Biology Commons^™

Component Trees For The Exploration Of Macromolecular Structures In Biology, Lucas Oliveira

Dissertations, Theses, and Capstone Projects

Understanding the three-dimensional structure of a macromolecular complex is essential for understanding its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. This dissertation presents a novel interactive framework for visual exploration of component trees of the density maps of macromolecular complexes, with the purpose of improved understanding of their structure. The interactive exploration of component trees together with a robust simplification methodology provide new insights in the study of macromolecular structures. An underlying mathematical theory is introduced and …

20141001.2: Religious Studies And Biological Sciences Departments, 1957-1975, College Of Liberal Arts, College Of Science

Guides to University Archives

These items include materials from the Religious Studies Department and the Biological Sciences Department at Marshall University from 1957-1975. Items were received in 2014 and include information about the "Bible & Religion" major that was changed to Religious Studies, and misc information about the biological sciences department.

Warming, Competition, And Bromus Tectorum Population Growth Across An Elevation Gradient, Aldo Compagnoni, Peter B. Adler

Green Canyon Environmental Research Area, Logan Utah

Cheatgrass (Bromus tectorum) is one of the most problematic invasive plant species in North America and climate change threatens to exacerbate its impacts. We conducted a two‐year field experiment to test the effect of warming, competition, and seed source on cheatgrass performance across an elevation gradient in northern Utah. We hypothesized that warming would increase cheatgrass performance, but that warming effects would be limited by competing vegetation and by local adaptation of cheatgrass seed sources. The warming treatment relied on open top chambers, we removed vegetation to assess the effect of competition from neighboring vegetation, and we reciprocally …

Selenite Activates The Alternative Oxidase Pathway And Alters Primary Metabolism In Brassica Napus Roots: Evidence Of A Mitochondrial Stress Response, Aleksandar Dimkovikj, Doug Van Hoewyk

Biology

Background: Human requirements for dietary selenium are met mainly by crops. However, excessive uptake of selenium in plants can restrict growth, and its toxicity has been postulated to target roots. Selenite toxicity can be attributed to its assimilation into selenocysteine, which can replace cysteine to yield malformed selenoproteins. Additionally, selenite has pro-oxidant properties. In this study, the effects of selenite on root tissue in Brassica napus (canola) were investigated to better understand its mode of toxicity and the metabolic adjustments needed to mediate a selenite-response.Results: Selenite induced the rapid formation of mitochondrial superoxide, which led to decreased aconitase activity and …

Natural Selection On Thermal Performance In A Novel Thermal Environment, Michael L. Logan, Robert M. Cox, Ryan Calsbeek

Dartmouth Scholarship

Tropical ectotherms are thought to be especially vulnerable to climate change because they are adapted to relatively stable temperature regimes, such that even small increases in environmental temperature may lead to large decreases in physiological performance. One way in which tropical organisms may mitigate the detrimental effects of warming is through evolutionary change in thermal physiology. The speed and magnitude of this response depend, in part, on the strength of climate-driven selection. However, many ectotherms use behavioral adjustments to maintain preferred body temperatures in the face of environmental variation. These behaviors may shelter individuals from natural selection, preventing evolutionary adaptation …

High Local Diversity Of Trypanosoma In A Common Bat Species, And Implications For The Biogeography And Taxonomy Of The T. Cruzi Clade, Veronika M. Cottontail, Elisabeth K. V. Kalko, Iain Cottontail, Nele Wellinghausen, Marco Tschapka, Susan L. Perkins, C. Miguel Pinto

Publications and Research

The Trypanosoma cruzi clade is a group of parasites that comprises T. cruzi sensu lato and its closest relatives. Although several species have been confirmed phylogenetically to belong to this clade, it is uncertain how many more species can be expected to belong into this group. Here, we present the results of a survey of trypanosome parasites of the bat Artibeus jamaicensis from the Panama´ Canal Zone, an important seed disperser. Using a genealogical species delimitation approach, the Poisson tree processes (PTP), we tentatively identified five species of trypanosomes – all belonging to the T. cruzi clade. A small monophyletic …

Identifying Candidate Genes For Variation In Sleep-Related Quantitative Traits, Shreyas Joshi, Bruce F. O'Hara

Biology Presentations

Background

Humans spend approximately one third of their lives sleeping, but compared with other biological processes, most of the molecular and genetic aspects of sleep have not been elucidated. A non-existent gene ontology and lack of a dedicated database containing a comprehensive list of sleep-related genes and their function presents a hurdle for sleep researchers.

Materials and methods

Using a two-pronged approach to solve this problem, publicly available microarray data from NCBI GEO (National Center for Biotechnology Information – Gene Expression Omnibus) database was used to develop a list of sleep-related genes for traits of interest. The data were analyzed …

Water‐Use Advantage For Lianas Over Trees In Tropical Seasonal Forests, Ya-Jun Chen, Kun-Fang Cao, Stefan A. Schnitzer, Za-Xin Fan, Jiao-Lin Zhang, Frans Bongers

Biological Sciences Faculty Research and Publications

• Lianas exhibit peak abundance in tropical forests with strong seasonal droughts, the eco‐physiological mechanisms associated with lianas coping with water deficits are poorly understood.
• We examined soil water partitioning, sap flow, and canopy eco‐physiological properties for 99 individuals of 15 liana and 34 co‐occurring tree species in three tropical forests that differed in soil water availability.
• In the dry season, lianas used a higher proportion of deep soil water in the karst forest (KF ; an area with severe seasonal soil water deficit (SSWD )) and in the tropical seasonal forest (TSF , moderate SSWD ), permitting them to maintain …

Hiv-1 Transgenic Rats Display Alterations In Immunophenotype And Cellular Responses Associated With Aging, Susan J. Abbondanzo

Seton Hall University Dissertations and Theses (ETDs)

Advances in anti-retroviral therapy over the last two decades have allowed life expectancy in patients infected with the human immunodeficiency virus to approach that of the general population. The process of aging in mammalian species, including rats, results in changes with immune response, immunological phenotypes, and ultimately, increased susceptibility to many infectious diseases. In order to investigate the immunological pathologies associated with chronic HIV-1 disease, particularly in aged individuals, the HIV-1 transgenic (HIV-1Tg) rat model was utilized. Age matched animals were challenged using lipopolysaccharide (LPS) to determine immunological modification of HIV-1Tg animals throughout the aging process. LPS is known to …

A Distinct Tethering Step Is Vital For Vacuole Membrane Fusion, Michael Zick, William T. Wickner

Dartmouth Scholarship

Past experiments with reconstituted proteoliposomes, employing assays that infer membrane fusion from fluorescent lipid dequenching, have suggested that vacuolar SNAREs alone suffice to catalyze membrane fusion in vitro. While we could replicate these results, we detected very little fusion with the more rigorous assay of lumenal compartment mixing. Exploring the discrepancies between lipid-dequenching and content-mixing assays, we surprisingly found that the disposition of the fluorescent lipids with respect to SNAREs had a striking effect. Without other proteins, the association of SNAREs in trans causes lipid dequenching that cannot be ascribed to fusion or hemifusion. Tethering of the SNARE-bearing proteoliposomes was …

An In Vitro Adult Mouse Muscle-Nerve Preparation For Studying The Firing Properties Of Muscle Afferents, Joy Franco, Heidi Kloefkorn, Shawn Hochman, Katherine Wilkinson

