William Thomas - US grants

Preferential cell associations arise in large part from differences in cellular adhesive properties with the result that regulation of those properties can in principle guide the organization of cells into anatomically "correct" structures. By corollary, errors in such regulation probably underlie at least in part the metastatic behavior of malignant cells and the morphogenetic aberrations leading to specific birth defects. A detailed knowledge of the molecular mechanisms generating cellular adhesive properties is thus essential to our understanding of diverse morphogenetic phenomena. In that context, this work proposes to investigate the role of the dual adhesion mechanisms described earlier in organizing the chick visual system. Recently generated monoclonals antibodies inhibitory of retinal Ca++ dependent (CD) aggregation will be used to identify and isolate components of the retinal CD adhesion mechanism. The molecules so identified will be characterized by molecular weight, pI and carbohydrate composition and their relationship to already identified CD molecules (ie., CaT, ligatin) determined. In exploring the regulatory potential of this mechanism, efforts will be made to elucidate the molecular basis for Ca++ dependent activity (cell-cell bonding) and protection from proteolysis. To complement this line of investigation experiments will also be performed to determine if molecules other than N-CAM contribute to retinal Ca++ independent (CI) adhesion. An array of monoclonal and monospecific polyclonal antibodies against CD and CI (non-CAM) adhesion molecules will then be used to 1) visualize the distribution of those molecules in the retina and other embryonic chick tissues, 2) to explore the structural relationship between functionally similar adhesion molecules from different tissues, 3) to investigate the role of CI and CD molecules in generating known adhesive gradients across the retina and tectum, and finally 4) to test the role of those in directing retino-tectal mapping. Cellular adhesiveness (rate, selectivity) will be tested using cell monolayer and aggregometer assays. Other work will be performed using various electrophoretic techniques, protein blotting, peptide mapping, affinity chromatography, immunochemistry and fluorescence microscopy.

This study concerns the effects of small-scale turbulence and its small scale shear on the growth rate, cell division, cell size distribution, and cell morphology of marine dinoflagellates. The aspect of turbulence most important to phytoplankton is the local shear, or rate-of-strain which varies over three orders of magnitude in the ocean. The rate-of-strain in turn, determines the relative velocities for separation distances smaller than the Kolmogoroff scale, and phytoplankton are smaller than this scale in the ocean. Based on previous results, the working hypothesis of this study will be that differences in species composition of experimental cultures can be brought about by the inhibitory effects of high turbulence. In controlled laboratory experiments, turbulence and shear levels will be computed for the linear velocity profile and small shears in laminar flow, or estimated from established turbulence formulae for higher shear rates. The estimates will be confirmed by hot wire anemometer and microconductivity probe measurements. Constant shear, or variable shear under microcomputer control will be produced between rotating cylinders over a wide range of Reynolds numbers, with or without time variation. Daily measurements of chlorophyll fluorescence and cell numbers will be made to asses culture growth rates. Changes in cell size distributions and cell division rates will also be measured due to turbulence and shear and examine the cells microscopically to assess morphological changes. The threshold turbulence and shear levels which result in effects on these parameters will be ascertained. The microscopic plants called phytoplankton that are responsible for most marine biological production must contend with unique environmental conditions. For example although (like their terrestrial counterparts) phytoplankton require light and nutrients, these small and in some cases delicate cells are subject to the small scale physical forces of the surrounding water, which is 1000 times more viscous than air. Such small scale turbulence is generated in the sea by wind, tidal, internal wave, and current motions. This work is a novel collaboration between a phytoplankton biologist and a physicist to examine the effect of these forces on the growth and selected other features of dinoflagellates, a type of phytoplankton that is suspected to be susceptible to turbulence. This laboratory study will be carried out in a specially built apparatus in which the physical turbulence the phytoplankton are exposed to can be carefully controlled. Although the work is a pilot project, the interdisciplinary nature of the work by two very capable scientists has generated great interest in the potential findings that may have broad implications beyond dinoflagellates.

Fold-thrust belts are formed as a result of translation of a wedge of sedimentary rocks along a system of interconnected faults that include decollement flats, frontal ramps, and lateral connectors (such as transverse faults, lateral ramps, and zones of displacement transfer). Lateral connectors are commonly aligned across strike of the fold-thrust belt; the transverse alignments of lateral connectors have been called cross-strike structural discontinuities (CSDs). CSDs are common features of fold-thrust belts and are potentially significant in exploration for petroleum, ground water, and ore deposits. The internal geometry and kinematics of the complete length of CSDs are not well known. Lateral connectors and CSDs are as important in the overall make-up of fold-thrust belts as frontal ramps, but the lateral connectors have been much less studied. Detailed studies of structure and stratigraphy within a CSD are designed to address the following important questions: whether or not inter- nal structural components of CSDs are systematically arrayed along the trend or with respect to stratigraphic and/or structural levels; whether or not CSDs are genetically linked to pre-thrust structures (basement faults), to stratigraphic varia- tions caused by synsedimentary pre-thrust structures, and/or structures in the autochthon; and how CSDs function kinematically within a fold-thrust belt.

