Biology Commons^™

High-Quality Permanent Draft Genome Sequence Of Bradyrhizobium Sp Th.B2, A Microsymbiont Of Amphicarpaea Bracteata Collected In Johnson City, New York, Rui Tian, Matthew Parker, Rekha Seshadri, T. B.K. Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Mohammed Baeshen, Nabih Baeshen, Nikos Kyrpides, Wayne Reeve

Biological Sciences Faculty Scholarship

Bradyrhizobium sp. Th.b2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Amphicarpaea bracteata collected in Johnson City, New York. Here we describe the features of Bradyrhizobium sp. Th.b2, together with high-quality permanent draft genome sequence information and annotation. The 10,118,060 high-quality draft genome is arranged in 266 scaffolds of 274 contigs, contains 9,809 protein-coding genes and 108 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

High-Quality Permanent Draft Genome Sequence Of Bradyrhizobium Sp Tv2a.2, A Microsymbiont Of Tachigali Versicolor Discovered In Barro Colorado Island Of Panama, Rui Tian, Matthew Parker, Rekha Seshadri, T. B.K. Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Mohammed Baeshen, Nabih Baeshen, Nikos Kyrpides, Wayne Reeve

Biological Sciences Faculty Scholarship

Bradyrhizobiumsp. Tv2a.2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Tachigali versicolor collected in Barro Colorado Island of Panama. Here we describe the features of Bradyrhizobiumsp. Tv2a.2, together with high-quality permanent draft genome sequence information and annotation. The 8,496,279 bp high-quality draft genome is arranged in 87 scaffolds of 87 contigs, contains 8,109 protein-coding genes and 72 RNA-only encoding genes. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Acute Sleep Fragmentation Induces Tissue-Specific Changes In Cytokine Gene Expression And Increases Serum Corticosterone Concentration, Jennifer Dumaine

Masters Theses & Specialist Projects

Sleep fragmentation induces acute inflammation and increases glucocorticosteroids in vertebrates. Obesity and sleep fragmentation are often concurrent pro-inflammatory conditions in patients with obstructive sleep apnea. Despite the association between the two, their simultaneous effects on immune and endocrine profiles have not been explored. In the first experiment, we investigated changes in proinflammatory (IL-1β, TNF-α) and anti-inflammatory (TGF-β1) cytokine gene expression in the periphery (liver, spleen, fat, and heart) and brain (hypothalamus, prefrontal cortex, and hippocampus) in mice exposed to various intervals of sleep fragmentation. Serum corticosterone concentration was also assessed. Sleep was disrupted in male C57BL/6J mice using an automated …

Global Research On Ultramafic (Serpentine) Ecosystems (8th International Conference On Serpentine Ecology In Sabah, Malaysia): A Summary And Synthesis, Antony Van Der Ent, Nishanta Rajakaruna, Robert Boyd, Guillaume Echevarria, Rimi Repin, Dick Williams

Biological Sciences

Since 1991, researchers from approximately 45 nations have participated in eight International Conferences on Serpentine Ecology (ICSE). The Conferences are coordinated by the International Serpentine Ecology Society (ISES), a formal research society whose members study geological, pedological, biological and applied aspects of ultramafic (serpentine) ecosystems worldwide. These conferences have provided an international forum to discuss and synthesise multidisciplinary research, and have provided opportunities for scientists in distinct fields and from different regions of the world to conduct collaborative and interdisciplinary research. The 8th ICSE was hosted by Sabah Parks in Malaysia, on the island of Borneo, and attracted the largest …

Habituation To Auditory Stimuli By Captive African Elephants (Loxodonta Africana), Sarah Elizabeth Goodyear

Masters Theses & Specialist Projects

Elephants are cognitive species that exhibit many types of learning. Associative, social, and insight learning have been investigated with elephants, but one of the simplest forms, habituation, has not. As an individual learns that a stimulus is neither harmful nor beneficial, it will decrease its response to the stimulus through the process of habituation. Elephants possess a well-developed sensory system and may habituate to stimuli that could be used for enrichment and/or management. The aim of this study was to examine the habituation process of elephants in response to repeated presentations of two auditory stimuli –buzzing by a disturbed beehive …

Epiphytic Diatom Community Structure In A Karst Riverine System, Gregory John Barren

