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Ka-Chun Wong
Motivation: In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter-enhancer pairs) systematically. Results: To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences...
June 13, 2017: Bioinformatics
Angelica Maldonado-Rodríguez, Othon Rojas-Montes, Guillermo Vazquez-Rosales, Adolfo Chavez-Negrete, Magdalena Rojas-Uribe, Araceli Posadas-Mondragon, Leopoldo Aguilar-Faisal, Ana Maria Cevallos, Beatriz Xoconostle-Cazares, Rosalia Lira
BACKGROUND: Dried blood and serum samples are useful resources for detecting antiviral antibodies. The conditions for elution of the sample need to be optimized for each disease. Dengue is a widespread disease in Mexico which requires continuous surveillance. In this study, we standardized and validated a protocol for the specific detection of dengue antibodies from dried serum spots (DSSs). METHODS: Paired serum and DSS samples from 66 suspected cases of dengue were collected in a clinic in Veracruz, Mexico...
2017: BioMed Research International
Sergei A Filichkin, Molly Megraw
Identifying cis-regulatory elements is critical in understanding the direct and indirect interactions that occur within gene regulatory networks. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high-throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. Yet, challenges still remain in processing recalcitrant tissues that have low DNA content. Here, we describe DNase I SIM (for Simplified In-nucleus Method), a protocol that simplifies and facilitates generation of DNase-seq libraries from plant tissues for high-resolution mapping of DNase I hypersensitive sites...
2017: Methods in Molecular Biology
Lucia Lauková, Barbora Konečná, Janka Bábíčková, Alexandra Wagnerová, Veronika Melišková, Barbora Vlková, Peter Celec
Sepsis is associated with the activation of white blood cells (WBCs) that leads to the production of extracellular traps. This process increases extracellular DNA (ecDNA) that can be recognized by the innate immune system and leads to inflammation. Previous studies have shown that by cleaving ecDNA deoxyribonuclease (DNase) prevents the antibacterial effects of extracellular traps, but also has beneficial effects in sepsis. The aim of our study was to analyze the effects of DNase on WBCs in vitro and on ecDNA in a mouse model of sepsis...
June 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Zhong Q Wang, Ruo D Liu, Ge G Sun, Yan Y Song, Peng Jiang, Xi Zhang, Jing Cui
The most commonly used serodiagnostic antigens for trichinellosis are the excretory-secretory (ES) antigens from T. spiralis muscle larvae (ML), but the specific antibodies against the ML ES antigens are usually negative during early stage of Trichinella infection. The recent studies demonstrated that T. spiralis adult worm (AW) antigens were recognized by mouse or swine infection sera on Western blot as early as 7-15 days post-infection (dpi), the AW antigens might contain the early diagnostic markers for trichinellosis...
2017: Frontiers in Microbiology
Xiaochun Zhang, Jingman Wang, Qiuxiang Cheng, Xuan Zheng, Guoping Zhao, Jin Wang
The clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9 system has been widely applied in both transcriptional regulation and epigenetic studies. However, for multiple targets, independent expression of multiple single guide RNAs (sgRNAs) is needed, which is less convenient. To address the problem, we employed a DNase-dead Cpf1 mutant (ddCpf1) for multiplex gene regulation. We demonstrated that ddCpf1 alone could be employed for gene repression in Escherichia coli, and the repression was more effective with CRISPR RNAs (crRNAs) specifically targeting to the template strand of its target genes, which was different from that of dCas9...
2017: Cell Discovery
Marina N Vassylyeva, Sergiy Klyuyev, Alexey D Vassylyev, Hunter Wesson, Zhuo Zhang, Matthew B Renfrow, Hengbin Wang, N Patrick Higgins, Louise T Chow, Dmitry G Vassylyev
Protein purification is an essential primary step in numerous biological studies. It is particularly significant for the rapidly emerging high-throughput fields, such as proteomics, interactomics, and drug discovery. Moreover, purifications for structural and industrial applications should meet the requirement of high yield, high purity, and high activity (HHH). It is, therefore, highly desirable to have an efficient purification system with a potential to meet the HHH benchmark in a single step. Here, we report a chromatographic technology based on the ultra-high-affinity (Kd ∼ 10(-14)-10(-17) M) complex between the Colicin E7 DNase (CE7) and its inhibitor, Immunity protein 7 (Im7)...
June 12, 2017: Proceedings of the National Academy of Sciences of the United States of America
Xianjun Lai, Sairam Behera, Zhikai Liang, Yanli Lu, Jitender S Deogun, James C Schnable
One method for identifying noncoding regulatory regions of a genome is to quantify rates of divergence between related species, as functional sequence will generally diverge more slowly. Most approaches to identifying these conserved noncoding sequences (CNS) based on alignment have had relatively large minimum sequence lengths (≥ 15 base pair) compared to the average length of known transcription factor binding sites. To circumvent this constraint, STAG-CNS integrates data from the promoters of conserved orthologous genes in three or more species simultaneously...
June 5, 2017: Molecular Plant
Luca Urbani, Panagiotis Maghsoudlou, Anna Milan, Maria Menikou, Charlotte Klara Hagen, Giorgia Totonelli, Carlotta Camilli, Simon Eaton, Alan Burns, Alessandro Olivo, Paolo De Coppi
Oesophageal tissue engineering is a therapeutic alternative when oesophageal replacement is required. Decellularised scaffolds are ideal as they are derived from tissue-specific extracellular matrix and are non-immunogenic. However, appropriate preservation may significantly affect scaffold behaviour. Here we aim to prove that an effective method for short- and long-term preservation can be applied to tissue engineered products allowing their translation to clinical application. Rabbit oesophagi were decellularised using the detergent-enzymatic treatment (DET), a combination of deionised water, sodium deoxycholate and DNase-I...
2017: PloS One
Luiz Gustavo Gardinassi, Thiago S DeSouza-Vieira, Naila O da Silva, Gustavo R Garcia, Valéria M Borges, Roseane N S Campos, Roque P de Almeida, Isabel K F de Miranda Santos, Elvira M Saraiva
BACKGROUND: Infections with parasites of the Leishmania donovani complex result in clinical outcomes that range from asymptomatic infection to severe and fatal visceral leishmaniasis (VL). Neutrophils are major players of the immune response against Leishmania, but their contribution to distinct states of infection is unknown. Gene expression data suggest the activation of the NETosis pathway during human visceral leishmaniasis. Thus, we conducted an exploratory study to evaluate NET-related molecules in retrospective sera from VL patients, asymptomatic individuals and uninfected endemic controls...
June 6, 2017: Parasites & Vectors
Jing Ye, Can Shao, Xu Zhang, Xuyun Guo, Ping Gao, Yunzhu Cen, Shiqing Ma, Ying Liu
The removal of mature biofilm from the surface of implant has been a formidable challenge in treating implant-associated infection. Prevention of biofilm formation rather than removal of existing biofilm is a more effective approach. Immobilization of biofilm-dispersing enzymes on material surfaces is regarded as one of the most promising strategies. Deoxyribonuclease I (DNase I) can degrade extracellular DNA (eDNA) and then destabilize biofilm. In this study, DNase I was immobilized on a titanium (Ti) surface by using dopamine as an intermediate...
September 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
Alzbeta Zinkova, Iva Brynychova, Alexander Svacina, Marie Jirkovska, Marie Korabecna
Circulating cell-free DNA (cfDNA) may be involved in immune response regulation. We studied the variations in abundance of telomeric sequences in plasma and serum in young healthy volunteers and the ability of cfDNA contained in these samples to co-activate the TNF-α m RNA expression in monocytes. We performed qPCR to determine relative telomere length (T/S ratios) in plasma, serum and whole blood of 36 volunteers. Using paired samples of plasma and serum and DNase treatment, we analysed the contribution of cfDNA to the co-activation of TNF-α mRNA expression in THP1 monocytic cell line...
June 1, 2017: Scientific Reports
Laiping Wong, Kaiyu Jiang, Yanmin Chen, James N Jarvis
Deep whole genome sequencing (WGS) allows for the comprehensive study of genetic landscapes at finer resolution than array based methods. We conducted deep WGS on children with the polyarticular form of juvenile idiopathic arthritis (JIA), using 2 independent cohorts to ascertain the sequencing fidelity. Genome wide SNP density analysis identified 18 SNP hotspots with comparison to the 1000 Genome Projects (1KGP) data. A subset of the genes adjacent to SNP hotspots showed statistically significant enrichment in immunological processes...