The overall objective of the proposed research is to investigate the reciprocal interactions and the dynamic effects of social class upon school practices through a cross cultural comparison of the knowledge transmission process in early 20th century elementary schools of Buffalo. The main hypothesis is that class was a greater factor than ethnicity or race in the schooling process. During the planning stages, the PI will identify and study southern-born white and black immigrants to the city and study the shifts which occurred within these two populations between 1910 and 1930. Having established their resettlement patterns in the city by social class, the PI will determine the elementary schools in which their children enrolled. Locating their schools would allow to investigate the responses of the public elementary schools to the children of immigrant populations. The PI also plans to analyze the content of articles published in the widely circulated School Magazine between 1918- 1932. Through a systematic analysis, the investigator expects to show similarities and differences in the types of school knowledge transmitted to the pupil populations under study.

The rates of photosynthesis of phytoplankton in the ocean are affected not only by the availability of light and nutrients, but also by the turbulence in the water column. Dr. Thomas will continue his studies on the effects of small scale turbulence on the growth rate, cell division, and cell morphology of marine phytoplankton using laboratory cultures. He will examine two red tide species using varying degrees of intermittent turbulence. In addition, he will investigate the effects of reduced temperature and turbulence on the viability and behavior of the organisms. This research will aid in the prediction of red tides in both time and space.

Dr. Thomas will study the effects of small scale turbulence on phytoplankton using a series of laboratory devices designed to expose the algae to varying levels of motion.He will then measure the growth rates and productivity of the organisms as well as their pigment composition, cell sizes and behavior to determine the impacts of the increased turbulence upon their physiology. It is hypothesized that the growth inhibition of dinoflagellates by small scale turbulence is the reason that red tides do not occur with moderate to strong wind conditions. This will aid in the prediction of the occurrence of many of the toxic outbreaks of red tides in the coastal regions.

9310504 Thomas This study of a longitudinal data base examines the distribution of cultural capital through extracurricular activities and the relative impact of race and gender upon this social process and its outcomes. It draws upon the theories of Bourdieu and Passeron to explain the interactive processes by which schools differentiate learning opportunities through the knowledge associated with their informal curricular outcomes. The researchers will study 12 randomly-selected desegregated public high schools in six southern cities over a retrospective 25 year period, employing both qualitative and quantitative methods, including content analysis of school yearbooks, validated with school site observations, accreditation reports, and interviews. %%% The results of this research will contribute to sociological theories of education, and they will strengthen the knowledge base for policy decisions concerning school tracking and support for various kinds of extracurricular activities. ***

9406216 Thomas Thrust belts worldwide are characterized by large-scale bends in trace: salients and recesses. As thrust belts advance they load the craton edge, producing foreland basins. Most previous studies of foreland basin formation use either salients or straight portions in order to avoid three-dimensional complexities in thrust direction. This study will take advantage of a large subsurface data base to model the development of a recess (the Black Warrior foreland basin) in which convergence of thrusting from different directions has resulted in a complex pattern of structural interference, diverse progradation of sediment wedges and numerous along-strike changes in thrusting, lading and subsidence. Results should help understand these more complex interactions, which will be of use in understanding foreland basins elsewhere.

The purpose of this study is to evaluate patients with diffuse skeletal disorders in an effort to determine the etiology and appropriate therapy of the skeletal disorders.

This research project is designed to investigate the significance of a recently discovered citrate-containing metabolite in the genesis and prevention of calcareous renal calculi.

9706735 Thomas One of the fundamental problems in early Paleozoic plate tectonic history of the Americas is where and how much the west coast of South America has interacted with the east coast of North America. One of the ways to test possible interactions of the continents is by testing lithostratigraphic correlations of Cambrian and Ordovician rocks. Thomas' study will do exactly that: compare and contrast the potential correlation of early Paleozoic sediments in the southeastern US with those of northwestern Argentina. The results will go a long way toward evaluating whether the correlations of these rocks permits a transfer in the Early Paleozoic of the Precordillera from Laurentia to Argentina .

Thomas
DEB-9972116

The coastal rain forest of Brazil once exteded 3,000 km along the coast of Brazil. Because of the high endemism of the flora and fauna and because of the rapid deforestation of the little that remains, the World Wildlfie Fund recognizes the Atlantic coastal forest of Brazil as one of the most endangered habitats on earth. Within the coastal forest biome, northeastern Brazil, including southern Bahia, is the most threatened, with less that 0.5% of the original forest remaining in a condition worth saving. This project will collect the vascular plants and bryophytes in the rain forests of three Brazilian reserves (Una Biological reserve, the Monte Pascoal National Park, and the Serra do Conduru State Park) in southern Bahia, Brazil. Approximately half of the specific diversity in these forests (estimated at around 1,500 species) is in the canopy and subcanopy trees, the most poorly collected and least documented part of the flora. By the end of the project, the PIs will have collected well-prepared, fertile specimens of a diverse flora; produced annotated checklists of the plants of each reserve; and compiled a cumulative checklist for all three reserves which will form a core checklist of the flora of the southern Bahian coastal forest.

