Microbiology Commons^™

Susceptibility Of Biofilms To Bdellovibrio Bacteriovorus Attack, Daniel Kadouri, George A. O'Toole

Dartmouth Scholarship

Biofilms are communities of microorganisms attached to a surface, and the growth of these surface attached communities is thought to provide microorganisms with protection against a range of biotic and abiotic agents. The capability of the gram-negative predatory bacterium Bdellovibrio bacteriovorus to control and reduce an existing Escherichia coli biofilm was evaluated in a static assay. A reduction in biofilm biomass was observed as early as 3 h after exposure to the predator, and an 87% reduction in crystal violet staining corresponding to a 4-log reduction in biofilm cell viability was seen after a 24-h exposure period. We observed that …

Review Of "The Microbial Models Of Molecular Biology: From Genes To Genomes" By R. H. Davis, Amy Cheng Vollmer, S. J. Vollmer

Biology Faculty Works

No abstract provided.

Crustacean Phylogenetic Systematics And Opsin Evolution, Megan L. Porter

Theses and Dissertations

Composed of a chromophore bound to an integral membrane protein (opsin), visual pigments are phenotypically characterized by the wavelength of maximal absorption (λmax). The underlying molecular mechanism controlling λmax is the interaction between the opsin amino acid sequence and the chromophore. While a plethora of studies have looked at structure/function relationships in vertebrate opsins, fewer studies have investigated similar issues in invertebrates. Furthermore, those few studies undertaken in invertebrate systems suggest different mechanisms of spectral tuning and photoactivation compared to vertebrate systems. This dissertation research is focused on expanding our knowledge of opsin evolution in invertebrate systems, particularly from non-insect …

Assessment Of Cell Death Parameters In Bovine Parvovirus-Infected Ebtr Cells, Lubna Salah Eldin Abdel Latif

Theses and Dissertations

Bovine parvovirus (BPV) is a helper-independent parvovirus. It has a small icosahedral capsid with a single stranded DNA genome. It is a highly stable virus with a narrow host range. It causes acute gastroenteritis in calves. It is considered to be a cytolytic virus because it kills the host cells. However, the mechanism by which the virus causes cell death is not known. The work described in this thesis assessed different parameters of cell death in BPV infected embryonic bovine tracheal (EBTr) cells. There are several ways for viruses to induce cell death. Viruses can induce apoptosis in the infected …

Intermediary Metabolism And Life History Trade-Offs: Lipid Metabolism In Lines Of The Wing-Polymorphic Cricket, Gryllus Firmus, Selected For Flight Capability Vs. Early Age Reproduction, Anthony J. Zera

Anthony Zera Publications

The extent to which modifications in intermediary metabolism contribute to life history variation and trade-offs is an important but poorly understood aspect of life history evolution. Artificial selection was used to produce replicate genetic stocks of the wing-polymorphic cricket, Gryllus firmus, that were nearly pure-breeding for either the flight-capable (LW[f]) morph, which delays ovarian growth, or the flightless (SW) morph, which exhibits enhanced early-age fecundity. LW(f) lines accumulated substantially more triglyceride, the main flight fuel in Gryllus, compared with SW-selected lines, and enhanced accumulation of triglyceride was strongly associated with reduced ovarian growth. Increased triglyceride accumulation in LW(f) lines resulted …

Mechanisms Of Virulence Regulation In Porphyromonas Gingivalis W83, Elaine Ann-Marie Vanterpool

Loma Linda University Electronic Theses, Dissertations & Projects

The expression of extracellular proteolytic activities is highly regulated in both prokaryotic and eukaryotic systems. This regulation can occur at multiple levels including expression of the protease genes, secretion, processing of an inactive secreted precursor to its active form and/or the posttranslational glycosylation of the proteins. These regulatory mechanisms are vital to ensure that expression is tightly controlled. Porphyromonas gingivalis has been associated with adult periodontitis and in the development of many systematic diseases. The major virulence factors of P. gingivalis, the gingipains, are responsible for pathogenesis including degradation of complement and immunoglobulin, inactivation of cytokines and their receptors, …

Oxygen Sensing By The Aer And Tsr Receptors Of Escherichia Coli, Jessica Claire Edwards

Loma Linda University Electronic Theses, Dissertations & Projects

Escherichia coli senses the oxygen concentration of its environment via the Aer and Tsr receptors, and swims to an oxygen concentration that provides optimal energy generation. Aer and Tsr do not sense oxygen per se but, sense the internal energy state via the electron transport system (ETS) in a previously unidentified mechanism. Proton motive force (PMF) and electron flow were proposed as possible sensory signals but, distinguishing between the two was not possible, previously, in live, motile cells. I differentiated PMF from electron flow by creating a series of ETS mutant strains that express ternary combinations of i) aerotaxis receptors, …

Surface Display Of Recombinant Proteins On Bacillus Thuringiensis Spores, Cheng Du, Wing C. Chan, Timothy W. Mckeithan, Kenneth W. Nickerson

Papers in Microbiology

The insecticidal protoxin from Bacillus thuringiensis has been shown to be a major component of the spore coat. We have developed a novel surface display system using B. thuringiensis spores in which the N-terminal portion of the protoxin is replaced with a heterologous protein. The expression vector with a sporulationspecific promoter was successfully used to display green fluorescent protein and a single-chain antibody (scFv) gene that encodes anti-4-ethoxymethylene-2-phenyl-2-oxazolin-5-one (anti-phOx) antibody. The spores that carry the anti-phOx antibody can bind to phOx specifically.

To Compare The Total Cholesterol And Hdl-Cholesterol Before And After Ultra-Centrifugation In Lipemic Samples, Jawaid Jabbar, Imran Siddiqui, Syed Qaiser Raza, Ayaz Baig

Department of Pathology and Laboratory Medicine

Objective: It is an everyday routine in laboratories to encounter interference in the analysis of lipids. These likely interferences (hemolysis, icterus and lipemia) are countered by asking physicians and patients to send fresh and properly collected samples. At the Aga Khan University (AKU) Laboratory, we receive 2-3 lipemic/turbid samples per day. Previously it was our departmental policy to advise these patients to go for lipoprotein electrophoresis, which though accurate was time consuming and not cost effective. We therefore studied ultra centrifugation/airfuge as an alternate method to clear lipid interference and provide accurate, reliable and cost effective results.
Methods: Daily 2-3 …

Cellulose Utilization By Clostridium Thermocellum: Bioenergetics And Hydrolysis Product Assimilation, Yi-Heng P. Zhang, Lee R. Lynd

Dartmouth Scholarship

The bioenergetics of cellulose utilization by Clostridium thermocellum was investigated. Cell yield and maintenance parameters, Y(X/ATP)True = 16.44 g cell/mol ATP and m = 3.27 mmol ATP/g cell per hour, were obtained from cellobiose-grown chemostats, and it was shown that one ATP is required per glucan transported. Experimentally determined values for G(ATP)P-T (ATP from phosphorolytic beta-glucan cleavage minus ATP for substrate transport, mol ATP/mol hexose) from chemostats fed beta-glucans with degree of polymerization (DP) 2-6 agreed well with the predicted value of (n-2)/n [corrected] (n = mean cellodextrin DP assimilated). A mean G(ATP)(P-T) value of 0.52 +/- 0.06 was calculated …

Integrated Recombinant Protein Expression And Purification Platform Based On Ralstonia Eutropha, Gavin C. Barnard, Jesse D. Mccool, David W. Wood, Tillman U. Gerngross

Dartmouth Scholarship

Protein purification of recombinant proteins constitutes a significant cost of biomanufacturing and various efforts have been directed at developing more efficient purification methods. We describe a protein purification scheme wherein Ralstonia eutropha is used to produce its own “affinity matrix,” thereby eliminating the need for external chromatographic purification steps. This approach is based on the specific interaction of phasin proteins with granules of the intracellular polymer poly

The Epigenomic Viewpoint On Cellular Differentiation Of Myeloid Progenitor Cells As It Pertains To Leukemogenesis, Vincent E. Sollars

Biochemistry and Microbiology

The new millennium has brought with it a surge of research in the field of epigenetics. This has included advances in our understanding of stem cell characteristics and mechanisms of commitment to cell lineages prior to differentiation. The nature of stem cells is similar to that of malignant cells in that they have unlimited self-renewal and protection from apoptosis, leading researchers to suspect that stem cells are the target of oncogenesis. This review will explore the idea of how epigenetic control of gene expression may contribute to mechanisms controlling differentiation of myeloid progenitor cells and its importance to our understanding …

Functional Mimicry Of A Human Immunodeficiency Virus Type 1 Coreceptor By A Neutralizing Monoclonal Antibody, Shi-Hua Xiang, Michael Farzan, Zhihai Si, Navid Madani, Liping Wang, Eric Rosenberg, James Robinson, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

Interaction of the human immunodeficiency virus type 1 (HIV-1) gp120 envelope glycoprotein with the primary receptor, CD4, promotes binding to a chemokine receptor, either CCR5 or CXCR4. The chemokine receptor-binding site on gp120 elicits CD4-induced (CD4i) antibodies in some HIV-1-infected individuals. Like CCR5 itself, the CD4i antibody 412d exhibits a preference for CCR5-using HIV-1 strains and utilizes sulfated tyrosines to achieve binding to gp120. Here, we show that 412d binding requires the gp120 β19 strand and the base of the V3 loop, elements that are important for the binding of the CCR5 N terminus. Two gp120 residues in the V3 …

Potential Microcin Production By Helicobacter Pylori Hpm8, Sarah R. Null

All-Inclusive List of Electronic Theses and Dissertations

Helicobacter pylori undergoes significant mutation during chronic infection. The organism adapts to its specific host allowing a selective advantage even after repeated exposure to new competing strains. Genetic drift does not fully explain the ability of some strains to outcompete pre-existing strains or newly introduced strains. The hypothesis behind this research is that H. pylori HPM8 produces a peptide encoded on a plasmid, pHPM8, which has antibacterial activity against other H. pylori strains. Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) was used to determine the stage of the growth cycle the peptide is being expressed. RT-PCR demonstrated peptide expression throughout the …

Requirements For Vibrio Cholerae Hapr Binding And Transcriptional Repression At The Hapr Promoter Are Distinct From Those At The Apha Promoter, Wei Lin, Gabriela Kovacikova, Karen Skorupski

Dartmouth Scholarship

Virulence gene expression in certain strains of Vibrio cholerae is regulated in response to cell density by a quorum-sensing cascade that influences the levels of the LuxR homolog HapR through small regulatory RNAs that control the stability of its message. At high cell density, HapR represses the expression of the gene encoding the virulence gene activator AphA by binding to a site between −85 and −58 in the aphA promoter. We show here that a second binding site for HapR lies within the hapR promoter from which it functions to repress its own transcription. This site, as determined by gel …

Assessment Of Student Skills For Critiquing Published Primary Scientific Literature: Using A Primary Trait Analysis Scale, Manuel F. Varela, Marvin M.F. Lutnesky, Marcy P. Osgood

Biology Faculty Publications (Archived)

Instructor evaluation of progressive student skills in the analysis of primary literature is critical for the development of these skills in young scientists. Students in a senior or graduate-level one-semester course in Immunology at a Masters-level comprehensive university were assessed for abilities (primary traits) to recognize and evaluate the following elements of a scientific paper: Hypothesis and Rationale, Significance, Methods, Results, Critical Thinking and Analysis, and Conclusions. We tested the hypotheses that average recognition scores vary among elements and that scores change with time differently by trait. Recognition scores (scaled 1 to 5), and differences in scores were analyzed using …

Collection, Isolation And Evaluation Of Nitrogen Fixing Bacteria In The Rio Grande Valley Of Texas, Thomas M. Eubanks

Theses and Dissertations - UTB/UTPA

Isolation from local soil samples with Phaseolus vulgaris (L.) produced 20 samples from which pure cultures were obtained. A commercial strain of Rhizobium #132 was obtained from Becker Underwood and included as a standard in the experiment. The results demonstrated that a variety of infective and effective of strains of Rhizobium nodulating Phaseolus vulgaris (L.) exist in the native soils of the Rio Grande Valley of Texas. A cluster of effective bacteria was identified and can serve as a basis for recommendations to inoculant industry in the Valley. An isolate collection has been established to serve as a source of …

Kaposi’S Sarcoma-Associated Herpesvirus/Human Herpesvirus 8 Replication And Transcription Activator Regulates Viral And Cellular Genes Via Interferon-Stimulated Response Elements, Jun Zhang, Jinzhang Wang, Charles Wood, Dongsheng Xu, Luwen Zhang

Nebraska Center for Virology: Faculty Publications

Kaposi’s sarcoma-associated herpesvirus (also called human herpesvirus 8 [HHV-8]) replication and transcription activator (RTA) is apparently necessary and sufficient for the switch from viral latency to lytic replication. RTA may regulate open reading frame (ORF) K14 (viral OX-2 homologue) and ORF74 (viral G-protein-coupled receptor homologue) genes through an interferon-stimulated response element (ISRE)-like sequence (K14 ISRE) in the promoter region. RTA strongly activated a K14 ISRE-containing K14-ORF74 promoter reporter construct and a heterologous promoter reporter construct containing K14 ISRE. RTA could bind to K14 ISRE and other ISREs, activate promoter reporter constructs from interferon-simulated genes (ISGs), and selectively induce three endogenous …

Identification Of Cis-Acting Elements That Mediate The Replication And Maintenance Of Human Papillomavirus Type 16 Genomes In Saccharomyces Cerevisiae, Kitai Kim, Peter C. Angeletti, Elizabeth C. Hassebroek, Paul F. Lambert

Nebraska Center for Virology: Faculty Publications

Papillomaviruses contain small double-stranded DNA genomes that are maintained in persistently infected mammalian host epithelia as nuclear plasmids and rely upon the host replication machinery for replication. Papillomaviruses encode a DNA helicase, E1, which can specifically bind to the viral genome and support DNA synthesis. Under some conditions in mammalian cells, E1 is not required for viral DNA synthesis, leading to the hypothesis that papillomavirus DNA can be replicated solely by the host replication machinery. This machinery is highly conserved among eukaryotes. We and others found that papillomavirus DNA could replicate in a simple eukaryote, Saccharomyces cerevisiae. Specifically, papillomavirus …

Comparative Genomics Of Foot-And-Mouth Disease Virus, C. Carrillo, E. R. Tuhlman, Gustavo A. Delhon, Z. Lu, A. Carreno, A. Vagnozzi, G. F. Kutish, D. L. Rock

Nebraska Center for Virology: Faculty Publications

Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5’ and 3’ untranslated regions (UTR), as was tolerance for insertions/deletions in the 5’ UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for …

Ductal Carcinoma In Situ (Dcis) In Karachi, Naila Kayani, Yasmin Bhurgri

Department of Pathology and Laboratory Medicine

Objective:
To study the frequency of ductal carcinoma in situ (DCIS) in a large pathology series. DCIS is a proliferation of non-invasive, malignant epithelial cells within the ductolobular system of the breast. It is a heterogeneous entity with several morphologic variants that differ in gross appearance, growth pattern, cytologic features, mammography, and malignant potential.
Methods:
The data of The Aga Khan University' Pathology Department, diagnosed on the basis of histopathology, during a 6-year period (1st January 1998 to 31st December 2003) was reviewed, all cases of DCIS studied, and data was analyzed with the help of analytical software SPSS.
Results: …

Trefoil Factor 2 (Tff2) Deficiency In Murine Digestive Tract Influences The Immune System, M. Baus- Loncar, J. Schmid, El-Nasir Lalani, I. Rosewell, R. A. Goodlad, H. G.W. Stamp, N. Blin, T. Kayademir

Department of Pathology and Laboratory Medicine

Background & Aims:

The gastrointestinal trefoil factor family (TFF1, TFF2, TFF3) peptides are considered to play an important role in maintaining the integrity of the mucosa. The physiological role of TFF2 in the protection of the GI tract was investigated in TFF2 deficiency.

Methods:

TFF2-/- mice were generated and differential expression of various genes was assessed by using a mouse expression microarray, quantitative real time PCR, Northern blots or immunohistochemistry.

Results:

On an mRNA level we found 128 differentially expressed genes. We observed modulation of a number of crucial genes involved in innate and adaptive immunity in the TFF2-/- mice. …

Insertional Polymorphisms Of Endogenous Feline Leukemia Viruses, Alfred L. Roca, William G. Nash, Joan C. Menninger, William J. Murphy, Stephen J. O'Brien

Biology Faculty Articles

The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one …

Sara Is An Essential Positive Regulator Of Staphylococcus Epidermidis Biofilm Development, Maria A. Tormo, Miguel Marti, Jaione Valle, Adhar C. Manna

Dartmouth Scholarship

Staphylococcus epidermidis biofilm formation is associated with the production of the polysaccharide intercellular adhesin (PIA)--poly-N-acetylglucosamine polysaccharide (PNAG) by the products of the icaADBC operon. Recent evidence indicates that SarA, a central regulatory element that controls the production of Staphylococcus aureus virulence factors, is essential for the synthesis of PIA/PNAG and the ensuing biofilm development in this species. Based on the presence of a sarA homolog, we hypothesized that SarA could also be involved in the regulation of the biofilm formation process in S. epidermidis. To investigate this, we constructed nonpolar sarA deletions in two genetically unrelated S. epidermidis clinical strains, …

Identification Of A Tcpc-Tcpq Outer Membrane Complex Involved In The Biogenesis Of The Toxin-Coregulated Pilus Of Vibrio Cholerae, Niranjan Bose, Ronald K. Taylor

Dartmouth Scholarship

The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonization. The TCP biogenesis apparatus is composed of at least nine proteins but is largely uncharacterized. TcpC is an outer membrane lipoprotein required for TCP biogenesis that is a member of the secretin protein superfamily. In the present study, analysis of TcpC in a series of strains deficient in each of the TCP biogenesis proteins revealed that TcpC was absent specifically in a tcpQ mutant. TcpQ is a predicted periplasmic protein required for TCP biogenesis. Fractionation …

The Defensin Gene In Dermacentor Variabilis And Ixodes Scapularis, Katherine Corbett Seguin

Biological Sciences Theses & Dissertations

In response to microbial challenge, invertebrates rely on their innate immune response to recognize and destroy harmful pathogens. One of the primary proteins produced by the response and that has been observed in many invertebrates, including insects, mussels, and ticks, is defensin. These proteins are responsible for forming pores in the membranes of invading microbes thereby destroying them. This study examined the gene coding region for defensin in two important tick disease vectors, Dermacentor variabilis and Ixodes scapularis. PCR amplification of the genes from tick chromosomal DNA resulted in the amplification of a 225 base pair amplicon. Sequencing of …

Mechanisms Of Cell Death Initiated In Herpes Simplex Virus Thymidine Kinase Expressing Colon Tumor Cells Treated With Ganciclovir And Ucn-01, Christina Elizabeth Ahn

Theses and Dissertations in Biomedical Sciences

Metastatic colon carcinoma is the second leading cause of death from malignancy in the United States, and development of more effective treatments is essential. Heterologous expression of Herpes Simplex Virus Thymidine Kinase (HSVtk) in combination with the prodrug, ganciclovir (GCV), has shown great promise for the genetic therapy of many cancers, but most patients have had only a partial or minimal response to the therapy. After screening a panel of two drug combinations, our laboratory has shown that the combination of GCV and the protein kinase inhibitor UCN-01 (7-hydroxystaurosporine) enhances tumor cell death more effectively than either drug alone. However …

Psychomotor Skills For The Undergraduate Medical Curriculum In A Developing Country--Pakistan, Rashida Ahmed, Zoon Naqvi, Ineke Wolfhagen

Department of Pathology and Laboratory Medicine

Objective: To identify essential psychomotor skills for all the medical graduates of an undergraduate programme in Pakistan.
Materials and Methods: Twenty-five physicians practising in a tertiary care centre and ninety primary care physicians used a Likert's scale, ranging from "very essential" to"not required at all", to mark 99 psychomotor skills in the undergraduate medical curriculum in Pakistan.
Results: Overall the opinions of both the groups about the essential skills matched except for a few areas.
Conclusion: This study provides baseline data about psychomotor skills that a medical graduate in developing countries should be able to perform. Further studies will be …

Connecting Branches To Student Activities, Amy Cheng Vollmer

Biology Faculty Works

No abstract provided.

Ovarian Primary Neuroendocrine Carcinoma Of Non-Small Cell Type: Report Of An Extremely Rare Neoplasm, Zubair Ahmed, Kanwal Aftab, Naila Kayani

Department of Pathology and Laboratory Medicine

Paraffin block sections of a uterus and ovarian mass from a 31 year old female were sent for second opinion to the Pathology Laboratory of Aga Khan University. Histologic examination and immunohistochemical features gave a diagnosis of primary neuroendocrine carcinoma of non-small cell type admixed with benign mucinous cystadenoma. This is a rare tumour with only eight being reported in literature.