Biology Commons^™

The Loss Of Hh Responsiveness By A Non-Ciliary Gli2 Variant, Jinling Liu, Huiqing Zeng, Aimin Liu

Engineering Management and Systems Engineering Faculty Research & Creative Works

Hedgehog signaling is crucial for vertebrate development and physiology. Gli2, the primary effector of Hedgehog signaling, localizes to the tip of the primary cilium, but the importance of its ciliary localization remains unclear. We address the roles of Gli2 ciliary localization by replacing endogenous Gli2 with Gli2^ΔCLR, a Gli2 variant not localizing to the cilium. The resulting Gli2^ΔCLRKI and Gli2^ΔCLRKI;Gli3 double mutants resemble Gli2-null and Gli2;Gli3 double mutants, respectively, suggesting the lack of Gli2^ΔCLR activation in development. Significantly, Gli2^ΔCLR cannot be activated either by pharmacochemical activation of Smo in vitro or by loss …

Long-Term Changes In Seasonal Fish Assemblage Dynamics In An Adventitious Desert Stream, Seiji Miyazono, Christopher M. Taylor

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

Tornillo Creek, a tributary of the Rio Grande in Texas, United States, has historically been an important nursery and spawning habitat for several native fish species. We examined variation in the seasonal fish assemblages in Tornillo Creek within and between two time periods (1967–1970 vs. 2009–2011), and contemporary fish assemblage–environment associations, in order to understand what environmental factors were associated with seasonal fish abundance and occupancy patterns. Our results indicated that fish assemblages were very different between the two time periods. Contemporary seasonal fish assemblage patterns in Tornillo Creek were less variable than historical assemblages and were linked to several …

Attraction, Repellence, And Predation: Role Of Companion Plants In Regulating Myzus Persicae (Sulzer) (Hemiptera: Aphidae) In Organic Kale Systems Of South Texas, Carlos R. Moreno, Alexis Racelis

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

Annual outbreaks of green peach aphid, Myzus persicae (Sulzer), limit commercial production of brassica crops, especially in organic systems in subtropical areas such as South Texas. We assessed the influence of companion plants that emit attractant, repellent, and natural enemy-attractant stimuli (i.e., insectary plants) on abundance of green peach aphid in organic kale (Brassica oleracaea L. var. acephala) fields in South Texas. We also monitored the assemblage of arthropod predators and parasitoids on kale and evaluated the response of numerically dominant species to companion plants. Indian mustard (Brassica juncea (L.) Vassiliĭ Matveievitch Czernajew; attractant), dill (Anethum graveolens L.; repellent), fennel …

The Fragile Fiber1 Kinesin Contributes To Cortical Microtubule-Mediated Trafficking Of Cell Wall Components, Chuanmei Zhu, Anindya Ganguly, Tobias I. Baskin, Daniel D. Mcclosky, Charles T. Anderson, Cliff Foster, Kristoffer A. Meunier, Ruth Okamoto, Howard Berg, Ram Dixit

Biology Faculty Research

The cell wall consists of cellulose microfibrils embedded within a matrix of hemicellulose and pectin. Cellulose microfibrils are synthesized at the plasma membrane, whereas matrix polysaccharides are synthesized in the Golgi apparatus and secreted. The trafficking of vesicles containing cell wall components is thought to depend on actin-myosin. Here, we implicate microtubules in this process through studies of the kinesin-4 family member, Fragile Fiber1 (FRA1). In an fra1-5 knockout mutant, the expansion rate of the inflorescence stem is halved compared with the wild type along with the thickness of both primary and secondary cell walls. Nevertheless, cell walls in fra1-5 …

Long-Term Changes In Seasonal Fish Assemblage Dynamics In An Adventitious Desert Stream, Seiji Miyazono, Christopher M. Taylor

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

Tornillo Creek, a tributary of the Rio Grande in Texas, United States, has historically been an important nursery and spawning habitat for several native fish species. We examined variation in the seasonal fish assemblages in Tornillo Creek within and between two time periods (1967–1970 vs. 2009–2011), and contemporary fish assemblage–environment associations, in order to understand what environmental factors were associated with seasonal fish abundance and occupancy patterns. Our results indicated that fish assemblages were very different between the two time periods. Contemporary seasonal fish assemblage patterns in Tornillo Creek were less variable than historical assemblages and were linked to several …

