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Yepez L.,Technical University of the North, Ibarra | Tenea G.N.,Technical University of the North, Ibarra
Romanian Biotechnological Letters | Year: 2015

Lactic acid bacteria found as sub-dominant component of the human and animal microbial gut represents one of the most significant groups of probiotic organisms. During the last decade probiotics become an important and viable ingredient in the functional foods as well as the pharmaceutical industry. In this paper, we shall review the most important findings with regards to the in vitro screening of specie-specific probiotic strains, the molecular mechanism of probiotic action, and applications in functional food. Moreover, we shall punctuate alternative sources for the isolation of novel probiotic strains to potentially satisfy the market need in the development of new functional products containing probiotic cultures more active and with better probiotic characteristics than those already existed. © 2015 University of Bucharest.

PubMed | University of Turku, Technical University of the North, Ibarra, James Cook University, University of Nottingham and 46 more.
Type: Journal Article | Journal: Proceedings. Biological sciences | Year: 2016

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change.

PubMed | Anglia, National University of Colombia, Technical University of the North, Ibarra, James Cook University and 49 more.
Type: Journal Article | Journal: Global ecology and biogeography : a journal of macroecology | Year: 2015

The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land-use planning. Remote sensing (RS) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset.Tropical forests of the Amazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1.Two recent pantropical RS maps of vegetation carbon are compared to a unique ground-plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area-based comparisons.The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north-east, to the light-wooded, shorter forests of the south-west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over- or under-estimated by >25%, whereas regional uncertainties for the maps were reported to be <5%.Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon-mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above-ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species assemblages can be reliably mapped from space.

PubMed | Anglia, National University of Colombia, Fundacion Puerto Rastrojo, New York Botanical Garden and 76 more.
Type: Journal Article | Journal: Science advances | Year: 2015

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the worlds >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

Vossen J.H.,Wageningen University | Dezhsetan S.,University of Mohaghegh | Esselink D.,Wageningen University | Arens M.,Wageningen University | And 5 more authors.
Plant Methods | Year: 2013

Background: Molecular profiling of gene families is a versatile tool to study diversity between individual genomes in sexual crosses and germplasm. Nucleotide binding site (NBS) profiling, in particular, targets conserved nucleotide binding site-encoding sequences of resistance gene analogs (RGAs), and is widely used to identify molecular markers for disease resistance (R) genes.Results: In this study, we used NBS profiling to identify genome-wide locations of RGA clusters in the genome of potato clone RH. Positions of RGAs in the potato RH and DM genomes that were generated using profiling and genome sequencing, respectively, were compared. Largely overlapping results, but also interesting discrepancies, were found. Due to the clustering of RGAs, several parts of the genome are overexposed while others remain underexposed using NBS profiling. It is shown how the profiling of other gene families, i.e. protein kinases and different protein domain-coding sequences (i.e., TIR), can be used to achieve a better marker distribution. The power of profiling techniques is further illustrated using RGA cluster-directed profiling in a population of Solanum berthaultii. Multiple different paralogous RGAs within the Rpi-ber cluster could be genetically distinguished. Finally, an adaptation of the profiling protocol was made that allowed the parallel sequencing of profiling fragments using next generation sequencing. The types of RGAs that were tagged in this next-generation profiling approach largely overlapped with classical gel-based profiling. As a potential application of next-generation profiling, we showed how the R gene family associated with late blight resistance in the SH*RH population could be identified using a bulked segregant approach.Conclusions: In this study, we provide a comprehensive overview of previously described and novel profiling primers and their genomic targets in potato through genetic mapping and comparative genomics. Furthermore, it is shown how genome-wide or fine mapping can be pursued by choosing different sets of profiling primers. A protocol for next-generation profiling is provided and will form the basis for novel applications. Using the current overview of genomic targets, a rational choice can be made for profiling primers to be employed. © 2013 Vossen et al.; licensee BioMed Central Ltd.

Pais-Chanfrau J.M.,Technical University of the North, Ibarra | Trujillo-Toledo L.E.,University las Fuerzas Armadas
Biology and Medicine | Year: 2016

The methylotrophic yeast Pichia pastoris became an excellent and successfully expression system for therapeutics and other useful heterologous proteins at large-scale. Its capacity to reach a high-cell-densityconcentration during its fed-batch fermentations in a chemically-defined culture medium is one of the main features of this system. The standard culture medium BSM developed by Invitrogen Co. has been the most widespread used. However, it contains certain components in improper ratios that lead to precipitation of some of its components during preparation, mainly after sterilization and/or during pH adjustment. In this study, we propose a modified version of the BSM culture medium, named MBSM. These simple modifications by employing a linear optimization technique solves the precipitation problems observed on BSM and other culture media. Beside it, is rather simple, easy to prepare, and inexpensive, and it has impact positively over the environment by reducing the pollution load of the fermentation waste and also diminish the cost of the industrial scale fermentation process. By using this modified medium, were reached cell densities of 100 gDCW · L-1 and 60 gDCW · L-1 for mini-proinsulin and exo-levanase under the inducible AOX1 and the constitutive GAPDH promoters, respectively. These results allow to get vast amounts of proteins able to be used in nanoscience and other biotechnological applications. © 2016 Pais-Chanfrau JM, et al.

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