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Padlock probes bound to bisulfitetreated genomic DNA in which cytosine residues (red) that are not methylated have been converted to uracils. Deng et al. and Ball et al. use customized padlock probes and next-generation sequencing to identify differences in DNA methylation between induced pluripotent stem cells and the fibroblasts from which they were derived (p 353, p 361).
If there is one thing that the new team at the US Food and Drug Administration should immediately implement, it is a comprehensive, open database of drug-related adverse events.
A gout drug has been approved by the FDA, the first in 40 years, with three more in the wings. What accounts for this sudden slew of gout therapies? Jill U. Adams investigates.
More needs to be done to tap the potential of drug discovery programs in mid-tier biotech companies for innovative treatments against neglected diseases.
Although fewer antibody fragments have entered the clinic than full-length monoclonal antibodies, proof-of-concept studies for these therapeutics remain the main hurdle.
Two groups have combined padlock probes and massively parallel sequencing to characterize cytosine methylation in targeted regions of the human genome.
Only a subset of single-nucleotide polymorphisms (SNPs) can be genotyped in genome-wide association studies. Imputation methods can infer the alleles of 'hidden' variants and use those inferences to test the hidden variants for association.
Although technically feasible, whole-genome analysis of cytosine methylation using bisulfite sequencing remains prohibitively expensive for large eukaryotic genomes. Deng et al. use 30,000 nondegenerate padlock probes to capture ∼66,000 bisulfite-converted sites in human CpG islands and compare their methylation in fibroblasts, embryonic stem cells and induced pluripotent stem cells.
Ball et al. exploit next-generation sequencing to detect methylation across the human genome. A targeted approach uses padlock probes and bisulfite-treated DNA, whereas an untargeted method relies on the methylation-sensitive restriction enzyme HpaII.
Knowing a drug's mode of action is invaluable for informing drug discovery efforts. Ho et al. construct an optimized yeast genomic library that enables rapid mutant cloning by complementation to guide mode-of-action studies.
Wollscheid et al. describe a multiplexed, mass spectrometry–based approach to catalog glycoproteins on the surfaces of live cells without the need for antibodies. They use it to monitor changes in the cell-surface glycoproteome during T-cell activation and the differentiation of embryonic stem cells to neural progenitors.
Many enzymes in eukaryotic and prokaryotic proteomes have no known substrate. Bachovchin et al. use the fluorescence polarization signal of broad-spectrum, activity-based probes to find inhibitors of such enzymes in high-throughput screens.