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Nature Biotechnology

Arjang Hassibi, Arun Manickam, Rituraj Singh, Sara Bolouki, Ruma Sinha, Kshama B Jirage, Mark W McDermott, Babak Hassibi, Haris Vikalo, Gelareh Mazarei, Lei Pei, Luc Bousse, Mark Miller, Mehrdad Heshami, Michael P Savage, Michael T Taylor, Nader Gamini, Nicholas Wood, Pallavi Mantina, Patrick Grogan, Peter Kuimelis, Piyush Savalia, Scott Conradson, Yuan Li, Rich B Meyer, Edmond Ku, Jessica Ebert, Benjamin A Pinsky, Gregory Dolganov, Tran Van, Kirsten A Johnson, Pejman Naraghi-Arani, Robert G Kuimelis, Gary Schoolnik
The emergence of pathogens resistant to existing antimicrobial drugs is a growing worldwide health crisis that threatens a return to the pre-antibiotic era. To decrease the overuse of antibiotics, molecular diagnostics systems are needed that can rapidly identify pathogens in a clinical sample and determine the presence of mutations that confer drug resistance at the point of care. We developed a fully integrated, miniaturized semiconductor biochip and closed-tube detection chemistry that performs multiplex nucleic acid amplification and sequence analysis...
July 16, 2018: Nature Biotechnology
Maria D Giraldez, Ryan M Spengler, Alton Etheridge, Paula M Godoy, Andrea J Barczak, Srimeenakshi Srinivasan, Peter L De Hoff, Kahraman Tanriverdi, Amanda Courtright, Shulin Lu, Joseph Khoory, Renee Rubio, David Baxter, Tom A P Driedonks, Henk P J Buermans, Esther N M Nolte-'t Hoen, Hui Jiang, Kai Wang, Ionita Ghiran, Yaoyu E Wang, Kendall Van Keuren-Jensen, Jane E Freedman, Prescott G Woodruff, Louise C Laurent, David J Erle, David J Galas, Muneesh Tewari
RNA-seq is increasingly used for quantitative profiling of small RNAs (for example, microRNAs, piRNAs and snoRNAs) in diverse sample types, including isolated cells, tissues and cell-free biofluids. The accuracy and reproducibility of the currently used small RNA-seq library preparation methods have not been systematically tested. Here we report results obtained by a consortium of nine labs that independently sequenced reference, 'ground truth' samples of synthetic small RNAs and human plasma-derived RNA. We assessed three commercially available library preparation methods that use adapters of defined sequence and six methods using adapters with degenerate bases...
July 16, 2018: Nature Biotechnology
Todd A Triplett, Kendra C Garrison, Nicholas Marshall, Moses Donkor, John Blazeck, Candice Lamb, Ahlam Qerqez, Joseph D Dekker, Yuri Tanno, Wei-Cheng Lu, Christos S Karamitros, Kyle Ford, Bing Tan, Xiaoyan M Zhang, Karen McGovern, Silvia Coma, Yoichi Kumada, Mena S Yamany, Enrique Sentandreu, George Fromm, Stefano Tiziani, Taylor H Schreiber, Mark Manfredi, Lauren I R Ehrlich, Everett Stone, George Georgiou
Increased tryptophan (Trp) catabolism in the tumor microenvironment (TME) can mediate immune suppression by upregulation of interferon (IFN)-γ-inducible indoleamine 2,3-dioxygenase (IDO1) and/or ectopic expression of the predominantly liver-restricted enzyme tryptophan 2,3-dioxygenase (TDO). Whether these effects are due to Trp depletion in the TME or mediated by the accumulation of the IDO1 and/or TDO (hereafter referred to as IDO1/TDO) product kynurenine (Kyn) remains controversial. Here we show that administration of a pharmacologically optimized enzyme (PEGylated kynureninase; hereafter referred to as PEG-KYNase) that degrades Kyn into immunologically inert, nontoxic and readily cleared metabolites inhibits tumor growth...
July 16, 2018: Nature Biotechnology
Michael Kosicki, Kärt Tomberg, Allan Bradley
CRISPR-Cas9 is poised to become the gene editing tool of choice in clinical contexts. Thus far, exploration of Cas9-induced genetic alterations has been limited to the immediate vicinity of the target site and distal off-target sequences, leading to the conclusion that CRISPR-Cas9 was reasonably specific. Here we report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors and a human differentiated cell line...
July 16, 2018: Nature Biotechnology
Li Tang, Yiran Zheng, Mariane Bandeira Melo, Llian Mabardi, Ana P Castaño, Yu-Qing Xie, Na Li, Sagar B Kudchodkar, Hing C Wong, Emily K Jeng, Marcela V Maus, Darrell J Irvine
Adoptive cell therapy (ACT) with antigen-specific T cells has shown remarkable clinical success; however, approaches to safely and effectively augment T cell function, especially in solid tumors, remain of great interest. Here we describe a strategy to 'backpack' large quantities of supporting protein drugs on T cells by using protein nanogels (NGs) that selectively release these cargos in response to T cell receptor activation. We designed cell surface-conjugated NGs that responded to an increase in T cell surface reduction potential after antigen recognition and limited drug release to sites of antigen encounter, such as the tumor microenvironment...
July 9, 2018: Nature Biotechnology
Lili Wang, Jeff Smith, Camilo Breton, Peter Clark, Jia Zhang, Lei Ying, Yan Che, Janel Lape, Peter Bell, Roberto Calcedo, Elizabeth L Buza, Alexei Saveliev, Victor V Bartsevich, Zhenning He, John White, Mingyao Li, Derek Jantz, James M Wilson
Clinical translation of in vivo genome editing to treat human genetic diseases requires thorough preclinical studies in relevant animal models to assess safety and efficacy. A promising approach to treat hypercholesterolemia is inactivating the secreted protein PCSK9, an antagonist of the LDL receptor. Here we show that single infusions in six non-human primates of adeno-associated virus vector expressing an engineered meganuclease targeting PCSK9 results in dose-dependent disruption of PCSK9 in liver, as well as a stable reduction in circulating PCSK9 and serum cholesterol...
July 9, 2018: Nature Biotechnology
Miao Jing, Peng Zhang, Guangfu Wang, Jiesi Feng, Lukas Mesik, Jianzhi Zeng, Huoqing Jiang, Shaohua Wang, Jess C Looby, Nick A Guagliardo, Linda W Langma, Ju Lu, Yi Zuo, David A Talmage, Lorna W Role, Paula Q Barrett, Li I Zhang, Minmin Luo, Yan Song, J Julius Zhu, Yulong Li
The neurotransmitter acetylcholine (ACh) regulates a diverse array of physiological processes throughout the body. Despite its importance, cholinergic transmission in the majority of tissues and organs remains poorly understood owing primarily to the limitations of available ACh-monitoring techniques. We developed a family of ACh sensors (GACh) based on G-protein-coupled receptors that has the sensitivity, specificity, signal-to-noise ratio, kinetics and photostability suitable for monitoring ACh signals in vitro and in vivo...
July 9, 2018: Nature Biotechnology
Maria Paz Zafra, Emma M Schatoff, Alyna Katti, Miguel Foronda, Marco Breinig, Anabel Y Schweitzer, Amber Simon, Teng Han, Sukanya Goswami, Emma Montgomery, Jordana Thibado, Edward R Kastenhuber, Francisco J Sánchez-Rivera, Junwei Shi, Christopher R Vakoc, Scott W Lowe, Darjus F Tschaharganeh, Lukas E Dow
CRISPR base editing enables the creation of targeted single-base conversions without generating double-stranded breaks. However, the efficiency of current base editors is very low in many cell types. We reengineered the sequences of BE3, BE4Gam, and xBE3 by codon optimization and incorporation of additional nuclear-localization sequences. Our collection of optimized constitutive and inducible base-editing vector systems dramatically improves the efficiency by which single-nucleotide variants can be created...
July 3, 2018: Nature Biotechnology
Ksenya Kveler, Elina Starosvetsky, Amit Ziv-Kenet, Yuval Kalugny, Yuri Gorelik, Gali Shalev-Malul, Netta Aizenbud-Reshef, Tania Dubovik, Mayan Briller, John Campbell, Jan C Rieckmann, Nuaman Asbeh, Doron Rimar, Felix Meissner, Jeff Wiser, Shai S Shen-Orr
Cytokines are signaling molecules secreted and sensed by immune and other cell types, enabling dynamic intercellular communication. Although a vast amount of data on these interactions exists, this information is not compiled, integrated or easily searchable. Here we report immuneXpresso, a text-mining engine that structures and standardizes knowledge of immune intercellular communication. We applied immuneXpresso to PubMed to identify relationships between 340 cell types and 140 cytokines across thousands of diseases...
