Biology Commons^™

A Conservation And Rigidity Based Method For Detecting Critical Protein Residues, Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel

All Faculty Scholarship for the College of the Sciences

Background

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine …

Silencing Synuclein At The Synapse With Plk2, Brendan D. Looyenga, Patrik Brundin

University Faculty Publications and Creative Works

No abstract provided.

Rapid Protocol For Preparation Of Electrocompetent Escherichia Coli And Vibrio Cholerae, Miguel F. Gonzales, Teresa Brooks, Stefan U. Pukatzki, Daniele Provenzano

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

Electroporation has become a widely used method for rapidly and efficiently introducing foreign DNA into a wide range of cells. Electrotransformation has become the method of choice for introducing DNA into prokaryotes that are not naturally competent. Electroporation is a rapid, efficient, and streamlined transformation method that, in addition to purified DNA and competent bacteria, requires commercially available gene pulse controller and cuvettes. In contrast to the pulsing step, preparation of electrocompetent cells is time consuming and labor intensive involving repeated rounds of centrifugation and washes in decreasing volumes of sterile, cold water, or non-ionic buffers of large volumes of …

Are Characiform Fishes Gondwanan In Origin? Insights From A Time-Scaled Molecular Phylogeny Of The Citharinoidei (Ostariophysi: Characiformes), Jairo Arroyave, John S. S. Denton, Melanie L. J. Stiassny

Publications and Research

Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating …

Luxs In Bacteria Isolated From 25- To 40-Million-Year-Old Amber, Tasha M. Santiago-Rodriguez, Ana R. Patrício, Jessica I. Rivera, Mariel Coradin, Alfredo Gonzalez, Gabriela Tirado, Raúl J. Cano, Gary A. Toranzos

Biological Sciences

Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25- to 40-million-year-old amber. The phylogenies and molecular clocks of luxS and the 16S rRNA gene from ancient and extant bacteria were determined as well. Luminescence assays using Vibrio harveyi BB170 aimed to determine the activity of luxS. While the phylogeny of luxS was very similar to that of extant Bacillus spp., …

Cervicothoracic Multisegmental Transpinal Evoked Potentials In Humans, Jonathan Einhorn, Alan Li, Royi Hazan, Maria Knikou

Publications and Research

The objectives of this study were to establish the neurophysiological properties of the transpinal evoked potentials (TEPs) following transcutaneous electric stimulation of the spine (tsESS) over the cervicothoracic region, changes in the amplitude of the TEPs preceded by median nerve stimulation at group I threshold, and the effects of tsESS on the flexor carpi radialis (FCR) H-reflex in thirteen healthy human subjects while seated. Two re-usable self-adhering electrodes, connected to function as one electrode (cathode), were placed bilaterally on the clavicles. A re-usable electrode (anode) was placed on the cervicothoracic region covering from Cervical 4 – Thoracic 2 and held …

The Repetitive Component Of The Sunflower Genome As Shown By Different Procedures For Assembling Next Generation Sequencing Reads, Lucia Natali, Rosa Maria Cossu, Elena Barghini, Tommaso Giordani, Matteo Buti, Flavia Mascagni, Michele Morgante, Navdeep Gill, Nolan Kane, Loren Rieseberg, Andrea Cavallini

Biology Faculty Articles

Background

Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries.

Results

By varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases …

Insertionmapper, A Pipeline Tool For The Identification Of Targeted Sequences From Multidimensional High Throughput Sequencing Data, Wenwei Xiong, Limei He, Yubin Li, Hugo K. Dooner, Chunguang Du

Department of Biology Faculty Scholarship and Creative Works

Background: The advent of next-generation high-throughput technologies has revolutionized whole genome sequencing, yet some experiments require sequencing only of targeted regions of the genome from a very large number of samples. These regions can be amplified by PCR and sequenced by next-generation methods using a multidimensional pooling strategy. However, there is at present no available generalized tool for the computational analysis of target-enriched NGS data from multidimensional pools.Results: Here we present InsertionMapper, a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. InsertionMapper consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution …

Zebrafish Ciliopathy Screen Plus Human Mutational Analysis Identifies C21orf59 And Ccdc65 Defects As Causing Primary Ciliary Dyskinesia, Christina Austin-Tse, Jan Halbritter, Maimoona A. Zariwala, Renée M. Gilberti, Heon Yung Gee, Nathan Hellman, Narendra Pathak, Yan Liu, Jennifer R. Panizzi, Ramila S. Patel-King, Douglas Tritschler, Raqual Bower, Eileen O'Toole, Jonathan D. Porath, Toby W. Hurd, Moumita Chaki, Katrina A. Diaz, Stefan Kohl, Svjetlana Lovric, Daw Yang Hwang, Daniela A. Braun, Markus Schueler, Rannar Airik, Edgar A. Otto, Margaret W. Leigh, Peadar G. Noone, Johnny L. Carson, Stephanie D. Davis, Jessica E. Pittman, Thomas W. Ferkol, Jeffry J. Atkinson, Kenneth N. Olivier

