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https://www.readbyqxmd.com/read/28548214/the-performance-of-malbac-and-mda-methods-in-the-identification-of-concurrent-mutations-and-aneuploidy-screening-to-diagnose-beta-thalassaemia-disorders-at-the-single-and-multiple-cell-levels
#1
WeiQiang Liu, HuiMin Zhang, Dan Hu, SiJia Lu, XiaoFang Sun
AIM: To select an optimal whole-genome amplification (WGA) method to improve the efficiency of the preimplantation genetic diagnosis and screening (PGD/PGS) of beta-thalassaemia disorders. METHODS: Fifty-seven fibroblast samples with defined beta-thalassaemia variations and forty-eight single-blastomere samples were amplified from single-, two-, and five-cell samples by multiple annealing and looping-based amplification cycles (MALBAC) and the multiple displacement amplification (MDA) method...
May 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28548177/specific-dna-sequences-allosterically-enhance-protein-protein-interaction-in-a-transcription-factor-through-modulation-of-protein-dynamics-implications-for-specificity-of-gene-regulation
#2
Abhishek Mazumder, Subrata Batabyal, Manas Mondal, Tanumoy Mondol, Susobhan Choudhury, Raka Ghosh, Tanaya Chatterjee, Dhananjay Bhattacharyya, Samir Kumar Pal, Siddhartha Roy
Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface...
May 26, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28548113/erratum-the-first-complete-genome-sequences-of-the-aci-lineage-the-most-abundant-freshwater-actinobacteria-obtained-by-whole-genome-amplification-of-dilution-to-extinction-cultures
#3
Ilnam Kang, Suhyun Kim, Md Rashedul Islam, Jang-Cheon Cho
This corrects the article DOI: 10.1038/srep42252.
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#4
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28548082/whole-genome-sequencing-and-imputation-in-isolated-populations-identify-genetic-associations-with-medically-relevant-complex-traits
#5
Lorraine Southam, Arthur Gilly, Dániel Süveges, Aliki-Eleni Farmaki, Jeremy Schwartzentruber, Ioanna Tachmazidou, Angela Matchan, Nigel W Rayner, Emmanouil Tsafantakis, Maria Karaleftheri, Yali Xue, George Dedoussis, Eleftheria Zeggini
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28546995/the-cost-and-cost-trajectory-of-whole-genome-analysis-guiding-treatment-of-patients-with-advanced-cancers
#6
Deirdre Weymann, Janessa Laskin, Robyn Roscoe, Kasmintan A Schrader, Stephen Chia, Stephen Yip, Winson Y Cheung, Karen A Gelmon, Aly Karsan, Daniel J Renouf, Marco Marra, Dean A Regier
BACKGROUND: Limited data exist on the real-world costs of applying whole-genome analysis (WGA) in a clinical setting. We estimated the costs of applying WGA to guide treatments for patients with advanced cancers and characterized how costs evolve over time. METHODS: The setting is the British Columbia Cancer Agency Personalized OncoGenomics (POG) program in British Columbia, Canada. Cost data were obtained for patients who enrolled in the program from 2012 to 2015...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546918/b-cell-receptor-signaling-pathway-involved-in-benign-lymphoepithelial-lesions-of-the-lacrimal-gland
#7
Xiao-Na Wang, Xin Ge, Jing Li, Xiao Liu, Jian-Min Ma
AIM: To detect the expression of B cell receptor signaling pathway (BCRSP) in lacrimal gland benign lymphoepithelial lesions (LGBLEL). METHODS: Gene microarray was used to compare whole-genome expression in lacrimal gland tissues from LGBLEL patients to tissues from orbital cavernous hemangioma (control tissues). Expression of BCRSP was confirmed by polymerase chain reaction (PCR) and immunohistochemistry. RESULTS: The expression of 22 genes of the BCRSP increased significantly in LGBLEL patients...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28546496/genome-sequence-of-brevibacillus-laterosporus-uniss-18-a-pathogen-of-mosquitoes-and-flies
#8
Salvatore Camiolo, Andrea Porceddu, Luca Ruiu
The entomopathogenic properties of Brevibacillus laterosporus UNISS 18 against insects are well documented. Here, we report the whole-genome sequence of this strain, which revealed the presence of several insecticide action-related genes. The deriving genetic information will help to elucidate the mechanisms underlying strain specificity and virulence against diverse target pests.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546493/whole-genome-sequence-of-the-bacteriophage-sensitive-strain-campylobacter-jejuni-nctc12662
#9
Yilmaz Emre Gencay, Martine C H Sørensen, Lone Brøndsted
Campylobacter jejuni NCTC12662 has been the choice bacteriophage isolation strain due to its susceptibility to C. jejuni bacteriophages. This trait makes it a good candidate for studying bacteriophage-host interactions. We report here the whole-genome sequence of NCTC12662, allowing future elucidation of the molecular mechanisms of phage-host interactions in C. jejuni.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546492/complete-genome-sequence-of-photobacterium-damselae-subsp-piscicida-strain-ot-51443-isolated-from-yellowtail-seriola-quinqueradiata-in-japan
#10
Takashi Aoki, Yuki Teru, Natsuki Morimoto, Tomoya Kono, Masahiro Sakai, Tomokazu Takano, John P Hawke, Yutaka Fukuda, Haruko Takeyama, Jun-Ichi Hikima
Pseudotuberculosis caused by infection of Photobacterium damselae subsp. piscicida has caused serious economic damages to aquaculture farms worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida strain OT-51443, isolated in Japan, was determined and suggests that this genome consists of two chromosomes and five plasmids.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546491/genome-sequence-of-acinetobacter-lactucae-otec-02-isolated-from-hydrocarbon-contaminated-soil
#11
Marco Antonio Rogel-Hernandez, Gabriela Guerrero, Clara Ivette Rincón-Molina, Víctor Manuel Ruiz-Valdiviezo, Crhistian Cisneros-Pérez, José Humberto Castañón-Gonzalez, Aline López-López, Esperanza Martinez-Romero, Reiner Rincón-Rosales
Acinetobacter lactucae OTEC-02 was isolated from hydrocarbon-contaminated soils. Whole-genome sequence analysis was performed to learn more about the strain's ability to degrade different types of recalcitrant toxic monoaromatic hydrocarbons. The genome of this bacterium revealed its genomic properties and versatile metabolic features, as well as a complete prophage.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546490/complete-genome-sequence-of-the-campylobacter-helveticus-type-strain-atcc-51209
#12
William G Miller, Emma Yee, James L Bono
Campylobacter helveticus has been isolated from domestic dogs and cats. Although C. helveticus is closely related to the emerging human pathogen C. upsaliensis, no C. helveticus-associated cases of human illness have been reported. This study describes the whole-genome sequence of the C. helveticus type strain ATCC 51209 (=CCUG 30682(T)).
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546483/finished-whole-genome-sequences-of-two-clostridium-botulinum-type-a-b-isolates
#13
Jessica L Halpin, Karen Hill, Shannon L Johnson, David Carlton Bruce, T Brian Shirey, Janet K Dykes, Carolina Lúquez
Clostridium botulinum secretes a potent neurotoxin that causes devastating effects when ingested, including paralysis and death if not treated. In the United States, some clinically significant strains produce toxin type A while also harboring a silent B gene. These are the first two closed genome sequences published for this subset.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546482/finished-whole-genome-sequence-of-clostridium-argentinense-producing-botulinum-neurotoxin-type-g
#14
Jessica L Halpin, Karen Hill, Shannon L Johnson, David Carlton Bruce, T Brian Shirey, Janet K Dykes, Carolina Lúquez
Here, we present a closed genome sequence for Clostridium argentinense strain 89G, the first strain identified to produce botulinum neurotoxin type G (BoNT/G). Although discovered in 1970, to date, there have been no reference quality sequences publicly available for this species.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546474/draft-genome-sequence-of-rhodococcus-sp-strain-66b
#15
Louise F Thatcher, Cindy A Myers, Cathryn A O'Sullivan, Margaret M Roper
We report here the draft genome sequence and annotation of Rhodococcus sp. strain 66b isolated from the soil of southwest Western Australia. This strain exhibits a range of bioactivities, including plant growth promotion, biosurfactant production, and wax degradation. Whole-genome sequencing was conducted to uncover the underlying mechanisms.
