Life Sciences Commons^™

Towards Quantitative Viromics For Both Double-Stranded And Single-Stranded Dna Viruses., Simon Roux, Natalie E Solonenko, Vinh T Dang, Bonnie T Poulos, Sarah M Schwenck, Dawn B Goldsmith, Maureen L Coleman, Mya Breitbart, Matthew B Sullivan

Marine Science Faculty Publications

BACKGROUND: Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).

METHODS: Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation …

Sea Surface Temperature Rises Shift Migration Patterns Due To Ecosystem Changes, Alexia Skrbic, Hesham El-Askary

Student Scholar Symposium Abstracts and Posters

The continuing climate change is negatively impacting ecosystems, specifically oceans which are declining and food webs are being altered by the increase of greenhouse gases. The increase of the carbon dioxide and other greenhouse gases is increasing sea surface temperature of the world’s oceans. Certain organisms lower on the food chain like phytoplankton and zooplankton are directly affected by the warming which alters how they process nutrients and their productivity. The limited amount of these primary producers in the oceans and specifically the location they inhabit directly affects all the organisms above them on the food chain. Several marine animals …

Manual And Automated Solid Phase Synthesis Of Peptides For Breast Cancer Cell Targeting, Savannah Carlson

Student Scholar Symposium Abstracts and Posters

Four peptides were synthesized using solid phase peptide synthesis. The two target peptides synthesized were based off peptide 18-4 and its negative analog. Each were synthesized once manually, and once using an automatic peptide synthesizer. Peptide 18-4 has a high affinity for breast cancer cells, allowing it to be used to detect circulating tumor cells (CTCs) in blood (Kaur et. al, 2015). Manual solid phase peptide synthesis is performed by anchoring the first amino acid to Wang resin and coupling each Fmoc protected amino acid individually until the target sequence is achieved. To synthesize the peptides automatically, the automated Tribute …

Lingnan Gardeners Newsletter (No. 25) = 嶺南彩園通訊 (第25期), Lingnan Gardeners, Kwan Fong Cultural Research And Development Programme, Lingnan University

Lingnan Gardeners Newsletter 嶺南彩園通訊

Winter Solstice 冬至

Lilliput Effect Dynamics Across The Cretaceous-Paleogene Mass Extinction: Approaches, Prevalence, And Mechanisms, Matthew Brett Jarrett

USF Tampa Graduate Theses and Dissertations

An organism's body size entails both physiological and ecological costs. Furthermore, as a parameter in analyzing organisms, it represents a fundamental and essential morphometric character. Reductions in size following mass extinction is a commonly observed phenomenon in the fossil record. This study examines the evolutionary significance of this phenomenon termed the: 'Lilliput Effect' by proposing that it represents a rapid evolutionary response to altered selection pressures during a mass extinction. This primary hypothesis is evaluated against two additional hypotheses of size reduction: 1) stunted growth as a response to stressed ecosystems, and/or 2) mass extinctions are size selective.

These hypotheses …

Polypores And Genus Concepts In Phanerochaetaceae (Polyporales, Basidiomycota), Otto Miettinen, Viacheslav Spirin, Josef Vlasák, Bernard Rivoire, Soili Stenroos, David S. Hibbett

Biology

We explored whether DNA-phylogeny-based and morphology-based genus concepts can be reconciled in the basidiomycete family Phanerochaetaceae. Our results show that macromorphology of fruiting bodies and hymenophore construction do not reflect monophyletic groups. However, by integrating micromor-phology and re-defining genera, harmonization of DNA phylogeny and morphological genus concepts is possible in most cases. In the case of one genus (Phlebiopsis), our genetic markers could not resolve genus limits satisfactorily and a clear morphological definition could not be identified. We combine extended species sampling, microscopic studies of fruiting bodies and phylogenetic analyses of ITS, nLSU and rpb1 to revise genus concepts. Three …

Characterization Of The Cytokinin-Responsive Transcriptome In Rice, Tracy Raines, Ivory C. Blakley, Yu-Chang Tsai, Jennifer M. Worthen, José M. Franco-Zorrilla, Roberto Solano, G. Eric Schaller

Dartmouth Scholarship

Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice.

Allelic Variation In Cxcl16 Determines Cd3+ T Lymphocyte Susceptibility To Equine Arteritis Virus Infection And Establishment Of Long-Term Carrier State In The Stallion, Sanjay Sarkar, Ernest Bailey, Yun Young Go, R. Frank Cook, Ted Kalbfleisch, John E. Eberth, R. Lakshman Chelvarajan, Kathleen M. Shuck, Sergey Artiushin, Peter J. Timoney, Udeni B. R. Balasuriya

Maxwell H. Gluck Equine Research Center Faculty Publications

Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of horses and other equid species. Following natural infection, 10–70% of the infected stallions can become persistently infected and continue to shed EAV in their semen for periods ranging from several months to life. Recently, we reported that some stallions possess a subpopulation(s) of CD3⁺ T lymphocytes that are susceptible to in vitro EAV infection and that this phenotypic trait is associated with long-term carrier status following exposure to the virus. In contrast, stallions not possessing the CD3⁺ T …

Forest Restoration Using Variable Density Thinning: Lessons From Douglas-Fir Stands In Western Oregon, Klaus J. Puettmann, Adrian Ares, Julia I. Burton, Erich Kyle Dodson

Wildland Resources Faculty Publications

A large research effort was initiated in the 1990s in western United States and Canada to investigate how the development of old-growth structures can be accelerated in young even-aged stands that regenerated following clearcut harvests, while also providing income and ecosystem services. Large-scale experiments were established to compare effects of thinning arrangements (e.g., spatial variability) and residual densities (including leave islands and gaps of various sizes). Treatment effects were context dependent, varying with initial conditions and spatial and temporal scales of measurement. The general trends were highly predictable, but most responses were spatially variable. Thus, accounting for initial conditions at …

Comparative Phylogeography In The Atlantic Forest And Brazilian Savannas: Pleistocene Fluctuations And Dispersal Shape Spatial Patterns In Two Bumblebees, Elaine Françoso, Alexander Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias

Publications and Research

Background: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.

Results: Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that …

Vectored Intracerebral Immunization With The Anti-Tau Monoclonal Antibody Phf1 Markedly Reduces Tau Pathology In Mutant Tau Transgenic Mice, Wencheng Liu, Lingzhi Zhao, Brittany Blackman, Mayur Parmar, Man Ying Wong, Thomas Woo, Fangmin Yu, Maria J. Chiuchiolo, Dolan Sondhi, Stephen M. Kaminsky, Ronald G. Crystal, Steven M. Paul

HPD Articles

UNLABELLED: Passive immunization with anti-tau monoclonal antibodies has been shown by several laboratories to reduce age-dependent tau pathology and neurodegeneration in mutant tau transgenic mice. These studies have used repeated high weekly doses of various tau antibodies administered systemically for several months and have reported reduced tau pathology of ∼40-50% in various brain regions. Here we show that direct intrahippocampal administration of the adeno-associated virus (AAV)-vectored anti-phospho-tau antibody PHF1 to P301S tau transgenic mice results in high and durable antibody expression, primarily in neurons. Hippocampal antibody levels achieved after AAV delivery were ∼50-fold more than those reported following repeated systemic …

Coral Recovery On Phase-Shifted Reefs Depend Upon The Type Of Macroalgae Present, Justin N. Voss

HCNSO Student Theses and Dissertations

The Florida Keys experienced some of the most drastic transitions from coral to macroalgae dominated states, known as phase-or regime-shifts, of any reefs in the Caribbean. Macroalgae on coral reefs lower coral recruitment by deterring coral settlement either directly through competition or indirectly by changing the chemical environment near the benthos. With evidence of species-specific interactions to coral-macroalgae competition, the type of macroalgae on a phase-shifted coral reef might be more important than just identifying a reef transition. To answer this question, I tested the effect of Laurencia intricata (a macroalgae related to the settlement inducing crustose coralline algae) and …

Recurring Patterns Among Scrambled Genes In The Encrypted Genome Of The Ciliate Oxytricha Trifallax, Jonathan Burns, Denys Kukushkin, Xiao Chen, Laura F Landweber, Masahico Saito, Nataša Jonoska

Mathematics and Statistics Faculty Publications

Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized "nano-chromosomes". During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90-98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt …

The Role Of Diverse Strategies In The Sustainability Of Online Communities, Lingfei Wu, Jacopo A. Baggio, Marco A. Janssen

Environment and Society Faculty Publications

Online communities are becoming increasingly important as platforms for large-scale human cooperation. These communities allow users seeking and sharing professional skills to solve problems collaboratively. To investigate how users cooperate to complete a large number of knowledge-producing tasks, we analyze Stack Exchange, one of the largest question and answer systems in the world. We construct attention networks to model the growth of 110 communities in the Stack Exchange system and quantify individual answering strategies using the linking dynamics on attention networks. We identify two answering strategies. Strategy A aims at performing maintenance by doing simple tasks, whereas strategy B aims …

Reber’S Caterpillar Offers No Help, Carl Safina

Animal Sentience

Reber’s target article “Caterpillars, consciousness and the origins of mind” seems only to shift but not to address the question of where the mind is and how minds occur.

Sneaky Salt Contributes To High Blood Pressure, Rodney Richmond

Faculty Research ​and Publications

No abstract provided.

A Novel Rrm3 Function In Restricting Dna Replication Via An Orc5-Binding Domain Is Genetically Separable From Rrm3 Function As An Atpase/Helicase In Facilitating Fork Progression, Salahuddin Syed, Claus Desler, Lene J Rasmussen, Kristina H Schmidt

Molecular Biosciences Faculty Publications

In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186-212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea. This novel Rrm3 function is independent of its established role …

Effects Of 17 Β-Estradiol And Progesterone On Acropora Cervicornis And Porites Astreoides Growth And Reproduction, Joshua L. Stocker

HCNSO Student Theses and Dissertations

Reef-building coral populations throughout the world are being threatened by numerous stressors and continue to decline. As potent endocrine-disrupting compounds, exogenous sex steroid contamination has been a largely overlooked stressor to corals. Previous research indicates these compounds are prevalent in marine environments, fluctuate annually along with reproductive cycles, can bioaccumulate, and have had variable effects on growth and reproduction in several cnidarian species. This project had three primary objectives: (1) establish environmental estradiol and progesterone concentrations in Broward County and lower Florida Keys reef environments, (2) conduct 17 β-estradiol and progesterone larval assays on P. astreoides larvae to determine the …

Invasive Species Impacts On Infrastructure, Invasive Species Advisory Committee

National Invasive Species Council

Executive Summary

Invasive species represent one of the most significant threats to ecosystems, human and animal health, infrastructure, the economy, and cultural resources. Because potentially invasive, non-native species typically enter the United States through ports of entry in urban environments, some of the first observable impacts may be to infrastructure, yet little is known about the economic costs associated with these impacts to the “built” environment. In addition, federal agencies currently lack the authority necessary to effectively prevent, eradicate, and control invasive species that impact the human-built environment. This lack of authority prevents rapid response to some of the most …

Control Of Gene Expression By Rna Binding Protein Action On Alternative Translation Initiation Sites, Angela Re, Levi Waldron, Alessandro Quattrone

Publications and Research

Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5' untranslated regions was strongly associated with improvement …

Calcium-Mediated Actin Reset (Caar) Mediates Acute Cell Adaptations, Pauline Wales, Christian Schuberth, Roland Aufschnaiter, Johannes Fels, Ireth Garcia-Aguilar, Annette Janning, Christopher D. Dlugos, Marco Schaefer-Herte, Christoph Klingner, Mike Waelte, Julian Kuhlmann, Ekaterina Menis, Hockaday Kang Hockaday Kang, Kerstin C. Maier, Wenya Hou, Antonella Russo, Henry N. Higgs

Dartmouth Scholarship

Actin has well established functions in cellular morphogenesis. However, it is not well understood how the various actin assemblies in a cell are kept in a dynamic equilibrium, in particular when cells have to respond to acute signals. Here, we characterize a rapid and transient actin reset in response to increased intracellular calcium levels. Within seconds of calcium influx, the formin INF2 stimulates filament polymerization at the endoplasmic reticulum (ER), while cortical actin is disassembled. The reaction is then reversed within a few minutes. This Calcium-mediated actin reset (CaAR) occurs in a wide range of mammalian cell types and in …

Striatal Dopaminergic Innervation Regulates Subthalamic Beta-Oscillations And Cortical-Subcortical Coupling During Movements: Preliminary Evidence In Subjects With Parkinson’S Disease, Andrea Canessa, Nicolo G. Pozzi, Gabriele Arnulfo, Joachim Brumberg, Martin M. Reich, Gianni Pezzoli, Maria F. Ghilardi, Cordula Matthies, Frank Steigerwald, Jens Volkman, Ioannis U. Isais

Publications and Research

Activation of the basal ganglia has been shown during the preparation and execution of movement. However, the functional interaction of cortical and subcortical brain areas during movement and the relative contribution of dopaminergic striatal innervation remains unclear. We recorded local field potential (LFP) activity from the subthalamic nucleus (STN) and high-density electroencephalography (EEG) signals in four patients with Parkinson’s disease (PD) off dopaminergic medication during a multi-joint motor task performed with their dominant and non-dominant hand. Recordings were performed by means of a fully-implantable deep brain stimulation (DBS) device at 4 months after surgery. Three patients also performed a single-photon …

The Impact Of Organic Farms: Biodiversity And Climate Change Resilience In The Southeast, Josie Newton

Earth and Environmental Sciences Presentations

Resilience to climate change serves as an indicator of the effectiveness of organic farming practices. Resilience means that an area is able to return to a stable state after a disturbance. In this context, it means that the area is able to function regularly even in the face of climate change, an instance that affects species health and biodiversity. By mapping the locations of organic farms across the southeastern United States along with the resilience scores of areas as evaluated by The Nature Conservancy and comparing this map to farm locations and biodiversity measures, we are able to determine the …

Mapping The Impact Of Intensive Rotational Grazing On Soil Fertility Over Time On Greenbrier Farms In Pickens County, South Carolina, Emily Kirby

Earth and Environmental Sciences Presentations

Intensive rotational grazing (IRG) is a management technique that involves a more intentional management approach which includes increased paddock numbers, shorter grazing periods, larger livestock presence per acre, and longer periods of rest on pastures. Potential advantages of this management technique include improved forage quality, greater yield, decreased erosion, stable production during adverse growing condition, and improved soil fertility. This study collects and analyzes data to understand the impact of rotational grazing on soil fertility as measured by SOC (soil organic carbon) and SON (soil organic nitrogen) on Greenbrier Farms in Easley, South Carolina. This study analyzes the transition from …

Habitat Quality Modeling For Bird Species At Furman University, Emma Cook

Earth and Environmental Sciences Presentations

In rapidly urbanizing areas, such as Greenville County in Upstate South Carolina, it is important to study habitat use and quality across land cover types in order to maximize conservation. Habitat fragmentation is a threat to many species of birds in areas with increasing development, especially those species that utilize larger forest patches for nesting and foraging. While land cover type and patch size are extremely important factors in determining habitat quality for birds, recent research has shown that the matrix of surrounding landscape proves to be very important as well. The landscape matrix, sometimes called landscape mosaic, considers the …

Spatial Distribution Of High Obesity Rates In South Carolina, Tom Bennett

Earth and Environmental Sciences Presentations

In 2015, the rate of adult obesity in South Carolina was nearly 32%, which places South Carolina as the 13th worst state when it comes to the prevalence of adult obesity. Along with overall rates of adult obesity, South Carolina has the 8th highest high school student obesity rate with 16.3% of high school students being obese. These statistics are troubling because obesity is a primary cause of Type II Diabetes, high blood pressure, and many other negative health effects. These health care issues then affect supply and demand for health care, advertising, physical exercise, and many other market segments, …

Inflammatory Gene Expression In Women Diagnosed With Polycystic Ovarian Syndrome, Myles K. Taylor

Electronic Theses & Dissertations

Polycystic ovarian syndrome (PCOS) is a common endocrine disorder in women of reproductive age. The pathophysiology of PCOS has conventionally thought to originate from androgen excess. However, recent evidence suggests that androgen excess is a downstream consequence to inflammatory dysregulation and subsequent metabolic abnormalities. Inflammatory mRNA gene expression of TNFa and IL-1ß in mononuclear cells isolated from women diagnosed with PCOS was explored using qPCR. Additionally, the correlations between body mass index (BMI) and fasting glucose on mRNA expression of TNFa and IL-1ß were explored. mRNA expression of both TNFa and IL-1ß were found to be significantly higher in PCOS …

Hnrnpa2 Is A Novel Histone Acetyltransferase That Mediates Mitochondrial Stress-Induced Nuclear Gene Expression, Manti Guha, Satish Srinivasan, Kip Guja, Edison Mejia, Miguel Garcia-Diaz, F. Brad Johnson, Gordon Ruthel, Brett A. Kaufman, Eric F. Rappaport, M. Rebecca Glineburg, Ji-Kang Fang, Andres J. Klein-Szanto, Hiroshi Nakagawa, Jeelan Basha, Tapas Kundu, Narayan G. Avadhani

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Reduced mitochondrial DNA copy number, mitochondrial DNA mutations or disruption of electron transfer chain complexes induce mitochondria-to-nucleus retrograde signaling, which induces global change in nuclear gene expression ultimately contributing to various human pathologies including cancer. Recent studies suggest that these mitochondrial changes cause transcriptional reprogramming of nuclear genes although the mechanism of this cross talk remains unclear. Here, we provide evidence that mitochondria-to-nucleus retrograde signaling regulates chromatin acetylation and alters nuclear gene expression through the heterogeneous ribonucleoprotein A2 (hnRNAP2). These processes are reversed when mitochondrial DNA content is restored to near normal cell levels. We show that the mitochondrial stress-induced …

Effect Of Diet On Mortality And Larval Duration In Chrysodeixis Includens (Lepidoptera: Noctuidae), Andrea Przygoda, Erin E. Barding, Margaret Smith

Georgia Journal of Science

Diet mediates many life history trade-offs and therefore is an important environmental component to consider. Because some organisms share food sources with humans, they encounter anthropogenic changes to their diet, such as genetically modified crops and chemical applications, which can contribute to additional complexity in their environment. To understand the effect of diet on the life history of the soybean looper, Chrysodeixis includens, we exposed larvae to several different food sources, including genetically modified soybean leaves and the pesticide spinosad. Significant differences in larval instar duration and timing of larval mortality among treatments were observed indicating that type of diet …

The Vertical And Horizontal Distribution Of Deep-Sea Crustaceans Of The Order Euphausiacea (Malacostraca: Eucarida) From The Northern Gulf Of Mexico With Notes On Reproductive Seasonality., Charles Douglas Fine

HCNSO Student Theses and Dissertations

The vertical and horizontal distributions of Euphausiacea in the northern Gulf of Mexico, including the location of the Deepwater Horizon oil spill, were analyzed from 340 trawl samples collected between April-June, 2011. This study is the first comprehensive survey of euphausiid distributions from depths deeper than 1000 m in the Gulf of Mexico and included stratified sampling from five discrete depth ranges (0-200 m, 200-600 m, 600-1000 m, 1000-1200 m, and 1200-1500 m). In addition, this study encompasses the region heavily impacted by the Deepwater Horizon oil spill. Data presented here could potentially be used in ecosystem models investigating trophic …