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https://www.readbyqxmd.com/read/28098911/diagnosis-for-choroideremia-in-a-large-chinese-pedigree-by-next%C3%A2-generation-sequencing-ngs-and-non%C3%A2-invasive-prenatal-testing-nipt
#1
Li Zhu, Jingliang Cheng, Boxu Zhou, Chunli Wei, Weichan Yang, Dong Jiang, Iqra Ijaz, Xiaojun Tan, Rui Chen, Junjiang Fu
To develop an effective strategy to isolate and use cell‑free fetal DNA (cffDNA) for the combined use of next‑generation sequencing (NGS) for diagnosing choroideremia and non‑invasive prenatal testing (NIPT) for Y chromosome determination, a large Chinese family with an X‑linked recessive disease, choroideremia, was recruited. Cell‑free DNA was extracted from maternal plasma, and SRY polymerase chain reaction amplification was performed using NIPT. Sanger sequencing was subsequently used for fetal amniotic fluid DNA verification...
January 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098143/efficient-dna-free-genome-editing-of-bread-wheat-using-crispr-cas9-ribonucleoprotein-complexes
#2
Zhen Liang, Kunling Chen, Tingdong Li, Yi Zhang, Yanpeng Wang, Qian Zhao, Jinxing Liu, Huawei Zhang, Cuimin Liu, Yidong Ran, Caixia Gao
Substantial efforts are being made to optimize the CRISPR/Cas9 system for precision crop breeding. The avoidance of transgene integration and reduction of off-target mutations are the most important targets for optimization. Here, we describe an efficient genome editing method for bread wheat using CRISPR/Cas9 ribonucleoproteins (RNPs). Starting from RNP preparation, the whole protocol takes only seven to nine weeks, with four to five independent mutants produced from 100 immature wheat embryos. Deep sequencing reveals that the chance of off-target mutations in wheat cells is much lower in RNP mediated genome editing than in editing with CRISPR/Cas9 DNA...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28096542/liquid-biopsy-in-2016-circulating-tumour-cells-and-cell-free-dna-in-gastrointestinal-cancer
#3
Klaus Pantel, Catherine Alix-Panabières
No abstract text is available yet for this article.
January 18, 2017: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28096488/novel-superspreader-bacteriophages-promote-horizontal-gene-transfer-by-transformation
#4
Eric C Keen, Valery V Bliskovsky, Francisco Malagon, James D Baker, Jeffrey S Prince, James S Klaus, Sankar L Adhya
: Bacteriophages infect an estimated 10(23) to 10(25) bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096456/antibody-conjugated-dna-based-nanocarriers-intercalated-with-doxorubicin-eliminate-myofibroblasts-in-explants-of-human-lens-tissue
#5
Jacquelyn Gerhart, Marvin Greenbaum, Lou Casta, Anthony Clemente, Keith Mathers, Robert Getts, Mindy George-Weinstein
Posterior capsule opacification (PCO) occurs in some adults and most children following cataract surgery. The fibrotic form of PCO arises, in part, from migratory, contractile myofibroblasts that deform the lens capsule and impair vision. In short-term cultures of human anterior lens tissue, myofibroblasts emerge from Myo/Nog cells that are identified with the G8 monoclonal antibody and by their expression of the MyoD transcription factor and bone morphogenetic protein inhibitor noggin. In this study, we tested the hypothesis that targeted depletion of Myo/Nog cells with the G8 mAb conjugated to three-dimensional DNA nanocarriers intercalated with Doxorubicin (G8:3DNA:Dox) would prevent the accumulation of myofibroblasts in long-term, serum and growth factor free cultures of human lens tissue obtained by capsulorhexis...
January 17, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28096270/mutation-enrichment-next-generation-sequencing-for-quantitative-detection-of-kras-mutations-in-urine-cell-free-dna-from-patients-with-advanced-cancers
#6
Takeo Fuji, Afsaneh Barzi, Andrea Sartore-Bianchi, Andrea Cassingena, Giulia Siravegna, Daniel Karp, Sarina Piha-Paul, Vivek Subbiah, Apostolia M Tsimberidou, Helen Huang, Sillvio Veronese, Federica Di Nicolantonio, Sandeep C Pingle, Cecile Rose T Vibat, Saege Hancock, David Berz, Vladislava O Melnikova, Mark G Erlander, Rajyalakshmi Luthra, Scott Kopetz, Funda Meric-Bernstam, Salvatore Siena, Heinz-Josef Lenz, Alberto Bardelli, Filip Janku
PURPOSE: Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers non-invasive biologic material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of KRAS. EXPERIMENTAL DESIGN: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA was developed and results were compared to clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer...
