Agriculture Research Services

Athens, GA, United States

Agriculture Research Services

Athens, GA, United States
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Spargo J.T.,University of Massachusetts Amherst | Cavigelli M.A.,Agriculture Research Services | Alley M.M.,Virginia Polytechnic Institute and State University | Maul J.E.,Agriculture Research Services | And 3 more authors.
Soil Science Society of America Journal | Year: 2012

The influence of no-tillage (NT) management on labile soil N is poorly defined. To quantify changes in soil C and N fractions with duration of NT, we sampled Kempsville sandy loam (fine-loamy, siliceous, subactive, thermic Typic Hapludults) soils in the Coastal Plain of Virginia from farm fields that had similar cropping histories and nutrient management but varied in amount of time in continuous NT from 0 to 11 yr. At the 0- to 2.5-cm soil depth, there was a linear increase with time in NT for total organic C, total organic N, particulate organic matter (POM)-C, POM-N, POM-C/total organic C, POM-N/total organic N, hydrolyzable unidentified-nitrogen (hUN-N) and NH4-N (hNH4-N), and various biochemical classes of pyrolysate compounds determined by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). At the 2.5- to 7.5-cm soil depth, there was a linear increase with time in NT for total organic C and N, hUN-N, hNH4-N, hydrolyzable α amino acid-nitrogen (AA-N) and amino sugar-nitrogen (AS-N) only; these rates of increase were lower than at the 0- to 2.5-cm depth. No measured C and N fractions increased at the 7.5- to 15-cm soil depth but POM-C/total organic C and POM-N/total organic N declined (p ≤ 0.10) at this depth, suggesting that the recalcitrance of C and N fractions increased at 7.5- to 15-cm in 11 yr. These patterns indicate that a new equilibrium level for these C and N fractions had not been reached but that their stratification of C and N pools with soil depth increased during 11 yr in NT. At the 0- to 2.5-cm depth, the labile N fractions, AA-N and AS-N approached or reached new equilibrium levels within 11 yr. Since these fractions are derived from soil microbial and plant biomass, the initial rapid increase in these fractions likely reflects an increase in N immobilization in the short term (3-6 yr) following adoption of NT. After this initial transition period, levels of AA-N and AS-N approach new elevated equilibrium levels, which would be reflected in a higher net N mineralization rate than under the previous tilled system. These results indicate that absolute values for labile soil N fractions such as AA-N and AS-N may not be readily interpretable with respect to soil fertility recommendations without considering whether these values are changing over time or are at an equilibrium level. Different patterns of change in POM-N vs. AA-N and AS-N indicate that these labile N fractions are distinct and may provide different types of information with respect to quantifying changes in soil fertility with time under NT. © Soil Science Society of America,.

Yoshida K.,Sainsbury Laboratory | Schuenemann V.J.,University of Tübingen | Cano L.M.,Sainsbury Laboratory | Pais M.,Sainsbury Laboratory | And 13 more authors.
eLife | Year: 2013

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity. Copyright Yoshida et al.

PubMed | Agriculture Research Services, Northwest Agriculture and Forestry University, University of Alberta, Washington State University and 2 more.
Type: | Journal: Journal of genomics | Year: 2014

There is a voluminous amount of scientific literature dealing with the involvement of adipocytes in molecular regulation of carcass composition, obesity, metabolic syndrome, or diabetes. To form adipocytes (process termed adipogenesis) nearly all scientific papers refer to the use of preadipocytes, adipofibroblasts, stromal vascular cells or adipogenic cell lines, and their differentiation to form lipid-assimilating cells containing storage triacylglyceride. However, mature adipocytes, themselves, possess ability to undergo dedifferentiation, form proliferative-competent progeny cells (the exact plasticity is unknown) and reinitiate formation of cells capable of lipid metabolism and storage. The progeny cells would make a viable (and alternative) cell system for the evaluation of cell ability to reestablish lipid assimilation, ability to differentially express genes (as compared to other adipogenic cells), and to form other types of cells (multi-lineage potential). Understanding the dedifferentiation process itself and/or dedifferentiated fat cells could contribute to our knowledge of normal growth processes, or to disease function. Indeed, the ability of progeny cells to form other cell types could turn-out to be important for processes of tissue reconstruction/engineering and may have implications in clinical, biochemical or molecular processes.

PubMed | Northwest Agriculture and Forestry University, Washington State University, Federal University of Viçosa, Auburn University and Agriculture Research Services
Type: | Journal: Journal of genomics | Year: 2014

Adipose tissue is derived from numerous sources, and in recent years this tissue has been shown to provide numerous cells from what seemingly was a population of homogeneous adipocytes. Considering the types of cells that adipose tissue-derived cells may form, these cells may be useful in a variety of clinical and scientific applications. The focus of this paper is to reflect on this area of research and to provide a list of potential (future) research areas.

Cooper L.,Oregon State University | Walls R.L.,New York Botanical Garden | Elser J.,Oregon State University | Gandolfo M.A.,Cornell University | And 19 more authors.
Plant and Cell Physiology | Year: 2013

The Plant Ontology (PO; is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. © 2012 The Author 2012. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.

Romao J.M.,University of Alberta | Jin W.,University of Alberta | Dodson M.V.,Washington State University | Hausman G.J.,Agriculture Research Services | And 2 more authors.
Experimental Biology and Medicine | Year: 2011

Adipogenesis, the complex development from preadipocytes or mesenchymal stem cells to mature adipocytes, is essential for fat formation and metabolism of adipose tissues in mammals. It has been reported to be regulated by hormones and various adipogenic transcription factors which are expressed as a transcriptional cascade promoting adipocyte differentiation, leading to the mature adipocyte phenotype. Recent findings indicate that microRNAs (miRNAs), a family of small RNA molecules of approximately 22 nucleotides in length, are involved in the regulatory network of many biological processes, including cell differentiation, through post-transcriptional regulation of transcription factors and/or other genes. In this review, we focus on the recent understanding of the roles of miRNAs in adipogenesis, including the most recent and relevant findings that support the role of several miRNAs as pro-or antiadipogenic factors regulating adipogenesis in mice, human and cattle to propose the future role of miRNA in adipogenesis of farm animal models. © 2011 by the Society for Experimental Biology and Medicine.

Poulos S.P.,The Coca-Cola Company | Hausman D.B.,University of Georgia | Hausman G.J.,Agriculture Research Services
Molecular and Cellular Endocrinology | Year: 2010

White adipose tissue is a mesenchymal tissue that begins developing in the fetus. Classically known for storing the body's fuel reserves, adipose tissue is now recognized as an endocrine organ. As such, the secretions from adipose tissue are known to affect several systems such as the vascular and immune systems and play major roles in metabolism. Numerous studies have shown nutrient or hormonal manipulations can greatly influence adipose tissue development. In addition, the associations between various disease states, such as insulin resistance and cardiovascular disease, and disregulation of adipose tissue seen in epidemiological and intervention studies are great. Evaluation of known adipokines suggests these factors secreted from adipose tissue play roles in several pathologies. As the identification of more adipokines and determination of their role in biological systems, and the interactions between adipocytes and other cells types continues, there is little doubt that we will gain a greater appreciation for a tissue once thought to simply store excess energy. © 2009 Elsevier Ireland Ltd.

Wei S.,Northwest University, China | Wei S.,Washington State University | Zan L.S.,Northwest University, China | Zan L.S.,National Beef Cattle Improvement Center | And 7 more authors.
Genetics and Molecular Research | Year: 2013

Fatty acid binding protein 4 (FABP4) is an important adipocyte gene, with roles in fatty acid transport and fat deposition in animals as well as human metabolic syndrome. However, little is known about the functional regulation of FABP4 at the cellular level in bovine. We designed and selected an effective shRNA (small hairpin RNA) against bovine FABP4, constructed a corresponding adenovirus (AD-FABP4), and then detected its influence on mRNA expression of four differentiation-related genes (PPARγ, CEBPA, CEBPB, and SREBF1) and three lipid metabolism-related genes (ADIPOQ, LEP and LEPR) of adipocytes. The FABP4 mRNA content, derived from bovine adipocytes, decreased by 41% (P < 0.01) after 24 h and 66% (P < 0.01) after 72 h of AD-FABP4 infection. However, lower mRNA content of FABP4 did not significantly alter levels of differentiation-related gene expression at 24 h following AD-FABP4 treatment of bovine-derived preadipocytes (P = 0.54, 0.78, 0.89, and 0.94, respectively). Meanwhile, knocking down (partially silencing) FABP4 significantly decreased ADIPOQ (P < 0.05) and LEP (P < 0.01) gene expression after 24 h of AD-FABP4 treatment, decreased ADIPOQ (P < 0.01) and LEP (P < 0.01) gene expression, but increased LEPR mRNA expression (P < 0.01) after a 72-h treatment of bovine preadipocytes. We conclude that FABP4 plays a role in fat deposition and metabolic syndrome by regulating lipid metabolism-related genes (such as ADIPOQ, LEP and LEPR), without affecting the ability of preadipocytes to differentiate into adipocytes. © FUNPEC-RP.

Hao X.,Chinese Academy of Agricultural Sciences | Hao X.,National Center for Tea Improvement | Hao X.,Agriculture Research Services | Hao X.,Northwest University, China | And 4 more authors.
PLoS ONE | Year: 2015

Leafy spurge (Euphorbia esula L.) is a noxious perennial weed that produces underground adventitious buds, which are crucial for generating new vegetative shoots following periods of freezing temperatures or exposure to various control measures. It is also capable of flowering and producing seeds, but requires vernalization in some cases. DORMANCY ASSOCIATED MADS-BOX (DAM) genes have been proposed to play a direct role in the transition to winter-induced dormancy and maintenance through regulation of the FLOWERING LOCUS T (FT) gene, which also is likely involved in the vernalization process. To explore the regulation of FT and DAM during dormancy transitions in leafy spurge, the transcript accumulation of two previously cloned DAM splice variants and two different previously cloned FT genes was characterized. Under long-photoperiods (16 h light), both DAM and FT transcripts accumulate in a diurnal manner. Tissue specific expression patterns indicated the tissues with high DAM expression had low FT expression and vice versa. DAM expression is detected in leaves, stems, shoot tips, and crown buds. FT transcripts were detected mainly in leaves and flowers. Under dormancy inducing conditions, DAM and FT genes had an inverse expression pattern. Additionally, chromatin immunoprecipitation assays were performed using DAM-like protein specific antibodies to demonstrate that DAM or related proteins likely bind to cryptic and/or conserved CArG boxes in the promoter regions of FT genes isolated from endodormant crown buds. These results are consistent with the hypothesis that DAM proteins play a crucial role in leafy spurge dormancy transition and maintenance, potentially by negatively regulating the expression of FT. © 2015, Public Library of Science. All rights reserved.

Karki A.,University of Wisconsin - Milwaukee | Horvath D.P.,Agriculture Research Services | Sutton F.,South Dakota State University
Functional and Integrative Genomics | Year: 2013

Winter wheat lines can achieve cold acclimation (development of tolerance to freezing temperatures) and vernalization (delay in transition from vegetative to reproductive phase) in response to low non-freezing temperatures. To describe cold-acclimation-specific processes and pathways, we utilized cold acclimation transcriptomic data from two lines varying in freeze survival but not vernalization. These lines, designated freeze-resistant (FR) and freeze-susceptible (FS), were the source of crown tissue RNA. Well-annotated differentially expressed genes (p ≤ 0.005 and fold change ≥ 2 in response to 4 weeks cold acclimation) were used for gene ontology and pathway analysis. "Abiotic stimuli" was identified as the most enriched and unique for FR. Unique to FS was "cytoplasmic components." Pathway analysis revealed the "triacylglycerol degradation" pathway as significantly downregulated and common to both FR and FS. The most enriched of FR pathways was "neighbors of DREB2A," with the highest positive median fold change. The "13-LOX and 13-HPL" and the "E2F" pathways were enriched in FR only with a negative median fold change. The "jasmonic acid biosynthesis" pathway and four "photosynthetic-associated" pathways were enriched in both FR and FS but with a more negative median fold change in FR than in FS. A pathway unique to FS was "binding partners of LHCA1," which was enriched only in FS with a significant negative median fold change. We propose that the DREB2A, E2F, jasmonic acid biosynthesis, and photosynthetic pathways are critical for discrimination between cold-acclimated lines varying in freeze survival. © 2012 Springer-Verlag Berlin Heidelberg.

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