Granted Patent
B2
US 12,405,193 · App. 16/794,849 · Granted Sep 2, 2025
Iterative direct expansion microscopy
Inventors:
Deblina Sarkar (Cambridge, MA); Edward Stuart Boyden (Chestnut Hill, MA); Asmamaw T. Wassie (Boston, MA); Jinyoung Kang (Cambridge, MA)
Assignee:
Massachusetts Institute of Technology
View Patent ↗
Loading inventors, assignments & file history…
Abstract
The present invention provides biological samples of interest that have been iteratively expanded in a method referred to herein as iterative direct expansion microscopy (id-ExM). In the id-ExM method, biological samples of interest are permeated with a swellable material that results in the sample becoming embedded in the swellable material, and then the sample can be expanded isotropically in three dimensions. The process of iteratively expanding the samples can be applied to expand samples one or more additional times such that, for example, a 5-fold expanded sample can be expanded again to achieve high expansion factors, for example, 20× to 100× or more linear expansion.
Claims (50)
1. A method for iteratively enlarging a sample of interest comprising biomolecules for microscopy, the method comprising the steps of:
a) contacting the sample with a biomolecule anchoring agent (BAA), wherein the BAA comprises a biomolecule binding moiety and an anchor;
b) embedding the sample in a first swellable material, wherein the biomolecules in the sample anchor to the first swellable material;
c) subjecting the sample to a disruption of the endogenous physical structure of the sample;
d) swelling the first swellable material resulting in an enlargement of the sample;
e) re-embedding the enlarged sample in a non-swellable material to form an enlarged sample hybrid;
f) embedding the enlarged sample hybrid in a second swellable material, wherein the second swellable material is the same as the first swellable material; and
g) swelling the second swellable material to further enlarge the sample,
wherein the biomolecules in the sample remain anchored to the first swellable material.
2. The method according to claim 1 , wherein embedding the sample in the first swellable material in step b) comprises permeating the sample with a composition comprising one or more water soluble monomer precursors; and polymerizing the composition within the sample to form the first swellable material, wherein said polymerizing results in anchoring of the biomolecules of the sample to the first swellable material to form a sample-swellable material complex.
3. The method according to claim 1 , wherein embedding the sample in the second swellable material in step f) comprises permeating the sample with a composition comprising one or more water soluble monomer precursors; and polymerizing the composition within the sample to form the second swellable material, wherein the biomolecules remain anchored to the first swellable material.
4. The method according to claim 2 , wherein the composition comprises at least one polyelectrolyte monomer and a covalent crosslinker.
5. The method according to claim 2 , wherein the first swellable material is a hydrogel.
6. The method according to claim 5 , wherein the hydrogel is a polyacrylate hydrogel.
7. The method according to claim 6 , wherein the composition comprises acrylate, acrylamide, and a crosslinker selected from N,N-methylenebisacrylamide (BIS), N,N′-(1,2-Dihydroxyethylene)bisacrylamide)(DHEBA), and N,N′-Bis(acryloyl)cystamine(BAC).
8. The method according to claim 1 , wherein re-embedding the enlarged sample in the non-swellable material in step e) comprises permeating the enlarged sample with a composition comprising precursors of a non-swellable material and polymerizing the composition within the enlarged sample to form a non-swellable material.
9. The method according to claim 1 , wherein prior to step g) a slice of the sample is taken and swelled.
10. The method according to claim 2 , wherein swelling the first swellable material in step d) comprises adding an aqueous solvent or liquid to cause the sample-swellable material complex to swell, thereby physically expanding the sample-swellable material complex, which results in an enlarged sample.
11. The method according to claim 10 , wherein the aqueous solvent or liquid is water.
12. The method according to claim 1 , further comprising the step of producing a high-resolution image of the sample by viewing the enlarged sample under a microscope.
13. The method according to claim 1 , further comprising the step of optically imaging the enlarged sample by viewing the sample under a microscope.
14. The method according to claim 3 , wherein the composition comprises at least one polyelectrolyte monomer and a covalent crosslinker.
15. The method according to claim 3 , wherein the second swellable material is a hydrogel.
16. The method according to claim 15 , wherein the hydrogel is a polyacrylate hydrogel.
17. The method according to claim 16 , wherein the composition comprises acrylate, acrylamide, and a crosslinker selected from N,N-methylenebisacrylamide (BIS), N,N′-(1,2-Dihydroxyethylene)bisacrylamide)(DHEBA), and N,N′-Bis(acryloyl)cystamine(BAC).
18. A method for iteratively enlarging a sample of interest comprising biomolecules for microscopy, the method comprising the steps of:
a) contacting the sample with a biomolecule anchoring agent (BAA), wherein the BAA comprises a biomolecule binding moiety and an anchor;
b) embedding the sample in a first swellable material, wherein the biomolecules in the sample anchor to the first swellable material;
c) subjecting the sample to a disruption of the endogenous physical structure of the sample;
d) swelling the first swellable material resulting in an enlargement of the sample;
e) re-embedding the enlarged sample in a non-swellable material to form an enlarged sample hybrid;
f) embedding the enlarged sample hybrid in a second swellable material, wherein the second swellable material is different than the first swellable material; and
g) swelling the second swellable material to further enlarge the sample,
wherein the biomolecules in the sample remain anchored to the first swellable material.
19. The method according to claim 18 , wherein embedding the sample in the first swellable material in step b) comprises permeating the sample with a composition comprising one or more water soluble monomer precursors; and polymerizing the composition within the sample to form the first swellable material, wherein said polymerizing results in anchoring of the biomolecules of the sample to the first swellable material to form a sample-swellable material complex.
20. The method according to claim 18 , wherein embedding the sample in the second swellable material in step f) comprises permeating the sample with a composition comprising one or more water soluble monomer precursors; and polymerizing the composition within the sample to form the second swellable material, wherein the biomolecules remain anchored to the first swellable material.
21. The method according to claim 19 , wherein the composition comprises at least one polyelectrolyte monomer and a covalent crosslinker.
22. The method according to claim 19 , wherein the first swellable material is a hydrogel.
23. The method according to claim 22 , wherein the hydrogel is a polyacrylate hydrogel.
24. The method according to claim 23 , wherein the composition comprises acrylate, acrylamide, and a crosslinker selected from N,N-methylenebisacrylamide (BIS), N,N′-(1,2-Dihydroxyethylene)bisacrylamide)(DHEBA), and N,N′-Bis(acryloyl)cystamine(BAC).
25. The method according to claim 18 , wherein re-embedding the enlarged sample in the non-swellable material in step e) comprises permeating the enlarged sample with a composition comprising precursors of a non-swellable material and polymerizing the composition within the enlarged sample to form a non-swellable material.
26. The method according to claim 18 , wherein prior to step g) a slice of the sample is taken and swelled.
27. The method according to claim 19 , wherein swelling the first swellable material in step d) comprises adding an aqueous solvent or liquid to cause the sample-swellable material complex to swell, thereby physically expanding the sample-swellable material complex, which results in an enlarged sample.
28. The method according to claim 27 , wherein the aqueous solvent or liquid is water.
29. The method according to claim 18 , further comprising the step of producing a high-resolution image of the sample by viewing the enlarged sample under a microscope.
30. The method according to claim 18 , further comprising the step of optically imaging the enlarged sample by viewing the sample under a microscope.
31. The method according to claim 20 , wherein the composition comprises at least one polyelectrolyte monomer and a covalent crosslinker.
32. The method according to claim 20 , wherein the second swellable material is a hydrogel.
33. The method according to claim 32 , wherein the hydrogel is a polyacrylate hydrogel.
34. The method according to claim 33 , wherein the composition comprises acrylate, acrylamide, and a crosslinker selected from N,N-methylenebisacrylamide (BIS), N,N′-(1,2-Dihydroxyethylene)bisacrylamide)(DHEBA), and N,N′-Bis(acryloyl)cystamine(BAC).
Assignments (2)
CONFIRMATORY LICENSE
Recorded Oct 2, 2023
From: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
To: NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT
Reel/Frame 065091/0077 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Jul 13, 2020
From: SARKAR, DEBLINA; BOYDEN, EDWARD STUART; WASSIE, ASMAMAW T.; KANG, JINYOUNG
To: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Reel/Frame 053187/0800 →
Continuity (2)
Provisional Application
62809062
· Feb 22, 2019
References Cited (400)
US 5840862A
· Bensimon et al.
