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Paper Potpourri


Prabakaran S, Everley RA, Landrieu I, et al. (2011). Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions. Molecular Systems Biology. Epub: doi 0.1038/msb.2011.15.
Researchers at Harvard Medical School compare four methods to measure phospho-form distribution: western blots with phospho-specific antibodies, peptide-based liquid chromatography and mass spectrometry, protein-based LC/MS, and nuclear magnetic resonance spectroscopy. The researchers found that "NMR also uncovered two additional phosphorylations, for which a combination of pepMS and proMS yielded an estimate of the 16-member phospho-form distribution. This combined MS strategy provides an optimal mixture of accuracy and coverage for quantifying distributions."

CNP Array
Campbell CD, Sampas N, Tsalenko A, et al. (2011). Population-genetic properties of differentiated human copy-number polymorphisms. The American Journal of Human Genetics. Epub: doi 10.1016/j.ajhg.2011.02.004.
Campbell et al. have developed a microarray design benchmarked against copy number variants determined from sequencing reads to obtain copy-number polymorphism genotypes for 1,495 CNPs from 487 human DNA samples. Their analysis revealed that CNPs in segmental duplications are more likely to be population differentiated than CNPs in unique regions, and that biallelic CNPs display greater stratification as compared to frequency-matched SNPs. "Our results suggest that CNPs ... might have contributed disproportionately to human diversity and selection," the authors write.

Infantile Exome Sequencing
Götz A, Tyynismaa H, Euro L, et al. (2011). Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. American Journal of Human Genetics. Epub: doi 10.1016/j.ajhg.2011.04.00.
The authors sequenced the exome of a 10-month-old patient who died of hypertrophic mitochondrial cardiomyopathy with combined cardiac respiratory chain complex I and IV deficiency. In their analysis, the researchers identified a homozygous missense mutation in AARS2, which encodes the mitochondrial alanyl-tRNA synthetase and has been shown to cause perinatal or infantile cardiomyopathy with near-total combined mitochondrial respiratory chain deficiency in the heart. "Exome sequencing is a powerful tool for identifying mutations in single patients," the authors write, adding that their study shows that mitochondrial disorders extend to prenatal life.

MicroRNA, HLA-C, and HIV
Kulkarni S, Savan R, Qi Y, et al. (2011). Differential microRNA regulation of HLA-C expression and its association with HIV control. Nature. Epub: doi 10.1038/nature09914.
In this paper, Kulkarnis et al. suggest that the -35 SNP of HLA-C marks a polymorphism that directly affects levels of HLA-C rather than acting as the causal variant for differential HLA-C expression itself. The authors demonstrate that variation within the 3' untranslated region of HLA-C results in relatively low surface expression of alleles that bind this microRNA and high expression of HLA-C alleles that escape post-transcriptional regulation. "The 3' UTR variant associates strongly with control of HIV, potentially adding to the effects of genetic variation encoding the peptide-binding region of the HLA class I loci. Variation in HLA-C expression adds another layer of diversity to this highly polymorphic locus," they add.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.