Masters Theses & Specialist Projects

The goal of this study was to assess the epiphytic diatom community structure of two host species along a karst gradient in the upper Green River, Kentucky to a gain a better understanding of the role of diatoms in the food web. The host species studied were Podostemum ceratophyllum and Cladophora. Percent cover of P. ceratophyllum and Cladophora were quantified in the four study reaches. The host species were sampled near-shore and mid-channel in each reach in September and October of 2013. After diatoms were extracted from the host and enumerated the density and diversity were quantified. Twelve genera were …

Role Of Aminoalcoholphosphotransferases 1 And 2 In Phospholipid Homeostasis In Arabidopsis, Xuemin Wang, Yu Liu, Geliang Wang

Biology Department Faculty Works

Aminoalcoholphosphotransferase (AAPT) catalyzes the synthesis of phosphatidylcholine (PC) and phosphotidylethanolamine (PE), which are the most prevalent membrane phospholipids in all eukaryotic cells. Here, we show that suppression of AAPTs results in extensive membrane phospholipid remodeling in Arabidopsis thaliana. Double knockout (KO) mutants that are hemizygous for either aapt1 or aapt2 display impaired pollen and seed development, leading to embryotic lethality of the double KO plants, whereas aapt1 or aapt2 single KO plants show no overt phenotypic alterations. The growth rate and seed yield of AAPT RNA interference (RNAi) plants are greatly reduced. Lipid profiling shows decreased total galactolipid and phospholipid …

Comprehensive Quantification Of Triacylglycerols In Soybean Seeds By Electrospray Ionization Mass Spectrometry With Multiple Neutral Loss Scans, Maoyin Li, Emily Butka, Xuemin Wang

Biology Department Faculty Works

Soybean seeds are an important source of vegetable oil and biomaterials. The content of individual triacylglycerol species (TAG) in soybean seeds is difficult to quantify in an accurate and rapid way. The present study establishes an approach to quantify TAG species in soybean seeds utilizing an electrospray ionization tandem mass spectrometry with multiple neutral loss scans. Ten neutral loss scans were performed to detect the fatty acyl chains of TAG, including palmitic (P, 16:0), linolenic (Ln, 18:3), linoleic (L, 18:2), oleic (O, 18:1), stearic (S, 18:0), eicosadienoic (20:2), gadoleic (20:1), arachidic (20:0), erucic (22:1), and behenic (22:0). The abundance of …

Phylogeography Of Darlingtonea Kentuckensis And Molecular Systematics Of Kentucky Cave Trechines, Olivia Frances Boyd

Masters Theses & Specialist Projects

The monotypic cave carabid genus Darlingtonea is widely distributed along the eastern band of the Mississippian/Pennyroyal plateau in Kentucky and northern Tennessee. DNA sequence data from the mitochondrial gene cytochrome oxidase subunit I (COI) was collected from one to four individuals from 27 populations, and patterns of phylogeography and population structure were inferred from COI haplotypes. A hierarchical analysis of molecular variance found low nucleotide diversity within populations and statistically significant variation among geographically-defined groups tested based on two a priori hypotheses of structure. Population structure among five distinct genetic clusters identifies approximate locations of barriers to gene flow among …

Hearing Sensitivity And The Effect Of Sound Exposure On The Axolotl (Ambystoma Mexicanum), Amy K. Fehrenbach

Masters Theses & Specialist Projects

The axolotl (Ambystoma mexicanum) has been used as a model organism for studying development, genetics, and regeneration. Although the sensory hair cells of the lateral line of this species have been shown to be able to regenerate, it is not known whether this also occurs in the inner ear. In fact, little is known about the hearing capabilities of the axolotl or other salamander species. I recorded auditory evoked potentials (AEPs) of six axolotls at eleven frequencies (0.1, 0.25, 0.4, 0.6, 0.8, 1, 1.5, 2, 3, 4, and 6 kHz) in order to produce baseline audiograms of underwater pressure sensitivity. …

Heterologous Expression Of Arabidopsis Thaliana Purple Acid Phosphatase Gene (Atpap15) In Crops For Phytoremediation Of Sites Contaminated With Excess Phosphorus, Jane Jeruto Bartonjo

Masters Theses & Specialist Projects

AtPAP15 is one of the purple acid phosphatases expressed by Arabidopsis thaliana that has been extensively studied. Purified AtPAP15 has been shown to exhibit both phytase and phosphomonoesterase activities in acidic pH with maximal activity at pH 4.5. AtPAP15 is a phosphorus starvation inducible (PSI) gene that is expressed highly during phosphorus deficient conditions. In the current study, AtPAP15 was overexpressed in Nicotiana tabaccum under cauliflower mosaic virus (CaMV35S) constitutive promoter. After PCR confirmation of the gene, plants were transferred to the greenhouse and allowed to grow in pots. The pots contained Sta-Green potting mix (Lowe’s Inc., Mooresville, North Carolina,U.S.). …

