Biology Commons^™

Comparative Studies Of Differential Gene Calling Methods For Rna-Seq Data, Ximeng Zheng

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

RNA-Seq is a recently developed technology that can reveal RNA expression profile by taking advantage of deep sequencing. This new technology has many advantages over microarray technologies. Although RNA-Seq is expected to overtake microarray experiments due to their massive amounts of data produced, it presents many challenges to bioinformatics research regarding efficient data processing and storage, and accuracy in data interpretation. One of the challenges and also an important aspect of expression profiling is to detect differentially expressed genes between different experimental conditions. Several statistical methods have been developed over the past few years. In this study, we chose two …

Metabolic Preconditioning Of Mammalian Cells : Mimetic Agents For Hypoxia Lack Fidelity In Promoting Phosphorylation Of Pyruvate Dehydrogenase., Apurva Borcar, Michael Menze, Mehmet Toner, Steven Hand

Faculty and Staff Scholarship

Induction of HIF-1α by oxygen limitation promotes increased phosphorylation and catalytic depression of mitochondrial pyruvate dehydrogenase (PDH) and an enhanced glycolytic poise in cells. Cobalt chloride and desferrioxamine are widely used as mimics for hypoxia because they increase the levels of HIF-1α. We evaluated the ability of these agents to elicit selected physiological responses to hypoxia as a means to metabolically precondition mammalian cells, but without the detrimental effects of hypoxia. We show that, while CoCl2 does increase HIF-1α in a dose-dependent manner, it unexpectedly and strikingly decreases PDH phosphorylation at E1α sites 1, 2, and 3 (Ser293, Ser300, and …

Nature And Function Of Insulator Protein Binding Sites In The Drosophila Genome, Yuri Schwartz, Daniela Linder-Basso, Peter Kharchenko, Michael Tolstorukov, Maria Kim, Hua-Bing Li, Andrey Gorchakov, Aki Minoda, Gregory Shanower, Artyom Alekseyenko, Nicole Riddle, Youngsook Jung, Tingting Gu, Annette Plachetka, Sarah C.R. Elgin, Mitzi Kuroda, Peter Park, Mikhail Savitsky, Gary Karpen, Vincenzo Pirrotta

Biology Faculty Research

Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but …

Internet Reviews: Biodiversity Heritage Library, John Creech

Library Scholarship

Review of the Biodiversity Heritage Library, emphasizing its value and appeal to a world-wide multi-lingual audience.

The Enzymes Of Biotin Dependent Co(2) Metabolism: What Structures Reveal About Their Reaction Mechanisms, Grover L. Waldrop, Hazel M. Holden, Martin St. Maurice

Biological Sciences Faculty Research and Publications

Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin-dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO₂ carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti-obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a …

Freq-Seq: A Rapid, Cost-Effective, Sequencing-Based Method To Determine Allele Frequencies Directly From Mixed Populations, Lon Chubiz, Ming-Chun Lee, Nigel Delaney, Christopher Marx

Biology Department Faculty Works

No abstract provided.

Functional And Structural Divergence Of An Unusual Ltr Retrotransposon Family In Plants, Dongying Gao, Jose Jimenez-Lopez, Aiko Iwata, Navdeep Gill, Scott Jackson

Biology Faculty Articles

Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 …

Constitutive Type Vi Secretion System Expression Gives Vibrio Cholerae Intra- And Interspecific Competitive Advantages, Daniel Unterweger, Maya Kitaoka, Sarah T. Miyata, Verena Bachmann, Teresa M. Brooks, Jessica Moloney, Oscar Sosa, David Silva, Jorge Duran-Gonzalez, Daniele Provenzano

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

The type VI secretion system (T6SS) mediates protein translocation across the cell membrane of Gram-negative bacteria, including Vibrio cholerae - the causative agent of cholera. All V. cholerae strains examined to date harbor gene clusters encoding a T6SS. Structural similarity and sequence homology between components of the T6SS and the T4 bacteriophage cell-puncturing device suggest that the T6SS functions as a contractile molecular syringe to inject effector molecules into prokaryotic and eukaryotic target cells. Regulation of the T6SS is critical. A subset of V. cholerae strains, including the clinical O37 serogroup strain V52, express T6SS constitutively. In contrast, pandemic strains …

Phylogenomics And A Posteriori Data Partitioning Resolve The Cretaceous Angiosperm Radiation Malpighiales, Peter Stevens, Zhenxiang Xi, Brad Ruhfel, Hanno Schaefer, André Amorim, M. Sugumaran, Kenneth Wurdack, Peter Endress, Merran Matthews, Sarah Mathews, Charles Davis

Biology Department Faculty Works

The angiosperm order Malpighiales includes ∼16,000 species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm systematics during the last 20 y, relationships within Malpighiales remain poorly resolved, possibly owing to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 additional clades in Malpighiales and substantially increased resolution along the backbone. This greatly improved phylogeny revealed a dynamic history of shifts in net diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas …

Scaling Flow Path Processes To Fluvial Landscapes: An Integrated Field And Model Assessment Of Temperature And Dissolved Oxygen Dynamics In A River-Floodplain-Aquifer System, Ashley M. Helton, Geoffrey C. Poole, Robert A. Payn, Clemente Izurieta, Jack Arthur Stanford

Biological Sciences Faculty Publications

Biogeochemical cycling within river ecosystems is strongly influenced by geomorphic and hydrologic dynamics. To scale point observations of temperature and dissolved oxygen (DO) to a hydrologically complex and dynamic three-dimensional river-floodplain-aquifer system, we integrated empirical models of temperature and biotic oxygen utilization with a recently published hydrogeomorphic model. The hydrogeomorphic model simulates channel flow, floodplain inundation, and surface-subsurface water exchange on the 16 km(2) Nyack Floodplain, Middle Fork Flathead River, Montana, USA. Model results were compared to observed data sets of DO to test the hypothesis that complexity in spatiotemporal patterns of biogeochemistry emerges from a comparatively simple representation of …

Naturally Selecting Solutions: The Use Of Genetic Algorithms In Bioinformatics, Timmy Manning, Roy D. Sleator, Paul Walsh

Department of Biological Sciences Publications

For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the …

Gene Expression Patterns Specific To The Regenerating Limb Of The Mexican Axolotl, James R. Monaghan, Antony Athippozhy, Ashley W. Seifert, Sri Putta, Arnold J. Stromberg, Malcolm Maden, David M. Gardiner, Stephen R. Voss

Biology Faculty Publications

Salamander limb regeneration is dependent upon tissue interactions that are local to the amputation site. Communication among limb epidermis, peripheral nerves, and mesenchyme coordinate cell migration, cell proliferation, and tissue patterning to generate a blastema, which will form missing limb structures. An outstanding question is how cross-talk between these tissues gives rise to the regeneration blastema. To identify genes associated with epidermis-nerve-mesenchymal interactions during limb regeneration, we examined histological and transcriptional changes during the first week following injury in the wound epidermis and subjacent cells between three injury types; 1) a flank wound on the side of the animal that …

Soil Nematodes And Their Prokaryotic Prey Along An Elevation Gradient In The Mojave Desert (Death Valley National Park, California, Usa), Amy M. Treonis, Kelsey Sutton, Brendan Kavanaugh, Archana Narla, Timothy Mcllarky, Jasmine Felder, Cecilia O'Leary, Megan Riley, Alyxandr Pikus, Sarah Thomas

Biology Faculty Publications

We characterized soil communities in the Mojave Desert across an elevation gradient. Our goal was to test the hypothesis that as soil quality improved with increasing elevation (due to increased productivity), the diversity of soil prokaryotes and nematodes would also increase. Soil organic matter and soil moisture content increased with elevation as predicted. Soil salinity did not correlate to elevation, but was highest at a mid-gradient, alluvial site. Soil nematode density, community trophic structure, and diversity did not show patterns related to elevation. Similar results were obtained for diversity of bacteria and archaea. Relationships between soil properties, nematode communities, and …

Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale

Biology Faculty Publications and Presentations

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an …

Acid Sensing Ion Channels Regulate Neuronal Excitability By Inhibiting Bk Potassium Channels, Elena Petroff, Vladislav Snitsarev, Huiyu Gong, Francois M. Abboud

Department of Biology Faculty Scholarship and Creative Works

Acid sensing ion channels (ASICs), Ca2+ and voltage-activated potassium channels (BK) are widely present throughout the central nervous system. Previous studies have shown that when expressed together in heterologous cells, ASICs inhibit BK channels, and this inhibition is relieved by acidic extracellular pH. We hypothesized that ASIC and BK channels might interact in neurons, and that ASICs may regulate BK channel activity. We found that ASICs inhibited BK currents in cultured wild-type cortical neurons, but not in ASIC1a/2/3 triple knockout neurons. The inhibition in the wild-type was partially relieved by a drop in extracellular pH to 6. To test the …

A Proposed Mechanism For Nitrogen Acquisition By Grass Seedlings Through Oxidation Of Symbiotic Bacteria, James F. White Jr., Holly Crawford, Mónica S. Torres, Robert Mattera, Ivelisse Irizarry, Marshall Bergen

All Faculty Scholarship for the College of the Sciences

In this paper we propose and provide evidence for a mechanism, oxidative nitrogen scavenging (ONS), whereby seedlings of some grass species may extract nitrogen from symbiotic diazotrophic bacteria through oxidation by plant-secreted reactive oxygen species (ROS). Experiments on this proposed mechanism employ tall fescue (Festuca arundinaceae) seedlings to elucidate features of the oxidative mechanism. We employed 15N₂ gas assimilation experiments to demonstrate nitrogen fixation, direct microscopic visualization of bacteria on seedling surfaces to visualize the bacterial oxidation process, reactive oxygen probes to test for the presence of H₂O₂ and cultural experiments to assess conditions …

Cartilage On The Move: Cartilage Lineage Tracing During Tadpole Metamorphosis, Ryan R. Kerney, Alison L. Brittain, Brian K. Hall, Daniel R. Buchholz

Biology Faculty Publications

The reorganization of cranial cartilages during tadpole metamorphosis is a set of complex processes. The fates of larval cartilage-forming cells (chondrocytes) and sources of adult chondrocytes are largely unknown. Individual larval cranial cartilages may either degenerate or remodel, while many adult cartilages appear to form de novo during metamorphosis. Determining the extent to which adult chondrocytes/cartilages are derived from larval chondrocytes during metamorphosis requires new techniques in chondrocyte lineage tracing. We have developed two transgenic systems to label cartilage cells throughout the body with fluorescent proteins. One system strongly labels early tadpole cartilages only. The other system inducibly labels forming …

Iqgap Family Members In Yeast, Dictyostelium, And Mammalian Cells, Katie Shannon

Biological Sciences Faculty Research & Creative Works

IQGAPs are a family of scaffolding proteins with multiple domains, named for the IQ motifs and GTPase activating protein (GAP) related domains. Despite their GAP homology, IQGAP proteins act as effectors for GTP-bound GTPases of the Ras superfamily and do not stimulate GTP hydrolysis. IQGAPs are found in eukaryotic cells from yeast to human, and localize to actin-containing structures such as lamellipodia, membrane ruffles, cell-cell adhesions, phagocytic cups, and the actomyosin ring formed during cytokinesis. Mammalian IQGAPs also act as scaffolds for signaling pathways. IQGAPs perform their myriad functions through association with a large number of proteins including filamentous actin …

Of Gardens, Microorganisms, And Long Island Sound, Judy Preston

Wrack Lines

How healthy soil can make an environmental difference.

"I happened to turn over a large rounded stone in my garden to find a mesmerizing world of organisms that had, just moments earlier, been going about their business before being exposed to the sunlit world, and me."

Lifelines Fall 2012, Southern Adventist University

Lifelines - Biology Department Newsletter

The Fall 2012 issue of Lifelines features articles on undergraduate research in biology, field ecology, and the addition of Dr. Aaron Corbit to the faculty.