January 17, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28096087/diffuse-large-b-cell-lymphoma-genotyping-on-the-liquid-biopsy
#7
Davide Rossi, Fary Diop, Elisa Spaccarotella, Sara Monti, Manuela Zanni, Silvia Rasi, Clara Deambrogi, Valeria Spina, Alessio Bruscaggin, Chiara Favini, Roberto Serra, Antonio Ramponi, Renzo Boldorini, Robin Foa', Gianluca Gaidano
Accessible and real-time genotyping for diagnostic, prognostic or treatment purposes is increasingly impelling in diffuse large B-cell lymphoma (DLBCL). Cell-free DNA (cfDNA) is shed into the blood by tumor cells undergoing apoptosis and can be used as source of tumor DNA for the identification of DLBCL mutations, clonal evolution, and genetic mechanisms of resistance. Here we aimed at tracking the basal DLBCL genetic profile and its modification upon treatment using plasma cfDNA. Ultra-deep targeted next generation sequencing of pre-treatment plasma cfDNA from DLBCL patients correctly discovered DLBCL-associated mutations that were represented in >20% of the alleles of the tumor biopsy with a >90% sensitivity and a ~100% specificity...
January 17, 2017: Blood
https://www.readbyqxmd.com/read/28095613/xenopus-egg-extract-to-study-regulation-of-genome-wide-and-locus-specific-dna-replication
#8
REVIEW
Erica Raspelli, Lucia Falbo, Vincenzo Costanzo
Faithful DNA replication, coupled with accurate repair of DNA damage, is essential to maintain genome stability and relies on different DNA metabolism genes. Many of these genes are involved in the assembly of replication origins, in the coordination of DNA repair to protect replication forks progression in the presence of DNA damage and in the replication of repetitive chromatin regions. Some DNA metabolism genes are essential in higher eukaryotes, suggesting the existence of specialized mechanisms of repair and replication in organisms with complex genomes...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28093244/novel-mutations-on-egfr-leu792-potentially-correlate-to-acquired-resistance-to-osimertinib-in-advanced-nsclc
#9
Kai Chen, Fei Zhou, Wenxiang Shen, Tao Jiang, Xue Wu, Xiaoling Tong, Yang W Shao, Songbing Qin, Caicun Zhou
Osimertinib is an irreversible third generation EGFR tyrosine kinase inhibitor (TKI) and has shown outstanding performances in treating EGFR T790M-positive advanced non-small cell lung cancer (NSCLC) patients, but acquired resistance is inevitable. EGFR C797S is the most notable resistance mechanism to this drug, but other EGFR mutations may also exist. In three lung adenocarcinoma patients resistant to osimertinib, we identified recurrent novel mutations at EGFR Leu792 codon by targeted next generation sequencing (NGS) of cell free DNA (cfDNA) from plasma or pleural effusion...
January 13, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28089353/cerebrospinal-fluid-mitochondrial-dna-in-the-alzheimer-s-disease-continuum
#10
Laura Cervera-Carles, Daniel Alcolea, Ainara Estanga, Mirian Ecay-Torres, Andrea Izagirre, Montserrat Clerigué, Maite García-Sebastián, Jorge Villanúa, Clàudia Escalas, Rafael Blesa, Pablo Martínez-Lage, Alberto Lleó, Juan Fortea, Jordi Clarimón
Low levels of cell-free mitochondrial DNA (mtDNA) in the cerebrospinal fluid (CSF) of Alzheimer's disease (AD) patients have been identified and proposed as a novel biomarker for the disease. The lack of validation studies of previous results prompted us to replicate this finding in a comprehensive series of patients and controls. We applied droplet digital polymerase chain reaction in CSF specimens from 124 patients representing the AD spectrum and 140 neurologically healthy controls. The following preanalytical and analytical parameters were evaluated: the effect of freeze-thaw cycles on mtDNA, the linearity of mtDNA load across serial dilutions, and the mtDNA levels in the diagnostic groups...
