SRI International

About: SRI International is a nonprofit organization based out in Menlo Park, California, United States. It is known for research contribution in the topics: Ionosphere & Laser. The organization has 7222 authors who have published 13102 publications receiving 660724 citations. The organization is also known as: Stanford Research Institute & SRI.

Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media

Abstract: Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation.

Formal Methods and their Role in the Certification of Critical Systems

Abstract: This article describes the rationale for formal methods and considers the benefits, weaknesses, and difficulties in applying these methods to digital systems used in critical applications. It suggests factors for consideration when formal methods are offered in support of certification in a context such as DO-178B (the guidelines for software used on board civil aircraft) [40]. The presentation is intended for those to whom these topics are new. A more technical discussion of formal methods is available as a technical report [42].