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An algorithm for linear mixed models substantially reduces memory usage and run time for genome-wide association studies. The improved algorithm scales linearly in cohort size, allowing the application of these models to much larger samples.
Reprogramming to induced pluripotency of cells from the endangered silver-maned drill and the northern white rhinoceros is reported. Induced pluripotent stem cells from endangered species may prove useful for species preservation in the future.
Expression profiles of several hundred microRNAs in the blood of individuals with disease, including autoimmune disease, cancers, cardiovascular disease and chronic inflammatory disease are reported.
A method for performing quantitative proteomics experiments in Caenorhabditis elegans using stable-isotope labeling of lysine is described. The method can be coupled with RNA interference to examine global effects on the proteome. Also in this issue, Larance et al. describe a very similar method.
A method for performing quantitative proteomics experiments in Caenorhabditis elegans using stable-isotope labeling with amino acids in cell culture (SILAC) is described. The authors used the method to identify heat shock–responsive proteins in worms. Also in this issue, Fredens et al. describe a very similar method.
SourceTracker finds the proportion and origin of contaminants in a given sample. Its database will prove useful in screening of metagenomic datasets for contaminants.
Single-stranded oligonucleotides are used as donor templates for zinc-finger nucleases to create targeted genomic deletions and mutations in mammalian cell lines.
Two-photon excitation in scanned light-sheet microscopy allows deeper imaging than the one-photon implementation and faster three-dimensional imaging of organism development with no evidence of phototoxicity compared to conventional two-photon point scanning microscopy.
Quantitative, large-scale in vivo phosphoproteomics analyses are made possible with a form of spike-in stable-isotope labeling with amino acids in cell culture (SILAC), in which SILAC-labeled cell lines act as an internal standard for mass spectrometry–based tissue phosphoproteome analysis.
This digital PCR device arrays samples into one million small-volume reactors, achieving a dynamic range of 107, measurement precision better than 1% and the ability to detect single-nucleotide variants present at less than 1:100,000.
A new method called functional ultrasound (fUS) is reported that allows imaging of transient changes in blood volume in the whole rat brain with a spatiotemporal resolution not attained by other functional brain imaging modalities.
Two sequence-verified, clonal, publicly available collections of human open reading frames are reported. One collection is in a lentiviral vector for expression in mammalian cells; the other is in the Gateway vector system.
Fiducial marks that can be visualized by both light and electron microscopy are generated by 'branding' fixed tissue with a near-infrared laser and will facilitate correlative light and electron microscopy.
The performance of low-power, continuous-wave stimulated emission depletion microscopy is improved by combining pulsed excitation with time-gated detection. This combination also simplifies super-resolution fluorescence correlation spectroscopy.
A linear, one-tube amplification procedure generates sufficient amounts of material from chromatin immunoprecipitation (ChIP) and reChIP experiments to allow high-throughput sequencing.
An algorithm to combine the results of different quantitative proteomics data processing workflows is presented. The method substantially increases the number of proteins that can be quantified in a proteomics experiment.
The combination of in situ hybridization of fluorescent probes onto chromosomes in solution and flow cytometry allows the quantitative identification of repeat sequences in individual chromosomes.
A combination of PCR stitching with next-generation sequencing results in Stitch-seq, a massively parallel method for interactome mapping. The approach is applied to human protein-protein interactions assayed in yeast two-hybrid screens.