· 1998
[cited by applicant]
US 5952232A
· Rothman
· 1999
[cited by applicant]
US 6107081A
· Feeback et al.
· 2000
[cited by applicant]
US 6204064B1
· Alberts et al.
· 2001
[cited by applicant]
US 6271278B1
· Park et al.
· 2001
[cited by applicant]
US 6287870B1
· Wardlaw et al.
· 2001
[cited by applicant]
US 6548255B2
· Bensimon et al.
· 2003
[cited by applicant]
US 9376677B2
· Mir
· 2016
[cited by applicant]
US 20040115629A1
· Panzer et al.
· 2004
[cited by applicant]
US 20040214211A1
· Gilmanshin et al.
· 2004
[cited by applicant]
US 20050034990A1
· Crooks et al.
· 2005
[cited by applicant]
US 20050069877A1
· Gandhi et al.
· 2005
[cited by applicant]
US 20060003356A1
· Shaw et al.
· 2006
[cited by applicant]
US 20060110760A1
· Kim et al.
· 2006
[cited by applicant]
US 20070134902A1
· Bertino et al.
· 2007
[cited by applicant]
US 20080139407A1
· Slootstra et al.
· 2008
[cited by applicant]
US 20090241681A1
· Machauf et al.
· 2009
[cited by applicant]
US 20100041128A1
· Banes et al.
· 2010
[cited by applicant]
US 20100055161A1
· Ahn
· 2010
[cited by applicant]
US 20100056445A1
· Sharma et al.
· 2010
[cited by applicant]
US 20110091717A1
· Weiss et al.
· 2011
[cited by applicant]
US 20110291357A1
· Boyle
· 2011
[cited by applicant]
US 20120220478A1
· Shaffer
· 2012
[cited by applicant]
US 20120251527A1
· Reiser
· 2012
[cited by applicant]
US 20130045503A1
· Miyawaki et al.
· 2013
[cited by applicant]
US 20140364330A1
· Mershin et al.
· 2014
[cited by applicant]
US 20150226743A1
· Weiss et al.
· 2015
[cited by applicant]
US 20150353989A1
· Fraser et al.
· 2015
[cited by applicant]
US 20170182220A1
· Song et al.
· 2017
[cited by applicant]
US 20190064037A1
· Boyden et al.
· 2019
[cited by applicant]
US 20190113423A1
· Goodman et al.
· 2019
[cited by applicant]
US 20200277664A1
· Frenz
· 2020
[cited by applicant]
US 20230332207A1
· Cui et al.
· 2023
[cited by applicant]
CN 104350372A
· 2015
[cited by applicant]
CN 111848855A
· 2020
[cited by applicant]
CN 112574089A
· 2021
[cited by applicant]
EP 3159361A1
· 2017
[cited by applicant]
JP 2005291759A
· 2005
[cited by applicant]
JP 2006036957A
· 2006
[cited by applicant]
JP 2008286694A
· 2008
[cited by applicant]
JP 2009191125A
· 2009
[cited by applicant]
JP 2014005231A
· 2014
[cited by applicant]
WO 0008212A1
· 2000
[cited by applicant]
WO 2007103665A2
· 2007
[cited by applicant]
WO 2008058302A1
· 2008
[cited by applicant]
WO 2010048605A1
· 2010
[cited by applicant]
WO 2012112689A1
· 2012
[cited by applicant]
WO 2012142664A1
· 2012
[cited by applicant]
WO 2014025392A1
· 2014
[cited by applicant]
WO 2014152984A1
· 2014
[cited by applicant]
WO 2015041755A1
· 2015
[cited by applicant]
WO 2015127183A2
· 2015
[cited by applicant]
WO 2016040489A1
· 2016
[cited by applicant]
WO 2017027367A1
· 2017
[cited by applicant]
WO 2017027368A1
· 2017
[cited by applicant]
WO 2017031249
· 2017
[cited by applicant]
WO 2017079406A1
· 2017
[cited by applicant]
WO 2017147435A1
· 2017
[cited by applicant]
WO 2018157074A1
· 2018
[cited by applicant]
WO 2019144391A1
· 2019
[cited by applicant]
WO 2021051011A1
· 2021
[cited by applicant]
WO 2021183667A1
· 2021
[cited by applicant]
WO 2022100696A1
· 2022
[cited by applicant]
Chen et al., Nature Methods 13(8): 679-684 (2016).
