Digital Commons Network^™

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel Isaac Speiser, M Sabrina Pankey, Alexandera K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Faculty Publications

Background

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis …

Viability Costs Of Reproduction And Behavioral Compensation In Western Mosquitofish (Gambusia Affinis), Clinton T. Laidlaw, Jacob M. Condon, Mark C. Belk

Faculty Publications

The cost of reproduction hypothesis suggests that current reproduction has inherent tradeoffs with future reproduction. These tradeoffs can be both in the form of energy allocated to current offspring as opposed to somatic maintenance and future reproduction (allocation costs), or as an increase in mortality as a result of morphological or physiological changes related to reproduction (viability costs). Individuals may be able to decrease viability costs by altering behavior. Female western mosquitofish, Gambusia affinis experience a reduction in swimming ability as a consequence of pregnancy. We test for a viability cost of reproduction, and for behavioral compensation in pregnant female …

Genetic Dominance & Cellular Processes, Robert D. Seager

Faculty Publications

In learning genetics, many students misunderstand and misinterpret what “dominance” means. Understanding is easier if students realize that dominance is not a mechanism, but rather a consequence of underlying cellular processes. For example, metabolic pathways are often little affected by changes in enzyme concentration. This means that enzyme-producing alleles usually show complete dominance. For genes producing nonenzymatic proteins such as collagen or hemoglobin, the amount of product matters, and dominance relationships are more complicated. Furthermore, with hemoglobin, dominance can change depending on what aspect of the phenotype is being studied and on the environmental conditions. X-linked genes are a special …

Residency Time As An Indicator Of Reproductive Restraint In Male Burying Beetles, Ashlee N. Smith, Mark C. Belk, J. Curtis Creighton

Faculty Publications

The cost of reproduction theory posits that there are trade-offs between current and future reproduction because resources that are allocated to current offspring cannot be used for future reproductive opportunities. Two adaptive reproductive strategies have been hypothesized to offset the costs of reproduction and maximize lifetime fitness. The terminal investment hypothesis predicts that as individuals age they will allocate more resources to current reproduction as a response to decreasing residual reproductive value. The reproductive restraint hypotheses predicts that as individuals age they will allocate fewer resources to current reproduction to increase the chance of surviving for an additional reproductive opportunity. …

A Comparison Of The Caulobacter Na1000 And K31 Genomes Reveals Extensive Genome Rearrangements And Differences In Metabolic Potential, Kurt Ash, Theta Brown, Tynetta Watford, Latia E. Scott, Craig Stephens, Bert Ely

Faculty Publications

The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4°C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. …

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

Faculty Publications

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

Identification And Characterization Of An Operon, Msaabcr, That Controls Virulence And Biofilm Development In Staphlococcus Aureus, Gyan S. Sahukhal, Mohamed O. Elasri

Faculty Publications

Background

Community-acquired, methicillin-resistant Staphylococcus aureus strains often cause localized infections in immunocompromised hosts, but some strains show enhanced virulence leading to severe infections even among healthy individuals with no predisposing risk factors. The genetic basis for this enhanced virulence has yet to be determined. S. aureus possesses a wide variety of virulence factors, the expression of which is carefully coordinated by a variety of regulators. Several virulence regulators have been well characterized, but others have yet to be thoroughly investigated. Previously, we identified the msa gene as a regulator of several virulence genes, biofilm development, and antibiotic resistance. We also …

Male-Male Clasping May Be Part Of An Alternative Reproductive Tactic In Xenopus Laevis, Heather J. Rhodes, Rachel J. Stevenson, Courtney L. Ego

Faculty Publications

No abstract provided.

Prior Experience Affects Allocation To Current Reproduction In A Burying Beetle, Eric J. Billman, J. Curtis Creighton, Mark C. Belk

Faculty Publications

The cost of reproduction hypothesis predicts that the level of reproductive investment to current reproduction is constrained by an individual’s future reproductive potential or residual reproductive value. Therefore, age, or differences between young and old individuals in residual reproductive value, is expected to influence reproductive investment. However, recent theoretical work suggests that residual reproductive value is also influenced by an individual’s state or condition which may in part be determined by prior reproductive experience. We evaluated the reproductive investment of same-aged female burying beetles (Nicrophorus orbicollis) to determine how prior reproductive experience affects current reproduction. Consistent with previous …

Correction Of The Caulobacter Crescentus Na1000 Genome Annotation, Bert Ely, Latia Etheredge Scott

Faculty Publications

Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading …

Structural And Functional Analyses Of A Glutaminyl Cyclase From Ixodes Scapularis Reveal Metal-Independent Catalysis And Inhibitor Binding, Kai-Fa Huang, Hui-Ling Hsu, Shahid Karim, Andrew H.-J. Wang

Faculty Publications

Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10–1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-­sheet, resulting in an increased thermal stability. Is-QC contains ∼0.5 stoichiometric zinc ions, which could …

Morphological Divergence Driven By Predation Environment Within And Between Species Of Brachyrhaphis Fishes, Spencer J. Ingley, Eric J. Billman, Mark C. Belk, Jerald B. Johnson

Faculty Publications

Natural selection often results in profound differences in body shape among populations from divergent selective environments. Predation is a well-studied driver of divergence, with predators having a strong effect on the evolution of prey body shape, especially for traits related to escape behavior. Comparative studies, both at the population level and between species, show that the presence or absence of predators can alter prey morphology. Although this pattern is well documented in various species or population pairs, few studies have tested for similar patterns of body shape evolution at multiple stages of divergence within a taxonomic group. Here, we examine …

Intraspecific Variation In Carapace Morphology Among Fiddler Crabs (Genus Uca) From The Atlantic Coast Of Brazil, Kelsey R. Hampton, Melanie J. Hopkins, John C. Mcnamara, Carl L. Thurman

Faculty Publications

Isolation due to geographical barriers should promote genetic and morphological divergence among populations. Marine currents flowing in opposing directions along landmasses can constitute barriers that isolate populations dependent upon aquatic dispersal. The distribution of fiddler crabs (genus Uca) is regulated primarily by the oceanic transport of their planktonic larvae and by available adult habitat. Along the Brazilian coast of eastern South America, the flow of 2 major oceanic currents separates northern from southern Uca populations, which may promote intraspecific divergence in ‘trans-Brazilian’ species. Populations of 10 Uca species were sampled at 64 locations north and south of the Ponta …

Streamwise Vortices Destabilize Swimming Bluegill Sunfish, Anabela Maia, Alex P. Sheltzer, Eric D. Tytell

Faculty Publications

In their natural environment, fish must swim stably through unsteady flows and vortices, including vertical vortices, typically shed by posts in a flow, horizontal cross-flow vortices, often produced by a step or a waterfall in a stream, and streamwise vortices, where the axis of rotation is aligned with the direction of the flow. Streamwise vortices are commonly shed by bluff bodies in streams and by ships’ propellers and axial turbines, but we know little about their effects on fish. Here, we describe how bluegill sunfish use more energy and are destabilized more often in flow with strong streamwise vorticity. The …

Egg Cannibalism In A Gull Colony Increases With Sea Surface Temperature, Lynelle M. Weldon, Shandelle M. Henson, James Hayward, Brianna G. Payne, Libby C. Megna, Andre E. Moncrieff

Faculty Publications

Cannibalism occurs regularly across a broad range of taxa with a variety of ecological and evolutionary consequences. Rises in sea surface temperature (SST) have been linked to increased cannibalism in some species, including polar bears (Ursus maritimus), Peruvian anchovy (Engraulis ringens), and Peruvian hake (Merluccius gayi peruanus), and might be expected in birds that depend on marine food webs for sustenance. Increased SSTs are associated with lowered ocean thermoclines and weakened upwellings. These changes, in turn, lead to decreased productivity in surface water and movement of surviving forage fish to deeper water, thereby food-stressing surface feeders such as gulls, diminishing …

Feeding Interactions Between Juvenile And Adult Flightless Cormorants., James Hayward, Libby C. Megna, Brianna G. Payne

Faculty Publications

We report observations on chick feedings by adult Flightless Cormorants Phalacrocorax harrisi, indicating that, contrary to the literature, the sequence of interaction is similar to that of other Pelecaniformes.

A Course-Based Research Experience: How Benefits Change With Increased Investment In Instructional Time, Christopher D. Shaffer, Consuelo J. Alvarez, April E. Bednarski, David Dunbar, Anya L. Goodman, Catherine Reinke, Anne G. Rosenwald, Michael J. Wolyniak, Cheryl Bailey, Daron Barnard, Christopher Bazinet, Dale L. Beach, James E.J. Bedard, Satish Bhalla, John Braverman, Martin Burg, Vidya Chandrasekaran, Hui-Min Chung, Kari Clase, Randall J. Dejong, Justin R. Diangelo, Chunguang Du, Todd T. Eckdahl, Heather Eisler, Julia A. Emerson, Amy Frary, Donald Frohlich, Yuying Gosser, Shubha Govind, Adam Haberman, Amy T. Hark, Charles Hauser, Arlene Hoogewerf, Laura L.M. Hoopes, Carina E. Howell, Diana Johnson, Christopher J. Jones, Lisa Kadlec, Marian Kaehler, S. Catherine Silver Key, Adam Kleinschmit, Nighat P. Kokan, Olga Kopp, Gary Kuleck, Judith Leatherman, Jane Lopilato, Christy Mackinnon, Juan Carlos Martinez-Cruzado, Gerard Mcneil, Stephanie Mel, Hemlata Mistry, Alexis Nagengast, Paul Overvoorde, Don W. Paetkau, Susan Parrish, Celeste N. Peterson, Mary Preuss, Laura K. Reed, Dennis Revie, Srebrenka Robic, Jennifer Roecklein-Canfield, Michael R. Rubin, Kenneth Saville, Stephanie Schroeder, Karim Sharif, Mary Shaw, Gary Skuse, Christopher D. Smith, Mary A. Smith, Sheryl T. Smith, Eric Spana, Mary Spratt, Aparna Sreenivasan, Joyce Stamm, Paul Szauter, Jeffrey S. Thompson, Matthew Wawersik, James Youngblom, Leming Zhou, Elaine R. Mardis, Jeremy Buhler, Wilson Leung, David Lopatto, Sarah C.R. Elgin

Faculty Publications

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant …

Relationships Between The Weedy (Amaranthaceae) And The Grain Amaranths [Abstract], Kiel D. Kielinski, Felix Jimenez, Eric N. Jellen, Peter J. Maughan, Scott M. Smith, Donald B. Pratt

Faculty Publications

No abstract provided.

Intrinsic And Extrinsic Factors Influence Expression Of Defensive Behavior In Plains Hog‐Nosed Snakes [Abstract], Andrew M. Durso, Stephen J. Mullin

Faculty Publications

No abstract provided.

Assessing Multiple Endpoints Of Atrazine Ingestion On Gravid Northern Watersnakes (Nerodia Sipedon) And Their Offspring [Abstract], L. A. Neuman-Lee, K. F. Gaines, K. A. Baumgartner, J. R. Voorhees, J. M. Novak, Stephen J. Mullin

Faculty Publications

No abstract provided.

Cloning, Expression, Sequence Analysis And Homology Modeling Of The Prolyl Endoprotease From Eurygaster Integriceps Puton, Ravi Chandra Yandamuri, Ranjeeta Gautam, Charles Darkoh, Vanitha Dareddy, Mustapha El-Bouhssini, Beatrice A. Clack

Faculty Publications

Eurygaster integriceps Puton, commonly known as sunn pest, is a major pest of wheat in Northern Africa, the Middle East and Eastern Europe. This insect injects a prolyl endoprotease into the wheat, destroying the gluten. The purpose of this study was to clone the full length cDNA of the sunn pest prolyl endoprotease (spPEP) for expression in E. coli and to compare the amino acid sequence of the enzyme to other known PEPs in both phylogeny and potential tertiary structure. Sequence analysis shows that the 5ꞌ UTR contains several putative transcription factor binding sites for transcription factors known to be …

Effect Of Origanum Chemotypes On Broiler Intestinal Bacteria, Liliana Betancourt, Fernando Rodriguez, Vienvilay Phandanouvong, Claudia Ariza-Nieto, Michael Hume, David Nisbet, German Afanador-Tellez, Alexandra Martynova-Van Kley, Armen Nalian

Faculty Publications

Essential oils have been proposed as alternatives to antibiotic use in food animal production. This study evaluated 3 chemotypes of the Origanum genus, containing varying amounts of secondary metabolites carvacrol, thymol, and sabinene, in the broiler chicken diet. Aerial parts of Origanum vulgare L. (OL), O. vulgare L. ssp. hirtum (OH), and O. majorana (OM) were collected from a greenhouse located in the high altitude Sabana de Bogotá (Savanna of Bogotá) and O. vulgare L. ssp. hirtum (OG) produced and ground in Greece. Oregano essential oils (OEO) from these plants were obtained by steam distillation and analyzed by gas chromatography …

Multiple Roles For Hoxa3 In Regulating Thymus And Parathyroid Differentiation And Morphogenesis In Mouse, Jena L. Chojnowski, Kyoko Masuda, Heidi A. Trau, Kirk Thomas, Mario Capeechi, Nancy R. Manley

Faculty Publications

Hoxa3 was the first Hox gene to be mutated by gene targeting in mice and is required for the development of multiple endoderm and neural crest cell (NCC)-derived structures in the pharyngeal region. Previous studies have shown that the Hoxa3 null mutant lacks third pharyngeal pouch derivatives, the thymus and parathyroids by E18.5, and organ-specific markers are absent or downregulated during initial organogenesis. Our current analysis of the Hoxa3 null mutant shows that organ-specific domains did undergo initial patterning, but the location and timing of key regional markers within the pouch, including Tbx1, Bmp4 and Fgf8, were altered. …

Importation Of Exotic Ticks And Tick-Borne Spotted Fever Group Rickettsiae Into The United States By Migrating Songbirds, Nabanita Mukherjee, Lorenza Beati, Michael Sellers, Laquita Burton, Steven Adamson, Richard G. Robbins, Frank Moore, Shahid Karim

Faculty Publications

Birds are capable of carrying ticks and, consequently, tick-transmitted microorganisms over long distances and across geographical barriers such as oceans and deserts. Ticks are hosts for several species of spotted fever group rickettsiae (SFGR), which can be transmitted to vertebrates during blood meals. In this study, the prevalence of this group of rickettsiae was examined in ticks infesting migratory songbirds by using polymerase chain reaction (PCR). During the 2009 and 2010 spring migration season, 2064 northward-migrating passerine songbirds were examined for ticks at Johnson Bayou, Louisiana. A total of 91 ticks was removed from 35 individual songbirds for tick species …

Effects Of Landscape Composition And Configuration On Migrating Songbirds: Inference From An Individual-Based Model, Emily B. Cohen, Scott M. Pearson, Frank R. Moore

Faculty Publications

The behavior of long-distance migrants during stopover is constrained by the need to quickly and safely replenish energetic reserves. Replenishing fuel stores at stopover sites requires adjusting to unfamiliar landscapes with little to no information about the distribution of resources. Despite their critical importance to the success of songbird migration, the effects of landscape composition and configuration on fuel deposition rates (FDR [g/d]), the currency of migration, has not been tested empirically. Our objectives were to understand the effects of heterogeneous landscapes on FDR of forest-dwelling songbirds during spring migration. The results of field experiments were used to parameterize a …

Lack Of Sexual Size Dimorphism In Sceloporus Poinsettii From Durango, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, John B. Iverson, Juan Manuel Morales Sandoval

Faculty Publications

No abstract provided.

Leucistic Wood Frog Tadpole (Lithobates Sylvaticus) From Central Ohio, Geoffrey R. Smith

Faculty Publications

No abstract provided.