Life Sciences Commons^™

Determining The Impacts Of Corn Silage Mixing Ratios On Hydrogen Production From Beef Cattle Manure, Katya Faber-Quimby

Honors Theses

With global warming becoming an increasingly serious threat and a growing population requiring additional energy resources, interest in the production of clean energy from the agricultural sector has surged in popularity. Biohydrogen, also known as green hydrogen, is H₂ that has been produced using renewable energy, such as from agricultural byproducts or waste materials. It presents a promising alternative to nonrenewable resources due to its high potential for energy storage and lack of carbon emissions when used. Cattle manure has been explored as a resource for the production of biohydrogen. Selecting for hydrogen-producing microbes in the manure serves the …

Adherent-Invasive Escherichia Coli (Aiec) Promotes Mild Colitis In The C57bl/6 Il-10 Ko Mouse Model Of Crohn's Disease, Sarah Sm Zaw

Senior Theses

Crohn's disease (CD) is a chronic inflammatory bowel disease. Interleukin-10 knockout (IL-10 KO) mice are crucial in CD research. Adherent-invasive Escherichia coli (AIEC) is a subgroup of E. coli. In one study, IL-10 KO mice colonized with AIEC developed colitis in the distal colon compared to wild-type (WT) mice. I investigated how AIEC NC101 WT affects colitis severity in IL-10 KO mice of the C57BL/6 genetic background. Similar results in both genotypes would enhance mouse strain accessibility. Germ-free C57BL6 IL-10 KO mice were divided into groups: colonized with AIEC NC101 for 12, 15, or 18 weeks, or kept germ-free. Histopathological …

Novel Microbiological Medium Developed For The Isolation Of Bacteria Associated With Estuarine Anemones, Parker K. Lund, Catalina Cuellar-Gempeler

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Out of the nearly one trillion species of microbiota estimated to inhabit Earth only ten thousand have been cultured in the laboratory. Culturing continues to play a vital role in determining the physiology and ecologic function of individual bacteria in microbial communities and for microbes associated with host organisms one of the major challenges is developing microbiological media that mimics the bacteria’s natural environment enough to promote growth. Here, we target bacteria associated with the estuary anemones Diadumene lineata and Metridium senile by developing a novel medium that uses anemone tissue as the sole source of nutrients. We further measured …

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …

Bloom: A Microbial Self-Portrait, Emily Lauren Mulvaney

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Exploring Representation In Microbiology Introductory Courses Can Encourage A More Inclusive And Inspiring Environment For Students And Instructors, Jill A. Mikucki, Elizabeth Fozo

Feminist Pedagogy

Microbiology has a relatively brief history where significant discoveries are often linked with major events in human history - from disease outbreak to industrialization to climate change. The founders of key microbiological principles span across continents, genders, ethnicities, and socioeconomic status. However, the portrait described in many introductory textbooks center around a lone, typically white male scientist. Such narratives not only are misleading regarding the development of key principles in microbiology but can also reinforce inappropriate stereotypes as to whom belongs in microbiology. In our introductory microbiology course, we designed group work for Zoom break-out rooms to help engage students …

Allergic Bronchopulmonary Aspergillosis: Radiological And Microbiological Profile Of Patients Presented In An Outpatient Pulmonary Clinic In A Developing Country, Nousheen Iqbal, Muhammad Irfan, Mustafa Bin Ali Zubairi, Maaha Ayub, Safia Awan, Kauser Jabeen, Ali Bin Sarwar Zubairi

Section of Pulmonary & Critical Care

There is limited data available about allergic bronchopulmonary aspergillosis (ABPA) in Pakistan. The aim of the study was to describe the radiological and microbiological profile of ABPA patients presenting to the outpatient pulmonary clinic of a tertiary care hospital in Karachi, Pakistan. A retrospective study was conducted on ABPA patients who presented to the pulmonary outpatient clinic at Aga Khan University Hospital, Karachi, Pakistan, from January 2017 to December 2019. Data was collected on microbiology and radiology features on predesigned proforma. A total of 7759 asthmatic patients presented at the outpatient pulmonology clinic during the study period. Of the 245 …

Investigating The Ability Of Saltwater Isolates To Inhibit Biofilm Formation By Clinically Significant Pathogens, Monica Murphy

ORBioM (Open Research BioSciences Meeting)

Background

Nosocomial pathogens are responsible for chronic and persistent infections partly due to their ability to form protective biofilms which enhance their antibiotic tolerance. Biofilm disruption combats antimicrobial resistance as dispersed cells regain antibiotic susceptibility. The goal of this study was to evaluate the antibiofilm potential of isolates from marine environments against a pathogen panel consisting of MRSA and clinical Staphylococcus aureus strains, Acinetobacter baumannii and Escherichia coli pathogens.

Method

A large bank of saltwater bacterial isolates was cultured in glucose-supplemented trypticase soy broth (TSBg) and resulting colonies were screened against the pathogen panel. Isolates of interest were further examined …

Examining The Absorbance Maximum, Protein Concentration And Antimicrobial Activity Of Seaweed Extracts, Claudia Kenneally

ORBioM (Open Research BioSciences Meeting)

Background

The emergence of antimicrobial resistance (AMR) has highlighted the need for novel antimicrobials. Antimicrobial compounds can be isolated from various marine sources, including seaweed, which contain pigments and proteins. This study focuses on screening seaweeds for potential antimicrobial compounds.

Methods

Four seaweed types (A, B, C, D) were collected from beaches in Cork, Ireland, and extracts of each were prepared using both methanol (-M) and water (-H₂O). The absorbance maximum (λ_max)of seaweed extracts was determined from 220 – 800 nm to investigate potential pigment interference at 600 nm. The bicinchoninic acid (BCA) assay was preformed …

Investigating Potential Indicators Of Soil Health Through Microbiome Response To Environmental And Anthropogenic Stressors, Austin Cook

Theses and Dissertations

Traditionally, the analysis of soil health has overlooked the biological component of soil due to poor understanding of connections between the microbiome and empirically measured soil health indicators. The purpose of this study was to assess the effects of environmental and anthropogenic stressors on the soil microbiome, with the aim of identifying measurable soil biological indicators. Chosen soils were examined under distinct conditions to evaluate the effect of selected environmental and anthropogenic stressors on the microbiome. Soil biological responses were analyzed via enzymatic response, microbial functional genes, and microbial community. Environmental factors such as soil moisture and organic matter showed …

The Effect Of Algal Wastewater Treatment Systems On Microbial Communities, Alexis Leach

University Honors Program Senior Projects

In collaboration with the Metropolitan Water Reclamation District of Greater Chicago and Gross-Wen Technologies, I examined the microbial communities in experimental tertiary wastewater treatment systems employing algal phytoremediation. Three algal phytoremediation systems were examined: two vertical conveyor belt systems, known as the 10-foot belt system and the series 4 system, and a third system lacking a converter belt in which planktonic algae grew in a control pond. I used EcoPlates to measure carbon substrate utilization by microorganisms in each system. EcoPlates contain thirty-one different carbon substrates, with a dye that indicates microbial use of each substrate. I conducted a Principal …

Antimicrobial Resistance In Eskape Pathogens And Its Effect On Modern Medicine And Treatment, Cameran Runge

Honors Theses

Abstract

ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella

pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter

spp.) are seeing a growing resistance to multiple classes of antibiotics. Misuse and overuse of antibiotics have played directly into the resistance observed, and the problem is growing exponentially. Antibiotic resistance is partially due to several intrinsic factors limiting the drug's uptake. These include efflux pumps, increased biofilm production, and reduced cell wall permeability in the resistant bacteria. ESKAPE pathogens also acquire resistance through horizontal gene transfer and plasmids. As antibiotics have become less effective, the bacteria can continue to thrive, leading to a detrimental …

Confirming The Presence Of Staphylococcus Aureus Enterotoxin Seb From Campus Wide Swabbing, Isabella Mc Dory, Amanda Brosnahan, Taylor Mach

Research and Scholarship Symposium Posters

Samples taken from the CSP community were previously isolated and characterized as Staphylococcus aureus. In this study, the DNA from those positive samples were purified through a genomic prep and ran through a polymerase chain reaction for the SEB toxin gene. A DNA gel electrophoresis was ran and imaged displaying the results.