December 22, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/28081343/the-combined-effects-of-proteasome-inhibitor-bortezomib-with-topoisomerase-i-and-ii-inhibitors-on-topoisomerase-enzymes
#11
Emine Öksüzoğlu, Çiydem Tırınoğlu, Barış Kerimoğlu
BACKGROUND/AIM: DNA topoisomerases are ubiquitous enzymes that regulate conformational changes in DNA topology during essential cellular processes, and, for this reason, have been characterized as the cellular targets of a number of anticancer drugs. Bortezomib is a powerful proteasome inhibitor used in the treatment of hematological malignancies. In this study, we investigated the inhibitory effects of bortezomib on human topoisomerase I and II enzymes both alone and in combination modes with camptothecin and etoposide...
December 20, 2016: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/28081183/circulating-cell-free-dna-in-dogs-with-mammary-tumors-short-and-long-fragments-and-integrity-index
#12
Giorgia Beffagna, Alessandro Sammarco, Chiara Bedin, Chiara Romualdi, Marta Mainenti, Antonio Mollo, Laura Cavicchioli, Silvia Ferro, Davide Trez, Raffaella De Maria, Donato Nitti, Andrea Saccani, Michelangelo Campanella, Marco Agostini, Valentina Zappulli
Circulating cell-free DNA (cfDNA) has been considered an interesting diagnostic/prognostic plasma biomarker in tumor-bearing subjects. In cancer patients, cfDNA can hypothetically derive from tumor necrosis/apoptosis, lysed circulating cells, and some yet unrevealed mechanisms of active release. This study aimed to preliminarily analyze cfDNA in dogs with canine mammary tumors (CMTs). Forty-four neoplastic, 17 non-neoplastic disease-bearing, and 15 healthy dogs were recruited. Necrosis and apoptosis were also assessed as potential source of cfDNA on 78 CMTs diagnosed from the 44 dogs...
2017: PloS One
https://www.readbyqxmd.com/read/28079901/the-clinical-utility-of-dna-based-screening-for-fetal-aneuploidy-by-primary-obstetrical-care-providers-in-the-general-pregnancy-population
#13
Glenn E Palomaki, Edward M Kloza, Barbara M O'Brien, Elizabeth E Eklund, Geralyn M Lambert-Messerlian
OBJECTIVE: To assess the clinical utility of cell-free DNA (cfDNA)-based screening for aneuploidies offered through primary obstetrical care providers to a general pregnancy population. METHODS: Patient educational materials were developed and validated and providers were trained. Serum was collected for reflexive testing of cfDNA failures. Providers and patients were surveyed concerning knowledge, decision making, and satisfaction. Pregnancy outcome was determined by active or passive ascertainment...
January 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28078820/improvement-of-the-in-vivo-cellular-repopulation-of-decellularized-cardiovascular-tissues-by-a-detergent-free-non-proteolytic-actin-disassembling-regimen
#14
Alexander Assmann, Marc Struß, Franziska Schiffer, Friederike Heidelberg, Hiroshi Munakata, Elena V Timchenko, Pavel E Timchenko, Tim Kaufmann, Khon Huynh, Yukiharu Sugimura, Quentin Leidl, Antonio Pinto, Volker R Stoldt, Artur Lichtenberg, Payam Akhyari
Low immunogenicity and high repopulation capacity are crucial determinants for the functional and structural performance of acellular cardiovascular implants. The present study evaluates a detergent-free, non-proteolytic, actin-disassembling regimen (BIO) for decellularization of heart valve and vessel grafts, particularly focusing on their bio-functionality. Rat aortic conduits (rAoC; n = 89) and porcine aortic valve samples (n = 106) are decellularized using detergents (group DET) or the BIO regimen...
January 11, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28078248/origanum-vulgare-leaf-extract-protects-mice-bone-marrow-cells-against-ionizing-radiation
#15
Reza Ghasemnezhad Targhi, Vahid Changizi, Farhang Haddad, Mansour Homayoun, Shokouhozaman Soleymanifard
OBJECTIVE: Ionizing radiation produces free radicals which induce DNA damage and cell death. Origanum vulgare leaf extract (OVLE) is a natural compound and its capability of scavenging free radicals and its antioxidant activity have been demonstrated by many researchers. In this study, using micronucleus assay, radioprotective effect of OVLE against clastogenic and cytotoxic effect of gamma irradiation has been investigated in mice bone marrow cells. MATERIALS AND METHODS: OVLE was injected intraperitoneally to the BALB/c mice 1hr prior to gamma irradiation (3Gy) at the doses of 100 and 200 mg/kg...
