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2. Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape

Author

Tobias Ensslen, Kumar Sarthak, Aleksei Aksimentiev, and Jan C. Behrends

Subjects
Histones, Nanopores, Colloid and Surface Chemistry, Lysine, Humans, General Chemistry, Peptides, Protein Processing, Post-Translational, Biochemistry, Mass Spectrometry, Catalysis
Abstract

The chemical nature and precise position of posttranslational modifications (PTMs) in proteins or peptides are crucial for various severe diseases, such as cancer. State-of-the-art PTM diagnosis is based on elaborate and costly mass-spectrometry or immunoassay-based approaches, which are limited in selectivity and specificity. Here, we demonstrate the use of a protein nanopore to differentiate peptides─derived from human histone H4 protein─of identical mass according to the positions of acetylated and methylated lysine residues. Unlike sequencing by stepwise threading, our method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, thus eliminating the need for controlled translocation. Molecular dynamics simulations show that the sensitivity to molecular shape derives from a highly nonuniform electric field along the pore. This molecular shape-sensing principle offers a path to versatile, label-free, and high-throughput characterizations of protein isoforms.

Published
2022
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3. Activation energy for pore opening in lipid membranes under an electric field

Author

Eulalie J. Lafarge, Pierre Muller, André P. Schroder, Ekaterina Zaitseva, Jan C. Behrends, and Carlos M. Marques

Subjects
Multidisciplinary
Abstract

The standard model of pore formation was introduced more than fifty years ago, and it has been since, despite some refinements, the cornerstone for interpreting experiments related to pores in membranes. A central prediction of the model concerning pore opening under an electric field is that the activation barrier for pore formation is lowered proportionally to the square of the electric potential. However, this has only been scarcely and inconclusively confronted to experiments. In this paper, we study the electropermeability of model lipid membranes composed of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) containing different fractions of POPC-OOH, the hydroperoxidized form of POPC, in the range 0 to 100 mol %. By measuring ion currents across a 50-μm-diameter black lipid membrane (BLM) with picoampere and millisecond resolution, we detect hydroperoxidation-induced changes to the intrinsic bilayer electropermeability and to the probability of opening angstrom-size or larger pores. Our results over the full range of lipid compositions show that the energy barrier to pore formation is lowered linearly by the absolute value of the electric field, in contradiction with the predictions of the standard model.

Published
2023
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4. The Multifaceted Antibacterial Mechanisms of the Pioneering Peptide Antibiotics Tyrocidine and Gramicidin S

Author

Michaela Wenzel, Marina Rautenbach, J. Arnold Vosloo, Tjalling Siersma, Christopher H. M. Aisenbrey, Ekaterina Zaitseva, Wikus E. Laubscher, Wilma van Rensburg, Jan C. Behrends, Burkhard Bechinger, and Leendert W. Hamoen

Subjects
antibiotics, antimicrobial peptides, bacterial cell biology, bacterial cytological profiling, cell membranes, mode of action, Microbiology, QR1-502
Abstract

ABSTRACT Cyclic β-sheet decapeptides from the tyrocidine group and the homologous gramicidin S were the first commercially used antibiotics, yet it remains unclear exactly how they kill bacteria. We investigated their mode of action using a bacterial cytological profiling approach. Tyrocidines form defined ion-conducting pores, induce lipid phase separation, and strongly reduce membrane fluidity, resulting in delocalization of a broad range of peripheral and integral membrane proteins. Interestingly, they also cause DNA damage and interfere with DNA-binding proteins. Despite sharing 50% sequence identity with tyrocidines, gramicidin S causes only mild lipid demixing with minor effects on membrane fluidity and permeability. Gramicidin S delocalizes peripheral membrane proteins involved in cell division and cell envelope synthesis but does not affect integral membrane proteins or DNA. Our results shed a new light on the multifaceted antibacterial mechanisms of these antibiotics and explain why resistance to them is virtually nonexistent. IMPORTANCE Cyclic β-sheet decapeptides, such as tyrocidines and gramicidin S, were among the first antibiotics in clinical application. Although they have been used for such a long time, there is virtually no resistance to them, which has led to a renewed interest in this peptide class. Both tyrocidines and gramicidin S are thought to disrupt the bacterial membrane. However, this knowledge is mainly derived from in vitro studies, and there is surprisingly little knowledge about how these long-established antibiotics kill bacteria. Our results shed new light on the antibacterial mechanism of β-sheet peptide antibiotics and explain why they are still so effective and why there is so little resistance to them.

