Construction of DNA Barcode-Tagged Salmonella Strains.

This chapter provides a detailed protocol for construction of DNA barcode-tagged isogenic strains of Salmonella. The protocol is illustrated with S. Enteritidis in this chapter.

Preparation of Transposon Library and Tn-Seq Amplicon Library for Salmonella Typhimurium.

Transposon sequencing (Tn-seq) is a powerful tool for functional genomics of bacteria. Tn-seq combines transposon mutagenesis with next generation sequencing to assess genetic requirements at a genome-wide scale and identify essential and conditionally essential genes. An efficient application of this experimental approach relies on robust protocols for transposon mutagenesis system and Tn-seq amplicon library preparation method.

Prospective Development of Small Molecule Targets to Oncogenic Ras Proteins.

Abnormal expression or mutations in Ras proteins has been found in up to 30% of cancer cell types, making them excellent protein models to probe structure-function relationships of cell-signaling processes that mediate cell transformtion. Yet, there has been very little development of therapies to help tackle Ras-related diseased states. The development of small molecules to target Ras proteins to potentially inhibit abnormal Ras-stimulated cell signaling has been conceptualized and some progress has been made over the last 16 or so years.

Copper binding affinity of the C2B domain of synaptotagmin-1 and its potential role in the nonclassical secretion of acidic fibroblast growth factor.

Fibroblast growth factor 1 (FGF1) is a heparin-binding proangiogenic protein. FGF1 lacks the conventional N-terminal signal peptide required for secretion through the endoplasmic reticulum (ER)-Golgi secretory pathway. FGF1 is released through a Cu(2+)-mediated nonclassical secretion pathway.

A switch I mutant of Cdc42 exhibits less conformational freedom.

Cdc42 is a Ras-related small G-protein and functions as a molecular switch in signal transduction pathways linked with cell growth and differentiation. It is controlled by cycling between GTP-bound (active) and GDP-bound (inactive) forms. Nucleotide binding and hydrolysis are modulated by interactions with effectors and/or regulatory proteins.

Retinol-binding site in interphotoreceptor retinoid-binding protein (IRBP): a novel hydrophobic cavity.

Purpose: Interphotoreceptor retinoid-binding protein (IRBP) appears to target and protect retinoids during the visual cycle. X-ray crystallographic studies had noted a betabetaalpha-spiral fold shared with crotonases and C-terminal protein transferases. The shallow cleft formed by the fold was assumed to represent the retinol-binding site.

Role of arginine-163 and the 163REEK166 motif in the oligomerization of truncated alpha A-crystallins.

To gain insight into the mechanism by which Arg-163 influences oligomerization of alphaA-crystallin, we prepared a series of truncated alphaA-crystallins with or without mutation of the Arg-163 residue. Expression of the proteins was achieved in Escherichia coli BL21 (DE3) pLysS cells, and alphaA-crystallin was purified by size-exclusion chromatography. Molecular mass was determined by molecular sieve HPLC, chaperone activity was assayed with alcohol dehydrogenase as the target protein, and structural changes were ascertained by circular dichroism (CD) measurements.

Novel mutations in GJA3 associated with autosomal dominant congenital cataract in the Indian population.

Purpose: Connexin 46 (Cx46) is crucial in the maintenance of lens homeostasis and it is known to be expressed mainly in the terminally differentiated lens fiber cells. The present study aimed to identify the spectrum of mutations in Connexin 46 in the Indian population.

Methods: PCR based Single Stranded Conformational Polymorphism (SSCP) analysis was used to screen sixty probands with nonsyndromic congenital cataract for mutations in the Cx46 gene (GJA3), followed by direct sequencing of samples that showed an electrophoretic shift.