Biomedical subjects

Yair Benita

Publications and source records attributed to Yair Benita.

3 recordsLinked to original sources

PubMed2006

Analysis of high throughput protein expression in Escherichia coli.

The ability to efficiently produce hundreds of proteins in parallel is the most basic requirement of many aspects of proteomics. Overcoming the technical and financial barriers associated with high throughput protein production is essential for the development of an experimental platform to query and browse the protein content of a cell (e.g. protein and antibody arrays). Proteins are inherently different one from another in their physicochemical properties; therefore, no single protocol can be expected to successfully express most of the proteins. Instead of optimizing a protocol to express a specific protein, we used sequence analysis tools to estimate the probability of a specific protein to be expressed successfully using a given protocol, thereby avoiding a priori proteins with a low success probability. A set of 547 proteins, to be used for antibody production and selection, was expressed in Escherichia coli using a high throughput protein production pipeline. Protein properties derived from sequence alone were correlated to successful expression, and general guidelines are given to increase the efficiency of similar pipelines. A second set of 68 proteins was expressed to investigate the link between successful protein expression and inclusion body formation. More proteins were expressed in inclusion bodies; however, the formation of inclusion bodies was not a requirement for successful expression.

Cloning, Molecular↗

PubMed2005

Multi-antigen immunization using IgG binding domain ZZ as carrier.

This article describes a method in which multiple vaccine candidates can be tested in parallel for their immunogenicity. Antigens derived from the genome sequence of Neisseria meningitidis group B strain MC58 were cloned and expressed as recombinant proteins fused to the IgG-binding domain ZZ or to a His-tag. Immunization of mice with a mixture of 22 ZZ-fusion antigens applied with the adjuvant QuilA, induced an enhanced immune response as compared to the same antigen mixture without QuilA or a mixture containing the corresponding His-tagged antigens with QuilA. The enhanced immune response of the ZZ-fusion antigens/QuilA preparation was apparent from 1) the higher number of antigens in the mixture that elicited an antibody response and 2) the much lower antigen dose needed to get this response. Our approach using ZZ-fusion antigens/QuilA mixtures may serve as a high throughput discovery tool for new vaccine candidates.

Adjuvants, Immunologic↗

PubMed2003

Regionalized GC content of template DNA as a predictor of PCR success.

A set of 1438 human exons was subjected to nested PCR. The initial success rate using a standard PCR protocol required for ligation-independent cloning was 83.4%. Logistic regression analysis was conducted on 27 primer- and template-related characteristics, of which most could be ignored apart from those related to the GC content of the template. Overall GC content of the template was a good predictor for PCR success; however, specificity and sensitivity values for predicted outcome were improved to 84.3 and 94.8%, respectively, when regionalized GC content was employed. This represented a significant improvement in predictability with respect to GC content alone (P < 0.001; chi(2)) and is expected to increase in relative sensitivity as template size increases. Regionalized GC was calculated with respect to a threshold of 61% GC content and a sliding window of 21 bp across the target sequence. Fine-tuning of PCR conditions is not practicable for all target sequences whenever a large number of genes of different lengths and GC content are to be amplified in parallel, particularly if total open reading frame or domain coverage is essential for recombinant protein synthesis. Thus, the present method is proposed as a means of grouping subsets of genes possessing potentially difficult target sequences so that PCR conditions can be optimized separately in order to obtain improved outcomes.

Analysis of Variance↗