Assembly of BioBrick standard biological parts using three antibiotic assembly

This is a revised personal version of the text of the final journal article available via DOI: 10.1016/B978-0-12-385120-8.00013-9An underlying goal of synthetic biology is to make the process of engineering biological systems easier and more reliable. In support of this goal, we developed BioBrick assembly standard 10 to enable the construction of systems from standardized genetic parts. The BioBrick standard underpins the distributed efforts by the synthetic biology research community to develop a collection of more than 6000 standard genetic parts available from the Registry of Standard Biological Parts. Here, we describe the three antibiotic assembly method for physical composition of BioBrick parts and provide step-by-step protocols. The method relies on a combination of positive and negative selection to eliminate time- and labor-intensive steps such as column cleanup and agarose gel purification of DNA during part assembly

A 530kb YAC contig tightly linked to the Friedreich ataxia locus contains five CpG clusters and a new highly polymorphic microsatellite

Friedreich ataxia (FA) is a severe autosomal recessive neurodegenerative disease. The defective gene has been previously assigned to chromosome 9q13-q21 by demonstration of tight linkage to the two independent loci D9S15 and D9S5. Linkage data indicate that FRDA is at less than 1 c M from both markers. Previous physical mapping has shown that probes defining D9S15 (MCT112) and D9S5 (26P) are less than 260kb apart and are surrounded by at least six CpG clusters within 450 kb, which might indicate the presence of “candidate” genes for FA. We isolated and characterized a 530 kb YAC (yeast artificial chromosome) contig that contains five of the CpG clusters. The YACs were used to search for new polymorphic markers needed to map FRDA precisely with respect to the cloned segment. In particular, we found a (CA) n microsatellite polymorphism, GS4, that detects 13 alleles with a PIC value of 0.83 and allows the definition of haplotypes extending over 310kb when used in combination with polymorphic markers at D9S5 and D9S15.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47632/1/439_2004_Article_BF00219179.pd

A yeast artificial chromosome contig encompassing the type 1 neurofibromatosis gene

The yeast artificial chromosome (YAC) system (Burke et al., 1987, Science 236: 806-812) allows the direct cloning of large regions of the genome. A YAC contig map of approximately 700 kb encompassing the region surrounding the type 1 neurofibromatosis (NF1) locus on 17q11.2 has been constructed. A single YAC containing the entire NF1 locus has been constructed by homologous recombination in yeast. In the process of contig construction a novel method of YAC end rescue has been developed by YAC circularization in yeast and plasmid rescue in bacteria. YACs containing homology to the NF1 region but mapping to another chromosome have also been discovered. Sequences of portions of the homologous locus indicate that this other locus is a nonprocessed pseudogene.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29972/1/0000334.pd

A genomic storm in critically injured humans

Critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes