keyword
MENU ▼
Read by QxMD icon Read
search

DNA screening

keyword
https://www.readbyqxmd.com/read/28550367/in-vitro-study-of-antioxidant-and-antibacterial-activities-of-lactobacillus-probiotic-spp
#1
Z Pourramezan, R Kasra Kermanshahi, M Oloomi, A Aliahmadi, H Rezadoost
This study investigated the influence of aeration and minimal medium conditions on antioxidant and antibacterial activities of 21 probiotic Lactobacillus strains isolated from dairy products. The probiotic potential of the isolates was evaluated by pH and bile tolerance. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) was used to confirm the phenotypic identification of isolates. Antioxidant producer isolates were screened by resistance to reactive oxygen species (ROS). The antioxidant and antibacterial activities of extracellular materials after 48 h fermentation with antioxidative strains were determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and broth microdilution assays, respectively...
May 26, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28550064/transient-silencing-of-dna-repair-genes-improves-targeted-gene-integration-in-the-filamentous-fungus-trichoderma-reesei
#2
Pak Yang Chum, Georg Schmidt, Markku Saloheimo, Christopher P Landowski
Trichoderma reesei is a filamentous fungus that is used world-wide to produce industrial enzymes. Industrial strains have traditionally been created though systematic strain improvement by mutagenesis and screening approaches. It is also desirable to specifically manipulate genes of the organism to further improve and modify the strain. Targeted integration in filamentous fungi is typically hampered by very low frequencies of homologous recombination. To address this limitation we have developed a simple transient method for silencing genes in T...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28550017/a-lysine-desert-protects-a-novel-domain-in-the-slx5-slx8-sumo-targeted-ub-ligase-to-maintain-sumoylation-levels-in-saccharomyces-cerevisiae
#3
Pragati Sharma, Janet R Mullen, Minxing Li, Mikel Zaratiegui, Samuel F Bunting, Steven J Brill
Protein modification by the small ubiquitin-like modifier (SUMO) plays important roles in genome maintenance. In Saccharomyces cerevisiae, proper regulation of sumoylation is known to be essential for viability in certain DNA repair mutants. Here we find the opposite result; proper regulation of sumoylation is lethal in certain DNA repair mutants. Yeast cells lacking the repair factors TDP1 and WSS1 are synthetically lethal due to their redundant roles in removing Top1-DNA covalent complexes (Top1ccs). A screen for suppressors of tdp1∆ wss1∆ synthetic lethality isolated mutations in genes known to control global sumoylation levels including ULP1, ULP2, SIZ2 and SLX5 The results suggest that alternative pathways of repair become available when sumoylation levels are altered...
May 26, 2017: Genetics
https://www.readbyqxmd.com/read/28546921/a-novel-frameshift-mutation-in-cx46-associated-with-hereditary-dominant-cataracts-in-a-chinese-family
#4
Xiu-Kun Cui, Ke-Ke Zhu, Zheng Zhou, Si-Min Wan, Yi Dong, Xuan-Ce Wang, Jing Li, Jing Zhang, Hong-Mei Mu, Lei Qin, Yan-Zhong Hu
AIM: To investigate the genetic mutations that are associated the hereditary autosomal dominant cataract in a Chinese family. METHODS: A Chinese family consisting of 20 cataract patients (including 9 male and 11 female) and 2 unaffected individuals from 5 generations were diagnosed to be a typical autosomal dominant cataract pedigree. Genomic DNA samples were extracted from the peripheral blood cells of the participants in this pedigree. Exon sequence was used for genetic mutation screening...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28546763/mutation-analysis-of-%C3%AE-thalassemia-in-east-western-indian-population-a-recent-molecular-approach
#5
Parth S Shah, Nidhi D Shah, Hari Shankar P Ray, Nikunj B Khatri, Ketan K Vaghasia, Rutvik J Raval, Sandip C Shah, Mandava V Rao
BACKGROUND: β-Thalassemia is the most prevalent genetic disorder in India. Its traits and coinheritance vary from mild to severe conditions, resulting in thalassemia minor, intermediate, and major, depending upon many factors. PURPOSE: The objective of this study was to identify the incidence of β-thalassemia traits, their coinheritance, and mutations, as well as to support the patients already diagnosed with β-thalassemia in East-Western Indian population for better management...
2017: Application of Clinical Genetics
https://www.readbyqxmd.com/read/28546435/a-simple-pipeline-for-mapping-point-mutations
#6
Guy Wachsman, Jennifer L Modliszewski, Manuel Valdes, Philip N Benfey
A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost-efficiency and ease of data production afforded by next-generation sequencing has created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user-friendly, complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes...
May 25, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28546384/systematic-analysis-of-the-dna-damage-response-network-in-telomere-defective-budding-yeast
#7
Eva-Maria Holstein, Greg Ngo, Conor Lawless, Peter Banks, Matthew Greetham, Darren Wilkinson, David Lydall
Functional telomeres are critically important to eukaryotic genetic stability. Scores of proteins and pathways are known to affect telomere function. Here, we report a series of related genome-wide genetic interaction screens performed on budding yeast cells with acute or chronic telomere defects. Genetic interactions were examined in cells defective in Cdc13 and Stn1, affecting two components of CST, a single stranded DNA (ssDNA) binding complex that binds telomeric DNA. For comparison, genetic interactions were also examined in cells with defects in Rfa3, affecting the major ssDNA binding protein, RPA, which has overlapping functions with CST at telomeres...
May 25, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28545381/prevalence-and-clinical-significance-of-visible-oral-lesions-in-patients-with-fanconi-anemia-at-risk-for-head-and-neck-cancer
#8
Eunike Velleuer, Ralf Dietrich, Amy Frohnmayer, Natalia Pomjanski, Laura E Hays, Stefan Biesterfeld
Fanconi anemia is a genetic bone marrow failure syndrome, variably associated with congenital anomalies and a sharply increased risk for epithelial malignancies. During the past 20 years, hematopoietic stem cell transplantation (HSCT) has dramatically improved survival. However, compared to the general population, FA patients are at greatly increased risk, and at a much younger age, for squamous cell carcinomas (SCC) of the oral cavity, esophagus and the anogenital region. The relative risk and age of onset appears to negatively correlate with HSCT in FA patients...
May 24, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28545070/pou4f3-mutation-screening-in-japanese-hearing-loss-patients-massively-parallel-dna-sequencing-based-analysis-identified-novel-variants-associated-with-autosomal-dominant-hearing-loss
#9
Tomohiro Kitano, Maiko Miyagawa, Shin-Ya Nishio, Hideaki Moteki, Kiyoshi Oda, Kenji Ohyama, Hiromitsu Miyazaki, Hiroshi Hidaka, Ken-Ichi Nakamura, Takaaki Murata, Rina Matsuoka, Yoko Ohta, Nobuhiro Nishiyama, Kozo Kumakawa, Sakiko Furutate, Satoshi Iwasaki, Takechiyo Yamada, Yumi Ohta, Natsumi Uehara, Yoshihiro Noguchi, Shin-Ichi Usami
A variant in a transcription factor gene, POU4F3, is responsible for autosomal dominant nonsyndromic hereditary hearing loss, DFNA15. To date, 14 variants, including a whole deletion of POU4F3, have been reported to cause HL in various ethnic groups. In the present study, genetic screening for POU4F3 variants was carried out for a large series of Japanese hearing loss (HL) patients to clarify the prevalence and clinical characteristics of DFNA15 in the Japanese population. Massively parallel DNA sequencing of 68 target candidate genes was utilized in 2,549 unrelated Japanese HL patients (probands) to identify genomic variations responsible for HL...
2017: PloS One
https://www.readbyqxmd.com/read/28545043/a-multiplex-taqman-qpcr-assay-for-sensitive-and-rapid-detection-of-phytoplasmas-infecting-rubus-species
#10
Holger Linck, Erika Krüger, Annette Reineke
Rubus stunt is an economically important disease in the production of raspberries, blackberries, and loganberries. A fast, sensitive, and reliable diagnosis of phytoplasmas, the causal agent of the disease, is of prime importance to stop its spread by vegetative propagation and by insect vectors. Therefore, multiplex qPCR assays using TaqMan probes with different kinds of fluorophores in one reaction were developed, allowing the detection of phytoplasmas in general as well as a more specific detection of phytoplasmas belonging to group 16SrV and host DNA (either plant or insect)...
