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The Department of Agriculture and Agri-Food, also referred to as Agriculture and Agri-Food Canada , is the department of the government of Canada with responsibility for policies governing agriculture production, farming income, research and development, inspection, and the regulation of animals and plants. It also has responsibilities regarding rural development. It is popularly called Ag-Canada.The current Minister of Agriculture and Agri-Food is Gerry Ritz. The current Deputy Minister is Andrea Lyon. Wikipedia.

Gupta U.C.,Agriculture and Agri Food Canada | Gupta S.C.,Loma Linda University
Pedosphere | Year: 2014

Mineral nutrients are fundamentally metals and other inorganic compounds. The life cycle of these mineral nutrients begins in soil, their primary source. Soil provides minerals to plants and through the plants the minerals go to animals and humans; animal products are also the source of mineral nutrients for humans. Plant foods contain almost all of the mineral nutrients established as essential for human nutrition. They provide much of our skeletal structure, e.g., bones and teeth. They are critical to countless body processes by serving as essential co-factors for a number of enzymes. Humans can not utilize most foods without critical minerals and enzymes responsible for digestion and absorption. Though mineral nutrients are essential nutrients, the body requires them in small, precise amounts. We require them in the form found in crops and they can be classified into three different categories: major, secondary, and micro or trace minerals. This classification is based upon their requirement rather than on their relative importance. Major minerals such as potassium (K) and phosphorus (P) are required in amounts of up to 10 g d-1. The daily requirement of secondary and micro minerals ranges from 400 to 1 500 mg d-1 and 45 μg d-1 to 11 mg d-1, respectively. To protect humans from mineral nutrient deficiencies, the key is to consume a variety of foods in modest quantities, such as different whole grains, low fat dairy, and different meats, vegetables and fruits. For insurance purposes, a supplement containing various mineral nutrients can be taken daily. © 2014 Soil Science Society of China.

Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin. © 2015 Tarasov, Génier.

Kasuga T.,Crops Pathology and Genetics Research Unit | Gijzen M.,Agriculture and Agri Food Canada
Trends in Microbiology | Year: 2013

A feature of pathogenic and invasive organisms is their adaptability when confronted with host and environmental challenges. Recent studies have demonstrated that plant pathogens rely on epigenetic processes for this purpose. Epiallelic variation of effector genes that results in evasion of host immunity is one emerging phenomenon. Another is the epigenetically induced reprogramming and diversification of transcriptional patterns by de-repression of transposable elements. These observations indicate that epigenetic control of gene expression provides a versatile means of generating phenotypic diversity that is adaptable and heritable across generations. © 2013 .

Satchithanantham S.,University of Manitoba | Krahn V.,University of Manitoba | Sri Ranjan R.,University of Manitoba | Sager S.,Agriculture and Agri Food Canada
Agricultural Water Management | Year: 2014

Knowing the crop water uptake pattern and soil water movement within the root zone is important for the optimum design of irrigation and drainage systems. The objective of this study was to monitor the soil water redistribution within the potato root zone after irrigation and to quantify shallow groundwater contribution to water use by potatoes. The water uptake pattern in a vertical plane was monitored by TDR miniprobes installed at five different depths and at three different radial distances from the base of the potato plants. Three such planes of TDR miniprobes were used as replicates. The soil within the root zone was brought to field capacity by surface application of water. The water content measurements were carried out prior to this irrigation event and at periodic intervals thereafter over a four-day period, three times/day. The groundwater level was measured at 3h intervals. Soil core samples were taken at each TDR probe location to determine the root density. The soil water content and upward flux from the groundwater was simulated using HYDRUS-1D model and the results were compared with the upward flux estimated from the change in groundwater levels. The maximum root density was found to be 14.5 and 252g/m-3 at two and three months after planting. Soil layers at shallower depths showed signs of drying while the deeper layers remained wet. Model simulations closely matched the measured soil water contents and upward flux. In a fine sandy loam, up to 92% of the crop water demand was met by capillary rise from the shallow groundwater table. Knowing the shallow water table contribution can decrease the net depth of irrigation water applied and save water and energy needed for pumping. © 2013 Elsevier B.V.

The precursor messenger RNA (pre-mRNA) three-prime cleaved-off region (3′ COR) and the mRNA three-prime untranslated region (3′ UTR) play critical roles in regulating gene expression. The differences in base composition between these regions and the corresponding genomes are still largely uncharacterized in animals and plants. In this study, the base compositions of non-redundant 3′CORs and 3′ UTRs were compared with the corresponding whole genomes of eleven animals, four dicotyledonous plants, and three monocotyledonous (cereal) plants. Among the four bases (A, C, G, and U for adenine, cytosine, guanine, and uracil, respectively), U (which corresponds to T, for thymine, in DNA) was the most frequent, A the second most frequent, G the third most frequent, and C the least frequent in most of the species in both the 3′COR and 3′UTR regions. In comparison with the whole genomes, in both regions the U content was usually the most overrepresented (particularly in the monocotyledonous plants), and the C content was the most underrepresented. The order obtained for the species groups, when ranked from high to low according to the U contents in the 3′COR and 3′UTR was as follows: dicotyledonous plants, monocotyledonous plants, non-mammal animals, and mammals. In contrast, the genomic T content was highest in dicotyledonous plants, lowest in monocotyledonous plants, and intermediate in animals. These results suggest the following: 1) there is a mechanism operating in both animals and plants which is biased toward U and against C in the 3′COR and 3′UTR; 2) the 3′UTR and 3′COR, as functional units, minimized the difference between dicotyledonous and monocotyledonous plants, while the dicotyledonous and monocotyledonous genomes evolved into two extreme groups in terms of base composition. © 2014 Xiu-Qing Li.

Gonzalez L.A.,Agriculture and Agri Food Canada
Journal of animal science | Year: 2012

The objective of the present study was to document the relationships between selected welfare outcomes and transport conditions during commercial long haul transport of cattle (≥400 km; 6,152 journeys; 290,866 animals). Surveys were delivered to transport carriers to collect information related to welfare outcomes including the number of dead, non-ambulatory (downer) and lame animals during each journey. Transport conditions surveyed included the length of time animals spent on truck, ambient temperature, animal density, shrinkage, loading time, cattle origin, season, experience of truck drivers, and vehicle characteristics. Overall 0.012% of assessed animals became lame, 0.022% non-ambulatory and 0.011% died onboard. Calves and cull cattle were more likely to die and become non-ambulatory during the journey, feeders intermediate, and fat cattle appeared to be the most able to cope with the stress of transport (P ≤ 0.01). The likelihood of cattle becoming non-ambulatory, lame, or dead increased sharply after animals spent over 30 h on truck (P < 0.001). The likelihood of animal death increased sharply when the midpoint ambient temperature fell below -15°C (P = 0.01) while the likelihood of becoming non-ambulatory increased when temperatures rose above 30°C (P = 0.03). Animals that lost 10% of their BW during transport had a greater (P < 0.001) likelihood of dying and becoming non-ambulatory or lame. Animals were more likely to die at smaller space allowances (P < 0.05), particularly at allometric coefficients below 0.015 (P = 0.10), which occurred more frequently in the belly and deck compartments of the trailers, and also at high space allowances in the deck (allometric coefficients > 0.035). The proportion of total compromised animals decreased with more years of truck driving experience (P < 0.001). Mortality was greater in cattle loaded at auction markets compared with feed yards and ranches (P < 0.01). Cull cattle, calves and feeders appear to be more affected by transport based on the likelihood of becoming non-ambulatory and dying within a journey. Most important welfare concerns during long distance transport include the total journey duration, too low or high space allowances, too high or too low ambient temperature, and the experience of the truck drivers.

Wijesinghe W.A.J.P.,Jeju National University | Athukorala Y.,Jeju National University | Athukorala Y.,Agriculture and Agri Food Canada | Jeon Y.-J.,Jeju National University
Carbohydrate Polymers | Year: 2011

In this study, the anticoagulant activity of a sulfated polysaccharide purified from enzyme assistant extract of brown seaweed Ecklonia cava (ECSP) was investigated both in vitro and in vivo. The sulfated polysaccharide purified from AMG assistant extract of E. cava showed anticoagulant activity comparable to that of a commercial fucoidan in activated partial thromboplastin time (APTT), thrombin time (TT) and prothrombin time (PT) clotting assays in vitro. In Fourier transform infrared spectroscopy (FT-IR), similar transmittance was observed for the commercial fucoidan and ECSP with an intense absorption band at 1240 and 820 cm-1 indicating its high sulfate content. The administration of the anticoagulant drug in rats clearly extended the coagulation time in a dose dependent and time dependent manner in both APTT and TT assays, especially a clear effect was observed at 30 min after the initial sample treatment. In the tail bleeding assay, ECSP showed prolonged bleeding time (>1800 ± 05.1 s) than the control (900 ± 20.1 s) at the dosage of 300 μg/kg. With the current findings ECSP might be a promising candidate in pharmaceutical applications as a natural anticoagulant. © 2011 Elsevier Ltd All rights reserved.

The British Columbia sweet cherry industry, which neighbors a huge US industry, relies on export markets that pay premium prices. Premium export quality relies on having both high quality large fruit and green stems. Harvesting sweet cherries at later maturities results in superior eating quality and the focus has been to harvest a more mature fruit. While the stem is not edible, it is important to visual impact and is an indicator of freshness. The first research on sweet cherries for export focused on retaining a bright green stem up to six weeks storage and details of that work will be discussed. Development of late season cultivars was necessary to extend the season past the US crop. 'Sweetheart' has become the most reliable cultivar for containerized ocean shipment. Characteristics important to containerized shipment of sweet cherries were identified and data on shipping potential and respiratory heat will be presented. Logistics from harvest to packing and the impact of deviations in logistics on sweet cherry quality at market was evaluated to develop optimal handling specifications. It is critical to protect harvested fruit with reflective covers to prevent stem browning and improve fruit quality during shipping. Post-pack cooling is also mandatory to reliable quality retention for cherries harvested at later maturities. One factor that does not appear to have large effect on shipping quality is plastic packaging or box liner type. Success of containerized shipping of premium quality sweet cherries is dependent on numerous factors, all of which must be optimized.

Lester G.E.,U.S. Department of Agriculture | Makus D.J.,U.S. Department of Agriculture | Hodges D.M.,Agriculture and Agri Food Canada | Jifon J.L.,Texas AgriLife Research Center
Journal of Agricultural and Food Chemistry | Year: 2013

Comparison of spinach (Spinacia oleracea L.) cultivars Lazio and Samish grown during the summer solstice in the subarctic versus the winter solstice in the subtropics provided insight into interactions between production environment (light intensity), cultivar, and leaf age/maturity/position affecting bionutrient concentrations of vitamins (C, E, folate, K1, provitamin A), lutein, phenolics, and antioxidants. Growing spinach during the winter solstice in the subtropics resulted in increased leaf dry matter %, oxidized (dehydro) ascorbic acid (AsA), α- and γ-tocopherol, and total phenols but lower reduced (free) AsA, α-carotene, folate, and antioxidant capacity compared to summer solstice-grown spinach in the subarctic. Both cultivars had similar bionutrients, except for higher dehydroAsA, and lower α- and γ-tocopherol in 'Samish' compared to 'Lazio'. For most bionutrients measured, there was a linear, and sometimes quadratic, increase in concentrations from bottom to top canopy leaves. However, total phenolics and antioxidant capacity increased basipetally. The current study has thus demonstrated that dehydroAsA, α-tocopherol, and γ-tocopherol were substantially lower in subarctic compared to subtropical-grown spinach, whereas the opposite relationship was found for antioxidant capacity, α-carotene, and folates (vitamin B9). The observations are consistent with previously reported isolated effects of growth environment on bionutrient status of crops. The current results clearly highlight the effect of production environment (predominantly radiation capture), interacting with genetics and plant phenology to alter the bionutrient status of crops. While reflecting the effects of changing growing conditions, these results also indicate potential alterations in the nutritive value of foods with anticipated shifts in global climatic conditions. © 2013 American Chemical Society.

Soil amendment with fish emulsion (FE) can suppress potato scab and verticillium wilt, but the effective broadcast rates (20 000 L ha-1) may not be feasible for commercial use. The aim of this 4-year study was to establish suppressive conditions against soilborne potato diseases and increase tuber yield with economically feasible rates of FE. Diluted FE (1000 and 2000 L ha-1 or 0.05 and 0.1%) was applied to field plots or micro-plots twice a year before planting and after harvesting potatoes starting in autumn of 2007 and ending in spring of 2010. In the micro-plots, FE (0.1%) added to an infested potato soil (site BL) consistently reduced scab severity by 44.9% (2008), 44.8% (2009) and 30.9% (2010) compared with the control. Scab severity on tubers harvested from these plots was also low in 2011 when no further FE was applied, but the effect was not significant. In the field, FE (2000 L ha -1) consistently reduced scab severity by 45% (2008), 53% (2009), 44% (2010) and 38% (2011); reduced the percentage of tubers with deep-pitted scab by 48% (2008), 51% (2009), 66% (2010) and 77% (2011); and increased the percentage of marketable tubers by 37% (2008), 83% (2009), 20% (2010) and 8% (2011). These field plots also showed a low percentage of Verticillium dahliae-infected potato plants during the first 3 years of the field trial. Fish emulsion treatments increased total tuber yield by 7-20% in the first 3 years, but there was no effect in the fourth year when no FE was applied. Marketable tubers were consistently higher in the plots amended with FE (2000 L ha -1). Fish emulsion soil treatments increased soil bacteria but the numbers dropped to the control level in the fourth year when no FE application was made. There was no change in total fungal numbers. The results suggest that economically feasible rates of FE can provide disease suppression and enhance tuber yield and the effect may last a year or more after the last FE application. © 2013 The Canadian Phytopathological Society.

Reblova M.,Academy of Sciences of the Czech Republic | Gams W.,Molenweg 15 | Seifert A.,Agriculture and Agri Food Canada
Studies in Mycology | Year: 2011

We examined the phylogenetic relationships of two species that mimic Chaetosphaeria in teleomorph and anamorph morphologies, Chaetosphaeria tulasneorum with a Cylindrotrichum anamorph and Australiasca queenslandica with a Dischloridium anamorph. Four data sets were analysed: a) the internal transcribed spacer region including ITS1, 5.8S rDNA and ITS2 (ITS), b) nc28S (ncLSU) rDNA, c) nc18S (ncSSU) rDNA, and d) a combined data set of ncLSU-ncSSU-RPB2 (ribosomal polymerase B2). The traditional placement of Ch. tulasneorum in the Microascales based on ncLSU sequences is unsupported and Australiasca does not belong to the Chaetosphaeriaceae. Both holomorph species are nested within the Glomerellales. A new genus, Reticulascus, is introduced for Ch. tulasneorum with associated Cylindrotrichum anamorph; another species of Reticulascus and its anamorph in Cylindrotrichum are described as new. The taxonomic structure of the Glomerellales is clarified and the name is validly published. As delimited here, it includes three families, the Glomerellaceae and the newly described Australiascaceae and Reticulascaceae. Based on ITS and ncLSU rDNA sequence analyses, we confirm the synonymy of the anamorph genera Dischloridium with Monilochaetes. Consequently Dischloridium laeënse, type species of the genus, and three related species are transferred to the older genus Monilochaetes. The teleomorph of D. laeënse is described in Australiasca as a new species. The Plectosphaerellaceae, to which the anamorph genus Stachylidium is added, is basal to the Glomerellales in the three-gene phylogeny. Stilbella annulata also belongs to this family and is newly combined in Acrostalagmus. Phylogenetic analyses based on ncLSU, ncSSU, and combined ncLSU-ncSSU-RPB2 sequences clarify family relationships within the Microascales. The family Ceratocystidaceae is validated as a strongly supported monophyletic group consisting of Ceratocystis, Cornuvesica, Thielaviopsis, and the type species of Ambrosiella. The new family Gondwanamycetaceae, a strongly supported sister clade to the Ceratocystidaceae, is introduced for the teleomorph genus Gondwanamyces and its Custingophora anamorphs. Four families are accepted in the Microascales, namely the Ceratocystidaceae, Gondwanamycetaceae, Halosphaeriaceae, and Microascaceae. Because of a suggested affinity of a Faurelina indica isolate to the Microascales, the phylogenetic position of the Chadefaudiellaceae is reevaluated. Based on the results from a separate ncLSU analysis of the Dothideomycetes, Faurelina is excluded from the Microascales and placed in the Pleosporales. © 2011 by the CBS Fungal Biodiversity Centre.

Yan W.,Agriculture and Agri Food Canada
Crop Science | Year: 2013

As a graphical data analysis tool, biplot analysis has increasingly been used in analyzing genotype × environment data and other types of twoway data. One limitation of biplot analysis is that it requires a complete two-way table. This paper reports on a procedure for estimating missing values in a two-way table so that incomplete data can be effectively analyzed using biplots. This procedure involves iteration of missing values based on singular value decomposition (SVD), which is the basic technique for biplot analysis. Simulation indicates that the proposed procedure successfully predicts missing values and recovers patterns for two sample datasets. On a smaller wheat (Triticum aestivum L.) dataset, the estimation was successful only when the proportion of missing data was less than 40%; for a larger oat (Avena sativa L.) dataset, the estimation was successful even when 60% of the data were treated as missing. The use of the SVD-based missing-value-estimation procedure enabled incomplete multiple-year data to be effectively analyzed in a single biplot. As a result, genotypes not tested in the same environments can be reasonably compared, and genotypes that have not been fully tested can be critically evaluated. © Crop Science Society of America.

Boivin G.,Agriculture and Agri Food Canada | Boivin G.,McGill University
Entomologia Experimentalis et Applicata | Year: 2013

The paradigm that females produce few costly eggs, whereas males produce an unlimited quantity of sperm holds true when matings are dispersed over time and males can replenish their sperm supply. In such a system, the best strategy for males is to mate with as many females as possible, as more is always better. However, in parasitoid species, mating often occurs at the emergence site and males may have to mate successively several females in a short period of time. This can lead to sperm depletion that can be temporary in synspermatogenic species whose males produce sperm throughout their adult life, or definitive in prospermatogenic species whose males emerge with their full sperm complement and do not produce more during their adult life. Both the spermatogeny index and the mating structure of a species will therefore influence the probability and intensity of sperm depletion in males. Sperm-limited males can court and mate females even in prospermatogenic species. These males still gain some inclusive fitness by preventing competitor males to fully inseminate females, therefore increasing the representation of their daughters in the following generation. Females that mate with partially or completely sperm-depleted males produce a constrained sex ratio that decreases their lifetime fitness. In species where sperm-depleted males occur, female choosiness based on sperm supply is predicted, as the cost of mating sperm-depleted males can be high. In addition, males are also expected to be choosy in prospermatogenic species as mating with sub-optimal females can be costly when sperm is limited. © Her Majesty the Queen in Right of Canada 2012 Entomologia Experimentalis et Applicata © 2012 The Netherlands Entomological Society.

There are three phases of rapid mammary accretion in swine, namely, from 90 d of age until puberty, during the last third of gestation and throughout lactation. Nutrition, endocrine status and management of gilts or sows during those periods can affect mammary development. More specifically, in growing gilts, feed restriction as of 90 d of age hinders mammary development and either supplying the phytoestrogen genistein or increasing circulating concentrations of prolactin stimulates mammogenesis. In late gestation, inhibition of relaxin or prolactin drastically diminishes mammary development and overly increasing dietary energy has a detrimental effect on mammogenesis. It also appears that feeding of the gestating sow can affect the mammary development of her offspring once it reaches puberty. Various management factors such as litter size, nursing intensity and use or non-use of a teat in the previous lactation will affect the amount of mammary tissue present at the end of lactation. Mammary development is followed by the essential process of involution whereby a rapid and drastic regression in parenchymal tissue takes place. It can occur either after weaning or in early lactation when teats are not being regularly suckled. Despite our current knowledge, much remains to be learned in order to develop the best management strategies for replacement gilts, and gestating and lactating sows that will maximize their milk production.

Gibson J.F.,University of Guelph | Skevington J.H.,Agriculture and Agri Food Canada | Skevington J.H.,Carleton University
Zoological Journal of the Linnean Society | Year: 2013

All global genera of the fly family Conopidae are revised here. A cladistic analysis of 117 morphological characters recorded from 154 species, including representatives of 59 genera and subgenera, recovers a phylogenetic hypothesis for the family. This hypothesis is used as the basis of a new classification for the family. Both Sicini and Zodionini are removed from Myopinae and elevated to subfamilial status. A new tribe, Thecophorini, is proposed within Myopinae to accommodate Thecophora, Scatoccemyia, and Pseudoconops. Two genera, Pseudomyopa and Parazodion, are removed from Dalmanniinae and placed in Myopinae and Zodioninae, respectively. Conopinae is divided into 11 tribes, seven of which are newly described (Asiconopini, Caenoconopini, Gyroconopini, Microconopini, Neoconopini, and Siniconopini). Some examined species are transferred to different or new genera and subgenera. A new genus, Schedophysoconops gen. nov., and subgenus Asiconops (Aegloconops) subgen. nov. within Conopinae are described. A review of character evolution and phylogeography is included in light of the new classification. A catalogue of all genus-group names is included with new emendations noted. © 2013 The Linnean Society of London.

Chai T.-T.,University of Western Australia | Simmonds D.,Agriculture and Agri Food Canada | Day D.A.,Flinders University | Colmer T.D.,University of Western Australia | Finnegan P.M.,University of Western Australia
Plant Physiology | Year: 2010

The alternative oxidase (AOX) is a cyanide-resistant oxidase that provides an alternative outlet for electrons from the respiratory electron transport chain embedded in the inner membrane of plant mitochondria. Examination of soybean (Glycine max) plants carrying a GmAOX2b antisense gene showed AOX to have a central role in reproductive development and fecundity. In three independently transformed antisense lines, seed set was reduced by 16% to 43%, whereas ovule abortion increased by 1.2-to 1.7-fold when compared with nontransgenic transformation control plants. Reduced fecundity was associated with reductions in whole leaf cyanide-resistant, salicylhydroxamic acid-sensitive respiration and net photosynthesis, but there was no change in total respiration in the dark. The frequency of potential fertilization events was reduced by at least one-third in the antisense plants as a likely consequence of prefertilization defects. Pistils of the antisense plants contained a higher proportion of immature-sized, nonfertile embryo sacs compared with nontransgenic control plants. Increased rates of pollen abortion in vivo and reduced rates of pollen germination in vitro suggested that the antisense gene compromised pollen development and function. Reciprocal crosses between antisense and nontransgenic plants revealed that pollen produced by antisense plants was less active in fertilization. Taken together, the results presented here indicate that AOX expression has an important role in determining normal gametophyte development and function. © 2010 American Society of Plant Biologists.

Landry J.-F.,Agriculture and Agri Food Canada | Hebert P.D.N.,University of Guelph
ZooKeys | Year: 2013

The genus Plutella was thought to be represented in Australia by a single introduced species, P. xylostella (Linnaeus), the diamondback moth. Its status as a major pest of cruciferous crops, and the difficulty in developing control strategies has motivated broad-ranging studies on its biology. Prior genetic work has generally supported the conclusion that populations of this migratory species are connected by substantial gene flow. However, the present study reveals the presence of two genetically divergent lineages of this taxon in Australia. One shows close genetic and morphological similarity with the nearly cosmopolitan Plutella xylostella. The second lineage possesses a similar external morphology, but marked sequence divergence in the barcode region of the cytochrome c oxidase I gene, coupled with clear differences in genitalia. As a consequence, members of this lineage are described as a new species, P. australiana Landry & Hebert, which is broadly distributed in the eastern half of Australia. © J-F. Landry, P.D.N. Hebert.

Catling P.M.,Agriculture and Agri Food Canada | Layberry R.A.,6124 Carp Road
Canadian Field-Naturalist | Year: 2013

the couperi subspecies of the Silvery Blue (Glaucopsyche lygdamus couperi) has expanded its range southward in northeastern north America using introduced legumes and open anthropogenic habitats. The discovery of a population of the Silvery Blue (Glaucopsyche lygdamus) in an eastern Ontario alvar woodland in 2011 suggests that the Silvery Blue may have been long established (although restricted) in southern Ontario. three larvae from this population were reared from eggs deposited on native neglected Milk-Vetch (Astragalus neglectus) by free-flying females in 2012. The three larvae, pupae, and single reared adult, as well as other adults from the alvar woodland, are described and compared with specimens associated with open anthropogenic habitat and introduced legumes. The alvar woodland specimens were closer to the northern Ontario subsp. couperi than to the subsp. lygdamus of the eastern united States. Although the alvar woodland larvae were darker green than subsp. couperi and the spots on the adults were on average larger than in subsp. couperi, the alvar woodland Silvery Blues could not be definitively distinguished from subsp. couperi, including specimens from northern Ontario and those from southern Ontario associated with open habitats. nevertheless, there is a possibility that the alvar woodland population of the Silvery Blue dates from early postglacial times and represents a distinct race separate from the Silvery Blue of open habitats.

O'Hara J.E.,Agriculture and Agri Food Canada
ZooKeys | Year: 2013

The history of the classification of the Tachinidae (Diptera) is traced from Meigen to the present. The contributions of Robineau-Desvoidy, Townsend, Villeneuve, Mesnil, Herting, Wood and many others are discussed within a chronological, taxonomic, and geographic context. The gradual development of the Tachinidae into its modern concept as a family of the Oestroidea and the emergence of the classificatory scheme of tribes and subfamilies in use today are reviewed. Certain taxa that have in the past been difficult to place, or continue to be of uncertain affinity, are considered and some are given in a table to show their varied historical treatments. The more significant systematic works published on the Tachinidae in recent decades are enumerated chronologically. © Government of Canada.

Nie X.,Agriculture and Agri Food Canada | Singh M.,Agricultural Certification Services
Canadian Journal of Plant Pathology | Year: 2013

Post-harvest screening of potato 'Kennebec' revealed a Potato virus Y (PVY) incidence of 15.8%, a rate that is unusually high for a cultivar possessing a high level of field resistance to the virus. Randomly selected tubers were planted in a field plot and the resulting plants were monitored. Approximately 16% of plants developed symptoms ranging from mild mosaic symptoms to severe necrosis/rugosity/stunting. ELISA and RT-PCR analysis revealed that infections with Potato virus S (PVS), Potato virus X (PVX) and PVY, mostly in mixed-infections, occurred commonly in 14 sampled plants. Two strains, namely the common strain (PVY°) and the recombinant tuber necrotic strain (PVY NTN) were identified in the PVY-positive plants. In general, mild mosaic was associated with infections with PVX and PVS; intermediated mosaic was associated with PVS and PVYNTN infections; whereas severe leaf deformation/necrosis/drop symptoms were associated with PVYNTN and PVX co-infections, or with PVY° and either PVS or PVX co-infections. Virus-free plantlets of potato 'Kennebec' were mechanically inoculated with PVX, PVY°, and PVYNTN alone or with PVX+PVY° or PVX+PVY NTN combinations in the greenhouse. Single infections with PVY° or mixed-infections with PVX+PVY° or PVX+PVYNTN incited severe mosaic symptoms and systemic necrosis soon after inoculation; whereas single infections with PVX and PVYNTN induced mild to intermediate mosaic symptoms only. The most severe symptoms occurred in the mixed-inoculation with PVX+PVYNTN, demonstrating dramatic synergism between these strains. Similarly, profound PVX and PVYNTN synergism was also found in tobacco and Physalis floridana plants, suggesting that the strain of PVY plays an important role in the level of synergistic reactions between PVX and PVY on host plants. © 2013 The contribution of Xianzhou Nie.

Willenborg C.J.,University of Saskatchewan | Johnson E.N.,Agriculture and Agri Food Canada
Industrial Crops and Products | Year: 2013

There has been keen interest in the development of cow cockle (Vaccaria hispanica (Mill.) Rauschert) as a medicinal and industrial crop in North America. However, very limited agronomic information exists regarding the cultivation of cow cockle as a crop. The objective of this study was to determine how seeding date and rate affected stand establishment, seed yield, and seed weight of cow cockle at various sites across western Canada. Field experiments were conducted at three locations across western Canada from 2006 to 2010 to evaluate the effects of seeding date (early May, mid May, early June, mid June) and seeding rate (50, 100, 200, 400, 800, and 1600seedsm-2) on cow cockle stand establishment, seed yield, and thousand seed weight (TSW). Delayed seeding had an inconsistent effect on plant stand establishment, but resulted in significant declines in seed yield and TSW in nearly all site-years. Plant stand establishment increased linearly with increasing seeding rate. A significant curvilinear increase in seed yield occurred with increasing seeding rate, while TSW declined significantly at increased seeding rates. The results of this study clearly show that seeding at an optimum rate of 400seedsm-2 as early as practical in the growing season will maximize seed yield and TSW in cow cockle crops. © 2013 Elsevier B.V.

Sundh I.,Swedish University of Agricultural Sciences | Goettel M.S.,Agriculture and Agri Food Canada
BioControl | Year: 2013

Ever since the inclusion of microbial biocontrol agents (MBCAs) within the regulatory frameworks initially designed for chemical pesticides, there has been awareness that these frameworks are not optimal for assessment and registration of new microbial biocontrol products. It is often claimed that the regulatory situation has contributed to a relatively slow uptake of microbial biocontrol in practice. In contrast to the MBCAs, non-indigenous invertebrate biocontrol agents (IBCAs) are regulated in many countries through quarantine and other biosecurity related legislation for prevention of introduction of alien organisms, whereas use of indigenous IBCAs are generally unregulated. In this study, we investigate what scientific support there is for performing evaluations of these two main groups of biocontrol agents (BCAs) within different frameworks. We compare potential risks of MBCAs and IBCAs, present a retrospective analysis of the development and implementation of the regulatory frameworks, and compare current requirements for MBCAs with those for other applications with microorganisms. One conclusion is that the ecological risks are of similar types between the two groups of BCAs, and that for both groups the environmental safety is most pertinently evaluated according to biological and ecological principles. The main difference between MBCAs and IBCAs with respect to human health is that the former may cause infectious disease. However, we found no evidence that this hazard is more serious for microorganisms for biocontrol than for microbes used in other types of applications, which generally have substantially lower regulatory demands than those for MBCAs. Several international initiatives have produced helpful guidelines and recommendations for simplified assessments and authorisations of BCAs. Still, we conclude that as long as MBCAs are evaluated within systems initially developed for chemicals, the risk for inappropriate emphasis of chemical hazards and therefore unnecessarily complicated assessments will be maintained. Therefore, this study supports the idea that development of new systems for the regulatory oversight of MBCAs, possibly a mutual framework covering all living BCAs, should be considered. Research issues that need to be further explored are to what extent utilisation of MBCAs actually results in increased exposure of non-targets to microorganisms, the biogeography and microbial ecology of representative MBCAs, and finally development of better methodology for determining potential human toxicity and pathogenicity of candidate MBCAs. © 2012 International Organization for Biological Control (IOBC).

Lafontaine J.D.,Agriculture and Agri Food Canada | Schmidt B.C.,Canadian Food Inspection Agency
ZooKeys | Year: 2013

A total of 64 additions and corrections are listed and discussed for the check list of the Noctuoidea of North America north of Mexico published in 2010. One family-group name is inserted, four are changed in rank, one is deleted, one is changed in name, and three are changed in authorship. Taxo-nomic changes to species are six new or revised synonymies, one new combination, and one revision in status from species to subspecies. © J.D. Lafontaine, B.C. Schmidt.

Additional evidence supports the inclusion by Hamilton (2001) of Machaerotinae in Clastopteridae. The former Clastopteridae (Clastopterinae sensu Hamilton, 2001) is revised to include Sepulliini (tr. nov.) Clastopterini includes a fossil genus Prisciba Poinar & Brown and the extant Clastoptera with 2 new species both from North America, and Iba Schmidt from the old-world. The last of these has 3 species (1 new), 2 from the Philippines and 1 in subgenus Parahindoloides Lallemand, stat. nov., from Borneo. Sepulliini includes 5 genera and 52 species from Africa, India and southeast Asia that were formerly included in "Aphrophoridae" but are now transferred to the redefined subfamily Clastopterinae, linking Clastopterini to Zygonini of the subfamily Machaerotinae. Sepulliini includes 24 newly described species: 2 species of Beesoniella Lallemand from India, and 1 of Grellaphia Schmidt from the Philippine Islands; and from continental Africa 2 species of Sepullia Stål from Ethiopia and Angola, Taphrotylus insignificans gen. & sp. nov.from Madagascar and 18 new species of Tremapterus Spinola, making Tremapterus (including Abbalomba Distant, Nyanja Distant and Patriziana Lallemand as subgenera) the largest and most widespread genus in Sepulliini. Its 38 species in sub-Saharan Africa include 2 new subgenera: Selenion (1 species) and Tremiziana (4 species). In this study, 25 new combinations are created: 20 in Tremapterus with T. major Jacobi (1910), described from Mt. Kilimandjaro, and T. occidentalis Schumacher (1912), described from above 1800 m on Mt. Cameroon transferred to Witteella Lallemand (Cercopidae, Aphrophorinae); Penthimia maculipennis Spinola and Philaenus maculosa Walker are transferred to Clastoptera Germar, and Parahindoloides lumuana Lallemand to Iba. The many new species and new combinations in the old-world fauna of Clastopterinae are included in keys and a checklist. Copyright © 2015 Magnolia Press.

Janzen H.H.,Agriculture and Agri Food Canada
European Journal of Soil Science | Year: 2015

Summary: The prospect, so alluring, of sequestering carbon (C) to mitigate CO2 build-up in air has prompted a flurry of soil studies, but questions still linger about whether early optimism was fully justified. My objectives are to review briefly the mechanisms of carbon accrual, consider constraints on soil C sequestration for mitigating climate, and contemplate questions for further collective conversation. Carbon in soil is ever in flux; not a stagnant reservoir, but a stream of atoms flowing through. Its instantaneous stock can be increased by adding more atoms to the stream or by slowing their rate of flow to CO2. The latter (decay) is influenced by intrinsic recalcitrance of the substrate, by protective interactions of carbon with the mineral matrix, and by the favourability of localized conditions for biological activity. Together, these mechanisms create a continuum of susceptibility to decay. Although many practices can abet carbon accrual, their effectiveness is constrained by the finitude of carbon gain, possible effects on other greenhouse gas emissions, susceptibility to future loss, the difficulty of measuring gains precisely, and the complexity of landscape-scale dynamics. In the light of these problems and prospects, I propose, as a working hypothesis, that we focus less on carbon, and more on using wisely the energy it carries; in other words, maximizing carbon 'stocks' is less critical than maintaining 'flows' to sustain the manifold functions performed by ecosystems. Among its implications, this hypothesis (i) enforces an ecosystem perspective, considering all inevitable trade-offs in the use of finite energy, (ii) emphasizes the importance of sustaining energy capture via photosynthesis, (iii) promotes a long view, evaluating carbon flows over several decades or longer and (iv) enfolds human aspirations, which ultimately shape carbon flows by demands on lands. Far from deflating the urgency of soil carbon research, this reoriented perspective may move soil carbon beyond a segregated stock to its central place as a dynamic hub in the energy cycles of our ecosystems. © 2014 British Society of Soil Science.

Kathiria P.,University of Lethbridge | Sidler C.,University of Lethbridge | Golubov A.,University of Lethbridge | Kalischuk M.,University of Lethbridge | And 2 more authors.
Plant Physiology | Year: 2010

Our previous experiments showed that infection of tobacco (Nicotiana tabacum) plants with Tobacco mosaic virus (TMV) leads to an increase in homologous recombination frequency (HRF). The progeny of infected plants also had an increased rate of rearrangements in resistance gene-like loci. Here, we report that tobacco plants infected with TMV exhibited an increase in HRF in two consecutive generations. Analysis of global genome methylation showed the hypermethylated genome in both generations of plants, whereas analysis of methylation via 5-methyl cytosine antibodies demonstrated both hypomethylation and hypermethylation. Analysis of the response of the progeny of infected plants to TMV, Pseudomonas syringae, or Phytophthora nicotianae revealed a significant delay in symptom development. Infection of these plants with TMV or P. syringae showed higher levels of induction of PATHOGENESIS-RELATED GENE1 gene expression and higher levels of callose deposition. Our experiments suggest that viral infection triggers specific changes in progeny that promote higher levels of HRF at the transgene and higher resistance to stress as compared with the progeny of unstressed plants. However, data reported in these studies do not establish evidence of a link between recombination frequency and stress resistance. © 2010 American Society of Plant Biologists.

Daniels-Lake B.J.,Agriculture and Agri Food Canada
Potato Research | Year: 2013

Recently, it has been shown that the darkening of potato processing colour attributable to a trace concentration of ethylene gas is more severe when CO2 is also elevated. In view of the increasing use of ethylene gas for sprout suppression in potato storage facilities, it was considered important to determine whether this effect also occurs at the much higher ethylene concentration used in commercial practice. Sprouting and processing colour of the French fry cultivars Russet Burbank, Shepody and Innovator and the potato crisp cultivar Dakota Pearl were tested during the November to June storage season of two consecutive years. Treatments were 0 or 2 kPa CO2 and 0 or 10 μL L-1 ethylene in a factorial design, plus a chlorpropham check. The 0 CO2 + 0 ethylene treatment constituted an untreated control. The ethylene exposure was commenced abruptly to maximize its effect on colour. The main effect of ethylene resulted in darker processing colour in all cultivars, whereas darkening attributable to the main effect of CO2 was observed only in Innovator and Dakota Pearl. The statistical interaction of the CO2 and ethylene was not significant except in Dakota Pearl Hunter a (redness) scores, although a tendency to darker colour when both gases were present was seen in Russet Burbank and Innovator at all evaluation dates. The results indicate that both gases can affect processing colour when ethylene is used to control sprouting, although considerable variability in the response exists among cultivars. This variability in combination with management of storage conditions such as temperature and CO2 can be utilized to minimize the impact of these gases on the processing colour of stored potatoes. © 2013 © Her Majesty the Queen in Right of Canada.

Jian F.,University of Manitoba | Jayas D.S.,University of Manitoba | White N.D.G.,Agriculture and Agri Food Canada
Transactions of the ASABE | Year: 2013

Thermal properties (thermal conductivity, specific heat, and thermal diffusivity) and bulk density of canola seeds are important engineering parameters needed for the design of processing, storing, drying, and cooling systems for canola seeds. In this study, standard bulk densities and specific heats of 6.5%, 7.7%, 9.6%, 11.6%, 13.7%, and 15.9% moisture content (wet basis, all standard errors of the moisture were ≤0.04 percentage points with n = 3) canola seeds (cultivar NX4-105 RR with 45.4% ±0.4 percentage point oil content), stored at 30°C for 0, 30, and 60 d, were measured at temperatures from-20°C to 60°C. Thermal diffusivity was calculated using measured specific heat and bulk density and published thermal conductivity. Standard bulk density of the canola at different temperatures and moisture contents followed a parabolic equation. There was no significant difference among the specific heats of canola at different storage times, and specific heat of the canola linearly increased with the increase of moisture content and temperature when the temperature was >0°C. The calculated thermal diffusivity decreased with the increase of moisture content, increase of storage time, and decrease of temperature. © 2013 American Society of Agricultural and Biological Engineers.

Hamilton K.G.A.,Agriculture and Agri Food Canada
Zootaxa | Year: 2013

The tribe Orthoraphini is validated by diagnosis to include the new-world fauna of Orthorapha Westwood with 21 species from Brazil and 2 newly recorded from Bolivia, including 9 new species: boliviana from an unknown locality in Bolivia and decorata, inscripta, inflata, invidia, irregularis, oculata, sagittata and sphaerata from Brazil. There are also 10 new combinations from Lepyronia Amyot & Serville: bufo W a l k e r, concinna Stål, frontalis Stål, fusconotata Stål, gemi-nata Jacobi, obscurata Amyot & Serville, obliqua Jacobi, quadrimaculata Lallemand, rana Walker and subfasciata Amy-ot & Serville. Keys are presented to the new-world species and 3 subgenera, including Lepyronoxia Melichar, stat.nov. (= Balsana Metcalf, syn.nov.) and Balsania subg.nov. In addition, the tribe contains 15 genera of old-world Aphrophorinae with an estimated 290 species from Pacific islands; of these, the previously undescribed male genitalia from 25 species in 8 genera are illustrated and antennal characters for Orthorapha and 14 Pacific island genera of Orthoraphini are compared to those of Cloviini, Philaenini and Aphrophorini. This is the first tribe of Cercopoidea to be described as limited to the Southern Hemisphere. Copyright © 2013 Magnolia Press.

Lonsdale O.,Agriculture and Agri Food Canada
Zootaxa | Year: 2013

The African Japanagromyza Sasakawa are revised, including a key and genitalic illustrations, and the limits of the genus are discussed. Nine species are recognized, which include four previously described species and four newly described species: J. crinicolis spec. nov.; J. dolobrata spec. nov.; J. laureata spec. nov.; J. nesiota spec. nov. The ninth species ("fe-male 1") is described but not formally named as it is known only from females. Japanagromyza salicifolii is known from Palaearctic Africa on Populus and Salix. The remaining eight species are known from the Afrotropical Region; of these, only Japanagromyza parvula Spencer has a known host association [Fabaceae - Crotalaria]. Copyright © 2013 Magnolia Press.

Legere A.,Agriculture and Agri Food Canada | Vanasse A.,Laval University
Agronomy Journal | Year: 2013

Combining low-input systems with conservation tillage may be feasible for field crops under northeastern conditions. This study compared the effects of herbicide-free (HF), organic (ORG), conventional (CONV), and herbicide-tolerant (GM) cropping systems applied to three 20 yr-old tillage treatments (MP, moldboard plow; CP, chisel plow; NT, no-till) on weed biomass and crop productivity in a 4-yr barley (Hordeum vulgare L.)-red clover (Trifolium pratense L.)-corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] rotation. Barley yield (4.5 Mg ha-1), and red clover forage yield (two cuts: 5.3 Mg ha-1) were similar across treatments. With MP and CP tillage, silage corn yield for CONV and GM systems (15 Mg ha-1) was 25% greater than for HF and ORG (11 Mg ha-1), whereas HF-NT and ORG-NT systems produced no harvestable yield. Soybean yield for HF-MP and ORG-MP systems was similar to that for CONV and GM (2.4 Mg ha-1), whereas yield in for the HF and ORG systems with CP and NT was half or less than for other treatments. Some form of primary tillage (CP or MP) was needed in corn and soybean to achieve adequate weed control and yield in the ORG and HF systems. Midseason weed proportion of total biomass was greater in the HF and ORG systems with CP and NT, and provided good yield prediction in corn (R2 = 0.74) and soybean (R2 = 0.84). Nutrient availability appeared adequate in corn following N2-fixing red clover but limiting in NT and CP for soybean following corn. Improving crop sequence, fertilization, and weed management will be key to the adoption of low-input systems using conservation tillage practices in cool, humid climates. © 2013 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved.

Mumladze L.,Ilia State University | Murvanidze M.,Biocontrol | Behan-Pelletier V.,Agriculture and Agri Food Canada
Pedobiologia | Year: 2013

Soil inhabiting oribatid mites (Acari: Oribatida) are one of the most interesting groups of animals because of their ecological characteristics at the community level. However, existing knowledge does not provide comprehensive explanations of the mechanisms underlying their community or metacommunity structure. The aim of this study is to investigate peat bog inhabiting oribatid mite metacommunity distribution throughout the Holarctic region. Species incidence data was collected (mainly from published sources) for 46 peat bog localities, comprising a total of 410 species. Characteristics of species composition (coherence, turnover and boundary clumping) were analyzed to reveal patterns of peat bog oribatid metacommunity for different ecological guilds. We also applied correlation and regression analysis to detect whether peat bog oribatid communities show latitudinal gradient and distance decay in compositional similarity. Analysis of metacommunity structure showed non-random structure for all ecological guilds studied with dominating nested and Clementsian patterns. No significant evidence was found for latitudinal gradients in species composition whereas non-linear distance decay in compositional similarity is a common phenomenon for peat bog oribatid communities. We discuss these metacommunity patterns within the framework of existing hypotheses and conclude that the community level structure for peat bog oribatid species is largely determined by interspecific interactions and common biogeographical history, whereas metacommunity patterns are the result of postglacial colonization processes. © 2012 Elsevier GmbH.

Catling P.M.,Agriculture and Agri Food Canada
Canadian Field-Naturalist | Year: 2013

Field and herbarium studies of the three varieties of Sporobolus vaginiflorus (var. inaequalis, var. vaginiflorus, and var. ozarkanus) in eastern Ontario found that (1) there is a strong tendency for the varieties to occur alone; (2) var. inaequalis occurs primarily on roadside gravels, river shores, and granite barrens and is the only variety associated with acid as well as alkaline substrates; and (3) both var. vaginiflorus and var. ozarkanus are confined to alvar landscapes but occupy different geographical regions. The ecological and geographical differentiation of these taxa supports their taxonomic recognition and the protection of alvar landscapes to conserve subspecific variants.

Gruyer N.,Laval University | Dorais M.,Agriculture and Agri Food Canada | Zagury G.J.,Ecole Polytechnique de Montreal | Alsanius B.W.,Swedish University of Agricultural Sciences
Agricultural Water Management | Year: 2013

Because of the lack of high-quality water and the potential pollution of groundwater by leached nutrients, recirculation of nutrient solutions for greenhouse production is now unavoidable. Although closed growing systems offer several advantages from an environmental standpoint, the risk of pathogen dissemination is a major concern for growers. Constructed wetlands represent an ecological and low-cost alternative method for treating agricultural wastewaters. The objective of this study was to evaluate the effectiveness of three types of constructed wetlands for removing the waterborne plant pathogens, such as Pythium ultimum and Fusarium oxysporum, that can be found in greenhouse wastewater. The experiment was conducted in a greenhouse using three types of horizontal subsurface-flow constructed wetlands in eight replicates. The wetlands were filled with pozzolana, planted with common cattail (Typha latifolia) and supplemented with sucrose or compost carbon sources or left without an external carbon source. The wetland units received reconstituted greenhouse wastewater and were inoculated five times consecutively with P. ultimum and F. oxysporum at 106CFUmL-1. Physical, chemical and biological properties as well as environmental parameters were evaluated during 12 weeks to characterize conditions related to plant pathogen removal efficiency. Even though 99.62-99.99% efficiency for pathogen repression was observed for the constructed wetlands, the compost amendment to the wetland promoted the development of biofilm around the filter media and the production of cell-wall degrading enzymes. Depending on the source of carbon that was provided to promote microbial population growth and wetland activity, different possible modes of action for pathogen removal were predominant but resulted in very high efficiency, considering that the wetlands were inoculated with massive populations of plant pathogens that are not found at the commercial level. This study showed that constructed wetlands can constitute an efficient and safe alternative to treat and then reuse greenhouse wastewater. © 2012.

Behan-Pelletier V.M.,Agriculture and Agri Food Canada
Zootaxa | Year: 2013

In North America, species diversity in the oribatid family Oribatellidae is primarily in the genus Oribatella Banks, but the genera Adoribatella Woolley, Ferolocella Grabowski, Joelia Oudemans and Ophidiotrichus Grandjean are also represented. I provide detailed diagnoses for these genera and the previously described species, Adoribatella punctata Woolley, known from Colorado and Oregon, USA, and Alberta, Canada, Ferolocella tessalata Berlese known from Missouri, Virginia, West Virginia, Georgia, Wisconsin, Ohio, Alabama, Arkansas and Texas, USA, and Ophidiotrichus exastus Woolley, known from North Carolina, Alabama, Missouri, Tennessee and Georgia, USA. I describe Joelia appalachia sp. nov., based on adult specimens, from West Virginia. A key is given to distinguish adults of these genera from those of Oribatella. Character states shared by adults of Oribatellidae are discussed, the synonymy of Gendzella Kuliev with Ferolocella is rejected, and arguments are presented for movement of Adoribatella from Oribatellidae to the Ceratozetoidea. Copyright © 2013 Magnolia Press.

Ma L.,University of Amsterdam | Ma L.,Agriculture and Agri Food Canada | Cornelissen B.J.C.,University of Amsterdam | Takken F.L.W.,University of Amsterdam
Frontiers in Plant Science | Year: 2013

Plant pathogens secrete effector proteins to promote host colonization. During infection of tomato xylem vessels, Fusarium oxysporum f. sp. lycopersici (Fol) secretes the Avr2 effector protein. Besides being a virulence factor, Avr2 is recognized intracellularly by the tomato I-2 resistance protein, resulting in the induction of host defenses. Here, we show that AVR2 is highly expressed in root- and xylem-colonizing hyphae three days post inoculation of roots. Co-expression of I-2 with AVR2 deletion constructs using agroinfiltration in Nicotiana benthamiana leaves revealed that, except for the N-terminal 17 amino acids, the entire AVR2 protein is required to trigger I-2-mediated cell death. The truncated Avr2 variants are still able to form homo-dimers, showing that the central region of Avr2 is required for dimerization. Simultaneous production of I-2 and Avr2 chimeras carrying various subcellular localization signals in N. benthamiana leaves revealed that a nuclear localization of Avr2 is required to trigger I-2-dependent cell death. Nuclear exclusion of Avr2 prevented its activation of I-2, suggesting that Avr2 is recognized by I-2 in the nucleus. © 2013 Ma, Cornelissen and Takken.

The extinct Eocene Baltic amber genus Propelma Trjapitzin 1963 is removed from synonymy under Eupelmus Dalman 1820 (Hymenoptera, Eupelmidae, Eupelminae) and treated as a valid genus within Neanastatinae Kalina 1984 based on examination of the holotype female of P. rohdendorfi Trjapitzin. Propelma rohdendorfi is redescribed, illustrated by photomacrographs, and compared to other described extant and extinct genera of Neanastatinae. Taxonomic, morphological and geological diversity of Neanastatinae relative to Eupelminae and Calosotinae is also discussed relative to potential age of the subfamily. © Government of Canada.

Wang S.,Natural Resources Canada | McKenney D.W.,Natural Resources Canada | Shang J.,Agriculture and Agri Food Canada | Li J.,Natural Resources Canada
Journal of Geophysical Research D: Atmospheres | Year: 2014

This study examined the long-term water budget closures for 370 watersheds over Canada's landmass by using 30years' (1981-2010) data products recently produced for precipitation (P) gridded using climate station measurements, land surface evapotranspiration (ET), and water surface evaporation (E0) obtained by the Ecological Assimilation of Land and Climate Observations (EALCO) model, and observed streamflow (Q). The results show that 29%, 58%, and 83% of the watersheds were closed within 5%, 10%, and 20% of P, respectively. The positive and negative imbalances among the 370 watersheds are largely offset and the national scale average is 24 mm yr-1, or 4.2% of P. Water budget closures have large variation across the landmass. Regions with sparse or less accurate monitoring of P such as the mountainous region and the Arctic exhibit the largest water imbalances. Further efforts on enhancing the climate observation networks, improving spatial models for P and ET estimates, and streamflow measurements are all likely critical for a better understanding of Canada's water budgets. © 2014 Her Majesty the Queen in Right of Canada.

Cable J.W.,Nipissing University | Kovacs J.M.,Nipissing University | Jiao X.,Nipissing University | Shang J.,Agriculture and Agri Food Canada
Remote Sensing | Year: 2014

The purpose of this research is to analyze how changes in acquisition time and incidence angle affect various C-band synthetic aperture radar (SAR) polarimetric intensities, co-polarized phase information, polarimetric response plots and decomposition parameters for various crops typical of Northern Ontario, Canada. We examine how these parameters may be used to monitor the growth stages of five common cash crops, namely, barley (Hordeum vulgare), canola (Brassica napus), oat (Avena sativa), soybean (Glycine max) and wheat (Triticum spp.). In total, nine RADARSAT-2 polarimetric images were analyzed across a 14-week period beginning in June and ending in September 2011 using two incidence angles of approximately 26° and 41°. As expected, the backscatter intensities for all targets were found to show a higher response when acquired at the steeper incidence angle (26°). All cash crop targets showed a rise and fall in backscatter response over the course of the growing season, coinciding with changing growth stages. Slight phase differences were observed for cereal crops, possibly due to one of the polarizations penetrating between the rows allowing double-bounce to occur. The polarimetric response plots and decompositions offered insight into the scattering mechanisms of each crop type, generally showing an increase in volume scattering as the crops reached maturity. Specifically, the contributions of the crops increased towards the volume scattering component and zones 4 and 2, as the crops matured in regards to the Freeman-Durden and Cloude-Pottier decompositions respectively. Overall, soybean and canola showed a more similar response in comparison to the cereal cash crops. Although the study focused on Northern Ontario, it is anticipated that these results would be relevant in investigations of multi-temporal RADARSAT-2 for agricultural zones with similar crop types. © 2014 by the authors; licensee MDPI, Basel, Switzerland.

Cable J.F.,Nipissing University | Kovacs J.M.,Nipissing University | Shang J.,Agriculture and Agri Food Canada | Jiao X.,Nipissing University
Remote Sensing | Year: 2014

For successful applications of microwave remote sensing endeavors it is essential to understand how surface targets respond to changing synthetic aperture radar (SAR) parameters. The purpose of the study is to examine how two particular parameters, acquisition time and incidence angle, influences the response from various land use/land cover types (forests, urban infrastructure, surface water and marsh wetland targets) using nine RADARSAT-2 C-band fine-beam (FQ7 and FQ21) fully polarimetric SAR data acquired during the 2011 growing season over northern Ontario, Canada. The results indicate that backscatter from steep incidence angle acquisitions was typically higher than shallow angles. Wetlands showed an increase in HH and HV intensity due to the growth of emergent vegetation over the course of the summer. The forest and urban targets displayed little variation in backscatter over time. The surface water target showed the greatest difference with respect to incidence angle, but was also determined to be the most affected by wind conditions. Analysis of the co-polarized phase difference revealed the urban target as greatly influenced by the incidence angle. The observed phase differences of the wetland target for all acquisitions also suggested evidence of double-bounce interactions, while the forest and surface water targets showed little to no phase difference. In addition, Cloude-Pottier and Freeman-Durden decompositions, when analyzed in conjunction with polarimetric response plots, provided supporting information to confidently identify the various targets and their scattering mechanisms. © 2014 by the authors; licensee MDPI, Basel, Switzerland.

Gagnon P.,University of Quebec | Gagnon P.,Agriculture and Agri Food Canada | Rousseau A.N.,University of Quebec
Hydrology and Earth System Sciences | Year: 2014

Regional climate models (RCMs) are valuable tools to evaluate impacts of climate change (CC) at regional scale. However, as the size of the area of interest decreases, the ability of a RCM to simulate extreme precipitation events decreases due to the spatial resolution. Thus, it is difficult to evaluate whether a RCM bias on localized extreme precipitation is caused by the spatial resolution or by a misrepresentation of the physical processes in the model. Thereby, it is difficult to trust the CC impact projections for localized extreme precipitation. Stochastic spatial disaggregation models can bring the RCM precipitation data at a finer scale and reduce the bias caused by spatial resolution. In addition, disaggregation models can generate an ensemble of outputs, producing an interval of possible values instead of a unique discrete value.

The objective of this work is to evaluate whether a stochastic spatial disaggregation model applied on annual maximum daily precipitation (i) enables the validation of a RCM for a period of reference, and (ii) modifies the evaluation of CC impacts over a small area. Three simulations of the Canadian RCM (CRCM) covering the period 1961-2099 are used over a small watershed (130 km2) located in southern Québec, Canada. The disaggregation model applied is based on Gibbs sampling and accounts for physical properties of the event (wind speed, wind direction, and convective available potential energy - CAPE), leading to realistic spatial distributions of precipitation. The results indicate that disaggregation has a significant impact on the validation. However, it does not provide a precise estimate of the simulation bias because of the difference in resolution between disaggregated values (4 km) and observations, and because of the underestimation of the spatial variability by the disaggregation model for the most convective events. Nevertheless, disaggregation illustrates that the simulations used mostly overestimated annual maximum precipitation depth in the study area during the reference period. Also, disaggregation slightly increases the signal of CC compared to the RCM raw simulations, highlighting the importance of spatial resolution in CC impact evaluation of extreme events. © Author(s) 2014.

Schmidt P.J.,Public Health Agency of Canada | Pintar K.D.M.,Public Health Agency of Canada | Fazil A.M.,Public Health Agency of Canada | Topp E.,Agriculture and Agri Food Canada
Risk Analysis | Year: 2013

Dose-response models are the essential link between exposure assessment and computed risk values in quantitative microbial risk assessment, yet the uncertainty that is inherent to computed risks because the dose-response model parameters are estimated using limited epidemiological data is rarely quantified. Second-order risk characterization approaches incorporating uncertainty in dose-response model parameters can provide more complete information to decisionmakers by separating variability and uncertainty to quantify the uncertainty in computed risks. Therefore, the objective of this work is to develop procedures to sample from posterior distributions describing uncertainty in the parameters of exponential and beta-Poisson dose-response models using Bayes's theorem and Markov Chain Monte Carlo (in OpenBUGS). The theoretical origins of the beta-Poisson dose-response model are used to identify a decomposed version of the model that enables Bayesian analysis without the need to evaluate Kummer confluent hypergeometric functions. Herein, it is also established that the beta distribution in the beta-Poisson dose-response model cannot address variation among individual pathogens, criteria to validate use of the conventional approximation to the beta-Poisson model are proposed, and simple algorithms to evaluate actual beta-Poisson probabilities of infection are investigated. The developed MCMC procedures are applied to analysis of a case study data set, and it is demonstrated that an important region of the posterior distribution of the beta-Poisson dose-response model parameters is attributable to the absence of low-dose data. This region includes beta-Poisson models for which the conventional approximation is especially invalid and in which many beta distributions have an extreme shape with questionable plausibility. © 2013 Society for Risk Analysis.

Young M.R.,University of Guelph | Behan-Pelletier V.M.,Agriculture and Agri Food Canada | Hebert P.D.N.,University of Guelph
PLoS ONE | Year: 2012

Although mites are one of the most abundant and diverse groups of arthropods, they are rarely targeted for detailed biodiversity surveys due to taxonomic constraints. We address this gap through DNA barcoding, evaluating acarine diversity at Churchill, Manitoba, a site on the tundra-taiga transition. Barcode analysis of 6279 specimens revealed nearly 900 presumptive species of mites with high species turnover between substrates and between forested and non-forested sites. Accumulation curves have not reached an asymptote for any of the three mite orders investigated, and estimates suggest that more than 1200 species of Acari occur at this locality. The coupling of DNA barcode results with taxonomic assignments revealed that Trombidiformes compose 49% of the fauna, a larger fraction than expected based on prior studies. This investigation demonstrates the efficacy of DNA barcoding in facilitating biodiversity assessments of hyperdiverse taxa. © 2012 Young et al.

Aldughpassi A.,University of Toronto | Abdel-Aal E-S.M.,Agriculture and Agri Food Canada | Wolever T.M.S.,University of Toronto
Journal of Nutrition | Year: 2012

Barley has a low glycemic index (GI), but it is unknown whether its GI is affected by variation in carbohydrate composition in different cultivars and by food processing and food form. To examine the effect of these factors on GI, 9 barley cultivars varying in amylose and β-glucan content were studied in 3 experiments in separate groups of 10 healthy participants. In Expt. 1, 3 barley cultivars underwent 2 levels of processing: hull removal [whole-grain (WG)] and bran, germ, and crease removal [white pearled (WP)]. GI varied by cultivar (CDC Fibar vs. AC Parkhill, [mean ± SEM]: 26 ± 3 vs. 53 ± 4, respectively; P < 0.05) and pearling (WG vs. WP: 26 ± 4 vs. 35 ± 3, respectively; P < 0.05) with no cultivar × pearling interaction. In Expt. 2, the GI of 7 WG cultivars ranged from 21 ± 4 to 36 ± 8 (P = 0.09). In Expt. 3, WG and WP AC Parkhill and Celebrity cultivars were ground and made into wet pasta. The GI of AC Parkhill pasta (69 ± 3) was similar to that of Celebrity pasta (64 ± 4) but, unlike in Expt. 1, the GI of WP pasta (61 ± 3) was less than that of WG pasta (72 ± 4) (P < 0.05). Pooled data from Expts. 1 and 2 showed that GI was correlated with total fiber (r = -0.75, P = 0.002) but not with measures of starch characteristics. We conclude that the GI of barley is influenced by cultivar, processing, and food form but is not predicted by its content of amylose or other starch characteristics. © 2012 American Society for Nutrition.

Giles C.D.,University of Vermont | Cade-Menun B.J.,Agriculture and Agri Food Canada | Hill J.E.,University of Vermont
Canadian Journal of Soil Science | Year: 2011

This review focuses on recent advances in understanding the origins, abiotic and biotic cycling, and measurement of inositol phosphates (IPx) in manures and soils. With up to eight orthophosphates bound to inositol via ester linkages, this class of compounds has the potential to be unavailable to enzymatic hydrolysis when sorbed or in complex with soil metals, limiting the release of phosphorus (P) for uptake by plants. However, hydrolysis of IPx by microbial phytases in aquatic environments could result in a potent source of the eutrophication agent orthophosphate. This review discusses the forms and stereoisomers of IPx that have been identified in environmental samples. Next, it discusses the various techniques used to identify IPx, including extraction and concentration, separation techniques such as electrophoresis, spectroscopic methods such as phosphorus-31 nuclear magnetic resonance spectroscopy (31P-NMR), mass spectrometry and X-ray absorption near-edge structure (XANES), and enzymatic techniques, such as enzyme hydrolysis (EH). Recent advances in knowledge about abiotic and biotic factors controlling the cycling of IPx in soil, manure and water are summarised, including soil characteristics affecting IPx sorption, transportation processes, and the microbial production and degradation of IPx. Finally, areas for future research focus are discussed.

Lonsdale O.,Plant Pest Diagnostics Center | Lonsdale O.,Agriculture and Agri Food Canada
Zootaxa | Year: 2011

The Californian species of Liriomyza Mik are revised, including descriptions, illustrations, photographs and a key to species. Sixty-three species are now known to occur in the state, 12 of which are described here as new: L. bispinula, L. conclavis, L. cunicularia, L. merga, L. miserabilis, L. nebulosa, L. parabella, L. phyllodes, L. projecta, L. salpingion, L. tricornis and L. trixivora. Liriomyza virginica Spencer is included as a junior synonym of L. helianthi Spencer, and L. similis Spencer is included as a synonym of L. artemisiae Spencer. Two species are newly recorded in the United States: L. equiseti Meijere, previously known from Canada and Europe, and L. montana Sehgal, previously known from Canada. A number of specimens of L. brassicae (Riley) have been identified as potential new host "races" or species. Morphological characters are provided to diagnose the sister species L. huidobrensis (Blanchard) and L. langei Frick, previously recognizable only on the basis of molecular data. Numerous new state, county and host records are also presented, and hosts are compared for five of the most common North American agricultural pests: L. brassicae, L. huidobrensis, L. langei, L. sativae Blanchard and L. trifolii (Burgess). California contains the highest diversity of Liriomyza known to occur in North America, containing approximately 70% of all described species known from the lower 48 states. Copyright © 2011. Magnolia Press.

Bartlett C.R.,University of Delaware | Hamilton K.G.A.,Agriculture and Agri Food Canada
Zootaxa | Year: 2011

The new genus Aethodelphax gen. nov. is described to include one new species, Aethodelphax prairianus sp. nov. and 7 species transferred from Delphacodes: Aethodelphax aetocephalus (Beamer, 1948), comb. nov., A. alatus (Beamer, 1948), comb. nov., A. caninus (Beamer, 1947), comb. nov., A. concavus (Beamer, 1948), comb. nov., A. megadontus (Beamer, 1951), comb. nov., A. paraparvulus (Beamer, 1948), comb. nov., and A. sagittatus (Beamer, 1947), comb. nov. A diagnosis for all species, illustrations and an identification key is provided. All species are found in the midwestern and southeastern states of the U.S., except A. caninus which is recorded from Arizona and New Mexico, and are all associated with native grasslands. © 2011 Magnolia Press.

Carisse O.,Agriculture and Agri Food Canada | Morissette-Thomas V.,Universite de Sherbrooke
Plant Disease | Year: 2013

Anthracnose is a serious disease that affects several grape cultivars. Infected leaves drop prematurely, and severe epidemics result in poor or no yield. Because the factors associated with grape defoliation in vineyards with a history of anthracnose were not well known, this study was undertaken to investigate the relationship between weather-, disease-, and host-related factors and survival of leaves. From 2006 to 2008, weather, anthracnose severity, and leaf emergence were monitored in an unsprayed experimental vineyard naturally infested with Elsinoë ampelina. Each year, two to three times weekly, the number of leaves and the proportion of leaf area diseased (PLAD) were monitored on 10 vines and 2 shoots per vine, for a total of 785 leaves. Survival analysis was used to investigate the factors influencing defoliation and to model time-to-death of grape leaves. Estimated median survival time was 117 to 121 days. Based on Kaplan-Meier estimates of survival probabilities, season type, PLAD per leaf and PLAD per shoot at first assessment, duration and amount of rain at first infection, severity of infection and leaf age at first infection and at first severe infection significantly influenced leaf survival. Based on accelerated time failure modeling, using the Weibull distribution, the most significant variables were PLAD per leaf and PLAD per shoot at first assessment, leaf age at first infection, and duration of rain. Each additional percent increase in PLAD per leaf, in PLAD per shoot, or in rainy days accelerated the time-to-death of grape leaves by 2.84, 1.02, and 0.66%, respectively, whereas for each additional day of leaf age at time of first infection, there was a 2.88% deceleration of the time to death. Results suggested that to avoid premature leaf drop, disease severity should be maintained below 25% leaf area diseased, which can be achieved by sanitation measures designed to reduce inoculum levels and by applying fungicide early in the season to prevent infection of young leaves.

Lefevre P.L.C.,University of Montreal | Palin M.-F.,Agriculture and Agri Food Canada | Chen G.,McGill Group for Suicide Studies | Turecki G.,McGill Group for Suicide Studies | Murphy B.D.,University of Montreal
Endocrinology | Year: 2011

Embryonic diapause is a poorly understood phenomenon of reversible arrest of embryo development prior to implantation. In many carnivores, such as the mink (Neovison vison), obligate diapause characterizes each gestation. Embryo reactivation is controlled by the uterus by mechanisms that remain elusive. Because polyamines are essential regulators of cell proliferation and growth, it was hypothesized that they trigger embryo reactivation. To test this, mated mink females were treated with α-difluoromethylornithine, an inhibitor of ornithine decarboxylase 1, the rate-limiting enzyme in polyamine biosynthesis, or saline as a control during the first 5 d of reactivation. This treatment induced polyamine deprivation with the consequence of rearrest in embryo cell proliferation. A mink trophoblast cell line in vitro subjected to α-difluoromethylornithine treatment likewise displayed an arrest in cell proliferation, morphological changes, and intracellular translocation of ornithine decarboxylase 1 protein. The arrest in embryo development deferred implantation for a period consistent with the length of treatment. Successful implantation and parturition ensued. We conclude that polyamine deprivation brought about a reversible rearrest of embryo development, which returned the mink embryo to diapause and induced a second delay in embryo implantation. The results are the first demonstration of a factor essential to reactivation of embryos in obligate diapause. Copyright © 2011 by The Endocrine Society.

Seo S.,McGill University | Karboune S.,McGill University | L'Hocine L.,Agriculture and Agri Food Canada | Yaylayan V.,McGill University
LWT - Food Science and Technology | Year: 2013

Glycated lysozyme (LZM) with galactose, galactooligosaccharides (GOSs) and galactan, through the Maillard reaction, were produced and characterized structurally and functionally. The extent of glycation of LZM was evaluated by the measurement of the blocked lysine and the formed furosine. The results indicated a high initial reactivity of galactose as compared to GOSs and galactan. In the presence of GOSs, the oxidative and cross-linking side reactions competed with the initial formation of Amadori product. The longer chain carbohydrate galactan exhibited the lowest initial rate of glycation with no significant cross-linking side reaction. Electrospray ionization mass spectrometry revealed the formation of glycated LZM containing up to eight galactose moieties; while only mono- to tetra-glycated LZM with GOSs were detected. 2-3 mol of galactan were conjugated to 1 mol of LZM. Galactan:LZM conjugates exhibited higher solubility, thermal stability and emulsion stability as compared to the unmodified LZM and LZM:galactose conjugates. LZM:GOS conjugates demonstrated the most improvement in the emulsion stability than the other conjugates. Furthermore, the glycation of LZM with galactose/GOSs/galactan decreased its immunoreactivity. © 2013 Elsevier Ltd.

Thompson D.,Agriculture and Agri Food Canada
Canadian Journal of Plant Science | Year: 2013

Orchardgrass (Dactylis glomerata L.) is commonly grown for irrigated forage production in interior British Columbia. Tall fescue [Schedonorus phoenix (Schop.) Holub.] is also adapted to the area but no comparative trials have been reported. Three varieties of each grass species were grown in monocultures or in mixtures with alfalfa at three irrigated sites throughout southern interior British Columbia. Study objectives included comparing the forage yield and nutritive value of the following groups: (1) tall fescue and orchardgrass monocultures, (2) tall fescue and orchardgrass mixtures with alfalfa and (3) grass-alfalfa mixtures with monocultures. In monoculture, tall fescue yield was 9% greater than orchardgrass (significantly greater yield at 3 of 6 site-years), though forage nutritive values were similar. Mixtures of the two grasses with alfalfa had similar yields, but those containing tall fescue had superior nutritive value. Alfalfa contributed a greater percentage to total yield and had higher survival when mixed with tall fescue. Tall fescue is a viable alternative to orchardgrass for irrigated forage production in monoculture and may be more suitable for mixtures with alfalfa. Our findings demonstrate a functional diversity effect; grass-alfalfa mixtures over-yielded the mean of the alfalfa, orchardgrass, and tall fescue monocultures by 12%.

Li X.,Agriculture and Agri Food Canada
Plant signaling & behavior | Year: 2012

Isoflavonoids are plant natural compounds predominantly found in leguminous plant. They play important functions in both nitrogen fixation and stress resistance. Many clinical studies have linked dietary intake of isoflavonoids to human health benefits. Binding of 14-3-3 proteins to GmMYB176, an isoflavonoid regulator, modulates expression of key isoflavonoids gene expression and its biosynthesis. We have recently demonstrated that the interaction of 14-3-3 proteins with GmMYB176 regulates nuclear-cytoplasmic localization of GmMYB176 thereby affecting target gene expression. Here, we report GmMYB62 as a new R1 MYB client protein of soybean 14-3-3s that may function together with GmMYB176 for gene regulation in soybean.

He Z.,Southern Regional Research Center | Olk D.C.,U.S. Department of Agriculture | Cade-Menun B.J.,Agriculture and Agri Food Canada
Soil Science Society of America Journal | Year: 2011

Phosphorus has long been known to be present in soil humic fractions, but little is known about specific P forms in humic fractions or their lability. We extracted the mobile humic acid (MHA) and recalcitrant calcium humate (CaHA) fractions from a Nebraska Hord silt loam soil (a fine-silty, mixed, superactive, mesic Cumulic Haplustoll) under continuous corn (Zea mays L.) receiving either inorganic fertilizer or animal manure. Solution 31P nuclear magnetic resonance spectroscopy demonstrated that P in both MHA and CaHA was predominantly present in organic forms, mostly as orthophosphate monoesters. Spiking experiments indicated no phytate present in these humic fractions, but scyllo-inositol P was identified in all samples. Potato phosphatase hydrolyzed some humicbound P. Fungal phytase released more humic-bound P, which may come from scyllo-inositol P. No additional P was released by including nuclease. Ultraviolet (UV) irradiation increased soluble inorganic P in MHA fractions, but total hydrolyzable P in MHA fractions did not increase, suggesting that the portion of P that was UV labile was also enzymatically hydrolyzable. In contrast, UV irradiation increased soluble inorganic P and total hydrolysable P in CaHA fractions, which suggests that UV-labile P in CaHA fractions did not overlap wiThenzymatically hydrolyzable P. Fertilization management did not significantly alter the lability of humic P in these humic fractions. This research has the potential to improve P management by increasing our knowledge of P lability for more efficient crop uptake. © Soil Science Society of America.

Besides creating a reservoir of animals aimed at maintaining the constant speed of the slaughter line, the function of lairage is to allow the animals to recover from the stress of transport and unloading. However, inadequate treatment of slaughter pigs in this stage or lack of environmental control may result in additional stress leading to economic losses due to poor animal welfare (deads-on-arrival and downers), skin damage and poor meat quality. Short and long lairage times can result in increased incidences of pale, soft, exudative and dark firm, dry pork, respectively. However, these effects are influenced by the environmental conditions and the pig genotype. Mixing unfamiliar pigs increases skin damages due to fighting, but keeping pigs in small groups or at high stocking density may limit this effect. Research is needed to identify alternative tools to the electric prod and to design a stunning chute enabling a smooth flow of pigs into the stunner.

Boye J.,Agriculture and Agri Food Canada | Zare F.,McGill University | Pletch A.,McGill University
Food Research International | Year: 2010

Pulses (pea, chickpea, lentil, bean) are an important source of food proteins. They contain high amounts of lysine, leucine, aspartic acid, glutamic acid and arginine and provide well balanced essential amino acid profiles when consumed with cereals and other foods rich in sulphur-containing amino acids and tryptophan. The protein content of most pulse legumes fall within the range of 17-30% (d.w.b.). Apart from their nutritional properties, pulse proteins also possess functional properties that play an important role in food formulation and processing. Examples of such functional properties include solubility, water and fat binding capacity and foaming. Various research studies indicate that some functional properties of pulse proteins may be comparable to those of other frequently used proteins such as soy and whey. The functional properties of pulse proteins have been exploited in the preparation and development of products such as bakery products, soups, extruded products and ready to eat snacks. The growing body of research on the health benefits associated with the consumption of pulses has increased interest in developing innovative technologies to expand the use of pulses in food products. At the same time, there are growing global food security challenges and protein malnutrition continues to be a problem in many countries around the world. Pulses, especially when blended with cereal proteins, may offer a promising alternative source for nutritional and functional proteins. This review provides an overview of the characteristics of pulse proteins, current and emerging techniques for their fractionation, their major functional properties and opportunities for their use in various applications. Crown Copyright © 2009.

Bailey K.L.,Agriculture and Agri Food Canada
Canadian Journal of Plant Pathology | Year: 2010

This manuscript is an invited paper in recognition of the Outstanding Research Award granted to Dr K. L. Bailey by the Canadian Phytopathological Society For many years, researchers have been sceptical as to whether microbial biological control agents, and in particular biopesticides, would be developed for use in areas other than greenhouses and forestry. This perception is slowly changing as the increased development and use of biopesticides in Canada is moving from being a novelty to a reality. This paper examines the role of biopesticides in Canada and the nine stages required to take a microbial biopesticide from discovery through product development, striving for commercialization and adoption by the end user. It highlights examples of Canadian biopesticide innovations that have moved through the innovation chain, illustrating the challenges and rewards along the way. © 2010 The Canadian Phytopathological Society.

Silversides F.G.,Agriculture and Agri Food Canada
Poultry science | Year: 2012

The maintenance of bone strength has been an important issue in the debate over cage use for laying hens. Bone strength depends on adequate mechanical load and cages restrict movement. Four laying crosses (Lohmann White, Lohmann Brown, H&N White, and Rhode Island Red × Barred Plymouth Rock cross hens) were housed in conventional cages or in floor pens equipped with perches and nest boxes to measure the effect of the housing system on bone strength. Approximately 15 hens of each genotype from each housing system were killed at 50 wk of age and the radius and tibia of each were removed for analysis. There were no differences between the Lohmann White and H&N White (White Leghorn) hens, likely because of their similar genetic background. The Lohmann Brown and the cross hens (brown-egg layers) were larger and they had heavier bones, but the bone density was not different from that of the other lines. The radius was heavier for hens kept in floor pens than for those kept in cages, but the tibia was not. When hens were kept in floor pens, both bones had greater cortical bone density and cross-sectional area, but the difference between housing systems in cortical bone cross-sectional area was much greater for the radius than it was for the tibia. Although the movement of hens in cages is limited, they spend a great deal of time standing, which puts a mechanical load on the tibia. Hens in floor pens are able to stretch their wings or fly, in contrast to hens kept in cages, which likely explains why the difference between housing systems in cortical bone was greater for the radius than for the tibia.

Barra Caracciolo A.,CNR Water Research Institute | Topp E.,Agriculture and Agri Food Canada | Grenni P.,CNR Water Research Institute
Journal of Pharmaceutical and Biomedical Analysis | Year: 2015

Environmental microorganisms play a key role in fundamental ecological processes such as biogeochemical cycling and organic contaminant degradation. Microorganisms comprise a large unexplored reservoir of genetic diversity and metabolic capability providing several ecosystem services, most importantly the maintenance of soil and water quality. Pharmaceutical occurrence in the environment can compromise microbial community structure and activities in different ways. The fate of a pharmaceutical in soil or water depends on numerous factors, including its inherent physic-chemical properties (e.g. water solubility, lipophilicity, vapour pressure), environmental factors and climate conditions (e.g. temperature, incident radiation, pH) and most importantly the presence and activity of microorganisms that possess the ability to biodegrade it. The presence of a natural microbial community is a necessary prerequisite for an effective response to the various chemicals that can contaminate an ecosystem. The recovery from contamination is only possible if toxicity does not hamper microbial activity. This review presents current knowledge on the effects on natural microbial communities of some pharmaceuticals and of some biocides commonly found as environmental microcontaminants. © 2014 Elsevier B.V.

Campos-Vega R.,Autonomous University of Queretaro | Loarca-Pina G.,Autonomous University of Queretaro | Oomah B.D.,Agriculture and Agri Food Canada
Food Research International | Year: 2010

Pulses contain a number of bioactive substances including enzyme inhibitors, lectins, phytates, oligosaccharides, and phenolic compounds. Enzyme inhibitors can diminish protein digestibility, and lectins can reduce nutrient absorption, but both have little effect after cooking. Phytic acid can diminish mineral bioavailability. Some phenolic compounds can reduce protein digestibility and mineral bioavailability, and galactooligosaccharides may cause flatulence. On the other hand, these same compounds may have protective effects. Phytic acid exhibits antioxidant activity and protects DNA damage, phenolic compounds have antioxidant and other important physiological and biological properties, and galactooligosaccharides may elicit prebiotic activity. These compounds can have complementary and overlapping mechanisms of action, including modulation of detoxifying enzymes, stimulation of the immune system, regulation of lipid and hormone metabolism, antioxidant, antimutagen, and antiangiogenic effects, reduction of tumor initiation, and promotion and induction of apoptosis. Secondary metabolites are considerated antinutrients, simultaneously conferring health benefits, so these secondary metabolites are currently marketed as functional foods and nutraceuticals ingredients. © 2009.

Roy F.,McGill University | Boye J.I.,Agriculture and Agri Food Canada | Simpson B.K.,McGill University
Food Research International | Year: 2010

Pulse crops are cool season, annually grown legume crops, which are harvested for their seeds. They are invaluable agricultural commodities which are produced and imported by many regions of the world. Pulse seeds are a valuable source of dietary protein, carbohydrates, fiber and an important source of essential vitamins and minerals. Their nutritional characteristics have been associated with a reduction in the incidence of various cancers, HDL cholesterol, type-2 diabetes and heart disease. Pulses also contain protein and non-protein antinutritional factors, which may cause deleterious effects on the host when the seeds or processed seeds are consumed raw. Conversely, recent studies have demonstrated that protein antinutritional compounds such as lectins, protease inhibitors and the non-antinutritional component, angiotensin I-converting enzyme (ACE) inhibitor may have beneficial properties. Lectins have been associated with reducing certain forms of cancer, activating innate defense mechanisms and managing obesity. Protease inhibitors such as trypsin and chymotrypsin inhibitors have been demonstrated to reduce the incidence of certain cancers and demonstrate potent anti-inflammatory properties. Angiotensin I-converting enzyme (ACE) inhibitor has been associated with a reduction in hypertension. © 2009 Elsevier Ltd.

Tosh S.M.,Agriculture and Agri Food Canada | Yada S.,California Almond Board
Food Research International | Year: 2010

Pulses are a good source of dietary fibre and other important nutrients. Flours and fibre-rich fractions obtained from pulse crops can be incorporated into processed foods to increase dietary fibre content and/or serve as functional ingredients. This review focuses on research conducted in the past ten years on the non-starch polysaccharides and oligosaccharides found in dry beans (Phaseolus vulgaris), chickpeas (Cicer arietinum), lentils (Lens culinaris), and dry peas (Pisum sativum). The isolation, composition, and structure of these pulse fibres are described. Common terms used to describe the physicochemical properties of fibre fractions are defined and briefly discussed. Recent studies on the effects of processing on the ratio of insoluble to soluble dietary fibre and on the α-galacto-oligosaccharide content of pulses and fibre fractions are cited and summarized. Food applications for pulse fibre fractions and flours in fibre enrichment, nutrient enrichment, fat binding and retention, and texture modification, as well as some non-food applications, are reviewed. Crown Copyright © 2009.

Reblova M.,Academy of Sciences of the Czech Republic | Seifert K.A.,Agriculture and Agri Food Canada
Studies in Mycology | Year: 2011

Sterigmatobotrys macrocarpa is a conspicuous, lignicolous, dematiaceous hyphomycete with macronematous, penicillate conidiophores with branches or metulae arising from the apex of the stipe, terminating with cylindrical, elongated conidiogenous cells producing conidia in a holoblastic manner. The discovery of its teleomorph is documented here based on perithecial ascomata associated with fertile conidiophores of S. macrocarpa on a specimen collected in the Czech Republic; an identical anamorph developed from ascospores isolated in axenic culture. The teleomorph is morphologically similar to species of the genera Carpoligna and Chaetosphaeria, especially in its nonstromatic perithecia, hyaline, cylindrical to fusiform ascospores, unitunicate asci with a distinct apical annulus, and tapering paraphyses. Identical perithecia were later observed on a herbarium specimen of S. macrocarpa originating in New Zealand. Sterigmatobotrys includes two species, S. macrocarpa, a taxonomic synonym of the type species, S. elata, and S. uniseptata. Because no teleomorph was described in the protologue of Sterigmatobotrys, we apply Article 59.7 of the International Code of Botanical Nomenclature. We epitypify (teleotypify) both Sterigmatobotrys elata and S. macrocarpa to give the genus holomorphic status, and the name S. macrocarpa is adopted for the holomorph. To evaluate the ordinal and familial affinities of Sterigmatobotrys and its relationships with the morphologically similar genera Carpoligna and Chaetosphaeria, phylogenetic relationships were inferred based on aligned sequences of the large subunit nuclear ribosomal DNA (ncLSU rDNA). © 2011 by the CBS Fungal Biodiversity Centre.

Lin S.,Wuhan University of Technology | Huang J.,Wuhan University of Technology | Chang P.R.,Agriculture and Agri Food Canada | Wei S.,Wuhan University of Technology | And 2 more authors.
Carbohydrate Polymers | Year: 2013

New nanocomposites consisting of a castor oil-based polyurethane matrix filled with acetylated cellulose nanocrystals (ACNs) were developed. The ACN exhibited improved dispersion in tetrahydrofuran as a blending medium, and reduced polarity as compared with unmodified cellulose nanocrystals, resulting in a high loading level of 25 wt% in the nanocomposite. As the ACN loading-level increased from 0% to 25%, the tensile strength and Young's modulus of the nanocomposites increased from 2.79 MPa to 10.41 MPa and from 0.98 MPa to 42.61 MPa, respectively. When the ACN loading-level was 10 wt%, the breaking elongation of the nanocomposites reached the maximum value of more than twice that of the polyurethane. The enhanced mechanical performance was primarily attributed to the formation of a three-dimensional ACN network and strong interfacial interactions between filler and matrix. This work produced new polyurethane-based nanocomposites containing modified cellulose nanocrystal with a high biomass content. Its high performance could contribute to potential applications.

Tanino K.K.,University of Saskatchewan | Kalcsits L.,University of British Columbia | Silim S.,Agriculture and Agri Food Canada | Kendall E.,Memorial University of Newfoundland | Gray G.R.,University of Saskatchewan
Plant Molecular Biology | Year: 2010

The role of temperature during dormancy development is being reconsidered as more research emerges demonstrating that temperature can significantly influence growth cessation and dormancy development in woody plants. However, there are seemingly contradictory responses to warm and low temperature in the literature. This research/review paper aims to address this contradiction. The impact of temperature was examined in four poplar clones and two dogwood ecotypes with contrasting dormancy induction patterns. Under short day (SD) conditions, warm night temperature (WT) strongly accelerated timing of growth cessation leading to greater dormancy development and cold hardiness in poplar hybrids. In contrast, under long day (LD) conditions, low night temperature (LT) can completely bypass the short photoperiod requirement in northern but not southern dogwood ecotypes. These findings are in fact consistent with the literature in which both coniferous and deciduous woody plant species' growth cessation, bud set or dormancy induction are accelerated by temperature. The contradictions are addressed when photoperiod and ecotypes are taken into account in which the combination of either SD/WT (northern and southern ecotypes) or LD/LT (northern ecotypes only) are separated. Photoperiod insensitive types are driven to growth cessation by LT. Also consistent is the importance of night temperature in regulating these warm and cool temperature responses. However, the physiological basis for these temperature effects remain unclear. Changes in water content, binding and mobility are factors known to be associated with dormancy induction in woody plants. These were measured using non-destructive magnetic resonance micro-imaging (MRMI) in specific regions within lateral buds of poplar under SD/WT dormancing inducing conditions. Under SD/WT, dormancy was associated with restrictions in inter- or intracellular water movement between plant cells that reduces water mobility during dormancy development. Northern ecotypes of dogwood may be more tolerant to photoinhibition under the dormancy inducing LD/LT conditions compared to southern ecotypes. In this paper, we propose the existence of two separate, but temporally connected processes that contribute to dormancy development in some deciduous woody plant: one driven by photoperiod and influenced by moderate temperatures; the other driven by abiotic stresses, such as low temperature in combination with long photoperiods. The molecular changes corresponding to these two related but distinct responses to temperature during dormancy development in woody plants remains an investigative challenge. © 2010 Springer Science+Business Media B.V.

Debnath S.C.,Agriculture and Agri Food Canada
Journal of Horticultural Science and Biotechnology | Year: 2010

A procedure for the mass propagation of adventitious shoots regenerated from leaf expiants of red raspberry (Rubus idaeus L.) using a liquid medium-containing bioreactor system combined with gelled medium has been described. Leaf segments of the raspberry cultivars 'Festival', 'Heritage', and 'Latham' produced multiple buds and shoots in 4.5 μM thidiazuron (TDZ)-containing shoot induction medium within 6 - 8 weeks of culture initiation. The raspberry cultivars differed significantly with respect to their shoot regeneration and multiplication rate, with 'Heritage' producing the highest number of adventitious shoots per explant. TDZ supported rapid shoot proliferation at low concentrations (1.2 - 2.3 μM) in the bioreactor system, but shoot elongation was improved in medium containing 4.4 μM 6-benzyladenine (BA). BA-induced, elongated shoots rooted in the bioreactor vessel containing the same medium, but without any plant growth regulators. In vitro-derived plantlets were acclimatised and eventually established in a greenhouse and in the field. These results suggest the possibility of large-scale multiplication of raspberry shoots using a bioreactorbased system.

Viaud V.,French National Institute for Agricultural Research | Angers D.A.,Agriculture and Agri Food Canada | Walter C.,Agrocampus Ouest
Soil Science Society of America Journal | Year: 2010

Because of its role in soil functioning, our ability to predict soil organic matter (SOM) dynamics, as influenced by natural and anthropogenic processes, is essential to mitigating soil degradation, ensuring (bod security, and improving the global environment. Numerous mathematical models have been developed to predict the response of SOM to agricultural practices at the soil-profile or small-plot scales. The same models, coupled with spatial databases, have been applied to larger spatial extents, especially in response to the demand for national inventories of soil C sequestration potential. Modeling SOM dynamics must also be developed at an intermediate integrative level to better investigate the relative importance of transfer and transformation processes in SOM dynamics in agricultural landscapes. Predictive models at the landscape scale will facilitate the assessment of the impact of SOM dynamics on the environment and provide management guidelines at the farm and watershed levels. We review the existing approaches and outline the various needs toward an integrated modeling of SOM at the landscape scale, Landscape-scale modeling involves specific land area representation and model requirements, which include: modeling SOM dynamics in the uncultivated elements of a landscape; simulating SOM distribution and differential dynamics along the soil profile; modeling SOM vertical and lateral fluxes linked to erosion, dissolved organic matter fluxes, and litter transfer; and modeling the spatial distribution of organic matter input and management practices. Even though progress is being made toward all of these aspects, a fully integrated framework for SOM modeling at the landscape level has still to be developed. This will only be possible with the design of a flexible, three-dimensional, spatially explicit representation of the landscape system and with the integration of functional interactions and organic matter transfer functions into the classical SOM modeling frameworks. © Soil Science Society of America, 5585 (Guiltord Rd., Madison Wl 53711 USA All rignts reserved.

Gariepy T.D.,Agriculture and Agri Food Canada | Lindsay R.,Public Health Agency of Canada Zoonotic Diseases and Special Pathogens | Ogden N.,Public Health Agency of Canada | Gregory T.R.,University of Guelph
Molecular Ecology Resources | Year: 2012

Ticks are among the most important vectors of disease in the Northern Hemisphere, and a better understanding of their feeding behaviour and life cycle is critical to the management and control of tick-borne zoonoses. DNA-based tools for the identification of residual bloodmeals in hematophagous arthropods have proven useful in the investigation of patterns of host use in nature. Using a blind test approach, we challenged the utility of the DNA barcode library for the identification of vertebrate bloodmeals in engorged, field-collected Ixodes scapularis. Universal vertebrate primers for the COI barcode region successfully amplified DNA from the host bloodmeal and only rarely amplified tick DNA. Of the 61 field-collected ticks, conclusive genus- and species-level identification was possible for 72% of the specimens. In all but two cases, barcode-based identification of the bloodmeal was consistent with the morphological identification of the vertebrate host the ticks were collected from. Possible explanations for mismatches or ambiguities are presented. This study validates the utility of the DNA barcode library as a valuable and reliable resource for the identification of unknown bloodmeals in arthropod vectors of disease. Future directions aimed at the refinement of these techniques to gain additional information and to improve the amplification success of digested vertebrate DNA in tick bloodmeals are discussed. © 2012 Blackwell Publishing Ltd.

Bahlai C.A.,University of Guelph | Weiss R.M.,Agriculture and Agri Food Canada | Hallett R.H.,University of Guelph
Ecological Modelling | Year: 2013

Soybean aphid (Aphis glycines) is a severe pest of soybean in North America with a diverse natural enemy guild. A large body of literature exists examining aspects of the biology and ecology of this species, but these studies have not been synthesized in a quantitative context, limiting the understanding of the relative importance of environmental and ecological factors in the population dynamics of this species. Existing models for population dynamics of A. glycines are geographically restricted, and do not incorporate host plant phenology or natural enemy impact on aphid population dynamics and phenology. In this paper, a mechanistic tritrophic population and phenology model is developed for this species, incorporating environmental cues, host plant cues and natural enemy dynamics. Individual natural enemy species differ with respect to prey consumption rates and foraging behaviours and may occur at different times in the lifecycle of a prey species in response to environmental cues, densities, or the availability of alternate prey. Additionally, the natural enemy complex of A. glycines differs in composition and abundance in different parts of the aphids range. Because of these factors, we developed a strategy to quantify impact of the natural enemy guild that would facilitate the incorporation of natural enemy complexes occurring at multiple locations. In order to standardize the impact of natural enemy guilds on prey species, we used the Natural Enemy Unit (NEU), where NEU is defined as the number of individuals of a predatory species that can kill 100 individual prey in 24. h. After calibration of the NEU calculation to incorporate a type III functional response to prevent natural enemies from driving aphid populations to local extinction, the model performed very well in predicting the dynamics between populations of natural enemies and A. glycines when compared to field observations. Simulations suggest that natural enemy abundance impacts A. glycines abundance more strongly than environmental conditions, but host plant phenology also dramatically influences dynamics of this species. © 2013 Elsevier B.V.

Rawson A.,National University of Ireland | Patras A.,University of Guelph | Tiwari B.K.,Manchester Metropolitan University | Noci F.,University College Dublin | And 2 more authors.
Food Research International | Year: 2011

Exotic fruits play a vital role in human diet due to the presence of bioactive compounds. Recent research shows the importance of phytochemicals and antioxidants in human health and nutrition. This review summarizes the recent application of both thermal and non-thermal processing technologies on bioactive content of exotic fruits and their products. This review also discusses the impact of processing conditions on the stability of bioactive compounds in exotic fruits and their products. The information provided will be beneficial for further commercialization and exploration of these novel technologies. © 2011 Elsevier Ltd.

Yang B.,CAS South China Botanical Garden | Jiang Y.,CAS South China Botanical Garden | Shi J.,Agriculture and Agri Food Canada | Chen F.,Clemson University | Ashraf M.,University of Agriculture at Faisalabad
Food Research International | Year: 2011

Mature longan (Dimocarpus longan Lour.) fruit has a succulent, edible and white aril, which has gained popularity as an exotic fruit in temperate regions. It is prized on the international market resulting in an increased production with significant contributions to local economic development. Longan fruit contains significant amounts of bioactive compounds such as corilagin, ellagic acid and its conjugates, 4-O-methylgallic acid, flavone glycosides, glycosides of quercetin and kaempferol, ethyl gallate 1-β-O-galloyl-d-glucopyranose, grevifolin and 4-O-α-l-rhamnopyranosyl-ellagic acid. The fruit has been used in the traditional Chinese medicinal formulation, serving as an agent in relief of neural pain and swelling. The application of ultrasonic-assisted extraction or high pressure-assisted extraction greatly increases the yield from longan pericarp or seeds. In recent years, some pharmacological activities such as anti-tyrosinase, anti-glycated and anticancer activities, and memory-enhancing effects of longan aril, pericarp or seed extract have been found, implicating a significant contribution to human health. Regarding the increasing cultivation area and increasing quantity of longan fruit in the world, further utilization of this fruit is expected in an effort to use more efficiently the inherent bioactive compounds. The paper reviews the recent advances in the extraction and pharmacological activities of bioactive compounds from longan fruit. Some novel pharmacological potential of longan fruit is also discussed in this paper. © 2010 Elsevier Ltd.

Wang T.-C.,Henan Agricultural University | Wei L.,Henan Agricultural University | Wang H.-Z.,Chinese Academy of Agricultural Sciences | Ma S.-C.,Henan Polytechnic University | Ma B.L.,Agriculture and Agri Food Canada
Field Crops Research | Year: 2011

In the rain-fed areas of northern China, maize (Zea mays L.) is a main field crop, as it is well adapted to high temperatures and bright sunshine. However, low and variable rainfall and high evapotranspiration rates are common in water-limited environments during the growing season, and often mismatched rainfall events with the critical growth stages, making yield unstable. In this study, the performance of a furrow-planting and straw-mulching system was compared with the conventional flat-planting system in a double-crop culture of winter wheat (Triticum aestivum L.) and summer maize for two consecutive years (2005-2006 and 2006-2007). The four tested treatments were: conventional flat planting (F), furrow planting between ridges (B), flat planting with wheat straw-mulching (FS), and furrow planting between ridges with wheat-straw mulch (BS). Soil water content and leaf area index (LAI) were measured throughout the growing season each year, and grain yield and precipitation-use efficiency (PUEY) were determined.On average, ridge tillage combined with furrow planting increased maize yield by 430kgha-1 (7.3%) and PUEY by 10.7% (1.5kgha-1mm-1), compared with the conventional flat planting; furrow planting coupled with straw mulching increased yield by an additional 16.9% and PUEY by 19.4%, respectively. From jointing to maturity, LAI values of BS were significantly higher than those of F-system (55.6% vs. 26.1% in 2006 and 81.4% vs. 21.7% in 2007). Our data suggest that maize production adopted by furrow planting with straw-covered ridges performed best under seasonal average rainfall below 480mm, which was associated with better synchronization of seasonal soil water supply and crop needs, leading to improved maize yield and PUEY. © 2011.

Formation of plant virus membrane-associated replication factories requires the association of viral replication proteins and viral RNA with intracellular membranes, the recruitment of host factors and the modification of membranes to form novel structures that house the replication complex. Many viruses encode integral membrane proteins that act as anchors for the replication complex. These hydrophobic proteins contain transmembrane domains and/or amphipathic helices that associate with the membrane and modify its structure. The comovirus Co-Pro and NTP-binding (NTB, putative helicase) proteins and the cognate nepovirus X2 and NTB proteins are among the best characterized plant virus integral membrane replication proteins and are functionally related to the picornavirus 2B, 2C, and 3A membrane proteins. The identification of membrane association domains and analysis of the membrane topology of these proteins is discussed. The evidence suggesting that these proteins have the ability to induce membrane proliferation, alter the structure and integrity of intracellular membranes, and modulate the induction of symptoms in infected plants is also reviewed. Finally, areas of research that need further investigation are highlighted. © 2013 Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada.

Pomar J.,University of Lleida | Lopez V.,University of Lleida | Pomar C.,Agriculture and Agri Food Canada
Computers and Electronics in Agriculture | Year: 2011

On-farm implementation of the concept of precision livestock farming requires the design and development of new, advanced and often complex equipment. This article proposes an agent-based simulation framework to meet the challenges of designing, testing and evaluating the performance of the new, automated precision feeding equipment for farms. In this context, an agent is a piece of software performing defined system functions such as exchanging information or requesting services to other agents via a high-level agent communication language. The proposed approach sees each main component of the actual precision feeding system represented by a virtual domain agent. The agents are then assembled within a multi-agent system that models the automatic precision feeding equipment as a whole. The operational capacity of the virtual prototype is achieved through communication and collaboration between the multiple agents that make up the system. The capacity for dynamic modification of parameters such as workload during the simulation process helps analyze the behavior, robustness and performance of the system prior to its actual use and thus providing a computer-aid tool helping in the design process. One case study shows that agent-based composable simulation can predict the behavior and performance of the system as a whole. © 2011.

Sandeman R.M.,University of Vic | Bowles V.M.,University of Melbourne | Colwell D.D.,Agriculture and Agri Food Canada
Parasite Immunology | Year: 2014

The current state of myiasis vaccine technologies are reviewed mainly in the primary research genera of Lucilia and Hypoderma. The importance of myiasis flies as primary causes of morbidity and mortality in agricultural species and man has not diminished despite the existence of good control strategies. However, the development of vaccines against myiasis infections has been relatively quiescent for more than 10 years despite the rapid development of genomic and proteomic analysis and of skills in data interpretation. The value of vaccine research in an era of chemical primacy is analysed. In fact, recent findings of drug resistance and the impact of animal welfare concerns should mean a renewed interest in alternative controls. The reasons that this has not been true to date are explored and new possibilities discussed. © 2014 John Wiley & Sons Ltd.

Hannoufa A.,Agriculture and Agri Food Canada | Hossain Z.,Environmental Proteomics NB Inc.
Biocatalysis and Agricultural Biotechnology | Year: 2012

Carotenoids are plant secondary metabolites with a range of beneficial physiological, health and industrial traits. In this review, we summarize the carotenoid biosynthesis pathway and provide an update on research into its regulation in plants. We discuss some factors that determine the steady-state levels of carotenoids in different plant organs and tissues. These factors include the flux through the biosynthesis pathway, and how certain steps represent rate-limiting (bottlenecks), that were exploited in the metabolic engineering of carotenoids. In addition, we discuss carotenoid catabolism, storage and sequestration, and transcriptional and epigenetic regulation as factors affecting the rate of carotenoid accumulation. © 2012.

Kumar S.,University of Manitoba | Banks T.W.,Applied Genomics | Cloutier S.,University of Manitoba | Cloutier S.,Agriculture and Agri Food Canada
International Journal of Plant Genomics | Year: 2012

The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference. © 2012 Santosh Kumar et al.

Jacques J.,Laval University | Berthiaume R.,Agriculture and Agri Food Canada | Cinq-Mars D.,Laval University
Small Ruminant Research | Year: 2011

Forty male Dorset lambs were divided at weaning into four dietary treatment groups: ad libitum concentrates (C), restricted concentrates (RC), zero grazing (ZGR) and grazing (GR). All the lambs were weaned and slaughtered at similar weights, 24. kg for weaning and 47. kg for slaughter. The average daily gain (ADG) of the RC-fed lambs (347. g/d) was lower than that of the C-fed lambs (449. g/d) but higher than that of the lambs in the ZGR (267. g/d) and GR (295. g/d) treatments (P< 0.0001). There was no significant difference between the ZGR and GR lambs for ADG. To reach slaughter weight, the RC and ZGR-GR lambs required 20 and 40 additional days, respectively (P< 0.0001), compared to the C-fed lambs. The lambs fed C had better feed efficiency than the lambs on mixed (RC) or forage-based (ZGR, GR) diets (P< 0.0001). Values for body score, in vivo (P< 0.05) back fat thickness (P< 0.0001), and back fat thickness after slaughter (P< 0.05) were higher in the carcasses of the C-fed lambs compared to the values obtained with the other dietary treatments. No difference was observed among the treatments for leg and shoulder muscle classification (P> 0.05). However, the loins of the C-fed lambs obtained a higher classification score than those of the lambs raised under ZGR or GR (P< 0.05). Carcass yield was greater (P< 0.0001) for the C-fed lambs compared to the RC and ZGR lambs, mostly because of a lighter full digestive tract (P = 0.0007). The carcasses of the grazing lambs obtained a lower global rating classification (P< 0.05), mainly because of a lack of back fat thickness. Feeding system had a significant effect on subcutaneous fat lightness (L*) (P = 0.004) and yellowness (b*) (P< 0.0001) but did not affect redness (a*). Overall, forage-based diets may prevent excessive carcass fat in heavy lambs while producing similar muscle development, resulting in a leaner product for consumers. © 2010 Elsevier B.V.

Malhi S.S.,Agriculture and Agri Food Canada | Nyborg M.,University of Alberta | Goddard T.,Alberta Agriculture and Rural Development | Puurveen D.,University of Alberta
Nutrient Cycling in Agroecosystems | Year: 2011

Soil, crop and fertilizer management practices may affect the amount and quality of organic C and N in soil. A long-term field experiment (growing barley, wheat, or canola) was conducted on a Black Chernozem (Albic Argicryoll) loam at Ellerslie, Alberta, Canada, to determine the influence of 19 (1980 to 1998) or 27 years (1980 to 2006) of tillage (zero tillage [ZT] and conventional tillage [CT]), straw management (straw removed [S Rem]and straw retained [S Ret]) and N fertilizer rate (0, 50 and 100 kg N ha -1 in S Ret and 0 kg N ha -1 in S Rem plots) on total organic C (TOC) and N (TON), and light fraction organic C (LFOC) and N (LFON) in the 0-7.5 and 7.5-15 cm or 0-5, 5-10 and 10-15 cm soil layers. The mass of TOC and TON in soil was usually higher in S Ret than in S Rem treatment (by 3.44 Mg C ha -1 for TOC and 0.248 Mg N ha -1 for TON after 27 years), but there was little effect of tillage and N fertilization on these parameters. The mass of LFOC and LFON in soil tended to increase with S Ret (by 285 kg C ha -1 for LFOC and 12.6 kg N ha -1 for LFON with annual rate of 100 kg N ha -1 for 27 years) , increased with N fertilizer application (by 517 kg C ha -1 for LFOC and 36.0 kg N ha -1 for LFON after 27 years), but was usually higher under CT than ZT (by 451 kg C ha -1 for LFOC and 25.3 kg N ha -1 for LFON after 27 years). Correlations between soil organic C or N fractions were highly significant in most cases. Linear regressions between crop residue C input and soil organic C or N were significant in most cases. The effects of tillage, straw management and N fertilizer on soil were more pronounced for LFOC and LFON than TOC and TON, and also in the surface layers than in the deeper layers. Tillage and straw management had little or no effect on C:N ratios, but the C:N ratios in light organic fractions significantly decreased with increasing N rate (from 20. 06 at zero-N to 18. 91 at 100 kg N ha -1). Compared to the 1979 results, in treatments that did not receive N fertilizer (CTS Rem0, CTS Ret0, ZTS Rem0 and ZTS Ret0), CTS Rem0 resulted in a net decrease in TOC concentration (by 1.9 g C kg -1) in the 0-15 cm soil layer in 2007 (after 27 years), with little or no change in the CTS Ret0 and ZTS Rem0 treatments, while there was a net increase in TOC concentration (by 1.2 g C kg -1) in the ZTS Ret0 treatment. Straw retention and N fertilizer application at 50 and 100 kg N ha -1 rates showed a net positive effect on TOC concentration under both ZT (ZTS Ret50 by 2.3 g C kg -1 and ZTS Ret100 by 3.1 g C kg -1) and CT (CTS Ret50 by 3.5 g C kg -1 and CTS Ret100 by 1.6 g C kg -1) treatments in 2007 compared to 1979 data. In conclusion, the findings suggest that retention of straw, application of N fertilizer and elimination of tillage would improve soil quality, and this might increase the potential for N supplying power of the soil and sustainability of crop productivity. © 2011 Springer Science+Business Media B.V.

Redhead S.A.,Agriculture and Agri Food Canada
Taxon | Year: 2013

The Committee supports recognition of multiple official repositories over a single repository, and accepted three: Fungal Names, Index Fungorum, and MycoBank starting 1 January 2013, noting that parties representing the three have signed a Memorandum of Cooperation that expires immediately following the next International Botanical Congress in 2017. The effectiveness of this arrangement will be evaluated and reviewed by 2014 when the International Mycological Congress must ratify the NCF recommendations.

Three new species of old-world Clastopteridae belonging to Machaerotinae are described, two in new monobasic genera: Allox transfigurata (Hindolini) from Borneo and Irridiculum deformatum (Machaerotini) from Sulawesi. One new species Machaeropsis dramatica (Hindolini) is described from Borneo. It is the first male known from the genus and shows that Machaeropsis Melichar is not synonymous with Metaenderleinia Lallemand. Five other new species are described, belonging to a new, related tribe Zygonini. Two of these new species (Ambonga lanceolata and Pseudomachaerota cucullata) belong to formerly monobasic genera from Madagascar incorrectly assigned to Cercopidae and Aphrophoridae respectively. These are related to 3 new genera: (1) from Madagascar, Pseudoclastoptera with new species P. irrubesco and P. invidia; from sub-Saharan Africa, (2) Zygon with 1 new species Z. desegregatum, and (3) Hemizygon, the latter with 2 new combinations from Pseudomachaerota: H. grande (Maa) and H. saturnus (Linnavuori). Zygon is possibly the most basal genus in Clastopteridae, according to its remarkable antennal characters with 5 different types of sensilla that show how basiconic and coeloconic sensilla are homodynamous. Genera related to Zygon are widely divergent from other spittlebugs as measured by mDNA "barcode" data from the COI gene. Copyright © 2014 Magnolia Press.

Li X.-Q.,Agriculture and Agri Food Canada | Du D.,University of New Brunswick
PLoS ONE | Year: 2014

C+G content (GC content or G+C content) is known to be correlated with genome/chromosome size in bacteria but the relationship for other kingdoms remains unclear. This study analyzed genome size, chromosome size, and base composition in most of the available sequenced genomes in various kingdoms. Genome size tends to increase during evolution in plants and animals, and the same is likely true for bacteria. The genomic C+G contents were found to vary greatly in microorganisms but were quite similar within each animal or plant subkingdom. In animals and plants, the C+G contents are ranked as follows: monocot plants>mammals>non-mammalian animals>dicot plants. The variation in C+G content between chromosomes within species is greater in animals than in plants. The correlation between average chromosome C+G content and chromosome length was found to be positive in Proteobacteria, Actinobacteria (but not in other analyzed bacterial phyla), Ascomycota fungi, and likely also in some plants; negative in some animals, insignificant in two protist phyla, and likely very weak in Archaea. Clearly, correlations between C+G content and chromosome size can be positive, negative, or not significant depending on the kingdoms/groups or species. Different phyla or species exhibit different patterns of correlation between chromosome-size and C+G content. Most chromosomes within a species have a similar pattern of variation in C+G content but outliers are common. The data presented in this study suggest that the C+G content is under genetic control by both trans- and cis- factors and that the correlation between C+G content and chromosome length can be positive, negative, or not significant in different phyla. © 2014 Li, Du.

Sutherland A.B.,University of New Brunswick | Culp J.M.,University of New Brunswick | Benoy G.A.,Agriculture and Agri Food Canada
Limnology and Oceanography: Methods | Year: 2010

Numerous techniques are used to measure deposited sediment and quantify substrate quality in streams. We evaluated the relationship between land disturbance and stream habitat by comparing 25 commonly used deposited sediment parameters to watershed, riparian, and local-scale drivers. We also tested whether land use regressions were improved by accounting for geomorphic setting (measures of slope and channel incision) and how visual versus measurement-based estimations of percent fines and embeddedness were related to each other and to percent agriculture. Of the 16 metrics significantly related to watershed agriculture, subsurface percent fines was the best indicator of land use. Subsurface fines were more strongly related to both watershed and riparian percent agriculture than surface sediment metrics. The second best-performing parameter was the visual assessment of percent fines <2mm. Surface particle counts also performed moderately well. Sediment percentiles (d50, d84) and stability indices were among the weakest indicators of watershed land use. All measures of local percent agriculture were poor predictors of deposited sediment parameters. Mean slope within the entire stream network was nearly as good of a predictor of deposited sediment as watershed percent agriculture. This suggests that we may improve our ability to predict deposited sediment by considering land use within the appropriate geomorphic context. © 2010, by the American Society of Limnology and Oceanography, Inc.

Robitaille G.,Agriculture and Agri Food Canada
Journal of Dairy Research | Year: 2013

Caseinomacropeptide (CMP), a 7-kDa phosphoglycopolypeptide fragment released from κ-casein during milk renneting, is heterogeneous with respect to post-translational glycosylation. Several studies have reported that CMP has growth-promoting activity on lactic acid bacteria belonging to the genera Bifidobacterium. The aim of this study was to evaluate the effect of glycosylation and sequence variations between bovine and caprine CMP on the growth of two probiotics: Lactobacillus rhamnosus RW-9595-M and Bifidobacterium thermophilum RBL67. The growth-promoting activities of CMP (mixture of glycosylated (gCMP) and non-glycosylated (aCMP) fractions), aCMP and gCMP were measured in a basal minimal culture medium using turbidimetric microplate assay at 37Â °C. Supplementation of the culture media at 2 mg/ml significantly improved maximum growth by 1·5 to 1·8 times depending on the strain, the additive (CMP, aCMP, gCMP), and the bovine or caprine origin (PÂ <Â 0·05). CMP preparations also decreased the time needed to reach the inflexion point of the growth curve and increase the cell density at that time (PÂ <Â 0·05). The effects of CMP preparations were dose dependent and significantly superior to the effect of bovine β-lactoglobulin added to the culture media. As gCMP and aCMP were as efficient as bovine and caprine CMP (PÂ >Â 0·1), it was concluded that the presence of oligosaccharides linked to CMP was not essential for growth-promoting activity of CMP. Copyright © Proprietors of Journal of Dairy Research 2012.

Zifkin M.,University of Victoria | Jin A.,University of Alberta | Ozga J.A.,University of Alberta | Irina Zaharia L.,National Research Council Canada | And 6 more authors.
Plant Physiology | Year: 2012

Highbush blueberry (Vaccinium corymbosum) fruits contain substantial quantities of flavonoids, which are implicated in a wide range of health benefits. Although the flavonoid constituents of ripe blueberries are known, the molecular genetics underlying their biosynthesis, localization, and changes that occur during development have not been investigated. Two expressed sequence tag libraries from ripening blueberry fruit were constructed as a resource for gene identification and quantitative realtime reverse transcription-polymerase chain reaction primer design. Gene expression profiling by quantitative real-time reverse transcription-polymerase chain reaction showed that flavonoid biosynthetic transcript abundance followed a tightly regulated biphasic pattern, and transcript profiles were consistent with the abundance of the three major classes of flavonoids. Proanthocyanidins (PAs) and corresponding biosynthetic transcripts encoding anthocyanidin reductase and leucoanthocyanidin reductase were most concentrated in young fruit and localized predominantly to the inner fruit tissue containing the seeds and placentae. Mean PA polymer length was seven to 8.5 subunits, linked predominantly via B-type linkages, and was relatively constant throughout development. Flavonol accumulation and localization patterns were similar to those of the PAs, and the B-ring hydroxylation pattern of both was correlated with flavonoid-3'-hydroxylase transcript abundance. By contrast, anthocyanins accumulated late in maturation, which coincided with a peak in flavonoid-3-O-glycosyltransferase and flavonoid- 3'5'-hydroxylase transcripts. Transcripts of VcMYBPA1, which likely encodes an R2R3-MYB transcriptional regulator of PA synthesis, were prominent in both phases of development. Furthermore, the initiation of ripening was accompanied by a substantial rise in abscisic acid, a growth regulator that may be an important component of the ripening process and contribute to the regulation of blueberry flavonoid biosynthesis. © 2011 American Society of Plant Biologists. All Rights Reserved.

Sanfacon H.,Agriculture and Agri Food Canada
Viruses | Year: 2015

Plant viruses recruit cellular translation factors not only to translate their viral RNAs but also to regulate their replication and potentiate their local and systemic movement. Because of the virus dependence on cellular translation factors, it is perhaps not surprising that many natural plant recessive resistance genes have been mapped to mutations of translation initiation factors eIF4E and eIF4G or their isoforms, eIFiso4E and eIFiso4G. The partial functional redundancy of these isoforms allows specific mutation or knock-down of one isoform to provide virus resistance without hindering the general health of the plant. New possible targets for antiviral strategies have also been identified following the characterization of other plant translation factors (eIF4A-like helicases, eIF3, eEF1A and eEF1B) that specifically interact with viral RNAs and proteins and regulate various aspects of the infection cycle. Emerging evidence that translation repression operates as an alternative antiviral RNA silencing mechanism is also discussed. Understanding the mechanisms that control the development of natural viral resistance and the emergence of virulent isolates in response to these plant defense responses will provide the basis for the selection of new sources of resistance and for the intelligent design of engineered resistance that is broad-spectrum and durable. © 2015 by the authors; licensee MDPI, Basel, Switzerland.

Dettman J.R.,University of Ottawa | Rodrigue N.,Agriculture and Agri Food Canada | Melnyk A.H.,University of Ottawa | Wong A.,Carleton University | And 2 more authors.
Molecular Ecology | Year: 2012

Experimental evolution (EE) combined with whole-genome sequencing (WGS) has become a compelling approach to study the fundamental mechanisms and processes that drive evolution. Most EE-WGS studies published to date have used microbes, owing to their ease of propagation and manipulation in the laboratory and relatively small genome sizes. These experiments are particularly suited to answer long-standing questions such as: How many mutations underlie adaptive evolution, and how are they distributed across the genome and through time? Are there general rules or principles governing which genes contribute to adaptation, and are certain kinds of genes more likely to be targets than others? How common is epistasis among adaptive mutations, and what does this reveal about the variety of genetic routes to adaptation? How common is parallel evolution, where the same mutations evolve repeatedly and independently in response to similar selective pressures? Here, we summarize the significant findings of this body of work, identify important emerging trends and propose promising directions for future research. We also outline an example of a computational pipeline for use in EE-WGS studies, based on freely available bioinformatics tools. © 2012 Blackwell Publishing Ltd.

Koocheki A.,Ferdowsi University of Mashhad | Taherian A.R.,Agriculture and Agri Food Canada | Bostan A.,Ferdowsi University of Mashhad
Food Research International | Year: 2013

Flow properties of Lepidium perfoliatum gum, extracted from Qodume shahri seeds, as influences of concentrations (0.5%, 1%, 1.5% and 2%), temperatures (5, 25, 45, and 65°C), salts and pHs were investigated. Among the selected models, power law model well described the rheological behavior of the L. perfoliatum seed mucilage solutions with high determination coefficients, R2 and low root mean square error (RMSE). Non-Newtonian shear thinning behavior was observed at all temperatures and concentrations. While increase in temperature decreased the viscosity and increased the flow behavior indices, adverse effect was obtained by increasing the concentration. The temperature effect was more pronounced at 0.5% L. perfoliatum seed gum concentration and indicated the higher activation energy (Ea: 31614.56J/mol). The viscosity was dependent on type of salt addition, and decreased with salt concentration. This behavior was more evident when using divalent salt. A marked dependence of viscosity on pH was also observed, as pH increased from acidic to alkaline conditions, the viscosity increased until pH of 9 and afterward decreased. The hydrocolloid showed good water absorption capacity (WAC) and imparted relatively high stability to foam and oil-in-water emulsion. However, the gum solubility was low at all temperatures studied (30, 60 and 90°C). © 2011 Elsevier Ltd.

Hopkinson R.F.,Custom Climate Services Inc | Soroka J.J.,Agriculture and Agri Food Canada
Agricultural and Forest Meteorology | Year: 2010

Diamondback moth caused significant damage to the canola crop on the Canadian Prairies in 1995. This infestation caught farmers and agriculture agencies off guard and led to a joint initiative by Agriculture and Agri-Food Canada, Canola Council of Canada, and Environment Canada to determine if such infestations could be forecast. The diamondback moth rarely overwinters on the Prairies and must be advected with air currents from source regions far to the south. A network of pheromone trap sites was established across the agricultural areas of the Prairies in 1997 and 1998 and backward trajectories were generated by the Meteorological Service of Canada's Canadian Meteorological Centre (CMC) for these locations. Forward trajectories were produced from a number of potential source regions. The trajectories were examined to determine if they could explain the occurrence of diamondback moths in the traps. Some aspects of the observed moth populations in these years were successfully explained by backward trajectories that passed near the surface over southern Texas about four days prior to arrival over the eastern Prairies. The trajectory analysis failed to explain moth populations in Alberta. Forecast trajectories from potential source regions based on the Meteorological Service of Canada's Global Environmental Multiscale (GEM) model were occasionally successful as a predictive tool. The frequency of back trajectories from several locations across the southern Canadian Prairies for the summers of 1997-1999 demonstrated that very few originated in or crossed the potential moth source regions in Texas, California or Mexico. Used in conjunction with the network of moth trap sites, the backward trajectories were helpful in providing early detection of diamondback moth infestations. © 2009 Elsevier B.V.

Ziemienowicz A.,University of Lethbridge | Ziemienowicz A.,Agriculture and Agri Food Canada
Biocatalysis and Agricultural Biotechnology | Year: 2014

Agrobacterium has been widely used as a vector to create transgenic plants. Agrobacterium-mediated gene transfer is governed by various factors of bacterial, host and environmental origin. Applications of this technology include enhancement of plant tolerance to biotic/abiotic stresses, increased crop productivity, pest resistance, phytoremediation, production of biopharmaceuticals, and enhanced nutritional content of crop plants. Agrobacterium has been successfully used to transform various economically and horticulturally important monocot and dicot species by standard tissue culture and in planta transformation techniques. Moreover, a novel Agrobacterium T-DNA-derived nano-complex method has been developed which will be highly valuable for plant biology and biotechnology. •In this review we discuss bacterial, host and environmental factors which affect gene transfer during Agrobacterium-mediated plant transformation.•We demonstrate applications of Agrobacterium-mediated gene transfer for production of plants with desired traits.•Several examples of recent advances in Agrobacterium-mediated plant transgenesis are presented and discussed. © 2013 Elsevier Ltd.

This study investigated CO2 and N2O emissions from soil receiving long-term cattle feedlot manure applications under rainfed and irrigated conditions in semi-arid southern Alberta, Canada. Soil available N and CO2 and N2O fluxes were measured after fall crop harvesting and prior to next spring's seeding from plots that had received 0 and 60 t ha−1yr−1 cattle feedlot manure application with (Mi0 and Mi60) or without irrigation (Mr0 and Mr60) for 27 years. Both CO2 and N2O fluxes varied considerably over the 7-month nongrowing season. Cumulative CO2 emissions from manured treatments (Mr60 at 2.20 t ha−1 and Mi60 at 2.36 t ha−1) were 2.6 times values from nonmanured treatments (Mr0 at 0.83 t ha−1 and Mi0 at 0.92 t ha−1). Similarly, cumulative N2O emission from manured treatments (Mr60 at 4.54 kg ha−1 and Mi60 at 5.34 kg ha−1) were 8–12 times values from nonmanured treatments (Mr0 at 0.40 kg ha−1 and Mi0 at 0.70 kg ha−1). Growing season irrigation had no effect on CO2 and N2O emission over the nongrowing season. Copyright © 2015 Crown copyright.

Hugelius G.,University of Stockholm | Kuhry P.,University of Stockholm | Tarnocai C.,Agriculture and Agri Food Canada | Virtanen T.,University of Helsinki
Permafrost and Periglacial Processes | Year: 2010

We investigated total storage and landscape partitioning of soil organic carbon (SOC) in continuous permafrost terrain, central Canadian Arctic. The study is based on soil chemical analyses of pedons sampled to 1-m depth at 35 individual sites along three transects. Radiocarbon dating of cryoturbated soil pockets, basal peat and fossil wood shows that cryoturbation processes have been occurring since the Middle Holocene and that peat deposits started to accumulate in a forest-tundra environment where spruce was present (~6000 cal yrs BP). Detailed partitioning of SOC into surface organic horizons, cryoturbated soil pockets and non-cryoturbated mineral soil horizons is calculated (with storage in active layer and permafrost calculated separately) and explored using principal component analysis. The detailed partitioning and mean storage of SOC in the landscape are estimated from transect vegetation inventories and a land cover classification based on a Landsat satellite image. Mean SOC storage in the 0-100-cm depth interval is 33.8kg Cm 2, of which 11.8 kg C m 2 is in permafrost. Fifty-six per cent of the total SOC mass is stored in peatlands (mainly bogs), but cryoturbated soil pockets in Turbic Cryosols also contribute significantly (17%). Elemental C/N ratios indicate that this cryoturbated soil organic matter (SOM) decomposes more slowly than SOM in surface O-horizons. © 2010 John Wiley & Sons, Ltd.

Beckie H.J.,Agriculture and Agri Food Canada | Hall L.M.,University of Alberta
Crop Protection | Year: 2014

GMHR crops have been cultivated in the Americas for nearly 20 years. Prior to release, regulators asked the question, "will herbicide selection pressure for evolution of HR weeds increase significantly as a result of GMHR crop cultivation?" In hindsight, they could not have imagined the rapid, widespread adoption of glyphosate-resistant (GR) crops and subsequent chain of events: surge in glyphosate usage at the expense of other herbicides, sharp drop in investment in herbicide discovery, unrelenting rise of GR and multiple-HR weed populations, and increasing herbicide use in GMHR cropping systems. In this brief review, we outline grower adoption of GMHR soybean, maize, cotton, and oilseed rape (canola) in the Americas, and their impact on herbicide-use practices for weed management. Cultivars with stacked-HR traits (e.g., glyphosate + glufosinate + dicamba or 2,4-D) will provide a short-term respite from HR weeds, but will perpetuate the chemical treadmill and selection of multiple-HR weeds. The only sustainable solution is for government or end-users of commodities to set herbicide-use reduction targets in our major field crops similar to European Union member states, and include financial incentives or penalties in agricultural programs to support this policy. Concomitantly, industry incentives must expand to improve grower adoption of best management practices for HR weeds. New or emerging technologies will provide additional tools for reactive HR weed management in the future, but their time of arrival is uncertain. © 2014.

Yu J.,Tianjin University | Chang P.R.,Agriculture and Agri Food Canada | Chang P.R.,University of Saskatchewan | Ma X.,Tianjin University
Carbohydrate Polymers | Year: 2010

Dialdehyde starch (DAS) is prepared by periodate oxidation of starch, and DAS with different aldehyde contents is plasticized by glycerol to obtain thermoplastic DAS (TPDAS). DAS is characterized by Fourier transform infrared (FTIR), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The crystalline starch is destroyed and oxidized to form amorphous DAS, while amorphous starch inside of starch granules is degraded. As a result, DAS containing 93.05% aldehyde content formes a ring shape. Compared to thermoplastic native starch, the re-crystallization of DAS can not take place in TPDAS during the storage period, because periodate oxidation has destroyed the crystallization of starch. With the increasing of aldehyde contents of DAS, the tensile strength and the resistance of both moisture absorption and water vapor permeability of TPDAS are improved. It is ascribed to the cross-linking of aldehyde groups in TPDAS. © 2009 Elsevier Ltd. All rights reserved.

Reynolds W.D.,Agriculture and Agri Food Canada
Engineering Geology | Year: 2015

The variable-head borehole permeameter (VHBP) method is a long-standing international standard for in-situ measurement of field-saturated hydraulic conductivity, KFS, in natural and engineered porous media. Its applicability is restricted, however, because traditional VHBP theory does not apply for unsaturated or deformable porous media, and because precise knowledge of the boundary condition on the interface of the borehole outlet (screen) is required for accurate KFS determination. This study extends the traditional VHBP theory to include saturated, unsaturated, rigid and deformable porous media, and also clarifies the boundary condition at the screen interface. Using a recent VHBP analysis developed for rigid, unsaturated porous media, it is shown (via flow conservation and the total increment theorem) that change in porous medium water content, ▵θ, can be extended to include change in porosity (deformation) as well as change in degree of saturation. It is also shown that the appropriate boundary condition on the borehole screen is antecedent pore water pressure head, Ha, for saturated porous media, but effective wetting front pressure head, ψf (or sorptive number, α*), for unsaturated porous media. The KFS, ▵θ, Ha, and ψf (or α*) parameters can be determined using numerical optimization (e.g. "Solver" in the Excel spreadsheet) to curve-fit the extended VHBP analysis directly to borehole head versus time measurements; however, fitting to the velocity graph (borehole head plotted against change in head with time) is generally less problematic. In a cursory assessment of the extended VHBP analysis, KFS was determined with ≤7% error, ▵θ with ≤15% error, Ha with ≤1.4% error, and ψf with ≤0.5% error, which is more than sufficient accuracy for most applications. It was concluded that the VHBP method was successfully extended for application to saturated, unsaturated, rigid and deformable porous media. © 2014.

O'Hara J.E.,Agriculture and Agri Food Canada
Canadian Entomologist | Year: 2012

Euthera Loew is a small but cosmopolitan genus of Tachinidae with distinctive smoky black cross bands on the wings. There are three described species in North America, Euthera bicolor Coquillett, Euthera setifacies Brooks, and Euthera tentatrix Loew. A new species from California and New Mexico is described as Euthera woodi sp. nov. in honour of dipterist D. Monty Wood. A key and digital images are provided for the identification of the four species, and the three previously described species are diagnosed. Oebalus mexicana (Sailer) and Nezara viridula (L.) (Heteroptera: Pentatomidae) are new host records for E. bicolor and E. tentatrix, respectively. © 2012 Entomological Society of Canada.

Andre Levesque C.,Agriculture and Agri Food Canada
Fungal Diversity | Year: 2011

Transformative changes in biological sciences during the past 25 years have led to many significant advances in oomycete research. Before the last half century there were some hints that the oomycetes were related to some algae but it is now definitively demonstrated that they do not share an evolutionary path with kingdom Eumycota and are instead placed in a new kingdom Straminipila. Clarifying this once and for all has created many opportunities, but the rapid expansion of the research community has caused some fragmentation, probably much more so than in other groups of fungi because of a lack of a unifying forum for the members of the community working on issues such as taxonomy or phylogeny. Prior to the advent of molecular phylogenetics, mycologists working in zoosporic fungi were examining the ultrastructure of the zoospore, mainly focussing on the flagellar apparatus, and managed to generate phylogenies or define clades of zoospore producing fungi that remained for the most part valid after the advances in molecular biology. Comprehensive molecular phylogenies that have been published for some genera of the oomycetes have helped in recognising a large number of new species and in the development of a wide range of DNA-based diagnostic tools. The number of genomes available for this group is increasing rapidly, pushing further the discoveries of novel host-parasite interaction mechanisms in oomycetes. Some important plant diseases that were believed to be under control have re-emerged and many new diseases have appeared particularly in forestry and even in mammals. The research community has been able to respond rapidly and effectively to these new challenges. New ecological roles for the oomycetes were found in the suppression of plant diseases and reduction of plant invasineness in natural ecosystems. There are still many challenges ahead in the oomycete community, probably the most pressing one is to establish a robust tree of life foundation like the Assembling the Fungal Tree of Life initiative. The oomycete research community is dynamic and has put to very good use the many new technological advances. © Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada 2011.

Debnath S.C.,Agriculture and Agri Food Canada
Canadian Journal of Plant Science | Year: 2011

While berry fruits have long enjoyed huge popularity among consumers, tremendous progress in plant tissue culture, resulting in great advances in micropropagation, has occurred. Of particular significance has been the evolution of the technology permitting multiplication of berry plants in bioreactors containing liquid media. Although automation of micropropagation in bioreactors has been advanced as a possible way of reducing propagation cost, optimal plant production depends upon better understanding of physiological and biochemical responses of plant to the signals of culture microenvironment and an optimization of specific physical and chemical culture conditions to control the morphogenesis of berry plants in liquid culture systems. Clonal fidelity can be a serious problem, and molecular strategies have been developed in order to reduce the variation to manageable levels. Molecular markers have been introduced to tissue culture research and can potentially be used in various facets of pertinent studies with berry crops. The paper focuses on bioreactor systems combined with semi-solid media used for in vitro culture of berry crops, cultivation of micropropagules and employment of molecular markers in micropropagated plants for the assessment of genetic fidelity, uniformity, stability and trueness-to-type amongdonor plants and tissue culture regenerants. The pertinent literature is reviewed and the relative merits and shortcomings of the various molecular markers applied are presented with an emphasis on the nature of tissue culture-induced variation.

Chen D.,McMaster University | Lawton D.,McMaster University | Thompson M.R.,McMaster University | Liu Q.,Agriculture and Agri Food Canada
Carbohydrate Polymers | Year: 2012

This study investigated the effectiveness of cellulose nanocrystals derived from potato peel waste as a reinforcement and vapor barrier additive. The nanocrystals were derived from cellulosic material in the potato peel by alkali treatment and subsequently acid hydrolysis. TEM images revealed the average fiber length of the nanocrystals was 410 nm with an aspect ratio of 41; its aspect ratio being considerably larger than cotton-derived nanocrystals prepared using similar reaction conditions. Cellulose nanocrystals (CNC)-filled polyvinyl alcohol (PVA) and thermoplastic starch (TPS) films were prepared by solution casting method to maintain uniform dispersion of the 1-2% (w/w) filler content. An increase of 19% and 33% (starch composite) and 38% and 49% (PVA composite) in tensile modulus was observed for the 1% and 2% CNC-reinforced composites, respectively. Water vapor transmission measurements showed a marginal reduction of water permeability for the PVA composite, whereas no effect was observed for the thermoplastic starch composite. © 2012 Elsevier Ltd.

Gelinas P.,Agriculture and Agri Food Canada
International Journal of Food Science and Technology | Year: 2013

Constipation is a highly prevalent and difficult-to-cure health problem, forcing 10-20% of the worldwide population to seek medical care. Efficacy of treatments varies greatly among individuals, and problems are becoming more frequent despite higher consumption of fibre-rich foods, the most popular solution for preventing such gastrointestinal disorders. The evidence that consumption of fibre prevents and relieves constipation is unconvincing or uncertain. The food industry has made great efforts to develop fibre-rich ingredients, especially those from food by-products and wastes. Except for psyllium and wheat bran, most of these ingredients have intermediate or low laxative potential and their efficacy needs to be confirmed by more clinical studies. This review suggests that there are major discrepancies between the proposed fibre-enriched ingredients and the consumers' needs. As a lasting solution to prevent constipation, the true impact of dietary fibre and potent food-grade laxatives might also be limited by overeating. © 2012 Institute of Food Science and Technology.

Derksen H.,University of Manitoba | Rampitsch C.,Agriculture and Agri Food Canada | Daayf F.,University of Manitoba
Plant Science | Year: 2013

Hormone signaling crosstalk plays a major role in plant defense against a wide range of both biotic and abiotic stresses. While many reviews on plant-microbe interactions have well described the general trends of signaling pathways in shaping host responses to pathogens, few discussions have considered a synthesis of positive versus negative interactions among such pathways, or variations in the signaling molecules themselves. This review deals with the interaction trends between salicylic, jasmonic, and abscisic acids in the signaling pathways, as well as exceptions to such trends. Here we focused on antagonistic versus cooperative interactions between salicylic and jasmonic acids, two major disease resistance signaling molecules, and some interactions with abscisic acid, a known abiotic stress hormone, and another player in plant defense mechanisms. We provide a set of examples materializing either antagonism or cooperation for each interaction between two pathways, thereby showing the trends and pinpointing the exceptions. Such analyses are practical for researchers working on the subject and essential for a better exploitation of the data already available in plant disease resistance signaling, both in Arabidopsis and crop species, toward the development of better disease management strategies for economically important crops. © 2013 Elsevier Ireland Ltd.

Saady N.M.C.,Agriculture and Agri Food Canada
International Journal of Hydrogen Energy | Year: 2013

This paper is a comprehensive review of H2 consumption during anaerobic mixed culture H2 dark fermentation with a focus on homoacetogenesis. Homoacetogenesis consumed from 11% to 43% of the H2 yield in single and repeated batch fermentations, respectively. However, its quantification and extent during continuous fermentation are still not well understood. Models incorporating thermodynamic and kinetic controls are required to provide insight into the dynamic of homoacetogenesis during H2 dark fermentation. Currently, no adequate method exists to eliminate homoacetogenesis because it does not depend on the culture's source, pre-treatment, substrate, type of reactor, or operation conditions. Controlling CO2 concentrations during dark fermentation needs further investigation as a potential strategy towards controlling homoacetogenesis. Incorporating radioactive labeling technique in H2 fermentation research could provide information on simultaneous production and consumption of H2 during dark fermentation. Genetic studies investigating blocking H2 consuming pathways and enhancing H2 evolving hydrogenases are suggested towards controlling homoacetogenesis during dark fermentation. © 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Boye J.,Food and Agriculture Organization of the United Nations | Boye J.,Agriculture and Agri Food Canada | Wijesinha-Bettoni R.,Food and Agriculture Organization of the United Nations | Burlingame B.,Food and Agriculture Organization of the United Nations
British Journal of Nutrition | Year: 2012

In 1989 the Joint FAO/WHO Expert Consultation on Protein Quality Evaluation recommended the use of the Protein Digestibility Corrected Amino Acid Score (PDCAAS) method for evaluating protein quality. In calculating PDCAAS, the limiting amino acid score (i.e., ratio of first limiting amino acid in a gram of target food to that in a reference protein or requirement) is multiplied by protein digestibility. The PDCAAS method has now been in use for 20 years. Research emerging during this time has provided useful data on various aspects of protein quality evaluation that has made a review of the current methods used in assessing protein quality necessary. This paper provides an overview of the use of the PDCAAS method as compared to other methods and addresses some of the key challenges that remain in regards to protein quality evaluation. Furthermore, specific factors influencing protein quality including the effects of processing conditions and preparation methods are presented. Protein quality evaluation methods and recommended protein intakes currently used in different countries vis-à-vis the WHO/FAO/UNU standards are further provided. As foods are frequently consumed in complement with other foods, the significance of the PDCAAS of single protein sources may not be evident, thus, protein quality of some key food groups and challenges surrounding the calculation of the amino acid score for dietary protein mixtures are further discussed. As results from new research emerge, recommendations may need to be updated or revised to maintain relevance of methods used in calculating protein quality. © 2012 The Authors.

Beyaert R.P.,Agriculture and Agri Food Canada | Paul Voroney R.,University of Guelph
Canadian Journal of Soil Science | Year: 2011

Crop residues are the primary means of sustaining soil organic matter levels in agricultural soils. This study was undertaken to determine the effects of tillage practices on the rate of decomposition of crop residues over a 15-yr period under field conditions in southern Ontario. Microplots were amended with 14C-labelled above-ground residues of five annual agricultural crops: corn (Zea mays L.), soybean (Glycine max L.), winter wheat (Triticum aestivum L.), winter rye (Secale cereale L.) and tobacco (Nicotiana tobaccum L.). The crop residues were added to the soil immediately following harvest during the 1990 growing season using a simulated conventional mouldboard plough-disc management (CT) or conservation tillage management (RT), and the amounts of crop residues remaining were measured periodically. The rate of decomposition of the labile C was positively correlated to the levels of hot-water soluble C and N content and negatively correlated to the C:N ratio and hemicellulose concentration of the residues. Decomposition of the residue C was greater under CT during the initial phase of decomposition, indicating that the incorporated residues were exposed to a more favourable environment for microbial activity compared with surface-applied residues. Kinetic analysis of residue decomposition showed that residues managed under CT had a larger labile component and faster rate of decomposition and a smaller resistant component with a slower decomposition rate than RT. Comparisons of models describing the decomposition of combined crops/tillage practices did not describe the decomposition process as well as models for individual crop/tillage combinations.

Gonzalez L.A.,University of Manitoba | Manteca X.,Autonomous University of Barcelona | Calsamiglia S.,Autonomous University of Barcelona | Schwartzkopf-Genswein K.S.,Agriculture and Agri Food Canada | Ferret A.,Autonomous University of Barcelona
Animal Feed Science and Technology | Year: 2012

Ruminal acidosis in feedlot cattle is a common metabolic disorder of digestive origin with significant economic and welfare implications. The main risk factors are high grain, low roughage diets because of their high rate and extent of degradation by rumen microbes. Diet formulation should therefore consider the proportion, method of processing and type of grain; the proportion, fiber concentration and particle size of forages; and the use of feed additives. Grain and forage characteristics, and feed additives, may determine the rate and amount of organic acids produced in the rumen. In addition, diet formulation may also affect feeding behavior, i.e. feed intake and chewing behaviors, which has a great influence on ruminal fluid acid-base balance. Feeding characteristics associated with low ruminal fluid pH are: high dry matter intake and ingestion of large meals because of the greater amount of acid production per period of time, high eating rate because of lower feed ensalivation, short time spent chewing while eating and ruminating because of lower daily saliva production, and large variations in feeding behavior patterns throughout the day such as less frequent meals and rumination. The ruminal acid-base balance requires synchronization in time between acid production and neutralization through saliva, as well as elimination through absorption, wash-out from the rumen, and metabolization. Greater proportions of roughage in the diet and greater particle size leads to slower eating rate and longer chewing time which favors saliva production, and smaller meals which reduce the amount of acid production. Adaptation of feeding behavior to diets with greater proportion of concentrates also plays an important role, as smaller meals and more even distribution of intake throughout the day lead to a better synchronization in time between acid production and elimination or neutralization. Monensin increases the frequency of meals and reduces meal size which is beneficial for ruminal fluid pH, whereas sodium bicarbonate at high concentrations produces the opposite effects and reduces rumination. In addition to diet formulation, feeding management and the social environment may also affect feeding behavior and consequently, ruminal fluid pH. Delivering the feed twice daily results in better synchronization in time between feed intake (acid production), rumination (saliva production), and elimination of fermentation products from the rumen. In contrast, feeding programs that restrict feed amount and time available allow animals to become hungry, whereas restricted feeding space increases competition among group mates. Both situations lead to fewer and larger meals eaten at a faster rate, and consequently, greater risk of ruminal acidosis. © 2011 Elsevier B.V.

Skevington J.H.,Agriculture and Agri Food Canada | Thompson F.C.,Smithsonian Institution
Canadian Entomologist | Year: 2012

The 19 New World species of Sericomyia Meigen are reviewed, including one species new to North America (Sericomyia jakutica (Stackelberg)) and one previously undescribed species (Sericomyia vockerothi Skevington sp. nov. from Alberta, Minnesota, Northwest Territories, Quebec, and Yukon Territory). Mallota powelli Nayar and Cole is recognized as a junior synonym of Sericomyia flagrans (Osten Sacken). A description and illustrations of S. vockerothi and an illustrated key to New World Sericomyia are presented. DNA barcode data are presented for 14 New World species and a cytochrome oxidase subunit I gene tree is presented and discussed. Genetic evidence supports the contention that the subgenera of Sericomyia are not monophyletic. Arctophila Schiner and Conosyprhus Frey are thus proposed as junior synonyms of Sericomyia. © 2012 Entomological Society of Canada.

Boudjou S.,University of Abderrahmane Mira de Bejaia | Oomah B.D.,Agriculture and Agri Food Canada | Zaidi F.,University of Abderrahmane Mira de Bejaia | Hosseinian F.,Carleton University
Food Chemistry | Year: 2013

Two faba bean (Vicia faba L.) subspecies major and minor and lentil seeds grown in Algeria were separated into cotyledons and hulls. These fractions, together with their corresponding whole seeds, were extracted with two solvents, aqueous (70%) acetone and (80%) ethanol, and evaluated for antioxidant activity in relation to their phenolic contents. Acetone selectively extracted tannins from faba beans. The hulls always exhibited high antioxidant activity, measured using the reducing power (RP), antiradical activity (DPPH) or oxygen radical absorbance capacity (ORAC) assays. Aqueous ethanol (80%) extract of lentil hulls exhibited high antioxidant and anti-inflammatory activities preferentially inhibiting 15-LOX (IC50, 55 μg/ml), with moderate COX-1 (IC 50, 66 μg/ml) and COX-2 (IC50, 119 μg/ml) inhibitory effects on the COX pathway, whereas faba bean hull extracts exerted relatively mild LOX inhibitory activity. © 2012 Elsevier Ltd. All rights reserved.

Levy D.,Hebrew University of Jerusalem | Coleman W.K.,Agriculture and Agri Food Canada | Veilleux R.E.,Virginia Polytechnic Institute and State University
American Journal of Potato Research | Year: 2013

Agriculture that depends upon irrigation is challenged by the increasing scarcity of fresh water and global climate change, and increasing human populations aggravate this situation. The potato crop depends on a regular water supply to secure high quality yields. Abiotic stress factors, such as drought, heat and salinity, have severe, adverse effects on growth and yield. In this review, different approaches to cope with water stress are presented. These approaches include altering morphological, physiological and genetic characteristics of potato and the use of biotechnology. For example, native potato and alien genes have been identified by transcriptomics and may provide useful candidates for deployment against stress. Transgenic potato cultivars harboring many of these genes have been evaluated and show promise for future release as new, stress tolerant cultivars. Potential management tools for economizing water use include efficient irrigation systems and precision agriculture. The use of alternative water resources, such as greywater, recycled wastewater, agricultural drainage water, and desalinated water will contribute to the water requirements of the potato crop and should help meet future challenges. © 2013 Potato Association of America.

Malhat F.M.,Agriculture and Agri Food Canada
Food Analytical Methods | Year: 2012

An effective analytical method for the residue analysis of a novel insecticide chlorantraniliprole and its dissipation in grape were studied. Chlorantraniliprole residues were extracted from grape samples with ethyl acetate. The extract was cleaned up with QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) method and determined by high-performance liquid chromatography with photodiode array detector (HPLC-DAD). At fortification levels of 0. 06, 0. 5, and 1. 0 mg kg -1 in grape, it was shown that recoveries ranged from 95. 11 to 102 % with relative standard deviation (RSD) of 6 to 11 %. The limit of detection (LOD) and limit of quantification (LOQ) were found to be 0. 02 and 0. 06 mg kg -1, respectively. The dissipation half-life time of chlorantraniliprole residues in grape was 2. 70 days. According to maximum residue limit (MRL), the preharvest interval (PHI) of chlorantraniliprole on grape was 4 days after the treatment. Based on the results of this study and the relevant residue regulation, chlorantraniliprole residue levels will be acceptable when applied to grape in Egypt. © 2012 Springer Science+Business Media, LLC.

Abd-Alrahman S.H.,King Saud University | Ahmed N.S.,Agriculture and Agri Food Canada
Bulletin of Environmental Contamination and Toxicology | Year: 2012

Dissipation of penconazole was estimated in tomatoes fruits cultivated in field using QuEChERS method for sample preparation and high performance liquid chro-matography with diode array detector. Following one application of normal dose 25 mL 100 L-1 water, the average initial deposits of penconazole were observed to be 0.74 and 1.21 mg kg-1 for tomatoes fruits and soil, respectively. The residues dissipated below the maximum residues limit of 0.2 mg kg-1 after 15 days. The half-life value (T1/2) and preharvest interval of penconazole were 5.61 and 15 days, respectively. While (T1/2) of penconazole in soil was 15.51 days. Thus, a waiting period of 15 day was suggested for the safe consumption of penconazole treated Tomatoes. © Springer Science+Business Media, LLC 2012.

Edwards L.M.,Agriculture and Agri Food Canada
Canadian Journal of Soil Science | Year: 2013

The importance of aggregate size and integrity in soil productivity and crop production is paramount, and aggregate size reduction or increase invariably becomes a primary concern in such soil management practices as tillage and organic matter manipulation. In this regard, therefore, the present review looks particularly at the consequence of freeze-thaw cycling (FTC) on agricultural lands in Prince Edward Island (PEI) where an annual average of 40 cycles induce measurable aggregate breakdown with mixed consequences. On the one extreme, the consequences are manifest in increased soil erosion. On the other extreme, reduced (or reversed) soil compaction and improved seedbed conditions are welcomed consequences where temperature alternation breaks up hard pans or soil clods, or where the predominance of smaller aggregates can be an asset in seedbed environments, favouring improved crop emergence and early-spring establishment. In the PEI soils studied, the greatest changes in aggregate size distribution with FTC occurred in the largest and smallest size fractions wherein fractions <0.5 mm showed a 33% average increase while, simultaneously, the 4.75-9.5 mm fractions showed a 28% average decrease. This breakdown is reflected most contrastingly where FTCs to maximum (asymptotic) breakdown averaged up to 3.5 times for a loam as it did for a sandy loam or a fine sandy loam soil. This review also examines FTC in a broader agricultural and environmental context where it can potentially impact agro-sustainability. Where FTC effects on a fine sandy loam were measured in terms of erosion, there was a sediment mass increase of about 90% in interrill flow and about 25% in rill flow. Further, this review emphasizes methodology that has proven to be workable under the circumstances of PEI's dominant agricultural soils and the FTC research objectives that they helped to shape. It was considered important in this review, also, to highlight the need for expanded research (commencing with regional cooperation), particularly on frost depth, to feed into moisture-availability modelling towards improved clarity for end-user benefit.

Ma Z.,McGill University | Boye J.I.,Agriculture and Agri Food Canada
Food and Bioprocess Technology | Year: 2013

Reducing fat and cholesterol content is currently one of the primary trends in food product innovation. Fat plays an important role in maintaining food quality, particularly the texture, flavor, and stability of food emulsion products. The food industry faces major challenges in seeking to produce reduced-fat and low-cholesterol mayonnaise and dressings that have attributes similar to full-fat products. Efficient monitoring of products to ensure desirable quality requires knowledge of their physicochemical characteristics, including appearance, rheology, emulsion stability, microstructure, and flavor, as well as particle size and charge distribution. The purpose of this paper is to provide a comprehensive overview of trends in the development of reduced-fat and low-cholesterol dressings. The effects of reducing fat content or using various fat replacers on the physicochemical properties of dressing and mayonnaise products are detailed with supporting experimental results. The possibility of using plant-based ingredients or reduced-cholesterol egg yolk in the formulation of such products is also examined. © 2012 Her Majesty the Queen in Right of Canada.

Tantawi T.I.,Agriculture and Agri Food Canada | Sinclair B.J.,Canadian National Collection of Insects and Canadian Food Inspection Agency
Zootaxa | Year: 2013

Seven species of Calliphoridae are reported from the Galápagos Islands, Ecuador: Lucilia pionia (Walker), L. setosa (James), L. deceptor (Curran), L. eximia (Wiedemann), Cochliomyia macellaria (Fabricius), Chrysomya albiceps (Wiedemann), and Chrysomya megacephala (Fabricius). Lucilia eximia is newly recorded from the islands. Lucilia sp. near pionia is recorded from the island of Española. The distribution and collection records of these species are discussed and listed, and a key to their identification is provided. Chrysomya rufifacies (Macquart) is reported for the first time from mainland Ecuador and the identification of this species is outlined. Copyright © 2013 Magnolia Press.

Behan-Pelletier V.M.,Agriculture and Agri Food Canada | Walter D.E.,Invertebrate Zoology
Zootaxa | Year: 2013

Species in the oribatid mite genus Tectoribates are primarily Palaearctic and Neotropical, with scattered, unidentified records from North America. Herein, we describe 3 new Tectoribates species from dry forest and prairie habitats in North America: T. alcecampestris sp. nov., from Alberta, T. borealis sp. nov., from southern Alberta and Ontario, both on the basis of adults and nymphs, and T. campestris sp. nov., from dry grassland habitats in Ontario and Kansas, on the basis of adults. We provide a revised and expanded diagnosis for adults of Tectoribates. We assess relationships of Tectoribates, using characters of adults and newly discovered apheredermous, plicate immatures. We include observations on Pseudotectoribates which is closely related to Tectoribates. The closest relatives of these genera are hypothesised to be among the Tegoribatidae (Achipterioidea) rather than among the Achipteriidae (Achipterioidea), Oribatellidae (Oribatelloidea), or Ceratozetoidea, as suggested in previous classifications. Finally, we give a key to adults of the world fauna of Tectoribates. © 2013 Magnolia Press.

Gerzhova A.,Laval University | Mondor M.,Laval University | Mondor M.,Agriculture and Agri Food Canada | Benali M.,CANMET Energy | Aider M.,Laval University
Food Bioscience | Year: 2015

A novel technology of electro-activation was used for protein extraction from canola meal. An alkaline solution was generated in the cathodic compartment under the influence of electric field. It has been reported to have improved extractive properties when compared to chemically alkalized solutions. The study aims to verify the efficiency of electro-activated solutions for protein extraction from canola oil cake by analyzing the effect of extraction method on the extractability rates, composition, and secondary structure of extracted proteins. The tested parameters included NaCl concentration (0.01-1 M), duration of electro-activation (10-60 min), and current intensity (0.2, 0.3 A). The electro-activation was performed in a three-compartment cell separated by ion exchange membranes, after which the obtained solutions were used for 1-h extraction. Maximal protein extractability was 34.32±1.21% obtained with the electro-activated solution generated under 0.3 A irrespective of the activation time. The conventional extraction under the same conditions (pH 7-10) yielded 31.18±1.89% of proteins. Electrophoretic profiles of electro-activated protein concentrates and isolates analyzed by SDS-PAGE were clearly more distinguishable compared to those obtained by conventional method. FTIR study revealed considerable difference in proteins' secondary structures between different treatment conditions (pH and salt concentration) as well as between conventional and electro-activated samples, showing less denatured spectra for the latter. © 2015 Elsevier Ltd. © 2015 ElsevierLtd.All rights reserved.

Riley R.,University of Ottawa | Charron P.,University of Ottawa | Idnurm A.,University of Missouri - Kansas City | Farinelli L.,FASTERIS SA | And 3 more authors.
New Phytologist | Year: 2014

Summary: Arbuscular mycorrhizal fungi (AMF) are important plant symbionts that have long been considered evolutionary anomalies because of their apparent long-term lack of sexuality, but recent explorations of available DNA sequence have challenged this notion by revealing the presence of homologues of fungal mating type-high-mobility group (MATA-HMG) and core meiotic genes in these organisms. To obtain more insights into the sexual potential of AMF, homologues of MATA-HMGs were sought in the transcriptome of three AMF isolates, and their functional and evolutionary trajectories were studied in genetically divergent strains of Rhizophagus irregularis using conventional and quantitative PCR procedures. Our analyses revealed the presence of at least 76 homologues of MATA-HMGs in R. irregularis isolates. None of these was found to be surrounded by genes generally found near other known fungal mating type loci, but here we report the presence of a 9-kb-long region in the AMF R. irregularis harbouring a total of four tandem-repeated MATA-HMGs; a feature that highlights a potentially elevated intragenomic diversity in this AMF species. The present study provides intriguing insights into the genome evolution of R. irregularis, and represents a stepping stone for understanding the potential of these fungi to undergo cryptic sex. See also the Commentary by Lee et al. © 2013 New Phytologist Trust.

Abbott D.W.,Agriculture and Agri Food Canada | van Bueren A.L.,University of Groningen
Current Opinion in Structural Biology | Year: 2014

Generally, non-catalytic carbohydrate binding module (CBM) specificity has been shown to parallel the catalytic activity of the carbohydrate active enzyme (CAZyme) module it is appended to. With the rapid expansion in metagenomic sequence space for the potential discovery of new CBMs in addition to the recent emergence of several new CBM families that display diverse binding profiles and novel functions, elucidating the function of these protein modules has become a much more challenging task. This review summarizes several approaches that have been reported for using primary structure to inform CBM specificity and streamlining their biophysical characterization. In addition we discuss general trends in binding site architecture and several newly identified functions for CBMs. Streams of investigation that will facilitate the development and refinement of sequence-based prediction tools are suggested. © 2014.

Gariepy T.D.,University of Hawaii at Manoa | Gariepy T.D.,Agriculture and Agri Food Canada | Messing R.H.,University of Hawaii at Manoa
Biological Control | Year: 2012

There has been much debate regarding the impact of parasitoid competition and hyperparasitism on the successful biological control of aphid pests. Difficulty in the evaluation of interspecific interactions and trophic links using conventional rearing and dissection methods has prevented a deeper understanding of such relationships. The analysis of trophic links in the parasitoid community associated with the melon aphid (Aphis gossypii) in Hawaii provides a unique opportunity to assess complex interactions that occur in a system where all of the aphids and parasitoids have been introduced. Here, we developed and applied multiplex PCR assays to investigate the occurrence of in-host competition between parasitoids and/or hyperparasitoids on melon aphids collected from fields of Colocasia esculenta. To fully document the parasitoid-hyperparasitoid community within A. gossypii, both live and mummified aphids were examined. A total of 818 live and 245 mummified aphids were analyzed using the multiplex assays, with congruent rearing of over 600 mummified aphids serving as a basis for qualitative comparisons in terms of species composition and trophic linkages. The rearing and the DNA methods showed similar trends, with sharp declines in one parasitoid species followed by sharp increases in another during the course of the season. Molecular analyses revealed that hyperparasitism and multiparasitism of live aphids is remarkably low, whereas hyperparasitism of mummified aphids was extraordinarily high in both rearing and molecular analyses. In comparison to reared samples, molecular analysis of the parasitoid community was more complete and permitted the identification of previously unknown or unconfirmed trophic linkages. The potential of this approach in future studies on the biological control of aphids in Hawaii, particularly in light of new parasitoid introductions, is discussed. © 2011 Elsevier Inc.

Shaner D.L.,U.S. Department of Agriculture | Beckie H.J.,Agriculture and Agri Food Canada
Pest Management Science | Year: 2014

This review is both a retrospective (what have we missed?) and prospective (where are we going?) examination of weed control and technology, particularly as it applies to herbicide-resistant weed management (RWM). Major obstacles to RWM are discussed, including lack of diversity in weed management, unwillingness of many weed researchers to conduct real integrated weed management research or growers to accept recommendations, influence or role of agrichemical marketing and governmental policy and lack of multidisciplinary research. We then look ahead to new technologies that are needed for future weed control in general and RWM in particular, in areas such as non-chemical and chemical weed management, novel herbicides, site-specific weed management, drones for monitoring large areas, wider application of 'omics' and simulation model development. Finally, we discuss implementation strategies for integrated weed management to achieve RWM, development of RWM for developing countries, a new classification of herbicides based on mode of metabolism to facilitate greater stewardship and greater global exchange of information to focus efforts on areas that maximize progress in weed control and RWM. There is little doubt that new or emerging technologies will provide novel tools for RMW in the future, but will they arrive in time? © 2013 Society of Chemical Industry.

Smith T.W.,Eastern Kentucky University | Smith T.W.,Agriculture and Agri Food Canada | Lundholm J.T.,SaintMarys University
Journal of Vegetation Science | Year: 2012

Question: How are heterogeneity-diversity relationships (HDRs) influenced by spatial structure in environmental variables, sampling grain and the extent of niche differentiation? Methods: We developed a spatially explicit simulation model incorporating variable dispersal distances and competition strength on fractal landscapes. By varying the grain used to sample these models, we examined scaling patterns in HDR metrics at fine scales (sampling grain from 100 to 10 000 individuals, sampling extent ca. 260 000 individuals). Results: Environmental geometry exerts an important influence on the ecological processes responsible for HDRs. Unique geometric characteristics of individual landscapes can greatly influence emergent community properties; field studies frequently use inadequate sample sizes to account for this phenomenon. Two opposing processes influence spatial scaling of HDRs: variance partitioning, which favours smaller-grained samples, and mass effects, which favour larger-grained samples. In assessing HDRs, diversity is more sensitive than species richness, and should be the preferred measure in field studies. The environmental geometry and age of a community interact: compared to high fractal dimension landscapes, low fractal dimension landscapes are slower to develop HDRs, but in the long term their HDRs will be higher. Conclusions: Our study demonstrates that, despite the superficial simplicity of the concept, HDRs vary in complex and non-intuitive ways, and warrant further theoretical and empirical study. More generally, environmental geometry is likely to exert a strong influence on many emergent community processes, but we do not yet have a firm understanding of this relationship. © 2012 International Association for Vegetation Science.

Goyal R.K.,Agriculture and Agri Food Canada | Mattoo A.K.,U.S. Department of Agriculture
Plant Science | Year: 2014

Crop losses due to pathogens are a major threat to global food security. Plants employ a multilayer defense against a pathogen including the use of physical barriers (cell wall), induction of hypersensitive defense response (HR), resistance (R) proteins, and synthesis of antimicrobial peptides (AMPs). Unlike a complex R gene-mediated immunity, AMPs directly target diverse microbial pathogens. Many a times, R-mediated immunity breaks down and plant defense is compromised. Although R-gene dependent pathogen resistance has been well studied, comparatively little is known about the interactions of AMPs with host defense and physiology. AMPs are ubiquitous, low molecular weight peptides that display broad spectrum resistance against bacteria, fungi and viruses. In plants, AMPs are mainly classified into cyclotides, defensins, thionins, lipid transfer proteins, snakins, and hevein-like vicilin-like and knottins. Genetic distance lineages suggest their conservation with minimal effect of speciation events during evolution. AMPs provide durable resistance in plants through a combination of membrane lysis and cellular toxicity of the pathogen. Plant hormones - gibberellins, ethylene, jasmonates, and salicylic acid, are among the physiological regulators that regulate the expression of AMPs. Transgenically produced AMP-plants have become a means showing that AMPs are able to mitigate host defense responses while providing durable resistance against pathogens. © 2014.Published by Elsevier Ireland Ltd.

Warwick S.I.,Agriculture and Agri Food Canada
Weed Science | Year: 2010

ALS inhibitor-resistant biotypes are the fastest growing class of herbicide-resistant (HR) weeds. A Canadian ALS inhibitor-resistant biotype of Russian thistle was first reported in 1989. The molecular basis for ALS-inhibitor resistance is unknown for Canadian populations of this polyploid weed species, and was determined in this study for one Alberta and two Saskatchewan HR Russian thistle populations. HR plants survived spray application of the ALS-inhibitor mixture thifensulfuron:tribenuron in the greenhouse. All three HR Russian thistle populations were heterogeneous and contained both HR and herbicide-susceptible (HS) individuals. The molecular basis for resistance was determined by sequencing the ALS gene and/or conducting a TaqMan genotyping assay for single nucleotide polymorphism (SNP) for the Trp574Leu mutation. Two target-site mutations were observed: Trp574Leu in all three biotypes (554 individuals) and Pro197Gln in one biotype (one individual), suggesting multiple-founding events for Russian thistle HR populations in western Canada. Segregation patterns among F1 and F2 progeny arrays of HR lines sprayed under greenhouse conditions varied; some segregated (i.e., had HR and HS progeny), whereas other lines were exclusively HR. In contrast, no segregation of molecular types, i.e., Trp574, Trp/Leu574 and Leu574, as would be expected with heterozygosity at a single locus Trp/Leu574, was observed. Such lack of segregation is consistent with the polyploid genome structure of Russian thistle and the presence of two copies of the ALS gene. The presence of more than one ALS gene confounded the ability of the molecular techniques to accurately identify "true" heterozygotes in this study. © 2010 Weed Science Society of America.

Yan L.,Jiangxi Science and Technology Normal University | Chang P.R.,Agriculture and Agri Food Canada | Zheng P.,Jiangxi Science and Technology Normal University
Carbohydrate Polymers | Year: 2011

A starch/carboxylated multiwall carbon nanotube (CCNT) composite (CCNT-starch) was prepared by covalently grafting a natural polymer starch onto the surfaces of CCNT. The obtained CCNT-starches were characterized by Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), transmission electron microscopy (TEM), ultraviolet-visible spectroscopy (UV-vis) and electrochemical measurement. FTIR revealed that the covalent bonds between -OH groups of soluble starch and CCNT were formed in CCNT-starch. TEM and TG showed that CCNTs were covered with the grafted starch about 7.7 and 12.8 wt% in CCNT-starch, respectively. The grafted starch facilitated the dispersion of CCNT-starch in water and chitosan films because of the hydrophilic polysaccharide structure of starch components. CCNT-starch containing 12.8 wt% starch in water could form homogeneous solutions without obvious aggregation of CCNTs. The electrochemical properties of the CCNT-starch were characterized by casting CCNT-starch and chitosan solution on glassy carbon electrode. Compared to CCNT, CCNT-starch exhibited a couple of redox peaks in cyclic voltammograms testing. © 2011 Published by Elsevier Ltd. All rights reserved.

