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https://www.readbyqxmd.com/read/27913730/dna-recognition-by-the-swai-restriction-endonuclease-involves-unusual-distortion-of-an-8-base-pair-a-t-rich-target
#1
Betty W Shen, Daniel F Heiter, Keith D Lunnen, Geoffrey G Wilson, Barry L Stoddard
R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5'-ATTTAAAT-3', and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar 'PD-D/ExK' restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911718/attacking-hiv-1-rna-versus-dna-by-sequence-specific-approaches-rnai-versus-crispr-cas
#2
REVIEW
Elena Herrera-Carrillo, Ben Berkhout
Human immunodeficiency virus type 1 (HIV-1) infection can be effectively controlled by potent antiviral drugs, but this never results in a cure. The patient should therefore take these drugs for the rest of his/her life, which can cause drug-resistance and adverse effects. Therefore, more durable therapeutic strategies should be considered, such as a stable gene therapy to protect the target T cells against HIV-1 infection. The development of potent therapeutic regimens based on the RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats (CRISPR-Cas) mechanisms will be described, which can be delivered by lentiviral vectors...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27908936/genome-editing-technologies-principles-and-applications
#3
REVIEW
Thomas Gaj, Shannon J Sirk, Sai-Lan Shui, Jia Liu
Targeted nucleases have provided researchers with the ability to manipulate virtually any genomic sequence, enabling the facile creation of isogenic cell lines and animal models for the study of human disease, and promoting exciting new possibilities for human gene therapy. Here we review three foundational technologies-clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs)...
December 1, 2016: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/27903910/structural-insights-into-dynamics-of-recu-hj-complex-formation-elucidates-key-role-of-ntr-and-stalk-region-toward-formation-of-reactive-state
#4
Sagar Khavnekar, Sarath Chandra Dantu, Svetlana Sedelnikova, Sylvia Ayora, John Rafferty, Avinash Kale
Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902801/achieving-plant-crispr-targeting-that-limits-off-target-effects
#5
Jeffrey D Wolt, Kan Wang, Dipali Sashital, Carolyn J Lawrence-Dill
The CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein) has been used to generate targeted changes for direct modification of endogenous genes in an increasing number of plant species; but development of plant genome editing has not yet fully considered potential off-target mismatches that may lead to unintended changes within the genome. Assessing the specificity of CRISPR-Cas9 for increasing editing efficiency as well as the potential for unanticipated downstream effects from off-target mutations is an important regulatory consideration for agricultural applications...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27898282/comparative-fingerprinting-of-the-human-microbiota-in-diabetes-and-cardiovascular-disease
#6
Emanuel Vamanu, Diana Pelinescu, Ionela Sarbu
Diabetes and cardiovascular diseases are major causes of morbidity and mortality worldwide, and are associated with changes in the human gut microbiota. To better understand the relationships between diet, disease, and the colonic microbiome, we used the in vitro GIS1 system and repetitive element palindromic polymerase chain reaction (rep-PCR) to determine the microbial fingerprints in individuals with these diseases and compared them with the fingerprints in healthy controls. Clear differences were apparent in the three groups...
November 29, 2016: Journal of Medicinal Food
https://www.readbyqxmd.com/read/27898094/crispr-cas9-aav-mediated-knock-in-at-nrl-locus-in-human-embryonic-stem-cells
#7
Xianglian Ge, Haitao Xi, Fayu Yang, Xiao Zhi, Yanghua Fu, Ding Chen, Ren-He Xu, Ge Lin, Jia Qu, Junzhao Zhao, Feng Gu
Clustered interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome engineering technologies are sparking a new revolution in biological research. This technology efficiently induces DNA double strand breaks at the targeted genomic sequence and results in indel mutations by the error-prone process of nonhomologous end joining DNA repair or homologous recombination with a DNA repair template. The efficiency of genome editing with CRISPR/Cas9 alone in human embryonic stem cells is still low...
