BIOLOGICAL GENE SEQUENCE STUCTURE ANALYSIS USING HIDDEN MARKOV MODEL

Identification or prediction of coding sequences from within genomic DNA has been a major part of the search of the gene. In this work real hidden Markov models (HMMs) to denote the consensus and deliver a beneficial tool in determining the splicing junction sites Markov models which has a recurring nature in computational biology leads to statistical models, in every sequential analysis it plays a role of putting up a right label on each residue. In sequential alignment and as well as in gene identification namely exons, introns or intergenic sequences which make in a sequence with homologous residue with the target database. Under the gene identification methodology Condon bias, exons, introns have length preference which leads to a combination of splice site consensus. Parameters are fixed on the onset while weight of the different information are polled together leading to the interception of result probability, which could lead to identifying the best score based on score mean and how confident are the best scoring answers are perfect. This leads to the concept of extendibility, to perfect and ad hoc gene finder, which is a modeled transitional methodology leading to the consensus, alternate splicing and offers polyadenylation signal. This leads to piling of authenticity against a delicate ad hoc program which could make to breakdown under its individual weightiness.

Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort

Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).

Identification of PNG kinase substrates uncovers interactions with the translational repressor TRAL in the oocyte-to-embryo transition

The Drosophila Pan Gu (PNG) kinase complex regulates hundreds of maternal mRNAs that become translationally repressed or activated as the oocyte transitions to an embryo. In a previous paper (Hara et al., 2017), we demonstrated PNG activity is under tight developmental control and restricted to this transition. Here, examination of PNG specificity showed it to be a Thr-kinase yet lacking a clear phosphorylation site consensus sequence. An unbiased biochemical screen for PNG substrates identified the conserved translational repressor Trailer Hitch (TRAL). Phosphomimetic mutation of the PNG phospho-sites in TRAL reduced its ability to inhibit translation in vitro. In vivo, mutation of tral dominantly suppressed png mutants and restored Cyclin B protein levels. The repressor Pumilio (PUM) has the same relationship with PNG, and we also show that PUM is a PNG substrate. Furthermore, PNG can phosphorylate BICC and ME31B, repressors that bind TRAL in cytoplasmic RNPs. Therefore, PNG likely promotes translation at the oocyte-to-embryo transition by phosphorylating and inactivating translational repressors.

Transposition of Tn125encoding the NDM-1 carbapenemase inAcinetobacter baumannii

TheblaNDM-1gene encodes a carbapenemase that confers resistance to almost all β-lactams, including latest resort carbapenems. It is increasingly reported worldwide in nosocomial and community-acquired Gram-negative bacteria.Acinetobacter baumanniiis an important opportunistic pathogen considered as an intermediate reservoir for theblaNDM-1gene. In this species, theblaNDM-1gene is located within the Tn125composite transposon. The mechanism driving the mobility of Tn125has not yet been elucidated. Here we experimentally demonstrated transposition of Tn125inA. baumannii. Systematic 3-bp duplication of the target site, being signature of transposition, was evidenced. The target site consensus for Tn125transposition was found to be GC-enriched at the duplicated 3 bp and AT-rich in the vicinity. Transposition frequency was not influenced by temperature changes or by exposure to sub-inhibitory concentrations of various antibiotics. This work is the first direct evidence of the functionality of a composite transposon inA. baumannii. It provides a mechanistic clue for the dissemination of theblaNDM-1gene inAcinetobacterspp. and subsequently among Enterobacteriaceae.

Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions

The increasing diagnostic use of gene sequencing has led to an expanding dataset of novel variants that lie within consensus splice junctions. The challenge for diagnostic laboratories is the evaluation of these variants in order to determine if they affect splicing or are merely benign. A common evaluation strategy is to use in silico analysis, and it is here that a number of programmes are available online; however, currently, there are no consensus guidelines on the selection of programmes or protocols to interpret the prediction results. Using a collection of 222 pathogenic mutations and 50 benign polymorphisms, we evaluated the sensitivity and specificity of four in silico programmes in predicting the effect of each variant on splicing. The programmes comprised Human Splice Finder (HSF), Max Entropy Scan (MES), NNSplice, and ASSP. The MES and ASSP programmes gave the highest performance based on Receiver Operator Curve analysis, with an optimal cut-off of score reduction of 10%. The study also showed that the sensitivity of prediction is affected by the level of conservation of individual positions, with in silico predictions for variants at positions -4 and +7 within consensus splice sites being largely uninformative.

Multistress Regulation in Escherichia coli: Expression of osmB Involves Two Independent Promoters Responding either to σS or to the RcsCDB His-Asp Phosphorelay

ABSTRACT Transcription of the Escherichia coli osmB gene is induced by several stress conditions. osmB is expressed from two promoters, osmBp1 and osmBp2. The downstream promoter, osmBp2, is induced after osmotic shock or upon entry into stationary phase in a σS-dependent manner. The upstream promoter, osmBp1, is independent of σS and is activated by RcsB, the response regulator of the His-Asp phosphorelay signal transduction system RcsCDB. RcsB is responsible for the induction of osmBp1 following treatment with chlorpromazine. Activation of osmBp1 by RcsB requires a sequence upstream of its −35 element similar to the RcsB binding site consensus, suggesting a direct regulatory role. osmB appears as another example of a multistress-responsive gene whose transcription involves both a σS-dependent promoter and a second one independent of σS but controlled by stress-specific transcription factors.