R2C2+UMI: Combining concatemeric consensus sequencing with unique molecular identifiers enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers.

The sequencing of PCR amplicons is a core application of high-throughput sequencing technology. Using unique molecular identifiers (UMIs), individual amplified molecules can be sequenced to very high accuracy on an Illumina sequencer. However, Illumina sequencers have limited read length and are therefore restricted to sequencing amplicons shorter than 600bp unless using inefficient synthetic long-read approaches. Native long-read sequencers from Pacific Biosciences and Oxford Nanopore Technologies can, using consensus read approaches, match or exceed Illumina quality while achieving much longer read lengths. Using a circularization-based concatemeric consensus sequencing approach (R2C2) paired with UMIs (R2C2+UMI) we show that we can sequence ~550nt antibody heavy-chain (IGH) and ~1500nt 16S amplicons at accuracies up to and exceeding Q50 (<1 error in 100,0000 sequenced bases), which exceeds accuracies of UMI-supported Illumina paired sequencing as well as synthetic long-read approaches.

Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2.

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short-read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the rolling circle to concatemeric consensus (R2C2) method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, and regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.

Isolation of a myoglobin molten globule by selective cobalt(III)-induced unfolding.

Reaction of the Schiff-base complex [Co(acetylacetonate-ethylenediimine)(NH3)2]+ with metmyoglobin at pH 6.5 yields a partially folded protein containing six Co(III) complexes. Although half of its alpha-helical secondary structure is retained, absorption and CD spectra indicate that the tertiary structure in both B-F and AGH domains is disrupted in the partially folded protein. In analogy to proton-induced unfolding, it is likely that the loss of tertiary structure is triggered by metal-ion binding to histidines. Cobalt(III)-induced unfolding of myoglobin is unique in its selectivity (other proteins are unaffected) and in allowing the isolation of the partially folded macromolecule (the protein does not refold or aggregate upon removal of free denaturant).

Hair chromium content of women with gestational diabetes compared with nondiabetic pregnant women.

Hair chromium concentration (HCC) of normal and diabetic pregnant women was determined by atomic-absorption spectroscopy. For nondiabetic pregnant women the value from 68 hair samples was 472 +/- 61 ng/g (mean +/- 95% CI); for gestational diabetics it was 734 +/- 155 ng/g from 42 hair samples. The difference was highly significant (P less than 0.005). Intermediate hair chromium concentrations were observed in 20 pregnant women with pregestational, overt diabetes mellitus (mean: 575 +/- 182 ng/g). Fifty-two women had a second hair sample taken later during pregnancy that showed a significant decrease in HCC (P less than 0.05). However, this decrease was confirmed only for the diabetic pregnant group. Age and parity did not influence the HCC. The data suggest that impaired utilization of chromium may be a possible etiology for gestational diabetes mellitus.

Chromium in biological systems, I. Some observations on glucose tolerance factor in yeast.

Glucose tolerance factor (GTF) has been isolated from a commercially available yeast extract powder, by a simple procedure under mild conditions. This cationic yellow material enhances considerably CO2 production in several yeast strains, after a lag time which can be eliminated by preincubation with glucose. The enhancement of CO2 production by GTF is not specific for glucose, and its effect on galactose raises the possibility that it influences the transport of the sugar to the cells. The ineffectiveness of GTF on cell free extract and the results of a Michaelis plot for CO2 production support this hypothesis.