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This Week in PNAS: Jul 25, 2017

In the early, online edition of the Proceedings of the National Academy of Sciences, investigators from the Joint Genome Institute, the University of Maine, and elsewhere report on findings from a genome sequencing study of the red algae Porphyra umbicalis. Using a combination of Pacific Biosciences and Illumina sequencing, the team put together an almost 88 million base haploid genome for the red algae, which is capable of surviving in the harsh intertidal zone, uncovering 13,125 predicted gene loci. Comparing the genome with sequences from land plants and other red algae highlighted shared biology as well as features that appeared to be distinct to P. umbicalis.

A team from Canada and China outlines a deep neural network model for sequencing peptides de novo with tandem mass spectrometry. The approach, known as DeepNovo, is meant to learn tandem mass spectra, fragment ions, and peptide sequence patterns based on convolutional neural networks, long short-term memory recurrent neural networks, and local dynamic programming. When they applied DeepNovo to a handful of datasets from mouse, human, fruit fly, and other models, the researchers found that it compared favorably with other peptide sequencing approaches when it came to both amino acid level and peptide level accuracy.

A series of papers explores potential ties between cultural and biological co-evolution, bringing together findings from the Sackler Colloquium of Biology Through Culture. For one of the studies, Dalhousie University biology researcher Hal Whitehead considers mitochondrial DNA diversity in the context of social learning and ecotypes in whales and dolphins, for example, while other teams consider cultural contributions to everything from cognition and learning to brain volume, longevity, and sociality.