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Genes and genomes

Rosa Porcel, Antonio Bustamante, Roc Ros, Ramón Serrano, José Miguel Mulet
Beta vulgaris (sugar beet) is one of the most important industrial crops. Screening of a cDNA library for sugar beet genes able to confer cold tolerance upon overexpression in yeast identified a novel aquaporin, which we named BvCOLD1. The amino acid sequence of BvCOLD1 indicated that is an acidic protein (pI 5,18) similar to TIP aquaporins. RNA expression analysis indicated that BvCOLD1 is expressed in all sugar beet organs. Confocal microscopy of a GFP tagged version localized BvCOLD1 in the endoplasmic reticulum in yeast and in plant cells...
August 13, 2018: Plant, Cell & Environment
Tsong-Hai Lee, Jen-Tsung Yang, Jiann-Der Lee, Ku-Chou Chang, Tsung-I Peng, Ting-Yu Chang, Kuo-Lun Huang, Chi-Hung Liu, Shan-Jin Ryu, Alessandro P Burlina
BACKGROUND: Fabry disease is a X-linked disease, and enzyme-based screening methods are not suitable for female patients. METHODS: Totally, 1,000 young stroke patients (18-55 y/o, 661 with ischemic stroke and 339 with hypertensive intracerebral hemorrhage) were recruited. Sequenom iPLEX assay was used to detect 26 Fabry related mutation genes. The frequency of Fabry disease in young stroke was reviewed and compared between Asian and non-Asian countries. RESULTS: Two male patients with ischemic stroke were found to have genetic mutation of IVS4+919G>A...
August 13, 2018: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
Shen Li, Bryan Wehrenberg, Barbara C Waldman, Alan S Waldman
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site...
August 1, 2018: DNA Repair
Etienne Patin, Lluis Quintana-Murci
Central Africa, a forested region that supports an exceptionally high biodiversity, hosts the world's largest group of hunter-gatherers, who live in close proximity with groups that have adopted agriculture over the past 5000 years. Our understanding of the prehistory of these populations has been dramatically hampered by the almost total absence of fossil remains in this region, a limitation that has recently been circumvented by population genomics approaches. Different studies have estimated that ancestors of rainforest hunter-gatherers and Bantu-speaking farmers separated more than 60 000 years ago, supporting the occurrence of ancient population structure in Africa since the Late Pleistocene...
August 10, 2018: Current Opinion in Genetics & Development
Long Sun, Juan Xu, Fang He
OBJECTIVES: Escherichia coli is the leading cause of urinary tract infections worldwide. Carbapenemase producing clinical isolates leave few therapeutic options. Here we report the draft genome sequence of a NDM-5, CTX-M-15, and OXA-1 co-producing E. coli ST167: a multidrug-resistant strain isolated from urine sample of a male hospitalized patient diagnosed with intracranial injury from a traffic accident. METHODS: The genome of E. coli ECWJ1 was sequenced using the Illumina HiSeq™ 4000 platform...
August 10, 2018: Journal of Global Antimicrobial Resistance
K K Biggar, B E Luu, C W Wu, F Pifferi, M Perret, K B Storey
MicroRNA (miRNA) are endogenous small noncoding RNA gene products, on average 22 nt long, that play important regulatory roles in mediating gene expression by binding to and targeting mRNAs for degradation or translational repression. In this paper we identify both novel and conserved miRNA sequences present in the genome of the gray mouse lemur, Microcebus marinus. In total, 122 conserved and 44 novel miRNA were identified with high confidence from the lemur genome (Mmur_2.0) and were used for expression analysis...
August 10, 2018: Gene
Bingzheng Shen, Jinchun Song, Yonghui Zhao, Yaoyun Zhang, Gaomin Liu, Xueke Li, Xingchen Guo, Wenxin Li, Zhijian Cao, Yingliang Wu
Since there is a symbiotic and competitive relationship between microorganisms in the same ecological niche, fungal defensins have been found to be important resources for antimicrobial peptides. Here, a fungal defensin, triintsin, was characterized in a clinical isolate of Trichophytoninterdigitale from a patient with onychomycosis. The comparison of its genomic and mRNA sequences showed the gene organization and structure of three coding exons separated by two introns. The precursor peptide of triintsin contained 85 amino acid residues, which were composed of three parts including an N-terminal signal domain of 21 residues, a pro-peptide of 47 residues that ended at lysine-arginine and a mature peptide of 38 residues at the C-terminus...
August 10, 2018: Peptides
Tamryn Marsberg, Michael D Jukes, Martyna Krejmer-Rabalska, Lukasz Rabalski, Caroline M Knox, Sean D Moore, Martin P Hill, Boguslaw Szewczyk
Cryptophlebia peltastica is an agricultural pest of litchis and macadamias in South Africa with phytosanitary status for certain markets. Current control methods rely on chemical, cultural and classical biological control. However, a microbial control option has not been developed. An Alphabaculovirus from C. peltastica was recovered from a laboratory reared colony and morphologically characterised by transmission electron microscopy (TEM). Analysis of occlusion bodies indicated a single NPV (SNPV) varying in size from 421 to 1263 nm...
August 10, 2018: Journal of Invertebrate Pathology
Jiahui Guo, Liurong Fang, Xu Ye, Jiyao Chen, Shangen Xu, Xinyu Zhu, Yimin Miao, Dang Wang, Shaobo Xiao
Porcine epidemic diarrhea virus (PEDV), which re-emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re-emerging and historic strains worldwide. Here, we analyzed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI-a, GI-b, GII-a, GII-b, and GII-c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII-c exhibited inconsistent topologies between the spike gene and other genes...
August 13, 2018: Transboundary and Emerging Diseases
Ming-Nan Chien, Po-Sheng Yang, Yi-Chiung Hsu, Tsang-Pai Liu, Jie-Jen Lee, Shih-Ping Cheng
BACKGROUND: Telomerase reverse transcriptase (TERT) promoter mutations have recently been identified as an important prognostic factor in thyroid cancer. Studies suggest that TERT may have noncanonical functions beyond telomere maintenance. METHODS: Clinicopathological information and transcriptome data for papillary thyroid carcinoma (PTC) samples were obtained from The Cancer Genome Atlas (TCGA). Propensity score matching was performed to adjust for potential confounding variables between the TERT promoter wild-type group and the mutant group...
August 13, 2018: Head & Neck
Silvia Sookoian, Marco Arrese, Carlos J Pirola
Knowledge of the genetic component of nonalcoholic fatty liver disease (NAFLD) has significantly contributed to the understanding of the disease pathogenesis. Genetic studies based either on genome wide association-strategies or candidate-genes approaches showed that variants in loci involved in lipid metabolism and/or lipid-droplets biology have predominant and reproducible effects on the disease phenotype (1). However, it has been a major challenge to translate this information into molecularly-plausible and clinically-safe therapeutic targets...
August 13, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Yu Zhang, Yun Zhang, Xiuling Shang, Bo Wang, Qitiao Hu, Shuwen Liu, Tingyi Wen
trans-4-Hydroxy-l-proline (Hyp) is an abundant component of mammalian collagen, and functions as a chiral synthon for the syntheses of anti-inflammatory drugs in the pharmaceutical industry. Proline 4-hydroxylase (P4H) can catalyze the conversion of l-proline to Hyp, however, it is still challenging for the fermentative production of Hyp from glucose using P4H due to the low yield and productivity. Here, we report the metabolic engineering of Corynebacterium glutamicum for the fermentative production of Hyp by reconstructing tricarboxylic acid (TCA) cycle together with heterologously expressing the p4h gene from Dactylosporangium sp...
August 13, 2018: Biotechnology and Bioengineering
Fernanda Almeida, Amanda Aparecida Seribelli, Marta Inês Cazentini Medeiros, Dália Dos Prazeres Rodrigues, Alessandro de MelloVarani, Yan Luo, Marc W Allard, Juliana Pfrimer Falcão
Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis...
2018: PloS One
Momina Hussain, Muhammad Atif Iqbal, Bradley J Till, Mehboob-Ur- Rahman
Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease...
2018: PloS One
Jean-Noël Hubert, Tatiana Zerjal, Frédéric Hospital
Devil Facial Tumor Disease (DFTD) is an aggressive cancer notorious for its rare etiology and its impact on Tasmanian devil populations. Two regions underlying an evolutionary response to this cancer were recently identified using genomic time-series pre- and post-DTFD arrival. Here, we support that DFTD shaped the genome of the Tasmanian devil in an even more extensive way than previously reported. We detected 97 signatures of selection, including 148 protein coding genes having a human orthologue, linked to DFTD...
2018: PloS One
Ying Chen, Melissa A Gilbert, Christopher M Grochowski, Deborah McEldrew, Jessica Llewellyn, Orith Waisbourd-Zinman, Hakon Hakonarson, Joan E Bailey-Wilson, Pierre Russo, Rebecca G Wells, Kathleen M Loomes, Nancy B Spinner, Marcella Devoto
Biliary atresia (BA) is a rare pediatric cholangiopathy characterized by fibrosclerosing obliteration of the extrahepatic bile ducts, leading to cholestasis, fibrosis, cirrhosis, and eventual liver failure. The etiology of BA remains unknown, although environmental, inflammatory, infectious, and genetic risk factors have been proposed. We performed a genome-wide association study (GWAS) in a European-American cohort of 343 isolated BA patients and 1716 controls to identify genetic loci associated with BA. A second GWAS was performed in an independent European-American cohort of 156 patients with BA and other extrahepatic anomalies and 212 controls to confirm the identified candidate BA-associated SNPs...
August 13, 2018: PLoS Genetics
Megumi Hara, Tsuyoshi Hachiya, Yoichi Sutoh, Keitaro Matsuo, Yuichiro Nishida, Chisato Shimanoe, Keitaro Tanaka, Atsushi Shimizu, Keizo Ohnaka, Takahisa Kawaguchi, Isao Oze, Fumihiko Matsuda, Hidemi Ito, Sayo Kawai, Asahi Hishida, Rieko Okada, Tae Sasakabe, Akie Hirata, Rie Ibusuki, Yora Nindita, Norihiro Furusyo, Hiroaki Ikezaki, Nagato Kuriyama, Etsuko Ozaki, Haruo Mikami, Yohko Nakamura, Sadao Suzuki, Akihiro Hosono, Sakurako Katsuura-Kamano, Kokichi Arisawa, Kiyonori Kuriki, Kaori Endoh, Naoyuki Takashima, Aya Kadota, Masahiro Nakatochi, Yukihide Momozawa, Michiaki Kubo, Mariko Naito, Kenji Wakai
PURPOSE: Although several genetic factors may play a role in leisure-time exercise behavior, there is currently no evidence of a significant genome-wide association, and candidate gene replication studies have produced inconsistent results. METHODS: We conducted a two-stage genome-wide association study (GWAS) and candidate single nucleotide polymorphisms (SNPs) association study on leisure-time exercise behavior using 13,980 discovery samples from the Japan Multi-Institutional Collaborative Cohort (J-MICC) study, and 2,036 replication samples from the Hospital-based Epidemiologic Research Program at Aichi Cancer Center-2 (HERPACC-2) study...
August 10, 2018: Medicine and Science in Sports and Exercise
Caio Santiago, Vivian Pereira, Luciano Digiampietri
Homologous sequences are widely used to understand the functions of certain genes or proteins. However, there is no consensus to solve the automatic assignment of functions to protein problem and many algorithms have different ways of identifying homologous clusters in a given set of sequences. In this article, we present an algorithm to deal with specific sets, the set of coding sequences obtained from phylogenetically close genomes (of the same species, genus, or family). When modeled as a graph, these sets have their own characteristics: they form more homogeneous and denser clusters...
August 13, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Esra Tuğ, M Ali Ergün, E Ferda Perçin
Tuğ E, Ergün MA, Perçin EF. Clinical findings in cases with 9q deletion encompassing the 9q21.11q21.32 region. Turk J Pediatr 2018; 60: 94-98. We report on a case with developmental delay and dysmorphic craniofacial features, and a novel~15.2 Mb interstitial deletion within 9q21.11q21.32 confirmed with array comparative genomic hybridization (aCGH). A twenty-two month old boy with inability to walk without support, absent speech, and attention deficit and hyperactivity disorder was seen in our clinic. His craniofacial examination revealed relative macrocephaly, facial asymmetry, frontal bossing, sparse medial eyebrows, hypertelorism, broad base to nose, smooth philtrum, large mouth, operated cleft lip and wide spaced teeth...
2018: Turkish Journal of Pediatrics
Ben Niu, Denise M Coslo, Alain R Bataille, Istvan Albert, B Franklin Pugh, Curtis J Omiecinski
The constitutive androstane receptor (CAR; NR1I3) is a nuclear receptor orchestrating complex roles in cell and systems biology. Species differences in CAR's effector pathways remain poorly understood, including its role in regulating liver tumor promotion. We developed transgenic mouse models to assess genome-wide binding of mouse and human CAR, following receptor activation in liver with direct ligands and with phenobarbital, an indirect CAR activator. Genomic interaction profiles were integrated with transcriptional and biological pathway analyses...
August 8, 2018: Nucleic Acids Research
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