Organisms Commons^™

Complex History Of Codiversification And Host Switching Of A Newfound Soricid-Borne Orthohantavirus In North America, Schuyler W. Liphardt, Hae Ji Kang, Laurie J. Dizney, Luis A. Ruedas, Joseph A. Cook, Richard Yanagihara

Biology Faculty Publications and Presentations

Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus …

Phylogenetic Estimates Of Hiv-1 Gp120 Indel Rates Across The Group M Subtypes, John Palmer, Art Poon

Western Research Forum

Insertions and deletions (indels) in the HIV-1 envelope glycoprotein gp120 play a significant role in the evolution of HIV pathogenesis and transmission fitness. While substitution rates in HIV-1 are well characterized by phylogenetic models, there is a lack of quantitative measures of indel rates in HIV-1. Here we use a dated-tip phylogenetic analysis of gp120 sequences to estimate indel rates for 7 subtypes and CRFs of HIV-1 group M.

We obtained and processed 26,359 HIV-1 gp120 sequences from the Los Alamos National Laboratory HIV Sequence database. After filtering these sequences, we extracted the conserved and variable regions from the remaining …

A Rapid Viability And Drug‑Susceptibility Assay Utilizing Mycobacteriophage As An Indicator Of Drug Susceptibilities Of Anti‑Tb Drugs Against Mycobacterium Smegmatis Mc2 155, Gillian Catherine Crowley, Jim O'Mahony, Aidan Coffey, Riona G. Sayers, Paul D. Cotter

Department of Biological Sciences Publications

Background: A rapid in-house TM4 mycobacteriophage-based assay, to identify multidrug resistance against various anti-tuberculosis drugs, using the fast-growing Mycobacterium smegmatis mc² 155 in a microtiter plate format was evaluated, based on phage viability assays. Methods: A variety of parameters were optimized before the study including the minimum incubation time for the drugs, phage and M. smegmatis mc² 155 to be in contact. An increase in phage numbers over 2 h was indicative that M. smegmatis mc² 155 is resistant to the drugs under investigation, however when phage numbers remained static, M. smegmatis mc² 155 found to …

A Multivalent Kaposi Sarcoma-Associated Herpesvirus-Like Particle Vaccine Capable Of Eliciting High Titers Of Neutralizing Antibodies In Immunized Rabbits, David H. Mulama, Lorraine Z. Mustvunguma, Jennifer Totonchy, Peng Ye, Joslyn Foley, Gabriela M. Escalante, Esther Rodriguez, Ramina Nabiee, Murali Muniraju, Felix Wussow, Anne K. Barasa, Javier Gordon Ogembo

Pharmacy Faculty Articles and Research

Kaposi sarcoma-associated herpesvirus (KSHV) is an emerging pathogen and the causative agent of multiple cancers in immunocompromised patients. To date, there is no licensed prophylactic KSHV vaccine. In this study, we generated a novel subunit vaccine that incorporates four key KSHV envelope glycoproteins required for viral entry in diverse cell types (gpK8.1, gB, and gH/gL) into a single multivalent KSHV-like particle (KSHV-LP). Purified KSHV-LPs were similar in size, shape, and morphology to KSHV virions. Vaccination of rabbits with adjuvanted KSHV-LPs generated strong glycoprotein-specific antibody responses, and purified immunoglobulins from KSHV-LP-immunized rabbits neutralized KSHV infection in epithelial, endothelial, fibroblast, and B …

Determining Remote Sensing Spatial Resolution Requirements For The Monitoring Of Harmful Algal Blooms In The Great Lakes, John Lekki, Eric Deutsch, Michael Sayers, Karl Bosse, Robert Anderson, Roger Tokars, Reid W. Sawtell

Michigan Tech Publications, Part 1

Harmful algal blooms (HABs) have become a major health and environmental concern in the Great Lakes. In 2014, severe HABs prompted the State of Ohio to request NASA Glenn Research Center (GRC) to assist with monitoring algal blooms in Lake Erie. The most notable species of HAB is Microcystis aeruginosa, a hepatotoxin producing cyanobacteria that is responsible for liver complications for humans and other fauna that come in contact with these blooms. NASA GRC conducts semiweekly flights in order to gather up-to-date imagery regarding the blooms' spatial extents and concentrations. Airborne hyperspectral imagery is collected using two hyperspectral imagers, HSI-2 …

Satellite Monitoring Of Harmful Algal Blooms In The Western Basin Of Lake Erie: A 20-Year Time-Series, Michael Sayers, Amanda Grimm, Robert Shuchman, Karl Bosse, Gary L. Fahnenstiel, Steven A. Ruberg, George A. Leshkevich

Michigan Tech Publications, Part 1

Blooms of harmful cyanobacteria (cyanoHABs) have occurred on an annual basis in western Lake Erie for more than a decade. Previously, we developed and validated an algorithm to map the extent of the submerged and surface scum components of cyanoHABs using MODIS ocean-color satellite data. The algorithm maps submerged cyanoHABs by identifying high chlorophyll concentrations (>18 mg/m3) combined with water temperature >20 °C, while cyanoHABs surface scums are mapped using near-infrared reflectance values. Here, we adapted this algorithm for the SeaWiFS sensor to map the annual areal extents of cyanoHABs in the Western Basin of Lake Erie for the …

Crispr/Cas9 In Yeast: A Multi-Week Laboratory Exercise For Undergraduate Students, Randi J. Ulbricht

Open Educational Resources

Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan for a laboratory-based course with the goal of editing the genome of budding yeast, Saccharomyces cerevisiae. Students apply knowledge regarding advanced topics such as: CRISPR/Cas9 gene editing, DNA repair, genetics, and cloning. The lesson requires students to master skills such as bioinformatics analysis, restriction enzyme digestion, ligation, basic microbiology skills, polymerase chain reaction, and plasmid purification. Instructors are led through the technical aspects of the protocols, …

The Association Between Herpes Simplex Virus Type 1 Reactivation And Alzheimer’S Disease, Andrew Allee

BIO 410 Spring 2019 Research Papers

This review will focus on the interaction of herpes simplex virus type 1 (HSV-1) and its causative role in pathogenesis of Alzheimer’s disease (AD) noting specifically, the epidemiological relevance of addressing this problem, as well as the molecular pathways associated. HSV-1 reactivation tends to be one of the primary causative events that is responsible for many of the pathologies associated with AD, such as: amyloid beta (Aβ) accumulation caused by malfunctioning cleavage of amyloid precursor protein (APP) as well as tau hyperphosphorylation. HSV-1 reactivation is a primary causative event in downstream dysfunction and is also shown to be directed by …

Author Correction: Fuctional Eubacteria Species Along With Transdomain Gut Inhabitants Favour Dysgenic Diversity In Oxalate Stone Disease, Mangesh V. Suryananshi, Shrikant S. Bhute, Rahul P. Gune, Yogesh S. Shouche

Life Sciences Faculty Research

This Article contains an error in the order of the Figures. Figures 2, 3 and 4 were published as Figures 4, 2, and 3 respectively. The correct Figures 2, 3 and 4 appear below as Figs 1, 2 and 3respectively. The Figure legends are correct.

Network Analyses Of Glomerular Capillaries, Jason Cory Brunson, Justin Sardi, Mark Terasaki

Biology and Medicine Through Mathematics Conference

No abstract provided.

Anti-Crispr Vs. Crispr: The Evolutionary Arms Race Between Microorganisms, Rachael M. St. Jacques

Masters Theses, 2010-2019

CRISPR arrays are a defense mechanism employed by bacteria against viral invaders. Cas proteins do the work in detecting, capturing, and integrating the viral DNA into the CRISPR array (Barrangou et al., 2007). Anti-CRISPR proteins are produced by phages, viruses that infect bacteria, to stop the bacterial host’s CRISPR-Cas complex from interrupting the phage life cycle (Bondy-Denomy, et al., 2015).

SEA-PHAGES is a course-based bacteriophage research network composed of 120 colleges and known at James Madison University as Viral Discovery. JMU uses the unsequenced Streptomyces griseus ATCC10137 as a host for bacteriophage discovery and propagation, and in this study we …

Amphotercin Washout Of Fungal Peritonitis In Liver Transplant Recipient: A Novel Approach, Ann Thompson, Mara Piltin, Alyssa Imperatore, Ely Sebastian, Sandra Paluzzi

Rowan-Virtua Research Day

Invasive fungal infection has a significant prevalence among organ transplant patients and is associated with high rates of morbidity and mortality. Fungal infection is difficult to identify early and subsequently difficult to effectively treat. In this case presentation we have a 45 y/o orthotopic liver transplant recipient who was profoundly sick from fungal peritonitis and due to the appearance of her abdomen and intestines, with the help of infectious disease, decided to proceed with direct amphotercin washout of the abdomen in the operating room. The patient had complete resolution of her fungal peritonitis and is doing well.

Investigation Of The In Vitro Interactions Between Two Common Cystic Fibrosis Pathogens, Staphylococcus Aureus And Stenotrophomonas Maltophilia., Matthew Hill

College of Arts & Sciences Senior Theses

Cystic Fibrosis (CF) is one of the most common autosomal disorders in Caucasian populations. This disorder creates a very opportune environment for many pathogens within the patient’s lung. Two common pathogens that infect CF patient’s lungs are Staphylococcus aureusand Stenotrophomonas maltophilia. These two species of bacteria can colonize host environments and establish mats of cells known as biofilms that become very difficult to eradicate with antibiotics. Once inside a CF lung, these pathogens must not only evade the host immune response but they also interact and compete with each other; however, how bacterial pathogens interact inside the host lung …

Effects Of Ambient And Laser Light On Water Evaporation From The Surface Of Polyurethane Swabs Doped With Surfactant, Collin Campbell

Chemical Engineering Undergraduate Honors Theses

Polyurethane swabs are a common instrument for environmental sampling in the food, medical, and forensic fields due to their high recovery of organisms like viruses, spores, and bacteria. For sampling microbes in food and medical facilities, storage of the collected samples occurs under the absence of light to promote growth for more accurate testing. In the forensic fields, microbial growth results in sample contamination so the inhibition of this growth requires the drying of the swabs. This work studies the evaporation rates of water from polyurethane swabs under zero watt incident light, 30 W fluorescent bulb, 50 mW 532 nm …

Reporting Charcoal Rot In Chia And Developing A Susceptibility Assay, Reis M. Misaka, Hagop S. Atamian Dr., Julien Besnard Dr.

Student Scholar Symposium Abstracts and Posters

Chia (Salvia Hispanica) cross breeds were planted in the summer of 2018 with the intent of selective breeding for agricultural benefit. Preexisting pathogens in the soil caused 40-50% fatality of adult plants. This was surprising due to the precursory knowledge that chia has antibiotic and antifungal oils (Elshafie et. al. 2018); chia was only recently documented to be susceptible to Fusarium wilt (Fusarium oxysporum). The primary pathogen responsible was identified as Macrophomina phaseolina (aka charcoal rot); a widespread soilborne pathogen which has multiple commercial hosts (Su et. al. 2001).

M. phaesolina on wheat seed vector where used as …

Automated Peak Detection Method For Behavioral Event Identification Detecting Balaenoptera Musculus And Grampus Griseus Feeding Attempts, David A. Sweeney, Stacy L. Deruiter, Ye Joo Mcnamara-Oh, Tiago A. Marques

University Faculty Publications and Creative Works

The desire of animal behaviorists for more flexible methods of conducting inter-study and inter-specific comparisons and meta-analysis of various animal behaviors compelled us to design an automated, animal behavior peak detection method that is potentially generalizable to a wide variety of data types, animals, and behaviors. We detected the times of feeding attempts by 12 Risso's dolphins (Grampus griseus) and 36 blue whales (Balaenoptera musculus) using the norm-jerk (rate of change of acceleration) time series. The automated peak detection algorithm identified median true-positive rates of 0.881 for blue whale lunges and 0.410 for Risso's dolphin prey capture attempts, with median …

Human Gut Microbiome, Enrico José Aveiro Johannsen, Mandy Peak

Posters

The human gut microbiome has been an area of interest for researchers due to its established link with human metabolism, nutrition, physiology, and immune functions. The research presented further investigates the microbiome to better understand it. Stools from two healthy young African males and a French obese individual were analyzed using MALDI-TOF MS and the enrichment culture technique. For the identification of bacterial species metagenomics, genomics, and culturomics were used. The results showed a much broader biodiversity in the human gut than previously predicted, as well as better results when using culturomics for measuring biodiversity in large-scale isolation.

Regulation Of Vaccinia Virus Replication: A Story Of Viral Mimicry And A Novel Antagonistic Relationship Between Vaccinia Kinase And Pseudokinase, Annabel T. Olson

School of Biological Sciences: Dissertations, Theses, and Student Research

Poxviruses employ sophisticated signaling pathways that thwart cellular defense mechanisms and simultaneously ensure viral factors are modulated properly. Yet, our understanding of these complex signaling networks are incomplete. For example, the vaccinia B1 kinase plays a vital role in inactivating the cellular antiviral factor BAF, and is suggested to orchestrate other pathways. B1 is highly conserved among poxviruses and exhibits a remarkable degree of similarity to VRKs, a family of cellular kinases, suggesting that the viral enzyme has evolved to mimic VRK activity. Indeed, B1 and VRKs have been demonstrated to target a shared substrate, the DNA binding protein BAF, …

Characterizing Aft1/2-Grx3/4 Interaction And The Role Of Bol2 During Iron Regulation In Saccharomyces Cerevisiae, William Rivers

Senior Theses

Iron dysregulation has been linked to a variety of human diseases, such as anemia, Friedreich’s ataxia, X-linked sideroblastic anemia, sideroblastic-like microcytic anemia, and myopathy. Thus, it is vitally important to understand the mechanisms for regulating intracellular iron. Here, we use fluorescence microscopy techniques in live cells to study interactions of the yeast proteins Grx3/4, Aft1/2, and Bol2, which have been shown to be involved in turning off iron import when the cell has adequate iron. Modified versions of genes encoding these proteins have been incorporated into several yeast backgrounds to use fluorescence to monitor interactions under varying iron levels.

The Effects Of Bacterial Endotoxin Lps On Synaptic Transmission At The Neuromuscular Junction, Robin L. Cooper, Micaiah Mcnabb, Jeremy Nadolski

Biology Faculty Publications

The direct action of bacterial lipopolysaccharides (LPS) endotoxin was shown to enhance synaptic transmission and hyperpolarize the membrane potential at low doses, but block glutamatergic receptors and decrease observable spontaneous events at a high dosage. The dosage effects are LPS type specific. The hyperpolarization is not due to voltage-gated potassium channels or to activation of nitric oxide synthase (NOS). The effects are induced directly by LPS, independent of an immune response.