Biology Commons^™

" Diversity, Endemism, And Conservation Of The Freshwater Crabs Of China" , Neil Cumberlidge, Peter Kl Ng, Darren Cj Yeo, Tohru Naruse, Kirstin S. Meyer, Lara J. Esser

Journal Articles

No abstract provided.

Class Discovery And Prediction Of Tumor With Microarray Data, Bo Liu

All Graduate Theses, Dissertations, and Other Capstone Projects

Current microarray technology is able take a single tissue sample to construct an Affymetrix oglionucleotide array containing (estimated) expression levels of thousands of different genes for that tissue. The objective is to develop a more systematic approach to cancer classification based on Affymetrix oglionucleotide microarrays. For this purpose, I studied published colon cancer microarray data. Colon cancer, with 655,000 deaths worldwide per year, has become the fourth most common form of cancer in the United States and the third leading cause of cancer - related death in the Western world. This research has been focuses in two areas: class discovery, …

Analysis Of The Genetic Structure Of Bithynia Tentaculata Snail Populations In Wisconsin And Minnesota, Sarah J. Whalen

All Graduate Theses, Dissertations, and Other Capstone Projects

In recent years, there have been tens of thousands of waterfowl mortalities in Wisconsin and Minnesota. An invasive species of snail, Bithynia tentaculata, is a host for the trematode parasites (Cyathocotyle bushiensis and Sphaeridiotrema globulus) that have caused these deaths. A microsatellite-enriched genomic library was detected using DNA from a B. tentaculata specimen from Lake Onalaska (Pool 7 of the Upper Mississippi River). Seven polymorphic microsatellite loci were used to genotype snails collected from Lake Butte des Morts, Shawano Lake, and Lake Onalaska in Wisconsin, as well as Lake Winnibigoshish in Minnesota. The genetic diversity of each population was measured …

Reduced Density Of Calbindin Immunoreactive Gabaergic Neurons In Major Depressive Disorder: Relevance To Neuroimaging Studies And Future Directions, Jonathan Hughes

Honors Theses

Background: Several lines of evidence suggest dysfunction of the γ-aminobutyric acid (GABA)ergic system in major depressive disorder. Neuroimaging studies report reduced levels of GABA in the dorsolateral prefrontal and occipital cortex of depressed patients. Our previous postmortem study re-vealed a reduction in the density and size of calbindin-immunoreactive (CB-IR) GABAergic neurons in the prefrontal cortex in major depressive disorder. The goal of this study was to test whether the changes in CB-IR neurons can also be detected in the occipital cortex, where neuroimaging studies report a prominent GABA decrease. Methods: A three-dimensional cell counting probe was used to assess the …

Lea Proteins During Water Stress : Not Just For Plants Anymore., Steven Hand, Michael Menze, Mehmet Toner, Leaf Boswell, Daniel Moore

Faculty and Staff Scholarship

Late embryogenesis abundant (LEA) proteins are extremely hydrophilic proteins that were first identified in land plants. Intracellular accumulation is tightly correlated with acquisition of desiccation tolerance, and data support their capacity to stabilize other proteins and membranes during drying, especially in the presence of sugars like trehalose. Exciting reports now show LEA proteins are not restricted to plants; multiple forms are expressed in desiccation-tolerant animals from at least four phyla. We evaluate here the expression, subcellular localization, biochemical properties and potential functions of LEA proteins in animal species during water stress. LEA proteins are intrinsically unstructured in aqueous solution, but …

Functional Characterization Of Putative Cilia Genes By High-Content Analysis, Cary Lai, Nidhi Gupta, Xiaohui Wen, Linda Rangell, Ben Chih, Andrew S. Peterson, J Fernando Bazan, Li Li, Suzie J. Scales

Biology Faculty Publications

Cilia are microtubule-based protrusions from the cell surface that are involved in a number of essential signaling pathways, yet little is known about many of the proteins that regulate their structure and function. A number of putative cilia genes have been identified by proteomics and comparative sequence analyses, but functional data are lacking for the vast majority. We therefore monitored the effects in three cell lines of small interfering RNA (siRNA) knockdown of 40 of these genes by high-content analysis. We assayed cilia number, length, and transport of two different cargoes (membranous serotonin receptor 6-green fluorescent protein [HTR6-GFP] and the …

Quantifying The Impact Of Gene Flow On Phenotype-Environment Mismatch: A Demonstration With The Scarlet Monkeyflower Mimulus Cardinalis, John R. Paul, Seema N. Sheth, Amy L. Angert

Biology Faculty Publications

Geographic range margins offer testing grounds for limits to adaptation. If range limits are concordant with niche limits, range expansions require the evolution of new phenotypes that can maintain populations beyond current range margins. However, many species' range margins appear static over time, suggesting limits on the ability of marginal populations to evolve appropriate phenotypes. A potential explanation is the swamping gene flow hypothesis, which posits that asymmetrical gene flow from large, well-adapted central populations prevents marginal populations from locally adapting. We present an empirical framework for combining gene flow, environment, and fitness-related phenotypes to infer the potential for maladaptation, …

Evolution And Personal Religious Belief: Christian University Biology-Related Majors’ Search For Reconciliation, Mark Winslow, John Staver, Lawrence C. Scharmann

Department of Teaching, Learning, and Teacher Education: Faculty Publications

The goal of this study was to explore Christian biology-related majors’ perceptions of conflicts between evolution and their religious beliefs. This naturalistic study utilized a case study design of 15 undergraduate biology-related majors at or recent biology-related graduates from a mid-western Christian university. The broad sources of data were interviews, course documents, and observations. Outcomes indicate that most participants were raised to believe in creationism, but came to accept evolution through evaluating evidence for evolution, negotiating the literalness of Genesis, recognizing evolution as a non-salvation issue, and observing professors as Christian role models who accept evolution. This study lends heuristic …

Phospholipid Analysis In Trypanosoma Cruzi, Melissa Rashonda Harris

Open Access Theses & Dissertations

Chagas disease, caused by the flagellate protozoan Trypanosoma cruzi is one of the most endemic and deadly infectious diseases. T.cruzi is distributed throughout most of South and Central America, where it infects 12 to 19 million people, with an annual incidence of 561,000. Another 35 million are exposed to infection, 2 to 3 million people have clinical symptoms of chronic Chagas disease, and about 45,000 of these may die every year due to cardiac failure. In addition to the growing number of incidences in other countries the disease is an emerging infectious disease in the U.S due to the migration …

Altered Leptin Signaling On Dendritic Cells As A Potential Mechanism For Cancer Immunotherapy, Lorena Y. De Los Santos

Open Access Theses & Dissertations

Leptin is a pleiotropic hormone synthesized primarily by white adipocytes and its receptors are expressed in a variety of tissues and cells such as in the hypothalamus and cells of the immune system. Multiple cell types can produce a considerable amount of leptin such as skeletal muscle, placenta, and osteoblasts to name a few and its synthesis has been shown to be regulated by sex hormones and a broad range of inflammatory mediators. Although leptin has been shown to directly affect immune response, we are interested in how leptin affects dendritic cell function and their ability to induce a proper …

Phylogeography Of Northern Populations Of The Black-Tailed Rattlesnake (Crotalus Molossus Baird And Girard, 1853) With The Revalidation Of C. Ornatus Hallowell, 1854, Christopher Anderson

Open Access Theses & Dissertations

The black-tailed rattlesnake (Crotalus molossus Baird and Girard, 1853) is a wide-ranging species complex with representatives from the southwestern United States through the highlands of central and southern Mexico. The systematics of this group has received little attention and in the past six decades only two taxonomic revisions have been proposed (the transfer of C. basiliscus oaxacus to C. molossus and the elevation of C. m. estebanensis to full species). However, a recent revision of the Neotropical rattlesnakes (C. durissus and C. simus) recovered a polyphyletic C. molossus. Sequenced data were obtained from three mitochondrial genes …

Relative Changes In Krillabundance Inferred From Antarctic Fur Seal, T. Huang, L. Sun, John M. Stark, Y. Wang, Z. Cheng, Q. Yang, S. Sun

Biology Faculty Publications

Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (d13C) and nitrogen (d15N) isotopes of …

The Selaginella Genome Identifies Changes In Gene Content Associated With The Evolution Of Vascular Plants, J. A. Banks, T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in …

De Novo Characterization Of The Gametophyte Transcriptome In Bracken Fern, Pteridium Aquilinum, J. P. Der, M. S. Barker, N. J. Wickett, C. W. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.

