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: 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: Genetic Mechanisms | Award Amount: 399.00K | Year: 2015
This study will investigate a novel RNA-based mechanism that allows plants to respond to stress that affects the DNA, and to transmit a signal that protects chromosome integrity, which is important for plant fertility, growth and disease prevention. This project will develop fundamental knowledge valuable for breeding and growing healthier plants. This project will integrate basic plant science research with the teaching and training of the next-generation of plant scientists. As part of this effort, laboratory management workshops for postdoctoral fellows and new faculty will be conducted, and a graduate course on this topic will be developed.
The overarching goal of this project is to elucidate the molecular mechanism and regulation of TER2, a novel telomerase-associated long noncoding RNA (lncRNA) from the model plant Arabidopsis thaliana. TER2 is a negative regulator of telomerase that is rapidly stabilized in response to DNA double-strand breaks. Induction of TER2 represses telomerase activity and is hypothesized to promote faithful repair of DNA damage. TER2 is also necessary for reproductive fitness through an unknown mechanism. A combination of biochemical, genetic, cell biological and computational strategies will be used to study TER2. Objective 1 will define key structural elements that regulate TER2 processing/metabolism for the purpose of identifying the DNA damage sensor within TER2 and the elements that control TER2 stability. Objective 2 will investigate the role of small RNA processing machinery in promoting TER2 turnover by testing if TER2 is a substrate for cleavage by Dicer 2. Objective 3 will examine the contribution of TER2 in Arabidopsis reproduction by testing whether the fertility-related defects in ter2 mutants reflect aberrant male gametogenesis or the effect of a paternally expressed imprinted gene. Altogether, the results of this work will establish new paradigms for lncRNA regulation and increase understanding of RNA-based pathways that promote genome stability.
Agency: NSF | Branch: Standard Grant | Program: | Phase: Biodiversity: Discov &Analysis | Award Amount: 89.36K | Year: 2016
Chalcidoidea (jewel wasps) are among the most species rich, ecologically important, and biologically diverse groups of terrestrial organisms. Their diversity is staggering, with more than 500,000 species thought to exist. These minute wasps (mostly 1-2 mm in size) are numerically abundant and common in almost every habitat. The smallest of these wasps are smaller than a typical single-celled organism, and yet the adults can fly, locate their hosts, deposit their eggs, and as larvae, consume their insect hosts. Most chalcidoid wasps are parasitoids; they feed on their insect hosts, eventually killing them. A few groups have also evolved to attack plant hosts and some serve as pollinators. Species attack all life stages from eggs to adults, and live and feed either internally or externally. Some are parasitoids of other parasitoids and some may even feed on their own species. Because they kill other insects, these wasps are extremely important for the control of pests of agricultural and forest crops, as well as vectors of human disease and veterinary pests. The economic importance of these wasps in pest management is unparalleled. They are widely used in biological control programs against major pests, with outcomes documented to result in decreases in pesticide, increases in yield, and in landmark cases direct savings of billions of dollars or permanent pest control. The evolutionary events leading to this enormous diversity in morphology, biology and rates of diversification are poorly understood, leading to an artificial system of taxonomic classification. In this research project, researchers will use a diverse array of molecular, morphological and bioinformatics approaches to develop a solid understanding of the hierarchy of relationships across the entire group. These relationships will then be used to reclassify major groups to reflect common ancestry, to provide a framework for a web-accessible portal to manage and deliver information on their diverse biology, and to explore the evolutionary changes that have driven and shaped this enormous radiation of terrestrial insects.
The objectives of the research project are to 1) generate a robust molecular phylogeny of the Chalcidoidea using new data from transcriptomes and targeted DNA enrichment for over 400 species, 2) generate morphological data for over 200 fossils from Eocene and Cretaceous amber and combine these with a comprehensive morphological data set for extant taxa, 3) develop a revised classification of Chalcidoidea in book form through a series of workshops and worldwide collaborations, and 4) make available information on the taxonomy, biology and distribution of over 31,000 available names and information in over 40,000 references. The project will train two postdoctoral researchers, one graduate student and several undergraduates. To involve the wider scientific community, a worldwide group of biocontrol researchers and taxonomists will develop a new classification for Chalcidoidea. With groups of Research and Extension Specialists, the project will develop posters, fliers, specimen education kits, and other educational materials for use in the classroom and by extension specialists, agricultural advisors, master naturalists and master gardeners, and the general public to develop a greater interest and understanding of this charismatic and and important group of insects.
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.
