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https://www.readbyqxmd.com/read/29652489/predominance-of-n6-methyladenine-specific-dna-fragments-enriched-by-multiple-immunoprecipitation
#1
Xiaoling Liu, Weiyi Lai, Ning Zhang, Hailin Wang
N6-methyladenine (6mA) is a re-discovered DNA modification in eukaryotic genomes. To explore the distribution and functions of 6mA, it is of paramount option to use immunoprecipitation to select 6mA-containing DNA fragments for genome-wide sequencing. Presumably, most of 6mA-free fragments is removed, and the co-pulling down of the residual is stochastic and sequence-independent and thus they should not be called as peaks by computation. Surprisingly, here we show the pre-dominance of 6mA-free fragments in the pulled-down fractions...
April 13, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29619629/effect-of-kynurenic-acid-on-pupae-viability-of-drosophila-melanogaster-cinnabar-and-cardinal-eye-color-mutants-with-altered-tryptophan-kynurenine-metabolism
#2
Valeriya Navrotskaya, Artur Wnorowski, Waldemar Turski, Gregory Oxenkrug
Kynurenic acid (KYNA) is one of the metabolites of evolutionary conserved tryptophan (Trp)/kynurenine (Kyn) metabolic pathway. Elevation of KYNA contributes to development of psychosis in schizophrenia but attenuates neurodegeneration in Drosophila model of Huntington's disease. We have reported that KYNA increased lethality of pupae of wild-type flies, but not of vermilion (v) mutants with impaired formation of Kyn from Trp, suggesting that KYNA toxicity depends on its interaction with downstream Kyn metabolites [i...
April 4, 2018: Neurotoxicity Research
https://www.readbyqxmd.com/read/29522145/golabeler-improving-sequence-based-large-scale-protein-function-prediction-by-learning-to-rank
#3
Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
Motivation: Gene Ontology (GO) has been widely used to annotate functions of proteins and understand their biological roles. Currently only <1% of more than 70 million proteins in UniProtKB have experimental GO annotations, implying the strong necessity of automated function prediction (AFP) of proteins, where AFP is a hard multilabel classification problem due to one protein with a diverse number of GO terms. Most of these proteins have only sequences as input information, indicating the importance of sequence-based AFP (SAFP: sequences are the only input)...
March 7, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29504913/circadian-succession-of-molecular-processes-in-living-tissues
#4
Abeer Fadda, Mohammed El Anbari, Andrey Ptitsyn
BACKGROUND: Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression activity. Timing of gene expression is controlled by internal molecular clock keeping steady periodic expression. In this study, we shift attention towards a broad range of periodically expressed genes involved in multiple cellular functions which may or may not be under direct control of the intrinsic circadian clock...
February 13, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29472763/-rhachotropis-eusiroidea-amphipoda-from-the-north-east-atlantic
#5
Anne-Nina Lörz, Anne Helene S Tandberg, Endre Willassen, Amy Driskell
The genus Rhachotropis has the widest geographic and bathymetric distribution of all amphipod genera worldwide. Molecular and morphological investigations of specimens sampled around Iceland and off the Norwegian coast allow the first insights into the relationships of North East Atlantic Rhachotropis . The 31 cytochrome oxidase subunit I (COI) sequences generated for this study were assigned 13 Barcode Index Numbers (BINs) in the Barcode of Life database (BOLD), of which 12 are new to the database. Molecular analyses of COI and 16S sequences could not confirm a theory that depth has a greater influence on the phylogeny of Rhachotropis than geographic distance...
