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https://www.readbyqxmd.com/read/28438015/genome-characteristics-of-lactobacillus-fermentum-strain-jdfm216-for-application-as-probiotic-bacteria
#1
Sung Yong Jang, Jaeyoung Heo, Mi Ri Park, Min-Ho Song, Jong Nam Kim, Sung Ho Jo, Do-Youn Jeong, Hak Kyo Lee, Younghoon Kim, Sangnam Oh
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces, possesses an enhancement of longevity and immune response on Caenorhabditis elegans host. To explore the molecular characteristics of strain JDFM216, we performed a whole-genome sequencing using PacBio system. The single circular DNA chromosome of 2,076,427 bp was completely assembled and 2,623 encoding sequences were predicted. Phylogenetically featured five genes possibly related to longevity and immune response of host were identified in L...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28437568/insights-into-deep-sea-adaptations-and-host-symbiont-interactions-a-comparative-transcriptome-study-on-bathymodiolus-mussels-and-their-coastal-relatives
#2
Ping Zheng, Minxiao Wang, Chaolun Li, Xiaoqing Sun, Xiaocheng Wang, Yan Sun, Song Sun
Mussels (Bivalve: Mytilidae) have adapted to various habitats, from freshwater to the deep sea. To understand their adaptive characteristics in different habitats, particularly in the bathymodiolin mussels in deep-sea chemosynthetic ecosystems, we conducted a comparative transcriptomic analysis between deep-sea bathymodiolin mussels and their shallow-water relatives. A number of gene families related to stress responses were shared across all mussels, without specific or significantly expanded families in deep-sea species, indicating that all mussels are capable of adapting to diverse harsh environments, but that different members of the same gene family may be preferentially utilized by different species...
April 24, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28437432/genome-wide-identification-and-expression-analysis-of-calcium%C3%A2-dependent-protein-kinase-and-its-related-kinase-gene-families-in-melon-cucumis-melo-l
#3
Haifei Zhang, Chunhua Wei, Xiaozhen Yang, Hejie Chen, Yongchao Yang, Yanling Mo, Hao Li, Yong Zhang, Jianxiang Ma, Jianqiang Yang, Xian Zhang
The calcium-dependent protein kinase (CDPK) is a ser/thr protein kinase that plays vital roles in plant growth, development, and responses to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CDPK genes in melon. Herein, a total of 18 CDPK genes and 7 CDPK-related protein kinases (CRK) genes were identified in the melon genome via bioinformatic analysis, which were unevenly distributed across eleven chromosomes with an apparent exception for chromosome 3...
2017: PloS One
https://www.readbyqxmd.com/read/28437136/enumeration-of-ancestral-configurations-for-matching-gene-trees-and-species-trees
#4
Filippo Disanto, Noah A Rosenberg
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the recursive computation of the conditional probability under the multispecies coalescent model of a gene tree topology given a species tree, the cost of this computation being affected by the number of ancestral configurations of the gene tree in the species tree. For matching gene trees and species trees, we obtain enumerative results on ancestral configurations...
April 24, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28436993/corrigendum-putative-wrkys-associated-with-regulation-of-fruit-ripening-revealed-by-detailed-expression-analysis-of-the-wrky-gene-family-in-pepper
#5
Yuan Cheng, Golam Jalal Ahammed, Jiahong Yu, Zhuping Yao, Meiying Ruan, Qingjing Ye, Zhimiao Li, Rongqing Wang, Kun Feng, Guozhi Zhou, Yuejian Yang, Weiping Diao, Hongjian Wan
No abstract text is available yet for this article.
