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This Week in Nature: Feb 26, 2009

In early online publication, scientists performed a genome-wide SNP scan in patients with cystic fibrosis to identify IFRD1 as a modifier of cystic fibrosis lung disease severity. In vivo, IFRD1 deficiency caused delayed bacterial clearance from the airway, suggesting that IFRD1 has its effect by regulating neutrophil effector function.

Also in early online, researchers have looked at host-pathogen co-evolution in HIV by studying the immunity-activating human leukocyte antigen. HLA puts epitopes of HIV proteins on the surface of infected cells, to activate the immune system to killing them, but mutations in these proteins can increase HIV virulence. They looked at viral sequences and HLA alleles from 2,800 subjects, drawn from 9 distinct study cohorts spanning 5 continents, and found strong correlations between mutant epitopes and HIV adaptation. "This process of viral adaptation ... highlights the challenge for a vaccine to keep pace with the changing immunological landscape presented by HIV," they say.

Researchers used a genome-wide screen to identify the prion protein (PrP) as having the greatest affinity for amyloid-beta (AB) peptides, that when they form oligomers cause Alzheimer's disease. Interaction between the oligomers and PrP did not require the highly pathogenic form of the protein, which is a misfolded version of the normal PrP. Further studies show that long-term potentiation is not blocked in mice that have AB oligomers but not PrP. "So [PrP] seems to be a main receptor for [AB] oligomers, mediating their deleterious effects on synaptic function," says this related news story.

In a paper published this week in Nature Nanotechnology, Oxford Nanopore researchers show proof-of-concept work that their sequencing technology can identify unlabelled nucleoside 5'-monophosphate molecules with accuracies averaging 99.8 percent. It could also tell apart methylated cytosine from the four standard DNA bases. A story at Tech Review says that while they haven't yet shown that they can run complete DNA sequences, it's an important step forward for nanopore sequencing in general. "They've shown the feasibility of all the steps," says Jeffrey Schloss at NHGRI.

The Scan

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.

DNA Biobank Developed for French Kidney Donors, Recipients

The KiT-GENIE biobank described in the European Journal of Human Genetics contains DNA samples, genotyping profiles, immune patterns, and clinical features for thousands of kidney donors or transplant recipients in Nantes, France.

Cardiometabolic Disease May Have Distinct Associations With Microbial Metabolites in Blood, Gut

By analyzing gut microbes in combination with related metabolites in feces and blood, researchers in Nature Communications found distinct cardiometabolic disease relationships at each site.

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.