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https://www.readbyqxmd.com/read/28431230/structural-basis-for-guide-rna-processing-and-seed-dependent-dna-targeting-by-crispr-cas12a
#1
Daan C Swarts, John van der Oost, Martin Jinek
The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28430877/the-accessible-chromatin-landscape-during-conversion-of-human-embryonic-stem-cells-to-trophoblast-by-bmp4
#2
Yajun Liu, Dewu Ding, Hongde Liu, Xiao Sun
Human embryonic stem cells (hESC) exposed to the growth factor bone morphogenic protein 4 (BMP4) in the absence of FGF2 have been used as a model to study the development of placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. In this study, we used the public available chromatin accessibility data of hESC H1 cells and BMP4-induced trophoblast (TB)cell lines to identify DNase I hypersensitive sites (DHSs) in the two cell lines, as well as the transcription factor binding sites within the DHSs...
April 18, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28421088/non-host-resistance-dna-damage-is-associated-with-sa-signaling-for-induction-of-pr-genes-and-contributes-to-the-growth-suppression-of-a-pea-pathogen-on-pea-endocarp-tissue
#3
Lee A Hadwiger, Kiwamu Tanaka
Salicylic acid (SA) has been reported to induce plant defense responses. The transcriptions of defense genes that are responsible for a given plant's resistance to an array of plant pathogens are activated in a process called non-host resistance. Biotic signals capable of carrying out the activation of pathogenesis-related (PR) genes in pea tissue include fungal DNase and chitosan, two components released from Fusarium solani spores that are known to target host DNA. Recent reports indicate that SA also has a physical affinity for DNA...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28417999/a-tiling-deletion-based-genetic-screen-for-cis-regulatory-element-identification-in-mammalian-cells
#4
Yarui Diao, Rongxin Fang, Bin Li, Zhipeng Meng, Juntao Yu, Yunjiang Qiu, Kimberly C Lin, Hui Huang, Tristin Liu, Ryan J Marina, Inkyung Jung, Yin Shen, Kun-Liang Guan, Bing Ren
Millions of cis-regulatory elements are predicted to be present in the human genome, but direct evidence for their biological function is scarce. Here we report a high-throughput method, cis-regulatory element scan by tiling-deletion and sequencing (CREST-seq), for the unbiased discovery and functional assessment of cis-regulatory sequences in the genome. We used it to interrogate the 2-Mb POU5F1 locus in human embryonic stem cells, and identified 45 cis-regulatory elements. A majority of these elements have active chromatin marks, DNase hypersensitivity, and occupancy by multiple transcription factors, which confirms the utility of chromatin signatures in cis-element mapping...
April 17, 2017: Nature Methods
https://www.readbyqxmd.com/read/28414715/transcriptional-regulatory-logic-of-the-diurnal-cycle-in-the-mouse-liver
#5
Jonathan Aryeh Sobel, Irina Krier, Teemu Andersin, Sunil Raghav, Donatella Canella, Federica Gilardi, Alexandra Styliani Kalantzi, Guillaume Rey, Benjamin Weger, Frédéric Gachon, Matteo Dal Peraro, Nouria Hernandez, Ueli Schibler, Bart Deplancke, Felix Naef
Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in the mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28412325/designing-metal-contained-enzyme-mimics-for-prodrug-activation
#6
REVIEW
Baoji Du, Dan Li, Jin Wang, Erkang Wang
Enzyme-activated prodrug therapy (EAPT) is a widely-used and effective treatment method for cancer by converting the prodrugs into the drugs at the demanded time and space, whose key step is prodrug activation. Traditional prodrug activations are mostly dependent on the natural enzymes, which are unstable, expensive and hard to be functionalized. The emerging enzyme mimics, especially the metal-contained enzyme mimics (MEMs), provide a potential chance for improving the traditional EAPT because of their high stability, low cost and easiness of preparation and functionalization...
April 12, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28411822/label-free-and-sensitive-assay-for-deoxyribonuclease-i-activity-based-on-enzymatically-polymerized-superlong-poly-thymine-hosted-fluorescent-copper-nanoparticles
#7
Lan Luo, Fengzhou Xu, Hui Shi, Xiaoxiao He, Taiping Qing, Yanli Lei, Jinlu Tang, Dinggeng He, Kemin Wang
Deoxyribonuclease I (DNase I) is an important physiological indicator and diagnostic biomarker, but traditional methods for assessing its activity are time-consuming, laborious, and usually radioactive. Herein, by effectively combining the special functions of DNase I and terminal deoxynucleotidyl transferase (TdT), a simple, green, cost-effective, label-free and ultrasensitive assay for DNase I activity has been constructed based on superlong poly(thymine)-hosted copper nanoparticles (poly T-CuNPs). In this strategy, a 3'-phosphorylated DNA primer is designed to block TdT polymerization...
July 1, 2017: Talanta
https://www.readbyqxmd.com/read/28407149/determination-of-the-biological-form-of-human-cytomegalovirus-dna-in-the-plasma-of-solid-organ-transplant-recipients
#8
Yupin Tong, Xiaoli L Pang, Curtis Mabilangan, Jutta K Preiksaitis
Background.: Whether cytomegalovirus (CMV) DNA exists in plasma as virion-associated or free DNA is uncertain. Methods.: An assay combining DNase I digestion and CMV quantitative polymerase chain reaction (DNase-CMV-qPCR) was developed to differentiate free naked DNA from virion DNA. One hundred three frozen and 10 fresh CMV DNA-positive plasma samples from solid-organ transplant recipients (SOTRs) were tested. Three sets of paired qPCR (P-qPCR) assays with amplicons of variable length were used to study CMV DNA fragmentation in 20 SOTR plasma samples, viral stocks (Towne, Merlin, AD169) and the first World Health Organization (WHO) international standard (IS) for CMV DNA...
April 12, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28394916/survey-of-single-nucleotide-polymorphisms-in-the-gene-encoding-human-deoxyribonuclease-i-like-2-producing-loss-of-function-potentially-implicated-in-the-pathogenesis-of-parakeratosis
#9
Misuzu Ueki, Haruo Takeshita, Natsuko Utsunomiya, Takanao Chino, Noritaka Oyama, Minoru Hasegawa, Kaori Kimura-Kataoka, Junko Fujihara, Reiko Iida, Toshihiro Yasuda
Dysfunction of DNase I-like 2 (DNase 1L2) has been assumed to play a role in the etiology of parakeratosis through incomplete degradation of DNA in the epidermis. However, the pathogenetic background factor for such pathophysiologic conditions remains unknown. In this context, non-synonymous single-nucleotide polymorphisms (SNPs) in DNASE1L2 that would potentially result in loss of in vivo DNase 1L2 activity might serve as a genetic risk factor for such pathophysiologic conditions. Our aim was to effectively survey the non-synonymous SNPs of DNASE1L2 that would produce a loss-of-function variant of the enzyme together with a genetic distribution in the various populations...
2017: PloS One
https://www.readbyqxmd.com/read/28393439/effect-of-intracoronary-administration-of-aav1-serca2a-on-ventricular-remodelling-in-patients-with-advanced-systolic-heart-failure-results-from-the-agent-hf-randomized-phase-2-trial
#10
Jean-Sébastien Hulot, Joe-Elie Salem, Alban Redheuil, Jean-Philippe Collet, Shaida Varnous, Patrick Jourdain, Damien Logeart, Estelle Gandjbakhch, Claude Bernard, Stéphane N Hatem, Richard Isnard, Philippe Cluzel, Claude Le Feuvre, Pascal Leprince, Nadjib Hammoudi, François M Lemoine, David Klatzmann, Eric Vicaut, Michel Komajda, Gilles Montalescot, Anne-Marie Lompré, Roger J Hajjar
AIMS: Restoration of sarco/endoplasmic reticulum Ca(2+) ATPase (SERCA2a) activity through gene transfer improved cardiac function in experimental and pilot studies in humans with heart failure. The AGENT-HF (NCT01966887) trial investigated the impact of adeno-associated virus (AAV1)/SERCA2a on ventricular remodelling using multimodality non-invasive cardiac imaging. METHODS AND RESULTS: AGENT-HF was a single centre, randomized, double-blind, placebo-controlled trial in adult patients with NYHA class III-IV ischaemic or non-ischaemic heart failure and left ventricular ejection fraction ≤35%...
April 10, 2017: European Journal of Heart Failure
https://www.readbyqxmd.com/read/28391960/rapid-detection-of-urinary-tract-infections-via-bacterial-nuclease-activity
#11
Katie S Flenker, Elliot L Burghardt, Nirmal Dutta, William J Burns, Julia M Grover, Elizabeth J Kenkel, Tyler M Weaver, James Mills, Hyeon Kim, Lingyan Huang, Richard Owczarzy, Catherine A Musselman, Mark A Behlke, Bradley Ford, James O McNamara
Rapid and accurate bacterial detection methods are needed for clinical diagnostic, water, and food testing applications. The wide diversity of bacterial nucleases provides a rich source of enzymes that could be exploited as signal amplifying biomarkers to enable rapid, selective detection of bacterial species. With the exception of the use of micrococcal nuclease activity to detect Staphylococcus aureus, rapid methods that detect bacterial pathogens via their nuclease activities have not been developed. Here, we identify endonuclease I as a robust biomarker for E...
April 5, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28384859/evaluation-of-hiaureus-tm-coagulase-confirmation-kit-in-identification-of-staphylococcus-aureus
#12
Arunagiri Subramanian, Vidushi K Chitalia, Kushminda Bangera, Shashikant P Vaidya, Rajas Warke, Abhay Chowdhary, Ranjana A Deshmukh
INTRODUCTION: Staphylococcus aureus is a facultative anaerobic Gram positive coccal bacterium whose incidence ranges to different infections. It is a cause of various uncomplicated skin infections, abscesses, septicaemia/bacteraemia, gastroenteritis, endocarditis, toxic shock syndrome and food intoxications. Various methods with varied time, sensitivities, specificities and costs are available, but may not be used as a reliable test for the identification and differentiation of S. aureus...
February 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28379579/discovery-of-novel-heart-rate-associated-loci-using-the-exome-chip
#13
Marten E van den Berg, Helen R Warren, Claudia P Cabrera, Niek Verweij, Borbala Mifsud, Jeffrey Haessler, Nathan A Bihlmeyer, Yi-Ping Fu, Stefan Weiss, Henry J Lin, Niels Grarup, Ruifang Li-Gao, Giorgio Pistis, Nabi Shah, Jennifer A Brody, Martina Müller-Nurasyid, Honghuang Lin, Hao Mei, Albert V Smith, Leo-Pekka Lyytikäinen, Leanne M Hall, Jessica van Setten, Stella Trompet, Bram P Prins, Aaron Isaacs, Farid Radmanesh, Jonathan Marten, Aiman Entwistle, Jan A Kors, Claudia T Silva, Alvaro Alonso, Joshua C Bis, Rudolf de Boer, Hugoline G de Haan, Renée de Mutsert, George Dedoussis, Anna F Dominiczak, Alex S F Doney, Patrick T Ellinor, Ruben N Eppinga, Stephan B Felix, Xiuqing Guo, Yanick Hagemeijer, Torben Hansen, Tamara B Harris, Susan R Heckbert, Paul L Huang, Shih-Jen Hwang, Mika Kähönen, Jørgen K Kanters, Ivana Kolcic, Lenore J Launer, Man Li, Jie Yao, Allan Linneberg, Simin Liu, Peter W Macfarlane, Massimo Mangino, Andrew D Morris, Antonella Mulas, Alison D Murray, Christopher P Nelson, Marco Orrú, Sandosh Padmanabhan, Annette Peters, David J Porteous, Neil Poulter, Bruce M Psaty, Lihong Qi, Olli T Raitakari, Fernando Rivadeneira, Carolina Roselli, Igor Rudan, Naveed Sattar, Peter Sever, Moritz F Sinner, Elsayed Z Soliman, Timothy D Spector, Alice V Stanton, Kathleen E Stirrups, Kent D Taylor, Martin D Tobin, André Uitterlinden, Ilonca Vaartjes, Arno W Hoes, Peter van der Meer, Uwe Völker, Melanie Waldenberger, Zhijun Xie, Magdalena Zoledziewska, Andrew Tinker, Ozren Polasek, Jonathan Rosand, Yalda Jamshidi, Cornelia M van Duijn, Eleftheria Zeggini, J Wouter Jukema, Folkert W Asselbergs, Nilesh J Samani, Terho Lehtimäki, Vilmundur Gudnason, James Wilson, Steven A Lubitz, Stefan Kääb, Nona Sotoodehnia, Mark J Caulfield, Colin N A Palmer, Serena Sanna, Dennis O Mook-Kanamori, Panos Deloukas, Oluf Pedersen, Jerome I Rotter, Marcus Dörr, Chris J O'Donnell, Caroline Hayward, Dan E Arking, Charles Kooperberg, Pim van der Harst, Mark Eijgelsheim, Bruno H Stricker, Patricia B Munroe
Background Resting heart rate is a heritable trait, and an increase in heart rate is associated with increased mortality risk. GWAS analyses have found loci associated with resting heart rate, at the time of our study these loci explained 0.9% of the variation.Aim To discover new genetic loci associated with heart rate from Exome Chip meta-analyses.Methods Heart rate was measured from either elecrtrocardiograms or pulse recordings. We meta-analysed heart rate association results from 104,452 European-ancestry individuals from 30 cohorts, genotyped using the Exome Chip...
