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4. Dynamic instabilities in the kinetics of growth and disassembly of microtubules

Author

Katrukha, Eugene

Subjects
Quantitative Biology - Subcellular Processes
Abstract

Dynamic instability of microtubules is considered using frameworks of non-linear thermodynamics and non-equilibrium reaction-diffusion systems. Stochastic assembly/disassembly phases in the polymerization dynamics of microtubules are treated as a result of collective clusterization of microdefects (holes in structure). The model explains experimentally observed power law dependence of catastrophe frequency from the microtubule growth rate. Additional reaction-diffusion-precipitation model is developed to account for kinetic limitations in microtubule dynamics. It is shown that large scale periodic microtubules length fluctuations are accompanied by concentration autowaves. We built corresponding parametric diagram mapping areas of stationary, non-stationary and metastable solutions. The loss of stability for the stationary solutions happens through bifurcation of Andronov-Hopf. Using parametric diagram we classify cytostatic effect of microtubule stabilizing drugs in four major classes and analyze their compatibility and possible synergistic effect for cancer treatment therapy., Comment: thesis (in Russian)

Published
2016

7. Optimization of Curvi-Linear Tracing Applied to Solar Physics and Biophysics

Author

Aschwanden, Markus J., De Pontieu, Bart, and Katrukha, Eugene A.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We developed an automated pattern recognition code that is particularly well suited to extract one-dimensional curvi-linear features from two-dimensional digital images. A former version of this {\sl Oriented Coronal CUrved Loop Tracing (OCCULT)} code was applied to spacecraft images of magnetic loops in the solar corona, recorded with the NASA spacecraft {\sl Transition Region And Coronal Explorer (TRACE)} in extreme ultra-violet wavelengths. Here we apply an advanced version of this code ({\sl OCCULT-2}) also to similar images from the {\sl Solar Dynamics Observatory (SDO)}, to chromospheric H-$\alpha$ images obtained with the {\sl Swedish Solar Telescope (SST)}, and to microscopy images of microtubule filaments in live cells in biophysics. We provide a full analytical description of the code, optimize the control parameters, and compare the automated tracing with visual/manual methods. The traced structures differ by up to 16 orders of magnitude in size, which demonstrates the universality of the tracing algorithm., Comment: Entropy, Special Issue on Advanced Signal Processing in Heliospheric Physics, (in press)

Published
2013
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11. Taxanes convert regions of perturbed microtubule growth into rescue sites

Author

Rai, Ankit, Liu, Tianyang, Glauser, Simon, Katrukha, Eugene A, Estévez-Gallego, Juan, Rodríguez-García, Ruddi, Fang, Wei-Shuo, Díaz, J Fernando, Steinmetz, Michel O, Altmann, Karl-Heinz, Kapitein, Lukas C, Moores, Carolyn A, Akhmanova, Anna, Sub Cell Biology, Celbiologie, Sub Cell Biology, Celbiologie, European Research Council, Netherlands Organization for Scientific Research, Biotechnology and Biological Sciences Research Council (UK), Ministerio de Economía y Competitividad (España), Swiss National Science Foundation, Rai, Ankit, Liu, Tianyang, Glauser, Simon, Katrukha, Eugene A., Estévez-Gallego, Juan, Rodríguez-García, Ruddi, Díaz, José Fernando, Steinmetz, Michel O., Altmann, Karl-Heinz, Kapitein, Lukas C., Moores, Carolyn A., Akhmanova, Anna, Rai, Ankit [0000-0002-3732-3597], Liu, Tianyang [0000-0003-2598-8572], Glauser, Simon [0000-0001-5911-5820], Katrukha, Eugene A. [0000-0002-9971-3603], Estévez-Gallego, Juan [0000-0003-3889-8488], Rodríguez-García, Ruddi [0000-0001-9676-4053], Díaz, José Fernando [0000-0003-2743-3319], Steinmetz, Michel O. [0000-0001-6157-3687], Altmann, Karl-Heinz [0000-0002-0747-9734], Kapitein, Lukas C. [0000-0001-9418-6739], Moores, Carolyn A. [0000-0001-5686-6290], and Akhmanova, Anna [0000-0002-9048-8614]

Subjects
Drug development, 02 engineering and technology, Epothilone, 010402 general chemistry, Microtubules, 01 natural sciences, Fluorescence imaging, Cryoelectron microscopy, Tubulin, Microtubule, Taverne, medicine, Humans, General Materials Science, Total internal reflection microscopy, Biological sciences, Cytoskeleton, Taxane, biology, Chemistry, Mechanical Engineering, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, 0104 chemical sciences, Kinetics, Mechanics of Materials, biology.protein, Biophysics, Taxoids, 0210 nano-technology, HeLa Cells, medicine.drug
Abstract

