Phylogeography and Genetic Diversity of the Seal Salamander (Desmognathus monticola)

Phylogeography is defined as the spatial distribution of taxa with respect to geologic and geographic events. It is well documented that the distributions of many taxa have been affected by glacial events during the Pleistocene Era. The patterns generated can be very complex and result from shifts in climate and/or vegetation. The Seal salamander, (Desmognathus monticola), is one species that still has questions pertaining to its phylogeography. The range of this species extends from southwestern Pennsylvania to northern Alabama and Georgia, with a highly disjunct, state-endangered population in the Red Hills of Alabama. The main goal of this study is to determine the origin of this disjunct population through an extensive field survey. In addition, the utility of a relatively new genetic technique will be tested, with possible conservation implication for this population. Three hypotheses were proposed to explain the origin of the southern population. First, it is possible that this population may not be disjunct, but instead may have a continuous range extending throughout the state of Alabama. If disjunct, then two additional hypotheses could be proposed. The southern population may represent a recent derivative from the main range, or it may be a relictual population formed through historic glacial events in the Appalachian region. Based upon a review of topographic maps and an extensive field survey of this intervening region, we concluded that D. monticola were not present in this area and that the Red Hills population is truly disjunct. Thus, the first hypothesis could be rejected. To address the final two hypotheses, Intersimple Sequence Repeats were employed, and networks of relatedness were constructed using parsimony and neighbor-joining methods. These data indicate the Red Hills population (10 bands) and the Tubmill population (8 bands), in the northern extreme of the range, harbor the highest numbers of population-specific bands. Remaining populations had three or fewer population-specific bands, and held only a subset of the bands present in the Red Hills and Tubmill populations. The Tubmill population was sister to the remaining populations; wherever, the Red Hills population was nested within each tree generated. To address this situation, constraint analyses were conducted to place the Red Hills as sister to all other populations. The tree generated was the same length of the unconstrained tree (L=570), which indicates that the Red Hills population could be sister to the remainder of the populations sampled. Our data thus indicate the potential for two refugial populations, possibly isolated during glacial events of the Pleistocene Era. A bi-directional recolonization from the northern and southern extremes may have occurred. The southern population was probably isolated due to shifts in climate and/or vegetation, while the northern population may be a more traditional glacial refugium

The Indiana Center for Breast Cancer Research: Progress towards a SPORE Proposal

poster abstractAbstract The Indiana Center for Breast Cancer Research (ICBCR) was funded under the IUPUI Signature Center Initiative in 2010. Its mission is to address the full range of prevention, early detection, and treatment of breast cancer through translational projects, supportive cores, and synergistic programs. This poster details our efforts to date towards applying for a National Cancer Institute Specialized Program of Research Excellence (SPORE) in January 2013. The proposed IU Breast Cancer SPORE will include 4-5 individual research projects, 3 cores, developmental research and career development programs. The SPORE Biostatistics and Bioinformatics core has developed the Breast Cancer Prognostics Database (BCDB), an online tool to study prognostic implications of genes of interest in publically available breast cancer databases. The BCDB can be used to study overall, recurrence free and metastasis free survival in large patient series. Supporting the SPORE Biospecimen/Pathology core, the IU Breast Cancer Tissue Bank includes a total sample of N = 500 cases with 30% non-Caucasian cases from Wishard Memorial Hospital. Currently there are N = 333 cases with tissue microarray data and complete clinical data with an additional 200 cases pending tissue confirmation. Dr. Clark D. Wells together with S. Badve and G. Sandusky are collaborating on the project: “Histologic Analysis of the Protein Levels of Amot130, AmotL1 and YAP in Normal, Hyperplastic and Invasive Breast Cancer Tissues”, a candidate SPORE individual research project. This project is investigating localized protein expression in paraffin-embedded tissues to associate expression levels with disease subtype and patient outcome. Dr. David P. Gilley together with N. Kannan, N. Huda, L. Tu, R. Droumeva, R. Brinkman, J. Emerman, S. Abe, and C. Eaves, are collaborating on the project: “Luminal mammary progenitors are a unique site of telomere dysfunction”, a candidate SPORE developmental research project. This project is investigating the relationship between telomere dysfunction and breast cancer tumorigenesis. These SPORE projects and cores were discussed at the IUSCC Breast Cancer Program retreat held on 1/13/12. Two additional planning meetings were held on 1/5 and 2/23. A timeline was generated to include final project selection in April, internal review in June, external review in August-September, and draft completion by 12/1, to meet the 1/20/13 NIH receipt deadline

Managing Invasive Plants on Great Plains Grasslands: A Discussion of Current Challenges

The Great Plains of North America encompass approximately 1,300,000 km2 of land from Texas to Saskatchewan. The integrity of these lands is under continual assault by long-established and newly-arrived invasive plant species, which can threaten native species and diminish land values and ecological goods and services by degrading desired grassland resources. The Great Plains are a mixture of privately and publicly owned lands, which leads to a patchwork of varying management goals and strategies for controlling invasive plants. Continually updated knowledge is required for efficient and effective management of threats posed by changing environments and invasive plants. Here we discuss current challenges, contemporary management strategies, and management tools and their integration, in hopes of presenting a knowledge resource for new and experienced land managers and others involved in making decisions regarding invasive plant management in the Great Plains

Managing Invasive Plants on Great Plains Grasslands: A Discussion of Current Challenges

The Great Plains of North America encompass approximately 1,300,000 km2 of land from Texas to Saskatchewan. The integrity of these lands is under continual assault by long-established and newly-arrived invasive plant species, which can threaten native species and diminish land values and ecological goods and services by degrading desired grassland resources. The Great Plains are a mixture of privately and publicly owned lands, which leads to a patchwork of varying management goals and strategies for controlling invasive plants. Continually updated knowledge is required for efficient and effective management of threats posed by changing environments and invasive plants. Here we discuss current challenges, contemporary management strategies, and management tools and their integration, in hopes of presenting a knowledge resource for new and experienced land managers and others involved in making decisions regarding invasive plant management in the Great Plains

A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources.

OBJECTIVE: The Genomic Medicine Working Group of the National Advisory Council for Human Genome Research virtually hosted its 13th genomic medicine meeting titled Developing a Clinical Genomic Informatics Research Agenda . The meeting\u27s goal was to articulate a research strategy to develop Genomics-based Clinical Informatics Tools and Resources (GCIT) to improve the detection, treatment, and reporting of genetic disorders in clinical settings. MATERIALS AND METHODS: Experts from government agencies, the private sector, and academia in genomic medicine and clinical informatics were invited to address the meeting\u27s goals. Invitees were also asked to complete a survey to assess important considerations needed to develop a genomic-based clinical informatics research strategy. RESULTS: Outcomes from the meeting included identifying short-term research needs, such as designing and implementing standards-based interfaces between laboratory information systems and electronic health records, as well as long-term projects, such as identifying and addressing barriers related to the establishment and implementation of genomic data exchange systems that, in turn, the research community could help address. DISCUSSION: Discussions centered on identifying gaps and barriers that impede the use of GCIT in genomic medicine. Emergent themes from the meeting included developing an implementation science framework, defining a value proposition for all stakeholders, fostering engagement with patients and partners to develop applications under patient control, promoting the use of relevant clinical workflows in research, and lowering related barriers to regulatory processes. Another key theme was recognizing pervasive biases in data and information systems, algorithms, access, value, and knowledge repositories and identifying ways to resolve them

Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life.

Neonates have heightened susceptibility to infections. The biological mechanisms are incompletely understood but thought to be related to age-specific adaptations in immunity due to resource constraints during immune system development and growth. We present here an extended analysis of our proteomics study of peripheral blood-plasma from a study of healthy full-term newborns delivered vaginally, collected at the day of birth and on day of life (DOL) 1, 3, or 7, to cover the first week of life. The plasma proteome was characterized by LC-MS using our established 96-well plate format plasma proteomics platform. We found increasing acute phase proteins and a reduction of respective inhibitors on DOL1. Focusing on the complement system, we found increased plasma concentrations of all major components of the classical complement pathway and the membrane attack complex (MAC) from birth onward, except C7 which seems to have near adult levels at birth. In contrast, components of the lectin and alternative complement pathways mainly decreased. A comparison to whole blood messenger RNA (mRNA) levels enabled characterization of mRNA and protein levels in parallel, and for 23 of the 30 monitored complement proteins, the whole blood transcript information by itself was not reflective of the plasma protein levels or dynamics during the first week of life. Analysis of immunoglobulin (Ig) mRNA and protein levels revealed that IgM levels and synthesis increased, while the plasma concentrations of maternally transferred IgG1-4 decreased in accordance with their in vivo half-lives. The neonatal plasma ratio of IgG1 to IgG2-4 was increased compared to adult values, demonstrating a highly efficient IgG1 transplacental transfer process. Partial compensation for maternal IgG degradation was achieved by endogenous synthesis of the IgG1 subtype which increased with DOL. The findings were validated in a geographically distinct cohort, demonstrating a consistent developmental trajectory of the newborn's immune system over the first week of human life across continents. Our findings indicate that the classical complement pathway is central for newborn immunity and our approach to characterize the plasma proteome in parallel with the transcriptome will provide crucial insight in immune ontogeny and inform new approaches to prevent and treat diseases

Acute ingestion of a novel whey-derived peptide improves vascular endothelial responses in healthy individuals: a randomized, placebo controlled trial

<p>Abstract</p> <p>Background</p> <p>Whey protein is a potential source of bioactive peptides. Based on findings from <it>in vitro </it>experiments indicating a novel whey derived peptide (NOP-47) increased endothelial nitric oxide synthesis, we tested its effects on vascular function in humans.</p> <p>Methods</p> <p>A randomized, placebo-controlled, crossover study design was used. Healthy men (n = 10) and women (n = 10) (25 ± 5 y, BMI = 24.3 ± 2.3 kg/m²) participated in two vascular testing days each preceded by 2 wk of supplementation with a single dose of 5 g/day of a novel whey-derived peptide (NOP-47) or placebo. There was a 2 wk washout period between trials. After 2 wk of supplementation, vascular function in the forearm and circulating oxidative stress and inflammatory related biomarkers were measured serially for 2 h after ingestion of 5 g of NOP-47 or placebo. Macrovascular and microvascular function were assessed using brachial artery flow mediated dilation (FMD) and venous occlusion strain gauge plethysmography.</p> <p>Results</p> <p>Baseline peak FMD was not different for Placebo (7.7%) and NOP-47 (7.8%). Placebo had no effect on FMD at 30, 60, and 90 min post-ingestion (7.5%, 7.2%, and 7.6%, respectively) whereas NOP-47 significantly improved FMD responses at these respective postprandial time points compared to baseline (8.9%, 9.9%, and 9.0%; <it>P </it>< 0.0001 for time × trial interaction). Baseline reactive hyperemia forearm blood flow was not different for placebo (27.2 ± 7.2%/min) and NOP-47 (27.3 ± 7.6%/min). Hyperemia blood flow measured 120 min post-ingestion (27.2 ± 7.8%/min) was unaffected by placebo whereas NOP-47 significantly increased hyperemia compared to baseline (29.9 ± 7.8%/min; <it>P </it>= 0.008 for time × trial interaction). Plasma myeloperoxidase was increased transiently by both NOP-47 and placebo, but there were no changes in markers inflammation. Plasma total nitrites/nitrates significantly decreased over the 2 hr post-ingestion period and were lower at 120 min after placebo (-25%) compared to NOP-47 (-18%).</p> <p>Conclusion</p> <p>These findings indicate that supplementation with a novel whey-derived peptide in healthy individuals improves vascular function.</p

The Hobby–Eberly Telescope Dark Energy Experiment (HETDEX) Survey Design, Reductions, and Detections

We describe the survey design, calibration, commissioning, and emission-line detection algorithms for the Hobby–Eberly Telescope Dark Energy Experiment (HETDEX). The goal of HETDEX is to measure the redshifts of over a million Lyα emitting galaxies between 1.88 < z < 3.52, in a 540 deg2 area encompassing a comoving volume of 10.9 Gpc3. No preselection of targets is involved; instead the HETDEX measurements are accomplished via a spectroscopic survey using a suite of wide-field integral field units distributed over the focal plane of the telescope. This survey measures the Hubble expansion parameter and angular diameter distance, with a final expected accuracy of better than 1%. We detail the project’s observational strategy, reduction pipeline, source detection, and catalog generation, and present initial results for science verification in the Cosmological Evolution Survey, Extended Groth Strip, and Great Observatories Origins Deep Survey North fields. We demonstrate that our data reach the required specifications in throughput, astrometric accuracy, flux limit, and object detection, with the end products being a catalog of emission-line sources, their object classifications, and flux-calibrated spectra

Priorities for synthesis research in ecology and environmental science

ACKNOWLEDGMENTS We thank the National Science Foundation grant #1940692 for financial support for this workshop, and the National Center for Ecological Analysis and Synthesis (NCEAS) and its staff for logistical support.Peer reviewedPublisher PD