Bull, Marta; Learn, Gerald; Genowati, Indira; McKernan, Jennifer; Hitti, Jane; Lockhart, David; Tapia, Kenneth; Holte, Sarah; Dragavon, Joan; Coombs, Robert; Mullins, James; Frenkel, Lisa (2009)
aPair-wise distance were used to identify whether the nearest neighbor to each genital DNA sequence was another genital sequence or from blood, as described in materials and methods. The actual proportion indicates the proportion of genital DNA sequences that had a nearest neighbor that is also from the genital tract; generalized estimating equations (GEE) was used to obtain confidence intervals for the actual proportion. The expected proportion indicates the proportion of sequences that woul...
Gu, Jingjing; Orr, Nick; D. Park, Stephen; M. Katz, Lisa; Sulimova, Galina; E. MacHugh, David; W. Hill, Emmeline (2009)
Candidate genes located within regions that have been subject to positive selection in Thoroughbred ranked by FST; the locus with the strongest evidence for selection is listed first. Heterozygosity values for Thoroughbred (TB), Akhal-Teke (AH), Connemara (CON) and Tuva (TU) are shown. Loci with lowest heterozygosity in Thoroughbred were included. Loci were localised to chromosomes and their positions were determined by in silico ePCR (Table S1). Each selected region was defined by loci flank...
Fàbrega, Anna; du Merle, Laurence; Le Bouguénec, Chantal; Teresa Jiménez de Anta, M.; Vila, Jordi (2009)
aCHL chloramphenicol, TET tetracycline, AMX amoxicillin, CRO ceftriaxone, FOX cefoxitin, ERY erythromycin, KAN kanamycin, TMP trimethoprim.
D. Champion, Mia; Zeng, Qiandong; B. Nix, Eli; E. Nano, Francis; Keim, Paul; D. Kodira, Chinnappa; Borowsky, Mark; Young, Sarah; Koehrsen, Michael; Engels, Reinhard; Pearson, Matthew; Howarth, Clint; Larson, Lisa; White, Jared; Alvarado, Lucia;... (2009)
Phylogenetic Differentiation Associated with Gene Gain and Loss.
Windschiegl, Barbara; Orth, Alexander; Römer, Winfried; Berland, Ludwig; Stechmann, Bahne; Bassereau, Patricia; Johannes, Ludger; Steinem, Claudia (2009)
The homopentameric B-subunit of bacterial protein Shiga toxin (STxB) binds to the glycolipid Gb3 in plasma membranes, which is the initial step for entering cells by a clathrin-independent mechanism. It has been suggested that protein clustering and lipid reorganization determine toxin uptake into cells. Here, we elucidated the molecular requirements for STxB induced Gb3 clustering and for the proposed lipid reorganization in planar membranes. The influence of binding site III of the B-subuni...
Kolodkin-Gal, Ilana; Verdiger, Reut; Shlosberg-Fedida, Ayalla; Engelberg-Kulka, Hanna (2009)
Toxin-antitoxin (TA) modules are gene pairs specifying for a toxin and its antitoxin and are found on the chromosomes of many bacteria including pathogens. Here we report how each of five such TA systems in E. coli affect bacterial cell death differently in liquid media and during biofilm formation. Of all these systems, only the TA system mazEF mediated cell death both in liquid media and during biofilm formation. At the other extreme, as our results have revealed here, the TA system dinJ-Ya...
L. Taylor-Cousar, Jennifer; A. Zariwala, Maimoona; H. Burch, Lauranell; G. Pace, Rhonda; L. Drumm, Mitchell; Calloway, Hollin; Fan, Haiying; W. Weston, Brent; A. Wright, Fred; R. Knowles, Michael (2009)
BackgroundThe pulmonary phenotype in cystic fibrosis (CF) is variable; thus, environmental and genetic factors likely contribute to clinical heterogeneity. We hypothesized that genetically determined ABO histo-blood group antigen (ABH) differences in glycosylation may lead to differences in microbial binding by airway mucus, and thus predispose to early lung infection and more severe lung disease in a subset of patients with CF.Methods and Principal FindingsClinical information and DNA was co...
Amleh, Asma; J. Nair, Sreejith; Sun, Jianlong; Sutherland, Ann; Hasty, Paul; Li, Rong (2009)
BackgroundNegative elongation factor (NELF) is a four-subunit protein complex conserved from Drosophila to humans. In vitro biochemical and tissue culture-based studies have demonstrated an important role of NELF in controlling RNA polymerase II (Pol II) pausing in transcription. However, the physiological significance of NELF function is not clear due to the lack of any genetic systems for studying NELF.Principal FindingsHere we show that disruption of the mouse B subunit of NELF (NELF-B), a...
W. Kijas, James; Townley, David; Dalrymple, Brian P.; P. Heaton, Michael; F. Maddox, Jillian; McGrath, Annette; Wilson, Peter; G. Ingersoll, Roxann; McCulloch, Russell; McWilliam, Sean; Tang, Dave; McEwan, John; Cockett, Noelle; Hutton Oddy, V.; W. Nicholas, Frank;... (2009)
The number and proportion of SNP in minor allele frequency (MAF) bins is given for three sets of markers. Set 1 includes all SNP identified during the re-sequencing experiment, with MAF being calculated from sequencing data. Set 2 is the subset of markers selected for inclusion in the SNP array, for which MAF was calculated from sequencing data. Set 3 includes SNP which passed all of the quality control filters, for which MAF was calculated from genotypic data.
Okimoto, Noriaki; Futatsugi, Noriyuki; Fuji, Hideyoshi; Suenaga, Atsushi; Morimoto, Gentaro; Yanai, Ryoko; Ohno, Yousuke; Narumi, Tetsu; Taiji, Makoto (2009)
We performed MM calculations (MM energy minimization) or MD simulations of a complex, a protein, and a ligand, and evaluated 12 types of binding free energies by combining the respective coordinate sets. The enthalpy contributions of Gprotein and Gligand in equation 2 were calculated in the following two ways: (1) by using the coordinate sets of a protein (or ligand) obtained from the MD simulations (or MM calculations) of the protein (or ligand) and (2) by using the coordinate sets extracted...