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This Week in PLoS: Dec 9, 2008

A study in PLoS Genetics used genotype and gene expression data from 89 African-American samples to study the relationship between local gene expression and genetic ancestry. Surprisingly, the researchers found that only about 12 percent of difference in gene expression is due to cis-acting variants. Daniel MacArthur thinks this doesn't bode well for personal genomics: considering that the other 88 percent must be trans-variants, it will not only be even more difficult to describe genetic pathways involved in many complex diseases, but, "making de novo predictions about the effect of a novel sequence variant on distant genes will be immensely more challenging," he writes at Genetic Future.

Another paper in PLoS Genetics studied lactic acidosis in a tumor's microenvironment, which directly affects how the tumor grows. Looking at breast cancer gene expression data sets, scientists found that lactic acidosis response was associated with good survival rates and that "may relate to the role of lactic acidosis in directing energy generation toward aerobic respiration and utilization of other energy sources via inhibition of glycolysis," they say in the abstract.

In PLoS Biology, Cold Spring Harbor's Rob Martienssen used chromatin immunoprecipitation and DNA methylation profiling to map histone modifications in a cell suspension culture of Arabidopsis. While some genes show an increase in DNA methylation, some transposable elements undergo significant loss of DNA methylation and transcriptional activation. Plus, after sequencing siRNA, transposable elements activated in culture have increased levels of 21-nucleotide siRNA, suggesting that RNAi plays a role in epigenetic restructuring for plants grown in cell culture.

Two studies look at TB resistance. In one published in PLoS One, researchers used a high-content peptide microarray with 61 M. tuberculosis proteins to perform antibody profiling of a total of 7446 individual peptide epitopes. They found that the difference between TB+ and TB- can be found not in specific TB serum proteins, but in "peptide epitope 'hotspots' at different locations within the same protein," they say in the abstract. In another study in PLoS Pathogens, scientists used gene expression profiling to study the susceptibility to tuberculosis, finding that CCL1 is one gene involved in susceptibility to TB.


The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.