CiteULike: jyuh's McDowall

Calculation of threshold and saturation points of sigmoidal baroreflex function curves.

LM McDowall — 2007-12-11T16:03:15-00:00

Am J Physiol Heart Circ Physiol, Vol. 291, No. 4. (October 2006)

The logistic sigmoid function curve provides an accurate description of the baroreflex input-output relationship and is the most commonly used equation for this purpose. The threshold (Thr) and saturation (Sat) values for the baroreflex are commonly defined as the values of mean arterial pressure (MAP) at which the reflexly controlled variable (e.g., heart rate or sympathetic nerve activity) is within 5% of the upper or lower plateau, respectively, of the sigmoid function. These values are referred to here as Thr(5%) and Sat(5%). In many studies, Thr and Sat are calculated with the equations Thr = A(3) - 2.0/A(2) and Sat = A(3) + 2.0/A(2), where A(3) is the value of MAP at the point where the reflexly controlled variable is at the midpoint of its range and A(2) is the gain coefficient. Although it is commonly stated that the values of Thr and Sat calculated with these equations represent Thr(5%) and Sat(5%), we show here that instead they are significantly greater and less than Thr(5%) and Sat(5%), respectively. Furthermore, the operating range (difference between Thr and Sat) calculated with these equations is 32% less than the difference between Thr(5%) and Sat(5%). We further show that the equations that provide correct values of Thr(5%) and Sat(5%) are Thr(5%) = A(3) - 2.944/A(2) and Sat(5%) = A(3) + 2.944/A(2). We propose that these be used as the standard equations for calculating threshold and saturation values when a logistic sigmoid function is used to model the open-loop baroreflex function curve.

New developments in the InterPro database.

NJ Mulder — 2007-05-18T20:25:15-00:00

Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.

Two-dimensional gel electrophoresis for identifying proteins that bind DNA or RNA.

JA Stead — 2007-08-26T14:38:11-00:00

Nat Protoc, Vol. 2, No. 8. (2007), pp. 1839-1848.

Electrophoretic mobility shift assays (EMSAs) are commonly used to analyze nucleic acid-protein interactions. When nucleic acid is bound by protein, its mobility during gel electrophoresis is reduced. Similarly, the final position of protein within a complex is shifted when compared to its free state. Here we provide a protocol for a simple approach that uses these mobility differences to identify nucleic acid-binding proteins. Following EMSA, denaturing gel electrophoresis is implemented to provide a second dimension of separation. Protein that binds a specific nucleic acid is identified as a spot(s) whose presence at a particular position(s) is dependent on nucleic acid within the initial binding reaction. The polypeptide in a spot can be subsequently identified by mass spectrometry. As EMSAs can be performed using partially purified or cell extracts, this approach substantially reduces the need for protein purification. It should facilitate the identification of a nucleic acid-binding protein within approximately 4 d.

The identification of nucleic acid-interacting proteins using a simple proteomics-based approach that directly incorporates the electrophoretic mobility shift assay.

JA Stead — 2007-08-26T14:38:18-00:00

Mol Cell Proteomics, Vol. 5, No. 9. (September 2006), pp. 1697-1702.

Proteins that interact with nucleic acids are central to numerous cellular processes, and their continuing characterization represents one of the foremost challenges in the postgenomic era. Here we describe a simple proteomics-based approach for the identification by mass spectrometry of proteins in crude extracts that interact with nucleic acids. It incorporates the electrophoretic mobility shift assay and is based on the finding that when a protein forms a complex with nucleic acid its electrophoretic mobility is affected as well as that of the nucleic acid. Our method should greatly reduce and in some cases may even eliminate the need for extensive protein purification and as such should contribute significantly to the functional annotation of the proteome. Furthermore it requires no prior knowledge of the molecular mass, quaternary structure, or pI of the interacting protein. Proof of principle is demonstrated using a recently discovered transcription factor; however, the approach should also have application in the identification of proteins that interact with RNA.