Person:

Presser, Aviva

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics,’ focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

Two billion people world-wide use kerosene-burning lamps for household lighting. These lamps produce large quantities of soot. In Chapter 2, I describe our field study examining 230 people in rural Uganda. I show that kerosene lamps are a major source of smoke exposure in the developing world, and that replacing such lamps with solar-powered lights reduces indoor soot levels 17-fold, leading to significant improvements in health within months. This finding is particularly notable because respiratory disease is the #1 cause of death in children under 5 worldwide.

Because solar cells are a challenge to manufacture in the developing world, I next examined the potential of harvesting electrons from soil-based microbes as a source of clean energy. Such devices are known as microbial fuel cells (MFCs); because soil is available everywhere, MFCs can, in principle, be locally constructed all over the world. In Chapter 3, I describe our exploration of the biology of MFCs, using high-throughput DNA sequencing to demonstrate a role for genus Pseudomonas in energy production. I also examine numerous agricultural products available throughout the developing world to determine whether any could serve as a suitable ‘feed’ for MFC soil. I find that dried animal blood increases MFC energy production 10-fold. In Chapter 4, I describe our design of a modular, stackable MFC, demonstrate that it can be easily constructed in rural Africa, and use it to power lights and to charge a cell phone battery.

In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes—the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.

The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.