2017: PloS One
https://www.readbyqxmd.com/read/28545020/microtubule-inhibitor-sp-6-27-inhibits-angiogenesis-and-induces-apoptosis-in-ovarian-cancer-cells
#11
Arpita Kulshrestha, Gajendra K Katara, Safaa A Ibrahim, Renukadevi Patil, Shivaputra A Patil, Kenneth D Beaman
In ovarian cancer (OVCA), treatment failure due to chemo-resistance is a serious challenge. It is therefore critical to identify new therapies that are effective against resistant tumors and have reduced side effects. We recently identified 4-H-chromenes as tubulin depolymerizing agents that bind to colchicine site of beta-tubulin. Here, we screened a chemical library of substituted 4-H-chromenes and identified SP-6-27 to exhibit most potent anti-proliferative activity towards a panel of human cisplatin sensitive and resistant OVCA cell lines with 50% inhibitory concentration (IC50; mean ± SD) ranging from 0...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544631/spermatozoa-from-males-with-reduced-fecundity-exhibit-differential-dna-methylation-patterns
#12
M Laqqan, S Tierling, Y Alkhaled, C Lo Porto, E F Solomayer, M Hammadeh
Infertility affects 10-15% of couples, and approximately 50% of cases are linked to male factor infertility. The purpose of this study was to evaluate the DNA methylation patterns in spermatozoa from males who are suffering from a reduction in fecundity. Thirty samples were subjected to 450K arrays as a screening study to evaluate the variation in sperm DNA methylation levels between cases and controls groups, and then four CpG sites (cg05799088, cg07227024, cg16338278, and cg08408433) underwent to deep bisulfite sequencing to validate the observed methylation differences in 111 samples (56 proven fertile males as 'controls' and 55 males suffering from a reduction in fecundity as 'cases')...
May 23, 2017: Andrology
https://www.readbyqxmd.com/read/28543018/multiple-ice-binding-proteins-of-probable-prokaryotic-origin-in-an-antarctic-lake-alga-chlamydomonas-sp-ice-mdv-chlorophyceae
#13
James A Raymond
Ice-associated algae produce ice-binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE-MDV (Chlamy-ICE). Genomic DNA and total RNA were sequenced and screened for known ice-associated genes...
May 19, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28542606/what-is-in-your-cup-of-tea-dna-verity-test-to-characterize-black-and-green-commercial-teas
#14
Olga De Castro, Maria Comparone, Antonietta Di Maio, Emanuele Del Guacchio, Bruno Menale, Jacopo Troisi, Francesco Aliberti, Marco Trifuoggi, Marco Guida
In this study, we used several molecular techniques to develop a fast and reliable protocol (DNA Verity Test, DVT) for the characterization and confirmation of the species or taxa present in herbal infusions. As a model plant for this protocol, Camellia sinensis, a traditional tea plant, was selected due to the following reasons: its historical popularity as a (healthy) beverage, its high selling value, the importation of barely recognizable raw product (i.e., crushed), and the scarcity of studies concerning adulterants or contamination...
2017: PloS One
https://www.readbyqxmd.com/read/28542326/the-murine-cytomegalovirus-m35-protein-antagonizes-type-i-ifn-induction-downstream-of-pattern-recognition-receptors-by-targeting-nf-%C3%AE%C2%BAb-mediated-transcription
#15
Baca Chan, Vladimir Gonçalves Magalhães, Niels A W Lemmermann, Vanda Juranić Lisnić, Markus Stempel, Kendra A Bussey, Elisa Reimer, Jürgen Podlech, Stefan Lienenklaus, Matthias J Reddehase, Stipan Jonjić, Melanie M Brinkmann
The type I interferon (IFN) response is imperative for the establishment of the early antiviral immune response. Here we report the identification of the first type I IFN antagonist encoded by murine cytomegalovirus (MCMV) that shuts down signaling following pattern recognition receptor (PRR) sensing. Screening of an MCMV open reading frame (ORF) library identified M35 as a novel and strong negative modulator of IFNβ promoter induction following activation of both RNA and DNA cytoplasmic PRR. Additionally, M35 inhibits the proinflammatory cytokine response downstream of Toll-like receptors (TLR)...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542229/thermodynamic-framework-to-assess-low-abundance-dna-mutation-detection-by-hybridization
#16
Hanny Willems, An Jacobs, Wahyu Wijaya Hadiwikarta, Tom Venken, Dirk Valkenborg, Nadine Van Roy, Jo Vandesompele, Jef Hooyberghs
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform...
2017: PloS One
https://www.readbyqxmd.com/read/28541665/identification-of-small-molecule-translesion-synthesis-inhibitors-that-target-the-rev1-ct-rir-protein-protein-interaction
#17
Vibhavari Sail, Alessandro A Rizzo, Nimrat Chatterjee, Radha Charan Dash, Zuleyha Ozen, Graham C Walker, Dmitry M Korzhnev, M Kyle Hadden
Translesion synthesis (TLS) is an important mechanism through which proliferating cells tolerate DNA damage during replication. The mutagenic Rev1/Polζ-dependent branch of TLS helps cancer cells survive first-line genotoxic chemotherapy and introduces mutations that can contribute to the acquired resistance so often observed with standard anti-cancer regimens. As such, inhibition of Rev1/Polζ-dependent TLS has recently emerged as a strategy to enhance the efficacy of first-line chemotherapy and reduce the acquisition of chemoresistance by decreasing tumor mutation rate...
May 25, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28541661/a-complementary-isothermal-amplification-method-to-the-us-epa-qpcr-approach-for-the-detection-of-enterococci-in-environmental-waters
#18
Claudia Kolm, Roland Martzy, Kurt Brunner, Robert L Mach, Rudolf Krska, Georg Heinze, Regina Sommer, Georg H Reischer, Andreas H Farnleitner
We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of the US Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci...
May 25, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28541628/high-risk-human-papillomavirus-genotype-distribution-and-attribution-to-cervical-cancer-and-precancerous-lesions-in-a-rural-chinese-population
#19
Xue Lian Zhao, Shang Ying Hu, Qian Zhang, Li Dong, Rui Mei Feng, Ross Han, Fang Hui Zhao
OBJECTIVE: To explore the genotype distribution of high-risk human papillomavirus (HR-HPV) and its attribution to different grades of cervical lesions in rural China, which will contribute to type-specific HPV screening tests and the development of new polyvalent HPV vaccines among the Chinese population. METHODS: One thousand two hundred ninety-two subjects were followed based on the Shanxi Province Cervical Cancer Screening Study I (SPOCCS-I), and screened by HPV DNA testing (hybrid capture® 2 [HC2]), liquid-based cytology (LBC), and if necessary, directed or random colposcopy-guided quadrant biopsies...
July 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/28541280/a-quantitative-csmart-assay-for-noninvasive-prenatal-screening-of-autosomal-recessive-nonsyndromic-hearing-loss-caused-by-gjb2-and-slc26a4-mutations
#20
Mingyu Han, Zhifeng Li, Wenlu Wang, Shasha Huang, Yanping Lu, Zhiying Gao, Longxia Wang, Dongyang Kang, Linwei Li, Yiqian Liu, Mengnan Xu, David S Cram, Pu Dai
PurposeThe aim of this study was to assess the performance of a noninvasive prenatal screening (NIPS) assay for accurate fetal genotyping of pregnancies at genetic risk for autosomal recessive nonsyndromic hearing loss (ARNSHL).MethodsA total of 80 pregnant couples carrying known mutations in either the GJB2 or SLC26A4 genes associated with a risk for ARNSHL were recruited to the study. Fetal amniocyte samples were genotyped by invasive prenatal screening (IPS), whereas the cell-free fetal DNA present in maternal plasma samples was genotyped using a novel NIPS method based on circulating single-molecule amplification and resequencing technology (cSMART)...
May 25, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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"