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Article ; Online: Applying transcriptomics to studyglycosylation at the cell type level.

Dworkin, Leo Alexander / Clausen, Henrik / Joshi, Hiren Jitendra

iScience

2022 Volume 25, Issue 6, Page(s) 104419

Abstract: The complex multi-step process of glycosylation occurs in a single cell, yet current analytics generally cannot measure the output (the glycome) of a single cell. Here, we addressed this discordance by investigating how single cell RNA-seq data can be ... ...

Abstract	The complex multi-step process of glycosylation occurs in a single cell, yet current analytics generally cannot measure the output (the glycome) of a single cell. Here, we addressed this discordance by investigating how single cell RNA-seq data can be used to characterize the state of the glycosylation machinery and metabolic network in a single cell. The metabolic network involves 214 glycosylation and modification enzymes outlined in our previously built atlas of cellular glycosylation pathways. We studied differential mRNA regulation of enzymes at the organ and single cell level, finding that most of the general protein and lipid oligosaccharide scaffolds are produced by enzymes exhibiting limited transcriptional regulation among cells. We predict key enzymes within different glycosylation pathways to be highly transcriptionally regulated as regulatable hotspots of the cellular glycome. We designed the Glycopacity software that enables investigators to extract and interpret glycosylation information from transcriptome data and define hotspots of regulation.
Language	English
Publishing date	2022-05-18
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.104419
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Article ; Online: Towards universally acceptable blood.

Clausen, Henrik / Olsson, Martin L

Nature microbiology

2019 Volume 4, Issue 9, Page(s) 1426–1427

MeSH term(s)	ABO Blood-Group System ; Bacterial Proteins/metabolism ; Blood Group Antigens/metabolism ; Blood Group Incompatibility/prevention & control ; Blood Grouping and Crossmatching ; Blood Transfusion ; Erythrocyte Membrane/immunology ; Gastrointestinal Microbiome ; Glycoside Hydrolases/metabolism ; Humans
Chemical Substances	ABO Blood-Group System ; Bacterial Proteins ; Blood Group Antigens ; Glycoside Hydrolases (EC 3.2.1.-)
Language	English
Publishing date	2019-08-07
Publishing country	England
Document type	Journal Article
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-019-0548-9
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Article ; Online: Polypeptide

Kato, Kentaro / Hansen, Lars / Clausen, Henrik

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 18

Abstract: ... Mucin- ... ...

Abstract	Mucin-type
MeSH term(s)	Animals ; Glycosylation ; N-Acetylgalactosaminyltransferases/metabolism ; Phenotype ; Substrate Specificity ; Polypeptide N-acetylgalactosaminyltransferase
Chemical Substances	N-Acetylgalactosaminyltransferases (EC 2.4.1.-)
Language	English
Publishing date	2021-09-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26185504
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Book ; Online: Measurement-Based Control for Minimizing Energy Functions in Quantum Systems

Clausen, Henrik Glavind / Rahman, Salahuddin Abdul / Karabacak, Özkan / Wisniewski, Rafal

2023

Abstract: In variational quantum algorithms (VQAs), the most common objective is to find the minimum energy eigenstate of a given energy Hamiltonian. In this paper, we consider the general problem of finding a sufficient control Hamiltonian structure that, under a ...

Abstract	In variational quantum algorithms (VQAs), the most common objective is to find the minimum energy eigenstate of a given energy Hamiltonian. In this paper, we consider the general problem of finding a sufficient control Hamiltonian structure that, under a given feedback control law, ensures convergence to the minimum energy eigenstate of a given energy function. By including quantum non-demolition (QND) measurements in the loop, convergence to a pure state can be ensured from an arbitrary mixed initial state. Based on existing results on strict control Lyapunov functions, we formulate a semidefinite optimization problem, whose solution defines a non-unique control Hamiltonian, which is sufficient to ensure almost sure convergence to the minimum energy eigenstate under the given feedback law and the action of QND measurements. A numerical example is provided to showcase the proposed methodology. Comment: Accepted for IFAC 2023 - 22nd World Congress of the International Federation of Automatic Control
Keywords	Quantum Physics ; Electrical Engineering and Systems Science - Systems and Control ; Mathematics - Optimization and Control
Subject code	531
Publishing date	2023-04-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Bump-and-Hole Approach to Dissect Regulation of Protein O-Glycosylation.

Schjoldager, Katrine T / Clausen, Henrik / Hurtado-Guerrero, Ramon

Molecular cell

2020 Volume 78, Issue 5, Page(s) 803–805

Abstract: In this issue of Molecular Cell, Schumann et al. (2020) present a novel strategy to dissect the regulation of protein O-glycosylation by a large family of isoenzymes in cells. They employ a bump-and-hole engineering approach to capture the specific ... ...

Abstract	In this issue of Molecular Cell, Schumann et al. (2020) present a novel strategy to dissect the regulation of protein O-glycosylation by a large family of isoenzymes in cells. They employ a bump-and-hole engineering approach to capture the specific contribution of individual isoenzymes to O-glycosylation of proteins.
MeSH term(s)	Glycosylation ; Glycosyltransferases ; Isoenzymes ; Proteins
Chemical Substances	Isoenzymes ; Proteins ; Glycosyltransferases (EC 2.4.-)
Language	English
Publishing date	2020-06-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2020.05.019
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Zs.A 5055: Show issues

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Article: A Bump-and-Hole Approach to Dissect Regulation of Protein O-Glycosylation

Schjoldager, Katrine T / Clausen, Henrik / Hurtado-Guerrero, Ramon

Molecular cell. 2020 June 04, v. 78, no. 5

2020

Abstract	In this issue of Molecular Cell, Schumann et al. (2020) present a novel strategy to dissect the regulation of protein O-glycosylation by a large family of isoenzymes in cells. They employ a bump-and-hole engineering approach to capture the specific contribution of individual isoenzymes to O-glycosylation of proteins.
Keywords	engineering ; glycosylation ; isozymes ; proteins
Language	English
Dates of publication	2020-0604
Size	p. 803-805.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2020.05.019
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Article ; Online: The incorrect use of CD75 as a synonym for ST6GAL1 has fostered the expansion of commercial "ST6GAL1" antibodies that do not recognize ST6GAL1.

Haldar, Barnita / Hwang, Jihye / Narimatsu, Yoshiki / Clausen, Henrik / Bellis, Susan L

Glycobiology

2022 Volume 32, Issue 9, Page(s) 736–742

Abstract: The ST6GAL1 Golgi sialyltransferase is upregulated in many human malignancies, however, detection of ST6GAL1 protein in cancer tissues has been hindered by the prior lack of antibodies. Recently, numerous commercial antibodies for ST6GAL1 have become ... ...

Abstract	The ST6GAL1 Golgi sialyltransferase is upregulated in many human malignancies, however, detection of ST6GAL1 protein in cancer tissues has been hindered by the prior lack of antibodies. Recently, numerous commercial antibodies for ST6GAL1 have become available, however, many of these do not, in fact, recognize ST6GAL1. Decades ago, the CD75 cell-surface epitope was mistakenly suggested to be the same molecule as ST6GAL1. While this was rapidly disproven, the use of CD75 as a synonym for ST6GAL1 has persisted, particularly by companies selling "ST6GAL1" antibodies. CD75 is reportedly a sialylated epitope which appears to encompass a range of glycan structures and glycan carriers. In this study, we evaluated the LN1 and ZB55 monoclonal antibodies, which are advertised as ST6GAL1 antibodies but were initially developed as CD75-recognizing antibodies (neither was raised against ST6GAL1 as the immunogen). Importantly, the LN1 and ZB55 antibodies have been widely used by investigators, as well as the Human Protein Atlas database, to characterize ST6GAL1 expression. Herein, we used cell and mouse models with controlled expression of ST6GAL1 to compare LN1 and ZB55 with an extensively validated polyclonal antibody to ST6GAL1. We find that LN1 and ZB55 do not recognize ST6GAL1, and furthermore, these 2 antibodies recognize different targets. Additionally, we utilized the well-validated ST6GAL1 antibody to determine that ST6GAL1 is overexpressed in bladder cancer, a finding that contradicts prior studies which employed LN1 to suggest ST6GAL1 is downregulated in bladder cancer. Collectively, our studies underscore the need for careful validation of antibodies purported to recognize ST6GAL1.
MeSH term(s)	Animals ; Antigens, CD/metabolism ; Epitopes ; Humans ; Mice ; Polysaccharides ; Sialyltransferases/metabolism ; Urinary Bladder Neoplasms
Chemical Substances	Antigens, CD ; Epitopes ; Polysaccharides ; Sialyltransferases (EC 2.4.99.-) ; ST6GAL1 protein, human (EC 2.4.99.1)
Language	English
Publishing date	2022-07-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1067689-2
ISSN	1460-2423 ; 0959-6658
ISSN (online)	1460-2423
ISSN	0959-6658
DOI	10.1093/glycob/cwac043
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Zs.A 3150: Show issues

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Article ; Online: H3N2 influenza A virus gradually adapts to human-type receptor binding and entry specificity after the start of the 1968 pandemic.

Liu, Mengying / Bakker, A Sophie / Narimatsu, Yoshiki / van Kuppeveld, Frank J M / Clausen, Henrik / de Haan, Cornelis A M / de Vries, Erik

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 31, Page(s) e2304992120

Abstract: To become established upon zoonotic transfer, influenza A viruses (IAV) need to switch binding from "avian-type" α2-3-linked sialic acid receptors (2-3Sia) to "human-type" Siaα2-6-linked sialic acid receptors (2-6Sia). For the 1968 H3N2 pandemic virus, ... ...

Abstract	To become established upon zoonotic transfer, influenza A viruses (IAV) need to switch binding from "avian-type" α2-3-linked sialic acid receptors (2-3Sia) to "human-type" Siaα2-6-linked sialic acid receptors (2-6Sia). For the 1968 H3N2 pandemic virus, this was accomplished by two canonical amino acid substitutions in its hemagglutinin (HA) although a full specificity shift had not occurred. The receptor repertoire on epithelial cells is highly diverse and simultaneous interaction of a virus particle with a range of low- to very low-affinity receptors results in tight heteromultivalent binding. How this range of affinities determines binding selectivity and virus motility remains largely unknown as the analysis of low-affinity monovalent HA-receptor interactions is technically challenging. Here, a biolayer interferometry assay enabled a comprehensive analysis of receptor-binding kinetics evolution upon host-switching. Virus-binding kinetics of H3N2 virus isolates slowly evolved from 1968 to 1979 from mixed 2-3/2-6Sia specificity to high 2-6Sia specificity, surprisingly followed by a decline in selectivity after 1992. By using genetically tuned HEK293 cells, presenting either a simplified 2-3Sia- or 2-6Sia-specific receptor repertoire, receptor-specific binding was shown to correlate strongly with receptor-specific entry. In conclusion, the slow and continuous evolution of entry and receptor-binding specificity of seasonal H3N2 viruses contrasts with the paradigm that human IAVs need to rapidly acquire and maintain a high specificity for 2-6Sia. Analysis of the kinetic parameters of receptor binding provides a basis for understanding virus-binding specificity, motility, and HA/neuraminidase balance at the molecular level.
MeSH term(s)	Humans ; Influenza A virus/metabolism ; Influenza A Virus, H3N2 Subtype/genetics ; Binding Sites ; HEK293 Cells ; Pandemics ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry ; Influenza, Human ; Receptors, Virus/metabolism
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus ; Receptors, Virus
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2304992120
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Article ; Online: Characterization of galactosyltransferase and sialyltransferase genes mediating the elongation of the extracellular O-GlcNAc glycans.

Tsukamoto, Yohei / Tsukamoto, Natsumi / Saiki, Wataru / Tashima, Yuko / Furukawa, Jun-Ichi / Kizuka, Yasuhiko / Narimatsu, Yoshiki / Clausen, Henrik / Takeuchi, Hideyuki / Okajima, Tetsuya

Biochemical and biophysical research communications

2024 Volume 703, Page(s) 149610

Abstract: O-GlcNAc is a unique post-translational modification found in cytoplasmic, nuclear, and mitochondrial proteins. In a limited number of extracellular proteins, O-GlcNAc modifications occur through the action of EOGT, which specifically modifies subsets of ...

