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gene cluster

María Muñoz-Amatriaín, Hamid Mirebrahim, Pei Xu, Steve I Wanamaker, MingCheng Luo, Hind Alhakami, Matthew Alpert, Ibrahim Atokple, Benoit Joseph Batieno, Ousmane Boukar, Serdar Bozdag, Ndiaga Cisse, Issa Drabo, Jeffrey D Ehlers, Andrew Farmer, Christian Fatokun, Yong Q Gu, Yi-Ning Guo, Bao-Lam Huynh, Scott A Jackson, Francis Kusi, Cynthia T Lawley, Mitchell R Lucas, Yaqin Ma, Michael P Timko, Jiajie Wu, Frank You, Philip A Roberts, Stefano Lonardi, Timothy J Close
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4,355 BACs...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
José Alcaraz-Quiles, Esther Titos, Mireia Casulleras, Marco Pavesi, Cristina López-Vicario, Bibiana Rius, Aritz Lopategi, Andrea de Gottardi, Ivo Graziadei, Henning Gronbaek, Pere Ginès, Mauro Bernardi, Vicente Arroyo, Joan Clària
: Acute-on-chronic liver failure (ACLF) in cirrhosis is an increasingly recognized syndrome characterized by acute decompensation, organ failure(s) and high short-term mortality. Recent findings suggest that an over-exuberant systemic inflammation plays a primary role in ACLF progression. In this study, we examined whether genetic factors shape systemic immune responses in patients with decompensated cirrhosis. Six single nucleotide polymorphisms (SNPs) in inflammation-related genes (IL-1β: rs1143623, IL-1ra: rs4251961, IL-10: rs1800871, SOCS3: rs4969170, NOD2: rs3135500 and CMKLR1: rs1878022) were genotyped in 279 cirrhotic patients with (n=178) and without (n=101) ACLF from the CANONIC study of the CLIF consortium...
October 24, 2016: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Kathleen Marie Burchhardt, Megan E Miller, William O Cline, Marc Cubeta
The fungus Monilinia vaccinii-corymbosi (Mvc), a pathogen of Vaccinium spp., requires asexual and sexual spore production to complete its life cycle. A recent study found population structuring of Mvc over a broad spatial scale in the US. In this study, we examined fine-scale genetic structuring, temporal dynamics, and reproductive biology within a 125 x 132m blueberry plot from 2010 to 2012. A total of 395 isolates of Mvc were sampled from infected shoots and fruits to examine their multilocus haplotype (MLH) using microsatellite markers...
October 24, 2016: Phytopathology
Keiichi Mochida, Tetsuya Sakurai, Hikaru Seki, Takuhiro Yoshida, Kotaro Takahagi, Satoru Sawai, Hiroshi Uchiyama, Toshiya Muranaka, Kazuki Saito
Chinese liquorice/licorice (Glycyrrhiza uralensis) is a leguminous plant species whose roots and rhizomes have been widely used as a herbal medicine and natural sweetener. Whole-genome sequencing is essential for gene discovery studies and molecular breeding in liquorice. Here, we report a draft assembly of the approximately 379-Mb whole-genome sequence of strain 308-19 of G. uralensis; this assembly contains 34 445 predicted protein-coding genes. Comparative analyses suggested well-conserved genomic components and collinearity of gene loci (synteny) between the genome of liquorice and those of other legumes such as Medicago and chickpea...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
C Elizabeth Oakley, Manmeet Ahuja, Wei-Wen Sun, Ruth Entwistle, Tomohiro Akashi, Junko Yaegashi, Chun-Jun Guo, Gustavo C Cerqueira, Jennifer Russo Wortman, Clay C C Wang, Yi-Ming Chiang, Berl R Oakley
Fungal secondary metabolites (SMs) are extremely important in medicine and agriculture, but regulation of their biosynthesis is incompletely understood. We have developed a genetic screen in Aspergillus nidulans for negative regulators of fungal SM gene clusters and we have used this screen to isolate mutations that upregulate transcription of the non-ribosomal peptide synthetase gene required for nidulanin A biosynthesis. Several of these mutations are allelic and we have identified the mutant gene by genome sequencing...
October 24, 2016: Molecular Microbiology
Zhiyuan Yao, Tingting Dong, Guo Zheng, Jinzhong Fu, Shuqiang Li
Endemism, which is typically high on islands and in caves, has rarely been studied in the cave entrance ecotone. We investigated the endemism of the spider genus Uthina at cave entrances. Totally 212 spiders were sampled from 46 localities, from Seychelles across Southeast Asia to Fiji. They mostly occur at cave entrances but occasionally appear at various epigean environments. Phylogenetic analysis of DNA sequence data from COI and 28S genes suggested that Uthina was grouped into 13 well-supported clades. We used three methods, the Bayesian Poisson Tree Processes (bPTP) model, the Bayesian Phylogenetics and Phylogeography (BPP) method, and the general mixed Yule coalescent (GMYC) model, to investigate species boundaries...
October 24, 2016: Scientific Reports
Gorana G Stamenković, Valentina S Ćirković, Marina M Šiljić, Jelena V Blagojević, Aleksandra M Knežević, Ivana D Joksić, Maja P Stanojević
The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973-2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1...
October 24, 2016: Scientific Reports
F Chen, Y Zhang, E Parra, J Rodriguez, C Behrens, R Akbani, Y Lu, J M Kurie, D L Gibbons, G B Mills, I I Wistuba, C J Creighton
Non-small-cell lung cancer (NSCLC) demonstrates remarkable molecular diversity. With the completion of The Cancer Genome Atlas (TCGA), there is opportunity for systematic analyses of the entire TCGA NSCLC cohort, including comparisons and contrasts between different disease subsets. On the basis of multidimensional and comprehensive molecular characterization (including DNA methylation and copy, and RNA and protein expression), 1023 NSCLC cases-519 from TCGA adenocarcinoma (AD) project and 504 from TCGA squamous cell carcinoma (SQCC) project-were classified using a 'cluster-of-clusters' analytic approach...
October 24, 2016: Oncogene
Joanna Melonek, James D Stone, Ian Small
Hybrid seed production in rice relies on cytoplasmic male sterility (CMS) induced by specific mitochondrial proteins, whose deleterious effects are suppressed by nuclear Restorer of Fertility (RF) genes. The majority of RF proteins belong to a specific clade of the RNA-binding pentatricopeptide repeat protein family. We have characterised 'restorer-of-fertility-like' (RFL) sequences from 13 Oryza genomes and the Brachypodium distachyon genome. The majority of the RFL sequences are found in genomic clusters located at two or three chromosomal loci with only a minor proportion being present as isolated genes...
October 24, 2016: Scientific Reports
Fang Chen, Weifeng Zhang, Junli Zhao, Peiyan Yang, Rui Ma, Haibin Xia
Objective To prepare Rev-erbβ knockout HEK293 cells using clustered regularly interspaced short palindromic repeats/Cas 9 nuclease (CRISPR/Cas9) gene editing technology. Methods The knock-in or knockout of Rev-erbβ gene could be realized by single-guide RNA (sgRNA)-mediated Cas9 cutting of target DNA, and followed by DNA homologous recombination or non-homologous end joining-mediated DNA repair. Firstly, four sgRNAs were designed for Rev-erbβ gene. The sgRNA1 and sgRNA2 with the higher activity were respectively used to construct pCMV-hCas9-U6-Rev-erbβ sgRNA1 and pCMV-hCas9-U6-Rev-erbβ sgRNA2...
November 2016: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
Elisete P Rodrigues, Cleiton de Paula Soares, Patrícia G Galvão, Eddie L Imada, Jean L Simões-Araújo, Luc F M Rouws, André L M de Oliveira, Márcia S Vidal, José I Baldani
Gluconacetobacter diazotrophicus is a beneficial nitrogen-fixing endophyte found in association with sugarcane plants and other important crops. Beneficial effects of G. diazotrophicus on sugarcane growth and productivity have been attributed to biological nitrogen fixation process and production of phytohormones especially indole-3-acetic acid (IAA); however, information about the biosynthesis and function of IAA in G. diazotrophicus is still scarce. Therefore, the aim of this work was to identify genes and pathways involved in IAA biosynthesis in this bacterium...
2016: Frontiers in Microbiology
Julieta Bonacina, Nadia Suárez, Ricardo Hormigo, Silvina Fadda, Marcus Lechner, Lucila Saavedra
The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner...
October 23, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Nicolas Argy, Gwladys I Bertin, Jacqueline Milet, Véronique Hubert, Jérôme Clain, Sandrine Cojean, Pascal Houzé, Nicaise Tuikue-Ndam, Eric Kendjo, Philippe Deloron, Sandrine Houzé
OBJECTIVES: Severe Plasmodium falciparum malaria (SM) involves cytoadhesion of parasitized red blood cells, mediated by P. falciparum erythrocyte membrane protein 1, which are encoded by var genes. Expression of var gene group A and B or encoding domain cassettes DC4, DC5, DC8 and 13 has been implicated in SM in African children, but no data exist in the context of imported malaria. The aim of this study was to investigate var gene expression linked to clinical presentation and host factors in SM imported in France...
October 20, 2016: Clinical Microbiology and Infection
En-Ming He, Cheng-Wen Chen, Yong Guo, Mei-Hua Hsu, Liang Zhang, Hsiu-Ling Chen, Guo-Ping Zhao, Cheng-Hsun Chiu, Yan Zhou
Streptococcus agalactiae (GBS) causes serious infections in humans and other species. A total of 25 complete GBS genomes, including the first sequenced serotype VI genome (GBS-M002), were compared in this study. The power law model suggested that the pan-genome of GBS is open, with approximately 1300 genes in the core genome of GBS, accounting for approximately 60% of the average genome content. GBS-M002 has 73 specific genes and is one of the five strains containing >60 specific genes. Based on COG (Cluster of Orthologous Groups of proteins) functional classification, 24% of the genes related to defense mechanisms are specific among the strains...
October 20, 2016: Gene
Kevin J Galinsky, Po-Ru Loh, Swapan Mallick, Nick J Patterson, Alkes L Price
Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for using population differentiation to detect selection and enables an analysis of the UK population structure at fine resolution. In this study, analyses of 113,851 UK Biobank samples showed that population structure in the UK is dominated by five principal components (PCs) spanning six clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters...
October 14, 2016: American Journal of Human Genetics
Ilona F Persoon, Mark J Buijs, Ahmet R Özok, Wim Crielaard, Bastiaan P Krom, Egija Zaura, Bernd W Brandt
OBJECTIVES: Bacterial infection of the root canal system causes apical periodontitis. Less is known about the role of fungi in these infections. This study aimed to assess the fungal prevalence, abundance, and diversity of root canal infections, as well as the relation between fungi and bacteria present in different parts of the root canal. MATERIALS AND METHODS: Twenty-six teeth with primary apical periodontitis were extracted, split in apical and coronal root segments, and cryo-pulverized...
October 22, 2016: Clinical Oral Investigations
Seketoulie Keretsu, Rosy Sarmah
: Protein complex detection from protein-protein interaction (PPI) network has received a lot of focus in recent years. A number of methods identify protein complexes as dense sub-graphs using network information while several other methods detect protein complexes based on topological information. While the methods based on identifying dense sub-graphs are more effective in identifying protein complexes, not all protein complexes have high density. Moreover, existing methods focus more on static PPI networks and usually overlook the dynamic nature of protein complexes...
October 8, 2016: Computational Biology and Chemistry
Lingling Qiu, Teng Ma, Guobin Chang, Xiangping Liu, Xiaomin Guo, Lu Xu, Yang Zhang, Wenming Zhao, Qi Xu, Guohong Chen
NLRC5, a protein belonging to the NOD-like receptor protein family (NLRs), is highly expressed in immune tissues and cells. NLRC5 plays an important role in the immune response of humans, where its regulatory mechanism has been elucidated. However, the function and regulation of NLRC5 in chickens remains unclear. In this study, temporal expression characteristics of NLRC5 and associated genes in the STAT1 pathway in chickens following infection with Salmonellapullorum were investigated using quantitative real-time polymerase chain reaction and hierarchical cluster analyses...
October 20, 2016: Gene
Dimitry A Chistiakov, Alexandra A Melnichenko, Alexander N Orekhov, Yuri V Bobryshev
In humans, three paraoxonase (PON1, PON2, and PON3) genes are clustered on chromosome 7 at a locus that spans a distance around 170 kb. These genes are highly homologous to each other and have a similar protein structural organization. PON2 is the intracellular enzyme, which is expressed in many tissues and organs, while two other members of PON gene family are produced by liver and associate with high density lipoprotein (HDL). The lactonase activity is the ancestral. Besides lactones and organic phosphates, PONs can hydrolyze and therefore detoxify oxidized low density lipoprotein and homocysteine thiolactone, i...
October 19, 2016: Biochimie
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