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Article ; Online: DART-ID increases single-cell proteome coverage.

Albert Tian Chen / Alexander Franks / Nikolai Slavov

PLoS Computational Biology, Vol 15, Iss 7, p e

2019 Volume 1007082

Abstract: Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller ... ...

Abstract	Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30-50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net.
Keywords	Biology (General) ; QH301-705.5
Subject code	381
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest

Albert Tian Chen / Kevin Altschuler / Shing Hei Zhan / Yujia Alina Chan / Benjamin E Deverman

eLife, Vol

2021 Volume 10

Abstract: COVID-19 CG (covidcg.org) is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs), lineages, and clades using the virus genomes on the GISAID database while filtering by location, date, gene, and mutation of interest. COVID-19 CG ... ...

Abstract	COVID-19 CG (covidcg.org) is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs), lineages, and clades using the virus genomes on the GISAID database while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to projects on SARS-CoV-2 transmission, evolution, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 spike receptor binding domain (RBD) across different geographical regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the emergence of a dominant lineage harboring an S477N RBD mutation in Australia in 2020. To accelerate COVID-19 efforts, COVID-19 CG will be upgraded with new features for users to rapidly pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.
Keywords	SARS-CoV-2 ; COVID-19 ; pandemic ; browser ; mutation tracking ; resource ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Josephson junction with

Tian, Jifa / Jauregui, Luis A / Wilen, C D / Rigosi, Albert F / Newell, David B / McDermott, R / Chen, Yong P

Journal of physics. Condensed matter : an Institute of Physics journal

2021 Volume 33, Issue 49

Abstract: Decoherence in quantum bits (qubits) is a major challenge for realizing scalable quantum computing. One of the primary causes of decoherence in qubits and quantum circuits based on superconducting Josephson junctions is the critical current fluctuation. ... ...

Abstract	Decoherence in quantum bits (qubits) is a major challenge for realizing scalable quantum computing. One of the primary causes of decoherence in qubits and quantum circuits based on superconducting Josephson junctions is the critical current fluctuation. Many efforts have been devoted to suppressing the critical current fluctuation in Josephson junctions. Nonetheless, the efforts have been hindered by the defect-induced trapping states in oxide-based tunnel barriers and the interfaces with superconductors in the traditional Josephson junctions. Motivated by this, along with the recent demonstration of 2D insulator
Language	English
Publishing date	2021-10-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/1361-648X/ac268f
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DART-ID increases single-cell proteome coverage.

Chen, Albert Tian / Franks, Alexander / Slavov, Nikolai

PLoS computational biology

2019 Volume 15, Issue 7, Page(s) e1007082

Abstract	Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30-50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net.
MeSH term(s)	Bayes Theorem ; Chromatography, Liquid/methods ; Proteome ; Single-Cell Analysis ; Tandem Mass Spectrometry/methods
Chemical Substances	Proteome
Language	English
Publishing date	2019-07-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1007082
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest.

Chen, Albert Tian / Altschuler, Kevin / Zhan, Shing Hei / Chan, Yujia Alina / Deverman, Benjamin E

eLife

2021 Volume 10

Abstract	COVID-19 CG (covidcg.org) is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs), lineages, and clades using the virus genomes on the GISAID database while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to projects on SARS-CoV-2 transmission, evolution, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 spike receptor binding domain (RBD) across different geographical regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the emergence of a dominant lineage harboring an S477N RBD mutation in Australia in 2020. To accelerate COVID-19 efforts, COVID-19 CG will be upgraded with new features for users to rapidly pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.
MeSH term(s)	Amino Acid Sequence ; Binding Sites/genetics ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Computational Biology/methods ; Genome, Viral/genetics ; Geography ; Global Health ; Humans ; Internet ; Mutation ; Pandemics ; Patient Identification Systems/methods ; Phylogeny ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Sequence Homology, Amino Acid ; Software ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-02-23
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.63409
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Article ; Online: Interfacial Stability in Bi

Wang, Chun-Hsien / Hsieh, Hsien-Chien / Sun, Zhen-Wei / Ranganayakulu, V K / Lan, Tian-Wey / Chen, Yang-Yuan / Chang, Ying-Yi / Wu, Albert T

ACS applied materials & interfaces

2020 Volume 12, Issue 24, Page(s) 27001–27009

Abstract: Bismuth telluride ( ... ...

Abstract	Bismuth telluride (Bi
Language	English
Publishing date	2020-06-04
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.9b22853
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers.

He, Haoran / Zhou, Jingxiong / Wang, Yunqiang / Jiao, Shuo / Qian, Xun / Liu, Yurong / Liu, Ji / Chen, Ji / Delgado-Baquerizo, Manuel / Brangarí, Albert C / Chen, Li / Cui, Yongxing / Pan, Haibo / Tian, Renmao / Liang, Yuting / Tan, Wenfeng / Ochoa-Hueso, Raúl / Fang, Linchuan

Global change biology

2023 Volume 30, Issue 1, Page(s) e17028

Abstract: Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to ... ...

Abstract	Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
MeSH term(s)	Bacteria/metabolism ; Archaea ; Microbiota ; Soil/chemistry ; Water/metabolism ; Soil Microbiology
Chemical Substances	Soil ; Water (059QF0KO0R)
Language	English
Publishing date	2023-11-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1281439-8
ISSN	1365-2486 ; 1354-1013
ISSN (online)	1365-2486
ISSN	1354-1013
DOI	10.1111/gcb.17028
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution.

Chen, Yen-Hsi / Tian, Weihua / Yasuda, Makiko / Ye, Zilu / Song, Ming / Mandel, Ulla / Kristensen, Claus / Povolo, Lorenzo / Marques, André R A / Čaval, Tomislav / Heck, Albert J R / Sampaio, Julio Lopes / Johannes, Ludger / Tsukimura, Takahiro / Desnick, Robert / Vakhrushev, Sergey Y / Yang, Zhang / Clausen, Henrik

Frontiers in bioengineering and biotechnology

2023 Volume 11, Page(s) 1128371

Abstract: Currently available enzyme replacement therapies for lysosomal storage diseases are limited in their effectiveness due in part to short circulation times and suboptimal biodistribution of the therapeutic enzymes. We previously engineered Chinese hamster ... ...

Abstract	Currently available enzyme replacement therapies for lysosomal storage diseases are limited in their effectiveness due in part to short circulation times and suboptimal biodistribution of the therapeutic enzymes. We previously engineered Chinese hamster ovary (CHO) cells to produce α-galactosidase A (GLA) with various N-glycan structures and demonstrated that elimination of mannose-6-phosphate (M6P) and conversion to homogeneous sialylated N-glycans prolonged circulation time and improved biodistribution of the enzyme following a single-dose infusion into Fabry mice. Here, we confirmed these findings using repeated infusions of the glycoengineered GLA into Fabry mice and further tested whether this glycoengineering approach, Long-Acting-GlycoDesign (LAGD), could be implemented on other lysosomal enzymes. LAGD-engineered CHO cells stably expressing a panel of lysosomal enzymes [aspartylglucosamine (AGA), beta-glucuronidase (GUSB), cathepsin D (CTSD), tripeptidyl peptidase (TPP1), alpha-glucosidase (GAA) or iduronate 2-sulfatase (IDS)] successfully converted all M6P-containing N-glycans to complex sialylated N-glycans. The resulting homogenous glycodesigns enabled glycoprotein profiling by native mass spectrometry. Notably, LAGD extended the plasma half-life of all three enzymes tested (GLA, GUSB, AGA) in wildtype mice. LAGD may be widely applicable to lysosomal replacement enzymes to improve their circulatory stability and therapeutic efficacy.
Language	English
Publishing date	2023-02-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2023.1128371
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Article: COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest.

Chen, Albert Tian / Altschuler, Kevin / Zhan, Shing Hei / Chan, Yujia Alina / Deverman, Benjamin E

bioRxiv : the preprint server for biology

2020

Abstract: COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse ... ...

Abstract	COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 Spike receptor binding domain (RBD) across different geographic regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the recent emergence of a dominant lineage harboring an S477N RBD mutation in Australia. To accelerate COVID-19 research and public health efforts, COVID-19 CG will be continually upgraded with new features for users to quickly and reliably pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.
Keywords	covid19
Language	English
Publishing date	2020-09-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.09.23.310565
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Article ; Online: A multisample 7 T dynamic nuclear polarization polarizer for preclinical hyperpolarized MR.

Cheng, Tian / Gaunt, Adam P / Marco-Rius, Irene / Gehrung, Marcel / Chen, Albert P / van der Klink, Jacques J / Comment, Arnaud

NMR in biomedicine

2020 Volume 33, Issue 5, Page(s) e4264

Abstract: Dynamic nuclear polarization (DNP) provides the opportunity to boost liquid state magnetic resonance (MR) signals from selected nuclear spins by several orders of magnitude. A cryostat running at a temperature of ~ 1 K and a superconducting magnet set to ...

Abstract	Dynamic nuclear polarization (DNP) provides the opportunity to boost liquid state magnetic resonance (MR) signals from selected nuclear spins by several orders of magnitude. A cryostat running at a temperature of ~ 1 K and a superconducting magnet set to between 3 and 10 T are required to efficiently hyperpolarize nuclear spins. Several DNP polarizers have been implemented for the purpose of hyperpolarized MR and recent systems have been designed to avoid the need for user input of liquid cryogens. We herein present a zero boil-off DNP polarizer that operates at 1.35 ± 0.01 K and 7 T, and which can polarize two samples in parallel. The samples are cooled by a static helium bath thermally connected to a 1 K closed-cycle
Language	English
Publishing date	2020-01-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1000976-0
ISSN	1099-1492 ; 0952-3480
ISSN (online)	1099-1492
ISSN	0952-3480
DOI	10.1002/nbm.4264
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