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This Week in Science: Aug 3, 2018

In Science this week, an international research team publishes a genetic study of Homo floresiensis, an extinct species of pygmies that arose twice and independently tens of thousands of years apart on the Indonesian island of Flores. The scientists generated genome-scale SNP data and whole-genome sequences from a group of modern-day pygmy humans living near the site on Flores whereH. floresiensis was discovered, finding "a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins." They also show that the short stature of the current Flores pygmy population is the result of polygenic selection acting on standing variation. Taken together, the findings suggest that the insular dwarfism observed on Flores arose independently in two separate hominin lineages. GenomeWeb has more on this study, here.

In Science Translational Medicine, an international group of industry and academic researchers reports a new method for counting immune cells based on DNA signatures that overcomes some of the limitations of current approaches such as flow cytometry. The new technique relies on epigenetic qPCR to analyze subpopulations of human leukocytes and was shown to be comparable to flow cytometry in a study of liquid blood samples from 97 HIV-positive patients and 25 healthy donors. Importantly, the new method was also able to detect abnormal immune cell counts in dried blood samples from 24 infants with immunodeficiency syndromes. The findings suggest that epigenetic qPCR is a precise and accurate method for immune monitoring and may be a useful addition to current immune diagnostics.

And in Science Advances, a Johns Hopkins-led team describes the identification of two genes associated with the restriction of HIV by type 1 interferon, which inhibits viral replication. The scientists sequenced RNA from activated CD4+ T cells — cells that support HIV replication — in 19 HIV-infected individuals before and after treatment with interferon alpha 2b. They identified a number of genes whose expression were altered with the interferon treatment including CMPK2 and BCL-G, which were upregulated and confirmed to restrict HIV in immune cells.