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Chao Huang, Hong Liu, Xiuli Gong, Bin Wen, Dan Chen, Jinyuan Liu, Fengliang Hu
Owing to an oversight during the proof checking stage, the above article has been published with the incorrect author listed for correspondence. The first author, Chao Huang, is listed as the corresponding author, although he was only intended to have been temporarily assigned to handle queries during the pre-press stages of the publication. The correct corresponding author should have been listed as Professor Bin Wen (also at the Spleen‑Stomach Institute, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510000, P...
October 25, 2016: Molecular Medicine Reports
Chirag J Patel, Nam Pho, Michael McDuffie, Jeremy Easton-Marks, Cartik Kothari, Isaac S Kohane, Paul Avillach
The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly available in hundreds of files. This Data Descriptor describes a single unified and universally accessible data file, merging across 255 separate files and stitching data across 4 surveys, encompassing 41,474 individuals and 1,191 variables. The variables consist of phenotype and environmental exposure information on each individual, specifically (1) demographic information, physical exam results (e...
October 25, 2016: Scientific Data
Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I Webb, Jiangning Song, Trevor Lithgow
Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance...
October 24, 2016: Briefings in Bioinformatics
Yuan Wang, Fuquan Chen, Man Zhao, Zhe Yang, Shuqin Zhang, Lihong Ye, Hongwei Gao, Xiaodong Zhang
BACKGROUND AND AIM: Aberrant expression of miR-107 is involved in the development of several human cancers. However, the role of miR-107 in hepatocellular carcinoma (HCC) is not well documented. In the present study, we aim to explore the function of miR-107 in hepatocarcinogenesis. METHODS: Bioinformatics analysis was applied to predict the target genes of miR-107. Luciferase reporter gene assay was performed to verify the miR-107 binding sites in 3'-untranslated region (3'UTR) of high mobility group A2 (HMGA2) mRNA...
October 20, 2016: Biochemical and Biophysical Research Communications
Fenix W D Huang, Christian M Reidys
: In this paper we introduce a novel, context-free grammar, RNAFeatures(*), capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures as orientable fatgraphs, which naturally leads to a filtration by their topological genus. Within this framework, RNA secondary structures correspond to pk-structures of genus zero. RNAFeatures(*) acts on formal, arc-labeled RNA secondary structures, called λ-structures. λ-structures correspond one-to-one to pk-structures together with some additional information...
October 20, 2016: Mathematical Biosciences
Christine Yueh, David R Hall, Bing Xia, Dzmitry Padhorny, Dima Kozakov, Sandor Vajda
ClusPro-DC ( implements a straightforward approach to the discrimination between crystallographic and biological dimers by docking the two subunits to exhaustively sample the interaction energy landscape. If a substantial number of low energy docked poses cluster in a narrow vicinity of the native structure of the dimer, then one can assume that there is a well-defined free energy well around the native state, which makes the interaction stable. In contrast, if the interaction sites in the docked poses do not form a large enough cluster around the native structure, then it is unlikely that the subunits form a stable biological dimer...
October 19, 2016: Journal of Molecular Biology
Huma Siddiqui, Tsute Chen, Ardita Aliko, Piotr M Mydel, Roland Jonsson, Ingar Olsen
BACKGROUND: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present. OBJECTIVE: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation...
2016: Journal of Oral Microbiology
Johanna Flygt, Fredrik Clausen, Niklas Marklund
BACKGROUND: Injury to the white matter may lead to impaired neuronal signaling and is commonly observed following traumatic brain injury (TBI). Although endogenous repair of TBI-induced white matter pathology is limited, oligodendrocyte progenitor cells (OPCs) may be stimulated to proliferate and regenerate functionally myelinating oligodendrocytes. Even though OPCs are present throughout the adult brain, little is known about their proliferative activity following axonal injury caused by TBI...
October 17, 2016: Restorative Neurology and Neuroscience
Sujoy Roy, Brandon C Curry, Behrouz Madahian, Ramin Homayouni
BACKGROUND: The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs. RESULTS: For approximately 900 human miRNAs indexed in miRBase, text documents were created by concatenating titles and abstracts of MEDLINE citations which refer to the miRNAs...
October 6, 2016: BMC Bioinformatics
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. RESULTS: In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks...
October 6, 2016: BMC Bioinformatics
Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung
In the post-genomic era, the number of unreviewed protein sequences is remarkably larger and grows tremendously faster than that of reviewed ones. However, existing methods for protein subchloroplast localization often ignore the information from these unlabelled proteins. This paper proposes a multi-label predictor based on ensemble linear neighborhood propagation (LNP), namely LNP-Chlo, which leverages hybrid sequence-based feature information from both labelled and unlabelled proteins for predicting localization of both single- and multi-label chloroplast proteins...
