Microbiology Commons^™

Mycobacterial Contamination Of Bronchoscopes: Challenges And Possible Solutions In Low Resource Settings, Dania Khalid Saeed, Sadia Shakoor, Seema Irfan, Rumina Hasan

Department of Pathology and Laboratory Medicine

The use of bronchoscopes has increased in tuberculosis (TB) diagnostics to circumvent the diagnostic challenges that are associated with low sputum volume and smear-negative TB. In healthcare facilities situated in low income countries that have a high burden of TB, adequate decontamination of bronchoscopes is a challenge and often overlooked to save on time and costs. This amplifies the risk of outbreaks and pseudo-outbreaks due to Mycobacterium tuberculosis and nontuberculosis mycobacteria. In this minireview, we review published literature of contaminated bronchoscopes causing pseudo-outbreaks of M. tuberculosis and nontuberculosis mycobacteria in an effort to determine common sources, and possible mitigation strategies …

Pulmonary Infections After Tuberculosis, Kauser Jabeen

Department of Pathology and Laboratory Medicine

Aims and Objective: Despite effective treatment of pulmonary tuberculosis (TB) patients, destruction of lung parenchyma may lead to complications including repeated infections. These infections are often misdiagnosed or wrongly identified as TB recurrence, and hence are not treated effectively. The frequency and severity of these infections vary with the extent of damage, and are much more prominent in patients with post-TB bronchiectasis and fibrocavitary diseases. This presentation will focus on the epidemiology, treatment, and management of post-TB infections and challenges, and the impact of these infections on public health in high-TB-burden countries.
Methods: Published literature and review articles were evaluated …

Tuberculosis In Vulnerable Populations In Eastern Mediterranean Region-Implications For Control, Sadia Shakoor, Rumina Hasan

Department of Pathology and Laboratory Medicine

Objectives: Socially and economically disadvantaged or "vulnerable" people are at high risk of tuberculosis (TB) and also contribute to active chains of TB transmission. Included in such vulnerable populations are children, women, prisoners, people living with human immunodeficiency virus, the homeless, and displaced people. The ongoing active transmission of TB among such populations is made more difficult to assess and control by difficult access, health inequities, poverty, and other chronic and debilitating health conditions at individual, domestic, and community levels.
Methods: The 22 Eastern Mediterranean Region member states encompass diverse sociopolitical and socioeconomic situations with far-reaching effects on vulnerable populations …

Massive Pulmonary Embolism Presenting As Seizures, Shahrukh Hashmani, Fateh Ali Tipoo Sultan, Murtaza Kazmi, Amammarah Yasmeen

Department of Pathology and Laboratory Medicine

Pulmonary embolism can present in various ways, though seizure activity has been rarely reported. We report a 38 years old male who had met a road traffic accident, underwent surgery, presented a month later with seizures, chest pain, shortness of breath and low blood pressure. Massive pulmonary embolism was diagnosed on CTPA, with classical features on ECG and echocardiogram and the patient was successfully managed with thrombolysis. Massive pulmonary embolism (MPE) should be kept in mind in patients who present with seizures, chest pain and haemodynamic instability.

Alternate Efflux Pump Mechanism May Contribute To Drug Resistance In Extensively Drug-Resistant Isolates Of Mycobacterium Tuberculosis, Akbar Kanji, Rumina Hasan, Ambreen Zaver, Asho Ali, Kehkashan Imtiaz, Mussarat Ashraf, Taane G. Clark, Ruth Mc Nerney, Samreen Shafiq, Zahra Hasan

Department of Pathology and Laboratory Medicine

No abstract provided.

The Role Of Streptococcus Gallolyticus Subspecies Gallolyticus In Colon Cancer Development, Jennifer L. Herold

Dissertations and Theses (Open Access)

Colorectal cancer (CRC) is the third most common cancer in men and women and is also the third most common cause of cancer death. A large body of evidence points towards the possibility that bacteria can have a significant impact on the development of cancer. It has been suggested that Streptococcus gallolyticus subsp. gallolyticus, a group D streptococci, may play a role in the development of CRC. Sg, formerly S. bovis biotype I, has been shown to be highly associated with CRC. In observing patients with either Sg bacteremia or endocarditis it was found that 25-80% of …

Oral Microbial Burden Of Periodontal Pathogens Among Orthodontic Patients, David Jolley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Objectives

Many research studies involving orthodontic patients have a natural inclination to focus on changes in levels of cariogenic pathogens after bracket placement, and very few studies examine the role of changes of periodontal pathogens – particularly among adult patients. Interestingly, recent evidence suggests that increased levels of a specific periodontal pathogen, Fusobacterium nucleatum, may elevate risk for development of colon cancer in adults through direct pathways. Based upon this new evidence, the objective of the current study was to screen saliva samples taken from orthodontic patients to determine the prevalence of periodontal pathogens, including F. Nucleatum, T. denticola, and …

Development Of The K-State (Competence) And Mutagenesis In Stressed Bacillus Subtillis Cells, Amanda Kidman

UNLV Theses, Dissertations, Professional Papers, and Capstones

Mutagenesis is central to the evolutionary process. We currently view evolution as a gradual process affecting all cells within a population. However, my project studied an underestimated part of the evolutionary process: mutations generated during stationary phase (caused by nutritional stress or growth arrest) within a subpopulation of cells. I used Bacillus subtilis, a bacterial model for cell growth and differentiation. Stationary-phase cultures of B. subtilis differentiate subpopulations that exhibit different survival strategies including competence, secondary metabolite production, biofilm formation, cannibalism, and endospore formation. The development of competence permits cells to uptake exogenous DNA and incorporate it into their genome. …

Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate

Biology Faculty Publications and Presentations

Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the …

Visualizing A Plant Cell, Rudaba R. Hasan

The Transdisciplinary STEAM+ Journal

Why visualizing science is important, especially as a school student.

The Subject Librarian Newsletter, Biology, Fall 2016, Sandy Avila

Libraries' Newsletters

No abstract provided.

Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates …

Current Antibiotics And Future Herbal Extract Methods To Treat Methicillin-Resistant Staphylococcus Aureus (Mrsa): Focusing On Inhibition Of Penicillin-Binding Protein 2a (Pbp2a), Mgayya R. Makullah

Senior Honors Theses

Methicillin-Resistant Staphylococcus aureus (MRSA) has developed resistance towards a number of antibiotics. This resistance creates a challenge when trying to treat MRSA with a number of antibiotics. This is mainly caused by the penicillin-binding proteins 2a (PBP2a). PBP2a have significantly less affinity for beta-lactam antibiotics compared to the other penicillin-binding proteins (PBPs) expressed by non-resistant strains. New treatments involving a combination of antibiotics and herbal extracts are being developed and used to inactivate PBP2a, allowing the previous ineffective antibiotics to be more effective.

Otopathogenic Pseudomonas Aeruginosa Enters And Survives Inside Macrophages, Rahul Mittal, Christopher V. Lisi, Hansi Kumari, M'Hamed Grati, Patricia Blackwelder, Denise Yan, Chaitanya Jain, Kalai Mathee, Paulo H. Weckwerth, Xue Zhong Liu

Biology Faculty Articles

Otitis media (OM) is a broad term describing a group of infectious and inflammatory disorders of the middle ear. Despite antibiotic therapy, acute OM can progress to chronic suppurative otitis media (CSOM) characterized by ear drum perforation and purulent discharge. Pseudomonas aeruginosa is the most common pathogen associated with CSOM. Although, macrophages play an important role in innate immune responses but their role in the pathogenesis of P. aeruginosa-induced CSOM is not known. The objective of this study is to examine the interaction of P. aeruginosa with primary macrophages. We observed that P. aeruginosa enters and multiplies inside human …

Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe

Bioinformatics Faculty Publications

A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N₅₀ of 109,831 bp.

