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Article ; Online: Intracellular drug binding affinities by NMR.

Madl, Tobias

Acta crystallographica. Section D, Structural biology

2021 Volume 77, Issue Pt 10, Page(s) 1216–1217

MeSH term(s)	Binding Sites ; Ligands ; Magnetic Resonance Spectroscopy ; Protein Binding
Chemical Substances	Ligands
Language	English
Publishing date	2021-10-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798321010135
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Conference proceedings ; Online: Security Concept with Distributed Trust-Levels for Autonomous Cooperative Vehicle Networks

Madl, Tobias

Fraunhofer AISEC

2021

Abstract: The newly proposed cooperative intelligent transportation system (cITS) is a big step towards completely autonomous driving. It is a key requirement for vehicles to exchange crucial information. Only with exchanged data, such as hazard warnings or route ... ...

Abstract	The newly proposed cooperative intelligent transportation system (cITS) is a big step towards completely autonomous driving. It is a key requirement for vehicles to exchange crucial information. Only with exchanged data, such as hazard warnings or route planning each vehicle will have enough information to find its way without a driver. However, this data has to be authentic and trustworthy, since it will directly influence the behavior of every vehicle inside such a network. For authentic messages, public key infrastructure (PKI)-based asymmetric cryptography mechanisms were already proposed by different organizations, such as the European Telecommunications Standards Institute (ETSI). The second crucial information of trustworthiness is still missing. In this paper, a new security concept is presented, which introduces a trust-level for each vehicle to enable an assessment, whether data is trustworthy or not. Besides, a Pretty Good Privacy (PGP)-inspired certificate administration is proposed to manage the certificates and their affiliated trust-level. The new concept mitigates sybil attacks and increases the speed of data processing inside vehicles.
Keywords	privacy ; ETSI ; PKI ; sensor fusion ; CITS ; security
Subject code	629
Language	English
Publishing country	de
Document type	Conference proceedings ; Online
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Conference proceedings ; Online: Security Concept with Distributed Trust-Levels for Autonomous Cooperative Vehicle Networks

Madl, Tobias

2021

Abstract: S.321-328 ... The newly proposed cooperative intelligent transportation system (cITS) is a big step towards completely autonomous driving. It is a key requirement for vehicles to exchange crucial information. Only with exchanged data, such as hazard ... ...

Abstract	S.321-328 The newly proposed cooperative intelligent transportation system (cITS) is a big step towards completely autonomous driving. It is a key requirement for vehicles to exchange crucial information. Only with exchanged data, such as hazard warnings or route planning each vehicle will have enough information to find its way without a driver. However, this data has to be authentic and trustworthy, since it will directly influence the behavior of every vehicle inside such a network. For authentic messages, public key infrastructure (PKI)-based asymmetric cryptography mechanisms were already proposed by different organizations, such as the European Telecommunications Standards Institute (ETSI). The second crucial information of trustworthiness is still missing. In this paper, a new security concept is presented, which introduces a trust-level for each vehicle to enable an assessment, whether data is trustworthy or not. Besides, a Pretty Good Privacy (PGP)-inspired certificate administration is proposed to manage the certificates and their affiliated trust-level. The new concept mitigates sybil attacks and increases the speed of data processing inside vehicles.
Keywords	privacy ; ETSI ; PKI ; sensor fusion ; CITS ; security ; 003 ; 005 ; 006 ; 518
Subject code	629
Language	English
Publishing country	de
Document type	Conference proceedings ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Patchy proteins form a perfect lens.

Madl, Tobias

Science (New York, N.Y.)

2017 Volume 357, Issue 6351, Page(s) 546–547

MeSH term(s)	Lens, Crystalline ; Lenses ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2017-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aao1456
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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: Genetically encoded fluorescent sensor to monitor intracellular arginine methylation.

