Biology Commons^™

Mojave Applied Ecology Notes Fall 2011, E. Cayenne Engel, Scott R. Abella, Kathryn A. Prengaman, Jason Whited, Peter Michel

Mojave Applied Ecology Notes

Paper on impacts of Mojave wildfires through time published, possibilities of catastrophic Mt. Charleston forest fires, vegetation mapping at three national parks, UNLV library’s special collections, and the benefits of scientific publications to managers and stakeholders

Fall 2011; Biology @ Su, Syracuse University Biology Department

Biology @ SU

No abstract provided.

A Tight Coupling Between Β2Y97 And Β2F200 Of The GabaA Receptor Mediates Gaba Binding, Phu N. Tran, Kurt T. Laha, David A. Wagner

Biological Sciences Faculty Research and Publications

The GABA_A receptor is an oligopentameric chloride channel that is activated via conformation changes induced upon the binding of the endogenous ligand, GABA, to the extracellular inter-subunit interfaces. Although dozens of amino acid residues at the α/β interface have been implicated in ligand binding, the structural elements that mediate ligand binding and receptor activation are not yet fully described. In this study, double-mutant cycle analysis was employed to test for possible interactions between several arginines (α₁R67, α₁R120, α₁R132, and β₂R207) and two aromatic residues (β₂Y97 and β₂F200) …

Mouse Versus Rat: Profound Differences In Meiotic Regulation At The Level Of The Isolated Oocyte, Stephen M. Downs

Biological Sciences Faculty Research and Publications

Cumulus cell-enclosed oocytes (CEO), denuded oocytes (DO), or dissected follicles were obtained 44–48 hr after priming immature mice (20–23 days old) with 5 IU or immature rats (25–27 days old) with 12.5 IU of equine chorionic gonadotropin, and exposed to a variety of culture conditions. Mouse oocytes were more effectively maintained in meiotic arrest by hypoxanthine, dbcAMP, IBMX, milrinone, and 8-Br-cGMP. Atrial natriuretic peptide, a guanylate cyclase activator, suppressed maturation in CEO from both species, but mycophenolic acid reversed IBMX-maintained meiotic arrest in mouse CEO with little activity in rat CEO. IBMX-arrested mouse, but not rat, CEO were induced to …

Breeding Biology Of Oryzomys Palustris, The Marsh Rice Rat, In Eastern Virginia, Robert K. Rose, Erin A. Dreelin

Virginia Journal of Science

The objectives of our study were to determine the age of maturity, litter size, and the timing of the breeding season of marsh rice rats (Oryzomys palustris) of coastal Virginia. From May 1995 to May 1996, monthly samples of rice rats were live-trapped in two coastal tidal marshes of eastern Virginia, and then necropsied. Sexual maturity was attained at 30-40 g for both sexes. Mean litter size of 4.63 (N= 16) did not differ among months or in mass or parity classes. Data from two other studies conducted in the same county, one of them contemporaneous, also were …

Death Of The Tonb Shuttle Hypothesis, Ray A. Larsen, Michael G. Gresock, Marina I. Savenkova, Anne A. Ollis, Kathleen Postle

Biological Sciences Faculty Publications

A complex of ExbB, ExbD, andTonB couples cytoplasmic membrane (CM) proton motive force (pmf) to the active transport of large, scarce, or important nutrients across the outer membrane (OM). TonB interacts with OM transporters to enable ligand transport. Several mechanical models and a shuttle model explain how TonB might work. In the mechanical models, TonB remains attached to the CM during energy transduction, while in the shuttle model theTonB N terminus leaves the CM to deliver conformationally stored potential energy to OM transporters. Previous studies suggested thatTonB did not shuttle based on the activity of a GFP-TonB fusion that was …

The Discovery And Exploration Of A Universal Targeting Mechanism In Eukaryotic Cells, Priyanka Sivadas

Dissertations (1934 -)

