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gene cluster

Ana Kovacic, Martina Seruga Music, Svjetlana Dekic, Marija Tonkic, Anita Novak, Zana Rubic, Jasna Hrenovic, Ivana Goic-Barisic
Acinetobacter baumannii origin and its epidemiology is under a great concern worldwide since this microorganism has become a leading nosocomial pathogen of the 21th century among the "ESKAPE" group of microorganisms. The aim of the study was to monitor and explore the epidemiology of this important hospital pathogen in the second largest clinical university hospital in Croatia. The presence of A. baumannii in hospital wastewater, as a route for possible transmission outside of the hospital setting, as well as its survival in environmental conditions including seawater, was investigated...
December 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
Anna Maikova, Johann Peltier, Pierre Boudry, Eliane Hajnsdorf, Nicolas Kint, Marc Monot, Isabelle Poquet, Isabelle Martin-Verstraete, Bruno Dupuy, Olga Soutourina
Clostridium difficile, a major human enteropathogen, must cope with foreign DNA invaders and multiple stress factors inside the host. We have recently provided an experimental evidence of defensive function of the C. difficile CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system important for its survival within phage-rich gut communities. Here, we describe the identification of type I toxin-antitoxin (TA) systems with the first functional antisense RNAs in this pathogen...
February 26, 2018: Nucleic Acids Research
Samuel Beck, Catherine Rhee, Jawon Song, Bum-Kyu Lee, Lucy LeBlanc, Laurie Cannon, Jonghwan Kim
CpG islands (CGIs) have long been implicated in the regulation of vertebrate gene expression. However, the involvement of CGIs in chromosomal architectures and associated gene expression regulations has not yet been thoroughly explored. By combining large-scale integrative data analyses and experimental validations, we show that CGIs clearly reconcile two competing models explaining nuclear gene localizations. We first identify CGI-containing (CGI+) and CGI-less (CGI-) genes are non-randomly clustered within the genome, which reflects CGI-dependent spatial gene segregation in the nucleus and corresponding gene regulatory modes...
February 26, 2018: Nucleic Acids Research
Damla Tas, Luca Stickley, Federico Miozzo, Rafael Koch, Nicolas Loncle, Virginie Sabado, Bettina Gnägi, Emi Nagoshi
Forkhead box (FOXO) proteins are evolutionarily conserved, stress-responsive transcription factors (TFs) that can promote or counteract cell death. Mutations in FOXO genes are implicated in numerous pathologies, including age-dependent neurodegenerative disorders, such as Parkinson's disease (PD). However, the complex regulation and downstream mechanisms of FOXOs present a challenge in understanding their roles in the pathogenesis of PD. Here, we investigate the involvement of FOXO in the death of dopaminergic (DA) neurons, the key pathological feature of PD, in Drosophila...
March 12, 2018: PLoS Genetics
Artem S Rogovskyy, Sara Lawhon, Kathryn Kuczmanski, David C Gillis, Jing Wu, Helen Hurley, Yuliya V Rogovska, Kranti Konganti, Ching-Yuan Yang, Kay Duncan
Trueperella pyogenes is an opportunistic pathogen that causes suppurative infections in animals including humans. Data on phenotypic and genotypic properties of T. pyogenes isolated from ruminants, particularly goats and sheep, are lacking. We characterized, by phenotypic and genotypic means, T. pyogenes of caprine and ovine origin, and established their phylogenetic relationship with isolates from other ruminants. T. pyogenes isolates ( n = 50) from diagnostic specimens of bovine ( n = 25), caprine ( n = 19), and ovine ( n = 6) origin were analyzed...
March 1, 2018: Journal of Veterinary Diagnostic Investigation
Jasmin Frey, Fabian Schneider, Thomas Huhn, Dieter Spiteller, Bernhard Schink, David Schleheck
Degradation of acetone by the sulfate-reducing bacterium Desulfococcus biacutus involves an acetone-activation reaction different from that used by aerobic or nitrate-reducing bacteria, because the small energy budget of sulfate-reducing bacteria does not allow for major expenditures into ATP-consuming carboxylation reactions. In the present study, an inducible coenzyme B12 -dependent conversion of 2-hydroxyisobutyryl-CoA to 3-hydroxybutyryl-CoA was demonstrated in cell-free extracts of acetone-grown D. biacutus cells, together with a NAD+ -dependent oxidation of 3-hydroxybutyryl-CoA to acetoacetyl-CoA...
March 12, 2018: Environmental Microbiology Reports
Lifeng Zhu, Qi Wu, Cao Deng, Mengjie Zhang, Chenglin Zhang, Hua Chen, Guoqing Lu, Fuwen Wei
Carnivorous members of the Carnivora reside at the apex of food chains and consume meat-only diets, rich in purine, fats and protein. Here, we aimed to identify potential adaptive evolutionary signatures compatible with high purine and fat metabolism based on analysis of host genomes and symbiotic gut microbial metagenomes. We found that the gut microbiomes of carnivorous Carnivora (e.g. Felidae, Canidae) clustered in the same clade, and other clades comprised omnivorous and herbivorous Carnivora (e.g. badgers, bears and pandas)...
March 12, 2018: Environmental Microbiology
Qun Yue, Yan Li, Li Chen, Xiaoling Zhang, Xingzhong Liu, Zhiqiang An, Gerald F Bills
The echinocandins are antifungal lipopeptides targeting fungi via noncompetitive inhibition of the β-1,3-D-glucan synthase FKS1 subunit. A novel echinocandin resistance mechanism involving an auxiliary copy of FKS1 in echinocandin-producing fungus Pezicula radicicola NRRL 12192 was discovered. We sequenced the genome of NRRL 12192 and predicted two FKS1-encoding genes (prfks1n and prfks1a), rather than a single FKS1 gene typical of filamentous ascomycetes. The prfks1a gene sits immediately adjacent to an echinocandin (sporiofungin) gene cluster which was confirmed by disruption of prnrps4 and abolishment of sporiofungin production...
March 12, 2018: Environmental Microbiology
Artem Pankin, Janine Altmüller, Christian Becker, Maria von Korff
Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions...
March 12, 2018: New Phytologist
Dana Szabóová, Ivan Hapala, Pavol Sulo
The complete mitochondrial DNA (mtDNA) sequence from Kazachstania sinensis was analyzed and compared to mtDNA from related yeasts. It contained the same set of genes; however, it only contained 23 tRNAs, as the trnR2 gene was absent. Most of the 12 introns within cox1, cob and rnl genes were inserted in the same sites as in other yeasts; however, two introns in rnl were in unusual positions. Traits such as gene order and GC cluster number were more related to Saccharomyces than to the other Kazachstania or linked clades...
March 8, 2018: FEMS Yeast Research
Maria Gomes Fernandes, Monika Bialecka, Daniela C F Salvatori, Susana M Chuva de Sousa Lopes
STUDY QUESTION: Which set of antibodies can be used to identify migratory and early post-migratory human primordial germ cells (hPGCs)? STUDY FINDING: We validated the specificity of 33 antibodies for 31 markers, including POU5F1, NANOG, PRDM1 and TFAP2C as specific markers of hPGCs at 4.5 weeks of development of Carnegie stage (CS12-13), whereas KIT and SOX17 also marked the intra-aortic hematopoietic stem cell cluster in the aorta-gonad-mesonephros (AGM). WHAT IS KNOWN ALREADY: The dynamics of gene expression during germ cell development in mice is well characterized and this knowledge has proved crucial to allow the development of protocols for the in-vitro derivation of functional gametes...
March 8, 2018: Molecular Human Reproduction
Yi-Feng Wu, Yu Zhao, Xin-Yan Liu, Shuai Gao, Ai-Xia Cheng, Hong-Xiang Lou
Liverworts, a section of the bryophyte plants which pioneered the colonization of terrestrial habitats, produce cyclic bisbibenzyls as a secondary metabolite. These compounds are generated via the phenylpropanoid pathway, similar with flavonoid biosynthesis for which bHLH transcription factors have been identified as one of the improtant regulators in higher plants. Here, a bHLH homolog (PabHLH) was isolated from the liverwort species Plagiochasma appendiculatum and its contribution to bisbibenzyl biosynthesis was explored...
March 8, 2018: Plant & Cell Physiology
Xiongying Chen, Zhifang Zhang, Qiumei Zhang, Wan Zhao, Jinguo Zhai, Min Chen, Boqi Du, Xiaoxiang Deng, Feng Ji, Chuanyue Wang, Yu-Tao Xiang, Hongjie Wu, Qi Dong, Chuansheng Chen, Jun Li
ZNF804A rs1344706 (A/C) was the first SNP that reached genome-wide significance for schizophrenia. Recent studies have linked rs1344706 to functional connectivity among specific brain regions. However, no study thus far has examined the role of this SNP in the entire functional connectome. In this study, we used degree centrality to test the role of rs1344706 in the whole-brain voxel-wise functional connectome during the resting state. 52 schizophrenia patients and 128 healthy controls were included in the final analysis...
2018: NeuroImage: Clinical
Katherine E Manning, Roger Tait, John Suckling, Anthony J Holland
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder of genomic imprinting, presenting with a characteristic overeating disorder, mild to moderate intellectual disability, and a variable range of social and behavioral difficulties. Consequently, widespread alterations in neural structure and developmental and maturational trajectory would be expected. To date, there have been few quantitative and systematic studies of brain morphology in PWS, although alterations of volume and of cortical organisation have been reported...
2018: NeuroImage: Clinical
Norman Junge, Qinggong Yuan, Thu Huong Vu, Simon Krooss, Christien Bednarski, Asha Balakrishnan, Toni Cathomen, Michael P Manns, Ulrich Baumann, Amar Deep Sharma, Michael Ott
AIM: To stably correct tyrosinaemia in proliferating livers of fumarylacetoacetate-hydrolase knockout ( Fah -/-) mice by homologous-recombination-mediated targeted addition of the Fah gene. METHODS: C57BL/6 Fah∆exon5 mice served as an animal model for human tyrosinaemia type 1 in our study. The vector was created by amplifying human Fah cDNA including the TTR promoter from a lentivirus plasmid as described. The Fah expression cassette was flanked by homologous arms (620 bp and 749 bp long) of the Rosa26 gene locus...
February 27, 2018: World Journal of Hepatology
Susanne Ledig, Peter Wieacker
The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome [MIM 277000] is characterised by the absence of a uterus and vagina in otherwise phenotypically normal women with karyotype 46,XX. Clinically, the MRKH can be subdivided into two subtypes: an isolated or type I form can be delineated from a type II form, which is characterised by extragenital malformations. The so-called Müllerian hypoplasia, renal agenesis, cervicothoracic somite dysplasia (MURCS) association can be seen as the most severe phenotypic outcome...
2018: Medizinische Genetik: Mitteilungsblatt des Berufsverbandes Medizinische Genetik E.V
Xue-Min Han, Zhi-Ling Yang, Yan-Jing Liu, Hai-Ling Yang, Qing-Yin Zeng
Glutathione S-transferases are ubiquitous enzyme in plants, playing vital roles in several physiological and developmental processes. In this study we identified 73 GST genes from the genome of Medicago truncatula. The Medicago GSTs were divided to eight classes with tau and phi being the most numerous. Six clusters were found on four Medicago chromosomes. The local gene duplication mainly contributed to the expansion of this large gene family. Functional divergence was found in their gene structures, gene expression patterns, and enzyme properties...
March 3, 2018: Plant Physiology and Biochemistry: PPB
Olga V Sizova, Alexander S Shashkov, Anna N Kondakova, Yuriy A Knirel, Rima Z Shaikhutdinova, Sergei A Ivanov, Angelina A Kislichkina, Lidia A Kadnikova, Aleksandr G Bogun, Svetlana V Dentovskaya
Lipopolysaccharide was isolated from bacteria Yersinia intermedia H9-36/83 (O:17) and degraded with mild acid to give an O-specific polysaccharide, which was isolated by GPC on Sephadex G-50 and studied by sugar analysis and 1D and 2D NMR spectroscopy. The polysaccharide was found to contain 3-deoxy-3-[(R)-3-hydroxybutanoylamino]-d-fucose (d-Fuc3NR3Hb) and the following structure of the heptasaccharide repeating unit was established: The structure established is consistent with the gene content of the O-antigen gene cluster...
February 28, 2018: Carbohydrate Research
Sof'ya N Senchenkova, Wenqi Hou, Olesya I Naumenko, Peng Geng, Alexander S Shashkov, Andrei V Perepelov, Bin Yang, Yuriy A Knirel
An O-specific polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Escherichia coli O33 followed by gel-permeation chromatography on Sephadex G-50. The polysaccharide was found to contain glycerol 2-phosphate (Gro-2-P), and the following structure of its tetrasaccharide repeat was established by sugar analysis, dephosphorylation, and 1D and 2D1 H and13 C NMR spectroscopy: The O33-antigen gene cluster was analyzed and found to be essentially consistent with the O-polysaccharide structure...
February 17, 2018: Carbohydrate Research
Lei Liu, Yuanyuan Fu, Fang Zhu, Changkao Mu, Ronghua Li, Weiwei Song, Ce Shi, Yangfang Ye, Chunlin Wang
The swimming crab (Portunus trituberculatus) is among the most economically important seawater crustacean species in Asia. Despite its commercial importance and being well-studied status, genomic and transcriptomic data are scarce for this crab species. In the present study, limb bud tissue was collected at different developmental stages post amputation for transcriptomic analysis. Illumina RNA-sequencing was applied to characterise the limb regeneration transcriptome and identify the most characteristic genes...
March 7, 2018: Gene
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