Zhang, Fangrong / Bischof, Helmut / Burgstaller, Sandra / Bourgeois, Benjamin M R / Malli, Roland / Madl, Tobias

Journal of photochemistry and photobiology. B, Biology

2024 Volume 252, Page(s) 112867

Abstract: Arginine methylation (ArgMet), as a post-translational modification, plays crucial roles in RNA processing, transcriptional regulation, signal transduction, DNA repair, apoptosis and liquid-liquid phase separation (LLPS). Since arginine methylation is ... ...

Abstract	Arginine methylation (ArgMet), as a post-translational modification, plays crucial roles in RNA processing, transcriptional regulation, signal transduction, DNA repair, apoptosis and liquid-liquid phase separation (LLPS). Since arginine methylation is associated with cancer pathogenesis and progression, protein arginine methyltransferases have gained interest as targets for anti-cancer therapy. Despite considerable process made to elucidate (patho)physiological mechanisms regulated by arginine methylation, there remains a lack of tools to visualize arginine methylation with high spatiotemporal resolution in live cells. To address this unmet need, we generated an ArgMet-sensitive genetically encoded, Förster resonance energy transfer-(FRET) based biosensor, called GEMS, capable of quantitative real-time monitoring of ArgMet dynamics. We optimized these biosensors by using different ArgMet-binding domains, arginine-glycine-rich regions and adjusting the linkers within the biosensors to improve their performance. Using a set of mammalian cell lines and modulators, we demonstrated the applicability of GEMS for monitoring changes in arginine methylation with single-cell and temporal resolution. The GEMS can facilitate the in vitro screening to find potential protein arginine methyltransferase inhibitors and will contribute to a better understanding of the regulation of ArgMet related to differentiation, development and disease.
MeSH term(s)	Animals ; Arginine/chemistry ; Methylation ; Fluorescence Resonance Energy Transfer ; Gene Expression Regulation ; Coloring Agents ; Protein Processing, Post-Translational ; Mammals/metabolism
Chemical Substances	Arginine (94ZLA3W45F) ; Coloring Agents
Language	English
Publishing date	2024-02-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	623022-2
ISSN	1873-2682 ; 1011-1344
ISSN (online)	1873-2682
ISSN	1011-1344
DOI	10.1016/j.jphotobiol.2024.112867
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Zs.A 2347: Show issues

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Article ; Online: Brain regions show different metabolic and protein arginine methylation phenotypes in frontotemporal dementias and Alzheimer's disease.

Zhang, Fangrong / Rakhimbekova, Anastasia / Lashley, Tammaryn / Madl, Tobias

Progress in neurobiology

2022 Volume 221, Page(s) 102400

Abstract: Frontotemporal dementia (FTD) is a heterogeneous neurodegenerative disease with multiple histopathological subtypes. FTD patients share similar symptoms with Alzheimer's disease (AD). Hence, FTD patients are commonly misdiagnosed as AD, despite the ... ...

Abstract	Frontotemporal dementia (FTD) is a heterogeneous neurodegenerative disease with multiple histopathological subtypes. FTD patients share similar symptoms with Alzheimer's disease (AD). Hence, FTD patients are commonly misdiagnosed as AD, despite the consensus clinical diagnostic criteria. It is therefore of great clinical need to identify a biomarker that can distinguish FTD from AD and control individuals, and potentially further differentiate between FTD pathological subtypes. We conducted a metabolomic analysis on post-mortem human brain tissue from three regions: cerebellum, frontal cortex and occipital cortex from control, FTLD-TDP type A, type A-C9, type C and AD. Our results indicate that the brain subdivisions responsible for different functions show different metabolic patterns. We further explored the region-specific metabolic characteristics of different FTD subtypes and AD patients. Different FTD subtypes and AD share similar metabolic phenotypes in the cerebellum, but AD exhibited distinct metabolic patterns in the frontal and occipital regions compared to FTD. The identified brain region-specific metabolite biomarkers could provide a tool for distinguishing different FTD subtypes and AD and provide the first insights into the metabolic changes of FTLD-TDP type A, type A-C9, type C and AD in different regions of the brain. The importance of protein arginine methylation in neurodegenerative disease has come to light, so we investigated whether the arginine methylation level contributes to disease pathogenesis. Our findings provide new insights into the relationship between arginine methylation and metabolic changes in FTD subtypes and AD that could be further explored, to study the molecular mechanism of pathogenesis.
MeSH term(s)	Humans ; Alzheimer Disease/diagnosis ; Alzheimer Disease/pathology ; Frontotemporal Dementia/diagnosis ; Methylation ; Neurodegenerative Diseases/pathology ; Brain/pathology ; Biomarkers ; Phenotype
Chemical Substances	Biomarkers
Language	English
Publishing date	2022-12-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	185535-9
ISSN	1873-5118 ; 0301-0082
ISSN (online)	1873-5118
ISSN	0301-0082
DOI	10.1016/j.pneurobio.2022.102400
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Article ; Online: Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems.

Lenard, Aneta J / Mulder, Frans A A / Madl, Tobias

Progress in nuclear magnetic resonance spectroscopy

2022 Volume 132-133, Page(s) 113–139

Abstract: Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on ... ...

Abstract	Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
MeSH term(s)	Solvents/chemistry ; Intrinsically Disordered Proteins/chemistry ; Magnetic Resonance Spectroscopy ; Solutions ; Nuclear Magnetic Resonance, Biomolecular/methods
Chemical Substances	Solvents ; Intrinsically Disordered Proteins ; Solutions
Language	English
Publishing date	2022-09-21
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	209325-x
ISSN	1873-3301 ; 0079-6565
ISSN (online)	1873-3301
ISSN	0079-6565
DOI	10.1016/j.pnmrs.2022.09.001
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Zs.A 2654: Show issues

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Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Reduced olfactory performance is associated with changed microbial diversity, oralization, and accumulation of dead biomaterial in the nasal olfactory area.

Kumpitsch, Christina / Fischmeister, Florian Ph S / Lackner, Sonja / Holasek, Sandra / Madl, Tobias / Habisch, Hansjörg / Wolf, Axel / Schöpf, Veronika / Moissl-Eichinger, Christine

Microbiology spectrum

2024 Volume 12, Issue 2, Page(s) e0154923

Abstract: The partial or complete loss of the sense of smell, which affects about 20% of the population, impairs the quality of life in many ways. Dysosmia and anosmia are mainly caused by aging, trauma, infections, or even neurodegenerative disease. Recently, the ...

Abstract	The partial or complete loss of the sense of smell, which affects about 20% of the population, impairs the quality of life in many ways. Dysosmia and anosmia are mainly caused by aging, trauma, infections, or even neurodegenerative disease. Recently, the olfactory area-a site containing the olfactory receptor cells responsible for odor perception-was shown to harbor a complex microbiome that reflects the state of olfactory function. This initially observed correlation between microbiome composition and olfactory performance needed to be confirmed using a larger study cohort and additional analyses. A total of 120 participants (middle-aged, no neurodegenerative disease) were enrolled in the study to further analyze the microbial role in human olfactory function. Olfactory performance was assessed using the Sniffin' Stick battery, and participants were grouped accordingly (normosmia:
MeSH term(s)	Middle Aged ; Humans ; Smell/physiology ; Anosmia/complications ; Quality of Life ; RNA, Ribosomal, 16S/genetics ; Neurodegenerative Diseases/complications ; Olfaction Disorders/complications
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2024-01-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01549-23
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Article ; Online: p53 Transactivation Domain Mediates Binding and Phase Separation with Poly-PR/GR.

Usluer, Sinem / Spreitzer, Emil / Bourgeois, Benjamin / Madl, Tobias

International journal of molecular sciences

2021 Volume 22, Issue 21

Abstract: The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the presence of poly-PR/GR dipeptide repeats, which are encoded by the chromosome 9 open reading frame 72 (C9orf72) gene. Recently, it was shown ... ...

Abstract	The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the presence of poly-PR/GR dipeptide repeats, which are encoded by the chromosome 9 open reading frame 72 (C9orf72) gene. Recently, it was shown that poly-PR/GR alters chromatin accessibility, which results in the stabilization and enhancement of transcriptional activity of the tumor suppressor p53 in several neurodegenerative disease models. A reduction in p53 protein levels protects against poly-PR and partially against poly-GR neurotoxicity in cells. Moreover, in model organisms, a reduction of p53 protein levels protects against neurotoxicity of poly-PR. Here, we aimed to study the detailed molecular mechanisms of how p53 contributes to poly-PR/GR-mediated neurodegeneration. Using a combination of biophysical techniques such as nuclear magnetic resonance (NMR) spectroscopy, fluorescence polarization, turbidity assays, and differential interference contrast (DIC) microscopy, we found that p53 physically interacts with poly-PR/GR and triggers liquid-liquid phase separation of p53. We identified the p53 transactivation domain 2 (TAD2) as the main binding site for PR25/GR25 and showed that binding of poly-PR/GR to p53 is mediated by a network of electrostatic and/or hydrophobic interactions. Our findings might help to understand the mechanistic role of p53 in poly-PR/GR-associated neurodegeneration.
MeSH term(s)	Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/pathology ; Binding Sites ; C9orf72 Protein/genetics ; C9orf72 Protein/metabolism ; Dipeptides/metabolism ; Fluorescence Polarization ; Frontotemporal Dementia/genetics ; Frontotemporal Dementia/pathology ; Humans ; Intrinsically Disordered Proteins/genetics ; Intrinsically Disordered Proteins/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Interaction Domains and Motifs/physiology ; Transcriptional Activation/genetics ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism
Chemical Substances	C9orf72 Protein ; C9orf72 protein, human ; Dipeptides ; Intrinsically Disordered Proteins ; TP53 protein, human ; Tumor Suppressor Protein p53
Language	English
Publishing date	2021-10-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222111431
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Article ; Online: Exploring the Arginine Methylome by Nuclear Magnetic Resonance Spectroscopy.

Habisch, Hansjörg / Zhang, Fangrong / Zhou, Qishun / Madl, Tobias

Journal of visualized experiments : JoVE

2021 , Issue 178

Abstract: Protein-bound arginine is commonly methylated in many proteins and regulates their function by altering the physicochemical properties, their interaction with other molecules, including other proteins or nucleic acids. This work presents an easily ... ...

Abstract	Protein-bound arginine is commonly methylated in many proteins and regulates their function by altering the physicochemical properties, their interaction with other molecules, including other proteins or nucleic acids. This work presents an easily implementable protocol for quantifying arginine and its derivatives, including asymmetric and symmetric dimethylarginine (ADMA and SDMA, respectively) and monomethyl arginine (MMA). Following protein isolation from biological body fluids, tissues, or cell lysates, a simple method for homogenization, precipitation of proteins, and protein hydrolysis is described. Since the hydrolysates contain many other components, such as other amino acids, lipids, and nucleic acids, a purification step using solid-phase extraction (SPE) is essential. SPE can either be performed manually using centrifuges or a pipetting robot. The sensitivity for ADMA using the current protocol is about 100 nmol/L. The upper limit of detection for arginine is 3 mmol/L due to SPE saturation. In summary, this protocol describes a robust method, which spans from biological sample preparation to NMR-based detection, providing valuable hints and pitfalls for successful work when studying the arginine methylome.
MeSH term(s)	Arginine/chemistry ; Epigenome ; Magnetic Resonance Spectroscopy ; Reproducibility of Results ; Solid Phase Extraction
Chemical Substances	Arginine (94ZLA3W45F)
Language	English
Publishing date	2021-12-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/63245
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