2018: ZooKeys
https://www.readbyqxmd.com/read/29116686/protocols-for-the-design-of-kinase-focused-compound-libraries
#6
Edgar Jacoby, Berthold Wroblowski, Christophe Buyck, Jean-Marc Neefs, Christophe Meyer, Maxwell D Cummings, Herman van Vlijmen
Protocols for the design of kinase-focused compound libraries are presented. Kinase-focused compound libraries can be differentiated based on the design goal. Depending on whether the library should be a discovery library specific for one particular kinase, a general discovery library for multiple distinct kinase projects, or even phenotypic screening, there exists today a variety of in silico methods to design candidate compound libraries. We address the following scenarios: 1) Datamining of SAR databases and kinase focused vendor catalogues; 2) Predictions and virtual screening; 3) Structure-based design of combinatorial kinase inhibitors; 4) Design of covalent kinase inhibitors; 5) Design of macrocyclic kinase inhibitors; and 6) Design of allosteric kinase inhibitors and activators...
November 8, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28828200/pathedex-uncovering-high-explanatory-visual-diagnostics-heuristics-using-digital-pathology-and-multiscale-gaze-data
#7
Dmitriy Shin, Mikhail Kovalenko, Ilker Ersoy, Yu Li, Donald Doll, Chi-Ren Shyu, Richard Hammer
BACKGROUND: Visual heuristics of pathology diagnosis is a largely unexplored area where reported studies only provided a qualitative insight into the subject. Uncovering and quantifying pathology visual and nonvisual diagnostic patterns have great potential to improve clinical outcomes and avoid diagnostic pitfalls. METHODS: Here, we present PathEdEx, an informatics computational framework that incorporates whole-slide digital pathology imaging with multiscale gaze-tracking technology to create web-based interactive pathology educational atlases and to datamine visual and nonvisual diagnostic heuristics...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28822333/virtual-screening-and-repositioning-of-inconclusive-molecules-of-beta-lactamase-bioassays-a-data-mining-approach
#8
Akshata Gad, Andrew Titus Manuel, Jinuraj K R, Lijo John, Sajeev R, Shanmuga Priya V G, Abdul Jaleel U C
This study focuses on the best possible way forward in utilizing inconclusive molecules of PubChem bioassays AID 1332, AID 434987 and AID 434955, which are related to beta-lactamase inhibitors of Mycobacterium tuberculosis (Mtb). The inadequacy in the experimental methods that were observed during the invitro screening resulted in an inconclusive dataset. This could be due to certain moieties present within the molecules. In order to reconsider such molecules, insilico methods can be suggested in place of invitro methods For instance, datamining and medicinal chemistry methods: have been adopted to prioritise the inconclusive dataset into active or inactive molecules...
October 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28755319/a-novel-family-of-proline-serine-rich-proteins-which-are-phospho-targets-of-stress-related-mitogen-activated-protein-kinases-differentially-regulates-growth-and-pathogen-defense-in-arabidopsis-thaliana
#9
Mieder Anthony Thomas Palm-Forster, Lennart Eschen-Lippold, Joachim Uhrig, Dierk Scheel, Justin Lee
The molecular actions of mitogen-activated protein kinases (MAPKs) are ultimately accomplished by the substrate proteins where phosphorylation affects their molecular properties and function(s), but knowledge regarding plant MAPK substrates is currently still fragmentary. Here, we uncovered a previously uncharacterized protein family consisting of three proline/serine-rich proteins (PRPs) that are substrates of stress-related MAPKs. We demonstrated the importance of a MAPK docking domain necessary for protein-protein interaction with MAPKs and consequently also for phosphorylation...
September 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28740629/comparison-of-coronary-artery-disease-guidelines-with-extracted-knowledge-from-data-mining
#10
Peyman Rezaei-Hachesu, Azadeh Oliyaee, Naser Safaie, Reza Ferdousi
Introduction: Coronary artery disease (CAD) is one of the major causes of disability and death in the world. Accordingly utilizing from a national and update guideline in heart-related disease are essential. Finding interesting rules from CAD data and comparison with guidelines was the objectives of this study. Methods: In this study 1993 valid and completed records related to patients (from 2009 to 2014) who had suffered from CAD were recruited and analyzed. Total of 25 variable including a target variable (CAD) and 24 inputs or predictor variables were used for knowledge discovery...
