Digital Commons Network^™

Single-Cell Enumeration Of An Uncultivated Tm7 Subgroup In The, Cleber C. Ouverney, Gary C. Armitage, David A. Relman

Faculty Publications, Biological Sciences

Specific oligonucleotide hybridization conditions were established for single-cell enumeration of uncultivated TM7 and IO25 bacteria by using clones expressing heterologous 16S rRNA. In situ analysis of human subgingival crevice specimens revealed that a greater proportion of samples from sites of chronic periodontitis than from healthy sites contained TM7 subgroup IO25. In addition, IO25 bacterial cells from periodontitis site samples were more abundant and fourfold longer than IO25 cells from healthy site samples.

Cultivation Of Tropheryma Whipplei From Cerebrospinal Fluid, Matthias Maiwald, Axel Von Herbay, David N. Fredricks, Cleber C. Ouverney, Jon C. Kosek, David A. Relman

Faculty Publications, Biological Sciences

Whipple disease (WD) is a systemic disorder caused by the bacterium Tropheryma whipplei. Since the recognition of a bacterial etiology in 1961, many attempts have been made to cultivate this bacterium in vitro. It was eventually isolated, in 2000, from an infected heart valve, in coculture with human fibroblasts. Here we report the isolation of 2 new strains of T. whipplei from cerebrospinal fluid (CSF) of 2 patients with intestinal WD but no neurological signs or symptoms. One culture-positive specimen was obtained before treatment; the other was obtained 12 months after discontinuation of therapy, at a time of intestinal remission. …

Quorum Sensing In Candida Albicans: Probing Farnesol’S Mode Of Action With 40 Natural And Synthetic Farnesol Analogs, Roman Shchepin, Jacob M. Hornby, Erin Burger, Timothy Niessen, Patrick H. Dussault, Kenneth Nickerson

Kenneth Nickerson Papers

The dimorphic fungus Candida albicans produces extracellular farnesol (3,7, 11-trimethyl-2,6,10-dodecatriene- 1-ol) which acts as a quorum-sensing molecule (QSM) to suppress filamentation. Of four possible geometric isomers of farnesol, only the E,E isomer possesses QSM activity. We tested 40 natural and synthetic analogs of farnesol for their activity in an N-acetylglucosamine-induced differentiation assay for germ tube formation (GTF). Modified structural features include the head group, chain length, presence or absence of the three double bonds, substitution of a backbone carbon by S, O, N, and Se heteroatoms, presence or absence of a 3-methyl branch, and the bulkiness of the hydrophobic …

Isolation And Characterization Of Thermophilic, Calcium-Precipitating Bacteria Form Calcite Deposits At Yucca Mountain, Terry Ann Else, Curtis R. Pantle, Penny S. Amy, Mark P. Buttner, Amy J. Smiecinski

Publications (YM)

Calcite deposits, composed of a mixture of calcium carbonate and silicon dioxide, were found in fractures and small cavities within the welded tuff of Yucca Mountain. This research investigation involves determining the presence of thermophilic, calciumprecipitating bacteria within these deposits. The possible existence of thermophilic bacteria may help to resolve the issue of whether these calcite deposits formed from precipitation of dissolved calcium carbonate in rain water transported from the overlying soil environment or as a result of upwelling of geothermally-heated waters transported from below the mountain. Evidence for microbially-influenced calcite precipitation in these deposits is indicated by the presence …

Morphological Biosignatures And The Search For Life On Mars, Sherry L. Cady, Jack D. Farmer, John P. Grotzinger, J. William Schopf, Andrew Steele

Geology Faculty Publications and Presentations

This report provides a rationale for the advances in instrumentation and understanding needed to assess claims of ancient and extraterrestrial life made on the basis of morphological biosignatures. Morphological biosignatures consist of bona fide microbial fossils as well as microbially influenced sedimentary structures. To be recognized as evidence of life, microbial fossils must contain chemical and structural attributes uniquely indicative of microbial cells or cellular or extracellular processes. When combined with various research strategies, high-resolution instruments can reveal such attributes and elucidate how morphological fossils form and become altered, thereby improving the ability to recognize them in the geological record …

