The UCSC Proteome Browser

The University of California Santa Cruz (UCSC) Proteome Browser provides a wealth of protein information presented in graphical images and with links to other protein-related Internet sites. The Proteome Browser is tightly integrated with the UCSC Genome Browser. For the first time, Genome Browser users have both the genome and proteome worlds at their fingertips simultaneously. The Proteome Browser displays tracks of protein and genomic sequences, exon structure, polarity, hydrophobicity, locations of cysteine and glycosylation potential, Superfamily domains and amino acids that deviate from normal abundance. Histograms show genome-wide distribution of protein properties, including isoelectric point, molecular weight, number of exons, InterPro domains and cysteine locations, together with specific property values of the selected protein. The Proteome Browser also provides links to gene annotations in the Genome Browser, the Known Genes details page and the Gene Sorter; domain information from Superfamily, InterPro and Pfam; three-dimensional structures at the Protein Data Bank and ModBase; and pathway data at KEGG, BioCarta/CGAP and BioCyc. As of August 2004, the Proteome Browser is available for human, mouse and rat proteomes. The browser may be accessed from any Known Genes details page of the Genome Browser at http://genome.ucsc.edu. A user's guide is also available on this website

Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage

Taking advantage of the complete genome sequences of several mammals, we developed a novel method to detect losses of well-established genes in the human genome through syntenic mapping of gene structures between the human, mouse, and dog genomes. Unlike most previous genomic methods for pseudogene identification, this analysis is able to differentiate losses of well-established genes from pseudogenes formed shortly after segmental duplication or generated via retrotransposition. Therefore, it enables us to find genes that were inactivated long after their birth, which were likely to have evolved nonredundant biological functions before being inactivated. The method was used to look for gene losses along the human lineage during the approximately 75 million years (My) since the common ancestor of primates and rodents (the euarchontoglire crown group). We identified 26 losses of well-established genes in the human genome that were all lost at least 50 My after their birth. Many of them were previously characterized pseudogenes in the human genome, such as GULO and UOX. Our methodology is highly effective at identifying losses of single-copy genes of ancient origin, allowing us to find a few well-known pseudogenes in the human genome missed by previous high-throughput genome-wide studies. In addition to confirming previously known gene losses, we identified 16 previously uncharacterized human pseudogenes that are definitive losses of long-established genes. Among them is ACYL3, an ancient enzyme present in archaea, bacteria, and eukaryotes, but lost approximately 6 to 8 Mya in the ancestor of humans and chimps. Although losses of well-established genes do not equate to adaptive gene losses, they are a useful proxy to use when searching for such genetic changes. This is especially true for adaptive losses that occurred more than 250,000 years ago, since any genetic evidence of the selective sweep indicative of such an event has been erased

The accretion and spreading of matter on white dwarfs

For a slowly rotating non-magnetized white dwarf the accretion disk extends all the way to the star. Here the matter impacts and spreads towards the poles as new matter continuously piles up behind it. We have solved the 3d compressible Navier-Stokes equations on an axisymmetric grid to determine the structure of this boundary layer for different viscosities corresponding to different accretion rates. The high viscosity cases show a spreading BL which sets off a gravity wave in the surface matter. The accretion flow moves supersonically over the cusp making it susceptible to the rapid development of gravity wave and/or Kelvin-Helmholtz instabilities. This BL is optically thick and extends more than 30 degrees to either side of the disk plane after 3/4 of a Keplerian rotation period (t=19s). The low viscosity cases also show a spreading BL, but here the accretion flow does not set off gravity waves and it is optically thin.Comment: 6 pages, 5 figures, requires autart.cl

Radical-initiated P,P-metathesis reactions of diphosphanes: evidence from experimental and computational studies