Bioremediation With White-Rot Fungi At Fisherville Mill: Analyses Of Gene Expression And Number 6 Fuel Oil Degradation, Darcy Young, Ma

Mosakowski Institute for Public Enterprise

Extracellular enzymes that white-rot fungi secrete during lignin decay have been proposed as promising agents for oxidizing pollutants. We investigated the abilities of the white-rot fungi Punctularia strigosozonata, Irpex lacteus, Trichaptum biforme, Phlebia radiata, Trametes versicolor, and Pleurotus ostreatus to degrade Number 6 fuel oil in wood sawdust cultures. Our goals are to advise bioremediation efforts at a brownfield redevelopment site on the Blackstone River in Grafton, Massachusetts and to contribute to the understanding of decay mechanisms in white-rot fungi. All species tested degraded a C10 alkane. When cultivated for 6 months, Irpex lacteus, T. biforme, P. radiata, T. versicolor …

Rapid Invasion Of Indo-Pacific Lionfishes (Pterois Volitans And Pterois Miles) In The Florida Keys, Usa: Evidence From Multiple Pre- And Post-Invasion Data Sets, Benjamin I. Ruttenberg, Pamela J. Schofield, J. Lad Akins, Alejandro Acosta, Michael W. Feeley, Jeremiah Blondeau, Steven G. Smith, Jerald S. Ault

Biological Sciences

Over the past decade, Indo-Pacific lionfishes, Pterois volitans (Linnaeus, 1758) and Pterois miles (Bennett, 1828), venomous members of the scorpionfish family (Scorpaenidae), have invaded and spread throughout much of the tropical and subtropical northwestern Atlantic Ocean and Caribbean Sea. These species are generalist predators of fishes and invertebrates with the potential to disrupt the ecology of the invaded range. Lionfishes have been present in low numbers along the east coast of Florida since the 1980s, but were not reported in the Florida Keys until 2009. We document the appearance and rapid spread of lionfishes in the Florida Keys using multiple …

Dynamics Of An Acute Coral Disease Outbreak Associated With The Macroalgae Dictyota Spp. In Dry Tortugas National Park, Florida, Usa, Marilyn E. Brandt, Benjamin I. Ruttenberg, Rob Waara, Jeff Miller, Brian Witcher, Andrew J. Estep, Matt Patterson

Biological Sciences

Reports of coral disease outbreaks have increased in recent decades, but often few details are known about these outbreaks, such as environmental triggers, associated biological variables, or even the precise temporal span of the outbreak. Here we document an acute outbreak of a rapid tissue loss disease on the highest live coral cover (15%–30%) reefs within Dry Tortugas National Park, Florida, USA. This disease exhibited similar signs to white plague disease with the notable exception that a white film often was observed on the recently denuded skeleton. The temporal span of the disease was short (<2 mo). Partial mortality was recorded but there was no detectable impact to overall coral cover. A significant increase and then decrease in the cover of macroalgae, primarily of the genus Dictyota, occurred simultaneously …

Characterization Of Biofilm Formation By Borrelia Burgdorferi In Vitro, Eva Sapi, Scott L. Bastian, Cedric L. Mpoy, Shernea Scott, Amy Rattelle, Namrata Pabbati, Akhila Poruri, Divya Burugu, Priyanka A. Theophilus, Truc V. Pham, Akshita Datar, Navroop K. Dhaliwal, Alan Macdonald, Michael J. Rossi, Saion K. Sinha, David F. Luecke

Biology and Environmental Science Faculty Publications

Borrelia burgdorferi, the causative agent of Lyme disease, has long been known to be capable of forming aggregates and colonies. It was recently demonstrated that Borrelia burgdorferi aggregate formation dramatically changes the in vitro response to hostile environments by this pathogen. In this study, we investigated the hypothesis that these aggregates are indeed biofilms, structures whose resistance to unfavorable conditions are well documented. We studied Borrelia burgdorferi for several known hallmark features of biofilm, including structural rearrangements in the aggregates, variations in development on various substrate matrices and secretion of a protective extracellular polymeric substance (EPS) matrix using several modes …

