The Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) Framework: Encouraging Reduction, Replacement, and Refinement in Animal Research.

While significant medical breakthroughs have been achieved through using animal models, our experience shows that often there is surplus material remaining that is frequently never revisited but could be put to good use by other scientists. Recognising that most scientists are willing to share this material on a collaborative basis, it makes economic, ethical, and academic sense to explore the option to utilise this precious resource before generating new/additional animal models and associated samples. To bring together those requiring animal tissue and those holding this type of archival material, we have devised a framework called Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) with the aim of making remaining material derived from animal studies in biomedical research more visible and accessible to the scientific community. We encourage journals, funding bodies, and scientists to unite in promoting a new way of approaching animal research by adopting the SEARCH framework.

SEARCHBreast: a new resource to locate and share surplus archival material from breast cancer animal models to help address the 3Rs.

Animal models have contributed to our understanding of breast cancer, with publication of results in high-impact journals almost invariably requiring extensive in vivo experimentation. As such, many laboratories hold large collections of surplus animal material, with only a fraction being used in publications relating to the original projects. Despite being developed at considerable cost, this material is an invisible and hence an underutilised resource, which often ends up being discarded. Within the breast cancer research community there is both a need and desire to make this valuable material available for researchers. Lack of a coordinated system for visualisation and localisation of this has prevented progress. To fulfil this unmet need, we have developed a novel initiative called Sharing Experimental Animal Resources: Coordinating Holdings-Breast (SEARCHBreast) which facilitates sharing of archival tissue between researchers on a collaborative basis and, de facto will reduce overall usage of animal models in breast cancer research. A secure searchable database has been developed where researchers can find, share, or upload materials related to animal models of breast cancer, including genetic and transplant models. SEARCHBreast is a virtual compendium where the physical material remains with the original laboratory. A bioanalysis pipeline is being developed for the analysis of transcriptomics data associated with mouse models, allowing comparative study with human and cell line data. Additionally, SEARCHBreast is committed to promoting the use of humanised breast tissue models as replacement alternatives to animals. Access to this unique resource is freely available to all academic researchers following registration at https://searchbreast.org.

SEARCHBreast Workshop Proceedings: 3D Modelling of Breast Cancer.

SEARCHBreast, a UK initiative supported by the NC3Rs, organised a workshop entitled 3D Modelling of Breast Cancer. The workshop focused on providing researchers with solutions to overcome some of the perceived barriers to working with human-derived tumour cells, cell lines and tissues, namely: a) the limited access to human-derived material; and b) the difficulty in working with these samples. The workshop presentations provided constructive advice and information on how to best prepare human cells or tissues for further downstream applications. Techniques in developing primary cultures from patient samples, and considerations when preserving tissue slices, were discussed. A common theme throughout the workshop was the importance of ensuring that the cells are grown in conditions as similar to the in vivo microenvironment as possible. Comparisons of the advantages of several in vitro options, such as primary cell cultures, cell line cultures, explants or tissue slices, suggest that all offer great potential applications for breast cancer research, and highlight that it need not be a case of choosing one over the other. The workshop also offered cutting-edge examples of on-chip technologies and 3-D tumour modelling by using virtual pathology, which can contribute to clinically relevant studies and provide insights into breast cancer metastatic mechanisms.

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.

The Gene3D structural domain database provides domain annotations for 7 million proteins, based on the manually curated structural domain superfamilies in CATH. These annotations are integrated with functional, genomic and molecular information from external resources, such as GO, EC, UniProt and the NCBI Taxonomy database. We have constructed a set of web services that provide programmatic access to this integrated database, as well as the Gene3D domain recognition tool (Gene3DScan) and protein sequence annotation pipeline for analysing novel protein sequences. Example queries include retrieving all curated GO terms for a domain superfamily or all the multi-domain architectures for the human genome. The services can be accessed using simple HTTP calls and are able to return results in a range of formats for quick downloading and easy parsing, graphical rendering and data storage. Hence, they provide a simple, but flexible means of integrating domain annotations and associated data sets into locally run pipelines and analysis software. The services can be found at http://gene3d.biochem.ucl.ac.uk/WebServices/.

Elucidating global epidemiology of Burkholderia multivorans in cases of cystic fibrosis by multilocus sequence typing.

Burkholderia multivorans is a prominent B. cepacia complex (BCC) species causing infection in people with cystic fibrosis. Despite infection control measures being introduced to reduce the spread of BCC there is a continued emergence of infections by B. multivorans. Our objective was to analyze a global collection of B. multivorans isolates, comparing those from environmental and clinical sources with those from reported outbreaks. Multilocus sequence typing (MLST) was performed on 107 B. multivorans isolates to provide a detailed analysis of the global population biology of this species. MLST resolved 64 B. multivorans sequence types. Twelve of these were globally distributed and associated with human infection; two of these (ST-21 and ST-375) were also composed of environmental isolates. These global lineages included strains previously linked to large outbreaks (e.g., French epidemic clone ST-16). Though few environmental isolates of B. multivorans were available for analysis, of six strains identified, three were identical to strains recovered from cystic fibrosis (CF) infection. Although the ability of B. multivorans to cause CF outbreaks is known, our report here concerning the existence of globally distributed B. multivorans CF strains is a new observation for this emerging B. cepacia complex pathogen and suggests that certain strain types may be better adapted to human infection than others. Common transmission-associated risk factors were not obviously linked to the globally distributed strains; however, the overlap in strains recovered from water environments, industrial products, and human infection suggests that environmental sources may be an important reservoir for infection with B. multivorans.

The assessment and treatment of adult heterosexual men with self-perceived problematic pornography use: A review.

Self-Perceived Problematic Porn Use (SPPPU) refers to an individual who self-identifies as addicted to porn because they feel they are unable to regulate their porn consumption, and that use interferes with everyday life. Although porn addiction has not been formally classified as its own distinct behavioral addiction, therapists and clinicians are advised to educate themselves on the current state of literature pertaining to pornography consumption given the widespread availability and consumption of sexually explicit material online. This review article begins with a general overview of pornography and porn use so that therapists and researchers can discern between non-intrusive and problematic pornography consumption patterns within their practice and understand the common characteristics of those that most commonly present with SPPPU. Thereafter, an overview and examination of therapeutic interventions for SPPPU will be identified and analysed. Finally, the review concludes with recommendations for therapists, clinicians, and future research.

NLSdb: database of nuclear localization signals.

NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using 'in silico mutagenesis' this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. NLSdb can be accessed via the web site: http://cubic.bioc.columbia.edu/db/NLSdb/.

PEP: Predictions for Entire Proteomes.

PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life: eukaryotes, prokaryotes and archaea. All proteins publicly available for organisms were aligned against SWISS-PROT, TrEMBL and PDB. Additionally, the following annotations are provided: secondary structure, transmembrane helices, coiled coils, regions of low complexity, signal peptides, PROSITE motifs, nuclear localization signals and classes of cellular function. Proteins that contain long regions without regular secondary structure are also identified. We have produced a related database of structural domain-like fragments derived from PEP and clusters based on homology between all fragments. The PEP database, fragments and clusters are distributed freely as a set of flat files and have been integrated into SRS. The PEP group of databases can be accessed from: http://cubic.bioc.columbia.edu/pep.

DSSPcont: Continuous secondary structure assignments for proteins.

The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces 'static' by 'dynamic' states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure.

Introducing SEARCHBreast: a virtual resource to facilitate sharing of surplus animal material developed for breast cancer research.

Animals studies have made significant contribution to expanding our knowledge of breast cancer. Often material is leftover and archived. SEARCHBreast provides a platform for collaborative sharing of archived material via a dedicated on-line database whereby users can both share and search available tissue. The SEARCHBreast database has information on over 50 different mouse models, including tissue from PDX models, available to share. With thousands of samples freely available, SEARCHBreast should be the first point of call for any researcher looking for animal material to aid their breast cancer research.

Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.

In rounds 3-5 of CAPRI, the community-wide experiment on the comparative evaluation of protein-protein docking for structure prediction, we applied the 3D-Dock software package to predict the atomic structures of nine biophysical interactions. This approach starts with an initial grid-based shape complementarity search. The product of this is a large number of potential interacting conformations that are subsequently ranked by interface residue propensities and interaction energies. Refinement through detailed energetics and optimization of side-chain positions using a rotamer library is also performed. For rounds 3, 4, and 5 of the CAPRI evaluation, where possible, we clustered functional residues on the surfaces of the monomers as an indication of binding sites, using sequence based evolutionary conservations. In certain targets this provided a very useful tool for identifying the areas of interaction. During round 5, we also applied the techniques of side-chain trimming and geometrical clustering described in the literature. Of the nine target complexes in rounds 3-5, we predicted conformations that contained at least some correct contact residues for seven of these systems. For two of the targets, we submitted predictions that were considered as medium-quality. These were a nidogen-laminin complex for target 8 (T08) and a serine-threonine phosphatase bound to a targeting subunit (T14). For a further three target systems, we produced models that were rated as acceptable predictions.

Haemophilus influenzae type b disease in Auckland children during the Hib vaccination era: 1995-2009.

AIM: To characterise Haemophilus influenzae type b (Hib) invasive disease in the era of Hib vaccination, in children of the greater Auckland region of New Zealand. METHOD: Identification of sterile site culture positive Hib via the Auckland hospital laboratories databases and national laboratory surveillance database in the time period; 1995 to 2009. RESULTS: There were a total of 26 cases in the Auckland Region. Over the 15-year period, the annual incidence of invasive Hib disease was 0.61 per 100,000 (95% CI: 0.4-0.9) for children aged under 15 years and 1.65 per 100,000 (95% CI: 1.1-2.5) for children aged under 5 years. Ninety-two percent were under 5 years and 54% were under 1 year. Sixty percent of the children were of Maori and Pacific ethnicity. The predominant diagnosis was meningitis, accounting for 15 cases (60%). There were no fatalities. Forty-eight percent of affected children were completely unimmunised with the Hib vaccine which has been fully funded on the National Immunisation Schedule since 1994. CONCLUSION: Since the introduction of the Hib vaccine, the disease rates have greatly reduced in the Auckland region. Although ethnic disparities have improved amongst the cases that occur, immunisation rates in cases are low and infants remain most at risk. Current emphasis on intensifying immunisation programmes to achieve higher vaccination rates and timeliness of delivery will help in efforts to achieve elimination of the disease in New Zealand.

Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space.

Structural genomics aims to solve the three-dimensional structures of proteins at a rapid rate and in a cost-effective manner, with the hope of significantly impacting on the life sciences, biotechnology, and drug discovery in the long-term. Structural genomics initiatives started in Japan in 1997 with the advent of the Protein Folds Project. Since then many new initiatives have begun worldwide, with diverse aims motivating the selection of proteins for structure determination. In this chapter, we consider the biological goals of high-throughput structural biology, while focusing on the Protein Structure Initiative in the United States. This is the most productive of the structural genomics initiatives, having solved 3,363 new structures between September 2000 and October 2008.