Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions

Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that is emerging in the field of proteomics as a complement to untargeted shotgun methods. SRM is particularly useful when predetermined sets of proteins, such as those constituting cellular networks or sets of candidate biomarkers, need to be measured across multiple samples in a consistent, reproducible and quantitatively precise manner. Here we describe how SRM is applied in proteomics, review recent advances, present selected applications and provide a perspective on the future of this powerful technology.     

Veterinary vaccines

Vaccination of animals for the prevention of infectious diseases has been practised for a number of years with little change in product composition. Recent advances in molecular biology, pathogenesis and immunology have laid the groundwork for the development of a new generation of veterinary vaccines based on pure subunits as well as live vectored bacteria and viruses. Along with novel methods of antigen preparation, the use of new adjuvants and delivery systems will permit targeting of the appropriate immune response as well as offering flexibility in terms of vaccination protocols. These new technologies are also being applied to the development of vaccines to enhance animal productivity and to control reproduction.     

Blastocystis: past pitfalls and future perspectives

Blastocystis is a genetically heterogeneous protist found in the intestinal tract (IT) of many vertebrates, and although it is implicated in a variety of human intestinal disorders, data regarding the clinical relevance of Blastocystis is at best speculative. Several research issues, including a lack of standardization across studies, the potential for intrasubtype variation in pathogenicity, and difficulties associated with diagnostics for many idiopathic disorders of the human IT have led to conflicting reports in support of a role for Blastocystis pathogenicity. Here, several research areas and methodologies are reviewed that if integrated appropriately into a prospective study may prove useful and facilitate a better understanding of the role of Blastocystis in human health and disease.     

Aromatase inhibitors: future directions

Estrogen and its cognate estrogen receptor are key players in the etiology and progression of breast cancer. Aromatase inhibitors, suppressing tumor and plasma estrogen levels by blocking testosterone conversion to estrogen, have been proven to provide the most effective endocrine therapy for postmenopausal breast cancer patients. Aromatase inhibitors are now the first choice endocrine therapy in the metastatic setting for postmenopausal women. These endocrine agents also seem likely to soon become the standard adjuvant therapy, either alone or in sequence with tamoxifen, though their long-term toxicity and the optimum duration of therapy still remain to be defined. Advanced experimental studies and some clinical observations reveal the importance of blocking both the genomic and non-genomic activities of the estrogen receptor, as well as its crosstalk with growth factor and other cellular signaling, for greatest effectiveness of endocrine therapy. Consequently, these studies provide a mechanistic explanation for the superb performance of aromatase inhibitors, and also suggest how inhibiting selected growth factor receptors might delay or prevent the onset of resistance to aromatase inhibitors and other endocrine therapies.     

Habitat complexity: approaches and future directions

Habitat complexity is one of the most important factors structuring biotic assemblages, yet we still lack basic understanding of the underlying mechanisms. Although it is one of the primary targets in conservation management, no methods are available for comparing complexity across ecosystems, and system-specific qualitative assessment predominates. Despite its overwhelming importance for faunal diversity and abundance, there has been surprisingly little interest in examining its effects on other community and ecosystem attributes. We discuss possibilities of such effects, outlining potentially fruitful areas for future research, and argue that complexity may be implicated in community persistence and ecosystem stability by acting as a decoupling mechanism in predator–prey interactions. We provide a brief overview of methods used to quantify complexity in different ecosystems, highlighting contributions of the current issue of Hydrobiologia, and discuss potential application of these approaches for cross-ecosystem comparisons. Better understanding of the role of habitat complexity resulting from such comparisons is critically important for preservation of biodiversity and ecosystem function in an era of unprecedented habitat loss.     

Bio-ontologies: current trends and future directions

In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.     

DNA vaccines: designing strategies against parasitic infections

The complexity of parasitic infections requires novel approaches to vaccine design. The versatility of DNA vaccination provides new perspectives. This review discusses the use of prime-boost immunizations, genetic adjuvants, multivalent vaccines and codon optimization for optimal DNA vaccine design against parasites.     

Anti-idiotype cancer vaccines: past and future

 Anti-idiotypic antibodies (Ab2) binding to the antigen-combining site of antitumor antibodies (Ab1) can induce anti-anti-idiotypic antibodies (Ab3) that specifically bind to the tumor antigen recognized by Ab1. Furthermore, Ab2, mimicking tumor antigens, have been shown to induce anti-anti-idiotypic proliferative T lymphocytes of the helper and suppressor type, as well as cytotoxic lymphocytes. The immunomodulatory activities of Ab2 have been demonstrated both in animals and in patients. The demonstration of tumor growth inhibition by anti-idiotypes in preclinical and phase I clinical studies emphasizes that randomized control trials should be performed to demonstrate clinical efficacy of Ab2 vaccines. Received: 25 July 1996 / Accepted: 22 August 1996     

Multiple sclerosis: etiological mechanisms and future directions

Multiple sclerosis (MS) is a complex human autoimmune-type disease with a predominantly unknown etiology. Immunologic destruction of myelin basic protein (MBP) throughout the nervous system is the major pathology of multiple sclerosis. This review will attempt to update new information about basic mechanisms and therapeutic management of the disease. The significance of the structure of MBP is discussed with respect to the contribution of such structures to the disease process. A number of MBP peptides that serve as the immunodominant antigens in MS patients have been identified. These peptides have been studied in animal models for their antigenic characteristics and ability to induce disease. Evidence for genetic contributions is reviewed with multigenerational twin studies providing the best evidence for susceptible haplotypes. The role of microorganisms/viruses and environmental agents are discussed as potential etiological factors but are now thought to be of minor importance to the primary causal development of the disease. Of major consideration are immunological mechanisms that contribute to the development of autoimmunity. In particular, antigen expression, cytokine and leukocyte interactions, and regulatory T-cells are discussed. Particular attention is given to regulatory T-cells (Treg), which help balance/modulate other T-cells such as Th1 and Th2 cells, and how such Treg regulate autoimmunity is addressed. The importance of the role of Tregs is exemplified by the demonstration that administration of oral antigens can induce specific Tregs that counteract experimental autoimmune encephalomyelitis in animal models. The significance of animal studies to human multiple sclerosis is discussed. A potential role for natural antibodies and innate immune mechanisms to help provide resistance to disease development is also reviewed. Finally, a variety of therapeutic agents that have been and continue to be utilized for multiple sclerosis is reviewed. Trials with oral antigens, such as glatirmer acetate (copolymer 1) especially in combination with interferon-beta, have shown promise. Antibody therapy and bone marrow transplantation are also briefly discussed.     

Paleobotany: Recent developments and future research directions

The current state of research in the field of paleobotany is reviewed, with emphasis on those areas that deal with more biological approaches to paleobotany. These would include such subjects as the reproductive biology of fossil plants, pollination biology in selected groups, paleobiochemistry, and information on the interaction of plants with other organisms (plant/animal interactions) and their environment (paleoecology). Also discussed are some of the more recent contributions to our understanding of Precambrian paleobiology and early angiosperm reproduction and evolution. Finally, we offer some speculation on the contributions that various areas of paleobotany may provide in the future.     

Cancer metabolism: current perspectives and future directions

Cellular metabolism influences life and death decisions. An emerging theme in cancer biology is that metabolic regulation is intricately linked to cancer progression. In part, this is due to the fact that proliferation is tightly regulated by availability of nutrients. Mitogenic signals promote nutrient uptake and synthesis of DNA, RNA, proteins and lipids. Therefore, it seems straight-forward that oncogenes, that often promote proliferation, also promote metabolic changes. In this review we summarize our current understanding of how ‘metabolic transformation'' is linked to oncogenic transformation, and why inhibition of metabolism may prove a cancer′s ‘Achilles'' heel''. On one hand, mutation of metabolic enzymes and metabolic stress sensors confers synthetic lethality with inhibitors of metabolism. On the other hand, hyperactivation of oncogenic pathways makes tumors more susceptible to metabolic inhibition. Conversely, an adequate nutrient supply and active metabolism regulates Bcl-2 family proteins and inhibits susceptibility to apoptosis. Here, we provide an overview of the metabolic pathways that represent anti-cancer targets and the cell death pathways engaged by metabolic inhibitors. Additionally, we will detail the similarities between metabolism of cancer cells and metabolism of proliferating cells.     

Ecological traps: current evidence and future directions

Ecological traps, which occur when animals mistakenly prefer habitats where their fitness is lower than in other available habitats following rapid environmental change, have important conservation and management implications. Empirical research has focused largely on assessing the behavioural effects of traps, by studying a small number of geographically close habitat patches. Traps, however, have also been defined in terms of their population-level effects (i.e. as preferred habitats of sufficiently low quality to cause population declines), and this is the scale most relevant for management. We systematically review the ecological traps literature to (i) describe the geographical and taxonomic distribution of efforts to study traps, (ii) examine how different traps vary in the strength of their effects on preference and fitness, (iii) evaluate the robustness of methods being used to identify traps, and (iv) determine whether the information required to assess the population-level consequences of traps has been considered. We use our results to discuss key knowledge gaps, propose improved methods to study traps, and highlight fruitful avenues for future research.     

Rotavirus vaccines: recent developments and future considerations

Two new vaccines have recently been shown to be safe and effective in protecting young children against severe rotavirus gastroenteritis. Although both vaccines are now marketed worldwide, it is likely that improvements to these vaccines and/or the development of future generations of rotavirus vaccines will be desirable. This Review addresses recent advances in our knowledge of rotavirus, the host immune response to rotavirus infection and the efficacy and safety of the new vaccines that will be helpful for improving the existing rotavirus vaccines, or developing new rotavirus vaccines in the future.     

Antigenic glycans in parasitic infections: implications for vaccines and diagnostics

Infections by parasitic protozoans and helminths are a major world-wide health concern, but no vaccines exist to the major human parasitic diseases, such as malaria, African trypanosomiasis, amebiasis, leishmaniasis, schistosomiasis, and lymphatic filariasis. Recent studies on a number of parasites indicate that immune responses to parasites in infected animals and humans are directed to glycan determinants within cell surface and secreted glycoconjugates and that glycoconjugates are important in host-parasite interactions. Because of the tremendous success achieved recently in generating carbohydrate-protein conjugate vaccines toward microbial infections, such as Haemophilus influenzae type b, there is renewed interest in defining parasite-derived glycans in the prospect of developing conjugate vaccines and new diagnostics for parasitic infections. Parasite-derived glycans are compelling vaccine targets because they have structural features that distinguish them from mammalian glycans. There have been exciting new developments in techniques for glycan analysis and the methods for synthesizing oligosaccharides by chemical or combined chemo-enzymatic approaches that now make it feasible to generate parasite glycans to test as vaccine candidates. Here, we highlight recent progress made in elucidating the immunogenicity of glycans from some of the major human and animal parasites, the potential for developing conjugate vaccines for parasitic infections, and the possible utilization of these novel glycans in diagnostics.