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28546117/analysis-on-pathogenic-and-virulent-characteristics-of-the-cronobacter-sakazakii-strain-baa-894-by-whole-genome-sequencing
#16
Xuerui Bao, Ling Yang, Lequn Chen, Bing Li, Lin Li, Yanyan Li, Zhenbo Xu
Cronobacter sakazakii is an opportunistic pathogen responsible for necrotizing enterocolitis, meningitis and septicaemia especially to infant and neonate, with high lethality ranging in 40%-80%. This strain is able to survive in infant milk formula and possesses capability of pathogenicity and virulence, biofilm formation, and high resistance to elevated osmotic, low pH, heat, oxidation, and desiccasion. This study is aims to investigate the molecular characteristics of Cronobacter sakazakii BAA 894, including mechanisms of its invasion and adherence, biofilm formation, unusual resistance to environmental stress employing whole genome sequencing and comparative genomics...
May 22, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28545488/genetic-diversity-of-mycobacterium-tuberculosis-isolates-from-tochigi-prefecture-a-local-region-of-japan
#17
Fuminori Mizukoshi, Tohru Miyoshi-Akiyama, Hiroki Iwai, Takako Suzuki, Reiko Kiritani, Teruo Kirikae, Keiji Funatogawa
BACKGROUND: Foreign-born patients with tuberculosis (TB) may introduce globally disseminated isolates of Mycobacterium tuberculosis into large cities in Japan. The risk of dissemination of these isolates into local regions, however, has not been determined. This study analyzed the molecular epidemiology of M. tuberculosis isolates obtained from TB patients living in a local region of Japan. METHODS: Whole genome sequences of 169 M. tuberculosis isolates, obtained from 148 Japanese-born and 21 foreign-born patients living in Tochigi, Japan, were analyzed using the Comprehensive analysis server for the Mycobacterium t u b erculosis complex (CASTB)...
May 25, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28545477/optimizing-complex-phenotypes-through-model-guided-multiplex-genome-engineering
#18
Gleb Kuznetsov, Daniel B Goodman, Gabriel T Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J Lajoie, George M Church
We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide mutations that recover 59% of the fitness defect exhibited by the 63-codon E. coli strain C321.∆A. By introducing targeted combinations of changes in multiplex we generate rich genotypic and phenotypic diversity and characterize clones using whole-genome sequencing and doubling time measurements. Regularized multivariate linear regression accurately quantifies individual allelic effects and overcomes bias from hitchhiking mutations and context-dependence of genome editing efficiency that would confound other strategies...
May 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28545446/whole-genome-sequencing-reveals-within-host-genetic-changes-in-paired-meningococcal-carriage-isolates-from-ethiopia
#19
Guro K Bårnes, Ola Brønstad Brynildsrud, Bente Børud, Bereket Workalemahu, Paul A Kristiansen, Demissew Beyene, Abraham Aseffa, Dominique A Caugant
BACKGROUND: Meningococcal colonization is a prerequisite for transmission and disease, but the bacterium only very infrequently causes disease while asymptomatic carriage is common. Carriage is highly dynamic, showing a great variety across time and space within and across populations, but also within individuals. The understanding of genetic changes in the meningococcus during carriage, when the bacteria resides in its natural niche, is important for understanding not only the carriage state, but the dynamics of the entire meningococcal population...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545403/long-lasting-effect-of-obesity-on-skeletal-muscle-transcriptome
#20
Ilhem Messaoudi, Mithila Handu, Maham Rais, Suhas Sureshchandra, Byung S Park, Suzanne S Fei, Hollis Wright, Ashley E White, Ruhee Jain, Judy L Cameron, Kerri M Winters-Stone, Oleg Varlamov
BACKGROUND: Reduced physical activity and increased intake of calorically-dense diets are the main risk factors for obesity, glucose intolerance, and type 2 diabetes. Chronic overnutrition and hyperglycemia can alter gene expression, contributing to long-term obesity complications. While caloric restriction can reduce obesity and glucose intolerance, it is currently unknown whether it can effectively reprogram transcriptome to a pre-obesity level. The present study addressed this question by the preliminary examination of the transcriptional dynamics in skeletal muscle after exposure to overnutrition and following caloric restriction...
May 25, 2017: BMC Genomics
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