The Evolution Of Chloroplast Genes And Genomes In Ferns, Paul G. Wolf, J. P. Der, A. M. Duffy, J. B. Davidson, A. L. Grusz, K. M. Pryer

Biology Faculty Publications

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene …

Pcr Detection Of Nearly Any Dengue Virus Strain Using A Highly Sensitive Primer ‘Cocktail’, Charul Gijavanekal, Maria Anez-Lingerfelt, Chen Feng, Catherine Putonti, George E. Fox, Aniko Sabo, Yuriy Fofanov, Richard C. Wilson

Bioinformatics Faculty Publications

PCR detection of viral pathogens is extremely useful, but suffers from thechallenge of detecting the many variant strains of a given virus that ariseover time. Here, we report the computational derivation and initial experi-mental testing of a combination of 10 PCR primers to be used in a singlehigh-sensitivity mixed PCR reaction for the detection of dengue virus. Pri-mer sequences were computed such that their probability of misprimingwith human DNA is extremely low. A ‘cocktail’ of 10 primers was shownexperimentally to be able to detect cDNA clones representing the four sero-types and dengue virus RNA spiked into total human whole blood …

Invasion By Exotic Earthworms Alters Litter- And Soil-Dwelling Oribatid Mites, Jordan L. Burke, John C. Maerz, Joseph Milanovich, Melanie C. Fisk, Kamal J.K. Gandhi

Biology: Faculty Publications and Other Works

Exotic earthworms are drivers of biotic communities in invaded North American forest stands. Here we used ecologically important oribatid mite (Arachnida: Acari) communities, as model organisms to study the responses of litter- and soil-dwelling microarthropod communities to exotic earthworm invasion in a northern temperate forest. Litter- and soil-dwelling mites were sampled in 2008–2009 from forest areas: (1) with no earthworms; (2) those with epigeic and endogeic species, including Lumbricus rubellus Hoffmeister; and (3) those with epigeic, endogeic, and anecic earthworms including L. terrestris L. Species richness and diversity of litter- and soil-dwelling (0–2 cm soil depth) oribatid mites was 1–2 …

Homoplastic Microinversions And The Avian Tree Of Life, Edward L. Braun, Rebecca T. Kimball, Kin-Lan Han, Naomi R. Iuhasz-Velez, Amber J. Bonilla

Biology: Faculty Publications and Other Works

Background

Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution.

Results

We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate …

Diets Of Three Species Of Bufonids (Amphibia, Anura) From Northern Mexico, Geoffrey R. Smith, J. A. Lemos-Espinal, A. B. Burner, K. E. Winter, C. B. Dayer

Faculty Publications

No abstract provided.

Effects Of Mosquitofish (Gambusia Affinis) Cues On Wood Frog (Lithobates Sylvaticus) Tadpole Activity, K. F. Buttermore, P. N. Litkenhaus, D. C. Torpey, Geoffrey R. Smith, Jessica E. Rettig

Faculty Publications

No abstract provided.

Body Temperatures Of Hyla Arenicolor From Sierra De Tepozotlan, Estado De Mexico, Mexico, F. Correa-Sanchez, Geoffrey R. Smith, G. A. Woolrich-Pina, J. A. Lemos-Espinal

Faculty Publications

No abstract provided.

The Effects Of Temperature And Salinity On Wood Frog (Lithobates Sylvaticus) Tadpole Growth And Survival, J. H. Clemmer, E. Z. Miller, Geoffrey R. Smith, Jessica E. Rettig

Faculty Publications

No abstract provided.

Allotetraploid Origin And Divergence In Eleusine (Chloridoideae, Poaceae): Evidence From Low-Copy Nuclear Gene Phylogenies And A Plastid Gene Chronogram, Qing Liu, Jimmy K. Triplett, Jun Wen, Paul M. Peterson

Research, Publications & Creative Work

Background and Aims: Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa.

Methods: Two low-copy nuclear (LCN) markers, Pepc4 and EF-1a, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and …

Determining Impediments To Gene Flow In A Natural Population Of Cornus Florida L. Cornaceae, Using Integrative Landscape Genetic Techniques, Crystal Meadows

Theses and Dissertations

This study examined the impact intervening environment has on gene flow in the insect pollinated understory tree, Cornus florida L., by combining GIS and landscape genetic techniques (Least Cost Path Analysis, Circuit Theory, and Conditional Genetic Distance). Traditional population genetic analysis indicated pair-wise relatedness was significantly correlated to distance (Pearson; r = -0.312, P < 0.001) suggesting a spatial component to offspring relatedness. Dispersal throughout the study site was non-random, exhibiting a high degree of pollen pool structure due to restricted gene flow (Two-Generation Analysis; Φft = 0.161, P = 0.001). Forest structure was quantified in GIS layers representing coniferous canopies, mixed hardwood canopies, C. florida canopies, open understory (roads), and open understory/canopy due to tree removal. Of these layers, landscape isolation for the roads layer provided the best-fit model for describing genetic differentiation among sampled pollen pools (Mantel; r = 0.542, P = 0.001). These data also suggest that improved biological inferences can be gained by examining a range of landscape isolation models.

Changing The Culture Of Science Education At Research Universities, W. Anderson, U Banerjee, C Drennan, Sarah C.R. Elgin, I Epstein, J Handelsman, G Hatfull, R Losick, D O'Dowd, B Olivera, S Strobel, G Walker, I Warner

Biology Faculty Research

No abstract provided.

Population Genetics Of Amphiuma Means And Siren Lacertina In Central Florida, Anna C. Deyle

USF Tampa Graduate Theses and Dissertations

Population structure can be defined as a difference in the frequencies of alleles among populations, and it is often caused by barriers to dispersal. I used mitochondrial DNA sequences to examine the population structure of two large, aquatic salamanders, Amphiuma means (the Two-Toed Amphiuma) and Siren lacertina (the Greater Siren), at two spatial scales in peninsular Florida. Both species appear to have similar life histories, including poor dry land dispersal capabilities, and I hypothesized that they would exhibit significant population structure at both broad and fine scales. Wetland loss and landscape fragmentation are certain to have caused decreases in abundance …

Evaluating The Effects Of Beach Nourishment On Loggerhead Sea Turtle (Caretta Caretta) Nesting In Pinellas County, Florida, Corey R. Leonard Ozan

USF Tampa Graduate Theses and Dissertations

The health of Florida's beaches are vital to the survival of loggerhead sea turtles (Caretta caretta), as nearly half of the world's loggerheads nest on the states beaches. Many of the beaches utilized by the turtles have undergone nourishment projects in hopes of combating erosion of the shoreline, protecting beachfront property, and creating more suitable beaches for tourism. Although it is argued that beach nourishment benefits sea turtles by providing more nesting habitat, the effects of the Pinellas County nourishment projects on loggerhead nesting are unknown. Beach nourishment can alter the compaction, moisture content, and temperature of the sand, all …

Nutritional Properties Of The Invasive Lionfish: A Delicious And Nutritious Approach For Controlling The Invasion, James A. Morris, Jr., Amber Thomas, Andrew L. Rhyne, Nancy Breen E. Breen, Lad Akins, Barry Nash

Arts & Sciences Faculty Publications

Lionfish, Pterois volitans and P. miles, are native to the Indo-Pacific and have recently invaded the Western Atlantic Ocean. Strategies for control of this invasion have included limited removal programs and promotion of lionfish consumption at both local and commercial scales. We demonstrate that lionfish meat contains higher levels of healthy n-3 fatty acids than some frequently consumed native marine fish species. Mean lionfish fillet yield was 30.5% of the total body wet weight, a value that is similar to that of some grouper and porgy species. A sensory evaluation indicated that lionfish meet the acceptability threshold of most consumers.

Two Distinct, Geographically Overlapping Lineages Of The Corallimorpharian Ricordea Florida (Cnidaria: Hexacorallia: Ricordeidae), H. Torres-Pratts, T. Lado-Insua, Andrew L. Rhyne, L. Rodríguez-Matos, N. V. Schizas

Arts & Sciences Faculty Publications

We examined the genetic variation of the corallimorpharian Ricordea florida; it is distributed throughout the Caribbean region and is heavily harvested for the marine aquarium trade. Eighty-four distinct individuals of R. florida were sequenced from four geographically distant Caribbean locations (Curaçao, Florida, Guadeloupe, and Puerto Rico). Analysis of the ribosomal nuclear region (ITS1, 5.8S, ITS2) uncovered two geographically partially overlapping genetic lineages in R. florida, probably representing two cryptic species. Lineage 1 was found in Florida and Puerto Rico, and Lineage 2 was found in Florida, Puerto Rico, Guadeloupe, and Curaçao. Because of the multi-allelic nature of the ITS …

The Jackprot Simulation Couples Mutation Rate With Natural Selection To Illustrate How Protein Evolution Is Not Random, Guillermo Paz-Y-Miño C, Avelina Espinosa, Chunyan Bai

Arts & Sciences Faculty Publications

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective …