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Article ; Online: DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions.

Sidore, Angus M / Plesa, Calin / Samson, Joyce A / Lubock, Nathan B / Kosuri, Sriram

2020 Volume 48, Issue 16, Page(s) e95

Abstract: Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene ... ...

Abstract	Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene libraries by compartmentalizing and assembling microarray-derived oligonucleotides in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.
MeSH term(s)	Emulsions/chemistry ; Escherichia coli/genetics ; Gene Library ; Genes, Synthetic ; Nucleic Acid Amplification Techniques/methods ; Oligonucleotides/genetics
Chemical Substances	Emulsions ; Oligonucleotides
Language	English
Publishing date	2020-08-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa600
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Article ; Online: Multiplexed gene synthesis in emulsions for exploring protein functional landscapes.

Plesa, Calin / Sidore, Angus M / Lubock, Nathan B / Zhang, Di / Kosuri, Sriram

Science (New York, N.Y.)

2018 Volume 359, Issue 6373, Page(s) 343–347

Abstract: Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled ( ... ...

Abstract	Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled (multiplexed) manner. DropSynth uses a library of barcoded beads that pull down the oligonucleotides necessary for a gene's assembly, which are then processed and assembled in water-in-oil emulsions. We used DropSynth to successfully build more than 7000 synthetic genes that encode phylogenetically diverse homologs of two essential genes in
MeSH term(s)	Emulsions ; Escherichia coli/genetics ; Gene Knockout Techniques ; Genes, Essential ; Genes, Synthetic ; Genetic Complementation Test ; Oligonucleotides/chemical synthesis ; Oligonucleotides/chemistry ; Oligonucleotides/genetics ; Proteins/genetics ; Proteins/physiology ; Synthetic Biology/methods
Chemical Substances	Emulsions ; Oligonucleotides ; Proteins
Language	English
Publishing date	2018-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aao5167
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: A systematic comparison of error correction enzymes by next-generation sequencing.

Lubock, Nathan B / Zhang, Di / Sidore, Angus M / Church, George M / Kosuri, Sriram

Nucleic acids research

2017 Volume 45, Issue 15, Page(s) 9206–9217

Abstract: Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by ...

Abstract	Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared six different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.
MeSH term(s)	Benchmarking ; Chemistry Techniques, Synthetic/standards ; DNA/chemical synthesis ; DNA/genetics ; Deoxyribonuclease I/genetics ; Deoxyribonuclease I/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Genes, Synthetic ; High-Throughput Nucleotide Sequencing ; MutS DNA Mismatch-Binding Protein/genetics ; MutS DNA Mismatch-Binding Protein/metabolism ; Oligodeoxyribonucleotides/chemistry
Chemical Substances	Escherichia coli Proteins ; Oligodeoxyribonucleotides ; DNA (9007-49-2) ; Deoxyribonuclease I (EC 3.1.21.1) ; MutS DNA Mismatch-Binding Protein (EC 3.6.1.3) ; MutS protein, E coli (EC 3.6.1.3)
Language	English
Publishing date	2017-09-06
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx691
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Article ; Online: Structural and functional characterization of G protein-coupled receptors with deep mutational scanning.

Jones, Eric M / Lubock, Nathan B / Venkatakrishnan, A J / Wang, Jeffrey / Tseng, Alex M / Paggi, Joseph M / Latorraca, Naomi R / Cancilla, Daniel / Satyadi, Megan / Davis, Jessica E / Babu, M Madan / Dror, Ron O / Kosuri, Sriram

eLife

2020 Volume 9

Abstract: The >800 human G protein-coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it ... ...

Abstract	The >800 human G protein-coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β
MeSH term(s)	Cloning, Molecular ; DNA Barcoding, Taxonomic ; DNA Mutational Analysis/methods ; Gene Editing ; HEK293 Cells ; Humans ; Machine Learning ; Models, Molecular ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/metabolism
Chemical Substances	Receptors, G-Protein-Coupled
Language	English
Publishing date	2020-10-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.54895
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Article ; Online: Reliable and accurate diagnostics from highly multiplexed sequencing assays.

Booeshaghi, A Sina / Lubock, Nathan B / Cooper, Aaron R / Simpkins, Scott W / Bloom, Joshua S / Gehring, Jase / Luebbert, Laura / Kosuri, Sri / Pachter, Lior

Scientific reports

2020 Volume 10, Issue 1, Page(s) 21759

Abstract: Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet ... ...

Abstract	Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/genetics ; COVID-19 Nucleic Acid Testing ; Humans ; Molecular Diagnostic Techniques ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/genetics
Language	English
Publishing date	2020-12-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-78942-7
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Article ; Online: Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design.

Mabanglo, Mark F / Hast, Michael A / Lubock, Nathan B / Hellinga, Homme W / Beese, Lorena S

Protein science : a publication of the Protein Society

2014 Volume 23, Issue 3, Page(s) 289–301

Abstract: Species of the fungal genus Aspergillus are significant human and agricultural pathogens that are often refractory to existing antifungal treatments. Protein farnesyltransferase (FTase), a critical enzyme in eukaryotes, is an attractive potential target ... ...

Abstract	Species of the fungal genus Aspergillus are significant human and agricultural pathogens that are often refractory to existing antifungal treatments. Protein farnesyltransferase (FTase), a critical enzyme in eukaryotes, is an attractive potential target for antifungal drug discovery. We report high-resolution structures of A. fumigatus FTase (AfFTase) in complex with substrates and inhibitors. Comparison of structures with farnesyldiphosphate (FPP) bound in the absence or presence of peptide substrate, corresponding to successive steps in ordered substrate binding, revealed that the second substrate-binding step is accompanied by motions of a loop in the catalytic site. Re-examination of other FTase structures showed that this motion is conserved. The substrate- and product-binding clefts in the AfFTase active site are wider than in human FTase (hFTase). Widening is a consequence of small shifts in the α-helices that comprise the majority of the FTase structure, which in turn arise from sequence variation in the hydrophobic core of the protein. These structural effects are key features that distinguish fungal FTases from hFTase. Their variation results in differences in steady-state enzyme kinetics and inhibitor interactions and presents opportunities for developing selective anti-fungal drugs by exploiting size differences in the active sites. We illustrate the latter by comparing the interaction of ED5 and Tipifarnib with hFTase and AfFTase. In AfFTase, the wider groove enables ED5 to bind in the presence of FPP, whereas in hFTase it binds only in the absence of substrate. Tipifarnib binds similarly to both enzymes but makes less extensive contacts in AfFTase with consequently weaker binding.
MeSH term(s)	Antifungal Agents/pharmacokinetics ; Aspergillus fumigatus/chemistry ; Aspergillus fumigatus/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Drug Design ; Farnesyltranstransferase/chemistry ; Farnesyltranstransferase/metabolism ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Humans ; Peptides/antagonists & inhibitors ; Peptides/chemistry ; Polyisoprenyl Phosphates/antagonists & inhibitors ; Polyisoprenyl Phosphates/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Quinolones/pharmacokinetics ; Sesquiterpenes/antagonists & inhibitors ; Sesquiterpenes/chemistry ; Sulfonamides/pharmacokinetics ; Benzenesulfonamides
Chemical Substances	Antifungal Agents ; Fungal Proteins ; Peptides ; Polyisoprenyl Phosphates ; Quinolones ; Sesquiterpenes ; Sulfonamides ; farnesyl pyrophosphate (79W6B01D07) ; Farnesyltranstransferase (EC 2.5.1.29) ; tipifarnib (MAT637500A)
Language	English
Publishing date	2014-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.2411
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing.

Jones, Eric M / Jajoo, Rishi / Cancilla, Daniel / Lubock, Nathan B / Wang, Jeffrey / Satyadi, Megan / Chong, Rockie / de March, Claire / Bloom, Joshua S / Matsunami, Hiroaki / Kosuri, Sriram

Cell systems

2019 Volume 8, Issue 3, Page(s) 254–260.e6

Abstract: G protein-coupled receptors (GPCRs) are central to how mammalian cells sense and respond to chemicals. Mammalian olfactory receptors (ORs), the largest family of GPCRs, mediate the sense of smell through activation by small molecules, though for most ... ...

