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https://www.readbyqxmd.com/read/28728396/characterization-and-functional-inferences-of-a-genome-wide-dna-methylation-profile-in-the-loin-longissimus-dorsi-muscle-of-swine
#1
Woonsu Kim, Hyesun Park, Kang-Seok Seo, Seongwon Seo
Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates)...
May 14, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728367/comparative-analysis-on-genome-wide-dna-methylation-in-longissimus-dorsi-muscle-between-small-tailed-han-and-dorper-%C3%A3-small-tailed-han-crossbred-sheep
#2
Yang Cao, Hai-Guo Jin, Hui-Hai Ma, Zhihui Zhao
Objective: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle (LDM) between Small Tailed Han and Dorper × Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods: Six samples were subjected to MeDIP-seq and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results: 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728341/dna-microarray-technology-in-hbv-genotyping
#3
Payam Behzadi, Elham Behzadi, Seyed M Alavian
No abstract text is available yet for this article.
October 2017: Minerva Medica
https://www.readbyqxmd.com/read/28728275/-changes-and-differences-of-dna-methylation-in-human-macrophages-infected-with-virulent-and-avirulent-mycobacterium-tuberculosis
#4
L N Lyu, H Y Jia, Z H Li, Z Q Liu, Z D Zhang
Objective: To profile DNA methylation and compare differentially methylated region (DMR) of macrophages infected with virulent and avirulent strains of Mycobacterium tuberculosis (MTB). Methods: PMA(50 ng/ml) treated THP-1 macrophages were left uninfected or infected with the virulent H37Rv(THP-1/Rv) or avirulent H37Ra(THP-1/Ra). The genomic DNA was then extracted and DNA methylation was profiled via Reduced Representation Bisulfite Sequencing (RRBS). The DNA methylation pattern and DMRs between the tested samples were indentified...
July 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28728263/-identification-of-mutations-associated-with-coronary-artery-lesion-susceptibility-in-kawasaki-disease-by-targeted-enrichment-of-genomic-region-sequencing-technique
#5
D Y Zhu, S R Song, L J Xie, F Qiu, J Yang, T T Xiao, M Huang
Objective: To screen and identify the mutations in Kawasaki disease by targeted enrichment of genomic region sequencing technique and investigate susceptibility genes associated with coronary artery lesion. Method: This was a case-control study.A total of 114 patients diagnosed as Kawasaki disease treated in Shanghai Children's Hospital between December 2015 and November 2016 were studied and another 45 healthy children who were physically examined in outpatient department were enrolled as control group. Patients were divided into two groups based on the results of echocardiogram...
July 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28728156/predicting-the-risk-to-develop-preeclampsia-in-the-first-trimester-combining-promoter-variant-98a-c-of-lgals13-placental-protein-13-black-ethnicity-previous-preeclampsia-obesity-and-maternal-age
#6
Liora Madar-Shapiro, Ido Karady, Alla Trahtenherts, Argryo Syngelaki, Ranjit Akolekar, Liona Poon, Ruth Cohen, Adi Sharabi-Nov, Berthold Huppertz, Marei Sammar, Kata Juhasz, Nandor Gabor Than, Zoltan Papp, Roberto Romero, Kypros H Nicolaides, Hamutal Meiri
BACKGROUND: LGALS13 (placental protein 13 [PP13]) promoter DNA polymorphisms was evaluated in predicting preeclampsia (PE), given PP13's effects on hypotension, angiogenesis, and immune tolerance. METHODS: First-trimester plasma samples (49 term and 18 intermediate) of PE cases matched with 196 controls were collected from King's College Hospital, London, repository. Cell-free DNA was extracted and the LGALS13 exons were sequenced after PCR amplification. Expression of LGALS13 promoter reporter constructs was determined in BeWo trophoblast-like cells with luciferase assays...
July 21, 2017: Fetal Diagnosis and Therapy
https://www.readbyqxmd.com/read/28728145/extracellular-dna-contributes-to-dental-biofilm-stability
#7
Sebastian Schlafer, Rikke L Meyer, Irene Dige, Viduthalai R Regina
Extracellular DNA (eDNA) is a major matrix component of many bacterial biofilms. While the presence of eDNA and its role in biofilm stability have been demonstrated for several laboratory biofilms of oral bacteria, there is no data available on the presence and function of eDNA in in vivo grown dental biofilms. This study aimed to determine whether eDNA was part of the matrix in biofilms grown in situ in the absence of sucrose and whether treatment with DNase dispersed biofilms grown for 2.5, 5, 7.5, 16.5, or 24 h...
July 21, 2017: Caries Research
https://www.readbyqxmd.com/read/28728135/prostate-cancer-risk-and-dna-methylation-signatures-in-aging-rats-following-developmental-bpa-exposure-a-dose-response-analysis
#8
Gail S Prins, Shu-Hua Ye, Lynn Birch, Xiang Zhang, Ana Cheong, Han Lin, Esther Calderon-Gierszal, Jacob Groen, Wen-Yang Hu, Shuk-Mei Ho, Richard B van Breemen
BACKGROUND: Previous studies have uncovered heightened prostatic susceptibility to hormone-induced neoplasia from early-life exposure to low-dose bisphenol A (BPA). However, significant data gaps remain that are essential to address for biological relevance and necessary risk assessment. OBJECTIVES: A complete BPA dose-response analysis of prostate lesions across multiple prostatic lobes was conducted that included internal BPA dosimetry, progression to adenocarcinoma with aging and mechanistic connections to epigenetically reprogramed genes...
July 11, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28728127/is-bacterial-luminescence-response-to-low-dose-radiation-associated-with-mutagenicity
#9
T V Rozhko, O A Guseynov, V E Guseynova, A A Bondar, A N Devyatlovskaya, N S Kudryasheva
Luminous marine bacteria are widely used in bioassays with luminescence intensity being a physiological parameter tested. The purpose of the study was to determine whether bacterial genetic alteration is responsible for bioluminescence kinetics change under low-dose radiation exposure. The alpha-emitting radionuclide (241)Am and beta-emitting radionuclide (3)H were used as the sources of low-dose ionizing radiation. Changes of bioluminescence kinetics of Photobacterium phosphoreum in solutions of (241)Am(NO3)3, 7 kBq/L, and tritiated water, 100 MBq/L, were studied; bioluminescence kinetics stages (absence of effect, activation, and inhibition) were determined...
July 17, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28728099/endogenous-viruses-of-parasitic-wasps-variations-on-a-common-theme
#10
REVIEW
Jean-Michel Drezen, Matthieu Leobold, Annie Bézier, Elisabeth Huguet, Anne-Nathalie Volkoff, Elisabeth A Herniou
In a remarkable example of convergent evolution, several parasitic wasp lineages have independently captured and maintained complex DNA virus machineries, used to transfer virulence factors. Parasitic wasps, which develop inside the larvae of their insect hosts, may inject Polydnaviruses (PDVs) or Virus-Like particles (VLPs), derived from the recurrent endogenization of several large DNA viruses. PDVs evolved from the domestication in braconid and ichneumonid wasps of viruses from different families and function as gene transfer agents...
July 17, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28728057/integrating-the-microbiome-as-a-resource-in-the-forensics-toolkit
#11
Thomas H Clarke, Andres Gomez, Harinder Singh, Karen E Nelson, Lauren M Brinkac
The introduction of DNA fingerprinting to forensic science rapidly expanded the available evidence that could be garnered from a crime scene and used in court cases. Next generation sequencing technologies increased available genetic data that could be used as evidence by orders of magnitude, and as such, significant additional genetic information is now available for use in forensic science. This includes DNA from the bacteria that live in and on humans, known as the human microbiome. Next generation sequencing of the human microbiome demonstrates that its bacterial DNA can be used to uniquely identify an individual, provide information about their life and behavioral patterns, determine the body site where a sample came from, and estimate postmortem intervals...
June 27, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28728056/sequence-based-diversity-of-23-autosomal-str-loci-in-koreans-investigated-using-an-in-house-massively-parallel-sequencing-panel
#12
Eun Hye Kim, Hwan Young Lee, So Yeun Kwon, Eun Young Lee, Woo Ick Yang, Kyoung-Jin Shin
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles...
July 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28728055/investigation-of-length-heteroplasmy-in-mitochondrial-dna-control-region-by-massively-parallel-sequencing
#13
Chun-Yen Lin, Li-Chin Tsai, Hsing-Mei Hsieh, Chia-Hung Huang, Yu-Jen Yu, Bill Tseng, Adrian Linacre, James Chun-I Lee
Accurate sequencing of the control region of the mitochondrial genome is notoriously difficult due to the presence of polycytosine bases, termed C-tracts. The precise number of bases that constitute a C-tract and the bases beyond the poly cytosines may not be accurately defined when analyzing Sanger sequencing data separated by capillary electrophoresis. Massively parallel sequencing has the potential to resolve such poor definition and provides the opportunity to discover variants due to length heteroplasmy...
July 10, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28728054/an-artificial-neural-network-system-to-identify-alleles-in-reference-electropherograms
#14
Duncan Taylor, Ash Harrison, David Powers
Electropherograms are produced in great numbers in forensic DNA laboratories as part of everyday criminal casework. Before the results of these electropherograms can be used they must be scrutinised by analysts to determine what the identified data tells them about the underlying DNA sequences and what is purely an artefact of the DNA profiling process. This process of interpreting the electropherograms can be time consuming and is prone to subjective differences between analysts. Recently it was demonstrated that artificial neural networks could be used to classify information within an electropherogram as allelic (i...
July 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28728009/bridged-rebar-graphene-functionalized-aptasensor-for-pathogenic-e-coli-o78-k80-h11-detection
#15
Harmanjit Kaur, Munish Shorie, Manju Sharma, Ashok K Ganguli, Priyanka Sabherwal
We report a novel fabrication method of functionalised Bridged Rebar Graphene (BRG) onto newly designed nanostructured aptasensor for label free impedimetric sensing of pathogenic bacteria E. coli O78:K80:H11. The chemical facilitated unscrolling of MWCNT and subsequent bridging with terephthalaldehyde (TPA) to form 3D-hierarchical BRG nanoconstruct exhibited synergistic effect by combining enhanced electrical properties and facile chemical functionality for stable bio-interface. The bacteria-DNA interactions were captured on BRG nanostructured electrode by using specific anti-E...
July 5, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28728008/pen-on-paper-strategy-for-point-of-care-testing-rapid-prototyping-of-fully-written-microfluidic-biosensor
#16
Zedong Li, Fei Li, Yue Xing, Zhi Liu, Minli You, Yingchun Li, Ting Wen, Zhiguo Qu, Xiao Ling Li, Feng Xu
Paper-based microfluidic biosensors have recently attracted increasing attentions in point-of-care testing (POCT) territories benefiting from their affordable, accessible and eco-friendly features, where technologies for fabricating such biosensors are preferred to be equipment free, easy-to-operate and capable of rapid prototyping. In this work, we developed a pen-on-paper (PoP) strategy based on two custom-made pens, i.e., a wax pen and a conductive-ink pen, to fully write paper-based microfluidic biosensors through directly writing both microfluidic channels and electrodes...
July 1, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28728006/an-electrochemical-impedance-biosensor-for-hg-2-detection-based-on-dna-hydrogel-by-coupling-with-dnazyme-assisted-target-recycling-and-hybridization-chain-reaction
#17
Wei Cai, Shunbi Xie, Jin Zhang, Dianyong Tang, Ying Tang
In this work, an electrochemical impedance biosensor for high sensitive detection of Hg(2+) was presented by coupling with Hg(2+)-induced activation of Mg(2+)-specific DNAzyme (Mg(2+)-DNAzyme) for target cycling and hybridization chain reaction (HCR) assembled DNA hydrogel for signal amplification. Firstly, we synthesized two different copolymer chains P1 and P2 by modifying hairpin DNA H3 and H4 with acrylamide polymer, respectively. Subsequently, Hg(2+) was served as trigger to activate the Mg(2+)-DNAzyme for selectively cleavage ribonucleobase-modified substrate in the presence of Mg(2+)...
July 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28727985/comparative-study-and-analytical-verification-of-pcr-methods-for-the-diagnosis-of-congenital-chagas-disease
#18
Carolina Inés Cura, Juan Carlos Ramírez, Marcelo Rodríguez, Constanza Lopez-Albízu, Lucía Irazu, Karenina Scollo, Sergio Sosa-Estani
Congenital infection is currently the first cause of new cases of Chagas disease in Argentina and nonendemic areas worldwide. Its diagnosis is of utmost importance to guarantee curative treatment. To improve such diagnosis, a transfer process of PCR tests to the national laboratory network has been initiated. We performed a comparative study of four PCR assays [two end-point PCR and two duplex real-time quantitative PCR (qPCR) procedures] to detect Trypanosoma cruzi DNA in blood samples. Because satellite DNA and kinetoplastid DNA qPCR methods have the best performance and the use of two different molecular targets for confirmatory purposes has been recommended, these methods selected to perform the transfer process and, in consequence, subjected to an analytical verification protocol based on international guidelines...
July 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28727982/genome-wide-dna-methylation-profile-of-prepubertal-porcine-testis
#19
Xi Chen, Liu-Hong Shen, Li-Xuan Gui, Fang Yang, Jie Li, Sui-Zhong Cao, Zhi-Cai Zuo, Xiao-Ping Ma, Jun-Liang Deng, Zhi-Hua Ren, Zhong-Xu Chen, Shu-Min Yu
The biological structure and function of the mammalian testis undergo important developmental changes during prepuberty and DNA methylation is dynamically regulated during testis development. In this study, we generated the first genome-wide DNA methylation profile of prepubertal porcine testis using methyl-DNA immunoprecipitation (MeDIP) combined with high-throughput sequencing (MeDIP-seq). Over 190 million high-quality reads were generated, containing 43642 CpG islands. There was an overall downtrend of methylation during development, which was clear in promoter regions but less so in gene-body regions...
July 21, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28727877/genetic-predisposition-to-breast-cancer-due-to-mutations-other-than-brca1-and-brca2-founder-alleles-among-ashkenazi-jewish-women
#20
Tom Walsh, Jessica B Mandell, Barbara M Norquist, Silvia Casadei, Suleyman Gulsuner, Ming K Lee, Mary-Claire King
Importance: Among Ashkenazi Jewish women, 3 mutations in BRCA1 and BRCA2 severely increase the risk of breast and ovarian cancer. However, among Ashkenazi Jewish patients with breast cancer who do not carry one of these founder mutations, the likelihood of carrying another pathogenic mutation in BRCA1 or BRCA2 or another breast cancer gene is not known. This information would be valuable to the patient and family for cancer prevention and treatment. Objective: To determine the frequency of cancer-predisposing mutations other than the BRCA1 and BRCA2 founder alleles among patients of Ashkenazi Jewish ancestry with breast cancer...
July 20, 2017: JAMA Oncology
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