Tsst-1 Superantigen Is Present At Low Levels In Staphylococcus Aureus, Clara Hipp, Amanda Brosnahan, Taylor Mach

Research and Scholarship Symposium Posters

No abstract provided.

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

The Antibacterial Efficacy Of Silver (I) Cyanoximates Against Streptococcus Mutans Ua159 Biofilm Growth And Infection In Galleria Mellonella Larvae, Jill Hughes

Honors Program Theses

Streptococcus mutans is the known etiological agent of dental caries. S. mutans’ virulence factors, namely biofilm formation and lactic acid fermentation, contribute to its pathogenic behavior within the oral cavity. Biofilms are thick, antibiotically resistant communities of bacteria that are much more difficult to treat than planktonic or free-floating bacteria. Continued misuse of antibiotics against dynamic communities, like biofilms, has led to increased research on non-antibiotic alternatives. Amongst these alternatives, there are silver and silver-based compounds. Silver is commonly incorporated into medicine due to its inhibitory and bactericidal effects and antibacterial properties. Silver (I) cyanoximates have demonstrated promising antibacterial activity …

Examining The Effect Of Varying Dilutions Of Octopamine On The Gut Microbiome Of Lab-Raised And Wild Acheta Domesticus By Brandon Nelson University Of Puget Sound Biology, Brandon Nelson

Summer Research

For my research I am comparing the gut microbiome of lab raised A. Domesticus that are given various levels of Octopamine, a stress hormone, and comparing that to the gut microbiome of wild cricket types. Crickets are a widely used organism across the world for various experiments as both subject and feed. Knowing how the gut microbiome of these crickets is affected by various levels of stress will allow us to better take care of these crickets. This could also help us determine if there are any diseases that lab raised crickets may be susceptible to. A large part of …

Frankenbacteriosis Targeting Interactions Between Pathogen And Symbiont To Control Infection In The Tick Vector, Lorena Mazuecos, Pilar Alberdi, Angélica Hernández-Jarguín, Marinela Contreras, Margarita Villar, Alejandro Cabezas-Cruz, Ladislav Simo, Almudena González-García, Sandra Díaz-Sánchez, Girish Neelakanta, Sarah I. Bonnet, Erol Fikrig, José De La Fuente

Biological Sciences Faculty Publications

(Summary) Tick microbiota can be targeted for the control of tick-borne diseases such as human granulocytic anaplasmosis (HGA) caused by model pathogen, Anaplasma phagocytophilum. Frankenbacteriosis is inspired by Frankenstein and defined here as paratransgenesis of tick symbiotic/commensal bacteria to mimic and compete with tick-borne pathogens. Interactions between A. phagocytophilum and symbiotic Sphingomonas identified by metaproteomics analysis in Ixodes scapularis midgut showed competition between both bacteria. Consequently, Sphingomonas was selected for frankenbacteriosis for the control of A. phagocytophilum infection and transmission. The results showed that Franken Sphingomonas producing A. phagocytophilum major surface protein 4 (MSP4) mimic pathogen and reduce infection …

Application Of Nitrate To An Anaerobic Subsurface Bioremediation, Cassie Marie Roberts

Masters Theses

"The highly contaminated subsurface matrix of the Baird and McGuire Superfund site is currently threatening the health and safety of the surrounding environment of Holbrook, MA. Contaminants of significant concern due to high concentration are inorganic arsenite and petroleum hydrocarbons, such as naphthalene. Parsons Corporation and the Massachusetts Department of Environmental Protection have implemented a bioremediation pilot to attempt to degrade the hydrocarbons and arsenic with the application of nitrate. The nitrate would act as an electron acceptor for biodegradation of the hydrocarbon contaminants, produce nitrite that would oxidize reduced iron, and iron oxides would sequester arsenic. Preliminary data showed …

Contrast Of Smokeless Tobacco And It's Microbiological Footprint In Users And Non-Users, Monayjia Brown, Katie Robbins, Elyse Mckinney, Sydney Snell

Humboldt Journal of Microbiology

Smokeless tobacco products such as vapes have gained significant popularity over the last 20 years (7), and it is clear that the effects of these products are primarily unknown. This study examines how the microbial profiles found in smokeless tobacco products, such as vapes, can be used in forensic science. By linking these profiles to their owners, investigators can identify suspects in cases where traditional evidence is lacking. This information could provide valuable assistance in tracking victims and matching perpetrators or victims to crime scenes. Forensic science involves any evidence found at a crime scene that is examined and analyzed …

Occurrence Of Kanamycin-Resistant Bacteria Relative To Anthropogenic Pollution Along Richland Creek In Nashville, Tn​, Jolene Ho Mach, Annie Le, Brandon Torres Ramirez

Science University Research Symposium (SURS)

The overuse of antibiotics has caused an increase in antibiotic-resistant (AR) bacteria, which is a serious public health concern. Previous studies showed a significant correlation between anthropogenic pollution and AR bacteria. This project aims to identify AR bacteria in Richland Creek relative to local anthropogenic pollution. Water samples were collected at four locations along Richland Creek in Nashville, Tennessee. Bacteria resistant to the antibiotic kanamycin were isolated from the water samples, identified to genera using DNA barcoding, and compared among the sites. We expect to see a greater abundance and diversity of kanamycin-resistant bacteria closer to the end than near …

Effects Of Mass Death On Community Structure And Ecosystem Function, Abby Kimpton Jones

Theses and Dissertations

Death and decomposition are natural processes that are generally well-understood. However, large events of death, such as mass mortality events (MMEs) are increasing in frequency and their impacts on the ecosystem are largely unknown. These events may have both bottom-up effects from increased nutrient input as well as top-down effects from loss of an ecological functional group by the affected population. Different functional MMEs may result in different top-down effects, creating cascading effects. In Chapter 1, I test the hypothesis that scavenger and herbivore simulated MMEs generate novel bottom-up and top-down effects. Results indicate that MMEs have a significant effect …

Discovering Novel Polyextremotolerant Fungi, And Determining Their Ecological Role Within The Biological Soil Crust Consortium, Erin Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

The ecological niche of polyextremotolerant fungi within oligotrophic ecosystems such as biological soil crusts has not yet been determined. These fungi persist in locations where nutrients are depleted while simultaneously surrounded by autotrophic microbes such as algae and cyanobacteria. Yet it has not been shown that they are engaging in any exchange of nutrients the way lichens do. However, there is seemingly no other way for these fungi to obtain vital nutrients, such as carbon or nitrogen, other than from these microbes. Here we have isolated polyextremotolerant fungi from cold desert biological soil crusts which are a microbial biofilm that …

Methanogen Metabolic Flexibility, Sean Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are …

An Investigation Of The Novel Use Of Bacteriophages To Diagnose And Treat Johne's Disease In Cattle, Max Kevane-Campbell

ORBioM (Open Research BioSciences Meeting)

Johne’s disease is a scourge to dairy farmers all over the world. It is an infectious disease that causes chronic inflammation and lesions along the inside of the small intestine of, primarily, ruminant animals (i.e., cattle and sheep). It is an incurable disease and urgently requires new and radical intervention strategies. Apart from careful on-site farm management practices, little can be offered to farmers to reduce the risk of infection, and nothing short of livestock culling is effective once an animal becomes infected. Currently, there are no vaccines licensed in Ireland or antibiotic treatment strategies available for Johne’s disease. This …

