Review Articles in 2010

Network inference is the construction of biological networks using an algorithm to assess biological data. Many different programs taking various approaches are available, and here De Smet and Marchal review these programs and provide a guide to using the right one for a particular data set.

The mechanisms that allow bacteria to swim through liquid environments are well understood, but much less is known about how bacteria migrate across solid surfaces, a process known as swarming. In this Review, Daniel Kearns describes the requirements and phenotypes associated with swarming motility.

Secretory antibodies are immune effectors that protect mucosal epithelia from infection by pathogens. Here, Strugnell and Wijburg describe the mechanisms for the production of secretory antibodies and their methods of action and discuss possible explanations for the evolution of the secretory immune system.

Most bacteria live in biofilms, the structure of which depends on the biofilm matrix. This matrix is composed of extracellular polymeric substances, which are compounds that are produced by the bacteria. Here, Flemming and Wingender describe the properties of the matrix and provide an overview of the individual matrix components.

Phage-related chromosomal islands, which include theStaphylococcus aureuspathogenicity islands, often encode virulence factors and co-opt a helper phage to spread to other cells. Richard Novick and colleagues describe the life cycle of these genetic elements, the regulation of their mobility and their effects on helper phages.

In this article the authors review what mouse models of intestinal inflammation using gene-targeted mice and defined bacteria have contributed to our understanding of the mechanisms underlying inflammatory bowel disease (IBD), focusing on the specific contribution of bacteria and bacterial components.

Integrative and conjugative elements are self-transmissible genetic elements that encode a core set of genes for their propagation and transfer and can also carry various other genes, including drug resistance markers. Here, Wozniak and Waldor describe the transmission of these elements and how this is regulated.

Chikungunya virus is a re-emerging alphavirus that recently caused an epidemic in countries of the Indian Ocean. At the time, little was known about the biology and pathogenesis of this virus compared with other viruses, but recent multidisciplinary efforts have furthered our understanding of this pathogen and its interaction with the host.

As the emergence of antibiotic resistance has increased, there has been a concurrent decline in the discovery and development of new classes of antibiotics. Fishwick and colleagues explore the possibility that structure-based drug design will plug this hole in the antimicrobial pipeline.

Demand for renewable alternatives to petrochemical-based products is increasing. In this Review, Bernd Rehm describes how a better understanding ofin vivobacterial biopolymer biosynthesis is enabling the production of tailor-made renewable biopolymers with a diverse range of material properties.

Oral biofilms are the paradigm of multispecies biofilms. Paul Kolenbrander and colleagues describe the different steps in the formation of these biofilms, the importance of intercellular cooperation and signalling, and how this can lead to pathogenesis. In all these aspects, the distance between the bacteria is an important factor.

Fe–S proteins participate in a wide array of cellular processes, from metabolism to gene regulation and DNA replication. Here, Py and Barras discuss the basic requirements for a bacterial cell to build and insert Fe–S clusters into apoproteins and summarize our current knowledge and understanding of this processin vivo.

The health of the periodontium, the tissue surrounding the teeth, is a delicate balance between host factors and bacterial stimulation. Richard Darveau discusses the factors that are involved in maintaining a healthy periodontium and how pathogens shift the balance to induce disease.

Despite the great promise of bacterial bioreporters in the laboratory, their uptake for commercial use has been limited. In this Review, van der Meer and Belkin describe the current design of bacterial bioreporters and discuss how integrating synthetic microbiology and microengineering will increase bioreporter use in the field.

With new technologies enabling researchers to get a better picture of microbial metabolismin vivo, Werner Goebel and colleagues describe our current understanding of the major carbon sources and metabolic pathways used by intracellular bacterial pathogens.

To date, three different autotrophic carbon fixation mechanisms have been found in archaea. Here, Georg Fuchs and colleagues describe these mechanisms and their phylogenetic distribution. As most cultivated autotrophic archaea live in conditions that resemble the conditions of early life, these pathways can serve as models for an ancestral autotrophic carbon fixation pathway.

Bacterial responses to antibiotics are complex and involve many genetic and biochemical pathways. This Review describes the effects of bactericidal antibiotics on bacterial cellular processes, the associated responses that contribute to killing and recent insights into these processes revealed through the study of biological networks.

In addition to being a major worldwide contributor to diarrhoeal disease,Giardia intestinalisis a useful model system for studying basic eukaryotic cellular processes owing to its reduced complexity. Here, Svärd and colleagues review the recent advances in our understanding of giardial cell biology and pathogenesis.

Dendritic cells form an important arm of the innate immune defence and provide protection against various pathogens. Heidi Barth and colleagues provide an overview of the interaction of dendritic cells with hepatitis B virus, hepatitis C virus and HIV.

Diseases spread across the world more than ever. Sarah Randolph and David Rogers use six examples of diseases to explore the factors that are involved in the spread and establishment of diseases and discuss how this information can be used to predict where new infections can take hold and become established.