keyword
MENU ▼
Read by QxMD icon Read
search

Dna fragmentation

keyword
https://www.readbyqxmd.com/read/29156792/liquid-biopsy-in-colon-cancer-comparison-of-different-circulating-dna-extraction-systems-following-absolute-quantification-of-kras-mutations-using-intplex-allele-specific-pcr
#1
Vera Kloten, Nadine Rüchel, Nadina Ortiz Brüchle, Janina Gasthaus, Nils Freudenmacher, Florian Steib, Jolein Mijnes, Julian Eschenbruch, Marcel Binnebösel, Ruth Knüchel, Edgar Dahl
Non-invasive molecular analysis of circulating tumor DNA (ctDNA) is a promising application in personalized cancer management, although there is still much to learn about the biological characteristics of ctDNA. The present study compared absolute amounts of KRAS mutated ctDNA and total circulating cell-free DNA (cfDNA) in colorectal cancer (CRC) patients (n=50) from various stages and healthy controls (n=8) by Intplex allele-specific and digital droplet PCR. In addition, the impact of two prominent extraction techniques (silica-based membrane vs...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156741/screening-epitopes-on-systemic-lupus-erythematosus-autoantigens-with-a-peptide-array
#2
Lin Wang, Chenjun Hao, Yongqiu Deng, Yanbo Liu, Shiliang Hu, Yangang Peng, Manna He, Jinhu Fu, Ming Liu, Jia Chen, Xiaoming Chen
Systemic lupus erythematosus (SLE) is a common autoimmune disease. Many autoantibodies are closely associated with SLE. However, the specific epitopes recognized and bound by these autoantibodies are still unclear. This study screened the binding epitopes of SLE-related autoantibodies using a high-throughput screening method. Epitope prediction on 12 SLE-related autoantigens was performed using the Immune Epitope Database and Analysis Resource (IEDB) software. The predicted epitopes were synthesized into peptides and developed into a peptide array...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156625/gene-based-pathogen-detection-can-we-use-qpcr-to-predict-the-outcome-of-diagnostic-metagenomics
#3
Sandra Christine Andersen, Mette Sofie Rousing Fachmann, Kristoffer Kiil, Eva Møller Nielsen, Jeffrey Hoorfar
In microbial food safety, molecular methods such as quantitative PCR (qPCR) and next-generation sequencing (NGS) of bacterial isolates can potentially be replaced by diagnostic shotgun metagenomics. However, the methods for pre-analytical sample preparation are often optimized for qPCR, and do not necessarily perform equally well for qPCR and sequencing. The present study investigates, through screening of methods, whether qPCR can be used as an indicator for the optimization of sample preparation for NGS-based shotgun metagenomics with a diagnostic focus...
November 20, 2017: Genes
https://www.readbyqxmd.com/read/29156308/modulatory-effects-of-green-tea-extract-against-the-hepatotoxic-effects-of-4-nonylphenol-in-catfish-clarias-gariepinus
#4
A H Sayed, Hamdy A M Soliman
The antioxidant role of the green tea (Camellia sinensis) extract (GTE) was examined to remedy the toxic effects of (0.2mgl(-1)) 4-nonylphenol(4-NP). Biochemical parameters, antioxidant enzymes, liver lipid peroxidation (LPO), DNA fragmentation, and apoptosis as well as histopathology of liver of African catfish Clarias gariepinus were considered. Catfishes were divided into four groups: first group (control), second group (0.2mgl(-1) of 4-NP), third group (0.2mgl(-1)of 4-NP +100mg GTE l(-1)water), and fourth group (0...
November 17, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29156123/a-nanopore-based-label-free-and-real-time-monitoring-assay-for-dna-methyltransferase-activity-and-inhibition
#5
Sana Rauf, Ling Zhang, Asghar Ali, Jalal Ahmad, Yang Liu, Jinghong Li
DNA methylation catalyzed by DNA methyltransferase plays an important role in many biological processes. However, conventional assays proposed for DNA methyltransferase activity are laborious and discontinuous. We describe a novel method for real-time monitoring of the activity and kinetics of Escherichia coli DNA adenine methyltransferase (Dam), using nanopore technique coupled with enzyme-linkage reactions. A double-stranded DNA probe AB having a recognition sequence 5'-GATC-3' for both Dam and MboI restriction endonuclease was prepared...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155942/detergent-based-decellularization-strategy-preserves-macro-and-microstructure-of-heart-valves
#6
Jessica Haupt, Georg Lutter, Stanislav N Gorb, Dan T Simionescu, Derk Frank, Jette Seiler, Alina Paur, Irma Haben
OBJECTIVES: Biological tissue has great potential to function as bioprostheses in patients for heart valve replacement. As these matrices are mainly xenogenic, the immunogenicity needs to be reduced by decellularization steps. Reseeding of bioscaffolds has tremendous potential to prevent calcification upon implantation, so intact microstructure of the material is mandatory. An optimal decellularization protocol of heart valves resulting in adequate preservation of the extracellular architecture has still not been developed...
October 9, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/29155723/one-step-protocol-for-evaluation-of-the-mode-of-radiation-induced-clonogenic-cell-death-by-fluorescence-microscopy
#7
Daijiro Kobayashi, Atsushi Shibata, Takahiro Oike, Takashi Nakano
Research on ionizing radiation (IR)-induced clonogenic cell death is important for understanding the effect of IR on malignant tumors and normal tissues. Here, we describe a quick and cost-effective one-step assay for simultaneously assessing the major modes of clonogenic cell death induced by IR, i.e., apoptosis, mitotic catastrophe, and cellular senescence. In this method, cells grown on a cover slip are irradiated with X-rays and stained with 4',6-diamidino-2-phenylindole dihydrochloride (DAPI). Using fluorescence microscopy, apoptosis, mitotic catastrophe, and cellular senescence are identified based on the characteristic morphologies of the DAPI-stained nuclei...
October 23, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155576/chronic-arsenic-exposure-increases-a%C3%AE-1-42-production-and-rage-expression-in-rat-brain
#8
Sandra Aurora Niño, Guadalupe Martel-Gallegos, Adriana Castro-Zavala, Benita Ortega-Berlanga, Juan Manuel Delgado, Hector Hernandez-Mendoza, E Romero-Guzman, Judith Rios-Lugo, Sergio Rosales-Mendoza, María Esther Jiménez-Capdeville, Sergio Zarazua
Chronic arsenic exposure during development is associated with alterations of chemical transmission and demyelination, which result in cognitive deficits and peripheral neuropathies. At cellular level, arsenic toxicity involves increased generation of reactive species that induce severe cellular alterations such as DNA fragmentation, apoptosis and lipid peroxidation. It has been proposed that arsenic-associated neurodegeneration could evolve to Alzheimer disease in later life.1,2 In this study, the effects of chronic exposure to inorganic arsenic (3 ppm by drinking water) in Wistar rats on the production and elimination of Amyloid-β (Aβ) were evaluated...
November 20, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29155212/effect-of-isoquercitrin-on-membrane-dynamics-and-apoptosis-like-death-in-escherichia-coli
#9
JiEun Yun, Eun-Rhan Woo, Dong Gun Lee
Minimum inhibitory concentration (MIC) is defined as the lowest concentration of a compound that completely inhibits microbial growth. Antibacterial mechanisms of compounds have been investigated at their sub-MICs as well as at their MIC. In this study, the effects of sub-MIC and MIC of isoquercitrin on Escherichia coli were investigated. The antibacterial effect of isoquercitrin was tested using the microdilution method. Sub-MICs of isoquercitrin induced the production of reactive oxygen species and depletion of glutathione...
