The vertebrate genome annotation (Vega) database.

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome. In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

The LRC haplotype project: a resource for killer immunoglobulin-like receptor-linked association studies.

There is increasing evidence for epistatic interactions between gene products (e.g. KIR) encoded within the Leukocyte Receptor Complex (LRC) with those (e.g. HLA) of the Major Histocompatibility Complex (MHC), resulting in susceptibility to disease. Identification of such associations at the DNA level requires comprehensive knowledge of the genetic variation and haplotype structure of the underlying loci. The LRC haplotype project aims to provide this knowledge by sequencing common LRC haplotypes.

The genomic sequence and analysis of the swine major histocompatibility complex.

We describe the generation and analysis of an integrated sequence map of a 2.4-Mb region of pig chromosome 7, comprising the classical class I region, the extended and classical class II regions, and the class III region of the major histocompatibility complex (MHC), also known as swine leukocyte antigen (SLA) complex. We have identified and manually annotated 151 loci, of which 121 are known genes (predicted to be functional), 18 are pseudogenes, 8 are novel CDS loci, 3 are novel transcripts, and 1 is a putative gene. Nearly all of these loci have homologues in other mammalian genomes but orthologues could be identified with confidence for only 123 genes. The 28 genes (including all the SLA class I genes) for which unambiguous orthology to genes within the human reference MHC could not be established are of particular interest with respect to porcine-specific MHC function and evolution. We have compared the porcine MHC to other mammalian MHC regions and identified the differences between them. In comparison to the human MHC, the main differences include the absence of HLA-A and other class I-like loci, the absence of HLA-DP-like loci, and the separation of the extended and classical class II regions from the rest of the MHC by insertion of the centromere. We show that the centromere insertion has occurred within a cluster of BTNL genes located at the boundary of the class II and III regions, which might have resulted in the loss of an orthologue to human C6orf10 from this region.

Preserving transfer independence among individuals with spinal cord injury.

STUDY DESIGN: Literature review. OBJECTIVES: Upper extremity (UE) joint degeneration, particularly at the shoulder, detrimentally influences functional independence, quality of life, cardiovascular disease risk, and life expectancy of individuals following spinal cord injury (SCI). This review (1) describes UE use for transfers among individuals with SCI; (2) describes contributing factors associated with UE joint degeneration and loss of transfer independence; (3) summarizes and identifies gaps in existing research; and (4) provides suggestions for future research. RESULTS: Investigations of wheelchair transfer related UE joint and function preservation among individuals with SCI should consider factors including age and length of time from SCI onset, interface between subject-wheelchair, pain, shoulder joint range of motion (ROM) and muscle strength deficiencies or imbalances, exercise capacity and tolerance for the physical strain of activities of daily living (ADL), body mass and composition, previous UE injury or disease history, and transfer techniques. Existing studies of transfers among individuals with SCI have relied on small groups of either asymptomatic or non-impaired subjects, with minimal integration of kinematic, kinetic and electromyographic data. Descriptions of UE joint ROM, forces, and moments produced during transfers are lacking. CONCLUSIONS: Biomechanical measurement and computer modeling have provided increasingly accurate tools for acquiring the data needed to guide intervention planning to prevent UE joint degeneration and preserve function among individuals with SCI. The identification of stressful sub-components during transfers will enable intervening clinicians and engineers who design and modify assistive and adaptive devices to better serve individuals with SCI.

Prescriptions for medical research. I--Management within the Medical Research Council.

In their submission to the government in advance of the white paper on science policy in the United Kingdom the Medical Research Council commends the MRC's own approach to managing directly funded research. But a series of semi-structured interviews with the directors of some of the MRC's units suggests a gap between the MRC's model of managed research and the reality. Although such units are theoretically managed from MRC head office (and units are charged an overhead for this), in practice each unit runs its own affairs. Between major reviews average contact time with the head office contact person is seven hours a year. The first paper argues that a purchaser-provider split would recognise the benefits of decentralisation and allow units to bid for research funds from several sources, the successful ones guaranteeing their survival through a rolling series of research programmes. The second paper criticises the MRC's cumbersome peer review system. Reliance on outside experts atrophies the scientific skills of head office staff and builds delays into decision making. A purchaser-provider model would allow the head office scientific staff to act like commercial research and development managers, commissioning research, and using the outcome, rather than peer review, as a criterion for continued funding.

Progress and problems in understanding the involvement of calcium in heart function.

In this article we have briefly reviewed the role of Ca2+ in the excitation contraction coupling in the myocardium and have indicated that cardiac contraction and relaxation are initiated upon raising and lowering the intracellular concentration of free Ca2+, respectively. Different mechanisms for the entry of Ca2+ through sarcolemma as well as release of Ca2+ from sarcoplasmic reticulum and possibly mitochondria have been outlined for initiating cardiac contraction. Relaxation of the cardiac muscle appears to be intimately dependent upon efflux of Ca2+ through sarcolemma as well as sequestration of Ca2+ by the intracellular storage sites, particularly sarcoplasmic reticulum and possibly mitochondria. The actions of some pharmacological and pathophysiological interventions have been explained on the basis of changes in subcellular Ca2+ movements in myocardium. Quinidine, which produced an initial positive inotropic action on rat heart was also found to increase sarcolemmal Ca2+-ATPase activity without any changes in the Na+-K+ ATPase. Other antiarrhythmic agents, procainamide and lidocaine, also increased sarcolemmal Ca2+-ATPase activity without affecting the Na+-K+ ATPase. On the other hand, both Ca2+-ATPase and Na+-K+ ATPase activities were increased in heart sarcolemma obtained from cardiomyopathic hamsters. In this model the increased Ca2+-ATPase activity may promote the occurrence of intracellular Ca2+ overload in the cardiac cell whereas the increased Na+-K+ ATPase activity may increase Ca2+ efflux through Na+-Ca2+ exchange systems as an adaptive mechanism. It has been suggested that some caution should be exercised while interpreting the data from in vitro experiments in terms of functional changes in the myocardium. Furthermore, it has been proposed that the pathophysiology and pharmacology of Ca2+ movements at different membrane sites be understood fully in normal and diseased myocardium in order to improve the therapy of heart disease.

Energy production and utilization in contractile failure due to intracellular calcium overload.

Intracellular calcium overload was produced by perfusing the Ca2+- deprived rat hearts for 5 or 10 min with normal medium containing 1.25 mM Ca2+ for 10 min and changes in the myofibrillar and membrane ATPase, sarcolemmal adenylate cyclase, mitochondrial oxidative phosphorylation and high energy phosphate stores in failing hearts were examined. Myocardial creatine phosphate and ATP were decreased by the intracellular calcium overload whereas the myofibrillar, mitochondrial and microsomal ATPase activities were not altered. The intracellular calcium overload markedly depressed the mitochondrial oxidative phosphorylation as well as sarcolemmal Ca2+ ATPase, Mg2+ ATPase, Na+ - K+ ATPase and adenylate cyclase. These results suggest that abnormalities in the process of energy production rather than energy utilization may primarily account for the depressed energy state of hearts failing due to an intracellular calcium overload.

Pressure control of ultrafiltration rate with high-flux dialysis membranes.

Control of ultrafiltration with high-flux dialysis membranes is normally achieved using complex, expensive, volumetric control methods. By using high-flux dialyzers with distensible membranes (parallel-plate dialyzers) in the cocurrent rather than in the countercurrent mode, ultrafiltration can be controlled simply and inexpensively by controlling the outlet pressure differential. Since this is the traditional method of ultrafiltration control, only minor, inexpensive equipment modifications are needed. As expected from transport theory, small molecule clearances are lower with cocurrent than with countercurrent flow. They are, however, adequate and superior to those achieved with post-dilutional hemofiltration (urea clearance greater than 110 ml/min with cocurrent single-pass, high-flux dialysis). Ultrafiltration control with this method is so simple and predictable that clearances at zero net ultrafiltration rates can easily be measured rather than extrapolated. Since dialysate pressure is always positive, no deaeration systems would be needed in dialysis equipment designed for use with cocurrent single-pass, high-flux dialysis.

Portable system for simultaneous measurements of blood electrolytes.

Miniature, rugged Chemfet sensors have been developed by coating field-effect transistors with ion-sensitive membranes. These sensors have been combined with a flow injection analysis manifold to demonstrate feasibility of a small portable system capable of simultaneous determinations in 10 seconds of hydrogen, potassium and calcium ion activities in 20 microliters samples of whole blood, serum or dialysate.

Selective chromatolysis of neurons in the gerbil brain: a possible consequence of "epileptic" activity produced by common carotid artery occlusion.

Unilateral (50 to 118 minutes) and bilateral (2 to 33 minutes) carotid artery occlusion in gerbils resulted in two distinct types of neuronal alteration: ischemic cell change (ICC) in selectively vulnerable brain regions, and selective chromatolysis (SC) confined to the deeper layers of the cortex, the Sommer sector of zone h-1, and the paramedian region (PM) of the hippocampus. In typical SC the nucleus was eccentric and the Nissl substance was lost in the central eosinophilic cytoplasm. In electron micrographs this area of cytoplasm showed disruption of smooth and rough endoplasmic reticulum with disaggregation of polyribosomes and accumulation of mitochrondria and various dense bodies. SC was identified at 2 to 3 hours and was still recognizable at five days. When bilateral carotid artery occlusion lasted 5 to 6 minutes, SC was seen in the hippocampal Sommer sector and cerebral cortex, while ICC was restricted to the endfolium (h3-5). Unlike ICC, the frequency of SC was not related to the duration of ischemia but probably to the epileptic seizures (overt and subclinical) initiated by ischemia in the gerbil. These changes must be considered when the gerbil is employed as a model of experimental stroke.