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When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki 2021 CUNY City College

When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki

Publications and Research

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic …


Mining Selected Metagenomes/Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes, Ahmed Yamany 2021 American University in Cairo

Mining Selected Metagenomes/Metatranscriptomes For Biosynthetic Gene Clusters And Antimicrobial Resistance Genes, Ahmed Yamany

Theses and Dissertations

Antimicrobial resistance is one of the serious global challenges in the current century. The fact that resistance genes transfer between bacteria, coupled with the fact that the world is connected through complex dynamics. Studying microbial behavior and understanding the different factors coffering microbial resistance to a broad spectrum of the available drug classes, parallel with a comprehensive analysis of the natural microbial products as the primary source of the novel antibiotics, might shed some light on solutions for this problem. Microbial environments harbor a wide range of secondary metabolites (SM) with different functional groups. SMs are not directly involved in …


Mfd Affects Global Transcription And The Physiology Of Stressed Bacillus Subtilis Cells, Holly Anne Martin, Anitha Sundararajan, Tatiana S. Ermi, Robert Heron, Jason Gonzales, Kaiden Lee, Diana Anguiano-Mendez, Faye Schilkey, Mario Pedraza-Reyes, Eduardo A. Robleto 2021 University of Nevada, Las Vegas

Mfd Affects Global Transcription And The Physiology Of Stressed Bacillus Subtilis Cells, Holly Anne Martin, Anitha Sundararajan, Tatiana S. Ermi, Robert Heron, Jason Gonzales, Kaiden Lee, Diana Anguiano-Mendez, Faye Schilkey, Mario Pedraza-Reyes, Eduardo A. Robleto

Life Sciences Faculty Publications

© Copyright © 2021 Martin, Sundararajan, Ermi, Heron, Gonzales, Lee, Anguiano-Mendez, Schilkey, Pedraza-Reyes and Robleto. For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found …


Inhibition Of Biofilm Formation By The Synergistic Action Of Egcg-S And Antibiotics, Shrameeta Shinde, Lee Lee, Tinchun Chu 2021 Miami University - Oxford

Inhibition Of Biofilm Formation By The Synergistic Action Of Egcg-S And Antibiotics, Shrameeta Shinde, Lee Lee, Tinchun Chu

Department of Biology Faculty Scholarship and Creative Works

Biofilm, a stress-induced physiological state, is an established means of antimicrobial tolerance. A perpetual increase in multidrug resistant (MDR) infections associated with high mortality and morbidity have been observed in healthcare settings. Multiple studies have indicated that the use of natural products can prevent bacterial growth. Recent studies in the field have identified that epigallocatechin gallate (EGCG), a green tea polyphenol, could disrupt bacterial biofilms. A modified lipid-soluble EGCG, epigallocatechin-3-gallate-stearate (EGCG-S), has enhanced the beneficial properties of green tea. This study focuses on utilizing EGCG-S as a novel synergistic agent with antibiotics to prevent or control biofilm. Different formulations of …


A Peek Inside The Machines Of Bacterial Nucleotide Excision Repair, Thanyalak Kraithong, Silas Hartley, David Jeruzalmi, Danaya Pakotiprapha 2021 Mahidol University

A Peek Inside The Machines Of Bacterial Nucleotide Excision Repair, Thanyalak Kraithong, Silas Hartley, David Jeruzalmi, Danaya Pakotiprapha

Publications and Research

Double stranded DNA (dsDNA), the repository of genetic information in bacteria, archaea and eukaryotes, exhibits a surprising instability in the intracellular environment; this fragility is exacerbated by exogenous agents, such as ultraviolet radiation. To protect themselves against the severe consequences of DNA damage, cells have evolved at least six distinct DNA repair pathways. Here, we review recent key findings of studies aimed at understanding one of these pathways: bacterial nucleotide excision repair (NER). This pathway operates in two modes: a global genome repair (GGR) pathway and a pathway that closely interfaces with transcription by RNA polymerase called transcription-coupled repair (TCR). …


Investigating The Development Of Fecal Bacterial Communities In Growing Dairy Calves, Emily Fowler 2021 South Dakota State University

Investigating The Development Of Fecal Bacterial Communities In Growing Dairy Calves, Emily Fowler

Electronic Theses and Dissertations

The gut development of young calves is crucial for the producer and the calf's future. Many factors can affect the development of a young calf's gastrointestinal system, and there has been little research into the fecal microbiome development of calves from 0 to 12 weeks of age. To gain further insight into this process, development of the fecal microbiome in 12 dairy calves was investigated. Fecal bacterial composition was determined at four time points (weeks 0, 4, 8 and 12) using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from fecal microbial genomic DNA, followed by Illumina MiSeq …


The Influence Of Infant Formula On The Growth Of Commensal And Pathogenic Streptococcus Species In The Infant Oral Cavity, Geneva Waynick 2021 Hollins University

The Influence Of Infant Formula On The Growth Of Commensal And Pathogenic Streptococcus Species In The Infant Oral Cavity, Geneva Waynick

Undergraduate Honors Theses

The oral microbiome is a complex community of microorganisms that can both reflect and greatly influence the health of the human host. A number of diseases are associated with dysbiotic oral microflora in infants and children, including dental (e.g. dental caries, gingivitis, and periodontal disease), and gastrointestinal diseases (e.g. pediatric appendicitis, celiac disease, and pediatric inflammatory bowel disease). A variety of factors can influence the composition of the oral microbial community in infants, including gestation length, mode of delivery, feeding method, and diet. This study focuses on the effects of diet on the growth of a commensal bacterium (Streptococcus …


Circadian Rhythmicity And Melatonin Sensitivity In The Human Gut Commensal Bacterium Klebsiella Aerogenes, Kinga Graniczkowska 2021 University of Kentucky

Circadian Rhythmicity And Melatonin Sensitivity In The Human Gut Commensal Bacterium Klebsiella Aerogenes, Kinga Graniczkowska

Theses and Dissertations--Biology

While the expression of circadian rhythms is nearly universal among multicellular eukaryotic organisms, demonstration of this phenomenon in prokaryotes has been largely restricted to photosynthetic cyanobacteria until very recently. Further, growing interest in gastrointestinal microbiomes has revealed a complex temporal relationship between the gastrointestinal clock and the bacterial microbiome within. At least one member of the gut microbiome, Klebsiella (née Enterobacter) aerogenes, responds to the indoleamine hormone melatonin, secreted by the gastrointestinal system itself. Further research revealed that K. aerogenes also expresses a circadian rhythm in motility and gene expression that is temperature compensated. Although rhythmicity is unaltered …


Comparing Capabilities Of Shewanella Oneidensis Mr-1 And The Microbial Community Of Iron Caves To Reduce Fe(Iii), Aaron Douglas Pham 2021 University of Akron

Comparing Capabilities Of Shewanella Oneidensis Mr-1 And The Microbial Community Of Iron Caves To Reduce Fe(Iii), Aaron Douglas Pham

Williams Honors College, Honors Research Projects

Caves are generally formed by the erosion and/or dissolution of rock and its subsequent removal by water. Iron ore caves (IOCs) form despite being hosted by relatively insoluble and weathering-resistant rock. Due to the discovery of a microbial community behind the walls of these caves, it was hypothesized that these bacteria could be responsible for speleogenesis. Iron ore exists in an oxidized (Fe(III)) state, but reduced (Fe(II)) form is soluble. It was further reasoned that the bacteria might be able to reduce Fe(III) through direct metabolic activity, which uses iron as an electron acceptor. Here we show that cave microorganisms …


Il-36g Cytokine Induction In Oral Epithelial Cells Triggered By Treponema Denticola And Their Role In Chronic Periodontitis, Christopher Blake 2021 Virginia Commonwealth University

Il-36g Cytokine Induction In Oral Epithelial Cells Triggered By Treponema Denticola And Their Role In Chronic Periodontitis, Christopher Blake

Theses and Dissertations

Periodontal disease is a polymicrobial disease affecting 10-15% of the population. Periodontal disease affects the quality of life by reducing mastication and potentially causing tooth loss. Periodontal disease is also linked to more severe, systemic diseases such as cardiovascular disease and rheumatoid arthritis. Development of the diseased state occurs when the plaque biofilm shifts from healthy to dysbiotic. The shift to a dysbiotic biome brings with it a shift in bacterial presence, specifically an increase in gram-negative bacteria, such as T. denticola. T. denticola is a gram-negative, anaerobic spirochete whose relationship with oral epithelial cells is poorly understood. Preliminary data …


Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė 2021 Old Dominion University

Advancing Cyanobacteria Biomass Estimation From Hyperspectral Observations: Demonstrations With Hico And Prisma Imagery, Ryan E. O'Shea, Nima Pahlevan, Brandon Smith, Mariano Bresciani, Todd Egerton, Claudia Giardino, Lin Li, Tim Moore, Antonio Ruiz-Verdu, Steve Ruberg, Stefan G.H. Simis, Richard Stumpf, Diana Vaičiūtė

Biological Sciences Faculty Publications

Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆Rrs) resulting from atmospheric correction and instrument radiometric noise. Although several individual algorithms have been proven to capture local variations in cyanobacteria biomass in specific regions, their performance has not been assessed on hyperspectral images from satellite sensors. Our work leverages a machine-learning model, Mixture Density Networks (MDNs), trained on a large (N = 939) dataset of collocated in situ chlorophyll-a concentrations (Chla), …


Pandemic Vibrio Cholerae Shuts Down Site-Specific Recombination To Retain An Interbacterial Defence Mechanism, Francis J. Santoriello, Lina Michel, Daniel Unterweger, Stefan Pukatzki 2020 CUNY City College

Pandemic Vibrio Cholerae Shuts Down Site-Specific Recombination To Retain An Interbacterial Defence Mechanism, Francis J. Santoriello, Lina Michel, Daniel Unterweger, Stefan Pukatzki

Publications and Research

Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily …


Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted 2020 University of Tennessee, Knoxville

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …


Examining Pathogenesis And Preventatives In Spontaneous And Staphylococcus-Induced Bacterial Chondronecrosis With Osteomyelitis In Broilers, Nnamdi Simon Ekesi 2020 University of Arkansas, Fayetteville

Examining Pathogenesis And Preventatives In Spontaneous And Staphylococcus-Induced Bacterial Chondronecrosis With Osteomyelitis In Broilers, Nnamdi Simon Ekesi

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis is the most important cause of lameness in broilers. This is important to poultry production, as it poses animal welfare issues, and causes a significant loss in revenue. The remediation of this disease requires the study of its etiology with fitting models and evaluating preventatives. The research reported herein covers genomic virulence analysis of BCO isolates, mainly Staphylococcus aureus, and Escherichia coli retrieved from lame birds. We found that S. aureus isolates were closest to chicken strains in Europe but may have been in the Arkansas area for a decade. Phylogenomics suggest our S. aureus is …


Molecular Detection Of Host-Specific Fecal Bacteria In Three Major Watersheds Of Piedmont Georgia, Muhammad Amar 2020 Georgia College

Molecular Detection Of Host-Specific Fecal Bacteria In Three Major Watersheds Of Piedmont Georgia, Muhammad Amar

Biology Theses

Abstract

Fecal pollution is a major concern in creeks and rivers. The aim of this study was to enumerate fecal coliform bacteria and identify the source of contamination using Microbial Source Tracking at three different creeks (Mountain Oak, Long Cane, and Ulcohatchee) in the Piedmont region of Georgia. Data collected in this research will be used to formulate watershed rehabilitation plans to decrease the transfer of fecal indicator bacteria (FIB) into these creeks. Samples were collected at several sites along the creeks (4 sites at Mountain Oak, 10 sites at Long Cane, and 5 sites at Ulcohatchee). The site locations …


Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier 2020 University of Tennessee, Knoxville

Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier

Masters Theses

Subaerial biofilms (SABs) grow at the interface between the atmosphere and rock surfaces in terrestrial and subterranean environments around the world. Multi-colored SABs colonizing relatively dry and nutrient-limited cave surfaces are known to contain microbes putatively involved in chemolithoautotrophic processes using inorganic carbon like carbon dioxide (CO2) or methane (CH4). However, the importance of CO2 and CH4 to SAB biomass production has not been quantified, the environmental conditions influencing biomass production and diversity have not been thoroughly evaluated, and stable carbon and nitrogen isotope compositions have yet to be determined from epigenic cave SABs. …


