Pathogenic Microbiology Commons^™

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits …

Improved Methods For The Quantification Of Viable Ascaris Suum And Application To Biosolids, Tanner Keyzers

Dissertations, Master's Theses and Master's Reports

The current method for detection of Ascaris ova in biosolids and wastewater has several drawbacks including being labor and time intensive as well as being difficult to quantify viable ova that have larvated during treatment. The goal of this thesis was to improve several methods for the detection and quantification of Ascaris ova during long term-storage of biosolids including improvement of quantifying viable ova using a heat and bleach treatment to promote movement of larvae inside of ova, and comparison of the traditional microscopic method with qPCR and PMA-qPCR to prevent the false-positive results. Improved methods to promote movement of …

Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form, Bliss Nicole Lambert

LSU Doctoral Dissertations

Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic …

Harnessing The Anopheles Microbiome To Conditionally Express Anti-Plasmodial Effectors During The Blood Meal, Jackie Shane

Electronic Theses and Dissertations

The control of vector-borne diseases such as malaria has been an extremely important research subject for hundreds of years. Because of the complex lifecycles of the pathogens that cause these diseases, finding a comprehensive treatment or preventative strategy has proven extremely difficult. Malaria alone is responsible for almost half a million deaths annually, most of them children under 5 years old. This disease is caused by parasitic protists in the genus Plasmodium that are transmitted to humans from Anopheles sp. mosquitoes. Most preventative strategies that are in use today revolve around controlling the vectors, including bed nets, insecticides, and larval …

Green Tea Polyphenol Epigallocatechin-3-Gallate-Stearate Inhibits The Growth Of Streptococcus Mutans: A Promising New Approach In Caries Prevention, Amy Lynn Melok, Lee Lee, Siti Ayuni Mohamed Yussof, Tinchun Chu

Department of Biology Faculty Scholarship and Creative Works

Streptococcus mutans (S. mutans) is the main etiological bacteria present in the oral cavity that leads to dental caries. All of the S. mutans in the oral cavity form biofilms that adhere to the surfaces of teeth. Dental caries are infections facilitated by the development of biofilm. An esterified derivative of epigallocatechin-3-gallate (EGCG), epigallocatechin-3-gallate-stearate (EGCG-S), was used in this study to assess its ability to inhibit the growth and biofilm formation of S. mutans. The effect of EGCG-S on bacterial growth was evaluated with colony forming units (CFU) and log reduction; biofilm formation was qualitatively determined by Congo red assay, …

Synthesis, Secretion, And Perception Of Abscisic Acid Regulates Stress Responses In Chlorella Sorokiniana, Maya Khasin, Rebecca E. Cahoon, Sophie Alvarez, Richard Beckeris, Seong-Il Eyun, Qidong Jia, Jean-Jack Riethoven, Kenneth Nickerson, Wayne R. Riekhof

Kenneth Nickerson Papers

Abscisic acid (ABA) is a phytohormone that has been extensively characterized in higher plants for its roles in seed and bud dormancy, leaf abscission, and stress responses. Genomic studies have identified orthologs for ABA-related genes throughout the Viridiplantae, including in unicellular algae; however, the role of ABA in algal physiology has not been characterized, and the existence of such a role has been a matter of dispute. In this study, we demonstrate that ABA is involved in regulating algal stress responses. Chlorella sorokiniana strain UTEX 1230 contains genes orthologous to those of higher plants which are essential for ABA …

Relationships Between Factors Influencing Biofilm Formation And Pathogen Retention In Complex Rhizosphere Microbial Communities, Aaron Coristine

Theses and Dissertations (Comprehensive)

Riparian wetlands are unique habitats facilitating all forms of life. The riverbanks of these environments provide ideal conditions for bacteria, plants, and higher organisms. Of particular interest to this research was the variation in microbial community structure at high, intermediate and poor water quality impacted areas. Assessing the capabilities of plants to retain microbial pathogens was identified. Root systems and corresponding soil are ideal locations for bacterial deposition, resulting in attachment at these areas. Biofilm production in these regions is important for long-term establishment, leading to persistence and potential naturalization. Opportunistic pathogens originating from mammalian fecal matter are introduced into …

