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Nature Biotechnology

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https://www.readbyqxmd.com/read/28714966/nanoscale-imaging-of-clinical-specimens-using-pathology-optimized-expansion-microscopy
#1
Yongxin Zhao, Octavian Bucur, Humayun Irshad, Fei Chen, Astrid Weins, Andreea L Stancu, Eun-Young Oh, Marcello DiStasio, Vanda Torous, Benjamin Glass, Isaac E Stillman, Stuart J Schnitt, Andrew H Beck, Edward S Boyden
Expansion microscopy (ExM), a method for improving the resolution of light microscopy by physically expanding a specimen, has not been applied to clinical tissue samples. Here we report a clinically optimized form of ExM that supports nanoscale imaging of human tissue specimens that have been fixed with formalin, embedded in paraffin, stained with hematoxylin and eosin, and/or fresh frozen. The method, which we call expansion pathology (ExPath), converts clinical samples into an ExM-compatible state, then applies an ExM protocol with protein anchoring and mechanical homogenization steps optimized for clinical samples...
July 17, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28714965/a-wellness-study-of-108-individuals-using-personal-dense-dynamic-data-clouds
#2
Nathan D Price, Andrew T Magis, John C Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T McDonald, Ulrike Kusebauch, Christopher L Moss, Yong Zhou, Shizhen Qin, Robert L Moritz, Kristin Brogaard, Gilbert S Omenn, Jennifer C Lovejoy, Leroy Hood
Personal data for 108 individuals were collected during a 9-month period, including whole genome sequences; clinical tests, metabolomes, proteomes, and microbiomes at three time points; and daily activity tracking. Using all of these data, we generated a correlation network that revealed communities of related analytes associated with physiology and disease. Connectivity within analyte communities enabled the identification of known and candidate biomarkers (e.g., gamma-glutamyltyrosine was densely interconnected with clinical analytes for cardiometabolic disease)...
July 17, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28671662/long-time-lapse-nanoscopy-with-spontaneously-blinking-membrane-probes
#3
Hideo Takakura, Yongdeng Zhang, Roman S Erdmann, Alexander D Thompson, Yu Lin, Brian McNellis, Felix Rivera-Molina, Shin-Nosuke Uno, Mako Kamiya, Yasuteru Urano, James E Rothman, Joerg Bewersdorf, Alanna Schepartz, Derek Toomre
Imaging cellular structures and organelles in living cells by long time-lapse super-resolution microscopy is challenging, as it requires dense labeling, bright and highly photostable dyes, and non-toxic conditions. We introduce a set of high-density, environment-sensitive (HIDE) membrane probes, based on the membrane-permeable silicon-rhodamine dye HMSiR, that assemble in situ and enable long time-lapse, live-cell nanoscopy of discrete cellular structures and organelles with high spatiotemporal resolution. HIDE-enabled nanoscopy movies span tens of minutes, whereas movies obtained with labeled proteins span tens of seconds...
July 3, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28650462/haplotype-phasing-of-whole-human-genomes-using-bead-based-barcode-partitioning-in-a-single-tube
#4
Fan Zhang, Lena Christiansen, Jerushah Thomas, Dmitry Pokholok, Ros Jackson, Natalie Morrell, Yannan Zhao, Melissa Wiley, Emily Welch, Erich Jaeger, Ana Granat, Steven J Norberg, Aaron Halpern, Maria C Rogert, Mostafa Ronaghi, Jay Shendure, Niall Gormley, Kevin L Gunderson, Frank J Steemers
Haplotype-resolved genome sequencing promises to unlock a wealth of information in population and medical genetics. However, for the vast majority of genomes sequenced to date, haplotypes have not been determined because of cumbersome haplotyping workflows that require fractions of the genome to be sequenced in a large number of compartments. Here we demonstrate barcode partitioning of long DNA molecules in a single compartment using "on-bead" barcoded tagmentation. The key to the method that we call "contiguity preserving transposition" sequencing on beads (CPTv2-seq) is transposon-mediated transfer of homogenous populations of barcodes from beads to individual long DNA molecules that get fragmented at the same time (tagmentation)...
June 26, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28650461/a-light-and-calcium-gated-transcription-factor-for-imaging-and-manipulating-activated-neurons
#5
Wenjing Wang, Craig P Wildes, Tanyaporn Pattarabanjird, Mateo I Sanchez, Gordon F Glober, Gillian A Matthews, Kay M Tye, Alice Y Ting
Activity remodels neurons, altering their molecular, structural, and electrical characteristics. To enable the selective characterization and manipulation of these neurons, we present FLARE, an engineered transcription factor that drives expression of fluorescent proteins, opsins, and other genetically encoded tools only in the subset of neurons that experienced activity during a user-defined time window. FLARE senses the coincidence of elevated cytosolic calcium and externally applied blue light, which together produce translocation of a membrane-anchored transcription factor to the nucleus to drive expression of any transgene...