[cited by examiner]
New England BioLabs, “Proteinase K”, P8102S product datasheet, 1 page, accessed Nov. 17, 2020.
[cited by applicant]
Product information brochure, FLOCRYLTM MBA, SNF Floerger, pp. 1-4, accessed Nov. 17, 2020.
[cited by applicant]
“Crosslinking and Photoactivatable Reagents”, Invitrogen, Chapter 5 in “Molecular Probes™ Handbook A Guide to Fluorescent Probes and Labeling Technologies”, 11th Edition, 2010, 171-188.
[cited by applicant]
“Proteinase K from Tritirachium album, solution”, Serva Electrophoresis, Instruction Manual, Cat. No. 33755, 1 page, publicly available prior to Feb. 1, 2017.
[cited by applicant]
Akhavan, A. et al., “Molecular Epizootiology of Rodent Leishmaniasis in a Hyperendemic Area of Iran”, Iranian J Publ Health, vol. 39, No. 1, 2010, 1-7.
[cited by applicant]
Asano, S. M. et al., “Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues”, Current Protocols in Cell Bio., vol. 80, No. 1, Online: DOI: 10.1002/cpcb.56. Retrieved from the Internet: URL:ht…
[cited by applicant]
Meng, H. , “Localization of a Blood Pressure Quantitative Trait Locus (QTL) to a 1.7cM Interval on Rat Chromosome 9”, Medical College of Ohio, dissertation, 2002, 1-158.
[cited by applicant]
Parang, B. et al., “Myeloid translocation genes differentially regulate colorectal cancer programs”, Oncogene, vol. 35, 2016, 6341-6349.
[cited by applicant]
Yu, C-C et al., “Expansion microscopy of C. elegans”, ELIFE, [Online] DOI: 10.7554/eLife.46249. Retrieved from the Internet: URL:https://elifesciences.org/articles/46249> [retrieved on Feb. 26, 2021], May 1, 2020, pp. 1…
[cited by applicant]
Office Action dated Apr. 4, 2018 from U.S. Appl. No. 14/627,310, filed Feb. 20, 2015.
[cited by applicant]
“Epitope Recovery Methods for IHC”, Nov. 7, 2015, ThermoFisher Scientific, pp. 1-2.
[cited by applicant]
Al, H. et al., “Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins”, Biochemistry, 46, 2007, 5904-10.
[cited by applicant]
Bates, M. et al., “Multicolor super-resolution imaging with photo-switchable fluorescent probes”, Science, 317, 2007, 1749-1753.
[cited by applicant]
Batish, M. et al., “Neuronal mRNAs Travel Singly into Dendrites”, PNAS, vol. 109(12), 2012, 4645-4650.
[cited by applicant]
Beliveau, B. et al., “Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes”, PNAS, vol. 109(52): pfa, 2012, 21301-21306.
[cited by applicant]
Bi, X. et al., “In situ-forming cross-linking hydrogel systems: chemistry and biomedical applications”, In: “Emerging Concepts in Analysis and Applications of Hydrogels”, INTECH, Aug. 24, 2016, 131-158.
[cited by applicant]
Bleckmann, J. et al., “Surface-Layer Lattices as Patterning Element for Multimeric Extremozymes”, Small Journal, 2013, 1-8.
[cited by applicant]
Bokman, S. H. et al., “Renaturation of Aequorea gree-fluorescent protein”, Biochem. Biophys. Res. Commun., 101, 1981, 1372-80.
[cited by applicant]
Bossi, M. et al., “Multicolor far-field fluorescence nanoscopy through isolated detection of distinct molecular species”, Nano Lett., 8, 2008, 2463-8.
[cited by applicant]
Breitwieser, A. et al., “Magnetic Beads Functionalized with Recombinant S-Layer Protein Exhibit High Human IgG-Binding and Anti-Fouling Properties”, Current Topics in Peptide & Protein Research, vol. 17, 2016, 45-55.