Faculty Publications, Biological Sciences

Muscle sensory neurons innervating muscle spindles and Golgi tendon organs encode length and force changes essential to proprioception. Additional afferent fibers monitor other characteristics of the muscle environment, including metabolite buildup, temperature, and nociceptive stimuli. Overall, abnormal activation of sensory neurons can lead to movement disorders or chronic pain syndromes. We describe the isolation of the extensor digitorum longus (EDL) muscle and nerve for in vitro study of stretch-evoked afferent responses in the adult mouse. Sensory activity is recorded from the nerve with a suction electrode and individual afferents can be analyzed using spike sorting software. In vitro preparations allow …

Zooplankton Density Increases In An Irrigation Reservoir During Drought Conditions, Brett P. Olds, Brian C. Peterson, Keith D. Koupal, Casey W. Schoenebeck, Kerri M. Farnsworth-Hoback, W. Wyatt Hoback

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Harlan County Reservoir, located in south-central Nebraska, entered a drought in 2003, providing an opportunity to monitor the effects of drought on the zooplankton community in this irrigation reservoir. We sampled the zooplankton community at 15 standardized locations every other week from April through the third week of October from 2003-2011. Total zooplankton densities were higher (131.8 ±13.1 L^-1) in drought reservoir conditions (2003-2006) than under normal conditions (66.6 ±9.0 L^-1) (2007-2011). The zooplankton community was dominated by copepods throughout the study, with adult and immature (nauplii) copepods contributing 86.5% of the total zooplankton, while Daphnia …

De Novo Assembly Of The Common Marmoset Transcriptome From Nextgen Mrna Sequences, Mnirnal D. Maudhoo, Dongren Ren, Julien S. Gradnigo, Robert M. Gibbs, Austin C. Lubker, Etsuko N. Moriyama, Jeffrey A. French, Robert B. Norgen Jr.

School of Biological Sciences: Faculty Publications

Background: Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released …

Trait-Based Diversification Shifts Reflect Differential Extinction Among Fossil Taxa, Peter J. Wagner, George F. Estabrook

School of Biological Sciences: Faculty Publications

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Traitbased diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among …

Inter-Calibration Of Satellite Passive Microwave Land Observations From Amsr-E And Amsr2 Using Overlapping Fy3b-Mwri Sensor Measurements, Jinyang Du, John S. Kimball, Jiancheng Shi, Lucas Alan Jones, Shengli Wu, Ruijing Sun, Hu Yang

Biological Sciences Faculty Publications

The development and continuity of consistent long-term data records from similar overlapping satellite observations is critical for global monitoring and environmental change assessments. We developed an empirical approach for inter-calibration of satellite microwave brightness temperature (T_b) records over land from the Advanced Microwave Scanning Radiometer for EOS (AMSR-E) and Microwave Scanning Radiometer 2 (AMSR2) using overlapping Tb observations from the Microwave Radiation Imager (MWRI). Double Differencing (DD) calculations revealed significant AMSR2 and MWRI biases relative to AMSR-E. Pixel-wise linear relationships were established from overlapping T_b records and used for calibrating MWRI and AMSR2 records to the AMSR-E …

Retrievals Of All-Weather Daily Air Temperature Using Modis And Amsr-E Data, Keunchang Jang, Sinkyu Kang, John S. Kimball, Suk Young Hong

Biological Sciences Faculty Publications

Satellite optical-infrared remote sensing from the Moderate Resolution Imaging Spectroradiometer (MODIS) provides effective air temperature (T_a) retrieval at a spatial resolution of 5 km. However, frequent cloud cover can result in substantial signal loss and remote sensing retrieval error in MODIS T_a. We presented a simple pixel-wise empirical regression method combining synergistic information from MODIS Ta and 37 GHz frequency brightness temperature (T_b) retrievals from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) for estimating surface level T_a under both clear and cloudy sky conditions in the United …

Park Rangers' Behaviors And Their Effects On Tourists And Tibetan Macaques (Macaca Thibetana) At Mt. Huangshan, China, Rie Usui, Lori K. Sheeran, Jin-Hua Li, Lixing Sun, Xi Wang, Alexander J. Pritchard, Alexander S. Duvall-Lash, R. Steven Wagner

Biology Faculty Scholarship

Previous studies have reported the negative impacts of tourism on nonhuman primates (NHPs) and tourists and advocated the improvement of tourism management, yet what constitutes good quality management remains unclear. We explored whether rates of macaque aggression and self-directed behaviors (SDBs) differed under the supervision of two park ranger teams at the Valley of the Wild Monkeys (VWM) in Mt. Huangshan, Anhui Province, China. The two ranger teams provisioned and managed a group of macaques on an alternating monthly basis. Monkey, tourist and ranger behaviors were collected from August 16–September 30, 2012. Macaque aggression and SDB rates did not differ …

2014 Scas Annual Meeting Program

Journal of the South Carolina Academy of Science

No abstract provided.

Genotypic And Phenotypic Characterization Of Aerosolized Bacteria Collected From African Dust Events, Christina A. Wilson, Robin L. Brigmon, Chris Yeager, Garriet W. Smith, Shawn W. Polson

Journal of the South Carolina Academy of Science

Twenty-one bacteria were isolated and characterized from air samples collected in Africa and the Caribbean by the United States Geological Survey (USGS). Isolates were selected based on preliminary characterization as possible pathogens. Identification of the bacterial isolates was achieved using 16S rRNA gene sequence analysis, fatty acid methyl esters (FAMEs) profiling, the BIOLOG Microlog^® System (carbon substrate assay), and repetitive extragenic palindromic (REP)-PCR analysis. The majority of isolates (18/21) were identified as species of the genus Bacillus. Three isolates were classified within the Bacillus cereus senso lato group, which includes Bacillus anthracis, Bacillus thuringiensis, and Bacillus …

Remembering To Perform Actions In The Future: Can Intentions Pop Into Mind?, Gilles O. Einstein

Journal of the South Carolina Academy of Science

No abstract provided.

Role Of Vitamin A In Retinal Diseases, Rosalie K. Crouch, Masahiro Kono, Peter H. Tang

Journal of the South Carolina Academy of Science

Vitamin A has an essential role in vision in that it forms the photosensitive pigments that absorb light and initiate the visual process. However, vitamin A and its analogues also have critical roles in maintaining the structural integrity of the retina. Disruption of the metabolism of vitamin A results in several blinding diseases. This review focuses on our recent studies on the role of a protein critical to the processing of vitamin A, RPE65. The absence or dysfunction of this protein causes the childhood blinding disease Leber congenital amaurosis.

Scas Officers And Council Members 2014-2015

Journal of the South Carolina Academy of Science

No abstract provided.

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Evidence For Transfer Of Membranes From Mesenchymal Stem Cells To Hl-1 Cardiac Cells, Robert Boomsma, David Geenen

Open Access Publishing Support Funded Articles

This study examined the interaction of mouse bone marrow mesenchymal stem cells (MSC) with cardiac HL-1 cells during coculture by fluorescent dye labeling and then flow cytometry. MSC were layered onto confluent HL-1 cell cultures in a 1 : 4 ratio. MSC gained gap junction permeant calcein from HL-1 cells after 4 hours which was partially reduced by oleamide. After 20 hours, 99% MSC gained calcein, unaffected by oleamide. Double-labeling HL-1 cells with calcein and the membrane dye DiO resulted in transfer of both calcein and DiO to MSC. When HL-1 cells were labeled with calcein and MSC with DiO, …

High Mrsa Carriage Rate Among Nursing Microbiology Students, Alan Lee Gillen, Whitney O. Daycock, Andrew Serafin

Faculty Publications and Presentations

Staphylococcus aureus is a common cause of disease, particularly in colonized persons. Although methicillin-resistant S. aureus (MRSA) infections have become increasingly reported, populationbased studies of students preparing for the health professions having S. aureus and MRSA colonization are lacking. We have found that students in microbiology classes having more contact with individuals in a healthcare setting are more likely to carry MRSA in their nares and axilla. The classes who had the highest rate of MRSA carriage during the school year, 2013-2014, were those with nursing students, who had a greater exposure to clinical settings and nursing homes. The class …

