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François P Douillard, Diego Mora, Robyn T Eijlander, Michiel Wels, Willem M de Vos
Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials...
2018: PloS One
Alyson G Weidmann
CRISPR-based approaches to genetic engineering are progressing at a rapid pace and present exciting new avenues for science, medicine, and technology. Many of the most cutting-edge advances in genome engineering are encompassed in the Research Articles, Reviews, and Perspectives in this special issue, often with an eye toward future directions for the field. Yet, many questions remain at this new frontier. We asked over 100 CRISPR researchers, including our contributing authors, for their perspectives on some of the most pressing questions surrounding the future of genome engineering and the CRISPR-Cas platform, the challenges that lie ahead, and opportunities for chemists and chemical biologists to drive creative molecular solutions...
February 16, 2018: ACS Chemical Biology
Minmin Yen, Andrew Camilli
This review highlights recent findings on the evolutionary arms race between the causative agent of cholera Vibrio cholerae and virulent bacteriophages (phages) ICP1, ICP2, and ICP3 isolated from cholera patient stool samples. We discuss mechanisms of phage resistance such as a unique phage-inhibitory chromosomal island and mutations that affect phage receptor expression. We also discuss the molecular characterization of ICP1 and its unique CRISPR-Cas system, which it uses to combat the phage-inhibitory chromosomal island...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
Felipe Cava
In this monographic issue, we have the pleasure to present contributions from six of the leading laboratories at the forefront of Vibrio cholerae genetics, ecology and evolution, together with a brief tribute by Diego Romero to Doctor Jaime Ferrán y Clua, a pioneering Spanish bacteriologist who developed the first vaccine against this pathogen. V. cholerae is a free-living aquatic bacterium that interacts with and infects a variety of organisms. In humans it causes cholera, the deadly diarrhoea that was responsible for millions of deaths during seven pandemics since 1817, and still thousands every year...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
Chun-Qing Song, Wen Xue
No abstract text is available yet for this article.
February 14, 2018: Nature Reviews. Gastroenterology & Hepatology
Bridget N J Watson, Raymond H J Staals, Peter C Fineran
A powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immunity. Although the benefits of resisting phage infection are evident, this can come at a cost of inhibiting the acquisition of other beneficial genes through HGT...
February 13, 2018: MBio
Jiazhang Lian, Mohammad HamediRad, Huimin Zhao
Thanks to its ease of use, modularity, and scalability, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been increasingly used in the design and engineering of Saccharomyces cerevisiae, one of the most popular hosts for industrial biotechnology. This review summarizes the recent development of this disruptive technology for metabolic engineering applications, including CRISPR-mediated gene knock-out and knock-in as well as transcriptional activation and interference. More importantly, multi-functional CRISPR systems that combine both gain- and loss-of-function modulations for combinatorial metabolic engineering are highlighted...
February 13, 2018: Biotechnology Journal
Gokul Kesavan, Juliane Hammer, Stefan Hans, Michael Brand
New genome-editing approaches, such as the CRISPR/Cas system, have opened up great opportunities to insert or delete genes at targeted loci and have revolutionized genetics in model organisms like the zebrafish. The Cre-loxp recombination system is widely used to activate or inactivate genes with high spatial and temporal specificity. Using a CRISPR/Cas9-mediated knock-in strategy, we inserted a zebrafish codon-optimized CreER T2 transgene at the otx2 gene locus to generate a conditional Cre-driver line. We chose otx2 as it is a patterning gene of the anterior neural plate that is expressed during early development...
February 12, 2018: Cell and Tissue Research
Zubair Ahmed Ratan, Young-Jin Son, Mohammad Faisal Haidere, Bhuiyan Mohammad Mahtab Uddin, Md Abdullah Yusuf, Sojib Bin Zaman, Jong-Hoon Kim, Laila Anjuman Banu, Jae Youl Cho
Bacteria and archaea possess adaptive immunity against foreign genetic materials through clustered regularly interspaced short palindromic repeat (CRISPR) systems. The discovery of this intriguing bacterial system heralded a revolutionary change in the field of medical science. The CRISPR and CRISPR-associated protein 9 (Cas9) based molecular mechanism has been applied to genome editing. This CRISPR-Cas9 technique is now able to mediate precise genetic corrections or disruptions in in vitro and in vivo environments...
2018: Therapeutic Advances in Medical Oncology
Albert Jeltsch
Genome targeting of restriction enzymes and DNA methyltransferases has many important applications including genome and epigenome editing. 15-20 years ago, my group was involved in the development of approaches for programmable genome targeting, aiming to connect enzymes with an oligodeoxynucleotide (ODN), which could form a sequence-specific triple helix at the genomic target site. Importantly, the target site of such enzyme-ODN conjugate could be varied simply by altering the ODN sequence promising great applicative values...
2018: Frontiers in Genetics
Jong-Hoon Lee, Sojeong Heo, Do-Won Jeong
BACKGROUND: Our previous comparative genomic analysis of Staphylococcus equorum KS1039 with five S. equorum strains illuminated the genomic basis of its safety and salt tolerance. However, a comprehensive picture of the cellular components and metabolic pathways involved in the degradation of macromolecules and development of sensory properties has not been obtained for S. equorum. Therefore, in this study, we examined the general metabolism of S. equorum based on information obtained from published complete genome sequences of six S...
February 13, 2018: BMC Genomics
Huanhuan Zhu, Linjie Zhang, Jianmin Xu, Chunhua Zhu, Hui Zhao, Yongkang Zhu, Guoqiang Lv
The prevention and treatment efficiency of ethanol-induced gastric epithelial injury are not satisfied. We have previously shown that AMP-activated protein kinase (AMPK) activation exerts a pro-survival function in human gastric epithelial cells (GECs). miroRNA-451 ("miR-451")'s inhibitor, antagomiR-451, can activate AMPK signaling. In the present study, we show that forced-expression of antagomiR-451 via a lentiviral vector depleted miR-451, leading to AMPK activation in established GES-1 cells and primary human GECs...
February 9, 2018: Biochemical and Biophysical Research Communications
Tomeu Viver, Luis Orellana, Pedro González-Torres, Sara Díaz, Mercedes Urdiain, María Eugenia Farías, Vladimir Benes, Peter Kaempfer, Azadeh Shahinpei, Mohammad Ali Amoozegar, Rudolf Amann, Josefa Antón, Konstantinos T Konstantinidis, Ramon Rosselló-Móra
The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability...
January 31, 2018: Systematic and Applied Microbiology
Hafiz Ishfaq Ahmad, Muhammad Jamil Ahmad, Akhtar Rasool Asif, Muhammad Adnan, Muhammad Kashif Iqbal, Khalid Mehmood, Sayyed Aun Muhammad, Ali Akbar Bhuiyan, Abdelmotaleb Elokil, Xiaoyong Du, Changzhi Zhao, Xiangdong Liu, Shengsong Xie
Precise nucleic acid editing technologies have facilitated the research of cellular function and the development of novel therapeutics, especially the current programmable nucleases-based editing tools, such as the prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases (Cas). As CRISPR-based therapies are advancing toward human clinical trials, it is important to understand how natural genetic variation in the human population may affect the results of these trials and even patient safety...
February 11, 2018: Current Issues in Molecular Biology
Misha Klein, Behrouz Eslami-Mossallam, Dylan Gonzalez Arroyo, Martin Depken
Due to their specificity, efficiency, and ease of programming, CRISPR-associated nucleases are popular tools for genome editing. On the genomic scale, these nucleases still show considerable off-target activity though, posing a serious obstacle to the development of therapies. Off targeting is often minimized by choosing especially high-specificity guide sequences, based on algorithms that codify empirically determined off-targeting rules. A lack of mechanistic understanding of these rules has so far necessitated their ad hoc implementation, likely contributing to the limited precision of present algorithms...
February 6, 2018: Cell Reports
Min-Soo Kim, Jin-Woo Bae
Bacteriophages are central members and potential modulators of the gut microbiome; however, the ecological and evolutionary relationships of gut bacteria and phages are poorly understood. Here we investigated the abundance and diversity of lysogenic bacteria (lysogens) in the bacterial community of C57BL/6J mice by detecting integrated prophages in genomes reconstructed from the metagenome of commensal bacteria. For the activities of lysogens and prophages, we compared the prophage genomes with the metagenome of free phages...
February 7, 2018: ISME Journal
Ioannis Mougiakos, Elleke F Bosma, Joyshree Ganguly, John van der Oost, Richard van Kranenburg
High engineering efficiencies are required for industrial strain development. Due to its user-friendliness and its stringency, CRISPR-Cas-based technologies have strongly increased genome engineering efficiencies in bacteria. This has enabled more rapid metabolic engineering of both the model host Escherichia coli and non-model organisms like Clostridia, Bacilli, Streptomycetes and cyanobacteria, opening new possibilities to use these organisms as improved cell factories. The discovery of novel Cas9-like systems from diverse microbial environments will extend the repertoire of applications and broaden the range of organisms in which it can be used to create novel production hosts...
February 1, 2018: Current Opinion in Biotechnology
Dong-Yan Jin, Ben Berkhout
No abstract text is available yet for this article.
January 15, 2018: Virus Research
Juliane Behler, Kundan Sharma, Viktoria Reimann, Annegret Wilde, Henning Urlaub, Wolfgang R Hess
Specialized RNA endonucleases for the maturation of clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs) are critical in CRISPR-CRISPR-associated protein (Cas) defence mechanisms. The Cas6 and Cas5d enzymes are the RNA endonucleases in many class 1 CRISPR-Cas systems. In some class 2 systems, maturation and effector functions are combined within a single enzyme or maturation proceeds through the combined actions of RNase III and trans-activating CRISPR RNAs (tracrRNAs). Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp...
February 5, 2018: Nature Microbiology
Jasper Edgar Neggers, Bert Kwanten, Tim Dierckx, Hiroki Noguchi, Arnout Voet, Lotte Bral, Kristien Minner, Bob Massant, Nicolas Kint, Michel Delforge, Thomas Vercruysse, Erkan Baloglu, William Senapedis, Maarten Jacquemyn, Dirk Daelemans
Unraveling the mechanism of action and molecular target of small molecules remains a major challenge in drug discovery. While many cancer drugs target genetic vulnerabilities, loss-of-function screens fail to identify essential genes in drug mechanism of action. Here, we report CRISPRres, a CRISPR-Cas-based genetic screening approach to rapidly derive and identify drug resistance mutations in essential genes. It exploits the local genetic variation created by CRISPR-Cas-induced non-homologous end-joining (NHEJ) repair to generate a wide variety of functional in-frame mutations...
February 5, 2018: Nature Communications
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