[cited by applicant]
Bruchez, M. et al., “Semiconductor nanocrystals as fluorescent biological labels”, Science, vol. 281, 1998, 2013-6.
[cited by applicant]
Buckley, P. et al., “Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons”, Neuron, vol. 69, 2011, 877-884.
[cited by applicant]
Buenrostro, J. D. et al., “ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide : ATAC-seq for Assaying Chromatin Accessibility”, In: “Current Protocols in Molecular Biology”, Wiley, New York, NY, Jan. 5,…
[cited by applicant]
Buxbaum, A. et al., “Single-Actin mRNA Detection in Neurons Reveals a Mechanism for Regulating Its Translatability”, Science, vol. 343, 2014, 419-422.
[cited by applicant]
Cabili, M. et al., “Localization and abundance analysis of human IncRNAs at single-cell and single-molecule resolution”, Genome Biology, vol. 16(20), 2015.
[cited by applicant]
Cal, et al., Nat Meth., 10, 2013, 540-547.
[cited by applicant]
Cajigas, I. et al., “The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging”, Neuron 74, 2012, 453-466.
[cited by applicant]
Cao, W. , “DNA ligases and ligase-based technologies”, Clinical and Applied Immunology Reviews, Elsevier, Amsterdam, NL, vol. 2, No. 1, Jan. 15, 2001, 33-43.
[cited by applicant]
Carpenter, A. E. et al., “CellProfiler: image analysis software for identifying and quantifying cell phenotypes”, Genome Biol., 7, 2006, R100.
[cited by applicant]
Chang, J-B et al., “Iterative expansion microscopy”, Nature Methods, 14(6), Jun. 2017, 593-599.
[cited by applicant]
Chen, F. et al., “Expansion Microscopy”, Science, 347(6621):, Jan. 15, 2015, 1-18.
[cited by applicant]
Chen, F. et al., “Nanoscale Imaging of RNA with Expansion Microscopy”, Nature Methods, 13(8):, Aug. 2016, 679-684.
[cited by applicant]
Chen, F. et al., “Supplementary Material for Expansion Microscopy”, Science, 347(6221), Jan. 15, 2015, 543-548.
[cited by applicant]
Chen, K. et al., “Spatially resolved, highly multiplexed RNA profiling in single cells”, Science. vol. 348(6233), 2015, aaa6090-aaa6090.
[cited by applicant]
Choi, H. et al., “Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability”, ACS Nano 8(5), 2014, 4284-4294.
[cited by applicant]
Choi, H. et al., “Programmable in situ amplification for multiplexed imaging of mRNA expression”, Nature Biotechnology, 28(11), 2010, 1208-1212.
[cited by applicant]
Chozinski, T. et al., “Expansion microscopy with conventional antibodies and fluorescent proteins”, Nature Methods, vol. 13(6), 2016, 485-491.
[cited by applicant]
Chu, J. et al., “Non-invasive intravital imaging of cellular differentiation with a bright red-excitable fluorescent protein”, Nat. Methods, 11, 2014, 572-8.
[cited by applicant]
Clemson, C. et al., “An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles”, Molecular Cell, 33, 2009, 717-26.
[cited by applicant]
Cormack, B. P. et al., “FACS-optimized mutants of the green fluorescent protein (GFP)”, Gene, 173, 1996, 33-8.
[cited by applicant]
Cubitt, A. B. et al., “Understanding structure-function relationships in the
[cited by applicant]
Dedecker, P. et al., “Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy”, J. Biomed. Opt., 17, 2012, 126008.
[cited by applicant]
Dilorenzo, F. et al., “Nanostructural Heterogeneity in Polymer Networks and Gels”, Polymer Chemistry, vol. 6, 215, 5515-5528.
[cited by applicant]
Edelstein, A. et al., “Computer control of microscopes using μManager”, Curr. Protoc. Mol. Biol. Chapter 14, Unit14.20, 2010.