.0208364
Thomas

One of the fundamental goals of biology is to understand how genome structure and function evolves in response to environmental change and how genetic constraints limit the natural distribution, abundance, and adaptive evolution of species. Toward these goals, Dr. Thomas is proposing to develop Bacterial Artificial Chromosome (BAC) libraries for diverse crustacean taxa. These libraries are specifically intended to support both comparative developmental studies and investigations into how organisms respond to environmental change. The Crustacea are ideal for comparative developmental studies because of their extraordinary morphological diversity, and close relationship to the premier developmental model organism, Drosophila melanogaster. Crustacean taxa are also the focus of many ecological studies aimed at understanding the fundamental interactions between organisms and their environment. The proposed BAC library resources and their distribution will provide critical tools in support of developmental evolution and environmental genomics.

Dr. Thomas is specifically proposing to develop BAC libraries for three taxa representing three crustacean classes. The Branchiopods are represented by the water flea, Daphnia pulex. The Maxillapoda are represented by a copepod Tigriopus californicus, and the class Malacostraca is represented by an amphipod, Parhyale hawaiensis. Daphnia and Parhyale are already the subjects of comparative developmental studies in numerous laboratories.

This work will take place in collaboration with a set of primary users who are actively participating in this proposal by consulting on the appropriate taxa, supplying specimens for DNA extraction and helping to make these resources available and useful to their taxon- or discipline-specific communities. These collaborators represent disparate fields of biological research and represent a broad spectrum of the potential user community. The generation and distribution of each library will take place at the Hubbard Center for Genome Studies (HCGS) at the University of New Hampshire under the direction of the PI (co-director of the center). The HCGS has a primary focus of comparative and environmental genomics, and in conjunction with this proposal will be offering intensive summer workshops in genomic technologies to support the use of BAC libraries by students and postdocs.

BAC library resources from each taxon will be made available to all academic and non-academic users in two ways: 1) as complete arrayed copies of the library; and 2) arrayed at high density on nylon filters. The BAC resources and associated information will be accessible via the WWW. The HCGS will maintain and distribute these resources for a minimum of five years after the end of the granting period.

A grant has been awarded to Dr. William K Thomas at the University of New Hampshire and his colleagues Dr. James Baldwin and Dr. Paul De Ley (University of California, Riverside), Dr. David Fitch (New York University) and Dr. Steven Nadler (University of California, Davis) to examine the evolutionary history and biodiversity of nematodes. The phylum Nematoda (roundworms) is argued to be one of the most abundant and genetically diverse animal phyla on earth. In addition, they play a key position in animal evolution and understanding of controversial invertebrate evolutionary relationships. Phylogenetic studies of this enormous phylum have been impeded by the difficulty of working with such diverse taxa, most of which are microscopic and known by relatively few experts. Nematode phylogenetics has also been impeded by the fragmentation of taxonomic specialists among different disciplines and by bias toward economically or medically important parasites of plants, vertebrates and invertebrates. Accordingly, understanding their evolutionary history is a critical component in the NSF's Assembling the Tree of Life program.
This project will develop a higher-level tree for the nematodes to provide a framework for interpreting their diversity. The work will use both molecular (18S ribosomal genes) and morphological data for over 1000 species. In a parallel effort, they will use the results of this work as a basis for selecting 50 nematode species for construction of cDNA libraries to provide greater insight into genetic diversity in the phylum and to possibly resolve the longstanding questions about of the deepest branches of the nematode tree or even its phylogenetic position in the animal kingdom.

Coupled natural-human ecosystems now tessellate the terrestrial surface of the Earth. There is little land that is not to some degree a consequence of its human inhabitants. Given the capacity of modern societies to alter both the atmosphere and ocean, even remote and unpopulated landscapes are to some degree altered by human activity. But does this human activity affect the stability of the natural-human system? What is the natural-human system's resistance to change? What is its resilience (the likelihood of returning to its original state after being disturbed)? While people often assume that the answer to these questions must be in the affirmative, this project will assess the question quantitatively and qualitatively through advanced socio-environmental systems analysis. This proposal will characterize, quantify, and model the spectrum of coupled natural-human dynamics on the Eastern Shore of Virginia over the past 500 years as, first, Native Americans and, later, European and African colonists and their descendents interacted with their environment. This interdisciplinary study is designed to improve understanding of the complex dynamics of a tightly coupled natural-human system in a single locale, but at varying spatial and temporal scales and under differing social and environmental pressures. These efforts will culminate in the development of integrated human-ecosystem models, which will be parameterized, calibrated, and validated by historical, archaeological, ecological, and geochemical data to simulate natural-human systems during specific historical periods that represent changes in human demographic patterns, land-use practices, and technological capabilities: Protohistoric (1550-1610); Colonial (1650-1700); Late Plantation (1800-1850); Commercial/Industrial (1850-1950); and Modern/Conservation (1950-present). Three working hypotheses will be investigated to understand and compare a range of landscape- and seascape-scale ecosystems in terms of their dynamic responses: (1) Systems with more technological societies are better able to resist change from environmental perturbation. (2) Systems with more technological societies are more resilient to environmental perturbation. (3) Technological societies are themselves the critical environmental perturbation that drives the future status of the system. Principal component analysis and other quantitative procedures will be employed to assess system stability, resiliency, and resistance to change during and between these time periods and to identify those system components within time periods that are most critical to resistance, resilience, and stability.

Anticipated intellectual contributions of this project include identifying constraints imposed by nature on humans in order to explain the range of adaptive poses assumed by human societies, assessing the response of the greater natural-human system to the activities of human societies over a broad range of time periods and through examination of distinctive demographic, land use, and technological regimes within the same locale. Anticipated broader impacts of this project include increase knowledge about natural-human dynamics on the Eastern Shore of Virginia, in particular, and countless other inhabited land-water interfaces throughout the world in general. The project will identify variables critical to system resistance, resilience, and stability, thereby informing policymaking in the Chesapeake Bay watershed and similar locales throughout the world. The project also will provide education and training opportunities for K-12 students, undergraduate and graduate students, and the general public. This project is supported by an award resulting from the FY 2003 special competition in Biocomplexity in the Environment focusing on the Dynamics of Coupled Natural and Human Systems.

Abstract: DEB-0315829
A grant has been awarded to Dr. James G. Baldwin and Dr. Paul De Ley of the University of California-Riverside and Dr. William K. Thomas of the University of New Hampshire to collaborate in a systematic inventory of marine nematodes. The inventory will include and preserve morphological records linked by database to DNA sequences selected to highlight unique features of each nematode species. The research site is Mexico's ecologically threatened Gulf of California and specifically the work will focus on five divergent Gulf localities designated as urgent priorities for biodiversity research by Mexican and international agencies. Special emphasis will be given to the ecologically rich northern region, adversely impacted by diversion of Colorado River freshwater and by agricultural runoff. Why focus on nematodes? Nematodes are the most abundant invertebrate on the planet, and yet most species, particularly subtropical and tropical marine forms, remain undiscovered and unnamed. By developing an inventory of nematode species in this unique region, new insight will be gained into the planet's biodiversity; the impact will be enhanced because new methods employed with this study are designed to accelerate bioinventory of marine nematodes at additional sites worldwide. The study will provide the "raw material" for ecological conservation work and as a source of previously undiscovered specimens it will support separate studies designed to understand nematode evolution. Outreach is enhanced by providing databases resources on marine nematodes that will be available worldwide to scientists, the public, teachers and policy makers. The project will develop new identification aids for nematodes that will assist scientists in various systematic and ecological work, including non-specialists (in nematodes), worldwide. This study is designed to train undergraduate and graduate students including a significant proportion from underrepresented groups.

The Precordillera in northwestern Argentina is an exotic Laurentian (North American) terrane that collided with and was accreted to western Gondwana (South America). General consensus holds that the Precordillera was rifted from the Ouachita embayment of southern Laurentia, and the Precordillera arguably has the best-constrained original location of any known exotic continental terrane. For that reason, the Precordillera provides a place to address fundamental questions of mechanisms and rates of transfer of a continental terrane from one continent to another. In addition, the Precordillera may serve as model for processes and responses that characterize the collision of a microcontinent (small plate) with a continent. Finally, the history of the transfer of the Precordillera from Laurentia to Gondwana is an important constraint on global paleogeographic reconstructions.

Even with the consensus both for the original location of the Argentine Precordillera in the Ouachita embayment and for collision of the Precordillera with western Gondwana, interpretations of the time of collision differ from Middle-Late Ordovician to Silurian-Devonian. Middle-Late Ordovician events are recognized in each of the interpretations, but those events are considered to represent collision with Gondwana in some interpretations and to represent rifting from Laurentia in others. New data gathered in this research help to constrain both the timing and mechanism(s) of collision of the Precordillera with Gondwana. This research integrates the history of subsidence and sedimentary filling of the Precordillera foreland basin in the context of temporal and mechanical links to the Famatina volcanic arc and a continental suture zone between the rocks of western Gondwana and the eastern Precordillera. Specifically, the research is examining the subsidence history of the basin, role of high-relief fault blocks as sources of carbonate olistoliths, significance of possible fault blocks for extension or transpression/transtension, provenance of igneous and metamorphic clasts, patterns of clastic sediment dispersal on Precordillera platform, relation of Famatina arch and suture zone to basin subsidence and sediment progradation on platform, and relation of succession to southern Laurentia.

The Atlantic coastal forest of Brazil is one of the World's biodiversity "hotspots." It suffers severe deforestation and has high biological diversity, especially of species found nowhere else (endemic species). Collection of biological specimens from these highly fragmented forests is unevenly distributed, with most collections made in proximity to cities or large protected areas, or in more easily accessible areas near the coast. This narrow fringe of forest comprises several areas of high endemism for plants and many groups of animals. These include the coastal montane forests of Sao Paulo and Rio de Janeiro (Paulista area) and the moist forests of southern Bahia. The division between the Paulista area and the Bahia area coincides with a very poorly collected region of forests in northern Espirito Santo and extreme southern Bahia. It is hypothesized that increased collecting in the gap between the Paulista area and the Bahia area will show that this gap does not exist. It will demonstrate that species now known only from the submontane forests of Bahia will be found occurring in similar forests farther south and that plants known only from the montane forests of the Serra do Mar of Rio de Janeiro and Sao Paulo will be found in the high elevation forests of northern Espirito Santo and southern Bahia. Staff of The New York Botanical Garden (NY), the Center for Cocoa Research (CEPEC), the State University of Santa Cruz, Bahia (UESC), and the Mello Leitao Biological Museum (MBML) of Santa Teresa, Espirito Santo, will collaborate and collect the vascular plants in the submontane and montane forests of southern Bahia and northern Espirito Santo, Brazil. The project, with support from the Office of International Science and Engineering and the Biodiversity Surveys and Inventories program , will have: 1) tested the hypotheses that there is no gap between the Paulista and Bahia centers of endemism, and that many montane and submontane species are less restricted in distribution than previously believed; 2) produced specimens that will be used by present and future biologists for expert identification, study, and descriptions of new species; 3) compiled a core checklist of the flora of the southern Bahian and northern Espirito Santo; and 4) reassessed patterns of plant endemism in the forests of eastern Brazil.
This project will be critical to intelligent conservation in the Atlantic forest of eastern Brazil. The project team will find and highlight areas of submontane and montane forest for possible conservation. In addition, distributions of rare plant species will be better defined, permitting an assessment of criteria for the inclusion of each species on IUCN's Red List of threatened species. It is expected that these distributions will be seen to follow patterns of ecological zonation and the presence or absence of certain species in a given forest fragment will be predictable. Training of Brazilian botanists and NY graduate students will be another important byproduct of our research, as the US students travel to Brazil they will develop important collaborations for future work.

[unreadable] DESCRIPTION (provided by applicant): The aims of the NCMHD-RIMI program are to reduce health disparities by providing resources to institutions that prepare significant number of minority students and faculty in biomedical sciences. Based on these aims, Virginia State University (VSU) proposes a RIMI program that is aimed to augment and strengthen the infrastructure and capacity of VSU to conduct basic biomedical research which will address and ultimately eliminate health disparities. The program will develop infrastructure to enhance research at VSU, infuse innovative educational experiences to students and faculty, expose faculty and students to cutting-edge biomedical research, and through collaborations enhance minority faculty/student participation in biomedical research. [unreadable] [unreadable] VSU-RIMI program objectives are: I) to build research capacity for biomedical research at VSU, ii) to promote the participation of faculty and students in biomedical and behavioral research, and iii) to enhance academic programs in biomedical sciences and health disparities. VSU-RIMI program proposes four major cores: administrative core, shared resources/infrastructure core, faculty developmental research core, and academic enhancement core. These four cores with the proposed specific aims consist of all major aims which are goals of NCMHD-RIMI program. Within the faculty research core, we propose three research projects which deal with health disparities and human health issues. These subprojects are: 1) Comparative Genomics Strategies for Finding Susceptibility Components for Inherited Human Disease-Diabetes, 2) Study of interaction between presenilin mutations and amyloid protein in development of Alzheimer's disease, and 3) A Comparative and Functional Genomic Approach to Host Susceptibility or Resistance and Immune Responses to Internal Parasite Infections. [unreadable] [unreadable] Our proposed RIMI program will include a team of personnel that will be headed by project director, Dr. Brown, a program coordinator, a research associate and three faculty members serving as co-PIs. Management team will be advised by an institutional advisory committee and overall RIMI program will have an oversight of an external advisory committee. The program includes University of Virginia, Louisiana State University, Utah State University, and College of William and Mary as collaborating institutions which are research intensive institutions. The RIMI program will be evaluated annually by an external consultant and proposed and actual accomplishments will be evaluated and a report will be provided to the external advisory committee and the RIMI program director. With the proposed well-planned RIMI program, within the five year of the project period, we anticipate to double the research productivity which could be measured in the number of publications, funded proposals, number of students entering graduate school and total number of faculty participating in biomedical research. [unreadable] [unreadable] [unreadable]

