Organisms Commons^™

Relationships Between Landscape Factors And Crayfish Density And The Interacting Effects Of Grazing And Increased Sedimentation On Algal Biomass, Katheryn Haley Rose

Graduate Theses and Dissertations

In recent years in the United States there has been a rapid expansion in anthropogenic sources of sediment in streams including construction, agriculture, and drilling for natural gas. Potential effects land disturbance associated with activities from natural gas development on aquatic biota in surrounding streams have not yet been well documented. An increase in inorganic sediment in streams can be detrimental to organisms through a variety of mechanisms including alteration of dominant substrate type, higher turbidity resulting in lower visibility, and burial of food resources such as algae and detritus. Increasing sedimentation in stream environments through anthropogenic disturbance is a …

Development Of Novel Antifungal Peptides Based On A Natural Model Of Histatin-5 Peptide, Duy Tu Nguyen

Graduate Theses and Dissertations

Our research group is working toward the development of novel antifungal peptides based on a natural model of peptide histatin-5. Histatin-5 is found in human saliva and known to protect our body against oral infections by Candida species. Candidiasis, or an infection caused by Candida species, is considered one of the most medically important fungal infections worldwide. Blood stream infections caused by Candida species are the fourth leading cause of hospital-acquired fungal infections that is associated with high mortality rates and high costs of treatment. This study investigated the modes of action of histatin-5 with the use of one 16-mer …

Taxis Toward Hydrogen Gas By Methanococcus Maripaludis, Kristen A. Brileya, James M. Connolly, Carey Downey, Robin Gerlach, Matthew W. Fields

Biology Faculty Publications and Presentations

Knowledge of taxis (directed swimming) in the Archaea is currently expanding through identification of novel receptors, effectors, and proteins involved in signal transduction to the flagellar motor. Although the ability for biological cells to sense and swim toward hydrogen gas has been hypothesized for many years, this capacity has yet to be observed and demonstrated. Here we show that the average swimming velocity increases in the direction of a source of hydrogen gas for the methanogen, Methanococcus maripaludis using a capillary assay with anoxic gas-phase control and time-lapse microscopy. The results indicate that a methanogen couples motility to hydrogen concentration …

Regulation Of Hyaluronate Lyase (Hyla) Expression By Regr A Transcriptional Repressor In Streptococcus Pyogenes, Alexis A. Kordis

Biological Sciences Theses & Dissertations

Streptococcus pyogenes, group A streptococci (GAS), causes diseases ranging from asymptomatic to life threatening. Some strains of S. pyogenes produce extracellular hyaluronate lyase (HylA), a potential virulence factor. HylA is an enzyme that degrades hyaluronic acid, which is found in the extracellular matrix of human tissues. The breakdown of the host tissue contributes to the spread of infection. The hylA gene is not constitutively expressed in vitro, which implies regulation.

A proposed regulator of hyaluronate lyase expression is RegR, a LacI/GalR like protein. A vector containing disrupted regR was electro-transformed into S. pyogenes M-type 22 strain 10403. Growth characteristics …

Effects Of Environmental Factors And Nutrient Availability On The Biochemical Composition Of Algae For Biofuels Production: A Review, Ankita Juneja, Ruben Michael Ceballos, Ganti S. Murthy

Biological Sciences Faculty Publications and Presentations

Due to significant lipid and carbohydrate production as well as other useful properties such as high production of useful biomolecular substrates (e.g., lipids) and the ability to grow using non-potable water sources, algae are being explored as a potential high-yield feedstock for biofuels production. In both natural and engineered systems, algae can be exposed to a variety of environmental conditions that affect growth rate and cellular composition. With respect to the latter, the amount of carbon fixed in lipids and carbohydrates (e.g., starch) is highly influenced by environmental factors and nutrient availability. Understanding synergistic interactions between multiple environmental variables and …

Regulating Rsma Expression In Pseudomonas Aeruginosa, Sean D. Stacey

Electronic Theses and Dissertations

Pseudomonas aeruginosa, a Gram-negative bacillus, commonly infects immunocompromised individuals and uses a variety of virulence factors to persist in these hosts. The posttranscriptional regulator, RsmA, plays a role in the expression of many virulence factors in P. aeruginosa. RsmA up regulates virulence factors used in colonizing hosts. However, regulation of rsmA is not well elucidated. Transposon mutagenesis was performed on P. aeruginosa containing a transcriptional rsmA-lacZ fusion to answer this question. Mutants were screened via β-galactosidase assay and transposon insertions identified via arbitrary PCR. A probable MFS transporter, we named mtpX, was one significant transposon mutant identified. …

Studies On Tracheorelaxant And Anti-Inflammatory Activities Of Rhizomes Of Polygonatum Verticillatum, Haroon Khan, Muhammad Saeed, Hassan Mehmood, Najeeb-Ur Rehman, Naveed Muhammad, Ikram-Ul Haq, Nadeem Ashraf, Kamal Eldin H El-Tahir, Anwar Gilani

Department of Biological & Biomedical Sciences

Background: The present study describes the tracheorelaxant and anti-inflammatory effects of Polygonatum verticillatum which may support its medicinal use in hyperactive airway complaints and inflammatory disorders.
Methods: The tracheorelaxant activity of crude extract of the rhizomes of P. verticillatum (PR) was assessed in isolated guinea-pig tracheal tissues immersed in tissue organ bath filled with Tyrode's solution and a continuous supply of carbogen gas (95% O2 and 5% CO2). The contractile and relaxant responses of the tissue were measured using isometric transducers coupled with Power-Lab data acquisition system. The anti-inflammatory effect was evaluated in carrageenan-induced rat paw edema model, while the …

Influence Of Media Composition On The Growth Rate Of Chlorella Vulgaris And Scenedesmus Acutus Utilized For Co2 Mitigation, Czarena L. Crofcheck, Xinyi E, Aubrey Shea, Michael D. Montross, Mark Crocker, Rodney Andrews

Biosystems and Agricultural Engineering Faculty Publications

Atmospheric carbon dioxide levels have increased since the industrial revolution due to increasing combustion of fossil fuels. One possible CO₂ mitigation strategy is the use of microalgae for mitigation of CO₂. This paper focuses on the influence of media composition on the growth rate of two microalgae strains, Chlorella vulgaris and Scenedesmus actus. A KNO₃ based medium was found to work better for Chlorella, while a urea based equivalent worked better for Scenedesmus. The urea based media investigated here resulted in growth similar to that found with previously reported KNO₃ based media. …

A Literature Review Of The Health Effects Of A Plant Based Diet Versus An Animal Based Diet, James Cote

Senior Honors Theses

Health and nutrition can mean a myriad of things to many people in today’s culture. The majority of the time people are unaware of the proper nutrients their body needs and how to get them from food. This thesis will seek to expose the health benefits that are associated with consuming a raw plant-based die, offering a more profound and encompassing view on nutrition. Investigating further into today’s most common diseases such as diabetes, heart disease, obesity, cancer and autoimmune disorders, it will seek to discover and answer why we have so many health issues. This thesis will discuss the …

Maternal Obesity Alters Fetal Development Due To Impaired Placental Function And Has Lasting Effects On Adult Offspring, Kristin Ann Norwood

Department of Animal Science: Dissertations, Theses, and Student Research

Obesity is an epidemic in many developed nations and maternal obesity can result in developmental alterations in offspring that have long-lasting effects. Two experiments were conducted to determine the impact of maternal obesity on placental development and early embryonic growth and muscle development. Experiment one utilized obese Lethal Yellow (LY) and normal weight C57BL/6 (B6) dams to assess how maternal obesity alters skeletal muscle development in mid-gestational embryos. Embryos from LY dams exhibited decreased embryo and placental weights as well as an increase in the myogenic marker desmin. Furthermore, the adipogenic marker PPARG expression was predominately localized to the neural …

The Voltage-Sensing Domain Of A Phosphatase Gates The Pore Of A Potassium Channel, Cristina Arrigoni, Indra Schroeder, Giulia Romani, James L. Van Etten, Gerhard Thiel, Anna Moroni

James Van Etten Publications

The modular architecture of voltage-gated K⁺ (Kv) channels suggests that they resulted from the fusion of a voltage-sensing domain (VSD) to a pore module. Here, we show that the VSD of Ciona intestinalis phosphatase (Ci-VSP) fused to the viral channel Kcv creates Kv_Synth1, a functional voltage-gated, outwardly rectifying K⁺ channel. Kv_Synth1 displays the summed features of its individual components: pore properties of Kcv (selectivity and filter gating) and voltage dependence of Ci-VSP (V1/2 = +56 mV; z of approx. 1), including the depolarizationinduced mode shift. The degree of outward rectification of the channel is critically …

A Virus-Encoded Potassium Ion Channel Is A Structural Protein In The Chlorovirus Paramecium Bursaria Chlorella Virus 1 Virion, Giulia Romani, Adrianna Piotrowski, Stefan Hillmer, James Gurnon, James L. Van Etten, Anna Moroni, Gerhard Thiel, Brigitte Hertel

James Van Etten Publications

Most chloroviruses encode small K+ channels, which are functional in electrophysiological assays. The experimental finding that initial steps in viral infection exhibit the same sensitivity to channel inhibitors as the viral K+ channels has led to the hypothesis that the channels are structural proteins located in the internal membrane of the virus particles. This hypothesis was questioned recently because proteomic studies failed to detect the channel protein in virions of the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1). Here, we used a mAb raised against the functional K+ channel from chlorovirus MA-1D to search for the viral K+ channel …

The Effect Of Visual Wulst Lesions And Trigeminal Nerve Sectioning On The Discrimination Of Magnetic Inclination In The Homing Pigeon (Columba Livia), Merissa Acerbi

Honors Projects

The ability of homing pigeons to return to their loft from unknown places has fascinated scientists for centuries. It is well established that homing pigeons, like migratory birds, posses an innate magnetic inclination compass to determine direction by measuring the angle between the magnetic field vector and the Earth's surface. Recent work has indicated that the avian magnetic compass is light mediated and appears to mediate magnetic information to the brain. This occurs via a visual pathway with processing in the visual Wulst area of the forebrain. There is, however, also evidence from other avian species that magnetic direction may …

Bmp7 Gene Transfer Via Gold Nanoparticles Into Stroma Inhibits Corneal Fibrosis In Vivo, Ashish Tandon, Ajay Sharma, Jason T. Rodier, Alexander M. Klibanov, Frank G. Rieger, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

This study examined the effects of BMP7 gene transfer on corneal wound healing and fibrosis inhibition in vivo using a rabbit model. Corneal haze in rabbits was produced with the excimer laser performing -9 diopters photorefractive keratectomy. BMP7 gene was introduced into rabbit keratocytes by polyethylimine-conjugated gold nanoparticles (PEI2- GNPs) transfection solution single 5-minute topical application on the eye. Corneal haze and ocular health in live animals was gauged with stereo- and slit-lamp biomicroscopy. The levels of fibrosis [a-smooth muscle actin (aSMA), F-actin and fibronectin], immune reaction (CD11b and F4/80), keratocyte apoptosis (TUNEL), calcification (alizarin red, vonKossa and osteocalcin), and …

A Virus-Encoded Potassium Ion Channel Is A Structural Protein In The Chlorovirus Paramecium Bursaria Chlorella Virus 1 Virion, Giulia Romani, Adrianna Piotrowski, Stefan Hillmer, James Gurnon, James L. Van Etten, Anna Morani, Gerhard Thiel, Brigitte Hertel

James Van Etten Publications

Most chloroviruses encode small K+ channels, which are functional in electrophysiological assays. The experimental finding that initial steps in viral infection exhibit the same sensitivity to channel inhibitors as the viral K+ channels has led to the hypothesis that the channels are structural proteins located in the internal membrane of the virus particles. This hypothesis was questioned recently because proteomic studies failed to detect the channel protein in virions of the prototype chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1). Here, we used a mAb raised against the functional K+ channel from chlorovirus MA-1D to search for the viral K+ channel …

Potassium Ion Channels: Could They Have Evolved From Viruses?1[W], Gerhard Thiel, Anna Moroni, Guillaume Blanc, James L. Van Etten

James Van Etten Publications

Cells communicate among themselves by electrical activity. Sophisticated membrane-embedded proteins, called ion channels, catalyze rapid, selective, and regulated ion fluxes across membranes (Hille, 2001). The resulting membrane currents are responsible for neuronal activity and the systemic propagation of electrical signals in animals. The activity of some channels is important for muscle movement in animals or growth in plants; other channels sense the concentration of physiological signals and modulate key processes in all kinds of eukaryotic cells. Among the many diverse ion channels in higher organisms, K+ channels are among the most important. One feature of K+ channels is that they …

Effects Of Intranasally Administered Dnsp-11 On The Central Dopamine System Of Normal And Parkinsonian Fischer 344 Rats, James H. Sonne

Theses and Dissertations--Neuroscience

Due to the blood-brain barrier, delivery of many drugs to the brain has required intracranial surgery which is prone to complication. Here we show that Dopamine Neuron Stimulating Peptide 11 (DNSP-11), following non-invasive intranasal administration, protects dopaminergic neurons from a lesion model of Parkinson’s disease in the rat. A significant and dose-dependent increase in an index of dopamine turnover (the ratio of DOPAC to dopamine) was observed in the striatum of normal young adult Fischer 344 rats by whole-tissue neurochemistry compared to vehicle administered controls.

Among animals challenged with a moderate, unilateral 6-hydroxy-dopamine (6-OHDA) lesion of the substantia nigra, those …

Nanoparticles Of Cobalt-Substituted Hydroxyapatite In Regeneration Of Mandibular Osteoporotic Bones, Nenad Ignjatović, Zorica Ajduković, Vojin Savić, Stevo Najman, Dragan Mihailović, Perica Vasilijević, Zoran Stojanović, Vuk Uskoković, Dragab Uskoković

Pharmacy Faculty Articles and Research

Indications exist that paramagnetic calcium phosphates may be able to promote regeneration of bone faster than their regular, diamagnetic counterparts. In this study, analyzed was the influence of paramagnetic cobalt-substituted hydroxyapatite nanoparticles on osteoporotic alveolar bone regeneration in rats. Simultaneously, biocompatibility of the material was tested in vitro, on osteoblastic MC3T3-E1 and epithelial Caco-2 cells in culture. The material was shown to be biocompatible and nontoxic when added to epithelial monolayers in vitro, while it caused a substantial decrease in the cell viability as well as deformation of the cytoskeleton and cell morphology when incubated with the osteoblastic …

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben Michael Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biological Sciences Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are “lemon” or “spindle”-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …

Composition Of The Adult Digestive Tract Bacterial Microbiome Based On Seven Mouth Surfaces, Tonsils, Throat And Stool Samples, Nicola Segata, Susan Kinder Haake, Peter Mannon, Katherine P. Lemon, Levi Waldron, Dirk Gevers, Curtis Huttenhower, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Background: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body’s greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

Results: The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; …

Cell-Mediated Immunity In Porcine Reproductive And Respiratory Syndrome Virus, Rajeshwari Parida

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Porcine reproductive and respiratory syndrome virus is a significant swine pathogen which exhibits considerable sequence diversity. In an attempt to identify highly conserved T-cell epitopes contained in proteins of this virus, we examined heptadecamer peptides spanning the sequence of the PRRSV nonstructural proteins 9, 10 and 11, all of them are highly conserved, for their ability to elicit a recall proliferative and interferon-gamma response in peripheral blood mononuclear cells obtained from pigs immunized against the type-II PRRSV strain FL-12. These studies led to the identification of seven peptides, two from each NSP 9 and NSP 10 and, three from NSP …

Role Of Lactic Acid Bacteria As A Bio-Sanitizer To Prevent Attachment Of Listeria Monocytogenes On Deli Slicer Contact Surfaces, And The Influence Of Listeria Innocua On The Attachment Of L. Monocytogenes On Selected Materials Located In The Food-Processing Environment, Jean Baptiste Ndahetuye

Graduate Theses and Dissertations

Listeria monocytogenes an important foodborne pathogen that continues to be a serious problem for the food industry. This pathogen contaminates food primarily during post-harvest in the food-processing environment. Its ecology in the food-processing environment is not well understood but previous research has demonstrated the ability of L. monocytogenes to survive on food contact surfaces after cleaning and disinfection. The current study explored the attachment of three lactic acid bacteria (LAB) strains, Lactobacillus animalis , Lb. amylovorus and Pediococcus acidilactici , their combination in a cocktail, and their influence to prevent the attachment of L. monocytogenes at room temperature by examining …

Vorinostat: A Potent Agent To Prevent And Treat Laser-Induced Corneal Haze, Ashish Tandon, Jonathan C. K. Tovey, Michael R. Waggoner, Ajay Sharma, John W. Cowden, Daniel J. Gibson, Yuanjing Liu, Gregory S. Schultz, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

PURPOSE—This study investigated the efficacy and safety of vorinostat, a deacetylase (HDAC) inhibitor, in the treatment of laser-induced corneal haze following photorefractive keratectomy (PRK) in rabbits in vivo and transforming growth factor beta 1 (TGFβ1) -induced corneal fibrosis in vitro.

METHODS—Corneal haze in rabbits was produced with −9.00 diopters (D) PRK. Fibrosis in cultured human and rabbit corneal fibroblasts was activated with TGFβ1. Vorinostat (25 μm) was topically applied once for 5 minutes on rabbit cornea immediately after PRK for in vivo studies. Vorinostat (0 to 25 μm) was given to human/rabbit corneal fibroblasts for 5 minutes or 48 …

Attenuation Of Corneal Myofibroblast Development Through Nanoparticle-Mediated Soluble Transforming Growth Factor-Β Type Ii Receptor (Stgfβrii) Gene Transfer, Ajay Sharma, Jason T. Rodier, Ashish Tandon, Alexander M. Klibanov, Rajiv R. Mohan

Pharmacy Faculty Articles and Research

Purpose: To explore (i) the potential of polyethylenimine (PEI)-DNA nanoparticles as a vector for delivering genes into human corneal fibroblasts, and (ii) whether the nanoparticle-mediated soluble extracellular domain of the transforming growth factor–β type II receptor (sTGFβRII) gene therapy could be used to reduce myofibroblasts and fibrosis in the cornea using an in vitro model.

