[{"external_id":{"isi":["001025621500002"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41592-023-01937-5","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoDa"}],"author":[{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"}],"related_material":{"record":[{"relation":"extended_version","status":"public","id":"13267"}]},"date_updated":"2024-01-10T08:37:48Z","date_created":"2024-01-10T08:07:15Z","volume":20,"publication":"Nature Methods","citation":{"chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5"},"article_type":"letter_note","page":"1141-1142","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14770","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","status":"public","intvolume":" 20","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}],"issue":"8"},{"extern":"1","issue":"4","type":"journal_article","oa_version":"None","volume":42,"date_updated":"2024-03-20T10:58:33Z","date_created":"2024-03-20T10:43:19Z","author":[{"full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","last_name":"Bravo"}],"publisher":"Mary Ann Liebert","intvolume":" 42","publication_status":"published","title":"SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9","status":"public","_id":"15144","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","publication_identifier":{"issn":["1935-472X"],"eissn":["1937-8661"]},"article_processing_charge":"No","day":"01","month":"04","keyword":["Management of Technology and Innovation","Biomedical Engineering","Bioengineering","Biotechnology"],"scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2022-04-01T00:00:00Z","doi":"10.1089/gen.42.04.03","page":"12","quality_controlled":"1","article_type":"letter_note","citation":{"ista":"Bravo JPK. 2022. SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9. Genetic Engineering & Biotechnology News. 42(4), 12.","apa":"Bravo, J. P. K. (2022). SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9. Genetic Engineering & Biotechnology News. Mary Ann Liebert. https://doi.org/10.1089/gen.42.04.03","ieee":"J. P. K. Bravo, “SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9,” Genetic Engineering & Biotechnology News, vol. 42, no. 4. Mary Ann Liebert, p. 12, 2022.","ama":"Bravo JPK. SuperFi-Cas9 exceeds fidelity, matches speed of original Cas9. Genetic Engineering & Biotechnology News. 2022;42(4):12. doi:10.1089/gen.42.04.03","chicago":"Bravo, Jack Peter Kelly. “SuperFi-Cas9 Exceeds Fidelity, Matches Speed of Original Cas9.” Genetic Engineering & Biotechnology News. Mary Ann Liebert, 2022. https://doi.org/10.1089/gen.42.04.03.","mla":"Bravo, Jack Peter Kelly. “SuperFi-Cas9 Exceeds Fidelity, Matches Speed of Original Cas9.” Genetic Engineering & Biotechnology News, vol. 42, no. 4, Mary Ann Liebert, 2022, p. 12, doi:10.1089/gen.42.04.03.","short":"J.P.K. Bravo, Genetic Engineering & Biotechnology News 42 (2022) 12."},"publication":"Genetic Engineering & Biotechnology News"},{"citation":{"short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” BMC Biology, vol. 18, 2, Springer Nature, 2020, doi:10.1186/s12915-019-0733-6.","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” BMC Biology. Springer Nature, 2020. https://doi.org/10.1186/s12915-019-0733-6.","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 2020;18. doi:10.1186/s12915-019-0733-6","ieee":"H. Rampelt et al., “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” BMC Biology, vol. 18. Springer Nature, 2020.","apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0733-6","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2."},"publication":"BMC Biology","article_type":"original","date_published":"2020-01-06T00:00:00Z","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"article_processing_charge":"No","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8402","intvolume":" 18","title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins."}],"oa":1,"external_id":{"pmid":["31907035"]},"main_file_link":[{"url":"https://doi.org/10.1186/s12915-019-0733-6","open_access":"1"}],"quality_controlled":"1","doi":"10.1186/s12915-019-0733-6","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1741-7007"]},"month":"01","pmid":1,"year":"2020","publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Rampelt, Heike","first_name":"Heike","last_name":"Rampelt"},{"last_name":"Sucec","first_name":"Iva","full_name":"Sucec, Iva"},{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"last_name":"Horten","first_name":"Patrick","full_name":"Horten, Patrick"},{"first_name":"Inge","last_name":"Perschil","full_name":"Perschil, Inge"},{"first_name":"Jean-Claude","last_name":"Martinou","full_name":"Martinou, Jean-Claude"},{"first_name":"Martin","last_name":"van der Laan","full_name":"van der Laan, Martin"},{"last_name":"Wiedemann","first_name":"Nils","full_name":"Wiedemann, Nils"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"},{"full_name":"Pfanner, Nikolaus","last_name":"Pfanner","first_name":"Nikolaus"}],"volume":18,"date_created":"2020-09-17T10:26:53Z","date_updated":"2021-01-12T08:19:02Z","article_number":"2","extern":"1"},{"month":"08","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"language":[{"iso":"eng"}],"doi":"10.1002/smll.202002135","quality_controlled":"1","external_id":{"pmid":["32783385"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/smll.202002135"}],"extern":"1","article_number":"2002135","date_created":"2023-08-01T09:36:48Z","date_updated":"2023-08-07T10:11:41Z","volume":16,"author":[{"first_name":"Silvia","last_name":"Moreno","full_name":"Moreno, Silvia"},{"full_name":"Sharan, Priyanka","first_name":"Priyanka","last_name":"Sharan"},{"full_name":"Engelke, Johanna","first_name":"Johanna","last_name":"Engelke"},{"last_name":"Gumz","first_name":"Hannes","full_name":"Gumz, Hannes"},{"full_name":"Boye, Susanne","last_name":"Boye","first_name":"Susanne"},{"first_name":"Ulrich","last_name":"Oertel","full_name":"Oertel, Ulrich"},{"full_name":"Wang, Peng","last_name":"Wang","first_name":"Peng"},{"first_name":"Susanta","last_name":"Banerjee","full_name":"Banerjee, Susanta"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"},{"full_name":"Voit, Brigitte","last_name":"Voit","first_name":"Brigitte"},{"full_name":"Lederer, Albena","first_name":"Albena","last_name":"Lederer"},{"first_name":"Dietmar","last_name":"Appelhans","full_name":"Appelhans, Dietmar"}],"publication_status":"published","publisher":"Wiley","year":"2020","pmid":1,"day":"11","article_processing_charge":"No","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"scopus_import":"1","date_published":"2020-08-11T00:00:00Z","article_type":"original","publication":"Small","citation":{"ama":"Moreno S, Sharan P, Engelke J, et al. Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. 2020;16(37). doi:10.1002/smll.202002135","ista":"Moreno S, Sharan P, Engelke J, Gumz H, Boye S, Oertel U, Wang P, Banerjee S, Klajn R, Voit B, Lederer A, Appelhans D. 2020. Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. 16(37), 2002135.","apa":"Moreno, S., Sharan, P., Engelke, J., Gumz, H., Boye, S., Oertel, U., … Appelhans, D. (2020). Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. Wiley. https://doi.org/10.1002/smll.202002135","ieee":"S. Moreno et al., “Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors,” Small, vol. 16, no. 37. Wiley, 2020.","mla":"Moreno, Silvia, et al. “Light‐driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors.” Small, vol. 16, no. 37, 2002135, Wiley, 2020, doi:10.1002/smll.202002135.","short":"S. Moreno, P. Sharan, J. Engelke, H. Gumz, S. Boye, U. Oertel, P. Wang, S. Banerjee, R. Klajn, B. Voit, A. Lederer, D. Appelhans, Small 16 (2020).","chicago":"Moreno, Silvia, Priyanka Sharan, Johanna Engelke, Hannes Gumz, Susanne Boye, Ulrich Oertel, Peng Wang, et al. “Light‐driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors.” Small. Wiley, 2020. https://doi.org/10.1002/smll.202002135."},"abstract":[{"lang":"eng","text":"Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand."}],"issue":"37","type":"journal_article","oa_version":"Published Version","title":"Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors","status":"public","intvolume":" 16","_id":"13363","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"04","publication_identifier":{"issn":["0006-3592"]},"external_id":{"pmid":["27748519"]},"quality_controlled":"1","doi":"10.1002/bit.26200","language":[{"iso":"eng"}],"extern":"1","year":"2017","pmid":1,"publication_status":"published","publisher":"Wiley","author":[{"full_name":"Kick, Benjamin","last_name":"Kick","first_name":"Benjamin"},{"full_name":"Hensler, Samantha","last_name":"Hensler","first_name":"Samantha"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"},{"first_name":"Dirk","last_name":"Weuster-Botz","full_name":"Weuster-Botz, Dirk"}],"date_updated":"2023-11-07T12:36:20Z","date_created":"2023-09-06T12:08:29Z","volume":114,"scopus_import":"1","keyword":["Applied Microbiology and Biotechnology","Bioengineering","Biotechnology"],"day":"01","article_processing_charge":"No","publication":"Biotechnology and Bioengineering","citation":{"ista":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 114(4), 777–784.","ieee":"B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production,” Biotechnology and Bioengineering, vol. 114, no. 4. Wiley, pp. 777–784, 2017.","apa":"Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2017). Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. Wiley. https://doi.org/10.1002/bit.26200","ama":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 2017;114(4):777-784. doi:10.1002/bit.26200","chicago":"Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz, and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology and Bioengineering. Wiley, 2017. https://doi.org/10.1002/bit.26200.","mla":"Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology and Bioengineering, vol. 114, no. 4, Wiley, 2017, pp. 777–84, doi:10.1002/bit.26200.","short":"B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology and Bioengineering 114 (2017) 777–784."},"article_type":"original","page":"777-784","date_published":"2017-04-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784.","lang":"eng"}],"issue":"4","_id":"14286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production","intvolume":" 114","oa_version":"None"},{"language":[{"iso":"eng"}],"doi":"10.1039/c3mb70245f","quality_controlled":"1","month":"08","publication_identifier":{"eissn":["1742-2051"],"issn":["1742-206X"]},"date_updated":"2024-03-25T11:45:46Z","date_created":"2024-03-21T07:58:57Z","volume":9,"author":[{"first_name":"Marcos H.","last_name":"Woehrmann","full_name":"Woehrmann, Marcos H."},{"full_name":"Bray, Walter M.","last_name":"Bray","first_name":"Walter M."},{"first_name":"James K.","last_name":"Durbin","full_name":"Durbin, James K."},{"last_name":"Nisam","first_name":"Sean C.","full_name":"Nisam, Sean C."},{"full_name":"Michael, Alicia Kathleen","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia Kathleen"},{"first_name":"Emerson","last_name":"Glassey","full_name":"Glassey, Emerson"},{"full_name":"Stuart, Joshua M.","first_name":"Joshua M.","last_name":"Stuart"},{"full_name":"Lokey, R. Scott","first_name":"R. Scott","last_name":"Lokey"}],"publication_status":"published","publisher":"Royal Society of Chemistry","year":"2013","extern":"1","article_number":"2604","date_published":"2013-08-20T00:00:00Z","article_type":"original","publication":"Molecular BioSystems","citation":{"ama":"Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 2013;9(11). doi:10.1039/c3mb70245f","ista":"Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 9(11), 2604.","ieee":"M. H. Woehrmann et al., “Large-scale cytological profiling for functional analysis of bioactive compounds,” Molecular BioSystems, vol. 9, no. 11. Royal Society of Chemistry, 2013.","apa":"Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. Royal Society of Chemistry. https://doi.org/10.1039/c3mb70245f","mla":"Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular BioSystems, vol. 9, no. 11, 2604, Royal Society of Chemistry, 2013, doi:10.1039/c3mb70245f.","short":"M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey, J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013).","chicago":"Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular BioSystems. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3mb70245f."},"day":"20","article_processing_charge":"No","keyword":["Molecular Biology","Biotechnology"],"scopus_import":"1","oa_version":"None","title":"Large-scale cytological profiling for functional analysis of bioactive compounds","status":"public","intvolume":" 9","_id":"15162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cytological profiling (CP) is an unbiased image-based screening technique that uses automated microscopy and image analysis to profile compounds based on numerous quantifiable phenotypic features. We used CP to evaluate a library of nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide range of biological pathways. We developed informatics techniques for generating dosage-independent phenotypic “fingerprints” for each compound, and for quantifying the likelihood that a compound's CP fingerprint corresponds to its annotated MOA. We identified groups of features that distinguish classes with closely related phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis vs. proteasome inhibitors. We tested several cases in which cytological profiles indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma ligand that acts as a proteasome inhibitor, using independent biochemical assays to confirm the MOAs predicted by the CP signatures. We also applied maximal-information statistics to identify correlations between cytological features and kinase inhibitory activities by combining the CP fingerprints of 24 kinase inhibitors with published data on their specificities against a diverse panel of kinases. The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities.","lang":"eng"}],"issue":"11","type":"journal_article"},{"publication":"Small","citation":{"ista":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. 2012. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 8(5), 654–660.","ieee":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S. G. Wolf, S. Das, and R. Klajn, “Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles,” Small, vol. 8, no. 5. Wiley, pp. 654–660, 2012.","apa":"Ridelman, Y., Singh, G., Popovitz-Biro, R., Wolf, S. G., Das, S., & Klajn, R. (2012). Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. Wiley. https://doi.org/10.1002/smll.201101882","ama":"Ridelman Y, Singh G, Popovitz-Biro R, Wolf SG, Das S, Klajn R. Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles. Small. 2012;8(5):654-660. doi:10.1002/smll.201101882","chicago":"Ridelman, Yonatan, Gurvinder Singh, Ronit Popovitz-Biro, Sharon G. Wolf, Sanjib Das, and Rafal Klajn. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small. Wiley, 2012. https://doi.org/10.1002/smll.201101882.","mla":"Ridelman, Yonatan, et al. “Metallic Nanobowls by Galvanic Replacement Reaction on Heterodimeric Nanoparticles.” Small, vol. 8, no. 5, Wiley, 2012, pp. 654–60, doi:10.1002/smll.201101882.","short":"Y. Ridelman, G. Singh, R. Popovitz-Biro, S.G. Wolf, S. Das, R. Klajn, Small 8 (2012) 654–660."},"article_type":"original","page":"654-660","date_published":"2012-03-12T00:00:00Z","scopus_import":"1","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"day":"12","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13408","status":"public","title":"Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles","intvolume":" 8","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as “protecting groups” during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls."}],"issue":"5","external_id":{"pmid":["22392681"]},"quality_controlled":"1","doi":"10.1002/smll.201101882","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"year":"2012","pmid":1,"publication_status":"published","publisher":"Wiley","author":[{"full_name":"Ridelman, Yonatan","last_name":"Ridelman","first_name":"Yonatan"},{"full_name":"Singh, Gurvinder","first_name":"Gurvinder","last_name":"Singh"},{"first_name":"Ronit","last_name":"Popovitz-Biro","full_name":"Popovitz-Biro, Ronit"},{"full_name":"Wolf, Sharon G.","last_name":"Wolf","first_name":"Sharon G."},{"full_name":"Das, Sanjib","first_name":"Sanjib","last_name":"Das"},{"first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"date_updated":"2023-08-08T07:55:10Z","date_created":"2023-08-01T09:47:55Z","volume":8,"extern":"1"},{"extern":"1","author":[{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Browne, Kevin P.","last_name":"Browne","first_name":"Kevin P."},{"first_name":"Siowling","last_name":"Soh","full_name":"Soh, Siowling"},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"volume":6,"date_updated":"2023-08-08T08:15:25Z","date_created":"2023-08-01T09:48:38Z","pmid":1,"year":"2010","publisher":"Wiley","publication_status":"published","publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"month":"07","doi":"10.1002/smll.200902272","language":[{"iso":"eng"}],"external_id":{"pmid":["20521264"]},"quality_controlled":"1","issue":"13","abstract":[{"text":"Photoresponsive gold nanoparticles dispersed in a solid/frozen matrix provide a basis for sensors that “remember” whether the sample has ever exceeded the melting temperature of the matrix. The operation of these sensors rests on the ability to photoinduce metastable electric dipoles on NP surfaces – upon melting, these dipoles drive NP aggregation, precipitation, and crosslinking. These events are manifested by a pronounced color change.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"13411","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","status":"public","title":"Nanoparticles that “remember” temperature","article_processing_charge":"No","day":"05","scopus_import":"1","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"date_published":"2010-07-05T00:00:00Z","citation":{"ama":"Klajn R, Browne KP, Soh S, Grzybowski BA. Nanoparticles that “remember” temperature. Small. 2010;6(13):1385-1387. doi:10.1002/smll.200902272","ista":"Klajn R, Browne KP, Soh S, Grzybowski BA. 2010. Nanoparticles that “remember” temperature. Small. 6(13), 1385–1387.","ieee":"R. Klajn, K. P. Browne, S. Soh, and B. A. Grzybowski, “Nanoparticles that ‘remember’ temperature,” Small, vol. 6, no. 13. Wiley, pp. 1385–1387, 2010.","apa":"Klajn, R., Browne, K. P., Soh, S., & Grzybowski, B. A. (2010). Nanoparticles that “remember” temperature. Small. Wiley. https://doi.org/10.1002/smll.200902272","mla":"Klajn, Rafal, et al. “Nanoparticles That ‘Remember’ Temperature.” Small, vol. 6, no. 13, Wiley, 2010, pp. 1385–87, doi:10.1002/smll.200902272.","short":"R. Klajn, K.P. Browne, S. Soh, B.A. Grzybowski, Small 6 (2010) 1385–1387.","chicago":"Klajn, Rafal, Kevin P. Browne, Siowling Soh, and Bartosz A. Grzybowski. “Nanoparticles That ‘Remember’ Temperature.” Small. Wiley, 2010. https://doi.org/10.1002/smll.200902272."},"publication":"Small","page":"1385-1387","article_type":"original"},{"quality_controlled":"1","external_id":{"pmid":["19771567"]},"language":[{"iso":"eng"}],"doi":"10.1002/smll.200900902","month":"12","publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"publication_status":"published","publisher":"Wiley","year":"2009","pmid":1,"date_updated":"2023-08-08T08:49:22Z","date_created":"2023-08-01T09:50:12Z","volume":5,"author":[{"full_name":"Browne, Kevin P.","first_name":"Kevin P.","last_name":"Browne"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"},{"full_name":"Villa, JulieAnn","last_name":"Villa","first_name":"JulieAnn"},{"first_name":"Bartosz A.","last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A."}],"extern":"1","article_type":"original","page":"2656-2658","publication":"Small","citation":{"ama":"Browne KP, Klajn R, Villa J, Grzybowski BA. Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates. Small. 2009;5(23):2656-2658. doi:10.1002/smll.200900902","ista":"Browne KP, Klajn R, Villa J, Grzybowski BA. 2009. Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates. Small. 5(23), 2656–2658.","ieee":"K. P. Browne, R. Klajn, J. Villa, and B. A. Grzybowski, “Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates,” Small, vol. 5, no. 23. Wiley, pp. 2656–2658, 2009.","apa":"Browne, K. P., Klajn, R., Villa, J., & Grzybowski, B. A. (2009). Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates. Small. Wiley. https://doi.org/10.1002/smll.200900902","mla":"Browne, Kevin P., et al. “Mechanofabrication of Pancake and Rodlike Nanostructures from Deformable Nanoparticle Aggregates.” Small, vol. 5, no. 23, Wiley, 2009, pp. 2656–58, doi:10.1002/smll.200900902.","short":"K.P. Browne, R. Klajn, J. Villa, B.A. Grzybowski, Small 5 (2009) 2656–2658.","chicago":"Browne, Kevin P., Rafal Klajn, JulieAnn Villa, and Bartosz A. Grzybowski. “Mechanofabrication of Pancake and Rodlike Nanostructures from Deformable Nanoparticle Aggregates.” Small. Wiley, 2009. https://doi.org/10.1002/smll.200900902."},"date_published":"2009-12-01T00:00:00Z","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Mechanofabrication of pancake and rodlike nanostructures from deformable nanoparticle aggregates","intvolume":" 5","_id":"13414","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","abstract":[{"text":"Supraspherical aggregates of crosslinked metal nanoparticles are transformed into pancakes and nanorods by mechanical stresses and shears imparted by macroscopic objects (see image). The dimensions of both types of nanostructures can be controlled by the pressures applied.","lang":"eng"}],"issue":"23"},{"date_published":"2008-10-09T00:00:00Z","page":"1635-1639","article_type":"original","citation":{"short":"Y. Wei, R. Klajn, A.O. Pinchuk, B.A. Grzybowski, Small 4 (2008) 1635–1639.","mla":"Wei, Yanhu, et al. “Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’” Small, vol. 4, no. 10, Wiley, 2008, pp. 1635–39, doi:10.1002/smll.200800511.","chicago":"Wei, Yanhu, Rafal Klajn, Anatoliy O. Pinchuk, and Bartosz A. Grzybowski. “Synthesis, Shape Control, and Optical Properties of Hybrid Au/Fe3O4 ‘Nanoflowers.’” Small. Wiley, 2008. https://doi.org/10.1002/smll.200800511.","ama":"Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small. 2008;4(10):1635-1639. doi:10.1002/smll.200800511","ieee":"Y. Wei, R. Klajn, A. O. Pinchuk, and B. A. Grzybowski, “Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 ‘nanoflowers,’” Small, vol. 4, no. 10. Wiley, pp. 1635–1639, 2008.","apa":"Wei, Y., Klajn, R., Pinchuk, A. O., & Grzybowski, B. A. (2008). Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers.” Small. Wiley. https://doi.org/10.1002/smll.200800511","ista":"Wei Y, Klajn R, Pinchuk AO, Grzybowski BA. 2008. Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”. Small. 4(10), 1635–1639."},"publication":"Small","article_processing_charge":"No","day":"09","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"scopus_import":"1","oa_version":"None","intvolume":" 4","status":"public","title":"Synthesis, shape control, and optical properties of hybrid Au/Fe3O4 “nanoflowers”","_id":"13422","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","abstract":[{"lang":"eng","text":"Make like a leaf: The synthesis and characterization of a family of “flowerlike” Au/Fe3O4 nanoparticles is described, whereby Fe3O4 “leaves” adhere to a gold core (see image). The size and numbers of iron oxide domains can be adjusted flexibly by changing the proportion of the starting materials and the reaction time."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1002/smll.200800511","quality_controlled":"1","external_id":{"pmid":["18636405"]},"publication_identifier":{"eissn":["1613-6829"],"issn":["1613-6810"]},"month":"10","volume":4,"date_created":"2023-08-01T10:30:42Z","date_updated":"2023-08-08T11:14:50Z","author":[{"first_name":"Yanhu","last_name":"Wei","full_name":"Wei, Yanhu"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"},{"first_name":"Anatoliy O.","last_name":"Pinchuk","full_name":"Pinchuk, Anatoliy O."},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2008","extern":"1"}]