Plant systems biology: network matters

Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology.     

PCI comes to age as age increasingly comes to PCI

Percutaneous coronary intervention (PCI) has evolved as the standard procedure for the treatment of acute coronary syndromes and for the majority of situations with stable coronary artery disease. Patients aged 75 and older represent one third of those hospitalised with acute ischaemic events and account for more than half of all cardiac deaths. 1 However, evidence-based data to guide coronary revascularisation in the elderly have been limited to 1) the randomised clinical trials that routinely under-enrol elderly patients, and 2) observational studies that represent single institution experience with small samples. 2 Nevertheless, the Western society is an ageing population and the percentage of the population above 80 years of age, the so-called octogenarians, is rapidly increasing in Europe and will almost triple by 2050. 3     

Genetics in the age of systems biology

Systems biology has become a fashionable label for a new generation of large-scale experiments. This essay explores how classical approaches such as forward genetics fit into this emerging framework.     

Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events

The extensive mechanistic and regulatory interconnections between the various events of mRNA biogenesis are now recognized as a fundamental principle of eukaryotic gene expression, yet the specific details of the coupling between the various steps of mRNA biogenesis do differ, and sometimes dramatically, between the different kingdoms. In this review, we emphasize examples where plants must differ in this respect from other eukaryotes, and highlight a recurring trend of recruiting the conserved, versatile functional modules, which have evolved to support the general mRNA biogenesis reactions, for plant-specific functions. We also argue that elucidating the inner workings of the plant 'mRNA factory' is essential for accomplishing the ambitious goal of building the 'virtual plant'.     

MGED comes of age

A report on the Sixth International Meeting of the Microarray Gene Expression Data Society ('MGED6'), Aix-en-Provence, France, 6-8 September 2003.     

Nanoproteomics comes of age

ABSTRACT

Introduction: Nanoproteomics, which is defined as quantitative proteome profiling of small populations of cells (<5000 cells), can reveal critical information related to rare cell populations, hard-to-obtain clinical specimens, and the cellular heterogeneity of pathological tissues.

Areas covered: We present a brief review of the recent technological advances in nanoproteomics. These advances include new technologies or approaches covering major areas of proteomics workflow ranging from sample isolation, sample processing, high-resolution separations, to MS instrumentation.

Expert commentary: We comment on the current state of nanoproteomics and discuss perspectives on both future technological directions and potential enabling applications.     

Molecular biology of the chromo domain: an ancient chromatin module comes of age

The chromo domain motif is found in proteins from fungi, protists, plants, fish, insects, amphibians, birds, and mammals. The chromo domain peptide fold may have its origins as a chromosomal protein in a common ancestor of archea and eukaryota, making it a particularly ancient protein structural module. Chromo domains have been found in single or multiple copies in proteins with diverse structures and activities, most or all of which are connected with chromosome structure/function. In this review, our current knowledge of chromo domain properties is summarized and a variety of contexts in which chromo domains participate in aspects of chromatin metabolism are discussed.     

Migration comes of age

The Age of Migration has been uniquely successful as a student text on international migration, not only filling a niche but defining the field. This review article documents the evolution of the five editions of the book in terms of its core structure and enlarging scope. In a more critical vein, I note some omissions and potential shortcomings, while acknowledging the subjectivity of my perspective. More attention could have been given to the mobilities paradigm, transnationalism, internal and return migration, and quantitative analyses. Nevertheless, this book has done more than any other to ensure that the academic study of migration now occupies a central place in the social sciences.     

Immunoinformatics comes of age

With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the adaptive immune response and summaries of immunoinformatics resources, emphasizing those with Web interfaces. These resources include searchable databases of epitopes and immune-related molecules, and analysis tools for T cell and B cell epitope prediction, vaccine design, and protein structure comparisons. There is an agreeable synergy between the growing collections in immune-related databases and the growing sophistication of analysis software; the databases provide the foundation for developing predictive computational tools, which in turn enable more rapid identification of immune responses to populate the databases. Collectively, these resources contribute to improved understanding of immune responses and escape, and evolution of pathogens under immune pressure. The public health implications are vast, including designing vaccines, understanding autoimmune diseases, and defining the correlates of immune protection.