[cited by applicant]
English, B. P. et al., “A three-camera imaging microscope for high-speed single-molecule tracking and super-resolution imaging in living cells”, in SPIE Nanosci. + Eng. (Mohseni, H., Agahi, M. H. & Razeghi, M.) 955008 (…
[cited by applicant]
Engreitz, J. et al., “The Xist IncRNA exploits three-dimensional genome architecture to spread across the X chromosome”, Science 341, 2013, 1237973.
[cited by applicant]
Femino, A. et al., “Visualization of Single RNA Transcripts in Situ”, Science, vol. 280, 1998, 585-590.
[cited by applicant]
Feng, G. et al., “Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP”, Neuron, 28, 2000, 41-51.
[cited by applicant]
Filonov, G. S. et al., “Bright and stable near-infrared fluorescent protein for in vivo imaging”, Nat. Biotechnol., 29, 2011, 757-61.
[cited by applicant]
Fouz, M. et al., “Bright Fluorescent Nanotags from Bottlebrush Polymers with DNA-Tipped Bristles”, ACS Central Science, vol. 1, 2015, 431-438.
[cited by applicant]
Freifeld, L. et al., “Expansion microscopy of zebrafish for neuroscience and developmental biology studies”, PNAS (online), Nov. 21, 2017, E10799-E10808.
[cited by applicant]
Goedhardt, J. et al., “Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%”, Nat. Commun., 3, 2012, 751.
[cited by applicant]
Goor, Olga J. et al., “Introduction of anti-fouling coutings at the surface of supramolecular elastomeric materials via post-modification of reactive supramolecular additives”, Polymer Chem., vol. 8, No. 34, Jan. 1, 201…
[cited by applicant]
Griesbeck, O. et al., “Reducing the environmental sensitivity of yellow fluorescent protein. Mechanism and applications”, J. Biol. Chem., 276, 2001, 29188-94.
[cited by applicant]
Gurskaya, N. G. et al., “Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light”, Nat. Biotechnol., 24, 2006, 461-5.
[cited by applicant]
Gyorvary, E. S. et al., “Self-Assembly and Recrystallization of Bacterial S-Layer Proteins at Silicon Supports Imaged in Real Time by Atomic Force Microscopy”, Journal of Microscopy, vol. 212, 2003, 300-306.
[cited by applicant]
Habuchi, S. et al., “mKikGR, a monomeric photoswitchable fluorescent protein”, PLoS One, 3, 2008, e3944.
[cited by applicant]
Hackstadt, T. , “Steric hindrance of antibody binding to surface proteins of Coxiella burnetti by phase I lipopolysaccharide”, Infect Immun, 56, 1998, 802-807.
[cited by applicant]
Heim, R. et al., “Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer”, Curr. Biol., 6, 1996, 178-82.
[cited by applicant]
Heim, R. et al., “Wavelength mutations and posttranslational autoxidation of green fluorescent protein”, Proc. Natl. Acad. Sci. U.S.A., 91, 1994, 12501-4.
[cited by applicant]
Hoffman, T. L. et al., “A Biosensor Assay for Studying Ligand-Membrane Receptor Interactions: Binding of Antibodies and HIV-1 Env to Chemokine Receptors”, PNAS, 97(21), 2000, 11215-11220.
[cited by applicant]
Huang, B. et al., “Whole-cell 3D Storm reveals interactions between cellular structures with nanometer-scale resolution”, Nat. Methods, 5, 2008, 1047-1052.
[cited by applicant]
Huisken, J. et al., “Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy”, Science. vol. 305, 2004, 1007-1009.
[cited by applicant]
Hunt, et al., “High temperature antigen retrieval and loss of nuclear morphology: a comparison of microwave\rand autoclave techniques”, J. Clin. Pathol. 49, 1996, 767-770.
[cited by applicant]
Jekel, P A. et al., “Use of endoproteinase Lys-C from Lysobacter enzymogenes in protein sequence analysis”, Anal. Biochem., 134, 1983, 347-354.
[cited by applicant]
Jiang, Y. et al., “Click hydrogels, microgels and nanogels: emerging platforms for drug delivery and tissue engineering”, Biomaterials, vol. 35, No. 18, Jun. 1, 2014, 4969-4985.
[cited by applicant]
Jimenez, N. et al., “A Novel Approach for Intracellular 3D Immuno-Labeling for Electron Tomography”, Traffic, 13, 2012, 926-933.