Chang P.R.,Agriculture and Agri Food Canada | Yu J.,Tianjin University | Ma X.,Tianjin University
Carbohydrate Polymers | Year: 2011

In this communication, a facile and green method is introduced for the preparation of porous starch (PS), citric acid-modified PS (CAPS) and porous ZnO. PS was created by replacing ice crystals in frozen starch gel with selected solvent using a solvent exchange technique. The porosity of PS was greatly affected by the ethanol/water volume ratios. PS was further modified with citric acid (CA) in order to preserve or maintain its porous state, especially upon contact with aqueous solution. CAPS was subsequently used as a structure-directing agent to prepare ZnO with a porous network structure. The thus obtained PS, CAPS and porous ZnO may find their niche in applications such as adsorbent, structure-directing agents for porous metal oxides or as sensors. © 2010 Elsevier Ltd. All rights reserved.

The objective of this study was to characterize antimicrobial resistance and virulence determinants of Escherichia coli from soil amended with litter from 36-day-old broiler chickens ( Gallus gallus domesticus ) fed with diets supplemented with a variety of antimicrobial agents. Soil samples were collected from plots before and periodically after litter application in August to measure E. coli numbers. A total of 295 E. coli were isolated from fertilized soil samples between August and March. Antibiotic susceptibility was determined by Sensititre, and polymerase chain reaction was performed to detect the presence of resistance and virulence genes. The results confirmed that E. coli survived and could be quantified by direct plate count for at least 7 months in soil following litter application in August. The effects of feed supplementation were observed on E. coli numbers in November and January. Among the 295 E. coli, the highest antibiotic resistance level was observed against tetracycline and β-lactams associated mainly with the resistance genes tetB and bla(CMY-2), respectively. Significant treatment effects were observed for phylogenetic groups, antibiotic resistance profiles, and virulence gene frequencies. Serotyping, phylogenetic grouping, and pulsed-field gel electrophoresis confirmed that multiple-antibiotic-resistant and potentially pathogenic E. coli can survive in soil fertilized with litter for several months regardless of antimicrobials used in the feed.

Seo S.,McGill University | Karboune S.,McGill University | Yaylayan V.,McGill University | L'Hocine L.,Agriculture and Agri Food Canada
Process Biochemistry | Year: 2012

The production of glycated lysozyme (LZM), with galactose, galactooligosaccharides (GOSs) and potato galactan through the Maillard reaction, was investigated. The percent blocked lysine, estimated from the furosine content, reached a maximum value of 11.2% for LZM:galactan conjugates after 1 day incubation at a a w of 0.65. A maximum percent blocked lysine of 7.0 and 13.5% were obtained for LZM:galactose/GOS conjugates at a lower a w of 0.45 after 3 and 7 days, respectively. However, the low percent blocked lysine and the high protein aggregation index of LZM:galactose/GOS conjugates at a w 0.79 and 0.65 revealed the prevalence of the degradation of the Amadori compounds and the protein cross-linking. Mass spectrometry of LZM conjugates revealed the formation of different glycoforms. Glycated LZMs containing up to seven galactose moieties were formed; while only mono- and diglycated LZMs with GOSs were detected. 2-3 mol of galactan were conjugated to 1 mol of LZM. Response surface methodology, based on a 5-level and 3-factor central composite design, revealed that molar ratio and temperature were the most significant variables for the glycation of LZM with GOSs. The optimal conditions leading to a high percent blocked lysine (16.11%) with a low protein aggregation index (0.11) were identified: temperature of 49.5 °C, LZM:GOS molar ratio of 1:9 and a w of 0.65. To the best of our knowledge, this is the first study on the optimization of LZM glycation with GOSs. © 2011 Elsevier Ltd. All rights reserved.

Helgason B.L.,Agriculture and Agri Food Canada | Walley F.L.,University of Saskatchewan | Germida J.J.,University of Saskatchewan
Soil Biology and Biochemistry | Year: 2010

No-till (NT) management greatly reduces soil physical disturbance and can result in a stratification of nutrients and organic matter in the soil profile due to the retention of crop residues on the soil surface potentially affecting the dynamics of microbial interactions in the soil. Microbial abundance and diversity can be used to assess the relative impact of management on the long-term sustainability of cropping systems. The objective of this study was to assess the impact of long-term NT vs. conventional tillage (CT) management on soil microbial community structure at four different sites on the Canadian prairies using phospholipid fatty acid analysis (PLFA) and DNA fingerprinting. Analysis of 16S and 18S rDNA using denaturing gradient gel electrophoresis revealed high inherent variability within bacterial and fungal community fingerprints among replicate field plots. Differences in bacterial and fungal phylogeny were related to depth in the soil profile but not to tillage management. Abundance of individual PLFA biomarkers were 7 to 86% greater in NT surface soils (0- to 5-cm depth), except at the Ellerslie site in 2005 where biomass was greater in CT. Responses at the 5- to 10-cm and 10- to 15-cm depths were more varied, in some cases with greater biomass in CT than NT soils. Ordination analysis of PLFA profiles showed clear community separation with depth but not tillage. Physiological stress biomarkers were correlated with simple measures of nutrient concentration and indicated that resource availability was likely the main factor determining community structure. It was concluded that tillage disturbance was not an overriding factor in determining microbial community composition in the long-term NT and CT soils studied. Further study of the interaction of cropping frequency with tillage management is needed to understand the effects of tillage disturbance on microbial turnover of plant derived residues. © 2010.

Rampitsch C.,Agriculture and Agri Food Canada | Bykova N.V.,Memorial University of Newfoundland
Proteomics | Year: 2012

The study of plant disease and immunity is benefiting tremendously from proteomics. Parallel streams of research from model systems, from pathogens in vitro and from the relevant pathogen-crop interactions themselves have begun to reveal a model of how plants succumb to invading pathogens and how they defend themselves without the benefit of a circulating immune system. In this review, we discuss the contribution of proteomics to these advances, drawing mainly on examples from crop-fungus interactions, from Arabidopsis-bacteria interactions, from elicitor-based model systems and from pathogen studies, to highlight also the important contribution of non-crop systems to advancing crop protection. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Danforth B.N.,Cornell University | Cardinal S.,Agriculture and Agri Food Canada | Praz C.,University of Neuchatel | Almeida E.A.B.,University of Sao Paulo | Michez D.,University of Mons
Annual Review of Entomology | Year: 2013

Our understanding of bee phylogeny has improved over the past fifteen years as a result of new data, primarily nucleotide sequence data, and new methods, primarily model-based methods of phylogeny reconstruction. Phylogenetic studies based on single or, more commonly, multilocus data sets have helped resolve the placement of bees within the superfamily Apoidea; the relationships among the seven families of bees; and the relationships among bee subfamilies, tribes, genera, and species. In addition, molecular phylogenies have played an important role in inferring evolutionary patterns and processes in bees. Phylogenies have provided the comparative framework for understanding the evolution of host-plant associations and pollen specialization, the evolution of social behavior, and the evolution of parasitism. In this paper, we present an overview of significant discoveries in bee phylogeny based primarily on the application of molecular data. We review the phylogenetic hypotheses family-by-family and then describe how the new phylogenetic insights have altered our understanding of bee biology. © 2013 by Annual Reviews. All rights reserved.

Kalischuk L.D.,Agriculture and Agri Food Canada | Buret A.G.,University of Calgary
American Journal of Physiology - Gastrointestinal and Liver Physiology | Year: 2010

The inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are T cell-mediated diseases that are characterized by chronic, relapsing inflammation of the intestinal tract. The pathogenesis of IBD involves the complex interaction between the intestinal microflora, host genetic and immune factors, and environmental stimuli. Epidemiological analyses have implicated acute bacterial enteritis as one of the factors that may incite or exacerbate IBD in susceptible individuals. In this review, we examine how interactions between the common enteric pathogen Campylobacter jejuni (C. jejuni), the host intestinal epithelium, and resident intestinal microflora may contribute to the pathogenesis of IBD. Recent experimental evidence indicates that C. jejuni may permit the translocation of normal, noninvasive microflora via novel processes that implicate epithelial lipid rafts. This breach in intestinal barrier function may, in turn, prime the intestine for chronic inflammatory responses in susceptible individuals. Insights into the interactions between enteric pathogens, the host epithelia, and intestinal microflora will improve our understanding of disease processes that may initiate and/or exacerbate intestinal inflammation in patients with IBD and provide impetus for the development of new therapeutic approaches for the treatment of IBD. Copyright © 2010 the American Physiological Society.

King R.R.,Agriculture and Agri Food Canada | Calhoun L.A.,University of New Brunswick
Magnetic Resonance in Chemistry | Year: 2012

The normal levels and types of glycoalkaloids found in commercial varieties of potato (Solanum tuberosum) appear to present no hazard to human health. However when wild Solanum species are used in breeding endeavors, new and untested glycoalkaloids may be introduced. Recent studies of domestic crosses with a wild Solanum oplocense accession indicated that the levels of a non-indigenous glycoalkaloid appeared associated with reduced defoliation by the Colorado potato beetle. The non-indigenous glycoalkaloid was isolated from foliage of the wild S. oplocense accession and unambiguously characterized by high-resolution electrospray ionization mass spectrometry and NM analysis as the glycoalkaloid dehydrocommersonine. Copyright © 2012 John Wiley & Sons, Ltd.

Santercole V.,Porto Conte Ricerche S.r.l | Delmonte P.,U.S. Food and Drug Administration | Kramer J.K.G.,Agriculture and Agri Food Canada
Lipids | Year: 2012

Commercial fish oils and foods containing fish may contain trans and/or isomerized fatty acids (FA) produced during processing or as part of prepared foods. The current American Oil Chemists' Society (AOCS) official method for marine oils (method Ce 1i-07) is based on separation by use of poly(ethylene glycol) (PEG) columns, for example Supelcowax-10 or equivalent, which do not resolve most unsaturated FA geometric isomers. Highly polar 100-m cyanopropyl siloxane (CPS) columns, for example SP-2560 and CP Sil 88 are recommended for separation of geometric FA isomers. Complementary separations were achieved by use of two different elution temperature programs with the same CPS column. This study is the first direct comparison of the separations achieved by use of 30-m Supelcowax-10 and 100-m SP-2560 columns for fatty acid methyl esters (FAME) prepared from the same fish oil and fish muscle sample. To simplify the identification of the FA in these fish samples, FA were fractionated on the basis of the number and type of double bonds by silver-ion solid-phase extraction (Ag +-SPE) before GC analysis. The results showed that a combination of the three GC separations was necessary to resolve and identify most of the unsaturated FA, FA isomers, and other components of fish products, for example phytanic and phytenic acids. Equivalent chain length (ECL) values of most FAME in fish were calculated from the separations achieved by use of both GC columns; the values obtained were shown to be consistent with previously reported values for the Supelcowax-10 column. ECL values were also calculated for the FA separated on the SP-2560 column. The calculated ECL values were equally valid under isothermal and temperature-programmed elution GC conditions, and were valuable for confirmation of the identity of several unsaturated FAME in the fish samples. When analyzing commercially prepared fish foods, deodorized marine oils, or foods fortified with marine oils it is strongly recommended that quantitative data acquired by use of PEG columns is complemented with data obtained from separations using highly polar CPS columns. © AOCS 2011.

Kwit C.,University of Tennessee at Knoxville | Moon H.S.,University of Tennessee at Knoxville | Warwick S.I.,Agriculture and Agri Food Canada | Stewart C.N.,University of Tennessee at Knoxville
Trends in Biotechnology | Year: 2011

Incorporation of crop genes into wild and weedy relative populations (i.e. introgression) has long been of interest to ecologists and weed scientists. Potential negative outcomes that result from crop transgene introgression (e.g. extinction of native wild relative populations; invasive spread by wild or weedy hosts) have not been documented, and few examples of transgene introgression exist. However, molecular evidence of introgression from non-transgenic crops to their relatives continues to emerge, even for crops deemed low-risk candidates for transgene introgression. We posit that transgene introgression monitoring and mitigation strategies are warranted in cases in which transgenes are predicted to confer selective advantages and disadvantages to recipient hosts. The utility and consequences of such strategies are examined, and future directions provided. © 2011 Elsevier Ltd.

Dietary fiber from fenugreek blunts glucose and cholesterol after a meal and regulates the production of cholesterol in the liver. The mechanisms for these effects have not been fully elucidated. Fenugreek seeds contain 45.4% dietary fiber (32% insoluble and 13.3% soluble), and the gum is composed of galactose and mannose. The latter compounds are associated with reduced glycemia and cholesterolemia. Fenugreek's hypoglycemic effect has been especially documented in humans and animals with type 1 and type 2 diabetes mellitus. In addition, this dietary fiber has potential for widespread use in the food industry because its galactomannan composition has emulsifying and stabilizing properties. Flour supplemented with 8%-10% fenugreek dietary fiber has been used in the production of baked goods such as bread, pizza, muffins, and cakes. This application to flour allows for the production of functional foods that may be widely acceptable to consumers observing western diets. © 2011, Mary Ann Liebert, Inc. and Korean Society of Food Science and Nutrition.

Marleau J.,University of Montreal | Dalpe Y.,University of Montreal | Dalpe Y.,Agriculture and Agri Food Canada | St-Arnaud M.,University of Montreal | Hijri M.,University of Montreal
BMC Evolutionary Biology | Year: 2011

Background: A conventional tenet of classical genetics is that progeny inherit half their genome from each parent in sexual reproduction instead of the complete genome transferred to each daughter during asexual reproduction. The transmission of hereditary characteristics from parents to their offspring is therefore predictable, although several exceptions are known. Heredity in microorganisms, however, can be very complex, and even unknown as is the case for coenocytic organisms such as Arbuscular Mycorrhizal Fungi (AMF). This group of fungi are plant-root symbionts, ubiquitous in most ecosystems, which reproduce asexually via multinucleate spores for which sexuality has not yet been observed. Results: We examined the number of nuclei per spore of four AMF taxa using high Z-resolution live confocal microscopy and found that the number of nuclei was correlated with spore diameter. We show that AMF have the ability, through the establishment of new symbioses, to pass hundreds of nuclei to subsequent generations of multinucleated spores. More importantly, we observed surprising heterogeneity in the number of nuclei among sister spores and show that massive nuclear migration and mitosis are the mechanisms by which AMF spores are formed. We followed spore development of Glomus irregulare from hyphal swelling to spore maturity and found that the spores reached mature size within 30 to 60 days, and that the number of nuclei per spores increased over time. Conclusions: We conclude that the spores used for dispersal of AMF contain nuclei with two origins, those that migrate into the spore and those that arise by mitosis in the spore. Therefore, these spores do not represent a stage in the life cycle with a single nucleus, raising the possibility that AMF, unlike all other known eukaryotic organisms, lack the genetic bottleneck of a single-nucleus stage. © 2011 Marleau et al; licensee BioMed Central Ltd.

Behan-Pelletier V.M.,Agriculture and Agri Food Canada
Acarologia | Year: 2015

Expressions of strong sexual dimorphism have been found in 77 species of Brachypylina, representing 36 genera, in the superfamilies Gustavioidea, Ameroidea, Oppioidea, Limnozetoidea, Ameronothroidea, Licneremaeoidea, Oripodoidea, Oribatelloidea, Ceratozetoidea and Galumnoidea. There are many examples of convergences, e.g., modifications of tarsus I setae in Cosmogneta (Autognetidae), Hydrozetes (Hydrozetidae) and Erogalumna (Galumnidae), and of possible behavioural constraints, e.g., the paraxial position of modified setae in sexually dimorphic species in these genera. Similarly, there is strong convergence in position and modification of presumed secretory porose organs in species of Autogneta (Autognetidae), Mochloribatula (Mochlozetidae), Symbioribates (Symbioribatidae), Oribatella (Oribatellidae), Zachvatkinibates, Nuhivabates (Punctoribatidae), Xiphobates (Chamobatidae) and Psammogalumna (Galumnidae). The number of superfamilies with sexually dimorphic species and the range of expression of sexual dimorphism suggest multiple independent origins in Brachypylina, as congeneric species in 20 of these 36 genera do not show such modifications. Despite 1% of brachypyline species being strongly sexually dimorphic, the evidence for courtship behaviour is limited to the Galumnidae and an undescribed species of Mochloribatula (Mochlozetidae). Evolution of strongly sexually dimorphic species in Oribatida seems to be in response to intermittent dryness, or aquatic habitats, or spatially discrete microhabitats. The littoral habitat is represented by 11 species showing strong sexual dimorphism, coastal vegetation by 6, the semiaquatic by 5, dry soil by 4 species and crustose lichens by 3 species. Arguably, these 29 species and some of the 19 species reported from arboreal habitats (including lichens and moss) live in microhabitats that can be intermittently dry, with wet-dry periods of varying lengths and intensity. Seven sexually dimorphic species of Hydrozetes are found in aquatic habitats; males of these all show modifications of one or more paraxial seta on tarsus I which may be used to orient the female. The 5 sexually dimorphic species of Autogneta, and Unguizetes mauritius (Jacot) are associated with decaying wood, bark and fungal sporophores, suggesting evolution of sexual dimorphism in this spatially discrete habitat. Undoubtedly, there are many other undiscovered cases of sexual dimorphism in Brachypylina, as microhabitats where they predominantly occur are rarely studied. © 2015, Les Amis d'Acarologia. All rights reserved.

A total of 32 Holstein cows were allotted at calving to eight groups of four cows blocked to determine the effects of feeding increased levels of whole flaxseed (WF) in the diet on dry matter (DM) intake (DMI), milk production and composition, milk fatty acid (FA) profile, concentration of some blood metabolites and energy balance. Cows within each block were assigned to one of four iso-net energy for lactation total mixed rations: no whole flaxseed (0WF), and diets with preplanned inclusions of 50 (50WF), 100 (100WF) or 150 (150WF). g/kg DM WF. Diets were fed for ad libitum intake from calving to week 24 of lactation. There was a trend for an interaction between treatment and week for DMI, milk yield, and logsomatic cell count (P=0.08, 0.07, and 0.09, respectively). Values of DMI averaged for the 24 week experiment, yields of fat, protein and total solids and proportions of short- and medium-chain FA in milk fat decreased linearly with higher proportions of WF in the diet. Milk yield was similar among diets. Proportions of 18:0, cis9-18:1, trans9-18:1, cis9,. trans11-18:2, cis9,12,15-18:3 19:0 and 20:0 in milk fat increased linearly and those of cis9,12-18:2, trans9,12-18:2 and 20:4 decreased linearly with higher concentrations of WF in the diet. Although milk FA profile was enhanced, feeding more than preplanned inclusions of 50 g/kg DM WF had negative effects on yield of milk components. © 2015.

Yan L.,Jiangxi Science and Technology Normal University | Chang P.R.,Agriculture and Agri Food Canada | Zheng P.,Jiangxi Science and Technology Normal University | Ma X.,Tianjin University
Carbohydrate Polymers | Year: 2012

The hydrophobicity of carbon nanotubes (CNTs) limits their extensive application. The hydrophilicity and biocompatibility of CNTs can be improved by modifying them with biopolymers. As a natural biopolymer, guar gum (GG) was covalently grafted on the surfaces of multiwall carbon nanotube (MWCNT) to obtain GG-MWCNT composite. Then iron oxide nanoparticles were synthesized on the GG-MWCNT to prepare the magnetic GG-MWCNT-Fe 3O 4. The obtained nanocomposites were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, transmission electron microscopy, ultraviolet-visible (UV-vis) spectroscopy and X-ray diffraction. GG-MWCNT was composed of about 21.6 wt% GG components, which enhanced the dispersion of GG-MWCNT in aqueous solution and also acted as a template for growth of iron oxide nanoparticles. GG-MWCNT-Fe 3O 4 exhibited superparamagnetic with a saturation magnetization (13.3 emu g -1), and good adsorption on neutral red and methylene blue. GG-MWCNT-Fe 3O 4 could be easily separated from the aqueous solution in a magnetic field. © 2011 Elsevier Ltd. All rights reserved.

May W.E.,Agriculture and Agri Food Canada
Weed Technology | Year: 2015

Niger is a potential crop for the Northern Great Plains, but not until volunteer canola can be controlled. A study at Indian Head, SK, was conducted from 2007 to 2009 to determine the tolerance of niger to flucarbazone, a herbicide that controls volunteer canola. The tolerance was determined by applying three rates of flucarbazone (19, 28.5, and 38 g ai ha-1) at four application stages (two, four, six, and eight-leaf stage). Mean injury did not exceed 22% for any year by treatment combination. Injury was most prominent in 2007, and dissipated as the growing season progressed. Increasing the rate of flucarbazone increased crop injury depending on the year, application timing, and evaluation timing. Injury under 20% in 2007 and under 10% in 2008 and 2009 was observed at the start of flowering when flucarbazone was applied at the two, four, and six-leaf stage. Injury from applications at the two, four, and six-leaf stage decreased as the growing season progressed. When the labelled rate of flucarbazone for wheat (19 g ha-1) was applied at the two, four, or six leaf stage, injury was below 10%. Injury when flucarbazone was applied at the eight-leaf stage was highest during seed filling. Volunteer canola was controlled by flucarbazone. The application of flucarbazone relative to a weedy control increased yield by about 50% (138 to 213 kg ha-1) in 2008 and 2009. Flucarbazone rate did not affect niger yield except in 2007 where yield was about 100 kg ha-1 less with the two highest rates. Delaying flucarbazone application decreased niger yield, especially in the year (2007) with most niger injury. Flucarbazone application at the two- or four-leaf niger stage at a rate of 19 g ha-1 provided a good balance of weed control and crop tolerance. Nomenclature: Flucarbazone; volunteer canola, Brassica napus L.; niger, Guizotia abbysinica (L.f.) Cass.; wheat, Triticum aestivum L. © 2015, BioOne. All rights reserved.

Van Kempen T.A.T.G.,Provimi Research and Innovation Center | Van Kempen T.A.T.G.,North Carolina State University | Regmi P.R.,University of Alberta | Matte J.J.,Agriculture and Agri Food Canada | Zijlstra R.T.,University of Alberta
Journal of Nutrition | Year: 2010

In vitro starch digestion is used for predicting the in vivo glucose response, but their relationship has not been defined thoroughly. To clarify, in vitro starch digestion using a modified Englyst-assay was compared to portal glucose appearance in pigs. Four portal vein-catheterized pigs (43.2 ± 4.8 kg body weight) were fed 4 diets containing 70% purified starch ranging from slowly to rapidly digestible [maximal rate of in vitro digestion (%)/min: 0.22 (slowly), 0.38, 0.73, and 1.06 (rapidly)] for 7-d periods in a 4 x 4 Latin square. In vivo (R2 = 0.964) and in vitro (R2 = 0.998) data were modeled using a Chapman-Richards model that accurately described the sigmoidal glucose-release profiles. Across samples, the extent of glucose recovered was less in vivo than in vitro (69 vs. 42% of starch). The rate of glucose release adjusted for plateau effects was lower in vivo (0.35 vs. 0.89%/min), whereas the shape parameter adjusted for plateau effects (sigmoidal modifier) was higher in vivo (37.9 vs. 13.7). Consequently, peak glucose release in vivo occurred 69 min postprandial, whereas it occurred only 6 min into the second stage of digestion in vitro. Cumulative portal glucose appearance was strongly related (R2 = 0.89; P < 0.001) to in vitro glucose release, although a nonlinear bias was observed. After correcting in vitro release with predicted gastric emptying, the relationship improved and became linear (R2 = 0.95; P < 0.001). In conclusion, in vitro starch digestion kinetics predict portal glucose appearance up to 8 h postprandial accurately provided that in vitro data are corrected for gastric emptying. © 2010 American Society for Nutrition.

Hannoufa A.,Agriculture and Agri Food Canada | Pillai B.V.S.,Dow AgroSciences | Chellamma S.,Dow AgroSciences
Transgenic Research | Year: 2014

The ultimate value of the Brassica napus (canola) seed is derived from the oil fraction, which has long been recognized for its premium dietary attributes, including its low level of saturated fatty acids, high content of monounsaturated fatty acids, and favorable omega-3 fatty acid profile. However, the protein (meal) portion of the seed has also received favorable attention for its essential amino acids, including abundance of sulfur-containing amino acids, such that B. napus protein is being contemplated for large scale use in livestock and fish feed formulations. Efforts to optimize the composition of B. napus oil and protein fractions are well documented; therefore, this article will review research concerned with optimizing secondary metabolites that affect the quality of seed oil and meal, from undesirable anti-nutritional factors to highl value beneficial products. The biological, agronomic, and economic values attributed to secondary metabolites have brought much needed attention to those in Brassica oilseeds and other crops. This review focuses on increasing levels of beneficial endogenous secondary metabolites (such as carotenoids, choline and tochopherols) and decreasing undesirable antinutritional factors (glucosinolates, sinapine and phytate). Molecular genetic approaches are given emphasis relative to classical breeding. © 2013 Her Majesty the Queen in Right of Canada.

Malhat F.,Agriculture and Agri Food Canada
Bulletin of Environmental Contamination and Toxicology | Year: 2011

The distribution patterns of some metals (zinc, iron, copper, cadmium and lead) in fish samples collected from El Menofiya Governorate, Egypt were studied. The samples were collected from El Menofiya, canal water supplies (El Sarsawia, El Bagoria and Bahr Shebin), in addition to El Embaby, El Menofi and Miet Rabiha drainage canals each 2 month during periods of 16 month, June 2007-Septemper 2008. In the present investigation, the high concentrations of metals were found in fish samples collected from the drainage canal. The highest mean concentration of lead (1.864 μg/g), copper (1.495 μg/g) and cadmium (1.840 μg/g) were found in fish samples collected from El-Embaby drain. While the highest mean concentration of iron (108.26 μg/g) and zinc (24.35 μg/g) were present in fish samples collected from Miet-Rabiha drain. Lead and cadmium were found in higher concentration than those recommended by FAO for fish. © 2011 Springer Science+Business Media, LLC.

Ojo E.R.,University of Manitoba | Bullock P.R.,University of Manitoba | Fitzmaurice J.,Agriculture and Agri Food Canada
Soil Science Society of America Journal | Year: 2015

The increased use of soil moisture retrieval from satellites has heightened The need for improved accuracy of point measurements that are used to validate remotely sensed soil moisture products. A wide range of devices can be installed for operational monitoring of soil moisture; however, many of The se devices have not been tested in situ in soils with a very high reactive clay content. The objective of this study was to evaluate The accuracy in field performance of five soil moisture sensors: The EnviroSCAN probe, The Diviner 2000 (both from Sentek Technologies), The Hydra Probe soil sensor (Stevens Water Monitoring Systems), The ThetaProbe ML2x (Delta-T Devices), and The ECH2O EC-5 (Decagon Devices) in soils that had about 71 % clay content. The instruments' default calibrations were tested against observed soil moisture from core samples using The The rmogravimetric method. New calibration equations were developed for each device, which were evaluated using an independent data set. The ThetaProbe had The lowest root mean square error (RMSE) of 0.025 m3 m3 and mean bias error (MBE) of 0.002 m3 m3 in The precalibration analysis. Although The Hydra Probe showed The highest precalibration errors, The instrument made The greatest improvement in post-calibration analysis, with an RMSE of 0.129 m3 m3 using The default equation reduced to 0.014 m3 m3 using in situ calibration, and The 0.110 m3 m3 MBE was reduced to 0 after applying in situ calibration. © Soil Science Society of America, 5585 Guilford Rd., Madison WI 53711 USA. All rights reserved.

Gossen B.D.,Agriculture and Agri Food Canada | Adhikari K.K.C.,University of Guelph | Mcdonald M.R.,University of Guelph
Plant Pathology | Year: 2012

Controlled-environment studies were conducted on two Brassica crops (canola, Brassica napus; and Shanghai pak choi, B. rapa subsp. chinensis var. communis) to examine the effects of temperature on infection and subsequent development of clubroot caused by Plasmodiophora brassicae. In the first experiment, canola seedlings were grown in infested soil for 3weeks at 14-26°C to assess the impact on primary and secondary infection and transferred to 20°C for 3weeks to assess symptom development under uniform conditions, or started at 20°C for 3weeks and then placed at the treatment temperatures for the final 3weeks to assess the impact of temperature on symptom development. A second experiment examined a wider range of temperatures (10-30°C). Similar experiments were also conducted on Shanghai pak choi. The studies demonstrated that clubroot severity was affected by temperature during both infection and vegetative development of the crop. Both early and late in crop development, little or no clubroot developed at temperatures at or below 17°C, and development was slower above 26°C than at 23-26°C for both crops throughout the study. In canola, the high levels of inoculum used in the study resulted in a high incidence of clubroot irrespective of temperature, but in pak choi incidence showed the same pattern as severity. This is the first study to demonstrate under controlled conditions that temperature during vegetative growth of the crop affects symptom development of clubroot. © 2011 Her Majesty the Queen in Right of Canada. Plant Pathology © 2011 BSPP.

Rodrigue N.,Agriculture and Agri Food Canada | Rodrigue N.,University of Ottawa
Genetics | Year: 2013

Phylogeny-based modeling of heterogeneity across the positions of multiple-sequence alignments has generally been approached from two main perspectives. The first treats site specificities as random variables drawn from a statistical law, and the likelihood function takes the form of an integral over this law. The second assigns distinct variables to each position, and, in a maximum-likelihood context, adjusts these variables, along with global parameters, to optimize a joint likelihood function. Here, it is emphasized that while the first approach directly enjoys the statistical guaranties of traditional likelihood theory, the latter does not, and should be approached with particular caution when the site-specific variables are high dimensional. Using a phylogeny-based mutation-selection framework, it is shown that the difference in interpretation of site-specific variables explains the incongruities in recent studies regarding distributions of selection coefficients. © 2013 Her Majesty the Queen in the Right of Canada.

The presence and distribution of two species of Notanisus Walker (Hymenoptera: Pteromalidae) in North America is reported. Notanisus sexramosus (Erdos), originally described from Hungary and previously reported from Maryland, USA, is recorded also from Massachusetts and Pennsylvania based on a male and macropterous and brachypterous females. Males of Notanisus are shown to have two types of flagellar structure, ramose and pedicellate, and diagnostic features are given for the previously unknown males of N. clavatus Bouček to differentiate these from those of N. sexramosus and N. versicolor Walker. Five other species are newly described, Notanisus kansensis n. sp. based on a female from Nebraska, USA, and four species from Sub-Saharan Africa and the Arabian Peninsula-Notanisus brevipetiolus n. sp. based on two females from Uganda and Zambia, Notanisus longipetiolus n. sp. based on a female from Zimbabwe and a female and two males from Mozambique, Notanisus vanharteni n. sp. based on a female and several males from United Arab Emirates, and Notanisus yemenensis n. sp. based on a female and male from Yemen. The latter five species are included with the Palaearctic species N. oulmesiensis (Delucchi) and N. gracilis (Yang) in the oulmesiensis species group, defined by the presence of reduced stigmal and postmarginal veins in both sexes. The seven oulmesiensis-group species are differentiated in a key and all treated species are illustrated through macrophotography. Monophyly and relationships of Notanisus within Cleonymini are discussed, including features that indicate it could be paraphyletic relative to Callocleonymus Masi. Copyright © 2015 Magnolia Press.

Roberts K.T.,Agriculture and Agri Food Canada | Roberts K.T.,University of Guelph
Food Research International | Year: 2011

The high molecular weight polysaccharide Guar gum has a plethora of uses in the food, pharmaceutical and paint industries. This polysaccharide is also employed as a dietary fibre, but the quantity used in food is limited due to its viscous properties. Guar gum may be modified enzymatically or chemically to reduce its molecular weight and by extension its viscosity. This modification though is believed to reduce its physiological efficacy, for example the attenuation of postprandial glycemia. However, a number of studies have shown the viscosity effects alone of this fibre in vitro and in vivo is not always correlated with blunted glycemia. The absolute mechanisms behind the benefits seen with guar gum consumption are not known and studies have shown factors such as food composition, food matrix and food and fibre processing conditions may all play a significant role. © 2011 Elsevier Ltd.

Challacombe C.A.,University of Guelph | Abdel-Aal E.S.M.,Agriculture and Agri Food Canada | Seetharaman K.,University of Guelph | Duizer L.M.,University of Guelph
Journal of Cereal Science | Year: 2012

Despite the health benefits of wholegrain, consumer acceptance of wholegrain products remains an issue due to the presence of characteristic flavours that some consumers consider to be unacceptable. It was hypothesized that phenolic acids could be contributing to the perceived unacceptable flavours described in wholegrain products. The purpose of this study was to examine the relationship between total phenolic acid content (TPAC) and phenolic acids as quantified by HPLC, to the sensory properties of wholegrain products using partial least squares (PLS) mapping. Red and white wheat flours were investigated in an intermediate (bread) and low (cracker) moisture product system. Red and white wheat demonstrated different phenolic acid profiles despite having similar TPAC. Within the bread crumb, the free and bound phenolic acids provided the best predictive scores; whereas only bound phenolic acids provided high predictive scores in crackers. This suggests that the contribution of phenolic acids to flavour characteristics of wholegrain products varies depending upon the product moisture. © 2012 Elsevier Ltd.

Kirk A.P.,University of Manitoba | Fox S.L.,Agriculture and Agri Food Canada | Entz M.H.,University of Manitoba
Plant Breeding | Year: 2012

With 1 figure and 8 tables An important research question is whether wheat cultivars for organic production should be selected under organic field conditions. Yield, protein content and kernel weight (KWT) of seven populations of wheat (Triticum aestivum L.) selected in both organic and conventional growing conditions (termed selection environments) were compared at four organically and four conventionally managed sites (termed management environments). Selection environment was found to affect yield, protein and KWT in both management environments. At most sites, populations selected in organic environments had higher yields at organically managed sites relative to conventionally selected populations. When organically managed site-years were combined, the yields of organically selected populations were significantly higher than those of conventionally selected populations. Populations selected under organic management had higher protein content and KWT under both management environments. Direct selection in organically managed field conditions for genotypes targeted to organic agriculture offers advantages over indirect selection in conventionally managed field conditions. © 2012 Blackwell Verlag GmbH.

Pozniak C.J.,University of Saskatchewan | Clarke J.M.,University of Saskatchewan | Clarke F.R.,Agriculture and Agri Food Canada
Molecular Breeding | Year: 2012

Identification of marker-trait associations in germplasm relevant to a breeding program can be an effective way to identify quantitative trait loci (QTL) useful for selection and is critical to the success of genome-wide selection strategies. This approach is most cost-effective if phenotypic data routinely collected by breeding programs is used, necessitating only addition of genotypic data. The objective of this work was to evaluate such an approach using unbalanced phenotypic data from durum wheat (Triticum turgidum L. var. durum) registration trials genotyped with diversity arrays technology (DArT) markers. Plant height, grain cadmium concentration and yellow colour loss during pasta manufacture were chosen as example traits because all are influenced by major genes associated with known QTL. A further evaluation was performed on semolina yellow pigment concentration, a more complexly-inherited trait, but with numerous QTL identified. In total, 870 informative DArT markers were used to detect marker-trait associations. The genome coverage of markers was uneven, with low coverage of chromosomes 4B and 5A. The DArT coverage of chromosome 4B was too sparse to identify markers strongly associated with the semidwarf height locus Rht-B1 and the lipoxygenase locus Lpx-B1, both known to reside on 4B. The 20 DArT markers associated with pigment concentration localized to chromosomes 1B, 2A, 5B, 6A, 7A and 7B, linked to the trait in other studies. One DArT clone showed sequence identity to a single wheat expressed sequence tag that maps to the same deletion bin as Psy1-A1, a gene previously associated with yellow pigment concentration in durum wheat. Three markers were associated with grain cadmium and explained similar proportions of the phenotypic variance as the Xusw14 marker known to be physically linked to Cdu-B1, a major locus on 5B regulating cadmium accumulation. The sequences of these three DArT markers were 98 % identical, and were used to identify a single gene in rice that is physically linked to other rice genes that co-localize with Cdu-B1 in durum wheat. The results suggest that this historical phenotypic dataset is useful for QTL discovery and would potentially be a 'training population' for genomic selection when a high-density, low-cost marker platform becomes available. © 2012 Springer Science+Business Media B.V.

Abbott D.W.,Agriculture and Agri Food Canada | Boraston A.B.,University of Victoria
Methods in Enzymology | Year: 2012

Carbohydrate-binding modules (CBMs) are important components of carbohydrate-active enzymes. Their primary functions are to assist in substrate turnover by targeting appended catalytic modules to substrate and concentrating appended catalytic modules on the surface of substrate. Presented here are four well-established methodologies for investigating and quantifying the CBM-polysaccharide binding relationship. These methods include: (1) the solid state depletion assay, (2) affinity gel electrophoresis, (3) UV difference and fluorescence spectroscopy, and (4) isothermal titration calorimetry. In addition, entropy-driven CBM-crystalline cellulose binding events and differential approaches to calculating stoichiometry with polyvalent polysaccharide ligands are also discussed. © 2012 Elsevier Inc. All rights reserved.

Milbury P.E.,Tufts University | Kalt W.,Agriculture and Agri Food Canada
Journal of Agricultural and Food Chemistry | Year: 2010

A compelling body of literature suggests berry phytochemicals play beneficial roles in reversing age-related cognitive impairment and protect against neurodegenerative disorders. Anthocyanins are bioactive phytochemicals in berries suspected to be responsible for some of these neuroprotective effects. The plausible mechanisms of anthocyanin bioactivity in brain tissue are dependent on their bioavailability to the brain. Pigs were fed 2% whole freeze-dried, powdered blueberry in the diet for 8 weeks. Anthocyanin and anthocyanin glucuronides were measured in the cortex, cerebellum, and midbrain and diencephalon by LC-MS/MS. Anthocyanins and their glucuronides were found in the range of femtomoles per gram of fresh weight of tissue at 18 h postprandial, after anthocyanins had been removed from the blood by xenobiotic metabolism. Xenobiotic metabolism, anthocyanin interaction, and transporter barriers to brain bioavailability are briefly discussed. The plausible mechanism of neuroprotective action of anthocyanins may be via modulation of signal transduction processes and/or gene expression in brain tissue rather than by direct antioxidant radical quenching. © 2010 American Chemical Society.

Bibliographic references to works pertaining to the taxonomy of Coleoptera published between 1758 and 1900 in the non-periodical literature are listed. Each reference includes the full name of the author, the year or range of years of the publication, the title in full, the publisher and place of publication, the pagination with the number of plates, and the size of the work. This information is followed by the date of publication found in the work itself, the dates found from external sources, and the libraries consulted for the work. Overall, more than 990 works published by 622 primary authors are listed. For each of these authors, a biographic notice (if information was available) is given along with the references consulted. © Fu-Ming Shi et al.

The paper deals with additional brachypterous species of the Quedius muscicola-group of the subgenus Raphirus Stephens, 1829 of the genus Quedius Stephens, 1829. Quedius nujiang sp. nov. and Q. angustiarum sp. nov. (both from Gaoligong Shan in Yunnan), Q. oros sp. nov. (Sichuan) and Q. chion sp. nov. (Yunnan) are described as new. New distributional data are given for Q. io and Q. li. A key to the brachypterous species of the Q. muscicola-group known at present from mainland China is attached.

Paz A.,Malardalen University | Thorin E.,Malardalen University | Topp C.,Agriculture and Agri Food Canada
Wood Science and Technology | Year: 2011

The aim of this study is to determine the dielectric constant of woody biomass at different water contents and describe its behavior with a dielectric mixing model. The use of the model for determination of water content is also verified. Dielectric constants were calculated from the travel times of electromagnetic waves with a center frequency of 555 MHz through collected biomass samples. The power law, Maxwell-Garnett, and Polder van Santen mixing models were applied to the experimental data. In the models, biomass was considered as a mixture of three phases: a solid solution composed of wood cellular material and bound water, free water, and air. The experimental data was found to be better described by the Maxwell-Garnett model. The use of this model along with an independent validation set for the determination of volumetric water content resulted in a root mean square error of prediction of 0.03 within the investigated volumetric water content range of 0.07-0.29. © 2010 Springer-Verlag.

Eissa S.,INRS - Institute National de la Recherche Scientifique | L'Hocine L.,Agriculture and Agri Food Canada | Siaj M.,University of Quebec at Montreal | Zourob M.,Cranfield University
Analyst | Year: 2013

A graphene-based label-free voltammetric immunosensor for the sensitive detection of the egg white allergen ovalbumin has been developed. Graphene-modified screen printed carbon electrodes have been covalently functionalized using electrochemical reduction of in situ generated aryl diazonium salt forming a carboxyphenyl film on the graphene surface. The blocking property of the carboxyphenyl film grafted on to the graphene electrodes using different cyclic voltammetry cycles has been characterized using differential pulse voltammetry in [Fe(CN)6]3-/4- solution. Then, the terminal carboxylic groups on the graphene surface were activated using EDC/NHS and used to immobilize the ovalbumin antibody and construct the immunosensor. The fabrication steps of the immunosensor have also been characterized using differential pulse voltammetry. The decrease in the [Fe(CN)6]3-/4- reduction peak current after the immunochemical reaction with ovalbumin has been used for the ovalbumin detection. The developed immunosensor has been used for ovalbumin detection in the concentration range of 1 pg mL-1 to 0.5 μg mL-1 with a detection limit of 0.83 pg mL-1 in PBS buffer. The food matrix effect studied with ovalbumin spiked cake extract showed a good percentage of recovery, indicating the possible applicability of the developed immunosensor in real food samples. © 2013 The Royal Society of Chemistry.

Lumba S.,University of Toronto | Toh S.,University of Toronto | Handfield L.-F.,University of Toronto | Swan M.,University of Toronto | And 8 more authors.
Developmental Cell | Year: 2014

The sesquiterpenoid abscisic acid (ABA) mediates an assortment of responses across a variety of kingdoms including both higher plants and animals. In plants, where most is known, a linear core ABA signaling pathway has been identified. However, the complexity of ABA-dependent gene expression suggests that ABA functions through an intricate network. Here, using systems biology approaches that focused on genes transcriptionally regulated by ABA, we defined an ABA signaling network of over 500 interactions among 138 proteins. This map greatly expanded ABA core signaling but was still manageable for systematic analysis. For example, functional analysis was used to identify an ABA module centered on two sucrose nonfermenting (SNF)-like kinases. We also used coexpression analysis of interacting partners within the network to uncover dynamic subnetwork structures in response to different abiotic stresses. This comprehensive ABA resource allows for application of approaches to understanding ABA functions in higher plants. © 2014 Elsevier Inc.

Ali A.,University of Selangor | Ong M.K.,University of Selangor | Forney C.F.,Agriculture and Agri Food Canada
Food Chemistry | Year: 2014

The objective of this study was to compare the physico-chemical characteristics and antioxidant activity of ozone-treated papaya fruit and untreated fruit. Freshly harvested papaya fruit were exposed continuously to ozone fumigation (0, 1.5, 2.5, 3.5 and 5 ppm) for 96 h prior to ambient storage at 25 ± 3 °C and 70 ± 5% relative humidity (RH) for up to 14 days. The fruit exposed to 2.5 ppm ozone had higher levels of total soluble solids (25.0%), ascorbic acid content (12.4%), b-carotene content (19.6%), lycopene content (52.1%), and antioxidant activity (30.9%), and also reduced weight loss (11.5%) at day 10 compared to the control. The sensory attributes of papaya treated with 2.5 ppm ozone was superior in sweetness and overall acceptability. These results support the application of ozone as a non-thermal and safe food preservation technique for papaya which can benefit both the producers and consumers. © 2013 Elsevier Ltd. All rights reserved.

Cheung L.K.Y.,University of British Columbia | Aluko R.E.,University of Manitoba | Cliff M.A.,Agriculture and Agri Food Canada | Li-Chan E.C.Y.,University of British Columbia
Journal of Functional Foods | Year: 2015

The objectives of this study were to investigate the effects of exopeptidase treatment on ACE-inhibitory activity, antihypertensive activity and taste of whey protein hydrolysates (WPHs). WPH with high ACE-inhibitory activity (IC50 = 0.15 mg/mL) was treated with carboxypeptidase (Accelerzyme® CPG), aminopeptidase (Peptidase R), or an aminopeptidase and proteinase mixture (ProteAX). The exopeptidase-treated hydrolysates exhibited ACE-inhibitory activity (IC50 = 0.24-0.34 mg/mL) and decreased systolic blood pressure (-12 to -31 mm Hg) in spontaneously hypertensive rats for 24 h after a single administration of 100 mg/kg body weight. The highest ACE-inhibitory activity was associated with the 200-1000 Da fractions in all exopeptidase-treated hydrolysates. Exopeptidase treatment significantly lowered bitterness, increased umami and salty tastes, and increased overall acceptability of the starting WPH, changes that may be due to release of certain terminal amino acids. Therefore, exopeptidase treatment may be a viable debittering method for bitter-tasting, antihypertensive protein hydrolysates, before incorporation into functional foods. © 2014 Elsevier Ltd.

Wei S.,Jiangsu Academy of Agricultural Sciences | Wei S.,Agriculture and Agri Food Canada
Plant Growth Regulation | Year: 2010

Madagascar periwinkle (Catharanthus roseus) produces diverse terpenoid indole alkaloids (TIAs), including the anti-cancer drugs vincristine and vinblastine. In this study, the effects of methyl jasmonic acid (MeJA) treatment on TIA metabolism and gene expression in seedlings were analyzed. Several reference genes were also isolated from periwinkle. These reference genes, as well as ribosomal protein (RSP9) and cyclophilin (CYC) genes, were characterized to determine which are most suitable for use as expression profiling control genes. The results show that TIA genes exhibit significant variation in the magnitude and timing of induction by MeJA. ORCA3, a jasmonate-responsive APETALA2 (AP2)-domain transcription factor gene, exhibited the greatest increase in transcript levels, with increases up to 25 fold observed 0.5 h after MeJA treatment. MeJA-induced increases in transcript levels occurred in the following order: ORCA3, desacetoxyvindoline 4-hydroxylase (D4H), strictosidine synthase (STR), tryptophan decarboxylase (TDC), geraniol 10-hydroxylase (G10H) and cytochrome P-450 reductase (CPR). The results suggest that variations in the timing of MeJA induced increases in TIA transcript levels might be related to complex interactions between different transcription factors, such as ORCA3, and other factors. CrEF1α and CrUBQ11 are the most stable genes out of the 8 tested under the conditions of these experiments. © 2010 Springer Science+Business Media B.V.

Manns H.R.,University of Guelph | Berg A.A.,University of Guelph | Bullock P.R.,University of Manitoba | Mcnairn H.,Agriculture and Agri Food Canada
Hydrological Processes | Year: 2014

The accuracy of soil water content (WC) interpretation from satellites and its application in hydrological modelling is dependent on our understanding of the effects of field-scale surface soil properties on soil WC variability. Soil texture, surface roughness and surface residue were evaluated for their influence on soil WC variability with data obtained from satellite ground verification sampling near Carman, Manitoba, within a 28 km2 area. Over the course of five selected dates from 23 April to 18 May 2008, soil WC and other physical variables were obtained in 38 agricultural fields covering three distinct soil textural classifications. Within each field, at each of 16 sampling locations, four individual soil WC measurements were taken, including sampling points with and without the influence of crop residue left on the soil surface. A principal component analysis and multiple linear regression both identified soil texture as the primary physical process controlling variability in soil WC and coefficient of variation (CV) among fields during the campaign. Residue cover was also a significant factor representing a second principal component that explained 37% of variability in average soil WC and contributed to 31% of variability in CV. Whereas soil texture predominated in soil WC and CV on most sampling dates, residue cover was of equal significance as texture in dry soils. This study identified specific effects of tillage and residue management contributing to field-scale soil WC variability that could contribute significant improvements to interpretation of remotely sensed soil WC and subsequent scaling efforts over agricultural regions. © 2014 John Wiley & Sons, Ltd.

O'Rourke S.M.,University College Dublin | O'Rourke S.M.,University of Sydney | Angers D.A.,Agriculture and Agri Food Canada | Holden N.M.,University College Dublin | Mcbratney A.B.,University of Sydney
Global Change Biology | Year: 2015

Mechanistic understanding of scale effects is important for interpreting the processes that control the global carbon cycle. Greater attention should be given to scale in soil organic carbon (SOC) science so that we can devise better policy to protect/enhance existing SOC stocks and ensure sustainable use of soils. Global issues such as climate change require consideration of SOC stock changes at the global and biosphere scale, but human interaction occurs at the landscape scale, with consequences at the pedon, aggregate and particle scales. This review evaluates our understanding of SOC across all these scales in the context of the processes involved in SOC cycling at each scale and with emphasis on stabilizing SOC. Current synergy between science and policy is explored at each scale to determine how well each is represented in the management of SOC. An outline of how SOC might be integrated into a framework of soil security is examined. We conclude that SOC processes at the biosphere to biome scales are not well understood. Instead, SOC has come to be viewed as a large-scale pool subjects to carbon flux. Better understanding exists for SOC processes operating at the scales of the pedon, aggregate and particle. At the landscape scale, the influence of large- and small-scale processes has the greatest interaction and is exposed to the greatest modification through agricultural management. Policy implemented at regional or national scale tends to focus at the landscape scale without due consideration of the larger scale factors controlling SOC or the impacts of policy for SOC at the smaller SOC scales. What is required is a framework that can be integrated across a continuum of scales to optimize SOC management. © 2015 John Wiley & Sons Ltd.

McGinn S.M.,Agriculture and Agri Food Canada
Animal : an international journal of animal bioscience | Year: 2013

Micrometeorological techniques can be applied to estimate methane (CH4) emissions from ruminants and livestock manure using CH4 concentration measured within the internal surface boundary layer. The main advantage of these techniques is that they are non-intrusive, thereby eliminating the impact of the measurement set-up on the calculated CH4 emission. This review focuses on four micrometeorological techniques, namely, the integrated horizontal flux (IHF), flux gradient (FG), eddy covariance (EC) and the dispersion modelling using the backward Lagrangian stochastic method (BLS). Each technique has unique advantages and limitations when used for estimating enteric (ruminant) and manure CH4 emissions. The IHF technique may be theoretically simpler then the FG, EC or BLS techniques, but all require high-resolution instruments to measure concentration. The EC and BLS techniques also require a measurement of the wind statistics. This review discusses the appropriate use of these four micrometeorological techniques for estimating CH4 emissions in animal agriculture and the recent advances in measurement technology.

Ragaee S.,University of Guelph | Seetharaman K.,University of Guelph | Abdel-Aal E.-S.M.,Agriculture and Agri Food Canada
Critical Reviews in Food Science and Nutrition | Year: 2014

Consumption of wholegrain foods has been recommended for healthy diets. The beneficial health properties of wholegrain products have been associated with the presence of higher amounts of dietary fiber and antioxidants and lower calories as compared to their respective refined ones. Phenolic compounds are mainly attributed to antioxidant properties of wholegrain foods. This review article provides a single comprehensive source that describes effects of milling and thermal processing on phenolic compounds and antioxidant properties in cereals. In general, milling and pearling processes affect the distribution of phenolic, compounds and thus antioxidant properties vary among the milling fractions. Thermal processes such as baking and extrusion could cause negative or positive effects on phenolic compounds and antioxidant properties of the end product subject to grain type and processing conditions. Thus factors that enhance health benefits of wholegrain cereal products have been discussed. © 2014 Copyright Taylor and Francis Group, LLC.

Abd-Alrahman S.H.,King Saud University | Abd-Alrahman S.H.,Agriculture and Agri Food Canada
Food Chemistry | Year: 2014

The dissipation kinetics and residual levels of thiamethoxam in potato and soil under field ecosystem were determined using a QuEChERS method with HPLC-DAD. At fortification levels of 0.05, 0.1, 0.25, 0.5, 1.0 and 5.0 mg kg-1, it was shown recovery was 99.4% (95.3-103.5%) for potato tubers, and 88.5% (86-91%) for soil with coefficient variation of the method (CV%) was less than 4% in potato tubers, and in soil less than 11%. For repeatability ranged from 1.27% to 4.77%. The LOD and LOQ were estimated to be 0.02 and 0.06 mg kg-1, respectively. The half-lives were 2.92 and 1.4 days, respectively. The terminal residues of thiamethoxam were below the maximum residue limit (MRL 0.2 mg kg-1) after 6 days, which considered to be safe for human beings. These results contribute to establishing the scientific basis of the dosage of thiamethoxam for use in vegetable-field ecosystems. © 2014 Elsevier Ltd. All rights reserved.

Zhang Y.,University of Manitoba | Rempel C.,Canola Council of Canada | Liu Q.,Agriculture and Agri Food Canada
Critical Reviews in Food Science and Nutrition | Year: 2014

Canola Council of Canada, Winnipeg, Manitoba, Canada The rising costs of nonrenewable feedstocks and environmental concerns with their industrial usage have encouraged the study and development of renewable products, including thermoplastic starch (TPS). Starch is an abundant, plant-based biodegradable material with interesting physicochemical characteristics that can be exploited, and this has received attention for development of TPS products. Starch exhibits usable thermoplastic properties when plasticizers, elevated temperatures, and shear are present. The choice of plasticizer has an effect on TPS, even when these have similar plasticization principles. Most TPS have glass transition temperature, Tg, in the range of approximately -75 to 10°C. Glassy transition of TPS is detected by differential scanning calorimeter (DSC) and thermodynamic analyzer (DMA), although DMA has been found to be more sensitive and effective. TPS has low tensile properties, typically below 6 MPa in tensile strength (TS). The addition of synthetic polymers, nanoclay, and fiber can improve TS and water-resistance ability. The moisture sorption behavior of TPS is described in GAB and BET models, from which monolayer moisture content and specific area are derived. Current studies on surface tension, gas permeability, crystallinity, and so on of the TPS are also reviewed. © 2014 Copyright Taylor and Francis Group, LLC.

Prosser R.S.,University of Guelph | Lissemore L.,University of Guelph | Topp E.,Agriculture and Agri Food Canada | Sibley P.K.,University of Guelph
Environmental Toxicology and Chemistry | Year: 2014

Biosolids generally contain the microbiocidal agents triclosan (TCS) and triclocarban (TCC) that are persistent during wastewater treatment and sorp to organic material. The present study investigated the concentration of TCS in tissues of radish, carrot, and soybean grown in potted soil amended with biosolids. Highest mean concentrations of TCS in radish, carrot, and soybean root tissue midway through the life cycle were 24.8ng/g, 49.8ng/g, and 48.1ng/g dry weight, respectively; by the conclusion of the test, however, concentrations had declined to 2.1ng/g, 5.5ng/g, and 8.4ng/g dry weight, respectively. Highest mean concentrations of TCS in radish and carrot shoot tissue were 33.7 and 18.3ng/g dry weight at days 19 and 45, respectively, but had declined to 13.7ng/g and 5.5ng/g dry weight at days 34 and 69, respectively. Concentration of TCS in all samples of soybean seeds was below method detection limit (i.e., 2.8ng/g dry wt). The present study also examined the concentration of TCS and TCC in edible portions of green pepper, carrot, cucumber, tomato, radish, and lettuce plants grown in a field amended with biosolids. Triclosan was detected only in cucumber and radish up to 5.2ng/g dry weight. Triclocarban was detected in carrot, green pepper, tomato, and cucumber up to 5.7ng/g dry weight. On the basis of the present study and other studies, we estimate that vegetable consumption represents less than 0.5% of the acceptable daily intake of TCS and TCC. These results demonstrate that, if best management practices for land application of biosolids in Ontario are followed, the concentration of TCS and TCC in edible portions of plants represents a negligible exposure pathway to humans. © 2013 SETAC.

Gorzelak M.A.,University of British Columbia | Gorzelak M.A.,University of Northern British Columbia | Hambleton S.,Agriculture and Agri Food Canada | Massicotte H.B.,University of Northern British Columbia
Fungal Ecology | Year: 2012

The ecological plasticity of Vaccinium membranaceum (Ericaceae) to grow from valley bottoms to alpine habitats allowed us to test if fungal community structure varies along an elevation gradient in east-central British Columbia. Using the shrub as an independent variable, and plant and soil features along the gradient to model a changing climate, communities of root-associated fungi were investigated. The colonized roots from 40 individuals were examined using culture-dependent sequencing and ARISA (automated ribosomal intergenic spacer analysis). Our results demonstrated that high elevation fungal communities, characterised by Rhizoscyphus ericae, differ from lower elevation communities, where Phialocephala fortinii was the most frequently isolated fungus. Co-occurrence analysis indicated that, overall, fungi tended to occur together more often than would be expected by chance. At the scale of the individual host plant, facilitation may play a more important role than competition in shaping fungal communities in these ecosystems. © 2011 Elsevier Ltd and The British Mycological Society.

Marambe H.K.,University of Saskatchewan | Shand P.J.,University of Saskatchewan | Wanasundara J.P.D.,University of Saskatchewan | Wanasundara J.P.D.,Agriculture and Agri Food Canada
Journal of Agricultural and Food Chemistry | Year: 2011

The scope of this study was to determine the ability of flaxseed (Linum usitatissimum L.) proteins to release angiotensin I-converting enzyme inhibitory (ACEI) peptides during simulated gastrointestinal (GI) digestion using a static (SM; no absorption in the intestinal phase) and a dynamic model (DM; simultaneous absorption of digested products in the intestinal phase via passive diffusion). Gastric and gastric + small intestinal digests of flaxseed proteins of both models possessed ACEI activity. The ACEI activity of the gastric + small intestinal digest in the DM (IC 50 unabsorbed, 0.05 mg N/mL; IC 50 absorbed, 0.04 mg N/mL) was significantly higher (p < 0.05) than that of the SM (IC 50, 0.39 mg N/mL). Two peptides, a pentapeptide (Trp-Asn-Ile/Leu-Asn-Ala) and a hexapeptide (Asn-Ile/Leu-Asp-Thr- Asp-Ile/Leu), were identified in the most active ACEI fraction (0.5-1 kDa) of the absorbable flaxseed protein digest by de novo sequencing. © 2011 American Chemical Society.

Urbez-Torres J.R.,Agriculture and Agri Food Canada | Peduto F.,University of California at Davis | Striegler R.K.,University of Missouri | Urrea-Romero K.E.,University of Arkansas | And 3 more authors.
Fungal Diversity | Year: 2012

Grapevine trunk diseases are a major concern to the wine- and table-grape industries worldwide, limiting both vineyard longevity and productivity. Field surveys conducted throughout the grape-growing regions of Arkansas and Missouri revealed the presence of three economically important grapevine trunk diseases including, Botryosphaeria canker, Eutypa dieback and esca. Morphological studies along with multi-gene phylogenetical analyses confirmed the identification of 15 different fungal taxa associated with different vascular symptoms. These include Botryosphaeria dothidea, Diatrypella sp., Diplodia seriata, Dothiorella americana, Eutypa lata, Eutypella vitis, Lasiodiplodia missouriana, Lasiodiplodia viticola, Neofusicoccum ribis, Neofusicoccum vitifusiforme, Pestalotiopsis sp., Pestalotiopsis uvicola, Phaeomoniella chlamydospora, Phomopsis viticola, Schyzophyllum commune, and Togninia minima. All of these represent new records on grapevines in Arkansas and Missouri. Dothiorella americana, L. missouriana and L. viticola are described as new species, and both N. ribis and N. vitifusiforme are first reported as grapevine pathogens in North America. Koch's postulates confirmed the pathogenicity of all fungal species except S. commune in the interspecific hybrids Vignoles, Chambourcin, Norton, and Traminette. Lasiodiplodia spp., N. ribis, and P. viticola were the most virulent fungi, while D. americana, E. vitis and N. vitifusiforme were considered to be weak pathogens. This research highlights the importance that grapevine trunk diseases have on grapevine health in growing regions where, due to different climatological conditions, interspecific hybrid cultivars are predominantly grown. © Kevin D. Hyde 2011.

Xing T.,Carleton University | Laroche A.,Agriculture and Agri Food Canada
Plant Signaling and Behavior | Year: 2011

The regulation mechanisms of any plant-pathogen interaction are complex and dynamic. A proteomic approach is necessary in understanding regulatory networks because it identifies new proteins in relation to their function and ultimately aims to clarify how their expression, accumulation and modification is controlled. One of the major control mechanisms for protein activity in plant-pathogen interactions is protein phosphorylation, and an understanding of the significance of protein phosphorylation in plant-pathogen interaction can be overwhelming. Due to the high number of protein kinases and phosphatases in any single plant genome and specific limitations of any technologies, it is extremely challenging for us to fully delineate the phosphorylation machinery. Current proteomic approaches and technology advances have demonstrated their great potential in identifying new components. Recent studies in well-developed plantpathogen systems have revealed novel phosphorylation pathways, and some of them are off the core phosphorylation cascades. Additional phosphoproteomic studies are needed to increase our comprehension of the different mechanisms and their fine tuning involved in the host resistance response to pathogen attacks. © 2011 Landes Bioscience.

Huang H.,McGill University | Liu L.,McGill University | Ngadi M.O.,McGill University | Gariepy C.,Agriculture and Agri Food Canada
Talanta | Year: 2014

Having acquired near infrared (NIR) hyperspectral images of intact pork loin samples through an NIR hyperspectral imaging system, the efficiency of a variety of image processing techniques including texture pattern analysis techniques were applied to process hyperspectral images so as to determine the intramuscular fat (IMF) content non-destructively. After the segmentation of region of interest (ROI), the raw spectral, texture-based spectral and textural characteristics of pork images were extracted by spectral averaging and pattern recognition techniques namely Gabor filter and improved gray level co-occurrence matrix (GLCM), respectively. First derivatives of the non-filtered and the Gabor filtered spectra were also investigated. Full waveband partial least squares regression (PLSR) was employed to determine the optimal parameters of Gabor filter and GLCM, and to select optimal wavelengths for IMF prediction. A stepwise procedure was applied to the optimal wavelengths to further optimize them to key wavelengths. Multiple linear regression (MLR) models were built based on the key wavelengths. Mean spectra and the Gabor filtered spectra outperformed GLCM. The best result, represented by correlation coefficients of calibration (Rc), cross validation (Rcv) and prediction (Rp) of 0.89, 0.89, and 0.86, respectively, was achieved using the first derivative of Gabor filtered spectra at 1193 and 1217 nm. To visualize the IMF content in pork, the distribution maps of IMF content in pork were drawn using a mean spectra-based MLR model. These promising results highlight the great potential of NIR hyperspectral imaging for non-destructive prediction of IMF content of intact pork. © 2013 Elsevier Ltd. All rights reserved.

Masse D.I.,Agriculture and Agri Food Canada
Journal of animal science | Year: 2010

Environmental issues associated with swine production are becoming a major concern among the general public and are thus an important challenge for the swine industry. There is now a renewed interest in environmental biotechnologies that can minimize the impact of swine production and add value to livestock by-products. An anaerobic biotechnology called psychrophilic anaerobic digestion (PAD) in sequencing batch reactors (SBR) has been developed at Agriculture and Agri-Food Canada. This very stable biotechnology recovers usable energy, stabilizes and deodorizes manure, and increases the availability of plant nutrients. Experimental results indicated that PAD of swine manure slurry at 15 to 25 degrees C in intermittently fed SBR reduces the pollution potential of manure by removing up to 90% of the soluble chemical oxygen demand. The process performs well under intermittent feeding, once to 3 times a week, and without external mixing. Bioreactor feeding activities can thus be easily integrated into the routine manure removal procedures in the barn, with minimal interference with other farm operations and use of existing manure-handling equipment. Process stability was not affected by the presence of antibiotics in manure. The PAD process was efficient in eliminating populations of zoonotic pathogens and parasites present in raw livestock manure slurries. Psychrophilic anaerobic digestion in SBR could also be used for swine mortality disposal. The addition of swine carcasses, at loading rates representing up to 8 times the normal mortality rates on commercial farms, did not affect the stability of SBR. No operational problems were related to the formation of foam and scum. The biotechnology was successfully operated at semi-industrial and full commercial scales. Biogas production rate exceeded 0.20 L of methane per gram of total chemical oxygen demand fed to the SBR. The biogas was of excellent quality, with a methane concentration ranging from 70 to 80%. The recovery of green energy, the production of a value-added odorless fertilizer, the elimination of manure pathogens, and the proper disposal of swine mortalities will substantially reduce the carbon and environmental footprints on products of swine origin.