How Science Makes America Great, Kenneth Nickerson

Kenneth Nickerson Papers

The proposed Federal Budget cuts funding for NIH, NSF, and CDC by 16% each and for the EPA by a whopping 31%. Ouch! The situation seems ironic because of President Trump’s slogan “Make America great again!”, which I agree with wholeheartedly. In addition to being a scientist, I also love history (especially military history) and science is at the top of my list of what has made the United States great. ... Why do we do it? I’m in science because it is rewarding. It is invigorating to discover how nature works. Scientists may act individually and in relative obscurity, …

Quorum Sensing Signals Produced By Heterotrophic Bacteria In Black Band Disease (Bbd) Of Corals And Their Potential Role In Bbd Pathogenesis, Chinmayee D. Bhedi

FIU Electronic Theses and Dissertations

Black band disease (BBD) of corals is a temperature dependent, highly virulent, polymicrobial disease affecting reef-building corals globally. The microbial consortium of BBD is primarily comprised of functional physiological groups that include photosynthetic cyanobacteria, sulfate reducers, sulfide oxidizers and a vast repertoire of heterotrophic bacteria. Quorum sensing (QS), the cell-density dependent communication phenomenon in bacteria, is known to induce expression of genes for a variety of virulence factors in diseases worldwide. Microbes capable of QS release signals such as acyl homoserine lactones (AHLs) and autoinducer-2 (AI-2), which coordinate microbial interaction. The focus of the present study was to investigate the …

Phenomenological And Molecular Basis Of The Cnidarian Immune System, Tanya Brown

FIU Electronic Theses and Dissertations

Coral reefs are one of the most diverse ecosystems on the planet due partially to the habitat structure provided by corals. Corals are long lived organisms that can live for hundreds of years and as a result growth of many species is very slow. As a result of this, recovery of corals from disease outbreaks is very slow and difficult and therefore the ecosystem is deteriorating rapidly. Due to this increase in disease and its detrimental effect on coral reefs, it has become imperative to study how corals respond to disease outbreaks. The response of the coral to pathogens is …

Burkholderia Cenocepacia J2315-Mediated Destruction Of Staphylococcus Aureus Nrs77 Biofilms., Rachel Thompson

College of Arts & Sciences Senior Honors Theses

Cystic fibrosis (CF) is an inherited disorder that affects over 30,000 people in the US and more than 70,000 people worldwide. Recurring bacterial infections in CF patients result in tissue damage that dramatically lowers respiratory function and are ultimately fatal. The formation of bacterial biofilms in the mucus and on lung epithelial tissue allows pathogens to be protected from antibiotics and the host immune system, making treatment of infection difficult. The interactions between CF pathogens in co-culture biofilms are not well understood and were examined in this study. Staphylococcus aureus and Burkholderia cenocepacia, two common CF pathogens, were used …

Range-Wide Prevalence And Impacts Of Pseudocercosporella Inconspicua On Lilium Grayi And An Assessment Of L. Superbum And L. Michauxii As Reservoirs, Cindy L. Barrett

Electronic Theses and Dissertations

Lilium grayi (Gray’s Lily), a southern Appalachian endemic species, is threatened by a Lilium-specific fungal pathogen, Pseudocercosporella inconspicua. The disease is characterized by tan lesions that can cause early senescence, while also lowering seed production and viability. This project tested for P. inconspicua conidia and accessed health at nine locations. The disease was present and ubiquitous across the range of L. grayi. Through identification of P. inconspicua conidia in the field, L. superbum (Turk’s Cap Lily) was identified as an additional host, while L. michauxii (Michaux’s Lily) was disease-free. However, infection was inducible in both species. With …

Quorum Sensing In Candida Albicans: Farnesol Versus Farnesoic Acid, Wayne R. Riekhof, Kenneth Nickerson

Kenneth Nickerson Papers

Candida albicans is a clinically important dimorphic fungus that exhibits either a budding yeast or a mycelial-hyphal or pseudohyphal growth, depending on environmental conditions. The yeast-to-mycelia morphologic transition, which is generally regarded as an important virulence determinant, depends on the inoculum size of liquid cultures. The yeast form is favored when cultures are inoculated at > 10⁶ cells∙mL^–1, whereas the mycelial form is favored at inoculum densities < 10⁶∙mL^–1. Farnesoic acid (FA) and farnesol (FOH) are two related sesquiterpene quorum- sensing molecules that, upon accumulation, prevent the yeast-to-mycelial conversion. Oh et al. showed that C. albicans …

Deciphering Fungal Dimorphism: Farnesol’S Unanswered Questions, Kenneth Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

Candida albicans excretes E,E-farnesol as a virulence factor and quorum sensing molecule that prevents the yeast to hyphal conversion. Polke et al. (2016) identified eed1Δ/Δ as the first farnesol hypersensitive mutant of C. albicans. eed1Δ/Δ also excretes 10X more farnesol and while able to form hyphae, it cannot maintain hyphae. This mutant enables new research into unanswered questions, including the existence of potential farnesol receptors and transporters, regulation of farnesol synthesis, and relationships among farnesol, germ tube formation and hyphal maintenance. The eed1 farnesol hypersensitivity can be explained by higher internal concentrations of farnesol or lower thresholds for response. One …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

Genomic Plasticity And Rapid Host Switching Can Promote The Evolution Of Generalism: A Case Study In The Zoonotic Pathogen Campylobacter, Dan J. Woodcock, Peter Krusche, Norval J. C. Strachan, Ken J. Forbes, Frederick M. Cohan, Guillaume Meric, Samuel K. Sheppard

Frederick M. Cohan

Distribution Of Enterotoxigenic Clostridium Perfringens Spores In U.S. Retail Spices, Chi-An Lee

Masters Theses

246 samples of bulk and packaged spices from retail stores in the western, southeastern, southern, midwestern, and northeastern areas of the U.S. were examined for the presence of Clostridium -perfringens. Isolates were checked for the presence of the lecithinase gene (cpa) and enterotoxin genes (cpe) by PCR. Enterotoxin formation during sporulation was investigated using the Oxoid Toxin Detection Kit. Forty-three confirmed isolates (from 17% of total samples) were cpa-positive. Of those, 27 were cpe-positive. Together, levels of C. perfringens spores ranged from 3.6-2400/gm. The amount of enterotoxin in cell extracts ranged from …

Novel Advancements For Improving Sprout Safety, Kyle S. Landry

Doctoral Dissertations

All varieties of bean sprouts (mung bean, alfalfa, broccoli, and radish) are classified as a “super-food” and are common staples for health conscious consumers. Along with the proposed health benefits, there is also an inherent risk of foodborne illness. When sprouts are cooked, there is little risk of illness. The purpose of this dissertation was to explore novel techniques to minimize or prevent the incidence of foodborne illness associated with the consumption of sprouts. Three areas were investigated: 1) the use of a biocontrol organism, 2) the use of a novel spontaneous carvacrol nanoemulsion, and 3) the influence of the …

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …

Killer Toxin From Several Food-Derived Debaryomyces Hansenii Strains Effective Against Pathogenic Candida Yeasts, Nabaraj Banjara, Kenneth Nickerson, Mallory J. Suhr, Heather E. Hallen-Adams

Kenneth Nickerson Papers

Candida yeasts are the dominant fungi in the healthy human microbiome, but are well-known for causing disease following a variety of perturbations. Evaluation of fungal populations from the healthy human gut revealed a significant negative correlation between the foodborne yeast, Debaryomyces hansenii, and Candida species. D. hansenii is reported to produce killer toxins (mycocins) effective against other yeast species. In order to better understand this phenomenon, a collection of 42 D. hansenii isolates was obtained from 22 cheeses and evaluated for killer activity against Candida albicans and Candida tropicalis over a range of temperatures and pH values. Twenty three …

Super-Killers: Environmental Isolates That Antagonize Pathogenic Vibrio, Abigail Joy

Honors Projects

Vibrio are members of a bacterial group that thrive in diverse aquatic environments including on the surface of aquatic animals, free-living in the water column, and in association with suspended particles. The total Vibrio counts in the coastal ocean ranges from 10³-10⁵ per milliliter of water depending on seasons and water temperature. Although many different species of Vibrio persist in the water column, pathogenic strains, such as Vibrio cholerae and Vibrio parahaemolyticus are absent or rare in marine environments. We hypothesize that the low abundance of these pathogenic species may be due to interspecific competition among environmental …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Prokaryotic Diversity In The Rhizosphere Of Organic, Intensive, And Transitional Coffee Farms In Brazil, Adam Caldwell, Livia Silva, Cynthia Da Silva, Cleber Ouverney

Faculty Publications, Biological Sciences

Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 …

The Shellfish Corner -- Vibrios And Shellfish, Michael Rice

Michael A Rice

Pathogenic Vibrios are becoming an increasing problem for shellfish producers in North America and elsewhere. This paper reviews current research into the pathogenic nature of Vibrios and provides some practical advice for avoiding the propagation of Vibrios on shellfish farms nd in wild harvest molluscan shellfish.

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 …

Concomitant Uptake Of Antimicrobials And Salmonella In Soil And Into Lettuce Following Wastewater Irrigation, J. Brett Sallach, Yuping Zhang, Laurie Hodges, Daniel D. Snow, Xu Li, Shannon L. Bartelt-Hunt

Department of Civil and Environmental Engineering: Faculty Publications

The use of wastewater for irrigation may introduce antimicrobials and human pathogens into the food supply through vegetative uptake. The objective of this study was to investigate the uptake of three antimicrobials and Salmonella in two lettuce cultivars. After repeated subirrigation with synthetic wastewater, lettuce leaves and soil were collected at three sequential harvests. The internalization frequency of Salmonella in lettuce was low. A soil horizon-influenced Salmonella concentration gradient was determined with concentrations in bottom soil 2 log CFU/g higher than in top soil. Lincomycin and sulfamethoxazole were recovered from lettuce leaves at concentrations as high as 822 ng/g and …

Candida Albicans Quorum Sensing Molecules Stimulate Mouse Macrophage Migration, Jessica C. Hargarten, Tyler C. Moore, Thomas M. Petro, Kenneth W. Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

The polymorphic commensal fungus Candida albicans causes life-threatening disease via bloodstream and intra-abdominal infections in immunocompromised and transplant patients. Although host immune evasion is a common strategy used by successful human fungal pathogens, C. albicans provokes recognition by host immune cells less capable of destroying it. To accomplish this, C. albicans white cells secrete a low-molecular-weight chemoattractive stimulant(s) of macrophages, a phagocyte that they are able to survive within and eventually escape from. C. albicans opaque cells do not secrete this chemoattractive stimulant( s). We report here a physiological mechanism that contributes to the differences in the interaction of C. …

Proteomic Adaptations To Starvation Prepare Escherichia Coli For Disinfection Tolerance, Zhe Du, Renu Nandakumar, Kenneth W. Nickerson, Xu Li

Kenneth Nickerson Papers

Despite the low nutrient level and constant presence of secondary disinfectants, bacterial re-growth still occurs in drinking water distribution systems. The molecular mechanisms that starved bacteria use to survive low-level chlorine-based disinfectants are not well understood. The objective of this study is to investigate these molecular mechanisms at the protein level that prepare starved cells for disinfection tolerance. Two commonly used secondary disinfectants chlorine and monochloramine, both at 1 mg/L, were used in this study. The proteomes of normal and starved Escherichia coli (K12 MG1655) cells were studied using quantitative proteomics. Over 60-min disinfection, starved cells showed significantly higher disinfection …

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …

Methane Production By A Packed-Bed Anaerobic Digester Fed Dairy Barn Flush Water, Sean Richard Thomson

Master's Theses

Packed-bed digesters are an alternative to covered lagoon digesters for methane production and anaerobic treatment of dilute wastewaters such as dairy barn flush water. The physical media of packed-beds retain biofilms, often allowing increased treatment rates. Previous studies have evaluated several types of media for digestion of dilute wastewaters, but cost and media fouling have setback commercial development. A major operational cost has been effluent recirculation pumping.

In the present effort, a novel approach to anaerobic digestion of flush dairy water was developed at pilot-scale: broken walnut shells were used as a low-cost packed-bed medium and effluent recirculation was replaced …