Abstract	O-GlcNAc is a unique post-translational modification found in cytoplasmic, nuclear, and mitochondrial proteins. In a limited number of extracellular proteins, O-GlcNAc modifications occur through the action of EOGT, which specifically modifies subsets of epidermal growth factor-like (EGF) domain-containing proteins such as Notch receptors. The abnormalities due to EOGT mutations in mice and humans and the increased EOGT expression in several cancers signify the importance of EOGT pathophysiology and extracellular O-GlcNAc. Unlike intracellular O-GlcNAc monosaccharides, extracellular O-GlcNAc extends to form elongated glycan structures. However, the enzymes involved in the O-GlcNAc glycan extension have not yet been reported. In our study, we comprehensively screened potential galactosyltransferase and sialyltransferase genes related to the canonical O-GlcNAc glycan pathway and revealed the essential roles of B4GALT1 and ST3GAL4 in O-GlcNAc glycan elongation in human HEK293 cells. These findings were confirmed by sequential glycosylation of Drosophila EGF20 in vitro by EOGT, β4GalT-1, and ST3Gal-IV. Thus, the findings from our study throw light on the specific glycosyltransferases that mediate O-GlcNAc glycan elongation in human HEK293 cells.
MeSH term(s)	Humans ; Animals ; Mice ; HEK293 Cells ; Acetylglucosamine/metabolism ; Receptors, Notch/metabolism ; Galactosyltransferases/genetics ; Glycosyltransferases ; Drosophila/metabolism ; Sialyltransferases/genetics ; Polysaccharides
Chemical Substances	Acetylglucosamine (V956696549) ; Receptors, Notch ; Galactosyltransferases (EC 2.4.1.-) ; Glycosyltransferases (EC 2.4.-) ; Sialyltransferases (EC 2.4.99.-) ; Polysaccharides
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2024.149610
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Article ; Online: Structure and function of Semaphorin-5A glycosaminoglycan interactions.

Nagy, Gergely N / Zhao, Xiao-Feng / Karlsson, Richard / Wang, Karen / Duman, Ramona / Harlos, Karl / El Omari, Kamel / Wagner, Armin / Clausen, Henrik / Miller, Rebecca L / Giger, Roman J / Jones, E Yvonne

Nature communications

2024 Volume 15, Issue 1, Page(s) 2723

Abstract: Integration of extracellular signals by neurons is pivotal for brain development, plasticity, and repair. Axon guidance relies on receptor-ligand interactions crosstalking with extracellular matrix components. Semaphorin-5A (Sema5A) is a bifunctional ... ...

Abstract	Integration of extracellular signals by neurons is pivotal for brain development, plasticity, and repair. Axon guidance relies on receptor-ligand interactions crosstalking with extracellular matrix components. Semaphorin-5A (Sema5A) is a bifunctional guidance cue exerting attractive and inhibitory effects on neuronal growth through the interaction with heparan sulfate (HS) and chondroitin sulfate (CS) glycosaminoglycans (GAGs), respectively. Sema5A harbors seven thrombospondin type-1 repeats (TSR1-7) important for GAG binding, however the underlying molecular basis and functions in vivo remain enigmatic. Here we dissect the structural basis for Sema5A:GAG specificity and demonstrate the functional significance of this interaction in vivo. Using x-ray crystallography, we reveal a dimeric fold variation for TSR4 that accommodates GAG interactions. TSR4 co-crystal structures identify binding residues validated by site-directed mutagenesis. In vitro and cell-based assays uncover specific GAG epitopes necessary for TSR association. We demonstrate that HS-GAG binding is preferred over CS-GAG and mediates Sema5A oligomerization. In vivo, Sema5A:GAG interactions are necessary for Sema5A function and regulate Plexin-A2 dependent dentate progenitor cell migration. Our study rationalizes Sema5A associated developmental and neurological disorders and provides mechanistic insights into how multifaceted guidance functions of a single transmembrane cue are regulated by proteoglycans.
MeSH term(s)	Glycosaminoglycans/metabolism ; Proteoglycans/metabolism ; Heparitin Sulfate/metabolism ; Cell Movement ; Semaphorins/genetics ; Semaphorins/metabolism
Chemical Substances	Glycosaminoglycans ; Proteoglycans ; Heparitin Sulfate (9050-30-0) ; Semaphorins
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46725-7
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