Microbiology Commons^™

Generation And Assessment Of Muscular Mutations In Caenorhabditis Elegans, Katie N. Reget

DePaul Discoveries

A study of egg laying muscular mutations in C. elegans was conducted over a span of ten weeks. Parent (EGL-19) and wild type (N2) were exposed to mutagenesis and integration mutation techniques to generate genetic and physical different mutants. Overall, four genetic, physical and phenotypically unique worms were generated for the process of mutagenesis. The worms used in the process of integration were found to have shortened life spans, reduced size and decrease numbers of progeny.

Chronic Inflammation As A Result Of Hepatitis C Virus Infection: A Review Of The Literature, Samantha L. Lane

DePaul Discoveries

Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide^5,6. It is estimated that roughly 80% of those infected suffer from persistent infection with the virus; this persistence of infection is progressive, and over time can lead to fibrosis, cirrhosis, and hepatocellular carcinoma⁷. Chronic inflammation and apoptotic deregulation are both hallmarks of chronic HCV infection, and many molecular pathways are initiated in both the innate and adaptive immune responses during infection with this viral pathogen. The aim of this review was to survey some of the major molecular mechanisms responsible for the induction of …

Analysis Of Anti-Dengue Antibodies, Lauren Syndergaard, Brian Poole

Journal of Undergraduate Research

Dengue virus is a mosquitoes-borne virus that causes dengue fever. It is found primarily in tropical areas with over a third of the world’s population living in at-risk areas (WHO). The number of infections has grown rapidly in recent years with as many as 50 to 100 million infections occur each year (WHO). Though not widely present in the United States (small outbreaks occur with some regularity in Texas from the Mexican border; Hawaii and Florida relatively recently had cases), many travelers endemic areas contract the virus. Though several are being studied, as yet, there are no vaccines available for …

Engineering A Pathogen Specific High Affinity T-Cell Receptor Called Llo56, John Hancock, Dr. Scott Weber

Journal of Undergraduate Research

CD4+ helper T-cells play a vital role in the body’s immune response. When infectious agents attack the body, phagocytes engulf these invaders and present a peptide segment of the pathogen on a receptor (called MHCII). These receptors are located on the surface of the cell and the displayed peptide is termed an epitope. CD4+ T-cells with T-cell receptors (TCRs) specific for the displayed peptide bind to the MHCII complex. It is this binding that releases chemical signals to initiate an immune response. A disadvantage of TCRs is that their wild-type affinity for MHC is low and that they are membrane …

Discovery And Characterization Of Bacteriophage To Control Mrsa, Jacob B. Hatch, Bradford Berges

Journal of Undergraduate Research

About 20% of humans are carriers of Staphylococcus aureus (SA). There were an estimated 11,000 deaths in the United States in 2005 attributed to SA, with the majority caused by MRSA (Methicillin Resistant Staphylococcus Aureus) isolates [1]. Many MRSA isolates have developed resistance to all but one antibiotic drug: vancomycin. However, other bacteria have developed resistance to vancomycin, suggesting that in time MRSA will likewise become non-responsive to this last available drug and MRSA infections will be untreatable. This project looks to find an alternate method of MRSA treatment. Bacteriophage (phage) are viruses that infect bacterial cells in order …

Use Of Humanized Mice To Study The Production Of Human Antibodies, Steven Hallam, Dr. Bradford Berges

Journal of Undergraduate Research

The human immune system is composed of two main subsets: innate and adaptive immunities. Among the adaptive immune cells, B cells play a vital role in stopping infectious agents through the production of antigen specific antibodies. Human B cells are important targets of infection for many human-specific viruses that are poorly understood. Since the infection and study of human subjects is not possible, animal models have been developed to mimic the human immune environment. Rag2-/-γc-/- mice engrafted with human hematopoietic stem cells produce human B lymphocytes and these cells are capable of mounting antigen-specific human antibody responses. However, there is …

Mapping Interaction Through Compensatory Phou Mutants In Escherichia Coli, Tanner Dean, William Mccleary

Journal of Undergraduate Research

The purpose of this experiment was to identify the physical interaction site between two proteins in Escherichia Coli. These two proteins, PhoU and PhoR, are two proteins involved in Phosphate signal transduction. When these two proteins are mutated, so they no longer interact, the pathway is broken and signaling is inhibited. To break this pathway, we mutated one protein (PhoR) until we developed several mutations that no longer interact with PhoU. This loss of interaction is caused by a physical change to the site of interaction between the two proteins. We hypothesized that we could find a naturally occurring PhoU …

Fire Blight Treatment With Lytic Bacteriophage, Todd Jarvis, Julianne Grose

Journal of Undergraduate Research

Fire Blight, caused by the bacteria Erwinia amylovora, is a highly contagious fruit tree disease that is difficult to treat. This disease causes a tree to whither away, as if it had been burned. It is estimated that Fire Blight causes more than a 100 million dollar loss in agricultural goods each year¹. In an attempt to treat fire blight and prevent it from spreading, large doses of antibiotics are sprayed on infected trees. These antibiotics do little in the way of helping to treat the trees. In addition, the antibiotic run off from the treatment finds …

Lymphoblastoid Cell Line Generation From Sle Patient Lymphocytes, Vera Mayhew, Brian Poole

Journal of Undergraduate Research

Epstein-Barr Virus (EBV) is one of the viruses found most frequently in the human population. Approximately 95% of the population is infected in the United Sates by the age of 40. When primary infection occurs is young adulthood approximately 50% of cases result in infectious mononucleosis. Whether EBV infection results in mononucleosis manifestations or not, the virus stays latent in the infected individual’s B cells for the rest of their life.

How Chemokine Ccl28 Binds To Yersinia Pseudotuberculosis, Jeffrey Moffat, David Erickson

Journal of Undergraduate Research

Chemokines are tiny proteins that play a valuable role in defending our bodies against bacteria and other pathogens. Chemokines are best known for their role in attracting immune cells to areas of infection. Some chemokines, however, have demonstrated the ability to not only recognize pathogens and/or recruit white blood cells, but also to kill various classes of bacteria and fungi¹. One of these antimicrobial chemokines is CCL28.

P. Larvae Bacteriophages As A Treatment For American Foulbrood In Honeybees, Bryan Merrill, Sandra Burnett

Journal of Undergraduate Research

The deadly honey bee disease American Foulbrood (AFB) is caused by the bacterium Paenibacillus larvae. The widespread use of antibiotics to prevent or treat AFB has led to many drug-resistant strains of P. larvae. Bacteriophages can target and destroy specific strains of bacteria and can be used to treat bacterial infections. This study accomplished two main goals. We determined the efficacy of previously isolated P. larvae phages as a treatment for AFB by applying a phage spray to infected beehives. We also isolated P. larvae bacteria from the infected hives we treated and identified phages to better counteract …

Cofactor Specificity Of The Bifunctional Alcohol And Aldehyde Dehydrogenase (Adhe) In Wild-Type And Mutant Clostridium Thermocellum And Thermoanaerobacterium Saccharolyticum, Tianyong Zheng, Daniel G. Olson, Liang Tian, Yannick J. Bomble, Michael Himmel, Jonathan Lo, Shuen Hon, A. Joe Shaw, Johannes P. Van Dijken, Lee Lynd

Dartmouth Scholarship

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic bacteria that have been engineered to produce ethanol from the cellulose and hemicellulose fractions of biomass, respectively. Although engineered strains of T. saccharolyticum produce ethanol with a yield of 90% of the theoretical maximum, engineered strains of C. thermocellum produce ethanol at lower yields (∼50% of the theoretical maximum). In the course of engineering these strains, a number of mutations have been discovered in their adhE genes, which encode both alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes. To understand the effects of these mutations, the adhE genes from six strains of C. …

Effect Of Ebi2 On B Cell Migration, Jeffrey Mella, Brian Poole

Journal of Undergraduate Research

My mentored research project was a terrific experience. I have been mentored with Dr. Brian Poole for the last three years. As a result of the project that was made possible by the ORCA grant, I was the first author on an abstract submitted and accepted by the International Immunology Summit. This last October I attended the International Immunology Summit in Las Vegas, Nevada. Dr. Poole and I presented our research and I responded to questions from the audience. I am currently an author on a manuscript that in progress that has been submitted for review. I have enjoyed my …

The Effects Of Sustained, High-Velocity Exercise On Gene Expression In California Yellowtail (Seriola Lalandi), Kelli Hatter

Undergraduate Honors Theses

California Yellowtail muscle fibers have been observed to exhibit two drastically different development patterns resulting from the speeds at which they are exercised. When fish are exercised at a moderate rate their epaxial fast-twitch muscle fibers grow in diameter—hypertrophy; when they are exercised at a fast speed, more new epaxial fast-twitch muscle fibers are produced—hyperplasia. To determine the underlying reason for this difference in muscle development, my summer research project and honors thesis exercised fish at: fast, moderate, and control speeds for a sustained amount of time to determine what is happening on a cellular level to cause the observed …

Histone Modifications And Their Effects On Nucleosome Positioning And Gene Expression, Jordon Ritchie, Steven Johnson

Journal of Undergraduate Research

Nucleosome positioning plays an important role in gene regulation and expression. Nucleosomes consist of DNA-histone interactions that comprise the first order of DNA compaction into chromatin in the cell. Modifications to the histone in the nucleosome have been hypothesized to influence the location of the nucleosome on the DNA and therefore the regulation of the gene the nucleosome is forming on. In our original proposal, we proposed to show the effects that different modifications had on the position of the nucleosome on the DNA and the DNA sequence that had the highest affinity for nucleosome formation given a specific histone …

Analysis Of The Adjuvant Effect Of Vitamin D3 In Enhancing Mucosal Immune Responses, Cameron Sargent, Dr. Eric Wilson

Journal of Undergraduate Research

Because skin provides an effective physical barrier, most pathogens that invade the body do so at mucosal sites like the nose and mouth. As such, finding methods of improving mucosal immunity is key to providing greater defense against communicable diseases, the cause of approximately one-quarter of all deaths worldwide [1]. Improving vaccination, the technique in which the body is exposed to a weakened or nonvirulent dosage of a pathogen or toxin to promote an immune response specific to that foreign material, is a potential way of enhancing mucosal immunity. Vaccination has been used for several decades in medicine, nearly eradicating …

How Yersinia Pseudotuberculosis Biofilm Formation Is Regulated By Global Regulator Csra, Jeffrey Schachterle, David Erickson

Journal of Undergraduate Research

The bacteria Yersinia pestis is the causative agent of bubonic plague, and its ability to form biofilm in fleas is essential for plague transmission by fleas [1]. Y. pestis recently evolved from Y. pseudotuberculosis (Y. pstb), and the two have nearly identical genomes. Y. pestis forms a biofilm in fleas that is capable of blocking the flea’s feeding. These biofilms are made up of a community of bacteria adhering to a polysaccharide matrix that is made by the hmsHFRS gene products. Y. pstb is capable of infecting fleas, but will not block the flea’s feeding [1]. Since the …

A Method Of Introducing Site Specific Mutations Into The Phor Gene Of The E. Coli Chromosome, Cameron Woodward, William Mccleary

Journal of Undergraduate Research

Phosphate intake by Escherichia coli serves as a good model system to study phosphate intake by other bacteria. The pho phosphate uptake system used by E. coli is well conserved in pathogens like Vibrio cholerae (1). To better understand this important mode of phosphate uptake a study was performed to examine the interactions between the phoR and phoU proteins of this system. PhoU interacts with the pstSCAB complex, which brings phosphate into the cell. After communicating with pstSCAB the phoU protein interacts with phoR to tell it if phosphate is present in the environment or not. PhoR has been shown …

Detection Of Hcmv Viral Il-10 (Vil-10) In Healthy Blood Donors, Vivian P. Young

Master's Theses

Human cytomegalovirus (HCMV) is widespread in the general population and can establish lifelong latency with expression of a limited subset of viral genes. The UL111A gene is expressed during both lytic and latent infection, and at least two protein isoforms are produced. During lytic infection, the full length transcript yields cmvIL-10, a potent immunosuppressive viral ortholog of human IL-10 (hIL-10). Alternative splicing of the UL111A transcript yields a truncated protein, LAcmvIL-10, which is expressed during both lytic and latent infection but with a limited range of immunosuppressive functions. The two viral cytokines, collectively termed viral IL-10 (vIL-10), are identical in …

Functional Analysis Of The Molluscum Contagiosum Virus Mc160 Death Effector Domain-Containing Protein Rxdl Motif, Sarah Weber

Seton Hall University Dissertations and Theses (ETDs)

The Molluscum contagiosum virus (MCV) is a member of the Poxviridae family that causes benign skin lesions. MCV lesions persist on average for 8-12 months in otherwise healthy individuals. MCV lesions are characterized by reduced inflammation. The persistence and reduction of inflammation at the site of MCV lesions have been attributed to MCV immune evasion genes. MCV encodes two death effector domain (DED) containing proteins, MC159 and MC160. DEDs are found in cellular proteins such as FADD and procaspase-8. These cellular proteins are involved in several innate immune responses such as apoptosis and activation of interferon (IFN). Presumably, MC159 and …

The C-Terminal Linker Of Ftsz Acts As An Intrinsically Disordered Peptide During Cell Division In Bacillus Subtilis, Steven Grigsby

Undergraduate Theses—Unrestricted

The bacterial tubulin homologue FtsZ polymerizes in vitro in a GTP-dependent manner to form long, single stranded filaments. In cells, these filaments assemble at the nascent division site, interacting laterally to form the contractile Z ring. The Z ring serves as a scaffold for the rest of the division machinery and constricts at the leading edge of the invaginating septum during cytokinesis. The FtsZ polypeptide consists of three primary domains: the N-terminal globular core consisting of 315 residues that contains the GTP binding site, a variable and flexible C-terminal linker (CTL) consisting of 50 residues, and a conserved region at …

Characterizing Dna2 In Model Plant Arabidopsis, Connor Woodward, Brent Nielsen

Journal of Undergraduate Research

Dna2 is a protein that is known to be essential for DNA replication in human and yeast mitochondria. In these organisms it acts as both a helicase and an endonuclease. In the model plant Arabidopsis thaliana an ortholog of Dna2 exists but has never been studied. Two questions were answered in this study. The first question is “What would happen to A. thaliana plants that lacked Dna2?”. The second is “Where is Dna2 localized in plant cells?”

Draft Genome Sequences Of Six Different Staphylococcus Epidermidis Clones, Isolated Individually From Preterm Neonates Presenting With Sepsis At Edinburgh's Royal Infirmary, Paul Walsh, M. Bekaert, J. Carroll, T. Manning, B. Kelly, A. O'Driscoll, X. Lu, C. Smith, P. Dickinson, K. Templeton, P. Ghazal, Roy D. Sleator

Department of Biological Sciences Publications

Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis clones, cultivated from blood taken from different preterm neonatal sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Addressing The Black Box Phenomenon Of Genome Sequencing And Assembly, Brandon Carter

Senior Honors Projects, 2010-2019

Genomics, a study of all genetic material in an organism, is a new discipline having a great impact on medicine, agriculture, and environmental phenomena. Most undergraduate faculty members were not formally trained in genomics and must retool themselves in order to stay current with these evolving technologies. Advances in sequencing technology have resulted in an explosion of “big data” that can only be managed and analyzed using digital methods. Multiple complex computer programs are required to teach students the concepts using hands-on methods. These programs are challenging to use, especially since the same faculty members lacking genomics training were not …

Transduction As The Method Of Horizontal Gene Transfer Of The Staphylococcal Chromosomal Cassette Mec (Sccmec), Amber B. Sauder

Senior Honors Projects, 2010-2019

Methicillin-resistant Staphylococcus aureus (MRSA) gains resistance to β-lactam antibiotics through a mutated penicillin binding protein (PBP2a) encoded on the SCCmec element. In combination with the recombinase encoded by ccr, these two genes are used as markers of the mobile genetic element (SCCmec). Due to recent increases in community acquired MRSA infections, the mechanisms of antibiotic resistance gene transfer have gained attention. Transduction, a method of horizontal gene transfer mediated by bacteriophage, is believed to be responsible for the movement of the SCCmec element. Recent studies have shown the transduction of the SCCmec element in clinical isolates; however, this study is …

Tricistronic Lentivirus Vector Construction Using Scar-Less Dna Assembly Methods And Web-Based Software J5 To Help Study Grk4, Christophe Langouet-Astrie

Senior Honors Projects, 2010-2019

About one third of the world’s population is affected by hypertension, or high blood pressure, which increases an individual’s risk for cardiovascular disease. A major contributor to hypertension is dietary sodium intake. To assess an individual’s risk for hypertension, patients are put on a low sodium diet. However, research has shown that low salt intake can also have different and potentially harmful effects. Because of this, a genetic screen for salt sensitivity is needed to asses an individual’s salt sensitivity classification before testing and these results matched to a recommended dietary change. The kidney regulates the body’s fluid volume, so …

Comparative Analysis Of Anti-Bd Bacteria From Six Malagasy Frog Species Of Ranomafana National Park, Kelsey Savage

Senior Honors Projects, 2010-2019

As Malagasy amphibians are facing an impending extinction crisis from the lethal skin fungus Batrachochytrium dendrobatidis (Bd), it has become imperative to proactively mitigate the threat. Bd sporangia develop in the skin of infected amphibians and cause the skin to thicken, leading to ionic imbalance and eventual heart failure. It has been shown that certain bacterial species are able to inhibit Bd growth on amphibians by producing antifungal metabolites. Community-based probiotics are one approach used to combat chytridomycosis by inoculating an environment with Bd-inhibitory bacteria so that many amphibian species are treated at once. With this method, it is important …

Cave Cyanobacteria Showing Antibacterial Activity, Vasiliki Lamprinou, Kyriaki Tryfinopoulou, Emmanuel N. Velonakis, Alkiviadis Vatopoulos, Smaragdi Antonopoulou, Elizabeth Fragopoulou, Adriani Pantazidou, Athena Economou-Amilli

International Journal of Speleology

Cave Cyanobacteria - thriving in an ‘extreme’ environment with interesting species biodiversity - are supposed to be a potential source of bioactive compounds. Lipid extracts from pure cultures of two recently established Cyanobacteria from Greek caves, Toxopsis calypsus and Phormidium melanochroun, were used for antibacterial screening against human pathogenic bacteria (reference and clinical isolates). Antimicrobial Susceptibility testing for both taxa was carried out using the disc-diffusion (Kirby Bauer) method, while preliminary data applying the standard broth microdilution method for the determination of the Minimal Inhibitory Concentration (MIC) are given only for T. calypsus. Antibacterial activity was demonstrated against the …

Comparison Of The Antibacterial, Colloidal, And Hemolytic Properties Of Novel Triple-Headed, Triscationic Amphiphiles, Tara Gallagher

Masters Theses, 2010-2019

Antibiotic resistant bacteria were first reported in the 1940s, several years after the clinical introduction of penicillin. Since then, antibiotic resistance has contributed to increasing bacterial infections, mortality rates, and treatment costs. One promising alternative to traditional antibiotics is the development and use of amphiphiles, compounds with at least one hydrophilic head group and one hydrophobic tail. Three novel series of triple-headed amphiphiles with variations in the third head group composition, tail length and number of tails (one or two) were synthesized. Isothermal titration calorimetry was used to determine the critical micelle concentration – the concentration at which amphiphiles aggregate …

Effect Of Cmvil-10 On Exosome Production By Human Breast Cancer Cells, Susanna N. Basappa

Undergraduate Honors Theses

Human cytomegalovirus (HCMV) is a ubiquitous virus that infects 70-90% of the general population, primarily the immunocompromised, but has been implicated in several forms of cancer, including breast cancer. Breast cancer is the second leading cause of cancer related deaths in women in North America, usually from metastasis. Exosomes are 30-100nm vesicles produced by most cells which carry protein and RNA to cells in their microenvironment. The aim of this study is to investigate the impact of HCMV-infection of a secreted viral cytokine, cmvIL-10, on exosome production by highly metastatic breast cancer cells.

MDA-MB-231 cells were cultured in vitro, …