Biology Commons^™

Biotechnology, Biologics And Biosimilars Bps 446, Joanna Burkhardt

Library Impact Statements

No abstract provided.

Big Brains Stabilize Populations And Facilitate Colonization Of Variable Habitats In Birds, Trevor S. Fristoe, Andrew N. Iwaniuk, Carlos A. Botero

Biology Faculty Research

The cognitive buffer hypothesis posits that environmental variability can be a major driver of the evolution of cognition because an enhanced ability to produce flexible behavioural responses facilitates coping with the unexpected. Although comparative evidence supports different aspects of this hypothesis, a direct connection between cognition and the ability to survive a variable and unpredictable environment has yet to be demonstrated. Here, we use complementary demographic and evolutionary analyses to show that among birds, the mechanistic premise of this hypothesis is well supported but the implied direction of causality is not. Specifically, we show that although population dynamics are more …

Zarnoch Studies The Health Of Our Waters, Aldemaro Romero Jr.

Publications and Research

Some people look at scientists and think of them as narrowly focused on obscure issues, but that is not the case with Dr. Chester Zarnoch. “You’re not just exploring the biology and the chemistry associated with the problem you’re working on, but also thinking about social implications, about economic implications,” he says.

A native of Manhattan, Zarnoch has studied and worked his entire life in New York, from receiving his bachelor’s degree at Southampton College of Long Island University, his master’s in the philosophy of biology at the City University of New York (CUNY) Graduate Center, a master’s in biology …

A Retrospective Look At The Physiological Stresses Response Of Southern Beaufort Sea Polar Bears, Susannah S. French

Funded Research Records

No abstract provided.

Filtering Out Parasites: Sand Crabs (Lepidopa Benedicti) Are Infected By More Parasites Than Sympatric Mole Crabs (Emerita Benedicti), Zen Faulkes

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

Two digging decapod crustaceans, the sand crab species Lepidopa benedicti and the mole crab species Emerita benedicti, both live in the swash zone of fine sand beaches. They were examined for two parasites that infect decapod crustaceans in the region, an unidentified nematode previously shown to infect L. benedicti, and cestode tapeworm larvae, Polypocephalus sp., previously shown to infect shrimp (Litopenaeus setiferus). Lepidopa benedicti were almost always infected with both parasite species, while E. benedicti were rarely infected with either parasite species. This difference in infection pattern suggests that tapeworms are ingested during sediment feeding in …

Melanoblast Development Coincides With The Late Emerging Cells From The Dorsal Neural Tube In Turtle Trachemys Scripta, R. Rice, J. Cebra-Thomas, M. Haugas, J. Partanen, D. P. C. Rice, Scott F. Gilbert

Biology Faculty Works

Ectothermal reptiles have internal pigmentation, which is not seen in endothermal birds and mammals. Here we show that the development of the dorsal neural tube-derived melanoblasts in turtle Trachemys scripta is regulated by similar mechanisms as in other amniotes, but significantly later in development, during the second phase of turtle trunk neural crest emigration. The development of melanoblasts coincided with a morphological change in the dorsal neural tube between stages mature G15 and G16. The melanoblasts delaminated and gathered in the carapacial staging area above the neural tube at G16, and differentiated into pigment-forming melanocytes during in vitro culture. The …

The Parasite Extinction Assessment & Red List: An Open-Source, Online Biodiversity Database For Neglected Symbionts, Colin J. Carlson, Oliver C. Muellerklein, Anna J. Phillips, Kevin R. Burgio, Giovanni Castaldo, Carrie A. Cizauskas, Graeme S. Cumming, Tad Dallas, Jorge Doña, Nyeema Harris, Roger Jovani, Zhongqi Miao, Heather Proctor, Hyun Seok Yoon, Wayne M. Getz

Faculty Publications

Parasite conservation is a rapidly growing field at the intersection of ecology, epidemiology, parasitology, and public health. The overwhelming diversity of parasitic life on earth, and recent work showing that parasites and other symbionts face severe extinction risk, necessitates infrastructure for parasite conservation assessments. Here, we describe the release of the Parasite Extinction Assessment & Red List (PEARL) version 1.0, an open-access database of conservation assessments and distributional data for almost 500 macroparasitic invertebrates. The current approach to vulnerability assessment is based on range shifts and loss from climate change, and will be expanded as additional data (e.g., host-parasite associations …

