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Weslaco, TX, United States

Muir J.P.,Texas AgriLife Research Center
Small Ruminant Research | Year: 2011

This manuscript seeks to summarize much, but by no means all, we already know about condensed tannins (CT) in goat ecosystems. Herbage CT influences much more than simply nutrition. From before the goat ingests the herbage, to what it selects, how it interacts with the rumen environment and the rest of the ruminant gastro-intestinal tract (GIT), to even the fecal environment and the soil to which it eventually returns, the picture is fascinatingly complex. A decade ago most goat scientists thought we knew all there was to know about CT and the goat; yet today we realize that we learn something new each time we examine both the broad picture as well as the details that comprise that picture. What we have yet to uncover may be vastly more important and involved than what we already know. The world that herbage CT and goats share is only gradually revealing itself, waiting for scientists of all disciplines to turn the next page in our quest for a complete understanding of the multiple roles CT play in the goat ecosystem. © 2011 Elsevier B.V.

Agency: NSF | Branch: Continuing grant | Program: | Phase: ADVANCES IN BIO INFORMATICS | Award Amount: 143.13K | Year: 2016

Phages, the viruses of bacteria, are the most numerous genetic entities in the biosphere, outnumbering bacteria by 10-100-fold, and contain most of its DNA diversity. Phage biology is a driver in global ecology and in the global dynamics of gene transfer. Phages, as the natural predators of bacteria, have recognized potential as antibacterial agents, both in human health and in animal husbandry and agriculture. Phages, because they can be restricted to specific bacterial species or genera, represent the only currently available tool for manipulating the diverse populations of bacteria in microbiomes, now known to be an essential component of health and development. Despite all of these factors, only a tiny fraction of phage biodiversity is captured by sequenced genomes; in fact, phages are by far the most under-sequenced genetic entity. As Next Generation Sequencing advances, the flow of phage DNA sequence is going to increase enormously. However, phage genomes represent special problems in genomic analysis, in part because of biological factors, including rapid sequence divergence, the compression of gene sizes and extensive gene overlap. Even more problematic is the general lack of expertise in phage biology, which makes quality annotation of phage genomes inaccessible to most of the scientific public.

The project will implement scalable infrastructure for bioinformatics analyses, focusing on the automated structural and functional annotation of phages. Publicly accessible infrastructure will be developed and deployed, from new and existing components to support community re-annotation of paradigm phages into gold standard curated annotation sets. Additionally the infrastructure will develop components focused on the acquisition and annotation of new phage genomes going forward, as the field of bacteriophage genomics rapidly expands. Tools will be developed and released encoding expert annotation knowledge to improve the state of the art in automated, quality, phage annotation. The entire project will be developed as open source software under an OSI approved license, permitting the re-implementation of the projects infrastructure in other genome annotation communities where it will provide value. Phage Genomics Education resources developed as part of our well-established course in Phage Genomics at TAMU will be improved to take advantage of the new community resources being built. As implementation progresses, the infrastructure deployed and progress updates will be available at https://cpt.tamu.edu/phagedb/

Agency: NSF | Branch: Continuing grant | Program: | Phase: ANIMAL BEHAVIOR | Award Amount: 384.29K | Year: 2015

Locusts are grasshoppers that can form enormous migrating swarms. They are major pests of agriculture throughout the world, causing millions of dollars in losses. In nature, locusts exist as one of two forms depending on local population density. At low density, locusts are inconspicuously colored and avoid each other, but at high density, they transform into conspicuously colored individuals that are attracted to each other. When the high-density condition persists, they eventually form swarms. This ability to change in response to density is known as density-dependent phenotypic plasticity. However, it is poorly understood how this phenomenon has evolved, why locusts swarm, and what makes them different from typical grasshoppers. Therefore, the main goal of this Faculty Early Career Development (CAREER) project is to understand why some grasshoppers respond to crowding by forming swarms and others do not. The project aims to unravel the genetic basis of locust swarming using behavioral experiments and cutting-edge molecular techniques.

The core of this CAREER project is the seamless integration of research and education from K-12 to undergraduate and graduate students. The partnership with local public schools, enhanced by service-learning, will provide unique and relevant science education opportunities for both elementary school and college-level students. Specifically, the CAREER-enabled course development will fill a much-needed void in providing authentic research experience to the biology curriculum at the University of Central Florida. One primary goal of the broader impact activities will be to broaden participation of underrepresented minority students, particularly those who seek careers in science after transferring from community colleges. Graduate students supported by this project will be exposed to high-impact research with international and interdisciplinary opportunities. The broad nature of this project will establish a strong and long-lasting international network for future collaborations.