Exploring The Niche Of Rickettsia Montanensis (Rickettsiales: Rickettsiaceae) Infection Of The American Dog Tick (Acari: Ixodidae), Using Multiple Species Distribution Model Approaches, Catherine A. Lippi, Holly Gaff, Alexis L. White, Heidi K. St. John, Allen L. Richards, Sadie J. Ryan 2020 Old Dominion University

Exploring The Niche Of Rickettsia Montanensis (Rickettsiales: Rickettsiaceae) Infection Of The American Dog Tick (Acari: Ixodidae), Using Multiple Species Distribution Model Approaches, Catherine A. Lippi, Holly Gaff, Alexis L. White, Heidi K. St. John, Allen L. Richards, Sadie J. Ryan

Biological Sciences Faculty Publications

The American dog tick, Dermacentor variabilis (Say) (Acari: Ixodidae), is a vector for several human diseasecausing pathogens such as tularemia, Rocky Mountain spotted fever, and the understudied spotted fever group rickettsiae (SFGR) infection caused by Rickettsia montanensis. It is important for public health planning and intervention to understand the distribution of this tick and pathogen encounter risk. Risk is often described in terms of vector distribution, but greatest risk may be concentrated where more vectors are positive for a given pathogen. When assessing species distributions, the choice of modeling framework and spatial layers used to make predictions are important. …


The Role Of The Msaabcr Operon In Implant-Associated Chronic Osteomyelitis In Staphylococcus Aureus Usa300 Lac, Gyan S. Sahukhal, Michelle Tucci, Hamed Benghuzzi, Gerri Wilson, Mohamed O. Elasri 2020 University of Southern Mississippi

The Role Of The Msaabcr Operon In Implant-Associated Chronic Osteomyelitis In Staphylococcus Aureus Usa300 Lac, Gyan S. Sahukhal, Michelle Tucci, Hamed Benghuzzi, Gerri Wilson, Mohamed O. Elasri

Faculty Publications

The msaABCR operon regulates several staphylococcal phenotypes such as biofilm formation, capsule production, protease production, pigmentation, antibiotic resistance, and persister cells formation. The msaABCR operon is required for maintaining the cell wall integrity via affecting peptidoglycan cross-linking. The msaABCR operon also plays a role in oxidative stress defense mechanism, which is required to facilitate persistent and recurrent staphylococcal infections. Staphylococcus aureus is the most frequent cause of chronic implant-associated osteomyelitis (OM). The CA-MRSA USA300 strains are predominant in the United States and cause severe infections, including bone and joint infections.


Increasing Antibiotic Resistance In Shigella Bacteria In The United States, William J. Pharr 2020 Georgia College and State University

Increasing Antibiotic Resistance In Shigella Bacteria In The United States, William J. Pharr

The Corinthian

Shigella bacteria cause half a million infections, 6,000 hospitalizations, and 70 deaths annually in the United States. These bacteria are of particular concern due to their high survivability, low infectious dose, and high adaptability. Cases of shigellosis from Shigella sonnei are becoming a more prevalent issue in the U.S. as the bacteria continues to develop higher resistance to today’s strongest antibiotics. Much of this resistance is connected to the exchange of genes between strains of Shigella due to insertion sequences (IS), intercontinental travel, and men who have sex with men (MSM). As a result of increased resistance, the use of …


Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík 2020 Comenius University in Bratislava

Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The aim of this work was to evaluate the transformation of manganese oxide (hausmannite) by microscopic filamentous fungus Aspergillus niger and the effects of the transformation on mobility and bioavailability of arsenic. Our results showed that the A. niger strain CBS 140837 greatly affected the stability of hausmannite and induced its transformation into biogenic crystals of manganese oxalates—falottaite and lindbergite. The transformation was enabled by fungal acidolysis of hausmannite and subsequent release of manganese ions into the culture medium. While almost 45% of manganese was bioextracted, the arsenic content in manganese precipitates increased throughout the 25-day static cultivation of fungus. …


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