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Bioinformatics Research

04:16 EDT 17th October 2018 | BioPortfolio

High-resolution frequency tuning but not temporal coding in the human cochlea.

Frequency tuning and phase-locking are two fundamental properties generated in the cochlea, enabling but also limiting the coding of sounds by the auditory nerve (AN). In humans, these limits are unknown, but high resolution has been postulated for both properties. Electrophysiological recordings from the AN of normal-hearing volunteers indicate that human frequency tuning, but not phase-locking, ...

SCALOP: sequence-based antibody canonical loop structure annotation.

Canonical forms of the antibody complementarity-determining regions (CDRs) were first described in 1987 and have been redefined on multiple occasions since. The canonical forms are often used to approximate the antibody binding site shape as they can be predicted from sequence. A rapid predictor would facilitate the annotation of CDR structures in the large amounts of repertoire data now becoming ...

ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes.

Coalescent- and reconciliation-based methods are now widely used to infer species phylogenies from genomic data. They typically use per-gene phylogenies as input, which requires conducting multiple individual tree inferences on a large set of multiple sequence alignments (MSAs). At present, no easy-to-use parallel tool for this task exists. Ad hoc scripts for this purpose do not only induce additi...

CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes.

Identification of conserved syntenic blocks across microbial genomes is important for several problems in comparative genomics such as gene annotation, study of genome organization and evolution, and prediction of gene interactions. Current tools for syntenic block discovery do not scale up to the large quantity of prokaryotic genomes available today.

Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana).

Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an ...

The contribution of purifying selection, linkage and mutation bias to the negative correlation between gene expression and polymorphism density in yeast populations.

The negative correlation between the rate of protein evolution and expression level of a gene has been recognized as a universal law of the evolutionary biology (Koonin 2011). In our study we apply a population-based approach to systematically investigate the relative importance of unequal mutation rate, linkage and selection in the origin of the expression-polymorphism anticorrelation. We analyze...

The fascinating world of non-coding RNA and how it may help to unravel the mysteries of tooth movement regulation.

The innovative study presented by Huang and co-workers in this issue of the European Journal of Orthodontics is one of the first giving insight into the mostly disregarded world of non-coding ribonucleic acids in orthodontics. In other fields of science non-coding ribonucleic acids have been shown to play a major role in the regulation of cell metabolism as well as the aetiology of diseases such a...

Highlight: The Evolutionary Arsenal of Aphids.

Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.

Phase-variation of Type I restriction-modification systems can rapidly alter the sequence motifs they target, diversifying both the epigenetic patterns and endonuclease activity within clonally descended populations. Here, we characterize the Streptococcus pneumoniae SpnIV phase-variable Type I RMS, encoded by the translocating variable restriction (tvr) locus, to identify its target motifs, mecha...

Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX.

A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5' and 3' end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially thoug...

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops.

The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding co...

Genome-wide identification of genic and intergenic neuronal DNA regions bound by Tau protein under physiological and stress conditions.

Tauopathies such as Alzheimer's Disease (AD) are neurodegenerative disorders for which there is presently no cure. They are named after the abnormal oligomerization/aggregation of the neuronal microtubule-associated Tau protein. Besides its role as a microtubule-associated protein, a DNA-binding capacity and a nuclear localization for Tau protein has been described in neurons. While questioning th...

Proteomic and Metabolomic Profiling Identify Plasma Biomarkers for Exposure to Ultra-low Levels of Carfentanil.

Despite the recent epidemic of fentanyl abuse, there are few validated assays capable of rapidly detecting these compounds. In order to improve the ability to detect carfentanil at physiologically relevant concentrations, we developed a systems biology approach to discover host-based markers which are specifically amplified upon exposure in a rabbit model. For this work, two 'omics' pipelines util...

New approach for understanding genome variations in KEGG.

KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of healt...

Longitudinal Cognitive Performance in Individuals at Ultrahigh Risk for Psychosis: A 10-year Follow-up.

It remains unclear whether the onset of psychosis is associated with deterioration in cognitive performance. The aim of this study was to examine the course of cognitive performance in an ultrahigh risk (UHR) cohort, and whether change in cognition is associated with transition to psychosis and change in functioning. Consecutive admissions to Personal Assessment and Crisis Evaluation (PACE) Clinic...

Investigation of the global protein content from healthy human tears.

Considering absence of invasiveness and side effects, tears emerge as a particularly attractive fluid for biomarker discovery and therefore for daily clinical use. However, to date this fluid remains poorly studied in healthy condition. Here, we present an updated in-depth characterisation of the human healthy tear protein composition using proteomics approach. Both eyes of 8 healthy controls (4 m...

Identification of subcellular targeting sequences of Cten reveals its role in cell proliferation.

Spatial and temporal subcellular localization plays critical roles in regulating protein function. Cten (C-terminal tensin like) is a member of the tensin family. Cten recruits signaling molecules, such as DLC1, to focal adhesions, modulates homeostasis of receptor tyrosine kinases, including EGFR and c-Met, and promotes cell migration. These functions are likely controlled by Cten localization at...

On the structure-function of MHC class ii molecules and how single amino acid polymorphisms could alter intracellular trafficking.

Classical HLA class II molecules are highly polymorphic heterodimeric transmembrane proteins encoded by a polygenic cluster on chromosome 6. Polymorphic residues in the membrane-distal domains ensure that a large collection of microbial peptides can be bound in the human population. Still, the HLA-DR, -DP and -DQ isotypes show a high degree of conservation in their overall tertiary and quaternary ...

The MHC in the Era of Next-Generation Sequencing: Implications for Bridging Structure with Function.

The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in tra...

Computational analysis of alternative splicing in plant genomes.

Computational analyses play crucial roles in charactering splicing isoforms in plant genomes. In this review, we provide a survey of computational tools used in recently published, genome-scale splicing analyses in plants. We summarize the commonly used software and pipelines for read mapping, isoform reconstruction, isoform quantification, and differential expression analysis. We also discuss met...

Characterization of quorum sensing genes and N-acyl homoserine lactones in Citrobacter amalonaticus strain YG6.

In the phylum of Proteobacteria, quorum sensing (QS) system is widely driven by synthesis and response of N-acyl homoserine lactone (AHL signalling molecules). AHL is synthesized by LuxI homologue and sensed by LuxR homologue. Once the AHL concentration achieved a threshold level, it triggers the regulation of target genes. In this study, QS activity of Citrobacter amalonaticus strain YG6 which wa...

The correlation of TGFβ1 gene polymorphisms with congenital heart disease susceptibility.

The aim of this study was to investigate the relationship between single nucleotide polymorphisms (SNPs) in transforming growth factor beta 1 (TGFβ1) gene (rs1982073 and rs1800471) and congenital heart disease (CHD) susceptibility.

Comparative transcriptome analysis explores maternal to zygotic transition during Eriocheir sinensis early embryogenesis.

The maternal genome directs almost all aspects of early animal development. As development proceeds, the elimination of maternal gene products and zygotic genome activation (ZGA) occur during the maternal to zygotic transition (MZT). To study the molecular mechanisms regulating this developmental event in Eriocheir sinensis, RNA-Seq technology was applied to generate comprehensive information on t...

The pollution level of the bla carbapenemase gene in coastal water and its host bacteria characteristics.

This paper investigated 10 carbapenemase genes and selected the hosts of these genes in the estuary of Bohai Bay. The results showed that the OXA-58 producer accounted for a large percentage of carbapenem resistant bacteria in the sampling points, whereas the VIM, KPC, NDM, IMP, GES, OXA-23, OXA-24, OXA-48 and OXA-51 producers were not detected in the study. In addition, 9 bacterial genera with 10...

MicroRNA profile analysis for discrimination of monozygotic twins using massively parallel sequencing and real-time PCR.

In general, it is extremely problematic to discriminate between monozygotic twins (MZTs), who share the same genomic DNA sequence, using traditional DNA-based identification methods such as short tandem repeat profiling. MicroRNAs (miRNAs) have shown potential in forensic applications owing to their low molecular weight, abundant and tissue-specific expression. In this study, we utilized massively...

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