Microbiology Commons^™

Investigations Of Potential Microbial Methanogenic And Carbon Monoxide Utilization Pathways In Ultra-Basic Reducing Springs Associated With Present-Day Continental Serpentinization: The Tablelands, Nl, Can, P. Morrill, W. Brazelton, L. Kohl, A. Rietze, S. Miles, H. Kavanagh, M. Schrenk, S. Ziegler, Susan Lang

Susan Q. Lang

Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface environment with H2 and CH4 present. Very little, however, is known about the carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms that live in this ultra-basic environment. The potential for microbial methanogenesis with bicarbonate, formate, acetate, and propionate precursors and carbon monoxide (CO) utilization pathways were tested in laboratory experiments by adding substrates to water and sediment from the Tablelands, NL, CAD, a site of present-day continental serpentinization. Microbial methanogenesis was not observed after bicarbonate, formate, acetate, or propionate addition. …

Positive Selection Drives Preferred Segment Combinations During Influenza Virus Reassortment, Konstantin Zeldovich, Ping Liu, Nicholas Renzette, Matthieu Foll, Serena Pham, Sergey Venev, Glen Gallagher, Daniel Bolon, Evelyn Kurt-Jones, Jeffrey Jensen, Daniel Caffrey, Celia Schiffer, Timothy Kowalik, Jennifer Wang, Robert Finberg

Celia A. Schiffer

Influenza A virus (IAV) has a segmented genome that allows for the exchange of genome segments between different strains. This reassortment accelerates evolution by breaking linkage, helping IAV cross species barriers to potentially create highly virulent strains. Challenges associated with monitoring the process of reassortment in molecular detail have limited our understanding of its evolutionary implications. We applied a novel deep sequencing approach with quantitative analysis to assess the in vitro temporal evolution of genomic reassortment in IAV. The combination of H1N1 and H3N2 strains reproducibly generated a new H1N2 strain with the hemagglutinin and nucleoprotein segments originating from H1N1 …

A Computational Analysis Of The Structural Determinants Of Apobec3'S Catalytic Activity And Vulnerability To Hiv-1 Vif, Shivender Shandilya, Markus-Frederik Bohn, Celia Schiffer

Celia A. Schiffer

APOBEC3s (A3) are Zn(2+) dependent cytidine deaminases with diverse biological functions and implications for cancer and immunity. Four of the seven human A3s restrict HIV by 'hypermutating' the reverse-transcribed viral genomic DNA. HIV Virion Infectivity Factor (Vif) counters this restriction by targeting A3s to proteasomal degradation. However, there is no apparent correlation between catalytic activity, Vif binding, and sequence similarity between A3 domains. Our comparative structural analysis reveals features required for binding Vif and features influencing polynucleotide deaminase activity in A3 proteins. All Vif-binding A3s share a negatively charged surface region that includes residues previously implicated in binding the highly-positively …

Effects Of Temperature, Nutrients, Organic Matter And Coral Mucus On The Survival Of The Coral Pathogen, Serratia Marcescens, Erin Looney, Kathryn Sutherland, Erin Lipp

Kathryn Patterson Sutherland PhD

Serratia marcescens is an enteric bacterium that causes white pox disease in elkhorn coral, Acropora palmata; however, it remains unclear if the pathogenic strain has adapted to seawater or if it requires a host or reservoir for survival. To begin to address this fundamental issue, the persistence of strain PDL100 was compared among seawater and coral mucus microcosms. Median survival time across all conditions ranged from a low of 15 h in natural seawater [with a first-order decay constant (k) = −0.173] at 30°C to a maximum of 120 h in glucose-amended A. palmata mucus (k = −0.029) at 30°C. …

Human Sewage Identified As Likely Source Of White Pox Disease Of The Threatened Caribbean Elkhorn Coral, Kathryn Sutherland, James Porter, Jeffrey Turner, Brian Thomas, Erin Looney, Trevor Luna, Meredith Meyers, J. Futch, Erin Lipp

Kathryn Patterson Sutherland PhD

Caribbean elkhorn coral, Acropora palmata, has been decimated in recent years, resulting in the listing of this species as threatened under the United States Endangered Species Act. A major contributing factor in the decline of this iconic species is white pox disease. In 2002, we identified the faecal enterobacterium, Serratia marcescens, as an etiological agent for white pox. During outbreaks in 2003 a unique strain of S. marcescens was identified in both human sewage and white pox lesions. This strain (PDR60) was also identified from corallivorious snails (Coralliophila abbreviata), reef water, and two non-acroporid coral species, Siderastrea siderea and Solenastrea …

