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Article ; Online: Particle ID: A Multiplexed Hydrogel Bead Platform for Biomedical Applications.

Alpsoy, Lokman / Sedeky, Abanoub Selim / Rehbein, Ulrike / Thedieck, Kathrin / Brandstetter, Thomas / Rühe, Jürgen

ACS applied materials & interfaces

2023 Volume 15, Issue 48, Page(s) 55346–55357

Abstract: We present a new platform based on hydrogel beads for multiplex analysis that can be fabricated, barcoded, and functionalized in a single step using a simple microfluidic assembly and a photo-cross-linking process. The beads are generated in a two-phase ... ...

Abstract	We present a new platform based on hydrogel beads for multiplex analysis that can be fabricated, barcoded, and functionalized in a single step using a simple microfluidic assembly and a photo-cross-linking process. The beads are generated in a two-phase flow fluidic system and photo-cross-linking of the polymer in the aqueous phase by C,H insertion cross-linking (CHic). The size and shape of the hydrogel particles can be controlled over a wide range by fluidic parameters. During the fabrication of the beads, they are barcoded by using physical and optical barcoding strategies. Magnetic beads and fluorescent particles, which allow identification of the production batch number, are added simultaneously as desired, resulting in complex, multifunctional beads in a one-step reaction. As an example of biofunctionalization,
MeSH term(s)	Humans ; Hydrogels ; Enzyme-Linked Immunosorbent Assay
Chemical Substances	Hydrogels
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c12122
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Finding new edges: systems approaches to MTOR signaling.

Heberle, Alexander Martin / Rehbein, Ulrike / Rodríguez Peiris, Maria / Thedieck, Kathrin

Biochemical Society transactions

2021 Volume 49, Issue 1, Page(s) 41–54

Abstract: Cells have evolved highly intertwined kinase networks to finely tune cellular homeostasis to the environment. The network converging on the mechanistic target of rapamycin (MTOR) kinase constitutes a central hub that integrates metabolic signals and ... ...

Abstract	Cells have evolved highly intertwined kinase networks to finely tune cellular homeostasis to the environment. The network converging on the mechanistic target of rapamycin (MTOR) kinase constitutes a central hub that integrates metabolic signals and adapts cellular metabolism and functions to nutritional changes and stress. Feedforward and feedback loops, crosstalks and a plethora of modulators finely balance MTOR-driven anabolic and catabolic processes. This complexity renders it difficult - if not impossible - to intuitively decipher signaling dynamics and network topology. Over the last two decades, systems approaches have emerged as powerful tools to simulate signaling network dynamics and responses. In this review, we discuss the contribution of systems studies to the discovery of novel edges and modulators in the MTOR network in healthy cells and in disease.
MeSH term(s)	Animals ; Gene Regulatory Networks/physiology ; Homeostasis/physiology ; Humans ; Protein Interaction Maps/physiology ; Signal Transduction/physiology ; Systems Integration ; TOR Serine-Threonine Kinases/metabolism ; TOR Serine-Threonine Kinases/physiology
Chemical Substances	MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2021-02-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20190730
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Article ; Online: Cardiac PI3K p110α attenuation delays aging and extends lifespan.

Abdellatif, Mahmoud / Eisenberg, Tobias / Heberle, Alexander Martin / Thedieck, Kathrin / Kroemer, Guido / Sedej, Simon

Cell stress

2022 Volume 6, Issue 8, Page(s) 72–75

Abstract: Phosphoinositide 3-kinase (PI3K) is a key component of the insulin signaling pathway that controls cellular me-tabolism and growth. Loss-of-function mutations in PI3K signaling and other downstream effectors of the insulin signaling pathway extend the ... ...

Abstract	Phosphoinositide 3-kinase (PI3K) is a key component of the insulin signaling pathway that controls cellular me-tabolism and growth. Loss-of-function mutations in PI3K signaling and other downstream effectors of the insulin signaling pathway extend the lifespan of various model organisms. However, the pro-longevity effect appears to be sex-specific and young mice with reduced PI3K signaling have increased risk of cardiac disease. Hence, it remains elusive as to whether PI3K inhibition is a valid strategy to delay aging and extend healthspan in humans. We recently demonstrated that reduced PI3K activity in cardiomyocytes delays cardiac growth, causing subnormal contractility and cardiopulmonary functional capacity, as well as increased risk of mortality at young age. In stark contrast, in aged mice, experi-mental attenuation of PI3K signaling reduced the age-dependent decline in cardiac function and extended maximal lifespan, suggesting a biphasic effect of PI3K on cardiac health and survival. The cardiac anti-aging effects of reduced PI3K activity coincided with enhanced oxida-tive phosphorylation and required increased autophagic flux. In humans, explanted failing hearts showed in-creased PI3K signaling, as indicated by increased phos-phorylation of the serine/threonine-protein kinase AKT. Hence, late-life cardiac-specific targeting of PI3K might have a therapeutic potential in cardiac aging and related diseases.
Language	English
Publishing date	2022-08-08
Publishing country	Austria
Document type	Journal Article ; Comment
ISSN	2523-0204
ISSN (online)	2523-0204
DOI	10.15698/cst2022.08.270
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Article ; Online: Differential control of ageing and lifespan by isoforms and splice variants across the mTOR network.

