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 …

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 …

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, …

Hplc-Uv Quantitation Of Folate Synthesized By Rickettsia Endosymbiot Ixodes Pacificus (Reip), Junyan Chen

Cal Poly Humboldt theses and projects

Ticks are the most important vector of many infectious diseases in the United States. Understanding the nature of the relationship between Rickettsia endosymbiont Ixodes pacificus (REIP) and Exudes pacificus will help develop strategies for the control of tick-borne diseases, such as Lyme disease, and Rocky Mountain spotted fever. Folate, also known as vitamin B9, is a necessary vitamin for tick survival, and plays a central role in one-carbon metabolism in cells. Folate exist as a large family of structurally related forms that transfer one-carbon groups among biomolecules that are important to cell growth, differentiation, and survival. In Dr. Zheng’s lab, …

Metabolic Characteristics Of Macrophage Activation With Phenotype Microarrays, Tanya Kathryn D'Souza

Theses

Inflammation is a natural protective response and is characterised by the activation of numerous immune cells, including macrophages which can release a variety of inflammatory mediators. Macrophages play a flexible role in the initiation and effector phases of the immune response and change their behaviour to respond to environmental stimuli. The main objectives in this study were to create and characterise different macrophage behaviours and employ a novel metabolic characterisation platform the Phenotype Microarray^TM to attribute additional characteristics to the currently well recognised phenotypes. Five activated macrophage states were demonstrated and characterised. Unactivated macrophages (MO) demonstrated undetectable levels of …

Effects Of Myrrh On Hsv-1 Using Plaque Assay, Badrieah Mohammad Alamri

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Herpes simplex virus type 1 (HSV-1) is a highly infective human pathogen which infects a wide range of population in North America and worldwide. HSV-1 infection has two phases, lytic and latent. Recurrence of HSV-1 is a major challenge to clinicians to control the infection especially in immune depleted individuals. Acyclovir (ACV) is an antiviral drug used to treat HSV-1 infection. Low solubility of ACV in water, mutation of viral thymidine kinase, and mutation of viral DNA polymerase are major problems that cause usage limitations of ACV. Myrrh has been used as an analgesic and anti-inflammatory natural product in middle …

A Nutrient-Regulated Cyclic Diguanylate Phosphodiesterase Controls Clostridium Difficile Biofilm And Toxin Production During Stationary Phase, Erin B. Purcell, Robert W. Mckee, David S. Courson, Elizabeth M. Garrett, Shonna M. Mcbride, Richard E. Cheney, Rita Tamayo

Chemistry & Biochemistry Faculty Publications

The signaling molecule cyclic diguanylate (c-di-GMP) mediates physiological adaptation to extracellular stimuli in a wide range of bacteria. The complex metabolic pathways governing c-di-GMP synthesis and degradation are highly regulated, but the specific cues that impact c-di-GMP signaling are largely unknown. In the intestinal pathogen Clostridium difficile, c-di-GMP inhibits flagellar motility and toxin production and promotes pilus-dependent biofilm formation, but no specific biological functions have been ascribed to any of the individual c-di-GMP synthases or phosphodiesterases (PDEs). Here, we report the functional and biochemical characterization of a c-di-GMP PDE, PdcA, 1 of 37 confirmed or putative c-di-GMP metabolism proteins …

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 …

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

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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

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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 …

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 …

Contribution Of A Class Ii Ribonucleotide Reductase To The Manganese Dependence Of Streptococcus Sanguinis, John L. Smith

Theses and Dissertations

Manganese-deficient Streptococcus sanguinis mutants exhibit a dramatic decrease in virulence for infective endocarditis and in aerobic growth in manganese-limited media. Loss of activity of a manganese-dependent, oxygen-dependent ribonucleotide reductase (RNR) could explain the decrease in virulence. When the genes encoding this RNR are deleted, there is no growth of the mutant in aerobic broth culture or in an animal model. Testing the contribution of the aerobic RNR to the phenotype of a manganese transporter mutant, a heterologous class II RNR from Lactobacillus leichmannii called NrdJ that requires B₁₂ rather than manganese as a cofactor was previously introduced into an …

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

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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

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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 …

Effect Of Exposure Of Raw264.7 Macrophages To Salmonella Typhimurium Components On Cell Viability, Cytoskeleton Re-Arrangement And Cytokine Secretion, Khalid Abdullah Alyahya

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Innate immune system plays an important role in individual's protection against pathogens and in activation of adaptive immune system. Utilizing RAW 264.7 murine macrophages as an innate immune response representative in this study, we analyzed the effect of invasive pathogen's components (e.g. flagellin) on the arrangement of macrophage's cytoskeleton, on viability of immune cells and on secretion of pro-inflammatory and anti-inflammatory cytokines and on fluorescence intensity of cytoskeleton after rearrangement. Additionally, we studied the similarity and differences between bacterial (Salmonella typhimurium) and synthetic TLR4 agonist (synthetic lipid-A) on viability, fluorescence intensity, cytokine secretion, and cytoskeleton rearrangements. Similarly, we studied the …

A Novel Molecular Relationship Between Parn And Pld That, When Deregulated, Contributes To The Aggressive Phenotype Of Breast Cancer Cell Lines., Taylor Elaine Miller

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The removal of mRNA transcript poly(A) tails by 3'-5' exonucleases is the rate-limiting step for controlled mRNA decay in eukaryotes. Poly(A)-specific ribonuclease (PARN) is one such exonuclease that degrades poly(A) tails, and although its in vitro activity is well-characterized, PARN’s patho-physiological roles in the cell are not well understood. Prior studies have found a possible role for PARN in cancer, in that PARN expression levels in human breast cancer tissues are often decreased compared to normal control tissues. Indeed, data mined from the ONCOMINE cancer array database showed that PARN is downregulated in patient invasive breast carcinoma samples compared to …

Antimicrobial Activity Of Fractionated Borohydride-Capped And Electrochemical Colloidal Silver, Marjorie M. Markopoulos

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Silver nanoparticles (AgNPs) and ionic silver (Ag+) are known to be broad-spectrum antimicrobial agents. Recent studies show these agents may be an alternative to the most widely used drinking water disinfectant, chlorine. Chlorine is a toxic industrial chemical with a lethal concentration of 430 ppm after 30 minutes. Additionally, chlorine can react with naturally occurring materials to produce a number of disinfection byproducts such as chloroform and trihalomethanes. Some of these byproducts pose cancer risks in addition to other negative impacts to human health. These would be eliminated with the use of Ag+ or AgNPs. The main goal of this …

Season, But Not Symbiont State, Drives Microbiome Structure In The Temperate Coral Astrangia Poculata., Koty H. Sharp, Zoe A. Pratte, Allison H. Kerwin

Arts & Sciences Faculty Publications

BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome …