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Nature Biotechnology

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https://www.readbyqxmd.com/read/29334370/scaffolds-that-mimic-antigen-presenting-cells-enable-ex-vivo-expansion-of-primary-t-cells
#1
Alexander S Cheung, David K Y Zhang, Sandeep T Koshy, David J Mooney
Therapeutic ex vivo T-cell expansion is limited by low rates and T-cell products of limited functionality. Here we describe a system that mimics natural antigen-presenting cells (APCs) and consists of a fluid lipid bilayer supported by mesoporous silica micro-rods. The lipid bilayer presents membrane-bound cues for T-cell receptor stimulation and costimulation, while the micro-rods enable sustained release of soluble paracrine cues. Using anti-CD3, anti-CD28, and interleukin-2, we show that the APC-mimetic scaffolds (APC-ms) promote two- to tenfold greater polyclonal expansion of primary mouse and human T cells compared with commercial expansion beads (Dynabeads)...
January 15, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29334369/dual-gene-activation-and-knockout-screen-reveals-directional-dependencies-in-genetic-networks
#2
Michael Boettcher, Ruilin Tian, James A Blau, Evan Markegard, Ryan T Wagner, David Wu, Xiulei Mo, Anne Biton, Noah Zaitlen, Haian Fu, Frank McCormick, Martin Kampmann, Michael T McManus
Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair...
January 15, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29334368/visualizing-detailed-postdoctoral-employment-trends-using-a-new-career-outcome-taxonomy
#3
Hong Xu, Richard S T Gilliam, Shyamal D Peddada, Gregory M Buchold, Tammy R L Collins
No abstract text is available yet for this article.
January 15, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29309060/functional-interrogation-and-mining-of-natively-paired-human-vh-vl-antibody-repertoires
#4
Bo Wang, Brandon J DeKosky, Morgan R Timm, Jiwon Lee, Erica Normandin, John Misasi, Rui Kong, Jonathan R McDaniel, George Delidakis, Kendra E Leigh, Thomas Niezold, Chang W Choi, Elise G Viox, Ahmed Fahad, Alberto Cagigi, Aurélie Ploquin, Kwanyee Leung, Eun Sung Yang, Wing-Pui Kong, William N Voss, Aaron G Schmidt, M Anthony Moody, David R Ambrozak, Amy R Henry, Farida Laboune, Julie E Ledgerwood, Barney S Graham, Mark Connors, Daniel C Douek, Nancy J Sullivan, Andrew D Ellington, John R Mascola, George Georgiou
We present a technology to screen millions of B cells for natively paired human antibody repertoires. Libraries of natively paired, variable region heavy and light (VH:VL) amplicons are expressed in a yeast display platform that is optimized for human Fab surface expression. Using our method we identify HIV-1 broadly neutralizing antibodies (bNAbs) from an HIV-1 slow progressor and high-affinity neutralizing antibodies against Ebola virus glycoprotein and influenza hemagglutinin.
January 8, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29291348/retrieval-of-a-million-high-quality-full-length-microbial-16s-and-18s-rrna-gene-sequences-without-primer-bias
#5
Søren M Karst, Morten S Dueholm, Simon J McIlroy, Rasmus H Kirkegaard, Per H Nielsen, Mads Albertsen
Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied ecosystems and subject to primer bias and chimerism, which results in an incomplete view of the diversity present in a sample. We combine poly(A)-tailing and reverse transcription of SSU rRNA molecules with synthetic long-read sequencing to generate high-quality, full-length SSU rRNA sequences, without primer bias, at high throughput...
January 1, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29251732/aligning-stars-of-all-colors
#6
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29251731/mentoring-for-diversity-in-technology
#7
Maggie Werner-Washburne
No abstract text is available yet for this article.
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29251730/biotech-s-pale-shadow
#8
Brady Huggett
No abstract text is available yet for this article.
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29251729/virus-stamping-for-targeted-single-cell-infection-in-vitro-and-in-vivo
#9
Rajib Schubert, Stuart Trenholm, Kamill Balint, Georg Kosche, Cameron S Cowan, Manuel A Mohr, Martin Munz, David Martinez-Martin, Gotthold Fläschner, Richard Newton, Jacek Krol, Brigitte Gross Scherf, Keisuke Yonehara, Adrian Wertz, Aaron Ponti, Alexander Ghanem, Daniel Hillier, Karl-Klaus Conzelmann, Daniel J Müller, Botond Roska
Genetic engineering by viral infection of single cells is useful to study complex systems such as the brain. However, available methods for infecting single cells have drawbacks that limit their applications. Here we describe 'virus stamping', in which viruses are reversibly bound to a delivery vehicle-a functionalized glass pipette tip or magnetic nanoparticles in a pipette-that is brought into physical contact with the target cell on a surface or in tissue, using mechanical or magnetic forces. Different single cells in the same tissue can be infected with different viruses and an individual cell can be simultaneously infected with different viruses...
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29251728/viruses-leave-their-stamp-on-single-cells
#10
Ede A Rancz, Andreas T Schaefer
No abstract text is available yet for this article.
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29251727/labeling-and-identifying-cell-specific-proteomes-in-the-mouse-brain
#11
Toke P Krogager, Russell J Ernst, Thomas S Elliott, Laura Calo, Václav Beránek, Ernesto Ciabatti, Maria Grazia Spillantini, Marco Tripodi, Michael H Hastings, Jason W Chin
We develop an approach to tag proteomes synthesized by specific cell types in dissociated cortex, brain slices, and the brains of live mice. By viral-mediated expression of an orthogonal pyrrolysyl-tRNA synthetase-tRNAXXX pair in a cell type of interest and providing a non-canonical amino acid with a chemical handle, we selectively label neuronal or glial proteomes. The method enables the identification of proteins from spatially and genetically defined regions of the brain.
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29251726/orthologous-crispr-cas9-enzymes-for-combinatorial-genetic-screens
#12
Fadi J Najm, Christine Strand, Katherine F Donovan, Mudra Hegde, Kendall R Sanson, Emma W Vaimberg, Meagan E Sullender, Ella Hartenian, Zohra Kalani, Nicolo Fusi, Jennifer Listgarten, Scott T Younger, Bradley E Bernstein, David E Root, John G Doench
Combinatorial genetic screening using CRISPR-Cas9 is a useful approach to uncover redundant genes and to explore complex gene networks. However, current methods suffer from interference between the single-guide RNAs (sgRNAs) and from limited gene targeting activity. To increase the efficiency of combinatorial screening, we employ orthogonal Cas9 enzymes from Staphylococcus aureus and Streptococcus pyogenes. We used machine learning to establish S. aureus Cas9 sgRNA design rules and paired S. aureus Cas9 with S...
December 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29227470/multiplexed-droplet-single-cell-rna-sequencing-using-natural-genetic-variation
#13
Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata, Rachel E Gate, Sara Mostafavi, Alexander Marson, Noah Zaitlen, Lindsey A Criswell, Chun Jimmie Ye
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29227469/integrative-single-cell-analysis-of-transcriptional-and-epigenetic-states-in-the-human-adult-brain
#14
Blue B Lake, Song Chen, Brandon C Sos, Jean Fan, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko, Kun Zhang
Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29227468/metagenomic-binning-and-association-of-plasmids-with-bacterial-host-genomes-using-dna-methylation
#15
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29176614/inhibition-of-53bp1-favors-homology-dependent-dna-repair-and-increases-crispr-cas9-genome-editing-efficiency
#16
Marella D Canny, Nathalie Moatti, Leo C K Wan, Amélie Fradet-Turcotte, Danielle Krasner, Pedro A Mateos-Gomez, Michal Zimmermann, Alexandre Orthwein, Yu-Chi Juang, Wei Zhang, Sylvie M Noordermeer, Eduardo Seclen, Marcus D Wilson, Andrew Vorobyov, Meagan Munro, Andreas Ernst, Timothy F Ng, Tiffany Cho, Paula M Cannon, Sachdev S Sidhu, Frank Sicheri, Daniel Durocher
Programmable nucleases, such as Cas9, are used for precise genome editing by homology-dependent repair (HDR). However, HDR efficiency is constrained by competition from other double-strand break (DSB) repair pathways, including non-homologous end-joining (NHEJ). We report the discovery of a genetically encoded inhibitor of 53BP1 that increases the efficiency of HDR-dependent genome editing in human and mouse cells. 53BP1 is a key regulator of DSB repair pathway choice in eukaryotic cells and functions to favor NHEJ over HDR by suppressing end resection, which is the rate-limiting step in the initiation of HDR...
November 27, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29176613/global-landscape-of-cell-envelope-protein-complexes-in-escherichia-coli
#17
Mohan Babu, Cedoljub Bundalovic-Torma, Charles Calmettes, Sadhna Phanse, Qingzhou Zhang, Yue Jiang, Zoran Minic, Sunyoung Kim, Jitender Mehla, Alla Gagarinova, Irina Rodionova, Ashwani Kumar, Hongbo Guo, Olga Kagan, Oxana Pogoutse, Hiroyuki Aoki, Viktor Deineko, J Harry Caufield, Erik Holtzapple, Zhongge Zhang, Ake Vastermark, Yogee Pandya, Christine Chieh-Lin Lai, Majida El Bakkouri, Yogesh Hooda, Megha Shah, Dan Burnside, Mohsen Hooshyar, James Vlasblom, Sessandra V Rajagopala, Ashkan Golshani, Stefan Wuchty, Jack F Greenblatt, Milton Saier, Peter Uetz, Trevor F Moraes, John Parkinson, Andrew Emili
Bacterial cell envelope protein (CEP) complexes mediate a range of processes, including membrane assembly, antibiotic resistance and metabolic coordination. However, only limited characterization of relevant macromolecules has been reported to date. Here we present a proteomic survey of 1,347 CEPs encompassing 90% inner- and outer-membrane and periplasmic proteins of Escherichia coli. After extraction with non-denaturing detergents, we affinity-purified 785 endogenously tagged CEPs and identified stably associated polypeptides by precision mass spectrometry...
November 27, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29131148/structure-guided-chemical-modification-of-guide-rna-enables-potent-non-viral-in-vivo-genome-editing
#18
Hao Yin, Chun-Qing Song, Sneha Suresh, Qiongqiong Wu, Stephen Walsh, Luke Hyunsik Rhym, Esther Mintzer, Mehmet Fatih Bolukbasi, Lihua Julie Zhu, Kevin Kauffman, Haiwei Mou, Alicia Oberholzer, Junmei Ding, Suet-Yan Kwan, Roman L Bogorad, Timofei Zatsepin, Victor Koteliansky, Scot A Wolfe, Wen Xue, Robert Langer, Daniel G Anderson
Efficient genome editing with Cas9-sgRNA in vivo has required the use of viral delivery systems, which have limitations for clinical applications. Translational efforts to develop other RNA therapeutics have shown that judicious chemical modification of RNAs can improve therapeutic efficacy by reducing susceptibility to nuclease degradation. Guided by the structure of the Cas9-sgRNA complex, we identify regions of sgRNA that can be modified while maintaining or enhancing genome-editing activity, and we develop an optimal set of chemical modifications for in vivo applications...
November 13, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29131147/accurate-assembly-of-transcripts-through-phase-preserving-graph-decomposition
#19
Mingfu Shao, Carl Kingsford
We introduce Scallop, an accurate reference-based transcript assembler that improves reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range phasing paths extracted from reads, while producing a parsimonious set of transcripts and minimizing coverage deviation. On 10 human RNA-seq samples, Scallop produces 34.5% and 36.3% more correct multi-exon transcripts than StringTie and TransComb, and respectively identifies 67.5% and 52.3% more lowly expressed transcripts. Scallop achieves higher sensitivity and precision than previous approaches over a wide range of coverage thresholds...
November 13, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29121011/assisted-reproductive-technologies-to-prevent-human-mitochondrial-disease-transmission
#20
Andy Greenfield, Peter Braude, Frances Flinter, Robin Lovell-Badge, Caroline Ogilvie, Anthony C F Perry
Mitochondria are essential cytoplasmic organelles that generate energy (ATP) by oxidative phosphorylation and mediate key cellular processes such as apoptosis. They are maternally inherited and in humans contain a 16,569-base-pair circular genome (mtDNA) encoding 37 genes required for oxidative phosphorylation. Mutations in mtDNA cause a range of pathologies, commonly affecting energy-demanding tissues such as muscle and brain. Because mitochondrial diseases are incurable, attention has focused on limiting the inheritance of pathogenic mtDNA by mitochondrial replacement therapy (MRT)...
November 9, 2017: Nature Biotechnology
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