Open Access. Powered by Scholars. Published by Universities.®
- Discipline
- Institution
- Publication Year
- File Type
Articles 1 - 30 of 41
Full-Text Articles in Microbiology
The Molecular Dimension Of Microbial Species: 3. Comparative Genomics Of Synechococcus Strains With Different Light Responses And In Situ Diel Transcription Patterns Of Associated Putative Ecotypes In The Mushroom Spring Microbial Mat, Millie Olsen, Shane Nowack, Jason Wood, Eric Becraft, Kurt Labutti, Anna Lipzen, Joel Martin, Wendy Shackwitz, Douglas Rusch, Frederick Cohan, Donald Bryant, David Ward
The Molecular Dimension Of Microbial Species: 3. Comparative Genomics Of Synechococcus Strains With Different Light Responses And In Situ Diel Transcription Patterns Of Associated Putative Ecotypes In The Mushroom Spring Microbial Mat, Millie Olsen, Shane Nowack, Jason Wood, Eric Becraft, Kurt Labutti, Anna Lipzen, Joel Martin, Wendy Shackwitz, Douglas Rusch, Frederick Cohan, Donald Bryant, David Ward
Frederick M. Cohan
Genomes were obtained for three closely related strains of Synechococcus that are representative of putative ecotypes that predominate at different depths in the 1 mm-thick, upper-green layer in the 60°C mat of Mushroom Spring, Yellowstone National Park, and exhibit different light adaptation and acclimation responses. The genomes were compared to the published genome of a previously obtained, closely related strain from a neighboring spring, and differences in both gene content and orthologous gene alleles between high-light-adapted and low-light-adapted strains were identified. Evidence of genetic differences that relate to adaptation to light intensity and/or quality, CO2 uptake, nitrogen metabolism, organic carbon …
The Molecular Dimension Of Microbial Species: 1. Ecological Distinctions Among, And Homogeneity Within, Putative Ecotypes Of Synechococcus Inhabiting The Cyanobacterial Mat Of Mushroomspring,Yellowstone National Park, Eric D. Becraft, Jason M. Wood, Douglas B. Rusch, Michael Kuhl, Sheila Jensen, Donald A. Bryant, David W. Roberts, Frederick M. Cohan, David M. Ward
The Molecular Dimension Of Microbial Species: 1. Ecological Distinctions Among, And Homogeneity Within, Putative Ecotypes Of Synechococcus Inhabiting The Cyanobacterial Mat Of Mushroomspring,Yellowstone National Park, Eric D. Becraft, Jason M. Wood, Douglas B. Rusch, Michael Kuhl, Sheila Jensen, Donald A. Bryant, David W. Roberts, Frederick M. Cohan, David M. Ward
Frederick M. Cohan
Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes (encoding a photosystem I reaction center protein subunit) and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species (putative ecotypes), which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper …
Characterization Of Fusobacterium Isolates From The Respiratory Tract Of White-Tailed Deer (Odocoileus Virginianus ), Amit Kumar, Dvm, Ms, Phd
Characterization Of Fusobacterium Isolates From The Respiratory Tract Of White-Tailed Deer (Odocoileus Virginianus ), Amit Kumar, Dvm, Ms, Phd
Amit Kumar, DVM, MS, PhD
A total of 23 clinical isolates of Fusobacterium spp. were recovered at necropsy over a 2-year period from the respiratory tract of white-tailed deer (Odocoileus virginianus). Isolates were identified as Fusobacterium varium (18/23),Fusobacterium necrophorum subsp. funduliforme (3/23), and Fusobacterium necrophorum subsp. necrophorum (2/23). Usingpolymerase chain reaction–based detection of virulence genes, all F. necrophorum isolates were positive for the promoter region of the leukotoxin operon and the hemagglutinin-related protein gene, while all F. varium isolates were negative. The presence of the leukotoxin gene in F. necrophorum isolates and the absence of this gene in F. varium isolates were confirmed by Southern …
Accuracy And Efficiency Of Algorithms For The Demarcation Of Bacterial Ecotypes From Dna Sequence Data, Juan Carlos Francisco, Frederick M. Cohan, Danny Krizanc
Accuracy And Efficiency Of Algorithms For The Demarcation Of Bacterial Ecotypes From Dna Sequence Data, Juan Carlos Francisco, Frederick M. Cohan, Danny Krizanc
Frederick M. Cohan
Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such ‘ecotypes’. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than …
Adhesion Of Fusobacterium Necrophorum To Bovine Endothelial Cells Is Mediated By Outer Membrane Proteins, Amit Kumar
Adhesion Of Fusobacterium Necrophorum To Bovine Endothelial Cells Is Mediated By Outer Membrane Proteins, Amit Kumar
Amit Kumar, DVM, MS, PhD