November 29, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27892857/genotyping-of-german-and-austrian-taylorella-equigenitalis-isolates-using-repetitive-extragenic-palindromic-rep-pcr-and-pulsed-field-gel-electrophoresis-pfge
#8
Reinhard Sting, Christoph Seeh, Norman Mauder, Michaela Maurer, Igor Loncaric, Beatrix Stessl, Peter Kopp, Klaus Banzhaf, Brigitte Martin, Falk Melzer, Astrid Raßbach, Joachim Spergser
A total of 124 Taylorella (T.) equigenitalis and five T. asinigenitalis field isolates collected between 2002 and 2014 were available for genotyping using REP- (repetitive extragenic palindromic) PCR and PFGE (pulsed-field gel electrophoresis). The study comprised 79 T. equigenitalis field isolates originating from ten defined breeds of German horses and revealed a spectrum of five REP (rep-E1-E4, rep-E3a) and 15 PFGE (TE-A1-A9, TE-B1-B3, TE-C, TE-E1, and TE-E2) genotypes. T. equigenitalis field isolates (n=40) obtained from Austrian Lipizzaner horses were differentiated into three REP (rep-E1, rep-E3a, and rep-E4) and three PFGE genotypes (TE-A2, TE-A5, and TE-D); those isolated from four Austrian Trotters belonged to the REP/PFGE genotype rep-E2/TE-A1...
October 4, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/27889248/comprehensive-study-to-investigate-the-role-of-various-aminoglycoside-resistance-mechanisms-in-clinical-isolates-of-acinetobacter-baumannii
#9
Vajihe Sheikhalizadeh, Alka Hasani, Mohammad Ahangarzadeh Rezaee, Mohammad Rahmati-Yamchi, Akbar Hasani, Reza Ghotaslou, Hamid Reza Goli
Therapeutic resistance towards most of the current treatment regime by Acinetobacter baumannii has reduced the prescribing antibiotic pattern and option is being re-shifted towards more toxic agents including aminoglycosides. The present investigation aimed at to study various mechanisms towards aminoglycoside non-susceptibility in clinical isolates of A. baumannii. The bacteria were subjected to genetic basis assessment for the presence of aminoglycoside modifying enzymes (AME), 16S rRNA methylase encoding genes and relative expression of AdeABC and AbeM efflux pumps in relation to their susceptibility to five aminoglycosides...
November 23, 2016: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/27881651/alternative-polyadenylation-of-human-bocavirus-at-its-3-end-is-regulated-by-multiple-elements-and-affects-capsid-expression
#10
Sujuan Hao, Junmei Zhang, Zhen Chen, Huanzhou Xu, Hanzhong Wang, Wuxiang Guan
: Alternative processing of human bocavirus (HBoV) P5 promoter-transcribed RNA is critical for generating the structural and nonstructural protein-encoding mRNA transcripts. The regulatory mechanism by which HBoV RNA transcripts are polyadenylated at proximal [(pA)p] or distal [(pA)d] polyadenylation sites is yet unclear. We constructed a recombinant HBoV infectious clone to study the alternative polyadenylation regulation of HBoV. Surprisingly, in addition to the reported distal polyadenylation site (pA)d, a novel distal polyadenylation site (pA)d2 which is located in the right end hairpin (REH), was identified during infectious clone transfection or recombinant virus infection...
November 23, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27877210/in-vivo-antitumor-effect-of-an-hpv-specific-promoter-driving-il-12-expression-in-an-hpv-16-positive-murine-model-of-cervical-cancer
#11
Victor Hugo Bermúdez-Morales, Geny Fierros-Zarate, Celina García-Meléndrez, Juan Manuel Alcocer-Gonzalez, Ausencio Morales-Ortega, Oscar Peralta-Zaragoza, Kirvis Torres-Poveda, Ana Isabel Burguete-García, Eva Hernández-Márquez, Vicente Madrid-Marina
Human papillomavirus (HPV) is a DNA virus that infects epithelial cells and has been implicated in the development of cervical cancer. Few therapeutic strategies have been designed for the treatment of cervical intraepithelial neoplasia, a precursor of cervical cancer. In these early stages, the HPV E2 protein is the most important viral factor involved in viral gene expression and plays crucial roles during the vegetative viral cycle in epithelial cells. Papillomavirus E2 binds specifically to palindromic ACCN6GGT sequences, referred to as the E2 binding sites (E2BS), which are concentrated within the viral long control region, and which are responsible for regulation of the HPV protein's expression...
