Biology Commons^™

Proteins: Form And Function, Roy D. Sleator

Department of Biological Sciences Publications

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

The Mayfly Newsletter, Peter M. Grant

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Research, Monitoring, Assessment And Development Plan 2011 – 2012, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

The Bird Of Time: Cognition And The Avian Biological Clock, Vincent M. Cassone, David F. Westneat

Biology Faculty Publications

Avian behavior and physiology are embedded in time at many levels of biological organization. Biological clock function in birds is critical for sleep/wake cycles, but may also regulate the acquisition of place memory, learning of song from tutors, social integration, and time-compensated navigation. This relationship has two major implications. First, mechanisms of the circadian clock should be linked in some way to the mechanisms of all these behaviors. How is not yet clear, and evidence that the central clock has effects is piecemeal. Second, selection acting on characters that are linked to the circadian clock should influence aspects of the …

Vincristine And Bortezomib Cause Axon Outgrowth And Behavioral Defects In Larval Zebrafish, Tahsin M. Khan, Nathan Benaich, Clare F. Malone, Rebecca L. Bernardos, Amy R. Russell, Gerald B. Downes, Michael J. Barresi, Lara D. Hutson

Biological Sciences: Faculty Publications

Peripheral neuropathy is a common side effect of a number of pharmaceutical compounds, including several chemotherapy drugs. Among these are vincristine sulfate, a mitotic inhibitor used to treat a variety of leukemias, lymphomas, and other cancers, and bortezomib, a 26S proteasome inhibitor used primarily to treat relapsed multiple myeloma and mantle cell lymphoma. To gain insight into the mechanisms by which these compounds act, we tested their effects in zebrafish. Vincristine or bortezomib given during late embryonic development caused significant defects at both behavioral and cellular levels. Intriguingly, the effects of the two drugs appear to be distinct. Vincristine causes …

Akirin Links Twist-Regulated Transcription With The Brahma Chromatin Remodeling Complex During Embryogenesis, Scott J. Nowak, Hitoshi Aihara, Katie Gonzalez, Yutaka Nibu, Mary K. Baylies

Faculty Articles

The activities of developmentally critical transcription factors are regulated via interactions with cofactors. Such interactions influence transcription factor activity either directly through protein–protein interactions or indirectly by altering the local chromatin environment. Using a yeast double-interaction screen, we identified a highly conserved nuclear protein, Akirin, as a novel cofactor of the key Drosophila melanogaster mesoderm and muscle transcription factor Twist. We find that Akirin interacts genetically and physically with Twist to facilitate expression of some, but not all, Twist-regulated genes during embryonic myogenesis. akirin mutant embryos have muscle defects consistent with altered regulation of a subset of Twistregulated genes. To …

Implication Of The Mir-184 And Mir-204 Competitive Rna Network In Control Of Mouse Secondary Cataract, Andrea Hoffmann, Yusen Huang, Rinako Suetsugu-Maki, Carol S. Ringelberg, Craig R. Tomlinson, Katia Del Rio-Tsonis, Panagiotis A. Tsonis

Biology Faculty Publications

The high recurrence rate of secondary cataract (SC) is caused by the intrinsic differentiation activity of residual lens epithelial cells after extra-capsular lens removal. The objective of this study was to identify changes in the microRNA (miRNA) expression profile during mouse SC formation and to selectively manipulate miRNA expression for potential therapeutic intervention. To model SC, mouse cataract surgery was performed and temporal changes in the miRNA expression pattern were determined by microarray analysis. To study the potential SC counterregulative effect of miRNAs, a lens capsular bag in vitro model was used. Within the first 3 wks after cataract surgery, …

The Genome Of The Xerotolerant Mold Wallemia Sebi Reveals Adaptations To Osmotic Stress And Suggests Cryptic Sexual Reproduction, Mahajabeen Padamsee, Arun T.K. Kumar, Robert Riley, Manfred Binder, Alex Boyd, Ana M. Calvo, Kentaro Furukawa, Cedar Hesse, Stefan Hohmann, Tim Y. James, Kurt Labutti, Alla Lapidus, Erika Lindquist, Susan Lucas, Kari Miller, Sourabha Shantappa, Igor V. Grigoriev, David S. Hibbett, David J. Mclaughlin, Joseph W. Spatafora, M. Catherine Aime

Biology

Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8. Mb), with few repeats and the largest fraction of genes with functional domains compared with …

A Streamlined Strategy For Biohydrogen Production With Halanaerobium Hydrogeniformans, An Alkaliphilic Bacterium, Matthew B. Begemann, Melanie R. Mormile, Oliver C. Sitton, Judy D. Wall, Dwayne A. Elias

Biological Sciences Faculty Research & Creative Works

Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium hydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5-and 6-carbon sugars derived from hemicellulose and cellulose …

Insights Into Migration And Development Of Coral Black Band Disease Based On Fine Structure Analysis, Aaron Miller, Patricia Blackwelder, Husain Al-Sayegh, Laurie L. Richardson

Biology Faculty Articles

In many diverse ecosystems, ranging from natural surfaces in aquatic ecosystems to the mammalian gut and medical implants, bacterial populations and communities exist as biofilms. While the process of biofilm development has been well-studied for those produced by unicellular bacteria such Pseudomonas aeruginosa, little is known about biofilm development associated with filamentous microorganisms. Black band disease (BBD) of corals is characterized as a polymicrobial biofilm (mat) community, visually-dominated by filamentous cyanobacteria. The mat migrates across a living coral host, completely lysing coral tissue and leaving behind exposed coral skeleton. It is the only known cyanobacterial biofilm that migrates across …

Antibiotic And Bacteriocin Sensitivity Of Listeria Monocytogenes Strains Isolated From Different Foods, Evrim Gunes Altuntas, Deniz Kocan, Serap Cosansu, Kamuran Ayhan, Vijay K. Juneja, Luis A. Materon

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

This study aimed to determine the antibiotic and bacteriocin sensitivity of Listeria monocytogenes strains isolated from animal derived foods. With disc diffusion assay, all fourteen L. monocytogenes strains were suscepti-ble to the antibiotics, including penicillin G, vancomycin, tetracycline, chloramphenicol, rifampicin, erythromycin, gentamicin and trime- thoprim. However, the percentages of fosfomycin and streptomycin resistances were 92.9% and 7.1%, respectively. Multiple resistances were not observed among the tested strains. The results of well diffusion assays showed that all strains were inhibited by the cell-free supernatant of a bacteriocin-producing strain, Pediococcus acidilactici 13, with the inhibition zones ranging from 16.00 to 24.50 mm. …

Comparing The Demographics Of Two Steelhead Populations And Their Habitat Characteristics, Eileen Ann Baglivio

Master's Theses

Currently, little is known about the demographics of the Oncorhynchus mykiss irideus, or steelhead trout, populations in San Luis Obispo County. Specifically, demographic information including length, age, and condition when first leaving a watershed for the open ocean is lacking. This thesis takes a closer look at a biological and environmental data collected by the California Department of Fish and Game Central Coast Steelhead and Coho Salmon project under the direction of Associate Biologist Jennifer Nelson. The main goal of this thesis is to analyze demographic and habitat data from the steelhead populations of two northern San Luis Obispo …

Assessing Patterns Of Hybridization And Multiple Mechanisms Of Reproductive Isolation Between Erythronium Albidum And Its Congener E. Mesochoreum, Kathy Roccaforte

School of Biological Sciences: Dissertations, Theses, and Student Research

Although there are approximately 250,000 extant angiosperm species, we still have much to learn about the speciation process, including the ways in which species boundaries are maintained among closely related taxa. Species are formed when populations become reproductively isolated from each other via genetic and morphological barriers that act before hybrid formation (prezygotic) or after hybrids are formed (postzygotic).

