keyword
MENU ▼
Read by QxMD icon Read
search

DNA screening

keyword
https://www.readbyqxmd.com/read/29792916/flow-cytometry-based-method-facilitates-optimization-of-pma-treatment-condition-for-pma-qpcr-method
#1
Zhiqing Huang, Jianwei Zheng, Chunmei Shi, Qiang Chen
Coupling propidium monoazide (PMA) with quantitative PCR (PMA-qPCR) has been successfully applied to specific detection and quantification of viable cells in various samples. The optimal PMA treatment condition is usually determined through qPCR. However, it is a tedious, time consuming and costly process including DNA extraction and qPCR. To overcome this problem, a flow cytometry-based (FCM-based) method was first proposed in this study to replace qPCR for screening of the optimal PMA treatment condition for Helicobacter pylori, since the pure culture treated with PMA was actually a single cell suspension with fluorescent dye...
May 21, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29792221/sex-differences-in-cardiovascular-epigenetics-a-systematic-review
#2
REVIEW
Robin J G Hartman, Sarah E Huisman, Hester M den Ruijter
BACKGROUND: Differences in cardiovascular diseases are evident in men and women throughout life and are mainly attributed to the presence of sex hormones and chromosomes. Epigenetic mechanisms drive the regulation of the biological processes that may lead to CVD and are possibly influenced by sex. In order to gain an overview of the status quo on sex differences in cardiovascular epigenetics, we performed a systematic review. MATERIALS AND METHODS: A systematic search was performed on PubMed and Embase for studies mentioning cardiovascular disease, epigenetics, and anything related to sex differences...
May 23, 2018: Biology of Sex Differences
https://www.readbyqxmd.com/read/29790943/mutalisk-a-web-based-somatic-mutation-analyis-toolkit-for-genomic-transcriptional-and-epigenomic-signatures
#3
Jongkeun Lee, Andy Jinseok Lee, June-Koo Lee, Jongkeun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong
Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790932/selex-screen-for-zona-pellucida-binding-dna-aptamers
#4
Paul S Miller, Janice P Evans
No abstract text is available yet for this article.
May 22, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29790807/study-of-mitochondrial-dna-a1555g-and-c1494t-mutations-in-a-large-cohort-of-women-individuals
#5
Lin Wang, Xiaobin Wang, Xiaolong Cai, Rong Qiang
Mammalian mitochondrial A1555G and C1494T mutations are the most common causes of aminoglycoside-induced and non-syndromic hearing loss. However, these two mutations always are studied in the subject of pedigrees analysis. In the present study, we aimed to investigate the genetic characteristic of the A1555G and C1494T mutations on the population-level sampling, and to study the A1555G pattern of maternal transmission in three heteroplasmic families. Four thousand two hundred and ten unrelated women with normal hearing were enrolled as subjects...
May 23, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29790588/the-lncrna-casc9-and-rna-binding-protein-hnrnpl-form-a-complex-and-co-regulate-genes-linked-to-akt-signaling
#6
Marcel Klingenberg, Matthias Groß, Ashish Goyal, Maria Polycarpou-Schwarz, Thilo Miersch, Anne-Sophie Ernst, Jörg Leupold, Nitin Patil, Uwe Warnken, Heike Allgayer, Thomas Longerich, Peter Schirmacher, Michael Boutros, Sven Diederichs
The identification of viability-associated long non-coding RNAs (lncRNA) might be a promising rationale for new therapeutic approaches in liver cancer. Here, we applied the first RNAi screening approach in hepatocellular carcinoma (HCC) cell lines to find viability-associated lncRNAs. Among the multiple identified lncRNAs with a significant impact on HCC cell viability, we selected CASC9 (Cancer Susceptibility 9) due to the strength of its phenotype, expression, and upregulation in HCC versus normal liver. CASC9 regulated viability across multiple HCC cell lines as shown by CRISPR interference, single siRNA- and siPOOL-mediated depletion of CASC9...
May 23, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29790491/advancements-in-microfluidic-technologies-for-isolation-and-early-detection-of-circulating-cancer-related-biomarkers
#7
REVIEW
Ankit Rana, Yuqian Zhang, Leyla Esfandiari
Early stage detection of cancer is essential for the improved long-term survival of patients. Currently, costly, extensively complex and invasive procedures, such as surgical tissue biopsies, are used for cancer screening. Thus, over the past few decades, advancements in microfluidics and lab-on-a-chip approaches have been made to develop minimally invasive and miniaturized platforms to identify and segregate circulating cancer biomarkers such as exosomes, circulating tumor cells (CTCs) and cell-free DNA (cfDNA) from body fluids...
May 23, 2018: Analyst
https://www.readbyqxmd.com/read/29789573/high-throughput-screening-of-prostate-cancer-risk-loci-by-single-nucleotide-polymorphisms-sequencing
#8
Peng Zhang, Ji-Han Xia, Jing Zhu, Ping Gao, Yi-Jun Tian, Meijun Du, Yong-Chen Guo, Sufyan Suleman, Qin Zhang, Manish Kohli, Lori S Tillmans, Stephen N Thibodeau, Amy J French, James R Cerhan, Li-Dong Wang, Gong-Hong Wei, Liang Wang
Functional characterization of disease-causing variants at risk loci has been a significant challenge. Here we report a high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) technology to simultaneously screen hundreds to thousands of SNPs for their allele-dependent protein-binding differences. This technology takes advantage of higher retention rate of protein-bound DNA oligos in protein purification column to quantitatively sequence these SNP-containing oligos. We apply this technology to test prostate cancer-risk loci and observe differential allelic protein binding in a significant number of selected SNPs...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789540/rapid-host-strain-improvement-by-in-vivo-rearrangement-of-a-synthetic-yeast-chromosome
#9
B A Blount, G-O F Gowers, J C H Ho, R Ledesma-Amaro, D Jovicevic, R M McKiernan, Z X Xie, B Z Li, Y J Yuan, T Ellis
Synthetic biology tools, such as modular parts and combinatorial DNA assembly, are routinely used to optimise the productivity of heterologous metabolic pathways for biosynthesis or substrate utilisation, yet it is well established that host strain background is just as important for determining productivity. Here we report that in vivo combinatorial genomic rearrangement of Saccharomyces cerevisiae yeast with a synthetic chromosome V can rapidly generate new, improved host strains with genetic backgrounds favourable to diverse heterologous pathways, including those for violacein and penicillin biosynthesis and for xylose utilisation...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789312/development-of-diagnostic-snp-markers-to-monitor-hybridization-between-sika-deer-cervus-nippon-and-wapiti-cervus-elaphus
#10
Hengxing Ba, Zhipeng Li, Yifeng Yang, Chunyi Li
Sika deer ( Cervus Nippon ) and wapiti ( Cervus elaphus ) are closely related species and their hybridization can result in significant allele-shift of their gene pool. Additive genetic effects and putative heterotic effects of their hybridization on growth performance could confer considerable economic advantage in deer farming. Here, we used double-digest restriction site-associated DNA sequencing technology (ddRAD-seq) and detected ∼320,000 genome-wide SNPs from 30 captive individuals: 7 sika deer, 6 wapiti and 17 F1 hybrids (reciprocal cross)...
May 22, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29788895/synthesis-of-nucleosides-and-non-nucleosides-based-4-6-disubstituted-2-oxo-dihydropyridine-3-carbonitriles-as-antiviral-agents
#11
Tarek S Ibrahim, Hassan A El-Sayed, Maan T Khayat, Amany M M Al-Mahmoudy, Ahmed H Moustafa, Ayat K Saad El-Deen, Sherif A F Rostom, Siva S Panda
BACKGROUND: Viral diseases are considered main threats that face the humanity worldwide. The emergence of new viruses like influenza viruses emphasizes the significance of designing novel antiviral drugs. METHOD: The aim of this work is to synthesize a new set of nucleoside and non-nucleoside cyanopyridine, characterized and evaluated for their in vitro antiviral properties against various strains. CONCLUSION: More than compounds showed variable antiviral potential against a panel of eighteen DNA and RNA viruses...
May 22, 2018: Medicinal Chemistry
https://www.readbyqxmd.com/read/29788264/mpk-1-erk-pathway-regulates-dna-damage-response-during-development-through-daf-16-foxo
#12
Julien N Bianco, Björn Schumacher
Ultraviolet (UV) induces distorting lesions to the DNA that can lead to stalling of the RNA polymerase II (RNAP II) and that are removed by transcription-coupled nucleotide excision repair (TC-NER). In humans, mutations in the TC-NER genes CSA and CSB lead to severe postnatal developmental defects in Cockayne syndrome patients. In Caenorhabditis elegans, mutations in the TC-NER genes csa-1 and csb-1, lead to developmental growth arrest upon UV treatment. We conducted a genetic suppressor screen in the nematode to identify mutations that could suppress the developmental defects in csb-1 mutants...
May 21, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29788025/does-100-rapid-review-improve-cervical-cancer-screening
#13
José Queiroz Filho, José Eleutério, Ricardo Ney Cobucci, Janaina Cristiana de Oliveira Crispim, Paulo César Giraldo, Ana Katherine Gonçalves
OBJECTIVE: The aim of this work was to evaluate 100% rapid review (100% RR) as a useful tool to detect false negative (FN) results. STUDY DESIGN: A sample of 8,677 swabs was investigated; the unsatisfactory and negative results were referred to 100% RR, concordant results were taken as the final diagnosis, while the discordant results were debated in a consensus meeting to reach a conclusion. The positive results were examined by 2 cytologists. The data were entered into SAS statistical software, and the agreement of the 100% RR results with the final diagnosis was tested with the weighted kappa statistic...