Fusobacterium necrophorum, a Gram-negative anaerobe, is frequently associated with suppurative and necrotic infections of animals and humans. The organism is a major bovine pathogen, and in cattle, the common fusobacterial infections are hepatic abscesses, foot rot, and necrotic laryngitis. The species comprises two subspecies: F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme. Bacterial adhesion to the host cell surface is a critical initial step in the pathogenesis, and outer membrane proteins (OMP) play an important role in adhesion and establishment of certain Gram-negative bacterial infections. The means by which F. necrophorum attaches to epithelial or endothelial cells has not …
Production Of Nitrogen-Based Platform Chemical: Cyanophycin Biosynthesis Using Recombinant Escherichia Coli And Renewable Media Substitutes, Amit Kumar
Amit Kumar, DVM, MS, PhD
BACKGROUND:Cyanophycin (CGP) is a sustainable polymer that can be converted to a derivative with reduced arginine content, or to completely biodegradable poly-aspartic acid, which can substitute for non-biodegradable polyacrylates. In nature, it is produced by most cyanobacteria; however, these microbes are not suitable for large-scale production due to slow growth and low polymer content. RESULTS: Cyanophycin synthetase gene (cphA) from Anabaena variabilis ATCC 29413 was PCR amplified and cloned into Escherichiacoli.Differentrenewablemediacomponents,suchassoybeanmeal,potatowastesandcorn-derivedzein hydrolysate, were evaluated for their feasibility for CGP production at shake flask level. The optimized conditions were then tested in a 7 L bioreactor; a maximum cell weight of …
Characterization Of Fusobacterium Necrophorum Isolated From Llama And Alpaca, Amit Kumar
Characterization Of Fusobacterium Necrophorum Isolated From Llama And Alpaca, Amit Kumar
Amit Kumar, DVM, MS, PhD
Fusobacterium necrophorum, a Gram-negative, anaerobic bacterium, is an opportunistic animal and human pathogen that causes a variety of infections termed necrobacillosis. There are 2 subspecies of F. necrophorum (subsp. necrophorum and subsp. funduliforme) that differ morphologically and biochemically and in virulence. Leukotoxin, a secreted protein, is considered to be the major virulence factor. In camelids, F. necrophorum causes a variety of infections, generally involving the lips, tongue, pharynx, interdigital spaces, foot pad, larynx, mandible, or maxillary bones. The objective of the current study was to characterize the presumptive Fusobacterium isolates from a variety of necrotic infections in llama (Lama glama) …
Outer Membrane Proteins Of Fusobacterium Necrophorum, Amit Kumar
Outer Membrane Proteins Of Fusobacterium Necrophorum, Amit Kumar
Amit Kumar, DVM, MS, PhD
Fusobacterium necrophorum, classified into subsp. necrophorum (Fnn) and subsp. funduliforme (Fnf), is frequently associated with necrotic infections of animals and humans. The outer membrane proteins (OMP) of many Gram negative bacteria play an important role in bacterial adhesion and establishment of infection. The OMP profile of F. necrophorum has not been well characterized. We analyzed OMP of bovine strains of Fnn and Fnf and human strains of F. necrophorum. Electrophoretic separations of extracted OMP of Fnn and Fnf strains of cattle showed a total of 19 and 20 protein bands, respectively. The most prominent protein band was 40 kDa in …
A New Class Of Homoserine Lactone Quorum-Sensing Signals, Amy Schaefer, E Greenberg, Colin Oliver, Yasuhiro Oda, Jean Huang, Gili Bittan-Banin, Caroline Peres, Silke Schmidt, Katarina Juhaszova, Janice Sufrin, Caroline Harwood
A New Class Of Homoserine Lactone Quorum-Sensing Signals, Amy Schaefer, E Greenberg, Colin Oliver, Yasuhiro Oda, Jean Huang, Gili Bittan-Banin, Caroline Peres, Silke Schmidt, Katarina Juhaszova, Janice Sufrin, Caroline Harwood
Jean J. Huang
Quorum sensing is a term used to describe cell-to-cell communication that allows cell-density-dependent gene expression. Many bacteria use acyl-homoserine lactone (acyl-HSL) synthases to generate fatty acyl-HSL quorum-sensing signals, which function with signal receptors to control expression of specific genes. The fatty acyl group is derived from fatty acid biosynthesis and provides signal specificity, but the variety of signals is limited. Here we show that the photosynthetic bacterium Rhodopseudomonas palustris uses an acyl-HSL synthase to produce p-coumaroyl-HSL by using environmental p-coumaric acid rather than fatty acids from cellular pools. The bacterium has a signal receptor with homology to fatty acyl-HSL receptors …
Acyl‐Hsl Signal Decay: Intrinsic To Bacterial Cell–Cell Communications, Ya-Juan Wang, Jean Huang, Jared Leadbetter
Acyl‐Hsl Signal Decay: Intrinsic To Bacterial Cell–Cell Communications, Ya-Juan Wang, Jean Huang, Jared Leadbetter
Jean J. Huang
No abstract available.
The Acid Stress Response Of The Cyanobacterium Synechocystis Sp. Strain Pcc 6308, Jean Huang, Nancy Kolodny, Jennifer Redfearn, Mary Allen
The Acid Stress Response Of The Cyanobacterium Synechocystis Sp. Strain Pcc 6308, Jean Huang, Nancy Kolodny, Jennifer Redfearn, Mary Allen
Jean J. Huang
The cyanobacterium Synechocystis sp. strain PCC 6308 has been shown to exhibit predictable physiological responses to acid stress. Originally isolated from a Wisconsin lake, this cyanobacterium grows optimally under alkaline conditions in the laboratory. After acid stress at a pH of between 4.4 and 7.7, cells return to exponential growth following a lag phase. The organism's response to this tolerable acid stress involves cell concentration-dependent neutralization of the external medium to pH 6 or above within 5 min, maintenance of a transmembrane pH gradient, and maintenance of photosystem II efficiency. Lethal acid stress, at a pH below 4.4, results in …
Identification Of Quip, The Product Of Gene Pa1032, As The Second Acyl-Homoserine Lactone Acylase Of Pseudomonas Aeruginosa Pao1, Jean Huang, Ashley Petersen, Marvin Whiteley, Jared Leadbetter
Identification Of Quip, The Product Of Gene Pa1032, As The Second Acyl-Homoserine Lactone Acylase Of Pseudomonas Aeruginosa Pao1, Jean Huang, Ashley Petersen, Marvin Whiteley, Jared Leadbetter
Jean J. Huang
The relevance of the acyl homoserine lactone (acyl-HSL) quorum signals N-3-oxododecanoyl-homoserine lactone (3OC12HSL) and N-butanoyl-homoserine lactone to the biology and virulence of Pseudomonas aeruginosa is well investigated. Previously, P. aeruginosa was shown to degrade long-chain, but not short-chain, acyl-HSLs as sole carbon and energy sources (J. J. Huang, J.-I. Han, L.-H. Zhang, and J. R. Leadbetter, Appl. Environ. Microbiol. 69:5941-5949, 2003). A gene encoding an enzyme with acyl-HSL acylase activity, pvdQ (PA2385), was identified, but it was not required for acyl-HSL utilization. This indicated that P. aeruginosa encodes another acyl-HSL acylase, which we identify here. A comparison …
Utilization Of Acyl-Homoserine Lactone Quorum Signals For Growth By A Soil Pseudomonad And Pseudomonas Aeruginosa Pao1, Jean Huang, Jong-In Han, Lian-Hui Zhang, Jared Leadbetter
Utilization Of Acyl-Homoserine Lactone Quorum Signals For Growth By A Soil Pseudomonad And Pseudomonas Aeruginosa Pao1, Jean Huang, Jong-In Han, Lian-Hui Zhang, Jared Leadbetter
Jean J. Huang
Acyl-homoserine lactones (AHLs) are employed by several Proteobacteria as quorum-sensing signals. Past studies have established that these compounds are subject to biochemical decay and can be used as growth nutrients. Here we describe the isolation of a soil bacterium, Pseudomonas strain PAI-A, that degrades 3-oxododecanoyl-homoserine lactone (3OC12HSL) and other long-acyl, but not short-acyl, AHLs as sole energy sources for growth. The small-subunit rRNA gene from strain PAI-A was 98.4% identical to that of Pseudomonas aeruginosa, but the soil isolate did not produce obvious pigments or AHLs or grow under denitrifying conditions or at 42°C. The quorum-sensing bacterium P. aeruginosa, which …
Method Of Identifying Agents That Inhibit Quorum Sensing Activity Of Gamma-Proteobacteria, Jean Huang, Jared Leadbetter
Method Of Identifying Agents That Inhibit Quorum Sensing Activity Of Gamma-Proteobacteria, Jean Huang, Jared Leadbetter
Jean J. Huang
Screening assays that allow for the identification of agents that increase acyl homoserine lactone (AHL) acylase expression and/or AHL acylase activity in γ-proteobacteria such as Pseudomonas aeruginosa. Such agents are useful, for example, for inhibiting quorum sensing activity of such bacteria by increasing degradation of long chain, but not short chain, AHLs and, therefore, can be useful for treating infections by such bacteria.
Production Of Hydrogen Gas From Light And The Inorganic Electron Donor Thiosulfate By Rhodopseudomonas Palustris, Jean Huang
Jean J. Huang
A challenge for photobiological production of hydrogen gas (H2) as a potential biofuel is to find suitable electron-donating feedstocks. Here, we examined the inorganic compound thiosulfate as a possible electron donor for nitrogenase-catalyzed H2 production by the purple nonsulfur phototrophic bacterium (PNSB) Rhodopseudomonas palustris. Thiosulfate is an intermediate of microbial sulfur metabolism in nature and is also generated in industrial processes. We found that R. palustris grew photoautotrophically with thiosulfate and bicarbonate and produced H2 when nitrogen gas was the sole nitrogen source (nitrogen-fixing conditions). In addition, illuminated nongrowing R. palustris cells converted about 80% of available electrons from thiosulfate …
Demarcation Of Bacterial Ecotypes From Dna Sequence Data: A Comparative Analysis Of Four Algorithms, Juan Francisco, Frederick Cohan, Danny Krizanc
Demarcation Of Bacterial Ecotypes From Dna Sequence Data: A Comparative Analysis Of Four Algorithms, Juan Francisco, Frederick Cohan, Danny Krizanc
Frederick M. Cohan
No abstract provided.
Diversity Of Bacteria And Archaea In Hypersaline Sediment From Death Valley National Park, California, J.-S. Kim, M. Makama, J. Petito, N.-H. Park, Frederick M. Cohan, R. S. Dungan
Diversity Of Bacteria And Archaea In Hypersaline Sediment From Death Valley National Park, California, J.-S. Kim, M. Makama, J. Petito, N.-H. Park, Frederick M. Cohan, R. S. Dungan
Frederick M. Cohan
No abstract provided.
The Variable Subdomain Of Escherichia Coli Seca Functions To Regulate Seca Atpase Activity And Adp Release, Sanchaita Das, Lorry M. Grady, Jennifer Michtavy, Yayan Zhou, Frederick M. Cohan, Manju M. Hingorani, Donald B. Oliver
The Variable Subdomain Of Escherichia Coli Seca Functions To Regulate Seca Atpase Activity And Adp Release, Sanchaita Das, Lorry M. Grady, Jennifer Michtavy, Yayan Zhou, Frederick M. Cohan, Manju M. Hingorani, Donald B. Oliver
Frederick M. Cohan
No abstract provided.
Diversity Of Bacteria And Archaea In Hypersaline Sediment From Death Valley National Park, California, J.-S. Kim, M. Makama, J. Petito, N.-H. Park, Frederick M. Cohan, R. S. Dungan
Diversity Of Bacteria And Archaea In Hypersaline Sediment From Death Valley National Park, California, J.-S. Kim, M. Makama, J. Petito, N.-H. Park, Frederick M. Cohan, R. S. Dungan
Frederick M. Cohan
No abstract provided.
Fine-Scale Distribution Patterns Of Synechococcus Ecological Diversity In The Microbial Mat Of Mushroom Spring, Yellowstone National Park, Eric Becraft, Frederick Cohan, Michael Kuhl, Sheila Jensen, David Ward
Fine-Scale Distribution Patterns Of Synechococcus Ecological Diversity In The Microbial Mat Of Mushroom Spring, Yellowstone National Park, Eric Becraft, Frederick Cohan, Michael Kuhl, Sheila Jensen, David Ward
Frederick M. Cohan
No abstract provided.
Catecholamines Increase Conjugative Gene Transfer Between Enteric Bacteria., Amit Kumar
Catecholamines Increase Conjugative Gene Transfer Between Enteric Bacteria., Amit Kumar
Amit Kumar, DVM, MS, PhD
The ability of pathogenic bacteria to sense and respond to periods of host stress is critical to their lifestyle. Adrenaline and norepinephrine are catecholamines that mediate acute host stress in vertebrates and invertebrates. Catecholamines are also used as environmental cues to enhance growth, motility and virulence of bacterial pathogens via specific binding receptors. Incidence of multidrug resistant and highly virulent bacterial pathogens is on the rise, and majority of the genes for antimicrobial resistance (AMR) and virulence are carried on horizontally transferable genetic elements. Conjugation machinery offers an efficient method for acquisition of AMR and virulence genes, which may be …
Influence Of Molecular Resolution On Sequence-Based Discovery Of Ecological Diversity Among Synechococcus Populations In An Alkaline Siliceous Hot Spring Microbial Mat, Melanie C. Melendrez, R. K. Lange, Frederick M. Cohan, David M. Ward
Influence Of Molecular Resolution On Sequence-Based Discovery Of Ecological Diversity Among Synechococcus Populations In An Alkaline Siliceous Hot Spring Microbial Mat, Melanie C. Melendrez, R. K. Lange, Frederick M. Cohan, David M. Ward
Frederick M. Cohan
No abstract provided.
The Ecology Of Speciation In Bacillus, Nora Connor, Johannes Sikorski, Alejandro P. Rooney, Sarah Kopac, Alexander F. Koeppel, Andrew Burger, Scott G. Cole, Elizabeth B. Perry, Danny Krizanc, Nicholas C. Field, Michele Slaton, Frederick M. Cohan
The Ecology Of Speciation In Bacillus, Nora Connor, Johannes Sikorski, Alejandro P. Rooney, Sarah Kopac, Alexander F. Koeppel, Andrew Burger, Scott G. Cole, Elizabeth B. Perry, Danny Krizanc, Nicholas C. Field, Michele Slaton, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.
Tracking Bacterial Responses To Global Warming With An Ecotype-Based Systematics, Frederick M. Cohan
Tracking Bacterial Responses To Global Warming With An Ecotype-Based Systematics, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.
Identifying The Fundamental Units Of Bacterial Diversity: A Paradigm Shift To Incorporate Ecology Into Bacterial Systematics, A. F. Koeppel, E. B. Perry, J. Sikorski, A. Warner, D. M. Ward, A. P. Rooney, E. Brambilla, N. Connor, E. Nevo, R. M. Ratcliff, Frederick M. Cohan
Identifying The Fundamental Units Of Bacterial Diversity: A Paradigm Shift To Incorporate Ecology Into Bacterial Systematics, A. F. Koeppel, E. B. Perry, J. Sikorski, A. Warner, D. M. Ward, A. P. Rooney, E. Brambilla, N. Connor, E. Nevo, R. M. Ratcliff, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.
Toward A Conceptual And Operational Union Of Bacterial Systematics, Ecology, And Evolution, Frederick M. Cohan
Toward A Conceptual And Operational Union Of Bacterial Systematics, Ecology, And Evolution, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.
Cyanobacterial Ecotypes In The Microbial Mat Community Of Mushroom Spring (Yellowstone National Park, Wyoming) As Species-Like Units Linking Microbial Community Composition, Structure And Function, D. M. Ward, M. M. Bateson, M. J. Ferris, M. Kuhl, A. Wieland, A. Koeppel, Frederick M. Cohan
Cyanobacterial Ecotypes In The Microbial Mat Community Of Mushroom Spring (Yellowstone National Park, Wyoming) As Species-Like Units Linking Microbial Community Composition, Structure And Function, D. M. Ward, M. M. Bateson, M. J. Ferris, M. Kuhl, A. Wieland, A. Koeppel, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.
Which Species Concept For Bacteria?—An E-Debate, S. Godreuil, Frederick M. Cohan, H. Shah, M. Tibayrenc
Which Species Concept For Bacteria?—An E-Debate, S. Godreuil, Frederick M. Cohan, H. Shah, M. Tibayrenc
Frederick M. Cohan
No abstract provided.
Gradual Evolution In Bacteria: Evidence From Bacillus Systematics, M. Feldgarden, N. Byrd, Frederick M. Cohan
Gradual Evolution In Bacteria: Evidence From Bacillus Systematics, M. Feldgarden, N. Byrd, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.
What Are Bacterial Species?, Frederick M. Cohan
What Are Bacterial Species?, Frederick M. Cohan
Frederick M. Cohan
No abstract provided.