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https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#1
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29771955/crispr-cas9-mediated-high-efficiency-knockout-of-the-eye-color-gene-vermillion-in-helicoverpa-zea-boddie
#2
Omaththage P Perera, Nathan S Little, Calvin A Pierce
Among various genome editing tools available for functional genomic studies, reagents based on clustered regularly interspersed palindromic repeats (CRISPR) have gained popularity due to ease and versatility. CRISPR reagents consist of ribonucleoprotein (RNP) complexes formed by combining guide RNA (gRNA) that target specific genomics regions and a CRISPR associated nuclease (Cas). The gRNA targeting specific gene sequences may be delivered as a plasmid construct that needs to be transcribed or as a synthetic RNA...
2018: PloS One
https://www.readbyqxmd.com/read/29766738/the-role-of-gene-editing-in-neurodegenerative-diseases
#3
Hueng-Chuen Fan, Ching-Shiang Chi, Yih-Jing Lee, Jeng-Dau Tsai, Shinn-Zong Lin, Horng-Jyh Harn
Neurodegenerative diseases (NDs), at least including Alzheimer's, Huntington's, and Parkinson's diseases, have become the most dreaded maladies because there are no precise diagnostic tools or definite treatments for these debilitating diseases. The increased prevalence and a substantial impact on the social-economic and medical care of NDs propel governments to develop policies to counteract the impact. Although the etiologies of NDs are still unknown, growing evidence suggests that genetic, cellular, and circuit alternations may cause the generation of abnormal misfolded proteins, which uncontrolledly accumulate to damage and eventually overwhelm the protein-disposal mechanisms of these neurons, leading to a common pathological feature of NDs...
January 1, 2018: Cell Transplantation
https://www.readbyqxmd.com/read/29755603/bacterial-crispr-regions-general-features-and-their-potential-for-epidemiological-molecular-typing-studies
#4
REVIEW
Zahra Karimi, Ali Ahmadi, Ali Najafi, Reza Ranjbar
Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements...
2018: Open Microbiology Journal
https://www.readbyqxmd.com/read/29754234/rapid-control-of-genome-editing-in-human-cells-by-chemical-inducible-crispr-cas-systems
#5
Kaiwen Ivy Liu, Muhammad Nadzim Bin Ramli, Norfala-Aliah Binte Sutrisnoh, Meng How Tan
Genome editing using programmable DNA endonucleases enables the engineering of eukaryotic cells and living organisms with desirable properties or traits. Among the various molecular scissors that have been developed to date, the most versatile and easy-to-use family of nucleases derives from CRISPR-Cas, which exists naturally as an adaptive immune system in bacteria. Recent advances in the CRISPR-Cas technology have expanded our ability to manipulate complex genomes for myriad biomedical and biotechnological applications...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29754224/transformation-of-an-exotic-yeast-species-into-a-platform-organism-a-case-study-for-engineering-glycolipid-production-in-the-yeast-starmerella-bombicola
#6
Sofie Lodens, Marilyn De Graeve, Sophie L K W Roelants, Sofie L De Maeseneire, Wim Soetaert
In this chapter, a step-by-step approach on how to transform non-conventional yeasts or fungi into platform organisms is described. The non-conventional glycolipid producing yeast Starmerella bombicola (and in some cases also Pseudohyphozyma bogoriensis) is used as a case study. And more specifically how to engineer it toward production of new-to-nature glycolipids like bola sophorolipids. When starting genetic engineering efforts for non-lab strains, one should start at the very basis: identifying selection markers and possibly developing auxotrophic strains...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29752075/towards-a-more-predictable-plant-breeding-pipeline-with-crispr-cas-induced-allelic-series-to-optimize-quantitative-and-qualitative-traits
#7
REVIEW
Armin Scheben, David Edwards
The rate of crop improvement must increase to meet rising global demand for food. Crop breeding pipelines can be hampered by the imprecision and multi-generational timeframe of methods such as intercrossing and stochastic mutagenesis used to generate variation. Genome editing can generate targeted allelic series of trait-related genes and regulatory elements, creating a series of variable phenotypes for breeding within a single generation. Disrupting genic and regulatory regions is particularly effective for engineering quantitative traits...
