Genome sequence of AM6, isolated from a Parkinson's disease patient.

Here, we report the genome sequence of AM6, isolated from a fecal sample obtained from a Parkinson's disease patient. The bacterial genome was sequenced using Illumina technology on a NextSeq 500 platform. The assembled genome of comprises 4,318,463 base pairs with a G + C content of 47.

PolyCrit: An Online Collaborative Platform for Polymer Characterization.

Polymer liquid chromatography at critical conditions (LCCC) is a chromatographic separation condition achieved by carefully balancing the interaction of a polymer with stationary and mobile phases to make the elution time of a polymer in chromatography independent of its molecular weight. By removing the dependence of elution time on polymer molecular weight, the LCCC then allows separation of polymer samples on the basis of secondary differences, such as topology, branching, and end-group functionality, that are otherwise difficult to resolve. Despite its potential, LCCC remains under-employed due to the complexity of its optimization and the scattered nature of existing data.

Engineering mtDNA deletions by reconstituting end joining in human mitochondria.

Recent breakthroughs in the genetic manipulation of mitochondrial DNA (mtDNA) have enabled precise base substitutions and the efficient elimination of genomes carrying pathogenic mutations. However, reconstituting mtDNA deletions linked to mitochondrial myopathies remains challenging. Here, we engineered mtDNA deletions in human cells by co-expressing end-joining (EJ) machinery and targeted endonucleases.

Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding.

Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecules by DNA sequencing. However, the solution properties of individual protein molecules cannot be probed using such approaches because they are completely altered by DNA attachment. Mass spectrometry enables parallel evaluation of protein properties amenable to physical fractionation such as solubility and oligomeric state, but current approaches are limited to libraries of 1,000 or fewer proteins.

Genome-wide profiling of highly similar paralogous genes using HiFi sequencing.

Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes.