Cell Tales - Volume 10

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In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. A Nature Research Journal. Releasing intact membrane protein complexes in bicelles or nanodiscs into the gas phase for observation by mass spectrometry. Brief Communication p Editorial 26 November This Month 26 November Software can be like music, but an evaluation of software tools can involve some hard-to-play chords.

Research Highlights 26 November GFP targeted to satellite repeats via transcription activator—like effectors TALEs allows the imaging of nuclear dynamics early in mouse development. Researchers define conditions in which human stem cells can be maintained in the ground state of pluripotency. Methods in Brief 26 November Tools in Brief 26 November An imaging strategy based on telecommunications technology dramatically accelerates fluorescence microscopy.

Chromatin interaction dynamics are quantified using a modified ChIP method that measures cross-linking kinetics. Laser-guided assembly of protein microscaffolds lets researchers construct multispecies cellular communities.

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Bacteria's ability to withstand broad genomic editing offers a potential route toward more robust and useful genetically modified organisms. Technology Feature 26 November Imaging with better than nanometer resolution brings new subcellular-scale details into focus. Practitioners share how they weigh trade-offs in speed, resolution and phototoxicity.

RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression.

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Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results. Perspective 26 November This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses which indices are best suited for specific tasks. Analysis 03 November open.

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Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge. Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis. Brief Communication 03 November Discrepancies between model prediction and experimental measurements enable molecular-level discovery with a whole-cell model of Mycoplasma genitalium.

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Brief Communication 20 October A method and software for profiling microbial communities from shotgun sequence data uses universal single-copy marker sequences for accurate species-level assignment. The method can classify species lacking a reference genome sequence, making it possible to analyze the large fraction of unknown microbes in the human gut.

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Brief Communication 29 September The metagenomeSeq tool robustly detects the differential abundance of microbes in marker-based microbial surveys by tackling the problems of data sparsity and undersampling common to these data sets. Brief Communication 13 October A simple method for preparing entirely monovalent quantum dots is described. These reagents can be targeted to protein and lipid tags and used as imaging probes in live cells. Amphipols, bicelles and nanodiscs are used to study intact membrane protein complexes by mass spectrometry, with better preservation of oligomeric complexes than traditional detergent micelles.

A database of known drug-gene interactions, with information derived from many public sources, allows the identification of genes that are currently targeted by a drug and the membership of genes in a category, such as kinase genes, that have a high potential for drug development. Brief Communication 06 October Article 06 October ATAC-seq queries the location of open chromatin, the binding of DNA-associated proteins and chromatin compaction at nucleotide resolution. Article 27 October The Spinach2 RNA aptamer provides substantially improved imaging over its predecessor Spinach, enabling live-cell imaging of many tagged RNA species including toxic trinucleotide repeat—containing RNAs.

Article 20 October Cover art by Erin Dewalt.

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Editorial 14 February A collection of articles illustrates ways that synthetic biology tools and tactics both draw from and stimulate chemical biology research. Elements 14 February Ryan Mehl is on a mission to make unnatural amino acids part of the natural order at the Unnatural Protein Facility. Research Highlights 14 February The bacterial halogenase SyrB2 catalyzes selective installation of halogens in place of unactivated aliphatic C-H bonds. TRPM3 can permeate ions through two distinct pores—the central pore and a likely alternative 'omega pore'.

Entry of ions through the alternative pore of TRPM3 contributes to pain generation, making it an attractive target for the design of new analgesics. System-wide approaches are gaining popularity over traditional studies of individual molecular components. A new NMR approach unravels the interaction hierarchy of these different components by placing them in direct competition for the same target.

Brief Communication 02 February A stable replication system, based on a DNA polymerase that replicates cytoplasmic plasmids with unique terminal proteins, decouples plasmid gene replication from host genome replication, allowing for continuous targeted evolution in vivo. Translational reprogramming, which enables site-specific incorporation of non-natural amino acids into proteins, offers practical tools for studying protein function but also provides insights into the genetic code.

Bacteriophages engineered with a amino-acid genetic code make use of the additional noncanonical amino acid during in vitro evolution.

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  • Article 05 January Inhibitor GSK inhibits the phosphatase and oncogenic activities in cell lines and a xenograft tumor model. This peripheral pore is inwardly rectifying, whereas the canonical central axis pore is outwardly rectifying. Article 12 January Optogenetic systems permit the temporal and spatial control of gene expression using light.

    A variant of the LOV domain—containing EL protein displays responsive blue light—gated transcriptional control of genes in zebrafish and in mammalian cell lines.

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    Synthetic biology requires orthogonal inputs and outputs to avoid undesired crosstalk between genetic constructs. Transcription activator—like effectors TALEs , which bind diverse DNA sequences and can thus be orthogonal, are now employed to construct NOR gates and logic circuits in mammalian cells.

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    Article 26 January Halogenases differ from hydroxylases by coordination of a chloride ion at the reactive iron center, which is taken up by an activated substrate. Biochemical and spectroscopic evidence now show other anions can be used, resulting in the first enzymatic incorporation of nitrogen onto unactivated aliphatic carbons. Article 02 February