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https://www.readbyqxmd.com/read/29343972/targeting-histone-methyltransferase-and-demethylase-in-acute-myeloid-leukemia-therapy
#1
REVIEW
Germana Castelli, Elvira Pelosi, Ugo Testa
Acute myeloid leukemia (AML) is a clonal disorder of myeloid progenitors characterized by the acquisition of chromosomal abnormalities, somatic mutations, and epigenetic changes that determine a consistent degree of biological and clinical heterogeneity. Advances in genomic technologies have increasingly shown the complexity and heterogeneity of genetic and epigenetic alterations in AML. Among the genetic alterations occurring in AML, frequent are the genetic alterations at the level of various genes involved in the epigenetic control of the DNA methylome and histone methylome...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29343702/analysis-of-mitochondrial-function-in-human-induced-pluripotent-stem-cells-from-patients-with-mitochondrial-diabetes-due-to-the-a3243g-mutation
#2
Masaki Matsubara, Hajime Kanda, Hiromi Imamura, Mayumi Inoue, Michio Noguchi, Kiminori Hosoda, Akira Kakizuka, Kazuwa Nakao
We previously established human induced pluripotent stem (iPS) cells in two diabetic patients from different families with the mitochondrial A3243G mutation and isolated isogenic iPS cell clones with either undetectable or high levels of the mutation in both patients. In the present study, we analyzed the mitochondrial functions of two mutation-undetectable and two mutation-high clones in each patient through four methods to assess complex I activity, mitochondrial membrane potential, mitochondrial respiration, and mitochondrial ATP production...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343653/establishment-of-a-screening-system-to-identify-novel-gata-2-transcriptional-regulators
#3
Keiichi Ohashi, Tohru Fujiwara, Koichi Onodera, Yo Saito, Satoshi Ichikawa, Masahiro Kobayashi, Yoko Okitsu, Noriko Fukuhara, Yasushi Onishi, Hideo Harigae
Hematopoietic stem cells can self-renew and differentiate into all blood cell types. The transcription factor GATA-2 is expressed in hematopoietic stem and progenitor cells and is essential for cell proliferation and differentiation. Heterozygous germline GATA2 mutations induce GATA-2 deficiency syndrome, characterized by monocytopenia, a predisposition to myelodysplasia and acute myeloid leukemia, and a profoundly reduced dendritic cell (DC) population, which is associated with increased susceptibility to viral infections...
2018: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29342270/whole-genome-analysis-reveals-the-evolution-and-transmission-of-an-mdr-dh-nap11-106-clostridium-difficile-clone-in-a-paediatric-hospital
#4
Larry K Kociolek, Egon A Ozer, Dale N Gerding, David W Hecht, Sameer J Patel, Alan R Hauser
Background: Clostridium difficile strain DH/NAP11/106, a relatively antibiotic-susceptible strain, is now the most common cause of C. difficile infection (CDI) among adults in the USA. Objectives: To identify mechanisms underlying the evolution and transmission of an MDR DH/NAP11/106 clone. Methods: WGS (Illumina MiSeq), restriction endonuclease analysis (REA) and antibiotic susceptibility testing were performed on 134 C. difficile isolates collected from paediatric patients with CDI over a 2 year period...
January 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#5
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29337882/functional-analysis-of-promoters-from-three-subtypes-of-the-pi3k-family-and-their-roles-in-the-regulation-of-lipid-metabolism-by-insulin-in-yellow-catfish-pelteobagrus-fulvidraco
#6
Mei-Qin Zhuo, Zhi Luo, Yi-Huan Xu, Dan-Dan Li, Ya-Xiong Pan, Kun Wu
In the present study, the length of 360, 1848 and 367 bp sequences of promoters from three subtypes of PI3K family (PI3KCa, PI3KC2b and PI3KC3) of yellow catfish Pelteobagrus fulvidraco were cloned and characterized. Bioinformatics analysis revealed that PI3KCa, PI3KC2b and PI3KC3 had different structures in their core promoter regions. The promoter regions of PI3KCa and PI3KC2b had CpG islands but no CAAT and TATA box. In contrast, the promoter of PI3KC3 had the canonical TATA and CAAT box but no CpG island...