June 26, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28650460/a-calcium-and-light-gated-switch-to-induce-gene-expression-in-activated-neurons
#6
Dongmin Lee, Jung Ho Hyun, Kanghoon Jung, Patrick Hannan, Hyung-Bae Kwon
Despite recent advances in optogenetics, it remains challenging to manipulate gene expression in specific populations of neurons. We present a dual-protein switch system, Cal-Light, that translates neuronal-activity-mediated calcium signaling into gene expression in a light-dependent manner. In cultured neurons and brain slices, we show that Cal-Light drives expression of the reporter EGFP with high spatiotemporal resolution only in the presence of both blue light and calcium. Delivery of the Cal-Light components to the motor cortex of mice by viral vectors labels a subset of excitatory and inhibitory neurons related to learned lever-pressing behavior...
June 26, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28604659/inference-and-quantification-of-peptidoforms-in-large-sample-cohorts-by-swath-ms
#7
George Rosenberger, Yansheng Liu, Hannes L Röst, Christina Ludwig, Alfonso Buil, Ariel Bensimon, Martin Soste, Tim D Spector, Emmanouil T Dermitzakis, Ben C Collins, Lars Malmström, Ruedi Aebersold
Consistent detection and quantification of protein post-translational modifications (PTMs) across sample cohorts is a prerequisite for functional analysis of biological processes. Data-independent acquisition (DIA) is a bottom-up mass spectrometry approach that provides complete information on precursor and fragment ions. However, owing to the convoluted structure of DIA data sets, confident, systematic identification and quantification of peptidoforms has remained challenging. Here, we present inference of peptidoforms (IPF), a fully automated algorithm that uses spectral libraries to query, validate and quantify peptidoforms in DIA data sets...
June 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28581492/engineered-cpf1-variants-with-altered-pam-specificities
#8
Linyi Gao, David B T Cox, Winston X Yan, John C Manteiga, Martin W Schneider, Takashi Yamano, Hiroshi Nishimasu, Osamu Nureki, Nicola Crosetto, Feng Zhang
The RNA-guided endonuclease Cpf1 is a promising tool for genome editing in eukaryotic cells. However, the utility of the commonly used Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) and Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1) is limited by their requirement of a TTTV protospacer adjacent motif (PAM) in the DNA substrate. To address this limitation, we performed a structure-guided mutagenesis screen to increase the targeting range of Cpf1. We engineered two AsCpf1 variants carrying the mutations S542R/K607R and S542R/K548V/N552R, which recognize TYCV and TATV PAMs, respectively, with enhanced activities in vitro and in human cells...
June 5, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28504668/hla-e-expressing-pluripotent-stem-cells-escape-allogeneic-responses-and-lysis-by-nk-cells
#9
Germán G Gornalusse, Roli K Hirata, Sarah E Funk, Laura Riolobos, Vanda S Lopes, Gabriel Manske, Donna Prunkard, Aric G Colunga, Laïla-Aïcha Hanafi, Dennis O Clegg, Cameron Turtle, David W Russell
Polymorphisms in the human leukocyte antigen (HLA) class I genes can cause the rejection of pluripotent stem cell (PSC)-derived products in allogeneic recipients. Disruption of the Beta-2 Microglobulin (B2M) gene eliminates surface expression of all class I molecules, but leaves the cells vulnerable to lysis by natural killer (NK) cells. Here we show that this 'missing-self' response can be prevented by forced expression of minimally polymorphic HLA-E molecules. We use adeno-associated virus (AAV)-mediated gene editing to knock in HLA-E genes at the B2M locus in human PSCs in a manner that confers inducible, regulated, surface expression of HLA-E single-chain dimers (fused to B2M) or trimers (fused to B2M and a peptide antigen), without surface expression of HLA-A, B or C...
May 15, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28504667/rapid-cloning-of-genes-in-hexaploid-wheat-using-cultivar-specific-long-range-chromosome-assembly
#10
Anupriya Kaur Thind, Thomas Wicker, Hana Šimková, Dario Fossati, Odile Moullet, Cécile Brabant, Jan Vrána, Jaroslav Doležel, Simon G Krattinger
Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes...
May 15, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700562/single-cell-genomics-for-the-masses
#11
Susannah G Tringe
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700561/recent-patents-in-optogenetics-and-optochemistry
#12
(no author information available yet)
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700560/ai-powered-drug-discovery-captures-pharma-interest
#13
Eric Smalley
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700559/people
#14
(no author information available yet)
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700558/algal-oil-productivity-gets-a-fat-bonus
#15
Matthew C Posewitz
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700557/around-the-world-in-a-month
#16
(no author information available yet)
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700556/permeability-rules-for-antibiotic-design
#17
Susan Jones
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700555/an-emerging-model-for-life-sciences-commercialization
#18
Ashley J Stevens
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700554/faster-deeper-smaller-the-rise-of-antibody-like-scaffolds
#19
Brian Owens
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28700553/first-rounders-jan-vilcek
#20
(no author information available yet)
No abstract text is available yet for this article.
July 12, 2017: Nature Biotechnology
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