Nunhems United States Inc.

Davis, CA, United States

Nunhems United States Inc.

Davis, CA, United States
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Al-Mulla H.M.N.,University of Reading | Al-Mulla H.M.N.,University of Baghdad | Turrell L.,University of Oxford | Smith N.M.,University of Reading | And 11 more authors.
mBio | Year: 2014

Positive-stranded viruses synthesize their RNA in membrane-bound organelles, but it is not clear how this benefits the virus or the host. For coronaviruses, these organelles take the form of double-membrane vesicles (DMVs) interconnected by a convoluted membrane network. We used electron microscopy to identify murine coronaviruses with mutations in nsp3 and nsp14 that replicated normally while producing only half the normal amount of DMVs under low-temperature growth conditions. Viruses with mutations in nsp5 and nsp16 produced small DMVs but also replicated normally. Quantitative reverse transcriptase PCR (RT-PCR) confirmed that the most strongly affected of these, the nsp3 mutant, produced more viral RNA than wild-type virus. Competitive growth assays were carried out in both continuous and primary cells to better understand the contribution of DMVs to viral fitness. Surprisingly, several viruses that produced fewer or smaller DMVs showed a higher fitness than wild-type virus at the reduced temperature, suggesting that larger and more numerous DMVs do not necessarily confer a competitive advantage in primary or continuous cell culture. For the first time, this directly demonstrates that replication and organelle formation may be, at least in part, studied separately during infection with positive-stranded RNA virus. © 2014 Al-Mulla et al.

Eckert A.J.,University of California at Davis | Eckert M.L.,Nunhems United States Inc. | Hall B.D.,University of Washington
American Journal of Botany | Year: 2010

The density and dispersion of individuals, nonequilibrium demographics, and habitat fragmentation all affect the magnitude and extent of spatial genetic structure within forest tree populations. Here, we investigate the link between historical demography and spatial genetic structure within ecologically contrasting stands of foxtail pine (Pinus balfouriana) in the Klamath Mountains of northern California. We defined two stand types a priori, based largely on differences in foxtail pine density and basal area, and for each type we sampled two stands. Population expansions, likely from Pleistocene bottlenecks, were detected in three of the four stands. The magnitude and extent of spatial autocorrelation among genotypes at five nuclear microsatellites differed dramatically among stands, with those having lower foxtail pine density exhibiting strong patterns of isolation by distance. Moran' s I statistics were 7-fold higher for the first distance class (< 25 m) in these stands relative to those observed in stands with higher foxtail pine density (I25 = 0.14 vs. 0.02). We conclude that differences in spatial genetic structure between stand types are due to differences in ecological attributes that affected expansion from inferred bottlenecks. © 2010 Botanical Society of America.

Martinez-Garcia P.J.,University of California at Davis | Parfitt D.E.,University of California at Davis | Bostock R.M.,University of California at Davis | Fresnedo-Ramirez J.,University of California at Davis | And 5 more authors.
PLoS ONE | Year: 2013

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar 'Dr. Davis' and a brown rot resistant introgression line, 'F8,1-42', derived from an initial almond x peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot. © 2013 Martínez-García et al.

Jeknic Z.,Oregon State University | Pillman K.A.,Oregon State University | Pillman K.A.,University of Adelaide | Pillman K.A.,Center for Cancer Biology | And 10 more authors.
Plant Molecular Biology | Year: 2014

