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https://www.readbyqxmd.com/read/29677397/two-ancestral-genes-shaped-the-xanthomonas-campestris-tal-effector-gene-repertoire
#1
Nicolas Denancé, Boris Szurek, Erin L Doyle, Emmanuelle Lauber, Lisa Fontaine-Bodin, Sébastien Carrère, Endrick Guy, Ahmed Hajri, Aude Cerutti, Tristan Boureau, Stéphane Poussier, Matthieu Arlat, Adam J Bogdanove, Laurent D Noël
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome)...
April 20, 2018: New Phytologist
https://www.readbyqxmd.com/read/29677184/elasticity-based-boosting-of-neuroepithelial-nucleokinesis-via-indirect-energy-transfer-from-mother-to-daughter
#2
Tomoyasu Shinoda, Arata Nagasaka, Yasuhiro Inoue, Ryo Higuchi, Yoshiaki Minami, Kagayaki Kato, Makoto Suzuki, Takefumi Kondo, Takumi Kawaue, Kanako Saito, Naoto Ueno, Yugo Fukazawa, Masaharu Nagayama, Takashi Miura, Taiji Adachi, Takaki Miyata
Neural progenitor cells (NPCs), which are apicobasally elongated and densely packed in the developing brain, systematically move their nuclei/somata in a cell cycle-dependent manner, called interkinetic nuclear migration (IKNM): apical during G2 and basal during G1. Although intracellular molecular mechanisms of individual IKNM have been explored, how heterogeneous IKNMs are collectively coordinated is unknown. Our quantitative cell-biological and in silico analyses revealed that tissue elasticity mechanically assists an initial step of basalward IKNM...
April 20, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29677173/what-does-this-mutation-mean-the-tools-and-pitfalls-of-variant-interpretation-in-lymphoid-malignancies
#3
REVIEW
Guillermin Yann, Lopez Jonathan, Chabane Kaddour, Hayette Sandrine, Bardel Claire, Salles Gilles, Sujobert Pierre, Huet Sarah
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS...
April 20, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29676726/rhodohalobacter-barkolensis-sp-nov-isolated-from-a-saline-lake-and-emended-description-of-the-genus-rhodohalobacter
#4
Shuai-Bo Han, Yang-Huan Yu, Zhao Ju, Yu Li, Ran Zhang, Xin-Jun Hou, Xin-Yuan Ma, Xiao-Yun Yu, Cong Sun, Min Wu
A Gram-stain-negative, non-motile, aerobic, rod-shaped bacterium, designated 15182T , was isolated from a saline lake in China. The novel strain 15182T was able to grow at 10-40 °C (optimum, 37 °C), pH 7.0-8.0 (optimum, 7.5) and with 0.5-4 % NaCl (optimum, 2-3 %, w/v). The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 15182T was most closely related to the genus Rhodohalobacter by sharing the highest sequence similarity of 97.0 % with Rhodohalobacter halophilus JZ3C29T ...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676722/siphonobacter-curvatus-sp-nov-isolated-from-a-freshwater-river
#5
Yunho Lee, Che Ok Jeon
A novel orange-pigmented, Gram-stain-negative and strictly aerobic bacterium, designated strain HR-UT , was isolated from a water sample of the Han River located in the Republic of Korea. Cells were catalase-positive and oxidase-positive, and non-motile curved rods without flagella. The strain grew at 5-35 °C (optimum 25 °C), pH 6-10 (optimum of 7-8) and 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-UT formed a tight phylogenic lineage with Siphonobacter aquaeclarae DSM 21668T and 'Siphonobacter intestinalis' 63MJ-2...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676719/vibrio-gangliei-sp-nov-a-novel-member-of-vibrionaceae-isolated-from-sawdust-in-a-pigpen
#6
Yu-Chen Meng, Hong-Can Liu, Yu-Guang Zhou, Man Cai, Yingqian Kang
A Gram-stain-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic, and motile bacterium, designated strain SZDIS-1T , was isolated from pigpen sawdust bedding in Xiamen, Fujian Province, China. Cells grew at 10-50 °C, pH 6.0-9.0, up to 12 % (w/v) NaCl, resisted vibriostatic agent O/129 and were negative for gelatin and alginate hydrolysis. No growth on thiosulfate citrate bile salts sucrose agar medium. Based on 16S rRNA gene sequences and multilocus sequence analysis, this strain should be assigned to the genus Vibrio, with the closest relatives being Vibrio aphrogenes CA-1004T (97...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676245/structure-and-interaction-prediction-in-prokaryotic-rna-biology
#7
Patrick R Wright, Martin Mann, Rolf Backofen
Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in "wet" laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29676073/overexpression-of-mir-155-5p-inhibits-the-proliferation-and-migration-of-il-13-induced-human-bronchial-smooth-muscle-cells-by-suppressing-tgf-%C3%AE-activated-kinase-1-map3k7-binding-protein-2
#8
Yujia Shi, Xingli Fu, Qi Cao, Zhengdao Mao, Yi Chen, Yun Sun, Zhiguang Liu, Qian Zhang
PURPOSE: Molecular mechanisms leading to asthma is still ill-defined. Though the function of microRNAs (miRNAs) in asthma was previously reported, the involvement of miR-155 in important features of this disease remains unknown. The present study was designed to uncover the probable involvement of miR-155-5p in the proliferation and migration of IL-13-induced human bronchial smooth muscle cells (BSMCs) and the intrinsic regulatory mechanism. METHODS: The effects of different concentrations of IL-13 on the proliferation and migration of BSMCs as well as the expression of miR-155-5p and its predicted target transforming growth factor (TGF)-β-activated kinase 1/MAP3K7-binding protein 2 (TAB2) were investigated...
May 2018: Allergy, Asthma & Immunology Research
https://www.readbyqxmd.com/read/29676051/genetic-dissection-of-photosynthetic-efficiency-traits-for-enhancing-seed-yield-in-chickpea
#9
Udita Basu, Deepak Bajaj, Akash Sharma, Naveen Malik, Anurag Daware, Laxmi Narnoliya, Virevol Thakro, Hari D Upadhyaya, Rajendra Kumar, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, QTL mapping and expression profiling. This identified 16 potential SNP loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea...
April 20, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29675401/analysis-of-the-antigenic-and-prophylactic-properties-of-the-leishmania-translation-initiation-factors-eif2-and-eif2b-in-natural-and-experimental-leishmaniasis
#10
Esther Garde, Laura Ramírez, Laura Corvo, José C Solana, M Elena Martín, Víctor M González, Carlos Gómez-Nieto, Aldina Barral, Manoel Barral-Netto, José M Requena, Salvador Iborra, Manuel Soto
Different members of intracellular protein families are recognized by the immune system of the vertebrate host infected by parasites of the genus Leishmania . Here, we have analyzed the antigenic and immunogenic properties of the Leishmania eIF2 and eIF2B translation initiation factors. An in silico search in Leishmania infantum sequence databases allowed the identification of the genes encoding the α, β, and γ subunits and the α, β, and δ subunits of the putative Leishmania orthologs of the eukaryotic initiation factors F2 (LieIF2) or F2B (LieIF2B), respectively...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29675014/the-resistome-of-low-impacted-marine-environments-is-composed-by-distant-metallo-%C3%AE-lactamases-homologs
#11
Erica L Fonseca, Bruno G N Andrade, Ana C P Vicente
The worldwide dispersion and sudden emergence of new antibiotic resistance genes (ARGs) determined the need in uncovering which environment participate most as their source and reservoir. ARGs closely related to those currently found in human pathogens occur in the resistome of anthropogenic impacted environments. However, the role of pristine environment as the origin and source of ARGs remains underexplored and controversy, particularly, the marine environments represented by the oceans. Here, due to the ocean nature, we hypothesized that the resistome of this pristine/low-impacted marine environment is represented by distant ARG homologs...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29674965/development-of-matrix-metalloproteinase-2-inhibitors-for-cardioprotection
#12
Péter Bencsik, Krisztina Kupai, Anikó Görbe, Éva Kenyeres, Zoltán V Varga, János Pálóczi, Renáta Gáspár, László Kovács, Lutz Weber, Ferenc Takács, István Hajdú, Gabriella Fabó, Sándor Cseh, László Barna, Tamás Csont, Csaba Csonka, György Dormán, Péter Ferdinandy
The objective of our present study is to develop novel inhibitors for MMP-2 for acute cardioprotection. In a series of pilot studies, novel substituted carboxylic acid derivatives were synthesized based on imidazole and thiazole scaffolds and then tested in a screeening cascade for MMP inhibition. We found that the MMP-inhibiting effects of imidazole and thiazole carboxylic acid-based compounds are superior in efficacy in comparison to the conventional hydroxamic acid derivatives of the same molecules. Based on these results, a 568-membered focused library of imidazole and thiazole compounds was generated in silico and then the library members were docked to the 3D model of MMP-2 followed by an in vitro medium throughput screening (MTS) based on a fluorescent assay employing MMP-2 catalytic domain...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29674657/emergence-of-vancomycin-resistant-enterococcus-faecium-at-an-australian-hospital-a-whole-genome-sequencing-analysis
#13
Kelvin W C Leong, Louise A Cooley, Tara L Anderson, Sanjay S Gautam, Belinda McEwan, Anne Wells, Fiona Wilson, Lucy Hughson, Ronan F O'Toole
In 2015, a marked increase in vancomycin-resistant Enterococcus faecium (VREfm) isolation was detected at the Royal Hobart Hospital, Australia. The primary objective of this work was to examine the dynamics of VREfm transmission using whole genome data mapped to public health surveillance information. Screening and clinical isolates of VREfm from patients were typed for the specific vancomycin-resistance locus present. Of total isolates collected from 2014-2016 (n = 222), 15.3% and 84.7% harboured either the vanA or the vanB vancomycin-resistance locus, respectively...
April 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29674548/draft-genome-sequence-of-mycobacterium-porcinum-csurp1564
#14
A Bouam, A Levasseur, M Drancourt
Mycobacterium porcinum is a rapidly growing environmental mycobacterium responsible for opportunistic infections. The 7,025,616-bp draft genome of M. porcinum strain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding genes, and 65 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex.
April 19, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29674534/draft-genome-sequence-of-nocardia-suismassiliense-strain-s-137-csur-p4007
#15
Mustapha Fellag, Anthony Levasseur, Jérémy Delerce, Fadi Bittar, Jean-Lou Marié, Bernard Davoust, Michel Drancourt
" Nocardia suismassiliense " strain S-137 isolated from Sus scrofa feces exhibits a 9.4-Mb (67.1% GC content) draft genome sequence containing 8,658 protein-coding genes, 66 tRNAs, and 9 rRNAs. In silico DNA-DNA hybridization confirmed strain S-137 as representative of a new species, " Nocardia suismassiliense ," closely related to N. tenerifensis and N. brasiliensis .
April 19, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29674177/current-view-on-phylogeny-within-the-genus-flabellula-schaeffer-1926-amoebozoa-leptomyxida
#16
Tomáš Tyml, Martina Lisnerová, Martin Kostka, Iva Dyková
The molecular phylogeny of Flabellula Schaeffer, 1926 has been updated by analysing 18S rRNA and actin gene sequences of 19 new strains collected and characterised by the authors over the past ten years. The genus Flabellula Schaeffer, 1926 (Amoebozoa: Leptomyxida) is a taxon in which species delineation based on morphological data by themselves is insufficient or even misleading. The description of two novel species, F. schaefferi n. sp. and F. sawyeri n. sp., is justified by the congruence of morphological data with 18S rRNA and actin gene sequence phylogenies, in-silico secondary structure prediction of the V2 region in the 18S rRNA, and by recognition of species-specific sequential motifs within this region...