Published
2018
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5. A chip-based array for high-resolution fluorescence characterization of free-standing horizontal lipid membranes under voltage clamp

Author

Tobias Ensslen and Jan C. Behrends

Subjects
Microscopy, Fluorescence, Lipid Bilayers, Biomedical Engineering, Membrane Proteins, Bioengineering, General Chemistry, Ion Channel Gating, Microelectrodes, Biochemistry
Abstract

Optical techniques, such as fluorescence microscopy, are of great value in characterizing the structural dynamics of membranes and membrane proteins. A particular challenge is to combine high-resolution optical measurements with high-resolution voltage clamp electrical recordings providing direct information on e.g. single ion channel gating and/or membrane capacitance. Here, we report on a novel chip-based array device which facilitates optical access with water or oil-immersion objectives of high numerical aperture to horizontal free-standing lipid membranes while conrolling membrane voltage and recroding currents using micropatterned Ag/AgCl-electrodes. We demonstrate both wide-field and confocal imaging, as well as time-resolved single photon counting on free-standing membranes spanning sub-picoliter cavities are demonstrated while electrical signals, including single channel activity, are simultaneously acquired. This optically addressable microelectrode cavity array will allow combined electrical-optical studies of membranes and membrane proteins to be performed as a routine experiment.

Published
2022
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11. The radiosensitizing effect of platinum nanoparticles in proton irradiations is not caused by an enhanced proton energy deposition at the macroscopic scale

Author

C Behrends, C M Bäcker, I Schilling, S Zwiehoff, J Weingarten, K Kröninger, C Rehbock, S Barcikowski, J Wulff, C Bäumer, and B Timmermann

Subjects
Radiation-Sensitizing Agents, Radiological and Ultrasound Technology, Medizin, Chemie, Metal Nanoparticles, Radiosensitizing effect, Proton therapy, Gelatin, Energy deposition, Radiology, Nuclear Medicine and imaging, Protons, Reactive Oxygen Species, Noble metal nanoparticles, Platinum
Abstract

Objective. Due to the radiosensitizing effect of biocompatible noble metal nanoparticles (NPs), their administration is considered to potentially increase tumor control in radiotherapy. The underlying physical, chemical and biological mechanisms of the NPs' radiosensitivity especially when interacting with proton radiation is not conclusive. In the following work, the energy deposition of protons in matter containing platinum nanoparticles (PtNPs) is experimentally investigated. Approach. Surfactant-free monomodal PtNPs with a mean diameter of (40 ± 10) nm and a concentration of 300 μg ml−1, demonstrably leading to a substantial production of reactive oxygen species (ROS), were homogeneously dispersed into cubic gelatin samples serving as tissue-like phantoms. Gelatin samples without PtNPs were used as control. The samples' dimensions and contrast of the PtNPs were verified in a clinical computed tomography scanner. Fields from a clinical proton machine were used for depth dose and stopping power measurements downstream of both samples types. These experiments were performed with a variety of detectors at a pencil beam scanning beam line as well as a passive beam line with proton energies from about 56–200 MeV. Main results. The samples' water equivalent ratios in terms of proton stopping as well as the mean proton energy deposition downstream of the samples with ROS-producing PtNPs compared to the samples without PtNPs showed no differences within the experimental uncertainties of about 2%. Significance. This study serves as experimental proof that the radiosensitizing effect of biocompatible PtNPs is not due to a macroscopically increased proton energy deposition, but is more likely caused by a catalytic effect of the PtNPs. Thus, these experiments provide a contribution to the highly discussed radiobiological question of the proton therapy efficiency with noble metal NPs and facilitate initial evidence that the dose calculation in treatment planning is straightforward and not affected by the presence of sensitizing PtNPs., Physics in medicine and biology;67(15)

Published
2022
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14. Resolving isomeric posttranslational modifications using a nanopore

Author

Aleksei Aksimentiev, Kumar Sarthak, Jan C. Behrends, and Tobias Ensslen

Subjects
chemistry.chemical_classification, Molecular dynamics, chemistry.chemical_compound, Nanopore, chemistry, Acetylation, Histone protein, Biophysics, Peptide, Mass spectrometry, DNA, Function (biology)
Abstract

Posttranslational modifications (PTMs) of proteins are crucial for cellular function but pose analytical problems, especially in distinguishing chemically identical PTMs at different nearby locations within the same protein. Current methods, such as liquid chromatography-tandem mass spectrometry, are technically tantamount to de novo protein sequencing1. Nanopore techniques may provide a more efficient solution, but applying the concepts of nanopore DNA strand sequencing to proteins still faces fundamental problems2–4. Here, we demonstrate the use of an engineered biological nanopore to differentiate positional isomers resulting from acetylation or methylation of histone protein H4, an important PTM target5,6. In contrast to strand sequencing, we differentiate positional isomers by recording ionic current modulations resulting from the stochastic entrapment of entire peptides in the pore’s sensing zone, with all residues simultaneously contributing to the electrical signal. Molecular dynamics simulations show that, in this whole-molecule sensing mode, the non-uniform distribution of the electric potential within the nanopore makes the added resistance contributed by a PTM dependent on its precise location on the peptide. Optimization of the pore’s sensitivity in combination with parallel recording and automated and standardized protein fragmentation may thus provide a simple, label-free, high-throughput analytical platform for identification and quantification of PTMs.

Published
2021
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18. Retracted Article: Microelectrochemical cell arrays for whole-cell currents recording through ion channel proteins based on trans-electroporation approach

Author

Tianyang Zheng, Gerhard Baaken, Jan C. Behrends, and Jürgen Rühe

Subjects
Electrochemistry, Environmental Chemistry, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 0210 nano-technology, 01 natural sciences, Biochemistry, Spectroscopy, 0104 chemical sciences, Analytical Chemistry
Abstract

A novel chip based method is able to record the whole-cell currents through biological cell membrane with high electrostability.

