Microbiology Commons^™

Draft Genome Sequence Of Ruoffia Tabacinasalis Isolated From A Bovine Nasal Swab: A Novel Member Of The Bovine Nasal Microbiota, Samantha Howe, Xiaoyuan Wei, Jasna Kovac, Jiangchao Zhao

Animal Science Faculty Publications and Presentations

We report the isolation and draft genome sequence of Ruoffia tabacinasalis, a novel member of the bovine nasal microbiota. The genome, which is estimated to be 90.5% complete, is composed of one contig comprising 2,363,349 bp with a GC content of 36.66%.

Leaf Diseases And Their Management In Oats, Department Of Primary Industries And Regional Development, Western Australia

Grains and other field crops factsheets

Leaf diseases of oats impact on grain yield and quality and reduce hay quality characteristics, such as colour and digestibility. This page outlines the symptoms, factors favouring disease risk and spread, and management.

Major leaf diseases of oats are septoria avenae blotch, stem rust, leaf rust, and barley yellow dwarf virus. Their severity changes with seasons.

Tulane Virus Persistence And Microbial Stability In 3d Food Ink Under Various Storage Conditions: A Pre- And Post-Printing Analysis, Allyson N. Hamilton, Kristen E. Gibson

Food Science Faculty Publications and Presentations

3D food printers facilitate novel customization of the physicochemical properties of food. This study aimed to investigate the impact of storage conditions on the inactivation of the human norovirus surrogate, Tulane virus (TuV), within 3D printed foods. TuV-inoculated protein cookie food ink (∽ 4 log PFU/g) was distributed into 18 3D food printer capsules (50 g each); half immediately underwent extrusion. Storage of the capsules and printed food products at 20 °C (0, 6, 12, and 24 h), 4 °C (0, 1, 3, and 5d), and − 18 °C (0, 1, 3, and 5d) was completed before analysis for TuV …

Complete Genome Sequence Of An Indian Outbreak Strain Of Chikungunya Virus, Eshna Laha, Deepak Jena, Viplov K. Biswas, Sharad Singh, Sunil K. Raghav, Asit K. Pattnaik, Soma Chattopadhyay

Nebraska Center for Virology: Faculty Publications

Here, we report the complete genome sequence of an Indian strain of chikungunya virus isolated from an infected patient from Hyderabad, Andhra Pradesh, India, during a massive outbreak in 2005–2006. The genome length spans 11,811 nucleotides and has a poly(A) tail of 29 residues at the 3′ end.

Horizontal Gene Transfer In Intergenomic Conflicts Between Bacteria And Their Genetic Parasites, Pavithra A.S

Theses and Dissertations

Bacteria are constantly infected by obligate acellular genetic parasites, such as plasmids and phages. The genetic conflicts between bacteria and their parasites, aggravated by horizontal gene transfer, exert significant ecological and evolutionary pressure on their respective genomes. The eco-evolutionary significance of parasite-derived elements on bacterial genomes is not well understood.

This study explored the genomics of plasmid-derived genetic elements such as antimicrobial resistance genes (ARGs), type II endonuclease toxin-antitoxin systems (TAs) and endonuclease colicin-like bacteriocin (CLB) operons, and phage-derived prophages of Escherichia coli using bioinformatics and developing novel hybrid agent-based models. We sequenced eight E. coli isolated from local wastewater …

Antibiotic-Resistant Gram-Negative Bacteria In A Local Wastewater Treatment Plant In North Georgia, Nou Moua, Lindsay Mccuen, Sarah White, Swapna Bhat, Margi Flood, Jeanelle Morgan

Georgia Journal of Science

Antibiotics are some of the most essential lifesaving drugs currently available to us against infectious diseases. Several pathogens are developing resistance to these drugs and many have become resistant to multiple antibiotics. Such multi-drug resistance is becoming a global issue and has been found in many environments including wastewater treatment plants (WWTPs). In this study, we sampled a local WWTP for antibiotic-resistant bacteria. This WWTP is in North Georgia and runs directly into Lake Lanier, which is the main source of drinking water for the Atlanta area as well as a popular spot for water recreation. We obtained treated and …

Avicennia Marina Mangrove Plant Mediated Selenium Nanoparticles And Their Therapeutic Activity Against Oral Pathogens And Other Biological Properties, Kannan Kamala, Pitchiah Sivaperumal, Dhanraj Ganapathy

Journal of Dentistry Indonesia

In the last few decades nanoparticles are widely used in the control of many pathogenic bacteria, fungi, viruses, and cancer growth both in-vitro and in-vivo. A marine plant of Avicennia marina is widely used in traditional medicine for diabetes, inflammation and skin diseases. Objective: In general Avicennia marina has been used as a traditional medicine to treat various diseases and it has shown significant inhibition against various pathogen and the formation of free radicals. Also, the plant A.marina mediated selenium nanoparticles has therapeutic activity has promising to develop biocompatible new cost effective treatment for various oral diseases. Methods: …

Using Origami And Shrinky Dinks To Create Active Learning Activities To Tackle Two Microbiology Concepts: Cell Structure Differences And Operon Regulation, Manuela Tripepi, Hannah M. Schapiro

College of Life Sciences Faculty Papers

This paper presents two low-cost hands-on activities designed to enhance student understanding and address the pedagogical challenges faced by microbiology professors in teaching concepts related to cell structure and gene regulation. In the first activity, we used Shrinky Dinks and Jeopardy-style game questions to explore the differences between prokaryotic and eukaryotic cells. Students have to collect pieces and physically build their cell models. The second activity uses origami organelles sets from Edvotek to illustrate the regulation of gene expression in the lac and trp operons, incorporating mutation scenarios for analysis. The intended audience comprises undergraduate students in microbiology, including biology, …

Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2, John Vincent Mcguire

Electronic Theses and Dissertations

The SARS-CoV-2 virus was recently able to cause a global pandemic, largely due to the asymptomatic period that occurs during initial infection. During this period, patients are infectious but do not exhibit symptoms, resulting in the unintentional spread of the virus. This occurs because the virus effectively avoids detection by the immune system during the early stages of infection, and as symptoms are the result of immune system activation, they never manifest. Non-structural Protein 15 (Nsp15) is one of the tools the virus uses to remain undetected, via its degradation of Pathogen-Associated Molecular Patterns (PAMPs) that would otherwise be recognized …

Multidrug-Resistant Esbl-Producing Escherichia Coli Coexisting With Colistin-Resistance Genes In Pig Farms, Central Thailand, Wipawee Songsaeng, Nutthee Am-In, Nuvee Prapasarakul, Wandee Sirichokchatchawan

The Thai Journal of Veterinary Medicine

The presence of extended-spectrum beta-lactamase and colistin resistance E. coli in food-producing animals is a public health concern. This study was conducted using a rigorous methodology to survey the prevalence of ESBL-producing and colistin-resistant E. coli from pig farms in the central part of Thailand. A total of 519 samples were collected from fecal, feed, and waste in 53 farms located in central Thailand. All samples were inoculated onto selective agar, and species identification was performed using biochemical assays and MAlDI-TOF MS. Antimicrobial susceptibility was determined by broth microdilution, and ESBL production was confirmed by the combination disc diffusion method. …

Development Of A Urothelial Cell Line Expressing A Caspase-1 Biosensor To Measure Cellular Inflammatory Responses To Potential Uropathogens, Nikita Riya Kesav

Master's Theses

Urinary tract infections are one of the most common bacterial infections, historically implicating Escherichia coli as the causative pathogen. However, it is now known that there are a variety of bacteria that exist within the urinary tract, acting as either beneficial uroprotectives or opportunistic uropathogens. Furthermore, there are significant gaps in our understanding as to how these bacteria interact with the urothelium and what role each plays in maintaining or disrupting homeostasis. Research has shown that Toll-like receptor 4 (TLR4) signaling and Nod-like Receptor Protein 3 play a role in inflammasome activation during infection, triggering caspase-1 activation and inducing release …

Investigating The Roles Of Sirtuins During Cvb3 Infection And Innate Immunity, Bridget M. Hulsebosch

Master's Theses

Coxsackievirus B3 (CVB3) is an enterovirus that chronically infects heart tissue, leading to dilated cardiomyopathy. However, no vaccines or antivirals exist for CVB3 infection or to treat CVB3-induced dilated cardiomyopathy, except for a heart transplant. Sirtuins (SIRTs), class III lysine deacetylases, have diverse and complex roles in cellular functions, contributing to energy production, NF-κB signaling, cell cycle regulation, and inflammation. Previous studies showed that SIRTs are essential for hepatitis B and A viral replication and regulate the IFN response during viral infection. However, the role of SIRT1 and 2 during CVB3 infection is entirely unknown. CVB3-infected SIRT1 and SIRT2 knockout …

Elucidating Enterococcal Mechanisms Underlying Recurrent Urinary Tract Infections, Baylie Hochstedler-Kramer

