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https://www.readbyqxmd.com/read/29906448/genomic-dissection-of-bipolar-disorder-and-schizophrenia-including-28-subphenotypes
#1
(no author information available yet)
Schizophrenia and bipolar disorder are two distinct diagnoses that share symptomology. Understanding the genetic factors contributing to the shared and disorder-specific symptoms will be crucial for improving diagnosis and treatment. In genetic data consisting of 53,555 cases (20,129 bipolar disorder [BD], 33,426 schizophrenia [SCZ]) and 54,065 controls, we identified 114 genome-wide significant loci implicating synaptic and neuronal pathways shared between disorders. Comparing SCZ to BD (23,585 SCZ, 15,270 BD) identified four genomic regions including one with disorder-independent causal variants and potassium ion response genes as contributing to differences in biology between the disorders...
June 14, 2018: Cell
https://www.readbyqxmd.com/read/29905836/knotgenome-a-server-to-analyze-entanglements-of-chromosomes
#2
Joanna I Sulkowska, Szymon Niewieczerzal, Aleksandra I Jarmolinska, Jonathan T Siebert, Peter Virnau, Wanda Niemyska
The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial...
June 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29905763/idp-denovo-de-novo-transcriptome-assembly-and-isoform-annotation-by-hybrid-sequencing
#3
Shuhua Fu, Yingke Ma, Hui Yao, Zhichao Xu, Shilin Chen, Jingyuan Song, Kin Fai Au
Motivation: In the past years, the long read (LR) sequencing technologies, such as Pacific Biosciences and Oxford Nanopore Technologies, have been demonstrated to substantially improve the quality of genome assembly and transcriptome characterization. Compared to the high cost of genome assembly by LR sequencing, it is more affordable to generate LRs for transcriptome characterization. That is, when informative transcriptome LR data are available without a high-quality genome, a method for de novo transcriptome assembly and annotation is of high demand...
February 23, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29904936/tpx2-gene-silencing-inhibits-cell-proliferation-and-promotes-apoptosis-through-negative-regulation-of-akt-signaling-pathway-in-ovarian-cancer
#4
Yuan Tian, Lian-Lian Liu, Dong-Mei Guo, Yan Wang, Wen-Hui Zha, Yang Li, Fu-Ju Wu
Ovarian cancer (OC) is the leading cause of death from gynecological malignancy. Accumulated studies have revealed that targeting protein for Xklp2 (TPX2) was tightly associated with the development and progression of OC. The present study further determined a novel mechanism of TPX2 in OC via the AKT signaling pathway. The differentially expressed genes were screened in GEO database for gene expression microarray of OC. Bioinformatics was used to analyze the key differentially expressed genes in OC. We prepared CD133/1+ OC stem cells...
June 15, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29904535/clips-communication-learning-in-practice-for-scientists-a-new-online-resource-leverages-assessment-to-help-students-and-academics-improve-science-communication
#5
Susan Rowland, James Hardy, Kay Colthorpe, Rhianna Pedwell, Louise Kuchel
The ability to communicate is a crucial graduate outcome for science students; however, crowded curricula and large class sizes make it difficult to find time to explicitly teach foundational communication skills. In response to these challenges, we developed an online resource called Communication Learning in Practice for Scientists, or CLIPS. CLIPS provides a multi-point mentoring model that has allowed us to successfully integrate the teaching and learning of a complex set of tacitly-understood skills across multiple scientific disciplines...
2018: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/29904147/dpubchem-a-web-tool-for-qsar-modeling-and-high-throughput-virtual-screening
#6
Othman Soufan, Wail Ba-Alawi, Arturo Magana-Mora, Magbubah Essack, Vladimir B Bajic
High-throughput screening (HTS) performs the experimental testing of a large number of chemical compounds aiming to identify those active in the considered assay. Alternatively, faster and cheaper methods of large-scale virtual screening are performed computationally through quantitative structure-activity relationship (QSAR) models. However, the vast amount of available HTS heterogeneous data and the imbalanced ratio of active to inactive compounds in an assay make this a challenging problem. Although different QSAR models have been proposed, they have certain limitations, e...
June 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29899538/assigning-biological-function-using-hidden-signatures-in-cystine-stabilized-peptide-sequences
#7
S M Ashiqul Islam, Christopher Michel Kearney, Erich J Baker
Cystine-stabilized peptides have great utility as they naturally block ion channels, inhibit acetylcholine receptors, or inactivate microbes. However, only a tiny fraction of these peptides has been characterized. Exploration for novel peptides most efficiently starts with the identification of candidates from genome sequence data. Unfortunately, though cystine-stabilized peptides have shared structures, they have low DNA sequence similarity, restricting the utility of BLAST and even more powerful sequence alignment-based annotation algorithms, such as PSI-BLAST and HMMER...
June 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29899418/linc00462-promotes-pancreatic-cancer-invasiveness-through-the-mir-665-tgfbr1-tgfbr2-smad2-3-pathway
#8
Bin Zhou, Weidong Guo, Chuandong Sun, Bingyuan Zhang, Fang Zheng
Emerging evidence has identified that long non-coding RNAs (lncRNAs) may play an important role in the pathogenesis of many cancers, pancreatic cancer (PC) included. However, the role of linc00462 in PC remains unclear. The aim of our present study was to investigate the potential functions of linc00462 in PC and to identify the underlying mechanisms of action. CCK8 assay, transwell assay, cell cycle assay, cell apoptosis assay, EdU assay, western blot assay, cell adhesion assay, HE staining, IF staining, ELISA assay, vivo growth and metastasis assay, and colony formation assay were performed...
June 13, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29899261/-c-ebp%C3%AE-promotes-stat3-expression-and-affects-cell-apoptosis-and-proliferation-in-porcine-ovarian-granulosa-cells
#9
Xiaolong Yuan, Xiaofeng Zhou, Yingting He, Yuyi Zhong, Ailing Zhang, Zhe Zhang, Hao Zhang, Jiaqi Li
Previous studies suggest that signal transducer and activator of transcription 3 (STAT3) and CCAAT/enhancer binding protein beta (C/EBPβ) play an essential role in ovarian granulosa cells (GCs) for mammalian follicular development. Several C/EBPβ putative binding sites were previously predicted on the STAT3 promoter in mammals. However, the molecular regulation of C/EBPβ on STAT3 and their effects on cell proliferation and apoptosis remain virtually unexplored in GCs. Using porcine GCs as a model, the 5′-deletion, luciferase report assay, mutation, chromatin immunoprecipitation, Annexin-V/PI staining and EdU assays were applied to investigate the molecular mechanism for C/EBPβ regulating the expression of STAT3 and their effects on the cell proliferation and apoptosis ability...
June 13, 2018: Genes
https://www.readbyqxmd.com/read/29897582/pirscan-a-webserver-to-predict-pirna-targeting-sites-and-to-avoid-transgene-silencing-in-c-elegans
#10
Wei-Sheng Wu, Wei-Che Huang, Jordan S Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng-Chi Lee
pirScan is a web-based tool for identifying C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence. The purpose of our tool is to allow C. elegans researchers to predict piRNA targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable. pirScan fulfills this purpose by first enumerating the predicted piRNA-targeting sites present in an input sequence. This prediction can be exported in a tabular or graphical format. Subsequently, pirScan suggests silent mutations that can be introduced to the input sequence that would allow the modified transgene to avoid piRNA targeting...
April 20, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29897488/glycostore-a-database-of-retention-properties-for-glycan-analysis
#11
Sophie Zhao, Ian Walsh, Jodie L Abrahams, Louise Royle, Terry Nguyen-Khuong, Daniel Spencer, Daryl L Fernandes, Nicolle H Packer, Pauline M Rudd, Matthew P Campbell
Summary: GlycoStore is a curated chromatographic, electrophoretic and mass-spectrometry composition database of N-, O-, glycosphingolipid (GSL) glycans and free oligosaccharides associated with a range of glycoproteins, glycolipids and biotherapeutics. The database is built on publicly available experimental data sets from GlycoBase developed in the Oxford Glycobiology Institute and then the National Institute for Bioprocessing Research and Training (NIBRT). It has now been extended to include recently published and in-house data collections from the Bioprocessing Technology Institute (BTI) A*STAR, Macquarie University and Ludger Ltd...