Razquin Navas, Patricia / Thedieck, Kathrin

Essays in biochemistry

2017 Volume 61, Issue 3, Page(s) 349–368

Abstract: Ageing can be defined as the gradual deterioration of physiological functions, increasing the incidence of age-related disorders and the probability of death. Therefore, the term ageing not only reflects the lifespan of an organism but also refers to ... ...

Abstract	Ageing can be defined as the gradual deterioration of physiological functions, increasing the incidence of age-related disorders and the probability of death. Therefore, the term ageing not only reflects the lifespan of an organism but also refers to progressive functional impairment and disease. The nutrient-sensing kinase mTOR (mammalian target of rapamycin) is a major determinant of ageing. mTOR promotes cell growth and controls central metabolic pathways including protein biosynthesis, autophagy and glucose and lipid homoeostasis. The concept that mTOR has a crucial role in ageing is supported by numerous reports on the lifespan-prolonging effects of the mTOR inhibitor rapamycin in invertebrate and vertebrate model organisms. Dietary restriction increases lifespan and delays ageing phenotypes as well and mTOR has been assigned a major role in this process. This may suggest a causal relationship between the lifespan of an organism and its metabolic phenotype. More than 25 years after mTOR's discovery, a wealth of metabolic and ageing-related effects have been reported. In this review, we cover the current view on the contribution of the different elements of the mTOR signalling network to lifespan and age-related metabolic impairment. We specifically focus on distinct roles of isoforms and splice variants across the mTOR network. The comprehensive analysis of mouse knockout studies targeting these variants does not support a tight correlation between lifespan prolongation and improved metabolic phenotypes and questions the strict causal relationship between them.
Language	English
Publishing date	2017-07-15
Publishing country	England
Document type	Journal Article ; Review
ISSN	1744-1358 ; 0071-1365
ISSN (online)	1744-1358
ISSN	0071-1365
DOI	10.1042/EBC20160086
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: systems medicine for rare tumor types. MAPTor-NET - personalized therapy for pancreatic neuroendocrine tumors

Sers, Christine / Thedieck, Kathrin

Systembiologie.de

2018 Volume -, Issue 12 May, Page(s) 34

Language	German
Document type	Article
ZDB-ID	2558263-X
ISSN	2191-2505
Database	Current Contents Medicine

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Article: Breaking the Interface: Efficient Extraction of Magnetic Beads from Nanoliter Droplets for Automated Sequential Immunoassays

Metzler, Lukas / Rehbein, Ulrike / Schönberg, Jan-Niklas / Brandstetter, Thomas / Thedieck, Kathrin / Rühe, Jürgen

Analytical chemistry. 2020 June 05, v. 92, no. 15

2020

Abstract: Droplet-based microfluidic systems offer a high potential for miniaturization and automation. Therefore, they are becoming an increasingly important tool in analytical chemistry, biosciences, and medicine. Heterogeneous assays commonly utilize magnetic ... ...

Abstract	Droplet-based microfluidic systems offer a high potential for miniaturization and automation. Therefore, they are becoming an increasingly important tool in analytical chemistry, biosciences, and medicine. Heterogeneous assays commonly utilize magnetic beads as a solid phase. However, the sensitivity of state of the art microfluidic systems is limited by the high bead concentrations required for efficient extraction across the water–oil interface. Furthermore, current systems suffer from a lack of technical solutions for sequential measurements of multiple samples, limiting their throughput and capacity for automation. Taking advantage of the different wetting properties of hydrophilic and hydrophobic areas in the channels, we improve the extraction efficiency of magnetic beads from aqueous nanoliter-sized droplets by 2 orders of magnitude to the low μg/mL range. Furthermore, the introduction of a switchable magnetic trap enables repetitive capture and release of magnetic particles for sequential analysis of multiple samples, enhancing the throughput. In comparison to conventional ELISA-based sandwich immunoassays on microtiter plates, our microfluidic setup offers a 25–50-fold reduction of sample and reagent consumption with up to 50 technical replicates per sample. The enhanced sensitivity and throughput of this system open avenues for the development of automated detection of biomolecules at the nanoliter scale.
Keywords	analytical chemistry ; automation ; biochemical compounds ; enzyme-linked immunosorbent assay ; hydrophilicity ; hydrophobicity ; magnetism ; medicine ; oil-water interface
Language	English
Dates of publication	2020-0605
Size	p. 10283-10290.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.0c00187
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Breaking the Interface: Efficient Extraction of Magnetic Beads from Nanoliter Droplets for Automated Sequential Immunoassays.