Dissertations

Urinary tract infection (UTI) is one of the most common bacterial infections globally and can lead to life-threatening complications. UTI disproportionately affects females, with the majority of females being treated for at least one UTI in their lifetime. Of the females who develop UTI in their lifetime, almost one third will develop recurrence within six months after initial treatment and many will struggle with UTI recurrence for long spans of their lives. Although recurrent UTI has previously been attributed to persistence of Escherichia coli, recent studies utilizing more sensitive detection methods have shown Enterococcus faecalis is strongly associated with recurrent …

Time-Transgressive Microbial Diversity In A Tropical Bat Guano Accumulation, Deer Cave, Mulu, Borneo, Joyce Lundberg, Donald A. Mcfarlane

International Journal of Speleology

Bat guano accumulations in caves can constitute large deposits of organic material, particularly chitin and its degradation products, that host a diverse microbiome. Previous microbiological studies have not addressed the stratified nature of these deposits in the context of the timeframe of the decomposition process. We present such data (temperature, pH, DNA sampling of eight carbon-dated strata) for a 75 cm-deep tropical guano accumulation that undergoes complete decomposition over a timescale of ~120 years. The aerobic, surface layer of freshly-fallen guano has the greatest diversity of taxa, with Bacteroidota co-dominant with Pseudomonadota, and includes many taxa unique to this …

The Experience Of Homelessness And Its Effects On Gut Eubiosis, Kamerin Villagomez

University Honors Theses

Microorganisms which populate the human gastrointestinal tract (GIT) have a profound effect on overall human health. The relationship between host health and eubiosis, or balance, of the GIT microbiome is symbiotic and can have reciprocal relationships with quality of sleep, quality of diet, stress and mental health, and the experience of pain. These specific aspects of health are unique in populations experiencing homelessness due to the multi-dimensional and complex nature of their lived experience. Very few studies explore populations experiencing homelessness, with even fewer investigating the intersection between this population and the human GIT microbiome. It is important to do …

Investigating The Presence Of Bacterial Phytoplasma Disease In Grasses Of Central Texas And Their Associated Hemiptera, Danielle Rios

Masters Theses (Archived)

No abstract provided.

The Molecular Detection Of Hemotropic Mycoplasma Species In Dogs, Hafize Tuğba Yüksel Dolgun, Şükrü Kirkan

The Thai Journal of Veterinary Medicine

Hemotropic mycoplasmas are uncultured bacteria that cause different degrees of hemolytic anemia in infected hosts. Molecular approaches are used to diagnose hemotropic mycoplasmas since they are difficult to identify using conventional methods. The aim of this study was to use molecular approaches to determine hemotropic mycoplasmas in dogs. Blood samples were collected in tubes (with EDTA) from 100 dogs. After DNA extraction, 100 DNA samples were investigated by PCR. Hemotropic mycoplasma was detected in 12 (12%) samples and positive samples were subjected to Sanger sequencing. Mycoplasma haemocanis was detected in 6 (50.0%) of the samples, Candidatus Mycoplasma hematoparvum in 5 …

Targeting Aspergillus Fumigatus Hypoxia Response Pathways For Novel Antifungal Drug Development., Cecilia Gutierrez Perez

Dartmouth College Ph.D Dissertations

Invasive fungal disease present are difficult to diagnose and treat and present a high mortality rate across the world with approximately 1.5 million people a year succumbing to fungal infections worldwide. Currently, there are limited antifungal classes used therapeutically, and antifungal drug resistance on the rise further exacerbates the dire need for novel therapeutics with innovative mode of actions. The filamentous fungi, Aspergillus fumigatus is the causative agent of invasive pulmonary aspergillosis (IPA). It is estimated that contemporary antifungals fail in about 50% of patients with invasive filamentous fungal infections, likely due to the biofilm mode of growth exhibited in …

Microbial Phosphate Solubilization Mechanisms In P Solubilizing In Andisol, Agustina Erlinda Marpaung, Tengku Sabrina, Abdul Rauf, Dwi Ningsih Susilowati, Luthfi Aziz Mahmud Siregar

Jurnal Kultivasi

Phosphate (P) nutrient plays a significant role in plant growth and yield. P is an essential element that plays an important role in photosynthesis and root development. Phosphate nutrient availability is deficient in some soil types due to retention, such as in Andisol soil types. High phosphate retention in Andisol soil types causes P nutrients to be unavailable to plants and can reduce crop yields. The availability of P in Andisol soils can be done, among others, by applying phosphate solubilizing microbes. Phosphate solubilizing microorganisms are soil microorganisms consisting of bacteria and fungi that can mineralize organic P, dissolve inorganic …

Inactivated Rabies-Based Lassa Fever Virus Vaccine Candidate Lassarab Protects Nonhuman Primates From Lethal Disease, Gabrielle Scher, Catherine Yankowski, Drishya Kurup, Nicole Josleyn, Eric Wilkinson, Jay Wells, Jesse Steffens, Ginger Lynn, Sean Vantongeren, Xiankun Zeng, Nancy Twenhafel, Kathleen Cashman, Matthias Schnell

Department of Microbiology and Immunology Faculty Papers

Lassa fever virus (LASV), a member of the Arenavirus family, is the etiological agent of Lassa fever, a severe hemorrhagic disease that causes considerable morbidity and mortality in the endemic areas of West Africa. LASV is a rodent-borne CDC Tier One biological threat agent and is on the World Health Organization's (WHO) Priority Pathogen list. Currently, no FDA-licensed vaccines or specific therapeutics are available. Here, we describe the efficacy of a deactivated rabies virus (RABV)-based vaccine encoding the glycoprotein precursor (GPC) of LASV (LASSARAB). Nonhuman primates (NHPs) were administered a two-dose regimen of LASSARAB or an irrelevant RABV-based vaccine to …

Rna Secondary Structures: Structure-Function Studies In Viral And Neurodegenerative Diseases, Caylee Cunningham

Electronic Theses and Dissertations

The studies within this dissertation highlight the importance of RNA structure and function, highlighting potential mechanisms in the pathogenesis of the SARS-CoV-2 virus and hallmarks of ALS. Specifically, the s2m, a 41-nt structure found within the hyper variable region of the 3’ UTR of the SARS-CoV-2 virus, was investigated as this element has no definitive role in viruses but its high conservation in several viral families warrants investigation. We used various biophysical techniques to determine if a palindromic sequence in the terminal loop could participate in dimerization activities, which may have implications in recombination and the longevity of the virus. …

Growth Response Of Tomatoes To Application Of Bacterial-Coated Npk Fertilizer In A Pot Experiment, Reginawanti Hindersah, Ruhnayati Kaffah, Ayu Siti Aisyah, Mieke Rochimi Setiawati, Mahfud Arifin

Jurnal Kultivasi

Nitrogen-fixer and phosphate-solubilizer bacteria increase the chemical-fertilizer efficiency and soil health. Bacterial-coated NPK fertilizer is a novel approach for intensifying biofertilizer application in vegetable production. The study aimed to observe the compatibility between two Azotobacter species and two Bacillus species, their population on two formulations of bacterial-coated NPK fertilizer (BCN), and the effect of BCN dose on growth, N and P content, and their uptake in tomato shoots. The compatibility test was performed using the streak method. The population of Azotobacter and Bacillus were counted for two formulations of NPK fertilizer coated by solid biofertilizer (5% and 10%) and zeolite …

Growth Improvement Of Immature Quinine By Applying Coffee Husk Compost And Biofertilizer, Yudithia Maxiselly, Dinda Rachmatis Sa'adah, Mira Ariyanti, Muhammad Khais Prayoga, Heri Syahrian Khomaeni

Jurnal Kultivasi

The growth of immature Cinchona ledgeriana can be optimized by applying fertilizers to fill the nutritional needs of plants. Nutrients can be provided through the help of microorganisms derived from organic fertilizers and biofertilizers. This study aims to evaluate the effect of applying coffee husk compost and biofertilizer consortium on the growth of immature quinine plants. This research was conducted from November 2023 – January 2024 at Gambung Tea and Cinchona Research Center, Pasir Jambu District, Bandung Regency, West Java. The research used a randomized block design with four replications and six treatments, namely control (Urea 17 g.plant-1 + SP36 …

Exploring The Interaction Between Klebsiella Pneumoniae And Clostridioides Difficile At The Mucosal Interface, Taylor D. Ticer

MUSC Theses and Dissertations

The gut microbiota plays a major role in human diseases. The impact of these microbes on human health comes not only from individual microbes but also from their interactions with each other. A prime example of this is Clostridioides difficile, an intestinal pathobiont that causes severe gastrointestinal illness. C. difficile works cooperatively with other gut bacteria, including Klebsiella pneumoniae. We hypothesized that K. pneumoniae would work synergistically with C. difficile and promote its pathogenesis. We screened over 40 K. pneumoniae strains to assess their interaction with the intestinal mucus layer, a key colonization site for C. difficile. …

The Role Of Efflux Pump Inhibitor In Enhancing Antimicrobial Efficiency Of Silver Nanoparticles And Methylene Blue As An Effective Photodynamic Therapy Agent, Yaran Allamyradov

Masters Theses & Specialist Projects

Efflux pumps are critical active transport systems utilized by cells to expel toxic substances, including antibiotics and photosensitizer complexes, thereby contributing to antimicrobial resistance. Efflux pump inhibitors (EPIs), which are compounds that obstruct the transport of molecules through these pumps, play a pivotal role in enhancing the effectiveness of antimicrobial therapies against pathogens. This study investigates the effects of the EPI reserpine on the photodeactivation rate of pathogens when used in conjunction with silver nanoparticles (Ag NPs) and methylene blue (MB), a common photosensitizer.

Our research reveals that the application of reserpine, in combination with Ag NPs and MB, leads …

Lanthanide-Dependent Methanol Metabolism In Sinorhizobium Meliloti, Enish Pathak

Masters Theses

Lanthanides, also known as rare earth elements, were thought to be biologically inert. However, the recent discovery of XoxF, a lanthanide-dependent methanol dehydrogenase, shed new light on the roles of lanthanides in biology. Lanthanide-dependent methanol metabolism was even found in bacterial genera that previously have not been described as methylotrophs, including Sinorhizobium. A homolog of the xoxF gene was found to be present in Sinorhizobium meliloti. S. meliloti is a soil bacterium that undergoes a symbiotic relationship with alfalfa plants by fixing atmospheric nitrogen within root nodules. While many studies on lanthanide-dependent methylotrophy have been performed mainly in the model …

Functional Characterization Of A Lncrna Afu-254 In Stress Response And Pathogenesis Of Aspergillus Fumigatus, Ritu Devkota

All Theses

Aspergillus fumigatus is a saprophytic fungus that can cause a collection of diseases termed aspergillosis; the most severe is invasive pulmonary aspergillosis (IPA). Azole is a major class of antifungal drugs used to treat invasive pulmonary aspergillosis. However, in recent years, there has been an increase in fungal resistance to azole drugs, making the treatment of IPA even more challenging. It is becoming increasingly clear that long non-coding RNAs (lncRNAs), i.e., the RNAs that do not translate into proteins, mediated regulation is vital in stress response and pathogenesis; however, the mechanisms of how lncRNA contribute to fungal stress resistance and …

Phylogenomic Analyses Of Three Distinct Lineages Uniting Staphylococcus Cohnii Snd Staphylococcus Urealyticus From Diverse Hosts, L. Caroline House, Amer Hasan, Andi Asnayanti, Adnan A. Alrubaye, Jeff Pummill, Douglas Rhoads

Poultry Science Faculty Publications and Presentations

We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50–440 kbp. The transfer of a 186 kbp region from …

Evaluating The Impact Of The Poultrystar®Bro Probiotic On The Incidence Of Bacterial Chondronecrosis With Osteomyelitis Using The Aerosol Transmission Challenge Model, Ruvindu Perera, Khawla Alharbi, Amer Hasan, Andi Asnayanti, Anh Dang Trieu Do, Abdulkarim Shwani, Raj Murugesan, Shelby Ramirez, Michael Kidd, Adnan A. Alrubaye

Poultry Science Faculty Publications and Presentations

Bacterial chondronecrosis with osteomyelitis (BCO) lameness is a major welfare issue for broiler production worldwide affecting approximately 1.5% of broilers over 42 days old. Excessive body weight gain causes mechanical stress on long bones, leading to micro-fractures. This condition induces a bacterial infection of fractures, resulting in bone necrosis and eventual BCO lameness. Increasing gut integrity and supporting Calcium metabolism contribute to the optimal bone structure and subsequently reduce BCO lameness. Probiotics thus provide an excellent strategy for alleviating BCO due to the improvement of intestinal integrity and barrier function. Accordingly, the present study investigated the lameness reduction through the …

Manipulation Of Cellular Proliferating Cell Nuclear Antigen (Pcna) During Herpes Simplex Virus Type 1 Infection, Jessica Packard, Jill A. Dembowski

Electronic Theses and Dissertations

Herpes simplex virus type 1 (HSV-1) is a double stranded DNA virus that replicates within the nucleus of host cells. Using accelerated native isolation of proteins on nascent DNA (aniPOND), cellular proteins were found to associate with HSV-1 replication forks. One host factor of interest is proliferating cell nuclear antigen (PCNA), the DNA sliding clamp that tethers DNA polymerases and DNA damage response proteins to replicating cellular DNA. Although HSV-1 encodes its own DNA polymerase processivity factor (UL42), PCNA plays a key role in HSV-1 infection. We used commercially available PCNA inhibitors and short hairpin RNAs (shRNA) to investigate how …