Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes

Abstract Background Bacterial promoters, which increase the efficiency of gene expression, differ from other promoters by several characteristics. This difference, not yet widely exploited in bioinformatics, looks promising for the development of relevant computational tools to search for strong promoters in bacterial genomes. Results We describe a new triad pattern algorithm that predicts strong promoter candidates in annotated bacterial genomes by matching specific patterns for the group I σ70 factors of Escherichia coli RNA polymerase. It detects promoter-specific motifs by consecutively matching three patterns, consisting of an UP-element, required for interaction with the α subunit, and then optimally-separated patterns of -35 and -10 boxes, required for interaction with the σ70 subunit of RNA polymerase. Analysis of 43 bacterial genomes revealed that the frequency of candidate sequences depends on the A+T content of the DNA under examination. The accuracy of in silico prediction was experimentally validated for the genome of a hyperthermophilic bacterium, Thermotoga maritima, by applying a cell-free expression assay using the predicted strong promoters. In this organism, the strong promoters govern genes for translation, energy metabolism, transport, cell movement, and other as-yet unidentified functions. Conclusion The triad pattern algorithm developed for predicting strong bacterial promoters is well suited for analyzing bacterial genomes with an A+T content of less than 62%. This computational tool opens new prospects for investigating global gene expression, and individual strong promoters in bacteria of medical and/or economic significance.</p

Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling

<p>Abstract</p> <p>Background</p> <p>Seminal fluid plays an important role in successful fertilization, but knowledge of the full suite of proteins transferred from males to females during copulation is incomplete. The list of ejaculated proteins remains particularly scant in one of the best-studied mammalian systems, the house mouse (<it>Mus domesticus</it>), where artificial ejaculation techniques have proven inadequate. Here we investigate an alternative method for identifying ejaculated proteins, by isotopically labeling females with ¹⁵N and then mating them to unlabeled, vasectomized males. Proteins were then isolated from mated females and identified using mass spectrometry. In addition to gaining insights into possible functions and fates of ejaculated proteins, our study serves as proof of concept that isotopic labeling is a powerful means to study reproductive proteins.</p> <p>Results</p> <p>We identified 69 male-derived proteins from the female reproductive tract following copulation. More than a third of all spectra detected mapped to just seven genes known to be structurally important in the formation of the copulatory plug, a hard coagulum that forms shortly after mating. Seminal fluid is significantly enriched for proteins that function in protection from oxidative stress and endopeptidase inhibition. Females, on the other hand, produce endopeptidases in response to mating. The 69 ejaculated proteins evolve significantly more rapidly than other proteins that we previously identified directly from dissection of the male reproductive tract.</p> <p>Conclusion</p> <p>Our study attempts to comprehensively identify the proteins transferred from males to females during mating, expanding the application of isotopic labeling to mammalian reproductive genomics. This technique opens the way to the targeted monitoring of the fate of ejaculated proteins as they incubate in the female reproductive tract.</p

Hypogene Speleogenesis in the Guadalupe Mountains, New Mexico and Texas, USA

The Guadalupe Mountains consist of an uplift of Permian carbonate shelf deposits in a semiarid landscape. A variety of speleogenetic processes, mostly hypogene, have made them one of the world’s best-known cave regions. The most notable caves are Carlsbad Cavern, which contains the largest known cave room in the USA, and Lechuguilla Cave, now the world’s 7th longest. Because the caves are no longer active, there was early confusion about their origin. This was resolved when long-dormant sulfuric acid processes were recognized, with H2S supplied by nearby oil fields. Potassium-argon dating of the by-product mineral alunite in the Guadalupes indicates speleogenetic ages from 12 to 4 million years, decreasing with lower elevation. Caves show abundant evidence for subaerial corrosion, both by sulfuric acid and carbonic acid in water films. Many seemingly phreatic features have resulted from this subaerial process. Microbial alteration of bedrock has contributed to weathering. There is evidence that isolated caves of greater age, lined by large scalenohedral calcite, were formed by supercritical CO2 in deep thermal water

The Saccharomyces cerevisiae NPR1 gene required for the activity of ammonia-sensitive amino acid permeases encodes a protein kinase homologue.

The NPR1 gene of Saccharomyces cerevisiae plays a central role in controlling permease activity; its product is required to promote the activity of at least six distinct transport systems for nitrogenous nutrients under conditions of nitrogen catabolite derepression. We report here the nucleotide sequence of the cloned NPR1 gene. The predicted amino acid sequence indicates that NPR1 encodes a protein of 86 kDa which appears to be organized into two distinct structural domains. The amino-terminal domain of NPR1 (residues 1 to 440) contains 26% serine residues and several regions strongly enriched for PEST residues and several regions strongly enriched for PEST residues suggesting a short half-life for the NPR1 protein. The carboxy-terminal region of NPR1 contains consensus sequences characteristic of the catalytic domains of protein kinases. Therefore, NPR1-dependent positive control of nitrogen transport systems most likely involves protein phosphorylation. Northern analysis indicates that the absence of general amino acid permease (GAP1) activity in npr1 mutants is not due to reduction in transcription or messenger stability. Hence, the NPR1 protein probably acts at the post-transcriptional level. Proteins that may serve as substrates for phosphorylation are discussed.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Chesapeake Bay Impact Structure Deep Drilling Project Completes Coring

The Chesapeake Bay Impact Structure Deep Drilling Project (CBIS Project) completed its coring operations during September–December 2005 and April–May 2006. Cores were collected continuously to a total depth of 1766 m. The recovered section consists of 1322 m of impactites beneath 444 m of post-impact continental shelf sediments.The CBIS Project is a joint venture of the International Continental Scientifi c Drilling Program (ICDP) and the U.S. Geological Survey (USGS). Project activities began with a planning workshop in September 2003 attended by sixtythree scientists from ten countries. Field operations began with site preparation in July 2005, and coring began in September 2005. Drilling, Observation and Sampling of theEarth’s Continental Crust (DOSECC) was the general contractor for the drilling operations throughout 2005