A fundamental and hard question in biology is identification of organisms. This proposal focuses on identification of nematodes, which are particularly difficult to identify, with the average identification requiring significant time and high level of expertise. Nematodes have direct and significant effect on humans, other animals, and agriculture. Four species of nematode parasites infect over 2 billion people worldwide, and one type of nematode causes one-third of the total estimated worldwide annual yield losses to all soybean pathogens. The current limiting factors for identification are the lack of tools and automation, the need for image comparison off-line and a need for significant expertise. To enable seasoned researchers as well as students to use resources, the team will build on image searching work, using a set of images that will make nematode identification a simple process of point and click. In addition to enabling research by harnessing data and experience of experts, the work may make biology more accessible. The team will build a computer-assisted interactive navigator that will intelligently assist and learn from the user. The work can be extended to many other biological data sets. The research challenges include extraction of features and similarity functions, and the mining, clustering, and anomaly detection for image and non-image data. Graduate students are engaged in the research and outreach involving high school students is also planned.

An award has been made to the New York Botanical Garden under the direction of Dr. Barbara M. Thiers for the enhancement of an online, virtual herbarium of plant specimens from Amazonian Brazil. The Garden holds over one-half million specimens from this biologically diverse and important country, and the grant will allow them to capture images and data from the specimens that can be accessed by researchers worldwide in studies of this flora. The Garden will work closely with Brazilian colleagues to ensure accuracy of the data for the specimens, and the electronic data will be made available to the Brazilian National Institute for Amazonian Research, which will support complementary efforts in that country. The data and information will be used by conservation biologists and botanists to document species distributions and inform decision makers dealing with this region, which contains many threatened species. Students in the US and Brazil will be involved in the project and will be trained in herbarium curation, database construction and management, and botanical research.

The University of New Hampshire (UNH) plans to acquire a high-performance computer from IBM, funded by the National Science Foundation and supplemented by an IBM University Research grant. This machine is powered by 84 PowerXCell 8i processors with a total of 756 computational cores. Beyond substantially increasing UNH's scientific computing capabilities, it provides access to a state-of-the-art accelerator-based architecture, as employed in the world's most advanced supercomputers like Roadrunner at Los Alamos National Laboratory. This research involves grand science challenges in the fields of magnetospheric
physics (space weather), plasma physics, and computational fluid dynamics, lattice quantum chromodynamics and genomics.
The investigators on this project conduct research on algorithms and program-
ming models for modern hardware architectures. Since computational capabilities have advanced from being driven by enhancements in speed to increasing the number of processors and computational cores, efficient exploitation of highly parallel machines challenges conventional programming models and increases the complexity of algorithms. The researchers plan to develop and deploy new computational approaches for describing, at a higher level of abstraction, the equations to be solved and then uses specific computer software,
including source-to-source translation, to generate highly optimized implementations tailored to the hardware to be used. The program also provides first-hand experience using a cutting-edge supercomputer to students in UNH.

Oceanic sediments harbor most of the world?s biodiversity, primarily comprised of minute organisms that perform key ecological functions such as nutrient cycling, critical to the biodegradation of hydrocarbons. Unfortunately, knowledge of these communities of organisms in the Gulf of Mexico (GOM) is sparse, thus precluding informed mitigation and remediation of the BP Deepwater Horizon oil spill. Knowledge-based action requires that three key questions be addressed: 1) How unique are the communities in the GOM? 2) How structured are the communities within the GOM? and 3) What has been the effect of anthropogenic disturbance on these communities? Cutting-edge, high-throughput DNA sequencing technologies will be utilized alongside traditional taxonomic methods to assay the diversity of virtually all complex organisms from sediment samples collected prior to the April 2010 spill, representing diverse habitats across the GOM.

The BP Deepwater Horizon oil spill represents one of the most dramatic anthropogenic events in human history. It will both require and inspire the interest of future biologists for decades. This funding will specifically provide new opportunities for student engagement in the long-term characterization of biodiversity, using new tools to understand the response of organisms to environmental change and the consequences, mitigation and remediation of such a severe environmental disturbance. Training will include support for undergraduate students to attend a workshop in GOM biodiversity assessment as well as graduate and postdoctoral training. In all cases participation by underrepresented groups in science will be actively encouraged. Most importantly, all data collected will be made openly accessible to the public and scientific communities to facilitate ongoing research and maximize the engagement of all stakeholders.

The Atlantic coastal forests of Brazil are considered one of the World's biodiversity "hotspots"; nearly half of the plant species in the Atlantic forests are unique to this region. Within these coastal forests, those in northeastern Brazil (from Bahia to Rio Grande do Norte) are the most biodiverse and the most critically endangered. Nevertheless, the distributions of the plant species in this region and their relationship to species in adjacent regions are not known. The goal of this project is to study the vegetation of these northeastern forests and demonstrate that the forests of the southern portion (Bahia) and those of the northern portion (Pernambuco) are not as distinct as previously hypothesized. This will be accomplished by collecting and identifying plant specimens in targeted forest fragments throughout the region which will make it possible to map and predict the distribution of plant species.

