1,575,585 results match your criteria DNA Repair [Journal]


Evaluation of Genotoxicity of Nanoparticles in Mouse Models.

Methods Mol Biol 2019 ;1894:301-312

Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, USA.

Owing to new and unique properties, engineered nanoparticles (NPs) likely pose different risks than their constituent chemicals and these risks need to be understood. In particular, it is important to assess genotoxicity, since genotoxicity is a precursor to carcinogenicity. Here we describe a battery of tests for the assessment of genotoxicity of NPs in vivo in mice. Read More

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January 2019
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DNA Methylation Analysis.

Methods Mol Biol 2019 ;1894:181-227

Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, P. R. China.

DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Read More

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January 2019

Determination of Phosphorylated Histone H2AX in Nanoparticle-Induced Genotoxic Studies.

Methods Mol Biol 2019 ;1894:145-159

Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, USA.

DNA double-strand breaks (DSBs), one of the most severe lesions of DNA damage triggered by various genotoxic insults, can lead to chromosome change, genomic instability, and even tumorigenesis if not repaired efficiently. In response to DNA damage, histone H2AX molecules are rapidly phosphorylated at serine 139 near the site of DNA DSBs and form γ-H2AX foci. As an early important cellular event linked to DNA damage and repair, γ-H2AX is a highly sensitive biomarker for "monitoring" DNA damage and consequently is a useful tool in genetic toxicology screen. Read More

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January 2019
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In Vitro Approaches for Assessing the Genotoxicity of Nanomaterials.

Methods Mol Biol 2019 ;1894:83-122

Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany.

Genotoxicity is associated with serious health effects and includes different types of DNA lesions, gene mutations, structural chromosome aberrations involving breakage and/or rearrangements of chromosomes (referred to as clastogenicity) and numerical chromosome aberrations (referred to as aneuploidy). Assessing the potential genotoxic properties of chemicals, including nanomaterials (NMs), is a key element in regulatory safety assessment. State-of-the-art genotoxicity testing includes a battery of assays covering gene mutations, structural and numerical chromosome aberrations. Read More

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January 2019

Genetic diversity between two Egyptian clover varieties and QTL analysis for some agro-morphological traits.

Mol Biol Rep 2018 Dec 13. Epub 2018 Dec 13.

Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.

Genetic diversity between two ecotypes of Egyptian clover varieties, namely Fahl (mono-cut) and Helaly (multi-cut) have been assessed based on forage yield and yield components as well as molecular marker systems. The two parental genotypes were crossed to produce seeds of F and F progenies. Analyses of variance indicated significant differences between four populations (P (Fahl), P (Helaly), F and F) for fresh forage yield, number of florets/inflorescence, number of seeds/inflorescence and 1000 seed weight. Read More

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December 2018

The bacteriology in adult patients with pneumonia and parapneumonic effusions: increased yield with DNA sequencing method.

Eur J Clin Microbiol Infect Dis 2018 Dec 13. Epub 2018 Dec 13.

Department of Medicine, Solna, Infectious Diseases Unit, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden.

The aim of this study was to use a 16S rDNA sequencing method in combination with conventional culture in patients with parapneumonic effusions (PPE) to evaluate the methods, study the microbiological spectrum, and examine the presence of bacteria within the different stages of PPE. Adults with community-acquired pneumonia (CAP) and PPE (n = 197) admitted to the Departments of Infectious Diseases at four hospitals in Stockholm County during 2011-2014 were prospectively studied. All patients underwent thoracentesis. Read More

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December 2018

Early Hereditary Diffuse Gastric Cancer (eHDGC) is Characterized by Subtle Genomic Instability and Active DNA Damage Response.

Pathol Oncol Res 2018 Dec 13. Epub 2018 Dec 13.

Division of Biomedical Science and Biochemistry, Research School of Biology, ANU College of Medicine, Biology and Environment, Australian National University, P.O. Box: 2601, Canberra, Australia.

Diffuse gastric cancer (DGC) is one of the two primary types of stomach cancer. Carriers of germline mutations in the gene encoding E-cadherin are predisposed to DGC. The primary aim of the present study was to determine if genomic instability is an early event in DGC and how it may lead to disease progression. Read More

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December 2018
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Measurement of IL-17AA and IL-17FF as Pharmacodynamic Biomarkers to Demonstrate Target Engagement in the Phase I Study of MCAF5352A.

AAPS J 2018 Dec 13;21(1). Epub 2018 Dec 13.

Department of OMNI Biomarker Development, Genentech Inc, South San Francisco, California, USA.

The interleukin (IL)-17 pathway has been implicated in the pathophysiology of many autoimmune diseases. MCAF5352A is a humanized monoclonal antibody which targets both IL-17A and IL-17F, thereby inhibiting the activity of IL-17 dimers (IL-17AA, IL-17AF, and IL-17FF). The pharmacokinetic profile of MCAF5352A has been characterized in both a Phase Ia single ascending dose study and a Phase Ib multiple ascending dose study. Read More

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December 2018

Identification of potential genes involved in triterpenoid saponins biosynthesis in Gleditsia sinensis by transcriptome and metabolome analyses.

J Nat Med 2018 Dec 13. Epub 2018 Dec 13.

Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.

Gleditsia sinensis is widely used as a medicinal plant in Asia, especially in China. Triterpenes, alkaloids, and sterols were isolated from Gleditsia species. Among them, triterpenoid saponins are very important metabolites owing to their various pharmacological activities. Read More

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December 2018

Chemical transformation mediated CRISPR/Cas9 genome editing in Escherichia coli.

Biotechnol Lett 2018 Dec 13. Epub 2018 Dec 13.

College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.

Objectives: To develop a convenient chemical transformation mediated CRISPR/Cas9 (CT-CRISPR/Cas9) system for genome editing in Escherichia coli.

Results: Here, we have constructed a CT-CRISPR/Cas9 system, which can precisely edit bacterial genome (replacing, deleting, inserting or point mutating a target gene) through chemical transformation. Compared with the traditional electroporation mediated CRISPR/Cas9 (ET-CRISPR/Cas9) system, genome editing with the CT-CRISPR/Cas9 system is much cheaper and simpler. Read More

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December 2018

Mitochondrial polymorphisms contribute to aging phenotypes in MNX mouse models.

Cancer Metastasis Rev 2018 Dec 14. Epub 2018 Dec 14.

Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA.

Many inbred strains of mice develop spontaneous tumors as they age. Recent awareness of the impacts of mitochondrial DNA (mtDNA) on cancer and aging has inspired developing a mitochondrial-nuclear exchange (MNX) mouse model in which nuclear DNA is paired with mitochondrial genomes from other strains of mouse. MNX mice exhibit mtDNA influences on tumorigenicity and metastasis upon mating with transgenic mice. Read More

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December 2018
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The Influence of a Xanthine-Catechin Chemical Matrix on in vitro Macrophage-Activation Triggered by Antipsychotic Ziprasidone.

Inflammation 2018 Dec 14. Epub 2018 Dec 14.

Postgraduate Program of Pharmacology, Federal University of Santa Maria (UFSM), Santa Maria, RS, Brazil.

Ziprasidone (ZIP) is an effective antipsychotic with low side effects than other second-generation antipsychotics. Despite this, there are reports of adverse events and previous studies associating the use of ZIP the inflammatory response. It is possible to infer that bioactive molecules present in some foods could attenuate peripheral inflammatory and oxidative stress potentially triggered ZIP. Read More

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December 2018

SIU-ICUD consultation on bladder cancer: basic science.

World J Urol 2018 Dec 13. Epub 2018 Dec 13.

Scott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.

Purpose: To provide a condensed summary of the Basic Science chapter that was included in the Third International Consultation on Bladder Cancer.

Methods: World bladder cancer basic science experts used the published literature to create summaries of recent progress in their areas of expertise.

Results: The completion of several large-scale genomics projects coupled with a strong collaborative culture within the research community and the exciting clinical activity of immune checkpoint blockade have combined to transform the bladder cancer research landscape. Read More

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December 2018

Breaking the curse of dimensionality to identify causal variants in Breeding 4.

Theor Appl Genet 2018 Dec 13. Epub 2018 Dec 13.

Institute for Genomic Diversity, Institute of Biotechnology, Cornell University, 175 Biotechnology Building, Ithaca, NY, 14853, USA.

In the past, plant breeding has undergone three major transformations and is currently transitioning to a new technological phase, Breeding 4. This phase is characterized by the development of methods for biological design of plant varieties, including transformation and gene editing techniques directed toward causal loci. The application of such technologies will require to reliably estimate the effect of loci in plant genomes by avoiding the situation where the number of loci assayed (p) surpasses the number of plant genotypes (n). Read More

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December 2018
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Draft genome sequence of the moderately halophilic bacterium sp. BBL2006.

Data Brief 2018 Dec 17;21:2410-2413. Epub 2018 Nov 17.

Department of Biology, Indiana University Southeast, New Albany, IN, USA.

We present the draft genome sequence of sp. BBL2006, a moderately halophilic, gram positive bacterium isolated from a sulfidic salt spring in Big Bone Lick State Park, Boone County, Kentucky. The genome of sp. Read More

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December 2018

Lentiviral Vector Purification Using Genetically Encoded Biotin Mimic in Packaging Cell.

Mol Ther Methods Clin Dev 2018 Dec 23;11:155-165. Epub 2018 Oct 23.

UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.

Lentiviral vectors (LVs) have recently witnessed an increasing demand in research and clinical applications. Their current purification processes represent the main bottleneck in their widespread use, as the methods used are cumbersome and yield low recoveries. We aimed to develop a one-step method to specifically purify LVs, with high yields and reduced levels of impurities, using the biotin-streptavidin system. Read More

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December 2018

A Comparative Review of Neutrophil Extracellular Traps in Sepsis.

Front Vet Sci 2018 28;5:291. Epub 2018 Nov 28.

Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis Davis, CA, United States.

Sepsis is the leading cause of critical illness and mortality in human beings and animals. Neutrophils are the primary effector cells of innate immunity during sepsis. Besides degranulation and phagocytosis, neutrophils also release neutrophil extracellular traps (NETs), composed of cell-free DNA, histones, and antimicrobial proteins. Read More

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November 2018

mutation and DNA repair and synthesis genes in non-small-cell lung cancer.

Mol Clin Oncol 2018 Dec 1;9(6):689-696. Epub 2018 Oct 1.

Department of Medical Oncology, Santa Maria della Misericordia Hospital, AOU di Perugia, I-06129 Perugia, Italy.

The aim of the present study was to assess the expression of select DNA repair and synthesis genes in non-small-cell lung cancer (NSCLC) according to mutation status. ERCC1, TS, RRM1, and BRCA1 mRNA expression levels were assessed from either primary or metastatic tumor specimens of patients diagnosed with epidermal growth factor receptor () wild-type (WT) advanced NSCLC. Total RNA was isolated from paraffin-embedded tumor specimens using the RNeasy FFPE kit and automatically purified using a QiaCube instrument. Read More

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December 2018

Epigenetic modulation during hippocampal development.

Biomed Rep 2018 Dec 18;9(6):463-473. Epub 2018 Oct 18.

Department of Pharmacology, Medical School of Yangtze University, Jingzhou, Hubei 434023, P.R. China.

The hippocampus is located in the limbic system and is vital in learning ability, memory formation and emotion regulation, and is associated with depression, epilepsy and mental retardation in an abnormal developmental situation. Several factors have been found to modulate the development of the hippocampus, and epigenetic modification have a crucial effect in this progress. The present review summarizes the epigenetic modifications, including DNA methylation, histone acetylation, and non-coding RNAs, regulating all stages of hippocampal development, focusing on the growth of Ammons horn and the dentate gyrus in humans and rodents. Read More

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December 2018

Monitoring BRAF and NRAS mutations with cell-free circulating tumor DNA from metastatic melanoma patients.

