Biology Commons^™

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Two Distinct Modes Of Metal Ion Binding In The Nuclease Active Site Of A Viral Dna-Packaging Terminase: Insight Into The Two-Metal-Ion Catalytic Mechanism, Haiyan Zhao, Zihan Lin, Anna Y. Lynn, Brittany Varnado, John A. Beutler, Ryan P. Murelli, Stuart F.J. Le Grice, Liang Tang

Publications and Research

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A° . Such proximity of the two metal ions may play an essential role in catalysis by …

The Effects Of Modafinil And Atomoxetine On Dopamine Signaling In The Striatal Subregions Of The Rat, Martin Bobak

Theses and Dissertations

In an effort to combat diseases and disorders that impede our health, comfort and well-being, an abundance of prescription drugs have emerged in the past 60 years. Many prescription drugs have remarkable efficacy for treating the primary symptoms of these diseases and disorders; however, some drugs carry negative side effects that impose their own adverse symptoms, albeit, often to a lesser degree than the primary symptoms. Thus, one of the main objectives of the pharmaceutical industry is to innovate and develop novel therapeutics, which remediate the primary symptoms of disease and lack undesirable negative side effects. However, in order to …

Intramolecular Phenotypic Capacitance In A Modular Rna Molecule, Eric J. Hayden, Devin P. Bendixsen, Andreas Wagner

Biology Faculty Publications and Presentations

Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second …

Colonization Of Lutzomyia Verrucarum And Lutzomyia Longipalpis Sand Flies (Diptera: Psychodidae) By Bartonella Bacilliformis, The Etiologic Agent Of Carrion's Disease, James M. Battisti, Phillip G. Lawyer, Michael F. Minnick

Biological Sciences Faculty Publications

Bartonella bacilliformis is a pathogenic bacterium transmitted to humans presumably by bites of phlebotomine sand flies, infection with which results in a bi-phasic syndrome termed Carrion's disease. After constructing a low-passage GFP-labeled strain of B. bacilliformis, we artificially infected Lutzomyia verrucarum and L. longipalpis populations, and subsequently monitored colonization of sand flies by fluorescence microscopy. Initially, colonization of the two fly species was indistinguishable, with bacteria exhibiting a high degree of motility, yet still confined to the abdominal midgut. After 48h, B. bacilliformis transitioned from bacillus-shape to a non-motile, small coccoid form and appeared to be digested along with …

Mapping The Movement Of Overwintering Western Monarch Butterflies (Danaus Plexippus) At The Pismo Beach Monarch Butterfly Grove Using Arcgis Software, Brett Johnson, Jesse Wycko, Daniel Goldthwaite, Tyler Brown

Symposium

Dr. Villablanca of the Cal Poly Biology Department commissioned this project with the goal of tracking Monarch Butterfly spatial redistribution in anticipation of or response to severe weather events. We believe that Monarchs cluster non-preferentially on introduced Eucalyptus trees until midwinter when they begin to cluster preferentially on native conifers. Based on the efforts of a previous group of students, it has been deter- mined that, over a two-week time period in mid-winter, Monarchs spend the majority of their time on native conifers. We set out to clearly demonstrate Monarch Butterfly spatial redistribution in either anticipation of or response to …

The Influence Of Psychological Factors On Reducing Recovery Time From Total Knee Replacement Surgery, Melissa Geiger

Symposium

Osteoarthritis is the most common cause of physical disability that Americans face, leading to destruction of the joints of the body. The primary joint affected is the knee, and the leading treatment is total knee replacement. The incidence of total knee replacement surgery is rising–and will continue to rise–as a treatment for knee pain resulting from osteoarthritis (Mizner et al., 2005). Various psychological factors have been proven to influence a person’s well-being in general and, more specifically, with recovery from illness or surgery (Taylor, 2011). Pre- surgical psychological screenings are an important factor in determining how the patient will recover …

Protocols For Cleaning And Articulating Large Mammal Skeleton, Brandon Rowley

Symposium

This protocol will refer to Panthera tigris as an example for each cleaning method and articulation because that was the organism subject to this procedure. However, the processes and methods discussed here can be used as reference for any large mammal. The key is to make sure the skeleton is clean, which entails removing the meat from the bones, degreasing, and whitening. Once this is done, articulation can begin. The protocol is divided into three major sections: cleaning the skeleton, whitening and degreasing, and articulation. The cleaning section contains three contemporary methods for removing tissue. Each method can be performed …

Assessing The Synergistic Effect Of Caffeine And Sugar On Cognitive Performance In Undergraduate Students, Sandra P. Urquiza, Michelle Vieyra

Journal of the South Carolina Academy of Science

Working independently, both caffeine and sugar provide benefits to attention and memory. However, there is sparse literature on the synergistic effects on improved cognitive performance between caffeine and sugar when taken together. This study explored the dynamics between caffeine and sugar when consumed under ordinary conditions – as a cup of coffee. Twenty-four undergraduate students (15 women and 9 men) were asked to complete a baseline cognitive test, and one of the three variables was given at random in the form of a cup of coffee: decaffeinated with sugar, caffeinated with no sugar, and caffeinated with sugar. The remaining two …

Reactive Oxygen Species-Mediated Neurodegeneration Is Independent Of The Ryanodine Receptor In Caenorhabditis Elegans, Lyndsay E.A. Young, Daniel C. Williams

Journal of the South Carolina Academy of Science

Despite the significant impacts on human health caused by neurodegeneration, our understanding of the degeneration process is incomplete. The nematode Caenorhabditis elegans is emerging as a genetic model organism well suited for identification of conserved cellular mechanisms and molecular pathways of neurodegeneration. Studies in the worm have identified factors that contribute to neurodegeneration, including excitotoxicity and stress due to reactive oxygen species (ROS). Disruption of the gene unc-68, which encodes the ryanodine receptor, abolishes excitotoxic cell death, indicating a role for calcium (Ca²⁺) signaling in neurodegeneration. We tested the requirement for unc-68 in ROS-mediated neurodegeneration using the …

Incidence Of West Nile Virus In House Sparrow Nestlings In Relation To Parental Effort, Natalie Mickelsen

Kaleidoscope

The house sparrow, Passer domesticus, is known to be an important host of West Nile (WN) virus and may contribute to the transmission of WN virus to humans. However, little is known about the factors that influence the occurrence of WN virus in birds. I conducted a study to determine if parental care was related to the rates of WN virus infections among nestling birds. I observed house sparrow nests for one hour periods noting the time the male and female parent spent on the nest box, in the nest box, and the number of food trips, as measures …

Poster 7: Importance Of Protein Structure Prediction, Michael Qian '16, Sarah Dovgin '16, Esther Chung '16

Protein Folding & Structure Prediction Posters

Initially, drugs were discovered by either chance or by trial and error through screening methods. Because scientists did not have the ability to model protein structures, drug discovery was a very expensive process. Currently, researchers are working on technologies to determine protein ligands and potential drugs through the usage of predicted protein structures.

Poster 1: Protein Functions And Relationships Between Structure And Function, Mara Cardona '16, Max Shramuk '16

Protein Folding & Structure Prediction Posters

No abstract provided.

Poster 6: Chaperone Proteins, Grace Carlberg '16, Andy Xu '16, Andrew Adams '16

Protein Folding & Structure Prediction Posters

No abstract provided.

Telonicher Marine Laboratory, Hsu Telonicher Marine Laboratory

Newsletters

No abstract provided.

High-Quality Permanent Draft Genome Sequence Of The Mimosa Asperata - Nodulating Cupriavidus Sp Strain Amp6, Sofie E. De Meyer, Matthew Parker, Peter Van Berkum, Rui Tian, Rekha Seshadri, T. B.K. Reddy, Victor Markowitz, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides, John Howieson, Wayne Reeve

Biological Sciences Faculty Scholarship

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Moreover, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Therefore, the genome of Cupriavidus sp. strain AMP6 enables comparative analyses of symbiotic trait evolution in this genus and here we describe the general features, together …

The Incredible Shrinking Dewlap: Signal Size, Skin Elasticity, And Mechanical Design In The Green Anole Lizard (Anolis Carolinensis), Simon P. Lailvaux, Jack Leifer, Bonnie K. Kircher, Michele A. Johnson

Biology Faculty Research

The expression of male secondary sexual traits can be dynamic, changing size, shape, color, or structure over the course of different seasons. However, the factors underlying such changes are poorly understood. In male Anolis carolinensis lizards, a morphological secondary sexual signal called the dewlap changes size seasonally within individuals. Here, we test the hypothesis that seasonal changes in male dewlap size are driven by increased use and extension of the dewlap in spring and summer, when males are breeding, relative to the winter and fall. We captured male green anole lizards prior to the onset of breeding and constrained the …

Readings On Current Biology: Bibliography, Imsa Biology Team

Nature of Science

No abstract provided.

Foraging Behavior Links Climate Variability And Reproduction In North Pacific Albatrosses, Lesley Thorne, Elliott Hazen, Steven Bograd, David Foley, Melinda Conners, Michelle Kappes, Hyemi Kim, Daniel Costa, Yann Tremblay, Scott A. Shaffer

Faculty Publications, Biological Sciences

Background: Climate-driven environmental change in the North Pacific has been well documented, with marked effects on the habitat and foraging behavior of marine predators. However, the mechanistic linkages connecting climate-driven changes in behavior to predator populations are not well understood. We evaluated the effects of climate-driven environmental variability on the reproductive success and foraging behavior of Laysan and Black-footed albatrosses breeding in the Northwest Hawaiian Islands during both brooding and incubating periods. We assessed foraging trip metrics and reproductive success using data collected from 2002–2012 and 1981–2012, respectively, relative to variability in the location of the Transition Zone Chlorophyll Front …

The Examination Of Enrichment Using Space And Food For African Elephants (Loxodonta Africana) At The San Diego Zoo Safari Park, Charlotte Hacker

Masters Theses & Specialist Projects

Concern for elephant welfare in zoological facilities has prompted a number of exhibit and management modifications, including those involving enrichment. Knowledge of how these changes impact measures of health and wellbeing, such as elephant movement and behavior, is crucial as the effects of multiple enrichment types and their interactions are largely understudied. The present study used observations and GPS unit collected data to determine the effects of space and food on the walking distance and behavior of thirteen African elephants, whose dominance structure was ascertained by the handlers at the San Diego Zoo Safari Park (SDZSP). This facility has two …

A Newly Discovered Bordetella Species Carries A Transcriptionally Active Crispr-Cas With A Small Cas9 Endonuclease, Yury V. Ivanov, Nikki Shariat, Karen B. Register, Bodo Linz, Israel Rivera, Kai Hu, Edward G. Dudley, Eric T. Harvill

Biology Faculty Publications

Background

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR.

Methods

The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR.

Results

Here we …

An Invitation To Measure Insect Cold Tolerance: Methods, Approaches, And Workflow., Brent J Sinclair, Litza E Coello Alvarado, Laura V Ferguson

Biology Publications

Insect performance is limited by the temperature of the environment, and in temperate, polar, and alpine regions, the majority of insects must face the challenge of exposure to low temperatures. The physiological response to cold exposure shapes the ability of insects to survive and thrive in these environments, and can be measured, without great technical difficulty, for both basic and applied research. For example, understanding insect cold tolerance allows us to predict the establishment and spread of insect pests and biological control agents. Additionally, the discipline provides the tools for drawing physiological comparisons among groups in wider studies that may …

Science & Spaghetti Monsters: Understanding The Nature Of Scientific Knowledge & Research, Sarah O'Leary-Driscoll

Nature of Science

What is science?

When students are asked to define science, many of them define science as “a body of knowledge gained by performing experiments.”

A more appropriate definition, however, is that “Science is … a process of inquiry aimed at building a testable body of knowledge open to rejection or confirmation” (Shermer, 2005).

There are three important points that this definition makes:

Poster 2: Primary Structure, Max Shramuk '16, Mara Cardona '16

Protein Folding & Structure Prediction Posters

No abstract provided.

Poster 3: Secondary Structure, Michael Qian '16, Sarah Dovgin '16, Esther Chung '16

Protein Folding & Structure Prediction Posters

No abstract provided.

Poster 4: Tertiary Structure, Grace Carlberg '16, Andy Xu '16, Andrew Adams '16

Protein Folding & Structure Prediction Posters

When proteins form polypeptide chains, they form primary structure - their amino acid sequence - secondary structure - their local shapes - and tertiary structure - their global fold and shape. Tertiary structure and its prediction are of vital importance to the biology community because of its importance for manipulating gene expression, cell-wide processes, and more. Because of the innumerable possibilities for even a simple primary structure protein, prediction is incredibly difficult. As bioinformatics technologies advance, though, our understanding of tertiary folding advances.

Poster 5: Quaternary Structure, Arun Arjunakani '16, Joseph Jagusah '16

Protein Folding & Structure Prediction Posters

No abstract provided.

Poster 8: Predicting Structure: Current Techniques And Challenges, Arun Arjunakani '16, Joseph Jagusah '16

Protein Folding & Structure Prediction Posters

No abstract provided.

Flexibility Of Crab Chemosensory Hairs Enables Flicking Antennules To Sniff, Lindsay D. Waldrop, Matthew A. Reidenbach, M. A. R. Koehl

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The first step in smelling is capture of odorant molecules from the surrounding fluid. We used lateral flagella of olfactory antennules of crabs Callinectes sapidus to study the physical process of odor capture by antennae bearing dense tufts of hair-like chemosensory sensilla (aesthetascs). Fluid flow around and through aesthetasc arrays on dynamically scaled models of lateral flagella of C. sapidus was measured by particle image velocimetry to determine how antennules sample the surrounding water when they flick. Models enabled separate evaluation of the effects of flicking speed, aesthetasc spacing, and antennule orientation. We found that crab antennules, like those of …

Essential Questions, Imsa Biology Team

Evolution

In order to understand the current state of biological life and how it has changed over time, the following questions must be addressed: