Glutamate transporter: an unexpected target for some antibiotics

Molecular pain is a relatively new and rapidly expanding research field that represents an advanced step from conventional pain research. Molecular pain research addresses physiological and pathological pain at the cellular, subcellular and molecular levels. These studies integrate pain research with molecular biology, genomics, proteomics, modern electrophysiology and neurobiology. The field of molecular pain research has been rapidly expanding in the recent years, and has great promise for the identification of highly specific and effective targets for the treatment of intractable pain. Although several existing journals publish articles on classical pain research, none are specifically dedicated to molecular pain research. Therefore, a new journal focused on molecular pain research is needed. Molecular Pain, an Open Access, peer-reviewed, online journal, will provide a forum for molecular pain scientists to communicate their research findings in a targeted manner to others in this important and growing field.     

Systems analysis of adaptive immunity by utilization of high-throughput technologies

A new generation of high-throughput technologies for quantitative and clonal analysis of adaptive immune responses have been developed. Functional analysis of lymphocyte populations has been accomplished via microfluidic assay systems. Additionally, lymphocyte receptor repertoires have been characterized on proteomic and genomic levels with multiplexed protein microarrays and high-throughput DNA sequencing. These tools are providing an unprecedented level of information depth on the distribution of adaptive immune cell (B and T cell) functionalities and repertoires, which develop upon activation following vaccination, pathogenic infection, or in disease states. These various high-throughput technologies have unlocked the potential to transform immunology into an information-rich science that will enable rapid expansion of the field of experimental systems immunology.     

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope prediction methods depends on a community consensus on the data and metrics utilized to develop and evaluate such tools. A workshop, sponsored by the National Institute of Allergy and Infectious Disease (NIAID), was recently held in Washington, DC to discuss the current state of the B-cell epitope prediction field. Many of the currently available tools were surveyed and a set of recommendations was devised to facilitate improvements in the currently existing tools and to expedite future tool development. An underlying theme of the recommendations put forth by the panel is increased collaboration among research groups. By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools.     

New journal: Algorithms for Molecular Biology

This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions.     

Towards an integrated network of coral immune mechanisms

Reef-building corals form bio-diverse marine ecosystems of high societal and economic value, but are in significant decline globally due, in part, to rapid climatic changes. As immunity is a predictor of coral disease and thermal stress susceptibility, a comprehensive understanding of this new field will likely provide a mechanistic explanation for ecological-scale trends in reef declines. Recently, several strides within coral immunology document defence mechanisms that are consistent with those of both invertebrates and vertebrates, and which span the recognition, signalling and effector response phases of innate immunity. However, many of these studies remain discrete and unincorporated into the wider fields of invertebrate immunology or coral biology. To encourage the rapid development of coral immunology, we comprehensively synthesize the current understanding of the field in the context of general invertebrate immunology, and highlight fundamental gaps in our knowledge. We propose a framework for future research that we hope will stimulate directional studies in this emerging field and lead to the elucidation of an integrated network of coral immune mechanisms. Once established, we are optimistic that coral immunology can be effectively applied to pertinent ecological questions, improve current prediction tools and aid conservation efforts.     

Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

The 2010 International Conference on Bioinformatics, InCoB2010, which is the annual conference of the Asia-Pacific Bioinformatics Network (APBioNet) has agreed to publish conference papers in compliance with the proposed Minimum Information about a Bioinformatics investigation (MIABi), proposed in June 2009. Authors of the conference supplements in BMC Bioinformatics, BMC Genomics and Immunome Research have consented to cooperate in this process, which will include the procedures described herein, where appropriate, to ensure data and software persistence and perpetuity, database and resource re-instantiability and reproducibility of results, author and contributor identity disambiguation and MIABi-compliance. Wherever possible, datasets and databases will be submitted to depositories with standardized terminologies. As standards are evolving, this process is intended as a prelude to the 100 BioDatabases (BioDB100) initiative whereby APBioNet collaborators will contribute exemplar databases to demonstrate the feasibility of standards-compliance and participate in refining the process for peer-review of such publications and validation of scientific claims and standards compliance. This testbed represents another step in advancing standards-based processes in the bioinformatics community which is essential to the growing interoperability of biological data, information, knowledge and computational resources.     

A research agenda for helminth diseases of humans: basic research and enabling technologies to support control and elimination of helminthiases

Successful and sustainable intervention against human helminthiases depends on optimal utilisation of available control measures and development of new tools and strategies, as well as an understanding of the evolutionary implications of prolonged intervention on parasite populations and those of their hosts and vectors. This will depend largely on updated knowledge of relevant and fundamental parasite biology. There is a need, therefore, to exploit and apply new knowledge and techniques in order to make significant and novel gains in combating helminthiases and supporting the sustainability of current and successful mass drug administration (MDA) programmes. Among the fields of basic research that are likely to yield improved control tools, the Disease Reference Group on Helminth Infections (DRG4) has identified four broad areas that stand out as central to the development of the next generation of helminth control measures: 1) parasite genetics, genomics, and functional genomics; 2) parasite immunology; 3) (vertebrate) host-parasite interactions and immunopathology; and 4) (invertebrate) host-parasite interactions and transmission biology. The DRG4 was established in 2009 by the Special Programme for Research and Training in Tropical Diseases (TDR). The Group was given the mandate to undertake a comprehensive review of recent advances in helminthiases research in order to identify notable gaps and highlight priority areas. This paper summarises recent advances and discusses challenges in the investigation of the fundamental biology of those helminth parasites under the DRG4 Group's remit according to the identified priorities, and presents a research and development agenda for basic parasite research and enabling technologies that will help support control and elimination efforts against human helminthiases.     

Immunopharmacology: a new frontier

Immunopharmacology is a hybrid science which has been founded upon the principles, theory, and technical developments of both immunology and pharmacology, but which has a unique identity incorporating both basic and applied areas of research. Basic immunopharmacological research is concerned with the underlying mechanisms by which endogenous and synthetic chemicals interact with the cells of the immune system. Important areas of research include the actions of chemicals such as lymphokines, cytokines, complement, kinins, autacoids, drugs, and even neuropeptides on immune function. Applied immunopharmacology is concerned with the development and testing of new immunomodulatory drugs which will be of benefit to clinical medicine but also as basic research tools. In the past, the two fields of immunology and pharmacology have contributed to each other in many significant ways. Immunology has contributed to pharmacological research by the development of antibodies which are frequently used today as specific probes for the quantitative and qualitative analysis of many different classes of chemicals of interest. Pharmacology has contributed to the field of immunology by providing basic pharmacological information on subjects such as the mediators of hypersensitivity reactions and inflammation. In the future, the truly hybrid field of immunopharmacology promises to have an expanding role in clinical medicine and basic research. This prediction is based on the observation that recombinant lymphokines and newly discovered immunomodulatory substances have begun to enter the clinic in ever increasing numbers. Future immunopharmacological research will include the study of the pharmacology of these lymphokines but also the rational development of new drugs that act as antagonists or agonists for the endogenous lymphokines that normally regulate the immune response.(ABSTRACT TRUNCATED AT 250 WORDS)     

Tumor microenvironments,the immune system and cancer survival

The study of cancer immunology has recently been reinvigorated by the application of new research tools and technologies, as well as by refined bioinformatics methods for interpretation of complex datasets. Recent microarray analyses of lymphomas suggest that the prognosis of cancer patients is related to an interplay between cancer cells and their microenvironment, including the immune response.     

Reflections on classic papers in Ethnic and Racial Studies

This paper provides an overview of this Special Issue celebrating the 40th anniversary of Ethnic and Racial Studies. We discuss some of the themes that are covered in this issue in the context of the wider history of the journal. We argue that the journal has worked over the years both to publish the highest quality original research and to feature scholarship in emerging subfields that have helped to broaden both our scope and reach across the globe. In addition we highlight some of the contribution that the journal has made to the development of both established and new areas of scholarship in its field throughout the world.     

MIMOX: a web tool for phage display based epitope mapping

Background  

Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them.     

Zoom in on neurodegeneration

Despite the existence of several scientific journals that publish research papers and reviews related to neurodegenerative diseases, a journal specifically devoted to the molecular and cellular aspects of disease mechanisms is lacking. Molecular Neurodegeneration is an open-access, peer-reviewed, online journal created to publish original research articles that address i) the mechanisms of neurodegeneration at the cellular, subcellular and molecular levels and ii) potential therapeutic interventions for neurodegenerative diseases. Through publication of reviews, editorial commentaries, and meeting reports, Molecular Neurodegeneration will also provide a forum to enhance the exchange of ideas and promote debate that is essential for scientific progress. Molecular Neurodegeneration will enable scientists to rapidly communicate their important research discoveries to their colleagues around the world.     

Protist 2000

As Protist enters the year 2000, the third year of its existence, it may be appropriate to briefly evaluate the past and look forward to what readers and authors of the journal can expect in the near future.It is fair to say that editing the journal over the past two years has been an enlightening experience, more work but also more fun than I anticipated. Whatever has been achieved, it would not have been possible without the tremendous support I received from my co-editors, the publisher and his staff and my secretarial office. Of no less importance has been the constructive criticism of fellow protistologists, readers and authors alike.I wish to thank Paul Falkowski, Rick A Firtel, and Frances D Gillin who have resigned from the Editorial Board for all their help in getting the journal started, and I welcome Randall S Alberte, Donald M Anderson, Richard Kessin and Peter Upcroft as new Board members.Protist has rapidly become one of the premium international journals for protist research, its impact factor, to be issued later this year will testify to this. The journal is covered by MEDLINE and a full text (PDF) online version is now available free of charge through the year 2000 on the publisher's Web site (http://www.urbanfischer.de/journals/protist).Protist will continue to publish high quality original work in all areas of protist research using the highest quality reproduction methods available today. In addition the highly successful “Protist News” and “From the Archives” sections for which authors are usually invited, will remain regular features of the journal.Protist in the year 2000 opens a new chapter of protist research. I invite you to join in this as a reader and a contributor.     

Immunoinformatics analysis of H5N1 proteome for designing an epitope-derived vaccine and predicting the prevalence of pre-existing cellular-mediated immunity toward bird flu virus in Indonesian population

As an essential step of adaptive immune response, the recognition between antigen and antibody triggers a series of self-protection mechanisms. Therefore, the prediction of antibody-binding sites (B-cell epitope) for protein antigens is an important field in immunology research. The performance of current prediction methods is far from satisfying, especially for conformational epitope prediction. Here a multi-perspective analysis was carried on with a comprehensive B-cell conformational epitope dataset, which contains 161 immunoglobulin complex structures collected from PDB, corresponding to 166 unique computationally defined epitopes. These conformational epitopes were described with parameters from different perspectives, including characteristics of epitope itself, comparison to non-epitope surface areas, and interaction pattern with antibody. According to the analysis results, B-cell conformational epitopes were relatively constant both in the number of composing residues and the accessible surface area. Though composed of spatially clustering residues, there were sequentially linear segments exist in these epitopes. Besides, statistical differences were found between epitope and non-epitope surface residues with parameters in residual and structural levels. Compared to non-epitope surface residues, epitope ones were more accessible. Amino acid enrichment and preference for specific types of residue-pair set on epitope areas have also been observed. Several amino acid properties from AAindex have been proven to distinguish epitope residues from non-epitope surface ones. Additionally, epitope residues tended to be less conservative under the environmental pressure. Measured by topological parameters, epitope residues were surrounded with fewer residues but in a more compact way. The occurrences of residue-pair sets between epitope and paratope also showed some patterns. Results indicate that, certain rules do exist in conformational epitopes in terms of size and sequential continuity. Statistical differences have been found between epitope and non-epitope surface residues in residual and structural levels. Such differences indicate the existence of distinctiveness for conformation epitopes. On the other hand, there was no accordant estimation for higher or lower values derived from any parameter for epitope residues compared with non-epitope surface residues. This observation further confirms the complicacy of characteristics for conformational epitope. Under such circumstance, it will be a more effective and accurate approach to combine several parameters to predict the conformation epitope. Finding conformational epitopes and analysing their properties is an important step to identify internal formation mechanism of conformational epitopes and this study will help future development of new prediction tools.     

Systems biology driven software design for the research enterprise

Background  

In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools.