Microbiology Commons^™

Leveraging Bioinformatics To Understand Chlorophyll D Biosynthesis In Acaryochloris Spp., Dikshyant Gautam

Graduate Research Theses & Dissertations

Acaryochloris strains can adapt into far red region of the visible spectrum by utilizing its unique chlorophyll called chlorophyll d (Chl d). The genetic machinery behind Chl d has not been discovered yet. Biosynthetic pathway for other chlorophylls like chlorophyll a, chlorophyll b and chlorophyll f found in cyanobacteria are however well known. This research aims to understand the biosynthetic pathway responsible for chlorophyll d production. Bioinformatics approaches like comparative genomics, machine learning, and weighted gene co-expression network analysis (WGCNA) were central in this study to identify candidate genes and regulatory mechanisms potentially involved in chlorophyll d synthesis.

An important …

Ecophysiology Of Bradyrhizobium Diazoefficiens Usda 110, Armaan Kaur Sandhu

Electronic Theses and Dissertations

With increasing demand for soybean, maximizing plant yield is important yiel is dependent on nitrogen availability, but nitrogen fertilizers can meet the plant's needs but have severe environmental impacts. An economically and environmentally sustainable approach is to enhance nitrogen availability through Biological Nitrogen Fixation by symbiotic rhizobia, Bradyrhizobium, an efficient nitrogen fixer for soybean. This symbiosis begins with attachment of rhizobia to legume roots. Root and rhizobia surface properties play a significant role in this attachment. Another major factor affecting root colonization is bacterial competition ability. There is a lack of knowledge on the role of bacterial surface properties, competition …

Dust-Driven Mechanism For Marine Particle Aggregation: Interactions Between Clay Minerals, Heterotrophic Bacteria And Organic Matter Influences Aggregation In Marine Systems, Vignesh Gokuladas Menon

Dartmouth College Master’s Theses

Atmospheric dust deposition plays a crucial role in marine biogeochemical cycles, yet mechanisms underlying its impact on particle dynamics remain unclear. This study investigates the synergistic interactions between marine heterotrophic bacteria and clay minerals in seawater, focusing on their effect on Transparent Exopolymer Particles (TEP) production and organoclay aggregation. Field experiments in the Gulf of Maine and laboratory roller tank studies were conducted using natural microbial communities and model heterotrophic bacterial strains (Alteromonas sp. EZ55, Marinobacter adhaerens HP15, and Sulfitobacter sp. NAS-14.1). Results demonstrate that clay exposure significantly enhances TEP production by bloom-associated heterotrophic bacteria, with increases up to …

Scale And Habitat Effects On Measurement Of Streptomyces Biogeography And Biodiversity, Terilyn A. Stoflet

Cal Poly Humboldt theses and projects

Bacteria in the genus Streptomyces are detected in most soils around the world, as well as on and in seeds, plants, animals, insects and the wind. Currently, more than 700 valid species of Streptomyces have been identified worldwide. Streptomyces produce the majority of antibiotics, antivirals and antifungals, as well as important agricultural bioactive molecules due to their unique genetic capabilities. Their distinct genetic abilities allow them to produce an unlimited amount of biosynthetic gene clusters, or BGC’s. Although many compounds come from Streptomyces, scientists have not discovered the biogeographic patterns of this genus. The biogeography of Streptomyces is a …

Listeria Adhesion Protein Orchestrates Caveolae-Mediated Apical Junctional Remodeling Of Epithelial Barrier For Listeria Monocytogenes Translocation, Rishi Drolia, Donald B. Bryant, Shivendra Tenguria, Zuri A. Jules-Culver, Jessie Thind, Breanna Amelunke, Donqi Liu, Nicholas L. F. Gallina, Krishna K. Mishra, Manalee Samaddar, Manoj R. Sawale, Dharmendra K. Mishra, Abigail D. Cox, Arun K. Bhunia

Biological Sciences Faculty Publications

The cellular junctional architecture remodeling by Listeria adhesion protein-heat shock protein 60 (LAP-Hsp60) interaction for Listeria monocytogenes (Lm) passage through the epithelial barrier is incompletely understood. Here, using the gerbil model, permissive to internalin (Inl) A/B-mediated pathways like in humans, we demonstrate that Lm crosses the intestinal villi at 48 h post-infection. In contrast, the single isogenic (lap− or ΔinlA) or double (lap−ΔinlA) mutant strains show significant defects. LAP promotes Lm translocation via endocytosis of cell-cell junctional complex in enterocytes that do not display luminal E-cadherin. In comparison, InlA facilitates …

