Commentary

In their own defense, tissues send a panoply of signals that initiate immunity and guide the choice of effector class. T_H1-T_H2 and T_reg is far too simple a representation of the breathtaking variety of the resulting responses.

The immune system has co-evolved with microbes that cause acute infectious disease. Immune responses must be appropriate to allow survival of both the individual and the species. These responses involve complex interactions that often go unmeasured.

Communicating about and comprehending immune responses and immunity will be facilitated by greater attention to semantic precision and consistency and increased willingness to engage with the full dimensionality and quantitative nature of immunological phenomena.

A well functioning lab is a productive lab. Here the guiding principles of good lab management are discussed.

Recent advances in flow cytometry technologies are changing how researchers collect, look at and present their data.

Successful microarray experimentation can generate enormous amounts of data, potentially very rich but also very unwieldy. Bold outlooks and new methods for data analysis and presentation should yield additional insight into the complexities of the immune system.

RNA interference and chromatin immunoprecipitation are now firmly established as useful methods for studying mechanisms of gene regulation in vivo. Their combined use can help elucidate gene regulation 'logic' by aiding in target gene identification for transcription factors and chromatin-modifying complexes.

Disease-oriented, introductory medical curricula can help overcome educational and institutional barriers that separate aspiring translational scientists in PhD programs from the world of medicine.

Immunology had an unexpected and decisive part in challenging the claims of 'Intelligent Design' proponents at the US trial on the teaching of evolution in public schools in Dover, Pennsylvania.

The 100th anniversary of Robert Koch's receiving the Nobel Prize reminds us of his achievements as a founder of modern bacteriology and as a forefather of immunology.

Despite considerable advances in identifying the environmental agents that trigger allergy and the immunological mechanisms involved, progress in developing effective treatments remains frustratingly slow. Is it time to rethink some of the paradigms guiding this research?

Among the concerns surrounding genetically modified crops has been the possibility of expressing within a plant new proteins that may be allergenic. Using available technology, practical approaches have been adopted to help prevent the creation of foods that are allergenic.

The US has entered a new period of fiscal restraint. What does this mean for basic research? Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, discusses the way forward for research scientists in the US.

Lung mechanics, immunology, genetics, diet and endocrinology may act in a developmental context to link two complex traits: obesity and asthma.

HIV testing is now required for non-HIV-AIDS-related immunological studies in areas of high HIV prevalence. Ethical guidelines for testing in these circumstances need clarification and sensitive protocols need to be developed.

How does air pollution affect asthma and allergic rhinitis? Particulate and gaseous pollution drive proallergic inflammation through the generation of oxidative stress, which is regulated by individual genetic susceptibility.

The present shortage in the US influenza vaccine supply has finally focused public attention on recurrent problems faced by public health officials in ensuring the availability of many vaccines.

The natural history of human immunodeficiency virus (HIV) infection has been altered through the development of drugs targeting two key viral enzymes, reverse transcriptase and protease. Continued advances from basic science have unearthed many other points of attack in the HIV life cycle that could lead to new classes of HIV therapeutics.

As part of the national effort in the US to protect civilians from bioterrorist attacks, the US National Institute of Allergy and Infectious Diseases (NIAID) was charged with the development of diverse research resources. The NIAID Resources for Biodefense Research program is forging new collaborations between immunologists and infectious disease experts and is reinvigorating research in the general area of immune protection against pathogenic infection.

The combination of bioinformatic and biological approaches constitutes a powerful method for identifying gene regulatory elements. High-quality genome sequences are available in public databases for several vertebrate species. Comparative cross-species sequence analysis of these genomes shows considerable conservation of noncoding sequences in DNA. Biological analyses show that an unexpectedly high number of the conserved sequences correspond to functional cis-regulatory regions that influence gene transcription. Because research biologists are often unfamiliar with the bioinformatic resources at their disposal, this commentary discusses how to integrate biological and bioinformatic methods in the discovery of gene regulatory regions and includes a tutorial on widely available comparative genomics programs.