2017: Journal of Cardiovascular and Thoracic Research
https://www.readbyqxmd.com/read/28669163/analyzing-a-lung-cancer-patient-dataset-with-the-focus-on-predicting-survival-rate-one-year-after-thoracic-surgery
#11
Peyman Rezaei Hachesu, Nazila Moftian, Mahsa Dehghani, Taha Samad Soltani
Background: Data mining, a new concept introduced in the mid-1990s, can help researchers to gain new, profound insights and facilitate access to unanticipated knowledge sources in biomedical datasets. Many issues in the medical field are concerned with the diagnosis of diseases based on tests conducted on individuals at risk. Early diagnosis and treatment can provide a better outcome regarding the survival of lung cancer patients. Researchers can use data mining techniques to create effective diagnostic models...
June 25, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28574840/methylation-regulates-hey1-expression-in-glioblastoma
#12
Andrew J Tsung, Maheedhara R Guda, Swapna Asuthkar, Collin M Labak, Ian J Purvis, Yining Lu, Neha Jain, Sarah E Bach, Durbaka V R Prasad, Kiran K Velpula
Glioblastoma (GBM) remains one of the most lethal and difficult-to-treat cancers of the central nervous system. The poor prognosis in GBM patients is due in part to its resistance to available treatments, which calls for identifying novel molecular therapeutic targets. In this study, we identified a mediator of Notch signaling, HEY1, whose methylation status contributes to the pathogenesis of GBM. Datamining studies, immunohistochemistry and immunoblot analysis showed that HEY1 is highly expressed in GBM patient specimens...
July 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28413565/enrichment-of-in-vivo-transcription-data-from-dietary-intervention-studies-with-in-vitro-data-provides-improved-insight-into-gene-regulation-mechanisms-in-the-intestinal-mucosa
#13
Marcel Hulst, Alfons Jansman, Ilonka Wijers, Arjan Hoekman, Stéphanie Vastenhouw, Marinus van Krimpen, Mari Smits, Dirkjan Schokker
BACKGROUND: Gene expression profiles of intestinal mucosa of chickens and pigs fed over long-term periods (days/weeks) with a diet rich in rye and a diet supplemented with zinc, respectively, or of chickens after a one-day amoxicillin treatment of chickens, were recorded recently. Such dietary interventions are frequently used to modulate animal performance or therapeutically for monogastric livestock. In this study, changes in gene expression induced by these three interventions in cultured "Intestinal Porcine Epithelial Cells" (IPEC-J2) recorded after a short-term period of 2 and 6 hours, were compared to the in vivo gene expression profiles in order to evaluate the capability of this in vitro bioassay in predicting in vivo responses...
2017: Genes & Nutrition
https://www.readbyqxmd.com/read/28346329/cardiac-computed-tomography-radiomics-a-comprehensive-review-on-radiomic-techniques
#14
Márton Kolossváry, Miklós Kellermayer, Béla Merkely, Pál Maurovich-Horvat
Radiologic images are vast three-dimensional data sets in which each voxel of the underlying volume represents distinct physical measurements of a tissue-dependent characteristic. Advances in technology allow radiologists to image pathologies with unforeseen detail, thereby further increasing the amount of information to be processed. Even though the imaging modalities have advanced greatly, our interpretation of the images has remained essentially unchanged for decades. We have arrived in the era of precision medicine where even slight differences in disease manifestation are seen as potential target points for new intervention strategies...
March 24, 2017: Journal of Thoracic Imaging
https://www.readbyqxmd.com/read/27966577/salivary-and-pellicle-proteome-a-datamining-analysis
#15
Hardy Schweigel, Michael Wicht, Falk Schwendicke
We aimed to comprehensively compare two compartmented oral proteomes, the salivary and the dental pellicle proteome. Systematic review and datamining was used to obtain the physico-chemical, structural, functional and interactional properties of 1,515 salivary and 60 identified pellicle proteins. Salivary and pellicle proteins did not differ significantly in their aliphatic index, hydrophaty, instability index, or isoelectric point. Pellicle proteins were significantly more charged at low and high pH and were significantly smaller (10-20 kDa) than salivary proteins...
December 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924046/new-data-and-features-for-advanced-data-mining-in-manteia
#16
Olivier Tassy
Manteia is an integrative database available online at http://manteia.igbmc.fr which provides a large array of OMICs data related to the development of the mouse, chicken, zebrafish and human. The system is designed to use different types of data together in order to perform advanced datamining, test hypotheses or provide candidate genes involved in biological processes or responsible for human diseases. In this new version of the database, Manteia has been enhanced with new expression data originating from microarray and next generation sequencing experiments...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27622813/pits-a-protein-interacting-with-ttk69-and-sin3a-has-links-to-histone-deacetylation
#17
Gwo-Jen Liaw
Histone deacetylation plays an important role in transcriptional repression. Previous results showed that the genetic interaction between ttk and rpd3, which encodes a class I histone deacetylase, is required for tll repression. This study investigated the molecular mechanism by which Ttk69 recruits Rpd3. Using yeast two-hybrid screening and datamining, one novel protein was found that weakly interacts with Ttk69 and Sin3A, designated as Protein interacting with Ttk69 and Sin3A (Pits). Pits protein expressed in the early stages of embryos and bound to the region of the tor response element in vivo...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27553711/analyses-of-htlv-1-sequences-suggest-interaction-between-orf-i-mutations-and-ham-tsp-outcome
#18
Fernanda Khouri Barreto, Ricardo Khouri, Filipe Ferreira de Almeida Rego, Luciane Amorim Santos, Maria Fernanda de Castro-Amarante, Izabela Bialuk, Cynthia A Pise-Masison, Bernardo Galvão-Castro, Antoine Gessain, Steven Jacobson, Genoveffa Franchini, Luiz Carlos Alcantara
The region known as pX in the 3' end of the human T-cell lymphotropic virus type 1 (HTLV-1) genome contains four overlapping open reading frames (ORF) that encode regulatory proteins. HTLV-1 ORF-I produces the protein p12 and its cleavage product p8. The functions of these proteins have been linked to immune evasion and viral infectivity and persistence. It is known that the HTLV-1 infection does not necessarily imply the development of pathological processes and here we evaluated whether natural mutations in HTLV-1 ORF-I can influence the proviral load and clinical manifestation of HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP)...
November 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27505347/the-methanogenic-redox-cofactor-f-420-is-widely-synthesized-by-aerobic-soil-bacteria
#19
Blair Ney, F Hafna Ahmed, Carlo R Carere, Ambarish Biswas, Andrew C Warden, Sergio E Morales, Gunjan Pandey, Stephen J Watt, John G Oakeshott, Matthew C Taylor, Matthew B Stott, Colin J Jackson, Chris Greening
F420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F420 biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes...
January 2017: ISME Journal
https://www.readbyqxmd.com/read/27491037/improving-trnascan-se-annotation-results-via-ensemble-classifiers
#20
Quan Zou, Jiasheng Guo, Ying Ju, Meihong Wu, Xiangxiang Zeng, Zhiling Hong
tRNAScan-SE is a tRNA detection program that is widely used for tRNA annotation; however, the false positive rate of tRNAScan-SE is unacceptable for large sequences. Here, we used a machine learning method to try to improve the tRNAScan-SE results. A new predictor, tRNA-Predict, was designed. We obtained real and pseudo-tRNA sequences as training data sets using tRNAScan-SE and constructed three different tRNA feature sets. We then set up an ensemble classifier, LibMutil, to predict tRNAs from the training data...
November 2015: Molecular Informatics
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