Biology Commons^™

Diet Of Juvenile Alabama Shad (Alosa Alabamae) In Two Northern Gulf Of Mexico Drainages, Paul F. Mickle, Jacob F. Schaefer, Donald A. Yee, Susan B. Adams

Faculty Publications

Understanding food-web ecology is valuable to conservation by linking interactions of multiple species together and illustrating the functionality of trophic exchange. Alosa alabamae (Alabama Shad), an anadromous species, reproduces in northern Gulf of Mexico drainages from February through May, and for this study, the Pascagoula and Apalachicola rivers were chosen to sample juvenile Alabama Shad. The age-0 fish mature within these rivers and have the potential to impact the food web of the systems in which maturation occurs. The focus was to determine if diet changes as Alabama Shad mature, and to identify diet differences between drainages. Diets of Alabama …

Sugar Promotes Vegetative Phase Change In Arabidopsis Thaliana By Repressing The Expression Of Mir156a And Mir156c, Li Yang, Mingli Xu, Yeonjong Koo, Jia He, R. Scott Poethig

Faculty Publications

Nutrients shape the growth, maturation, and aging of plants and animals. In plants, the juvenile to adult transition (vegetative phase change) is initiated by a decrease in miR156. In Arabidopsis, we found that exogenous sugar decreased the abundance of miR156, whereas reduced photosynthesis increased the level of this miRNA. This effect was correlated with a change in the timing of vegetative phase change, and was primarily attributable to a change in the expression of two genes, MIR156A and MIR156C, which were found to play dominant roles in this transition. The glucose-induced repression of miR156 was dependent on the …

Genomic Reconstruction Of Transcriptional Regulatory Networks In Lactic Acid Bacteria, Dmitri A. Ravcheev, Aaron A. Best, Natalia V. Sernova, Marat D. Kazanov, Pavel S. Novichkov, Dmitri A. Rodionov

Faculty Publications

Background

Genome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms having a large economic impact, including both human and animal pathogens and strains used in the food industry. Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group.

Results

A comparative genomics approach was used for reconstruction of transcriptional regulatory networks in 30 selected genomes of lactic acid bacteria. The inferred networks comprise regulons for 102 orthologous transcription factors (TFs), including 47 novel regulons for previously uncharacterized …

Lake Macrophyte Nutrient Index Of Standing Waters In Serbia (Limnis), Dušanka Laketić, Snežana Radulović, Milica Živković, Tamara Jurca, Mac H. Alford

Faculty Publications

The aim of this study was to derive a Macrophyte Nutrient Index for standing waters in Serbia, based on the LEAFPACS method and to correlate it against existing Lake Typology.

A single data matrix of 46 species and 1463 sample quadrats was compiled from two datasets: a revised phytocenological database given according to Braun-Blanquet Cover Abundance Scale and a database of sample quadrats collected during the summer months of 2009, 2010 and 2011 at 31 lakes in Serbia. The nutrient indices (MSI) for 46 lake hydrophytes were calculated using the Reprediction Algorithm on N-Ellenberg's values. A Macrophyte …

Pan-Arctic Distributions Of Continental Runoff In The Arctic Ocean, Cédric G. Fichot, Karl Kaiser, Stanford B. Hooker, Rainer M.W. Amon, Marcel Babin, Simon Bélanger, Sally A. Walker, Ronald Benner

Faculty Publications

Continental runoff is a major source of freshwater, nutrients and terrigenous material to the Arctic Ocean. As such, it influences water column stratification, light attenuation, surface heating, gas exchange, biological productivity and carbon sequestration. Increasing river discharge and thawing permafrost suggest that the impacts of continental runoff on these processes are changing. Here, a new optical proxy was developed and implemented with remote sensing to determine the first pan-Arctic distribution of terrigenous dissolved organic matter (tDOM) and continental runoff in the surface Arctic Ocean. Retrospective analyses revealed connections between the routing of North American runoff and the recent freshening of …

Contact Hypersensitivity To Oxazolone Provokes Vulvar Mechanical Hyperalgesia In Mice, Tijana Martinov, Rose Glenn-Finer, Sarah Burley, Elena Tonc, Evelyn Balsells, Alyssa Ashbaugh, Linnea Swanson, Randy S. Daughters, Devavani Chatterjea

Faculty Publications

The interplay among pain, allergy and dysregulated inflammation promises to yield significant conceptual advances in immunology and chronic pain. Hapten-mediated contact hypersensitivity reactions are used to model skin allergies in rodents but have not been utilized to study associated changes in pain perception in the affected skin. Here we characterized changes in mechanical hyperalgesia in oxazolone-sensitized female mice challenged with single and repeated labiar skin exposure to oxazolone. Female mice were sensitized with topical oxazolone on their flanks and challenged 1-3 times on the labia. We then measured mechanical sensitivity of the vulvar region with an electronic pressure meter and …

Effects Of Storage Conditions On The Morphology And Titer Of Lentiviral Vectors, H. Rahman, Josephine Taylor, Beatrice Clack, R. S. Stewart, Sarah C. Canterberry

Faculty Publications

Lentiviral vectors are commonly used in laboratory experiments to stably integrate transgenes into host genomes. It has long been observed that storage of virus stocks leads to a decrease in viral titer, but the mechanisms driving this decrease have yet to be identified. To that end, lentiviral vector stocks were generated and stored as follows: room temperature for less than one hour, -80ºC for 24 hours, 4ºC for three days and 4ºC for 7 days. These stocks were subsequently evaluated with regard to their transducing ability and their morphology, specifically particle diameter. The vector that was stored at room temperature …

Differential Habitat Use By Common Watersnakes (Nerodia Sipedon), Lorin A. Neuman-Lee, Andrew M. Durso, Nicholas M. Kiriazis, Melanie J. Olds, Stephen J. Mullin

Faculty Publications

Understanding intraspecific variation in habitat use is important for the management of any species. In many studies of reptiles, habitat use by juveniles is poorly understood when compared to their adult conspecifics because of capture biases and logistical constraints. We compared habitat use between sexes and age classes of Common Watersnakes (Nerodia sipedon) at a reservoir in central Illinois. Juvenile N. sipedon occurred more frequently in habitat with high canopy cover, whereas adult N. sipedon, especially reproductive females, were found exclusively in habitat with no canopy cover. Adult males used both locations equally. We emphasize the need to investigate ontogenetic …

Differential Jumping Performance In Newly Metamorphosed Blanchard's Cricket Frogs, Acris Blanchardi (Anura: Hylidae), From Fish- And Invertebrate-Dominated Ponds, Taylor L. Hall, Daniel Saenz, Matthew Kwiatkowski

Faculty Publications

Organisms that adopt phenotypically plastic anti-predator strategies during larval stages may incur fitness costs later in development. These costs are typically difficult to define in many species. The difficulty of identifying ecological trade-offs may result from experimental comparisons that do not adequately mirror naturally occurring predator-prey relatioships. To examine this, we captured 61 newly metamorphosed Acris blanchardi from ponds dominated either by fish or invertebrate predators. These predators are known to induce alternate phenotypic anti-predator responses at the larval stage. We use jumping performance as a measure of post-metamorphic fitness, and compared the morphological traits and jumping ability of frogs …

Synergistic Effects Of The Invasive Chinese Tallow (Triadica Sebifera) And Climate Change On Aquatic Amphibian Survival, Daniel Saenz, Erin M. Fucik, Matthew Kwiatkowski

Faculty Publications

Changes in climate and the introduction of invasive species are two major stressors to amphibians, although little is known about the interaction between these two factors with regard to impacts on amphibians. We focused our study on an invasive tree species, the Chinese tallow (Triadica sebifera), that annually sheds its leaves and produces leaf litter that is known to negatively impact aquatic amphibian survival. The purpose of our research was to determine whether the timing of leaf fall from Chinese tallow and the timing of amphibian breeding (determined by weather) influence survival of amphibian larvae. We simulated a …

Assessment Of Genetic Diversity In Peruvian Amaranth (Amaranthus Caudatus And A. Hybridus) Germplasm Using Single Nucleotide Polymorphism Markers [Abstract], Felix Jimenez, Peter J. Maughan, Aquilino Alvarez, Kiel D. Kielinski, Scott M. Smith, Donald B. Pratt, David B. Elzinga, Eric N. Jellen

Faculty Publications

No abstract provided.