May 8, 2018: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29748239/shooting-the-messenger-rna-targeting-crispr-cas-systems
#8
Yifan Zhu, Sanne E Klompe, Marnix Vlot, John van der Oost, Raymond H J Staals
Since the discovery of CRISPR-Cas immune systems astonishing progress has been made on revealing their mechanistic foundations. Due to the immense potential as genome engineering tools, research has mainly focused on a subset of Cas nucleases that target DNA. In addition, however, distinct types of RNA-targeting CRISPR-Cas systems have been identified. The focus of this review will be on the interference mechanisms of the RNA targeting type III and type VI CRISPR-Cas systems, their biological relevance and their potential for applications...
May 10, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29743593/sox2-is-required-for-tumor-development-and-cancer-cell-proliferation-in-osteosarcoma
#9
Giulia Maurizi, Narendra Verma, Abhilash Gadi, Alka Mansukhani, Claudio Basilico
The stem cell transcription factor Sox2 is highly expressed in many cancers where it is thought to mark cancer stem cells (CSCs). In osteosarcomas, the most common bone malignancy, high Sox2 expression marks and maintains a fraction of tumor-initiating cells that show all the properties of CSC. Knockdown of Sox2 expression abolishes tumorigenicity and suppresses the CSC phenotype. Here we show that, in a mouse model of osteosarcoma, osteoblast-specific Sox2 conditional knockout (CKO) causes a drastic reduction in the frequency and onset of tumors...
May 10, 2018: Oncogene
https://www.readbyqxmd.com/read/29740742/prospects-for-engineering-dynamic-crispr-cas-transcriptional-circuits-to-improve-bioproduction
#10
REVIEW
Jason Fontana, William E Voje, Jesse G Zalatan, James M Carothers
Dynamic control of gene expression is emerging as an important strategy for controlling flux in metabolic pathways and improving bioproduction of valuable compounds. Integrating dynamic genetic control tools with CRISPR-Cas transcriptional regulation could significantly improve our ability to fine-tune the expression of multiple endogenous and heterologous genes according to the state of the cell. In this mini-review, we combine an analysis of recent literature with examples from our own work to discuss the prospects and challenges of developing dynamically regulated CRISPR-Cas transcriptional control systems for applications in synthetic biology and metabolic engineering...
May 8, 2018: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29732484/crispr-cas9-the-powerful-new-genome-editing-tool-for-putative-therapeutics-in-obesity
#11
REVIEW
María José Franco-Tormo, Mireille Salas-Crisostomo, Nuno Barbosa Rocha, Henning Budde, Sérgio Machado, Eric Murillo-Rodríguez
The molecular technology known as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is revolutionizing the field of medical research and deepening our understanding of numerous biological processes. The attraction of CRISPR/Cas9 lies in its ability to efficiently edit DNA or modulate gene expression in living eukaryotic cells and organisms, a technology that was once considered either too expensive or scientifically risky. CRISPR/Cas9 has been successfully applied in agriculture to develop the next generation of disease-resistant plants...
May 7, 2018: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/29729377/toolboxes-for-cyanobacteria-recent-advances-and-future-direction
#12
REVIEW
Tao Sun, Shubin Li, Xinyu Song, Jinjin Diao, Lei Chen, Weiwen Zhang
Photosynthetic cyanobacteria are important primary producers and model organisms for studying photosynthesis and elements cycling on earth. Due to the ability to absorb sunlight and utilize carbon dioxide, cyanobacteria have also been proposed as renewable chassis for carbon-neutral "microbial cell factories". Recent progresses on cyanobacterial synthetic biology have led to the successful production of more than two dozen of fuels and fine chemicals directly from CO2 , demonstrating their potential for scale-up application in the future...
May 2, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29717930/myoediting-toward-prevention-of-muscular-dystrophy-by-therapeutic-genome-editing
#13
Yu Zhang, Chengzu Long, Rhonda Bassel-Duby, Eric N Olson
Muscular dystrophies represent a large group of genetic disorders that significantly impair quality of life and often progress to premature death. There is no effective treatment for these debilitating diseases. Most therapies, developed to date, focus on alleviating the symptoms or targeting the secondary effects, while the underlying gene mutation is still present in the human genome. The discovery and application of programmable nucleases for site-specific DNA double-stranded breaks provides a powerful tool for precise genome engineering...
July 1, 2018: Physiological Reviews
https://www.readbyqxmd.com/read/29717009/an-attenuated-crispr-cas-system-in-enterococcus-faecalis-permits-dna-acquisition
#14
Karthik Hullahalli, Marinelle Rodrigues, Uyen Thy Nguyen, Kelli Palmer
Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis , since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E...
May 1, 2018: MBio
https://www.readbyqxmd.com/read/29710373/transforming-plant-biology-and-breeding-with-crispr-cas9-cas12-and-cas13
#15
REVIEW
Patrick Schindele, Felix Wolter, Holger Puchta
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone non-homologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change of plant genomes via homologous recombination have recently been developed...
April 30, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29706536/repetitive-dna-reeling-by-the-cascade-cas3-complex-in-nucleotide-unwinding-steps
#16
Luuk Loeff, Stan J J Brouns, Chirlmin Joo
CRISPR-Cas provides RNA-guided adaptive immunity against invading genetic elements. Interference in type I systems relies on the RNA-guided Cascade complex for target DNA recognition and the Cas3 helicase/nuclease protein for target degradation. Even though the biochemistry of CRISPR interference has been largely covered, the biophysics of DNA unwinding and coupling of the helicase and nuclease domains of Cas3 remains elusive. Here, we employed single-molecule Förster resonance energy transfer (FRET) to probe the helicase activity with high spatiotemporal resolution...
April 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29704747/non-viral-delivery-systems-for-crispr-cas9-based-genome-editing-challenges-and-opportunities
#17
REVIEW
Ling Li, Shuo Hu, Xiaoyuan Chen
In recent years, CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) genome editing systems have become one of the most robust platforms in basic biomedical research and therapeutic applications. To date, efficient in vivo delivery of the CRISPR/Cas9 system to the targeted cells remains a challenge. Although viral vectors have been widely used in the delivery of the CRISPR/Cas9 system in vitro and in vivo, their fundamental shortcomings, such as the risk of carcinogenesis, limited insertion size, immune responses and difficulty in large-scale production, severely limit their further applications...
April 18, 2018: Biomaterials
https://www.readbyqxmd.com/read/29702275/recent-advances-in-metabolic-engineering-of-saccharomyces-cerevisiae-new-tools-and-their-applications
#18
REVIEW
Jiazhang Lian, Shekhar Mishra, Huimin Zhao
Metabolic engineering aims to develop efficient cell factories by rewiring cellular metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae has been extensively engineered to produce a wide variety of products at high levels from various feedstocks. In this review, we summarize the recent development of metabolic engineering approaches to modulate yeast metabolism with representative examples. Particularly, we highlight new tools for biosynthetic pathway optimization (i.e. combinatorial transcriptional engineering and dynamic metabolic flux control) and genome engineering (i...
April 24, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29693372/biosynthesis-of-the-15-membered-ring-depsipeptide-neoantimycin
#19
Will Skyrud, Joyce Liu, Divya Thankachan, Maria Cabrera, Ryan F Seipke, Wenjun Zhang
Antimycins are a family of natural products possessing outstanding biological activities and unique structures, which have intrigued chemists for over a half century. Of particular interest are the ring-expanded antimycins that show promising anti-cancer potential and whose biosynthesis remains uncharacterized. Specifically, neoantimycin and its analogs have been shown to be effective regulators of the oncogenic proteins GRP78/BiP and K-Ras. The neoantimycin structural skeleton is built on a 15-membered tetralactone ring containing one methyl, one hydroxy, one benzyl and three alkylmoieties, as well as an amide linkage to a conserved 3-formamidosalicylic acid moiety...
April 25, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29690921/pathogen-detection-in-the-crispr-cas-era
#20
Dipali G Sashital
CRISPR-Cas systems have provided revolutionary tools for genome editing. The discovery of Cas proteins with alternative activities has now enabled sensitive and robust tools for detecting nucleic acids. Recent reports harnessing these new CRISPR-Cas technologies display their potential for providing low-cost and practical diagnostic tools for pathogen and disease detection.
April 24, 2018: Genome Medicine
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