Life Sciences Commons^™

A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron Adams, U. Gozel, K. Nguyen, R. Inserra, R. Giblin-Davis

Byron Adams

The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states …

Decline In A Dominant Invertebrate Species Contributes To Altered Carbon Cycling In A Low-Diversity Soil Ecosystem, Byron Adams, J. Barrett, Ross Virginia, Diana Wall

Byron Adams

Low-diversity ecosystems cover large portions of the Earth's land surface, yet studies of climate change on ecosystem functioning typically focus on temperate ecosystems, where diversity is high and the effects of individual species on ecosystem functioning are difficult to determine. We show that a climate-induced decline of an invertebrate species in a low-diversity ecosystem could contribute to significant changes in carbon © cycling. Recent climate variability in the McMurdo Dry Valleys of Antarctica is associated with changes in hydrology, biological productivity, and community composition of terrestrial and aquatic ecosystems. One of the greatest changes documented in the dry valleys is …

Topical Lipophilic Epigallocatechin-3-Gallate On Herpes Labialis: A Phase Ii Clinical Trial Of Averteax Formula, Man Zhao, Rong Zheng, Jinyan Jiang, Douglas Dickinson, Baiping Fu, Tin-Chun Chu, Lee Lee, Hanna Pearl, Stephen Hsu

Tin-Chun Chu, Ph.D.

Objectives The aim of this study was to clinically evaluate a topical proprietary formulation containing lipophilic catechins (AverTeaX) on recurrent herpes labialis. Methods A double blind, placebo-controlled, randomized trial with 40 participants initially in two groups. Results Compared to the vehicle group, AverTeaX applied topically 6-8 times daily resulted in a significant reduction of clinical episode duration (median 4.5 days, range 1-11 days vs. 9 days, range 2-11 days, p=0.003) and shortened blistering/ulceration stages within an episode from a median of 3 (range 0-6) days to 1 (range 0-3) day (p=0.0003). Median quality of life scores based on a multi-question …

Dorsoventral Boundary For Organizing Growth And Planar Polarity In The Drosophila Eye, Amit Singh, Janghoo Lim, Kwang-Wook Choi

Amit Singh

A fundamental feature of developing tissues and organs is generation of planar polarity of cells in an epithelium with respect to the body axis.

The Drosophila compound eye shows two-tier dorsoventral (DV) planar polarity. At the individual ommatidium level, the eight photoreceptors in each unit eye form a dorsoventrally asymmetric cluster. At the level of eye field, hundreds of ommatidia in the upper and lower halves of an eye are uniformly polarized dorsally or ventrally, respectively. This results in DV mirror symmetries about the equator. The uniform orientations of photoreceptor clusters over long distance in the eye field provide an …

Biosignatures In Chimney Structures And Sediment From The Loki’S Castle Low-Temperature Hydrothermal Vent Field At The Arctic Mid-Ocean Ridge, A. Jaeschke, B. Eickmann, Susan Lang, S. Bernasconi, H. Strauss, G. Früh-Green

Susan Q. Lang

No abstract provided.

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 …

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 …

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 …

Effect Of Intracellular Expression Of Antimicrobial Peptide Ll-37 On Growth Of Escherichia Coli Strain Top10 Under Aerobic And Anaerobic Conditions, Wei Liu, Shi Dong, Fei Xu, Xue Wang, T. Withers, Hongwei Yu, Xin Wang

Hongwei Yu

Antimicrobial peptides (AMPs) can cause lysis of target bacteria by directly inserting themselves into the lipid bilayer. This killing mechanism confounds the identification of the intracellular targets of AMPs. To circumvent this, we used a shuttle vector containing the inducible expression of a human cathelicidin-related AMP, LL-37, to examine its effect on Escherichia coli TOP10 under aerobic and anaerobic growth conditions. Induction of LL-37 caused growth inhibition and alteration in cell morphology to a filamentous phenotype. Further examination of the E. coli cell division protein FtsZ revealed that LL-37 did not interact with FtsZ. Moreover, intracellular expression of LL-37 results …

Gel Shift Analysis Of The Empa Promoter Region In Vibrio Anguillarum, Steven Denkin, Pedja Sekaric, David Nelson

David R. Nelson

BACKGROUND: The induction of metalloprotease encoded by empA in Vibrio anguillarum occurs at high cell density in salmon intestinal mucus. Previously we have shown that there are significant differences in empA expression in two strains of V. anguillarum, M93Sm and NB10. It is hypothesized that differences in empA regulation are due to differences in binding of regulatory elements.

RESULTS: Two strains of V. anguillarum, M93Sm and NB10, were examined and compared for the presence of DNA regulatory proteins that bind to and control the empA promoter region. Gel mobility shift assays, using a digoxigenin (DIG)-labeled oligomer containing a lux box-like …

A Diverse Assemblage Of Indole-3-Acetic Acid Producing Bacteria Associate With Unicellular Green Algae, Christopher Bagwell, Magdalena Piskorska, Tanya Soule, Angela Petelos, Christopher Yeager

Tanya Soule

Microalgae have tremendous potential as a renewable feedstock for the production of liquid transportation fuels. In natural waters, the importance of physical associations and biochemical interactions between microalgae and bacteria is generally well appreciated, but the significance of these interactions to algal biofuels production have not been investigated. Here, we provide a preliminary report on the frequency of co-occurrence between indole-3-acetic acid (IAA)-producing bacteria and green algae in natural and engineered ecosystems. Growth experiments with unicellular algae, Chlorella and Scenedesmus, revealed IAA concentration-dependent responses in chlorophyll content and dry weight. Importantly, discrete concentrations of IAA resulted in cell culture synchronization, …

Microbial Isolations From Olive Ridley (Lepidochelys Olivacea) And Eastern Pacific Green (Chelonia Mydas Agassizii) Sea Turtle Nests In Guanacaste, Costa Rica, And Standard Testing Of Cloacal Fluid Antimicrobial Properties, Erin Keene, Tanya Soule, Frank Paladino

Tanya Soule

Microorganisms associated with olive ridley and East Pacific green turtle nesting and potential cloacal fluid antimicrobial properties were studied in Guanacaste, Costa Rica. During the 2010–2011 season, bacteria and fungi were isolated from olive ridley cloacal fluid, nest chamber sand, and egg samples. Because of the lack of cloacal fluid bacteria isolated, the focus of the 2011–2012 season shifted to determine whether fluid contained antibacterial properties by using Kirby–Bauer disk diffusion assays, and cloacal fluid and sand samples were taken to see whether bacteria were unique to cloacal fluid. Assays were performed on 34 olive ridley and 5 East Pacific …

From The Centers For Disease Control And Prevention. Prevalence Of Penicillin-Resistant Streptococcus Pneumoniae--Connecticut, 1992-1993, E. Simpson

E. Hatheway Simpson

To determine the extent of antimicrobial susceptibility testing of Streptococcus pneumoniae and the prevalence of penicillin resistance among pneumococcal isolates from July 1992 through June 1993, in August 1993 the Connecticut Department of Public Health and Addiction Services (DPHAS) surveyed all 44 hospitals with clinical microbiology laboratories in Connecticut. This report summarizes the results of that survey.

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 …

Higher-Level Production Of Volatile Fatty Acids In Vitro By Chicken Gut Microbiotas Than By Human Gut Microbiotas As Determined By Functional Analyses, Fang Lei, Yeshi Yin, Yuezhu Wang, Bo Deng, Hongwei Yu, Lanjuan Li, Charlie Xiang, Shengyue Wang, Baoli Zhu, Xin Wang

Hongwei Yu

The aim of this study was to determine the relationship between the composition and function of gut microbiota. Here, we compared the bacterial compositions and fermentation metabolites of human and chicken gut microbiotas. Results generated by quantitative PCR (qPCR) and 454 pyrosequencing of the 16S rRNA gene V3 region showed the compositions of human and chicken microbiotas to be markedly different, with chicken cecal microbiotas displaying more diversity than human fecal microbiotas. The nutrient requirements of each microbiota growing under batch and chemostat conditions were analyzed. The results showed that chicken cecal microbiotas required simple sugars and peptides to maintain …

Ultraviolet Photoprotective Compounds From Cyanobacteria In Biomedical Applications, Tanya Soule, Ferran Garcia-Pichel

Tanya Soule

No abstract provided.