Erythronium albidum Nutt. and Erythronium mesochoreum Knerr (Liliaceae) differ in ploidy, are likely sister species, and have been reported to hybridize, making them well-suited for assessing the strength of multiple reproductive barriers. First, I assessed the frequency of hybrid occurrence at …

Pseudoscorpion Mitochondria Show Rearranged Genes And Genome-Wide Reductions Of Rna Gene Sizes And Inferred Structures, Yet Typical Nucleotide Composition Bias, Sergey Ovchinnikov, Susan E. Masta

Biology Faculty Publications and Presentations

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do …

Effects Of The Manipulation Of Aboveground Plant Diversity In Restoration Management On The Diversity Of Belowground Arthropod Assemblage, Claire E. Gilmore

College of Science and Health Theses and Dissertations

A missing element in restoring belowground soil systems to a relatively healthy state may lie in promoting microarthropod diversity. By contributing to healthy nutrient cycling and assisting in the breakdown of leaf litter a diverse microarthropod population helps improve the overall soil quality. My study evaluated how current restoration practices aimed at maintaining aboveground diversity affects belowground microarthropod populations. I examined how the aboveground manipulation of plant diversity in restoration management practices affects the hyperdiverse assemblage of belowground arthropod communities. Additionally, I examined the relationship between soil nutrient content and microarthropod diversity. This study was conducted within the boundaries of …

Phylogeny And Cryptic Diversity In Geckos (Phyllopezus; Phyllodactylidae; Gekkota) From South America’S Open Biomes, Tony Gamble, Guarino R. Colli, Miguel T. Rodrigues, Fernanda P. Werneck, Andrew M. Simons

Biological Sciences Faculty Research and Publications

The gecko genus Phyllopezus occurs across South America’s open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p. przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a …

Computer Simulation And Mathematical Models Of The Noncentrosomal Plant Cortical Microtubule Cytoskeleton, Ezgi Can Eren, Natarajan Gautam, Ram Dixit

Biology Faculty Research

There is rising interest in modeling the noncentrosomal cortical microtubule cytoskeleton of plant cells, particularly its organization into ordered arrays and the mechanisms that facilitate this organization. In this review, we discuss quantitative models of this highly complex and dynamic structure both at a cellular and molecular level. We report differences in methodologies and assumptions of different models as well as their controversial results. Our review provides insights for future studies to resolve these controversies, in addition to underlining the common results between various models. We also highlight the need to compare the results from simulation and mathematical models with …

Genetic Reporter System For Positioning Of Proteins At The Bacterial Pole, Kathryn R. Fixen, Anuradha Janakiraman, Sean Garritty, Daniel J. Slade, Andrew N. Gray, Nilay Karahan, Ann Hochschild, Marcia C. Goldberg

Publications and Research

Spatial organization within bacteria is fundamental to many cellular processes, although the basic mechanisms underlying localization of proteins to specific sites within bacteria are poorly understood. The study of protein positioning has been limited by a paucity of methods that allow rapid large-scale screening for mutants in which protein positioning is altered. We developed a genetic reporter system for protein localization to the pole within the bacterial cytoplasm that allows saturation screening for mutants in Escherichia coli in which protein localization is altered. Utilizing this system, we identify proteins required for proper positioning of the Shigella autotransporter IcsA. Autotransporters, widely …

The Chicken Challenge – What Contemporary Studies Of Fowl Mean For Science And Ethics, Carolynn L. Smith, Jane Johnson

Between the Species

Studies with captive fowl have revealed that they possess greater cognitive capacities than previously thought. We now know that fowl have sophisticated cognitive and communicative skills, which had hitherto been associated only with certain primates. Several theories have been advanced to explain the evolution of such complex behavior. Central to these theories is the enlargement of the brain in species with greater mental capacities. Fowl present us with a conundrum, however, because they show the behaviors anticipated by the theories but do not have the expected changes in the brain. Consequently fowl present two challenges of interest to us here. …

