scholarly journals A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8491 ◽  
Author(s):  
Xiaoli Liu ◽  
Xiujuan Zhou ◽  
Kang Li ◽  
Dehong Wang ◽  
Yuanhao Ding ◽  
...  
Keyword(s):  
Genome Editing ◽  
Genetic Basis ◽  
Restriction Enzymes ◽  
Expression Cassette ◽  
Destination Vector ◽  
Dna Ligation ◽  
Global View ◽  
Pcr Product ◽  
One Step ◽  
Set Up

Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing.

scholarly journals A CRISPR/Cas9-based method and primer design tool for seamless genome editing in fission yeast

2017 ◽  
Vol 1 ◽  
pp. 19 ◽  
Author(s):  
María Rodríguez-López ◽  
Cristina Cotobal ◽  
Oscar Fernández-Sánchez ◽  
Natalia Borbarán Bravo ◽  
Risky Oktriani ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Genome Editing ◽  
Point Mutations ◽  
Restriction Enzymes ◽  
Design Tool ◽  
Selection Marker ◽  
Guide Rna ◽  
Non Coding Rna ◽  
Pcr Product ◽  
Genomic Regions

In the fission yeast Schizosaccharomyces pombe the prevailing approach for gene manipulations is based on homologous recombination of a PCR product that contains genomic target sequences and a selectable marker. The CRISPR/Cas9 system has recently been implemented in fission yeast, which allows for seamless genome editing without integration of a selection marker or leaving any other genomic ‘scars’. The published method involves manual design of the single guide RNA (sgRNA), and digestion of a large plasmid with a problematic restriction enzyme to clone the sgRNA. To increase the efficiency of this approach, we have established and optimized a PCR-based system to clone the sgRNA without restriction enzymes into a plasmid with a dominant natMX6 (nourseothricin) selection marker. We also provide a web-tool, CRISPR4P, to support the design of the sgRNAs and the primers required for the entire process of seamless DNA deletion. Moreover, we report the preparation of G1-synchronized and cryopreserved S. pombe cells, which greatly increases the efficiency and speed for transformations, and may also facilitate standard gene manipulations. Applying this optimized CRISPR/Cas9-based approach, we have successfully deleted over 80 different non-coding RNA genes, which are generally lowly expressed, and have inserted 7 point mutations in 4 different genomic regions.

scholarly journals A CRISPR/Cas9-based method and primer design tool for seamless genome editing in fission yeast

2016 ◽  
Vol 1 ◽  
pp. 19 ◽  
Author(s):  
María Rodríguez-López ◽  
Cristina Cotobal ◽  
Oscar Fernández-Sánchez ◽  
Natalia Borbarán Bravo ◽  
Risky Oktriani ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Genome Editing ◽  
Point Mutations ◽  
Restriction Enzymes ◽  
Design Tool ◽  
Selection Marker ◽  
Guide Rna ◽  
Non Coding Rna ◽  
Pcr Product ◽  
Genomic Regions

In the fission yeast Schizosaccharomyces pombe the prevailing approach for gene manipulations is based on homologous recombination of a PCR product that contains genomic target sequences and a selectable marker. The CRISPR/Cas9 system has recently been implemented in fission yeast, which allows for seamless genome editing without integration of a selection marker or leaving any other genomic ‘scars’. The published method involves manual design of the single guide RNA (sgRNA), and digestion of a large plasmid with a problematic restriction enzyme to clone the sgRNA. To increase the efficiency of this approach, we have established and optimized a PCR-based system to clone the sgRNA without restriction enzymes into a plasmid with a dominant natMX6 (nourseothricin) selection marker. We also provide a web-tool, CRISPR4P, to support the design of the sgRNAs and the primers required for the entire process of seamless DNA deletion. Moreover, we report the preparation of G1-synchronized and cryopreserved S. pombe cells, which greatly increases the efficiency and speed for transformations, and may also facilitate standard gene manipulations. Applying this optimized CRISPR/Cas9-based approach, we have successfully deleted over 80 different non-coding RNA genes, which are generally lowly expressed, and have inserted 7 point mutations in 4 different genomic regions.

