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https://www.readbyqxmd.com/read/28214361/identification-of-arabidopsis-genic-and-non-genic-promoters-by-paired-end-sequencing-of-tss-tags
#1
Mutsutomo Tokizawa, Kazutaka Kusunoki, Hiroyuki Koyama, Atsushi Kurotani, Tetsuya Sakurai, Yutaka Suzuki, Tomoaki Sakamoto, Tetsuya Kurata, Yoshiharu Y Yamamoto
Information about transcription start sites (TSSs) provides foundational data for analyses of promoter architecture. In this report, we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers, and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324,461 promoters that covered 79.7% (21,672/27,206) of protein-coding genes in the Arabidopsis genome. In addition, we identified intragenic, antisense, and Orphan promoters that were not associated with any gene models...
February 18, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#2
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#3
Teresa Pankert, Thibaud Jegou, Maïwen Caudron-Herger, Karsten Rippe
Nuclear RNAs emerge as important factors to orchestrate the dynamic organization of the nucleus into functional subcompartments. By tethering RNAs to distinct genomic loci, the RNA-dependent chromatin changes can be dissected by fluorescence microscopic analysis. Here we describe how this approach is implemented in mammalian cells. It involves two high-affinity protein-nucleic acid interactions that can established with number of different protein domains and DNA and RNA sequences. A prototypic system is described here in detail: It consists of the binding of MS2 bacteriophage coat protein to its RNA recognition sequence and the interaction between the bacterial LacI repressor protein to its target lacO operator DNA sequences...
February 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28210467/diversity-and-distribution-of-culturable-lactic-acid-bacterial-species-in-indonesian-sayur-asin
#4
Wibowo Mangunwardoyo, Abinawanto, Andi Salamah, Endang Sukara, Sulistiani, Achmad Dinoto
BACKGROUND AND OBJECTIVES: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. MATERIALS AND METHODS: Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia...
August 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28209553/intraspecific-genetic-variability-in-a-population-of-moroccan-leishmania-infantum-revealed-by-pcr-rflp-of-kdna-minicircles
#5
Adil El Hamouchi, Rajaa Ejghal, Moustapha Hida, Meryem Lemrani
In Morocco, Leishmania infantum is the main etiologic agent of human and canine visceral leishmaniasis (VL). This species has been proven to be an opportunistic agent in HIV+ patients and is also responsible of sporadic cutaneous leishmaniasis (CL).This work aims to evaluate the genetic variability of Moroccan L. infantum strains based on PCR-RFLP analysis of the kinetoplastid DNA (kDNA) minicircles. A total of 75 DNA samples extracted from positive Giemsa-stained smears (n=32) and from L. infantum cultures (n=43) was studied...
February 13, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28209129/orthograph-a-versatile-tool-for-mapping-coding-nucleotide-sequences-to-clusters-of-orthologous-genes
#6
Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis
BACKGROUND: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28208686/identification-of-autophagy-related-genes-and-their-regulatory-mirnas-associated-with-celiac-disease-in-children
#7
Sergio Comincini, Federico Manai, Cristina Meazza, Sara Pagani, Carolina Martinelli, Noemi Pasqua, Gloria Pelizzo, Marco Biggiogera, Mauro Bozzola
Celiac disease (CD) is a severe genetic autoimmune disorder, affecting about one in 100 people, where the ingestion of gluten leads to damage in the small intestine. Diagnosing CD is quite complex and requires blood tests and intestinal biopsy examinations. Controversy exists regarding making the diagnosis without biopsy, due to the large spectrum of manifesting symptoms; furthermore, small-intestinal gastroscopy examinations have a relatively complex management in the pediatric population. To identify novel molecular markers useful to increase the sensitivity and specificity in the diagnosis of pediatric CD patients, the expression levels of two key autophagy executor genes (ATG7 and BECN1) and their regulatory validated miRNAs (miR-17 and miR-30a, respectively) were analyzed by relative quantitative real-time-PCR on a cohort of confirmed CD patients compared to age-related controls...
February 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28207822/identification-classification-and-transcription-profiles-of-the-b-type-response-regulator-family-in-pear
#8
Junbei Ni, Songling Bai, Ling Gao, Minjie Qian, Linbing Zhong, Yuanwen Teng
Type-B response regulators (B-RRs) are transcription factors that function in the final step of two-component signaling systems. In model plants, B-RRs have been shown to play important roles in cytokinin signal transduction. However, the functions of B-RRs in pear have not been well studied. In this report, we conducted a genome-wide analysis and identified 11 putative genes encoding B-PpRR proteins based on the published genome sequence of Pyrus bretschneideri. A phylogenetic tree of the B-PpRR family was constructed, and the motif distribution, chromosome localization, and gene structure of B-PpRR family genes were determined...
2017: PloS One
https://www.readbyqxmd.com/read/28207764/didehydrophenylalanine-an-abundant-modification-in-the-beta-subunit-of-plant-polygalacturonases
#9
Kjell Sergeant, Bruno Printz, Annelie Gutsch, Marc Behr, Jenny Renaut, Jean-Francois Hausman
The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described...
2017: PloS One
https://www.readbyqxmd.com/read/28205635/deciphering-the-distance-to-antibiotic-resistance-for-the-pneumococcus-using-genome-sequencing-data
#10
Fredrick M Mobegi, Amelieke J H Cremers, Marien I de Jonge, Stephen D Bentley, Sacha A F T van Hijum, Aldert Zomer
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205134/minimal-residual-disease-in-acute-lymphoblastic-leukemia-how-to-recognize-and-treat-it
#11
REVIEW
Nicholas J Short, Elias Jabbour
In recent years, the identification of minimal residual disease (MRD) that persists after chemotherapy has emerged as the most powerful tool in determining the prognosis of patients with ALL, often superseding historically relevant prognostic factors. Multiple methods to detect MRD exist, each with their own advantages and disadvantages. Multiparameter flow cytometry and quantitative polymerase chain reaction are the most commonly used methods of MRD detection in clinical practice, although there is promise in the use of more sensitive assays utilizing next-generation sequencing that may be able to further refine MRD-based risk stratification...
January 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28205112/autochthonous-sporadic-acute-hepatitis-e-caused-by-two-distinct-subgenotype-3b-hepatitis-e-virus-strains-with-only-90-nucleotide-identity
#12
Yasuko Yamaguchi, Hitoshi Takagi, Yuhei Suzuki, Kyoko Maruhashi, Takashi Kosone, Satoru Kakizaki, Ken Sato, Masanobu Yamada, Shigeo Nagashima, Masaharu Takahashi, Hiroaki Okamoto
Hepatitis E, which is caused by hepatitis E virus (HEV), is a public health concern in Japan, where the zoonotic food-borne transmission of HEV from domestic pigs and wild boars plays an important role. A 44-year-old Japanese man with autochthonous sporadic acute hepatitis E was admitted with general fatigue and moderate liver dysfunction. In the present study, two distinct HEV strains were recovered from the patient, who had consumed the raw or undercooked pig liver and intestine two or three times per week for 3 months before the disease onset...
February 15, 2017: Clinical Journal of Gastroenterology
https://www.readbyqxmd.com/read/28204975/surface-and-exoproteomes-of-gram-positive-pathogens-for-vaccine-discovery
#13
Massimiliano Biagini, Fabio Bagnoli, Nathalie Norais
Reverse vaccinology has been very successful in the discovery of vaccine candidates against many pathogenic bacteria by integrating genome and proteome mining. This great achievement was facilitated by the complementarity of the in silico prediction of antigens and the empirical data on protein localization, expression, and immunogenicity obtained through different techniques based on electrophoresis, immunoblotting and mass spectrometry. An iterative process between information provided by DNA sequence analysis and proteomic data has been established leading to precise antigen identification...
February 16, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28204905/transcriptome-assembly-and-identification-of-genes-and-snps-associated-with-growth-traits-in-largemouth-bass-micropterus-salmoides
#14
Shengjie Li, Hao Liu, Junjie Bai, Xinping Zhu
Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively...