Human Pathogen Shown To Cause Disease In The Threatened Elkhorn Coral Acropora Palmata, Kathryn Patterson Sutherland, Sameera Shaban, Jessica L. Joyner, James W. Porter, Erin K. Lipp

Kathryn Patterson Sutherland PhD

Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments …

The Shellfish Corner -- Vibrios And Shellfish, Michael Rice

Michael A Rice

Pathogenic Vibrios are becoming an increasing problem for shellfish producers in North America and elsewhere. This paper reviews current research into the pathogenic nature of Vibrios and provides some practical advice for avoiding the propagation of Vibrios on shellfish farms nd in wild harvest molluscan shellfish.

Isolation And Characterization Of Microalgae Strains For Live Food In Sulawesi, Indonesia, Wa Iba, Michael Rice

Michael A Rice

Four strains of diatoms were isolated from the waters of Kendari Bay in Southeast Sulawesi, Indonesia, including strains of Melosira moniliformis, Chaetoceros, sp. and a larger species that is likely to be Tetraselmis weissflogii. Isolated strains have exhibited a wide range of salinity tolerances in the 20 to 35 psu range. Strains of isolated phytoplankton were able to reach high densities consistent with strains suitable for use as aquaculture feeds. One strain Kbl-3 attained lipid content of 22.3 percent per gram dry weight at salinity of 35 psu, suggesting that it may be a good feed for shrimp larvae. Most …

Antiviral Activity Of Theaflavin Digallate Against Herpes Simplex Virus Type 1, Aline De Oliveira, Derek Prince, Chih-Yu Lo, Lee Lee, Tin-Chun Chu

Tin-Chun Chu, Ph.D.

Tea is the second most consumed drink in the world. The beneficial effects of tea have been mostly attributed to its catechin content. Black tea is derived from the leaves of Camellia sinensis plant, and it is rich in theaflavin polyphenols, in particular theaflavin (TF1), theaflavin-3-monogallate (TF2A), theaflavin-3′-monogallate (TF2B), and theaflavin-3,3′-digallate (TF3). Vero and A549 cells were used to evaluate the effect of purified individual black tea theaflavins as anti-herpes simplex virus 1 agents. With the rise of HSV resistant strains, there is a critical need to develop novel antiherpesviral treatments. Results of the cytotoxicity assay tested by MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium] …

Evolution Of The Influenza A Virus Genome During Development Of Oseltamivir Resistance In Vitro, Nicholas Renzette, Daniel Caffrey, Konstantin Zeldovich, Ping Liu, Glen Gallagher, Daniel Aiello, Alyssa Porter, Evelyn Kurt-Jones, Daniel Bolon, Yu-Ping Poh, Jeffrey Jensen, Celia Schiffer, Timothy Kowalik, Robert Finberg, Jennifer Wang

Glen R. Gallagher

Influenza A virus (IAV) is a major cause of morbidity and mortality throughout the world. Current antiviral therapies include oseltamivir, a neuraminidase inhibitor that prevents the release of nascent viral particles from infected cells. However, the IAV genome can evolve rapidly, and oseltamivir resistance mutations have been detected in numerous clinical samples. Using an in vitro evolution platform and whole-genome population sequencing, we investigated the population genomics of IAV during the development of oseltamivir resistance. Strain A/Brisbane/59/2007 (H1N1) was grown in Madin-Darby canine kidney cells with or without escalating concentrations of oseltamivir over serial passages. Following drug treatment, the H274Y …

The Shellfish Corner--Shellfish Sanitation And The Price Of Shellfish, Michael A. Rice

Michael A Rice

Prices of raw molluscan shellfish in different countries around the world are tied to perceived risk of becoming ill if consumed. Wholesale prices of oysters in the southern New England from 1880 to 2010 are analyzed in relation to introduction of flush toilets and sewer systems in the early 20th Century, the initiation of the US National Shellfish Sanitation Program in 1925 and renewed consumer interest in consuming raw shellfish in the latter half of the 20th Century.

Evolution Of The Influenza A Virus Genome During Development Of Oseltamivir Resistance In Vitro, Nicholas Renzette, Daniel R. Caffrey, Konstantin B. Zeldovich, Ping Liu, Glen R. Gallagher, Daniel Aiello, Alyssa J. Porter, Evelyn A. Kurt-Jones, Daniel N. Bolon, Yu-Ping Poh, Jeffrey D. Jensen, Celia A. Schiffer, Timothy F. Kowalik, Robert W. Finberg, Jennifer P. Wang

Celia A. Schiffer

Influenza A virus (IAV) is a major cause of morbidity and mortality throughout the world. Current antiviral therapies include oseltamivir, a neuraminidase inhibitor that prevents the release of nascent viral particles from infected cells. However, the IAV genome can evolve rapidly, and oseltamivir resistance mutations have been detected in numerous clinical samples. Using an in vitro evolution platform and whole-genome population sequencing, we investigated the population genomics of IAV during the development of oseltamivir resistance. Strain A/Brisbane/59/2007 (H1N1) was grown in Madin-Darby canine kidney cells with or without escalating concentrations of oseltamivir over serial passages. Following drug treatment, the H274Y …

A Sensitive Assay Using A Native Protein Substrate For Screening Hiv-1 Maturation Inhibitors Targeting The Protease Cleavage Site Between The Matrix And Capsid, Sook-Kyung Lee, Nancy Cheng, Emily Hull-Ryde, Marc Potempa, Celia Schiffer, William Janzen, Ronald Swanstrom

Celia A. Schiffer

The matrix/capsid processing site in the HIV-1 Gag precursor is likely the most sensitive target to inhibit HIV-1 replication. We have previously shown that modest incomplete processing at the site leads to a complete loss of virion infectivity. In the study presented here, a sensitive assay based on fluorescence polarization that can monitor cleavage at the MA/CA site in the context of the folded protein substrate is described. The substrate, an MA/CA fusion protein, was labeled with the fluorescein-based FlAsH (fluorescein arsenical hairpin) reagent that binds to a tetracysteine motif (CCGPCC) that was introduced within the N-terminal domain of CA. …

Interview With Celia Schiffer, Celia Schiffer

Celia A. Schiffer

Celia Schiffer, a Professor in Biochemistry and Molecular Pharmacology; a former Director of UMass Center for AIDS Research; and a Founder and Co-Director for the Institute for Drug Resistance (University of Massachusetts Medical School, MA, USA). Schiffer has an undergraduate degree in physics from the University of Chicago, with a PhD in biophysics from University of California, San Francisco (CA, USA). She was a postdoctoral associate first at the ETH in Zurich and then at Genentech in San Francisco. Schiffer has published more than 100 peer reviewed journal articles. Her laboratory primarily uses structural biology, biophysical and chemistry techniques to …

Hiv-1 Protease-Substrate Coevolution In Nelfinavir Resistance, Madhavi Kolli, Aysegul Ozen, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue …

Prototypical Recombinant Multi-Protease Inhibitor Resistant Infectious Molecular Clones Of Human Immunodeficiency Virus Type-1, Vici Varghese, Yumi Mitsuya, W. Jeffrey Fessel, Tommy F. Liu, George Melikian, David Katzenstein, Celia Schiffer, Susan Holmes, Robert Shafer

Celia A. Schiffer

The many genetic manifestations of HIV-1 protease inhibitor (PI) resistance present challenges to research into the mechanisms of PI-resistance and the assessment of new PIs. To address these challenges, we created a panel of recombinant multi-PI resistant infectious molecular clones designed to represent the spectrum of clinically relevant multi-PI resistant viruses. To assess the representativeness of this panel, we examined the sequences of the panel's viruses in the context of a correlation network of PI-resistance amino acid substitutions in sequences from more than 10,000 patients. The panel of recombinant infectious molecular clones comprised 29 of 41 study-defined PI-resistance amino acid …

Substrate Envelope-Designed Potent Hiv-1 Protease Inhibitors To Avoid Drug Resistance, Madhavi Nalam, Akbar Ali, G. S. Kiran Kumar Reddy, Hong Cao, Saima Anjum, Michael Altman, Nese Yilmaz, Bruce Tidor, Tariq Rana, Celia Schiffer

Celia A. Schiffer

The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing. The designed PIs share a common chemical scaffold but utilize various moieties that optimally fill the substrate envelope, as confirmed by crystal structures. The designed PIs retain robust binding to MDR protease variants and display exceptional antiviral potencies against …

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 …

The Effect Of Dissolved Polyunsaturated Aldehydes On Microzooplankton Growth Rates In The Chesapeake Bay And Atlantic Coastal Waters, Peter J. Lavrentyev, Gayantonia Franzè, James J. Pierson, Diane K. Stoecker

Peter J. Lavrentyev