Dna Methylation Differences In Monozygotic Twin Pairs Discordant For Schizophrenia Identifies Psychosis Related Genes And Networks, Christina A. Castellani, Benjamin I. Laufer, Melkaye G. Melka, Eric J. Diehl, Richard L. O'Reilly, Shiva M. Singh

Biology Publications

Background

Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental, random, and epigenetic factors. The involvement of DNA methylation in this disease appears logical, but remains to be established.

Methods

We have used blood DNA from two pairs of monozygotic twins discordant for schizophrenia and their parents in order to assess genome-wide methylation using a NimbleGen Methylation Promoter Microarray.

Results

The genome-wide results …

Urea Concentration And Hsp70 Expression In The Kidney Of Thirteen-Lined Ground Squirrels During Diuresis And Antidiuresis, Ryan M. O'Gara

Honors Theses, 1963-2015

During bouts of torpor hibernating animals have greatly reduced metabolic rates leading to profound decreases in body temperature and blood pressure. As a result of these conditions, kidney filtration and the ability to concentrate urine cease. Once a week, however, hibernators rewarm to euthermic body temperatures and regain kidney function. This is associated with rapid changes in extracellular osmotic gradients within the kidney, a remarkable feat but one that is potentially damaging to kidney cells. While hibernators deal with this stress by up-regulating expression of heat shock proteins (HSP’s) and protective organic osmolytes, little research has been done to see …

Development Of Quantitative Tools For The Characterization And Analysis Of The Blood Brain Barrier In Normal And Mps Iiib Mice, Sara M. Rigney

Dissertations, Masters Theses, Capstones, and Culminating Projects

The Blood Brain Barrier (BBB) functions to control homeostasis within the central nervous system (CNS) via strict control over the passage of molecules into and out of the brain. The goal of this barrier is to protect the CNS from harmful external factors while allowing entry of essential nutrients and removal of metabolic byproducts. This restrictive nature of the BBB is due to the protein network at the borders of adjoining cerebral endothelial cells known as the tight junctions (TJs) and the relationship of other supporting cells and proteins such as astrocytes, pericytes, microglia, and the basement membrane and extracellular …

Fisheries Management Paper No 274 - Finfish Resources Of The Peel-Harvey Estuary - Harvest Strategy 2015-2020 (Version 1.0), Department Of Fisheries, Western Australia

Fisheries Management Papers

WEST COAST ESTUARINE MANAGED FISHERY (AREA 2)

Harvest strategies for aquatic resources managed by the Western Australian Department of Fisheries (the Department) are formal documents prepared to support the decision-making processes required to ensure the management of these resources are consistent with the principles of Ecologically Sustainable Development (ESD). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA), Section 3, and the draft Aquatic Resources Management Bill 2013 (ARMB), Clause 9, which will replace the FRMA once enacted.

The publication of these strategies is intended to make the decision-making considerations and processes …

Antioxidant Capacity Of Wyoming Big Sagebrush (Artemisia Tridentata Ssp. Wyomingensis) Varies Spatially And Is Not Related To The Presence Of A Sagebrush Dietary Specialist, Xinzhu Pu, Lisa Lam, Kristina Gehlken, Amy C. Ulappa, Janet Rachlow, Jennifer Sorensen Forbey

Biology Faculty Publications and Presentations

Sagebrush (Artemisia spp.) in North America is an abundant native plant species that is ecologically and evolutionarily adapted to have a diverse array of biologically active chemicals. Several of these chemicals, specifically polyphenols, have antioxidant activity that may act as biomarkers of biotic or abiotic stress. This study investigated the spatial variation of antioxidant capacity, as well as the relationship between a mammalian herbivore and antioxidant capacity in Wyoming big sagebrush (Artemisia tridentata wyomingensis). We quantified and compared total polyphenols and antioxidant capacity of leaf extracts from sagebrush plants from different spatial scales and at different levels …

Multi-Level Adjustments In Singing Behavior By A Migratory Songbird In Response To Urbanization, Jacob Job

