Topics overview: Error-correction code (ECC) sequencing can improve sequencing accuracy, Higher affinity T cell receptors, Molecular afterglow imaging, Human fecal sample processing in metagenomic studies, Pearl millet genome sequence improves agronomic traits in arid environments.
1、Highly accurate fluorogenic DNA sequencing with information theory–based error correction.
Eliminating errors in next-generation DNA sequencing has proved challenging. Here Zitian Chen at Beijing Advanced Innovation Center for Genomics (ICG) in Beijing, China and his colleagues present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory–based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. They show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.
Read more, please click http://www.nature.com/articles/nbt.3982
2、Generation of higher affinity T cell receptors by antigen-driven differentiation of progenitor T cells in vitro.
Many promising targets for T-cell-based cancer immunotherapies are self-antigens. During thymic selection, T cells bearing T cell receptors (TCRs) with high affinity for self-antigen are eliminated. The affinity of the remaining low-avidity TCRs can be improved to increase their antitumor efficacy, but conventional saturation mutagenesis approaches are labor intensive, and the resulting TCRs may be cross-reactive. Here Thomas M Schmitt at Fred Hutchinson Cancer Research Center in Washington, USA and his colleagues describe the in vitro maturation and selection of mouse and human T cells on antigen-expressing feeder cells to develop higher-affinity TCRs. The approach takes advantage of natural Tcrb gene rearrangement to generate diversity in the length and composition of CDR3β. In vitro differentiation of progenitors transduced with a known Tcra gene in the presence of antigen drives differentiation of cells with a distinct agonist-selected phenotype. They purified these cells to generate TCRβ chain libraries pre-enriched for target antigen specificity. Several TCRβ chains paired with a transgenic TCRα chain to produce a TCR with higher affinity than the parental TCR for target antigen, without evidence of cross-reactivity.
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3、Molecular afterglow imaging with bright, biodegradable polymer nanoparticles.
Afterglow optical agents, which emit light long after cessation of excitation, hold promise for ultrasensitive in vivo imaging because they eliminate tissue autofluorescence. However, afterglow imaging has been limited by its reliance on inorganic nanoparticles with relatively low brightness and short-near-infrared (NIR) emission. Here Qingqing Miao at Nanyang Technological University in Singapore and her colleagues present semiconducting polymer nanoparticles (SPNs) <40 nm in diameter that store photon energy via chemical defects and emit long-NIR afterglow luminescence at 780 nm with a half-life of ∼6 min. In vivo, the afterglow intensity of SPNs is more than 100-fold brighter than that of inorganic afterglow agents, and the signal is detectable through the body of a live mouse. High-contrast lymph node and tumor imaging in living mice is demonstrated with a signal-to-background ratio up to 127-times higher than that obtained by NIR fluorescence imaging. Moreover, they developed an afterglow probe, activated only in the presence of biothiols, for early detection of drug-induced hepatotoxicity in living mice.
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4、Towards standards for human fecal sample processing in metagenomic studies.
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here Paul I Costea at European Molecular Biology Laboratory in Heidelberg, Germany and his colleagues tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. They compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. They found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, they considered resulting DNA quantity and quality, and they ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. They recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
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5、Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments.
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. Rajeev K Varshney at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in Hyderabad, Telangana State, India and his colleagues report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. They highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. They resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. They use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. They believe that these resources should empower researchers and breeders to improve this important staple crop.
Read more, please click http://www.nature.com/articles/nbt.3943