May 22, 2018: Acta Cytologica
https://www.readbyqxmd.com/read/29787887/human-pegivirus-persistence-in-the-human-blood-virome-after-allogeneic-haematopoietic-stem-cell-transplantation
#14
Diem-Lan Vu, Samuel Cordey, Federico Simonetta, Francisco Brito, Mylène Docquier, Lara Turin, Christian van Delden, Elsa Boely, Carole Dantin, Amandine Pradier, Eddy Roosnek, Yves Chalandon, Evgeny M Zdobnov, Stavroula Masouridi-Levrat, Laurent Kaiser
OBJECTIVES: As commensal viruses are defined by the immunological tolerance afforded to them, any immunomodulation, such as is received during haematopoietic stem cell transplantation, may shift the demarcation between innocuous viral resident and disease-causing pathogen. METHODS: We analysed by deep-sequencing the plasma virome of 40 allogeneic haematopoietic stem cell transplant (allo-HSCT) patients 1 month post-transplantation. As human pegivirus (HPgV) was highly prevalent, we performed a one-year screening of 122 plasma samples by specific rRT-PCR assay...
May 19, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29787863/validity-of-targeted-next-generation-sequencing-in-routine-care-for-identifying-clinically-relevant-molecular-profiles-in-non-small-cell-lung-cancer-results-of-a-2-year-experience-on-1-343-samples
#15
Antoine Legras, Marc Barritault, Anne Tallet, Elizabeth Fabre, Alice Guyard, Bastien Rance, William Digan, Nicolas Pecuchet, Etienne Giroux-Leprieur, Catherine Julie, Stéphane Jouveshomme, Véronique Duchatelle, Véronique Giraudet, Laure Gibault, Alain Cazier, Jean Pastre, Françoise LE Pimpec-Barthes, Pierre Laurent-Puig, Hélène Blons
Theranostic assays are based on single gene testing but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated. NGS performance was assessed following guidelines. TaqMan probes and NGS were compared for their ability to detect EGFR and KRAS mutations and NGS mutation profiles were analyzed on a large series of NSCLC (n=1,343)...
May 19, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29787635/abnormal-bone-remodeling-activity-of-dental-follicle-cells-from-a-cleidocranial-dysplasia-patient
#16
Yang Liu, Xianli Zhang, Xiangyu Sun, Xiaozhe Wang, Chenying Zhang, Shuguo Zheng
OBJECTIVES: To explore the role of dental follicle cells (DFCs) with a novel cleidocranial dysplasia (CCD) causative gene RUNX2 mutation (DFCsRUNX 2+/m ) in delayed permanent tooth eruption. MATERIALS AND METHODS: A CCD patient with typical clinical features was involved in this study. DFCsRUNX 2+/m were cultured and DNA was extracted for RUNX2 mutation screening. Measurements of cell proliferation, alkaline phosphatase (ALP) activity, alizarin red staining and osteoblast-specific genes expression were performed to assess osteogenesis of DFCsRUNX 2+/m ...
May 22, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29786943/integrating-a-comprehensive-dna-barcode-reference-library-with-a-global-map-of-yews-taxus-l-for-forensic-identification
#17
Jie Liu, Richard I Milne, Michael Möller, Guang-Fu Zhu, Lin-Jiang Ye, Ya-Huang Luo, Jun-Bo Yang, Moses Cheloti Wambulwa, Chun-Neng Wang, De-Zhu Li, Lian-Ming Gao
Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa...
May 22, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#18
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29785534/an-enzyme-free-homogenous-electrochemical-assay-for-sensitive-detection-of-the-plasmid-mediated-colistin-resistance-gene-mcr-1
#19
Bo Li, Zhixin Chai, Xiaohui Yan, Chunchen Liu, Bo Situ, Ye Zhang, Weilun Pan, Shihua Luo, Jianhua Liu, Lei Zheng
Antibiotic resistance associated with the mcr-1 gene of Gram-negative bacteria, which confers resistance to drugs of last resort and has the potential to spread via plasmids, is one of the most pressing issues facing global health today. Point-of-care testing for the mcr-1 gene is needed to aid in the identification of colistin resistance in the field and to control its horizontal transmission. Here, we report the successful development of an enzyme-free homogenous electrochemical strategy for sensitive detection of the antibiotic resistance gene mcr-1 using the hybridization chain reaction and mcr-1-specific toehold probe...
May 22, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29785231/advantages-of-evaluating-%C3%AE-h2ax-induction-in-non-clinical-drug-development
#20
REVIEW
Shigeki Motoyama, Akira Takeiri, Kenji Tanaka, Asako Harada, Kaori Matsuzaki, Junko Taketo, Saori Matsuo, Etsuko Fujii, Masayuki Mishima
γH2AX, the phosphorylated form of a histone variant H2AX at Ser 139, is already widely used as a biomarker to research the fundamental biology of DNA damage and repair and to assess the risk of environmental chemicals, pollutants, radiation, and so on. It is also beginning to be used in the early non-clinical stage of pharmaceutical drug development as an in vitro tool for screening and for mechanistic studies on genotoxicity. Here, we review the available information on γH2AX-based test systems that can be used to develop drugs and present our own experience of practically applying these systems during the non-clinical phase of drug development...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
keyword
keyword
33369
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"