Agency: NSF | Branch: Continuing grant | Program: | Phase: Cellular Dynamics and Function | Award Amount: 650.47K | Year: 2015

Almost every process in bacteria depends on the dynamic and specific localization of large molecules within the cell. This research addresses the question: how do bacteria make sure all of these molecules are organized into their correct positions? This project will probe the molecular and biophysical basis of cellular organization, including the role of positional constraints in regulating both essential and non-essential processes. The study will be carried out by undergraduate and graduate students in a highly mentored, collaborative research environment that emphasizes learning-through-teaching experiences and promotes critical thinking by allowing students to make decisions and learn from mistakes. The research will also produce a broadly useful and powerful community research tool that will facilitate the research efforts of over a hundred other laboratories. The project will provide multi-disciplinary training for graduate and undergraduate students.

The premise of this research is that the bacterial nucleoid encodes a largely overlooked reservoir of topological information, and the aim is to elucidate the mechanisms by which the nucleoid functions as a primary positional determinant in the 3D landscape of a bacterial cell. Biochemical, structural, genetic, and cell biological approaches will be employed to elucidate the role of the nucleoid in the regulation cell division. In addition, a systematized approach to gene function discovery will be undertaken to identify and characterize novel factors that interact with the nucleoid and the cell envelope to drive subcellular organization. The gene discovery pipeline developed for this study will be broadly applicable to other organisms and the ordered gene expression library will be made publicly available to accelerate gene function discovery and characterization efforts in other laboratories.

Agency: NSF | Branch: Continuing grant | Program: | Phase: PLANT GENOME RESEARCH RESOURCE | Award Amount: 1.52M | Year: 2016

Cassava (Manihot esculenta) is a tropical root crop with exceptional drought tolerance, making it a critical component of food security for 800 million people in tropical regions of Africa, Latin America, and Asia. Despite its importance, cassavas current 12 to 24 month crop cycle limits the economic prosperity of smallholder farmers due to the length of time between harvest cycles. Identifying new cassava varieties that bulk roots early in the crop cycle is an essential solution to overcome this time constraint. Selection for an early root bulking trait, however, is currently limited because it requires destructive digging of roots, unmanageable breeding trial sizes, and large labor costs. This project will improve trait selection by adapting a technology from geophysics called ground-penetrating radar to produce three-dimensional quantifiable images of cassava roots non-destructively. Using ground-penetrating radar, early bulking root masses can be imaged underground. The goal is to select for cassava varieties that increase cassava yields by 25 to 50% by selecting early stage root bulking from existing high yielding genotypes. The development of a commercial ground-penetrating radar instrument and associated data processing software for selecting early stage root bulking in cassava will provide cassava breeders throughout the world with the tools needed to develop new higher yielding cultivars.

Cassava is a tropical root crop that is exceptionally adapted to drought tolerance but has a prolonged life cycle of 12 to 24 months. This long duration limits harvest capabilities for smallholder farmers in the developing world, thus reducing the benefits of the crop as a component of global food security. Overcoming this limitation through selection of new cassava cultivars that exhibit early stage root bulking (ESRB) is an essential solution to ensure continued food security. This project will adapt ground-penetrating radar (GPR) to non-destructively develop 3-dimensional (3-D) quantifiable images of cassava roots. Current GPR instruments and analytical software are designed for subsurface imaging but not necessarily adapted for crop research. This project will use uncoupled GPR transmitters and antenna and an in vitro cassava trough assay system to develop an accurate and cost effective GPR instrument design for cassava breeding in terms of central frequencies emitted and antenna geometries. Ancillary soil matrix data will be combined to allow the development of broadband GPR filter processes of root versus soil matrix specific frequencies, derive root allometries, and begin to convert the individual data processing methods into a streamlined decision support software for ESRB selection. In the long term, the aim is to increase yield by 25 to 50% via GPR-based selection of ESRB from existing high yielding genotypes. The project will ultimately develop an ideal GPR instrument and an easy to use streamlined data processing and decision support software needed by cassava breeders to develop higher yielding early bulking cassava cultivars.

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