A wide range of eukaryotic organisms generate motile cilia and flagella. These slender organelles beat rhythmically to move the surrounding fluid or to propel cells in aqueous environment. Organisms use these powerful yet nimble organelles to forage, evade, adapt and mate. The machinery that drives this tightly controlled movement is the sophisticated microtubule-based axoneme. As it is critical for the survival of individual species, this machinery has largely been preserved to the molecular level throughout evolution. Proteomic studies have shown that most proteins in this biological machine consist of molecular modules commonly used in the cell body. But the usage …

Cluster K Mycobacteriophages: Insights Into The Evolutionary Origins Of Mycobacteriophage Tm4, Welkin Pope, Christina Ferreira, Deborah Jacobs-Sera, Robert Benjamin, Ariangela Davis, Randall Dejong, Sarah C.R. Elgin, Forrest Guilfoile, Mark Forsyth, Alexander Harris, Samuel Harvey, Lee Hughes, Peter Hynes, Arrykka Jackson, Marilyn Jalal, Elizabeth Macmurray, Coreen Manley, Molly Mcdonough, Jordan Mosier, Larissa Osterbann, Hannah Rabinowitz, Corwin Rhyan, Daniel Russell, Margaret Saha, Christopher Shaffer, Stephanie Simon, Erika Sims, Isabel Tovar, Emilie Weisser, John Wertz, Kathleen Weston-Hafer, Kurt Williamson, Bo Zhang, Steven Cresawn, Paras Jain, Mariana Piuri, William Jacobs, Roger Hendrix, Graham Hatfull

Biology Faculty Research

Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, …

Functional Characterization Of Putative Non-Specific Phospholipase C (Npc) In Arabidopsis Thaliana, Carlotta Antonetta Peters

Dissertations

Abstract Phospholipases are enzymes that hydrolyze phospholipids. In terms of the position of bond hydrolysis, phospholipases are classified into four major types: phospholipase C (PLC), phospholipase D (PLD), phospholipase A1 (PLA1) and phospholipase A2 (PLA2). PLC hydrolyzes phospholipids at the first phosphodiester bond, producing diacylglycerol (DAG) and a phosphorylated head group. Based on substrate specificity, PLC is divided into two distinctively different groups: phosphoinositide-specific phospholipase C (PI-PLC) and non-specific phospholipase C (NPC). There are six members of the NPC family in Arabidopsis, designated NPC1 through 6 that bears sequence homology to bacterial phosphatidylcholine hydrolyzing PLC (PC-PLC). However, their function remains …

Global Analysis Of Serine-Threonine Protein Kinase Genes In Neurospora Crassa, Gyungsoon Park, Jacqueline A. Servin, Gloria E. Turner, Lorena Altamirano

Dartmouth Scholarship

Serine/threonine (S/T) protein kinases are crucial components of diverse signaling pathways in eukaryotes, including the model filamentous fungus Neurospora crassa. In order to assess the importance of S/T kinases to Neurospora biology, we embarked on a global analysis of 86 S/T kinase genes in Neurospora. We were able to isolate viable mutants for 77 of the 86 kinase genes. Of these, 57% exhibited at least one growth or developmental phenotype, with a relatively large fraction (40%) possessing a defect in more than one trait. S/T kinase knockouts were subjected to chemical screening using a panel of eight chemical treatments, with …

Contagious Yawning And Seasonal Climate Variation, Andrew C. Gallup, Omar Tonsi Eldakar

Biology Faculty Articles

Recent evidence suggests that yawning is a thermoregulatory behavior. To explore this possibility further, the frequency of contagious yawning in humans was measured while outdoors in a desert climate in the United States during two distinct temperature ranges and seasons (winter: 22°C; early summer: 37°C). As predicted, the proportion of pedestrians who yawned in response to seeing pictures of people yawning differed significantly between the two conditions (winter: 45%; summer: 24%). Across conditions yawning occurred at lower ambient temperatures, and the tendency to yawn during each season was associated with the length of time spent outside prior to being tested. …

Composition Of Suspended And Benthic Particulate Matter In The Tidal Freshwater James River, Anne Schlegel

Theses and Dissertations

Investigating linkages between the compositions of suspended (seston) and benthic particulate matter is important to the understanding of organic matter (OM) cycling and nutrient retention in aquatic systems. We compared the quantity and quality of the truly suspended (TS) and settleable (SB) fractions of seston as well as benthic particulate matter in the tidal freshwater James River, Virginia. The mass of seston and OM was consistently higher in the TS fraction compared to the SB fraction. OM was preferentially retained in the TS fraction relative to seston. The proportional contribution of OM constituents (chlorophyll a, particulate organic carbon and nitrogen) …

Micrornas And Phylogenomics Resolve The Relationships Of Tardigrada And Suggest That Velvet Worms Are The Sister Group Of Arthropoda, Lahcen I. Campbell, Omar Rota-Stabelli, Gregory D. Edgecombe, Trevor Marchioro, Stuart J. Longhorn, Maximilian J. Telford, Hervé Philippe, Lorena Rebecchi, Kevin J. Peterson, Davide Pisani

Dartmouth Scholarship

Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and …

Quantification Of Protein Group Coherence And Pathway Assignment Using Functional Association., Meghana Chitale, Shriphani Palakodety, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

Genomics and proteomics experiments produce a large amount of data that are awaiting functional elucidation. An important step in analyzing such data is to identify functional units, which consist of proteins that play coherent roles to carry out the function. Importantly, functional coherence is not identical with functional similarity. For example, proteins in the same pathway may not share the same Gene Ontology (GO) terms, but they work in a coordinated fashion so that the aimed function can be performed. Thus, simply applying existing functional similarity measures might not be the best solution to identify functional units in omics …

Rhythmic Leptin Is Required For Weight Gain From Circadian Desynchronized Feeding In The Mouse, Deanna M. Arble, Martha H. Vitaterna, Fred W. Turek

Biological Sciences Faculty Research and Publications

The neuroendocrine and metabolic effects of leptin have been extensively researched since the discovery, and the later identification, of the leptin gene mutated within the ob/ob mouse. Leptin is required for optimal health in a number of physiological systems (e.g. fertility, bone density, body weight regulation). Despite the extensive leptin literature and many observations of leptin’s cyclical pattern over the 24-hour day, few studies have specifically examined how the circadian rhythm of leptin may be essential to leptin signaling and health. Here we present data indicating that a rhythmic leptin profile (e.g. 1 peak every 24 hours) leads to excessive …

Uncovering New Functions For Micrornas In Caenorhabditis Elegans, Allison L. Abbott

Biological Sciences Faculty Research and Publications

In the race to understand microRNA (miRNA) functions in development and physiology, Caenorhabditis elegans investigators were the first out of the gate with the cloning and analysis of the lin-4 and let-7 miRNAs [1,2]. The starting point of strong, penetrant loss of function phenotypes facilitated these advancements. However, subsequent functional analysis of miRNAs in C. elegans was hampered by the lack of easily observable loss-of-function phenotypes [3]. There are several possible models to account for this observation. First, redundancy between related miRNAs can account for the absence of phenotypes in mutants missing individual miRNA genes [4,5]. Second, miRNAs may also …

Effects Of Prescribed Burning On Vegetation And Swainson’S Warbler Space Use Patterns In Eastern Arkansas, Jeremy Lewis Everitts

Student Theses and Dissertations

The Swainson’s warbler Limnothlypis swainsonii) is a species of conservation concern throughout the southeastern U.S. An understanding of Swainson’s warbler habitat requirements has been documented, although little is known about how prescribed burning may improve or potentially negatively impact their populations. To learn more about the ecology of this secretive species and understand the effects of management on habitat use patterns, I studied the effects of prescribed burning on a population of Swainson’s warblers in the St. Francis National Forest in Arkansas. With the help of coworkers, I radio−tracked 45 Swainson’s warblers and collected habitat data at 1,043 sites within …

Cryopreservation Of Spin-Dried Mammalian Cells, Nilay Chakraborty, Michael A. Menze, Jason Malsam, Alptekin Aksan, Steven C. Hand, Mehmet Toner

Faculty Research & Creative Activity

This study reports an alternative approach to achieve vitrification where cells are pre-desiccated prior to cooling to cryogenic temperatures for storage. Chinese Hamster Ovary (CHO) cells suspended in a trehalose solution were rapidly and uniformly desiccated to a low moisture content (<0.12 g of water per g of dry weight) using a spin-drying technique. Trehalose was also introduced into the cells using a high-capacity trehalose transporter (TRET1). Fourier Transform Infrared Spectroscopy (FTIR) was used to examine the uniformity of water concentration distribution in the spin-dried samples. 62% of the cells were shown to survive spin-drying in the presence of trehalose following immediate rehydration. The spin-dried samples were stored in liquid nitrogen (LN2) at a vitrified state. It was shown that following re-warming to room temperature and re-hydration with a fully complemented cell culture medium, 51% of the spin-dried and vitrified cells survived and demonstrated normal growth characteristics. Spin-drying is a novel strategy that can be used to improve cryopreservation outcome by promoting rapid vitrification.

Relationships Among Reproductive Morphology, Behavior, And Testosterone In A Natural Population Of Green Anole Lizards, Michele A. Johnson, R. E. Cohen, J. R. Vandecar, J. Wade

Biology Faculty Research

Laboratory studies of reproductive systems have long supported the idea that neural and/or muscular structures used frequently are often enhanced in size. However, field studies integrating behavioral, morphological, and hormonal data are needed to better understand relationships in natural environments. We examined a natural population of green anole lizards (Anolis carolinensis) to determine whether variation in reproductive morphology both within and between the sexes paralleled differences in courtship and copulatory behaviors and circulating testosterone levels. Display rate in males was positively correlated with the sizes of the cartilage supporting the dewlap (a throat fan used in courtship and …

Educational Curriculum Standards & Standardized Educational Tests: Comparing Apples & Oranges?, William D. Stansfield

Biological Sciences

Mandated biology curriculum standards and standardized tests may vary widely from one state to another, making academic-performance comparisons among the states problematic. This report outlines the effects of the “No Child Left Behind” law and uses California as a test case against which teachers in other states may make comparisons of their own biology curriculum standards and tests. Several sources are cited that offer sample multiple-choice questions that have appeared on previous California standardized tests for sciences/life sciences/biology. These examples, and critique thereof, may help teachers better prepare their own tests to improve student performance in meeting the state's curriculum …

Season And Sex Of Host Affect Intensities Of Ectoparasites In Western Fence Lizards (Sceloporus Occidentalis) On The Central Coast Of California, Anthony S. Lumbad, Larisa K. Vredevoe, Emily N. Taylor

Biological Sciences

Seasonal variability in intensities of ectoparasites of western fence lizards (Sceloporus occidentalis) was quantified in spring, summer, and autumn 2008. Lizards were suspended over pans of water in the laboratory to enumerate replete western black-legged ticks (Ixodes pacificus) and mites. Intensity of ectoparasites was greatest in spring. On average, mites comprised the greatest proportion of ectoparasites, followed by larval and nymphal ticks, respectively. Mites were on lizards year-round. Overall intensity of ticks was greatest in spring, but low during summer and autumn. Males were more heavily parasitized by ticks than females in spring, whereas females had …

The Proteomic Response Of Sea Squirts (Genus Ciona) To Acute Heat Stress: A Global Perspective On The Thermal Stability Of Proteins, Loredana Serafini, Jay B. Hann, Dietmar Kültz, Lars Tomanek

Biological Sciences

Congeners belonging to the genus Ciona have disparate distributions limited by temperature. Ciona intestinalis is more widespread with a cosmopolitan distribution ranging from tropical to sub-arctic zones, while Ciona savignyi is limited to temperate-latitudes of the northern Pacific Ocean. To compare the heat stress response between congeners, we quantified changes in protein expression using proteomics. Animals were exposed to 22 °C, 25 °C, and 28 °C for 6 h, then recovered at a control temperature (13 °C) for 16 h (high heat stress experiment). In a second experiment we exposed animals to lower levels of heat stress at 18 °C, …

Human U6 Promoter Drives Stronger Shrna Activity Than Its Schistosome Orthologue In Schistosoma Mansoni And Human Fibrosarcoma Cells, Clarence Lee

Department of Biology Faculty Publications

Blood flukes or schistosomes are the causative agents of human schistosomiasis, one of the major neglected tropical diseases. Draft genome sequences have been reported for schistosomes, but functional genomics tools are needed to investigate the role and essentiality of the newly reported genes. Vector based RNA interference can contribute to functional genomics analysis for schistosomes. Using mRNA encoding reporter firefly luciferase as a model target, we compared the performance of a schistosome and a human promoter from the U6 gene in driving shRNA in human fibrosarcoma cells and in cultured schistosomes. Further, both a retroviral [Murine leukemia virus (MLV)] and …

Influence Of Iron-Chelated Growth Conditions On Outer Membrane Protein Production And Virulence Of Vibrio Tubiashii, Broderick Eribo

Department of Biology Faculty Publications

Growth of two Vibrio tubiashii strains under iron-chelated conditions resulted in the production of a hydroxymate-like siderophore, and expression of outer membrane proteins with homologies to proteins in Vibrio cholerae and Vibrio vulnificus which were not seen in cells grown under non-chelated growth conditions. PCR analysis using primers based on Listonella anguillarum's ferric uptake Repressor protein (fur) gene detected a 316 bp fur gene homolog which also had sequence homology to the fur genes of V. cholerae and V. vulnificus. V. tubiashii cultured under iron-chelated growth conditions induced a greater fluid accumulation (FA) response in suckling mice than cells which …

Development Of Novel Microsatellite Markers For High-Resolution Genetic Analysis Of The Western Slimy Salamander (Plethodon Albagula), Nathan Thomas Stephens

Student Theses and Dissertations

Polymorphic microsatellite DNA markers were developed and characterized for the western slimy salamander (Plethodon albagula). Salamanders from the Spillway Mine in Garland County, Arkansas were sampled for DNA and a microsatellite-enriched library was created for this species. The library yielded 1654 sequences from which 142 candidate loci containing simple tandem repeats were identified; 28 polymerase chain reaction primer pairs representing 28 candidate loci were tested in this study and eight were selected for development based on robust amplification and polymorphism in PCR-based analysis of P. albagula population samples. Of these eight loci, six were determined to be unlinked in a …

Cryopreservation Of Spin-Dried Mammalian Cells., Nilay Chakraborty, Michael Menze, Jason Malsam, Alptekin Aksan, Steven Hand, Mehmet Toner

Faculty and Staff Scholarship

This study reports an alternative approach to achieve vitrification where cells are pre-desiccated prior to cooling to cryogenic temperatures for storage. Chinese Hamster Ovary (CHO) cells suspended in a trehalose solution were rapidly and uniformly desiccated to a low moisture content (< 0.12 g of water per g of dry weight) using a spin-drying technique. Trehalose was also introduced into the cells using a high-capacity trehalose transporter (TRET1). Fourier Transform Infrared Spectroscopy (FTIR) was used to examine the uniformity of water concentration distribution in the spin-dried samples. 62% of the cells were shown to survive spin-drying in the presence of trehalose following immediate rehydration. The spin-dried samples were stored in liquid nitrogen (LN2) at a vitrified state. It was shown that following re-warming to room temperature and re-hydration with a fully complemented cell culture medium, 51% of the spin-dried and vitrified cells survived and demonstrated normal growth characteristics. Spin-drying is a novel strategy that can be used to improve cryopreservation outcome by promoting rapid vitrification.

University Of South Florida St. Petersburg Student Research Journal, Vol. 1, Issue 1, Article 3 : Modeling A Molecular Dynamic Simulation Of The Stat3 Monomer, Jessica Ruekberg, Demetrios Kiriopoulos, Kevin Moore, Deby L. Cassill, Leon Hardy

USF St. Petersburg Campus Faculty Publications

STAT3, also known as signal transducer and activator of transcription 3, is a DNA transcription enzyme. In mammals including humans, STAT3 regulates the expression of a variety of genes that play a role in embryonic development. Specifically, STAT3 regulates cell division, cell differentiation and cell death (apoptosis). During embryonic development, STAT3 proteins are phosphorylated in a cell's cytoplasm in response to chemical growth factors. Once phosphorylated, STAT3 proteins pair up to form homodimers that act like pliers. STAT3 homodimers are transferred into the cell nucleus, where they bind to DNA to regulate embryonic development. When mutations of the STAT3 gene …

Sex Chromosome Mosaicism And Hybrid Speciation Among Tiger Swallowtail Butterflies, Krushnamegh Kunte, Cristina Shea, Matthew Aardema, J. Mark Scriber, Thomas E. Juenger, Lawrence E. Gilbert, Marcus R. Kronforst

Department of Biology Faculty Scholarship and Creative Works

Hybrid speciation, or the formation of a daughter species due to interbreeding between two parental species, is a potentially important means of diversification, because it generates new forms from existing variation. However, factors responsible for the origin and maintenance of hybrid species are largely unknown. Here we show that the North American butterfly Papilio appalachiensis is a hybrid species, with genomic admixture from Papilio glaucus and Papilio canadensis. Papilio appalachiensis has a mosaic phenotype, which is hypothesized to be the result of combining sex-linked traits from P. glaucus and P. canadensis. We show that P. appalachiensis' Z-linked genes associated with …

Analyses Of Sorex Longirostris Distribution In Arkansas And Across The Mississippi River, Garrett Adam Mikel

Theses and Dissertations

The southeastern shrew (Sorex longirostris) is considered uncommon and a Species of Greatest Conservation Need in Arkansas, exhibiting an apparent gap in eastern Arkansas. Soricinae are exceptionally small and short-lived with limited dispersal, making them especially prone to speciation through long-term zoogeographic barriers to gene flow consistent with phylogeographic category 1. Therefore, I compiled Arkansas occurrences, evaluated persistence at previous capture sites in the state, surveyed additional counties, quantified microhabitat at my capture locations, and evaluated systematic status of S. longirostris east and west of the Mississippi River using mitochondrial DNA. Number of documented specimens in Arkansas has increased to …

Expression Of Hyp-O-Glycan Modified Protein In Plant Using Transient And Cell Culture Platforms, Di Wu

Student Theses and Dissertations

Plants have emerged as cost-effective, efficient factories to produce foreign proteins of pharmaceutical importance. Agrobacterium-mediated transient expression provides a rapid and simple plant system for production but is often linked with low protein recovery. Plant-specific hydroxyproline (Hyp)-O-glycosylation has been demonstrated to increase protein stability and solubility (termed Hyp-Glyco technology). To test if Hyp-glycans attached to a target protein can improve overall transiently expressed protein yields, EGFP reporter protein was expressed as fusion with a 5 or 32 repeats of Ser-Pro motif ((SP)5 or (SP)32 ) that directs extensive Hyp-O-glycosylation. My thesis project has provided the first demonstration that the Hyp-O-glcosylation …