Oncotarget 2018 Nov 16;9(90):36238-36249. Epub 2018 Nov 16.

Université Côte d'Azur, CHU Nice, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Nice, France.

The mutation status of the and genes in tumor tissue is used to select patients with metastatic melanoma for targeted therapy. Cell-free circulating DNA (cfDNA) represents an accessible, non-invasive surrogate sample that could provide a snapshot of the and genotype in these patients. We investigated the feasibility of the Idylla™ assay for detection of and mutations in cfDNA of 19 patients with metastatic melanoma at baseline and during the course of treatment. Read More

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November 2018

Identification of rare levels of methylated tumor DNA fragments using an optimized bias based pre-amplification-digital droplet PCR (OBBPA-ddPCR).

Oncotarget 2018 Nov 16;9(90):36137-36150. Epub 2018 Nov 16.

Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Dresden, Germany.

Background: The analysis of aberrant DNA methylations is used for the diagnosis of cancer as significant changes in the gene methylation pattern are often detected during early carcinogenesis. In this study, we evaluated the performance of a two-step method that combines pre-amplification with ddPCR technique.

Results: By using ddPCR, the dependence of amplification efficiency for methylated and unmethylated DNA fragments on the relevant MgCl concentration and the annealing temperature was established in addition to the primer design. Read More

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November 2018

Exosomes impact survival to radiation exposure in cell line models of nervous system cancer.

Oncotarget 2018 Nov 16;9(90):36083-36101. Epub 2018 Nov 16.

Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.

Radiation is utilized in the therapy of more than 50% of cancer patients. Unfortunately, many malignancies become resistant to radiation over time. We investigated the hypothesis that one method of a cancer cell's ability to survive radiation occurs through cellular communication via exosomes. Read More

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November 2018

Methylation level of Rap1GAP and the clinical significance in MDS.

Oncol Lett 2018 Dec 26;16(6):7287-7294. Epub 2018 Sep 26.

Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Suzhou, Jiangsu 215006, P.R. China.

Previous studies on the pathogenesis of myelodysplastic syndrome (MDS) have identified multiple associated gene mutations, including mutations of tetmethylcytosinedioxygenase 2, isocitrate dehydrogenase [NADP(+)] 1 cytosolic, isocitrate dehydrogenase [NADP(+)] 2 mitochondrial and additional sex combs like 1 transcriptional regulator, all of which may be considered epigenetic regulators. Furthermore, mutations of RAS type GTPase family genes have been identified in 10-15% patients with MDS. The authors' previous study on the gene expression profile of cluster of differentiation 34 cells using microarray analysis identified elevated expression of RAP1GTPase activating protein 1 (Rap1GAP) in patients with MDS compared with that in non-malignant blood diseases (NM) control group. Read More

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December 2018
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Targeted next-generation sequencing of cancer-related genes in thyroid carcinoma: A single institution's experience.

Oncol Lett 2018 Dec 2;16(6):7278-7286. Epub 2018 Oct 2.

Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.

Thyroid carcinoma (TC) has characteristic genetic alterations, including point mutations in proto-oncogenes and chromosomal rearrangements that vary by histologic subtype. Recent developments in next-generation sequencing (NGS) technology enable simultaneous analysis of cancer-associated genes of interest, thus improving diagnostic accuracy and allowing precise personalized treatment for human cancer. A total of 50 patients who underwent thyroidectomy between 2014 and 2016 at Hokuto Hospital were enrolled. Read More

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December 2018

Methylation of and together with HPV status in cytological cervical specimens serves an important role in the progression of cervical intraepithelial neoplasia.

Oncol Lett 2018 Dec 26;16(6):7166-7174. Epub 2018 Sep 26.

Department of Obstetrics and Gynecology, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, SK-03601 Martin, Slovakia.

