<p> The Archaea represent a fascinating domain of life where each species comprises a hybrid of bacterial and eukaryal features. Unfortunately, there have been few investigations of the Archaea and many fundamental questions remain regarding their biochemistry, genetics, and genomics. One reason for this is that few archaea are amenable to detailed experimental analysis; however, a few halophilic archaea (haloarchaea) can be easily manipulated in the laboratory and contain a sequenced genome, allowing for bioinformatics studies, such as recording changes in the transcriptomes. Haloarchaea are found wherever seawater is concentrated above 2 M NaCl and contain a similarly high concentration of salts internally, without producing compatible solutes. They exhibit a variety of novel molecular characteristics, including acidic proteins that resist the denaturing effects of salts, and DNA repair systems that minimize the deleterious effects of desiccation and intense solar radiation. In addition, haloarchaea are metabolically versatile and respond to a wide variety of environmental signals, including extremes of radiation, salinity, temperature, heavy metals, pollutants, and pH by modulating the activity of key genes. </p><p> Of the above naturally occurring stresses, all have been previously studied but one, pH. Haloarchaea are routinely isolated from both acidic and alkaline saline lakes; however, their ability to thrive under these conditions still remains an unexplored mystery. Therefore, I have endeavored to unlock a few of these secrets by growing sequenced haloarchaeal strains at extremes of pH and cataloging the changes in their transcriptomes compared to growth at optimal pH. For my experiments, RNA was isolated at the end of logarithmic growth and labeled cDNA was generated and hybridized to custom-designed microarray slides that I designed. Changes in the transcriptomes were cataloged and compared to each other as well as to changes from previously studied bacteria. The results from my experiments showed that haloarchaea are primarily responding to extremes of pH in a manner similar to known bacterial cells, making these responses similar across two domains of life. However, there are a few differences, compared to bacteria, due to the unique nature of the Archaea.</p>

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008. / Source: Dissertation Abstracts International, Volume: 69-11, Section: B, page: 6561. Adviser: Richard Tapping. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (M.S.)--University of California, San Francisco, 2009. / Source: Masters Abstracts International, Volume: 47-06, page: 3492. Advisers: John D.B. Featherstone; Ling Zhan.

<p> Viruses have long been noted to be composed simply of nucleic acid and protein. This thesis describes this confluence of science of viruses at the interface of genomics and proteomics. Chapter 2 describes the discovery of klassevirus, a new picornavirus in pediatric diarrhea. Chapter 3 shows that klassevirus is likely a human pathogen given the seroconversion of klassevirus-positive individuals against a klassevirus non-structural protein that is not present in the picornavirus virion. Subsequent work failed to obtain a culturable virus from klassevirus-positive stool samples, enabling the transition to culture-independent methods of characterizing picornavirus-host protein interactions. Chapter 4 describes the use of affinity purification mass spectrometry to discovery a novel picornavirus 3A-ACBD3-PI4KB complex that promotes viral replication in the enteroviruses and kobuviruses. Chapter 5 extends upon the methodology to describe a novel host protein interactor of ACBD3 (TBC1D22A/B), whose interaction is altered specifically by the kobuvirus 3A protein. This complex also demonstrates significant interaction with the klassevirus 3A protein, suggesting that the AP-MS work may inform the biology of the uncultured virus. Finally, chapter 6 describes future directions that are opened up by this work.</p>

<p> In most human immunodeficiency virus type 1 (HIV&minus;1) infected individuals, highly active antiretroviral therapy (HAART) suppresses viremia to levels below standard clinical detection limits and delays the progression to AIDS. More sensitive assays have demonstrated that low&minus;level residual viremia is present during HAART. Furthermore, viremia rebounds upon cessation of therapy and thus, life&minus;long treatment is required to prevent the progression to AIDS. This is presumably due to viral persistence within anatomical and cellular viral reservoirs that are not eliminated during long&minus;term HAART. During HAART, viral persistence has been principally attributed to a latent viral reservoir; however, instances of complete viral replication cycles, termed residual replication, may occur. Human studies have provided evidence for and against the hypothesis that residual replication occurs in tissues and contributes to residual viremia. </p><p> To address questions regarding viral persistence, this dissertation research utilized a rhesus macaque model of HIV&minus;1 HAART. This model uses RT&minus;SHIV, a chimeric simian immunodeficiency virus (SIV) with the HIV&minus;1 reverse transcriptase (RT) replacing the native SIV RT gene. This modification renders RT&minus;SHIV susceptible to non&minus;nucleoside RT inhibitors, which are an important component of frontline therapies. Chapter 2 describes a longitudinal phylogenetic analysis of residual viremia during 42 weeks of therapy in five macaques that initiated HAART eight weeks after infection. This is the first non&minus;human primate phylogenetic study to characterize residual viremia for a period greater than five weeks. The results did not provide substantial evidence that residual replication contributed to residual viremia. Additionally, one of the five macaques maintained a predominant plasma clone (PPC) population, which is an enigmatic feature of human residual viremia. Chapter 3 describes viral DNA diversification in lymphoid and gastrointestinal tissues relative to pre&minus;HAART viremia. Similar to many human studies, there was no discernible evidence of residual replication or selection of resistance mutations. The origins of PPC populations were also not identified. Importantly, this dissertation advances the relevancy of HAART in RT&minus;SHIV infected macaques as a model of human HAART. Thus, this model may be ideal in studies designed to improve human health, investigate the nature of viral persistence, and potentially develop a cure for HIV&minus;1.</p>

<p> Several methods of enumerating Enterococci in water are suggested in the literature, notably membrane filtration and mEA plating. To establish optimal growth conditions, including incubation time, (24 and 48 hr) and temperature (35&deg;C and 41&deg;C), samples of 0.1 mL, 1 mL and 10 mL filtered water collected from Lake Artemisia, MD, USA were amended with known concentrations of Enterococcus faecalis (ATCC 29212), filtered using 0.45 &micro;m membrane filters, and incubated on mEA agar under different conditions: 35&deg;C/24h, 35&deg;C/48h, and 41&deg;C/48h, following U. S. Environmental Protection Agency guidelines. Results demonstrated no significant difference among the volume and time of incubations used but a significant difference in the temperatures employed. Being the etiological agent of cholera, V. cholerae is a major public health problem in several developing countries. The prevalence of &beta;-lactamase-producing strains and their isolation from life-threatening infections as well as the environment is alarming and presents a major therapeutic challenge for clinicians. The extended-spectrum &beta;-lactamase profile of a collection of 210 V. cholerae O1 strains isolated from clinical and water samples was investigated. The strains were collected during ongoing epidemiological and ecological cholera surveillance in the provinces of Chhatak and Mathbaria in Bangladesh, between March 2009 and April 2012. Resistance to penicillins, monobactams, carbapenems, second-, third- and fourth- generation cephalosporins were tested by disk diffusion. Genotypic analysis of the resistance determinants was performed by PCR to detect ESBL (blaCTX, blaTEM, blaSHV), carbapenemases (blaIMP, blaSPM, blaVIM, blaBIC, blaNDM, blaKPC, blaAIM, blaSIM, blaDIM, and blaGIM). All strains were sensitive to the 4th-generation beta-lactam cefepime. This is the first report documenting such extensive resistance to monobactams and third-generation cephalosporin in V. cholerae.</p>

Thesis (Ph.D.)--University of California, San Francisco, 2005. / Source: Dissertation Abstracts International, Volume: 66-12, Section: B, page: 6402. Adviser: Alexander Johnson.

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2007. / Title from dissertation home page (viewed Sept. 29, 2008). Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0818. Adviser: Clay Fuqua.

Thesis (Ph.D.)--University of California, San Francisco, 2008. / Source: Dissertation Abstracts International, Volume: 69-12, Section: B, page: 7268. Adviser: Hiten D. Madhani.

Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2009. / Title from PDF t.p. (viewed on Jul 9, 2010). Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5968. Adviser: Patricia L. Foster.