Published
2020
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19. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

Author

Abdelghani Oukhaled, Hadjer Ouldali, Juan Pelta, Kumar Sarthak, Tobias Ensslen, Philippe Manivet, Aleksei Aksimentiev, Jan C. Behrends, and Fabien Piguet

Subjects
Pore Forming Cytotoxic Proteins, Bacterial Toxins, Biomedical Engineering, Aerolysin, Bioengineering, Sequence (biology), Molecular Dynamics Simulation, Applied Microbiology and Biotechnology, Nanopores, 03 medical and health sciences, 0302 clinical medicine, Protein sequencing, Electricity, Amino Acids, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Protein molecules, Extramural, Chemistry, Proteins, Amino acid, Nanopore, Biochemistry, Sufficient time, Molecular Medicine, Peptides, 030217 neurology & neurosurgery, Biotechnology
Abstract

Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.

Published
2019
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20. Prevalence and risk factors of undiagnosed diabetes mellitus among gastroenterological patients: a HbA1c-based single center experience - Prevalence of undiagnosed diabetes in gastroenterological patients

Author

Anne Lautenbach, Jörg Schrader, Angelique Hölzemer, Ansgar W. Lohse, Berit C. Behrends, Hans O. Pinnschmidt, Thomas Renné, T Fründt, Jocelyn de Heer, and Niko Schröder

Subjects
Blood Glucose, Liver Cirrhosis, medicine.medical_specialty, Cirrhosis, Population, 030209 endocrinology & metabolism, Disease, Primary sclerosing cholangitis, Prediabetic State, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Internal medicine, Diabetes mellitus, medicine, Diabetes Mellitus, Prevalence, Humans, 030212 general & internal medicine, Prediabetes, Risk factor, education, Retrospective Studies, Glycated Hemoglobin, education.field_of_study, business.industry, Gastroenterology, medicine.disease, Etiology, business
Abstract

Diabetes mellitus is a major risk factor for microvascular disease, leading to chronic kidney injury or cardiovascular disease, but there is a tremendous proportion of patients worldwide who suffer from undiagnosed diabetes. Until now, little is known about the prevalence of undiagnosed diabetes in gastroenterology inpatients.To improve detection of undiagnosed diabetes, a routine screening procedure for gastroenterology inpatients, based on hemoglobin AWe conducted a retrospective analysis of the implemented diabetes screening. Diabetes mellitus was diagnosed according to the guideline of the German Diabetes Association in patients with an HbAWithin a 3-month period, 606 patients were eligible for a diabetes screening. Pre-existing diabetes was documented in 120 patients (19.8 %), undiagnosed diabetes was found in 24 (3.9%), and 162 patients (26.7%) met the definition for prediabetes. Steroid medication use, age, and liver cirrhosis due to primary sclerosing cholangitis (PSC) were identified as risk factors for undiagnosed diabetes.The prevalence of undiagnosed diabetes in gastroenterology inpatients is markedly elevated in comparison to the general population, and a substantial number of inpatients are in a prediabetic status, underlining the need for diabetes screening. In addition to previously described risk factors of patient age and steroid medication use, we identified PSC-related liver cirrhosis (but not liver cirrhosis due to another etiology) as an independent risk factor for undiagnosed diabetes.Diabetes mellitus ist ein Hauptrisikofaktor für mikrovaskuläre Erkrankungen, die zu chronischer Niereninsuffizienz oder Herz-Kreislauf-Erkrankungen führen. Weltweit ist ein erheblicher Anteil der Bevölkerung an Diabetes erkrankt, ohne von der Erkrankung zu wissen. Über die Prävalenz und mögliche Risikofaktoren eines unerkannten Diabetes mellitus bei stationär behandelten Patienten ist bisher wenig bekannt. ZIEL: Um die Detektion von bis dato nicht diagnostiziertem Diabetes zu verbessern, wurde ein Routine-Screening-Verfahren für stationäre, gastroenterologische Patienten basierend auf der Messung von Hämoglobin A1c (HbA1c) und Nüchternplasmaglukose (FPG) etabliert.Retrospektive Analyse des durchgeführten Diabetes-Screenings. Bei Patienten mit einem HbA1c von ≥ 6,5% und/oder Nüchternplasmaglukose (FPG) ≥ 126 mg/dl wurde ein Diabetes mellitus gemäß Richtlinie des Deutschen Diabetesverbandes diagnostiziert. Risikofaktoren für einen unerkannten Diabetes mellitus wurden durch uni- und multivariate Analyse ermittelt.In dem Beobachtungszeitraum von drei Monaten wurde bei 606 Patienten ein Diabetes-Screening durchgeführt. Vorbestehender Diabetes wurde bei 120 Patienten (19,8%) dokumentiert, ein bis dato unerkannter Diabetes lag bei 24 Patienten (3,9%), 162 Patienten (26,7%) erfüllten die Definition eines Prädiabetes. Steroidmedikation, Alter und Leberzirrhose bei primär sklerosierender Cholangitis (PSC) wurden als Risikofaktor für unerkannten Diabetes identifiziert.Die Prävalenz eines unerkannten Diabetes bei stationären, gastroenterologischen Patienten ist im Vergleich zur Allgemeinbevölkerung deutlich erhöht, und ein erheblicher Anteil dieser Patienten befindet sich in einem prädiabetischen Status, was die Notwendigkeit eines Diabetes-Screenings unterstreicht. Zusätzlich zu bereits beschriebenen Risikofaktoren wie Alter und Steroidmedikation, identifizierten wir eine PSC-bedingte Leberzirrhose, jedoch keine Leberzirrhose aufgrund einer anderen Ätiologie als unabhängigen Risikofaktor für unerkannten Diabetes mellitus.