Abstract	G protein-coupled receptors (GPCRs) are central to how mammalian cells sense and respond to chemicals. Mammalian olfactory receptors (ORs), the largest family of GPCRs, mediate the sense of smell through activation by small molecules, though for most bonafide ligands, they have not been identified. Here, we introduce a platform to screen large chemical panels against multiplexed GPCR libraries using next-generation sequencing of barcoded genetic reporters in stably engineered human cell lines. We mapped 39 mammalian ORs against 181 odorants and identified 79 interactions that have not been reported to our knowledge, including ligands for 15 previously orphaned receptors. This multiplexed receptor assay allows the cost-effective mapping of large chemical libraries to receptor repertoires at scale.
MeSH term(s)	Animals ; Cell Line ; Gene Expression Profiling ; Humans ; Ligands ; Mammals/metabolism ; Mammals/physiology ; Odorants ; Receptors, Odorant/metabolism ; Sequence Analysis, RNA/methods ; Signal Transduction ; Smell
Chemical Substances	Ligands ; Receptors, Odorant
Language	English
Publishing date	2019-03-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2854138-8
ISSN	2405-4720 ; 2405-4712
ISSN (online)	2405-4720
ISSN	2405-4712
DOI	10.1016/j.cels.2019.02.009
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Book ; Article ; Online: Fast and accurate diagnostics from highly multiplexed sequencing assays

Booeshaghi, A. Sina / Lubock, Nathan B. / Cooper, Aaron R. / Simpkins, Scott W. / Bloom, Joshua S. / Gehring, Jase / Luebbert, Laura / Kosuri, Sriram / Pachter, Lior

2020

Abstract: Scalable, inexpensive, accurate, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays that rely on high-throughput sequencing (HMSAs) can, in ... ...

Abstract	Scalable, inexpensive, accurate, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays that rely on high-throughput sequencing (HMSAs) can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, the analysis and interpretation of HMSAs requires overcoming several computational and statistical challenges. Using recently acquired experimental data, we present and validate an accurate and fast computational testing workflow based on kallisto and bustools, that utilize robust statistical methods and fast, memory efficient algorithms for processing high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSAs.
Keywords	covid19
Subject code	518
Publishing date	2020-05-16
Publishing country	us
Document type	Book ; Article ; Online
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Article ; Online: Activation of peripheral nerve fibers by electrical stimulation in the sole of the foot.

Frahm, Ken Steffen / Mørch, Carsten Dahl / Grill, Warren M / Lubock, Nathan B / Hennings, Kristian / Andersen, Ole Kaeseler

BMC neuroscience

2013 Volume 14, Page(s) 116

Abstract: Background: Human nociceptive withdrawal reflexes (NWR) can be evoked by electrical stimulation applied to the sole of the foot. However, elicitation of NWRs is highly site dependent, and NWRs are especially difficult to elicit at the heel. The aim of ... ...