By combining the diphosphanes Ar2P–PAr2, where Ar = C6H5, 4-C6H4Me, 4-C6H4OMe, 3,5-C6H3(CF3)2, it has been shown that P,P-metathesis generally occurs rapidly under ambient conditions. DFT calculations have shown that the stability of unsymmetrical diphosphanes Z2P–PZ′2 is a function of the difference between the Z and Z′ substituents in terms of size and electronegativity. Of the mechanisms that were calculated for the P,P-metathesis, the most likely was considered to be one involving Ar2P˙ radicals. The observations that photolysis increases the rate of the P,P-metatheses and TEMPO inhibits it, are consistent with a radical chain process. The P,P-metathesis reactions that involve (o-Tol)2P–P(o-Tol)2 are anomalously slow and, in the absence of photolysis, were only observed to take place in CHCl3 and CH2Cl2. The role of the chlorinated solvent is ascribed to the formation of Ar2PCl which catalyses the P,P-metathesis. The slow kinetics observed with (o-Tol)2P–P(o-Tol)2 is tentatively attributed to the o-CH3 groups quenching the (o-Tol)2P˙ radicals or inhibiting the metathesis reaction sterically

Heterometathesis of diphosphanes (R2P–PR2) with dichalcogenides (R′E–ER′, E = O, S, Se, Te)

The reactions of R2P–PR2 with R′E–ER′, (where E = Se, S, O, Te) to give R2P–ER′ have been explored experimentally and computationally. The reaction of Ph2P–PPh2 with PhSe–SePh gives Ph2P–SePh (1) rapidly and quantitatively. The P–P/Se–Se reaction is inhibited by the addition of the radical scavenger TEMPO which is consistent with a radical mechanism for the heterometathesis reaction. Compound 1 has been fully characterised, including by X-ray crystallography. A range of other Ar2P–SeR (R = Ph, nBu or CH2CH2CO2H) have also been prepared and characterised. The reaction of 1 with [Mo(CO)4(nbd)] (nbd = norbornadiene) gives two products which, from their characteristic 31P NMR data, have been identified as cis-[Mo(CO)4(Ph2PSePh–P)2] (8) and the mixed-donor complex cis-[Mo(CO)4(Ph2P–SePh–P)(Ph2P–SePh–Se)] (9). It is deduced that the P and Se atoms in ligand 1 have comparable capacity to coordinate to Mo(0). The reaction of Ph2P–PPh2 with PhS–SPh gives Ph2P–SPh (2) quantitatively but no reaction was observed between Ph2P–PPh2 and PhTe–TePh. Heterometathesis between Ph2P–PPh2 and tBuO–OtBu does not occur thermally but has been observed under UV irradiation to give Ph2P–OtBu along with P(V) oxidation by-products. DFT calculations have been carried out to illuminate why heterometatheses with dichalcogenides R′E–ER′ occur readily when E = S and Se but not when E = O and Te. The calculations show that heterometathesis is predicted to be thermodynamically favourable for E = O, S and Se and unfavourable for E = Te. The fact that a metathesis reaction between Ph2P–PPh2 with tBuO–OtBu is not observed in the absence of UV radiation, is therefore due to kinetics

A patient survey of out-of-hours care provided by Emergency Care Practitioners

© 2007 Halter et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

The feasibility of using pattern recognition software to measure the influence of computer use on the consultation

BACKGROUND: A key feature of a good general practice consultation is that it is patient-centred. A number of verbal and non-verbal behaviours have been identified as important to establish a good relationship with the patient. However, the use of the computer detracts the doctor's attention away from the patient, compromising these essential elements of the consultation. Current methods to assess the consultation and the influence of the computer on them are time consuming and subjective. If it were possible to measure these quantitatively, it could provide the basis for the first truly objective way of studying the influence of the computer on the consultation. The aim was to assess whether pattern recognition software could be used to measure the influence and pattern of computer use in the consultation. If this proved possible it would provide, for the first time, an objective quantitative measure of computer use and a measure of the attention and responsiveness of the general practitioner towards the patient. METHODS: A feasibility study using pattern recognition software to analyse a consultation was conducted. A web camera, linked to a data-gathering node was used to film a simulated consultation in a standard office. Members of the research team enacted the role of the doctor and the patient, using pattern recognition software to try and capture patient-centred, non-verbal behaviour. As this was a feasibility study detailed results of the analysis are not presented. RESULTS: It was revealed that pattern recognition software could be used to analyse certain aspects of a simulated consultation. For example, trigger lines enabled the number of times the clinician's hand covered the keyboard to be counted and wrapping recorded the number of times the clinician nodded his head. It was also possible to measure time sequences and whether the movement was brief or lingering. CONCLUSION: Pattern recognition software enables movements associated with patient-centredness to be recorded. Pattern recognition software has the potential to provide an objective, quantitative measure of the influence of the computer on the consultation