Computational Biology Branch (CBB) is the research branch of the National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH).

We hold weekly seminars by CBB members each Tuesday at 11 AM in the Building 38A B2 NCBI Library. Visitors' presentations usually take place in the same room, but are scheduled on a different day of the week. If scheduling a visitor's presentation, please don't forget to book a seminar room.

To schedule a seminar, please click on the appropriate date in the calendar.

Contact Ivan Ovcharenko with questions or if you need help in scheduling a seminar.

About CBB

Location: 8th floor conference room
Affiliation: University of Alabama at Birmingham
Host: Ivan Ovcharenko
Studies of DNA gyrase activity in Escherichia coli and Salmonella enterica serovar typhimurium
“Gyrase introduces negative supercoils into bacterial DNA. In balance with topoisomerase I it contributes to the maintenance of constant negative DNA supercoiling. It was shown that in Escherichia coli negative supercoil density of pBR322 plasmid is higher than in Salmonella typhimurium. One of the possible explanations of this phenomenon is a difference of DNA gyrase activity between E. coli and S. typhimurium. We developed in vitro assay of gyrase activity which has shown that DNA gyrases of E. coli and S. typhimurium has the same supercoiling end point, but E. coli gyrase works faster then S. typhimurium enzyme. To see how this rate difference influence supercoiling on the chromosome, the in vivo assay based on excision of sequence surrounded by resolvase sites has been used. The efficiency of resolvase action correlates with supercoiling density between resolvase sites. This assay has shown that in strains carrying E. coli gyrB supercoiling density is increased, but it is decreased in strains carrying E. coli gyrA. This fact can be explained by inefficient interaction of E. coli GyrA with S. typhimurium molecular machinery. Introduction of E. coli gyrA or gyrB does not influence the doubling time of S. typhimurium, while introduction of S. typhimurium gyrA into E. coli causes the increase in doubling time. In the previous works was shown that transcription and translation rates correlate with the rate of negative supercoil introduction. It raises possibility that differences in E. coli and S. typhimurium gyrase rates correspond to differences in transcription and translation rates in these organisms.“

Dissecting polymorphic toxin systems by domain analysis and comparative genomics

Evolution and dynamics of transcriptional regulation in bacteria

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