Cervical cancer (CC) is the second most common type of cancer affecting the female population. The development of CC takes several years, and involves a precancerous stage known as cervical intraepithelial neoplasia (CIN). A key factor in the development of disease is the human papillomavirus (HPV) infection, which initiates carcinogenesis. Read More

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December 2018

Clinical application of plasma mitochondrial DNA content in patients with lung cancer.

Oncol Lett 2018 Dec 27;16(6):7074-7081. Epub 2018 Sep 27.

Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China.

Alterations of mitochondrial DNA (mtDNA) have been identified in several types of solid tumor. However, to the best of our knowledge, the clinical significance of plasma mtDNA content in lung cancer remains unknown. Thus, the current study explored the diagnostic and prognostic value of plasma mtDNA quantification in patients with lung cancer. Read More

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December 2018
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Microbiota dysbiosis is associated with HPV-induced cervical carcinogenesis.

Oncol Lett 2018 Dec 26;16(6):7035-7047. Epub 2018 Sep 26.

Department of Molecular Virology, Adam Mickiewicz University, 61-712 Poznan, Poland.

Cervical microbial communities serve a crucial role in the persistence and development of oncogenic human papilloma virus (HPV) infections. In the present study, the authors hypothesised that disturbed heterogeneity of microbial flora was associated with HPV-induced carcinogenesis. Swabs of the cervical microbiota were collected from 250 women and the 16S ribosomal DNA was sequenced using a high throughput assay. Read More

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December 2018

The development of simultaneous measurement of viral load and physical status for human papillomavirus 16 and 18 co-infection using multiplex quantitative polymerase chain reaction.

Oncol Lett 2018 Dec 4;16(6):6977-6987. Epub 2018 Oct 4.

Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.

Persistent infection with human papillomavirus (HPV) type 16 and 18 is known to be a major risk factor for cervical cancer. Increased prevalence of co-infection with these high-risk types has been observed in pre-cancerous and cancerous tissues. The determination of physical status and copy numbers of viruses is therefore useful in clinical settings. Read More

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December 2018

p53-Sensitive Epileptic Behavior and Inflammation in Hypomorphic Mice.

Front Genet 2018 27;9:581. Epub 2018 Nov 27.

Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy.

Epilepsy is a complex clinical condition characterized by repeated spontaneous seizures. Seizures have been linked to multiple drivers including DNA damage accumulation. Investigation of epilepsy physiopathology in humans imposes ethical and practical limitations, for this reason model systems are mostly preferred. Read More

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November 2018

Beta 1, Beta 2 and Beta 3 Adrenergic Receptor Gene Polymorphisms in a Southeastern European Population.

Front Genet 2018 28;9:560. Epub 2018 Nov 28.

Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Zografou, Greece.

Genetic polymorphisms in β-, β- and β-adrenergic receptors (β-ARs) have been associated with chronic non-communicable disorders, such as cardiovascular diseases, asthma, chronic obstructive pulmonary disease (COPD) and obesity, as well as β-agonists and antagonists response and toxicity. The purpose of this study was to determine the frequency distribution of genetic variants Ser49Gly and Arg389Gly, variants Gly16Arg and Gln27Glu, variant Trp64Arg in a Southeastern European Caucasian (SEC) population sample and to establish a comparison with existing data from other human populations. A sample of 431 men and 590 women volunteered to participate in this genotyping analysis after anonymization and de-identification. Read More

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November 2018

Non-coding RNAs Function as Immune Regulators in Teleost Fish.

Front Immunol 2018 28;9:2801. Epub 2018 Nov 28.

Institute for Translational Medicine, Medical College of Qingdao University, Qingdao, China.

Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Read More

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November 2018
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Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis.

Front Pharmacol 2018 28;9:1330. Epub 2018 Nov 28.

Telethon Kids Institute, Perth, WA, Australia.