Daily Energy Expenditure In Precocial Shorebird Chicks: Smaller Species Perform At Higher Levels, Robert Ricklefs, Karen Krijgsveld, G. Visser

Biology Department Faculty Works

We measured daily energy expenditure (DEE) during the development periods of precocial chicks of five species of Arctic shorebirds spanning a broad range in size, in order to investigate the relationships between DEE, body size, and growth rate. We also quantified the effect of weather conditions on the energy expenditure of chicks to establish the impact of cold arctic weather on their time and energy budgets. We used the doubly labeled water method to measure DEE at ambient temperatures in an outside enclosure on the subarctic tundra at Churchill, Manitoba, Canada. Growth rate was highest in the smallest species, and …

Arenavirus Infection Induces Discrete Cytosolic Structures For Rna Replication, Nicholas L. Baird, Joanne York, Jack H. Nunberg

Biological Sciences Faculty Publications

Arenaviruses are responsible for acute hemorrhagic fevers with high mortality and pose significant threats to public health and biodefense. These enveloped negative-sense RNA viruses replicate in the cell cytoplasm and express four proteins. To better understand how these proteins insinuate themselves into cellular processes to orchestrate productive viral replication, we have identified and characterized novel cytosolic structures involved in arenavirus replication and transcription. In cells infected with the nonpathogenic Tacaribe virus or the attenuated Candid#1 strain of Junin virus, we find that newly synthesized viral RNAs localize to cytosolic puncta containing the nucleoprotein (N) of the virus. Density gradient centrifugation …

Dispositional Depression And Hostility Are Associated With Inflammatory Markers Of Cardiovascular Disease In African Americans, Michael Lipscomb

Department of Biology Faculty Publications

Prior research has demonstrated that state depressive symptoms and hostility can modulate inflammatory immune responses and directly contribute to cardiovascular disease (CVD) onset and development. Previous studies have not considered the contribution of dispositional depressive symptoms to the inflammatory process. They have also largely excluded African Americans, despite their disproportionate risk for CVD. The first aim of the study was to examine the impact of state and dispositional depression and hostility on CVD-associated inflammatory biomarkers interleukin-6 (IL-6) and C-reactive protein (CRP) in an African American sample. The second aim was to examine synergistic influences of hostility and state and dispositional …

Integrating Technology, Field Experience And Collaboration In An Undergraduate Biology Research Course, Melissa M. Grigione, Dan Farkas

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Phylogeny Of A Neotropical Clade In The Gesneriaceae: More Tales Of Convergent Evolution, John L. Clark, Minde M. Funke, Aaron M. Duffy, James F. Smith

Biology Faculty Publications and Presentations

The Gesneriaceae is a family known for convergent evolution of complex floral forms. As a result, defining genera and resolving evolutionary relationships among such genera using morphological data alone has been challenging and often does not accurately reflect monophyletic lineages. The tribe Episcieae is the most diverse within Neotropical Gesneriaceae in terms of its number of species and morphological diversity. As a result, defining genera using floral characters has been historically troublesome. Here we investigate relationships among genera of the tribe using an array of chloroplast DNA, nuclear ribosomal genes, and low-copy nuclear genes to provide resolution for the monophyly …

The Importance Of Host Plant Limitation For Caterpillars Of An Arctiid Moth (Platyprepia Virginalis) Varies Spatially, Richard Karban, Patrick Grof-Tisza, John L. Maron, Marcel Holyoak

Biological Sciences Faculty Publications

Spatial dynamic theories such as source–sink models frequently describe habitat-specific demographies, yet there are surprisingly few field studies that have examined how and why interacting species vary in their dynamics across multiple habitat types. We studied the spatial pattern of interaction between a chewing herbivore and its primary larval host plant in two habitat types. We found that the interaction between an arctiid caterpillar (Platyprepia virginalis) and its host (Lupinus arboreus) differed in wet vs. upland dry habitats, as did yearly population dynamics for the caterpillar. In upland sites, there was a strong positive relationship between …