Microbiology Commons^™

The Development Of A Primer Payload With Microparticles For Uti Pathogen Identification Using Polythymidine- Modified Lamp Primers In Droplet Lamp, Jonas Otoo

KGI Theses and Dissertations

Nucleic acid amplification tests (NAATs) are among the diagnostic tests with the highest sensitivity and specificity. However, they are more complex to develop than other diagnostic tests such as biochemical tests and lateral flow immunoassay tests. Polymerase chain reaction (PCR) is the gold standard for NAATs. PCR requires thermal cycling to achieve clonal amplification of the target pathogen DNA for diagnosis. Thermal cycling poses a challenge in the development of PCR diagnostics for point-of-care (POC) settings. Loop-mediated isothermal amplification (LAMP) offers an isothermal method for NAATs diagnostics. The advancement of the microfluidics field significantly enhances the development of LAMP diagnostics …

Evaluación De Bacterias Con Potencial En La Promoción Del Crecimiento Vegetal En Agraz Silvestre Vaccinium Meridionale Swartz, Angie Sofia Barbosa Romero

Biología

El agraz (Vaccinium meridionale) es una planta promisoria con un fruto de gran aceptación en los mercados locales e internacionales por su alto valor en antioxidantes, antocianinas, vitaminas, y su amplia utilización gastronómica. Sin embargo, existen dificultades a la hora de establecer cultivos, las cuales están asociadas principalmente con la germinación de las semillas. Debido a que las bacterias promotoras de crecimiento vegetal son una alternativa sostenible para el manejo agrícola, con varios beneficios para la planta-bacteria. Como la fijación de nitrógeno y la producción de fitohormonas, el objetivo de esta investigación fue evaluar el efecto de bacterias con potencial …

Extension Of The Ergot Alkaloid Gene Cluster, Samantha Joy Fabian

Graduate Theses, Dissertations, and Problem Reports

Specialized metabolites produced by fungi impact human health. A large portion of the pharmaceuticals currently on the market are derived from metabolites biosynthesized by microbes. Ergot alkaloids are a class of fungal metabolites that are important in the interactions of environmental fungi with insects and mammals and also are used in the production of pharmaceuticals. In animals, ergot alkaloids can act as partial agonists or antagonists at receptors for 5-hydroxytryptamine (serotonin), dopamine, and noradrenaline as ergot alkaloids have chemical structures similar to those neurotransmitters. Therefore, they affect insects and mammals that consume them and can be used to produce drugs …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

Biomass Estimation Of Marine Biofilms On Plastic Surfaces, Kian Banihashemi, Fernando Javier Gil

Biological Sciences

Plastics have become a major source of marine pollution, which threatens food safety and quality, human health, and marine ecosystems. Due to the drastic negative effects of plastics in a marine environment, alternative biodegradable plastics are being generated that are more eco-friendly and have less environmental impact. Though some of these plastics are known to biodegrade, the process of degradation for bioplastics has not been heavily studied in a marine environment. This pilot project sought to both quantify the process of biodegradation and compare across different methods for effectiveness of biomass estimation, which serves as an indicator of biodegradation. Plastics …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

Size Progression Of Oxygenic Photogranules (Opgs) And Its Effect On Opg Wastewater Treatment, Ahmed S.A. Abouhend

Doctoral Dissertations

In recent years, the oxygenic photogranule (OPG) process has gained increasing interest because of its potential to treat wastewater without supplemental aeration. Oxygenic photogranules (OPGs) are dense spherical aggregates comprised of phototrophic and nonphototrophic microorganisms. In OPG wastewater treatment reactors, photogranules grow in number as well as in size. The primary goal of this dissertation was to investigate how OPGs grow in size and how the growth affects their structure and functions. We found that OPGs undergo structural changes as they grow bigger in size. As OPGs grow larger, filamentous cyanobacteria become enriched while other phototrophic microbes diminish significantly. OPGs …

Mapping Selected Polyphenols Metabolism By Gut Bacteria And Their Genes, Ermin Zhao

Doctoral Dissertations

The human gut microbiome is a huge enzyme repository for dietary polyphenols metabolism, especially considering most of the polyphenols cannot be digested in the host and their biological functions are limited. Poor bioaccessibility based on traditional pharmaceutical ADME (absorption, distribution, metabolism, and excretion) assessment is the main problem facing the widely medical application of most polyphenols. Gut bacteria have the potential to mediate a wide range of biotransformation reactions of polyphenols, which leads to the production of many bioactive metabolites. In the past decades, mounting evidence in traditional ADME study have demonstrated gut bacteria play an irreplaceable role in dietary …

Prospecting For And Isolation Of Microalgae In South Texas, Mauricio Alejandro Peña

