Summaries of newsworthy papers published online on 10 December 2006 in Nature and Nature Research Journals. Lightning strikes twice for milk drinkers, How shigella causes dysentery, Sensing fungal infections, and Improving metagenomics efforts.
NATURE AND THE NATURE RESEARCH JOURNALS PRESS RELEASE
For papers that will be published online on 10 December 2006
This press release is copyrighted to the Nature journals mentioned below.
This press release contains:
Summaries of newsworthy papers:
- Malaria parasite diversity – Nature Genetics
- Lightning strikes twice for milk drinkers – Nature Genetics
- How shigella causes dysentery – Nature Immunology
- Sensing fungal infections – Nature Immunology
- Improving metagenomics efforts – Nature Methods
Mention of papers to be published at the same time with the same embargo
Geographical listing of authors
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********************NATURE GENETICS *********************
,  &  Malaria parasite diversity
Three studies independently characterize the genetic diversity of the parasite that causes malaria in the January issue of Nature Genetics.
Two of the studies focus on Plasmodium falciparum, the most deadly of the Plasmodium species known to cause human malaria, while one study also compares it to the related Plasmodium reichenowi, which infects chimpanzees. Overall, these data constitute a valuable resource that should improve understanding of drug resistance in malaria, as well as identifying candidate targets for vaccines.
Dyann Wirth and colleagues present a genome-wide map of diversity in P. falciparum, including full genome sequencing of 16 new and geographically diverse strains, and targeted sequencing of an additional 54 worldwide isolates. In an accompanying study, Xin-zhuan Su, Philip Awadalla and colleagues focus on sequencing of genomic regions coding for proteins within 4 P. falciparum isolates. They sequenced approximately 3,500 genes, representing about 19% of the genome, develop a high-resolution map of genetic variation, and report 7 new candidate targets for vaccines. In the third study, Manolis Dermitzakis, Matthew Berriman and colleagues provide the first sequence of the P. reichenowi strain, as well as the sequence of two P. falciparum strains, and examine the evolutionary differences between the two. One of the P. falciparum strains, a new uncultured clinical isolate from an individual from Ghana, may provide a better model than strains cultured in the laboratory.
Dyann Wirth (Harvard School of Public Health, Boston, MA, USA)
Tel: +1 617 432 1563; E-mail: firstname.lastname@example.org
[Author paper 1]
Xin-zhuan Su (National Institutes of Health, Rockville, MD, USA)
Tel: +1 301 402 0876; E-mail: email@example.com
[Author paper 2]
Emmanouil Dermitzakis (Wellcome Trust Sanger Institute, Hinxton, UK)
Tel: +44 1223 494866; E-mail: firstname.lastname@example.org
[Author paper 3]
Additional contact for comment on the papers:
Jane Carlton (New York University School of Medicine, NY, USA)
Tel: +1 212 263 4377; E-mail: email@example.com
 Lightning strikes twice for milk drinkers
The ability of Africans and Europeans to digest milk as adults is a textbook example of a trait arising independently in two populations in response to the same strong selective pressure. This ability - known as lactase persistence - is analyzed in the January issue of Nature Genetics.
Lactase persistence is frequent in Northern European populations, but much lower elsewhere, and may have become established as a consequence of cattle domestication and a pastoralist lifestyle. Previous work had shown that genetically, it could be attributed to variants that control the expression of the gene encoding the enzyme lactase-phlorizin hydrolase (LPH). This enzyme breaks down lactose into more easily absorbed sugars such as glucose and galactose.
Sarah Tishkoff and colleagues asked whether the genetic basis of lactase persistence in certain pastoralist populations in East Africa might be attributed to the same variants. They studied 470 lactase-persistent and lactase non-persistent individuals from Kenya, Tanzania and Sudan and found a significant association between lactase persistence and one variant that is very close in location to the LPH variant previously associated with the trait in Europeans. Because other genetic markers in the region differed between the two populations, the authors conclude that the lactase persistent-associated LPH variants arose independently.
Sarah Tishkoff (University of Maryland, College Park, MD, USA)
Tel: +1 301 405 6038; E-mail: firstname.lastname@example.org
Other papers from Nature Genetics to be published online at the same time and with the same embargo:
 Mutations in SYNE1 lead to a newly discovered form of autosomal recessive cerebellar ataxia
******************* NATURE IMMUNOLOGY *******************
 How shigella causes dysentery
A report in the January issue of Nature Immunology explores how shigella bacteria survives and spreads in the gut to cause dysentery — a severe infection of the gastrointestinal tract that affects millions of people worldwide. The report finds that a protein produced by shigella is injected into host cells and blocks the production of immune signals required for preventing disease.
Laurence Arbibe and colleagues studied Shigella flexneri infection of human colon cells to understand the bacterial factors required to initiate disease. Shigella bacteria are known to inject up to 20 proteins into gut intestinal cells for the purpose of promoting infection and for dampening immune responses.
They found that one of the injected proteins from Shigella flexneri, called OpsF, could prevent gut cells from switching on genes involved in immune responses. As a consequence of OspF function, Shigella flexneri avoids being killed by immune cells of their host and is thus able to spread throughout the gut and cause disease.
This study highlights the precision with which pathogens such as shigella can dramatically alter host cells. It also suggests that blocking OspF may provide a therapeutic target for treating bacterial dysentery that kills hundreds of thousands of people annually.
Laurence Arbibe (Pasteur Institut, Paris, France)
Tel: +33 1 40 61 32 47; E-mail: email@example.com
Additional comment on the paper:
B. Brett Finlay (University of British Columbia, Vancouver, Canada)
Tel: + 1 604 822 2210; E-mail: firstname.lastname@example.org
 &  Sensing fungal infections
Two studies in the January issue of Nature Immunology demonstrate the importance of a host protein in recognizing the presence of fungal infections. Pathogenic fungi can cause life-threatening infections in individuals with immunodeficiencies, such as those with advanced HIV disease.
Two independent groups, led by Gordon Brown and Yoichiro Iwakura, produced mice that lack the protein Dectin-1, a cell-surface protein implicated in immune responses to fungal infections. Both groups show that mice that lack Dectin-1 are relatively normal except when infected with fungi, which causes more lethality in the mutant mice. The authors also evaluated the types of blunted immune responses that occur in the mutant mice and show that only specific immune functions are defective.
These studies substantially extend our understanding of how pathogenic fungi affect host tissues and the requirement of Dectin-1 in those processes.
Gordon Brown (University of Cape Town, South Africa)
Tel: +27 21 406 6684; E-mail: email@example.com
[Author Paper 7]
Yoichiro Iwakura (University of Tokyo, Japan)
Tel: + 81 3 5449 5536; E-mail: firstname.lastname@example.org
[Author Paper 8]
Additional comment on the paper:
Jürg Tschopp (University of Lausanne, Epalinges, Switzerland)
Tel: + 41 21 692 57 38; E-mail: email@example.com
 Improving metagenomics efforts
A novel technique for simplifying the study of important ecosystems is described in the January issue of Nature Methods.
Shotgun sequencing methods used in metagenomics efforts to study microbial communities produce massive collections of sequence fragments that are very difficult to analyze. A number of methods have been used to attempt to assemble and classify these sequences but they generally fail for highly complex samples and short fragments. Isidore Rigoutsos and colleagues describe a new sequence classification method that uses information from 340 completed genomes to classify and assemble sequence fragments from complex communities that have been resistant to previous efforts.
Isidore Rigoutsos (IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA)
Tel: +1 914 945 1384; E-mail: firstname.lastname@example.org
Other papers from Nature Methods to be published online at the same time and with the same embargo:
 Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization
 Retrograde neuronal tracing with a deletion-mutant rabies virus
 Major signal increase in fluorescence microscopy through dark-state relaxation
Items from other Nature journals to be published online at the same time and with the same embargo:
 Hsp70 regulates erythropoiesis by preventing caspase-3-mediated cleavage of GATA-1
 A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family
Nature PHYSICS (http://www.nature.com/naturephysics)
 Scaling of proton acceleration driven by petawatt-laser–plasma interactions
 Controllable valley splitting in silicon quantum devices
 Quasiparticle dynamics in graphene
NATURE MATERIALS (http://www.nature.com/naturematerials)
 Atomic structure of the binary icosahedral Yb–Cd quasicrystal
 Six-fold coordinated carbon dioxide VI
 A rack-and-pinion device at the molecular scale
 Triggering dynamics of the high-pressure benzene amorphization
Nature MEDICINE (http://www.nature.com/naturemedicine)
 NF-kappaB in breast cancer cells promotes osteolytic bone metastasis by inducing osteoclastogenesis via GM-CSF
 Loss of tumor suppressor PTEN function increases B7-H1 expression and immunoresistance in glioma
 Chromosome 5q deletion and epigenetic suppression of the gene encoding alpha-catenin (CTNNA1) in myeloid cell transformation
 Lactobacillus acidophilus modulates intestinal pain and induces opioid and cannabinoid receptors
Nature NEUROSCIENCE (http://www.nature.com/natureneuroscience)
 A new naturally occurring GABAA receptor subunit partnership with high sensitivity to ethanol
 Attractive axon guidance involves metric membrane transport and exocytosis in the growth cone
 Representation of body identity and body actions in extrastriate body area and ventral premotor cortex
 Essential function of HIPK2 in TGFbeta-dependent survival of midbrain dopamine neurons
NATURE CELL BIOLOGY (http://www.nature.com/naturecellbiology)
 Regulation of protein tyrosine phosphatase (PTP) 1B by sumoylation
 H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability
 Basal-to-apical cadherin flow at cell junctions
 Triggering neural differentiation of ES cells by subtype switching of importin-alpha
Nature STRUCTURAL & MOLECULAR BIOLOGY (http://www.nature.com/natstructmolbiol)
 Structural insight into the substrate specificity of DNA Polymerase mu
 Heme is involved in microRNA processing
 Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome
GEOGRAPHICAL LISTING OF AUTHORS
The following list of places refers to the whereabouts of authors on the papers numbered in this release. The listing may be for an author's main affiliation, or for a place where they are working temporarily. Please see the PDF of the paper for full details.
Quebec City: 5
Shanghai: 24, 27
Paris: 6, 13, 14, 25
Saint Martin d’Heres: 18
Berlin: 17, 20
Greifswald-Insel Riems: 11
Chieti Scalo: 28
Rome: 13, 21, 28
Osaka: 8, 33
Saitama: 18, 27
Cape Town: 7
Dar es Salaam: 4
Hinxton: 3, 4
London: 3, 7, 30
Oxford: 2, 3, 7
UNITED STATES OF AMERICA
Berkeley: 17, 31
La Jolla: 11, 27
Los Angeles: 22, 23, 26, 30, 35
Palo Alto: 24
San Francisco: 29
Walnut Creek: 9
Chicago: 4, 24
College Park: 4
Boston: 1, 24, 30
Cambridge: 1, 5
Ann Arbor: 22
New York: 3, 10, 16
Yorktown Heights: 9
Chapel Hill: 34
Research Triangle Park: 34
Pittsburgh: 7, 26
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Nature Materials (London)
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Nature Medicine (New York)
Juan Carlos Lopez
Tel: +1 212 726 9325; E-mail: email@example.com
Nature Methods (New York)
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Nature Neuroscience (New York)
Sandra Aamodt (based in California)
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Nature Physics (London)
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