January 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29337421/fenoxaprop-p-ethyl-resistance-conferred-by-cytochrome-p450s-and-target-site-mutation-in-alopecurus-japonicus
#7
Guoqi Chen, Hongle Xu, Teng Zhang, Congqiang Bai, Liyao Dong
BACKGROUND: Alopecurus japonicus has evolved serious resistance to acetyl-CoA carboxylase (ACCase) inhibiting herbicides. Although target-site resistance (TSR) to ACCase inhibitors in A. japonicus has been reported, but non-target site resistance (NTSR) has not. This study investigated both TSR and NTSR in a fenoxaprop-P-ethyl-resistant A. japonicus population (AHFD-3), which was collected in Feidong County, Anhui Province, China. RESULTS: We found that AHFD-3 exhibited high resistance to fenoxaprop-P-ethyl and low resistance to flucarbazone-sodium...
January 16, 2018: Pest Management Science
https://www.readbyqxmd.com/read/29337372/crispr-cas9-edited-site-sequencing-cres-seq-an-efficient-and-high-throughput-method-for-the-selection-of-crispr-cas9-edited-clones
#8
Yaligara Veeranagouda, Delphine Debono-Lagneaux, Hamida Fournet, Gilbert Thill, Michel Didier
The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells)...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29336152/mutation-of-phenylalanine-223-to-leucine-enhances-transformation-of-benzo-a-pyrene-by-ring-hydroxylating-dioxygenase-of-sphingobium-sp-fb3-by-increasing-accessibility-of-the-catalytic-site
#9
Bo Fu, Ting Xu, Zhongli Cui, Ho Leung Ng, Kai Wang, Ji Li, Qing X Li
Burning of agricultural biomass generates polycyclic aromatic hydrocarbons (PAHs) including the carcinogen benzo[a]pyrene, of which the catabolism is primarily initiated by a ring-hydroxylating dioxygenase (RHD). This study explores catalytic site accessibility and its role in preferential catabolism of some PAHs over others. The genes flnA1f, flnA2f, flnA3 and flnA4, encoding the oxygenase α and β subunits, ferredoxin, and ferredoxin reductase, respectively, of the RHD enzyme complex (FlnA) were cloned from Sphingobium sp...
January 16, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29335443/elucidating-the-genomic-architecture-of-asian-egfr-mutant-lung-adenocarcinoma-through-multi-region-exome-sequencing
#10
Rahul Nahar, Weiwei Zhai, Tong Zhang, Angela Takano, Alexis J Khng, Yin Yeng Lee, Xingliang Liu, Chong Hee Lim, Tina P T Koh, Zaw Win Aung, Tony Kiat Hon Lim, Lavanya Veeravalli, Ju Yuan, Audrey S M Teo, Cheryl X Chan, Huay Mei Poh, Ivan M L Chua, Audrey Ann Liew, Dawn Ping Xi Lau, Xue Lin Kwang, Chee Keong Toh, Wan-Teck Lim, Bing Lim, Wai Leong Tam, Eng-Huat Tan, Axel M Hillmer, Daniel S W Tan
EGFR-mutant lung adenocarcinomas (LUAD) display diverse clinical trajectories and are characterized by rapid but short-lived responses to EGFR tyrosine kinase inhibitors (TKIs). Through sequencing of 79 spatially distinct regions from 16 early stage tumors, we show that despite low mutation burdens, EGFR-mutant Asian LUADs unexpectedly exhibit a complex genomic landscape with frequent and early whole-genome doubling, aneuploidy, and high clonal diversity. Multiple truncal alterations, including TP53 mutations and loss of CDKN2A and RB1, converge on cell cycle dysregulation, with late sector-specific high-amplitude amplifications and deletions that potentially beget drug resistant clones...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29331527/construction-of-sake-yeast-with-low-production-of-dimethyl-trisulfide-precursor-by-a-self-cloning-method
#11
Yuriko Ikeda, Atsuko Isogai, Yuta Moriyoshi, Ryoko Kanda, Kazuhiro Iwashita, Tsutomu Fujii
Dimethyl trisulfide (DMTS) is the primary component responsible for "hineka", the stale aroma of Japanese sake. Deletion of the MRI1 or MDE1 gene of sake yeast, encoding 5'-methylthioribose-1-phosphate isomerase and 5'-methylthioribulose-1-phosphate dehydratase, respectively, has been reported to greatly reduce the amount of DMTS precursor (DMTS-P1) in sake and to suppress the formation of DMTS during storage. In this study, we constructed sake yeast strains lacking MRI1 gene function by a self-cloning method...
January 10, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29330918/leptosphaeria-maculans-avrlm9-a-new-player-in-the-game-of-hide-and-seek-with-avrlm4-7
#12
Kaveh Ghanbarnia, Lisong Ma, Nicholas J Larkan, Parham Haddadi, W G Dilantha Fernando, M Hossein Borhan
Blackleg disease of Brassica napus caused by Leptosphaeria maculans (Lm) is largely controlled by deploying race-specific resistance (R) genes. However, selection pressure exerted by R genes causes Lm to adapt and give rise to new virulent strains through mutation and deletion of effector genes. Therefore, knowledge of effector gene function is necessary for effective management of the disease. Here we report cloning of Lm effector AvrLm9 that is recognised by the resistance gene Rlm9 in B. napus cultivar Goéland...
January 13, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29330047/an-intrinsically-disordered-domain-in-polaribacter-irgensii-kopri-22228-cspb-confers-extraordinary-freeze-tolerance
#13
Youn Hong Jung, Ji-Hyun Uh, Kyunghee Lee, Hana Im
Organisms living in extremely cold environments possess mechanisms to survive low temperatures. Among the known cold-induced genes, cold-shock proteins (Csps) are the most prominent. A csp-homologous gene, cspBPi, has been cloned from the Arctic bacterium Polaribacter irgensii KOPRI 22228, and overexpression of this gene greatly increased the freezing tolerance of its host. This protein consists of a unique N-terminal domain and a well conserved C-terminal cold shock domain. To elucidate the detailed mechanisms involved in the extraordinary freeze-tolerance conferred by CspBPi, we identified the responsible domain by mutational analysis...
January 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29329928/cloning-and-characterization-of-%C3%A2-6-%C3%A2-5-fatty-acyl-desaturase-fad-gene-promoter-in-the-marine-teleost-siganus-canaliculatus
#14
Yewei Dong, Jianhong Zhao, Junliang Chen, Shuqi Wang, Yang Liu, Qinghao Zhang, Cuihong You, Óscar Monroig, Douglas R Tocher, Yuanyou Li
The rabbitfish Siganus canaliculatus was the first marine teleost demonstrated to have the ability of biosynthesizing long-chain polyunsaturated fatty acids (LC-PUFA) from C18 PUFA precursors, and all genes encoding the key enzymes for LC-PUFA biosynthesis have been cloned and functionally characterized, which provides us a potential model to study the regulatory mechanisms of LC-PUFA biosynthesis in teleosts. As the primary step to clarify such mechanisms, present research focused on promoter analysis of gene encoding ∆6/∆5 fatty acyl desaturase (Fad), a rate-limiting enzyme catalyzing the first step in the conversion of C18 PUFA to LC-PUFA...
January 9, 2018: Gene
https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#15
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29326868/essential-thrombocytemia-following-immune-thrombocytopenia-with-jak2v617f-mutation
#16
Giovanni Caocci, Sandra Atzeni, Monica Usai, Giorgio La Nasa
JAK2V617F mutation is found in about 60% of cases of essential thrombocytemia (ET) and represents a driving mutation. Immune thrombocytopenia (ITP) is an autoimmune disease characterized by a low platelet (PLT) count. So far, only 2 reports described ET following ITP. For the first time we analyzed in a patient the JAK2V617F allele burden at ITP onset occurred 13 years before the ET diagnosis and found the presence of a small clone JAK2V617F positive clone (3%) raised to 27% in the following years. The association of ET and ITP could suggest similar pathogenetic mechanisms that should be further investigated...
2018: Leukemia Research Reports
https://www.readbyqxmd.com/read/29326013/a-cluster-of-multidrug-resistant-mycobacterium-tuberculosis-among-patients-arriving-in-europe-from-the-horn-of-africa-a-molecular-epidemiological-study
#17
Timothy M Walker, Matthias Merker, Astrid M Knoblauch, Peter Helbling, Otto D Schoch, Marieke J van der Werf, Katharina Kranzer, Lena Fiebig, Stefan Kröger, Walter Haas, Harald Hoffmann, Alexander Indra, Adrian Egli, Daniela M Cirillo, Jérôme Robert, Thomas R Rogers, Ramona Groenheit, Anne T Mengshoel, Vanessa Mathys, Marjo Haanperä, Dick van Soolingen, Stefan Niemann, Erik C Böttger, Peter M Keller
BACKGROUND: The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. METHODS: On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis...
January 8, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29324785/phylogenetic-diversity-antimicrobial-susceptibility-and-virulence-gene-profiles-of-brachyspira-hyodysenteriae-isolates-from-pigs-in-germany
#18
Jessica Joerling, Stefanie A Barth, Karen Schlez, Hermann Willems, Werner Herbst, Christa Ewers
Swine dysentery (SD) is an economically important diarrheal disease in pigs caused by different strongly hemolytic Brachyspira (B.) species, such as B. hyodysenteriae, B. suanatina and B. hampsonii. Possible associations of epidemiologic data, such as multilocus sequence types (STs) to virulence gene profiles and antimicrobial susceptibility are rather scarce, particularly for B. hyodysenteriae isolates from Germany. In this study, B. hyodysenteriae (n = 116) isolated from diarrheic pigs between 1990 and 2016 in Germany were investigated for their STs, susceptibility to the major drugs used for treatment of SD (tiamulin and valnemulin) and genes that were previously linked with virulence and encode for hemolysins (tlyA, tlyB, tlyC, hlyA, BHWA1_RS02885, BHWA1_RS09085, BHWA1_RS04705, and BHWA1_RS02195), outer membrane proteins (OMPs) (bhlp16, bhlp17...
2018: PloS One
https://www.readbyqxmd.com/read/29323173/electroporation-of-mice-zygotes-with-dual-guide-rna-cas9-complexes-for-simple-and-efficient-cloning-free-genome-editing
#19
Marie Teixeira, Bénédicte F Py, Christophe Bosc, Daphné Laubreton, Marie-Jo Moutin, Jacqueline Marvel, Frédéric Flamant, Suzy Markossian
In this report, we present an improved protocol for CRISPR/Cas9 genome editing in mice. The procedure consists in the electroporation of intact mouse zygotes with ribonucleoprotein complexes prepared in vitro from recombinant Cas9 nuclease and synthetic dual guide RNA. This simple cloning-free method proves to be extremely efficient for the generation of indels and small deletions by non-homologous end joining, and for the generation of specific point mutations by homology-directed repair. The procedure, which avoids DNA construction, in vitro transcription and oocyte microinjection, greatly simplifies genome editing in mice...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321316/two-residues-in-nsp9-contribute-to-the-enhanced-replication-and-pathogenicity-of-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus
#20
Kuan Zhao, Jia-Cong Gao, Jun-Yao Xiong, Jin-Chao Guo, Yong-Bo Yang, Cheng-Gang Jiang, Yan-Dong Tang, Zhi-Jun Tian, Xue-Hui Cai, Guang-Zhi Tong, Tong-Qing An
Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) possesses greater replicative capacity and pathogenicity than classical PRRSV. However, the factors that lead to enhanced replication and pathogenicity remain unclear. In our study, an alignment of all available full-length sequences of North-American type PRRSVs (n = 204) revealed two consistent amino acid mutations that differed between HP-PRRSV and classical PRRSV and were located at positions 519 and 544 in non-structural protein 9...
January 10, 2018: Journal of Virology
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