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Jessica Cedervall, Anca Dragomir, Falk Saupe, Yanyu Zhang, Johan Ärnlöv, Erik Larsson, Anna Dimberg, Anders Larsson, Anna-Karin Olsson
Renal insufficiency is a frequent cancer-associated problem affecting more than half of all cancer patients at the time of diagnosis. To minimize nephrotoxic effects the dosage of anticancer drugs are reduced in these patients, leading to sub-optimal treatment efficacy. Despite the severity of this cancer-associated pathology, the molecular mechanisms, as well as therapeutic options, are still largely lacking. We here show that formation of intravascular tumor-induced neutrophil extracellular traps (NETs) is a cause of kidney injury in tumor-bearing mice...
2017: Oncoimmunology
I Mittra, K Pal, N Pancholi, A Shaikh, B Rane, P Tidke, S Kirolikar, N K Khare, K Agrawal, H Nagare, N K Nair
Background: Toxicity associated with chemotherapy is a major therapeutic challenge and is caused by chemotherapy-induced DNA damage and inflammation. We have recently reported that cell-free chromatin (cfCh) fragments released from dying cells can readily enter into healthy cells of the body to integrate into their genomes and induce DNA double-strand breaks, apoptosis and inflammation in them. We hypothesized that much of the toxicity of chemotherapy might be due to release of large quantities of cfCh from dying cells that could trigger an exaggerated DNA damage, apoptotic and inflammatory response in healthy cells over and above that caused by the drugs themselves...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Ron Schwessinger, Maria C Suciu, Simon J McGowan, Jelena Telenius, Stephen Taylor, Doug R Higgs, Jim R Hughes
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants...
September 13, 2017: Genome Research
Ya-Jun Liu, Feng Zhang, Hong-de Liu, Xiao Sun
The mechanism of transcriptional regulation has been the focus of many studies in the post-genomic era. The development of sequencing-based technologies for chromatin profiling enables current researchers to experimentally measure chromatin properties. Moreover, many studies aim at annotating the state of the chromatin into broad categories based on observed chromatin features and/or DNA sequences, then associating the resultant distal regulatory regions with the correct target genes based on DNA sequences, and predicting the dependence of epigenetic features on genetic variation...
August 20, 2017: Yi Chuan, Hereditas
L A Alexeeva, O A Patutina, A V Sen'kova, M A Zenkova, N L Mironova
After a long pause, the accumulation of data on the involvement of tumor-specific DNA and extracellular DNA in metastasis has again placed enzymes with deoxyribonuclease activity in the focus of the search for antitumor and antimetastatic drugs. In this work, the ability of bovine pancreatic DNase I to reduce the invasive potential of B16 melanoma has been investigated in vitro and in vivo. It was found that DNase I had a cytotoxic effect on B16 melanoma cells (IC50 ≈ 10^(4) U/mL). At the same time, significantly lower doses of DNase I (10^(2)-10^(3) U/mL) inhibited the migratory activity of melanoma cells in vitro, causing a decrease in the distance of cell front migration and in the area of scratch healing 48 h after the enzyme addition, as well as reducing the rate of cell migration...
July 2017: Molekuliarnaia Biologiia
Zuzana Garlikova, Ana Catarina Silva, Ana Rabata, David Potesil, Ivana Ihnatova, Jana Dumkova, Zuzana Koledova, Zbynek Zdrahal, Vladimir Vinarsky, Ales Hample, Perpetua Pinto-do-O, Diana S Nascimento
Extracellular matrix (ECM) is an essential component of the tissue microenvironment, actively shaping cellular behavior. In vitro culture systems are often poor in ECM constituents thus not allowing for naturally occurring cell-ECM interactions. This study reports on a straightforward and efficient method for generation of ECM scaffolds from lung tissue and its subsequent in vitro application using primary lung cells. Mouse lung tissue was subjected to decellularization with 0.2% sodium dodecyl sulfate, hypotonic solutions and DNase...
September 12, 2017: Tissue Engineering. Part C, Methods
Brad J Schmier, Claudiu M Nelersa, Arun Malhotra
NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3' → 5' exonuclease, but we show here that NrnA is bidirectional, degrading 2-5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker...
September 11, 2017: Scientific Reports
Carol Lai, Nurashikin Mohammad, Tidi Maharani Hassan, Mohamed Faisal Abdul Hamid
This case series reviews two cases of elderly patients who presented with fever, cough and shortness of breath. Clinical examinations and initial chest radiographs confirmed unilateral pleural effusion. Thoracenteses were consistent with exudative pleural effusion. We commenced intravenous antibiotics treating for parapneumonic effusions. The first case showed persistent effusion despite drainage, and the second case had a little aspirate from pleural tapping. Subsequent ultrasound of the thorax showed multiloculated effusions...
September 11, 2017: BMJ Case Reports
Steven Gazal, Hilary K Finucane, Nicholas A Furlotte, Po-Ru Loh, Pier Francesco Palamara, Xuanyao Liu, Armin Schoech, Brendan Bulik-Sullivan, Benjamin M Neale, Alexander Gusev, Alkes L Price
Recent work has hinted at the linkage disequilibrium (LD)-dependent architecture of human complex traits, where SNPs with low levels of LD (LLD) have larger per-SNP heritability. Here we analyzed summary statistics from 56 complex traits (average N = 101,401) by extending stratified LD score regression to continuous annotations. We determined that SNPs with low LLD have significantly larger per-SNP heritability and that roughly half of this effect can be explained by functional annotations negatively correlated with LLD, such as DNase I hypersensitivity sites (DHSs)...
September 11, 2017: Nature Genetics
Claudine Baraquet, Caroline S Harwood
The transition of bacteria from a planktonic lifestyle to a collaborative, sessile biofilm lifestyle is a regulated process orchestrated by the intracellular second-messenger c-di-GMP (bis-(3'-5')-cyclic dimeric guanosine monophosphate). To modulate this transition, c-di-GMP acts at the transcriptional, posttranscriptional, and posttranslational levels. In this chapter, we describe a method to study of how a transcriptional regulator modulates gene expression in response to c-di-GMP binding. DNase I footprinting is a valuable tool for use in analyzing how regulatory proteins bind to DNA, the location of their binding sites or how c-di-GMP affects their binding to DNA...
2017: Methods in Molecular Biology
Jing Zhu, Fan Zhang, Meijun Du, Peng Zhang, Songbin Fu, Liang Wang
Extrachromosomal circular DNAs (eccDNAs) have been reported in most eukaryotes. However, little is known about the cell-free eccDNA profiles in circulating system such as blood. To characterize plasma cell-free eccDNAs, we performed sequencing analysis in 26 libraries from three blood donors and negative controls. We identified thousands of unique plasma eccDNAs in the three subjects. We observed proportional eccDNA increase with initial DNA input. The detected eccDNAs were also associated with circular DNA enrichment efficiency...
September 8, 2017: Scientific Reports
Xuan Liao, Maurice K H Yap, Kim Hung Leung, Patrick Y P Kao, Long Qian Liu, Shea Ping Yip
Identification of genetic variations related to high myopia may advance our knowledge of the etiopathogenesis of refractive error. This study investigated the role of potassium channel gene (KCNQ5) polymorphisms in high myopia. We performed a case-control study of 1563 unrelated Han Chinese subjects (809 cases of high myopia and 754 emmetropic controls). Five tag single-nucleotide polymorphisms (SNPs) of KCNQ5 were genotyped, and association testing with high myopia was conducted using logistic regression analysis adjusted for sex and age to give Pasym values, and multiple comparisons were corrected by permutation test to give Pemp values...
2017: BioMed Research International
Yoshitaka Inoue, Yuk Ming Liu, Masayuki Otawara, Isabel Chico Calero, Ahhyun Stephanie Nam, Yong-Ming Yu, Philip Chang, Kathryn L Butler, Rosalynn M Nazarian, Jeremy Goverman, Benjamin J Vakoc, Daniel Irimia
Secondary burn necrosis is the expansion and deepening of the original burn injury several days after injury. Limiting the extent of secondary burn necrosis may improve outcomes. In this study, we examined the ability of the lipid mediator of inflammation-resolution resolvin D2 (RvD2) and chromatin-lysing enzyme (DNase) to reduce secondary burn necrosis. Male Wistar rats were injured using a brass comb with 4 prongs heated in boiling water. This method created 2 parallel rows of 4 rectangular burned areas separated by 3 unburned interspaces...
August 31, 2017: Journal of Burn Care & Research: Official Publication of the American Burn Association
B Reyneke, T Ndlovu, S Khan, W Khan
Ethidium monoazide (EMA) quantitative polymerase chain reaction (qPCR), propidium monoazide (PMA)-qPCR and DNase treatment in combination with qPCR were compared for the determination of microbial cell viability. Additionally, varying EMA and PMA concentrations were analysed to determine which dye and concentration allowed for the optimal identification of viable cells. Viable, heat treated (70 °C for 15 min) and autoclaved cultures of Legionella pneumophila, Pseudomonas aeruginosa, Salmonella typhimurium, Staphylococcus aureus and Enterococcus faecalis were utilised in the respective viability assays...