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: Standard Grant | Program: | Phase: Genetic Mechanisms | Award Amount: 503.95K | Year: 2015
Mutation induces genetic variation. Genetic variation, in turn, fuels evolutionary change. Experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution and biology. Mutation accumulation (MA) experiments have been instrumental in measuring the rate of origin of deleterious mutations. However, the vast majority of MA studies to date are compromised by two major limitations: (i) the use of phenotypic data to indirectly estimate key mutational parameters, and (ii) the use of experimental lines maintained at a single, minimum effective population size. Although population-genetics theory predicts a wide range of fitness consequences for all classes of spontaneous mutations, their distribution of fitness effects remains obscure. Furthermore, the loss or fixation of mutations and their consequences for population fitness additionally depend upon their individual effect and the efficacy of natural selection, the latter being influenced by the population size. Spontaneous MA lines of the nematode Caenorhabditis elegans were evolved in parallel over 400 generations at three varying effective population sizes to manipulate the efficacy of natural selection in different genomic backgrounds. This represents the most ambitious experiment of its kind within any species. The combination of long-term spontaneous MA lines under varying intensities of selection and use of powerful high-throughput genomic techniques will enable unprecedented insights into (i) the rates of origin of diverse mutations, (ii) their differential accumulation under varying regimes of natural selection, and (iii) a framework to assess the interaction between mutation and selection at the molecular level on a genome-wide scale. The aims are to identify all acquired mutations at the mitochondrial and nuclear level, investigate their differential rates of accumulation under varying population sizes and infer their distribution of fitness effects. Phenotypic fitness-assays will quantify the rate of fitness decay at different population sizes and determine the extent to which larger populations are buffered from mutational degradation. By providing a unified account of the consequences of spontaneous mutations at the genetic and phenotypic levels, this research will yield significant insights into the evolutionary process for several different topics, including the genetic basis of variation, the evolutionary dynamics of mutations under the forces of natural selection and genetic drift, and their range of fitness effects.
The experimental lines provide an unprecedented resource to study biological evolution at multiple scales, from phenotype to protein function. The experimental MA lines created as part of this research and the deposition of genome sequences in public databases represent an enormous community resource to be shared with colleagues in the scientific community. In addition to the training projects listed with individual aims, this project will have broad impacts in two areas: academic training/mentorship and public outreach in an environment with a large fraction of underrepresented minorities. Data generated by the research will be (i) disseminated to high school students and the general public via seminars and interactive panel discussions to communicate its evolutionary implications and promote scientific literacy, and (ii) employed in the creation of data sets and mini tutorials for high school students to demystify molecular evolution and introduce them to basic evolutionary computational methods for analyses of genomic sequences. The University of New Mexico is the only research-intensive University that is also Hispanic serving, with two extensive underrepresented student populations comprising Hispanics and Native Americans. This provides a unique opportunity to mentor undergraduate minority students, graduate students and postdocs, and instill in them an appreciation for interdisciplinary research in population-genomics and bioinformatics. Research stemming from this project is expected to greatly enhance our fundamental understanding of the evolutionary process and enable the quantification of several key rate parameters in biology, with implications for all spheres of biology including an understanding of the genetic and phenotypic consequences of maintaining populations at small sizes.
Agency: NSF | Branch: Standard Grant | Program: | Phase: Biodiversity: Discov &Analysis | Award Amount: 59.07K | Year: 2017
Understanding and documenting the worlds biodiversity is the first step in biological conservation. Among many biodiversity hotpots around the world, southern Africa is particularly well-known for its diverse and unique plants and animals. Over the past decade, scientists have documented more than 600 species of grasshoppers from this region. Grasshoppers are ecologically and economically important as they are critical components of terrestrial ecosystems, especially grasslands, and include several serious pest species. Despite the years of biodiversity research in southern Africa, scientists have recognized that there is a certain fauna that has never been fully explored - the flightless grasshoppers occupying the mountain forests in South Africa. The forest patches and isolated mountain peaks in this area represent habitat islands, and there is no other land-based system of habitat islands in the world with the number, size, and configurational complexity as the Afromontane zone in South Africa. This project focuses on understanding the total diversity of grasshoppers in this amazing and complex landscape and the processes shaping this diversity. The results from this project will provide critical information about species diversification in complex habitats and help researchers better understand species diversity and distributions in similar habitats in the US and around the world.
This project will focus on the grasshopper family Lentulidae, which is endemic to southern Africa, and address the following two questions: (i) What is the total species diversity of Lentulidae in the alpine and Afromontane regions in South Africa? and (ii) What are patterns of speciation and diversification in Lentulidae as related to their geographic distribution? Scientists will explore inselbergs (isolated mountain peaks rising abruptly from surroundings) and adjacent plateaus in the Drakensberg Escarpment and the Afromontane forest patches in South Africa in search of new species. Using modern taxonomic techniques, the scientists will rapidly describe this unique grasshopper fauna and make the resulting specimen-level data digitally available to the public. The project will also reconstruct the evolutionary relationships among the focal taxa to examine how these small flightless grasshoppers have colonized and diversified in isolated inselbergs and Afromontane forest patches. Specifically, genome-scale single nucleotide polymorphism (SNP) data will be generated using RAD-Seq to estimate phylogeographic patterns as well as for inferring population genetic structures for those species that appear to be widespread. The project will provide hands-on research and mentoring experience for undergraduate students at Texas A&M University and Drexel University.
