Digital Commons Network^™

The Valley-Of-Death: Reciprocal Sign Epistasis Constrains Adaptive Trajectories In A Constant, Nutrient Limiting Environment, Kami E. Chiotti, Daniel J. Kvitek, Karen H. Schmidt, Gregory Koniges, Katja Schwartz, Elizabeth A. Donckels, Frank Rosenzweig, Gavin Sherlock

Biological Sciences Faculty Publications

The fitness landscape is a powerful metaphor for describing the relationship between genotype and phenotype for a population under selection. However, empirical data as to the topography of fitness landscapes are limited, owing to difficulties in measuring fitness for large numbers of genotypes under any condition. We previously reported a case of reciprocal sign epistasis (RSE), where two mutations individually increased yeast fitness in a glucose-limited environment, but reduced fitness when combined, suggesting the existence of two peaks on the fitness landscape. We sought to determine whether a ridge connected these peaks so that populations founded by one mutant could …

Review Of "The Pku Paradox: A Short History Of A Genetic Disease" By D. B. Paul And J. P. Brosco, John B. Jenkins

Biology Faculty Works

No abstract provided.

Historical Species Distribution Models Predict Species Limits In Western Plethodon Salamanders, Tara A. Pelletier, Charlie Crisafulli, Steve Wagner, Amanda J. Zellmer, Brian C. Carstens

All Faculty Scholarship for the College of the Sciences

Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range, hindcast these models onto a climatic model 21 Ka, and use three molecular approaches to delimit species in an integrated fashion. In contrast to expectations …

Pathogenic Landscape Of Transboundary Zoonotic Diseases In The Mexico–Us Border Along The Rio Grande, Maria Dolores Esteve-Gassent, Adalberto A. Pérez De León, Dora Romero-Salas, Teresa Patricia Feria-Arroyo, Ramiro Patino, John A. Goolsby

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

Transboundary zoonotic diseases, several of which are vector borne, can maintain a dynamic focus and have pathogens circulating in geographic regions encircling multiple geopolitical boundaries. Global change is intensifying transboundary problems, including the spatial variation of the risk and incidence of zoonotic diseases.The complexity of these challenges can be greater in areas where rivers delineate international boundaries and encompass transitions between ecozones.The Rio Grande serves as a natural border between the US State ofTexas and the Mexican States of Chihuahua, Coahuila, Nuevo León, andTamaulipas. Not only do millions of people live in this transboundary region, but also a substantial amount …

Toxic Metal Effect On Filamentous Fungi Isolated From The Contaminated Soil Of Multan And Gujranwala, Anam Rasool, Shazia Irum

Journal of Bioresource Management

Considering the importance of filamentous fungi for bioremediation of wastewater and contaminated soils, this study was planned to investigate the metal tolerance potential of indigenous filamentous fungi. Certain metals are important to biological actions. However all metals, whether essential or inessential will show toxicity at certain levels. During 2012 total 17 fungi were isolated and preserved from contaminated peri-urban agricultural areas of Multan and Gujranwala for further detail investigation of heavy metal tolerance. Aspergillus niger, Aspergillus fumigatus and Aspergillus flavus isolated from both soil and water samples while Aspergillus terreus and Penicillium sp were only isolated from soil samples …

Measuring Immune Responsiveness In Xenopus Laevis Using Phytohaemagglutanin (Pha), Kevin Kinney, Skyler Majors, Madelyn Lee, Scott Espich, Erika Kischuk

Annual Student Research Poster Session

Phytohaemagglutanin (PHA) is a red kidney bean extract that has been used to stimulate an immunological T cell response in a variety of animals. This procedure has become very popular method to analyze an individual animal’s ability to trigger an immunological response.(Brown 2014) PHA skin testing has been used in a variety of avian, mice, lizard, and amphibian species where it is injected into the muscle, skin, or webbing of an animal and then recording the amount of swelling before and after the injection.(Smits 1999) We are using the amphibian Xenopus laevis to test 1) their immune reaction under normal …

Study The Quality Of Groundwater Of Al-Zoroup Area In Mahdah State, The Sultanate Of Oman, Fahad Khalifa Rashid Al-Shidi