April 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29897414/conics-integrates-scrna-seq-with-dna-sequencing-to-map-gene-expression-to-tumor-sub-clones
#12
Sören Müller, Ara Cho, Siyuan J Liu, Daniel A Lim, Aaron Diaz
Motivation: Single-cell RNA-sequencing (scRNA-seq) has enabled studies of tissue composition at unprecedented resolution. However, the application of scRNA-seq to clinical cancer samples has been limited, partly due to a lack of scRNA-seq algorithms that integrate genomic mutation data. Results: To address this, we present. CONICS: COpy-Number analysis In single-Cell RNA-Sequencing. CONICS is a software tool for mapping gene expression from scRNA-seq to tumor clones and phylogenies, with routines enabling: the quantitation of copy-number alterations in scRNA-seq, robust separation of neoplastic cells from tumor-infiltrating stroma, inter-clone differential-expression analysis, and intra-clone co-expression analysis...
April 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29897411/comorbidity-an-r-package-for-the-systematic-analysis-of-disease-comorbidities
#13
Alba Gutiérrez-Sacristán, Àlex Bravo, Alexia Giannoula, Miguel A Mayer, Ferran Sanz, Laura I Furlong
Motivation: The study of comorbidities is a major priority due to their impact on life expectancy, quality of life and healthcare cost. The availability of electronic health records for data mining offers the opportunity to discover disease associations and comorbidity patterns from the clinical history of patients gathered during routine medical care. This opens the need for analytical tools for detection of disease comorbidities, including the investigation of their underlying genetic basis...
April 20, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29895226/down-regulation-of-circ-prkci-inhibits-cell-migration-and-proliferation-in-hirschsprung-disease-by-suppressing-the-expression-of-mir-1324-target-plcb1
#14
Lingling Zhou, Yang Li, Weiwei Jiang, Hua Zhang, Zechao Wen, Yang Su, Feng Wu, Zhengke Zhi, Qiyang Shen, Hongxing Li, Xiaoqun Xu, Weibing Tang
Circular RNAs (circRNAs) are a novel class of noncoding RNAs (ncRNAs), which have been shown to participate in intracellular RNA regulatory networks and play vital roles in many pathological processes. Recently, circular RNA_PRKCI (circ-PRKCI) has been reported to regulate cell proliferation, migration and invasion in several human cancers. Hirschsprung disease (HSCR) is a well-known congenital gut motility disorder which roots in the aberrance of cranial-caudal neural crest cell migration. In this study, we investigated whether circ-PRKCI may affect cell migration and proliferation in HSCR...
June 12, 2018: Cell Cycle
https://www.readbyqxmd.com/read/29895149/improving-sequence-based-prediction-of-protein-peptide-binding-residues-by-introducing-intrinsic-disorder-and-a-consensus-method
#15
Zijuan Zhao, Zhenling Peng, Jianyi Yang
Protein-peptide interaction is crucial for many cellular processes. It is difficult to determine the interaction by experiments as peptides are often very flexible in structure. Accurate sequence-based prediction of peptide-binding residues can facilitate the study of this interaction. In this work, we developed two novel sequence-based methods SVMpep and PepBind to identify the peptide-binding residues. Recent studies demonstrate that the protein-peptide binding is closely associated with intrinsic disorder...
June 12, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29893550/autonomous-multi-modal-metabolomics-data-integration-for-comprehensive-pathway-analysis
#16
Tao Huan, Amelia Palermo, Julijana Ivanisevic, Duane Rinehart, David Edler, Thiery Phommavongsay, H Paul Benton, Carlos Guijas, Xavier Domingo-Almenara, Benedikt Warth, Gary Siuzdak
Comprehensive metabolomic data can be achieved using multiple orthogonal separation and mass spectrometry (MS) analytical techniques. However, drawing biologically relevant conclusions from this data and combining it with additional layers of data collected by other omic technologies present a significant bioinformatic challenge. To address this, a data processing approach was designed to automate the comprehensive prediction of dysregulated metabolic pathways/networks from multiple data sources. The platform autonomously integrates multiple MS-based metabolomics data types without constraints due to different sample preparation/extraction, chromatographic separation, or MS detection method...
June 12, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29892612/data-for-validation-of-osteometric-methods-in-forensic-anthropology
#17
Natalie R Langley, Lee Meadows Jantz, Shauna McNulty, Heli Maijanen, Stephen D Ousley, Richard L Jantz
Many techniques in forensic anthropology employ osteometric data, although little work has been done to investigate the intrinsic error in these measurements. These data were collected to quantify the reliability of osteometric data used in forensic anthropology research and case analyses. Osteometric data (n = 99 measurements) were collected on a random sample of William M. Bass Donated Collection skeletons (n = 50 skeletons). Four observers measured the left elements of 50 skeletons. After the complete dataset of 99 measurements was collected on each of the 50 skeletons, each observer repeated the process for a total of four rounds...
August 2018: Data in Brief
https://www.readbyqxmd.com/read/29891445/-role-of-allograft-inflammatory-factor-1-in-regulating-the-proliferation-migration-and-apoptosis-of-colorectal-cancer-cells
#18
Xiao-Lan Ai, Fang Yao, Xiao-Jing Wang, Dong-Bei Duan, Ke Li, Zi-You Hu, Guo Yin, Mei Wang, Bing-Yi Wu
OBJECTIVE: To investigate the role of allograft inflammatory factor-1 (AIF-1) in colorectal cancer (CRC) progression and explore the possible mechanism. METHODS: The expression levels of AIF-1 in 70 CRC tissues and paired adjacent tissues were detected using immunohistochemistry and Western blotting, and the correlation of AIF-1 expression with the clinicopathological features of the patients was analyzed. In the CRC cell line SW480, the functional role of AIF-1 in regulating tumor progression was investigated by transfecting the cells with an AIF-1-overexpressing plasmid (AIF-1) and a negative control plasmid (NC)...
May 20, 2018: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://www.readbyqxmd.com/read/29890119/flyxcdb-a-resource-for-drosophila-cell-surface-and-secreted-proteins-and-their-extracellular-domains
#19
Jimin Pei, Lisa N Kinch, Nick V Grishin
Genomes of metazoan organisms possess a large number of genes encoding cell surface and secreted (CSS) proteins that carry out crucial functions in cell adhesion and communication, signal transduction, extracellular matrix establishment, nutrient digestion and uptake, immunity, and developmental processes. We developed the FlyXCDB database (http://prodata.swmed.edu/FlyXCDB) that provides a comprehensive resource to investigate extracellular (XC) domains in CSS proteins of Drosophila melanogaster, the most studied insect model organism in various aspects of animal biology...
June 8, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29889867/tubular-cell-loss-in-early-inv-nphp2-mutant-kidneys-represents-a-possible-homeostatic-mechanism-in-cortical-tubular-formation
#20
Masaki Shigeta, Hirotaka Kanazawa, Takahiko Yokoyama
Inversion of embryonic turning (inv) cystic mice develop multiple renal cysts and are a model for type II nephronophthisis (NPHP2). The defect of planar cell polarity (PCP) by oriented cell division was proposed as the underlying cellular phenotype, while abnormal cell proliferation and apoptosis occur in some polycystic kidney disease models. However, how these cystogenic phenotypes are linked and what is most critical for cystogenesis remain largely unknown. In particular, in early cortical cytogenesis in the inv mutant cystic model, it remains uncertain whether the increased proliferation index results from changes in cell cycle length or cell fate determination...
2018: PloS One
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