September 5, 2017: Applied Microbiology and Biotechnology
Desmond M Schofield, Ernestas Sirka, Eli Keshavarz-Moore, John M Ward, Darren N Nesbeth
OBJECTIVES: To reduce unwanted Fab' leakage from an autonucleolytic Escherichia coli strain, which co-expresses OmpA-signalled Staphylococcal nuclease and Fab' fragment in the periplasm, by substituting in Serratial nuclease and the DsbA periplasm translocation signal as alternatives. RESULTS: We attempted to genetically fuse a nuclease from Serratia marcescens to the OmpA signal peptide but plasmid construction failed, possibly due to toxicity of the resultant nuclease...
September 5, 2017: Biotechnology Letters
Matteo D Antonio, Donate Weghorn, Agnieszka D Antonio-Chronowska, Florence Coulet, Katrina M Olson, Christopher DeBoever, Frauke Drees, Angelo Arias, Hakan Alakus, Andrea L Richardson, Richard B Schwab, Emma K Farley, Shamil R Sunyaev, Kelly A Frazer
Efforts to identify driver mutations in cancer have largely focused on genes, whereas non-coding sequences remain relatively unexplored. Here we develop a statistical method based on characteristics known to influence local mutation rate and a series of enrichment filters in order to identify distal regulatory elements harboring putative driver mutations in breast cancer. We identify ten DNase I hypersensitive sites that are significantly mutated in breast cancers and associated with the aberrant expression of neighboring genes...
September 5, 2017: Nature Communications
Gi Hoon Jung, Eun Seob Lim, Min-Ah Woo, Joo Young Lee, Joo-Sung Kim, Hyun-Dong Paik
Campylobacter jejuni and C. coli are important foodborne pathogenic bacteria, especially in poultry meat. In this study, the presence of extracellular DNase activity was investigated for biofilm-deficient Campylobacter strains versus biofilm-forming Campylobacter strains isolated from chickens to understand the relation between extracellular DNase activity and biofilm formation. Biofilm-forming reference strain, C. jejuni NCTC11168, was co-incubated with biofilm non-forming strains isolated from raw chickens or their supernatants...
September 5, 2017: Journal of Microbiology and Biotechnology
Ebrahim Rezazadeh Zarandi, Shahla Mansouri, Nouzar Nakhaee, Farhad Sarafzadeh, Mohammad Moradi
Clostridium difficile (C.difficile) infection is often established in the presence of antibiotics and probably antibiotics can influence surface layer protein A (slpA) expression as a colonization factor. The aim of this study is to evaluate the effect of vancomycin (VAN), clindamycin (CLI) alone and in combination with ceftazidime (CAZ) on slpA gene expression to determine whether such antibiotics can have any effect on slpA expression. About ∼10(6) CFU/mL was inoculated to medium containing an appropriate concentration of antibiotics alone and in combination...
September 1, 2017: Microbial Pathogenesis
Yue Zheng, Hwang-Soo Joo, Vinod Nair, Katherine Y Le, Michael Otto
Phenol-soluble modulins (PSMs) are alpha-helical, amphipathic peptides that have multiple functions in staphylococcal physiology and virulence. Recent research has suggested that PSMs form amyloid fibrils and amyloids are involved in PSM-mediated phenotypes such as cytolysis and biofilm stability. While we observed PSM amyloid formation using electron microscopy and dye assays, there were no apparent differences in the production of extracellular fibrous material between a PSM-deficient strain and the isogenic wild-type strain...
September 1, 2017: International Journal of Medical Microbiology: IJMM
Guotai Yu, Asyraf Hatta, Sambasivam Periyannan, Evans Lagudah, Brande B H Wulff
DNA is widely used in plant genetic and molecular biology studies. In this chapter, we describe how to extract DNA from wheat tissues. The tissue samples are ground to disrupt the cell wall. Then cetyltrimethylammonium bromide (CTAB) or sodium dodecyl sulfate (SDS) is used to disrupt the cell and nuclear membranes to release the DNA into solution. A reducing agent, β-mercaptoethanol, is added to break the disulfide bonds between the cysteine residues and to help remove the tanins and polyphenols. A high concentration of salt is employed to remove polysaccharides...
2017: Methods in Molecular Biology
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