Theses

The groundwater is the most important source of water in the Sultanate of Oman. Accordingly, the Oman Government has paid great attention commensurate with the importance of water resource in terms of their sources, quality, and ways to rationalize consumption to remain under the term of sustainability and validity of present and future generations. This study was conducted in Al Buraymi at Mahdah State in Al-Zoroub area targete a groundwater quality for 20 wells in private farms. The water samples were taken from these wells and subjected to analysis for microbial and geochemical aspects. For this analysis, the assorted devices …

Landscape Genetics Of The Endangered California Tiger Salamander (Ambystoma Californiense) In The Los Vaqueros Watershed, Ryan Neal Vincent

Mahurin Honors College Capstone Experience/Thesis Projects

Genetic diversity is essential for maintaining healthy biological systems, and dispersal-mediated gene flow increases genetic diversity by introducing new alleles to a gene pool. Populations that frequently experience gene flow will show characteristic similarities in allele frequencies. Measuring genetic diversity among many populations across a landscape has proven to be a powerful approach for assessing the ways that habitat discontinuities may affect patterns of gene flow, and in turn, influence allele frequencies and population dynamics. This study examines the landscape-level population genetic structure of the California tiger salamander, Ambystoma californiense, within the Los Vaqueros Watershed of Contra Costa County, …

Host Cell Death In Legionella Pneumophila Pathogenesis And Immunity, Wenhan Zhu

Open Access Dissertations

Legionella pneumophila is an intracellular pathogen that causes a severe, atypical pneumonia termed Legionnaires' disease. Upon entering the host cell, L. pneumophila resides in a membrane-bound vacuole, in which the bacterium evades lysosomal fusion and replicates. The establishment of the vacuole requires the Dot/Icm (Defect in organelle trafficking/ intracellular multiplication) transport system, which translocates a large number of substrates into host cells to re-orchestrate various cellular processes, such as intracellular trafficking, protein synthesis and host cell death pathways. Therefore, a key step in understanding the biology of Legionella is to dissect the mechanisms of action of the Dot/Icm substrates. By …

Hypogammaglobulinemia In Blt Humanized Mice – An Animal Model Of Primary Antibody Deficiency, Francisco Martinez-Torres, Tomonori Nochi, Angela Wahl, J. Victor Garcia, Paul W. Denton

Biology Faculty Publications

Primary antibody deficiencies present clinically as reduced or absent plasma antibodies without another identified disorder that could explain the low immunoglobulin levels. Bone marrow-liver-thymus (BLT) humanized mice also exhibit primary antibody deficiency or hypogammaglobulinemia. Comprehensive characterization of B cell development and differentiation in BLT mice revealed other key parallels with primary immunodeficiency patients. We found that B cell ontogeny was normal in the bone marrow of BLT mice but observed an absence of switched memory B cells in the periphery. PC-KLH immunizations led to the presence of switched memory B cells in immunized BLT mice although plasma cells producing PCor …

High Local Diversity Of Trypanosoma In A Common Bat Species, And Implications For The Biogeography And Taxonomy Of The T. Cruzi Clade, Veronika M. Cottontail, Elisabeth K. V. Kalko, Iain Cottontail, Nele Wellinghausen, Marco Tschapka, Susan L. Perkins, C. Miguel Pinto

Publications and Research

The Trypanosoma cruzi clade is a group of parasites that comprises T. cruzi sensu lato and its closest relatives. Although several species have been confirmed phylogenetically to belong to this clade, it is uncertain how many more species can be expected to belong into this group. Here, we present the results of a survey of trypanosome parasites of the bat Artibeus jamaicensis from the Panama´ Canal Zone, an important seed disperser. Using a genealogical species delimitation approach, the Poisson tree processes (PTP), we tentatively identified five species of trypanosomes – all belonging to the T. cruzi clade. A small monophyletic …

Hiv-1 Transgenic Rats Display Alterations In Immunophenotype And Cellular Responses Associated With Aging, Susan J. Abbondanzo

Seton Hall University Dissertations and Theses (ETDs)