15 p.-6 fig., Microtubules are polymers of tubulin dimers, and conformational transitions in the microtubule lattice drive microtubule dynamic instability and affect various aspects of microtubule function. The exact nature of these transitions and their modulation by anticancer drugs such as Taxol and epothilone, which can stabilize microtubules but also perturb their growth, are poorly understood. Here, we directly visualize the action of fluorescent Taxol and epothilone derivatives and show that microtubules can transition to a state that triggers cooperative drug binding to form regions with altered lattice conformation. Such regions emerge at growing microtubule ends that are in a pre-catastrophe state, and inhibit microtubule growth and shortening. Electron microscopy and in vitro dynamics data indicate that taxane accumulation zones represent incomplete tubes that can persist, incorporate tubulin dimers and repeatedly induce microtubule rescues. Thus, taxanes modulate the material properties of microtubules by converting destabilized growing microtubule ends into regions resistant to depolymerization., This work was supported by the European Research Council Synergy (grant no. 609822) and the Netherlands Organization for Scientific Research CW ECHO (grant no. 711.015.005 to A.A.), by a Biotechnology and Biological Sciences Research Council grant (no. BB/N018176/1 to C.A.M.), by an EMBO Long Term Fellowship to R.R.-G., by the CAMS Innovation Fund for Medical Sciences (grant no. 2016-I2M-1-010 to W.-S.F.), by grants from MINECO/FEDER (no. BFU2016-75319-R to J.F.D.) and by COST Action (no. CM1407 to J.F.D. and K.-H.A.). M.O.S is supported by a grant from the Swiss National Science Foundation (no. 31003A_166608).

Published
2019
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14. Uptake, Transport, and Toxicity of Pristine and Weathered Micro- and Nanoplastics in Human Placenta Cells

Author

Dusza, Hanna M, Katrukha, Eugene A, Nijmeijer, Sandra M, Akhmanova, Anna, Vethaak, A Dick, Walker, Douglas I, Legler, Juliette, IRAS OH Toxicology, Sub Cell Biology, Dep Population Health Sciences, Celbiologie, Environment and Health, AIMMS, Institute for Environmental Studies, IRAS OH Toxicology, Sub Cell Biology, Dep Population Health Sciences, and Celbiologie

Subjects
Polyethylene/metabolism, Polyethylene, Cell Survival, Pregnancy, Health, Toxicology and Mutagenesis, Placenta, Microplastics, Public Health, Environmental and Occupational Health, Placenta/metabolism, Humans, Polystyrenes, Female
Abstract

BACKGROUND: The first evidence of micro- and nanoplastic (MNP) exposure in the human placenta is emerging. However, the toxicokinetics and toxicity of MNPs in the placenta, specifically environmentally relevant particles, remain unclear. OBJECTIVES: We examined the transport, uptake, and toxicity of pristine and experimentally weathered MNPs in nonsyncytialized and syncytialized BeWo b30 choriocarcinoma cells. METHODS: We performed untargeted chemical characterization of pristine and weathered MNPs using liquid chromatography high-resolution mass spectrometry to evaluate compositional differences following particle weathering. We investigated cellular internalization of pristine and weathered polystyrene (PS; formula presented ) and high-density polyethylene (HDPE; formula presented ) particles using high-resolution confocal imaging and three-dimensional rendering. We investigated the influence of particle coating with human plasma on the cellular transport of PS particles using a transwell setup and examined the influence of acute MNP exposure on cell viability, damage to the plasma membrane, and expression of genes involved in steroidogenesis. RESULTS: Chemical characterization of MNPs showed a significantly higher number of unique features in pristine particles in comparison with weathered particles. Size-dependent placental uptake of pristine and weathered MNPs was observed in both placental cell types after 24 h exposure. Cellular transport was limited and size-dependent and was not influenced by particle coating with human plasma. None of the MNPs affected cell viability. Damage to the plasma membrane was observed only for formula presented PS particles in the nonsyncytialized cells at the highest concentration tested (formula presented ). Modest down-regulation of hsd17b1 was observed in syncytialized cells exposed to pristine MNPs. DISCUSSION: Our results suggest that pristine and weathered MNPs are internalized and translocated in placental cells in vitro. Effects on gene expression observed upon pristine PS and HDPE particle exposure warrant further examination. More in-depth investigations are needed to better understand the potential health risks of MNP and chemicals associated with them under environmentally relevant exposure scenarios. https://doi.org/10.1289/EHP10873.

Published
2022
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15. Lattice defects induced by microtubule-stabilizing agents exert a long-range effect on microtubule growth by promoting catastrophes

Author

European Commission, Netherlands Organization for Scientific Research, Biotechnology and Biological Sciences Research Council (UK), Fundación Tatiana Pérez de Guzmán el Bueno, Consejo Superior de Investigaciones Científicas (España), Ministerio de Ciencia, Innovación y Universidades (España), Medical Research Council (UK), Rai, Ankit [0000-0002-3732-3597], Liu, Tianyang [0000-0003-2598-8572], Katrukha, Eugene A. [0000-0002-9971-3603], Estévez-Gallego, Juan [0000-0003-3889-8488], Manka, Szymon W. [0000-0001-6733-146X], Paterson, Ian [0000-0002-8861-9136], Díaz, José Fernando [0000-0003-2743-3319], Kapitein, Lukas C. [0000-0001-9418-6739], Moores, Carolyn A. [0000-0001-5686-6290], Akhmanova, Anna [0000-0002-9048-8614], Rai, Ankit, Liu, Tianyang, Katrukha, Eugene A., Estévez-Gallego, Juan, Manka, Szymon W., Paterson, Ian, Díaz, José Fernando, Kapitein, Lukas C., Moores, Carolyn A., Akhmanova, Anna, European Commission, Netherlands Organization for Scientific Research, Biotechnology and Biological Sciences Research Council (UK), Fundación Tatiana Pérez de Guzmán el Bueno, Consejo Superior de Investigaciones Científicas (España), Ministerio de Ciencia, Innovación y Universidades (España), Medical Research Council (UK), Rai, Ankit [0000-0002-3732-3597], Liu, Tianyang [0000-0003-2598-8572], Katrukha, Eugene A. [0000-0002-9971-3603], Estévez-Gallego, Juan [0000-0003-3889-8488], Manka, Szymon W. [0000-0001-6733-146X], Paterson, Ian [0000-0002-8861-9136], Díaz, José Fernando [0000-0003-2743-3319], Kapitein, Lukas C. [0000-0001-9418-6739], Moores, Carolyn A. [0000-0001-5686-6290], Akhmanova, Anna [0000-0002-9048-8614], Rai, Ankit, Liu, Tianyang, Katrukha, Eugene A., Estévez-Gallego, Juan, Manka, Szymon W., Paterson, Ian, Díaz, José Fernando, Kapitein, Lukas C., Moores, Carolyn A., and Akhmanova, Anna

Abstract

icrotubules are dynamic cytoskeletal polymers that spontane ously switch between phases of growth and shrinkage. The probability of transitioning from growth to shrinkage, termed catastrophe, increases with microtubule age, but the underlying mechanisms are poorly understood. Here, we set out to test whether microtubule lattice defects formed during polymerization can affect growth at the plus end. To generate microtubules with lattice defects, we used microtubule-stabilizing agents that pro mote formation of polymers with different protofilament num bers. By employing different agents during nucleation of stable microtubule seeds and the subsequent polymerization phase, we could reproducibly induce switches in protofilament number and induce stable lattice defects. Such drug-induced defects led to fre quent catastrophes, which were not observed when microtubules were grown in the same conditions but without a protofilament number mismatch. Microtubule severing at the site of the defect was sufficient to suppress catastrophes. We conclude that struc tural defects within the microtubule lattice can exert effects that can propagate over long distances and affect the dynamic state of the microtubule end.

Published
2021

18. Taxanes convert regions of perturbed microtubule growth into rescue sites

Author

European Research Council, Netherlands Organization for Scientific Research, Biotechnology and Biological Sciences Research Council (UK), Ministerio de Economía y Competitividad (España), Swiss National Science Foundation, Rai, Ankit [0000-0002-3732-3597], Liu, Tianyang [0000-0003-2598-8572], Glauser, Simon [0000-0001-5911-5820], Katrukha, Eugene A. [0000-0002-9971-3603], Estévez-Gallego, Juan [0000-0003-3889-8488], Rodríguez-García, Ruddi [0000-0001-9676-4053], Díaz, José Fernando [0000-0003-2743-3319], Steinmetz, Michel O. [0000-0001-6157-3687], Altmann, Karl-Heinz [0000-0002-0747-9734], Kapitein, Lukas C. [0000-0001-9418-6739], Moores, Carolyn A. [0000-0001-5686-6290], Akhmanova, Anna [0000-0002-9048-8614], Rai, Ankit, Liu, Tianyang, Glauser, Simon, Katrukha, Eugene A., Estévez-Gallego, Juan, Rodríguez-García, Ruddi, Fang, Wei-Shuo, Díaz, José Fernando, Steinmetz, Michel O., Altmann, Karl-Heinz, Kapitein, Lukas C., Moores, Carolyn A., Akhmanova, Anna, European Research Council, Netherlands Organization for Scientific Research, Biotechnology and Biological Sciences Research Council (UK), Ministerio de Economía y Competitividad (España), Swiss National Science Foundation, Rai, Ankit [0000-0002-3732-3597], Liu, Tianyang [0000-0003-2598-8572], Glauser, Simon [0000-0001-5911-5820], Katrukha, Eugene A. [0000-0002-9971-3603], Estévez-Gallego, Juan [0000-0003-3889-8488], Rodríguez-García, Ruddi [0000-0001-9676-4053], Díaz, José Fernando [0000-0003-2743-3319], Steinmetz, Michel O. [0000-0001-6157-3687], Altmann, Karl-Heinz [0000-0002-0747-9734], Kapitein, Lukas C. [0000-0001-9418-6739], Moores, Carolyn A. [0000-0001-5686-6290], Akhmanova, Anna [0000-0002-9048-8614], Rai, Ankit, Liu, Tianyang, Glauser, Simon, Katrukha, Eugene A., Estévez-Gallego, Juan, Rodríguez-García, Ruddi, Fang, Wei-Shuo, Díaz, José Fernando, Steinmetz, Michel O., Altmann, Karl-Heinz, Kapitein, Lukas C., Moores, Carolyn A., and Akhmanova, Anna

Abstract

Microtubules are polymers of tubulin dimers, and conformational transitions in the microtubule lattice drive microtubule dynamic instability and affect various aspects of microtubule function. The exact nature of these transitions and their modulation by anticancer drugs such as Taxol and epothilone, which can stabilize microtubules but also perturb their growth, are poorly understood. Here, we directly visualize the action of fluorescent Taxol and epothilone derivatives and show that microtubules can transition to a state that triggers cooperative drug binding to form regions with altered lattice conformation. Such regions emerge at growing microtubule ends that are in a pre-catastrophe state, and inhibit microtubule growth and shortening. Electron microscopy and in vitro dynamics data indicate that taxane accumulation zones represent incomplete tubes that can persist, incorporate tubulin dimers and repeatedly induce microtubule rescues. Thus, taxanes modulate the material properties of microtubules by converting destabilized growing microtubule ends into regions resistant to depolymerization.