Abstract	Background: Human nociceptive withdrawal reflexes (NWR) can be evoked by electrical stimulation applied to the sole of the foot. However, elicitation of NWRs is highly site dependent, and NWRs are especially difficult to elicit at the heel. The aim of the present study was to investigate potential peripheral mechanisms for any site dependent differences in reflex thresholds. Results: The first part of the study investigated the neural innervation in different sites of the sole of the foot using two different staining techniques. 1) Staining for the Nav1.7 antigen (small nociceptive fibers) and 2) the Sihler whole nerve technique (myelinated part of the nerve). No differences in innervation densities were found across the sole of the foot using the two staining techniques: Nav1.7 immunochemistry (small nociceptive fibers (1-way ANOVA, NS)) and the Sihler's method (myelinated nerve fibers (1-way ANOVA, NS)). However, the results indicate that there are no nociceptive intraepidermal nerve fibers (IENFs) innervating the heel.Secondly, mathematical modeling was used to investigate to what degree differences in skin thicknesses affect the activation thresholds of Aδ and Aβ fibers in the sole of the foot. The modeling comprised finite element analysis of the volume conduction combined with a passive model of the activation of branching cutaneous nerve fibers. The model included three different sites in the sole of the foot (forefoot, arch and heel) and three different electrode sizes (diameters: 9.1, 12.9, and 18.3 mm). For each of the 9 combinations of site and electrode size, a total of 3000 Aβ fibers and 300 Aδ fibers was modeled. The computer simulation of the effects of skin thicknesses and innervation densities on thresholds of modeled Aδ and Aβ fibers did not reveal differences in pain and perception thresholds across the foot sole as have been observed experimentally. Instead a lack of IENFs at the heel decreased the electrical activation thresholds compared to models including IENFs. Conclusions: The nerve staining and modeling results do not explain differences in NWR thresholds across the sole of the foot which may suggest that central mechanisms contribute to variation in NWR excitability across the sole of the foot.
MeSH term(s)	Electric Stimulation ; Finite Element Analysis ; Foot/innervation ; Humans ; Nerve Fibers, Myelinated/ultrastructure ; Pain Threshold/physiology ; Reflex/physiology ; Silver Staining
Language	English
Publishing date	2013-10-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2202
ISSN (online)	1471-2202
DOI	10.1186/1471-2202-14-116
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Article ; Online: High-resolution measurement of electrically-evoked vagus nerve activity in the anesthetized dog.

Yoo, Paul B / Lubock, Nathan B / Hincapie, Juan G / Ruble, Stephen B / Hamann, Jason J / Grill, Warren M

Journal of neural engineering

2013 Volume 10, Issue 2, Page(s) 26003

Abstract: Objective: Not fully understanding the type of axons activated during vagus nerve stimulation (VNS) is one of several factors that limit the clinical efficacy of VNS therapies. The main goal of this study was to characterize the electrical recruitment ... ...

Abstract	Objective: Not fully understanding the type of axons activated during vagus nerve stimulation (VNS) is one of several factors that limit the clinical efficacy of VNS therapies. The main goal of this study was to characterize the electrical recruitment of both myelinated and unmyelinated fibers within the cervical vagus nerve. Approach: In anesthetized dogs, recording nerve cuff electrodes were implanted on the vagus nerve following surgical excision of the epineurium. Both the vagal electroneurogram (ENG) and laryngeal muscle activity were recorded in response to stimulation of the right vagus nerve. Main results: Desheathing the nerve significantly increased the signal-to-noise ratio of the ENG by 1.2 to 9.9 dB, depending on the nerve fiber type. Repeated VNS following nerve transection or neuromuscular block (1) enabled the characterization of A-fibers, two sub-types of B-fibers, and unmyelinated C-fibers, (2) confirmed the absence of stimulation-evoked reflex compound nerve action potentials in both the ipsilateral and contralateral vagus nerves, and (3) provided evidence of stimulus spillover into muscle tissue surrounding the stimulating electrode. Significance: Given the anatomical similarities between the canine and human vagus nerves, the results of this study provide a template for better understanding the nerve fiber recruitment patterns associated with VNS therapies.
MeSH term(s)	Action Potentials/physiology ; Anesthesia ; Animals ; Artifacts ; Data Interpretation, Statistical ; Dogs ; Electrodes, Implanted ; Electromyography ; Evoked Potentials/physiology ; Female ; Nerve Fibers, Myelinated/physiology ; Nerve Fibers, Unmyelinated/physiology ; Neuroimaging ; Neuromuscular Blockade ; Peripheral Nerves/physiology ; Reflex/physiology ; Signal-To-Noise Ratio ; Vagus Nerve/physiology ; Vagus Nerve Stimulation/methods ; Vagus Nerve Stimulation/statistics & numerical data
Language	English
Publishing date	2013-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2170901-4
ISSN	1741-2552 ; 1741-2560
ISSN (online)	1741-2552
ISSN	1741-2560
DOI	10.1088/1741-2560/10/2/026003
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