The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43 229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616 470 domain sequences classified into 23 876 sequence families. This results in the significant expansion of the CATHHMMmodel library to include models built from the CATH sequence relatives, giving a10%increase in coveragefor detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned

Partner randomized controlled trial: study protocol and coaching intervention

<p>Abstract</p> <p>Background</p> <p>Many children with asthma live with frequent symptoms and activity limitations, and visits for urgent care are common. Many pediatricians do not regularly meet with families to monitor asthma control, identify concerns or problems with management, or provide self-management education. Effective interventions to improve asthma care such as small group training and care redesign have been difficult to disseminate into office practice.</p> <p>Methods and design</p> <p>This paper describes the protocol for a randomized controlled trial (RCT) to evaluate a 12-month telephone-coaching program designed to support primary care management of children with persistent asthma and subsequently to improve asthma control and disease-related quality of life and reduce urgent care events for asthma care. Randomization occurred at the practice level with eligible families within a practice having access to the coaching program or to usual care. The coaching intervention was based on the transtheoretical model of behavior change. Targeted behaviors included 1) effective use of controller medications, 2) effective use of rescue medications and 3) monitoring to ensure optimal control. Trained lay coaches provided parents with education and support for asthma care, tailoring the information provided and frequency of contact to the parent's readiness to change their child's day-to-day asthma management. Coaching calls varied in frequency from weekly to monthly. For each participating family, follow-up measurements were obtained at 12- and 24-months after enrollment in the study during a telephone interview.</p> <p>The primary outcomes were the mean change in 1) the child's asthma control score, 2) the parent's quality of life score, and 3) the number of urgent care events assessed at 12 and 24 months. Secondary outcomes reflected adherence to guideline recommendations by the primary care pediatricians and included the proportion of children prescribed controller medications, having maintenance care visits at least twice a year, and an asthma action plan. Cost-effectiveness of the intervention was also measured.</p> <p>Discussion</p> <p>Twenty-two practices (66 physicians) were randomized (11 per treatment group), and 950 families with a child 3-12 years old with persistent asthma were enrolled. A description of the coaching intervention is presented.</p> <p>Trial registration</p> <p>ClinicalTrials.gov identifier <a href="http://www.clinicaltrials.gov/ct2/show/NCT00860834">NCT00860834</a>.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Evolutionary analysis of protein structural families to assist comparative modelling of genome sequences

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Relationships of the Escherichia coli O157, O111, and O55 O-Antigen Gene Clusters with Those of Salmonella enterica and Citrobacter freundii, Which Express Identical O Antigens

Escherichia coli O157, Salmonella enterica O30, and Citrobacter freundii F90 have identical O-antigen structures, as do E. coli O55 and S. enterica O50. The O-antigen gene cluster sequences for E. coli O157 and E. coli O55 have been published, and the genes necessary for O-antigen biosynthesis have been identified, although transferase genes for glycosidic linkages are only generic and have not been allocated to specific linkages. We determined sequences for S. enterica O30 and C. freundii F90 O-antigen gene clusters and compared them to the sequence of the previously described E. coli O157 cluster. We also determined the sequence of the S. enterica O50 O-antigen gene cluster and compared it to the sequence of the previously described E. coli O55 cluster. For both the S. enterica O30-C. freundii F90-E. coli O157 group and the S. enterica O50-E. coli O55 group of O antigens, the gene clusters have identical or nearly identical organizations. The two sets of gene clusters had comparable overall levels of similarity in their genes, which were lower than the levels determined for housekeeping genes for these species, which were 55 to 65% for the genes encoding glycosyltransferases and O-antigen processing proteins and 75 to 93% for the nucleotide-sugar pathway genes. Nonetheless, the similarity of the levels of divergence in the five gene clusters required us to consider the possibility that the parent gene cluster for each structure was in the common ancestor of the species and that divergence is faster than expected for the common ancestor hypothesis. We propose that the identical O-antigen gene clusters originated from a common ancestor, and we discuss some possible explanations for the increased rate of divergence that is seen in these genes

“They are gaining experience; we are gaining extra hands”: a mixed methods study to assess healthcare worker perceptions of a novel strategy to strengthen human resources for HIV in South Africa

Abstract Background Lay health workers (LHWs) can support the HIV response by bridging gaps in human resources for health. Innovative strategies are needed to expand LHW programs in many low- and middle-income countries. Youth Health Africa (YHA) is a novel LHW approach implemented in South Africa that places young adults needing work experience in one-year non-clinical internships at health facilities to support HIV programs (e.g., as HIV testers, data clerks). While research suggests YHA can increase HIV service delivery, we need to understand healthcare worker perceptions to know if this is an acceptable and appropriate approach to strengthen human resources for health and healthcare delivery. Methods We conducted a convergent mixed methods study to assess healthcare worker acceptance and perceived appropriateness of YHA as implemented in Gauteng and North West provinces, South Africa and identify issues promoting or hindering high acceptability and perceived appropriateness. To do this, we adapted the Johns Hopkins Measure of Acceptability and Appropriateness to survey healthcare workers who supervised interns, which we analyzed descriptively. In parallel, we interviewed frontline healthcare workers who worked alongside YHA interns and conducted an inductive, thematic analysis. We merged quantitative and qualitative results using the Theoretical Framework of Acceptability to understand what promotes or hinders high acceptance and appropriateness of YHA. Results Sixty intern supervisors responded to the survey (91% response rate), reporting an average score of 3.5 for acceptability and 3.6 for appropriateness, on a four-point scale. Almost all 33 frontline healthcare workers interviewed reported the program to be highly acceptable and appropriate. Perceptions that YHA was mutually beneficial, easy to integrate into facilities, and helped facilities be more successful promoted a strong sense of acceptability/appropriateness amongst healthcare workers, but this was tempered by the burden of training interns and limited program communication. Overall, healthcare workers were drawn to the altruistic nature of YHA. Conclusion Healthcare workers in South Africa believed YHA was an acceptable and appropriate LHW program to support HIV service delivery because its benefits outweighed its costs. This may be an effective, innovative approach to strengthen human resources for HIV services and the broader health sector

Genome and proteome annotation: organization, interpretation and integration

Recent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly analysed, annotated, stored and displayed. Consequently, a vast number of resources have been created to present the data to the wider community. Annotation tools and databases provide the means to disseminate these data and to comprehend their biological importance. This review examines the various aspects of annotation: type, methodology and availability. Moreover, it puts a special interest on novel annotation fields, such as that of phenotypes, and highlights the recent efforts focused on the integrating annotations

New tools for “hot-wiring” clathrin-mediated endocytosis with temporal and spatial precision

Clathrin-mediated endocytosis (CME) is the major route of receptor internalization at the plasma membrane. Analysis of constitutive CME is difficult because the initiation of endocytic events is unpredictable. When and where a clathrin-coated pit will form and what cargo it will contain are difficult to foresee. Here we describe a series of genetically encoded reporters that allow the initiation of CME on demand. A clathrin-binding protein fragment (“hook”) is inducibly attached to an “anchor” protein at the plasma membrane, which triggers the formation of new clathrin-coated vesicles. Our design incorporates temporal and spatial control by the use of chemical and optogenetic methods for inducing hook–anchor attachment. Moreover, the cargo is defined. Because several steps in vesicle creation are bypassed, we term it “hot-wiring.” We use hot-wired endocytosis to describe the functional interactions between clathrin and AP2. Two distinct sites on the β2 subunit, one on the hinge and the other on the appendage, are necessary and sufficient for functional clathrin engagement