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28436940/disruption-of-spatiotemporal-hypoxic-signaling-causes-congenital-heart-disease-in-mice
#6
Xuejun Yuan, Hui Qi, Xiang Li, Fan Wu, Jian Fang, Eva Bober, Gergana Dobreva, Yonggang Zhou, Thomas Braun
Congenital heart disease (CHD) represents the most prevalent inborn anomaly. Only a minority of CHD cases are attributed to genetic causes, suggesting a major role of environmental factors. Nonphysiological hypoxia during early pregnancy induces CHD, but the underlying reasons are unknown. Here, we have demonstrated that cells in the mouse heart tube are hypoxic, while cardiac progenitor cells (CPCs) expressing islet 1 (ISL1) in the secondary heart field (SHF) are normoxic. In ISL1+ CPCs, induction of hypoxic responses caused CHD by repressing Isl1 and activating NK2 homeobox 5 (Nkx2...
April 24, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28436588/reduced-erg-dosage-impairs-survival-of-hematopoietic-stem-and-progenitor-cells
#7
Ying Xie, Mia Lee Koch, Xin Zhang, Melanie J Hamblen, Frank J Godinho, Yuko Fujiwara, Huafeng Xie, Jan-Henning Klusmann, Stuart H Orkin, Zhe Li
ERG, an ETS family transcription factor frequently overexpressed in human leukemia, has been implicated as a key regulator of hematopoietic stem cells. However, how ERG controls normal hematopoiesis, particularly at the stem and progenitor cell level, and how it contributes to leukemogenesis remain incompletely understood. Using homologous recombination, we generated an Erg knockdown allele (Erg(kd) ) in which Erg expression can be conditionally restored by Cre recombinase. Erg(kd/kd) animals die at E10.5-E11...
April 24, 2017: Stem Cells
https://www.readbyqxmd.com/read/28436536/early-vertebrate-origin-and-diversification-of-small-transmembrane-regulators-of-cellular-ion-transport
#8
Sergej Pirkmajer, Henriette Kirchner, Leonidas Lundell, Pavel V Zelenin, Juleen R Zierath, Kira S Makarova, Yuri I Wolf, Alexander V Chibalin
Small transmembrane proteins are important for regulation of cellular ion transport. The most prominent among these proteins are members of the FXYD family (FXYD1-12), which regulate Na(+) -K(+) -ATPase, and phospholamban, sarcolipin, myoregulin, and DWORF, which regulate the sarco-endoplasmic reticulum Ca(2+) -ATPase (SERCA). FXYDs and regulators of SERCA are present in fishes, as well as terrestrial vertebrates; however, their evolutionary origins and phylogenetic relationships are obscure, thus hampering comparative physiological studies...
April 24, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28436534/a-novel-trpa1-variant-is-associated-with-carbamazepine-responsive-cramp-fasciculation-syndrome
#9
M J Nirenberg, R Chaouni, T M Biller, R M Gilbert, C Paisán-Ruiz
Cramp-fasciculation syndrome (CFS) is a rare muscle hyperexcitability syndrome that presents with muscle cramps, fasciculations, and stiffness, as well as pain, fatigue, anxiety, hyperreflexia, and paresthesias. Although familial cases have been reported, a genetic etiology has not yet been identified. We performed whole-exome sequencing followed by validation and cosegregation analyses on a father-son pair with CFS. Both subjects manifested other hypersensitivity-hyperexcitability symptoms, including asthma, gastroesophageal reflux, migraine, restless legs syndrome, tremor, cold hyperalgesia, and cardiac conduction defects...
April 24, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28436337/molecular-cloning-expression-and-characterization-of-e2f-transcription-factor-4-from-antheraea-pernyi
#10
M N Abbas, S Kausar, Y-X Sun, Y Sun, L Wang, C Qian, G-Q Wei, B-J Zhu, C-L Liu
The E2F transcription factor family is distributed widely in eukaryotes and has been well studied among mammals. In the present study, the E2F transcription factor 4 (E2F4) gene was isolated from fat bodies of Antheraea pernyi and sequenced. E2F4 comprised a 795 bp open reading frame encoding a deduced amino acid sequence of 264 amino acid residues. The recombinant protein was expressed in Escherichia coli (Transetta DE3), and anti-E2F4 antibodies were prepared. The deduced amino acid sequence displayed significant homology to an E2F4-like protein from Bombyx mori L...
