Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.
We present Interactome INSIDER, a tool to link genomic variant information with
structural protein-protein interactomes. Underlying this tool is the application of
machine learning to predict protein interaction interfaces for 185,957 protein
interactions with previously unresolved interfaces, in human and 7 model organisms,
including the entire experimentally determined human binary interactome. Predicted
interfaces exhibit similar functional properties as known interfaces, including enrichment
for disease mutations and recurrent cancer mutations. Through 2,164 de
novo mutagenesis experiments, we show that mutations of predicted and known
interface residues disrupt interactions at a similar rate, and much more frequently than
mutations outside of predicted interfaces. To spur functional genomic studies, Interactome
INSIDER (http://interactomeinsider.yulab.org) enables users to identify whether
variants or disease mutations are enriched in known and predicted interaction interfaces
at various resolutions. Users may explore known population variants, disease mutations,
and somatic cancer mutations, or upload their own set of mutations for this purpose.
We describe a method for producing high-resolution chemical patterns on surfaces to control the attachment and growth of cultured neurons. Microcontact printing has been extended to allow the printing of micron-scale protein lines aligned to an underlying pattern of planar microelectrodes. Poly-L-lysine (PL) lines have been printed on the electrode array for electrical studies on cultured neural networks. Rat hippocampal neurons showed a high degree of attachment selectivity to the PL and produced neurites that faithfully grew onto the electrode recording sites.
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