June 18, 2018: Nature Biotechnology
Sebastian Palluk, Daniel H Arlow, Tristan de Rond, Sebastian Barthel, Justine S Kang, Rathin Bector, Hratch M Baghdassarian, Alisa N Truong, Peter W Kim, Anup K Singh, Nathan J Hillson, Jay D Keasling
Oligonucleotides are almost exclusively synthesized using the nucleoside phosphoramidite method, even though it is limited to the direct synthesis of ∼200 mers and produces hazardous waste. Here, we describe an oligonucleotide synthesis strategy that uses the template-independent polymerase terminal deoxynucleotidyl transferase (TdT). Each TdT molecule is conjugated to a single deoxyribonucleoside triphosphate (dNTP) molecule that it can incorporate into a primer. After incorporation of the tethered dNTP, the 3' end of the primer remains covalently bound to TdT and is inaccessible to other TdT-dNTP molecules...
June 18, 2018: Nature Biotechnology
Luke W Koblan, Jordan L Doman, Christopher Wilson, Jonathan M Levy, Tristan Tay, Gregory A Newby, Juan Pablo Maianti, Aditya Raguram, David R Liu
Base editors enable targeted single-nucleotide conversions in genomic DNA. Here we show that expression levels are a bottleneck in base-editing efficiency. We optimize cytidine (BE4) and adenine (ABE7.10) base editors by modification of nuclear localization signals (NLS) and codon usage, and ancestral reconstruction of the deaminase component. The resulting BE4max, AncBE4max, and ABEmax editors correct pathogenic SNPs with substantially increased efficiency in a variety of mammalian cell types.
May 29, 2018: Nature Biotechnology
Yen-Wen Liu, Billy Chen, Xiulan Yang, James A Fugate, Faith A Kalucki, Akiko Futakuchi-Tsuchida, Larry Couture, Keith W Vogel, Clifford A Astley, Audrey Baldessari, Jason Ogle, Creighton W Don, Zachary L Steinberg, Stephen P Seslar, Stephanie A Tuck, Hiroshi Tsuchida, Anna V Naumova, Sarah K Dupras, Milly S Lyu, James Lee, Dale W Hailey, Hans Reinecke, Lil Pabon, Benjamin H Fryer, W Robb MacLellan, R Scott Thies, Charles E Murry
Pluripotent stem cell-derived cardiomyocyte grafts can remuscularize substantial amounts of infarcted myocardium and beat in synchrony with the heart, but in some settings cause ventricular arrhythmias. It is unknown whether human cardiomyocytes can restore cardiac function in a physiologically relevant large animal model. Here we show that transplantation of ∼750 million cryopreserved human embryonic stem cell-derived cardiomyocytes (hESC-CMs) enhances cardiac function in macaque monkeys with large myocardial infarctions...
August 2018: Nature Biotechnology
Brandon G Wong, Christopher P Mancuso, Szilvia Kiriakov, Caleb J Bashor, Ahmad S Khalil
Precise control over microbial cell growth conditions could enable detection of minute phenotypic changes, which would improve our understanding of how genotypes are shaped by adaptive selection. Although automated cell-culture systems such as bioreactors offer strict control over liquid culture conditions, they often do not scale to high-throughput or require cumbersome redesign to alter growth conditions. We report the design and validation of eVOLVER, a scalable do-it-yourself (DIY) framework, which can be configured to carry out high-throughput growth experiments in molecular evolution, systems biology, and microbiology...
August 2018: Nature Biotechnology
Karl W Barber, Paul Muir, Richard V Szeligowski, Svetlana Rogulina, Mark Gerstein, Jeffrey R Sampson, Farren J Isaacs, Jesse Rinehart
Post-translational phosphorylation is essential to human cellular processes, but the transient, heterogeneous nature of this modification complicates its study in native systems. We developed an approach to interrogate phosphorylation and its role in protein-protein interactions on a proteome-wide scale. We genetically encoded phosphoserine in recoded E. coli and generated a peptide-based heterologous representation of the human serine phosphoproteome. We designed a single-plasmid library encoding >100,000 human phosphopeptides and confirmed the site-specific incorporation of phosphoserine in >36,000 of these peptides...
August 2018: Nature Biotechnology
Bin Gu, Eszter Posfai, Janet Rossant
Rapid, efficient generation of knock-in mice with targeted large insertions remains a major hurdle in mouse genetics. Here, we describe two-cell homologous recombination (2C-HR)-CRISPR, a highly efficient gene-editing method based on introducing CRISPR reagents into embryos at the two-cell stage, which takes advantage of the open chromatin structure and the likely increase in homologous-recombination efficiency during the long G2 phase. Combining 2C-HR-CRISPR with a modified biotin-streptavidin approach to localize repair templates to target sites, we achieved a more-than-tenfold increase (up to 95%) in knock-in efficiency over standard methods...
August 2018: Nature Biotechnology
Ruwan Gunaratne, Shekhar Kumar, James W Frederiksen, Steven Stayrook, Jens L Lohrmann, Kay Perry, Kristin M Bompiani, Charlene V Chabata, Nabil K Thalji, Michelle D Ho, Gowthami Arepally, Rodney M Camire, Sriram Krishnaswamy, Bruce A Sullenger
Unfractionated heparin (UFH), the standard anticoagulant for cardiopulmonary bypass (CPB) surgery, carries a risk of post-operative bleeding and is potentially harmful in patients with heparin-induced thrombocytopenia-associated antibodies. To improve the activity of an alternative anticoagulant, the RNA aptamer 11F7t, we solved X-ray crystal structures of the aptamer bound to factor Xa (FXa). The finding that 11F7t did not bind the catalytic site suggested that it could complement small-molecule FXa inhibitors...
August 2018: Nature Biotechnology
Ross Thyer, Raghav Shroff, Dustin R Klein, Simon d'Oelsnitz, Victoria C Cotham, Michelle Byrom, Jennifer S Brodbelt, Andrew D Ellington
Incorporation of the rare amino acid selenocysteine to form diselenide bonds can improve stability and function of synthetic peptide therapeutics. However, application of this approach to recombinant proteins has been hampered by heterogeneous incorporation, low selenoprotein yields, and poor fitness of bacterial producer strains. We report the evolution of recoded Escherichia coli strains with improved fitness that are superior hosts for recombinant selenoprotein production. We apply an engineered β-lactamase containing an essential diselenide bond to enforce selenocysteine dependence during continuous evolution of recoded E...
August 2018: Nature Biotechnology
Robert M Bowers, Nikos C Kyrpides, Ramunas Stepanauskas, Miranda Harmon-Smith, Devin Doud, T B K Reddy, Frederik Schulz, Jessica Jarett, Adam R Rivers, Emiley A Eloe-Fadrosh, Susannah G Tringe, Natalia N Ivanova, Alex Copeland, Alicia Clum, Eric D Becraft, Rex R Malmstrom, Bruce Birren, Mircea Podar, Peer Bork, George M Weinstock, George M Garrity, Jeremy A Dodsworth, Shibu Yooseph, Granger Sutton, Frank O Glöckner, Jack A Gilbert, William C Nelson, Steven J Hallam, Sean P Jungbluth, Thijs J G Ettema, Scott Tighe, Konstantinos T Konstantinidis, Wen-Tso Liu, Brett J Baker, Thomas Rattei, Jonathan A Eisen, Brian Hedlund, Katherine D McMahon, Noah Fierer, Rob Knight, Rob Finn, Guy Cochrane, Ilene Karsch-Mizrachi, Gene W Tyson, Christian Rinke, Alla Lapidus, Folker Meyer, Pelin Yilmaz, Donovan H Parks, A M Eren, Lynn Schriml, Jillian F Banfield, Philip Hugenholtz, Tanja Woyke
No abstract text is available yet for this article.
July 6, 2018: Nature Biotechnology
(no author information available yet)
No abstract text is available yet for this article.
July 6, 2018: Nature Biotechnology
Cristiano Gonçalves Pereira, Virgínia Picanco-Castro, Dimas Tadeu Covas, Geciane Silveira Porto
No abstract text is available yet for this article.
July 6, 2018: Nature Biotechnology
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