Protein Sectors: Statistical Coupling Analysis Versus Conservation, Tiberiu Teşileanu, Lucy J. Colwell, Stanislas Leibler

Publications and Research

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be …

Winter Rye As A Bioenergy Feedstock: Impact Of Crop Maturity On Composition, Biological Solubilization And Potential Revenue, Xiongjun Shao, Kay Dimarco, Tom L. Richard, Lee R. Lynd

Dartmouth Scholarship

Background:

Winter annual crops such as winter rye (Secale cereale L) can produce biomass feedstock on seasonally fallow land that continues to provide high-value food and feed from summer annuals such as corn and soybeans. As energy double crops, winter grasses are likely to be harvested while still immature and thus structurally different from the fully senesced plant material typically used for biofuels. This study investigates the dynamic trends in biomass yield, composition, and biological solubilization over the course of a spring harvest season.

Results:

The water soluble fraction decreased with increasing maturity while total carbohydrate content stayed …

Prevalence Of Borrelia Burgdorferi-Infected Ticks From Wildlife Hosts, A Response To Norris Et Al., Maria Dolores Esteve-Gassent, Abha Grover, Teresa Patricia Feria-Arroyo, Ivan Castro-Arellano, Raul F. Medina, Guadalupe Gordillo Pérez, Adalberto A. Pérez De León

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

In a recent Letter to the Editor, Norris et al. questioned the validity of some of our data reported by Feria-Arroyo et al. The main issue investigated by us was the potential impact of climate change on the probable distribution of the tick vector Ixodes scapularis in the Texas-Mexico transboundary region. As an ancillary issue, an analysis of sequence data for the intergenic spacer of Borrelia burgdorferi was conducted. In the present letter, we provide further evidence supporting our original results, and advocate that extensive study of the population genetics of B. burgdorferi is needed in the Texas-Mexico transboundary …

A Bioinformatics Approach To Revealing The Genetic Basis For Host Range Specificity, Hayley A. Norian

James Madison Undergraduate Research Journal (JMURJ)

Bacteriophages, or phages, are viruses that infect bacteria. Mycobacteriophages are bacteriophages that specifically infect the genus Mycobacterium. This genus of bacteria includes human pathogens such as Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans, which cause tuberculosis, leprosy and Buruli ulcer, respectively. The full genome sequences of 654 mycobacteriophages are currently available. Collectively, these 654 phages encode 69,581 genes. Only 20.25% of these genes have at least one known homologue in NCBI, the National Center for Biotechnology Information, leaving roughly 80% of all known mycobacteriophage genes without even a predicted function. Bacteriophages are highly host-specific and typically only infect a small …

A Functional Chlorophyll Biosynthesis Pathway Identified In The Kleptoplastic Sea Slug, Elysia Chlorotica, Julie A. Schwartz

USF Tampa Graduate Theses and Dissertations

The sacoglossan sea slug, Elysia chlorotica, feeds upon and sequesters plastids from the heterokont alga, Vaucheria litorea, and maintains the metabolically active organelles for up to nine months under starvation conditions while utilizing the photosynthate to survive and reproduce. The photosynthetic pigment, chlorophyll a (Chla), is found in all oxygenic photosynthetic organisms and is responsible for capturing photons of light and converting them into chemical energy. Chlorophyll and its associated proteins involved in the light capturing process are subject to photo oxidative damage and must be continually replaced for ongoing photosynthesis to continue; however, genes encoding these proteins are present …

Predicting Invasion Rates For Phragmites Australis, Rachel Nydegger, Jacob Duncan, James A. Powell

Browse All Undergraduate research

In wetlands of Utah and southern Idaho as well as estuaries of the east coast, the ten-foot tall invasive grass Phragmites australis can be found near waterways, where it outcompetes native plants and degrades wildlife habitat. Phragmites australis is an obligate out-crossing plant that can spread sexually through seed disper- sal, or asexually via stolons and rhi- zomes (Kettenring and Mock 2012). Small patches are usually a single genetic individual, spreading vegetatively (and slowly) via runners; when patches become genetically diverse viable seeds are produced and invasion rates can be increase by an order of magnitude (Kettenring et al. 2011)

Colonization Of Lake Erie Tributaries By Allocapnia Recta (Capniidae), Alison L. Yasick, Robert A. Krebs, Julie Wolin