Theses and Dissertations

Microalgae is a very important microorganism that can be used for beneficial purposes for humans. One way to show the importance of algae in this planet is the contribution of Oxygen it provides to the atmosphere, which many organisms rely on (Medeiros et al., 2015). Carbon footprint has been one of the greatest causes for global warming and it is due to the use of fossils to create diesel. One of the ways to avoid contamination is to replace those fuels that are used on daily basis, such as for transportation. The microalgae are able to produce lipids that can …

Toward Lignin Valorization: Development Of Rhodococcus Opacus Pd630 As A Chassis For Triacylglycerol (Tag) Production From Recalcitrant Aromatic Feedstocks, Rhiannon R. Carr

McKelvey School of Engineering Theses & Dissertations

The advent of the industrial era was precipitated by the discovery of fossil fuels, and ushered in unprecedented changes for humanity included but not limited to the development of rapid transit and communications, improvements to food distribution and preservation, the mass production of goods, and a radical rearrangement of communities from relatively small enclaves to metropolises. With all the benefits, however, come considerable costs, especially to the global environment. Greenhouse gas emissions, built up over centuries of unregulated combustion, have precipitated a rate of global temperature change unparalleled in the 4.5 billion-year history of this planet. In order to preserve …

Developing A Toolbox To Engineer Quantitative Trait Variation In Legume Species Using Crispr/Cas Technologies., Petar Miletic

Electronic Thesis and Dissertation Repository

The impact of intensive agriculture on the environment is immense. This is especially dire with regard to the natural nitrogen (N) cycle, where the human driven interference, primarily associated with industrial fertilization, has reached unsustainable levels. Unlike cereals, legumes, such as soybean, alfalfa and common bean, have the ability to use atmospheric nitrogen, which limits the need for industrial fertilization. A more wide-spread use of legumes could alleviate some of the negative impacts on the biogeochemical cycle while also providing a useful alternative to meat consumption, an important factor in sustainability. To reach this goal, further improvements of legume crops …

Extracellular Polymeric Substances In Oxygenic Photogranules: Investigation Of Their Role In Photogranulation In A Hydrostatic Environment, Wenye Camilla Kuo-Dahab

Doctoral Dissertations

The purpose of this dissertation was to assess the critical role of extracellular polymeric substances (EPS) in the photogranulation of activated sludge, in a hydrostatic environment. The first section evaluates the fate and dynamics of different fractions of EPS in sludge-based photogranulation under hydrostatic conditions. The study shows that during the transformation of activated sludge into a photogranular biomass, sludge’s base-extractable proteins selectively degrade. Strong correlations between base-extracted proteins and the growth of chlorophyll a and chlorophyll a/b ratio suggest that the bioavailability of this organic nitrogen is linked with selection and enrichment of filamentous cyanobacteria under hydrostatic conditions. The …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Understanding The Adhesion Mechanism In Mycelium-Assisted Wood Bonding, Wenjing Sun

Electronic Theses and Dissertations

The increasing environmental awareness has led to an increased interest in developing more sustainable materials as alternatives to petroleum-derived products. Among different nature-based products, fungal-mycelium-based bio-composites have gained considerable attention in various applications. Multiple materials with different densities and structures and potential applications can be fabricated by inoculating filamentous white-rot fungi in lignocellulosic materials and other substrates. Different from lower-density as-grown foam-like mycelium composites, higher-density mycelium-lignocellulosic panels have the potential to replace commercial particleboard and fiberboard bonded by petroleum-based resins. This kind of composite can be produced by directly adding heat and pressure to the low-density foams or by assembling …

Partial Expression Of The Vbss Gene In Rhizobium Leguminosarum Atcc 14479 And In-Silico Analysis Of The Vbs Gene Cluster In Various Microorganisms, Afreen Siddiqui

Undergraduate Honors Theses

Iron is extremely important for many organisms. Despite its abundancy, it exists in insoluble forms that makes its usability difficult. Some organisms secrete siderophores, low molecular weight compounds, that can chelate iron and convert it into usable forms for cells. One such organism, Rhizobium leguminosarum, is a nitrogen fixing symbiont proteobacteria that infects leguminous plants. The genome of Rhizobium leguminosarum ATCC 14479, which infects the red clover, Trifoli pratense, has previously been completely sequenced in our lab. Our lab has identified several genes in this strain involved in the biosynthesis of a siderophore, vicibactin. The protein product of one of …

Unraveling Host-Gut Microbiota Dialogue And Its Impact On Response To Immune Checkpoint Blockade, Alexandria Cogdill

Dissertations & Theses (Open Access)