Published
2020

20. Uptake, Transport, and Toxicity of Pristine and Weathered Micro- and Nanoplastics in Human Placenta Cells

Author

IRAS OH Toxicology, Sub Cell Biology, Dep Population Health Sciences, Celbiologie, Dusza, Hanna M, Katrukha, Eugene A, Nijmeijer, Sandra M, Akhmanova, Anna, Vethaak, A Dick, Walker, Douglas I, Legler, Juliette, IRAS OH Toxicology, Sub Cell Biology, Dep Population Health Sciences, Celbiologie, Dusza, Hanna M, Katrukha, Eugene A, Nijmeijer, Sandra M, Akhmanova, Anna, Vethaak, A Dick, Walker, Douglas I, and Legler, Juliette

Published
2022

22. Organization and dynamics of the cortical complexes controlling insulin secretion in β-cells

Author

Noordstra, Ivar, primary, van den Berg, Cyntha M., additional, Boot, Fransje W. J., additional, Katrukha, Eugene A., additional, Yu, Ka Lou, additional, Tas, Roderick P., additional, Portegies, Sybren, additional, Viergever, Bastiaan J., additional, de Graaff, Esther, additional, Hoogenraad, Casper C., additional, de Koning, Eelco J. P., additional, Carlotti, Françoise, additional, Kapitein, Lukas C., additional, and Akhmanova, Anna, additional

Published
2022
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23. Organization and dynamics of the cortical complexes controlling insulin secretion in β-cells

Author

Noordstra, Ivar, van den Berg, Cyntha M, Boot, Fransje W J, Katrukha, Eugene A, Yu, Ka Lou, Tas, Roderick P, Portegies, Sybren, Viergever, Bastiaan J, de Graaff, Esther, Hoogenraad, Casper C, de Koning, Eelco J P, Carlotti, Françoise, Kapitein, Lukas C, Akhmanova, Anna, Celbiologie, Sub Cell Biology, Celbiologie, and Sub Cell Biology

Subjects
Insulin secretion, Cell cortex, Cell Biology, Knock-in mouse, Exocytosis, Focal adhesion, Liquid-liquid phase separation, Cytoskeletal Proteins, Glucose, Insulin-Secreting Cells, Insulin Secretion, Insulin, Single-molecule imaging
Abstract

Insulin secretion in pancreatic β-cells is regulated by cortical complexes that are enriched at the sites of adhesion to extracellular matrix facing the vasculature. Many components of these complexes, including bassoon, RIM, ELKS and liprins, are shared with neuronal synapses. Here, we show that insulin secretion sites also contain the non-neuronal proteins LL5β (also known as PHLDB2) and KANK1, which, in migrating cells, organize exocytotic machinery in the vicinity of integrin-based adhesions. Depletion of LL5β or focal adhesion disassembly triggered by myosin II inhibition perturbed the clustering of secretory complexes and attenuated the first wave of insulin release. Although previous analyses in vitro and in neurons have suggested that secretory machinery might assemble through liquid–liquid phase separation, analysis of endogenously labeled ELKS in pancreatic islets indicated that its dynamics is inconsistent with such a scenario. Instead, fluorescence recovery after photobleaching and single-molecule imaging showed that ELKS turnover is driven by binding and unbinding to low-mobility scaffolds. Both the scaffold movements and ELKS exchange were stimulated by glucose treatment. Our findings help to explain how integrin-based adhesions control spatial organization of glucose-stimulated insulin release.

Published
2021

24. Quantitative mapping of dense microtubule arrays in mammalian neurons

Author

Katrukha, Eugene A, Jurriens, Daphne, Salas Pastene, Desiree M, Kapitein, Lukas C, Sub Cell Biology, Celbiologie, Sub Cell Biology, and Celbiologie

Subjects
Male, Kinesins, super-resolution, Hippocampus, Cell membrane, Neurons/cytology, 0302 clinical medicine, Tubulin, Biology (General), Cytoskeleton, Neurons, 0303 health sciences, Absolute number, Chemistry, General Neuroscience, STED microscopy, cytoskeleton, Acetylation, General Medicine, medicine.anatomical_structure, Microtubules/metabolism, Medicine, Female, expansion microscopy, Research Article, Kinesins/metabolism, QH301-705.5, hippocampal neurons, Science, Hippocampus/metabolism, General Biochemistry, Genetics and Molecular Biology, microtubules, Motor protein, 03 medical and health sciences, Microtubule, Detyrosination, medicine, Animals, Protein Processing, 030304 developmental biology, General Immunology and Microbiology, Microtubule cytoskeleton, Post-Translational, Dendritic shaft, Cell Biology, Tubulin/metabolism, Superresolution, Rats, Biophysics, Rat, Developmental biology, Protein Processing, Post-Translational, 030217 neurology & neurosurgery, Intracellular transport, Developmental Biology
Abstract

The neuronal microtubule cytoskeleton underlies the polarization and proper functioning of neurons, amongst others by providing tracks for motor proteins that drive intracellular transport. Different subsets of neuronal microtubules, varying in composition, stability, and motor preference, are known to exist, but the high density of microtubules has so far precluded mapping their relative abundance and three-dimensional organization. Here, we use different super-resolution techniques (STED, Expansion Microscopy) to explore the nanoscale organization of the neuronal microtubule network in rat hippocampal neurons. This revealed that in dendrites acetylated microtubules are enriched in the core of the dendritic shaft, while tyrosinated microtubules are enriched near the plasma membrane, thus forming a shell around the acetylated microtubules. Moreover, using a novel analysis pipeline we quantified the absolute number of acetylated and tyrosinated microtubules within dendrites and found that they account for 65–75% and ~20–30% of all microtubules, respectively, leaving only few microtubules that do not fall in either category. Because these different microtubule subtypes facilitate different motor proteins, these novel insights help to understand the spatial regulation of intracellular transport., eLife digest Cells in the body need to control the position of the molecules and other components inside them. To do this, they use a system of proteins that work a bit like a road network. The ‘roads’ are tubular structures known as microtubules, while ‘vehicles’ are transporters, called motor proteins, that ‘walk’ along the microtubules. Microtubule networks are important in all cells, but especially in neurons, which can grow very large. These cells have tree-like branches called dendrites that receive messages from other neurons. Dendrites contain different types of microtubules with many chemical modifications. These modifications consist of specific molecules or ‘groups’ becoming attached to or removed from the microtubules to change their properties – for example, microtubules can be ‘acetylated’ or ‘detyrosinated’. Motor proteins prefer different kinds of microtubules, and so understanding transport inside cells involves creating a precise roadmap showing how many of each type of microtubule exist and where they go. Using different super-resolution microscopy techniques, Katrukha et al. created maps of the microtubules in rat neurons. These show that acetylated microtubules form a core in the centre of the dendrites, while tyrosinated microtubules (which did not undergo detyrosination) line the cell membrane of the dendrites. Katrukha et al. then used the maps to determine that acetylated microtubules account for 65 to 70% of all microtubules, while tyrosinated microtubules make up 20 to 30%. This means that most microtubules fall into these two categories. The work by Katrukha et al. provides one of the first quantitative estimates of the relative amount of acetylated and tyrosinated microtubules, starting to shed light on how cells control their transport network. This could ultimately allow researchers to explore how transport changes in health and disease.

Published
2021

26. Centrosome-mediated microtubule remodeling during axon formation in human iPSC-derived neurons

Author

Lindhout, Feline W., Portegies, Sybren, Kooistra, Robbelien, Herstel, Lotte J., Stucchi, Riccardo, Hummel, Jessica J.A., Scheefhals, Nicky, Katrukha, Eugene A., Altelaar, Maarten, MacGillavry, Harold D., Wierenga, Corette J., Hoogenraad, Casper C., Celbiologie, Biomolecular Mass Spectrometry and Proteomics, Sub Cell Biology, and Afd Biomol.Mass Spect. and Proteomics

Subjects
axon, centrosome, Biochemistry, Genetics and Molecular Biology(all), Neuroscience(all), Immunology and Microbiology(all), hiPSC-derived neuron, human, development, Molecular Biology
Abstract

Axon formation critically relies on local microtubule remodeling and marks the first step in establishing neuronal polarity. However, the function of the microtubule-organizing centrosomes during the onset of axon formation is still under debate. Here, we demonstrate that centrosomes play an essential role in controlling axon formation in human-induced pluripotent stem cell (iPSC)-derived neurons. Depleting centrioles, the core components of centrosomes, in unpolarized human neuronal stem cells results in various axon developmental defects at later stages, including immature action potential firing, mislocalization of axonal microtubule-associated Trim46 proteins, suppressed expression of growth cone proteins, and affected growth cone morphologies. Live-cell imaging of microtubules reveals that centriole loss impairs axonal microtubule reorganization toward the unique parallel plus-end out microtubule bundles during early development. We propose that centrosomes mediate microtubule remodeling during early axon development in human iPSC-derived neurons, thereby laying the foundation for further axon development and function.

Published
2021

27. Organization and dynamics of the cortical complexes controlling insulin secretion in β-cells

Author

Noordstra, Ivar, primary, van den Berg, Cyntha M., additional, Boot, Fransje W. J., additional, Katrukha, Eugene A., additional, Yu, Ka Lou, additional, Tas, Roderick P., additional, Portegies, Sybren, additional, Viergever, Bastiaan J., additional, de Graaff, Esther, additional, Hoogenraad, Casper C., additional, de Koning, Eelco J. P., additional, Carlotti, Françoise, additional, Kapitein, Lukas C., additional, and Akhmanova, Anna, additional

Published
2021
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29. Chemical Imaging of Hierarchical Porosity Formation within a Zeolite Crystal Visualized by Small‐Angle X‐Ray Scattering and In‐Situ Fluorescence Microscopy

Author

Filez, Matthias, Vesely, Martin, Garcia-Torregrosa, Ivan, Gambino, Marianna, Attila, Özgün, Meirer, Florian, Katrukha, Eugene A., Roeffaers, Maarten B.J., Garrevoet, Jan, Kapitein, Lukas C., Weckhuysen, Bert M., Sub Inorganic Chemistry and Catalysis, Sub Cell Biology, Inorganic Chemistry and Catalysis, Celbiologie, Sub Inorganic Chemistry and Catalysis, Sub Cell Biology, Inorganic Chemistry and Catalysis, and Celbiologie

Subjects
Materials science, Chemistry(all), Chemistry, Multidisciplinary, in situ fluorescence microscopy, 010402 general chemistry, 01 natural sciences, Catalysis, Crystal, Microscopy, zeolite, Zeolite, Porosity, Science & Technology, desilication, 010405 organic chemistry, Small-angle X-ray scattering, Scattering, Communication, small-angle X-ray scattering microscopy, General Medicine, General Chemistry, Microporous material, Communications, 0104 chemical sciences, Characterization (materials science), Chemistry, Chemical engineering, Zeolites | Very Important Paper, Physical Sciences, ddc:540, ddc:660, hierarchical nanoporosity
Abstract

Angewandte Chemie 133(25), 13922 - 13925 (2021). doi:10.1002/ange.202101747, Introducing hierarchical porosity to zeolites is vital for providing molecular access to microporous domains. Yet, the dynamics of meso- and macropore formation has remained elusive and pore space ill-characterized by a lack of (in situ) microscopic tools sensitive to nanoporosity. Here, we probe hierarchical porosity formation within a zeolite ZSM-5 crystal in real-time by in situ fluorescence microscopy during desilication. In addition, we introduce small-angle X-ray scattering microscopy as novel characterization tool to map intracrystal meso- and macropore properties. It is shown that hierarchical porosity formation initiates at the crystal surface and propagates to the crystal core via a pore front with decreasing rate. Also, hierarchical porosity only establishes in specific (segments of) subunits which constitute ZSM-5. Such space-dependent meso- and macroporosity implies local discrepancies in diffusion, performance and deactivation behaviors even within a zeolite crystal., Published by Wiley-VCH, Weinheim

Published
2021
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30. Direct observation of aggregate-triggered selective autophagy in human cells

Author

Janssen, Anne F J, Korsten, Giel, Nijenhuis, Wilco, Katrukha, Eugene A, Kapitein, Lukas C, Janssen, Anne F J, Korsten, Giel, Nijenhuis, Wilco, Katrukha, Eugene A, and Kapitein, Lukas C

Abstract

Degradation of aggregates by selective autophagy is important as damaged proteins may impose a threat to cellular homeostasis. Although the core components of the autophagy machinery are well characterized, the spatiotemporal regulation of many selective autophagy processes, including aggrephagy, remains largely unexplored. Furthermore, because most live-cell imaging studies have so far focused on starvation-induced autophagy, little is known about the dynamics of aggrephagy. Here, we describe the development and application of the mKeima-PIM assay, which enables live-cell observation of autophagic turnover and degradation of inducible protein aggregates in conjunction with key autophagy players. This allowed us to quantify the relative timing and duration of different steps of aggrephagy in human cells and revealed the short-lived nature of the autophagosome. The assay furthermore showed the spatial distribution of omegasome formation, highlighting that autophagy initiation is directly instructed by the cargo. Moreover, we found that nascent autophagosomes mostly remain immobile until acidification occurs. Thus, our assay provides new insights into the spatiotemporal regulation and dynamics of aggrephagy.

Published
2021

31. Lattice defects induced by microtubule-stabilizing agents exert a long-range effect on microtubule growth by promoting catastrophes

Author

Sub Cell Biology, Celbiologie, Rai, Ankit, Liu, Tianyang, Katrukha, Eugene A, Estévez-Gallego, Juan, Manka, Szymon W, Paterson, Ian, Díaz, J Fernando, Kapitein, Lukas C, Moores, Carolyn A, Akhmanova, Anna, Sub Cell Biology, Celbiologie, Rai, Ankit, Liu, Tianyang, Katrukha, Eugene A, Estévez-Gallego, Juan, Manka, Szymon W, Paterson, Ian, Díaz, J Fernando, Kapitein, Lukas C, Moores, Carolyn A, and Akhmanova, Anna

Published
2021

32. Centrosome-mediated microtubule remodeling during axon formation in human iPSC-derived neurons

Author

Celbiologie, Biomolecular Mass Spectrometry and Proteomics, Sub Cell Biology, Afd Biomol.Mass Spect. and Proteomics, Lindhout, Feline W., Portegies, Sybren, Kooistra, Robbelien, Herstel, Lotte J., Stucchi, Riccardo, Hummel, Jessica J.A., Scheefhals, Nicky, Katrukha, Eugene A., Altelaar, Maarten, MacGillavry, Harold D., Wierenga, Corette J., Hoogenraad, Casper C., Celbiologie, Biomolecular Mass Spectrometry and Proteomics, Sub Cell Biology, Afd Biomol.Mass Spect. and Proteomics, Lindhout, Feline W., Portegies, Sybren, Kooistra, Robbelien, Herstel, Lotte J., Stucchi, Riccardo, Hummel, Jessica J.A., Scheefhals, Nicky, Katrukha, Eugene A., Altelaar, Maarten, MacGillavry, Harold D., Wierenga, Corette J., and Hoogenraad, Casper C.

Published
2021

34. Chemical Imaging of Hierarchical Porosity Formation within a Zeolite Crystal Visualized by Small-Angle X-Ray Scattering and In-Situ Fluorescence Microscopy

Author

Sub Inorganic Chemistry and Catalysis, Sub Cell Biology, Inorganic Chemistry and Catalysis, Celbiologie, Filez, Matthias, Vesely, Martin, Garcia-Torregrosa, Ivan, Gambino, Marianna, Attila, Özgün, Meirer, Florian, Katrukha, Eugene A., Roeffaers, Maarten B.J., Garrevoet, Jan, Kapitein, Lukas C., Weckhuysen, Bert M., Sub Inorganic Chemistry and Catalysis, Sub Cell Biology, Inorganic Chemistry and Catalysis, Celbiologie, Filez, Matthias, Vesely, Martin, Garcia-Torregrosa, Ivan, Gambino, Marianna, Attila, Özgün, Meirer, Florian, Katrukha, Eugene A., Roeffaers, Maarten B.J., Garrevoet, Jan, Kapitein, Lukas C., and Weckhuysen, Bert M.

Published
2021

36. Centrosome-mediated microtubule remodeling during axon formation in human iPSC-derived neurons

Author

Cell Biology, Neurobiology and Biophysics, Biomolecular Mass Spectrometry and Proteomics, Sub Cell Biology, Afd Biomol.Mass Spect. and Proteomics, Lindhout, Feline W., Portegies, Sybren, Kooistra, Robbelien, Herstel, Lotte J., Stucchi, Riccardo, Hummel, Jessica J.A., Scheefhals, Nicky, Katrukha, Eugene A., Altelaar, Maarten, MacGillavry, Harold D., Wierenga, Corette J., Hoogenraad, Casper C., Cell Biology, Neurobiology and Biophysics, Biomolecular Mass Spectrometry and Proteomics, Sub Cell Biology, Afd Biomol.Mass Spect. and Proteomics, Lindhout, Feline W., Portegies, Sybren, Kooistra, Robbelien, Herstel, Lotte J., Stucchi, Riccardo, Hummel, Jessica J.A., Scheefhals, Nicky, Katrukha, Eugene A., Altelaar, Maarten, MacGillavry, Harold D., Wierenga, Corette J., and Hoogenraad, Casper C.

Published
2021

38. Inside Cover: Chemical Imaging of Hierarchical Porosity Formation within a Zeolite Crystal Visualized by Small‐Angle X‐Ray Scattering and In‐Situ Fluorescence Microscopy (Angew. Chem. Int. Ed. 25/2021)

Author

Filez, Matthias, primary, Vesely, Martin, additional, Garcia‐Torregrosa, Ivan, additional, Gambino, Marianna, additional, Attila, Özgün, additional, Meirer, Florian, additional, Katrukha, Eugene A., additional, Roeffaers, Maarten B. J., additional, Garrevoet, Jan, additional, Kapitein, Lukas C., additional, and Weckhuysen, Bert M., additional

Published
2021
Full Text
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39. Chemical Imaging of Hierarchical Porosity Formation within a Zeolite Crystal Visualized by Small‐Angle X‐Ray Scattering and In‐Situ Fluorescence Microscopy

Author

Filez, Matthias, primary, Vesely, Martin, additional, Garcia‐Torregrosa, Ivan, additional, Gambino, Marianna, additional, Attila, Özgün, additional, Meirer, Florian, additional, Katrukha, Eugene A., additional, Roeffaers, Maarten B. J., additional, Garrevoet, Jan, additional, Kapitein, Lukas C., additional, and Weckhuysen, Bert M., additional

Published
2021
Full Text
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40. Innentitelbild: Chemical Imaging of Hierarchical Porosity Formation within a Zeolite Crystal Visualized by Small‐Angle X‐Ray Scattering and In‐Situ Fluorescence Microscopy (Angew. Chem. 25/2021)

Author

Filez, Matthias, primary, Vesely, Martin, additional, Garcia‐Torregrosa, Ivan, additional, Gambino, Marianna, additional, Attila, Özgün, additional, Meirer, Florian, additional, Katrukha, Eugene A., additional, Roeffaers, Maarten B. J., additional, Garrevoet, Jan, additional, Kapitein, Lukas C., additional, and Weckhuysen, Bert M., additional

Published
2021
Full Text
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42. Mechanisms of Motor-Independent Membrane Remodeling Driven by Dynamic Microtubules

Author

Rodríguez-García, Ruddi, Volkov, Vladimir A, Chen, Chiung-Yi, Katrukha, Eugene A, Olieric, Natacha, Aher, Amol, Grigoriev, Ilya, López, Magdalena Preciado, Steinmetz, Michel O, Kapitein, Lukas C, Koenderink, Gijsje, Dogterom, Marileen, Akhmanova, Anna, Rodríguez-García, Ruddi, Volkov, Vladimir A, Chen, Chiung-Yi, Katrukha, Eugene A, Olieric, Natacha, Aher, Amol, Grigoriev, Ilya, López, Magdalena Preciado, Steinmetz, Michel O, Kapitein, Lukas C, Koenderink, Gijsje, Dogterom, Marileen, and Akhmanova, Anna

Abstract

Microtubule-dependent organization of membranous organelles occurs through motor-based pulling and by coupling microtubule dynamics to membrane remodeling. For example, tubules of endoplasmic reticulum (ER) can be extended by kinesin- and dynein-mediated transport and through the association with the tips of dynamic microtubules. The binding between ER and growing microtubule plus ends requires End Binding (EB) proteins and the transmembrane protein STIM1, which form a tip-attachment complex (TAC), but it is unknown whether these proteins are sufficient for membrane remodeling. Furthermore, EBs and their partners undergo rapid turnover at microtubule ends, and it is unclear how highly transient protein-protein interactions can induce load-bearing processive motion. Here, we reconstituted membrane tubulation in a minimal system with giant unilamellar vesicles, dynamic microtubules, an EB protein, and a membrane-bound protein that can interact with EBs and microtubules. We showed that these components are sufficient to drive membrane remodeling by three mechanisms: membrane tubulation induced by growing microtubule ends, motor-independent membrane sliding along microtubule shafts, and membrane pulling by shrinking microtubules. Experiments and modeling demonstrated that the first two mechanisms can be explained by adhesion-driven biased membrane spreading on microtubules. Optical trapping revealed that growing and shrinking microtubule ends can exert forces of ∼0.5 and ∼5 pN, respectively, through attached proteins. Rapidly exchanging molecules that connect membranes to dynamic microtubules can thus bear a sufficient load to induce membrane deformation and motility. Furthermore, combining TAC components and a membrane-attached kinesin in the same in vitro assays demonstrated that they can cooperate in promoting membrane tubule extension.

Published
2020

43. Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends

Author

Serra-Marques, Andrea, Martin, Maud, Katrukha, Eugene A, Grigoriev, Ilya, Peeters, Cathelijn A.E., Liu, Qingyang, Hooikaas, Peter Jan, Yao, Yao, Solianova, Veronika, Smal, Ihor, Pedersen, Lotte B, Meijering, Erik, Kapitein, Lukas C, Akhmanova, Anna, Serra-Marques, Andrea, Martin, Maud, Katrukha, Eugene A, Grigoriev, Ilya, Peeters, Cathelijn A.E., Liu, Qingyang, Hooikaas, Peter Jan, Yao, Yao, Solianova, Veronika, Smal, Ihor, Pedersen, Lotte B, Meijering, Erik, Kapitein, Lukas C, and Akhmanova, Anna

Abstract

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.

Published
2020

44. Comparing strategies for deep astigmatism-based single-molecule localization microscopy

Author

Siemons, Marijn, Cloin, Bas M C, Salas, Desiree M, Nijenhuis, Wilco, Katrukha, Eugene A, Kapitein, Lukas C, Siemons, Marijn, Cloin, Bas M C, Salas, Desiree M, Nijenhuis, Wilco, Katrukha, Eugene A, and Kapitein, Lukas C

Abstract

Single-molecule localization microscopy (SMLM) enables fluorescent microscopy with nanometric resolution. While localizing molecules close to the coverslip is relatively straightforward using high numerical aperture (NA) oil immersion (OI) objectives, optical aberrations impede SMLM deeper in watery samples. Adaptive optics (AO) with a deformable mirror (DM) can be used to correct such aberrations and to induce precise levels of astigmatism to encode the z-position of molecules. Alternatively, the use of water immersion (WI) objectives might be sufficient to limit the most dominant aberrations. Here we compare SMLM at various depths using either WI or OI with or without AO. In addition, we compare the performance of a cylindrical lens and a DM for astigmatism-based z-encoding. We find that OI combined with adaptive optics improves localization precision beyond the performance of WI-based imaging and enables deep (>10 µm) 3D localization.

Published
2020

45. Mechanisms of Motor-Independent Membrane Remodeling Driven by Dynamic Microtubules

Author

Sub Cell Biology, Celbiologie, Rodríguez-García, Ruddi, Volkov, Vladimir A, Chen, Chiung-Yi, Katrukha, Eugene A, Olieric, Natacha, Aher, Amol, Grigoriev, Ilya, López, Magdalena Preciado, Steinmetz, Michel O, Kapitein, Lukas C, Koenderink, Gijsje, Dogterom, Marileen, Akhmanova, Anna, Sub Cell Biology, Celbiologie, Rodríguez-García, Ruddi, Volkov, Vladimir A, Chen, Chiung-Yi, Katrukha, Eugene A, Olieric, Natacha, Aher, Amol, Grigoriev, Ilya, López, Magdalena Preciado, Steinmetz, Michel O, Kapitein, Lukas C, Koenderink, Gijsje, Dogterom, Marileen, and Akhmanova, Anna

Published
2020

46. Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends

Author

Sub Cell Biology, Celbiologie, Serra-Marques, Andrea, Martin, Maud, Katrukha, Eugene A, Grigoriev, Ilya, Peeters, Cathelijn A.E., Liu, Qingyang, Hooikaas, Peter Jan, Yao, Yao, Solianova, Veronika, Smal, Ihor, Pedersen, Lotte B, Meijering, Erik, Kapitein, Lukas C, Akhmanova, Anna, Sub Cell Biology, Celbiologie, Serra-Marques, Andrea, Martin, Maud, Katrukha, Eugene A, Grigoriev, Ilya, Peeters, Cathelijn A.E., Liu, Qingyang, Hooikaas, Peter Jan, Yao, Yao, Solianova, Veronika, Smal, Ihor, Pedersen, Lotte B, Meijering, Erik, Kapitein, Lukas C, and Akhmanova, Anna

Published
2020

47. Imaging of Tumor Spheroids, Dual-Isotope SPECT, and Autoradiographic Analysis to Assess the Tumor Uptake and Distribution of Different Nanobodies (vol 31, pg 1079, 2020)

Author

Hernandez, Beltran Irati, Rompen, Rene, Rossin, Raffaella, Xenaki, Katerina T., Katrukha, Eugene A., Nicolay, Klaas, Henegouwen, Paul van Bergen En, Gruell, Holger, Oliveira, Sabrina, Hernandez, Beltran Irati, Rompen, Rene, Rossin, Raffaella, Xenaki, Katerina T., Katrukha, Eugene A., Nicolay, Klaas, Henegouwen, Paul van Bergen En, Gruell, Holger, and Oliveira, Sabrina

Published
2020

49. Taxanes convert regions of perturbed microtubule growth into rescue sites

Author

Sub Cell Biology, Celbiologie, Rai, Ankit, Liu, Tianyang, Glauser, Simon, Katrukha, Eugene A, Estévez-Gallego, Juan, Rodríguez-García, Ruddi, Fang, Wei-Shuo, Díaz, J Fernando, Steinmetz, Michel O, Altmann, Karl-Heinz, Kapitein, Lukas C, Moores, Carolyn A, Akhmanova, Anna, Sub Cell Biology, Celbiologie, Rai, Ankit, Liu, Tianyang, Glauser, Simon, Katrukha, Eugene A, Estévez-Gallego, Juan, Rodríguez-García, Ruddi, Fang, Wei-Shuo, Díaz, J Fernando, Steinmetz, Michel O, Altmann, Karl-Heinz, Kapitein, Lukas C, Moores, Carolyn A, and Akhmanova, Anna

Published
2020

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