scholarly journals A CRISPR/Cas9-based method and primer design tool for seamless genome editing in fission yeast

2017 ◽  
Vol 1 ◽  
pp. 19 ◽  
Author(s):  
María Rodríguez-López ◽  
Cristina Cotobal ◽  
Oscar Fernández-Sánchez ◽  
Natalia Borbarán Bravo ◽  
Risky Oktriani ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Genome Editing ◽  
Point Mutations ◽  
Restriction Enzymes ◽  
Design Tool ◽  
Selection Marker ◽  
Guide Rna ◽  
Non Coding Rna ◽  
Pcr Product ◽  
Genomic Regions

In the fission yeast Schizosaccharomyces pombe the prevailing approach for gene manipulations is based on homologous recombination of a PCR product that contains genomic target sequences and a selectable marker. The CRISPR/Cas9 system has recently been implemented in fission yeast, which allows for seamless genome editing without integration of a selection marker or leaving any other genomic ‘scars’. The published method involves manual design of the single guide RNA (sgRNA), and digestion of a large plasmid with a problematic restriction enzyme to clone the sgRNA. To increase the efficiency of this approach, we have established and optimized a PCR-based system to clone the sgRNA without restriction enzymes into a plasmid with a dominant natMX6 (nourseothricin) selection marker. We also provide a web-tool, CRISPR4P, to support the design of the sgRNAs and the primers required for the entire process of seamless DNA deletion. Moreover, we report the preparation of G1-synchronized and cryopreserved S. pombe cells, which greatly increases the efficiency and speed for transformations, and may also facilitate standard gene manipulations. Applying this optimized CRISPR/Cas9-based approach, we have successfully deleted over 80 different non-coding RNA genes, which are generally lowly expressed, and have inserted 7 point mutations in 4 different genomic regions.

scholarly journals Development of the Multiple Gene Knockout System with One-Step PCR in Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

Archaea ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Shoji Suzuki ◽  
Norio Kurosawa
Keyword(s):  
Gene Knockout ◽  
Arginine Decarboxylase ◽  
Sulfolobus Acidocaldarius ◽  
Dna Photolyase ◽  
Genetic Studies ◽  
Multiple Gene ◽  
Plasmid Construction ◽  
Pcr Product ◽  
Optimized Protocol ◽  
One Step

Multiple gene knockout systems developed in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius are powerful genetic tools. However, plasmid construction typically requires several steps. Alternatively, PCR tailing for high-throughput gene disruption was also developed in S. acidocaldarius, but repeated gene knockout based on PCR tailing has been limited due to lack of a genetic marker system. In this study, we demonstrated efficient homologous recombination frequency (2.8 × 104 ± 6.9 × 103 colonies/μg DNA) by optimizing the transformation conditions. This optimized protocol allowed to develop reliable gene knockout via double crossover using short homologous arms and to establish the multiple gene knockout system with one-step PCR (MONSTER). In the MONSTER, a multiple gene knockout cassette was simply and rapidly constructed by one-step PCR without plasmid construction, and the PCR product can be immediately used for target gene deletion. As an example of the applications of this strategy, we successfully made a DNA photolyase- (phr-) and arginine decarboxylase- (argD-) deficient strain of S. acidocaldarius. In addition, an agmatine selection system consisting of an agmatine-auxotrophic strain and argD marker was also established. The MONSTER provides an alternative strategy that enables the very simple construction of multiple gene knockout cassettes for genetic studies in S. acidocaldarius.

scholarly journals Molecular Typing ofNeisseria gonorrhoeaeIsolates by Opa-Typing and Ribotyping in New Delhi, India

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
Author(s):  
Pejvak Khaki ◽  
Preena Bhalla ◽  
Ahmad Mir Fayaz ◽  
Sohiela Moradi Bidhendi ◽  
Majid Esmailzadeh ◽  
...  
Keyword(s):  
Molecular Typing ◽  
Preventive Measures ◽  
Restriction Enzymes ◽  
New Delhi ◽  
Pcr Product ◽  
Sexual Contacts ◽  
High Level ◽  
Epidemiological Characteristics ◽  
Epidemiological Characterization

Control and preventive measures for gonococcal infections are based on precise epidemiological characteristics ofN. gonorrhoeaeisolates. In the present study the potential utility of opa-typing and ribotyping for molecular epidemiological study of consecutive gonococcal strains was determined. Sixty gonococcal isolates were subjected to ribotyping with two restriction enzymes,AvaII andHincII, and opa-typing withTaqI andHpaII for epidemiological characterization of gonococcal population. Ribotyping withAvaII yielded 6 ribotype patterns while twelve RFLP patterns were observed withHincII. Opa-typing of the 60 isolates revealed a total 54 opa-types, which 48 were unique and 6 formed clusters. Fifty-two opa-types were observed withTaqI-digested PCR product while opa-typing withHpaII demonstrated 54 opa-types. The opa-types from isolates that were epidemiologically unrelated were distinct, whereas those from the sexual contacts were identical. The results showed that opa-typing is highly useful for characterizing gonococcal strains from sexual contacts and has more discriminatory than ribotyping that could differentiate between gonococci of the same ribotype. The technique even with a single restriction enzyme has a high level of discrimination (99.9%) between epidemiologically unrelated isolates. In conclusion, the molecular methods such as opa-typing and ribotyping can be used for epidemiological characterization of gonococcal strains.

scholarly journals Impact of a Novel W2027L Mutation and Non-Target Site Resistance on Acetyl-CoA Carboxylase-Inhibiting Herbicides in a French Lolium multiflorum Population

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1838
Author(s):  
Shiv Shankhar Kaundun ◽  
Joe Downes ◽  
Lucy Victoria Jackson ◽  
Sarah-Jane Hutchings ◽  
Eddie Mcindoe
Keyword(s):  
Lolium Multiflorum ◽  
Restriction Enzymes ◽  
Target Site ◽  
Cereal Crops ◽  
Acetyl Coa Carboxylase ◽  
Wild Type ◽  
Resistance Mutations ◽  
Acetyl Coa ◽  
Pcr Product ◽  
Target Site Resistance

Herbicides that inhibit acetyl-CoA carboxylase (ACCase) are among the few remaining options for the post-emergence control of Lolium species in small grain cereal crops. Here, we determined the mechanism of resistance to ACCase herbicides in a Lolium multiflorum population (HGR) from France. A combined biological and molecular approach detected a novel W2027L ACCase mutation that affects aryloxyphenoxypropionate (FOP) but not cyclohexanedione (DIM) or phenylpyraxoline (DEN) subclasses of ACCase herbicides. Both the wild-type tryptophan and mutant leucine 2027-ACCase alleles could be positively detected in a single DNA-based-derived polymorphic amplified cleaved sequence (dPACS) assay that contained the targeted PCR product and a cocktail of two discriminating restriction enzymes. Additionally, we identified three well-characterised I1781L, I2041T, and D2078G ACCase target site resistance mutations as well as non-target site resistance in HGR. The non-target site component endowed high levels of resistance to FOP herbicides whilst partially impacting on the efficacy of pinoxaden and cycloxydim. This study adequately assessed the contribution of the W2027L mutation and non-target site mechanism in conferring resistance to ACCase herbicides in HGR. It also highlights the versatility and robustness of the dPACS method to simultaneously identify different resistance-causing alleles at a single ACCase codon.