Metzler, Lukas / Rehbein, Ulrike / Schönberg, Jan-Niklas / Brandstetter, Thomas / Thedieck, Kathrin / Rühe, Jürgen

Analytical chemistry

2020 Volume 92, Issue 15, Page(s) 10283–10290

Abstract	Droplet-based microfluidic systems offer a high potential for miniaturization and automation. Therefore, they are becoming an increasingly important tool in analytical chemistry, biosciences, and medicine. Heterogeneous assays commonly utilize magnetic beads as a solid phase. However, the sensitivity of state of the art microfluidic systems is limited by the high bead concentrations required for efficient extraction across the water-oil interface. Furthermore, current systems suffer from a lack of technical solutions for sequential measurements of multiple samples, limiting their throughput and capacity for automation. Taking advantage of the different wetting properties of hydrophilic and hydrophobic areas in the channels, we improve the extraction efficiency of magnetic beads from aqueous nanoliter-sized droplets by 2 orders of magnitude to the low μg/mL range. Furthermore, the introduction of a switchable magnetic trap enables repetitive capture and release of magnetic particles for sequential analysis of multiple samples, enhancing the throughput. In comparison to conventional ELISA-based sandwich immunoassays on microtiter plates, our microfluidic setup offers a 25-50-fold reduction of sample and reagent consumption with up to 50 technical replicates per sample. The enhanced sensitivity and throughput of this system open avenues for the development of automated detection of biomolecules at the nanoliter scale.
MeSH term(s)	Antibodies/chemistry ; Automation/methods ; Enzyme-Linked Immunosorbent Assay/methods ; Fluorocarbons/chemistry ; Immunomagnetic Separation/methods ; Magnetic Phenomena ; Microfluidic Analytical Techniques/methods ; Nanostructures
Chemical Substances	Antibodies ; Fluorocarbons
Language	English
Publishing date	2020-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.0c00187
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Article ; Online: Phosphoproteomics Profiling Defines a Target Landscape of the Basophilic Protein Kinases AKT, S6K, and RSK in Skeletal Myotubes.

Fricke, Anna L / Mühlhäuser, Wignand W D / Reimann, Lena / Zimmermann, Johannes P / Reichenbach, Christa / Knapp, Bettina / Peikert, Christian D / Heberle, Alexander M / Faessler, Erik / Schäuble, Sascha / Hahn, Udo / Thedieck, Kathrin / Radziwill, Gerald / Warscheid, Bettina

Journal of proteome research

2023 Volume 22, Issue 3, Page(s) 768–789

Abstract: Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the phospho-signaling network are the protein kinases AKT, S6K, and RSK as part of the PI3K-AKT-mTOR- ... ...

Abstract	Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the phospho-signaling network are the protein kinases AKT, S6K, and RSK as part of the PI3K-AKT-mTOR-S6K and RAF-MEK-ERK-RSK pathways. However, despite their functional importance, knowledge about their specific targets is incomplete because these kinases share the same basophilic substrate motif RxRxx
MeSH term(s)	Muscle Fibers, Skeletal/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Phosphorylation ; Proto-Oncogene Proteins c-akt/genetics ; Proto-Oncogene Proteins c-akt/metabolism ; Signal Transduction/physiology ; Ribosomal Protein S6 Kinases, 90-kDa ; Ribosomal Protein S6 Kinases, 70-kDa
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Ribosomal Protein S6 Kinases, 90-kDa (EC 2.7.11.1) ; Ribosomal Protein S6 Kinases, 70-kDa (EC 2.7.11.1)
Language	English
Publishing date	2023-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00505
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Article ; Online: Proteome Coverage after Simultaneous Proteo-Metabolome Liquid-Liquid Extraction.

van Pijkeren, Alienke / Egger, Anna-Sophia / Hotze, Madlen / Zimmermann, Elisabeth / Kipura, Tobias / Grander, Julia / Gollowitzer, André / Koeberle, Andreas / Bischoff, Rainer / Thedieck, Kathrin / Kwiatkowski, Marcel

Journal of proteome research

2023 Volume 22, Issue 3, Page(s) 951–966

Abstract: Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, ...

Abstract	Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.
MeSH term(s)	Proteome/analysis ; Methanol ; Chloroform ; Metabolome ; Surface-Active Agents ; Liquid-Liquid Extraction/methods ; Urea
Chemical Substances	Proteome ; Methanol (Y4S76JWI15) ; Chloroform (7V31YC746X) ; Surface-Active Agents ; Urea (8W8T17847W)
Language	English
Publishing date	2023-02-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00758
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Article: systemmedizin für seltene tumoren. MAPTor-NET - personalisierte Therapie pankreatischer neuroendokriner Tumoren

Sers, Christine / Thedieck, Kathrin

Systembiologie.de

2017 Volume -, Issue 12 Dez., Page(s) 34

Language	German
Document type	Article
ZDB-ID	2558263-X
ISSN	2191-2505
Database	Current Contents Medicine

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