Agency: NSF | Branch: Standard Grant | Program: | Phase: BIOLOGICAL OCEANOGRAPHY | Award Amount: 196.30K | Year: 2017
Understanding how changes in environmental conditions affect biota in the oceans is critically important for maintaining biodiversity and sustainable fisheries and projecting potential responses to future climate scenarios. The aims of this project are to determine how the distribution of fish and invertebrates has changed over time along the Texas coast and to assess the extent to which these changes are attributable to changes in local environmental conditions, such as sea surface temperature, coastal sea level, salinity, turbidity, and river discharge rate. Studies of biological systems in the Gulf of Mexico are lacking compared to coastal research in the Atlantic and Pacific oceans. Addressing these regional knowledge gaps is crucial because the Gulf of Mexico supports a wide diversity of temperate and tropical species that are ecologically and economically important. Poleward shifts in species distributions associated with increasing sea surface temperature have been observed along the Atlantic and Pacific coasts. In contrast, the northern edge of the Gulf of Mexico is bound by land that places biogeographic constraints on the potential responses of coastal organisms to changing environmental conditions. This project will use advanced statistical methods to analyze long-term species composition data for the northwestern Gulf of Mexico and characterize past relationships of species composition and local environmental conditions. These findings will help guide the development of predictive models to assess potential biological responses to projected environmental conditions. Research results will be shared with local and state resource agencies responsible for managing coastal fisheries. As an integral part of this project, a three-level (faculty-graduate-undergraduate) mentoring system will be established to promote diversity in science through undergraduate and graduate training. Undergraduate students will be recruited through the Texas A&M University Chapter of the Society for Advancement of Chicano and Native Americans in Science (SACNAS), for which the principal investigator is currently a faculty advisor. Both graduate and undergraduate students will work as a team on the project and develop quantitative data analysis and other general scientific skills. Finally, the research program will be used as a case study for establishing mentoring systems for promoting diversity in science.
The availability of long-term species composition data provides a unique opportunity to substantially improve knowledge toward understanding the effects of climate change on marine organisms in a low latitude system. This project will examine species composition data for eight bays distributed over approximately 650 km of the Texas coast; comprehensive data of this type are uncommon elsewhere. The biological data have been collected over 35-40 years as part of a long-term monitoring program and includes information on more than 1000 species of fish and invertebrates. This unique dataset will be analyzed using modern statistical approaches, including occupancy data analysis, co-integration method, and state-space vector autoregressive modeling. These methods overcome common difficulties in statistical analyses, including datasets having multi-collinearity among independent variables and those involving non-stationarity. Based on the results of the statistical analyses, models enabling the prediction of species composition under projected local environmental conditions will be developed. As part of this project, undergraduate and graduate students will acquire expertise in contemporary analytical methods, research findings will be broadly shared with both the academic and resource management communities, and computational code will be made publically available. This project will provide better understanding of the effects of environmental conditions on fish and invertebrate distribution and will provide valuable information for improved fishery management and conservation efforts under changing environmental conditions.
Agency: NSF | Branch: Standard Grant | Program: | Phase: Genetic Mechanisms | Award Amount: 561.72K | Year: 2016
This project will study a unique mechanism of gene expression in ancient single-celled parasites called trypanosomes. Unlike most organisms that use the RNA copied from DNA as is for directing protein synthesis, in the energy-generating mitochondria of trypanosomes (and other organisms), the RNA is edited by addition or removal of specific information. Why editing occurs is not clear, but understanding how it happens may provide important clues about the function of this type of genetic alteration. The project will have broad educational impact by providing interdisciplinary training opportunities for postdoctoral, graduate, undergraduate, and high school students. In addition, specific efforts will target students from groups traditionally underrepresented in the STEM disciplines.
This project focuses on the process of RNA editing in the mitochondria of trypanosomes. Through the action of a central editing enzyme, called RECC, uridylates are inserted or deleted at thousands of specific sites in dozens of mRNAs. This extensive editing process is directed by hundreds of small non-coding guide RNAs and involves several auxiliary factors. However, the mechanistic basis of the regulation of editing remains a long-standing question in trypanosomal RNA biology. In previous work, a regulatory editing subcomplex, called REH2C, was identified and found to contain three protein subunits. Two of these, a helicase and a zinc-finger protein, appear to participate directly in editing. A combination of genetic, biochemical, bioinformatics, and proteomic approaches will be used to address how these proteins assemble with mRNAs and guide mRNAs into editosome complexes in vivo and how the complexes carry out editing functions. These studies may establish new paradigms in RNA editing regulation. In a broader sense, the studies will allow a better understanding of how this amazing process evolved. This system can be used to draw analogies with related RNA helicases and RNA processes that are directed by small guide RNAs and that evolved more recently in eukaryotic lineages.