Published
2021

21. Pore-forming toxins as tools for polymer analytics: From sizing to sequencing

Author

Fabien, Piguet, Tobias, Ensslen, Mazdak A, Bakshloo, Monasadat, Talarimoghari, Hadjer, Ouldali, Gerhard, Baaken, Ekaterina, Zaitseva, Manuela, Pastoriza-Gallego, Jan C, Behrends, and Abdelghani, Oukhaled

Subjects
Nanopores, Polymers, Nanotechnology, Peptides, Polyethylene Glycols
Abstract

We report here on the nanopore resistive pulse sensing (Np-RPS) method, involving pore-forming toxins as tools for polymer analytics at single molecule level. Np-RPS is an electrical method for the label-free detection of single molecules. A molecule interacting with the pore causes a change of the electrical resistance of the pore, called a resistive pulse, associated with a measurable transient current blockade. The features of the blockades, in particular their depth and duration, contain information on the molecular properties of the analyte. We first revisit the history of Np-RPS, then we discuss the effect of the configuration of the molecule/nanopore interaction on the molecular information that can be extracted from the signal, illustrated in two different regimes that either favor molecular sequencing or molecular sizing. Specifically, we focus on the sizing regime and on the use of two different pore-forming toxins, staphylococcal α-hemolysin (αHL) and aerolysin (AeL) nanopores, for the characterization of water-soluble polymers (poly-(ethylene glycol), (PEG)), homopeptides, and heteropeptides. We discuss how nanopore sizing of polymers could be envisioned as a new approach for peptide/protein sequencing.

Published
2021

22. 20 Vestibuläres System

Author

Jens Rettig, Erhard Wischmeyer, Rainer Deutzmann, Heimo Ehmke, Jan C. Behrends, Jens Leipziger, Claudia Pedain, Markus Hoth, Stephan Frings, Frank Müller, Stephan Grissmer, Armin Kurtz, Charlotte Wagner, and Josef Bischofberger

Published
2021
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23. 7 Immunsystem Immunsystem

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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25. 6 Blut Blut

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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27. Sachverzeichnis

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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28. 13 Ernährung, Verdauung und Absorption, Leber

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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29. Duale Reihe Physiologie

Author

Jan C. Behrends, Erhard Wischmeyer, Heimo Ehmke, Charlotte Wagner, Claudia Pedain, Markus Hoth, Josef Bischofberger, Stephan Frings, Stephan Grissmer, Frank Müller, Jens Rettig, Armin Kurtz, Jens Leipziger, and Rainer Deutzmann

Published
2021
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30. 10 Niere und Salz-/Wasserhaushalt Niere

Author

Rainer Deutzmann, Jan C. Behrends, Frank Müller, Jens Leipziger, Charlotte Wagner, Josef Bischofberger, Jens Rettig, Armin Kurtz, Heimo Ehmke, Erhard Wischmeyer, Claudia Pedain, Markus Hoth, Stephan Frings, and Stephan Grissmer

Published
2021
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32. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Author