Purification Of An Inducible Dnase From A Thermophilic Fungus, Kyle Landry, Andrea Vu, Robert Levin

Kyle S Landry

Purification And Characterization Of Iso-Ribonucleases From A Novel Thermophilic Fungus, Kyle Landry, Robert Levin

Kyle S Landry

The Chlorella Variabilis Nc64a Genome Reveals Adaptation To Photosymbiosis, Coevolution With Viruses, And Cryptic Sex, Guillaume Blanc, Gary Duncan, Irina Agarkova, Mark Borodovsky, James Gurnon, Alan Kuo, Erika Lindquist, Susan Lucas, Jasmyn Pangilinan, Juergen Polle, Asaf Salamov, Astrid Terry, Takashi Yamada, David Dunigan, Igor Grigoriev, Jean-Michel Claverie, James Van Etten

David D Dunigan Ph. D.

Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have …

Cooperative Effects Of Drug-Resistance Mutations In The Flap Region Of Hiv-1 Protease, Jennifer Foulkes-Murzycki, Christina Rosi, Nese Yilmaz, Robert Shafer, Celia Schiffer

Celia A. Schiffer

Understanding the interdependence of multiple mutations in conferring drug resistance is crucial to the development of novel and robust inhibitors. As HIV-1 protease continues to adapt and evade inhibitors while still maintaining the ability to specifically recognize and efficiently cleave its substrates, the problem of drug resistance has become more complicated. Under the selective pressure of therapy, correlated mutations accumulate throughout the enzyme to compromise inhibitor binding, but characterizing their energetic interdependency is not straightforward. A particular drug resistant variant (L10I/G48V/I54V/V82A) displays extreme entropy-enthalpy compensation relative to wild-type enzyme but a similar variant (L10I/G48V/I54A/V82A) does not. Individual mutations of sites …

Gene Transfer In Skeletal And Cardiac Muscle Using Recombinant Adeno-Associated Virus, Alisha Gruntman, Lawrence Bish, Christian Mueller, H. Lee Sweeney, Terence Flotte, Guangping Gao

Christian Mueller

Adeno-associated virus (AAV) is a DNA virus with a small ( approximately 4.7 kb) single-stranded genome. It is a naturally replication-defective parvovirus of the dependovirus group. Recombinant AAV (rAAV), for use as a gene transfer vector, is created by replacing the viral rep and cap genes with the transgene of interest along with promoter and polyadenylation sequences. Only the viral inverted terminal repeats (ITRs) are required in cis for replication and packaging during production. The ITRs are also necessary and sufficient for vector genome processing and persistence during transduction. The tissue tropism of the rAAV vector is determined by the …

Structural And Thermodynamic Basis Of Amprenavir/Darunavir And Atazanavir Resistance In Hiv-1 Protease With Mutations At Residue 50, Seema Mittal, Rajintha Bandaranayake, Nancy King, Moses Prabu-Jeyabalan, Madhavi Nalam, Ellen Nalivaika, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

Drug resistance occurs through a series of subtle changes that maintain substrate recognition but no longer permit inhibitor binding. In HIV-1 protease, mutations at I50 are associated with such subtle changes that confer differential resistance to specific inhibitors. Residue I50 is located at the protease flap tips, closing the active site upon ligand binding. Under selective drug pressure, I50V/L substitutions emerge in patients, compromising drug susceptibility and leading to treatment failure. The I50V substitution is often associated with amprenavir (APV) and darunavir (DRV) resistance, while the I50L substitution is observed in patients failing atazanavir (ATV) therapy. To explain how APV, …

Viral Perturbations Of Host Networks Reflect Disease Etiology, Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica Mar, Michael Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod Marto, Nicholas Christakis, Elliott Kieff, Frederick Roth, Jennifer Roecklein-Canfield, James Decaprio, Michael Cusick, John Quackenbush, David Hill, Karl Münger, Marc Vidal, Albert-László Barabási

Albert-László Barabási

Many human diseases, arising from mutations of disease susceptibility genes (genetic diseases), are also associated with viral infections (virally implicated diseases), either in a directly causal manner or by indirect associations. Here we examine whether viral perturbations of host interactome may underlie such virally implicated disease relationships. Using as models two different human viruses, Epstein-Barr virus (EBV) and human papillomavirus (HPV), we find that host targets of viral proteins reside in network proximity to products of disease susceptibility genes. Expression changes in virally implicated disease tissues and comorbidity patterns cluster significantly in the network vicinity of viral targets. The topological …