Salmonella Detection In Food Using A Hek-Htlr5 Reported Cell-Based Sensor, Esma Eser, Victoria A. Felton, Rishi Drolia, Arun K. Bhunia

Biological Sciences Faculty Publications

The development of a rapid, sensitive, specific method for detecting foodborne pathogens is paramount for supplying safe food to enhance public health safety. Despite the significant improvement in pathogen detection methods, key issues are still associated with rapid methods, such as distinguishing living cells from dead, the pathogenic potential or health risk of the analyte at the time of consumption, the detection limit, and the sample-to-result. Mammalian cell-based assays analyze pathogens’ interaction with host cells and are responsive only to live pathogens or active toxins. In this study, a human embryonic kidney (HEK293) cell line expressing Toll-Like Receptor 5 (TLR-5) …

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 …

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. …

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

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

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 …

Paper-Based Ratiometric Sensor Array For Pathogenic Bacterial Species Identification, Aayushi Laliwala

Theses & Dissertations

Bacterial infections are the leading cause of mortality worldwide due to the lack of accurate diagnosis of the pathogens causing infections. Currently, microbiological and molecular techniques are used to identify pathogenic bacteria. However, these techniques have limitations as they are time-consuming, cost-inefficient, and require trained personnel. Therefore, timely and precise identification of pathogenic bacteria is crucial for public safety. Our lab previously synthesized a fluorescent sensor array (3-hydroxyflavone derivatives) encapsulated in hyaluronic acid-based nanoparticles to identify bacterial species and recognize their Gram status. Though promising, this technique was relatively time-consuming and required high sample and volumes.

To overcome these limitations, …

Understanding The Effect Of Chikungunya Virus Infection On Bone Homeostasis, Enakshi Roy

Theses & Dissertations

Chikungunya virus (CHIKV) is a mosquito-borne virus that causes Chikungunya fever (CHIKF), characterized by high fever, headache, rash, and joint pain. With global travel on the rise, infections caused by CHIKV have emerged in new regions, expanding their geographic range and infecting susceptible hosts. Currently, no approved prophylactic or therapeutic measures exist to prevent or treat these infections, with prevention strategies primarily focused on vector control. However, these measures have proven inadequate due to the emergence of mutations that enhance viral transmission or vector range. Therefore, urgent attention is needed to develop therapies to treat the infection. Although CHIKV has …

Synergetic Signaling Between The Chlamydia Secreted Effectors Tarp And Tmea Regulates Actin Kinetics And Efficient Entry, Matthew Romero

Theses & Dissertations

Chlamydia trachomatis is both the leading cause of non-congenital preventable blindness in developing nations and the leading source of bacterial sexually transmitted infections. As an obligate intracellular pathogen, Chlamydia has an absolute requirement on gaining entry into its host, which is accomplished by manipulating the host actin cytoskeleton to assemble engulfment structures that drive pathogen entry. In support of this, Chlamydia secretes the effectors TarP and TmeA via a type-III secretion system, whose respective signaling outputs operate synergistically to generate rapid actin kinetics and efficient pathogen engulfment. Rapid actin recruitment characteristic of invading Chlamydia is derived from a collaborative interaction …

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

Gatekeeping At Bio, Daniel A Gorelick

Faculty, Staff and Students Publications

No abstract provided.

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 …

Establishing A Novel Lipid-Polyamine Metabolic Connection To Virus Replication, Yazmin Edith Cruz Pulido

Dissertations

Polyamines are small positively charged alkylamines found in all living cells. These ubiquitous molecules have been found to play a variety of roles ranging from stabilizing nucleic acids (DNA and RNA) to cellular proliferation. Studies have also identified roles for polyamines in viral packaging and viral enzyme function. However, the role of polyamines on cellular components and their effect on viral replication is less known. In our efforts to identify the lipid-polyamine metabolic connection to virus replication we utilized a human hepatocyte cell line in which polyamines were depleted via pharmacological or genetic approaches and studied the effects on lipid …

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 …

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 …