November 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29154952/in-vitro-mechanisms-of-beauvericin-toxicity-a-review
#10
REVIEW
Beatriz Mallebrera, Alessandra Prosperini, Guillermina Font, Maria-Jose Ruiz
Beauvericin (BEA) is a mycotoxin produced by many species of fungus Fusarium and by Beauveria bassiana; BEA is a natural contaminant of cereals and cereals based products and possesses a wide variety of biological properties. The mechanism of action seems to be related to its ionophoric activity, that increases ion permeability in biological membranes. As a consequence, BEA causes cytotoxicity in several cell lines and is capable to produce oxidative stress at molecular level. Moreover, BEA is genotoxic (produces DNA fragmentation, chromosomal aberrations and micronucleus) and causes apoptosis with the involvement of mitochondrial pathway...
November 15, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/29154928/sequence-analysis-of-the-thrombospondin-related-adhesive-protein-gene-and-heat-shock-protein-70-of-babesia-gibsoni-isolated-from-dogs-in-nanjing-china
#11
Huan-Ran Lin, Xiao-Ting Mei, Yu-Fang Hong, Yan-Bing Zhao, Xiao-Nan Guo, De-Ji Yang, Da-Wei Yao
In this study, the thrombospondin-related adhesive protein (TRAP) gene and the heat shock protein 70 (Hsp70) gene of Babesia gibsoni isolated from the naturally infected dog in the Nanjing area were cloned and sequenced. Twenty blood samples were collected from the suspected cases of babesiosis at the animal hospital of Nanjing Agriculture University. Genomic DNA was extracted from the blood samples, and the 18S rDNAs were amplified by PCR to confirm Babesia infection. As a result, 10 cases of Babesia 18S rDNA gene amplification were positive in the 20 blood samples, confirming that the 10 cases were infected with canine Babesia...
November 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29154161/effect-of-bovine-sperm-chromatin-integrity-evaluated-using-three-different-methods-on-in%C3%A2-vitro-fertility
#12
L S Castro, A F P Siqueira, T R S Hamilton, C M Mendes, J A Visintin, M E O A Assumpção
In vitro fertility potential of individual bulls is still relatively uncharacterized. Classical sperm analysis does not include the evaluation of all sperm characteristics and thus, some cell compartments could be neglected. In humans, sperm DNA integrity has already proven to have major influence in embryo development and assisted reproduction techniques successfully. In bovine, some studies already correlated chromatin integrity with field fertility. However, none of those have attempted to relate DNA assessment approaches such as chromatin deficiency (CMA3), chromatin stability (SCSA; AO+) and DNA fragmentation (COMET assay) to predict in vitro bull fertility...
November 10, 2017: Theriogenology
https://www.readbyqxmd.com/read/29153610/tdp-43-proteolysis-is-associated-with-astrocyte-reactivity-after-traumatic-brain-injury-in-rodents
#13
Chih-Yuan Huang, Yi-Che Lee, Ping-Chia Li, Po-Chou Liliang, Kang Lu, Kuo-Wei Wang, Li-Ching Chang, Li-Yen Shiu, Ming-Feng Chen, Yuan-Ting Sun, Hao-Kuang Wang
The aggregation and deposition of transactivation response DNA-binding protein 43 (TDP-43) in neurons and astrocytes is characteristic in a number of neurodegenerative diseases including Alzheimer's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis. Nevertheless, the exact role of TDP-43 in astrocytes is unknown. Recently, TDP-43 was identified in neurons but not astrocytes after traumatic brain injury (TBI) in humans. In the present study, we evaluated TDP-43 expression and proteolysis in astrocytes in a rat model of TBI...
December 15, 2017: Journal of Neuroimmunology
https://www.readbyqxmd.com/read/29152409/long-adapter-single-strand-oligonucleotide-probes-for-the-massively-multiplexed-cloning-of-kilobase-genome-regions
#14
Lorenzo Tosi, Viswanadham Sridhara, Yunlong Yang, Dongli Guan, Polina Shpilker, Nicola Segata, H Benjamin Larman, Biju Parekkadan
As the catalogue of sequenced genomes and metagenomes continues to grow, massively parallel approaches for the comprehensive and functional analysis of gene products and regulatory elements are becoming increasingly valuable. Current strategies to synthesize or clone complex libraries of DNA sequences are limited by the length of the DNA targets, throughput and cost. Here, we show that long-adapter single-strand oligonucleotide (LASSO) probes can capture and clone thousands of kilobase DNA fragments in a single reaction...
2017: Nature biomedical engineering
https://www.readbyqxmd.com/read/29152187/genetic-diversity-population-structure-and-traditional-culture-of-camellia-reticulata
#15
Tong Xin, Weijuan Huang, Jan De Riek, Shuang Zhang, Selena Ahmed, Johan Van Huylenbroeck, Chunlin Long
Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29151871/genetic-and-epigenetic-variation-in-spartina-alterniflora-following-the-deepwater-horizon-oil-spill
#16
Marta Robertson, Aaron Schrey, Ashley Shayter, Christina J Moss, Christina Richards
Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S...
September 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29151157/potent-apoptosis-inducing-activity-of-erypoegin-k-an-isoflavone-isolated-from-erythrina-poeppigiana-against-human-leukemia-hl-60-cells
#17
Kiyomi Hikita, Natsuki Hattori, Aya Takeda, Yuko Yamakage, Rina Shibata, Saori Yamada, Kuniki Kato, Tomiyasu Murata, Hitoshi Tanaka, Norio Kaneda
Erypoegin K is an isoflavone isolated from the stem bark of Erythrina poeppigiana. It contains a furan group at the A-ring of the core isoflavone structure and can inhibit the activity of glyoxalase I, an enzyme that catalyzes the detoxification of methylglyoxal (MG), a by-product of glycolysis. In the present study, we found that erypoegin K has a potent cytotoxic effect on human leukemia HL-60 cells. Its cytotoxic effect was much stronger than that of a known glyoxalase I inhibitor S-p-bromobenzylglutathione cyclopentyl diester...
November 18, 2017: Journal of Natural Medicines
https://www.readbyqxmd.com/read/29150736/effect-of-erythrocyte-sperm-separation-medium-on-nuclear-acrosomal-and-membrane-maturity-parameters-in-human-sperm
#18
Bikem Soygur, Soner Celik, Ciler Celik-Ozenci, Leyla Sati
PURPOSE: The purpose of this study is to investigate whether erythrocyte-sperm separation medium (ESSM) has effects on human sperm motility, morphology, viability, membrane maturity, acrosome integrity, and nuclear attributes before and after cryopreservation. METHODS: Semen samples from normozoospermic (n = 36) and oligozoospermic (n = 9) patients were analyzed. Samples from the same patient were divided into three aliquots: group 1 and group 2 were resuspended in sperm washing media and ESSM, respectively...
November 18, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29150665/a-streamlined-cloning-workflow-minimising-the-time-to-strain-pipeline-for-pichia-pastoris
#19
Kate E Royle, Karen Polizzi
Although recent advances in E. coli self-assembly have greatly simplified cloning, these have not yet been harnessed for the high-throughput generation of expression strains in the early research and discovery phases of biopharmaceutical production. Here, we have refined the technique and incorporated it into a streamlined workflow for the generation of Pichia pastoris expression strains, reducing the timeline by a third and removing the reliance on DNA editing enzymes, which often require troubleshooting and increase costs...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29149895/novel-insights-into-chromosomal-conformations-in-cancer
#20
REVIEW
Ruobing Jia, Peiwei Chai, He Zhang, Xianqun Fan
Exploring gene function is critical for understanding the complexity of life. DNA sequences and the three-dimensional organization of chromatin (chromosomal interactions) are considered enigmatic factors underlying gene function, and interactions between two distant fragments can regulate transactivation activity via mediator proteins. Thus, a series of chromosome conformation capture techniques have been developed, including chromosome conformation capture (3C), circular chromosome conformation capture (4C), chromosome conformation capture carbon copy (5C), and high-resolution chromosome conformation capture (Hi-C)...
November 17, 2017: Molecular Cancer
keyword
keyword
98571
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"