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Gut Dysbiosis Correlates With Covid-19 Severity, Ednita Escobar 2024 Claremont Colleges

Gut Dysbiosis Correlates With Covid-19 Severity, Ednita Escobar

CMC Senior Theses

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) impacts not only respiratory but also gut and oral microbiomes, influencing the manifestations of COVID-19. Each person’s unique microbiome consists of microorganisms such as bacteria, fungi, and viruses, some of which are symbiotic and others potentially harmful. Alterations in the gut microbiome, specifically, can affect the severity and symptoms of COVID-19. A review of studies indicate a pattern of gut dysbiosis in COVID-19 patients characterized by a decrease in beneficial microbiota and/or an increase in opportunistic pathogens. This gut imbalance correlates with disease severity, suggesting that the gut microbiome plays a significant role …


Microbes Mediated Keratin Extraction From Poultry Waste And Assessment Of Its Efficacy In Growth Promotion Of Zea Mays And Triticum Aestivum, Imran Ahmad, Aisha Waheed Qurashi, Roheela Yasmeen 2023 Department of Biology, Lahore Garrison University, Sector C, Phase-VI, DHA Lahore, Pakistan

Microbes Mediated Keratin Extraction From Poultry Waste And Assessment Of Its Efficacy In Growth Promotion Of Zea Mays And Triticum Aestivum, Imran Ahmad, Aisha Waheed Qurashi, Roheela Yasmeen

Journal of Bioresource Management

Feathers are a waste product of the poultry industry and are considered a major pollutant of the environment. Soil associated with poultry farms is a rich source of indigenous bacteria that are involved in biodegradation of keratin of the feathers of Gallus gallus domesticus. The present study was designed to understand the role of microbes in the degradation of a feather’s keratin and its possible utilization as a bio-protein for plants. In our studies, Keratinolytic activity was high at 37-45 ℃ and at 7.5-9.5 pH. Pseudomonas aeruginosa was identified by 16S rRNA sequencing as the most active keratinolytic strain. …


Consequences Of Spatial Structure In Soil–Geomorphic Data On The Results Of Machine Learning Models, Daehyun Kim, Insang Song, Lorrayne Miralha, Daniel R. Hirmas, Ryan W. McEwan, Tom G. Mueller, Pavel Samonil 2023 Seoul National University

Consequences Of Spatial Structure In Soil–Geomorphic Data On The Results Of Machine Learning Models, Daehyun Kim, Insang Song, Lorrayne Miralha, Daniel R. Hirmas, Ryan W. Mcewan, Tom G. Mueller, Pavel Samonil

Biology Faculty Publications

In this paper, we examined the degree to which inherent spatial structure in soil properties influences the outcomes of machine learning (ML) approaches to predicting soil spatial variability. We compared the performances of four ML algorithms (support vector machine, artificial neural network, random forest, and random forest for spatial data) against two non-ML algorithms (ordinary least squares regression and spatial filtering regression). None of the ML algorithms produced residuals that had lower mean values or were less autocorrelated over space compared with the non-ML approaches. We recommend the use of random forest when a soil variable of interest is weakly …


Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia 2023 Brigham Young University

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …


Isolation And Characterization Of Microbes From Agricultural Fields And Their Evaluation For The Control Of Plant Pests, Hira Liaqat Ali, Sumaira Mazhar, Afeefa Chaudhry 2023 Department of Biology, Lahore Garrison University, Lahore, Pakistan

Isolation And Characterization Of Microbes From Agricultural Fields And Their Evaluation For The Control Of Plant Pests, Hira Liaqat Ali, Sumaira Mazhar, Afeefa Chaudhry

Journal of Bioresource Management

Plant diseases due to pests cause huge loss to crop fields every year. For the control of plant pest, pesticides are under use. Fusarium wilt is caused by phytopathogen Fusarium oxysporum. More than 100 species were affected due to this disease caused by this virus. Fungi also affect onion plant crop yield every year, when chemical pesticides are applied to onion crop field. It will increase the cost of onion production and it is also dangerous for the environment and living organism other than the targeted pests. A number of microorganisms like fungi, bacteria and nematode are currently being …


Exploring Representation In Microbiology Introductory Courses Can Encourage A More Inclusive And Inspiring Environment For Students And Instructors, Jill A. Mikucki, Elizabeth Fozo 2023 University of Tennessee, Knoxville

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 …


Protocol For An Agent-Based Model Of Recombination In Bacteria Playing A Public Goods Game, Isaiah Paolo A. Lee, Omar T. Eldakar, J. Peter Gogarten, Cheryl P. Andam 2023 University of New Hampshire

Protocol For An Agent-Based Model Of Recombination In Bacteria Playing A Public Goods Game, Isaiah Paolo A. Lee, Omar T. Eldakar, J. Peter Gogarten, Cheryl P. Andam

Biology Faculty Articles

Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory.

For complete details on the use and execution of this protocol, please refer to Lee et al.1


Pseudomonas Aeruginosa Enhances Fluconazole Activity Against Candida During Polymicrobial Infection, Siham Hattab 2023 University of Maine

Pseudomonas Aeruginosa Enhances Fluconazole Activity Against Candida During Polymicrobial Infection, Siham Hattab

Electronic Theses and Dissertations

Polymicrobial infections pose a significant challenge in the field of medicine due to our incomplete understanding of how pathogens interact during infection and how these interactions impact the effectiveness of drug treatments. Among the opportunistic pathogens, Candida albicans and Pseudomonas aeruginosa stand out, as they are often found in similar infection sites, such as burn wounds, the lungs of patients with cystic fibrosis and those on mechanical ventilation. Candida albicans is an opportunistic fungus responsible for invasive candidiasis, a condition associated with a high mortality rate of 40% in hospitals. Pseudomonas aeruginosa, on the other hand, is the primary pathogen …


Assessing The Role Of The Microbiome, Parasite Infections, And Movement In Avian Health, Olivia N. Choi 2023 University of Maine

Assessing The Role Of The Microbiome, Parasite Infections, And Movement In Avian Health, Olivia N. Choi

Electronic Theses and Dissertations

Avian health encompasses the physical, physiological, and behavioral well-being of birds. Assessing avian health is not only important for the conservation and management of wild birds and the recreational economy, but also for the management of infectious diseases that threaten public health and agriculture. Birds, comprising approximately 10,000 species and an estimated 50 billion individuals worldwide, are known to be involved in the spread of pathogens, some of which are zoonotic (from animals to humans), such as avian influenza and West Nile viruses. Individual measures of avian health may include physical measurements (e.g., body mass, wing length), pathogen infection status, …


Interactions Between Streptococcus Agalactiae And Candida Albicans Affect Persistence And Virulence, Kathryn Patenaude 2023 University of Maine

Interactions Between Streptococcus Agalactiae And Candida Albicans Affect Persistence And Virulence, Kathryn Patenaude

Electronic Theses and Dissertations

Streptococcus agalactiae (Group B Streptococcus or GBS), a Gram-positive bacterium, and Candida albicans, a polymorphic fungus, are commensal microbes in most of the population they colonize but are also capable of causing severe and sometimes fatal infections in certain patient groups. Both organisms share similarities including the colonization the same tissue environments and causing infections in specific patient groups including those who are newborn, pregnant, suffering from chronic conditions like diabetes and HIV, as well as elderly patients. Previous research discovered that GBS and C. albicans can synergize to enhance the colonization of GBS in the bladders of mice, but …


Mutational Analysis Of The Nitrogenase Carbon Monoxide Protective Protein Cown Reveals That A Conserved C‑Terminal Glutamic Acid Residue Is Necessary For Its Activity, Dustin L. Willard, Joshuah J. Arellano, Mitch Underdahl, Terrence M. Lee, Avinash S. Ramaswamy, Gabriella Fumes, Agatha Kliman, Emily Y. Wong, Cedric P. Owens 2023 Chapman University

Mutational Analysis Of The Nitrogenase Carbon Monoxide Protective Protein Cown Reveals That A Conserved C‑Terminal Glutamic Acid Residue Is Necessary For Its Activity, Dustin L. Willard, Joshuah J. Arellano, Mitch Underdahl, Terrence M. Lee, Avinash S. Ramaswamy, Gabriella Fumes, Agatha Kliman, Emily Y. Wong, Cedric P. Owens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN’s protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work …


The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman 2023 Study Program of Microbiology, Department of Biology, Faculty of Mathematics and Natural Sciences, Institut Pertanian Bogor, Bogor 16680, Indonesia

The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman

Makara Journal of Science

Fusarium proliferatum decreases the productivity of shallot (Allium cepa L.). Endophytic bacteria are potential biocontrol agents in controlling the growth of F. proliferatum. This study aimed to select and characterize endophytic bacteria producing bioactive compounds that inhibit the growth of F. proliferatum. The endophytic bacteria used were isolated from the roots, stems, leaves, and soil of shallot plants from healthy and diseased shallot farming fields. The endophytic bacteria were selected using the dual culture method and extracted using ethyl acetate solvent. The results of the 16S rRNA identification suggested that isolate ABP5.2 is similar to Pseudomonas …


Enzymatic Screening And Genotypic Characterization Of Thermophilic Bacteria From The Hot Springs Of Sarawak, Malaysia, Seng Chiew Toh, Samuel Lihan, Sui Sien Leong, Azizul Hakim Lahuri, Wai Cheong Woon, Wing Woh Ng 2023 Department of Animal Sciences and Fishery, Faculty of Agricultural and Forestry Sciences, Universiti Putra Malaysia Bintulu Sarawak, Bintulu 97008, Malaysia

Enzymatic Screening And Genotypic Characterization Of Thermophilic Bacteria From The Hot Springs Of Sarawak, Malaysia, Seng Chiew Toh, Samuel Lihan, Sui Sien Leong, Azizul Hakim Lahuri, Wai Cheong Woon, Wing Woh Ng

Makara Journal of Science

Owing to their eccentric thermostable ability, thermophiles are among the most utilized extremophiles in various industries, such as manufacturing, and clinical research. Researchers believe that many unknown thermophiles are yet to be discovered. This study aimed to genotypically characterize the diversity of thermophiles and screen them for the potential production of enzymes in the recreational hot springs located at Northwest Coast of Borneo. Water samples were collected at 45 °C–50 °C from Annah Rais and Panchor hot springs during the sampling period from January 2018 to January 2019. Three samples (water and sediment) were collected twice in a 3-week interval …


Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan 2023 Medical University of South Carolina

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …


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 2023 Aga Khan University

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 …


Exploring Soil Microbial Dynamics In Southern Appalachian Forests: A Systems Biology Approach To Prescribed Fire Impacts, Saad Abd Ar Rafie 2023 University of Tennessee, Knoxville

Exploring Soil Microbial Dynamics In Southern Appalachian Forests: A Systems Biology Approach To Prescribed Fire Impacts, Saad Abd Ar Rafie

Doctoral Dissertations

Prescribed fires in Southern Appalachian forests are vital in ecosystem management and wildfire risk mitigation. However, understanding the intricate dynamics between these fires, soil microbial communities, and overall ecosystem health remains challenging. This dissertation addresses this knowledge gap by exploring selected aspects of this complex relationship across three interconnected chapters.

The first chapter investigates the immediate effects of prescribed fires on soil microbial communities. It reveals subtle shifts in porewater chemistry and significant increases in microbial species richness. These findings offer valuable insights into the interplay between soil properties and microbial responses during the early stages following a prescribed fire. …


The Identification Of Small Molecule Inhibitors To Candida Albicans Phosphatidylserine Synthase, Yue Zhou 2023 University of Tennessee, Knoxville

The Identification Of Small Molecule Inhibitors To Candida Albicans Phosphatidylserine Synthase, Yue Zhou

Doctoral Dissertations

Candida albicans phosphatidylserine (PS) synthase, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis due to its importance in virulence, absence in the host and conservation among fungal pathogens. This dissertation is focused on the identification of inhibitors for this membrane enzyme. Cho1 has two substrates: cytidyldiphosphate-diacylglycerol (CDP-DAG) and serine. Previous studies identified a conserved CDP-alcohol phosphotransferase (CAPT) binding motif present within Cho1, and here we revealed that mutations in all but one conserved amino acid within the CAPT motif resulted in decreased Cho1. For serine, we have predicted a …


Impact Of Cadmium Stress On Soil Virus Reproduction And The Persistence Of Viruses Under Abiotic Conditions, Zhibo Cheng 2023 University of Tennessee, Knoxville

Impact Of Cadmium Stress On Soil Virus Reproduction And The Persistence Of Viruses Under Abiotic Conditions, Zhibo Cheng

Doctoral Dissertations

Soil viruses are ubiquitous and greatly impact the structure and function of soil microbial communities, with their effects modulated by various environmental factors. This study investigates the inactivation of naturally occurring soil viruses in sterilized soil, as well as the effects of cadmium (Cd) exposure and carbon (C) and nitrogen (N) nutrient availability on the population dynamics of virus-host communities in agricultural soil.

Lab-scale slurry and unsaturated experiments were performed to examine virus inactivation in the absence of host bacteria in sterilized soil. In slurry experiments, virus abundance declined by over 90% after 10 days of incubation. The addition of …


Integration Of Raman Spectroscopy And Python-Based Data Analysis For Advancing Neurobiological Research, Natalie E. Dunn 2023 University of Tennessee, Knoxville

Integration Of Raman Spectroscopy And Python-Based Data Analysis For Advancing Neurobiological Research, Natalie E. Dunn

Doctoral Dissertations

The field of Raman spectroscopy continues to expand into biological applications due to its usefulness as a non-invasive technique that can be utilized qualitatively and quantitatively. However, the inherent weakness of Raman scattering leads to the need for each collected spectra to undergo a preprocessing step to remove noise, background drift, and cosmic rays. Biological research in particular needs large datasets due to the increased variability in samples. As datasets grow, the need to perform preprocessing on each individual spectra becomes daunting. Often, these steps are done by hand with the help of specialized software programs. Preprocessing can be accelerated …


Exploring The Regulation Of A Bacillus Pumilus Bioplastic Degrading Protein, Elise Keara Phillips 2023 University of Tennessee, Knoxville

Exploring The Regulation Of A Bacillus Pumilus Bioplastic Degrading Protein, Elise Keara Phillips

Doctoral Dissertations

Biodegradable plastics are being adopted to reduce the environmental impacts associated with petroleum-based plastics, including long residence times, and reliance on fossil fuels as a feedstock. Microbial degradation of bioplastics is still poorly understood, which leads to inconsistent degradation outcomes and challenges for implementation. Bacillus pumilus B12 degrades the biodegradable bioplastic polylactic acid (PLA) via the protease AprE, but the regulatory mechanisms controlling aprE expression in B. pumilus B12 are largely unknown. To explore this question, we established developed a conjugation- based method to introduce DNA into B. pumilus B12 and diverse Bacillus species that is applicable to environmental and …


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