Acceptance Of Evolution By America’S Educators Of Prospective Teachers, Guillermo Paz-Y-Miño-C, Avelina Espinosa

New England Science Public: Series Evolution

Paz-y-Miño-C G & Espinosa A. 2014. Acceptance of Evolution by America’s Educators of Prospective Teachers. New England Science Public: Series Evolution 2(1): 1-92 (ISSN: 2326-0971). In NESP Series Evolution Vol 2 No 1, Paz-y-Miño-C and Espinosa use the conceptual framework of the Incompatibility Hypothesis (i.e. science/evolution and belief in supernatural causation are incompatible) to document the patterns of acceptance of evolution of 495 Educators of Prospective Teachers affiliated with 281 colleges and universities widely distributed in 4 regions, 9 divisions, and 50 states in the United States. These higher-education professionals (65% PhD-, 22% doctorate-holders) were polled in five areas: (i) …

Induced Phytoextraction Of Lead From Contaminated Urban Soil Through Manipulation Of Rhizosphere And Plant Biogeochemical Functions In Switchgrass (Panicum Virgatum), Deayne M. Johnson

Master of Science in Integrative Biology Theses

Contamination of soils with lead (Pb) continues to pose a risk to the health of humans especially in residential urban areas. Remediation of these soils is necessary to reduce the amount of Pb and alleviate risk to human health. Phytoextraction of Pb through chemically induced accumulation of Pb in the harvestable foliage and removal of contaminated plant material has great potential in offering a solution to this environmental problem. The effects of the combined application of a soil fungicide (benomyl), synthetic chelates (ethylenediamineteteraacetic acid, EDTA), and foliar-Fe supplement on lead (Pb) phytoextraction from contaminated soil by switchgrass (Panicum virgatum) was …

Antiviral Responses In Mouse Embryonic Stem Cells: Differential Development Of Cellular Mechanisms In Type I Interferon Production And Response, Ruoxing Wang, Jundi Wang, Dhiraj Acharya, Amber M. Paul, Fengwei Bai, Faqing Huang, Yan-Lin Guo

Faculty Publications

We have recently reported that mouse embryonic stem cells (mESCs) are deficient in expressing type I interferons (IFNs) in response to viral infection and synthetic viral RNA analogs (Wang, R., Wang, J., Paul, A. M., Acharya, D., Bai, F., Huang, F., and Guo, Y. L. (2013) J. Biol. Chem. 288, 15926–15936). Here, we report that mESCs are able to respond to type I IFNs, express IFN-stimulated genes, and mediate the antiviral effect of type I IFNs against La Crosse virus and chikungunya virus. The major signaling components in the IFN pathway are expressed in mESCs. Therefore, the basic molecular mechanisms …

Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator

Department of Biological Sciences Publications

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants …

Genetic Evidence For Multiple Sources Of The Non-Native Fish Cichlasoma Urophtalmus (Günther; Mayan Cichlids) In Southern Florida, Elizabeth Harrison, Joel C. Trexler, Timothy M. Collins, Ella Vazquez-Domínguez, Ulises Razo-Mendivil, Wilfredo A. Matamoros, Christian Barrientos

Student Publications

The number and diversity of source populations may influence the genetic diversity of newly introduced populations and affect the likelihood of their establishment and spread. We used the cytochrome b mitochondrial gene and nuclear microsatellite loci to identify the sources of a successful invader in southern Florida, USA, Cichlasoma urophthalmus (Mayan cichlid). Our cytochrome b data supported an introduction from Guatemala, while our microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. The mismatch between mitochondrial and nuclear genomes suggests admixture of a female lineage from Guatemala, …