Biological, Geological, and Environmental Faculty Publications

Plecoptera display a variety of dispersal mechanisms. The most reduced of these, walking, is common for winter stoneflies in the family Capniidae. To examine dispersal in a winter stonefly, Allocapnia recta, we sequenced a fragment of the 16s rRNA mitochondrial gene from four adjacent Lake Erie drainages. Nineteen unique haplotypes were obtained from 107 specimens. The four watersheds explained 37% of the haplotype diversity and all pairwise contrasts among streams were statistically significant; not one haplotype was common to all four watersheds. This extreme level of divergence among populations separated briefly in both space and time suggest minimal if …

The Regulatory Function Of Sphingosine-1-Phosphate Signaling Axis On Regulatory T Cells In Colorectal Cancer, Andrew V. Nguyen, Yuan-Yuan Wu, Elaine Y. Lin

Publications and Research

In tumors associated with inflammation such as inflammatory bowel disease (IBD) and colorectal cancer (CRC), high numbers of regulatory T cells (Tregs) are associated with both favorable and poor prognoses. The functions of Tregs in CRC remain elusive and have yet to be clearly defined. With new evidence supporting many subsets of Tregs, the research on the development and functions of these cells has begun to come to fruition. The sphingosine 1 phosphate (S1P) pathway was recently reported to regulate the development and function of regulatory T cells. This pathway may shine new light into the pleiotropic nature of these …

Sister Remberta Westkaemper: A Fine Lady And Excellent Field Botanist, Stephen G. Saupe

Forum Lectures

Sister Remberta, the first full-time president of Saint Ben's and founding member of the CSB Biology Department, was the preeminent authority on the flora of Stearns County. This presentation will focus on Sister Remberta's botanical activities with an introduction to the CSB|SJU Bailey Herbarium. This work was supported by a Centennial Year Fellowship.

Herbivory And The Resilience Of Caribbean Coral Reefs: Knowledge Gaps And Implications For Management, Thomas C. Adam, Deron E. Burkepile, Benjamin I. Ruttenberg, Michelle J. Paddack

Biological Sciences

Herbivory is a key process on coral reefs that can facilitate reef-building corals by excluding algae that otherwise negatively impact coral settlement, growth, and survivorship. Over the last several decades, coral cover on Caribbean reefs has declined precipitously. On many reefs, large structurally complex corals have been replaced by algae and other non-reef-building organisms, resulting in the collapse of physical structure and the loss of critical ecosystem services. The drivers of coral decline on Caribbean reefs are complex and vary among locations. On many reefs, populations of key herbivores have been greatly reduced by disease and overfishing, and this has …

The Guanine Nucleotide Exchange Factor Ric-8a Induces Domain Separation And Ras Domain Plasticity In Gαi1, Ned Van Eps, Celestine J. Thomas, Wayne L. Hubbell, Stephen R. Sprang

Biological Sciences Faculty Publications

Heterotrimeric G proteins are activated by exchange of GDP for GTP at the G protein alpha subunit (Gα), most notably by G protein-coupled transmembrane receptors. Ric-8A is a soluble cytoplasmic protein essential for embryonic development that acts as both a guanine nucleotide exchange factor (GEF) and a chaperone for Gα subunits of the i, q, and 12/13 classes. Previous studies demonstrated that Ric-8A stabilizes a dynamically disordered state of nucleotide-free Gα as the catalytic intermediate for nucleotide exchange, but no information was obtained on the structures involved or the magnitude of the structural fluctuations. In the present study, site-directed spin …

Analyses Of Alternatively Processed Genes In Ciliates Provide Insights Into The Origins Of Scrambled Genomes And May Provide A Mechanism For Speciation, Feng Gao, Scott W. Roy, Laura A. Katz

Biological Sciences: Faculty Publications

Chromosome rearrangements occur in a variety of eukaryotic life cycles, including during the development of the somatic macronuclear genome in ciliates. Previous work on the phyllopharyngean ciliate Chilodonella uncinata revealed that macronuclear β-tubulin and protein kinase gene families share alternatively processed germ line segments nested within divergent regions. To study genome evolution in this ciliate further, we characterized two additional alternatively processed gene families from two cryptic species of the ciliate morphospecies C. uncinata: those encoding histidine acid phosphatase protein (Hap) and leishmanolysin family protein (Lei). Analyses of the macronuclear Hap and Lei sequences reveal that each gene family consists …

Use And Misuse Of Material Transfer Agreements: Lessons In Proportionality From Research, Repositories, And Litigation, Tania M. Bubela, Jenilee Guebert, Amrita Mishra

Office of the Provost

Material transfer agreements exist to facilitate the exchange of materials and associated data between researchers as well as to protect the interests of the researchers and their institutions. But this dual mandate can be a source of frustration for researchers, creating administrative burdens and slowing down collaborations. We argue here that in most cases in pre-competitive research, a simple agreement would suffice; the more complex agreements and mechanisms for their negotiation should be reserved for cases where the risks posed to the institution and the potential commercial value of the research reagents is high.