April 24, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28436329/molecular-mechanisms-underlying-the-function-diversity-of-arsr-family-metalloregulator
#11
Sai Ren, Qiming Li, Longxiang Xie, Jianping Xie
The ArsR family of transcriptional regulators are widespread among microorganisms and are involved in various important cellular events, such as metal ion homeostasis, biofilm formation, primary and secondary metabolism, symbiosis, response to adverse condition, and virulence. Its N-terminus contains a winged helix-turn-helix DNA-binding domain that can repress or activate transcription by binding to downstream target promoters. With the increasing number of members in this family identified over the past few decades, the ArsR family members have been intensively explored...
2017: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/28436179/monogenic-diabetes-prevalence-among-polish-children-summary-of-11%C3%A2-years-long-nationwide-genetic-screening-program
#12
Beata Małachowska, Maciej Borowiec, Karolina Antosik, Arkadiusz Michalak, Anna Baranowska-Jaźwiecka, Grażyna Deja, Przemysława Jarosz-Chobot, Agnieszka Brandt, Małgorzata Myśliwiec, Małgorzata Stelmach, Joanna Nazim, Jadwiga Peczyńska, Barbara Głowińska-Olszewska, Anita Horodnicka-Józwa, Mieczysław Walczak, Maciej T Małecki, Agnieszka Zmysłowska, Agnieszka Szadkowska, Wojciech Fendler, Wojciech Młynarski
BACKGROUND: Estimated monogenic diabetes (MD) prevalence increases as screening programs proceeds. OBJECTIVE: To estimate prevalence of MD among Polish children. SUBJECTS: Patients and their family members suspected of suffering from MD (defined as causative mutation in one of the Maturity Onset Diabetes of the Young or permanent neonatal diabetes mellitus genes) were recruited between January 2005 and December 2015. METHODS: Nationwide prevalence was estimated based on data from 6 administrative provinces (out of 16 in Poland) with high referral rates of patients (>10 per 100 000 children)...
April 24, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28435889/multidrug-resistance-salmonella-genomic-island-1-in-a-morganella-morganii-subsp-morganii-human-clinical-isolate-from-france
#13
Eliette Schultz, Olivier Barraud, Jean-Yves Madec, Marisa Haenni, Axel Cloeckaert, Marie-Cécile Ploy, Benoît Doublet
Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 (Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, blaVEB-6 and blaNDM-1, respectively...
March 2017: MSphere
https://www.readbyqxmd.com/read/28435885/phylogenomic-reconstruction-of-the-oomycete-phylogeny-derived-from-37-genomes
#14
Charley G P McCarthy, David A Fitzpatrick
The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus...
March 2017: MSphere
https://www.readbyqxmd.com/read/28435519/gt198-psmc3ip-germline-variants-in-early-onset-breast-cancer-patients-from-hereditary-breast-and-ovarian-cancer-families
#15
Stephanie Schubert, Tim Ripperger, Melanie Rood, Anthony Petkidis, Winfried Hofmann, Hildegard Frye-Boukhriss, Marcel Tauscher, Bernd Auber, Ursula Hille-Betz, Thomas Illig, Brigitte Schlegelberger, Doris Steinemann
GT198, located 470 kb downstream of BRCA1, encodes for the nuclear PSMC3-interacting protein, which functions as co-activator of steroid hormone-mediated gene expression, and is involved in RAD51 and DMC1-mediated homologous recombination during DNA repair of double-strand breaks. Recently, germline variants in GT198 have been identified in hereditary breast and ovarian cancer (HBOC) patients, mainly in cases with early-onset. We screened a cohort of 166 BRCA1/2 mutation-negative HBOC patients, of which 56 developed early-onset breast cancer before the age of 36 years, for GT198 variants...
January 2017: Genes & Cancer
https://www.readbyqxmd.com/read/28435477/acrodermatitis-enteropathica-in-a-pair-of-twins
#16
Abdullatif Al Rashed, Mohja Al Shehri, Feroze Kaliyadan
BACKGROUND: Acrodermatitis enteropathica (AE) is a rare autosomal recessive metabolic disorder. First described by Brandt in 1936 and was named by Danbolt. A mutation in the SLC39A4 gene on chromosome 8 q24.3 is responsible for this disorder, which encodes zinc transporter Zip4. The diagnosis is made by the clinical presentation and histopathology and laboratory tests. In this case, we reported a twin presented with a typical rash and low zinc level. To our knowledge, very few cases reported as a twin with typical acrodermatitis enteropathica presentation...
December 31, 2016: Journal of Dermatological Case Reports
https://www.readbyqxmd.com/read/28435087/the-complete-mitochondrial-genome-of-clostera-anachoreta-lepidoptera-notodontidae-and-phylogenetic-implications-for-noctuoidea-species
#17
Xiao-Yu Zhu, Zhao-Zhe Xin, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Zheng-Fei Wang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
In this study, the complete mitochondrial genome (mitogenome) of Clostera anachoreta (Lepidoptera: Notodontidae) was sequenced. It comprises 15,456 base pairs (bp), including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNA), 22 transfer RNAs (tRNA) and one non-coding control region (CR), as found in other lepidopterans. Gene order is identical to that of typical lepidopterans. There are 15 intergenic spacers ranging from 1 to 49bp, and 9 overlapping regions ranging from 1 to 8bp, occurring throughout the genome...
April 20, 2017: Genomics
https://www.readbyqxmd.com/read/28435073/evaluation-of-a-rapid-detection-for-coxsackievirus-b3-using-one-step-reverse-transcription-loop-mediated-isothermal-amplification-rt-lamp
#18
A Monazah, M Zeinoddini, A R Saeeidinia
Coxsackievirus B3 (CVB3) is a member of the genus Enterovirus within the family Picornaviridae and is an important pathogen of viral myocarditis, which accounts for more than 50% viral myocarditis cases. VP1 is major capsid protein that this region has a low homology in both amino acid and nucleotide sequences among Enteroviruses. Therefore we have chosen this region for designed a set of RT-LAMP primers for CVB3 detection. For this the total RNA was extracted from 24-h post infected-HeLa cells with complete cytopathic effect (CPE), and applied to a one-step reverse transcription loop-mediated isothermal amplification reaction (RT-LAMP) using CVB3-specific primers...
April 20, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28434086/the-inability-of-bacillus-licheniformis-perr-mutant-to-grow-is-mainly-due-to-the-lack-of-perr-mediated-fur-repression
#19
Jung-Hoon Kim, Yoon-Mo Yang, Chang-Jun Ji, Su-Hyun Ryu, Young-Bin Won, Shin-Yeong Ju, Yumi Kwon, Yeh-Eun Lee, Hwan Youn, Jin-Won Lee
PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes involved in peroxide stress response. Industrially important bacterium Bacillus licheniformis contains three PerR-like proteins (PerRBL, PerR2, and PerR3) compared to its close relative Bacillus subtilis. Interestingly, unlike other bacteria including B. subtilis, no authentic perR BL null mutant could be established for B. licheniformis. Thus, we constructed a conditional perR BL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28433919/identification-of-differentially-expressed-mirnas-through-high-throughput-sequencing-in-the-chicken-lung-in-response-to-mycoplasma-gallisepticum-hs
#20
Yabo Zhao, Yue Hou, Kang Zhang, Bo Yuan, Xiuli Peng
Mycoplasma gallisepticum (MG) infects chickens, causes chronic respiratory diseases (CRD) and severely damages the poultry industry. It has been suggested that micro-ribonucleic acids (miRNAs) are involved in microbial pathogenesis. Here, we identified miRNAs that are associated with MG infection in chicken lungs at 3 and 10days post-infection by deep sequencing. Thirty-six down-regulated and 9 up-regulated miRNAs belonging to 31 miRNA families were detected at 3days post-infection, whereas 50 down-regulated and 18 up-regulated miRNAs belonging to 41 miRNA families were found at 10days post-infection...
April 12, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
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