April 3, 2018: European Journal of Protistology
https://www.readbyqxmd.com/read/29674152/identification-and-functional-analysis-of-the-aspergillic-acid-gene-cluster-in-aspergillus-flavus
#17
Matthew D Lebar, Jeffrey W Cary, Rajtilak Majumdar, Carol H Carter-Wientjes, Brian M Mack, Qijian Wei, Valdet Uka, Sarah De Saeger, José Diana Di Mavungu
Aspergillus flavus can colonize important food staples and produce aflatoxins, a group of toxic and carcinogenic secondary metabolites. Previous in silico analysis of the A. flavus genome revealed 56 gene clusters predicted to be involved in the biosynthesis of secondary metabolites. A. flavus secondary metabolites produced during infection of maize seed are of particular interest, especially with respect to their roles in the biology of the fungus. A predicted nonribosomal peptide synthetase-like (NRPS-like) gene, designated asaC (AFLA_023020), present in the uncharacterized A...
April 16, 2018: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/29673960/systematic-metabolic-engineering-of-methylomicrobium-alcaliphilum-20z-for-2-3-butanediol-production-from-methane
#18
Anh Duc Nguyen, In Yeub Hwang, Ok Kyung Lee, Donghyuk Kim, Marina G Kalyuzhnaya, Rina Mariyana, Susila Hadiyati, Min Sik Kim, Eun Yeol Lee
Methane is considered a next-generation feedstock, and methanotrophic cell-based biorefinery is attractive for production of a variety of high-value compounds from methane. In this work, we have metabolically engineered Methylomicrobium alcaliphilum 20Z for 2,3-butanediol (2,3-BDO) production from methane. The engineered strain 20Z/pBudK.p, harboring the 2,3-BDO synthesis gene cluster (budABC) from Klebsiella pneumoniae, accumulated 2,3-BDO in methane-fed shake flask cultures with a titer of 35.66mg/L. Expression of the most efficient gene cluster was optimized using selection of promoters, translation initiation rates (TIR), and the combination of 2,3-BDO synthesis genes from different sources...
April 16, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29673582/in-silico-prediction-of-the-pathogenic-effect-of-a-novel-variant-of-bckdha-leading-to-classical-maple-syrup-urine-disease-identified-using-clinical-exome-sequencing
#19
Cynthia Fernández-Lainez, Carmen Aláez-Verson, Isabel Ibarra-González, Sergio Enríquez-Flores, Karol Carrillo-Sanchez, Leonardo Flores-Lagunes, Sara Guillén-López, Leticia Belmont-Martínez, Marcela Vela-Amieva
Maple syrup urine disease (MSUD) is a metabolic disorder caused by mutations in three of the branched-chain α-keto acid dehydrogenase complex (BCKDC) genes. Classical MSUD symptom can be observed immediately after birth and include ketoacidosis, irritability, lethargy, and coma, which can lead to death or irreversible neurodevelopmental delay in survivors. The molecular diagnosis of MSUD can be time-consuming and difficult to establish using conventional Sanger sequencing because it could be due to pathogenic variants of any of the BCKDC genes...
April 16, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29673423/experimental-and-in-silico-analysis-of-cordycepin-and-its-derivatives-as-endometrial-cancer-treatment
#20
Pedro Fong, Cheng N Ao, Kai I Tou, Ka M Huang, Chi C Cheong, Li R Meng
The aim of this study was to investigate the inhibition effects of cordycepin and its derivatives on endometrial cancercell growth. Cytotoxicity MTT assays, clonogenic assays and flow cytometry were used to observe the effects on apoptosis and regulation of the cell cycle of Ishikawa cells under various concentrations of cordycepin, cisplatin and combinations of the two. Validated in silico docking simulations were performed on 31 cordycepin derivatives against adenosine deaminase (ADA) to predict their binding affinities and hence their potential tendency to be metabolized by ADA...
April 19, 2018: Oncology Research
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