Biomedical subjects

David C Schwartz

Publications and source records attributed to David C Schwartz.

22 records · Page 2Linked to original sources

PubMed2003

Analysis of recombinant yeast decapping enzyme.

A critical step in the turnover of yeast mRNAs is decapping. Two yeast proteins, Dcp1p and Dcp2p, are absolutely required for decapping, although their precise roles in the decapping reaction have not been established. To determine the function of both Dcp1p and Dcp2p in decapping, we purified recombinant versions of these proteins from Escherichia coli and examined their properties. These experiments demonstrate that copurification of Dcp1p and Dcp2p yields active decapping enzyme under a variety of conditions. Moreover, Dcp2p alone can have decapping activity under some biochemical conditions. This suggests that Dcp2p can be a catalytic subunit of the decapping complex, and Dcp1p may function to enhance Dcp2p activity, or as an additional active subunit. In addition, recombinant Dcp1p/Dcp2p prefers long mRNA substrates and is sensitive to inhibition by sequestration of the 5' end but not the 3' end of the substrate. This suggests that Dcp1p/Dcp2p contains an additional RNA-binding site spatially distinct from the active site. Finally, using two RNA-binding proteins that enhance decapping in vivo (Edc1p and Edc2p), we can reconstitute the activation of decapping with recombinant proteins. This indicates that the Edc1 and Edc2 proteins act directly on the decapping enzyme.

Endoribonucleases↗

PubMed2002

Serial intracoronary ultrasound in children: feasibility, reproducibility, limitations, and safety.

Pediatric patients with heart transplants and Kawasaki disease are at risk to develop coronary artery disease. Selective coronary angiography underestimates vasculopathy in transplant patients and intimal changes in Kawasaki disease. Routine intracoronary ultrasound imaging in adults accurately identifies histopathologic features not visualized by angiography. Little data are available regarding safety and efficacy in children. This study provides sequential data and experience in children between the ages of 2 1/2 and 22 years. Thirty-two patients underwent 62 intracoronary ultrasound examinations at the time of coronary angiography. Careful correlation of the ultrasound crystal locations with the angiographic images of the vessels was made. Images were analyzed for intimal hyperplasia and luminal diameters. Intracoronary ultrasound was more sensitive than angiography in detecting vessel wall disease. Coronary vasospasm occurred in 11 of 62 studies after the intracoronary ultrasound study. All but 1 episode were asymptomatic and resolved after intracoronary nitroglycerine. When a standard protocol is followed and current technology is used, intracoronary ultrasound is feasible, reproducible, efficacious, and safe in the young patient. It allows earlier detection of vasculopathy and intimal disease at angiographically normal sites. As technology improves and greater experience is gained, the long-term safety and prognostic value of these studies in children should be forthcoming.

Adolescent↗

PubMed2002

A whole-genome shotgun optical map of Yersinia pestis strain KIM.

Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.

Genome, Bacterial↗

PubMed2002

Genome sequence of Yersinia pestis KIM.

We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing surprising amounts of locally colinear "backbone," or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of E. coli pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.

Bacteriophages↗