Protein structural domains: analysis of the 3Dee domains database.

The 3Dee database of domain definitions was developed as a comprehensive collection of domain definitions for all three-dimensional structures in the Protein Data Bank (PDB). The database includes definitions for complex, multiple-segment and multiple-chain domains as well as simple sequential domains, organized in a structural hierarchy. Two different snapshots of the 3Dee database were analyzed at September 1996 and November 1999.

Randomized trial of a specialist genetic assessment service for familial breast cancer.

Background: Because of the growing demand for genetic assessment, there is an urgent need for information about what services are appropriate for women with a family history of breast cancer. Our purpose was to compare the psychologic impact and costs of a multidisciplinary genetic and surgical assessment service with those of current service provisions.

Methods: We carried out a prospective randomized trial of surgical consultation with (the trial group) and without (the control group) genetic assessment in 1000 women with a family history of breast cancer.

Private psychiatric practice in an era of managed care.

Managed care is a given for private practice right now. It is important to develop a practice you can be proud of and be comfortable to work in by practicing ethically, with high standards for quality. Be persistent in expecting the same from the managed care companies, your colleagues, and your patients.

The social geography of AIDS and hepatitis risk: qualitative approaches for assessing local differences in sterile-syringe access among injection drug users.

While significant gains have been achieved in understanding and reducing AIDS and hepatitis risks among injection drug users (IDUs), it is necessary to move beyond individual-level characteristics to gain a fuller understanding of the impact of social context on risk. In this study, 6 qualitative methods were used in combination with more traditional epidemiologic survey approaches and laboratory bioassay procedures to examine neighborhood differences in access to sterile syringes among IDUs in 3 northeastern cities. These methods consisted of (1) neighborhood-based IDU focus groups to construct social maps of local equipment acquisition and drug use sites; (2) ethnographic descriptions of target neighborhoods; (3) IDU diary keeping on drug use and injection equipment acquisition; (4) ethnographic day visits with IDUs in natural settings; (5) interviews with IDUs about syringe acquisition and collection of syringes for laboratory analysis; and (6) focused field observation and processual interviewing during drug injection.

Application of multiple sequence alignment profiles to improve protein secondary structure prediction.

The effect of training a neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles derived from the same sequences, is shown to provide a range of accuracy from 70.5% to 76.4%.

ProtEST: protein multiple sequence alignments from expressed sequence tags.

Motivation: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed.

Results: A ProtEST search found a non-redundant, translated, error- and length-corrected EST sequence for > 58% of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe.

Interventions to improve uptake of breast screening in inner city Cardiff general practices with ethnic minority lists.

Objective: To increase the uptake of breast screening in three inner city GP practices with a high proportion of ethnic minority patients.

Setting: The study was carried out in May and June 1997 in the South East Wales division of Breast Test Wales (BTW). Three inner city general practices in Cardiff, with a low uptake in the previous round of breast screening and a high proportion of ethnic minority women on their lists, were targeted to receive interventions to increase uptake.

A model protocol evaluating the introduction of genetic assessment for women with a family history of breast cancer.

Randomised controlled trials allow comparisons to be made between different models of service delivery, but have not been used in the field of clinical genetics. With the advent of clinical governance, the evidence provided by such trials will be increasingly important in informing and shaping clinical genetics practice. The TRACE project (Trial of genetic assessment in breast cancer) is a randomised controlled trial of genetic assessment for women who are at increased risk of breast cancer because of their family history.

Evaluating peptide repertoires within the context of thymocyte development.

The process of antigen presentation by MHC molecules allows T cells to sample the proteins expressed within a particular cell. This sampling is in the form of short peptides bound within the grooves of MHC molecules displayed on the surface of cells. In the context of immune surveillance, this presentation allows the identification of infected cells by displaying peptides originating from foreign proteins within the cell.

Protein sequence alignment techniques.

The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison.

Deposition of macromolecular structures.

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimentalists to interpret the data.

Evaluation and improvement of multiple sequence methods for protein secondary structure prediction.

A new dataset of 396 protein domains is developed and used to evaluate the performance of the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR. The maximum theoretical Q3 accuracy for combination of these methods is shown to be 78%. A simple consensus prediction on the 396 domains, with automatically generated multiple sequence alignments gives an average Q3 prediction accuracy of 72.

JPred: a consensus secondary structure prediction server.

Unlabelled: An interactive protein secondary structure prediction Internet server is presented. The server allows a single sequence or multiple alignment to be submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction is also returned which improves the average Q3 accuracy of prediction by 1% to 72.

Requirement for diverse, low-abundance peptides in positive selection of T cells.

Whether a single major histocompatibility complex (MHC)-bound peptide can drive the positive selection of large numbers of T cells has been a controversial issue. A diverse population of self peptides was shown to be essential for the in vivo development of CD4 T cells. Mice in which all but 5 percent of MHC class II molecules were bound by a single peptide had wild-type numbers of CD4 T cells.

An altered invariant chain protein with an antigenic peptide in place of CLIP forms SDS-stable complexes with class II alphabeta dimers and facilitates highly efficient peptide loading.

We report an experimental system for abundant expression of specific peptide-class II complexes in vivo and in vitro. We have constructed a cassette which allows for the replacement of the CLIP region of invariant chain (Ii) with an antigenic peptide. In fibroblasts expressing an altered Ii protein, in which CLIP has been replaced with peptide 52-68 from the class II I-E alpha chain (pEalpha), pEalpha-I-Ab complexes are formed with high efficiency.

Analysis of the role of MKK-4/Sek-1 in T cell development and apoptosis.

The stress-activated protein kinases (SAPK) are a group of dual-specificity kinases with potential roles in the control of apoptosis and proliferation. In most cells they are regulated through phosphorylation by MKK-4. We have investigated the role of MKK-4 in T cell development and function by generating transgenic animals expressing catalytically inactive MKK-4 (dMKK-4) in the thymus.

Simulation and dynamic optimisation of animal cell culture.

In animal cell culture, there are some 25 substrates that both have a significant effect on the culture performance and which can be measured with relative ease. A detailed dynamic simulation for such a culture has been produced and an optimisation policy that use this model to identify ideal media conditions has been developed. This paper describes an extension of that work to include the dynamic optimisation of cultures under fed-batch operation.

The interpretation of relative momentum data to assess the contribution of the free limbs to the generation of vertical velocity in sports activities.

The contribution that the free limbs (the arms and lead leg) make to vertical velocity at take-off during jumping activities was determined by using a relative momentum approach. This requires the momentum of each free limb to be quantified relative to the joint at which the limb is attached to the body between the touchdown (or start of movement) and the take-off. The contribution that each makes to the vertical velocity at take-off requires interpretation of the momentum data.

Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation.

Analysis of the relationship between surface accessibility and amino acid conservation in multiple sequence alignments of homologous proteins confirms expected trends for hydrophobic amino acids, but reveals an unexpected difference between the conservation of Asp, Glu and Gln. Even when not in an active site, Asp is more highly conserved than Glu. There is a clear preference for conserved and buried Asp to be present in coil, but there is no tendency for Asp to conserve phi/psi in the ++ region of the Ramachandran map.

Protein fold recognition by mapping predicted secondary structures.

A strategy is presented for protein fold recognition from secondary structure assignments (alpha-helix and beta-strand). The method can detect similarities between protein folds in the absence of sequence similarity. Secondary structure mapping first identifies all possible matches (maps) between a query string of secondary structures and the secondary structures of protein domains of known three-dimensional structure.