Methods: PEI-DNA nanoparticles were prepared at a nitrogen-to-phosphate ratio of 30 by mixing linear PEI and a plasmid encoding sTGFβRII conjugated to the fragment crystallizable (Fc) portion of human immunoglobulin. The PEI-DNA polyplex formation was confirmed through gel retardation assay. Human corneal fibroblasts (HCFs) were …

Cyanobacteria Dominance In The Oligohaline Waters Of Back Bay, Virginia, Harold G. Marshall

Biological Sciences Faculty Publications

Back Bay and its flora have historically been influenced by the interaction of freshwater flow in combination with frequent intrusion of saline water into its basin. These events have resulted in a dynamic environmental setting influencing the abundance and composition of its phytoplankton community. Dominating these oligohaline waters is a diverse representation and high abundance of freshwater filamentous and colonial cyanobacteria. These include the nonheterocystous Planktolyngbya contorta, Planktolyngbya limnetica, and Pseudanabaena limnetica, taxa implicated as bloom producers in Bay waters with N:P molar ratios ranging from 23:1 to 74:1.

Efficient And Robust Rna-Seq Process For Cultured Bacteria And Complex Community Transcriptomes, Georgia Giannoukos, Dawn M. Ciulla, Katherine Huang, Brian J. Haas, Jacques Izard, Joshua Z. Levin, Jonathan Livny, Ashlee M. Earl, Dirk Gevers, Doyle V. Ward, Chad Nusbaum, Bruce W. Birren, Andreas Gnirke

Department of Food Science and Technology: Faculty Publications

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.

The Effects Of 17Α-Ethynylestradiol (Ee2) On Gonadal Development And Differentiation In The Estuarine Killifish, Fundulus Heteroclitus, Ibrahim Chehade

Theses and Dissertations (Comprehensive)

Endocrine disrupting substances (EDSs) comprise a wide variety of chemicals that perturb normal endocrine function including developmental and reproductive processes in vertebrates. The synthetic estrogen 17α-ethynylestradiol (EE₂) is a commonly-used model EDS because of its environmental relevance and its effects on the reproductive endocrine system. Early life-stage exposure of fish to estrogenic EDSs causes effects such as intersex (ovotestes in males) and feminization. This study aims to confirm the period of gonadal differentiation in the estuarine killifish or mummichog (Fundulus heteroclitus) and to determine the sensitivity of gonadal development to EE₂. Artificially-regressed mummichog were spawned, and …

Phylogenomics Of Reichenowia Parasitica, An Alphaproteobacterial Endosymbiont Of The Freshwater Leech Placobdella Parasitica, Sebastian Kvist, Apurva Narechania, Alejandro Oceguera-Figueroa, Bella Fuks, Mark E. Siddall

Publications and Research

Although several commensal alphaproteobacteria form close relationships with plant hosts where they aid in (e.g.,) nitrogen fixation and nodulation, only a few inhabit animal hosts. Among these, Reichenowia picta, R. ornata and R. parasitica, are currently the only known mutualistic, alphaproteobacterial endosymbionts to inhabit leeches. These bacteria are harbored in the epithelial cells of the mycetomal structures of their freshwater leech hosts, Placobdella spp., and these structures have no other obvious function than housing bacterial symbionts. However, the function of the bacterial symbionts has remained unclear. Here, we focused both on exploring the genomic makeup of R. parasitica and on …

African Elephants Change Gaits When Walking Downhill, Robert H.I. Dale, Robert Warren, Brock Ward, Eric Noble

Scholarship and Professional Work - LAS

Abstract from the International Elephant and Rhino Conservation and Research Symposium, Rotterdam, NL, October 10-14, 2011.

Action Spectrum For Photoentrainment Of The Circadian Clock In Wild-Type Chlamydomonas Reinhardtii, Jennifer Forbes=Stovall

Masters Theses & Specialist Projects

The circadian clock is an endogenous timer that oscillates with a period of approximately 24 hours and is reset upon environmental time cues such as the daily light/ dark or temperature cycles. Chlamydomonas reinhardtii is an ideal model organism for research on the circadian clock, because it shows several well-characterized behaviors that exhibit a circadian rhythm. Its circadian rhythm of phototaxis (swimming toward light) has been automated. Former action spectrum studies using the circadian phototaxis rhythm as an indicator surprisingly found that pulses of blue light were not effective in resetting the circadian clock of dark-adapted cells. This may have …