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Abstract Background When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statistically significant sites are revealed when a transcription factor binding site motif model is used to scan a genome-scale database. Methods We have developed a scanning algorithm, PhyloScan, which combines evidence from matching sites found in orthologous data from several related species with evidence from multiple sites within an intergenic region, to better detect regulons. The orthologous sequence data may be multiply aligned, unaligned, or a combination of aligned and unaligned. In aligned data, PhyloScan statistically accounts for the phylogenetic dependence of the species contributing data to the alignment and, in unaligned data, the evidence for sites is combined assuming phylogenetic independence of the species. The statistical significance of the gene predictions is calculated directly, without employing training sets. Results In a test of our methodology on synthetic data modeled on seven Enterobacteriales, four Vibrionales, and three Pasteurellales species, PhyloScan produces better sensitivity and specificity than MONKEY, an advanced scanning approach that also searches a genome for transcription factor binding sites using phylogenetic information. The application of the algorithm to real sequence data from seven Enterobacteriales species identifies novel Crp and PurR transcription factor binding sites, thus providing several new potential sites for these transcription factors. These sites enable targeted experimental validation and thus further delineation of the Crp and PurR regulons in E. coli. Conclusion Better sensitivity and specificity can be achieved through a combination of (1) using mixed alignable and non-alignable sequence data and (2) combining evidence from multiple sites within an intergenic region.

Rates of human papillomavirus (HPV) vaccine series completion among adolescent Hispanic females in Texas in 2014 (~39%) lag behind the Healthy People 2020 goal (80%). This qualitative study identifies Hispanic mothers' salient behavioral, normative and control beliefs regarding having their adolescent daughters complete the vaccine series. Thirty-two mothers of girls (aged 11-17) that had received at least one dose of the HPV vaccine, completed in-depth interviews. Six girls had received one dose of the HPV vaccine, 10 girls had received two doses, and 16 girls had received all three doses. The questions elicited salient: (i) experiential and instrumental attitudes (behavioral beliefs); (ii) supporters and non-supporters (normative beliefs) and (iii) facilitators and barriers (control beliefs). Directed content analysis was employed to select the most salient beliefs. Mothers: (i) expressed salient positive feelings (e.g. good, secure, happy and satisfied); (ii) believed that completing the series resulted in positive effects (e.g. protection, prevention); (iii) believed that the main supporters were themselves, their daughter's father and doctor with some of their friends not supporting series completion and (iv) believed that vaccine affordability, information, transportation, ease of scheduling and keeping vaccination appointments and taking their daughter's immunization card to appointments were facilitators. This study represents the first step in building theory-based framework of vaccine series completion for this population. The beliefs identified provide guidance for health care providers and intervention developers.

An in vitro method has been developed utilizing phytohemagglutinin (PHA) activated lymphocytes obtained from human tonsils and adenoids which permit the accumulation of multi-liter quantities of cell-free supernatants containing lymphotoxin and other lymphocyte effector molecules (LEM). An enriched media is employed which contains a large molecular weight, heat stable bovine serum fraction which supports lymphoid cell activation and levels of LEM secretion equal to that of cultures maintained in medium supplemented with whole serum. Elimination of whole serum from the media greatly reduces overall protein concentrations and facilitates concentration and purification studies. Various technical aspects of these cultures have been examined, i.e.: 1) cell concentration, 2) kinetics of LT production over a ten-day period, 3) mitogen dosage, and 4) types of media. Supernatants can be harvested repeatedly from a single culture over the ten day period, thus doubling the yield of LEM collected from a single culture.

Background: RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNAi efficiency, and it is of interest to have a convincing mechanistic interpretation of this observation. We here examine this issue by considering the secondary structures for both the target messenger RNA (mRNA) and the siRNA guide strand. Results: By analyzing a unique homogeneous data set of 101 shRNAs targeted to 100 endogenous human genes, we find that: 1) target site accessibility is more important than GC-content for efficient RNAi; 2) there is an appreciable negative correlation between GC-content and RNAi activity; 3) for the predicted structure of the siRNA guide strand, there is a lack of correlation between RNAi activity and either the stability or the number of free dangling nucleotides at an end of the structure; 4) there is a high correlation between target site accessibility and GC-content. For a set of representative structural RNAs, the GC content of 62.6% for paired bases is significantly higher than the GC content of 38.7% for unpaired bases. Thus, for a structured RNA, a region with higher GC content is likely to have more stable secondary structure. Furthermore, by partial correlation analysis, the correlation for GC-content is almost completely diminished, when the effect of target accessibility is controlled. Conclusion: These findings provide a target-structure-based interpretation and mechanistic insight for the effect of GC-content on RNAi efficiency. [ABSTRACT FROM AUTHOR]

Polyacrylamide gel electrophoresis of pure pancreatic juice from 14 healthy normal subjects, 11 chronic alcoholics without detectable pancreatic disease, 15 patients with pancreatitis, and two with cancer of the pancreas consistently demonstrated the presence of two variants of trypsinogen with different electrophoretic mobilities. In healthy normal subjects the proportion of cationic to anionic trypsinogen was invariably greater than 1 and averaged about 2. In chronic alcoholics, patients with pancreatitis or cancer of the pancreas, this ratio, with a single exception, was below one and averaged about 0·45. The extraordinary consistency of these findings suggests that the quantitative relationship between cationic and anionic trypsinogen in human pancreatic juice may be a very sensitive indicator of incipient or existing pancreatic pathology. The most acceptable explanation for the reversal of the normal zymogen ratio in pancreatic disease is a selective increase in the synthesis of the anionic variant relative to that of the cationic species. Total trypsinogen concentrations differed widely from one another in the three patient groups, but the ratio of cationic to anionic trypsinogen exhibited little change and remained below 1. Our results also demonstrate for the first time a specific effect of chronic alcohol abuse on the secretory profile of a pancreatic enzyme in human subjects. A newly discovered minor, trypsinogen-like component of human pancreatic juice was found to be significantly increased in pancreatic juice of chronic alcoholics, decreased in pancreatic secretions of patients with pancreatitis, and barely detectable in those of two patients with cancer of the pancreas. [ABSTRACT FROM PUBLISHER]

Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/.