Cancer is a disease with only one degree of separation, affecting one in two men and one in three women in their lifetimes; accounting for 1 of every 6 deaths. While cancer mortality rates continue to improve, incidence rates are expected to rise and shift through 2050 due to epidemiological and demographic transitions worldwide. As such, it is imperative to continue to investigate and improve our understanding of both disease etiology and hallmarks of response to treatment. Currently, conventional therapies include, but are not limited to, surgery, chemotherapy, and radiotherapy. However, within the past decade, major advances have been made …

Primer Payload System For Higher-Order Multiplex Lamp: Design And Development Of Unit Processes, Tochukwu Dubem Anyaduba

KGI Theses and Dissertations

Design and Development of Platforms for the Application of Loop-mediated Isothermal Nucleic Acid Amplification, LAMP, in the Diagnosis of Polymicrobial Diseases

Tochukwu Dubem Anyaduba, Travis Schlappi (PI)

For the past two decades, several isothermal nucleic acid amplification technologies have emerged. These are mostly in response to the need for robust molecular diagnostic tools amenable to point-of-care and limited-resource settings. Of these, loop-mediated isothermal amplification, LAMP, stands out as a highly specific and rapid alternative to the polymerase chain reaction, PCR. One of LAMP's significant characteristics involves using four essential and two loop (rate increasing) primers to recognize six to eight …

Mining Selected Metagenomes/Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes, Ahmed Yamany

Theses and Dissertations

Antimicrobial resistance is one of the serious global challenges in the current century. The fact that resistance genes transfer between bacteria, coupled with the fact that the world is connected through complex dynamics. Studying microbial behavior and understanding the different factors coffering microbial resistance to a broad spectrum of the available drug classes, parallel with a comprehensive analysis of the natural microbial products as the primary source of the novel antibiotics, might shed some light on solutions for this problem. Microbial environments harbor a wide range of secondary metabolites (SM) with different functional groups. SMs are not directly involved in …

Micro-Physiological Models To Mimic Mucosal Barrier Complexity Of The Human Intestine In Vitro, Abhinav Sharma

Doctoral Dissertations

The mucosal barrier in the intestine is vital to maintain selective absorption of nutrients while protecting internal tissues and maintaining symbiotic relationship with luminal microbiota. This bio-barrier consists of a cellular epithelial barrier and an acellular mucus barrier. Secreted mucus regulates barrier function via in situ biochemical and biophysical interaction with luminal content that continually evolves during digestion and absorption. Increasing evidence suggests that a mucus barrier is indispensable to maintain homeostasis in the gastrointestinal tract. However, the importance of mucus barrier is largely underrated for in vitro mucosal tissue modeling. The major gap is the lack of experimental material …

Development Of A Thermosensitive Endonuclease To Act As A Plasmid Kill-Switch, Christopher D. Leichthammer

Electronic Thesis and Dissertation Repository

Biocontainment is an integral part of biomedical research that aims to protect the environment and human health by containing hazardous or invasive organisms in the laboratory. Containment systems often rely on elaborate genetic circuits; however, cells may escape containment by developing mutations that render the genetic circuits inviable or resistant to killing mechanisms. The aim of this thesis was to create a site-specific nuclease for biocontainment of plasmids in the mammalian gastrointestinal tract. LAGLIDADG homing endonucleases would be good candidate nucleases for a biocontainment system as they are resistant to mutations in their coding sequence and their target sequence in …

Needles In A Haystack Of Protein Diversity: Interrogation Of Complex Biological Samples Through Specialized Strategies In Bottom-Up Proteomics Uncover Peptides Of Interest For Diverse Applications, Manuel I. Villalobos Solis

Doctoral Dissertations

Peptide identification is at the core of bottom-up proteomics measurements. However, even with state-of the-art mass spectrometric instrumentation, peptide level information is still lost or missing in these types of experiments. Reasons behind missing peptide identifications in bottom-up proteomics include variable peptide ionization efficiencies, ion suppression effects, as well as the occurrence of chimeric spectra that can lower the efficacy of database search strategies. Peptides derived from naturally abundant proteins in a biological system also have better chances of being identified in comparison to the ones produced from less abundant proteins, at least in regular discovery-based proteomics experiments. This dissertation …

Characterization Of The Overexpression Of The Native H+-Pumping Pyrophosphatase In The Microalga Picochlorum Soloecismus, Kimberly T. Wright

Biology ETDs

Microalgae are of interest for the creation of sustainable and cost competitive alternatives to petroleum-based fuels and chemicals. However, cultivation, extraction and processing of algal biomass requires improved yields to achieve economic feasibility. The advancement of microalgal biotechnology and various genetic engineering techniques allow the improvement of microalgae biomass for this purpose. Here, the characterization of the overexpression of the native vacuolar H+ pumping pyrophosphate (AVP1) in Picochlorum soloecismus was examined. AVP1 overexpression causes biomass increase in relevant plant crops. When overexpressed in this microalga it increases carbon storage in the form of starch in a closed laboratory photobioreactor. However, …

Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro

LSU Doctoral Dissertations

Cyanobacteria were the first organisms to use oxygenic photosynthesis, converting CO₂ into useful organic chemicals. However, the chemical industry has historically relied on fossil raw materials to produce organic precursors, which has contributed to global warming. Thus, cyanobacteria have emerged as sustainable stakeholders for biotechnological production. The filamentous cyanobacterium Anabaena sp. UTEX 2576 can metabolize multiple sources of Nitrogen and was studied as a platform for biotechnological production of high-value chemicals (i.e., pigments, antioxidants, vitamins and secondary metabolites). From a Chemical engineering perspective, the biomass generation in this organism was thoroughly studied by interpreting the cell as a microbial …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Neurodegenerative Modeling: Tau Protein, Degradative Pathways, And Gene Expression Profiling Of Human Ipsc-Derived Neural Precursors And Differentiated 3-D Neural Sphere Versus 2-D Monolayer Cultures, Kyle H. Anthoney

Cal Poly Humboldt theses and projects

Human induced pluripotent stem cells offer a model for human brain development and disease by differentiation into brain organoids; however, current neural culture systems lack the microenvironment, neuronal circuits and connectivity, vascular circulation, and immune system that exist in vivo. After differentiation and development of neuronal and non-neuronal cell types within two formats of cell cultures, we can visualize and recapitulate in vivo protein accumulation, gene expression, and degradative processes such as autophagy. Using RNA extraction, purification methods and reverse transcription I compared traditional monolayer cultures and novel 3-D neural sphere cultures via gene expression analysis. This analysis indicated …

Microbial Degradation Of Urea Oligomers: Potential Slow Release Nitrogen Fertilizers, Maddy Bygd

Departmental Honors Projects

Urea is the most commonly used nitrogen compound in fertilizers across the world. It provides the most nitrogen at the lowest cost. However, with the size and solubility of this compound, it is easily washed out of the soil. This results in the need to continuously add fertilizer to fields, creating adverse effects on the environment due to nitrogen runoff and leading to increased expenses for farmers. Triuret, a urea oligomer, is a compound with promising potential for use as a nitrogen source, providing a slower release of nitrogen into the soil. It is hypothesized that this compound can be …

The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi

Dissertations

Essential oils (EOs) are plant-derived products that have been long exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to the broad-range antimicrobial activity, low toxicity to human commensal bacteria, and the capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, many aspects of their mode of action remain inconclusive. The overarching aim of this work was to address these gaps by studying molecular interactions between antimicrobial plant aldehydes and the opportunistic human pathogen Pseudomonas aeruginosa. We initiated …

Study Of Paper Microbial Fuel Cells For Use In On-Site Wastewater Testing, William A. Tolmasoff

Master's Theses

This study demonstrated a technique for fabricating simple, low-cost Paper Microbial fuel cells (PMFC’s) in the model of a previous study to, for the first time, produce voltage from wastewater effluent. The PMFC’s were created by stacking and gluing the main components of an MFC together: reservoir layer; anode; cation exchange membrane (CEM); air cathode. A wax printer was used to create the hydrophobic borders of the PMFC’s on filter paper, and graphite paint was applied to the paper to create the anode. The CEM’s considered were filter paper, wax, and Nafion, with Nafion being the most efficient. Finally, the …

See The Forest For The Leaves: Foliar Fungal Community Composition And Volatile Organic Compound Production, Joshua Copeland

Master's Theses

Endophytes are microbes that live within plants without causing detectable illness. These microorganisms can emit volatile organic compounds (VOCs), airborne signaling molecules that can significantly affect plant growth. Despite the prevalence of endophytes and their VOCs, little is known about these factors important to plant health. With this in mind I isolated fungal endophytes from leaves of Populus trichocarpa and Populus fremontii, tree species with economic and environmental uses, to determine if endophyte communities are reserved between the closely related tree species and over seasons. Surface sterilized leaf fragments were plated onto malt extract agar and the resulting fungi were …

Characterization Of Bacterial Isolates Obtained From Commercial Poultry Feed And Retail Food Using Whole Genome Sequence Analysis And Selected Biochemical Tests, Elena George Olson

Electronic Theses & Dissertations

The goals of this study is two-fold. The first part investigates bacterial isolates from commercial poultry feed and the second part deals with bacterial isolates recovered from retail food. In order to reduce pathogen contamination in poultry products identification of overall microbial populations in poultry production processing steps have always been considered an important monitoring tool for assessing sanitizer effectiveness and the corresponding responses of bacteria load levels on poultry carcasses. Bacterial isolates recovered from corn-based chicken feed were purified on aerobic plate count agar and eleven morphologically different colonies were selected for whole genome sequencing. In this part, the …