Improving The Pcr Protocol To Amplify A Repetitive Dna Sequence, J. Riet, L.R. V. Ramos, Randolph V. Lewis, L. F. Marins

Biology Faculty Publications

Although PCR-based techniques have become an essential tool in the field of molecular and genetic research, the amplification of repetitive DNA sequences is limited. This is due to the truncated nature of the amplified sequences, which are also prone to errors during DNA polymerase-based amplification. The complex structure of repetitive DNA can form hairpin loops, which promote dissociation of the polymerase from the template, impairing complete amplification, and leading to the formation of incomplete fragments that serve as megaprimers. These megaprimers anneal with other sequences, generating unexpected fragments in each PCR cycle. Our gene model, MaSp1, is 1037-bp long, …

Inventory Of Gulf Of Mexico Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruises Dp03 And Dp04) May-August, 2016, April Cook, Tracey Sutton

DEEPEND Datasets

This data set includes the biological and environmental data for all of the species collected during the DP03 (May 2016) and DP04 cruises (August 2016). The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled to capture diel …

New Record Of Asian Pied Starling (Gracupica Contra Contra) From Kalar Kahar (Pakistan), Usman Hanif, Fakhar-I- Abbas, Zahid Iqbal Khan, Afsar Mian

Journal of Bioresource Management

A pair of Asian Pied Starling or Pied Myna (Gracupica contra contra) was sighted in reed vegetation present around Kalar Kahar Lake (northwestern Salt Range, Pakistan). Subspecies has been sighted for the first time west of Sialkot and Lahore. Further studies are required to determine the status of the population of the subspecies in Kalar Kahar to suggest an extension in distribution range of the species.

Coordinating Ipm Successes In Utah's Crops, Communities And Schools, Marion Murray

Funded Research Records

No abstract provided.

Monitoring Replication Protein A (Rpa) Dynamics In Homologous Recombination Through Site-Specific Incorporation Of Non-Canonical Amino Acids, Nilisha Pokhrel, Sofia Origanti, Eric Parker Davenport, Disha M. Gandhi, Kyle Kaniecki, Ryan A. Mehl, Eric C. Greene, Chris Dockendorff, Edwin Antony

Biological Sciences Faculty Research and Publications

An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as …

A First Linkage Map And Downy Mildew Resistance Qtl Discovery For Sweet Basil (Ocimum Basilicum) Facilitated By Double Digestion Restriction Site Associated Dna Sequencing (Ddradseq), Robert M. Pyne, Josh Honig, Jennifer Vaiciunas, Adolfina R. Koroch, Christian Wyenandt, Stacy Bonos, James Simon

Publications and Research

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed …

Efficacy Of Neutral And Negatively Charged Liposome-Loaded Gentamicin On Planktonic Bacteria And Biofilm Communities, Moayad Alhariri, Majad A. Majrashi, Ali H. Bahkali, Faisal S. Almajed, Ali Azghani, Mohammed A. Khiyami, Essam J. Alyamani, Sameera M. Aljohani, Majed A. Halwani

Biology Faculty Publications and Presentations

We investigated the efficacy of liposomal gentamicin formulations of different surface charges against Pseudomonas aeruginosa and Klebsiella oxytoca. The liposomal gentamicin formulations were prepared by the dehydration-rehydration method, and their sizes and zeta potential were measured. Gentamicin encapsulation efficiency inside the liposomal formulations was determined by microbiologic assay, and stability of the formulations in biologic fluid was evaluated for a period of 48h. The minimum inhibitory concentration and the minimum bactericidal concentration were determined, and the in vitro time kill studies of the free form of gentamicin and liposomal gentamicin formulations were performed. The activities of liposomal gentamicin in preventing …

Seeds From Fresh Conventional Tomatoes Germinate Faster Than Dried Or Organic Seeds, Christopher G. Brown, Kautz Evan, Cameron Kilpatrick, Mary Vu, Mallory Weaver

Georgia Journal of Science

Conventionally-grown and organically-grown tomato seeds sourced from both fresh tomatoes and store-bought packages were germinated for seven days to evaluate the effect of seed source on germination rates. Seeds from fresh Roma tomatoes were prepared by allowing them to ferment in their own pulp for 24 hours, while commercially packaged dry seeds did not require any preparation. Once prepared, the seeds were spaced evenly on wet paper towels and stored in resealable plastic bags in groups of 10 for a total sample size of 100 seeds in each of four treatments. The number of germinated seeds and the length of …

Chronic Plasmodium Brasilianum Infections In Wild Peruvian Tamarins, Gideon Erkenswick, Mrinalini Watsa, M. Pacheco, Ananias Escalante, Patricia Parker, Georges Snounou

Biology Department Faculty Works

There is an increased interest in potential zoonotic malarias. To date, Plasmodium malariae that infects humans remains indistinguishable from Plasmodium brasilianum, which is widespread among New World primates. Distributed throughout tropical Central and South America, the Callitrichidae are small arboreal primates in which detection of natural Plasmodium infection has been extremely rare. Most prior screening efforts have been limited to small samples, the use of low-probability detection methods, or both. Rarely have screening efforts implemented a longitudinal sampling design. Through an annual mark-recapture program of two sympatric callitrichids, the emperor (Saguinus imperator) and saddleback (Saguinus fuscicollis) tamarins, whole blood samples …

Prothonotary Warbler Nest Selection, Nest Survival, Demographic Parameters, And Spatial Plumage Color Variation, Morgan Christopher Slevin

Student Theses and Dissertations

(I) To aid conservation efforts for the declining Prothonotary Warbler (Protonotaria citrea), we studied warblers breeding in White River NWR to assess relationships between nest site microhabitat variables and both habitat selection patterns and nest survival; furthermore, we estimated demographic parameters of individuals breeding in natural cavities vs. nest boxes. Prothonotary Warblers preferred nesting in relatively high, shallow cavities in dead trees; however, canopy cover was negatively related to nest survival. Demographic parameters generally did not differ between nest type. (II) To explore how carotenoid-derived coloration and associated signaling vary spatially, we compared warblers breeding in Arkansas and Virginia, USA. …

Phytochemical-Rich Foods Inhibit The Growth Of Pathogenic Trichomonads, Sabrina M. Noritake, Jenny Liu, Sierra Kanetake, Carol E. Levin, Christina Tam, Luisa W. Cheng, Kirkwood M. Land, Mendel Friedman

College of the Pacific Faculty Articles

Plants produce secondary metabolites that often possess widespread bioactivity, and are then known as phytochemicals. We previously determined that several phytochemical-rich food-derived preparations were active against pathogenic foodborne bacteria. Trichomonads produce disease (trichomoniasis) in humans and in certain animals. Trichomonads are increasingly becoming resistant to conventional modes of treatment. It is of interest to test bioactive, natural compounds for efficacy against these pathogens.

Elevated Expression Of Hypoxanthine Guanine Phosphoribosyltransferase Within Malignant Tissue, Michelle H. Townsend, Abigail M. Felsted, Zachary E. Ence, Stephen R. Piccolo, Richard A. Robison, Kim L. O'Neill

Faculty Publications

Hypoxanthine Guanine Phosphoribosyltransferase (HPRT) is a housekeeping enzyme involved in the purine synthesis of guanine and inosine in the salvage pathway. While other salvage pathway enzymes, such as TK1, have been established as biomarkers for both cancer cell proliferation and cancer development, little research been done to evaluate whether HPRT has the same potential as a cancer biomarker. We designed this study to determine if HPRT has value as an identifier of malignancy within the most common types of cancer. We utilized histological samples from lung, colon, prostate, and breast cancer with additional normal tissue to evaluate whether there was …

Transcriptome Sequencing And Delimitation Of Sympatric Oscarella Species (O. Carmela And O. Pearsei Sp. Nov) From California, Usa, Alexander V. Ereskovsky, Daniel J. Richter, Dennis V. Lavrov, Klaske J. Schippers, Scott A. Nichols

Biological Sciences: Faculty Scholarship

The homoscleromorph sponge Oscarella carmela, first described from central California, USA is shown to represent two superficially similar but both morphologically and phylogenetically distinct species that are co-distributed. We here describe a new species as Oscarella pearsei, sp. nov. and re-describe Oscarella carmela; the original description was based upon material from both species. Further, we correct the identification of published genomic/transcriptomic resources that were originally attributed to O. carmela, and present new Illumina-sequenced transcriptome assemblies for each of these species, and the mitochondrial genome sequence for O. pearsei sp. nov. Using SSU and LSU …

Risking Our Reefs Bio 256g, Michael Cerbo

Library Impact Statements

No abstract provided.

Chloride Intracellular Channel Proteins Respond To Heat Stress In Caenorhabditis Elegans, Jun Liang, Yakov Shaulov, Cathy Savage-Dunn, Stéphane Boissinot, Tasmia Hoque

Publications and Research

Chloride intracellular channel proteins (CLICs) are multi-functional proteins that are expressed in various cell types and differ in their subcellular location. Two CLIC homologs, EXL-1 (excretory canal abnormal like-1) and EXC-4 (excretory canal abnormal± 4), are encoded in the Caenorhabditis elegans genome, providing an excellent model to study the functional diversification of CLIC proteins. EXC-4 functions in excretory canal formation during normal animal development. However, to date, the physiological function of EXL-1 remains largely unknown. In this study, we demonstrate that EXL-1 responds specifically to heat stress and translocates from the cytoplasm to the nucleus in intestinal cells and body …

Pteronura Brasiliensis (Carnivora: Mustelidae), Paula Noonan, Siobhan Prout, Virginia Hayssen

Biological Sciences: Faculty Publications

Pteronura brasiliensis (Zimmermann, 1780), the giant otter, is the largest freshwater otter. Found in South America, it inhabits slow-moving rivers and creeks and feeds predominantly on fish. Extinct in the southern portions of its former range, P. brasiliensis is listed as "Endangered" by the International Union for Conservation of Nature and Natural Resources. Threats to P. brasiliensis include habitat destruction, illegal hunting, and disease.

Stability At Low Densities Or Endangered? Spatiotemporal Population Dynamics Of The Caddo Madtom (Noturus Taylori), Brittany Latrice Mccall

Student Theses and Dissertations

Imperilment in North American freshwater fishes is primarily due to habitat alteration, deterioration, and fragmentation. In response to the aquatic biodiversity crisis, there has been a call for action by the Center for Biological Diversity, with a petition for the federal listing of 404 aquatic species in the southeastern U.S. This thesis focuses on a petitioned species, the Caddo Madtom, Noturus taylori. The chapters in this thesis address the genetic variation, habitat limitations, and status of the Arkansas endemic. In summation, N. taylori was found to have a high level of genetic variation for an endemic madtom, and is relatively …

Parasite Biodiversity Faces Extinction And Redistribution In A Changing Climate, Colin J. Carlson, Kevin R. Burgio, Eric R. Dougherty, Anna J. Phillips, Veronica M. Bueno, Christopher F. Clements, Giovanni Castaldo, Tad Dallas, Carrie A. Cizauskas, Graeme S. Cumming, Jorge Doña, Nyeema C. Harris, Roger Jovani, Sergey Mironov, Oliver C. Muellerklein, Heather C. Proctor, Wayne M. Getz

Faculty Publications

Climate change is a well-documented driver of both wildlife extinction and disease emergence, but the negative impacts of climate change on parasite diversity are undocumented. We compiled the most comprehensive spatially explicit data set available for parasites, projected range shifts in a changing climate, and estimated extinction rates for eight major parasite clades. On the basis of 53,133 occurrences capturing the geographic ranges of 457 parasite species, conservative model projections suggest that 5 to 10% of these species are committed to extinction by 2070 from climate-driven habitat loss alone. We find no evidence that parasites with zoonotic potential have a …

C. Elegans Avoids Toxin-Producing Streptomyces Using A Seven Transmembrane Domain Chemosensory Receptor, Alan Tran, Angelina Tang, Colleen O’Loughlin, Anthony Balistreri, Eric Chang, Doris Coto Villa, Joy Li, Aruna Varshney, Vanessa Jimenez, Jacqueline Pyle, Bryan Tsujimoto, Christopher Wellbrook, Christopher Vargas, Alex Duong, Nebat Ali, Sarah Matthews, Samantha Levinson, Sarah Woldemariam, Sami Khuri, Martina Bremer, Daryl Eggers, Noelle L’Etoile, Laura Miller Conrad, Miri Vanhoven

