[What can experimental research offer to rheumatology today--the viewpoint of molecular biology? Contribution of molecular biology to pathogenesis research in rheumatology using the example of rheumatoid arthritis]

Molecular biology plays an increasing role for the development of innovative approaches to analyze the pathogenesis of rheumatic diseases and to improve diagnosis and therapy of these disorders. Some of these approaches/techniques have recently yielded important results, e.g. the analysis of 1) chromosomal aberrations (numerical and, in part, structural aberrations in synovial fibroblasts/macrophages from chronic joint inflammation); 2) cell clonality (oligoclonal expansion of synovial T-cells, B-cells, but also fibroblasts); 3) the importance of genetic factors (genome-wide screening for arthritis susceptibility genes); 4) mutations in key genes of cell cycle and/or function (mutations in p53 and proto-oncogenes in the inflamed synovial membrane); and 5) gene expression patterns (e.g. by high-density microarrays, custom arrays, in situ hybridization, and real-time PCR). It can be expected that these analyses will result in central new findings concerning the understanding of the pathogenetic basis of chronic inflammatory rheumatic diseases, with the potential to develop differential diagnostic criteria for these hitherto extremely heterogeneous diseases, and to create the basis for individual-oriented therapy.

[Diagnosis and therapy monitoring applying methods of molecular medicine]

New experimental approaches are presented which are implemented in rheumatology research. DNA microarray technology and proteome analysis are two new methods which are applied to gain a global survey over the gene expression at the RNA and protein level under various conditions. Based on these methods of molecular medicine important functional proteins in the pathogenesis of rheumatoid arthritis (RA) as well as clinical relevant genetic polymorphisms shall be identified. New insights are expected which will help in the differentiation of clinical entities and in the search for new therapeutic strategies in the treatment of RA.

Ruminations of a geriatric Emeritus Regius Professor of Medicine

The potential for the holder of a senior academic post to influence the medical world is usually enshrined in their job description. Even though Oxford University failed to provide one, this account of 25 years of undirected activity suggests that such posts can influence events, albeit to a limited extent and not always in the expected direction.

Interview with Sydney Brenner by Soraya de Chadarevian

The following text is an edited version of a recent interview with Sydney Brenner who has been at the forefront of many developments in molecular biology since the 1950s. It provides a participant's view on current issues in the history and epistemology of molecular biology. The main issue raised by Brenner regards the relation of molecular biology to the new field of systems biology. Brenner defends the original programme of molecular biology-the molecular explanation of living processes-that in his view has yet to be completed. The programme of systems biology in contrast he views as either trivial or as not achievable since it purports to deal with inverse problems that are impossible to solve in complex living systems. Other issues covered in the conversation concern the impact of the human genome sequencing project, the commercial turn in molecular biology and the contested disciplinary status of the science.

Molecular genetics of human myopia: an update

Myopia, or nearsightedness, is the most common human eye disorder in the world, and is a significant global public health concern. Along with cataract, macular degeneration, infectious disease, and vitamin A deficiency, myopia is one of the most important causes of visual impairment worldwide. Severe or high-grade myopia is a leading cause of blindness because of its associated ocular morbidities of retinal detachment, macular choroidal degeneration, premature cataract, and glaucoma. Ample evidence documents the heritability of the non-syndromic forms of this condition, especially for high-grade myopia, commonly referred to as myopic spherical refractive power of 5 to 6 diopters or higher. Multiple high-grade myopia genetic loci have been identified, and confirmatory studies identifying high-grade and moderate myopia loci have also occurred. In general, myopia susceptibility genes are unknown with few association studies performed, and without confirmation in other research laboratories or testing of separate patient cohorts.

Why is modern medicine stuck in a rut?

There is a growing perception that modern medicine is approaching a state of crisis characterized by creative inertia, non-innovation, and non-productivity. Compared to the remarkable progress during the first 30 years after World War II, the last 30 years have been characterized by a self-congratulatory illusion of progress, the fruits of which have failed to reach our patients. The problem may lie with the fact that the (often lone) clinical innovator of the past who made all the difference to the spectacular progress of medicine during the golden age has been marginalized to the extent that he is now an endangered species. The two definable forces that have led to his alienation are the hegemony of molecular science and the primacy accorded to the randomized clinical trial in biomedical research. Both these stifle creative originality-the former by an overdependence on complex and technology-driven "big science" and a flawed founding philosophy, and the latter by putting limits on our intellectual expectations and a bureaucratic approach to scientific research.

Biomolecular simulation and modelling: status, progress and prospects

Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted.

The Future of Cancer Diagnostics: Next Generation Molecular Technologies - Cambridge Healthtech Institute's Inaugural Conference

Cambridge Health Tech Institute's first conference on 'The Future of Cancer Diagnostics: Next Generation Molecular Technologies' covered the following areas: regulatory requirements regarding the validation of new cancer diagnostics; how such validation processes might be suitably implemented from laboratory to clinical pipeline to the bedside; translational strategies, such as proteomics or methylation patterns; and novel biomarkers in oncology. Overall in this golden age of cancer research, the aims and objectives of the meeting were to explore how the implementation of new diagnostic strategies could be facilitated. This meeting examined various topics, including 'Early cancer detection', 'Differential diagnosis', 'Prognostic markers and therapy selection' and 'Circulating tumor cells'. The talks and sessions of the meeting are summarized in this report, with particular focus on preclinical and clinical therapies.

Gene concepts and genethics: beyond exceptionalism

The discursive explosion that was provoked by the new genetics could support the impression that the ethical and social problems posed by the new genetics are somehow exceptional in their very nature. According to this view we are faced with special ethical and social problems that create a challenge so fundamental that the special label of genethics is needless to justify. The historical account regarding the evolution of the gene concepts could serve us to highlight the limits of what we know about genes and what we can do with genes. The widespread notion about the exceptionality of genetic knowledge and its applicative possibilities is hardly justifiable and leads to misunderstandings regarding the conceptualization of the ethical and social problems we might face. Following a more realistic interpretation of the role of genes in human life we might avoid a whole set of fictive dilemmas and counterproductive regulatory efforts in bioethics. Bioethical discourse should move from the gene-centered scientific discourse toward the more sophisticated and complex discourses where human development represented as a matter of complex interactions between genomes and environments, between genes, educational factors, nutritional regimes, and other different developmental resources. If a gene is seen as one among the different developmental resources that are shaping a given human trait then both genethics and genetic exceptionalism could hardly be represented as a justified approach in discussing the ethical and social problems of genetics.

Acute aortic dissection

We summarise advances in the epidemiology, presentation, pathogenesis, diagnosis, and management of acute aortic dissection. Improved understanding of this problem has been assisted not only by establishment of an international registry but also by progress in molecular biology and genetics of connective-tissue diseases. Advances in endovascular products and techniques have provided new treatment options. Open surgical repair remains the main treatment for dissection in the ascending aorta, whereas endovascular treatment is increasingly being used in dissection that is limited to other parts of the aorta.

The genetics of suicide: a critical review of molecular studies

Genetic epidemiology research has shown that genes contribute to suicide risk. Unfortunately, the first 30 years of candidate-based association studies have provided little information about the specific genetic contributors. This article reviews genetic association studies of suicidal phenotypes published to date. Possible theoretical, methodological, and operational challenges accounting for the modest success of association studies in the field are also discussed. The authors conclude that future research may benefit from using a more systematic and comprehensive selection of candidate genes and variants, examining gene-environment and gene-gene interactions, and investigating higher-order moderators.

[Progress in molecular genetics of generalized epilepsy with febrile seizures plus]

Generalized epilepsy with febrile seizures plus (GEFS+) is a familial inherited epileptic syndrome characterized by phenotypic heterogeneity from the milder febrile seizures to the severest epileptic encephalopathy such as severe myoclonic epilepsy in infancy (SMEI). GEFS+ is a disorder with a genetic heterogeneity. Molecular genetics have revealed that four genes are associated with the pathogenesis of GEFS+. These include mutations in genes encoding subunits of neuronal voltage-gated sodium channels (SCN1A, SCN1B, SCN2A) and gamma(2) subunit of the gamma amino-butyric acid (GABA)(A) receptor (GABRG2). These genes have been confirmed as having a role in autosomal dominant GEFS+ families. In addition, the phenotypes of the affected members may depend on the types and locations of these gene mutations. This review states the molecular genetic progress of GEFS+ in brief.

[Physiology, biomedicine, medicine]

The physiology throughout centuries was considered as the basic fundamental science in medicine. Rapid development of molecular biology, genetics and of some other natural sciences in 2nd half XX demanded century not only the answer to a question on the sciences defining the base of development of medicine, but also key problems of its progress. The biomedicine is formed, its methods are discussed, is frequent in system of natural sciences, parities with physiology. The special attention is given unconditional necessity of finding-out of molecular mechanisms of functions, targets of action of physiologically active substances and obligatory correlation of data of modeling with the same processes in conditions in vivo in whole body. The role of various sciences in the decision of fundamental problems of medicine, a place and role of physiology in modern medicine is shown.

Molecular information obtained from radiobiological tissue archives: achievements of the past and visions of the future

Radiobiological archives have not been overwhelmed by applications to use their stored tissue materials, in part because of lack of technologies to conduct quantitative analysis of the tissues. Over the last decade, advances in methodology have made it possible to routinely extract both DNA and RNA from archival materials. The quantitative analysis of gene expression by reverse transcription real-time PCR (QRT-PCR), and of gene copy number by array-based CGH (aCGH), are now firmly established methods for the study of tissue samples stored as paraffin blocks. More recent developments in proteomic technology have enabled the extraction of proteins from formalin-fixed paraffin-embedded (FFPE) tissue samples. These protein extracts have been used to produce quantitative data by Western blotting and even to identify proteins through LC/MS analysis. The development of applications using gel-based proteomics (2D/MS) is still a future challenge. This report gives an overview of the methodology already applicable on FFPE tissue, as well as the novel technologies to be used in the future research. Our goal is to collect existing animal and human tissue samples for use by the radiation biology community, to test new technologies for preparation of material from tissue samples, and to actively pursue materials arising from ongoing research.

Pathophysiology of delirium in the intensive care unit

Delirium, or acute brain dysfunction, is a life-threatening global disturbance in cognitive functioning that frequently manifests in critically ill patients. This review examines the current status of knowledge regarding the pathophysiology of delirium in the ICU, in particular, evaluating the role of iatrogenic factors such as sedatives and analgesic administration in brain dysfunction. This hypothesis is considered along with several other plausible mechanisms of ICU delirium, including sepsis, postoperative cognitive dysfunction, and changes in biomarkers and neurotransmitters. The review concludes by highlighting potential future directions in molecular genetics for the elucidation of delirium and its long-term consequences.

Editorial: Synthesis themed issue

With this issue, NPR fully embraces the molecular and structural biology revolution by showcasing leading work in natural product synthesis, with emphasis on those areas allied to the chemical biology agenda.

[New tendencies in molecular genetics of bacteriophages]

The paper deals with development of molecular genetics of bacteriophages of phytopathogenic erwinia at the Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine.

Beyond chemotherapy--demystifying the new 'targeted' cancer treatments

It has been known for some time that key genetic changes are the principle mechanism of cancer development. These changes lead to abnormalities in the signalling pathways of cells and result in unregulated cell growth, angiogenesis and metastasis.

Adult zebrafish as a model for successful central nervous system regeneration

Adult fish, in contrast to mammals, are capable of regenerating axonal tracts as well as cells and even entire tissues in the central nervous system (CNS). The zebrafish is a powerful genetic model for studies on the developing CNS and is now emerging as a CNS regeneration model. Here we review recent progress in adult regeneration paradigms in zebrafish ranging from axonal re-growth models to those of tissue regeneration. Moreover, we review the tools that have become available in zebrafish to elucidate the factors contributing to successful CNS regeneration. Since many molecular pathways are shared between zebrafish and mammals, it is hoped that insights from zebrafish may contribute to future therapeutic approaches in CNS injury and disease.

Optimality criteria for the prediction of metabolic fluxes in yeast mutants

Constraint-based models of cellular metabolism, such as flux balance analysis (FBA), use convex analysis and optimization to study metabolic networks at a genome scale. The availability of reaction lists for numerous organisms, along with a variety of network analysis and optimization tools, is making these approaches increasingly popular for metabolic engineering and biomedical applications, as well as for addressing fundamental biological questions. It is therefore very important to assess the predictive capacity of these models and to understand how to interpret them in a biologically relevant manner. Typically, model assessment is limited to gauging the ability to predict phenotypes, such as viability under different environmental and genetic conditions. These types of assessments, for the most part, focus only on the growth phenotype of the cells, but ignore the underlying flux predictions. While this may be sufficient for certain types of study, the question of whether flux balance models can reliably predict intracellular and transport fluxes is crucial for more detailed analysis, and remains largely unanswered. Here we compare FBA model predictions of yeast metabolic fluxes to a previously published set of experimentally determined fluxes for 13 different single gene deletion mutants across a variety of possible objective functions. We find that the specific optimization criteria used to determine fluxes have a significant impact on the accuracy of the predicted fluxes. Interestingly, while different optimization methods provide very different levels of agreement relative to experimental fluxes, they tend to provide similar predictions with respect to the effect of the perturbation on growth. This demonstrates that assessment of models at the level of flux predictions is a critical step in assessing the biological validity of different models and optimization criteria.

Synthetic biology: lessons from the history of synthetic organic chemistry

The mid-nineteenth century saw the development of a radical new direction in chemistry: instead of simply analyzing existing molecules, chemists began to synthesize them--including molecules that did not exist in nature. The combination of this new synthetic approach with more traditional analytical approaches revolutionized chemistry, leading to a deep understanding of the fundamental principles of chemical structure and reactivity and to the emergence of the modern pharmaceutical and chemical industries. The history of synthetic chemistry offers a possible roadmap for the development and impact of synthetic biology, a nascent field in which the goal is to build novel biological systems.

Chemistry across scales: from molecules to cells

Many important biological functions are strongly dependent on specific chemical interactions. Modelling how the physicochemical molecular details emerge at much larger scales is an active area of research, currently pursued with a variety of methods. We describe a series of theoretical and computational approaches that aim to derive bottom-up descriptions that capture the specificity that ensues from atomistic detail by extracting relevant features at the different scales. The multiscale models integrate the descriptions at different length and time scales by exploiting the idea of mechanical responses. The methodologies bring together concepts and tools developed in seemingly unrelated areas of mathematics such as algebraic geometry, model reduction, structural graph theory and non-convex optimization. We showcase the applicability of the framework with examples from protein engineering and enzyme catalysis, protein assembly, and with the description of lipid bilayers at different scales. Many challenges remain as it is clear that no single methodology will answer all questions in such multidimensional complex problems.

The new biology: beyond the Modern Synthesis

BACKGROUND

The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century.

CONCLUSION

Like the physical sciences in the first half of the 20th Century, biology at the start of the 21st Century is achieving a substantive maturity of theory, experimental tools, and fundamental findings thanks to relatively secure foundations in genomics. Genomics has also forced biologists to connect evolutionary and molecular biology, because these formerly Balkanized disciplines have been brought together as actors on the genomic stage. Biologists are now addressing the evolution of genetic systems using more than the concepts of population biology alone, and the problems of cell biology using more than the tools of biochemistry and molecular biology alone. It is becoming increasingly clear that solutions to such basic problems as aging, sex, development, and genome size potentially involve elements of biological science at every level of organization, from molecule to population. The new biology knits together genomics, bioinformatics, evolutionary genetics, and other such general-purpose tools to supply novel explanations for the paradoxes that undermined Modernist biology.