Two in one: bifunctional derivatives of trolox acting as antimalarial and antioxidant agents

2020 ◽  
Vol 12 (20) ◽  
pp. 1845-1854
Author(s):  
Florence Souard ◽  
Edwige Nicolle ◽  
Delphine Cressend ◽  
Alexis Valentin ◽  
Ahcène Boumendjel
Keyword(s):  
Antioxidant Activity ◽  
Ascorbic Acid ◽  
In Vivo Studies ◽  
Chemical Libraries ◽  
Falciparum Strain ◽  
Antioxidant Agents ◽  
One Step ◽  
Set Up ◽  
Derivatives Of

Background: The aim of the present work was to set-up compounds that are able to act simultaneously as antimalarial and antioxidants. Trolox, a known antioxidant was chosen as a core structure to ensure the antioxidant activity and contribute to antiplasmodial effect. Results: Ten compounds were prepared in one step and evaluated on chloroquino-sensitive (3D7) and chloroquino-resistant (FcB1) strains of Plasmodium falciparum. The most active compound (3d) shows antiplasmodial activity in the range of chloroquine against chloroquino-sensitive and chloroquino-resistant P. falciparum strain. The antioxidant activity of (3d) was conducted through four tests and was found to be more potent than trolox itself and L-ascorbic acid. Conclusion: Compound (3d) can be considered as an excellent lead molecule for further in vivo studies. This study paves the way for building large chemical libraries to be investigated in the field of malaria.

scholarly journals Improving the Activity of Fe/C/N ORR Electrocatalyst Using Double Ammonia Promoted CO2 Laser Pyrolysis

2020 ◽  
Vol 6 (4) ◽  
pp. 63
Author(s):  
Henri Perez ◽  
Mathieu Frégnaux ◽  
Emeline Charon ◽  
Arnaud Etcheberry ◽  
Olivier Sublemontier
Keyword(s):  
Co2 Laser ◽  
Large Scale ◽  
Laser Energy ◽  
Reduction Reaction ◽  
Laser Pyrolysis ◽  
Highly Active ◽  
One Step ◽  
Orr Activity ◽  
Set Up ◽  
The One

Recently, we reported the use of CO2 laser pyrolysis for the synthesis of promising Fe/C/N electrocatalysts for Oxygen Reduction Reaction (ORR) in fuel cells. The set-up used single laser pyrolysis of an aerosolized solution of iron acetylacetonate in toluene with ammonia, both as laser energy transfer agent and nitrogen source. In the present paper, we investigate the effect of a second ammonia promoted CO2 laser pyrolysis on the feature and ORR activity of Fe/C/N electrocatalysts. Indeed, compared to single pyrolysis, the second ammonia promoted CO2 laser pyrolysis could be an interesting way to synthesize in one-step performing ORR electrocatalysts on a large scale. For this comparison, a two-stage reactor was built, allowing both single ammonia-induced CO2 laser pyrolysis as reported previously or double ammonia-induced CO2 laser pyrolysis. In the latter configuration, the catalyst nanopowder flow is formed at the first stage of the reactor, then mixed with a second ammonia flow and allowed to cross a second CO2 laser beam, thus undergoing a second ammonia-induced CO2 laser pyrolysis before being collected on filters. It is found that the second ammonia-induced CO2 laser pyrolysis significantly improves the ORR performances of the materials prepared by single CO2 laser pyrolysis. The effect is demonstrated for three different catalysts for which the onset potentials for the ORR from single-stage to double-stage configuration increase from 625 mV to 845 mV, 790 mV to 860 mV, and 800 mV to 885 mV, respectively. The selectivity of the ORR was determined at 600 mV/SHE and lie between 3.41 and 3.72. These promising performances suggesting potentialities for the one-step formation of highly active Fe/C/N ORR electrocatalysts are discussed, based on results of surface analysis by XPS, specific surface area measurements, and Raman spectroscopy.

Sign in / Sign up

Export Citation Format

Share Document