2016: Journal of Cancer
https://www.readbyqxmd.com/read/27877187/engineering-plant-immunity-using-crispr-cas9-to-generate-virus-resistance
#12
REVIEW
Syed Shan-E-Ali Zaidi, Manal Tashkandi, Shahid Mansoor, Magdy M Mahfouz
Plant viruses infect many economically important crops, including wheat, cotton, maize, cassava, and other vegetables. These viruses pose a serious threat to agriculture worldwide, as decreases in cropland area per capita may cause production to fall short of that required to feed the increasing world population. Under these circumstances, conventional strategies can fail to control rapidly evolving and emerging plant viruses. Genome-engineering strategies have recently emerged as promising tools to introduce desirable traits in many eukaryotic species, including plants...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27877161/an-enrichment-of-crispr-and-other-defense-related-features-in-marine-sponge-associated-microbial-metagenomes
#13
Hannes Horn, Beate M Slaby, Martin T Jahn, Kristina Bayer, Lucas Moitinho-Silva, Frank Förster, Usama R Abdelmohsen, Ute Hentschel
Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27870221/inductors-and-regulatory-properties-of-the-genomic-island-associated-fru2-metabolic-operon-of-streptococcus-agalactiae
#14
Kévin Patron, Philippe Gilot, Vanessa Rong, Aurélia Hiron, Laurent Mereghetti, Emilie Camiade
The fru2 metabolic operon of Streptococcus agalactiae encodes the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) enzyme II complex Fru2 (EIIB(Fru2) , EIIA(Fru2) , and EIIC(Fru2) ); Fru2 R, a transcriptional activator with PTS regulatory domains (PRDs); a D-allulose-6-phosphate 3-epimerase; a transaldolase; and a transketolase. We showed that the transcription of fru2 is induced during the stationary phase of growth in complex media and during incubation in human cerebrospinal or amniotic fluids...
November 21, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27857054/type-i-crispr-cas-targets-endogenous-genes-and-regulates-virulence-to-evade-mammalian-host-immunity
#15
Rongpeng Li, Lizhu Fang, Shirui Tan, Min Yu, Xuefeng Li, Sisi He, Yuquan Wei, Guoping Li, Jianxin Jiang, Min Wu
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems in bacteria and archaea provide adaptive immunity against invading foreign nucleic acids. Previous studies suggest that certain bacteria employ their Type II CRISPR-Cas systems to target their own genes, thus evading host immunity. However, whether other CRISPR-Cas systems have similar functions during bacterial invasion of host cells remains unknown. Here we identify a novel role for Type I CRISPR-Cas systems in evading host defenses in Pseudomonas aeruginosa strain UCBPP-PA14...
December 2016: Cell Research
https://www.readbyqxmd.com/read/27854339/two-novel-myoviruses-from-the-north-of-iraq-reveal-insights-into-clostridium-difficile-phage-diversity-and-biology
#16
Srwa J Rashid, Jakub Barylski, Katherine R Hargreaves, Andrew A Millard, Gurinder K Vinner, Martha R J Clokie
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq...