February 15, 2017: Genetica
https://www.readbyqxmd.com/read/28202731/microfluidic-droplet-platform-for-ultrahigh-throughput-single-cell-screening-of-biodiversity
#15
Stanislav S Terekhov, Ivan V Smirnov, Anastasiya V Stepanova, Tatyana V Bobik, Yuliana A Mokrushina, Natalia A Ponomarenko, Alexey A Belogurov, Maria P Rubtsova, Olga V Kartseva, Marina O Gomzikova, Alexey A Moskovtsev, Anton S Bukatin, Michael V Dubina, Elena S Kostryukova, Vladislav V Babenko, Maria T Vakhitova, Alexander I Manolov, Maja V Malakhova, Maria A Kornienko, Alexander V Tyakht, Anna A Vanyushkina, Elena N Ilina, Patrick Masson, Alexander G Gabibov, Sidney Altman
Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions...
February 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28197949/the-impact-of-next-generation-sequencing-on-the-diagnosis-and-treatment-of-epilepsy-in-paediatric-patients
#16
REVIEW
Davide Mei, Elena Parrini, Carla Marini, Renzo Guerrini
Next-generation sequencing (NGS) has contributed to the identification of many monogenic epilepsy syndromes and is favouring earlier and more accurate diagnosis in a subset of paediatric patients with epilepsy. The cumulative information emerging from NGS studies is rapidly changing our comprehension of the relations between early-onset severe epilepsy and the associated neurological impairment, progressively delineating specific entities previously gathered under the umbrella definition of epileptic encephalopathies, thereby influencing treatment choices and limiting the most aggressive drug regimens only to those conditions that are likely to actually benefit from them...
February 14, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28197140/molecular-characteristics-of-carbapenem-resistant-enterobacter-cloacae-in-ningxia-province-china
#17
Zhiyun Shi, Huizheng Zhao, Gang Li, Wei Jia
The emergence of carbapenem-resistant Enterobacteriaceae (CRE) has become a major public health concern worldwide and a new challenge in the treatment of infectious diseases. The molecular characteristics of Enterobacter cloacae in Ningxia China are unknown. In this study, we reported 10 carbapenem-resistant E. cloacae isolates from the General Hospital of Ningxia Medical University, the largest university hospital in Ningxia between January 2012 and December 2013. Bacteria isolates were identified by Vitek2 compact and the identity of non-duplicate E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28196471/characterization-and-expression-profiling-of-serine-protease-inhibitors-in-the-diamondback-moth-plutella-xylostella-lepidoptera-plutellidae
#18
Hailan Lin, Xijian Lin, Jiwei Zhu, Xiao-Qiang Yu, Xiaofeng Xia, Fengluan Yao, Guang Yang, Minsheng You
BACKGROUND: Serine protease inhibitors (SPIs) have been found in all living organisms and play significant roles in digestion, development and innate immunity. In this study, we present a genome-wide identification and expression profiling of SPI genes in the diamondback moth, Plutella xylostella (L.), a major pest of cruciferous crops with global distribution and broad resistance to different types of insecticides. RESULTS: A total of 61 potential SPI genes were identified in the P...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28195652/identification-of-the-anti-mycobacterial-functional-properties-of-piperidinol-derivatives
#19
Collette S Guy, Esther Tichauer, Gemma L Kay, Daniel J Phillips, Trisha L Bailey, James Harrison, Christopher M Furze, Andrew D Millard, Matthew I Gibson, Mark J Pallen, Elizabeth Fullam
BACKGROUND AND PURPOSE: Tuberculosis (TB) remains a major global health threat and is now the leading cause of death from a single infectious agent worldwide. The current TB drug regimen is inadequate and new anti-tubercular agents are urgently required to be able to successfully combat the increasing prevalence of drug-resistant TB. The purpose of this study was to investigate a piperidinol compound derivative that is highly active against the Mycobacterium tuberculosis bacillus. EXPERIMENTAL APPROACH: The antibacterial properties of the piperidinol compound and its corresponding bis-Mannich base analogue were evaluated against Mycobacterium smegmatis and Gram-negative organisms...
February 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28194922/identification-of-the-novel-hla-b-13-83-allele-by-polymerase-chain-reaction-sequence-based-typing-in-a-chinese-cord-blood-donor
#20
J He, N-Y Chen, Z-D Han, W Zhang, F-M Zhu
HLA-B*13:83 differs from HLA-B*13:01:01 by 2 nucleotide substitutions at positions 103 and 106.
February 13, 2017: HLA
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