Discovering new species and clarifying the distribution of forest plants in northeastern Brazil will enhance our understanding of the history of this unique region and its flora. In addition, data on species and their distributions will be provided to appropriate government bodies and local organizations so that decisions about conservation priorities can be made wisely. The PI and Co-PI will provide training in botany, ecology and conservation to student both in the U.S. and in Brazil.

A high throughput (HTP) sequencing system will be acquired by the University of New Hampshire (UNH) to enable Northern New England research groups using genome-enabled technologies to explore basic questions in ecology, evolution, and biodiversity. This research will catalyze the generation of new interdisciplinary knowledge of fundamental biological processes and advance the role of genomics and bioinformatics across traditional biological disciplines. The instrument, an Illumina HiSeq 2500, is both fast and flexible, suited to a large array of applications. It will support the research and training programs of 16 existing laboratories at UNH, four new UNH Assistant Professors, and 8 research groups at regional undergraduate institutions using genomics to address the basic biological question: ?How do organisms respond to changes in their environment?? Users will benefit from this local, well-managed, shared instrument through (1) dramatic reductions in wait times for sample analyses, (2) intensive sample management to contain costs and maximize data output, and (3) comprehensive onsite technical and bioinformatics support. The Illumina HiSeq 2500 will be housed in the UNH Hubbard Center for Genome Studies (HCGS), an established DNA core facility with a service-driven technical, management, and bioinformatics team. The HCGS also serves as a regional bioinformatics core facility, meeting the bioinformatics and connectivity needs of scientists throughout northern New England. Management, storage, and security of the data generated by the HTP sequencing system will be provided by a dedicated IT team and infrastructure in the UNH Research Computing and Instrumentation Core Facility. To interpret and utilize the data effectively, two full-time Ph.D.-level bioinformatics staff will be dedicated to HTP sequence analysis. In addition, the HCGS works extensively with computer science faculty and students to promote the cross-disciplinary development of bioinformatics expertise. This team approach and infrastructure will ensure the efficient operation of the sequencing platform and will allow its use by the broadest number of research programs.

UNH is a national leader in promoting research experiences for undergraduates; the anticipated major users of this HTP sequencing system exemplify this commitment in their own research programs. The new sequencing system will support such research experiences for undergraduate students, and also provide research opportunities for graduate students and postdoctoral fellows. To complement and support the research activities, a series of workshops will be held to provide training for students (and faculty) in HTP sequencing applications and the associated bioinformatics tools. In addition, data generated by this system will be integrated into courses in the biology curricula of participating institutions, supporting the adoption of these technologies in diverse fields. The research programs that will use this instrument already have a strong record of participation by diverse students and faculty, attracting students through programs such as the McNair Scholars, UNH Project SMART, and UNH REAP, and building faculty partnerships through collaborative research projects with historically black colleges and universities. This participation is expected to continue, and grow, as the new HTP sequencing system facilitates exploration of new areas of genomics and the application of informatics to answering a wider range of research questions.

EAGER: TESTING THE HYPOTHESIZED GRAND CANYON-APPALACHIAN CONNECTION

George Gehrels and William Thomas
University of Arizona

This project has a specific goal of testing the hypothesis that some of the sand that make up the sandstones of the Grand Canyon were supplied primarily from the Appalachian mountains, and a more general goal of reconstructing dispersal pathways for sediment across the US during late Paleozoic (350-245 million years ago) time. Conducting source area studies for this time period is challenging because of the complex interplay of mountian building processes and climate. During this time the Ouachita-Appalachian-Caledonian mountain range formed as result of collisional interactions during assembly of the supercontinent Pangea, the Cordilleran mountain range experienced arc-type magmatism and several phases of convergent tectonism, and the Ancestral Rocky Mountains were uplifted. There were also dramatic changes in regional and global paleoclimate as North America moved northward across the paleo-equator and as southern hemisphere glaciation created large changes in sea level. North America accordingly serves as a fabulous laboratory in which to examine the interplay between these disparate processes, potentially serving as an ancient analogue of our modern world. The hypothesized Grand Canyon-Appalachian connection is based on detrital zircon grains of ~720-280 Ma that appear in increasing abundance in Mississippian through Permian strata of the Grand Canyon, as reported in the June 2011 issue of Lithosphere by Gehrels and colleagues. These young grains were interpreted to have been shed from the Appalachian orogen primarily on the basis of similarities with crystallization ages of Appalachian plutons and detrital zircon ages reported from upper Paleozoic strata of the Appalachian foreland basin. This interpretation was challenged in the August 2011 issue of Lithosphere by Thomas because there is little evidence that clastic detritus was transported westward out of the Appalachian foreland basins, and because the young sediment could have been shed from other orogens (e.g. the Fanklinian system to the north) and in part from local igneous rocks. Thomas (2011) also proposed that testing these hypotheses by combining additional DZ provenance data with facies relations, thickness patterns, and petrographic characteristics of upper Paleozoic strata would enable reconstruction of the dispersal pathways of sediment transport across North America during late Paleozoic time. We propose to combine U-Pb age and Hf isotope determinations of ~60 samples with traditional stratigraphic information to specifically test the Grand Canyon-Appalachian hypothesis and more generally reconstruct late Paleozoic dispersal pathways of southern North America.

Three impacts beyond the geologic contributions noted above include:
(1) Providing opportunities for faculty members and undergraduate students at academic institutions near study areas to become involved in sample collection, analysis, and interpretation.
(2) Advancing the field of provenance analysis by integrating U-Pb geochronology, Hf isotope analysis, and traditional stratigraphic/sedimentologic analysis of sandstones in an effort to reconstruct dispersal pathways and to examine linkages between tectonics and climate.
(3) Sharing information with the public by providing operators of State and National Parks near our study areas with the results of our work, following the model of the 'Trail of Time' exhibits at the Grand Canyon.

This research will explain and predict of the distribution of animal and plant species in the endangered yet megadiverse Brazilian Atlantic forest. The investigators will correlate biogeographic and environmental patterns across major clades in order to understand patterns in this biodiversity hotspot. The project will entail study of both climate and landscape, and their changes over the last 120,000 years. This information will enable understanding of how species have responded to repeated environmental shifts of the past. Data from Earth-orbiting satellites will be combined with meteorological data and paleoenvironmental information from the fossil pollen record and ancient precipitation data derived from the geochemistry of deposits found in caves. These data, combined with information on modern species ranges, genetic diversity, physiological tolerances, host-pathogen dynamics, and regional shifts in the composition of the biota will demonstrate how the biodiversity of the Atlantic forest evolved over time.

This study will enable the reconstruction of historical factors influencing current biodiversity and, given a range of climate change scenarios, permit the prediction of the future composition of biodiversity in the Atlantic forest or elsewhere. Forest areas of geological stability, physical connectivity, and higher genetic diversity will be identified so that forests or species under extinction threat can be conserved. In response to current concern about the value of ecosystem services and climate change, this study provides a model of how to predict biodiversity change. A travelling exhibit will reach out to commuters in São Paulo and New York. Collaborations among research groups in Brazil and the US is central to the project?s student training plan. The project also strengthens a minority-serving campus, ensuring that North-American students underrepresented in science are exposed to trans-disciplinary, international work.

The University of New Hampshire and the University of California, Davis are awarded a grant to develop a Research Coordination Network focused on eukaryotic biodiversity research using high-throughput sequencing (RCN EukHiTS). Microscopic eukaryote species (organisms <1mm, such as nematodes, fungi, protists, etc.) are abundant and ubiquitous-yet invisible to the naked eye-in every ecosystem on earth. The biodiversity and geographic distributions for most of these species are largely unknown, and represent one of the major knowledge gaps in biology. High-throughput DNA sequencing technologies now allow for deep examination of virtually all microscopic organisms present in an environmental sample. For microbial eukaryote taxa, en masse biodiversity assessment using traditional loci (rRNA genes) can be conducted at a fraction of the time and cost required for traditional (morphological) approaches. Despite this promise, current bottlenecks include the lack of useful distributed tools for analysis and common data standards to allow global comparisons across individual studies as well as missing links between molecules and morphology. The EukHiTS RCN will focus on developing community capabilities for computational approaches focused on eukaryotic taxa and the infrastructure, both cyber and human, needed for effective interpretation of large high-throughput datasets. The steering committee of RCN EukHiTS includes expertise from computational biology, functional genomics, computer science, taxonomy, ecology, database resource management, and representatives of end‐user communities to ensure that all aspects of the community are well-represented.

RCN EukHiTs will offer extensive scientific outreach, education and training, including a heavy focus on technology and social media tools. Key network activities will be devoted to training the next generation of scientists to take up the challenges of global biodiversity assessment; a strong focus on undergraduate opportunities ("Bioinformatics Bootcamps" and institutional research exchanges) will enable students to develop their research skill set through interdisciplinary training, and gain career insight though planned social interactions with established researchers at different career stages. Research coordination activities will include yearly catalysis meetings (held as satellite events to well-attended, interdisciplinary scientific conferences), working groups, and RCN-sponsored conference symposia. An RCN portal website will disseminate RCN activities and inform the wider community of eukaryotic biodiversity research priorities and long-term goals. Similarly, web-based content, including blog posts and Twitter feeds, will serve to engage public audiences and raise awareness of new DNA sequencing technologies and the role of microbial eukaryotes in natural ecosystems.