Quantitative Proteomic Profiling Reveals Hepatic Lipogenesis And Liver X Receptor Activation In The Pander Transgenic Model., Mark G. Athanason, Whitney A. Ratliff, Dale Chaput, Catherine B. Marelia, Melanie N. Kuehl, Stanley M. Stevens Jr., Brant R. Burkhardt

Molecular Biosciences Faculty Publications

PANcreatic-DERived factor (PANDER) is a member of a superfamily of FAM3 proteins modulating glycemic levels by metabolic regulation of the liver and pancreas. The precise PANDER-induced hepatic signaling mechanism is still being elucidated and has been very complex due to the pleiotropic nature of this novel hormone. Our PANDER transgenic (PANTG) mouse displays a selective hepatic insulin resistant (SHIR) phenotype whereby insulin signaling is blunted yet lipogenesis is increased, a phenomena observed in type 2 diabetes. To examine the complex PANDER-induced mechanism of SHIR, we utilized quantitative mass spectrometry-based proteomic analysis using Stable Isotope Labeling by Amino Acids in Cell …

Plant-Biocrust Interactions Mediated By The Fungal Loop, Eva Dettweiler-Robinson

Biology ETDs

Plant-microbial interactions influence biogeochemical cycles. Plants and biological soil crusts are primary producers in drylands. Biocrusts include cyanobacteria, lichens, mosses, algae, fungi, bacteria, and archaea on the soil surface, some of which fix atmospheric nitrogen. I investigated controls on biocrust carbon fluxes and their contribution to ecosystem fluxes, the incorporation of plant-derived carbon into biocrusts, and the role of soil fungi in promoting performance of plants and biocrusts. Biocrusts responded to temperature and moisture differently by biome. Biocrusts in grasslands/shrublands contributed >25% of total summertime ecosystem respiration, but biocrusts in savannas/woodlands contributed < 1%. Biocrusts contributed < 2% to GPP in any biome. To augment their native photosynthesis, biocrusts may include 16% plant-derived carbon. Fungal connections improved plant and biocrust performance and reduced differences in the CN ratio between organisms compared to when connections were impeded. Investigation of interactions among biocrusts, plants, and fungi has improved understanding of resource cycling in drylands.

Pepper Mild Mottle Virus As A Surrogate For Enteric Viruses: Implications For Assessing Water Quality, Erin Michelle Symonds

USF Tampa Graduate Theses and Dissertations

Less than 10% of the world’s domestic wastewater is disinfected prior to discharge into surface waters; therefore, human exposure to diverse wastewater-related pathogens results in millions of cases of illness each year. Among the enteric pathogens, viruses represent an important group of emerging pathogens and are frequently the cause of food- and water-borne outbreaks of illness. Although the World Health Organization and many government agencies mandate the use of bacterial indicators to identify poor microbial water quality, it is well known that these indicators poorly correlate with fecal pollution contamination events and risk of disease. The field of public health-related …

Overlap In The Seasonal Infection Patterns Of Avian Malaria Parasites And West Nile Virus In Vectors And Hosts, Matthew Medeiros, Robert Ricklefs, Jeffrey Brawn, Marilyn Ruiz, Tony Goldberg, Gabriel Hamer

Biology Department Faculty Works

Multiple vector-borne pathogens often circulate in the same vector and host communities, and seasonal infection dynamics influence the potential for pathogen interactions. Here, we explore the seasonal infection patterns of avian malaria (Haemosporida) parasites (Plasmodium and Haemoproteus) and West Nile virus (WNV) in birds and mosquitoes in suburban Chicago. We show that both pathogens vary seasonally in Culex mosquitoes and avian hosts, but that patterns of covariation are complex. Different putative Plasmodium species varied asynchronously across the season in mosquitoes and birds, suggesting that different forces may govern their transmission. Infections of Culex mosquitoes with Plasmodium parasites were positively associated …

Ebola Vp40 In Exosomes Can Cause Immune Cell Dysfunction, Michelle Pleet, Allison Mathiesen, Catherine Demarino, Yao Akpamagbo, Robert Barclay, Sergey N. Iordanskiy, +6 Additional Authors

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Ebola virus (EBOV) is an enveloped, ssRNA virus from the family Filoviridae capable of causing severe hemorrhagic fever with up to 80–90% mortality rates. The most recent outbreak of EBOV in West Africa starting in 2014 resulted in over 11,300 deaths; however, long-lasting persistence and recurrence in survivors has been documented, potentially leading to further transmission of the virus. We have previously shown that exosomes from cells infected with HIV-1, HTLV-1 and Rift Valley Fever virus are able to transfer viral proteins and non-coding RNAs to naïve recipient cells, resulting in an altered cellular activity. In the current manuscript, we …

Transcriptomic Analysis Implicates The P53 Signaling Pathway In The Establishment Of Hiv-1 Latency In Central Memory Cd4 T Cells In An In Vitro Model, Cory White, Bastiaan Moesker, Nadejda Beliakova-Bethell, Laura Martins, Celsa Spina, Alberto Bosque, +4 Additional Authors

Microbiology, Immunology, and Tropical Medicine Faculty Publications

The search for an HIV-1 cure has been greatly hindered by the presence of a viral reservoir that persists despite antiretroviral therapy (ART). Studies of HIV-1 latency in vivo are also complicated by the low proportion of latently infected cells in HIV-1 infected individuals. A number of models of HIV-1 latency have been developed to examine the signaling pathways and viral determinants of latency and reactivation. A primary cell model of HIV-1 latency, which incorporates the generation of primary central memory CD4 T cells (TCM), full-length virus infection (HIVNL4-3) and ART to suppress virus replication, was used to investigate the …

P16ink4a Expression And Immunologic Aging In Chronic Hiv Infection, Susan Ribeiro, Jeffrey Milush, Edecio Cunha-Neto, Esper Kallas, Jorge Kalil, Luiz Felipe D. Passero, Peter W. Hunt, Steven Deeks, Douglas F. Nixon, Devi Sengupta

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Chronic HIV infection is characterized by increased immune activation and immunosenescence. p16 INK4a (p16) is a member of the cyclin-dependent kinase antagonist family that inhibits cellular proliferation, and its protein expression increases during normal chronological aging. However, some infectious diseases can increase the expression of this anti-proliferative protein, potentially accelerating immunological aging and dysfunction. In order to investigate the immunological aging in HIV patients, p16 protein expression was evaluated by flow cytometry, in T cell subsets in a cohort of chronically HIV-infected patients on and off ART as well as age-matched healthy controls. Results showed that untreated HIV-infected subjects exhibited …

Chemokine Levels In The Penile Coronal Sulcus Correlate With Hiv-1 Acquisition And Are Reduced By Male Circumcision In Rakai, Uganda., Jessica L Prodger, Ronald H Gray, Brett Shannon, Kamnoosh Shahabi, Xiangrong Kong, Kate Grabowski, Godfrey Kigozi, Fred Nalugoda, David Serwadda, Maria J Wawer, Steven J Reynolds, Cindy M. Liu, Aaron A R Tobian, Rupert Kaul

Environmental and Occupational Health Faculty Publications

Individual susceptibility to HIV is heterogeneous, but the biological mechanisms explaining differences are incompletely understood. We hypothesized that penile inflammation may increase HIV susceptibility in men by recruiting permissive CD4 T cells, and that male circumcision may decrease HIV susceptibility in part by reducing genital inflammation. We used multi-array technology to measure levels of seven cytokines in coronal sulcus (penile) swabs collected longitudinally from initially uncircumcised men enrolled in a randomized trial of circumcision in Rakai, Uganda. Coronal sulcus cytokine levels were compared between men who acquired HIV and controls who remained seronegative. Cytokines were also compared within men before …

Methods To Assess The Direct Interaction Of C. Jejuni With Mucins, Julie Ann Naughton, Marguerite Clyne, Gina Duggan, Billy Bourke

Books/Book chapters

Studies of the interaction of bacteria with mucus secreting cells can be complemented at a more mechanistic level by exploring the interaction of bacteria with purified mucins. Here we describe a far western blotting approach to show how C. jejuni proteins separated by SDS PAGE and transferred to a membrane or slot blotted directly onto a membrane can be probed biotinylated mucin. In addition we describe the use of novel mucin microarrays to assess bacterial interactions with mucins in a high throughput manner.

Microbiology, Openstax, Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Brian M. Forster, Philip Lister

Open Educational Resources Collection

Microbiology covers the scope and sequence requirements for a single-semester microbiology course for non-majors. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of the text make the material interesting and accessible while maintaining the career-application focus and scientific rigor inherent in the subject matter. Microbiology’s art program enhances students’ understanding of concepts through clear and effective illustrations, diagrams, and photographs.

Microbiology is produced through a collaborative publishing agreement between OpenStax and the American Society for Microbiology Press. The book aligns with the curriculum guidelines of the …

A Cryab Interactome Reveals Clientele Specificity And Dysfunction Of Mutants Associated With Human Disease, Whitney Katherine Hoopes

Theses and Dissertations

Small Heat Shock Proteins (sHSP) are critical molecular chaperones that function to maintain protein homeostasis (proteostasis) and prevent the aggregation of other proteins during cellular stress. Any disruption in the process of proteostasis can lead to prevalent diseases ranging from cancer and cataract to cardiovascular and Alzheimer's disease. CryAB (αB-crystallin, HspB5) is one of ten known human sHSP that is abundant in the lens, skeletal, and cardiac muscle. This protein is required for cardiac function and muscle cell integrity. When the cell experiences physiological stress, including heat shock, CryAB moves to the cytoskeleton to act as a chaperone and prevent …

The Roles Of Biotin In Candida Albicans Physiology, Nur Ras Aini Ahmad Hussin

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

Due to the increased number of immunocompromised patients, infections by Candida albicans have significantly increased in recent years. C. albicans transition from yeast to germ tubes is an essential factor for virulence. In this study we noted that Lee's medium, commonly used to induce filamentation, contained 500-fold more biotin than needed for growth. Thus, we investigated the effects of excess biotin on growth rate and filamentation by C. albicans in different media. At 37 °C, excess biotin (4 µM) enhanced germ tube formation (GTF) ca. 10-fold in both Lee's medium and a defined glucose proline medium, and ca. …

Genetic And Biochemical Analysis Of The Micrococcin Biosynthetic Pathway, Philip Ross Bennallack

Theses and Dissertations

Declining antibiotic discovery and flourishing antibiotic resistance have led to a modern antibiotic crisis which threatens to compromise our ability to treat infectious disease. Consequently, there is significant interest in developing new antibiotics with novel modes of action and chemical properties. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural compounds with the appealing attributes of being derived directly from a genetic template while possessing numerous exotic chemical features that contribute to stability and antimicrobial activity. Abundant in nature, their diverse range of biological activities makes them excellent prospects for antibiotic development. Thiopeptides, a RiPP family rich in chemical complexity, …

Computing And Applying Atomic Regulons To Understand Gene Expression And Regulation, Jose P. Faria, James J. Davis, Janaka N. Edirisinghe, Ronald C. Taylor, Pamela B. Weisenhorn, Robert D. Olson, Rick Stevens, Miguel Rocha, Isabel Rocha, Aaron A. Best, Matthew Dejongh, Nathan L. Tintle, Bruce Parrelo, Ross Overbeek, Christopher S. Henry

Faculty Work Comprehensive List

Understanding gene function and regulation is essential for the interpretation prediction and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets Atomic Regulons ARs represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes and to enable rational genetic engineering of cellular systems. Here we describe an approach for inferring ARs that leverages large-scale expression data sets gene context and functional …

Characterization Of Antimicrobial Activity Of Culturable Bacteria Isolated From Krubera-Voronja Cave, Aiste Klusaite, Vida Vickackaite, Birute Vaitkeviciene, Rasa Karnickaite, Dominykas Bukelskis, Ieva Kieraite-Aleksandrova, Nomeda Kuisiene

International Journal of Speleology

In the present study we aimed to perform the first analysis of antimicrobial activity of bacteria isolated from Krubera-Voronja Cave, with the main focus on their activity against Grampositive bacteria, including Gram-positive pathogens. Using five different media, in total 874 heterotrophic cultures were isolated from water and sediment samples collected in Krubera-Voronja Cave at a depth from 220 m to 1640 m. 14.0% of all isolates demonstrated antibacterial activity against Gram-positive and Gram-negative test microorganisms. Our results show that this percentage was not uniform; it increased with the sampling depth and was the highest in the lower part of the …