Antimicrobial-resistant microbes are an increasing threat to human health. In cystic fibrosis (CF), airway infections with remain a key driver of lung damage. With few new antibiotics on the development horizon, alternative therapeutic approaches are needed against antimicrobial-resistant pathogens. Read More

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November 2018
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Can Your DNA Influence Your Bet-Placing? The Impact of Cannabinoid Receptor 1 Gene on Gambling Tasks.

Front Hum Neurosci 2018 27;12:458. Epub 2018 Nov 27.

Sino-Britain Centre for Cognition and Ageing Research, Faculty of Psychology, Southwest University, Chongqing, China.

Are we placing a bet by ourselves or has our DNA already made the decision for us? Previous research has suggested that some genes related to dopamine or serotonin can influence our non-bet-placing decision-making, but little is known about whether cannabinoid-related genes can impact how much people bet. To investigate this issue, we focused on rs1049353, a single-nucleotide polymorphism of the cannabinoid receptor 1 (), because it is related to addictive behavior and reward processing. In this study ( = 377), we used a modified Cambridge gambling task to test the effect of polymorphism on how much people bet. Read More

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November 2018

Genomic Interventions in Medicine.

Bioinform Biol Insights 2018 3;12:1177932218816100. Epub 2018 Dec 3.

Department of Biological Sciences, Covenant University, Ota, Nigeria.

Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. Read More

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December 2018

Deciphering bacterial epigenomes using modern sequencing technologies.

Nat Rev Genet 2018 Dec 13. Epub 2018 Dec 13.

Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Read More

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December 2018

Exosome circRNA secreted from adipocytes promotes the growth of hepatocellular carcinoma by targeting deubiquitination-related USP7.

Oncogene 2018 Dec 13. Epub 2018 Dec 13.

Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.

Hepatocellular carcinoma (HCC), the major form of liver cancer, has shown increasing incidence and poor prognosis. Adipose tissue is known to function in energy storage and metabolism regulation by the secretion of adipokines. Circular RNAs (circRNAs), a novel type of noncoding RNA, have recently been recognized as key factors in tumor development, but the role of exosome circRNAs derived from adipose tissues has not been defined yet. Read More

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December 2018

A survey on incidence and management of adenovirus infection after allogeneic HSCT.

Bone Marrow Transplant 2018 Dec 13. Epub 2018 Dec 13.

Department of Pediatric Hematology and Oncology, University Hospital, Collegium Medicum UMK, Bydgoszcz, Poland.

To determine the current practices on the management of Adenovirus (ADV) infection after allogenic stem cell transplantation, a survey was undertook among EBMT centres. The response rate was 20% (91/446): 46% were adult, 44% were paediatric and 10% were mixed centres, respectively. The overall incidence of ADV infection was 7. Read More

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December 2018

Genomic and regulatory characteristics of significant transcription factors in colorectal cancer metastasis.

Authors:
Bin Zhou Rui Guo

Sci Rep 2018 Dec 13;8(1):17836. Epub 2018 Dec 13.

Department of Biochemistry and Molecular biology, Shanxi Medical University, Taiyuan, China.

The dysregulation of transcription factors has an important impact on the oncogenesis and tumor progression. Nonetheless, its functions in colorectal cancer metastasis are still unclear. In this study, four transcription factors (HNF4A, HSF1, MECP2 and RAD21) were demonstrated to be associated with the metastasis of colorectal cancer in both RNA and protein levels. Read More

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December 2018

The formation of chromatin domains involves a primary step based on the 3-D structure of DNA.

Authors:
Giorgio Bernardi

Sci Rep 2018 Dec 13;8(1):17821. Epub 2018 Dec 13.

Science Department, Roma Tre University, Viale Marconi 446, 00146, Rome, Italy.

The general model presented here for the formation of chromatin domains, LADs and TADs, is primarily based on the 3-D structures of the corresponding DNA sequences, the GC-poor and GC-rich isochores. Indeed, the low-heterogeneity GC-poor isochores locally are intrinsically stiff and curved because of the presence of interspersed oligo-Adenines. In contrast, the high-heterogeneity GC-rich isochores are in the shape of peaks characterized by increasing levels of GC and of interspersed oligo-Guanines. Read More

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December 2018

Crystal structure and mutation analysis revealed that DREP2 CIDE forms a filament-like structure with features differing from those of DREP4 CIDE.

Sci Rep 2018 Dec 13;8(1):17810. Epub 2018 Dec 13.

College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.

Cell death-inducing DFF45-like effect (CIDE) domain-containing proteins, DFF40, DFF45, CIDE-A, CIDE-B, and FSP27, play important roles in apoptotic DNA fragmentation and lipid homeostasis. The function of DFF40/45 in apoptotic DNA fragmentation is mediated by CIDE domain filament formation. Although our recent structural study of DREP4 CIDE revealed the first filament-like structure of the CIDE domain and its functional importance, the filament structure of DREP2 CIDE is unclear because this structure was not helical in the asymmetric unit. Read More

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December 2018

The short-sequence design of DNA and its involvement in the 3-D structure of the genome.

Sci Rep 2018 Dec 13;8(1):17820. Epub 2018 Dec 13.

Science Department, Roma Tre University, Viale Marconi 446, 00146, Rome, Italy.

Recent investigations have shown that isochores are characterized by a 3-D structure which is primarily responsible for the topology of chromatin domains. More precisely, an analysis of human chromosome 21 demonstrated that low-heterogeneity, GC-poor isochores are characterized by the presence of oligo-Adenines that are intrinsically stiff, curved and unfavorable for nucleosome binding. This leads to a structure of the corresponding chromatin domains, the Lamina Associated Domains, or LADs, which is well suited for interaction with the lamina. Read More

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December 2018

Virus-mediated export of chromosomal DNA in plants.

Nat Commun 2018 Dec 13;9(1):5308. Epub 2018 Dec 13.

Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, 10135, Italy.

The propensity of viruses to acquire genetic material from relatives and possibly from infected hosts makes them excellent candidates as vectors for horizontal gene transfer. However, virus-mediated acquisition of host genetic material, as deduced from historical events, appears to be rare. Here, we report spontaneous and surprisingly efficient generation of hybrid virus/host DNA molecules in the form of minicircles during infection of Beta vulgaris by Beet curly top Iran virus (BCTIV), a single-stranded DNA virus. Read More

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December 2018

Genetics and genomics of pulmonary arterial hypertension.

Eur Respir J 2018 Dec 13. Epub 2018 Dec 13.

Vanderbilt University Medical Center, Nashville, TN, USA.

Since 2000 there have been major advances in our understanding of the genetic and genomics of pulmonary arterial hypertension (PAH), although there remains much to discover. Based on existing knowledge, around 25-30% of patients diagnosed with idiopathic PAH have an underlying Mendelian genetic cause for their condition and should be classified as heritable PAH (HPAH). Here, we summarise the known genetic and genomic drivers of PAH, the insights these provide into pathobiology, and the opportunities afforded for development of novel therapeutic approaches. Read More

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December 2018

The DNA repair associated protein Gadd45 regulates the temporal coding of immediate early gene expression within the prelimbic prefrontal cortex and is required for the consolidation of associative fear memory.

J Neurosci 2018 Dec 13. Epub 2018 Dec 13.

Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD 4072, Australia

We have identified a member of the growth arrest and DNA damage (Gadd45) protein family, Gadd45, which is known to be critically involved in DNA repair, as a key player in the regulation of immediate early gene (IEG) expression underlying the consolidation of associative fear memory in adult male C57/Bl6 mice. Gadd45 temporally influences learning-induced IEG expression in the prelimbic prefrontal cortex (PLPFC) through its interaction with DNA double-strand break (DSB)-mediated changes in DNA methylation. Our findings suggest a two-hit model of experience-dependent IEG activity and learning that comprises 1) a first wave of IEG expression governed by DSBs and followed by a rapid increase in DNA methylation, and 2) a second wave of IEG expression associated with the recruitment of Gadd45 and active DNA demethylation at the same site, which is necessary for memory consolidation. Read More

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December 2018

Effective design principles for leakless strand displacement systems.

Proc Natl Acad Sci U S A 2018 Dec 13. Epub 2018 Dec 13.

Electrical and Computer Engineering, University of Texas at Austin, Austin, TX 78712;

Artificially designed molecular systems with programmable behaviors have become a valuable tool in chemistry, biology, material science, and medicine. Although information processing in biological regulatory pathways is remarkably robust to error, it remains a challenge to design molecular systems that are similarly robust. With functionality determined entirely by secondary structure of DNA, strand displacement has emerged as a uniquely versatile building block for cell-free biochemical networks. Read More

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December 2018

Inhibition of AZIN2-sv induces neovascularization and improves prognosis after myocardial infarction by blocking ubiquitin-dependent talin1 degradation and activating the Akt pathway.

EBioMedicine 2018 Dec 10. Epub 2018 Dec 10.

Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.. Electronic address:

Background: We previously found that loss of lncRNA-AZIN2 splice variant (AZIN2-sv) increases cardiomyocyte (CM) proliferation and attenuates adverse ventricular remodelling post-myocardial infarction (MI). However, whether inhibition of AZIN2-sv can simultaneously induce angiogenesis and thus improve prognosis after MI is unclear.

Methods: We used in situ hybridization and quantitative PCR to determine AZIN2-sv expression in endothelial cells. Read More

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December 2018

Comparison of DNA fragmentation levels in spermatozoa with different sex chromosome complements.

Reprod Biomed Online 2018 Nov 20. Epub 2018 Nov 20.

Assisted Conception Unit, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, 1E, Special Block, Prince of Wales Hospital, Ngan Shing Street, Hong Kong. Electronic address:

Research Question: Do spermatozoa with different sex chromosome complements (X and Y; aneuploidy and monosomy) exhibit different degrees of DNA damage?

Design: A prospective, observational study to measure the DNA fragmentation level and sex chromosome complement simultaneously using combined sperm chromosome dispersion (SCD) and fluorescence in-situ hybridization tests. Two methods were used to evaluate SCD images: a traditional semi-quantitative method to categorize halo size and a newly developed quantitative method based on the Matlab image analysis programme to more precisely measure the halo area and calculate the halo size index (HSI).

Results: The HSI (which was inversely proportional to DNA fragmentation level) of Y chromosome-bearing spermatozoa was significantly (P < 0. Read More

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November 2018

Label-free optical biosensor for target detection based on simulation-assisted catalyzed hairpin assembly.

Comput Biol Chem 2018 Dec 3. Epub 2018 Dec 3.

College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China. Electronic address:

The development of efficient and convenient strategy without involving enzyme or complex nanomaterial for the micro molecules detection has profound meaning in the diagnosis of diseases. Herein, taking the advantages of the strong affinity of aptamer and catalyzed hairpin assembly, we develop a new non-label optical amplified strategy for thrombin detection in this work. To support both biological inquiry and technological innovation, thermodynamic models are introduced to predict the minimum energy secondary structure of interacting nucleic acid strands and calculate the partition function and equilibrium concentration for complexes in our system. Read More

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December 2018

Stability and properties of Z-DNA containing artificial nucleobase 2'-O-methyl-8-methyl guanosine.

Bioorg Med Chem 2018 Dec 6. Epub 2018 Dec 6.

Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan. Electronic address:

We synthesized several DNA oligonucleotides containing one or several 2'-O-methyl-8-methyl guanosine (mGm) and demonstrated that these oligonucleotides not only stabilize the Z-DNA with a wide range of sequences under low salt conditions but also possess high thermal stability. Using artificial nucleobase-containing oligonucleotides, we studied the interaction of the Zα domain with Z-DNA. Furthermore, we showed that the mGm-contained oligonucleotides allow to study the photochemical reaction of Z-DNA. Read More

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December 2018
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