Biology Commons^™

Histomorphology Of Cutaneous Glands Associated With Conspicuous Coloration In Selected Arkansas Anurans, Christopher Shelton Thigpen

Student Theses and Dissertations

The histology and histochemistry of serous glands of Hyla chrysoscelis, H. cinerea, Lithobates palustris and L. sphenocephalus are described, herein for the first time. Light microscopy was used for examination of glands. The glands are merocrine, externally secreting and composed of a syncytium of secretory cells surrounding a central lumen bordered superficially by melanophores. Serous gland numbers were compared within individuals and between species within a genus to test for differences between skin patches and species with and without conspicuous coloration. It was hypothesized no significant differences would exist within individuals and between species of a genus. Significant differences were …

Structural Basis For Negative Allosteric Modulation Of Glun2a-Containing Nmda Receptors, Feng Yi, Tung-Chung Mou, Katherine N. Dorsett, Robert A. Volkmann, Frank S. Menniti, Stephen R. Sprang, Kasper B. Hansen

Biological Sciences Faculty Publications

NMDA receptors mediate excitatory synaptic transmission and regulate synaptic plasticity in the central nervous system, but their dysregulation is also implicated in numerous brain disorders. Here, we describe GluN2A-selective negative allosteric modulators (NAMs) that inhibit NMDA receptors by stabilizing the apo state of the GluN1 ligand-binding domain (LBD), which is incapable of triggering channel gating. We describe structural determinants of NAM binding in crystal structures of the GluN1/2A LBD heterodimer, and analyses of NAM-bound LBD structures corresponding to active and inhibited receptor states reveal a molecular switch in the modulatory binding site that mediate the allosteric inhibition. NAM binding causes …

Ifn-G Induces Histone 3 Lysine 27 Trimethylation In A Small Subset Of Promoters To Stably Silence Gene Expression In Human Macrophages, Yu Qiao, Kyuho Kang, Eugenia Giannopoulou, Celeste Fang, Lionel B. Ivashkiv

Publications and Research

The mechanisms by which IFN-g activates expression of interferon-stimulated genes that have inflammatory and host defense functions are well understood. In contrast, little is known about how IFN-g represses gene expression. By using transcriptomic and epigenomic analysis, we found that stable repression of a small group of genes by IFN-g is associated with recruitment of the histone methyltransferase EZH2 and deposition of the negative mark histone 3 lysine 27 trimethylation (H3K27me3) at their promoters. Repressed genes included MERTK, PPARG, and RANK, which have anti-inflammatory functions and promote osteoclast differentiation. Gene repression and H3K27me3 persisted after IFN-g signaling was terminated, and …

Receptor-Type Guanylyl Cyclase At 76c (Gyc76c) Regulates De Novo Lumen Formation During Drosophila Tracheal Development, Monn Monn Myat, Unisha Patel

Publications and Research

Lumen formation and maintenance are important for the development and function of essential organs such as the lung, kidney and vasculature. In the Drosophila embryonic trachea, lumena formde novo to connect the different tracheal branches into an interconnected network of tubes. Here, we identify a novel role for the receptor type guanylyl cyclase at 76C (Gyc76C) in de novo lumen formation in the Drosophila trachea.We show that in embryosmutant for gyc76C or its downsteam effector protein kinase G (PKG) 1, tracheal lumena are disconnected. Dorsal trunk (DT) cells of gyc76C mutant embryos migrate to contact each other and complete the …

Aspects Of Host Usage Of The Chestnut Lamprey (Ichthyomyzon Castaneus) In Arkansas, Jeremiah Max Salinger

Student Theses and Dissertations

Most native North American lamprey species are imperiled in some manner, but are curiously understudied. The research described in this thesis addresses the adult feeding biology of the Chestnut Lamprey (Ichthyomyzon castaneus), a freshwater parasitic lamprey native to the southeastern United States. This thesis addresses Chestnut Lamprey attachment site selection and size-selective parasitism of Rainbow Trout (Oncorhynchus mykiss) in an outdoor laboratory setting, as well as Chestnut Lamprey host usage and distribution in Arkansas. Approximately 75% of the 80 wounded Rainbow Trout studied were attacked in their dorsal mid-section. Chestnut Lampreys were found to select shorter hosts, with no mass …

The Role Of The Chloroplastic And Endoplasmic Reticulum Ascorbate Subcellular Pools In Plant Physiology, Jessica Patricia Yactayo-Chang

Student Theses and Dissertations

Vitamin C (L-ascorbic acid, AsA) is the most abundant water-soluble antioxidant in plants. Ascorbate scavenges free radicals, is an enzyme cofactor, and a donor/ acceptor of electrons in the chloroplast. Ascorbate protects tissues against damage caused by reactive oxygen species (ROS) produced through normal metabolism or generated from stress. The inositol route to AsA involves four enzymes: myo-inositol oxygenase, glucuronate reductase, gluconolactonase (GNL), and L-gulono-1,4-lactone oxidase (GulLO). The third enzyme, GNL, has been characterized in rat and bacteria but not in plants. Eighteen putative GNLs were identified in Arabidopsis, one of which, AtGNL, is interesting because it possesses a chloroplastic …

Partitioning Controls On Amazon Forest Photosynthesis Between Environmental And Biotic Factors At Hourly To Interannual Timescales, Jin Wu, Kaiyu Guan, Matthew Hayek, Natalia Restrepo-Coupe, Kenia T. Wiedemann, Xiangtao Xu, Richard Wehr, Bradley O. Christoffersen, Guofang Miao, Rodrigo Da Silva

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

Gross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance-derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light-use efficiency associated with changes in the parameters themselves. Our fitted model was …

Perceptions Of Active Learning Between Faculty And Undergraduates: Differing Views Among Departments, Lorelei E. Patrick, Leigh Ann Howell, William Wischusen

Biological Sciences Faculty Publications

There have been numerous calls recently to increase the use of active learning in university science, technology, engineering, and math (STEM) classrooms to more actively engage students and enhance student learning. However, few studies have investigated faculty and student perceptions regarding the effectiveness of active learning or the barriers to its implementation. Previous work surveying a single class in a single department has suggested that faculty and students have different perceptions of the effectiveness of active learning strategies and the barriers faculty face when implementing these teaching strategies. We expand on these previous findings by surveying a larger and more …

Environmental Conditions Of 2 River Drainages Into The Northern Gulf Of Mexico During Successful Hatching Of Alabama Shad (Alosa Alabamae), Paul F. Mickle, Jacob F. Schaefer, Susan B. Adams, Brian R. Kreiser, William T. Slack

Faculty Publications

In recent years, the Alabama shad (Alosa alabamae) has experienced dramatic declines and extirpations from portions of its native range. Habitat degradation and barriers to migration are considered contributing factors to contraction in the distributional range this species. To identify conditions during successful spawning, river temperatures and discharges in 2 drainages of the northern Gulf of Mexico (the Apalachicola and Pascagoula rivers) were characterized during successful hatching “windows.” Sampling during 2005–2009 yielded 400 juvenile Alabama shad of which 261 were aged from counts of rings on sagittal otoliths. Results from logistic regression revealed that successful spawning coincided with increases in …

Temporal Regularity Increases With Repertoire Complexity In The Australian Pied Butcherbird’S Song, Eathan Janney, Hollis Taylor, Constance Scharff, David Rothenberg, Lucas C. Parra, Ofer Tchernichovski

Publications and Research

Music maintains a characteristic balance between repetition and novelty. Here, we report a similar balance in singing performances of free-living Australian pied butcherbirds. Their songs include many phrase types. The more phrase types in a bird’s repertoire, the more diverse the singing performance can be. However, without sufficient temporal organization, avian listeners may find diverse singing performances difficult to perceive and memorize. We tested for a correlation between the complexity of song repertoire and the temporal regularity of singing performance. We found that different phrase types often share motifs (notes or stereotyped groups of notes). These shared motifs reappeared in …

A Gis Analysis Of Land Cover Effects On Water Systems: Nutrients And Algae In Stormwater Ponds, Nicole Lee Kappel

Theses and Dissertations

Anthropogenic land conversion is occurring rapidly and has the potential to impact our water quality. This study aims to explore the effect of watershed land characteristics on water quality within stormwater ponds (SWPs). Rapid land conversion is known to affect water quality of receiving water bodies, however not much is known about the effect of urbanization on SWPs. Geographic informational systems (GIS) was used to determine areas of land that drain into ponds. Water samples were collected and analyzed for total phosphorous, dissolved reactive phosphorous, nitrate, and ammonia. Algal pigment and percent cover measurements were taken in the field and …

Convergence In Nitrogen Deposition And Cryptic Isotopic Variation Across Urban And Agricultural Valleys In Northern Utah, Steven J. Hall, E. M. Ogata, Samantha R. Weintraub, Michelle A. Baker, James R. Ehleringer, C I. Czimczik, David R. Bowling

Biology Faculty Publications

The extent to which atmospheric nitrogen (N) deposition reflects land use differences and biogenic versus fossil fuel reactive N sources remains unclear yet represents a critical uncertainty in ecosystem N budgets. We compared N concentrations and isotopes in precipitation-event bulk (wet + dry) deposition across nearby valleys in northern Utah with contrasting land use (highly urban versus intensive agriculture/low-density urban). We predicted greater nitrate (NO3−) versus ammonium (NH4+) and higher δ15N of NO3− and NH4+ in urban valley sites. Contrary to expectations, annual N deposition (3.5–5.1 kg N ha−1 yr−1) and inorganic N concentrations were similar within and between valleys. …

Secondary Structure Adopted By The Gly-Gly-X Repetitive Regions Of Dragline Spider Silk, Geoffrey M. Gray, Arjan Van Der Vaart, Chengchen Guo, Justin A. Jones, David Onofrei, Brian R. Cherry, Randolph V. Lewis, Jeffery L. Yarger, Gregory P. Holland

Biology Faculty Publications

Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X) segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X) regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed.

Plastid Osmotic Stress Influences Cell Differentiation At The Plant Shoot Apex, Margaret E. Wilson, Matthew Mixdorf, R Howard Berg, Elizabeth S. Haswell

Biology Faculty Research

The balance between proliferation and differentiation in the plant shoot apical meristem is controlled by regulatory loops involving the phytohormone cytokinin and stem cell identity genes. Concurrently, cellular differentiation in the developing shoot is coordinated with the environmental and developmental status of plastids within those cells. Here, we employ an Arabidopsis thaliana mutant exhibiting constitutive plastid osmotic stress to investigate the molecular and genetic pathways connecting plastid osmotic stress with cell differentiation at the shoot apex. msl2 msl3 mutants exhibit dramatically enlarged and deformed plastids in the shoot apical meristem, and develop a mass of callus tissue at the shoot …

How Could Consciousness Emerge From Adaptive Functioning?, Max Velmans

Animal Sentience

The sudden appearance of consciousness that Reber posits in creatures with flexible cell walls and motility rather than non-flexible cells walls and no motility involves an evolutionary discontinuity. This kind of “miracle” is required by all “discontinuity” theories of consciousness. To avoid miraculous emergence, one may need to consider continuity theories, which accept that different forms of consciousness and material functioning co-evolve but assume the existence of consciousness to be primal in the way that matter and energy are assumed to be primal in physics.

Parallel Mutations Result In A Wide Range Of Cooperation And Community Consequences In A Two-Species Bacterial Consortium, Sarah Douglas, Lon Chubiz, William Harcombe, F. Ytreberg, Christopher Marx

Biology Department Faculty Works

Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium, we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determine community dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymous mutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica …

Grnsight: A Web Application And Service For Visualizing Models Of Small- To Medium-Scale Gene Regulatory Networks, Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi

Biology Faculty Works

GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of …

A Species-Level Phylogeny Of Extant Snakes With Description Of A New Colubrid Subfamily And Genus, Alex Figueroa, Alexander D. Mckelvy, L. Lee Grismer, Charles D. Bell, Simon P. Lailvaux

Publications and Research

Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higherlevel snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).

Results Increased taxon sampling resulted …

Review Of Experimental Compounds Demonstrating Anti-Toxoplasma Activity, Madalyn M. Mcfarland, Sydney J. Zach, Xiaofang Wang, Lakshmi-Prasad Potluri, Andrew J. Neville, Jonathan L. Vennerstrom, Paul H. Davis

Biology Faculty Publications

Toxoplasma gondii is a ubiquitous apicomplexan parasite capable of infecting humans and other animals. Current treatment options for T. gondii infection are limited and most have drawbacks, including high toxicity and low tolerability. Additionally, no FDA-approved treatments are available for pregnant women, a high-risk population due to transplacental infection. Therefore, the development of novel treatment options is needed. To aid this effort, this review highlights experimental compounds that, at a minimum, demonstrate inhibition of in vitro growth of T. gondii. When available, host cell toxicity and in vivo data are also discussed. The purpose of this review is to facilitate …

Identification Of Microorganisms Isolated From Mars-Bound Spacecraft Using Maldi-Tof, Melanie K. Phillips

STAR Program Research Presentations

The primary goal of the Biotechnology and Planetary Protection Group (BPPG) at the Jet Propulsion Laboratory (JPL) is to prevent microbial contamination between Earth and other planetary bodies. This helps preserve the ability to study other worlds as they exist in their natural states and protects our biosphere from extraterrestrial life. The process for identifying microbes located on space-bound hardware in JPL can be more efficient and precise by using the technique called matrix-assisted laser desorption and ionization time of flight (MALDI-TOF). Once this identification technique is fully implemented, the process time will be reduced from two weeks to one …

The Effects Of Drought On Diets Of Apex Predators In The South African Lowveld Inferred By Fecal Hair Analysis, Shelby Wade

Mahurin Honors College Capstone Experience/Thesis Projects

To properly manage offtake quotas and conservation efforts, Balule Nature Reserve (South Africa) instituted a study in 2014 to determine prey species selection by megapredators. In 2015, Balule Nature Reserve received about 190 mm less rainfall between the months of January and June than in 2014 (116 mm less than average). This study compares the diets of lions and hyaenas between 2014 and 2015. Prey species consumed were determined by fecal analysis, and results were compared to prey availability. Sixteen, 1 km2 plots were chosen from the 400 km2 Reserve. Between June and August 2015, we walked three, 1 km …

Identification Of Pathway-Specific Serum Biomarkers Of Response To Glucocorticoid And Infliximab Treatment In Children With Inflammatory Bowel Disease, Christopher R. Heier, Alyson A. Fiorillo, Ellen Chaisson, Heather A. Gordish-Dressman, Yetrib Hathout, Jesse M. Damsker, Eric P. Hoffman, Laurie S. Conklin

Genomics and Precision Medicine Faculty Publications

Objective:

Serum biomarkers may serve to predict early response to therapy, identify relapse, and facilitate drug development in inflammatory bowel disease (IBD). Biomarkers are particularly important in children, in whom achieving early remission and minimizing procedures are especially beneficial.

Methods:

We profiled protein and micro RNA (miRNA) in serum from patients pre- and post-therapy, to identify molecular markers of pharmacodynamic effect. Serum was obtained from children with IBD before and after treatment with either corticosteroids (prednisone; n=12) or anti-tumor necrosis factor-α biologic (infliximab; n=7). Over 1,100 serum proteins were assayed using aptamer-based SOMAscan proteomics, and 22 miRNAs analyzed …

Muscle Myeloid Type I Interferon Gene Expression May Predict Therapeutic Responses To Rituximab In Myositis Patients., Kanneboyina Nagaraju, Svetlana Ghimbovschi, Sree Rayavarapu, Aditi Phadke, Lisa G. Rider, Eric P. Hoffman, Frederick Miller

Genomics and Precision Medicine Faculty Publications

Objective. To identify muscle gene expression patterns that predict rituximab responses and assess the effects of rituximab on muscle gene expression in PM and DM.

Methods. In an attempt to understand the molecular mechanism of response and non-response to rituximab therapy, we performed Affymetrix gene expression array analyses on muscle biopsy specimens taken before and after rituximab therapy from eight PM and two DM patients in the Rituximab in Myositis study. We also analysed selected muscle-infiltrating cell phenotypes in these biopsies by immunohistochemical staining. Partek and Ingenuity pathway analyses assessed the gene pathways and networks.

Results. Myeloid type I IFN …

Principles And Practices Fostering Inclusive Excellence: Lessons From The Howard Hughes Medical Institute’S Capstone Institutions, P. M. Dibartolo, L. Gregg-Jolly, D. Gross, C. A. Manduca, E. Iverson, D. B. Cooke Iii, G. K. Davis, C. Davidson, P. E. Hertz, L. Hibbard, S. K. Ireland, C. Mader, A. Pai, S. Raps, Kathleen King Siwicki, J. E. Swartz

Biology Faculty Works

Best-practices pedagogy in science, technology, engineering, and mathematics (STEM) aims for inclusive excellence that fosters student persistence. This paper describes principles of inclusivity across 11 primarily undergraduate institutions designated as Capstone Awardees in Howard Hughes Medical Institute’s (HHMI) 2012 competition. The Capstones represent a range of institutional missions, student profiles, and geographical locations. Each successfully directed activities toward persistence of STEM students, especially those from traditionally underrepresented groups, through a set of common elements: mentoring programs to build community; research experiences to strengthen scientific skill/identity; attention to quantitative skills; and outreach/bridge programs to broaden the student pool. This paper grounds …

Review Of "A Primer Of Human Genetics" By G. Gibson, John B. Jenkins

Biology Faculty Works

No abstract provided.

Rapid Museum, Gary Barwin

The Goose

Poetry by Gary Barwin

The Role Of Retrotransposons In Gene Family Expansions In The Human And Mouse Genomes, Václav Janoušek, Christina M. Laukaitis, Alexey Yanchukov, Robert C. Karn

Scholarship and Professional Work - LAS

Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. …

Juvenile Winter Flounder (Pseudopleuronectes Americanus) And Summer Flounder (Paralichthys Dentatus) Utilization Of Southern New England Nurseries: Comparisons Among Estuarine, Tidal River, And Coastal Lagoon Shallow-Water Habitats, David L. Taylor, Jason Mcnamee, John Lake, Carissa L. Gervasi, Danial G. Palance

Arts & Sciences Faculty Publications

This study evaluated the relative importance of the Narragansett Bay estuary (RI and MA, USA), and associated tidal rivers and coastal lagoons, as nurseries for juvenile winter flounder, Pseudopleuronectes americanus, and summer flounder, Paralichthys dentatus. Winter flounder (WF) and summer flounder (SF) abundance and growth were measured from May to October (2009–2013) and served as indicators for the use and quality of shallow-water habitats (water depth < 1.5–3.0 m). These bioindicators were then analyzed with respect to physiochemical conditions to determine the mechanisms underlying intraspecific habitat selection. WF and SF abundances were greatest in late May and June (maximum monthly mean = 4.9 and 0.55 flounder/m2 for WF and SF, respectively) and were significantly higher in the tidal rivers relative to the bay and lagoons. Habitat-related patterns in WF and SF abundance were primarily governed by their preferences for oligohaline (0.1–5 ppt) and mesohaline (6–18 ppt) waters, but also their respective avoidance of hypoxic conditions (< 4 mg DO/L) and warm water temperatures (>25 °C). Flounder habitat usage was also positively related to sediment organic content, which may be due to these substrates having sufficiently high prey densities. WF growth rates (mean = 0.25 ± 0.14 mm/day) …

Insights Into The Molecular Roles Of Heparan Sulfate Proteoglycans (Hspgs-Syndecans) In Autocrine And Paracrine Growth Factor Signaling In The Pathogenesis Of Hodgkin's Lymphoma, Rajendra Ghardbaran

Publications and Research

Syndecans (SDC, SYND) comprise a group of four structurally related type 1 transmembrane heparan sulfate proteoglycans (HSPGs) that play important roles in tumorigenic processes. SDCs exert signaling via their protein cores and their conserved transmembrane and cytoplasmic domains or by forming complexes with growth factors (GFs). In classical Hodgkin's lymphoma (cHL), a lymphoid neoplasm of predominantly B cell origin, SDC1 and SDC4 are the active SDCs, and a number of GF (vascular endothelial growth factor, fibroblast growth factor, etc.) signaling pathways have been studied. However, despite extensive pre-clinical and clinical research on SDC-mediated GF signaling in many cancer types, there …

Genotypic Diversity Effects On Biomass Production In Native Perennial Bioenergy Cropping Systems, Geoffrey P. Morris, Zhenbin Hu, Paul P. Grabowski, Justin O. Borevitz, Marie-Anne De Graaff, R. Michael Miller, Julie D. Jastrow

Biology Faculty Publications and Presentations

The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) on perennial biomass cropping systems in two experiments conducted over 2008–2014 at a 5.4-ha fertile field site in northeastern Illinois, USA. We varied levels of switchgrass and big bluestem genotypic diversity using various local and nonlocal cultivars – under low or high species diversity, with or without nitrogen inputs – and …