Faculty Publications, Chemistry

Predators and prey co-evolve, each maximizing their own fitness, but the effects of predator–prey interactions on cellular and molecular machinery are poorly understood. Here, we study this process using the predator Caenorhabditis elegans and the bacterial prey Streptomyces, which have evolved a powerful defense: the production of nematicides. We demonstrate that upon exposure to Streptomyces at their head or tail, nematodes display an escape response that is mediated by bacterially produced cues. Avoidance requires a predicted G-protein-coupled receptor, SRB-6, which is expressed in five types of amphid and phasmid chemosensory neurons. We establish that species of Streptomyces secrete dodecanoic acid, …

Interest Exceeds Understanding In Public Support Of Bee Conservation, Joseph S. Wilson, Matthew L. Forister, Olivia Messinger Carril

Biology Faculty Publications

Recent analyses suggesting that certain populations of bees may be declining have led to a variety of conservation efforts, many of which rely on public support and participation. However, little is known about the public's knowledge of bee diversity. We carried out a survey to measure public understanding of bee diversity and found that although 99% of respondents believed that bees are critical or important, only 14% were able to guess within 1000 the actual number of bee species in the US. Furthermore, when reviewing a selection of photographs depicting various insects, many respondents were unable to discern bees from …

Riparian Plant Litter Quality Increases With Latitude, Luz Boyero, Manuel A. S. Graça, Alan M. Tonin, Javier Pérez, Andrew J. Swafford, Verónica Ferreira, Andrea Landeira-Dabarca, Markos A. Alexandrou, Mark O. Gessner, Brendan G. Mckie, Ricardo J. Albariño, Leon A. Barmuta, Marcos Castillo, Julián Chará, Eric Chauvet, Jose Checo Colón-Gaud, David Dudgeon, Andrea C. Encalada, Ridcardo Figueroa, Alexander S. Flecker, Tadeusz Fleituch, André Frainer, José F. Gonçalves Jr., Julie E. Helson, Tomoya Iwata, Jude Mathooko, Charles M'Erimba, Catherine M. Pringle, Alonso Ramírez, Christopher M. Swan, Catherine M. Yule, Richard G. Pearson

Biology: Faculty Publications

Plant litter represents a major basal resource in streams, where its decomposition is partly regulated by litter traits. Litter-trait variation may determine the latitudinal gradient in decomposition in streams, which is mainly microbial in the tropics and detritivore-mediated at high latitudes. However, this hypothesis remains untested, as we lack information on large-scale trait variation for riparian litter. Variation cannot easily be inferred from existing leaf-trait databases, since nutrient resorption can cause traits of litter and green leaves to diverge. Here we present the first global-scale assessment of riparian litter quality by determining latitudinal variation (spanning 107°) in litter traits (nutrient …

Urbanization Alters Communities Of Flying Arthropods In Parks And Gardens Of A Medium-Sized City, Edward Lagucki, Justin D. Burdine, Kevin E. Mccluney

Biological Sciences Faculty Publications

Urbanization transforms undeveloped landscapes into built environments, causing changes in communities and ecological processes. Flying arthropods play important roles in these processes as pollinators, decomposers, and predators, and can be important in structuring food webs. The goal of this study was to identify associations between urbanization and the composition of communities of flying (and floating) arthropods within gardens and parks in a medium-sized mesic city. We predicted that flying arthropod abundance and diversity would respond strongly to percent impervious surface and distance to city center, measurements of urbanization. Flying arthropods were sampled from 30 gardens and parks along an urbanization …

Plant Mechanosensitive Ion Channels: An Ocean Of Possibilities, Debarati Basu, Elizabeth S. Haswell

Biology Faculty Research

Mechanosensitive ion channels, transmembrane proteins that directly couple mechanical stimuli to ion flux, serve to sense and respond to changes in membrane tension in all branches of life. In plants, mechanosensitive channels have been implicated in the perception of important mechanical stimuli such as osmotic pressure, touch, gravity, and pathogenic invasion. Indeed, three established families of plant mechanosensitive ion channels play roles in cell and organelle osmoregulation and root mechanosensing - and it is likely that many other channels and functions await discovery. Inspired by recent discoveries in bacterial and animal systems, we are beginning to establish the conserved and …