Heterogeneity In Genetic Diversity Among Non-Coding Loci Fails To Fit Neutral Coalescent Models Of Population History, Jeffrey L. Peters, Trina E. Roberts, Kevin Winker, Kevin G. Mccracken

Biological Sciences Faculty Publications

Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to test for deviations from selective neutrality in the gadwall (Anas strepera), a Holarctic duck. Nucleotide diversity among these loci varied by nearly two …

Effects Of Road Salt On Photosynthetic And Enzyme Activity Of Stream Biofilms, Leah Cook

Master's Theses and Doctoral Dissertations

Road salt application and salt-laden run-off are common, yet little information exists about its influence on periphyton. I measured extracelluar enzyme activity and photosynthetic activity of natural winter stream periphyton communities under various short-term laboratory salt exposures. The results of this study suggest that short-term exposure to increased concentrations of salt did not affect extracelluar enzyme activity but could temporarily reduce the photosynthetic activity of the periphyton. Further work will be necessary to understand the longterm effects of increased salt concentrations on periphyton and extracellular enzyme activity.

A Putative P-Type Atpase Required For Virulence And Resistance To Haem Toxicity In Listeria Monocytogenes, Rosemary Rea, Roy D. Sleator, Et. Al.

Department of Biological Sciences Publications

Regulation of iron homeostasis in many pathogens is principally mediated by the ferric uptake regulator, Fur. Since acquisition of iron from the host is essential for the intracellular pathogen Listeria monocytogenes, we predicted the existence of Fur-regulated systems that support infection. We examined the contribution of nine Fur-regulated loci to the pathogenicity of L. monocytogenes in a murine model of infection. While mutating the majority of the genes failed to affect virulence, three mutants exhibited a significantly compromised virulence potential. Most striking was the role of the membrane protein we designate FrvA (Fur regulated virulence factor A; encoded by …

Lianas Have A Greater Competitive Effect Than Trees Of Similar Biomass On Tropical Canopy Trees, Michael F. Tobin, Alexandra Wright, Scott A. Mangan, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas (woody vines) reduce growth and survival of host trees in both temperate and tropical forests; however, the relative strength of liana‐tree competition in comparison to tree‐tree competition remains unexplored. When controlling for biomass, lianas may have greater competitive effects than trees because the unique morphology of lianas allows them to reach the forest canopy at relatively small stem diameters and deploy a substantial crown above their host. We tested the hypothesis that lianas have a greater negative effect on canopy trees than do trees of similar biomass with a liana‐ and tree sapling‐cutting experiment in a seasonal tropical moist …

Overexpression Of Fatty Acid Amide Hydrolase Induces Early Flowering In Arabidopsis Thaliana, Neal D. Teaster, Jantana Keereetaweep, Aruna Kilaru, Yuh-Shuh Wang, Yuhong Tang, Christopher N.-Q. Tran, Brian G. Ayre, Kent D. Chapman, Elison B. Blancaflor

ETSU Faculty Works

N-Acylethanolamines (NAEs) are bioactive lipids derived from the hydrolysis of the membrane phospholipid N-acylphosphatidylethanolamine (NAPE). In animal systems this reaction is part of the “endocannabinoid” signaling pathway, which regulates a variety of physiological processes. The signaling function of NAE is terminated by fatty acid amide hydrolase (FAAH), which hydrolyzes NAE to ethanolamine and free fatty acid. Our previous work in Arabidopsis thaliana showed that overexpression of AtFAAH (At5g64440) lowered endogenous levels of NAEs in seeds, consistent with its role in NAE signal termination. Reduced NAE levels were accompanied by an accelerated growth phenotype, increased sensitivity to abscisic acid (ABA), enhanced …

Matrix Metalloproteinase Genes Are Transcriptionally Regulated By E2f Transcription Factors: A Link Between Cell Cycle Control And Metastatic Progression, Jacqueline Lea Johnson

USF Tampa Graduate Theses and Dissertations

The RbµE2F transcriptional regulatory pathway plays a critical role in the cell cycle. Rb is inactivated through multiple waves of phosphorylation, mediated mainly by cyclin D and cyclin E associated kinases. Once Rb is inactivated, cells can enter Sµphase. Collectively, three Rb family members and ten E2F proteins coordinate every additional stage of the cell cycle, from quiescence to mitosis. However the RbµE2F pathway is frequently altered in cancer. Aside from cell proliferation, the RbµE2F pathway regulates other essential cellular processes including apoptosis, cell differentiation, angiogenesis and DNA damage repair pathways, but its role in invasion and cancer progression is …

Sendai Virus-Based Liposomes Enable Targeted Cytosolic Delivery Of Nanoparticles In Brain Tumor-Derived Cells, Veronica Dudu, Veronica Rotari, Maribel Vazquez

Publications and Research

BACKGROUND: Nanotechnology-based bioassays that detect the presence and/or absence of a combination of cell markers are increasingly used to identify stem or progenitor cells, assess cell heterogeneity, and evaluate tumor malignancy and/or chemoresistance. Delivery methods that enable nanoparticles to rapidly detect emerging, intracellular markers within cell clusters of biopsies will greatly aid in tumor characterization, analysis of functional state and development of treatment regimens.

RESULTS: Experiments utilized the Sendai virus to achieve in vitro, cytosolic delivery of Quantum dots in cells cultured from Human brain tumors. Using fluorescence microscopy and Transmission Electron Microscopy, in vitro experiments illustrated that these virus-based …

Library Impact Statement For Bio 501 Advanced Scientific Ethics, Michael A. Cerbo Ii

Library Impact Statements

Library Impact Statement for BIO 501 Advanced Scientific Ethics new course proposal. No new resources are required to support this course. Responding library faculty member: Michael A. Cerbo II. Requesting faculty member: Chris Lane.

Library Impact Statement For Bio 502 Advanced Scientific Communication, Michael A. Cerbo Ii

Library Impact Statements

Library Impact Statement for BIO 502 Advanced Scientific Communication new course proposal. No new resources are needed to support this course. Responding library faculty member: Michael A. Cerbo II. Requesting faculty member: Chris Lane.

Evolution Of Plant Sucrose Uptake Transporters, Anke Reinders, Alicia B. Sivitz, John M. Ward

Dartmouth Scholarship

In angiosperms, sucrose uptake transporters (SUTs) have important functions especially in vascular tissue. Here we explore the evolutionary origins of SUTs by analysis of angiosperm SUTs and homologous transporters in a vascular early land plant, Selaginella moellendorffii, and a non-vascular plant, the bryophyte Physcomitrella patens, the charophyte algae Chlorokybus atmosphyticus, several red algae and fission yeast, Schizosaccharomyces pombe. Plant SUTs cluster into three types by phylogenetic analysis. Previous studies using angiosperms had shown that types I and II are localized to the plasma membrane while type III SUTs are associated with vacuolar membrane. SUT homologs were …

Characterization Of Aquaporin 4 Protein Expression And Localization In Tissues Of The Dogfish (Squalus Acanthias), Christopher P. Cutler, Sheena Harmon, Jonathan Walsh, Kia Burch

Biology: Faculty Publications

The role of aquaporin water channels such as aquaporin 4 (Aqp4) in elasmobranchs such as the dogfish Squalus acanthias is completely unknown. This investigation set out to determine the expression and cellular and sub-cellular localization of Aqp4 protein in dogfish tissues. Two polyclonal antibodies were generated (AQP4/1 and AQP4/2) and these showed somewhat different characteristics in Western blotting and immunohistochemistry. Western blots using the AQP4/1 antibody showed two bands (35.5 and 49.5 kDa) in most tissues in a similar fashion to mammals. Liver had an additional band of 57 kDa and rectal gland two further faint bands of 37.5 and …