November 16, 2016: Viruses
https://www.readbyqxmd.com/read/27854212/non-random-distribution-of-dmd-deletion-breakpoints-and-implication-of-double-strand-breaks-repair-and-replication-error-repair-mechanisms
#17
Isabelle Marey, Rabah Ben Yaou, Nathalie Deburgrave, Aurélie Vasson, Juliette Nectoux, France Leturcq, Bruno Eymard, Pascal Laforet, Anthony Behin, Tanya Stojkovic, Michèle Mayer, Vincent Tiffreau, Isabelle Desguerre, François Constant Boyer, Aleksandra Nadaj-Pakleza, Xavier Ferrer, Karim Wahbi, Henri-Marc Becane, Mireille Claustres, Jamel Chelly, Mireille Cossee
BACKGROUND: Dystrophinopathies are mostly caused by copy number variations, especially deletions, in the dystrophin gene (DMD). Despite the large size of the gene, deletions do not occur randomly but mainly in two hot spots, the main one involving exons 45 to 55. The underlying mechanisms are complex and implicate two main mechanisms: Non-homologous end joining (NHEJ) and micro-homology mediated replication-dependent recombination (MMRDR). OBJECTIVE: Our goals were to assess the distribution of intronic breakpoints (BPs) in the genomic sequence of the main hot spot of deletions within DMD gene and to search for specific sequences at or near to BPs that might promote BP occurrence or be associated with DNA break repair...
May 27, 2016: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/27851729/in-vivo-genome-editing-via-crispr-cas9-mediated-homology-independent-targeted-integration
#18
Keiichiro Suzuki, Yuji Tsunekawa, Reyna Hernandez-Benitez, Jun Wu, Jie Zhu, Euiseok J Kim, Fumiyuki Hatanaka, Mako Yamamoto, Toshikazu Araoka, Zhe Li, Masakazu Kurita, Tomoaki Hishida, Mo Li, Emi Aizawa, Shicheng Guo, Song Chen, April Goebl, Rupa Devi Soligalla, Jing Qu, Tingshuai Jiang, Xin Fu, Maryam Jafari, Concepcion Rodriguez Esteban, W Travis Berggren, Jeronimo Lajara, Estrella Nuñez-Delicado, Pedro Guillen, Josep M Campistol, Fumio Matsuzaki, Guang-Hui Liu, Pierre Magistretti, Kun Zhang, Edward M Callaway, Kang Zhang, Juan Carlos Izpisua Belmonte
Targeted genome editing via engineered nucleases is an exciting area of biomedical research and holds potential for clinical applications. Despite rapid advances in the field, in vivo targeted transgene integration is still infeasible because current tools are inefficient, especially for non-dividing cells, which compose most adult tissues. This poses a barrier for uncovering fundamental biological principles and developing treatments for a broad range of genetic disorders. Based on clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) technology, here we devise a homology-independent targeted integration (HITI) strategy, which allows for robust DNA knock-in in both dividing and non-dividing cells in vitro and, more importantly, in vivo (for example, in neurons of postnatal mammals)...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27845770/crispr-cas9-system-as-a-versatile-tool-for-genome-engineering-in-human-cells
#19
REVIEW
Xuelian Wang, Xiumin Huang, Xiuli Fang, Youzhong Zhang, Wanpeng Wang
Targeted nucleases are influential instruments for intervening in genome revision with great accuracy. RNA-guided Cas9 nucleases produced from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have noticeably altered the means to modify the genomes of distinct organisms. They can be notably used to facilitate effective genome manipulation in eukaryotic cells by clearly detailing a 20-nt targeting sequence inside its directed RNA. We discuss the most recent advancements in the molecular basis of the type II CRISPR/Cas system and encapsulate applications and elements affecting its use in human cells...
November 15, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27845735/deletion-of-pr130-interrupts-cardiac-development-in-zebrafish
#20
Jie Yang, Zuhua Li, Xuedong Gan, Gang Zhai, Jiajia Gao, Chenling Xiong, Xueping Qiu, Xuebin Wang, Zhan Yin, Fang Zheng
Protein phosphatase 2 regulatory subunit B, alpha (PPP2R3A), a regulatory subunit of protein phosphatase 2A (PP2A), is a major serine/threonine phosphatase that regulates crucial function in development and growth. Previous research has implied that PPP2R3A was involved in heart failure, and PR130, the largest transcription of PPP2R3A, functioning in the calcium release of sarcoplasmic reticulum (SR), plays an important role in the excitation-contraction (EC) coupling. To obtain a better understanding of PR130 functions in myocardium and cardiac development, two pr130-deletion zebrafish lines were generated using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system...
November 11, 2016: International Journal of Molecular Sciences
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