October 21, 2016: Journal of Proteome Research
Fayyaz Ul Amir Afsar Minhas, Amina Asif, Muhammad Arif
: Feature selection and ranking is of great importance in the analysis of biomedical data. In addition to reducing the number of features used in classification or other machine learning tasks, it allows us to extract meaningful biological and medical information from a machine learning model. Most existing approaches in this domain do not directly model the fact that the relative importance of features can be different in different regions of the feature space. In this work, we present a context aware feature ranking algorithm called CAFÉ-Map...
October 11, 2016: Computers in Biology and Medicine
Jawed Iqbal, Mairaj Ahmed Ansari, Binod Kumar, Dipanjan Dutta, Arunava Roy, Leela Chikoti, Gina Pisano, Sujoy Dutta, Shahrooz Vahedi, Mohanan Valiya Veettil, Bala Chandran
IFI16 (gamma-interferon-inducible protein 16), a predominantly nuclear protein involved in transcriptional regulation, also functions as an innate immune response DNA sensor and induces the IL-1β and antiviral type-1 interferon-β (IFN-β) cytokines. We have shown that IFI16, in association with BRCA1, functions as a sequence independent nuclear sensor of episomal dsDNA genomes of KSHV, EBV and HSV-1. Recognition of these herpesvirus genomes resulted in IFI16 acetylation, BRCA1-IFI16-ASC-procaspase-1 inflammasome formation, cytoplasmic translocation, and IL-1β generation...
October 2016: PLoS Pathogens
Shery Park, Hu Zhao, Mark Urata, Yang Chai
Repair of calvarial bony defects remains challenging for craniofacial surgeons. Injury experiments on animal calvarial bones are widely used to study healing mechanisms and test tissue engineering approaches. Previously we identified Gli1+ cells within the calvarial sutures as stem cells supporting calvarial bone turnover and injury repair. In this study, we tested the regenerative capacity of the suture region compared to other areas of calvarial bone. Injuries were made to mouse sagittal sutures or other areas of the calvarial bone at varying distances from the suture...
October 20, 2016: Stem Cells and Development
Kelly L Stauch, Lance M Villeneuve, Phillip R Purnell, Sanjit Pandey, Chittibabu Guda, Howard S Fox
This article reports changes in the striatal non-synaptic mitochondrial proteome of DJ-1, Parkin, and PINK1 knockout (KO) rats at 3 months of age. DJ-1, Parkin, and PINK1 mutations cause autosomal-recessive parkinsonism. It is thought that loss of function of these proteins contributes to the onset and pathogenesis of Parkinson׳s disease (PD). As DJ-1, Parkin, and PINK1 have functions in the regulation of mitochondria, the dataset generated here highlights protein expression changes, which can be helpful for understanding pathological mitochondrial alterations...
December 2016: Data in Brief
Juan Antonio Garcia-Martin, Amir H Bayegan, Ivan Dotu, Peter Clote
BACKGROUND: RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary structure is identical to the target s 0. Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0. RESULTS: We introduce the program RNAdualPF, which computes the dual partition function Z (∗), defined as the sum of Boltzmann factors exp(-E(a,s 0)/RT) of all RNA nucleotide sequences a compatible with target structure s 0...
October 19, 2016: BMC Bioinformatics
Jiajie Huang, Kejie Li, Michael Gribskov
While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint)...
2016: PloS One
Jonathan Sandoval-Castillo, Catherine R M Attard, Shashikanth Marri, Chris J Brauer, Luciana M Möller, Luciano B Beheregaray
Captive breeding programs are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programs have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding...
October 18, 2016: Molecular Ecology Resources
Li Qin, Chan Liu, Ya-Guang Ni, Ya-Ning Shi, Bao-Xue Ao, Zheng Liu, Duan-Fang Liao
OBJECTIVE: Hypertension is closely associated with profound vascular remodeling, especially proliferation and hyperplasia of vascular smooth muscle cells (VSMCs). Aberrant Wnt5a signaling has been related to vascular diseases, but its role on the proliferation of VSMCs is unclear. The study evaluated the effect of Wnt5a on the proliferation of VSMCs and its possible mechanism. DESIGN AND METHOD: The capability of cell proliferation was detected by the assays of MTT, colony formation and EdU cell proliferation...
September 2016: Journal of Hypertension
Yi Wang, Ling Xu, Roger Thilmony, Frank M You, Yong Q Gu, Devin Coleman-Derr
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 ( or PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version...
October 13, 2016: Nucleic Acids Research
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