April 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28379095/an-insight-into-the-antibiofilm-properties-of-costa-rican-stingless-bee-honeys
#14
L G Zamora, C J Beukelman, A J J van den Berg, P C Aerts, H C Quarles van Ufford, R Nijland, M L Arias
OBJECTIVE: There is an increasing search for antibiofilm agents that either have specific activity against biofilms or may act in synergy with antimicrobials. Our objective is to examine the the antibiofilm properties of stingless bee honeys. METHOD: Meliponini honeys from Costa Rica were examined along with Medihoney as a reference. All honeys were submitted to a screening composed of minimum inhibitory concentration, inhibition of biofilm formation and biofilm destruction microplate-based assays against a Staphylococcus aureus biofilm forming strain...
April 2, 2017: Journal of Wound Care
https://www.readbyqxmd.com/read/28378498/rce1-a-novel-transcriptional-repressor-regulates-cellulase-gene-expression-by-antagonizing-the-transactivator-xyr1-in-trichoderma-reesei
#15
Yanli Cao, Fanglin Zheng, Lei Wang, Guolei Zhao, Guanjun Chen, Weixin Zhang, Weifeng Liu
Cellulase gene expression in the model cellulolytic fungus Trichoderma reesei is supposed to be controlled by an intricate regulatory network involving multiple transcription factors. Here, we identified a novel transcriptional repressor of cellulase gene expression, Rce1. Disruption of the rce1 gene not only facilitated the induced expression of cellulase genes but also led to a significant delay in terminating the induction process. However, Rce1 did not participate in Cre1-mediated catabolite repression...
April 5, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28375596/efficient-transcriptional-gene-repression-by-type-v-a-crispr-cpf1-from-eubacterium-eligens
#16
Seong Keun Kim, Haseong Kim, Woo-Chan Ahn, Kwang-Hyun Park, Eui-Jeon Woo, Dae-Hee Lee, Seung-Goo Lee
Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is an emerging technology for artificial gene regulation. Type II CRISPR-Cas endonuclease Cas9 is the most widely used protein for gene regulation with CRISPRi. Here, we present type V-A CRISPR-Cas endonuclease Cpf1-based CRISPRi. We constructed an l-rhamnose-inducible CRISPRi system with DNase-deactivated Cpf1 from Eubacterium eligens (EedCpf1) and compared its performance with catalytically deactivated Cas9 from Streptococcus pyogenes (SpdCas9)...
April 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28373968/streptococcus-suis-serotype-2-biofilms-inhibit-the-formation-of-neutrophil-extracellular-traps
#17
Fang Ma, Li Yi, Ningwei Yu, Guangyu Wang, Zhe Ma, Huixing Lin, Hongjie Fan
Invasive infections caused by Streptococcus suis serotype 2 (SS2) has emerged as a clinical problem in recent years. Neutrophil extracellular traps (NETs) are an important mechanism for the trapping and killing of pathogens that are resistant to phagocytosis. Biofilm formation can protect bacteria from being killed by phagocytes. Until now, there have only been a few studies that focused on the interactions between bacterial biofilms and NETs. SS2 in both a biofilm state and a planktonic cell state were incubated with phagocytes and NETs, and bacterial survival was assessed...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28369538/structure-of-acid-deoxyribonuclease
#18
Armando Varela-Ramirez, Jan Abendroth, Adrian A Mejia, Isabelle Q Phan, Donald D Lorimer, Thomas E Edwards, Renato J Aguilera
Deoxyribonuclease II (DNase II) is also known as acid deoxyribonuclease because it has optimal activity at the low pH environment of lysosomes where it is typically found in higher eukaryotes. Interestingly, DNase II has also been identified in a few genera of bacteria and is believed to have arisen via horizontal transfer. Here, we demonstrate that recombinant Burkholderia thailandensis DNase II is highly active at low pH in the absence of divalent metal ions, similar to eukaryotic DNase II. The crystal structure of B...
March 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369033/crispr-cas9-epigenome-editing-enables-high-throughput-screening-for-functional-regulatory-elements-in-the-human-genome
#19
Tyler S Klann, Joshua B Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B Hilton, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach
Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context...
April 3, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28359676/transplantation-of-the-decellularized-tracheal-allograft-in-animal-model-rabbit
#20
Reza Ershadi, Mohamadbagher Rahim, Siavash Jahany, Siamak Rakei
BACKGROUND: It has been difficult to perform tracheal allotransplantation without immunosuppression. To determine whether decellularized trachea can be used in tracheal replacement, we evaluated the viability of decellularized tracheal allografts in a rabbit model of immunosuppressant-free transplantation. METHOD: Half allograft (Group 1, n = 7) was harvested from adult New Zealand white rabbits, subjected to a detergent-enzymatic method (containing sodium deoxycholate/DNase lavations) of decellularization for as many cycles as needed, and the other half was stored in phosphate-buffered saline at 4°C as a control (Group 2, n = 7)...
March 27, 2017: Asian Journal of Surgery
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