June 1, 2017: Scientific Reports
Christina A Markunas, Eric O Johnson, Dana B Hancock
Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10(-8)) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits...
May 31, 2017: Human Genetics
Anderson B Guimarães-Costa, Natalia C Rochael, Fabiano Oliveira, Juliana Echevarria-Lima, Elvira M Saraiva
Monocyte-derived dendritic cells (mo-DCs) are essential for the development of a Th1 protective immune response against Leishmania parasites. It is well known that IL-4 and GM-CSF drive differentiation of human monocytes to dendritic cells (DCs). Here, we investigate if neutrophil extracellular traps (NETs) disrupt this process. NETs-enriched supernatants, generated after human neutrophil activation by Leishmania promastigotes, were added to monocytes and differentiation monitored by expression of molecules associated with macrophage and DCs phenotypes, cytokine production, and parasite killing...
2017: Frontiers in Immunology
Yawen Liu, Zhaozhu Zheng, He Gong, Meng Liu, Shaozhe Guo, Gang Li, Xiaoqin Wang, David L Kaplan
The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility...
May 31, 2017: Biomaterials Science
Nandhini Ponnuswamy, Maartje M C Bastings, Bhavik Nathwani, Ju Hee Ryu, Leo Y T Chou, Mathias Vinther, Weiwei Aileen Li, Frances M Anastassacos, David J Mooney, William M Shih
DNA nanostructures have evoked great interest as potential therapeutics and diagnostics due to ease and robustness of programming their shapes, site-specific functionalizations and responsive behaviours. However, their utility in biological fluids can be compromised through denaturation induced by physiological salt concentrations and degradation mediated by nucleases. Here we demonstrate that DNA nanostructures coated by oligolysines to 0.5:1 N:P (ratio of nitrogen in lysine to phosphorus in DNA), are stable in low salt and up to tenfold more resistant to DNase I digestion than when uncoated...
May 31, 2017: Nature Communications
Hidenobu Yaku, Yoshio Yoshida, Hidehiko Okazawa, Yasushi Kiyono, Yuko Fujita, Daisuke Miyoshi
A sensitive telomerase assay based on asymmetric polymerase chain reaction (A-PCR) on magnetic beads and subsequent application of cycling probe technology, STAMC, which is insusceptible to DNase and PCR inhibitors, was for the first time applied to clinical specimens in addition to a conventional telomeric repetitive amplification protocol (TRAP). The electrophoresis results showed that an increase in scraped cervical cancer cells not only reduced TRAP products but also increased smaller products, suggesting the unreliability of TRAP for clinical samples...
May 30, 2017: Analytical Chemistry
Shanxin Zhang, Zhiping Zhou, Xinmeng Chen, Yong Hu, Lindong Yang
DNase I hypersensitive sites (DHSs) are accessible chromatin regions hypersensitive to cleavages by DNase I endonucleases. DHSs are indicative of cis-regulatory DNA elements (CREs), all of which play important roles in global gene expression regulation. It is helpful for discovering CREs by recognition of DHSs in genome. To accelerate the investigation, it is an important complement to develop cost-effective computational methods to identify DHSs. However, there is a lack of tools used for identifying DHSs in plant genome...
May 26, 2017: Journal of Theoretical Biology
Lindsay R Stolzenburg, Rui Yang, Jenny L Kerschner, Sara Fossum, Matthew Xu, Andrew Hoffmann, Kay-Marie Lamar, Sujana Ghosh, Sarah Wachtel, Shih-Hsing Leir, Ann Harris
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), but are not good predictors of lung phenotype. Genome-wide association studies (GWAS) previously identified additional genomic sites associated with CF lung disease severity. One of these, at chromosome 11p13, is an intergenic region between Ets homologous factor (EHF) and Apaf-1 interacting protein (APIP). Our goal was to determine the functional significance of this region, which being intergenic is probably regulatory...
May 26, 2017: Nucleic Acids Research
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