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https://www.readbyqxmd.com/read/27918204/removal-of-listeria-monocytogenes-dual-species-biofilms-using-combined-enzyme-benzalkonium-chloride-treatments
#1
Pedro Rodríguez-López, Alba Carballo-Justo, Lorraine A Draper, Marta L Cabo
The effects of pronase (PRN), cellulase (CEL) or DNaseI alone or combined with benzalkonium chloride (BAC) against Listeria monocytogenes-carrying biofilms were assayed. The best removal activity against L. monocytogenes-Escherichia coli biofilms was obtained using DNaseI followed by PRN and CEL. Subsequently, a modified logistic model was used to quantify the combined effects of PRN or DNaseI with BAC. A better BAC performance after PRN compared to DNaseI eradicating L. monocytogenes was observed. In E. coli the effects were the opposite...
December 5, 2016: Biofouling
https://www.readbyqxmd.com/read/27903897/combining-atac-seq-with-nuclei-sorting-for-discovery-of-cis-regulatory-regions-in-plant-genomes
#2
Zefu Lu, Brigitte T Hofmeister, Christopher Vollmers, Rebecca M DuBois, Robert J Schmitz
: Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899623/combining-transcription-factor-binding-affinities-with-open-chromatin-data-for-accurate-gene-expression-prediction
#3
Florian Schmidt, Nina Gasparoni, Gilles Gasparoni, Kathrin Gianmoena, Cristina Cadenas, Julia K Polansky, Peter Ebert, Karl Nordström, Matthias Barann, Anupam Sinha, Sebastian Fröhler, Jieyi Xiong, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Barbara Hutter, Gideon Zipprich, Bärbel Felder, Jürgen Eils, Benedikt Brors, Wei Chen, Jan G Hengstler, Alf Hamann, Thomas Lengauer, Philip Rosenstiel, Jörn Walter, Marcel H Schulz
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#4
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27677919/smart-carbon-nanotubes-with-laser-controlled-behavior-in-gene-delivery-and-therapy-through-a-non-digestive-trafficking-pathway
#5
Fenfen Kong, Fei Liu, Wei Li, Xiaomeng Guo, Zuhua Wang, Hanbo Zhang, Qingpo Li, Lihua Luo, Yongzhong Du, Yi Jin, Jian You
Near-infrared (NIR) laser-controlled gene delivery presents some benefits in gene therapy, inducing enhanced gene transfection efficiency. In this study, a "photothermal transfection" agent is obtained by wrapping poly(ethylenimine)-cholesterol derivatives (PEI-Chol) around single-walled carbon nanotubes (SWNTs). The PEI-Chol modified SWNTs (PCS) are effective in compressing DNA molecules and protecting them from DNaseI degradation. Compared to the complexes formed by PEI with DNA (PEI/DNA), complexes of PCS and DNA that are formed (PCS/DNA) exhibit a little lower toxicity to HEK293 and HeLa cells under the same PEI molecule weight and weight ratios...
September 28, 2016: Small
https://www.readbyqxmd.com/read/27651453/identification-of-a-novel-distal-regulatory-element-of-the-human-neuroglobin-gene-by-the-chromosome-conformation-capture-approach
#6
Kin Tung Tam, Ping Kei Chan, Wei Zhang, Pui Pik Law, Zhipeng Tian, Godfrey Chi Fung Chan, Sjaak Philipsen, Richard Festenstein, Kian Cheng Tan-Un
Neuroglobin (NGB) is predominantly expressed in the brain and retina. Studies suggest that NGB exerts protective effects to neuronal cells and is implicated in reducing the severity of stroke and Alzheimer's disease. However, little is known about the mechanisms which regulate the cell type-specific expression of the gene. In this study, we hypothesized that distal regulatory elements (DREs) are involved in optimal expression of the NGB gene. By chromosome conformation capture we identified two novel DREs located -70 kb upstream and +100 kb downstream from the NGB gene...
September 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27446086/neutrophil-extracellular-traps-in-anca-associated-vasculitis
#7
REVIEW
Daniel Söderberg, Mårten Segelmark
A group of pauci-immune vasculitides, characterized by neutrophil-rich necrotizing inflammation of small vessels and the presence of antineutrophil cytoplasmic antibodies (ANCAs), is referred to as ANCA-associated vasculitis (AAV). ANCAs against proteinase 3 (PR3) (PR3-ANCA) or myeloperoxidase (MPO) (MPO-ANCA) are found in over 90% of patients with active disease, and these ANCAs are implicated in the pathogenesis of AAV. Dying neutrophils surrounding the walls of small vessels are a histological hallmark of AAV...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27244087/molecular-dynamics-and-high-throughput-binding-free-energy-calculation-of-anti-actin-anticancer-drugs-new-insights-for-better-design
#8
L Roopa, R Pravin Kumar, L M M Sudheer Mohammed
Actin cytoskeleton plays an important role in cancerous cell progression. Till date many anticancer toxins are discovered that binds to different sites of actin. Mechanism of action of these toxins varies with respect to the site where they bind to actin. Latrunculin A (LAT) binds closely to nucleotide binding site and Reidispongiolide binds to the barbed end of actin. LAT is reported to reduce the displacement of domain 2 with respect to domain 1 and allosterically modulate nucleotide exchange. On the other hand Reidispongiolide binds with the higher affinity to actin and competes with the DNaseI binding loop once the inter-monomer interaction has been formed...
May 24, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27213305/low-molecular-weight-polyethylenimine-modified-with-pluronic-123-and-rgd-or-chimeric-rgd-nls-peptide-characteristics-and-transfection-efficacy-of-their-complexes-with-plasmid-dna
#9
Jing Hu, Wenfang Zhao, Kehai Liu, Qian Yu, Yuan Mao, Zeyu Lu, Yaguang Zhang, Manman Zhu
To solve the problem of transfection efficiency vs. cytotoxicity and tumor-targeting ability when polyethylenimine (PEI) was used as a nonviral gene delivery vector, new degradable PEI polymers were synthesized via cross-linking low-molecular-weight PEI with Pluronic P123 and then further coupled with a targeting peptide R4 (RGD) and a bifunctional R11 (RGD-NLS), which were termed as P123-PEI-R4 and P123-PEI-R11, respectively. Agarose gel electrophoresis showed that both P123-PEI-R4 and P123-PEI-R11 efficaciously condense plasmid DNA at a polymer-to-pDNA w/w ratio of 3...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27078861/using-roadmap-data-to-identify-enhancers-associated-with-disorders-of-sex-development
#10
Thomas Ohnesorg, Brittany Croft, Jacqueline Tan, Andrew H Sinclair
Despite recent advances in our understanding, most cases of disorders of sex development (DSD) cannot be explained by mutations in known genes. In genome-wide screens of DSD patients, we and others detected duplications or deletions of potential regulatory regions of known or suspected DSD genes. It is therefore likely that a significant proportion of DSD cases may be explained by disrupted transcriptional regulation of gonad genes. Despite many recent technological advances, limited availability of relevant tissues - especially human embryonic material - can make the identification of long-range regulatory elements extremely difficult...
2016: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/27060133/polymorphic-tandem-repeats-within-gene-promoters-act-as-modifiers-of-gene-expression-and-dna-methylation-in-humans
#11
Javier Quilez, Audrey Guilmatre, Paras Garg, Gareth Highnam, Melissa Gymrek, Yaniv Erlich, Ricky S Joshi, David Mittelman, Andrew J Sharp
Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation...
May 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27052111/atlas-of-prostate-cancer-heritability-in-european-and-african-american-men-pinpoints-tissue-specific-regulation
#12
Alexander Gusev, Huwenbo Shi, Gleb Kichaev, Mark Pomerantz, Fugen Li, Henry W Long, Sue A Ingles, Rick A Kittles, Sara S Strom, Benjamin A Rybicki, Barbara Nemesure, William B Isaacs, Wei Zheng, Curtis A Pettaway, Edward D Yeboah, Yao Tettey, Richard B Biritwum, Andrew A Adjei, Evelyn Tay, Ann Truelove, Shelley Niwa, Anand P Chokkalingam, Esther M John, Adam B Murphy, Lisa B Signorello, John Carpten, M Cristina Leske, Suh-Yuh Wu, Anslem J M Hennis, Christine Neslund-Dudas, Ann W Hsing, Lisa Chu, Phyllis J Goodman, Eric A Klein, John S Witte, Graham Casey, Sam Kaggwa, Michael B Cook, Daniel O Stram, William J Blot, Rosalind A Eeles, Douglas Easton, Zsofia Kote-Jarai, Ali Amin Al Olama, Sara Benlloch, Kenneth Muir, Graham G Giles, Melissa C Southey, Liesel M Fitzgerald, Henrik Gronberg, Fredrik Wiklund, Markus Aly, Brian E Henderson, Johanna Schleutker, Tiina Wahlfors, Teuvo L J Tammela, Børge G Nordestgaard, Tim J Key, Ruth C Travis, David E Neal, Jenny L Donovan, Freddie C Hamdy, Paul Pharoah, Nora Pashayan, Kay-Tee Khaw, Janet L Stanford, Stephen N Thibodeau, Shannon K McDonnell, Daniel J Schaid, Christiane Maier, Walther Vogel, Manuel Luedeke, Kathleen Herkommer, Adam S Kibel, Cezary Cybulski, Dominika Wokolorczyk, Wojciech Kluzniak, Lisa Cannon-Albright, Craig Teerlink, Hermann Brenner, Aida K Dieffenbach, Volker Arndt, Jong Y Park, Thomas A Sellers, Hui-Yi Lin, Chavdar Slavov, Radka Kaneva, Vanio Mitev, Jyotsna Batra, Amanda Spurdle, Judith A Clements, Manuel R Teixeira, Hardev Pandha, Agnieszka Michael, Paula Paulo, Sofia Maia, Andrzej Kierzek, David V Conti, Demetrius Albanes, Christine Berg, Sonja I Berndt, Daniele Campa, E David Crawford, W Ryan Diver, Susan M Gapstur, J Michael Gaziano, Edward Giovannucci, Robert Hoover, David J Hunter, Mattias Johansson, Peter Kraft, Loic Le Marchand, Sara Lindström, Carmen Navarro, Kim Overvad, Elio Riboli, Afshan Siddiq, Victoria L Stevens, Dimitrios Trichopoulos, Paolo Vineis, Meredith Yeager, Gosia Trynka, Soumya Raychaudhuri, Frederick R Schumacher, Alkes L Price, Matthew L Freedman, Christopher A Haiman, Bogdan Pasaniuc
Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines...
April 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/26982363/pioneering-activity-of-the-c-terminal-domain-of-ebf1-shapes-the-chromatin-landscape-for-b-cell-programming
#13
Sören Boller, Senthilkumar Ramamoorthy, Duygu Akbas, Robert Nechanitzky, Lukas Burger, Rabih Murr, Dirk Schübeler, Rudolf Grosschedl
Lymphopoiesis requires the activation of lineage-specific genes embedded in naive, inaccessible chromatin or in primed, accessible chromatin. The mechanisms responsible for de novo gain of chromatin accessibility, known as "pioneer" function, remain poorly defined. Here, we showed that the EBF1 C-terminal domain (CTD) is required for the regulation of a specific gene set involved in B cell fate decision and differentiation, independently of activation and repression functions. Using genome-wide analysis of DNaseI hypersensitivity and DNA methylation in multipotent Ebf1(-/-) progenitors and derivative EBF1wt- or EBF1ΔC-expressing cells, we found that the CTD promoted chromatin accessibility and DNA demethylation in previously naive chromatin...
March 15, 2016: Immunity
https://www.readbyqxmd.com/read/26939122/enhancement-of-dnasei-salt-tolerance-by-mimicking-the-domain-structure-of-dnase-from-an-extremely-halotolerant-bacterium-thioalkalivibrio-sp-k90mix
#14
Gediminas Alzbutas, Milda Kaniusaite, Arunas Lagunavicius
In our previous work we showed that DNaseI-like protein from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix retained its activity at salt concentrations as high as 4 M NaCl and the key factor allowing this was the C-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix) motifs. The further investigations revealed that this domain originated from proteins related to bacterial competence ComEA/ComE proteins. It is likely that in the course of evolution the DNA-binding domain from these proteins was fused to a metallo-β-lactamase superfamily domain...
2016: PloS One
https://www.readbyqxmd.com/read/26901046/which-genetics-variants-in-dnase-seq-footprints-are-more-likely-to-alter-binding
#15
Gregory A Moyerbrailean, Cynthia A Kalita, Chris T Harvey, Xiaoquan Wen, Francesca Luca, Roger Pique-Regi
Large experimental efforts are characterizing the regulatory genome, yet we are still missing a systematic definition of functional and silent genetic variants in non-coding regions. Here, we integrated DNaseI footprinting data with sequence-based transcription factor (TF) motif models to predict the impact of a genetic variant on TF binding across 153 tissues and 1,372 TF motifs. Each annotation we derived is specific for a cell-type condition or assay and is locally motif-driven. We found 5.8 million genetic variants in footprints, 66% of which are predicted by our model to affect TF binding...
February 2016: PLoS Genetics
https://www.readbyqxmd.com/read/26877240/a-caps-based-binding-assay-provides-semi-quantitative-validation-of-protein-dna-interactions
#16
Yongyao Xie, Yaling Zhang, Xiucai Zhao, Yao-Guang Liu, Letian Chen
Investigation of protein-DNA interactions provides crucial information for understanding the mechanisms of gene regulation. Current methods for studying protein-DNA interactions, such as DNaseI footprinting or gel shift assays, involve labeling DNA with radioactive or fluorescent tags, making these methods costly, laborious, and potentially damaging to the environment. Here, we describe a novel cleaved amplified polymorphic sequence (CAPS)-based binding assay (CBA), which is a label-free method that can simplify the semi-quantitative validation of protein-DNA interactions...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26833627/streptomyces-coelicolor-xdhr-is-a-direct-target-of-p-ppgpp-that-controls-expression-of-genes-encoding-xanthine-dehydrogenase-to-promote-purine-salvage
#17
Smitha Sivapragasam, Anne Grove
The gene encoding Streptomyces coelicolor xanthine dehydrogenase regulator (XdhR) is divergently oriented from xdhABC, which encodes xanthine dehydrogenase (Xdh). Xdh is required for purine salvage pathways. XdhR was previously shown to repress xdhABC expression. We show that XdhR binds the xdhABC-xdhR intergenic region with high affinity (Kd ∼ 0.5 nM). DNaseI footprinting reveals that this complex formation corresponds to XdhR binding the xdhR gene promoter at two adjacent sites; at higher protein concentrations, protection expands to a region that overlaps the transcriptional and translational start sites of xdhABC...
May 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/26775567/aldosterone-alters-the-chromatin-structure-of-the-murine-endothelin-1-gene
#18
Amanda K Welch, I Jeanette Lynch, Michelle L Gumz, Brian D Cain, Charles S Wingo
UNLABELLED: Aldosterone increases sodium reabsorption in the renal collecting duct and systemic blood pressure. Paradoxically, aldosterone also induces transcription of the endothelin-1 (Edn1) gene to increase protein (ET-1) levels, which inhibits sodium reabsorption. AIMS: Here we investigated changes in the chromatin structure of the Edn1 gene of collecting duct cell lines in response to aldosterone treatment. The Edn1 gene has a CpG island that encompasses the transcription start site and four sites in the 5' regulatory region previously linked to transcriptional regulation...
August 15, 2016: Life Sciences
https://www.readbyqxmd.com/read/26541514/a-transient-ischemic-environment-induces-reversible-compaction-of-chromatin
#19
Ina Kirmes, Aleksander Szczurek, Kirti Prakash, Iryna Charapitsa, Christina Heiser, Michael Musheev, Florian Schock, Karolina Fornalczyk, Dongyu Ma, Udo Birk, Christoph Cremer, George Reid
BACKGROUND: Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. RESULTS: Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40-700 nm in dimension...
2015: Genome Biology
https://www.readbyqxmd.com/read/26474554/a-gntr-family-transcription-factor-positively-regulates-mycobacterial-isoniazid-resistance-by-controlling-the-expression-of-a-putative-permease
#20
Jialing Hu, Lei Zhao, Min Yang
BACKGROUND: Bacteria use transcriptional regulation to respond to environmental stresses. Specifically, exposure to antibacterial drugs is deemed to be an atypical stress, and altering transcriptional regulation in response to such stress can increase bacterial drug resistance. However, only a few transcription factors that regulate drug resistance have been reported. RESULTS: In the present study, a GntR family transcription factor, encoded by the MSMEG_0535 (Ms0535) gene, was shown to be an isoniazid (INH) resistance regulator in Mycobacterium smegmatis...
2015: BMC Microbiology
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