Neuroscience: Faculty Publications

Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Multiple causative PCD mutations account for only 65% of cases, suggesting that many genes essential for cilia function remain to be discovered. By using zebrafish morpholino knockdown of PCD candidate genes as an in vivo screening platform, we identified c21orf59, ccdc65, and c15orf26 as critical for cilia motility. c21orf59 and c15orf26 knockdown in zebrafish and planaria blocked outer dynein arm assembly, and ccdc65 knockdown altered cilia beat pattern. Biochemical analysis in Chlamydomonas revealed that the C21orf59 ortholog FBB18 is …

Neighborhoods Have Little Effect On Fungal Attack Or Insect Predation Of Developing Seeds In A Grassland Biodiversity Experiment, Noelle G. Beckman, Ray Dybzinski, G. David Tilman

Biology Faculty Publications

Numerous observational studies have documented conspecific negative density-dependence that is consistent with the Janzen–Connell Hypothesis (JCH) of diversity maintenance. However, there have been few experimental tests of a central prediction of the JCH: that removing host-specific enemies should lead to greater increases in per capita recruitment in areas of higher host density or lower relative phylogenetic diversity. Using spatially randomized plots of high and low host biomass in a temperate grassland biodiversity experiment, we treated developing seedheads of six prairie perennials to factorial applications of fungicide and insecticide. We measured predispersal seed production, seed viability, and seedling biomass. Results were …

Administration Of Murine Stromal Vascular Fraction Ameliorates Chronic Experimental Autoimmune Encephalomyelitis, Julie A. Semon, Xiujuan Zhang, Armitabh C. Pandey, Sandra M. Alandete, Catherine Maness, Shijia Zhang, Brittni A. Scruggs, Amy L. Strong, Steven A. Sharkey, For Full List Of Authors, See Publisher's Website.

Biological Sciences Faculty Research & Creative Works

Administration of adipose-derived stromal/stem cells (ASCs) represents a promising therapeutic approach for autoimmune diseases since they have been shown to have immunomodulatory properties. The uncultured, nonexpanded counterpart of ASCs, the stromal vascular fraction (SVF), is composed of a heterogeneous mixture of cells. Although administration of ex vivo culture-expanded ASCs has been used to study immunomodulatory mechanisms in multiple models of autoimmune diseases, less is known about SVF-based therapy. The ability of murine SVF cells to treat myelin oligodendrocyte glycoprotein_35-55-induced experimental autoimmune encephalitis (EAE) was compared with that of culture-expanded ASCs in C57Bl/6J mice. A total of 1 x …

Age Of The Donor Reduces The Ability Of Human Adipose-Derived Stem Cells To Alleviate Symptoms In The Experimental Autoimmune Encephalomyelitis Mouse Model, Brittni A. Scruggs, Julie A. Semon, Xiujuan Zhang, Shijia Zhang, Annie C. Bowles, Amitabh C. Pandey, Kathleen M. P. Imhof, Allan V. Kalueff, Jeffrey M. Gimble, Bruce A. Bunnell

Biological Sciences Faculty Research & Creative Works

There is a significant clinical need for effective therapies for primary progressive multiple sclerosis, which presents later in life (i.e., older than 50 years) and has symptoms that increase in severity without remission. With autologous mesenchymal stem cell therapy now in the early phases of clinical trials for all forms of multiple sclerosis (MS), it is necessary to determine whether autologous stem cells from older donors have therapeutic effectiveness. In this study, the therapeutic efficacy of human adipose-derived mesenchymal stem cells (ASCs) from older donors was directly compared with that of cells from younger donors for disease prevention. Mice were …

Origin And Differential Selection Of Allelic Variation At Tas2r16 Associated With Salicin Bitter Taste Sensitivity In Africa, Michael Campbell

Department of Biology Faculty Publications

Bitter taste perception influences human nutrition and health, and the genetic variation underlying this trait may play a role in disease susceptibility. To better understand the genetic architecture and patterns of phenotypic variability of bitter taste perception, we sequenced a 996 bp region, encompassing the coding exon of TAS2R16, a bitter taste receptor gene, in 595 individuals from 74 African populations, and in 94 non-Africans from 11 populations. We also performed genotype-phenotype association analyses of threshold levels of sensitivity to salicin, a bitter anti-inflammatory compound, in 296 individuals from Central and East Africa. In addition, we characterized TAS2R16 mutants in …

Neuropeptide W Increases Mean Arterial Pressure As A Result Of Behavioral Arousal, Alicia T. Pate, Gina L.C. Yosten, Willis K. Samson

Biological Sciences Faculty Research & Creative Works

Neuropeptide W (NPW), an endogenous ligand for G protein-coupled receptors NPBWR1 (GPR7) and NPBWR2 (GPR8), has been detected in neurons in limbic and reticular activating system areas known to be important in arousal, as well as hypothalamic nuclei known to be important in food and water intake and the neuroendocrine response to stress. In rat, central administration of NPW increased mean arterial pressure (MAP) and behaviors associated with locomotion and grooming. We hypothesized that the NPW-induced increase in MAP was secondary to those increases in physical activity. Since peptides that stimulate arousal have been shown to increase sympathetic activity (e.g., …

Sequestration And Scavenging Of Iron In Infection, Nermi Lee Parrow, Robert E. Fleming, Michael F. Minnick

Biological Sciences Faculty Publications

The proliferative capability of many invasive pathogens is limited by the bioavailability of iron. Pathogens have thus developed strategies to obtain iron from their host organisms. In turn, host defense strategies have evolved to sequester iron from invasive pathogens. This review explores the mechanisms employed by bacterial pathogens to gain access to host iron sources, the role of iron in bacterial virulence, and iron-related genes required for the establishment or maintenance of infection. Host defenses to limit iron availability for bacterial growth during the acute-phase response and the consequences of iron overload conditions on susceptibility to bacterial infection are also …

Lifelines Fall 2013, Southern Adventist University

Lifelines - Biology Department Newsletter

The Fall 2013 issue of Lifelines features articles on toxins found in nature, student missions in Tanzania, an alumni spotlight, undergraduate research, and updates on department happenings.

Increased Abundance Of Frost Mrna During Recovery From Cold Stress Is Not Essential For Cold Tolerance In Adult Drosophila Melanogaster., H Udaka, A Percival-Smith, B J Sinclair

Biology Publications

Frost (Fst) is a candidate gene associated with the response to cold in Drosophila melanogaster because Fst mRNA accumulation increases during recovery from low temperature exposure. We investigated the contribution of Fst expression to chill-coma recovery time, acute cold tolerance and rapid cold hardening (RCH) in adult D. melanogaster by knocking down Fst mRNA expression using GAL4/UAS-mediated RNA interference. In this experiment, four UAS-Fst and one tubulin-GAL4 lines were used. We predicted that if Fst is essential for cold tolerance phenotypes, flies with low Fst mRNA levels should be less cold tolerant than flies with normal levels of cold-induced Fst …

Cross-Tolerance And Cross-Talk In The Cold: Relating Low Temperatures To Desiccation And Immune Stress In Insects., Brent J Sinclair, Laura V Ferguson, Golnaz Salehipour-Shirazi, Heath A Macmillan

Biology Publications

Multiple stressors, both abiotic and biotic, often are experienced simultaneously by organisms in nature. Responses to these stressors may share signaling pathways ("cross-talk") or protective mechanisms ("cross-tolerance"). Temperate and polar insects that must survive the winter experience low temperatures accompanied by additional abiotic stressors, such as low availability of water. Cold and desiccation have many similar effects at a cellular level, and we present evidence that the cellular mechanisms that protect against cold stress also protect against desiccation, and that the responses to cold and dehydration likely evolved as cross-tolerance. By contrast, there are several lines of evidence suggesting that …

Acquisition Of An Electrochemical System Instrument For The Development Of Sensors, Elmer-Rico E. Mojico

Cornerstone 1 Reports : Expansion and Enhancements of the Thinkfinity Platform

No abstract provided.

Do Bacterial And Fungal Communities In Soils Of The Bolivian Altiplano Change Under Shorter Fallow Periods?, L. Gomez-Montano, A. Jumpponen, M. A. Gonzales, J. Cusicanqui, C. Valdivia, P. P. Motavalli, M. Herman, K. A. Garrett

School of Biological Sciences: Faculty Publications

Traditional fallow periods in the Bolivian highlands are being shortened in an effort to increase short-term crop yields, with potential long-term impacts on soil microbial communities and their functions. In addition, native vegetation, such as Parasthrephia sp. or Baccharis sp. (both locally known as “thola”) are often removed as a fuel for cooking. We evaluated the effects of fallow period and thola on soils in 29 farmers’ fields in two municipalities in the Bolivian Altiplano (Umala and Ancoraimes). Soil fungal and bacterial community responses were characterized using 454-pyrosequencing. Soils in Ancoraimes had significantly higher levels of organic matter, nitrogen, and …

Colorful Displays Signal Male Quality In A Tropical Anole Lizard, E. G. Cook, Troy G. Murphy, Michele A. Johnson

Biology Faculty Research

Parasites influence colorful ornaments and their behavioral display in many animal hosts. Because coloration and display behavior are often critical components of communication, variation in these traits may have important implications for individual fitness, yet it remains unclear whether such traits are signals of quality in many taxa. We investigated the association between ectoparasitic mite load and the color and behavioral use of the throat fan (dewlap) by male Anolis brevirostris lizards. We found that heavily parasitized lizards exhibited lower body condition, duller dewlaps, and less frequent dewlap displays than less parasitized individuals. Our results thus suggest that highly parasitized …

Characterization Of Caxck31, A Bacterial Calcium/Proton Antiporter, Marc Robert Ridilla

Open Access Dissertations

To better understand a class of transporters known as Calcium/Cation Antiporters (CaCAs), the bacterial calcium/proton antiporter CAXCK31 was purified and characterized. New methods were developed for its heterologous overexpression and purification. These methods help to define stress responses to toxic membrane overproduction in E. coli and may be broadly applicable to studies of membrane proteins. The results from a variety of biochemical and biophysical experiments demonstrated that CAXCK31 exists as a dimer in the membrane and can be purified in the dimeric state. The methods used include chemical cross-linking, FRET, and SEC-MALS. In addition, various transport properties of CAXCK31, including …

Tossing The Coin For Half Life, William L. Romine

Biological Sciences Faculty Publications

No abstract provided.

Exploring Life And Death At The Cellular Level: An Examination Of How Our Cells Can Live Without Us, Emily F. Schmitt Lavin

Biology Faculty Articles

No abstract provided.

Andrews Welcomes New Biology Faculty, Becky St. Clair

Lake Union Herald

No abstract provided.

Fight Or Flight: Parental Decisions About Predators At Nests Of Northern Bobwhites (Colinus Virginianus), Susan N. Ellis-Felege, Jonathan S. Burnam, William E. Palmer, D. Clay Sisson, John P. Carroll

Biology Faculty Publications

Patterns of nest defense against predators by ground-nesting bird species in the wild are poorly understood, largely because of a historical inability to directly monitor nests. Most nest-defense studies have observed responses elicited from artificial predators or human observers presented to nesting birds, and few have attempted to present these events in the context of predator—prey relationships found in the wild. We hypothesized that predator threat level (e.g., the threat posed to the clutch or to the clutch and the attending adult), parental characteristics, clutch investment, and future reproductive opportunities would influence avian nest-defense decisions. During 1999–2006, we examined predation …

The Deletion Of The Bre1 Gene In Aspergillus Nidulans Impairs Mitotic Growth, Meiosis, And Dna Damage Repair, Andrea J. Sitton, Steven W. James

Student Publications

Bre1 is a homotetrameric E3 ubiquitin-protein ligase that heterodimerizes with Rad6, an E2 ubiquitin-conjugating enzyme, in order to ubiquitinate lysine 123 in Aspergillus nidulans. This post-translational modification promotes methylation of lysines 4 and 79 on histone H3, which are required for certain damage repair pathways and for both optimal mitotic cell growth and meiosis [1-3, 12]. ΔBre1 mutants were generated by exposing protoplasts from strains auxotrophic for pyridoxine to a three-way fusion construct made from the Bre1 5’ and 3’ flanking regions and the Aspergillus fumigatus pyroA gene, which served as a selectable marker. Molecular diagnosis was confirmed via trans-locus …

Consequences Of Seed Dispersal For Plant Recruitment In Tropical Forests: Interactions Within The Seedscape, Noelle G. Beckman, Haldre S. Rogers

Biology Faculty Publications

Seed dispersal sets the stage for the suite of biotic and abiotic interactions that determine the fate of individual seeds. In this review, we first focus on how dispersal influences the 'seedscape', or the combination of abiotic and biotic factors that affect the probability of recruitment once a seed has reached its final location. We review recent papers that examine the effect of different dispersal vectors on (1) the quality of the habitat in which a seed lands; (2) the distance seeds are dispersed from the parent tree; and (3) the density and composition of plant s within the neighborhood …

High-Throughput Rna Sequencing Of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity And Novel Splice Variants, Brian E. Howard, Qiwen Hu, Ahmet Can Babaoglu, Manan Chandra, Monica Borghi, Xiaoping Tan, Luyan He, Heike Winter-Sederoff, Walter Gassmann, Paola Veronese, Steffen Heber

Biology Faculty Publications

We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events …

A Multi-Scale Analysis Of The Effects Of Local- And Landscape-Level Variables On Nuthatch Occupancy And Distribution, Jesse Wood

Earth and Environmental Sciences Presentations

The objectives of this study are to conduct a multi-scale analysis of the effects of habitat variables on Brownheaded Nuthatch (S. pusilla) occupancy and spatial distribution in the greater Greenville area of South Carolina. By understanding the local- and landscape-drivers of an ecologically sensitive species, we can build a predictive model of species occurrence and contribute to regional conservation efforts of both habitat and biodiversity.