Faculty Opinions recommendation of Selection of chromosomal DNA libraries using a multiplex CRISPR system.

Author(s):  
Corey Nislow
2014 ◽  
Author(s):  
Owen W Ryan ◽  
Jeffrey M Skerker ◽  
Matthew J Maurer ◽  
Xin Li ◽  
Jordan C Tsai ◽  
...  

2014 ◽  
Author(s):  
Owen W. Ryan ◽  
Jeffrey M. Skerker ◽  
Matthew J. Maurer ◽  
Xin Li ◽  
Jordan C. Tsai ◽  
...  

AbstractThe directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into the Saccharomyces cerevisiae genome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over ten-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function.


eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Owen W Ryan ◽  
Jeffrey M Skerker ◽  
Matthew J Maurer ◽  
Xin Li ◽  
Jordan C Tsai ◽  
...  

The directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. We developed quantitative gene assembly and DNA library insertion into the Saccharomyces cerevisiae genome by optimizing an efficient single-step and marker-free genome editing system using CRISPR-Cas9. With this Multiplex CRISPR (CRISPRm) system, we selected an improved cellobiose utilization pathway in diploid yeast in a single round of mutagenesis and selection, which increased cellobiose fermentation rates by over 10-fold. Mutations recovered in the best cellodextrin transporters reveal synergy between substrate binding and transporter dynamics, and demonstrate the power of CRISPRm to accelerate selection experiments and discoveries of the molecular determinants that enhance biomolecule function.


Author(s):  
B. D. Young ◽  
M. Jeanpierre ◽  
M. H. Goyns ◽  
G. D. Stewart ◽  
T. Elliot ◽  
...  

BioTechniques ◽  
2008 ◽  
Vol 44 (3) ◽  
pp. 351-360 ◽  
Author(s):  
Weihua Pan ◽  
Ping Xin ◽  
Gary A. Clawson
Keyword(s):  

1998 ◽  
Vol 120 (2) ◽  
pp. 193-200 ◽  
Author(s):  
T. NETHERWOOD ◽  
M. BINNS ◽  
H. TOWNSEND ◽  
J. L. N. WOOD ◽  
J. A. MUMFORD ◽  
...  

During a survey of foal diarrhoea between 1991 and 1994, Clostridium perfringens was significantly associated with disease with 56% of cases infected [1]. The contribution of enterotoxigenic C. perfringens to this association, was assessed by use of the reverse passive latex agglutination test for enterotoxin (RPLA; Oxoid Unipath) and vero cell toxicity neutralized by antitoxin on stored faecal samples and sporulated faecal isolates of C. perfringens. Polymerase chain reaction (PCR1) based on the DNA sequence for the whole enterotoxin gene [2] yielded a fragment from an equine isolate of the anticipated size which, cloned into plasmid M13 phage, had a sequence essentially identical to the published sequence. Consequently, all faecal isolates were also tested by PCR1 and for a part of the enterotoxin gene (PCR2).Significant association with diarrhoea (controls not in contact with cases) was found with positive RPLA tests on faeces (OR=13, P=0·002) and isolates (OR=4·57, P=<0·0001), vero cell toxicity of isolates (OR=1·78, P=0·026), and PCR1 (OR=nd, P=0·029) but not PCR2 or vero cell toxicity of faeces. Significant association with diarrhoea was also found for isolates negative by RPLA (OR=3·91; CI 2·05–7·57; P<0·0001) or PCR1 (OR=4·81; CI 2·84–8·20; P<0·0001). Many of the isolates from RPLA positive faeces and verotoxic isolates were PCR negative and no evidence could be found for the presence of the enterotoxin gene in a random selection of RPLA positive/PCR negative isolates by gene probe on chromosomal DNA and PCR reaction product or vero cell toxicity neutralized by specific antiserum. Failure of the vero cell toxicity on faeces to be associated with diarrhoea or for cytotoxicity of cultures and RPLA on cultures to agree with the PCRs was believed to be related to the presence of other cytotoxins, the inherent cytotoxicity of equine faeces and to the poor specificity of the commercial antiserum used in the test.Enterotoxigenic C. perfringens could not account for the overall association of C. perfringens with foal diarrhoea because (a) cultures positive by PCR, RPLA or cytotoxicity were not significantly more common amongst isolates from cases than controls; and (b) the proportion of isolates from cases positive by PCR (PCR1 or PCR2) was too small at 9·7%.


2002 ◽  
Vol 1 (6) ◽  
pp. 895-905 ◽  
Author(s):  
Thomas D. Sullivan ◽  
Peggy J. Rooney ◽  
Bruce S. Klein

ABSTRACT The dimorphic fungi Blastomyces dermatitidis and Histoplasma capsulatum cause systemic mycoses in humans and other animals. Forward genetic approaches to generating and screening mutants for biologically important phenotypes have been underutilized for these pathogens. The plant-transforming bacterium Agrobacterium tumefaciens was tested to determine whether it could transform these fungi and if the fate of transforming DNA was suited for use as an insertional mutagen. Yeast cells from both fungi and germinating conidia from B. dermatitidis were transformed via A. tumefaciens by using hygromycin resistance for selection. Transformation frequencies up to 1 per 100 yeast cells were obtained at high effector-to-target ratios of 3,000:1. B. dermatitidis and H. capsulatum ura5 lines were complemented with transfer DNA vectors expressing URA5 at efficiencies 5 to 10 times greater than those obtained using hygromycin selection. Southern blot analyses indicated that in 80% of transformants the transferred DNA was integrated into chromosomal DNA at single, unique sites in the genome. Progeny of B. dermatitidis transformants unexpectedly showed that a single round of colony growth under hygromycin selection or visible selection of transformants by lacZ expression generated homokaryotic progeny from multinucleate yeast. Theoretical analysis of random organelle sorting suggests that the majority of B. dermatitidis cells would be homokaryons after the ca. 20 generations necessary for colony formation. Taken together, the results demonstrate that A. tumefaciens efficiently transfers DNA into B. dermatitidis and H. capsulatum and has the properties necessary for use as an insertional mutagen in these fungi.


RSC Advances ◽  
2018 ◽  
Vol 8 (34) ◽  
pp. 19067-19074 ◽  
Author(s):  
Deng-Kai Yang ◽  
Chia-Fu Chou ◽  
Lin-Chi Chen

This study demonstrates a library-based approach to obtain aptamers with different binding properties for flexible design of AMACR detection.


2019 ◽  
Vol 65 (6) ◽  
pp. 477-484 ◽  
Author(s):  
S.P. Radko ◽  
S.A. Lapa ◽  
A.V. Chudinov ◽  
S.A. Khmeleva ◽  
M.M. Mannanova ◽  
...  

Using random (combinatorial) DNA-libraries with various degrees of diversity, it was shown that their amplification by polymerase chain reaction in real time resulted in appearance of a maximum on amplification curves. The relative decrease of fluorescence after passing the maximum was directly proportional to the logarithm of the number of oligonucleotide sequence variants in the random DNA-library provided that this number was within in the interval from 1 to 104 and remained practically unaltered when the number of variants was in the interval from 105 to 108. The obtained dependence was used in the course of SELEX to evaluate changes in the diversity of random DNA-libraries from round to round in selection of DNA-aptamers to the recombinant SMAD4 protein. As a result, oligonucleotides containing sequences able to form a site of SMAD4-DNA interactions known as SBE (SMAD-binding element) have been selected thus indicating that the SMAD4-SBE interaction dominates the aptamer selection.


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