Tnt1 Retrotransposon Mutagenesis: A Tool For Soybean Functional Genomics, Yaya Cui, Shyam Barampuram, Minviluz G. Stacey, C. Nathan Hancock, Seth Findley, Melanie Mathieu, Zhanyuan Zhang, Wayne A. Parrott, Gary Stacey

Faculty Publications

Insertional mutagenesis is a powerful tool for determining gene function in both model and crop plant species. Tnt1, the transposable element of tobacco (Nicotiana tabacum) cell type 1, is a retrotransposon that replicates via an RNA copy that is reverse transcribed and integrated elsewhere in the plant genome. Based on studies in a variety of plants, Tnt1 appears to be inactive in normal plant tissue but can be reactivated by tissue culture. Our goal was to evaluate the utility of the Tnt1 retrotransposon as a mutagenesis strategy in soybean (Glycine max). Experiments showed that the …

Enhancing Pcr Amplification Of Dna From Recalcitrant Plant Specimens Using A Trelahose-Based Additive, Tharangamala Samarakoon, Shiao Y. Wang, Mac H. Alford

Faculty Publications

Premise of the study: PCR amplification of DNA extracted from plants is sometimes difficult due to the presence of inhibitory compounds. An effective method to overcome the inhibitory effect of compounds that contaminate DNA from difficult plant specimens is needed.

Methods and Results: The effectiveness of a PCR additive reagent containing trehalose, bovine serum albumin (BSA), and polysorbate‐20 (Tween‐20) (TBT‐PAR) was tested. PCR of DNA extracted from fresh, silica‐dried, and herbarium leaf material of species of Achariaceae, Asteraceae, Lacistemataceae, and Samydaceae that failed using standard techniques were successful with the addition of TBT‐PAR.

Conclusions: The addition of TBT‐PAR during routine …

Neutrophil In Viral Infections, Friend Or Foe?, Brandon D. Drescher, Fengwei Bai

Faculty Publications

Polymorphonuclear leukocytes or neutrophils are the first immune cells to the site of injury and microbial infection. Neutrophils are crucial players in controlling bacterial and fungal infections, and in particular secondary infections, by phagocytosis, degranulation and neutrophil extracellular traps (NETs). While neutrophils have been shown to play important roles in viral pathogenesis, there is a lack of detailed investigation. In this article, we will review recent progresses toward understanding the role of neutrophils in viral pathogenesis. (C) 2012 Elsevier B.V. All rights reserved.

Presenting Fake Figures: A Tool To Teach Effective Scientific Figure Design, Verónica A. Segarra, Stephanie Pulford, Susan Walsh

Faculty Publications

No abstract provided.

An Allele Of Sequoia Dominantly Enhances A Trio Mutant Phenotype To Influence Drosophila Larval Behavior, Kathryn E. Dean, April Fields, Marcus J. Geer, Eric C. King, Eric C. Liebl

Faculty Publications

No abstract provided.

Diets Of Two Species Of Horned Lizards (Phrynosoma Modestum And P. Solare) From Mexico, J. A. Lemos-Espinal, Christopher J. Dibble, Geoffrey R. Smith

Faculty Publications

No abstract provided.

Orientocreadium Batrachoides Tubangui, 1931 (Orientocreadiidae): The Only Trematode Parasite Of Clarias Gariepinus (Burchell, 1822) (Clariidae) From The Asi River (Southern Turkey), Tayha Tepe, Mehmet Cemal Oğuz, Mark C. Belk, Remzi Özgen

Faculty Publications

Objective: Some information is available about the parasite fauna and incidence for Clarias gariepinus in Turkey, but digenean parasites have received little attention. The purpose of the study is to contribute to the parasite fauna of Turkey.

Methods: From 2007 to 2008, a total 63 Clarias gariepinus that were caught in the Asi River were purchased from the fish market in Hatay and brought on ice to the Parasitology Research Laboratory at Atatürk University. The fish were dissected. The obtained parasites were fixed with AFA, dyed with Mayer’s Carmalum, and mounted with Canada Balsam.

Results: Forty-eight fish were infected with …

Local Filters Limit Species Diversity, But Species Pools Determine Composition, Tara K. Rajaniemi, Deborah E. Goldberg, Roy Turkington, Andrew R. Dyer

Faculty Publications

In a series of three experiments, we tested for effects of species pools, resource stress, and species interactions on four aspects of community structure: species richness, evenness, species composition, and functional group composition. We also examined whether the impacts of species interactions on the community varied with resource availability or species pool. Communities of sand dune annuals grew from seed bank samples collected from two sites in three different years, so that the species pool differed at two levels: the source site and the year of seed bank collection. Communities experienced one of three irrigation treatments and a range of …

Stable Bifurcations In Semelparous Leslie Models, J. M. Cushing, Shandelle M. Henson

Faculty Publications

In this paper, we consider nonlinear Leslie models for the dynamics of semelparous age-structured populations. We establish stability and instability criteria for positive equilibria that bifurcate from the extinction equilibrium at R0=1. When the bifurcation is to the right (forward or super-critical), the criteria consist of inequalities involving the (low-density) between-class and within-class competition intensities. Roughly speaking, stability (respectively, instability) occurs if between-class competition is weaker (respectively, stronger) than within-class competition. When the bifurcation is to the left (backward or sub-critical), the bifurcating equilibria are unstable. We also give criteria that determine whether the boundary of the positive cone is …

The Role Of Individual Behavior Type In Mediating Indirect Interactions, Blaine D. Griffen, Benjamin J. Toscano, John Gatto

Faculty Publications

Trait-mediated indirect interactions (TMII) play an important role in structuring natural communities, and numerous studies have experimentally demonstrated their presence in a variety of systems. However, these studies have largely examined the presence or absence of traits that are responsible for these interactions, without considering natural variation between individuals in the extent to which these traits are manifested. We used a well-documented TMII to investigate the importance of individual behavior type for determining the strength of the TMII. The toadfish Opsanus tau has an indirect positive influence on bivalve survival because the mud crab Panopeus herbstii, a consumer of bivalves, …

A Plant Virus Substrate Induces Early Upregulation Of Bmp2 For Rapid Bone Formation, Pongkwan Sitasuwan, L. Andrew Lee, Peng Bo, Erin N. Davis, Yuan Lin, Qian Wang

Faculty Publications

Many nanoscale materials have been developed to investigate the effects on stem cell differentiations via topographical and chemical cues for applications in tissue engineering and regenerative medicine. The use of plant viruses as cell supporting substrates has been of particular interest due to the rapid induction of bone marrow derived mesenchymal stem cells (BMSCs) towards osteogenic cells. In this study, the role of Tobacco mosaic virus (TMV) and its early effects on osteoinduction with particular emphasis on the regulation of bone morphogenetic protein-2 (BMP2) was examined. We observed that the cells on the virus substrate immediately aggregated and formed bone-like …

Dispersal Behavior Correlates With Personality Of A North American Fish, Josh E. Rasmussen, Mark C. Belk

Faculty Publications

The process of dispersal is determined by the interaction of individual (intrinsic) traits and environmental (extrinsic) factors. Although many studies address and quantify dispersal, few evaluate both intrinsic and extrinsic factors jointly. We test the relative importance of intrinsic traits (exploration tendency and size) and extrinsic factors (population density and habitat quality) on dispersal of a medium-sized western United States minnow, southern leatherside chub Lepidomeda aliciae. A generalized linear model with a binomial response was used to determine the probability of individuals dispersing one year after tagging. Medium-sized individuals that were more prone to explore novel environments were 10.7 …

Tracing The Transport Of Colored Dissolved Organic Matter In Water Masses Of The Southern Beaufort Sea: Relationship With Hydrographic Characteristics, A. Matsuoka, A. Bricaud, Ronald Benner, J. Para, R. Sempéré, L. Prieur, S. Bélanger, M. Babin

Faculty Publications

Light absorption by colored dissolved organic matter (CDOM) [aCDOM(λ)] plays an important role in the heat budget of the Arctic Ocean, contributing to the recent decline in sea ice, as well as in biogeochemical processes. We investigated aCDOM(λ) in the Southern Beaufort Sea where a significant amount of CDOM is delivered by the Mackenzie River. In the surface layer, aCDOM(440) showed a strong and negative correlation with salinity, indicating strong river influence and conservative transport in the river plume. Below the mixed layer, a weak but positive correlation between aCDOM(440) and salinity was observed above the upper halocline, resulting from …

Caprg: Sequence Assembling Pipeline For Next Generation Sequencing Of Non-Model Organisms, Arun Rawat, Mohamed O. Elasri, Kurt A. Gust, Glover George, Don Pham, Leona D. Scanlan, Chris Vulpe, Edward J. Perkins

Faculty Publications

Our goal is to introduce and describe the utility of a new pipeline “Contigs Assembly Pipeline using Reference Genome” (CAPRG), which has been developed to assemble “long sequence reads” for non-model organisms by leveraging a reference genome of a closely related phylogenetic relative. To facilitate this effort, we utilized two avian transcriptomic datasets generated using ROCHE/454 technology as test cases for CAPRG assembly. We compared the results of CAPRG assembly using a reference genome with the results of existing methods that utilize de novo strategies such as VELVET, PAVE, and MIRA by employing parameter space comparisons (intra-assembling comparison). CAPRG performed …

Differences In Spectral Sensitivity Within And Among Species Of Darters (Genus Etheostoma), Jennifer M. Gumm, Ellis R. Lowe, Tamra C. Mendelson

Faculty Publications

We examined variation in the visual system both within and among seven species of darters, colorful freshwater fishes of the genus Etheostoma. Using microspectrophotometry, we found that darters possess rod photoreceptor cells, single cone photoreceptor cells containing middle wavelength sensitive (MWS) visual pigments, and twin photoreceptor cells containing (LWS) visual pigments. No variation in peak sensitivity was detected among species or individuals in the rod class. In the MWS class, significant variation was detected among species and a strong statistical trend suggests differences among individuals. By contrast, all differences in the LWS class could be attributed to variation among individuals. …

Reproductive Strategy Of Male And Female Eastern Spiny Lizards Sceloporus Spinosus (Squamata: Phrynosomatidae) From A Region Of The Chihuahuan Desert, Mexico, A. Ramirez-Bautista, B. P. Stephenson, X. Hernandez-Ibarra, U. Hernandez-Salinas, R. Cruz-Elizalde, A. Lozano, Geoffrey R. Smith

Faculty Publications

No abstract provided.

A Contribution To The Knowledge Of The Ochid Bes Of The Los Amigos Biological Station, Peru (Hymenoptera, Apidae, Euglossini) [Abstract], R. Niemack, Ismael A. Hinojosa-Diaz, Daniel J. Bennett, C. S. Chaboo

Faculty Publications

No abstract provided.

Effects Of An Invasive Plant, Chinese Tallow (Triadica Sebifera), On Development And Survival Of Anuran Larvae, Taylor B. Cotten, Matthew Kwiatkowski, Daniel Saenz, Michael Collyer

Faculty Publications

Amphibians are considered one of the most threatened vertebrate groups. Although numerous studies have addressed the many causes of amphibian population decline, little is known about effects of invasive plants. Chinese tallow (Triadica sebifera) is an exotic deciduous tree that has invaded the southeastern United States. Amphibian larvae in environments invaded by T. sebifera may be impacted negatively as autumn leaf litter decomposes in natal areas. We compared effects of leaf litter decomposition from T. sebifera and two native tree species on survival and development of four species of anuran larvae from eastern Texas. Larvae from Pseudacris fouquettei, Lithobates (Rana) …

New Species Of Macrocephalic Halictine Bees (Hymenoptera: Halictidae) [Abstract], Michael S. Engel, Ismael A. Hinojosa-Diaz, Daniel J. Bennett

Faculty Publications

No abstract provided.