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- 1From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedA physicist pushed microscopes beyond theoretical limits to provide a better look inside living cells. Author(s): Mats G L Gustafsson Author Affiliations: Mats Gustafsson, who died of brain cancer April 17, 2011,...
- 2From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedIn 2010, 31 billion dollars of the US federal budget were allocated to the 25 Institutes constituting the US National Institutes of Health (NIH), an investment that the research community should exploit to its fullest,...
- 3From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedTo the Editor: Only a small fraction of the human transcriptome (~1%) encodes proteins (1), but a large portion of transcripts is long noncoding RNAs (lncRNAs) and is an unexplored component of mammalian genomes (2)....
- 4From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedCombining proteome analysis with genome sequencing improves gene annotation and yields evidence that some genes presumed to be noncoding are actually expressed. Sequencing a genome is one thing; annotating all...
- 5From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedSoftware for fast and accurate alignment of brain images is used to generate a partial brain atlas for Drosophila melanogaster and should enable circuit mapping. Comparative brain anatomy is an old field that has...
- 6From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedNext-generation sequencing has not been applied to protein-protein interactome network mapping so far because the association between the members of each interacting pair would not be maintained in en masse sequencing....
- 7From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedComplex, curved three-dimensional DNA nanostructures can be created using new DNA origami folding techniques. In the traditional Japanese art of origami, pieces of ordinary paper are folded into extraordinary shapes....
- 8From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedSince my first column on color coding (1) appeared, we have received a number of e-mails asking us to highlight the issue of color blindness. One of those correspondences was published in the October 2010 issue (2)....
- 9From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedWe describe a conditional in vivo protein-trap mutagenesis system that reveals spatiotemporal protein expression dynamics and can be used to assess gene function in the vertebrate Danio rerio. Integration of pGBT-RP2.1...
- 10From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedTwo new reports describe variants of channelrhodopsin 2 with improved properties. Channelrhodopsin 2 (ChR2) has been a godsend tool to study brain function. This protein--originally found in tiny algae--is a...
- 11From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedMats Gustafsson, who died of brain cancer April 17, 2011, found thinking in terms of waves just as easy as thinking in terms of three-dimensional space. Rather than considering the nanometer-scale objects in a cell, he...
- 12From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedWochner et al. describe the evolution of an RNA polymerase ribozyme capable of synthesizing up to 95-nucleotide RNA strands, much longer than the capabilities of natural ribozymes. They used water-in-oil emulsion...
- 13From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedGoold et al. introduce an epitope tag into the cellular prion protein, PrPC, expressed in a neuroblastoma cell line in which endogenous PrP has been knocked down by RNA interference; the tagged PrPC supports prion...
- 14From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedStructural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently...
- 15From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedAlthough 5-hyrdoxymethyl-cytosine (5hmC) is thought to be important for genome function in certain cells, a lack of tools has made profiling difficult. Xu et al. used a 5hmC-specific antibody for methylated DNA...
- 16From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedWhereas genomic data are universally machine-readable, data from imaging, multiplex biochemistry, flow cytometry and other cell- and tissue-based assays usually reside in loosely organized files of poorly documented...
- 17From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedA paleoenzymology approach yields a thermostable thioredoxin enzyme that is functional at acidic pH; the underlying method could prove effective for generating other enzymes with such properties. "Wouldn't you want...
- 18From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedWe report super-resolution fluorescence imaging of live cells with high spatiotemporal resolution using stochastic optical reconstruction microscopy (STORM). By labeling proteins either directly or via SNAP tags with...
- 19From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedA transposon-insertion method can trap and mutate genes while simultaneously revealing their spatiotemporal expression pattern, all in a conditional manner in the live, transparent zebrafish. With over 20,000 human...
- 20From: Nature Methods. (Vol. 8, Issue 6) Peer-ReviewedAnalyzing Drosophila melanogaster neural expression patterns in thousands of three-dimensional image stacks of individual brains requires registering them into a canonical framework based on a fiducial reference of...