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https://www.readbyqxmd.com/read/29049890/dna-methylation-signatures-in-peripheral-blood-mononuclear-cells-from-a-lifestyle-intervention-for-women-at-midlife-a-pilot-rct
#1
Lisa M McEwen, Evan G Gatev, Meaghan J Jones, Julia L MacIsaac, Megan M McAllister, Rebecca E Goulding, Kenneth M Madden, Martin G Dawes, Michael S Kobor, Maureen C Ashe
OBJECTIVES: Physical activity confers many health benefits, but the underlying mechanisms require further exploration. In this pilot randomized controlled trial we tested the association between longitudinal measures of DNA methylation and changes in objective measures including physical activity, weight loss, and C-reactive protein levels in community-dwelling women aged 55 to 70 years. METHODS: We assessed DNA methylation from 20 healthy post-menopausal women (55-70 years of age), who did not have a mobility disability and allocated them to a group-based intervention, Everyday Activity Supports You (EASY), or a control group (monthly group-based health-related education sessions)...
October 19, 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/29049475/potential-of-aqueous-humor-as-a-surrogate-tumor-biopsy-for-retinoblastoma
#2
Jesse L Berry, Liya Xu, A Linn Murphree, Subramanian Krishnan, Kevin Stachelek, Emily Zolfaghari, Kathleen McGovern, Thomas C Lee, Anders Carlsson, Peter Kuhn, Jonathan W Kim, David Cobrinik, James Hicks
Importance: Retinoblastoma (Rb) is one of the first tumors to have a known genetic etiology. However, because biopsy of this tumor is contraindicated, it has not been possible to define the effects of secondary genetic changes on the disease course. Objective: To investigate whether the aqueous humor (AH) of Rb eyes has sufficient tumor-derived DNA to perform genetic analysis of the tumor, including DNA copy number alterations. Design, Setting, and Participants: This investigation was a case series study at a tertiary care hospital (Children's Hospital Los Angeles) with a large Rb treatment center...
October 12, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/29048578/genome-assembly-and-transcriptome-resource-for-river-buffalo-bubalus-bubalis-2n-50
#3
John L Williams, Daniela Iamartino, Kim D Pruitt, Tad Sonstegard, Timothy P L Smith, Wai Yee Low, Tommaso Biagini, Lorenzo Bomba, Stefano Capomaccio, Bianca Castiglioni, Angelo Coletta, Federica Corrado, Fabrizio Ferré, Leopoldo Iannuzzi, Cynthia Lawley, Nicolò Macciotta, Matthew McClure, Giordano Mancini, Donato Matassino, Raffaele Mazza, Marco Milanesi, Bianca Moioli, Nicola Morandi, Luigi Ramunno, Vincenzo Peretti, Fabio Pilla, Paola Ramelli, Steven Schroeder, Francesco Strozzi, Francoise Thibaud-Nissen, Luigi Zicarelli, Paolo Ajmone-Marsan, Alessio Valentini, Giovanni Chillemi, Aleksey Zimin
Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well annotated, reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are two species of domestic water buffalo, the river (2n = 50) and the swamp (2n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29048510/donor-derived-mycoplasma-hominis-and-an-apparent-cluster-of-m-hominis-cases-in-solid-organ-transplant-recipients
#4
Olivia C Smibert, Heather L Wilson, Asma Sohail, Shanti Narayanasamy, Mark B Schultz, Susan A Ballard, Jason C Kwong, Jim de Boer, C Orla Morrissey, Anton Y Peleg, Greg I Snell, Miranda A Paraskeva, Adam W J Jenney
Background: Invasive and disseminated Mycoplasma hominis infections are well recognized but uncommon complications in solid organ transplant recipients. In a single center, a cluster of M. hominis infections were identified in lung transplant recipients from the same thoracic intensive care unit (ICU). We sought to determine the source(s) of these infections. Methods: Medical records of the donor and infected transplant recipients were reviewed for clinical characteristics...
October 16, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29048487/the-genome-draft-of-coconut-cocos-nucifera
#5
Yong Xiao, Pengwei Xu, Haikuo Fan, Luc Baudouin, Wei Xia, Stéphanie Bocs, Junyang Xu, Qiong Li, Anping Guo, Lixia Zhou, Jing Li, Yi Wu, Zilong Ma, Alix Armero, Auguste Emmanuel Issali, Na Liu, Ming Peng, Yaodong Yang
Background: Coconut palm (Cocos nucifera, 2n = 32), a member of genus Cocos and family Arecaceae (Palmaceae), is an important tropical fruit and oil crop. Currently, coconut palm is cultivated in 93 countries, including Central and South America, East and West Africa, Southeast Asia and the Pacific island, with a total growth area of more than 12 million hectares (www.fao.org/faostat/en/). Coconut palm is generally classified into two main categories: "Tall" (flowering 8-10 years after planting) and "Dwarf" (flowering 4-6 years after planting), based on morphological characteristics and breeding habits...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29048483/draft-genome-of-the-gayal-bos-frontalis
#6
Ming-Shan Wang, Yan Zeng, Xiao Wang, Wen-Hui Nie, Jin-Huan Wang, Wei-Ting Su, Newton O Otecko, Zi-Jun Xiong, Sheng Wang, Kai-Xing Qu, Shou-Qing Yan, Min-Min Yang, Wen Wang, Yang Dong, Dong-Dong Wu, Ya-Ping Zhang
Background: Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history as well as genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. Findings: We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome...
October 5, 2017: GigaScience
https://www.readbyqxmd.com/read/29048369/effect-of-curcumin-on-the-diversity-of-gut-microbiota-in-ovariectomized-rats
#7
Zhiguo Zhang, Yanjing Chen, Lihua Xiang, Zhen Wang, Gary Guishan Xiao, Jingqing Hu
Curcumin has been proven to have a weight-loss effect in a menopausal rat model induced by ovariectomy. However, the effects of curcumin on gut microfloral communities of ovariectomized (OVX) rats remains unclear. Here, we used high-throughput 16S rDNA sequencing to explore the effects of curcumin on microbial diversity in the gut of OVX rats. Female Wistar rats were subjected to either ovariectomy or a sham operation (SHAM group). The OVX rats were treated with vehicle (OVX group) or curcumin (CUR group) by oral gavage...
October 19, 2017: Nutrients
https://www.readbyqxmd.com/read/29047347/the-dynamics-of-smoking-related-disturbed-methylation-a-two-time-point-study-of-methylation-change-in-smokers-non-smokers-and-former-smokers
#8
Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger, Melanie Waldenberger
BACKGROUND: The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. However, few large-scale investigations have explored the associations using observations for individuals at multiple time-points. Here, through the use of the Illumina 450K BeadChip and data collected at two time-points separated by approximately 7 years, we investigate changes in methylation over time associated with quitting smoking or remaining a former smoker, and those associated with continued smoking...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29045798/effects-of-reclamation-years-on-composition-and-diversity-of-soil-bacterial-communities-in-northwest-china
#9
Zhibo Cheng, Fenghua Zhang, William Jeffrey Gale, Weichao Wang, Wen Sang, Haichang Yang
The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after > 27 yr of abandonment and then farmed again for 1, 5, 10, and 15 yr. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in five aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (> 0.25 mm), as well as soil organic C, available N, and available P...
October 18, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/29045613/genome-structure-of-rosa-multiflora-a-wild-ancestor-of-cultivated-roses
#10
Noriko Nakamura, Hideki Hirakawa, Shusei Sato, Shungo Otagaki, Shogo Matsumoto, Satoshi Tabata, Yoshikazu Tanaka
The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures...
October 16, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29045404/transcriptomic-responses-of-biomphalaria-pfeifferi-to-schistosoma-mansoni-investigation-of-a-neglected-african-snail-that-supports-more-s-mansoni-transmission-than-any-other-snail-species
#11
Sarah K Buddenborg, Lijing Bu, Si-Ming Zhang, Faye D Schilkey, Gerald M Mkoji, Eric S Loker
BACKGROUND: Biomphalaria pfeifferi is highly compatible with the widespread human-infecting blood fluke Schistosoma mansoni and transmits more cases of this parasite to people than any other snail species. For these reasons, B. pfeifferi is the world's most important vector snail for S. mansoni, yet we know relatively little at the molecular level regarding the interactions between B. pfeifferi and S. mansoni from early-stage sporocyst transformation to the development of cercariae. METHODOLOGY/PRINCIPAL FINDINGS: We sought to capture a portrait of the response of B...
October 18, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29044499/identification-of-the-first-homozygous-1-bp-deletion-in-gdf9-gene-leading-to-primary-ovarian-insufficiency-by-using-targeted-massively-parallel-sequencing
#12
M M França, M F A Funari, M Y Nishi, A M Narcizo, S Domenice, E M F Costa, A M Lerario, B B Mendonca
Targeted massively parallel sequencing (TMPS) has been used in genetic diagnosis for Mendelian disorders. In the past few years, the TMPS has identified new and already described genes associated with primary ovarian insufficiency phenotype. Here, we performed a targeted gene sequencing to find a genetic diagnosis in idiopathic cases of Brazilian POI cohort. A custom SureSelect(XT) DNA target enrichment panel was designed and the sequencing was performed on Illumina NextSeq sequencer. We identified one homozygous 1-bp deletion variant (c...
October 16, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29044436/preterm-infant-associated-clostridium-tertium-clostridium-cadaveris-and-clostridium-paraputrificum-strains-genomic-and-evolutionary-insights
#13
Raymond Kiu, Shabhonam Caim, Cristina Alcon-Giner, Gusztav Belteki, Paul Clarke, Derek Pickard, Gordon Dougan, Lindsay J Hall
Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C...
October 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29044179/the-effect-of-insecticide-synergist-treatment-on-genome-wide-gene-expression-in-a-polyphagous-pest
#14
Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M Clark, Thomas Van Leeuwen, Wannes Dermauw
Synergists can counteract metabolic insecticide resistance by inhibiting detoxification enzymes or transporters. They are used in commercial formulations of insecticides, but are also frequently used in the elucidation of resistance mechanisms. However, the effect of synergists on genome-wide transcription in arthropods is poorly understood. In this study we used Illumina RNA-sequencing to investigate genome-wide transcriptional responses in an acaricide resistant strain of the spider mite Tetranychus urticae upon exposure to synergists such as S,S,S-tributyl phosphorotrithioate (DEF), diethyl maleate (DEM), piperonyl butoxide (PBO) and cyclosporin A (CsA)...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043445/the-role-of-intermediate-filaments-in-maintaining-integrity-and-function-of-intestinal-epithelial-cells-after-massive-bowel-resection-in-a-rat
#15
I Sukhotnik, Y Ben Shahar, Y Pollak, T Dorfman, H Kreizman Shefer, Z E Assi, N Mor-Vaknin, A G Coran
PURPOSE: Intermediate filaments (IFs) are a part of the cytoskeleton that extend throughout the cytoplasm of all cells and function in the maintenance of cell-shape by bearing tension and serving as structural components of the nuclear lamina. In normal intestine, IFs provide a tissue-specific three-dimensional scaffolding with unique context-dependent organizational features. The purpose of this study was to evaluate the role of IFs during intestinal adaptation in a rat model of short bowel syndrome (SBS)...
October 17, 2017: Pediatric Surgery International
https://www.readbyqxmd.com/read/29042801/investigating-a-rare-methicillin-resistant-staphylococcus-aureus-strain-first-description-of-genome-sequencing-and-molecular-characterization-of-cc15-mrsa
#16
Abiola C Senok, Ali M Somily, Peter Slickers, Muhabat A Raji, Ghada Garaween, Atef Shibl, Stefan Monecke, Ralf Ehricht
PURPOSE: Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA) have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain. METHODS: Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer...
2017: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29042494/insights-from-the-genome-sequence-of-mycobacterium-lepraemurium-massive-gene-decay-and-reductive-evolution
#17
Andrej Benjak, Tanvi P Honap, Charlotte Avanzi, Enrique Becerril-Villanueva, Iris Estrada-García, Oscar Rojas-Espinosa, Anne C Stone, Stewart T Cole
Mycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, Mycobacterium leprae and M. lepraemurium were once thought to be closely related, although it was later suggested that M. lepraemurium might be related to Mycobacterium avium In this study, the complete genome of M. lepraemurium was sequenced using a combination of PacBio and Illumina sequencing...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29042239/microbiota-of-field-collected-ixodes-scapularis-and-dermacentor-variabilis-from-eastern-and-southern-ontario-canada
#18
Katie M Clow, J Scott Weese, Joyce Rousseau, Claire M Jardine
The microbiota of hard ticks has been an area of growing interest due to the potential role that the broader microbial community may play in pathogen carriage and transmission. In the last two decades, Ontario, Canada has experienced rapid changes in the risk of tick-borne disease, primarily due to the range expansion of Ixodes scapularis. Another human-biter, Dermacentor variabilis, is a longstanding resident of the province, but currently poses minimal risk of pathogen transmission. To examine the microbiota of these two species, we collected adult and nymphal I...
September 20, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29041914/analysis-of-the-genome-of-the-new-zealand-giant-collembolan-holacanthella-duospinosa-sheds-light-on-hexapod-evolution
#19
Chen Wu, Melissa D Jordan, Richard D Newcomb, Neil J Gemmell, Sarah Bank, Karen Meusemann, Peter K Dearden, Elizabeth J Duncan, Sefanie Grosser, Kim Rutherford, Paul P Gardner, Ross N Crowhurst, Bernd Steinwender, Leah K Tooman, Mark I Stevens, Thomas R Buckley
BACKGROUND: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. RESULTS: Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×...
October 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29040920/ancestry-prediction-in-singapore-population-samples-using-the-illumina-forenseq-kit
#20
Anantharaman Ramani, Yongxun Wong, Si Zhen Tan, Bing Hong Shue, Christopher Syn
The ability to predict bio-geographic ancestry can be valuable to generate investigative leads towards solving crimes. Ancestry informative marker (AIM) sets include large numbers of SNPs to predict an ancestral population. Massively parallel sequencing has enabled forensic laboratories to genotype a large number of such markers in a single assay. Illumina's ForenSeq DNA Signature Kit includes the ancestry informative SNPs reported by Kidd et al. In this study, the ancestry prediction capabilities of the ForenSeq kit through sequencing on the MiSeq FGx were evaluated in 1030 unrelated Singapore population samples of Chinese, Malay and Indian origin...
August 15, 2017: Forensic Science International. Genetics
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