D. KLIONSKY, A. ABDEL-AZIZ, S. ABDELFATAH, M. ABDELLATIF, A. ABDOLI, S. ABEL, H. ABELIOVICH, M. ABILDGAARD, Y. ABUDU, A. ACEVEDO-AROZENA, I. ADAMOPOULOS, K. ADELI, T. ADOLPH, A. ADORNETTO, E. AFLAKI, G. AGAM, A. AGARWAL, B. AGGARWAL, M. AGNELLO, P. AGOSTINIS, J. AGREWALA, A. AGROTIS, P. AGUILAR, S. AHMAD, Z. AHMED, U. AHUMADA-CASTRO, S. AITS, S. AIZAWA, Y. AKKOC, T. AKOUMIANAKI, H. AKPINAR, A. AL-ABD, L. AL-AKRA, A. AL-GHARAIBEH, M. ALAOUI-JAMALI, S. ALBERTI, E. ALCOCER-GOMEZ, C. ALESSANDRI, M. ALI, M. AL-BARI, S. ALIWAINI, J. ALIZADEH, E. ALMACELLAS, A. ALMASAN, A. ALONSO, G. ALONSO, N. ALTAN-BONNET, D. ALTIERI, S. ALVES, C. DA COSTA, M. ALZAHARNA, M. AMADIO, C. AMANTINI, C. AMARAL, S. AMBROSIO, A. AMER, V. AMMANATHAN, Z. AN, S. ANDERSEN, S. ANDRABI, M. ANDRADE-SILVA, A. ANDRES, S. ANGELINI, D. ANN, U. ANOZIE, M. ANSARI, P. ANTAS, A. ANTEBI, Z. ANTON, T. ANWAR, L. APETOH, N. APOSTOLOVA, T. ARAKI, Y. ARAKI, K. ARASAKI, W. ARAUJO, J. ARAYA, C. ARDEN, M. AREVALO, S. ARGUELLES, E. ARIAS, J. ARIKKATH, H. ARIMOTO, A. ARIOSA, D. ARMSTRONG-JAMES, L. ARNAUNE-PELLOQUIN, A. AROCA, D. ARROYO, I. ARSOV, R. ARTERO, D. ASARO, M. ASCHNER, M. ASHRAFIZADEH, O. ASHUR-FABIAN, A. ATANASOV, A. AU, P. AUBERGER, H. AUNER, L. AURELIAN, R. AUTELLI, L. AVAGLIANO, Y. AVALOS, S. AVEIC, C. AVELEIRA, T. AVINWITTENBERG, Y. AYDIN, S. AYTON, S. AYYADEVARA, M. AZZOPARDI, M. BABA, J. BACKER, S. BACKUES, D. BAE, O. BAE, S. BAE, E. BAEHRECKE, A. BAEK, S. BAEK, G. BAGETTA, A. BAGNIEWSKA-ZADWORNA, H. BAI, J. BAI, X. BAI, Y. BAI, N. BAIRAGI, S. BAKSI, T. BALBI, C. BALDARI, W. BALDUINI, A. BALLABIO, M. BALLESTER, S. BALAZADEH, R. BALZAN, R. BANDOPADHYAY, S. BANERJEE, Y. BAO, M. BAPTISTA, A. BARACCA, C. BARBATI, A. BARGIELA, D. BARILA, P. BARLOW, S. BARMADA, E. BARREIRO, G. BARRETO, J. BARTEK, B. BARTEL, A. BARTOLOME, G. BARVE, S. BASAGOUDANAVAR, D. BASSHAM, R. JR, A. BASU, H. BATOKO, I. BATTEN, E. BAULIEU, B. BAUMGARNER, J. BAYRY, R. BEALE, I. BEAU, F. BEAUMATIN, L. BECHARA, G. BECK, M. BEERS, J. BEGUN, C. BEHRENDS, G. BEHRENS, R. BEI, E. BEJARANO, S. BEL, C. BEHL, A. BELAID, N. BELGAREH-TOUZE, C. BELLAROSA, F. BELLEUDI, M. PEREZ, R. BELLO-MORALES, J. BELTRAN, S. BELTRAN, D. BENBROOK, M. BENDORIUS, B. BENITEZ, I. BENITO-CUESTA, J. BENSALEM, M. BERCHTOLD, S. BEREZOWSKA, D. BERGAMASCHI, M. BERGAMI, A. BERGMANN, L. BERLIOCCHI, C. BERLIOZ-TORRENT, A. BERNARD, L. BERTHOUX, C. BESIRLI, S. BESTEIRO, V. BETIN, R. BEYAERT, J. BEZBRADICA, K. BHASKAR, I. BHATIA-KISSOVA, R. BHATTACHARYA, S. BHATTACHARYA, S. BHATTACHARYYA, M. BHUIYAN, S. BHUTIA, L. BI, X. BI, T. BIDEN, K. BIJIAN, V. BILLES, N. BINART, C. BINCOLETTO, A. BIRGISDOTTIR, G. BJORKOY, G. BLANCO, A. BLAS-GARCIA, J. BLASIAK, R. BLOMGRAN, K. BLOMGREN, J. BLUM, E. BOADA-ROMERO, M. BOBAN, K. BOESZEBATTAGLIA, P. BOEUF, B. BOLAND, P. BOMONT, P. BONALDO, S. BONAM, L. BONFILI, J. BONIFACINO, B. BOONE, M. BOOTMAN, M. BORDI, C. BORNER, B. BORNHAUSER, G. BORTHAKUR, J. BOSCH, S. BOSE, L. BOTANA, J. BOTAS, C. BOULANGER, M. BOULTON, M. BOURDENX, B. BOURGEOIS, N. BOURKE, G. BOUSQUET, P. BOYA, P. BOZHKOV, L. BOZI, T. BOZKURT, D. BRACKNEY, C. BRANDTS, R. BRAUN, G. BRAUS, R. BRAVO-SAGUA, J. BRAVO-SAN PEDRO, P. BREST, M. BRINGER, A. BRIONES-HERRERA, V. BROADDUS, P. BRODERSEN, E. ALVAREZ, J. BRODSKY, S. BRODY, P. BRONSON, J. BRONSTEIN, C. BROWN, R. BROWN, P. BRUM, J. BRUMELL, N. BRUNETTI-PIERRI, D. BRUNO, R. BRYSON-RICHARDSON, C. BUCCI, C. BUCHRIESER, M. BUENO, L. BUITRAGO-MOLINA, S. BURASCHI, S. BUCH, J. BUCHAN, E. BUCKINGHAM, H. BUDAK, M. BUDINI, G. BULTYNCK, F. BURADA, J. BURGOYNE, M. BURON, V. BUSTOS, S. BUTTNER, E. BUTTURINI, A. BYRD, I. CABAS, S. CABRERA-BENITEZ, K. CADWELL, J. CAI, L. CAI, Q. CAI, M. CAIRO, J. CALBET, G. CALDWELL, K. CALDWELL, J. CALL, R. CALVANI, A. CALVO, M. BARRERA, N. CAMARA, J. CAMONIS, N. CAMOUGRAND, M. CAMPANELLA, E. CAMPBELL, F. CAMPBELL-VALOIS, S. CAMPELLO, I. CAMPESI, J. CAMPOS, O. CAMUZARD, J. CANCINO, D. DE ALMEIDA, L. CANESI, I. CANIGGIA, B. CANONICO, C. CANTI, B. CAO, M. CARAGLIA, B. 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TUXWORTH, J. TYLER, E. TYUTEREVA, Y. UCHIYAMA, A. UGUNKLUSEK, H. UHLIG, I. ULASOV, M. UMEKAWA, C. UNGERMANN, R. UNNO, S. URBE, E. URIBE-CARRETERO, S. USTUN, V. UVERSKY, T. VACCARI, M. VACCARO, B. VAHSEN, H. VAKIFAHMETOGLU-NORBERG, R. VALDOR, M. VALENTE, A. VALKO, R. VALLEE, A. VALVERDE, G. VAN DEN BERGHE, S. VAN DER VEEN, L. VAN KAER, J. VAN LOOSDREGT, S. VAN WIJK, W. VANDENBERGHE, I. VANHOREBEEK, M. VANNIER-SANTOS, N. VANNINI, M. VANRELL, C. VANTAGGIATO, G. VARANO, I. VARELA-NIETO, M. VARGA, M. VASCONCELOS, S. VATS, D. VAVVAS, I. VEGANAREDO, S. VEGA-RUBIN-DE-CELIS, G. VELASCO, A. VELAZQUEZ, T. VELLAI, E. VELLENGA, F. VELOTTI, M. VERDIER, P. VERGINIS, I. VERGNE, P. VERKADE, M. VERMA, P. VERSTREKEN, T. VERVLIET, J. VERVOORTS, A. VESSONI, V. VICTOR, M. VIDAL, C. VIDONI, O. VIEIRA, R. VIERSTRA, S. VIGANO, H. VIHINEN, V. VIJAYAN, M. VILA, M. VILAR, J. VILLALBA, A. VILLALOBO, B. VILLAREJO-ZORI, F. VILLARROYA, J. VILLARROYA, O. VINCENT, C. VINDIS, C. VIRET, M. VISCOMI, D. VISNJIC, I. VITALE, D. VOCADLO, O. VOITSEKHOVSKAJA, C. VOLONTE, M. VOLTA, M. VOMERO, C. VON HAEFEN, M. VOOIJS, W. VOOS, L. VUCICEVIC, R. WADE-MARTINS, S. WAGURI, K. WAITE, S. WAKATSUKI, D. WALKER, M. WALKER, S. WALKER, J. WALTER, F. WANDOSELL, B. WANG, C. WANG, D. WANG, F. WANG, G. WANG, H. WANG, J. WANG, K. WANG, L. WANG, M. WANG, N. WANG, P. WANG, Q. WANG, W. WANG, X. WANG, Y. WANG, Z. WANG, G. WARNES, V. WARNSMANN, H. WATADA, E. WATANABE, M. WATCHON, T. WEAVER, G. WEGRZYN, A. WEHMAN, H. WEI, L. WEI, T. WEI, Y. WEI, O. WEIERGRABER, C. WEIHL, G. WEINDL, R. WEISKIRCHEN, A. WELLS, R. WEN, X. WEN, A. WERNER, B. WEYKOPF, S. WHEATLEY, J. WHITTON, A. WHITWORTH, K. WIKTORSKA, M. WILDENBERG, T. WILEMAN, S. WILKINSON, D. WILLBOLD, B. WILLIAMS, R. WILLIAMS, P. WILLIAMSON, R. WILSON, B. WINNER, N. WINSOR, S. WITKIN, H. WODRICH, U. WOEHLBIER, T. WOLLERT, E. WONG, J. WONG, R. WONG, V. WONG, W. WONG, A. WU, C. WU, J. WU, K. WU, M. WU, S. WU, W. WU, X. WU, Y. WU, R. XAVIER, H. XIA, L. XIA, Z. XIA, G. XIANG, J. XIANG, M. XIANG, W. XIANG, B. XIAO, G. XIAO, H. XIAO, J. XIAO, L. XIAO, S. XIAO, Y. XIAO, B. XIE, C. XIE, M. XIE, Y. XIE, Z. XIE, M. XILOURI, C. XU, E. XU, H. XU, J. XU, L. XU, W. XU, X. XU, Y. XUE, S. YAKHINE-DIOP, M. YAMAGUCHI, O. YAMAGUCHI, A. YAMAMOTO, S. YAMASHINA, S. YAN, Z. YAN, Y. YANAGI, C. YANG, D. YANG, H. YANG, J. YANG, L. YANG, M. YANG, P. YANG, Q. YANG, S. YANG, W. YANG, X. YANG, Y. YANG, H. YAO, S. YAO, X. YAO, Y. YAO, T. YASUI, M. YAZDANKHAH, P. YEN, C. YI, X. YIN, Y. YIN, Z. YIN, M. YING, Z. YING, C. YIP, S. YIU, Y. YOO, K. YOSHIDA, S. YOSHII, T. YOSHIMORI, B. YOUSEFI, B. YU, H. YU, J. YU, L. YU, M. YU, S. YU, V. YU, W. YU, Z. YU, J. YUAN, L. YUAN, S. YUAN, Y. YUAN, Z. YUAN, J. YUE, Z. YUE, J. YUN, R. YUNG, D. ZACKS, G. ZAFFAGNINI, V. ZAMBELLI, I. ZANELLA, Q. ZANG, S. ZANIVAN, S. ZAPPAVIGNA, P. ZARAGOZA, K. ZARBALIS, A. ZAREBKOHAN, A. ZARROUK, S. ZEITLIN, J. ZENG, E. ZEROVNIK, L. ZHAN, B. ZHANG, D. ZHANG, H. ZHANG, J. ZHANG, K. ZHANG, L. ZHANG, M. ZHANG, P. ZHANG, S. ZHANG, W. ZHANG, X. ZHANG, Y. ZHANG, Z. ZHANG, H. ZHAO, L. ZHAO, S. ZHAO, T. ZHAO, X. ZHAO, Y. ZHAO, G. ZHENG, K. ZHENG, L. ZHENG, S. ZHENG, X. ZHENG, Y. ZHENG, Z. ZHENG, B. ZHIVOTOVSKY, Q. ZHONG, A. ZHOU, B. ZHOU, C. ZHOU, G. ZHOU, H. ZHOU, J. ZHOU, K. ZHOU, R. ZHOU, X. ZHOU, Y. ZHOU, Z. ZHOU, B. ZHU, C. ZHU, G. ZHU, H. ZHU, W. ZHU, Y. ZHU, H. ZHUANG, X. ZHUANG, K. ZIENTARA-RYTTER, C. ZIMMERMANN, E. ZIVIANI, T. ZOLADEK, W. ZONG, D. ZOROV, A. ZORZANO, W. ZOU, Z. ZOU, S. ZURYN, W. ZWERSCHKE, B. BRAND-SABERI, C. KENCHAPPA, S. OSHIMA, Y. RONG, J. SLUIMER, and C. STALLINGS

