Science Watch® - Tracking Trends and Performance in Basic Research
January/February 2006


Gut Reactions: Toll-Like Receptors and Intestinal Microflora
by Jeremy Cherfas
WHAT'S HOT IN BIOLOGY
Rank      Paper Citations This Period (Jul-Aug 05) Rank Last Period (May-Jun 05)
1 J.D. Bendtsen, et al., "Improved prediction of signal peptides: SignalP 3.0," J. Mol. Biol., 340(4): 783-95, 16 July 2004. [Tech. U. Denmark, Lyngby; Stockholm U., Sweden] *838SU 56 8
2 K.N. Ferreira, et al., "Architecture of the photosynthetic oxygen-evolving center," Science, 303(5665): 1831-8, 19 March 2004. [Imperial Coll., London, U.K.; Japan Sci. Tech. Corp., Nagatsuta] *804EI  43
3 W. Ludwig, et al., "ARB: a software environment for sequence data," Nucl. Acids Res., 32(4): 1363-71, February 2004. [Tech. U. Munich, Germany; U. Heidelberg, Germany] *802RD 41
4 J.D. Storey, R. Tibshirani, "Statistical significance for genomewide studies," Proc. Natl. Acad. Sci. USA, 100(16): 9440-5, 5 August 2003. [U. Washington, Seattle; Stanford U., CA] *709HP 39
5 R.A. Gibbs, et al. (The International HapMap Consortium), "The International HapMap Project", Nature, 426(6968): 789-96, 18/25 December 2003. [74 institutions worldwide] *754QM 34 7
6 M. Stephens, P. Donnelly, "A comparison of Bayesian methods for haplotype reconstruction from population genotype data," Am. J. Hum. Genet., 73(5): 1162-9, November 2003. [U. Washington, Seattle] *742AR 33 10
7 L. Giot, et al., "A protein interaction map of Drosophila melanogaster", Science, 302(5651): 1727-36, 5 December 2003. [CuraGen Corp., New Haven, CT; Wayne St. U. Sch. Med., Detroit, MI; Yale U. Sch. Med., New Haven, CT] *750AX 32
8 A. Bateman, et al., "The Pfam protein families database," Nucl. Acids Res., 32: D138-41, 1 January 2004. [Wellcome Trust Sanger Inst., Cambridge, U.K.; Karolinska Inst., Stockholm, Sweden; Howard Hughes Med. Inst., Washington U. Sch. Med., St. Louis, MO] *763HM 32
9 W.-K. Huh, et al., "Global analysis of protein localization in budding yeast," Nature, 425(6959): 686-91, 16 October 2003. [U. Calif. San Francisco, Howard Hughes Med. Inst., San Francisco, CA] *732DA 30 6
10 W. Li, et al., "Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus," Nature, 426(6965): 450-4, 27 November 2003. [5 U.S. institutions] *747JE 30
 SOURCE: ISI’s Hot Papers DatabaseRead  the Legend.

The Top Ten is still dominated by software tools for the analysis of genome and protein sequences. These include one or two new entries; for example, at #3 is a new "environment" for sequence data, while the latest report from the Pfam protein family database is at #8. This clutter, though it reflects the importance of such analytical tools, may decrease in future. At #12 is a paper describing the amalgamation of three protein databases—Swiss-Prot, TrEMBL and PIR—into a single UniProt, the Universal Protein knowledgebase (R. Apweiler, et al., 32: D115-9, 1 January 2004; 28 citations this period): perhaps a single annual update will replace three.

Surprising science is still being highly cited, but only in the outer reaches of the Hot Topics, where two papers of potential medical interest arouse attention. Hyeryun Choe and Michael Farzan at Harvard University School of Medicine led a group that investigated how the virus responsible for severe acute respiratory syndrome (SARS) interacts with the cells of its host. Their paper, at #10, demonstrates that angiotensin-converting enzyme 2 (ICE-2), which is involved in the regulation of blood pressure, is a functional receptor for the SARS coronavirus. This has all sorts of implications, as the authors note. It hints that other molecules that bind to ICE-2, or even a soluble form of the ICE-2 receptor, could block the course of SARS infection. The structure of the binding region of ICE-2 could also point towards a suitable vaccine against SARS. And a cell line already approved for vaccine production could be enlisted to make SARS for an attenuated or killed virus vaccine by giving it the ability to express ICE-2, which is also essential for viral replication.

At #13 (S. Rakoff-Nahoum, et al., Cell, 118[2]: 229-41, 23 July 2004; 27 citations) is an entirely fresh insight into toll-like receptors (TLRs). These are the basis of the innate immune system. They recognize certain bacterial products such as lipopolysaccharides and mount a non-specific attack. The problem is that the mammalian body is host to bacteria that are not merely not pathogenic, but positively benign. The lower intestine and colon house an estimated 1013 bacteria of diverse species that confer multiple benefits. Why don’t the TLRs recognize and attack them? It had been thought that the TLRs were kept away from the benign bacteria by the epithelia of the gut, while pathogenic bacteria had virulence factors that enabled them to slip through the gut wall, and that brought them into contact with TLRs. Gut microflora have been implicated in inflammatory conditions such as Crohn’s diseases, and so there is considerable interest in the study of commensal bacteria.

Ruslan Medzhitov and his colleagues at Yale University School of Medicine thought that TLRs might be involved, and so studied mice deficient in MyD88, an adaptor molecule essential for TLRs to induce inflammatory cytokines. They dosed MyD88-negative mice with a toxin that destroys the colon epithelium, allowing commensal bacteria to come into contact with TLRs on white blood cells and elsewhere. Medzhitov reasoned that as these mice could not mount an effective TLR-mediated attack, they would not show as severe a response to the toxin as mice with an intact TLR pathway. To the team’s surprise, MyD88-deficient mice showed much higher morbidity and mortality than wild-type mice, which were essentially unharmed.

A painstaking series of experiments eliminated all kinds of alternative explanations and came up with several new ideas about the role and operation of TLRs, not related to immune functions. Interactions between commensal bacteria and the host’s TLRs prevent epithelial injury, perhaps by stimulating the normal production of protective compounds. TLRs also influence cell reproduction in the lining of the gut, maintaining a balance between cell death and proliferation and thus maintaining the integrity of the epithelium. This is of particular interest because medical interventions that involve intestinal damage, such as radiotherapy, chemotherapy, and colonic surgery, are often preceded by antibiotic treatment to reduce the risk of infections. Medzhitov’s work suggests this may not be such a good idea, and that deliberately stimulating TLRs might improve tissue repair and healing.

Medzhitov proposes two distinct functions for TLRs: protection against infection and regulation of tissue growth, at least in epithelia. Both depend on the recognition of bacteria, pathogens, and commensals. And some components, such as cytokines and chemokines, are involved in both functions. The big question he asks: "Which of the two TLR functions evolved first?"end

Dr. Jeremy Cherfas is Science Writer at the
International Plant Genetic Resources Institute, Rome, Italy.

View the top 10 scientists and/or top 3 Hot Papers in Biology.
Science Watch®, January/February 2006, Vol. 17, No. 1
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