Clinical applications of molecular biology for infectious diseases

Molecular biological methods for the detection and characterisation of microorganisms have revolutionised diagnostic microbiology and are now part of routine specimen processing. Polymerase chain reaction (PCR) techniques have led the way into this new era by allowing rapid detection of microorganisms that were previously difficult or impossible to detect by traditional microbiological methods. In addition to detection of fastidious microorganisms, more rapid detection by molecular methods is now possible for pathogens of public health importance. Molecular methods have now progressed beyond identification to detect antimicrobial resistance genes and provide public health information such as strain characterisation by genotyping. Treatment of certain microorganisms has been improved by viral resistance detection and viral load testing for the monitoring of responses to antiviral therapies. With the advent of multiplex PCR, real-time PCR and improvements in efficiency through automation, the costs of molecular methods are decreasing such that the role of molecular methods will further increase. This review will focus on the clinical utility of molecular methods performed in the clinical microbiology laboratory, illustrated with the many examples of how they have changed laboratory diagnosis and therefore the management of infectious diseases.     

Bringing systems biology to cancer,immunology and infectious disease

A report on the seventh annual ‘International Conference on Systems Biology of Human Disease’ held in Boston, Massachusetts, USA, 17–19 June, 2014.     

The impact of systems biology and biosimulation on drug discovery and development

Drug discovery and development involves a series of difficult, systematic decision-making exercises, each of which is based on data acquired from bioassays and clinical trials. Since assays and trials are designed to elucidate the underlying pathophysiology of a disease, it is not sufficient to merely acquire data, but one must also interpret those findings in the context of the physiology they are meant to represent. Recently, these efforts have been enhanced by the use of biosimulation as a means of integrating and interpreting the vast new data sets generated by classically designed systems biology studies. Only when data describing gene expression, cell function, and whole-body physiology are interpreted in the context of integrated system function, will current error rates experienced during drug discovery and development be minimized.     

Molecular biology and the diagnosis, epidemiology and pathogenesis of infectious diseases

Abstract In this short review, the impact of molecular biology on microbiology in general is described. Specifically, molecular biology is increasingly enlarging the available choice of methods for the diagnosis of microbial disease. In situ hybridization seems to be a particularly promising procedure. In epidemiology, an interesting facet is the high mutation rate of RNA viruses. In pathogenesis, molecular biology will help to elucidate pathways of infection and the targeting of pathogenic macromolecules within the cell and within an organism.     

Molecular biology and the diagnosis, epidemiology and pathogenesis of infectious diseases

In this short review, the impact of molecular biology on microbiology in general is described. Specifically, molecular biology is increasingly enlarging the available choice of methods for the diagnosis of microbial disease. In situ hybridization seems to be a particularly promising procedure. In epidemiology, an interesting facet is the high mutation rate of RNA viruses. In pathogenesis, molecular biology will help to elucidate pathways of infection and the targeting of pathogenic macromolecules within the cell and within an organism.     

Genomics and development: Taking developmental biology to new heights

The 2006 Arolla meeting brought together scientists from around the globe to discuss how genomic scale analyses can enhance progress in understanding developmental biology.     

Emerging infectious diseases and animal social systems

Emerging infectious diseases threaten a wide diversity of animals, and important questions remain concerning disease emergence in socially structured populations. We developed a spatially explicit simulation model to investigate whether—and under what conditions—disease-related mortality can impact rates of pathogen spread in populations of polygynous groups. Specifically, we investigated whether pathogen-mediated dispersal (PMD) can occur when females disperse after the resident male dies from disease, thus carrying infections to new groups. We also examined the effects of incubation period and virulence, host mortality and rates of background dispersal, and we used the model to investigate the spread of the virus responsible for Ebola hemorrhagic fever, which currently is devastating African ape populations. Output was analyzed using regression trees, which enable exploration of hierarchical and non-linear relationships. Analyses revealed that the incidence of disease in single-male (polygynous) groups was significantly greater for those groups containing an average of more than six females, while the total number of infected hosts in the population was most sensitive to the number of females per group. Thus, as expected, PMD occurs in polygynous groups and its effects increase as harem size (the number of females) increases. Simulation output further indicated that population-level effects of Ebola are likely to differ among multi-male–multi-female chimpanzees and polygynous gorillas, with larger overall numbers of chimpanzees infected, but more gorilla groups becoming infected due to increased dispersal when the resident male dies. Collectively, our results highlight the importance of social system on the spread of disease in wild mammals.     

Application of systems biology for bioprocess development

Random mutagenesis or genetic modification of an organism without consideration of its consequences to the entire system might cause unwanted changes in cellular metabolism. Systems metabolic engineering thus aims to develop strains by performing metabolic engineering within a systems biology framework, in which entire cellular networks are optimized and fermentation and downstream processes are considered at early stages. Thus, regulatory, metabolic and other cellular networks are engineered in an integrated manner. Here, we review the applications of systems biology for the development of strains and bioprocesses by means of several successful examples and, furthermore, discuss future prospects.     

System biology and synthetic biology modify drug discovery and development

Life Sciences are built on observations. Right now, a more systemic approach allowing to integrate the different organizational levels in Biology is emerging. Such an approach uses a set of technologies and strategies allowing to build models that appear to be more and more predictive (omics, bioinformatics, integrative biology, computational biology…). Those models accelerate the rational development of new therapies avoiding an engineering based only on trials and errors. This approach both holistic and predictive radically modifies the discovery and development modalities used today in health industries. Moreover, because of the apparition of new jobs at the interface of disciplines, of private and public sectors and of life sciences and engineering sciences, this implies to rethink the training programs in both their contents and their pedagogical tools.     

Genomics and computational molecular biology

There has been a dramatic increase in the number of completely sequenced bacterial genomes during the past two years as a result of the efforts both of public genome agencies and the pharmaceutical industry. The availability of completely sequenced genomes permits more systematic analyses of genes, evolution and genome function than was otherwise possible. Using computational methods - which are used to identify genes and their functions including statistics, sequence similarity, motifs, profiles, protein folds and probabilistic models - it is possible to develop characteristic genome signatures, assign functions to genes, identify pathogenic genes, identify metabolic pathways, develop diagnostic probes and discover potential drug-binding sites. All of these directions are critical to understanding bacterial growth, pathogenicity and host-pathogen interactions.     

Genomics and the second golden era of cancer drug development

The first golden era of cancer drug development was initiated in the 1940s and gave rise to the cytotoxic agents that dominate current cancer medicine. The second golden era is now underway in which cancer genomics will direct drug development.     

Predicting drug side-effects by chemical systems biology

The publication of the highest-quality and best-annotated personal genome yet tells us much about sequencing technology, something about genetic ancestry, but still little of medical relevance.     

Genomics and the biology of parasites

Despite the advances of modern medicine, the threat of chronic illness, disfigurement, or death that can result from parasitic infection still affects the majority of the world population, retarding economic development. For most parasitic diseases, current therapeutics often leave much to be desired in terms of administration regime, toxicity, or effectiveness and potential vaccines are a long way from market. Our best prospects for identifying new targets for drug, vaccine, and diagnostics development and for dissecting the biological basis of drug resistance, antigenic diversity, infectivity and pathology lie in parasite genome analysis, and international mapping and gene discovery initiatives are under way for a variety of protozoan and helminth parasites. These are far from ideal experimental organisms, and the influence of biological and genomic characteristics on experimental approaches is discussed, progress is reviewed and future prospects are examined.     

The discovery, biology, and drug development of sialyl Lea and sialyl Lex

The discoveries of sialylated, fucosylated lacto-, and neolacto-type carbohydrate structures were accomplished with the aid of analytical methods and monoclonal antibodies such as the immunostaining of thin layer chromatograms. Based on the use of such antibodies, these structures, notably sialyl Le(a) and sialyl Le(x), were demonstrated to be highly expressed in many malignant cancers. A diagnostic assay using one of these antibodies (CA19-9) is now established as one of the more commonly used assays for pancreatic and gastrointestinal cancers worldwide. Upon further study, several laboratories have demonstrated that the level of expression of these carbohydrate tumor markers is also positively correlated with patient survival and is a prognostic indicator of metastatic disease. Concurrent with this finding, both sialyl Le(a) and sialyl Le(x) were shown to bind to a family of carbohydrate-binding proteins involved in the extravasation of cells from the bloodstream, called the selectins. Thus, sialyl Le(a) and sialyl Le(x) expressed on cell surfaces play functional roles in medical conditions that require extravasation of cells from the bloodstream which include a wide range of inflammatory diseases and cancer metastasis. Many studies have confirmed the function of sialyl Le(a) and sialyl Le(x) in animal models of these diseases and the inhibition of binding of sialyl Le(a) and sialyl Le(x) to the selectins is a validated drug target in the pharmaceutical industry. Thus, a new class of drugs, arising from the field of glycobiology, is based on the rational design of small molecule drugs that mimic the structures sialyl Le(a) and sialyl Le(x) and can potently inhibit their functional binding to the selectins.