Dissertations

The spread of high-amplitude anthropogenic noise across natural landscapes is a serious issue for vocally communicating animals. Noise disrupts communication, which has implications for individual fitness and population persistence. In response, animals adjust their vocal signals with increasing noise. As the increase in noise has occurred on a relatively short time scale, evolutionary responses are likely not the primary cause of adjustments. Instead, short-term behavioral adjustments may drive population differences; however, such adjustments are currently not well understood. Moreover, noise is only one characteristic of urbanized landscapes and whether other characteristics, such as highly reverberant surfaces interact with noise to …

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species⁴. RNA-seq analysis showed that one gene, PPTG_16698 has the 5^th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of …

Investigating The Pathogenecity Of Chl1 Leu17phe Polymorphism In Schizophrenia, Brooke Nichole Hansen

Undergraduate Honors Capstone Projects

Schizophrenia is a devastating brain disorder that affects a surprising 1% of the world's population. Despite this prevalence, little is known about the molecular aspects of this disorder making it both difficult to diagnose and treat. Several studies have identified the CHL1 gene (Close Homolog of L1), sometimes referred to as CALL, as a risk gene for schizophrenia. CHL1, a neural cell adhesion molecule, has major roles in cell migration, and the development of dendritic and axonal projections. Therefore any deficiency in CHL1 may result in brain defects similar to those identified in schizophrenic populations. Moreover, in genetically engineered mice, …

Developing A Portable System For Measuring Human Motor Learning, Karen Elizabeth Tew

Undergraduate Honors Capstone Projects

Point-to-point reaching is a commonly used paradigm in the field of human motor control. By studying how people move their arms from one location in space to another, researchers have gained insight into how the central nervous system controls and learns skilled movement. Many experimental methods that are designed to study reaching are not portable. This makes it difficult for researchers to access certain clinical populations with limited mobility or motor dysfunction. We have addressed this issue by developing a point-to-point reaching system that can capture key movement variables (e.g. speed and accuracy) yet is portable and inexpensive. We have …

Sources Of Uncertainty In Stream Nutrient Sampling Below A Point Source, Alexandria Hayden Campbell

Undergraduate Honors Capstone Projects

The goal of this study was to determine what aspects of sampling and sample storage could lead to uncertainty when taking samples in a stream below a point source. Sources of uncertainty studied were the locations where the samples were taken to assess if nutrients were adequately mixed within a cross-section, different filtration techniques, dilution errors, analytical uncertainty, and freezing time. Bootstrapping analyses were used to determine whether mixing and dilution errors led to uncertainty, while one-way ANOVAs were used to evaluate filtration techniques and storage time. Sample spikes to determine percent recovery of nutrients and repeat sample analyses are …

The Effects Of Zno Nanoparticles On Egg, Larva, And Adult Rough-Skinned Newts (Taricha Granulosa), Austin Reid Spence

Undergraduate Honors Capstone Projects

The objective of this study was to examine the effects of zinc oxide (ZnO) nanoparticles on egg, larva, and adult rough-skinned newts, Taricha granulosa. To date, little research has been done to investigate the potentially detrimental effects of nanoparticles on amphibians, especially salamanders and newts (caudates). Chronic toxicity was tested on eggs and larvae, and acute toxicity was tested on eggs, larvae, and adults. For eggs, chronic exposure to ZnO nanoparticles caused higher mortality at 10.0 and 100.0 mg/L compared to 0.0, 0.1, and 1.0 mg/L. When given an acute exposure (24h) to nanoparticles at a late incubation stage, …

Increasing Vaccine Accessibility Through Cost Alternative Manufacturing And Elimination Of The Cold Chain, Jorgen Madsen

Undergraduate Honors Capstone Projects

Millions of people die each year from infectious diseases. This is partly due to the difficulty of transporting temperature dependent vaccines through what is called the cold chain in developing countries. I hypothesize that we can increase vaccine accessibility by finding cost effective alternatives to vaccine production and by eliminating the cold chain through vaccine stabilizers. The gold standard in purification of influenza virus is by means of ultracentrifugation. Although effective, this process is very expensive and thus impractical for developing countries. I hypothesize that column chromatography can be a cost efficient alternative that is as effective as ultracentrifugation. The …

Biogeography, Population Genetics, And Community Structure Of North American Bumble Bees, Jonathan Berenguer Koch

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In 2011, several wild North American bumble bee pollinator species were reported to have declined by up to 96% in relative abundance in comparison to historic estimates, and one species was speculated to be extinct. None of these species have yet been documented to have recovered from these declines and additional species are now suggested to be at risk. Imperiled species in particular show increased specificity to narrow climatic envelopes, as opposed to putatively stable species. My dissertation describes patterns of population genetic diversity, structure, and gene flow pathways associated with climate variation and historical biogeography of bumble bees distributed …

Scalable Bio-Production Of High Value Products In Bacteria, Yukie Kawasaki

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Natural products are structurally and chemically diverse bioactive compounds produced by living organisms. The complex structures of natural products are often difficult to duplicate synthetically and thus industrial production of natural products most often depends on use of the host organisms. In this dissertation research, scalable production of natural products was pursued in bacterial platforms.