C-Repeat Binding Factors (CBFs) are DNA-binding transcriptional activators of gene pathways imparting freezing tolerance. Poaceae contain three CBF subfamilies, two of which, HvCBF3/CBFIII and HvCBF4/CBFIV, are unique to this taxon. To gain mechanistic insight into HvCBF4/CBFIV CBFs we overexpressed Hv-CBF2A in spring barley (Hordeum vulgare) cultivar 'Golden Promise'. The Hv-CBF2A overexpressing lines exhibited stunted growth, poor yield, and greater freezing tolerance compared to non-transformed 'Golden Promise'. Differences in freezing tolerance were apparent only upon cold acclimation. During cold acclimation freezing tolerance of the Hv-CBF2A overexpressing lines increased more rapidly than that of 'Golden Promise' and paralleled the freezing tolerance of the winter hardy barley 'Dicktoo'. Transcript levels of candidate CBF target genes, COR14B and DHN5 were increased in the overexpressor lines at warm temperatures, and at cold temperatures they accumulated to much higher levels in the Hv-CBF2A overexpressors than in 'Golden Promise'. Hv-CBF2A overexpression also increased transcript levels of other CBF genes at FROST RESISTANCE-H2-H2 (FR-H2) possessing CRT/DRE sites in their upstream regions, the most notable of which was CBF12. CBF12 transcript levels exhibited a relatively constant incremental increase above levels in 'Golden Promise' both at warm and cold. These data indicate that Hv-CBF2A activates target genes at warm temperatures and that transcript accumulation for some of these targets is greatly enhanced by cold temperatures. © 2013 Springer Science+Business Media Dordrecht.

Martinez-Garcia P.J.,University of California at Davis | Peace C.P.,Washington State University | Parfitt D.E.,University of California at Davis | Ogundiwin E.A.,Nunhems United States Inc. | And 4 more authors.
Euphytica | Year: 2012

Chilling injury (CI) is a major physiological problem limiting consumption and export of peach and nectarine (Prunus persica (L.) Batsch). To clarify the genetic basis for chilling injury, inheritance of the major CI symptoms mealiness, flesh browning, flesh bleeding, and flesh leatheriness were examined over three years in two related peach progenies. In addition, genetic relationships among traits and the year-to-year variation in trait performance in these progenies were tracked. Both populations also segregated for Freestone-Melting flesh (F-M) and yellow flesh. There were significant differences in CI symptoms among years. The major gene endoPG, which controls the F-M locus, provides resistance to mealiness in non-melting flesh fruit. Only fruit with melting flesh can develop mealiness if the tree possesses other genetic susceptibility factors and/or experiences inducing conditions. The F-M locus also greatly influences susceptibility to flesh bleeding, although the physiological mechanism for this disorder is unclear and may be controlled by a different gene closely linked to endoPG. Unlike mealiness, flesh bleeding occurred primarily in non-melting flesh fruit, particularly when the fruit is white-fleshed. Flesh browning incidence was greater in mealy fruit and was not associated with flesh bleeding. Breeding for CI resistance is thus a viable long-term strategy to reduce losses in the fresh and processed peach and nectarine industries. This study is an important first step to understanding genetic control of CI symptoms in peach. © 2011 Springer Science+Business Media B.V.

Ziemienowicz A.,University of Lethbridge | Shim Y.-S.,Agriculture and Agri Food Canada | Shim Y.-S.,Nunhems United States Inc. | Matsuoka A.,University of Lethbridge | And 2 more authors.
Plant Physiology | Year: 2012

Genetic transformation of monocotyledonous plants still presents a challenge for plant biologists and biotechnologists because monocots are difficult to transform with Agrobacterium tumefaciens, whereas other transgenesis methods, such as gold particlemediated transformation, result in poor transgene expression because of integration of truncated DNA molecules. We developed a method of transgene delivery into monocots. This method relies on the use of an in vitro-prepared nano-complex consisting of transferred DNA, virulence protein D2, and recombination protein A delivered to triticale microspores with the help of a Tat 2 cell-penetrating peptide. We showed that this approach allowed for single transgene copy integration events and prevented degradation of delivered DNA, thus leading to the integration of intact copies of the transgene into the genome of triticale plants. This resulted in transgene expression in all transgenic plants regenerated from microspores transfected with the full transferred DNA/protein complex. This approach can easily substitute the bombardment technique currently used for monocots and will be highly valuable for plant biology and biotechnology. © 2012 American Society of Plant Biologists. All Rights Reserved.

Eudes F.,Agriculture and Agri Food Canada | Shim Y.-S.,Nunhems United States Inc. | Jiang F.,Agriculture and Agri Food Canada
Biocatalysis and Agricultural Biotechnology | Year: 2014

Microspore culture is not only a valuable system for the study of developmental plant biology, but can also be effectively exploited for biotechnological purposes. Microspore culture is an established platform for the production of large numbers of doubled haploid plants in a few crop species. The unique characteristics of this haploid cell and the rapid advancement of genome sequencing technology make the microspore a special target for genetic engineering. DNA and/or protein delivery into these cells has been studied during the past 25 years with mitigated success, and was often limited to daughter cells. A novel delivery method using short peptide nanocarriers has rendered microspore transformation more achievable and opened new opportunities for crop development. © 2013.

Alluvada J.,Texas Tech University | Alluvada J.,Nunhems United States Inc. | Fokar M.,Texas Tech University | Fokar M.,Institute for Agricultural Biosciences | Holaday A.S.,Texas Tech University
Acta Physiologiae Plantarum | Year: 2014

We compared gene expression levels for enzymes of carbohydrate metabolism in the twig xylem of two Populus species with the seasonal levels of starch and soluble sugars (sucrose, glucose, and fructose) and relative levels of the enzymes. Plants of Populus deltoides Bartr. ex Marsh and P. balsamifera L., 3-4 years old, were grown outside in Lubbock, TX, USA in 43 L pots. The xylem in the middle portion of the twigs was sampled during the dormant period (November-February), at bud break (for P. balsamifera), and during the growth flush (April-July). The gene expression for ADP-glucose pyrophosphorylase (AGPase), sucrose synthase (SuSy), and sucrose-phosphate synthase (SPS) generally coincided with the levels of the carbohydrates in whose metabolism these enzymes are involved. Gene expression for AGPase and its protein levels were high when the xylem starch content was high (growing period). However, P. balsamifera maintained high AGPase levels in dormant and growing twigs, unlike P. deltoides whose dormant twigs had low AGPase and low gene expression. Compared to growing twigs, gene expression for SuSy and SPS and their protein levels were higher in dormant twigs when soluble sugar content was higher. No down-regulation of these genes appears to occur when pools of the associated carbohydrates are high. Contrary to our expectation, the gene expression for β-amylase was highest in growing twigs when starch content was high. High β-amylase gene expression in growing twigs may be involved in maintaining a sufficient level of soluble sugars for growth through possibly controlling the extent of starch accumulation. © 2014 Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków.

Monihan S.M.,University of Arizona | Magness C.A.,University of Arizona | Magness C.A.,Nunhems United States Inc. | Yadegari R.,University of Arizona | And 2 more authors.
Plant Physiology | Year: 2016

The accumulation of sodium in soil (saline conditions) negatively affects plant growth and development. The Salt Overly Sensitive (SOS) pathway in Arabidopsis (Arabidopsis thaliana) functions to remove sodium from the cytosol during vegetative development preventing its accumulation to toxic levels. In this pathway, the SOS3 and CALCINEURIN B-LIKE10 (CBL10) calcium sensors interact with the SOS2 protein kinase to activate sodium/proton exchange at the plasma membrane (SOS1) or vacuolar membrane. To determine if the same pathway functions during reproductive development in response to salt, fertility was analyzed in wild type and the SOS pathway mutants grown in saline conditions. In response to salt, CBL10 functions early in reproductive development before fertilization, while SOS1 functions mostly after fertilization when seed development begins. Neither SOS2 nor SOS3 function in reproductive development in response to salt. Loss of CBL10 function resulted in reduced anther dehiscence, shortened stamen filaments, and aborted pollen development. In addition, cbl10 mutant pistils could not sustain the growth of wild-type pollen tubes. These results suggest that CBL10 is critical for reproductive development in the presence of salt and that it functions in different pathways during vegetative and reproductive development. © 2016 American Society of Plant Biologists. All rights reserved.

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