Butterfly Biology, Joshua Feingold

Quadrivium: A Journal of Multidisciplinary Scholarship

A photographic exploration of butterflies from larvae to adults in Davie, Florida.

Geographic Range Predicts Photosynthetic And Growth Response To Warming In Co-Occurring Tree Species, Peter B. Reich, Kerrie M. Sendall, Karen Rice, Roy L. Rich, Artur Stefanski, Sarah E. Hobbie, Rebecca A. Montgomery

Faculty Research & Creative Activity

No abstract provided.

Cold Truths: How Winter Drives Responses Of Terrestrial Organisms To Climate Change, Caroline M. Williams, Hugh A.L. Henry, Brent J. Sinclair

Biology Publications

Winter is a key driver of individual performance, community composition, and ecological interactions in terrestrial habitats. Although climate change research tends to focus on performance in the growing season, climate change is also modifying winter conditions rapidly. Changes to winter temperatures, the variability of winter conditions, and winter snow cover can interact to induce cold injury, alter energy and water balance, advance or retard phenology, and modify community interactions. Species vary in their susceptibility to these winter drivers, hampering efforts to predict biological responses to climate change. Existing frameworks for predicting the impacts of climate change do not incorporate the …

The Proteomic Response Of The Carcinus Maenas Y-Organ Over The Course Of The Molt Cycle, Mark S. Hamer

Master's Theses

Molting in arthropods is a complex process governed by regulatory mechanisms that have evolved and adapted over millennia to allow these animals to grow, despite being confined by a hardened exoskeleton. We isolated the molt-regulating Y-organs (YO) from the common shore crab Carcinus maenas at molt stages B, C_1-3, C₄, and D₀ to assess how changes in protein abundances might underline the unique physiology of each of these stages. We found that changes in protein abundance were most notable in the postmolt stages (B and C_1-3), where an increase in energy metabolism and …

Machine Learning For Predicting Soil Classes In Three Semi-Arid Landscapes, Colby W. Brungard, Janis L. Boettinger, Michael C. Duniway, Skye A. Wills, Thomas C. Edwards Jr.

Plants, Soils, and Climate Faculty Publications

Mapping the spatial distribution of soil taxonomic classes is important for informing soil use and management decisions. Digital soil mapping (DSM) can quantitatively predict the spatial distribution of soil taxonomic classes. Key components of DSM are the method and the set of environmental covariates used to predict soil classes. Machine learning is a general term for a broad set of statistical modeling techniques. Many different machine learning models have been applied in the literature and there are different approaches for selecting covariates for DSM. However, there is little guidance as to which, if any, machine learning model and covariate set …

Weekly Versus Monthly Testosterone Administration On Fast And Slow Skeletal Muscle Fibers In Older Adult Males, Robert H. Fitts, James R. Peters, E. Lichar Dillon, William J. Durham, Melinda A. Sheffield-Moore, Randall J. Urban

Biological Sciences Faculty Research and Publications

Context: In older adults, loss of mobility due to sarcopenia is exacerbated in men with low serum T. T replacement therapy is known to increase muscle mass and strength, but the effect of weekly (WK) vs monthly (MO) administration on specific fiber types is unknown.

Objective: To determine the efficacy of WK vs MO T replacement on the size and functional capacity of individual fast and slow skeletal muscle fiber types.

Design, Setting, and Patients:

Subjects were randomized into a 5-month, double-blind, placebo-controlled trial. All subjects (ages, 61–71 y) were community-dwelling men who had T levels < 500 ng/dL.

Intervention: Subjects were dosed …

Mechanisms Underlying Weight Loss And Metabolic Improvements In Rodent Models Of Bariatric Surgery, Deanna M. Arble, Darleen A. Sandoval, Randy J. Seeley

Biological Sciences Faculty Research and Publications

Obesity is a growing health risk with few successful treatment options and fewer still that target both obesity and obesity-associated comorbidities. Despite ongoing scientific efforts, the most effective treatment option to date was not developed from basic research but by surgeons observing outcomes in the clinic. Bariatric surgery is the most successful treatment for significant weight loss, resolution of type 2 diabetes and the prevention of future weight gain. Recent work with animal models has shed considerable light on the molecular underpinnings of the potent effects of these ‘metabolic’ surgical procedures. Here we review data from animal models and how …

Unique Competitive Effects Of Lianas And Trees In A Tropical Forest Understory, Alexandra Wright, Michael F. Tobin, Scott A. Mangan, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas are an important component of tropical forests, contributing up to 25 % of the woody stems and 35 % of woody species diversity. Lianas invest less in structural support but more in leaves compared to trees of similar biomass. These physiological and morphological differences suggest that lianas may interact with neighboring plants in ways that are different from similarly sized trees. However, the vast majority of past liana competition studies have failed to identify the unique competitive effects of lianas by controlling for the amount of biomass removed. We assessed liana competition in the forest understory over the course …

Intrinsically Disordered C-Terminal Tails Of E. Coli Single-Stranded Dna Binding Protein Regulate Cooperative Binding To Single-Stranded Dna, Alexander G. Kozlov, Elizabeth A. Weiland, Anuradha Mittal, Vince Waldman, Edwin Antony, Nicole Fazio, Rohit V. Pappu, Timothy M. Lohman

Biological Sciences Faculty Research and Publications

The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)₆₅ mode] or only two subunits [(SSB)₃₅ binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)₃₅ mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is …

Isolation Of Diverse Members Of The Aquificales From Geothermal Springs In Tengchong, China, Brian P. Hedlund, Anna-Louise Reysenbach, Liuquin Huang, John C. Ong, Zizhang Liu, Jeremy A. Dodsworth, Reham Ahmed, Amanda J. Williams, Brandon R. Briggs, Yitai Liu, Weiguo Hou, Hailiang Dong

Biology Faculty Publications and Presentations

The order Aquificales (phylum Aquificae) consists of thermophilic and hyperthermophilic bacteria that are prominent in many geothermal systems, including those in Tengchong, Yunnan Province, China. However, Aquificales have not previously been isolated from Tengchong. We isolated five strains of Aquificales from diverse springs (temperature 45.2–83.3°C and pH 2.6–9.1) in the Rehai Geothermal Field from sites in which Aquificales were abundant. Phylogenetic analysis showed that four of the strains belong to the genera Hydrogenobacter, Hydrogenobaculum, andSulfurihydrogenibium, including strains distant enough to likely justify new species ofHydrogenobacter and Hydrogenobaculum. The additional strain may represent a …

Functional Characterization Of The Plant 15-Cis-Zeta-Carotene Isomerase Z-Iso, Jesus Alonso Beltran Zambrano

Dissertations, Theses, and Capstone Projects

Vitamin A deficiency is a widespread health issue in the tropics. To solve this issue, efforts are underway to increase provitamin A carotenoids such as β-carotene in staple crops which can be achieved by breeding, metabolic engineering or a combination of both approaches. However, rational strategies to improve carotenoid content in crops require sufficient knowledge of pathway regulation. Therefore, to better understand how plants synthesize provitamin A and to guide metabolic engineering strategies in crops such as maize, the functional characterization of the new ζ-carotene isomerase (Z-ISO) is of significant importance.

Z-ISO was recently discovered in maize and Arabidopsis (Chen …

Tcr Alpha Lcr And Non-Lcr Cis-Elements Contributing To Tissue Specific Expression Of The Tcr Alpha Gene In Thymic And Peripheral T Cells, Martina Kucerova-Levisohn

Dissertations, Theses, and Capstone Projects

Orchestrated expression of multiple genes residing in the complex TCRα/δ/Dad1 locus requires tight control from multiple cis-acting elements. The TCRα locus control region (LCR), is positioned between TCRα and Dad1 gene, and has been implicated in the differential expression of both genes. In this study, we focus our work on the hypersensitive site (HS)1 prime (HS1'), located 3' of the classical Eα enhancer, within the TCRα LCR. We investigated its non- redundant role in TCRα expression in thymic and peripheral T cells as assayed by in vivo and in vitro studies. Furthermore, formation of HS1' in both lymphoid and …