Advances in anti-retroviral therapy over the last two decades have allowed life expectancy in patients infected with the human immunodeficiency virus to approach that of the general population. The process of aging in mammalian species, including rats, results in changes with immune response, immunological phenotypes, and ultimately, increased susceptibility to many infectious diseases. In order to investigate the immunological pathologies associated with chronic HIV-1 disease, particularly in aged individuals, the HIV-1 transgenic (HIV-1Tg) rat model was utilized. Age matched animals were challenged using lipopolysaccharide (LPS) to determine immunological modification of HIV-1Tg animals throughout the aging process. LPS is known to …

High Mrsa Carriage Rate Among Nursing Microbiology Students, Alan Lee Gillen, Whitney O. Daycock, Andrew Serafin

Faculty Publications and Presentations

Staphylococcus aureus is a common cause of disease, particularly in colonized persons. Although methicillin-resistant S. aureus (MRSA) infections have become increasingly reported, populationbased studies of students preparing for the health professions having S. aureus and MRSA colonization are lacking. We have found that students in microbiology classes having more contact with individuals in a healthcare setting are more likely to carry MRSA in their nares and axilla. The classes who had the highest rate of MRSA carriage during the school year, 2013-2014, were those with nursing students, who had a greater exposure to clinical settings and nursing homes. The class …

Enhanced Expression Of Codon Optimized Mycobacterium Avium Subsp. Paratuberculosis Antigens In Lactobacillus Salivarius, Christopher D. Johnston, John P. Bannatine, Rodney Govender, Lorraine Endersen, Daniel Pletzer, Helge Weingart, Aidan Coffey, Jim O'Mahony, Roy D. Sleator

Department of Biological Sciences Publications

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants …

Phenotypic Signatures Arising From Unbalanced Bacterial Growth, Cheemang Tan, Robert P. Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You

Biology Faculty Articles

Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify “phenotypic signatures” by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under …

Recent Shifts In The Occurrence, Cause, And Magnitude Of Animal Mass Mortality Events, Samuel B. Fey, Adam M. Siepielski, Sébastien Nusslé, Kristina Cervantes-Yoshida, Jason L. Hwan, Eric R. Huber, Maxfield J. Fey, Alessandro Catenazzi, Stephanie M. Carlson

Dartmouth Scholarship

Mass mortality events (MMEs) are rapidly occurring catastrophic demographic events that punctuate background mortality levels. Individual MMEs are staggering in their observed magnitude: re- moving more than 90% of a population, resulting in the death of more than a billion individuals, or producing 700 million tons of dead biomass in a single event. Despite extensive documentation of individual MMEs, we have no understanding of the major features characterizing the occurrence and magnitude of MMEs, their causes, or trends through time. Thus, no framework exists for contextualizing MMEs in the wake of ongoing global and regional perturbations to natural systems. Here …

Limitations To Estimating Bacterial Cross-Species Transmission Using Genetic And Genomic Markers: Inferences From Simulation Modeling, Julio A. Benavides, Paul C. Cross, Gordon Luikart, Scott Creel

Biological Sciences Faculty Publications

Cross-species transmission (CST) of bacterial pathogens has major implications for human health, livestock, and wildlife management because it determines whether control actions in one species may have subsequent effects on other potential host species. The study of bacterial transmission has benefitted from methods measuring two types of genetic variation: variable number of tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). However, it is unclear whether these data can distinguish between different epidemiological scenarios. We used a simulation model with two host species and known transmission rates (within and between species) to evaluate the utility of these markers for inferring CST. …

Historical Demography And Dispersal Patterns In The Eastern Pipistrelle Bat (Perimyotis Subflavus), Alynn M. Martin

Masters Theses

The recent emergence of threats to North American bat conservation has prompted increased population genetics research on high risk species. The eastern pipistrelle bat is affected by both white-nose syndrome and wind turbine mortality. However, little work has been done regarding the population structure and effective population size of this species. Using the HVI region of the mitochondria and eight microsatellite loci, I analyzed male and female structure across the sample range of P. subflavus and estimated the effective population size of their populations. Pairwise F_ST values indicate that there is one panmictic population based on microsatellite data, while …

An Inverse Association Between West Nile Virus Serostatus And Avian Malaria Infection Status, Robert Ricklefs, Matthew Medeiros, Tavis Anderson, Jenni Higashiguchi, Uriel Kitron, Edward Walker, Jeffrey Brawn, Bethany Krebs, Marilyn Ruiz, Tony Goldberg, Gabriel Hamer

Biology Department Faculty Works

BackgroundVarious ecological and physiological mechanisms might influence the probability that two or more pathogens may simultaneously or sequentially infect a host individual. Concurrent infections can have important consequences for host condition and fitness, including elevated mortality risks. In addition, interactions between coinfecting pathogens may have important implications for transmission dynamics.MethodsHere, we explore patterns of association between two common avian pathogens (West Nile virus and avian malaria parasites) among a suburban bird community in Chicago, IL, USA that share mosquito vectors. We surveyed 1714 individual birds across 13 species for both pathogens through established molecular protocols.ResultsField investigations of haemosporidian and West …

Controlling Pseudomonas Aeruginosa Biofilms And Persister Cells By Manipulating Cell-Cell Signaling, Shuyuan Ma

Theses - ALL

Bacterial cells often form sessile biofilms that are up to 1,000 times more resistant to antimicrobial agents than free-living cells. Meanwhile, bacteria produce a small subpopulation of slow-growing or non-growing persister cells that exhibit high tolerance to antibiotics. Both biofilms and persister cells play important roles in the recalcitrance of chronic infections. Recent studies have shown that bacterial cell-to-cell communication, named quorum sensing (QS), is involved in the biofilm and persister formation.

In this study, we investigated the effects of quorum sensing signals N-(3-oxododecanoyl)-homoserine lactone (3-oxo-C12-HSL) and N-butyryl homoserine lactone (C4-HSL) on isolated Pseudomonas aeruginosa PAO1 and PDO300 persister cells. …

Role Of Msaa Gene In Regulation Of The Msaabcr Operon And Biofilm Development In Staphylococcus Aureus, Ahmed Alzuway

Master's Theses

Staphylococcus aureus is an important human pathogen that causes wide variety of diseases ranging from chronic biofilm associated infection to acute life threatening infection such as bacteremia, pneumonia, osteomyelitis, or endocarditis, despite the progress with antibiotics used in the treatment of bacterial infections. Furthermore, increased use of prosthetic and indwelling devices in modern medical practices has led to increased infections due to S. aureus. Treating S. aureus infections have become difficult owing to its ability to resist most of the antibiotics; this problem is further exacerbated by ability of MRSA strains to form biofilms. Emergence of community-acquired methicillin resistance …

Are New Jersey Birds Involved In The Enzootic Cycle Of Lyme Disease?, Heather Kopsco

Theses, Dissertations and Culminating Projects

Birds are well-established in cycles of zoonotic diseases, generally as hosts of an infected arthropod vector such as a mosquito or tick. Since the 1980s, research in both the United States and Europe has focused on their role in the ecology of Lyme disease and its causative agent, Borrelia burgdorferi, since they are fed upon by larval and nymphal ticks and can transport them and their associated diseases geographically during migrations. Further, research has shown that a number of avian species exhibit reservoir competency for B. burgdorferi which demonstrates that birds are involved in the enzootic cycles of the disease …

The Avian Thrombocyte Is A Specialized Immune Cell, Farzana Ferdous

All Dissertations

Thrombocytes are the most abundant circulating cells next to red blood cells in avian blood. Avian thrombocytes are homologous in function to mammalian platelets. Avian thrombocytes and the mammalian platelet are widely recognized contributors to inflammatory responses upon stimulation with various microbial stimulants. However, some observed responses of the avian thrombocyte depart from a standardized model ascribed to innate cells. To help unravel the role of thrombocytes in innate immunity, and possibly adaptive immunity, first we examined the surface features of chicken thrombocytes. Chicken thrombocytes constitutively express transcripts for different Toll-like receptors (TLRs) that are crucial for the innate immune …

Oroya Fever And Verruga Peruana: Bartonelloses Unique To South America, Michael F. Minnick, Burt E. Anderson, Amorce Lima, James M. Battisti, Phillip G. Lawyer, Richard J. Birtles

Biological Sciences Faculty Publications

Bartonella bacilliformis is the bacterial agent of Carrión's disease and is presumed to be transmitted between humans by phlebotomine sand flies. Carrión's disease is endemic to high-altitude valleys of the South American Andes, and the first reported outbreak (1871) resulted in over 4,000 casualties. Since then, numerous outbreaks have been documented in endemic regions, and over the last two decades, outbreaks have occurred at atypical elevations, strongly suggesting that the area of endemicity is expanding. Approximately 1.7 million South Americans are estimated to be at risk in an area covering roughly 145,000 km2 of Ecuador, Colombia, and Peru. Although disease …

The Wonderfully Made Design Of The Skin And Its Microbiome, Alan L. Gillen

Faculty Publications and Presentations

Many microbes live in a mutualistic relationship with the human body, make up the human microbiome, and play a role in our health by modulating the immune system. Man is “covered” inside and outside his body with millions of microbes to maintain normal bodily functions and sustain life in our changing world. The skin is the largest organ in the human body and is colonized by millions of microbes. This external colonization of the integumentary system is termed our skin microbiome. Man cannot see it (except with a microscope), but we need it for normal functioning, certainly in a pathogenic …

Development Of An Efficient Human Hepatocyte Culture Platform For Assessing Novel Therapeutic Efficacy Against Plasmodium Liver Parasites, Steven Patrick Maher

USF Tampa Graduate Theses and Dissertations

Malaria is a critical and global public health problem, affecting over 200 million people every year, resulting in over 500,000 deaths. A vaccine is not currently available and only one drug, primaquine, is effective against the dormant stages of Plasmodium vivax. Preclinical assessment of novel therapeutic drugs and vaccines is hampered by the lack of an in vitro liver model for P. falciparum and P. vivax. To provide a stable human hepatocyte-based culture platform for parasite development, we engineered a microfluidic bilayer device capable of both simple and complex culture methods, including perfusion and co-culture, to better understand the requirements …

Aquastella Gen. Nov.: A New Genus Of Saprolegniaceous Oomycete Rotifer Parasites Related To Aphanomyces, With Unique Sporangial Outgrowths, Daniel P. Molloy, Sally L. Glockling, Clifford A. Siegfried, Gordon W. Beakes, Timothy Y. James, Sergey E. Mastitsky, Elizabeth S. Wurdak, Laure Giamberini, Michael J. Gaylo, Michael J. Nemeth

Biology Faculty Publications

The oomycete genus Aquastella is described to accommodate two new species of parasites of rotifers observed in Brooktrout Lake, New York State, USA. Three rotifer species – Keratella taurocephala,Polyarthra vulgaris, and Ploesoma truncatum – were infected, and this is the first report of oomycete infection in these species. Aquastella attenuata was specific to K. taurocephala and Aquastella aciculariswas specific to P. vulgaris and P. truncatum. The occurrence of infections correlated with peak host population densities and rotifers were infected in the upper layers of the water column. Sequencing of 18S rRNA and phylogenetic analysis of …

Population And Metapopulation Ecology Of Childhood Diseases, Christian E. Gunning

Biology ETDs

Researchers have long used mathematical models and empirical data to explore the population ecology of childhood diseases such as measles and whooping cough. These diseases have proven ideal model systems for studying population dynamics over space and time. Here we present a novel dataset of weekly measles and whooping cough case reports in pre-vaccine era U.S. cities and states, along with a previously- studied dataset of measles in England & Wales. We first estimate per-population disease reporting probabilities. We find that disease reporting is highly variable over space and between diseases, and correlated with socioeconomic covariates including ethnic composition and …

The Microbiome Of Rainbow Trout (Oncorhynchus Mykiss), Liam T. Lowrey

Biology ETDs

Commensal organisms are an integral part of all vertebrates, contributing heavily to development, pathogen defense, and metabolism. Commensals reside at different body sites within vertebrate animals creating unique and distinct communities that vary between locations. The human microbiome project has revealed distinct bacterial community compositions at the diverse range of body sites that have been sampled, providing evidence for different functional purposes of each microbiome. Rainbow trout, Oncorhynchus mykiss, serves as a model organism for the study of mucosal physiology and immunology. Teleost fish are evolutionarily important as one of the first jawed vertebrates with a dedicated adaptive mucosal immune …

Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park

Open Access Theses

Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …