Microbiology Commons^™

Fractionation And Characterization Of Lignin Streams From Genetically Engineered Switchgrass, Enshi Liu

Theses and Dissertations--Biosystems and Agricultural Engineering

Development of biomass feedstocks with desirable traits for cost-effective conversion is one of the main focus areas in biofuels research. As suggested by techno-economic analyses, the success of a lignocellulose-based biorefinery largely relies on the utilization of lignin to generate value-added products, i.e. fuels and chemicals. The fate of lignin and its structural/compositional changes during pretreatment have received increasing attention; however, the effect of genetic modification on the fractionation, depolymerization and catalytic upgrading of lignin from genetically engineered plants is not well understood. This study aims to fractionate and characterize the lignin streams from a wild-type and two genetically engineered …

Role Of Intracellular Growth During The Gastrointestinal Stage Of Listeria Monocytogenes Infection, Grant Steven Jones

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Listeria monocytogenes is a facultative intracellular bacterium that causes foodborne disease in humans. L. monocytogenes invade the gut mucosa and then disseminate, causing systemic infections associated with high mortality rates in immunocompromised individuals. It is unknown how L. monocytogenes traffic to the mesenteric lymph nodes, which represent an important bottleneck for systemic spread. In addition, little is known about the gastrointestinal stage of infection due to the general resistance of mice to oral infection with L. monocytogenes. Our laboratory developed a novel foodborne mouse model of listeriosis utilizing a murinized strain of L. monocytogenes to investigate the gastrointestinal stage …

Evolution Of Equine Arteritis Virus During Persistent Infection In The Reproductive Tract Of The Stallion And The Male Donkey, Bora Nam

Theses and Dissertations--Veterinary Science

Equine arteritis virus (EAV) establishes persistent infection in the stallion reproductive tract, and the carrier stallion continues to shed virus in semen for weeks to years or lifelong. The objective of this study was to elucidate the intra-host evolution of EAV during persistent infection in stallions. Seven EAV seronegative stallions were experimentally infected with EAV KY84 strain and followed for 726 days post-infection, and sequential clinical samples including semen were collected for virus isolation and next-generation sequencing (NGS). In addition, archived sequential semen samples from two stallions that were naturally infected with EAV KY84 for a long-period (up to 10 …

The Role Of The Dosage Compensation Complex As A Pathway For Spiroplasma To Induce Male Lethality In Drosophila Melanogaster, Becky Cheng

CMC Senior Theses

Drosophila melanogaster and many other insects harbor intracellular bacterial symbionts that are transmitted vertically from infected host mothers to their offspring. Many of these bacteria alter host reproductive developmental processes in order to increase their transmission success. For example, Spiroplasma, a spirochete that naturally infects D. melanogaster, selectively kills males during mid-embryogenesis while sparing females. Previous studies suggested that Spiroplasma interacts genetically with the male-specific dosage compensation pathway, which causes ~2-fold up-regulation of most genes located on the male’s single X chromosome so that their expression matches the levels found in females who have two Xs. To further …

Designing A Luminescence Assay To Measure In Vitro Binding Of The Fibronectin Attachment Protein (Fap) Of Mycobacterium Avium Subspecies Paratuberculosis To Fibronectin, Sirri Ngwa

All Graduate Theses, Dissertations, and Other Capstone Projects

The attachment and penetration of epithelial cells by Mycobacterium avium subsp. paratuberculosis (MAP) requires a bacterial fibronectin (FN) attachment protein FAP-P, which facilitates binding of FN by MAP. The region of FAP-P that interacts with FN is known, however, the region of FN that is bound by FAP-P is to be determined. Identification of the region of FN to which FAP-P binds would enable the synthesis of a competing peptide that could prevent FN binding by MAP. The first step toward locating this binding site is the design of a reliable FN binding assay. The purpose of this investigation was …

Development And Characterization Of Histidine-Tagged Hpv16 L2 And Ms2-Arginine-Tagged Recombinant Proteins For Downstream Processes, Tahiyat Alothaim

Dissertations, Master's Theses and Master's Reports

Human papillomaviruses (HPVs) are the most common sexually transmitted infections. Persistent infection with HPV can lead to anogenital cancers including head and neck cancers. Three prophylactic vaccines have been approved to prevent against some types of HPV infection. However, the vaccines are HPV-type specific and protect mostly against the HPV types included in the vaccines. To offer broader protection against more HPV types, studies in the field are developing candidate vaccines targeting a conserved minor capsid protein, L2. Nevertheless, reagents for developing and assessing L2 vaccines are limited. For example, antibodies to assess the antigenicity of some L2 epitopes are …

Fungal Iron Oxidation In Brazilian Iron Caves, Braxton L. Hornick

Williams Honors College, Honors Research Projects

The iron caves in Brazil are thought to form through a cycle of Fe(III)-reduction and Fe(II)-oxidation; the Fe(II) is washed out of the cave walls by rainwater, where it is oxidized to Fe(III) and deposited in iron-oxide crusts. Bacteria are known to reduce Fe(III) in the caves, but what species may be oxidizing Fe(II) is still unknown. Our hypotheses was another bacterial species was involved and our initial assays were aimed at isolating Fe(II)-oxidizing bacteria; however all our Fe(II)-oxidizing cultures were contaminated with fungi when Fe(II)-oxidation was seen. Antifungals were used to inhibit growth of fungal species, which inhibited both …

The Effects Of Polyunsaturated Aldehydes On Pelagic Microbial Food Webs In The Chesapeake Bay Area And Atlantic Coastal Waters, Chase Alfman

Williams Honors College, Honors Research Projects

Diatoms, one of the most common classes of phytoplankton, are autotrophic plankton, and are the primary food source for many organisms. Diatoms play a key role in nearly all oceanic food webs. Under stressful conditions, diatoms can undergo biological changes that produce cytotoxic secondary metabolites such as polyunsaturated aldehydes (PUA’s). This process is a form of allelopathy, utilized by many algae as a defense mechanism against predation, as well as to inhibit competitors. Microzooplankton are an essential part of these aquatic food webs as well, as they are a key herbivore in many oceanic environments. A set of experiments was …

Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting

Williams Honors College, Honors Research Projects

Visible light spectroscopy is a commonly used technique for measuring the growth of bacterial cultures, and growth curves provide broadly important data. However, the equipment and resources required for these experiments has been restricted to higher education and industry due to high cost and sophistication. We have previously reported on an inexpensive, 3D-printable photospectrometer called the SpecPhone. This device utilizes an iPhone as the camera, along with several other, inexpensive additions to make a fully functional spectrometer. Here, the application of the SpecPhone is expanded to the quantification of actively dividing E. coli cultures. Two protocols have been developed; one …

Genetic Interference And Receptor Biology Of Neglected Influenza Viruses, Runxia Liu

Electronic Theses and Dissertations

Influenza B virus (IBV) is an important pathogen that infects humans and causes seasonal influenza epidemics. By using next-generation sequencing (NGS) approach, we analyzed total mRNAs extracted from A549 cells infected with B/Brisbane/60/2008, and identified four defective genomes in IBV with two from the polymerase basic subunit 1 (PB1) segment and the other two from the matrix (M) segment. Each of them can potently inhibit the replication of IBV. One derived from PB1 segment was able to interfere modestly with influenza A virus (IAV) replication. The productions of the four defective RNAs are not dependent on the cell types. The …

A Survey Of Β-Lactam Antibiotic Resistance Genes And Culturable Ampicillin Resistant Bacteria In Minnesota Soils, Emily M. Wollmuth

Departmental Honors Projects

Since the discovery of penicillin, antibiotics have been an essential tool in the treatment of bacterial infections and diseases. It is estimated that antibiotics and antibiotic resistance genes have existed for billions of years. With the increasing appearance of resistant pathogenic bacteria, there has been growing concern. β-lactam antibiotics make up the largest portion of the global market, so resistance to these antibiotics is especially alarming. It has been theorized that frequency and type of antibiotic resistance genes vary by area. Previous studies suggest that these differences may be related to antibiotic use in agricultural and urban areas. To survey …

Antibiotic Resistance Genes In Minnesota Soil Bacteria From Areas Of High And Low Ferric Iron, Gunner L. Drossel, Presley Martin Phd

Departmental Honors Projects

Naturally-occurring antibiotic resistance genes in soil bacteria represent a potentially important reservoir of genes that could contribute to antibiotic resistance of human pathogens. It has been reported that over 40 genes in bacterial genomes are controlled by concentrations of ferric iron. We examined the effect of soil metal content on the level of resistance to two antibiotics, ampicillin (Amp) and tetracycline (Tet), and the presence of multiple genes that code for efflux pump-mediated resistance. These pumps act to export toxins (e.g. heavy metals and antibiotics, perhaps). Because of this, growth in heavy metal-contaminated soils might select for antibiotic resistance. Ninety-six …

Humboldt Journal Of Microbiology: Volume 19, Number 1- May 2017, Press Humboldt

Humboldt Journal of Microbiology

No abstract provided.

A First Look At The Microbial Community Of Rabidosa Rabida, A Wolf Spider In Searcy, Arkansas, Patricia Rivera, Ryan Stork, Amber Hug

Journal of the Arkansas Academy of Science

Many diverse animal models have been used to explore the interactions between host organisms and their microbiota. Increased understanding of microbe-host interactions could lead to improved healthcare and drug development. Spiders have venom, digestive fluid, and body fluid components that have been suggested to possess antimicrobial properties that could lead to new and interesting host-microbe interactions. While studies have been published on interactions between bacteria affecting the immune function and behavior of spiders, the spider microbiome has not been established to date. Excreta and body swabs were collected from Rabidosa rabida, a wolf spider typically found on tall grass …

Identification And Analysis Of Bacterial Genomic Metabolic Signatures, Nathaniel Bowerman, Nathan L. Tintle, Matthew Dejongh, Aaron A. Best

Faculty Work Comprehensive List

With continued rapid growth in the number and quality of fully sequenced and accurately annotated bacterial genomes, we have unprecedented opportunities to understand metabolic diversity. We selected 101 diverse and representative completely sequenced bacteria and implemented a manual curation effort to identify 846 unique metabolic variants present in these bacteria. The presence or absence of these variants act as a metabolic signature for each of the bacteria, which can then be used to understand similarities and differences between and across bacterial groups. We propose a novel and robust method of summarizing metabolic diversity using metabolic signatures and use this method …

An Undergraduate Cell Biology Lab: Western Blotting To Detect Proteins From Drosophila Eye, Neha Gogia, Ankita Sarkar, Amit Singh

Biology Faculty Publications

We have developed an undergraduate laboratory to allow detection and localization of proteins in the compound eye of Drosophila melanogaster, a.k.a fruit fly. This lab was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of Western Blotting technique to study protein localization in the adult eye of Drosophila. Western blotting, a two-day laboratory exercise, can be used to detect the presence of proteins of interests from total protein isolated from a tissue. The first day involves isolation of proteins from the tissue and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide) gel …

Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to develop a laboratory exercise, which allows students to get a hands-on experience of a molecular biology technique to analyze gene expression. The short duration of the biology laboratory for an undergraduate curriculum is the biggest challenge with the development of new labs. An important part of cell biology or molecular biology undergraduate curriculum is to study gene expression. There are many labs to study gene expression in qualitative manner. The commonly used reporter gene expression studies are primarily qualitative. However, there is no hands-on experience exercise to quantitatively determine gene expression. Therefore, …

Analysis Of Microbial Diversity In Disturbed Soil, Tyler G. Sanda

Williams Honors College, Honors Research Projects

This paper uses the composition and abundance of microbial species to analyze soil recovery in disturbed land. Surface mining disturbs ecological communities throughout the world. As organizations seek to reclaim these disturbed lands, a proper analysis of recovery is needed. In previous studies, recovery of disturbed land was limited to surface examinations, which do not characterize the possible unseen devastating effects of the subsoil. Soil microorganisms are extremely sensitive to environmental changes such as strip mining. It is proposed that these microorganisms may serve as better indicators of recovery post disturbance. Our analysis indicates microbial recovery, however it may not …

Vitamin D3 And Suppressor Of Cytokine Signaling Proteins Reduces Pro-Inflammatory Cytokines In An Alzheimer's Disease Like-Model Consisting Of Microglial And Neuronal Co-Cultures, Alexander Evdokiou

Browse all Theses and Dissertations

This study examined the inflammatory effects of amyloid-beta (A[beta]42) in a microglial-neuronal co-culture system and determined whether 1a, 25-dihydroxyvitamin D3 (1,25-(OH)2D3) along with suppressor of cytokine signaling (SOCS)1 and SOCS 3 mimetics would attenuate the inflammatory response to A[beta]42. This culture system, when seeded with A[beta]42, serves as an in vitro model for Alzheimer's disease (AD). In a neuronal-microglia co-culture, A[beta]42 stimulated microglia to secrete TNF-a, but with the addition of 1,25-(OH)2D3, TNF-a levels dropped by nearly eight-fold and to near zero values in the presence of both 1,25-(OH)2D3 and SOCS1 and SOCS 3 mimetics. The reduction of the inflammatory …

Dnp63a Suppresses Cell Invasion By Targeting Rac1 Through Mir-320a, Amjad Ahmed Aljagthmi

Browse all Theses and Dissertations

DNp63a, a member of the p53 family of transcription factors, is overexpressed in a number of cancers and known to play a role in proliferation, differentiation, migration and invasion. DNp63a has been shown to regulate several microRNAs that play a role in both development and cancer, but to date there has not been a global analysis of p63- regulated miRNA. Using next-generation sequencing of small RNA from wild type and sip63 transfected HaCaT cells, our laboratory recently identified a number of DNp63a- regulated miRNAs by RNA-Seq studies which may serve as biomarkers of cancer progression. We identified a novel miRNA, …

Biomarkers Of Sepsis: A Retrospective Approach, Jose M. Roberts

Williams Honors College, Honors Research Projects

Background: Biomarkers are taking the spotlight in becoming the norm for early diagnoses. Sepsis is an inflammatory disease that increases metabolic rate in children. The first biomarker is hyponatremia. Hyponatremia is a frequent electrolyte imbalance in clinical practice, often observed in children with inflammatory disease and infection. Presence of hyponatremia is associated with electrical signaling imbalances, inflammation and renal dysfunction. The clinical value of hyponatremia in pediatric patients is unknown. The C-reactive protein is a second biomarker. Its presence signifies that necrotic cells and inflammation are present.

Objectives: To evaluate the use of biomarkers in children seen in the Emergency …

Mycobacterium Species Identification In An Acute Hospital: Towards Rapid Identification, And Improved Epidemiology, Using Novel Mass Spectrometry Analysis, James Anthony O'Connor

Theses

Mycobacteria are a heterogeneous group of bacteria that cause a wide spectrum of disease, including Tuberculosis (TB), the single biggest killer worldwide. The genus also incorporates over 170 nontuberculosis (NTM) species, many of which are opportunistic pathogens. The aim of this project was to ascertain the burden of mycobacterial disease in the region and to determine the efficacy of Matrix-Assisted Laser Desorption/Ionisation time-of-flight (MALDI-tof) mass spectrometry (MS) for novel uses as a rapid identification method for clinical mycobacteria and as a typing tool for Mycobacterium tuberculosis complex isolates. A five-year retrospective epidemiological study of the region was conducted, the first …

Microbiota, Diet And Medication In Human Gut Disorders, Adam Clooney

Theses

The microbiota, a community of micro-organisms in a particular environment, have been intensely researched in the past decade and interest appears to continue to increase. The human body is richly populated with bacterial cells (3.8x10'^) and alterations in these communities are associated with disease. The work presented in this thesis explores aspects of microbiota research methodologies with regard to optimisation and concerns over a lack of reproducibility. Additionally, we investigated the effects of medication, in particular Proton Pump Inhibitors, on the human gut microbiota, along with comparisons between the microbiota of patients with active and inactive Inflammatory Bowel Disease.

Microbiota …

A Diagnostic And Control Programme For Johne’S Disease On Irish Dairy Farms, Aideen Kennedy

Theses

Johne’s disease (JD) is an enteritis of ruminants with potential zoonotic implications. JD diagnosis and control present difficulties given JDs prolonged subclinical nature. In order to improve JD control in Ireland, PhD aims included conducting a national survey documenting high-risk husbandry practices employed on Irish farms, thereby targeting areas for improved management. Furthermore as JD has been associated with on-farm economic losses internationally, this research programme aimed to analyse production losses associated with testing JD ELISA positive on Irish dairy farms. A longitudinal study was also conducted to assess if successful JD control can be achieved using gold-standard protocols. Due …

The Development Of New Molecular Tools To Detect Mycobacterium Avium Subspecies Paratuberculosis From A Bovine Faecal Environment By Real-Time Pcr, Marcel De Kruijf

Theses

The slow-growing intracellular pathogen Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne’s disease in domesticated and wild ruminants. Johne’s disease inflicts severe annual economic losses to the dairy industry worldwide. This thesis is divided into five chapters that consist of a literature review' chapter and four experimental chapters focusing on MAP strain genotyping and the development of novel molecular MAP detection tools using real-time PCR. Chapter 1 describes published information regarding MAP characteristics, Johne’s disease, MAP genomes, available MAP detection methods, MAP epidemiology and genotyping.

To efficiently control and monitor MAP infection, molecular t>ping of MAP strains provides extensive knowledge …

Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris, Amy L. Gallagher

Graduate Student Theses, Dissertations, & Professional Papers

Acaryochloris is a recently discovered genus of cyanobacteria, unique in its use of an uncommon chlorophyll as its major photosynthetic pigment, and in its peculiar genome dynamics. Members of this genus exhibit increased genic copy number variation (CNV), which is thought to be primarily derived from gene duplications and horizontal gene transfer (HGT). Acaryochloris provides an ideal system to explore mechanisms behind maintenance of gene duplicates and the influence of CNV in local adaptation. Here, I propose a mechanism for retention of gene duplicates of the bacterial recombinase, RecA, in Acaryochloris genomes and provide preliminary evidence that these paralogs are …

Molecular Biology Of A Surface-Exposed Protein Family Of Bartonella Bacilliformis, Hannah Fay

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Bartonella bacilliformis is a gram negative alpha-proteobacterium native to the Andes of South America. Bartonella causes Carrion’s disease, a potentially life threatening disease transmitted by the sand fly. It has a mortality rate of 88% when untreated and 10% when treated. Diagnostics and control measures for the disease are underdeveloped and no vaccine is available. Recent outbreaks indicate that the range of the pathogen is increasing with nearly 1.7 million people in western South America at risk. Little is known about the epidemiology and pathogenesis of B. bacilliformis. Recent research done by UC San Diego found a paralogous gene …

Vitamin D3 And Suppressor Of Cytokine Signaling Proteins Reduces Pro-Inflammatory Cytokines In An Alzheimer’S Disease Like-Model Consisting Of Microglial And Neuronal Co-Cultures, Alexander Evdokiou

Browse all Theses and Dissertations

This study examined the inflammatory effects of amyloid-ß (Aß42) in a microglial-neuronal co-culture system and determined whether 1a, 25-dihydroxyvitamin D3 (1,25-(OH)2D3) along with suppressor of cytokine signaling (SOCS)1 and SOCS 3 mimetics would attenuate the inflammatory response to Aß42. This culture system, when seeded with Aß42, serves as an in vitro model for Alzheimer’s disease (AD). In a neuronal-microglia co-culture, Aß42 stimulated microglia to secrete TNF-a, but with the addition of 1,25-(OH)2D3, TNF-a levels dropped by nearly eight-fold and to near zero values in the presence of both 1,25-(OH)2D3 and SOCS1 and SOCS 3 mimetics. The reduction of the inflammatory …

The Effect Of Gram-Positive Staphylococcus Aureus Cell Wall Components Lipoteichoic Acid And Peptidoglycan On Cytokine Production, Cytoskeletal Arrangement, And Cell Viability On Raw 264.7 Murine Macrophages, Gabrielle String

Browse all Theses and Dissertations

In this study, gram positive Staphylococcus aureus cell wall components such as lipoteichoic acid (LTA) and peptidoglycan (PGN) were used to study the potential inflammatory and anti-inflammatory cytokine response, cytoskeletal arrangement and cell viability on RAW264.7 murine macrophages over 24 hours. The effect of S.aureus LTA and PGN (5 [mu]g/mL) on RAW 264.7 macrophages was evaluated every six hours for twenty-four hours. Inflammatory cytokine (TNF-a) production peaked at 6 hours before decreasing over time. Anti-inflammatory cytokine (IL-10) production peaked between 12 and 18 hours. During the first twenty-four hours, cytotoxicity of treated macrophages, as defined as the release of lactate …

The Impact Of Socs1 And Socs3 Peptide Mimetics On Rho And Cdc42 Proteins Expression, F-Actin Cytoskeleton Rearrangements, And Cytokines Production Of Uninfected And Hsv-1 Infected M1 And M2 Raw 264.7 Murine Macrophages, Maha A. Elwardany

Browse all Theses and Dissertations

The immune system plays an essential role in the pathogenesis of HSV-1 during the lytic phase of the disease, orchestrating the inflammatory response, retaining the virus in its latent phase and preventing the recurrence of HSV-1 infection. Macrophages display a vital role in the innate and adaptive immune responses during multiple phases of HSV-1 infection. Polarized macrophages are categorized into two distinct classes with diverse functions. The classically activated M1 can engulf and destroy the microbial agents, produce proinflammatory cytokines, and participate in the pathogenesis of many inflammatory diseases. The alternatively activated M2 induces anti-inflammatory mediators and stimulates tissue remodeling …