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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; http://www.plantontology.org/) 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. Source


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. Source


Habib S.,NASA | Zaitchik B.,Johns Hopkins University | Alo C.,Johns Hopkins University | Ozdogan M.,University of Wisconsin - Madison | And 2 more authors.
International Geoscience and Remote Sensing Symposium (IGARSS) | Year: 2011

The Nile basin River system spans 3 million km2 distributed over ten nations. The eight upstream riparian nations, Ethiopia, Eretria, Uganda, Rwanda, Burundi, Congo, Tanzania and Kenya are the source of approximately 86% of the water inputs to the Nile, while the two downstream riparian countries Sudan and Egypt, presently rely on the river's flow for most of the their needs. Both climate and agriculture contribute to the complicated nature of Nile River management: precipitation in the headwaters regions of Ethiopia and Lake Victoria is variable on a seasonal and inter-annual basis, while demand for irrigation water in the arid downstream region is consistently high. The Nile is, perhaps, one of the most difficult trans-boundary water issue in the world1, and this study would be the first initiative to combine NASA satellite observations with the hydrologic models study the overall water balance in a comprehensive manner. The cornerstone application of NASA's Earth Science Research Results under this project are the NASA Land Data Assimilation System (LDAS)2 and the USDA Atmosphere-Land Exchange Inverse (ALEXI)3 model. The end-users such as Regional Center for Mapping of Resources for Development (RCMRD, Nairobi, Kenya), Eastern Nile Technical Regional Office (ENTRO, Addis Ababa, Ethiopia), Ethiopian and Kenya Meteorological and Famine Early Warning System Network (FEWSNet) will be the eventual benefactors of this work. © 2011 IEEE. Source


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. Source


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. Source

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