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https://www.readbyqxmd.com/read/29471546/longitudinal-analyses-of-blood-transcriptome-during-conversion-to-psychosis
#1
Boris Chaumette, Oussama Kebir, Juliette Pouch, Bertrand Ducos, Fekrije Selimi, Raphael Gaillard, Marie-Odile Krebs
The biological processes associated with the onset of schizophrenia remain largely unknown. Current hypotheses favor gene × environment interactions as supported by our recent report about DNA methylation changes during the onset of psychosis. Here, we conducted the first longitudinal transcriptomic analysis of blood samples from 31 at-risk individuals who later converted to psychosis and 63 at-risk individuals who did not. Individuals were followed for a maximum of 1 year. Blood samples were collected at baseline and at the end of follow-up and individuals served as their own controls...
February 17, 2018: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29471523/liver-transcriptomic-and-plasma-metabolomic-profiles-of-fattening-lambs-are-modified-by-feed-restriction-during-the-suckling-period
#2
A Santos, F J Giráldez, E Trevisi, L Lucini, J Frutos, S Andrés
The increasing world population is driving demand for improved efficiency of feed resources of livestock. However, the molecular mechanisms behind various feed efficiency traits and their regulation by nutrition remain poorly understood. Here we aimed to identify differentially expressed (DE) genes in the liver tissues of fattening Merino lambs and differences in metabolites accumulated in plasma to identify modified metabolic pathways as a consequence of milk restriction during the suckling period. Twenty-four male Merino lambs (4...
February 19, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29471506/a-translational-silencing-function-of-mcpip1-regnase-1-specified-by-the-target-site-context
#3
Gesine Behrens, Reinhard Winzen, Nina Rehage, Anneke Dörrie, Monika Barsch, Anne Hoffmann, Jörg Hackermüller, Christopher Tiedje, Vigo Heissmeyer, Helmut Holtmann
The expression of proteins during inflammatory and immune reactions is coordinated by post-transcriptional mechanisms. A particularly strong suppression of protein expression is exerted by a conserved translational silencing element (TSE) identified in the 3' UTR of NFKBIZ mRNA, which is among the targets of the RNA-binding proteins Roquin-1/2 and MCPIP1/Regnase-1. We present evidence that in the context of the TSE MCPIP1, so far known for its endonuclease activity toward mRNAs specified by distinct stem-loop (SL) structures, also suppresses translation...
February 19, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29471354/a-coliform-targeted-metagenomic-method-facilitating-human-exposure-estimates-to-escherichia-coli-borne-antibiotic-resistance-genes
#4
A F C Leonard, X L Yin, T Zhang, M Hui, W H Gaze
Background: Antimicrobial resistance and the spread of antibiotic resistance genes (ARGs) poses a threat to human health. Community-acquired infections resistant to treatment with first-line antibiotics are increasing, and there are few studies investigating environmental exposures and transmission. Aim: To develop a novel targeted metagenomic method to quantify the abundance and diversity of ARGs in a faecal indicator bacterium, and to estimate human exposure to resistant bacteria in a natural environment...
February 19, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29471115/targeted-next-generation-sequencing-is-a-sensitive-tool-for-differential-diagnosis-of-myelodysplastic-syndromes-in-bone-marrow-trephines
#5
Andreas Bräuninger, Wolfgang Blau, Kristin Kunze, Ann-Kathrin Desch, Alexander Brobeil, Mehmet Kemal Tur, Benjamin Etschmann, Ulrich Günther, Dieter Körholz, Georg Schliesser, Andreas Käbisch, Michael Kiehl, Mathias Rummel, Stefan Gattenlöhner
Myelodysplastic syndromes are hematological neoplasias in which immunohistological examination of bone-marrow trephines is important for a definite diagnosis. Unequivocal distinction from reactive bone-marrow changes is, however, sometimes difficult. As neoplastic clones in myelodysplastic syndrome carry mutations in recurrent genes, mutation detection by targeted next-generation sequencing may be a useful support for differential diagnosis. To elucidate the accuracy of this approach in the clinical diagnostic setting, we analyzed single and consecutive bone-marrow trephines processed for immunohistological examination from 145 patients by targeted next-generation sequencing of 12 genes recurrently mutated in myelodysplastic syndromes...
February 19, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29471113/validation-of-a-customized-bioinformatics-pipeline-for-a-clinical-next-generation-sequencing-test-targeting-solid-tumor-associated-variants
#6
Thomas Schneider, Geoffrey H Smith, Michael R Rossi, Charles E Hill, Linsheng Zhang
Bioinformatic analysis is an integral and critical part of clinical next-generation sequencing. It is especially challenging for some pipelines to consistently identify insertions and deletions. We present the validation of an open source tumor amplicon pipeline (OTA-pipeline) for clinical next-generation sequencing targeting solid tumor-associated variants. Raw data generated from 557 TruSight Tumor 26 samples as well as in silico data were analyzed by the OTA-pipeline and legacy pipeline and compared. Discrepant results were confirmed by orthogonal methods...
February 19, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29470497/most-yeast-sh3-domains-bind-peptide-targets-with-high-intrinsic-specificity
#7
Tom Brown, Nick Brown, Elliott J Stollar
A need exists to develop bioinformatics for predicting differences in protein function, especially for members of a domain family who share a common fold, yet are found in a diverse array of proteins. Many domain families have been conserved over large evolutionary spans and representative genomic data during these periods are now available. This allows a simple method for grouping domain sequences to reveal common and unique/specific binding residues. As such, we hypothesize that sequence alignment analysis of the yeast SH3 domain family across ancestral species in the fungal kingdom can determine whether each member encodes specific information to bind unique peptide targets...
2018: PloS One
https://www.readbyqxmd.com/read/29470107/leptospira-genomospecies-and-sequence-type-prevalence-in-small-mammal-populations-in-germany
#8
Stefan Fischer, Anne Mayer-Scholl, Christian Imholt, Nastasja G Spierling, Elisa Heuser, Sabrina Schmidt, Daniela Reil, Ulrike M Rosenfeld, Jens Jacob, Karsten Nöckler, Rainer G Ulrich
Leptospirosis is a worldwide emerging infectious disease caused by zoonotic bacteria of the genus Leptospira. Numerous mammals, including domestic and companion animals, can be infected by Leptospira spp., but rodents and other small mammals are considered the main reservoir. The annual number of recorded human leptospirosis cases in Germany (2001-2016) was 25-166. Field fever outbreaks in strawberry pickers, due to infection with Leptospira kirschneri serovar Grippotyphosa, were reported in 2007 and 2014. To identify the most commonly occurring Leptospira genomospecies, sequence types (STs), and their small mammal host specificity, a monitoring study was performed during 2010-2014 in four federal states of Germany...
February 22, 2018: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/29469858/high-performance-color-sequence-particle-streak-velocimetry-for-3d-airflow-measurement
#9
Huan Wang, Guijin Wang, Xianting Li
In this paper, a high-performance color sequence particle streak velocimetry (CSPSV) technique is proposed to measure the air velocity in a large three-dimensional (3D) space. Based on the basic principle of CSPSV, a new color sequence illumination pattern is designed to mark seeding bubbles for better imaging performance. Synchronized with the illumination system, cameras record the targets' paths at the start, middle, and end points with different color information more clearly. Thus, a rectification-based stereo corresponding algorithm is presented to reconstruct the 3D trajectory of the bubbles...
February 20, 2018: Applied Optics
https://www.readbyqxmd.com/read/29469596/genome-scale-metabolic-models-as-platforms-for-identification-of-novel-genes-as-antimicrobial-drug-targets
#10
Bashir Sajo Mienda, Rabiu Salihu, Aliyu Adamu, Shehu Idris
The growing number of multidrug-resistant pathogenic bacteria is becoming a world leading challenge for the scientific community and for public health. However, advances in high-throughput technologies and whole-genome sequencing of bacterial pathogens make the construction of bacterial genome-scale metabolic models (GEMs) increasingly realistic. The use of GEMs as an alternative platforms will expedite identification of novel unconditionally essential genes and enzymes of target organisms with existing and forthcoming GEMs...
February 22, 2018: Future Microbiology
https://www.readbyqxmd.com/read/29469323/-molecular-epidemiology-of-cryptosporidium-infection-in-infants-with-diarrhea-in-wuhan-city
#11
Liu Xiao-Jie, Mao Tie-Bo, Wu Peng, Zhou Rui
OBJECTIVE: To understand the prevalence of Cryptosporidium infection in diarrhea infants under 2 years old in Wuhan City, so as to provide the epidemiological evidence for the prevention and treatment of cryptosporidiosis. METHODS: The fecal samples from infants under 2 years old with diarrhea were collected in Hubei General Hospital and Central South Hospital in Wuhan City, Hubei Province from August 2014 to July 2015. The fecal samples were stored in 2.5% potassium dichromate at 4 ℃ after filtered...
March 14, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
https://www.readbyqxmd.com/read/29469149/technical-aspects-of-nicking-enzyme-assisted-amplification
#12
Liu Wang, Cheng Qian, Hui Wu, Wenjuan Qian, Rui Wang, Jian Wu
Nicking enzyme assisted amplification (NEAA) is an extremely rapid method for molecular diagnosis. However, this technology is not widely applied for real sample analysis because the overproduced non-specific products limit its sensitivity and raise the threshold of detection methods. Here, we have found that the non-specific amplification is mainly caused by the coexistence of Bst polymerase, nicking primers and dNTP. The highly active nicking enzyme directs and accelerates the non-specific amplification in a way which favors nicking...
February 22, 2018: Analyst
https://www.readbyqxmd.com/read/29468924/emerging-molecular-target-antagonists-for-the-treatment-of-biliary-tract-cancer
#13
Pasquale Lombardi, Donatella Marino, Elisabetta Fenocchio, Giovanna Chilà, Massimo Aglietta, Francesco Leone
Biliary tract cancers (BTCs) are a heterogeneous group of cancers, characterized by low incidence but poor prognosis. Even after complete surgical resection for early stage, relapse is frequent and the lack of effective treatments contributes to the dismal prognosis. To date, the only standard treatment in first-line is cisplatin/gemcitabine combination, whereas no standard in 2nd -line has been defined. Hence, the current goal is to better understand the biology of BTCs, discovering new treatment methods and improving clinical outcomes...
February 22, 2018: Expert Opinion on Emerging Drugs
https://www.readbyqxmd.com/read/29468660/spatiotemporal-homogeneity-and-distinctness-of-the-t-cell-receptor-%C3%AE-chain-repertoires-in-epstein-barr-virus-associated-primary-and-metastatic-nasopharyngeal-carcinomas
#14
Yih-Lin Chung, Mei-Ling Wu
Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated lymphoepithelioma. The aim of the present study was to characterize the homogeneity and distinctness of the T-cell repertoires within and between primary and metastatic NPCs. We used ultra-deep sequencing of the hypervariably rearranged antigen-binding CDR3 regions of T-cell receptor beta (TCRbeta ) to comprehensively profile the T-cell repertoires in NPC patients receiving definitive chemoradiotherapy with long-term follow-up. We observed not only various spatially heterogeneous patient-specific TCRbeta clone compositions that changed with time but also several commonly enriched TCRbeta subclones that were constantly shared between primary NPCs in the head and neck regions, locally recurrent tumors after treatment, and later-developed distant metastatic tumors in the liver, lung and bone...
February 22, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29468550/detection-of-e2f-dna-complexes-using-chromatin-immunoprecipitation-assays
#15
Miyoung Lee, Lorraine J Gudas, Harold I Saavedra
Chromatin immunoprecipitation (ChIP), originally developed by John T. Lis and David Gilmour in 1984, has been useful to detect DNA sequences where protein(s) of interest bind. ChIP is comprised of several steps: (1) cross-linking of proteins to target DNA sequences, (2) breaking genomic DNA into 300-1000 bp pieces by sonication or nuclease digestion, (3) immunoprecipitation of protein bound to target DNA with an antibody, (4) reverse cross-linking between target DNA and the bound protein to liberate the DNA fragments, and (5) amplification of target DNA fragment by PCR...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29468546/detection-of-ccnd1-locus-amplification-by-fluorescence-in-situ-hybridization
#16
Margit Balázs, Viktória Koroknai, István Szász, Szilvia Ecsedi
It is well known that chromosomal aberrations of tumors are associated with the initiation and progression of malignancy. Fluorescence in situ hybridization (FISH) is a powerful, rapid method to detect chromosome copy number and structural alterations in tissue sections, chromosome, or interphase cellular preparations via hybridization of complementary probe sequences. The technique is based on the complementary nature of DNA double strands, which allows fluorescently labeled DNA probes to be used as probes to label the complementary sequences of target cells, chromosomes, and tissues...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29467872/differential-microrna-expression-profiles-in-tamoxifen-resistant-human-breast-cancer-cell-lines-induced-by-two-methods
#17
Peng Ye, Cheng Fang, Hui Zeng, Yu Shi, Zhongya Pan, Nairui An, Keli He, Li Zhang, Xinghua Long
Tamoxifen (TAM) resistance has become a severe problem for endocrine therapy of breast cancer. The present study investigated the association between microRNA (miRNA) expression and TAM resistance in breast cancer. The TAM-resistant breast cancer MCF-7C and MCF-7T cell lines were established using the human breast cancer cell line MCF-7 as the parental cell line and 4-hydroxytamoxifen (OHT) as the screening drug in vitro . The MCF-7C cell line was established by dose stepwise induction beginning with a low concentration of OHT; the MCF-7T cell line was established by temporal stepwise induction beginning with a high concentration of OHT...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29467864/therapeutic-targeting-of-noncoding-rnas-in-hepatocellular-carcinoma-recent-progress-and-future-prospects
#18
Zhangang Xiao, Jing Shen, Lin Zhang, Mingxing Li, Wei Hu, Chihin Cho
Due to the high mortality rate and unsatisfactory treatment options available, hepatocellular carcinoma (HCC) remains one of the most common malignancies and a leading cause of cancer-associated mortality. Novel therapeutic targets for HCC are urgently required. Advanced RNA sequencing technology enables the identification of considerable amounts of noncoding RNAs (ncRNAs), including small noncoding RNAs and long noncoding RNAs, which exhibit no protein-coding activities. In this respect, ncRNAs and their regulatory processes are important factors in liver tumorigenesis...
March 2018: Oncology Letters
https://www.readbyqxmd.com/read/29467792/evaluation-of-bioinformatics-approaches-for-next-generation-sequencing-analysis-of-micrornas-with-a-toxicogenomics-study-design
#19
Halil Bisgin, Binsheng Gong, Yuping Wang, Weida Tong
MicroRNAs (miRNAs) are key post-transcriptional regulators that affect protein translation by targeting mRNAs. Their role in disease etiology and toxicity are well recognized. Given the rapid advancement of next-generation sequencing techniques, miRNA profiling has been increasingly conducted with RNA-seq, namely miRNA-seq. Analysis of miRNA-seq data requires several steps: (1) mapping the reads to miRBase, (2) considering mismatches during the hairpin alignment (windowing), and (3) counting the reads (quantification)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29467791/next-generation-sequencing-methods-for-diagnosis-of-epilepsy-syndromes
#20
REVIEW
Paul Dunn, Cassie L Albury, Neven Maksemous, Miles C Benton, Heidi G Sutherland, Robert A Smith, Larisa M Haupt, Lyn R Griffiths
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS)...
2018: Frontiers in Genetics
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