Subjects
flux, macroautophagy, phagophore, stress, vacuole, Autophagosome, LC3, lysosome, neurodegeneration, cancer
Abstract

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Published
2021

33. Vorwort

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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34. 5 Blutkreislauf Blutkreislauf

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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35. 9 Säure-Basen-Haushalt Säure-Basen-Haushalt

Author

Jens Leipziger, Jens Rettig, Charlotte Wagner, Josef Bischofberger, Rainer Deutzmann, Jan C. Behrends, Claudia Pedain, Markus Hoth, Stephan Frings, Stephan Grissmer, Armin Kurtz, Erhard Wischmeyer, Heimo Ehmke, and Frank Müller

Published
2021
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36. 1 Grundlagen der Zellphysiologie Zellphysiologie

Author

Rainer Deutzmann, Jan C. Behrends, Jens Rettig, Charlotte Wagner, Josef Bischofberger, Claudia Pedain, Markus Hoth, Frank Müller, Stephan Frings, Heimo Ehmke, Stephan Grissmer, Erhard Wischmeyer, Jens Leipziger, and Armin Kurtz

Published
2021
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37. 4 Herz Herz

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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38. 22 Sensomotorik Sensomotorik

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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39. 11 Hormonelle Regulation Hormone Regulation

Author

Rainer Deutzmann, Jan C. Behrends, Jens Rettig, Claudia Pedain, Markus Hoth, Stephan Frings, Frank Müller, Erhard Wischmeyer, Heimo Ehmke, Stephan Grissmer, Charlotte Wagner, Josef Bischofberger, Jens Leipziger, and Armin Kurtz

Published
2021
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41. 24 Antwortkommentare klinische Fallbeispiele

Author

Claudia Pedain, Charlotte Wagner, Markus Hoth, Josef Bischofberger, Stephan Frings, Rainer Deutzmann, Jan C. Behrends, Jens Rettig, Frank Müller, Stephan Grissmer, Armin Kurtz, Jens Leipziger, Erhard Wischmeyer, and Heimo Ehmke

Published
2021
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42. 3 Grundlagen der Muskelphysiologie

Author

Rainer Deutzmann, Jan C. Behrends, Armin Kurtz, Jens Leipziger, Claudia Pedain, Markus Hoth, Stephan Frings, Heimo Ehmke, Charlotte Wagner, Josef Bischofberger, Stephan Grissmer, Erhard Wischmeyer, Frank Müller, and Jens Rettig

Published
2021
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43. Pore-forming toxins as tools for polymer analytics: From sizing to sequencing

Author

Gerhard Baaken, Ekaterina Zaitseva, Manuela Pastoriza-Gallego, Jan C. Behrends, Hadjer Ouldali, Tobias Ensslen, Mazdak Afshar Bakshloo, Fabien Piguet, Monasadat Talarimoghari, Abdelghani Oukhaled, Laboratoire Analyse, Modélisation et Matériaux pour la Biologie et l'Environnement (LAMBE - UMR 8587), and Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY)

Subjects
chemistry.chemical_classification, 0303 health sciences, Resistive touchscreen, Analyte, Materials science, 030303 biophysics, Nanotechnology, Polymer, Sizing, 03 medical and health sciences, Nanopore, chemistry.chemical_compound, chemistry, Molecule, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Nanopore sequencing, Ethylene glycol, ComputingMilieux_MISCELLANEOUS
Abstract

We report here on the nanopore resistive pulse sensing (Np-RPS) method, involving pore-forming toxins as tools for polymer analytics at single molecule level. Np-RPS is an electrical method for the label-free detection of single molecules. A molecule interacting with the pore causes a change of the electrical resistance of the pore, called a resistive pulse, associated with a measurable transient current blockade. The features of the blockades, in particular their depth and duration, contain information on the molecular properties of the analyte. We first revisit the history of Np-RPS, then we discuss the effect of the configuration of the molecule/nanopore interaction on the molecular information that can be extracted from the signal, illustrated in two different regimes that either favor molecular sequencing or molecular sizing. Specifically, we focus on the sizing regime and on the use of two different pore-forming toxins, staphylococcal α-hemolysin (αHL) and aerolysin (AeL) nanopores, for the characterization of water-soluble polymers (poly-(ethylene glycol), (PEG)), homopeptides, and heteropeptides. We discuss how nanopore sizing of polymers could be envisioned as a new approach for peptide/protein sequencing.

Published
2021
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44. 8 Atmung Atmung

Author

Jan C. Behrends, Josef Bischofberger, Rainer Deutzmann, Heimo Ehmke, Stephan Frings, Stephan Grissmer, Markus Hoth, Armin Kurtz, Jens Leipziger, Frank Müller, Claudia Pedain, Jens Rettig, Charlotte Wagner, and Erhard Wischmeyer

Published
2021
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46. Electrophysiology on Channel-Forming Proteins in Artificial Lipid Bilayers: Next-Generation Instrumentation for Multiple Recordings in Parallel

Author

Jan C. Behrends, Alison Obergrussberger, Niels Fertig, Frank Bernhard, Christopher Hein, Ekaterina Zaitseva, Mordjane Boukhet, Gerhard Baaken, and Conrad Weichbrodt

Subjects
0303 health sciences, 03 medical and health sciences, Electrophysiology, Membrane, Materials science, Nanotechnology, 02 engineering and technology, Instrumentation (computer programming), 021001 nanoscience & nanotechnology, 0210 nano-technology, Lipid bilayer, Ion channel, 030304 developmental biology
Abstract

Artificial lipid bilayers have been used for several decades to study channel-forming pores and ion channels in membranes. Until recently, the classical two-chamber setups have been primarily used for studying the biophysical properties of pore forming proteins. Within the last 10 years, instruments for automated lipid bilayer measurements have been developed and are now commercially available. This chapter focuses on protein purification and reconstitution of channel-forming proteins into lipid bilayers using a classic setup and on the commercially available systems, the Orbit mini and Orbit 16.

Published
2020
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47. Electrophysiology on Channel-Forming Proteins in Artificial Lipid Bilayers: Next-Generation Instrumentation for Multiple Recordings in Parallel

Author

Ekaterina, Zaitseva, Alison, Obergrussberger, Conrad, Weichbrodt, Mordjane, Boukhet, Frank, Bernhard, Christopher, Hein, Gerhard, Baaken, Niels, Fertig, and Jan C, Behrends

Subjects
Lipid Bilayers, Mycobacterium smegmatis, Gene Expression, Porins, Equipment Design, Ion Channels, Electrophysiological Phenomena, Electrophysiology, Transformation, Genetic, Bacterial Proteins, Lab-On-A-Chip Devices, Escherichia coli, Animals, Humans, Point Mutation
Abstract

Artificial lipid bilayers have been used for several decades to study channel-forming pores and ion channels in membranes. Until recently, the classical two-chamber setups have been primarily used for studying the biophysical properties of pore forming proteins. Within the last 10 years, instruments for automated lipid bilayer measurements have been developed and are now commercially available. This chapter focuses on protein purification and reconstitution of channel-forming proteins into lipid bilayers using a classic setup and on the commercially available systems, the Orbit mini and Orbit 16.

Published
2020

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