Prevalence Of Bacteria Of Division Tm7 In Human Subgingival Plaque And Their Association With Disease, Mary M. Brinig, Paul W. Lepp, Cleber C. Ouverney, Gary C. Armitage, David A. Relman

Faculty Publications, Biological Sciences

Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site. Human subgingival plaque samples from healthy sites and sites exhibiting various stages of periodontal disease were analyzed for the presence of TM7 bacteria. TM7 ribosomal DNA (rDNA) was found in 96% of the samples, and it accounted for approximately 0.3%, on average, of all bacterial rDNA in the samples as determined by real-time quantitative PCR. Two new phylotypes of this division were identified, and members of the division were found to exhibit filamentous …

Trophic Uptake And Transfer Of Dmsp In Simple Planktonic Food Chains, Kw Tang, R Simo

VIMS Articles

Recent field studies suggest that a large portion of phytoplankton-DMSP could be lost to grazing by protozoans, but the fate of the grazed DMSP remains uncertain. In the laboratory we studied trophic uptake and transfer of phytoplankton-DMSP through simple planktonic food chains using 2 experimental approaches: (1) A direct approach measured the ingestion and retention of phytoplankton-DMSP by the heterotrophic dinoflagellate Gyrodinium dominans. Overall, DMSP content of G. dominans estimated by the direct approach was highly variable, likely because of the low G. dominans biomass relative to phytoplankton in the samples. (2) An indirect approach, in which the omnivorous copepod …

Comparison Of Methods For Dna Isolation From Food Samples For Detection Of Shiga Toxin-Producing Escherichia Coli By Real-Time Pcr, Loree C. Heller, Carisa R. Davis, K. Kealy Peak, David Wingfield, Andrew C. Cannons, Philip T. Amuso, Jacqueline Cattani

Bioelectrics Publications

In this study, food samples were intentionally contaminated with Escherichia coli O157:H7, and then DNA was isolated by using four commercial kits. The isolated DNA samples were compared by using real-time PCR detection of the Shiga toxin genes. The four kits tested worked similarly.

Bacterioplankton Dynamics In The York River Estuary: Primary Influence Of Temperature And Freshwater Inputs, G. E. Schultz, E. D. White, H. W. Ducklow

VIMS Articles

Bacterial community dynamics were investigated over seasonal and basin scales within the York River estuary, Virginia. Variables describing bacterioplankton dynamics were measured at 6 stations spanning the entire salinity gradient (0 to ca. 20 psu over 60 km). Samples were collected monthly from June 1996 through May 1997 and every other month from June 1997 through May 1998. Bacterial abundance and production were high throughout the estuary. Bacterial abundance ranged from 4.4 x 10(8) to 1.3 x 10(10) cells l(-1). Incorporation of (3)H-thymidine ranged from 10 to 863 pmol(-1) h(-1) while (3)H-leucine incorporation rates ranged from 25 to 1963 pmol …

Eight Gram-Negative Bacteria Are 10,000 Times More Sensitive To Cationic Detergents Than To Anionic Detergents, Soumitra Rajagopal, Nicole Eis, Kenneth Nickerson

Kenneth Nickerson Papers

In liquid culture, eight typical Gram-negative bacteria were ca. 10,000-fold more sensitive to cationic detergents than to the anionic detergent sodium dodecyl sulfate. Cetyltrimethylammonium bromide (CTAB) was inhibitory at concentrations ranging from 0.0006% to 0.01%. Four pseudomonads able to form biofilms were ca. 1000-fold more resistant to CTAB on Luria–Bertani agar plates than they were in liquid culture. A lasI mutant of Pseudomonas aeruginosa was only able to tolerate 0.1% CTAB on Luria–Bertani agar plates but could tolerate 5% CTAB when supplemented with homoserine lactone containing culture supernatants.

En culture liquide, huit bactéries Gram négatif typiques étaient ca. 10,000 fois …