November 2016: Avicenna Journal of Phytomedicine
https://www.readbyqxmd.com/read/28077981/dna-polymerase-kappa-protects-human-cells-against-mmc-induced-genotoxicity-through-error-free-translesion-dna-synthesis
#16
Yuki Kanemaru, Tetsuya Suzuki, Akira Sassa, Kyomu Matsumoto, Noritaka Adachi, Masamitsu Honma, Satoshi Numazawa, Takehiko Nohmi
BACKGROUND: Interactions between genes and environment are critical factors for causing cancer in humans. The genotoxicity of environmental chemicals can be enhanced via the modulation of susceptible genes in host human cells. DNA polymerase kappa (Pol κ) is a specialized DNA polymerase that plays an important role in DNA damage tolerance through translesion DNA synthesis. To better understand the protective roles of Pol κ, we previously engineered two human cell lines either deficient in expression of Pol κ (KO) or expressing catalytically dead Pol κ (CD) in Nalm-6-MSH+ cells and examined cytotoxic sensitivity against various genotoxins...
2017: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
https://www.readbyqxmd.com/read/28077404/high-throughput-sequencing-of-the-t-cell-receptor-repertoire-pitfalls-and-opportunities
#17
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28073590/objective-detection-of-apoptosis-in-rat-renal-tissue-sections-using-light-microscopy-and-free-image-analysis-software-with-subsequent-machine-learning-detection-of-apoptosis-in-renal-tissue
#18
Nayana Damiani Macedo, Aline Rodrigues Buzin, Isabela Bastos Binotti Abreu de Araujo, Breno Valentim Nogueira, Tadeu Uggere de Andrade, Denise Coutinho Endringer, Dominik Lenz
OBJECTIVE: The current study proposes an automated machine learning approach for the quantification of cells in cell death pathways according to DNA fragmentation. METHODS: A total of 17 images of kidney histological slide samples from male Wistar rats were used. The slides were photographed using an Axio Zeiss Vert.A1 microscope with a 40x objective lens coupled with an Axio Cam MRC Zeiss camera and Zen 2012 software. The images were analyzed using CellProfiler (version 2...
December 28, 2016: Tissue & Cell
https://www.readbyqxmd.com/read/28072763/epithelial-to-mesenchymal-transition-and-hpv-infection-in-squamous-cell-oropharyngeal-carcinomas-the-papillophar-study
#19
Marine Lefevre, Alexandra Rousseau, Thomas Rayon, Véronique Dalstein, Christine Clavel, Agnès Beby-Defaux, Jean-Luc Pretet, Patrick Soussan, Myriam Polette, Jean Lacau Saint Guily, Philippe Birembaut
BACKGROUND: Human Papillomavirus (HPV) infection is recognised as aetiological factor of carcinogenesis in oropharyngeal squamous cell carcinomas (OPC). HPV-related OPC respond better to treatments and have a significantly favourable outcome. Epithelial to mesenchymal transition (EMT) implicated in tumour invasion, is a hallmark of a poor prognosis in carcinomas. METHODS: We have studied the relationship of EMT markers (E-cadherin, β-catenin and vimentin) with HPV infection (DNA and E6/E7 mRNA detection), p16(INK4a) expression and survival outcomes in a cohort of 296 patients with OPC...
January 10, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28069892/post-translational-regulation-of-the-dicing-activities-of-arabidopsis-dicer-like-3-and-4-by-inorganic-phosphate-and-the-redox-state
#20
Atsushi Seta, Midori Tabara, Yuki Nishibori, Akihiro Hiraguri, Naoko Ohkama-Ohtsu, Tadashi Yokoyama, Satoshi Hara, Keisuke Yoshida, Toru Hisabori, Akihito Fukudome, Hisashi Koiwa, Hiromitsu Moriyama, Nobuhiro Takahashi, Toshiyuki Fukuhara
In Arabidopsis thaliana, small interfering RNAs (siRNAs) generated by two Dicer isoforms, DCL3 and DCL4, function in distinct epigenetic processes, i.e. RNA-directed DNA methylation and post-transcriptional gene silencing, respectively. Plants often respond to their environment by producing a distinct set of small RNAs; however, the mechanism for controlling the production of different siRNAs from the same dsRNA substrate remains unclear. We established a simple biochemical method to visualize the dsRNA-cleaving activities of DCL3 and DCL4 in cell-free extracts prepared from Arabidopsis seedlings...
January 9, 2017: Plant & Cell Physiology
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