Biliverdin IXα is a natural anti-inflammatory compound which is emerging as a potent cytoprotectant in the medical field. Syringomycin E is a natural fungicide expected to be an effective agrofungicide in organic farming. Both biliverdin IXα and syringomycin E have limited supplies in the market. …

Aqueous Solvation Method For Recombinant Spider Silk Proteins, Justin A. Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silk is a remarkable material that has recently garnered significant international interest due to its broad applicability and natural composition. Spider silk fibers demonstrate unparalleled mechanical properties and their biocompatability will allow them to replace products currently on the market such as fibers, threads and sutures that are made from traditional polymers. As spiders cannot be farmed, an emphasis in the Lewis lab is being placed on producing recombinant spider silk proteins (rSSP) in a variety of hosts, including alfalfa, goats, silkworms and Escherichia. coli. To this end, alfalfa, goats and silkworms are being generated with unique rSSP's …

Next-Gen Transcriptomics Reveals Variable Gene Expression In Stenotrophomonas Maltophilia K279a When Grown In Co-Culture With Pseudomonas Aeruginosa 2192., David Jensen 1984-

Electronic Theses and Dissertations

We are constantly surrounded by bacteria, many of which are found in cohabitation with other species in the same niches. These organisms can be particularly problematic when they infect the human body. Cystic fibrosis (CF) is of significant concern because of the frequency that those suffering from this autosomal recessive disease have in colonization by these infectious agents. Affecting more than 30,000 people in the U.S. alone. CF is due to a genetic mutation that causes a thick mucosal buildup in luminal surfaces. This viscous mucus creates a cultivation site for complex respiratory biofilms. Complications of CF include paralysis of …

Do Hydrocarbon And Salinity Disturbance Affect Marine Meiofauna Diversity And Community Structure?, Kyle Edward Anderson

Electronic Theses and Dissertations

Coastal areas around the world are subjected to numerous disturbances, both natural and anthropogenic. Coastal meiofauna are an ecologically important group of organisms that may be sensitive to disturbance and especially useful as indicators of habitat status following anthropogenic disturbances. In this research, I compared the effects of five different intensity levels of hydrocarbon contamination, salinity reduction, and random non-disturbance diversity manipulation on communities of marine meiofauna communities in a microcosm experiment. While I did find the expected negative relationship between intensity and morphogroup diversity in the random treatment, the hydrocarbon and salinity disturbance treatments had no effects on overall …

An Inquiry-Infused Introductory Biology Laboratory That Integrates Mendel's Pea Phenotypes With Molecular Mechanisms, Philip Kudish, E. Schlag, Nicholas J. Kaplinsky

Biology Faculty Works

We developed a multi-week laboratory in which college-level introductory biology students investigate Mendel's stem length phenotype in peas. Students collect, analyze and interpret convergent evidence from molecular and physiological techniques. In weeks 1 and 2, students treat control and experimental plants with Gibberellic Acid (GA) to determine whether uncharacterized short mutant lines are GA responsive. These data allow students to place the mutation in the GA signal transduction pathway. During weeks 2 and 3, plants are genotyped for Mendel's "le" mutation using a derived cleaved polymorphic sequences (dCAPS) PCR assay. This laboratory allows students to make a direct connection between …

Proteins Involved In Hdaci Induced Decay Of Erbb2 Transcripts In Breast Cancer, Sadaf Malik

Dissertations, Masters Theses, Capstones, and Culminating Projects

ERBB2-positive breast cancer is an aggressive disease form that can result in rapid tumor growth and metastasis driven by the overexpression of ERBB2 growth factor receptors present on the cell surface. Currently, approved agents can target and disable ERBB2 receptor function, but as few as 30% of patients with disseminated ERBB2-positive breast cancer will respond to these targeted therapeutics when given as single agents. Even then, many initial responders will soon develop resistance to these agents. Histone deacetylase inhibitors (HDACi) are a powerful new class of epigenetic therapeutics that have demonstrated potent antitumor activity. However, there are several concerns that …