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https://www.readbyqxmd.com/read/28742982/investigation-of-orthologous-pathogen-recognition-gene-rich-regions-in-solanaceous-species
#1
A Di Donato, Giuseppe Andolfo, A Ferrarini, M Delledonne, M R Ercolano
The genome architecture of pathogen receptor genes (PRGs) was extensively investigated in several plant species. However, we still know little about their elaborate reorganization arose during the plant speciation process. Using recently released pepper and eggplant genome sequences we were able to identify 1097 pathogen recognition genes in pepper Zunla-1 and 775 in eggplant Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping...
July 25, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28742980/disease-relevant-modifications-of-the-methylome-and-transcriptome-by-particulate-matter-pm2-5-from-biomass-combustion
#2
Katharina Heßelbach, Gwang-Jin Kim, Stephan Flemming, Thomas Häupl, Marc Bonin, Regina Dornhof, Stefan Günther, Irmgard Merfort, Matjaz Humar
Exposure to particulate matter (PM) is recognized as a major health hazard, but molecular responses are still insufficiently described. We analyzed the epigenetic impact of ambient PM2.5 from biomass combustion on the methylome of primary human bronchial epithelial BEAS-2B cells using the Illumina HumanMethylation450 BeadChip. The transcriptome was determined by the Affymetrix HG-U133 Plus 2.0 Array. PM2.5 induced genome wide alterations of the DNA methylation pattern, including differentially methylated CpGs in the promoter region associated with CpG islands...
July 25, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28742460/resistance-genes-in-global-crop-breeding-networks
#3
Karen A Garrett, Kelsey F Andersen, Frank Asche, Robert Bowden, Greg Forbes, Peter Kulakow, Bo Zhou
Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks...
July 25, 2017: Phytopathology
https://www.readbyqxmd.com/read/28742459/identification-of-clusters-that-condition-resistance-to-anthracnose-in-the-common-bean-differential-cultivars-ab136-and-mdrk
#4
Ana Campa, Noemi Trabanco, Juan Jose Ferreira
The correct identification of the anthracnose resistance systems present in the common bean cultivars AB136 and MDRK is important because both are included in the set of 12 differential cultivars proposed for use in classifying the races of the anthracnose causal agent, Colletrotrichum lindemuthianum. In this work, the responses against seven C. lindemuthianum races were analyzed in a recombinant inbred line population derived from the cross AB136 x MDRK. A genetic linkage map of 100 molecular markers distributed across the 11 bean chromosomes was developed in this population to locate the gene or genes conferring resistance against each race, based on linkage analyses and chi-square tests of independence...
July 25, 2017: Phytopathology
https://www.readbyqxmd.com/read/28742073/biological-nitrogen-fixation-in-the-oxygen-minimum-region-of-the-eastern-tropical-north-pacific-ocean
#5
Amal Jayakumar, Bonnie X Chang, Brittany Widner, Peter Bernhardt, Margaret R Mulholland, Bess B Ward
Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day(-1)) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day(-1)) were found in the anoxic region of offshore stations...
July 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28742008/development-of-a-crispr-cas9-mediated-gene-editing-tool-in-streptomyces-rimosus
#6
Haiyan Jia, Longmei Zhang, Tongtong Wang, Jin Han, Hui Tang, Liping Zhang
Clustered regularly interspaced short palindromic repeats, associated proteins (CRISPR/Cas), has been developed into a powerful, targeted genome-editing tool in a wide variety of species. Here, we report an extensive investigation of the type II CRISPR/Cas9 system for targeted gene editing in Streptomyces rimosus. S. rimosus is used in the production of the antibiotic oxytetracycline, and its genome differs greatly from other species of the genus Streptomyces in the conserved chromosome terminal and core regions, which is of major production and scientific research value...
July 26, 2017: Microbiology
https://www.readbyqxmd.com/read/28741995/merdimonas-faecis-gen-nov-sp-nov-isolated-from-human-faeces
#7
Boram Seo, Ju Eun Yoo, Yung Mi Lee, GwangPyo Ko
A strictly anaerobic Gram-stain-positive, non-motile and non-spore-forming bacterial strain, BR31T, was isolated from a faecal sample of a healthy human. Bacterial colonies were ivory-coloured on GAM agar and composed of rod-shaped cells with rounded ends approximately 1.4-2.1×0.5-0.6 µm in size. According to comparative analysis based on 16S rRNA gene sequences, strain BR31T formed a distinct phylogenetic lineage that reflects a new genus within Clostridium cluster XIVa in the family Lachnospiraceae, with highest similarity to Eubacterium contortum DSM 3982T (94...
July 26, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28740575/identification-of-novel-diagnostic-and-prognostic-mirna-signatures-in-endometrial-cancer
#8
Muralidharan Jayaraman, Rangasudhagar Radhakrishnan, Cara A Mathews, Mingda Yan, Sanam Husain, Katherine M Moxley, Yong Sang Song, Danny N Dhanasekaran
With the goal of identifying diagnostic and prognostic biomarkers in endometrial cancer, miRNA-profiling was carried out with formalin-fixed paraffin embedded (FFPE) tissue samples from 49 endometrial cancer patients. Results using an 84-cancer specific miRNA panel identified the upregulation of miR-141-3p and miR-96-5p along with a downregulation of miR-26, miR-126-3p, miR-23b, miR-195-5p, miR-374a and let-7 family of miRNAs in endometrial cancer. We validated the dysregulated expression of the identified miRNAs in a panel of endometrial cancer cell-lines...
May 2017: Genes & Cancer
https://www.readbyqxmd.com/read/28740351/partners-of-patients-with-ulcerative-colitis-exhibit-a-biologically-relevant-dysbiosis-in-fecal-microbial-metacommunities
#9
Guang-Lan Chen, Ye Zhang, Wang-Yue Wang, Xue-Liang Ji, Fei Meng, Pei-Song Xu, Ning-Min Yang, Fu-Qiang Ye, Xiao-Chen Bo
AIM: To investigate alterations in the fecal microbiome using 16S rRNA amplicon sequencing in couples in the same cohabitation environment. METHODS: Fecal samples were collected from eight ulcerative colitis (UC) patients and their healthy partners at Lishui People's Hospital, Zhejiang Province, China. DNA was extracted and the variable regions V3 and V4 of the 16S rRNA genes were PCR amplified using a two-step protocol. Clear reads were clustered into operational taxonomic units (OTUs) at the 97% sequence similarity level using UCLUST v1...
July 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28739820/efficient-plastid-transformation-in-arabidopsis
#10
Qiguo Yu, Kerry Ann Lutz, Pal Maliga
Plastid transformation is routine in tobacco, but 100-fold less frequent in Arabidopsis, preventing its use in plastid biology. A recent study revealed that null mutations in ACC2, encoding a plastid-targeted acetyl-CoA-carboxylase, cause hypersensitivity to spectinomycin. We hypothesized that plastid transformation efficiency should increase in the acc2 background, because when ACC2 is absent, fatty acid biosynthesis becomes dependent on translation of the plastid-encoded ACC β-Carboxylase subunit. We bombarded ACC2-defective Arabidopsis leaves with a vector carrying a selectable spectinomycin resistance (aadA) gene and gfp, encoding the green fluorescence protein GFP...
July 24, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28739729/the-axis-of-cxcr4-sdf-1-plays-a-role-in-colon-cancer-cell-adhesion-through-regulation-of-the-akt-and-igf1r-signalling-pathways
#11
Fei Zheng, Zhongtao Zhang, Valentina Flamini, Wen G Jiang, Yuxin Cui
BACKGROUND/AIM: Colorectal cancer (CRC) is the third most common cancer in the world. The high mortality of this tumor is mainly due to its invasive properties, as it forms metastases in multiple organs, preferentially in the liver. There has evidence showing that C-X-C chemokine receptor type 4 (CXCR-4) and its ligand, stromal cell-derived factor-1 (SDF-1), plays an important role in cancer progression and metastasis. However, the molecular mechanism underling the CRCR4-mediated CRC metastasis has not been well characterized...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28739220/beyond-native-cas9-manipulating-genomic-information-and-function
#12
REVIEW
Hitoshi Mitsunobu, Jun Teramoto, Keiji Nishida, Akihiko Kondo
Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated manipulation of genomic information is becoming more versatile by combining nuclease-deficient CRISPR systems with a wide variety of effectors including base-editing deaminases, transcriptional regulators, and epigenetic modifiers. The programmable binding ability of CRISPR systems is essential when the systems are employed as targeting domains to recruit the effectors to specific genomic loci. The discovery of a variety of Cas9 orthologs and engineered variants enables high-fidelity genome editing and a wider selection of genomic targets, and CRISPR-mediated deaminases enable more precise and predictable genome editing compared with CRISPR nuclease-based editing...
July 21, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28738914/characterization-of-group-b-coxsackieviruses-isolated-from-non-polio-acute-flaccid-paralysis-patients-in-pakistan-vital-assessment-before-polio-eradication
#13
M Angez, S Shaukat, R Zahra, M M Alam, S Sharif, A Khurshid, Y Arshad, M Suleman, G Mujtaba, S S Z Zaidi
Pakistan is at the verge of polio eradication but isolation of non-polio enteroviruses (NPEVs) from acute flaccid paralysis (AFP) cases may result in serious or even fatal outcome. Many enteroviruses share similar symptoms and epidemiology as is the case with poliovirus and coxsackievirus (CV). The present study was designed to genetically characterize coxsackievirus B (CV-B) serotypes isolated from non-polio acute flaccid paralytic children, as well as to understand their probable role in paralysis. A total of 63 (20·1%) out of 313 stool samples during 2013 were found positive for NPEVs in rhabdomyosarcoma cells...
July 25, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28738889/influence-of-the-pneumococcal-conjugate-vaccines-on-the-temporal-variation-of-pneumococcal-carriage-and-the-nasal-microbiota-in-healthy-infants-a-longitudinal-analysis-of-a-case-control-study
#14
Moana Mika, Josua Maurer, Insa Korten, Aurélie Allemann, Suzanne Aebi, Silvio D Brugger, Weihong Qi, Urs Frey, Philipp Latzin, Markus Hilty
BACKGROUND: Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland...
July 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28738846/long-non-coding-rnas-as-novel-players-in-%C3%AE-cell-function-and-type-1-diabetes
#15
REVIEW
Aashiq H Mirza, Simranjeet Kaur, Flemming Pociot
BACKGROUND: Long non-coding RNAs (lncRNAs) are a sub-class within non-coding RNA repertoire that have emerged as crucial regulators of the gene expression in various pathophysiological conditions. lncRNAs display remarkable versatility and wield their functions through interactions with RNA, DNA, or proteins. Accumulating body of evidence based on multitude studies has highlighted the role of lncRNAs in many autoimmune and inflammatory diseases, including type 1 diabetes (T1D). This review highlights emerging roles of lncRNAs in immune and islet β cell function as well as some of the challenges and opportunities in understanding the pathogenesis of T1D and its complications...
July 24, 2017: Human Genomics
https://www.readbyqxmd.com/read/28738804/oncogenic-long-noncoding-rna-landscape-in-breast-cancer
#16
Shouping Xu, Dejia Kong, Qianlin Chen, Yanyan Ping, Da Pang
BACKGROUND: Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified. METHODS: Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation...
July 24, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28738776/graph-based-clustering-of-mirna-sequences
#17
Viviani A Kasahara, Maria do Carmo Nicoletti
MicroRNAs (miRNAs) are approximately 22 nucleotide-long non-coding RNA molecules, that play important roles in gene regulation. They regulate several processes, such as development, metabolism and cell death, among many others. The many miRNAs discovered so far have been divided into biologically representative families, aiming at organizing and systematizing their study so to promote, mainly, a better understanding of their functionalities. Considering that members of the same miRNA family tend to biologically function in similar ways, a well-structured family can help detecting miRNA functions which have not been associated yet with any existing family...
July 24, 2017: MicroRNA
https://www.readbyqxmd.com/read/28738348/colistin-resistance-in-kpc-2-and-shv-5-producing-klebsiella-pneumoniae-clinical-isolates-in-bulgaria
#18
Encho Savov, Iva Todorova, Lida Politi, Angelina Trifonova, Maja Borisova, Elena Kioseva, Athanassios Tsakris
BACKGROUND/AIMS: Colistin resistance is increasingly recognized among carbapenemase-producing Klebsiella pneumoniae isolates in several European regions. The current study documents the appearance of colistin resistance among KPC-2 and SHV-5-produning K. pneumoniae strains in Bulgaria. METHODS: Four colistin-resistant K. pneumoniae isolates were recovered from 2 patients hospitalized in the anesthesiology and resuscitation clinic of a tertiary care university hospital in Sofia, Bulgaria...
July 22, 2017: Chemotherapy
https://www.readbyqxmd.com/read/28738062/analysis-of-novel-runx2-mutations-in-chinese-patients-with-cleidocranial-dysplasia
#19
Xianli Zhang, Yang Liu, Xiaozhe Wang, Xiangyu Sun, Chenying Zhang, Shuguo Zheng
Cleidocranial dysplasia (CCD) is an autosomal dominant inheritable skeletal disorder characterized by cranial dysplasia, clavicle hypoplasia and dental abnormalities. This disease is mainly caused by heterozygous mutations in RUNX2, a gene that encodes an osteoblast-specific transcription factor. In the present study, mutational analyses of RUNX2 gene were performed on four unrelated Chinese patients with CCD. Four different RUNX2 mutations were detected in these patients, including one nonsense mutation (c...
2017: PloS One
https://www.readbyqxmd.com/read/28737770/tissue-specific-ctcf-cohesin-mediated-chromatin-architecture-delimits-enhancer-interactions-and-function-in-vivo
#20
Lars L P Hanssen, Mira T Kassouf, A Marieke Oudelaar, Daniel Biggs, Chris Preece, Damien J Downes, Matthew Gosden, Jacqueline A Sharpe, Jacqueline A Sloane-Stanley, Jim R Hughes, Benjamin Davies, Douglas R Higgs
The genome is organized via CTCF-cohesin-binding sites, which partition chromosomes into 1-5 megabase (Mb) topologically associated domains (TADs), and further into smaller sub-domains (sub-TADs). Here we examined in vivo an ∼80 kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ∼1 Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF-cohesin sites that are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment...
July 24, 2017: Nature Cell Biology
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