Ells T.C.,Agriculture and Agri Food Canada | Hansen L.T.,Dalhousie University
Journal of Food Protection | Year: 2010

Mild thermal processing can enhance the shelf life of cut fruits and vegetables by delaying the onset of spoilage and preserving the organoleptic properties of shredded cabbage. However, food safety issues related to this process have not been fully investigated. Therefore, the survival and growth of Listeria spp. on cabbage treated in this manner was examined. Experimentally, 24 strains of Listeria spp. (including L. monocytogenes) were inoculated onto cut and intact cabbage tissues and stored at 5°C. All strains on intact tissues exhibited a moderate decline in numbers (up to 1.0 log CFU/cm2) over the 28-day storage period. Conversely, cut tissue supported growth of most strains during the first 7 to 14 days of incubation with maximum increases of 1.2 log CFU/cm2. Subsequently, the survival or growth on heat-treated (50°C for 3 min) and untreated shredded cabbage of four L. monocytogenes and four nonpathogenic Listeria spp. strains were compared during storage for 21 days at 5°C. Growth on untreated shred for all strains was similar to the results observed on cut tissue with a maximum increase of approximately 1.0 log CFU/g. However, in the heat-treated cabbage shred all strains displayed a rapid increase in growth (up to 2.5 log CFU/g) during the first 7 days of incubation, which may be indicative of the destruction of an endogenous growth-inhibiting compound within the cabbage. In conclusion, this study shows that mild thermal treatments of cut cabbage may promote pathogen growth if other inimical barriers are not implemented downstream of the thermal treatment. Copyright ©, Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture & Agri-Food Canada.

Amend A.S.,University of California at Berkeley | Seifert K.A.,Agriculture and Agri Food Canada | Bruns T.D.,University of California at Berkeley
Molecular Ecology | Year: 2010

Pyrosequencing technologies have revolutionized how we describe and compare complex microbial communities. In 454 pyrosequencing data sets, the abundance of reads pertaining to taxa or phylotypes is commonly interpreted as a measure of genic or taxon abundance, useful for quantitative comparisons of community similarity. Potentially systematic biases inherent in sample processing, amplification and sequencing, however, may alter read abundance and reduce the utility of quantitative metrics. Here, we examine the relationship between read abundance and biological abundance in a sample of house dust spiked with known quantities and identities of fungi along a dilution gradient. Our results show one order of magnitude differences in read abundance among species. Precision of quantification within species along the dilution gradient varied from R 2 of 0.96-0.54. Read-quality based processing stringency profoundly affected the abundance of one species containing long homopolymers in a read orientation-biased manner. Order-level composition of background environmental fungal communities determined from pyrosequencing data was comparable with that derived from cloning and Sanger sequencing and was not biased by read orientation. We conclude that read abundance is approximately quantitative within species, but between-species comparisons can be biased by innate sequence structure. Our results showed a trade off between sequence quality stringency and quantification. Careful consideration of sequence processing methods and community analyses are warranted when testing hypotheses using read abundance data. © 2010 Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada.

Qian D.,Tianjin University | Chang P.R.,Agriculture and Agri Food Canada | Ma X.,Tianjin University
Carbohydrate Polymers | Year: 2011

Porous starch (PS) was created by replacing ice crystals in frozen starch gel with ethanol using a solvent exchange technique. In the single freezing process, the porous structures of PSs were controlled by changing the starch paste concentrations. With the increasing of concentrations from 5 to 20%, pore size, moisture adsorption, oil adsorption capacity and methylene blue (MB) adsorption of PSs decreased greatly, while the apparent density increased from 0.093 to 0.689 g/cm3. In the dual freezing process, the porous structures of citric acid-modified PS (CAPS0) were full of starch pastes with different concentrations (1.5, 2.5 and 3.5%), and then frozen again. Compared to CAPS0, PSs from the dual freezing process exhibited larger apparent density and MB adsorption, but lower moisture adsorption and oil adsorption capacity. And the starch paste concentrations (1.5-3.5%) had few effects on the properties of PSs in the second freezing process. Copyright © 2011 Published by Elsevier Ltd. All rights reserved.

Andrew M.E.,Natural Resources Canada | Wulder M.A.,Natural Resources Canada | Coops N.C.,University of British Columbia | Baillargeon G.,Agriculture and Agri Food Canada
Global Ecology and Biogeography | Year: 2012

Aim: Several lines of evidence suggest that beta diversity, or dissimilarity in species composition, should increase with productivity: (1) the latitudinal species richness gradient is most closely related to productivity and associated latitudinal beta-diversity relationships have been described, and (2) the scale dependence of the productivity-diversity relationship implies that there should be a positive productivity-beta-diversity relationship. However, such a pattern has not yet been demonstrated at broad scales. We test if there is a gradient of increasing beta diversity with productivity. Location: Canada. Methods: Canada was clustered into regions of similar productivity regimes along three remotely sensed productivity axes (minimum and integrated annual productivity, seasonality of productivity) and elevation. The overall (β j), turnover (β sim) and nestedness (β nes) components of beta diversity within each productivity regime were estimated with pairwise dissimilarity metrics and related to cluster productivity with partial linear regression and with spatial autoregression. Tests were performed for all species, productivity breadth-based subsets (e.g. species occurring in many and a moderate number of productivity regimes), and pre- and post-1970 butterfly records. Beta diversity between adjacent clusters along the productivity gradients was also evaluated. Results: Within-cluster β j and β sim increased with productivity and decreased with seasonality. The converse was true for β nes. All species subsets responded similarly; however, productivity-beta-diversity relationships were weaker for the post-1970 temporal subset and strongest for species of moderate breadth. Between-cluster beta diversity (β j) and nestedness (β nes) declined with productivity. Main conclusions: As predicted, beta diversity of communities within productivity regimes was observed to increase with productivity. This pattern was driven largely by a gradient of species turnover. Therefore, beta diversity may make an important contribution to the broad-scale gradient of species richness with productivity. However, this species richness gradient dominates regional beta diversity between productivity regimes, resulting in decreasing between-productivity dissimilarity with productivity driven by a concurrent decline in nestedness. © 2011 Crown in the right of Canada.

Wu D.,Tianjin University | Chang P.R.,Agriculture and Agri Food Canada | Ma X.,Tianjin University
Carbohydrate Polymers | Year: 2011

The Zn-Al layered double hydroxide (LDH) was fabricated using carboxymethyl-cellulose sodium (CMC) as the stabilizer in aqueous solution, and then used as the filler to prepare LDH-CMC/glycerol plasticized-starch (GPS) nanocomposites in the casting process. Transmission electron microscopy exhibited the platelets of LDH-CMC with a lateral size of 30-60 nm and the thickness of 5-10 nm. X-ray diffraction showed that the presence of CMC decreased the thickness of LDH. The chemical formulas of LDH was [Zn 0.64·Al0.36·(OH)2]Cl 0.36·nH2O, and the content of CMC was about 37.5 wt%. LDH-CMC possessed the good stability in water because of hydrophilic CMC components and the smaller size of each LDH stack. A low loading of LDH-CMC (below 6 wt%) could obviously improve mechanical properties and water vapor barrier of the nanocomposites, because LDH-CMC could form the good interaction with GPS matrix.© 2011 Elsevier Ltd All rights reserved.

Brua R.B.,Environment Canada | Culp J.M.,Environment Canada | Benoy G.A.,Agriculture and Agri Food Canada
Hydrobiologia | Year: 2011

The assessment of benthic invertebrate community condition is an integral component of freshwater biomonitoring and water quality determination. Several sampling devices have been developed to collect benthic macroinvertebrates, including qualitative, semi-quantitative, and quantitative methods. In this study, we compared several benthic macroinvertebrate metrics and community assemblage measures calculated from data obtained from two sampling methods, namely the Kick- and U-net sampling devices. We reasoned that if the two methods produced similar values for benthic metrics and community composition, then samples collected by these methods should be able to be combined to build larger data sets for use in regional bioassessment analyses. No statistical differences between Kick- and U-net methods were found among standard benthic macroinvertebrate metrics, except for Kicknets collecting more Chironomidae. Invertebrate assemblages were very similar between collection methods, although slightly greater taxonomic richness was found in U-net samples. Bray-Curtis similarity was typically [75% between methods within a stream, while classification strengthsampling- method comparability, an approach for analyzing differences in similarity between groups, indicated invertebrate assemblage similarity between collection methods was virtually identical at approximately 100%. Since these two methods produce similar results, we conclude that benthic macroinvertebrate data collected by these methods can be combined for data analysis and bioassessments with the caveat that mesh size of the sample nets is similar. In addition, if the primary study objective is to assess macroinvertebrate biodiversity, then the U-net sampling device may be more appropriate, despite the slightly greater time needed to complete field sample collection, as it tended to collect a greater diversity of species. © Springer Science+Business Media B.V. 2010.

Gelinas P.,Agriculture and Agri Food Canada
Recent Patents on Food, Nutrition and Agriculture | Year: 2010

Baker's yeast is the gas-forming ingredient in bakery products. Methods have been invented to properly handle baker's yeast and optimize its activity at the bakery plant. Over the years, incentives for inventions on yeast storage and activation have greatly changed depending on trends in the baking industry. For example, retailer's devices for cutting bulk pressed yeast and techniques for activating dry yeast have now lost their importance. Review of patents for invention indicates that activation of baker's yeast activity has been a very important issue for bakers, for example, with baking ingredients called yeast foods. In the recent years and especially for highly automated bakeries, interest has moved to equipments and processes for optimized storage of liquid cream yeast to thoroughly control dough fermentation and bread quality. © 2010 Bentham Science Publishers Ltd.

Jianxiong Y.E.,University of Guelph | Kostrzynska M.,Agriculture and Agri Food Canada | Dunfield K.,University of Guelph | Warriner K.,University of Guelph
Journal of Food Protection | Year: 2010

The following reports on the application of a combination of antagonistic bacteria and lytic bacteriophages to control the growth of Salmonella on sprouting mung beans and alfalfa seeds. Antagonistic bacteria were isolated from mung bean sprouts and tomatoes by using the deferred plate assay to assess anti-Salmonella activity. From the isolates screened, an Enterobacter asburiae strain (labeled "JX1") exhibited stable antagonistic activity against a broad range of Salmonella serovars (Agona, Berta, Enteritidis, Hadar, Heidelberg, Javiana, Montevideo, Muenchen, Newport, Saint Paul, and Typhimurium). Lytic bacteriophages against Salmonella were isolated from pig or cattle manure effluent. A bacteriophage cocktail prepared from six isolates was coinoculated with E. asburiae JX1 along with Salmonella in broth culture. The combination of E. asburiae JX1 and bacteriophage cocktail reduced the levels of Salmonella by 5.7 to 6.4 log CFU/ml. Mung beans inoculated with Salmonella and sprouted over a 4-day period attained levels of 6.72 ± 0.78 log CFU/g. In contrast, levels of Salmonella were reduced to 3.31 ± 2.48 or 1.16 ± 2.14 log CFU/g when the pathogen was coinoculated with bacteriophages or E. asburiae JX1, respectively. However, by using a combination of E. asburiae JX1 and bacteriophages, the levels of Salmonella associated with mung bean sprouts were only detected by enrichment. The biocontrol preparation was effective at controlling the growth of Salmonella under a range of sprouting temperatures (20 to 30°C) and was equally effective at suppressing the growth of Salmonella on sprouting alfalfa seeds. The combination of E. asburiae JX1 and bacteriophages represents a promising, chemical-free approach for controlling the growth of Salmonella on sprouting seeds. Copyright ©, International Association for Food Protection.

Lysyk T.J.,Agriculture and Agri Food Canada
Journal of Medical Entomology | Year: 2014

The effects of temperature on oviposition by Dermacentor andersoni (Stiles) was examined using replete females ranging in weight from 30 to 1,198 mg. Survivorship was >96% during the preoviposition periods and declined during oviposition period. Egg production peaked earlier and at greater levels as temperature increased. Longevity, preoviposition period, and oviposition period declined as temperature increased. Replete weight had minor effects on measures of time, but smaller females tended to have greater longevity and preoviposition periods, and shorter oviposition periods. Temperature and replete weight both had large effects on measures of oviposition success such as the amount of eggs laid, the conversion efficiency index, and daily egg production. Lower temperatures and replete weight resulted in greater oviposition failure, and reduced egg production and conversion efficiency. Oviposition was greatly inhibited at 10°C, suggesting this is near the lower temperature limit for development. However, egg production was reduced at temperatures <20°C, suggesting that the northern edge of the distribution may be influenced by the effects of temperature on oviposition. © 2014 Entomological Society of America.

Ghoshal B.,University of British Columbia | Sanfacon H.,University of British Columbia | Sanfacon H.,Agriculture and Agri Food Canada
Virology | Year: 2015

The natural outcome of some plant-virus interactions is symptom recovery, which is characterized by the emergence of asymptomatic leaves following a systemic symptomatic infection. Symptom recovery is generally accompanied with reduced virus titers and sequence-specific resistance to secondary infection and has been linked with the induction of antiviral RNA silencing. Recent studies have revealed an unsuspected diversity of silencing mechanisms associated with symptom recovery in various host-virus interactions, including degradation or translation repression of viral RNAs and in the case of DNA viruses, transcriptional arrest of viral minichromosomes. RNA silencing may also contribute to symptom alleviation by regulating plant gene expression. In this review, we discuss the evidence supporting the role of various RNA silencing mechanisms in symptom recovery. We also discuss how a delicate equilibrium between RNA silencing and virus counter-defense responses in recovered leaves may help maintain virus titers at levels below the threshold required for symptom induction. © 2015 Published by Elsevier Inc.

Li X.-Q.,Agriculture and Agri Food Canada | Xing T.,Carleton University | Du D.,University of New Brunswick
Current Issues in Molecular Biology | Year: 2016

Somatic mutation of signal transduction genes or key nodes of the cellular protein network can cause severe diseases in humans but can sometimes genetically improve plants, likely because growth is determinate in animals but indeterminate in plants. This article reviews protein networks; human protein ranking; the mitogenactivated protein kinase (MAPK) and insulin (phosphoinositide 3kinase [PI3K]/phosphatase and tensin homolog [PTEN]/protein kinase B [AKT]) signaling pathways; human diseases caused by somatic mutations to the PI3K/PTEN/ AKT pathway; use of the MAPK pathway in plant molecular breeding; and protein domain evolution. Casitas B-lineage lymphoma (CBL), PTEN, MAPK1 and PIK3CA are among the top-ranked proteins in directional rankings. Eight proteins (ACVR1, CDC42, RAC1, RAF1, RHOA, TGFBR1, TRAF2, and TRAF6) are ranked in the top 50 key players in both signal emission and signal reception and in interaction with many other proteins. Top-ranked proteins likely have major impacts on the network function. Such proteins are targets for drug discovery, because their mutations are implicated in various cancers and overgrowth syndromes. Appropriately managing food intake may help reduce the growth of tumors or malformation of tissues. The role of the protein kinase C/ fatty acid synthase pathway in fat deposition in PTEN/PI3K patients should be investigated. Both the MAPK and insulin signaling pathways exist in plants, and MAPK pathway engineering can improve plant tolerance to biotic and abiotic stresses such as salinity. © 2016, Caister Academic Press. All rights reserved.

Most of the world's species at risk of extinction are neither particularly attractive nor obviously useful, and consequently lack conservation support. In contrast, the public, politicians, scientists, the media and conservation organisations are extremely sympathetic to a select number of well-known and admired species, variously called flagship, charismatic, iconic, emblematic, marquee and poster species. These are extremely attractive, large, entertaining or useful, and they receive the lion's share of public and private financial support, publicity, research, conservation and protective legislation. Such species have proven to be the best available means of increasing public awareness of the biodiversity crisis, and of mobilising financial support for conservation. They are widely touted as critical to the cause of conservation, not just symbolically, but also because preservation of their habitats, it has been claimed, can simultaneously preserve other species at risk. However, there is only limited evidence of 'trickle-down' benefits to rare, endemic and endangered species. Indeed, management strategies based on various ecologically-defined representative species (surrogate species, focal species, indicator species, keystone species, umbrella species) are only partially useful for aiding non-targeted species at risk. Aesthetic and commercial standards have become the primary determinants of which species in the natural world deserve conservation. Accordingly, the world's biodiversity is being beautified by selective conservation of attractive species, while the plight of the overwhelming majority of species is receiving limited attention. © 2012 Copyright Taylor and Francis Group, LLC.

Li X.-Q.,Agriculture and Agri Food Canada
Current Issues in Molecular Biology | Year: 2016

This article proposes the concept of genome network, describes different variations of the somatic genome network, and reviews the agricultural implications of such variations. All genetic materials in a cell constitute the genome network of the cell and can jointly influence the cell's function and fate. The somatic genome of a plant is the genome network of cells in somatic tissues and of nonreproductive cells in pollen and ovules. Somatic genome variation (SGV, approximately equivalent to somagenetic variation) occurs at multiple levels, including stoichiometric, ploidy, and sequence variations. For a multicellular organism, the term "somatic genome variation" covers both the variation in part of the organism and the generation of new genotype individuals through somatic means from a sexually produced original genotype. For unicellular organisms, genome variation in somatic nuclei occurs at the whole organism level because there is only a single cell per individual. Growth, development and evolution of living organisms require both stability and instability of their genomes. Somatic genome variation displays many more attributes than genetic mutation and has strong implications for agriculture. © 2016, Caister Academic Press. All rights reserved.

Fu Y.-B.,Agriculture and Agri Food Canada
G3: Genes, Genomes, Genetics | Year: 2014

Genotyping by sequencing (GBS) recently has emerged as a promising genomic approach for assessing genetic diversity on a genome-wide scale. However, concerns are not lacking about the uniquely large unbalance in GBS genotype data. Although some genotype imputation has been proposed to infer missing observations, little is known about the reliability of a genetic diversity analysis of GBS data, with up to 90% of observations missing. Here we performed an empirical assessment of accuracy in genetic diversity analysis of highly incomplete single nucleotide polymorphism genotypes with imputations. Three large single-nucleotide polymorphism genotype data sets for corn, wheat, and rice were acquired, and missing data with up to 90% of missing observations were randomly generated and then imputed for missing genotypes with three map-independent imputation methods. Estimating heterozygosity and inbreeding coefficient from original, missing, and imputed data revealed variable patterns of bias from assessed levels of missingness and genotype imputation, but the estimation biases were smaller for missing data without genotype imputation. The estimates of genetic differentiation were rather robust up to 90% of missing observations but became substantially biased when missing genotypes were imputed. The estimates of topology accuracy for four representative samples of interested groups generally were reduced with increased levels of missing genotypes. Probabilistic principal component analysis based imputation performed better in terms of topology accuracy than those analyses of missing data without genotype imputation. These findings are not only significant for understanding the reliability of the genetic diversity analysis with respect to large missing data and genotype imputation but also are instructive for performing a proper genetic diversity analysis of highly incomplete GBS or other genotype data. © 2014 Fu.

Lapointe J.,Agriculture and Agri Food Canada
Journal of Animal Physiology and Animal Nutrition | Year: 2014

Genetic selection and management changes during the last decades have significantly increased the average litter size of sows. However, this recent success has not correlated with an extension of longevity and reduction in replacement rate. Longevity or lifetime production of sows is determined by a combination of environmental and genetic factors. Nutrition is an environmental factor of importance, and it has long been appreciated that animals fed with specific diets may perform differently. The advent of modern science revealed that this is partly due to the ability of nutrients to act as signalling molecules that, through appropriate intracellular sensing mechanisms, can control gene expression and modulate cell functions. Based on this concept, nutrigenomics studies now aim to show that not only are certain nutrients essential for general health, but also that specific quantities of precise nutrients are necessary during critical periods of energy deficiency and oxidative stress such as gestation and lactation to ensure long-term productivity. The toxic molecules at the origin of oxidative stress, free radicals, are mainly generated as normal by-products of aerobic energy production by mitochondria. In all cells, mitochondria are dynamic organelles that are mainly known as the primary energy-generating system. Thus, when metabolic demands are elevated as it is for hyperprolific sows, mitochondria are heavily solicited for answering all energetic needs, and substantive amounts of free radicals are generated. As a result, optimal conditions in term of antioxidant protection and metabolic substrates availability are required to support mitochondrial function in these animals. This article discusses how performance and longevity of sows are linked to mitochondrial function and oxidative stress and reviews the major natural nutrients known for their antioxidant and/or energetic properties that are susceptible to impact mitochondria and likely improved sows productivity. © 2014 Blackwell Verlag GmbH.

Lartillot N.,University of Montreal | Lartillot N.,CNRS Montpellier Laboratory of Informatics, Robotics and Microelectronics | Rodrigue N.,Agriculture and Agri Food Canada | Rodrigue N.,University of Ottawa | And 2 more authors.
Systematic Biology | Year: 2013

Modeling across site variation of the substitution process is increasingly recognized as important for obtaining more accurate phylogenetic reconstructions. Both finite and infinite mixture models have been proposed and have been shown to significantly improve on classical single-matrix models. Compared with their finite counterparts, infinite mixtures have a greater expressivity.However, they are computationally more challenging. This has resulted in practical compromises in the design of infinite mixture models. In particular, a fast but simplified version of a Dirichlet process model over equilibrium frequency profiles implemented in PhyloBayes has often been used in recent phylogenomics studies, while more refined model structures, more realistic and empirically more fit, have been practically out of reach. We introduce a message passing interface version ofPhyloBayes,implementing the Dirichletprocess mixture models aswell as more classical empirical matrices and finite mixtures. The parallelization is made efficient thanks to the combination of two algorithmic strategies: a partial Gibbs sampling update of the tree topology and the use of a truncated stick-breaking representation for the Dirichlet process prior. The implementation shows close to linear gains in computational speed for up to 64 cores, thus allowing faster phylogenetic reconstruction under complex mixture models. PhyloBayes MPI is freely available from our website www.phylobayes.org. [Bayesian inference; Dirichlet process; mixture models; phylogenetics; phylogenomics.] © The Author(s) 2013.

Mahelka V.,Academy of Sciences of the Czech Republic | Kopecky D.,Academy of Sciences of the Czech Republic | Baum B.R.,Agriculture and Agri Food Canada
Molecular Biology and Evolution | Year: 2013

We employed sequencing of clones and in situ hybridization (genomic and fluorescent in situ hybridization [GISH and rDNA-FISH]) to characterize both the sequence variation and genomic organization of 45S (herein ITS1-5.8S-ITS2 region) and 5S (5S gene + nontranscribed spacer) ribosomal DNA (rDNA) families in the allohexaploid grass Thinopyrum intermedium. Both rDNA families are organized within several rDNA loci within all three subgenomes of the allohexaploid species. Both families have undergone different patterns of evolution. The 45S rDNA family has evolved in a concerted manner: internal transcribed spacer (ITS) sequences residing within the arrays of two subgenomes out of three got homogenized toward one major ribotype, whereas the third subgenome contained a minor proportion of distinct unhomogenized copies. Homogenization mechanisms such as unequal crossover and/or gene conversion were coupled with the loss of certain 45S rDNA loci. Unlike in the 45S family, the data suggest that neither interlocus homogenization among homeologous chromosomes nor locus loss occurred in 5S rDNA. Consistently with other Triticeae, the 5S rDNA family in intermediate wheatgrass comprised two distinct array types-the long-and short-spacer unit classes. Within the long and short units, we distinguished five and three different types, respectively, likely representing homeologous unit classes donated by putative parental species. Although the major ITS ribotype corresponds in our phylogenetic analysis to the E-genome species, the minor ribotype corresponds to Dasypyrum. 5S sequences suggested the contributions from Pseudoroegneria, Dasypyrum, and Aegilops. The contribution from Aegilops to the intermediate wheatgrass' genome is a new finding with implications in wheat improvement. We discuss rDNA evolution and potential origin of intermediate wheatgrass. © 2013 The Author.

Rasolofo E.A.,Laval University | St-Gelais D.,Agriculture and Agri Food Canada | LaPointe G.,Laval University | Roy D.,Laval University
International Journal of Food Microbiology | Year: 2010

Spoilage bacteria in milk are controlled by treatments such as thermization, microfiltration and addition of carbon dioxide. However, little information is known about the changes in microbial communities during subsequent cold storage of treated milk. Culture-dependent methods and a direct molecular approach combining 16S rRNA gene clone libraries and quantitative PCR (Q-PCR) were applied to obtain a better overview of the structure and the dynamics of milk microbiota. Raw milk samples were treated by the addition of carbon dioxide (CO2), thermization (TH) or microfiltration (MF) and stored at 4 °C or 8 °C up to 7 d. Untreated milk (UT) was used as a control. Psychrotrophic and staphylococci bacteria were enumerated in the milk samples by culture methods. For the molecular approach, DNA was extracted from milk samples and 16S rRNA gene was amplified by PCR with universal primers prior to cloning. The Q-PCR method was used to evaluate the dynamics of dominant bacterial species revealed by clone library analysis of 16S rRNA gene. Comparison of the 16S rRNA gene sequence indicated that the two most abundant operational taxonomic units (OTU), determined at 97% identity, belonged to the class Gammaproteobacteria (40.3% of the 1415 sequences) and Bacilli (40%). Dominant bacterial species in UT, CO2 and TH milk samples at day 3 were affiliated with Staphylococcus, Streptococcus, Clostridia, Aerococcus, Facklamia, Corynebacterium, Acinetobacter and Trichococcus. Dominant bacterial species detected in MF milk were Stenotrophomonas, Pseudomonas and Delftia, while Pseudomonas species dominated the bacterial population of UT, CO2 and MF milk samples at day 7. Staphylococcus and Delftia were the dominant bacterial species in thermized milk. Q-PCR results showed that populations of S. aureus, A. viridans, A. calcoaceticus, C. variabile and S. uberis were stable during 7 d of storage at 4 °C. Populations of P. fluorescens, S. uberis and total bacteria increased in UT and CO2 milk samples during 7 d of storage at 8 °C and were noticeable from day 3. This study shows new microbial species which can develop during cold storage after milk treatment and contributes to identifying causes of reduced shelf life and deterioration of technological properties of milk during storage. © 2010 Elsevier B.V.

Wong A.,Carleton University | Wong A.,University of Ottawa | Rodrigue N.,University of Ottawa | Rodrigue N.,Agriculture and Agri Food Canada | Kassen R.,University of Ottawa
PLoS Genetics | Year: 2012

Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF-like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates. © 2012 Wong et al.

Lonsdale O.,Agriculture and Agri Food Canada
African Invertebrates | Year: 2015

Phytomyza impunita sp. n. is described in the subgenus Ptochomyza Hering. This species is known from a single location in the Republic of South Africa, representing the fifth described species in the subgenus, and the second known Ptochomyza to occur outside of the Palaearctic Region, with P. asparagivora (Spencer) known from southern Europe, Pakistan, Ethiopia and Kenya. The new species is described and figured, and discussed in relation to congeners. © 2015, Council Natal Museum. All rights reserved.

de Jong H.,Agriculture and Agri Food Canada
American Journal of Potato Research | Year: 2016

The first impact of the potato on society was the intimate relationship between the domestication of the potato and the evolution of Andean civilization which affected Andean culture and religion. In addition to food potatoes were used for several non-food purposes. In the Inca Empire the freeze-dried chuño was collected as taxes from the peasants and disbursed from imperial storehouses to labor gangs for building roads, waging war, and erecting monuments. After the Spanish conquest chuño was used to feed the slaves in the Andean silver and gold mines. This in turn set the stage for flooding the Spanish and eventually the global market with these precious metals and subsequent world-wide inflation of consumer goods. The potato became the major contributor to the European population explosion of 1750–1850 which in turn resulted in increased urbanization and contributed to the underpinning of the Industrial Revolution in England in the nineteenth century. By feeding rapidly growing populations the potato permitted a small number of nations in northern Europe to assert dominion over much of the world between 1750 and 1950. The failure of the potato crop in Ireland in the 1840s led Britain to repeal the protectionist Corn Laws and set the country on a path of free trade. At least one million Irish refugees emigrated, mostly to North America where they left a great legacy. The past 50 years have seen a major global shift in potato production towards many developing countries in Asia, including China and India. Throughout its history the potato has provided bread for the poor. Today it contributes to food security on a global scale. The potato’s depiction on postage stamps demonstrates the esteem in which it is held worldwide and the many references to the potato in art, literature and folklore worldwide are evidence how it has become interwoven in the cultures of many societies today. © 2016 The Potato Association of America

Gunnaiah R.,McGill University | Kushalappa A.C.,McGill University | Duggavathi R.,McGill University | Fox S.,Agriculture and Agri Food Canada | Somers D.J.,Vineland Research and Innovation Center
PLoS ONE | Year: 2012

Background: Resistance in plants to pathogen attack can be qualitative or quantitative. For the latter, hundreds of quantitative trait loci (QTLs) have been identified, but the mechanisms of resistance are largely unknown. Integrated non-target metabolomics and proteomics, using high resolution hybrid mass spectrometry, were applied to identify the mechanisms of resistance governed by the fusarium head blight resistance locus, Fhb1, in the near isogenic lines derived from wheat genotype Nyubai. Findings: The metabolomic and proteomic profiles were compared between the near isogenic lines (NIL) with resistant and susceptible alleles of Fhb1 upon F. graminearum or mock-inoculation. The resistance-related metabolites and proteins identified were mapped to metabolic pathways. Metabolites of the shunt phenylpropanoid pathway such as hydroxycinnamic acid amides, phenolic glucosides and flavonoids were induced only in the resistant NIL, or induced at higher abundances in resistant than in susceptible NIL, following pathogen inoculation. The identities of these metabolites were confirmed, with fragmentation patterns, using the high resolution LC-LTQ-Orbitrap. Concurrently, the enzymes of phenylpropanoid biosynthesis such as cinnamyl alcohol dehydrogenase, caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, flavonoid O-methyltransferase, agmatine coumaroyltransferase and peroxidase were also up-regulated. Increased cell wall thickening due to deposition of hydroxycinnamic acid amides and flavonoids was confirmed by histo-chemical localization of the metabolites using confocal microscopy. Conclusion: The present study demonstrates that the resistance in Fhb1 derived from the wheat genotype Nyubai is mainly associated with cell wall thickening due to deposition of hydroxycinnamic acid amides, phenolic glucosides and flavonoids, but not with the conversion of deoxynivalenol to less toxic deoxynivalenol 3-O-glucoside. © 2012 Gunnaiah et al.

Hwang S.-F.,Crop Diversification Center North | Strelkov S.E.,University of Alberta | Feng J.,Crop Diversification Center North | Gossen B.D.,Agriculture and Agri Food Canada | Howard R.J.,Crop Diversification Center South
Molecular Plant Pathology | Year: 2012

Plasmodiophora brassicae causes clubroot disease in cruciferous plants, and is an emerging threat to Canadian canola (Brassica napus) production. This review focuses on recent studies into the pathogenic diversity of P. brassicae populations, mechanisms of pathogenesis and resistance, and the development of diagnostic tests for pathogen detection and quantification. Taxonomy: Plasmodiophora brassicae is a soil-borne, obligate parasite within the class Phytomyxea (plasmodiophorids) of the protist supergroup Rhizaria. Disease symptoms: Clubroot development is characterized by the formation of club-shaped galls on the roots of affected plants. Above-ground symptoms include wilting, stunting, yellowing and premature senescence. Disease cycle: Plasmodiophora brassicae first infects the root hairs, producing motile zoospores that invade the cortical tissue. Secondary plasmodia form within the root cortex and, by triggering the expression of genes involved in the production of auxins, cytokinins and other plant growth regulators, divert a substantial proportion of plant resources into hypertrophic growth of the root tissues, resulting in the formation of galls. The secondary plasmodia are cleaved into millions of resting spores and the root galls quickly disintegrate, releasing long-lived resting spores into the soil. A serine protease, PRO1, has been shown to trigger resting spore germination. Physiological specialization: Physiological specialization occurs in populations of P. brassicae, and various host differential sets, consisting of different collections of Brassica genotypes, are used to distinguish among pathotypes of the parasite. Detection and quantification: As P. brassicae cannot be cultured, bioassays with bait plants were traditionally used to detect the pathogen in the soil. More recent innovations for the detection and quantification of P. brassicae include the use of antibodies, quantitative polymerase chain reaction (qPCR) and qPCR in conjunction with signature fatty acid analysis, all of which are more sensitive than bioassays. Resistance in canola: Clubroot-resistant canola hybrids, recently introduced into the Canadian market, represent an important new tool for clubroot management in this crop. Genetic resistance must be carefully managed, however, as it has been quickly overcome in other regions. At least three resistance genes and one or two quantitative trait loci are involved in conferring resistance to P. brassicae. Root hair infection still occurs in resistant cultivars, but secondary plasmodia often remain immature and unable to produce resting spores. Fewer cell wall breakages occur in resistant hosts, and spread of the plasmodium through cortical tissue is restricted. More information on the genetics of clubroot resistance in canola is needed to ensure more effective resistance stewardship. © 2011 The Authors. Molecular Plant Pathology © 2011 BSPP and Blackwell Publishing Ltd.

Lefevre P.L.C.,University of Montreal | Palin M.-F.,Agriculture and Agri Food Canada | Murphy B.D.,University of Montreal