Implications Of Antibiotic And Bacteriophage Resistance In Environmentally Isolated E. Coli, Michael Connolly

Honors Theses

The increasing prevalence of antibiotic-resistant bacteria is an emerging problem for humans. Clinical misuse, overuse in agricultural and food settings, and limited numbers of new antibiotics have accelerated the proliferation of antibiotic-resistant bacteria. To confront this threat, scientists must develop new therapeutics that kill these antibiotic-resistant bacteria. In this study, we used Escherichia coli to analyze antibiotic and bacteriophage susceptibility. E. coli is a common, mostly benign, enteric, gram-negative bacteria. We isolated three E. coli strains from the Hans Groot Kill, a stream that runs through Union College’s campus. We sought to assess various E. coli strains’ antibiotic resistance, susceptibility …

Assembly Of The Peripheral Arm Subunits Of Escherichia Coli Complex I And Analysis Of Clinical Mutations, Hind Alkhaldi

Biological Sciences Theses and Dissertations

Respiratory Complex I from E. coli is a proto-type of the mitochondrial enzyme, consisting of a 6-subunit peripheral arm (B-CD-E-F-G-I) and a 7-subunit membrane arm. When subunits E-F-G (N-module), were expressed alone they formed an active complex as determined by co-immunoprecipitation and native gel electrophoresis. When co-expressed with subunits B and CD, only a complex of E-F-G was found. When these five subunits were co-expressed with subunit I and two membrane subunits, A and H, a complex of B-CD-E-F-G-I was membrane-bound, constituting the N- and Q-modules. Assembly of Complex I was also followed by splitting the genes between two plasmids, …

Antibiotic-Resistant Bacteria In Freshwater Crayfish, Colby Finch

Honors Theses

The presence of antibiotic-resistant bacteria is increasing in natural aquatic environments. Alongside this, organisms that live in these ecosystems are increasingly harboring antibiotic-resistant bacteria. In this study, I analyzed the capacity for the crayfish species Procambarus vioscai paynei to harbor antibiotic-resistant bacteria. Crayfish, as well as water and sediment, were sampled from a pond at the University of Mississippi Field Station. The guts of crayfish were plated on TSA agar, as well as agar containing vancomycin, erythromycin, penicillin, tetracycline, or ciprofloxacin. Following incubation, counts of bacteria were determined. Selected bacterial isolates were tested for multiple antibiotic-resistance. Bacterial isolates were also …

A Comparison Of Heterotroph Isolation And Sequencing Methods From Various Cyanobacterial And Algal Microbiomes, Victoria Starks

Honors Theses

Cyanobacteria have provided a vast, new source of natural products to be utilized in drug development. Because of their non-axenic nature, cyanobacteria typically have an abundance of symbiotic heterotrophs living in association with them. These bacteria can play significant roles in the survival of its cyanobacterial host as well as provide the potential production of unique compounds. The possibility of unknown natural products is only increased by the flexible nature of these bacteria, as altering its environmental state can change the activity of biosynthetic pathways and even activate novel production. Our research team’s intent is to isolate cyanobacterial strains from …

Analysis And Identification Of Lipolytic Bacterial Species For The Degradation Of Wastewater Lipids, Lindsay C. Smoak

Honors College Theses

The aim of this study was to isolate native bacterial strains from the wastewater treatment facilities of Statesboro, GA to identify their lipolytic activities. Obtained bacterial strains were further assessed via morphological and biochemical methods to determine their enzymatic capabilities. Use of the detergent Tween-20 in growth mediums was the first criteria to assess lipase activity, and these isolates were further investigated to quantitatively measure lipase presence and activity. Lipase protein was precipitated and dialyzed to perform a lipase activity assay, followed by Sodium Dodecyl Sulphate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) to confirm the presence of the lipolytic enzymes. Sanger sequencing was …