[cited by applicant]
Jung, H. et al., “Axonal mRNA localization and local protein synthesis in nervous system assembly, maintenance and repair”, Nat. Rev. Neurosci., vol. 13(5), 2012, 308-24.
[cited by applicant]
Kakimoto, K. et al., “Hypothesis for the mechanism for heat-induced antigen retrieval occurring on fresh frozen sections without formalin-fixation in immunohistochemistry”, J Mol Histol., 39, 2008, 389-399.
[cited by applicant]
Kaur, et al., Biochemistry 45, 2006, 7347-7355.
[cited by applicant]
Ke, R. et al., “In situ sequencing for RNA analysis in preserved tissue and cells”, Nature Methods, vol. 10(9), 2013, 857-60.
[cited by applicant]
Ke, Rongqin et al., “Supplementary Material In situ sequencing for RNA analysis in preserved tissue and cells”, Nature Methods 10(9):857-60, 2013, 1-29.
[cited by applicant]
Kroon, D.-J , “B-spline Grid, Image and Point based Registration”, Matlab Cent. at <http://www.mathworks.com/matlabcentral/fileexchange/20057-b-spline-grid--image-and-point-based-registration>.
[cited by applicant]
Laemmli, U. K. , “Cleavage of structural proteins during the assembly of the head of bacteriophage T4”, Nature, 227, 1970, 680-685.
[cited by applicant]
Lam, A. J. et al., “Improving FRET dynamic range with bright green and red fluorescent proteins”, Nat. Methods, 9, 2012, 1005-12.
[cited by applicant]
Lee, J. H. et al., “Highly Multiplexed Subcellular RNA Sequencing in Situ”, Sciencexpress, online http://www.sciencemag.org/content/early/recent, 6 pages (Science, vol. 343), This May Be the Same as Lee (FIP Ref No. 304…
[cited by applicant]
Lein, E. et al., “Genome-wide atlas of gene expression in the adult mouse brain”, Nature, vol. 445, 2007, 168-76.
[cited by applicant]
Levsky, J. et al., “Fluorescence in situ hybridization: past, present and future”, Journal of Cell Science, 116, 2003, 2833-2838.
[cited by applicant]
Lieberman-Aiden, E. et al., “Comprehensive mapping of long-range interactions reveals folding principles of the human genome”, Science 326, 2009, 289-93.
[cited by applicant]
Livet, J. et al., “Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system”, Nature, 450, 2007, 56-62.
[cited by applicant]
Lowe, D. G. , “Distinctive Image Features from Scale-Invariant Keypoints”, Int. J. Comput. Vis., 60, 2004, 91-110.
[cited by applicant]
Lubeck, E. et al., “Single-cell in situ RNA profiling by sequential hybridization”, Nature Methods, vol. 11(4), 2014, 360-1.
[cited by applicant]
Lubeck, E. et al., “Single-cell systems biology by super-resolution imaging and combinatorial labeling”, Nature Methods, vol. 9, 2012, 743-8.
[cited by applicant]
Majcher, M. J. et al., “Hydrogel synthesis and design”, In: “Cellulose-Based Superabsorbent Hydrogels”, Springer International Publishing, Jan. 1, 2018, 1-41.
[cited by applicant]
Markwardt, M. L. et al., “An improved cerulean fluorescent protein with enhanced brightness and reduced reversible photoswitching”, PLoS One, 6, 2011, e17896.
[cited by applicant]
McKinney, S. A. et al., “A bright and photostable photoconvertible fluorescent protein”, Nat. Methods, 6, 2009, 131-3.
[cited by applicant]
Mito, M. et al., “Simultaneous multicolor detection of RNA and proteins using super-resolution microscopy”, Methods, doi:10.1016/j.ymeth.2015.11.007., 2015.
[cited by applicant]
Mortensen, K. I. et al., “Optimized localization analysis for singlemolecule tracking and super-resolution microscopy”, Nat. Methods, 7, 2010, 377-81.
[cited by applicant]
Nagai, T. et al., “A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications”, Nat. Biotechnol., 20, 2002, 87-90.
[cited by applicant]
Nagre, R. D. et al., “Thermosaline Resistant Acrylamide-Based Polyelectrolyte as Filtration Control Additive in Aqueous-Based Mud”, Petroleum and Coal, vol. 56, No. 3, 2014, 222-230.
[cited by applicant]
Nilsson, M. et al., “RNA-templated DNA ligation for transcript ananlysis”, Nucleic Acids Research, Information Retrieval LTD., vol. 29, No. 2, Jan. 15, 2001, 578-581.
[cited by applicant]
Orakdogen, N. et al., “Correlation Between Crosslinking Efficiency and Spatial Inhomogeneity in Poly(acrylamide) Hydrogels”, Polymer Bulletin, vol. 57, 2006, 631-641.
[cited by applicant]
Ormo, M. et al., “Crystal structure of the Aequorea victoria green fluorescent protein”, Science, 273, 1996, 1392-5.
[cited by applicant]
Oshima, K. et al., “Model Polyelectrolyte Gels Synthesized by End-Linking of Tetra-Arm Polymers with Click Chemistry: Synthesis and Mechanical Properties”, Macromolecules, vol. 47, 2014, 7573-7580.
[cited by applicant]
Panning, B. et al., “X chromosome Inactivation is Mediated by by Xist RNA stabilization”, Cell. vol. 90, 1997, 907-16.
[cited by applicant]
Park, Y. N. et al., “Detection of Hepatitis C Virus RNA Using Ligation-Dependent Polymerase Chain Reaction in Formalin-Fixed, Paraffin-Embedded Liver Tissues”, Amer. J. of Pathol., vol. 149, No. 5, Nov. 1, 1996, 1485-14…
[cited by applicant]
Plath, K. et al., “Xist RNA and the mechanism of X chromosome inactivation”, Annu. Rev. Genet. 36, 2002, 233-78.
[cited by applicant]
Pum, D. et al., “Reassembly of S-Layer Proteins”, Nanotechnology, 2014, 1-15.
[cited by applicant]
Raj, A. et al., “Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes”, Methods in Enzymology, vol. 472 (Elsevier Inc.), 2010, 365-386.
[cited by applicant]
Raj, A. et al., “Imaging individual mRNA molecules using multiple singly labeled probes”, Nat. Methods 5(10), 2008, 877-879.
[cited by applicant]
Randall, K. J. et al., “A dual-label technique for the immunohistochemical demonstration of T-lymphocyte subsets in formalin-fixed, paraffin-embedded rat lymphoid tissue”, Toxicol. Pathol., 36, 2008, 795-804.
[cited by applicant]
Rego, E. H. et al., “Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution”, Proc. Natl. Acad. Sci. U.S.A., 109, 2012, E135-43.
[cited by applicant]
Reinhart-King, C. A. et al., “Dynamics and Mechanics of EndothelialCell Spreading”, Biophysical J, 89(1):, Jul. 1, 2005, 676-689.
[cited by applicant]
Rose, R. et al., “Ocular ascorbate transport and metabolism”, A. Comp. Physiol., 100, 1991, 273-85.
[cited by applicant]
Rothbauer, M. et al., “Exploitation of S-Layer Anisotropy: pH-Dependent Nanolayer Orientation for Cellular Micropatterning,”, Acs NANO, published online, 2013.
[cited by applicant]
Sakai, T. et al., “Design and Fabrication of a High-Strength Hydrogel with Ideally Homogenous Network Structure from Tetrahedron-Like Macromonomers”, Macromolecules, vol. 41, 2008, 5379-5384.
[cited by applicant]
Schindelin, J. et al., “Fiji: an open-source platform for biological-image analysis”, Nature Methods, vol. 9, 2012, 676-82.
[cited by applicant]
Schnell, U. et al., “Immunolabeling artifacts and the need for live-cell imaging”, Nat. Methods, 9, 2012, 152-158.
[cited by applicant]
Seneviratne, U. et al., “S-nitrosation of proteins relevant to Alzheimer's disease during early stages of neurodegeneration”, Proc. Natl. Acad. Sci. U. S. A. 1521318113—(2016). doi:10.1073/pnas.1521318113.
[cited by applicant]
Shah, S. et al., “Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing”, Development In Review, 2016.
[cited by applicant]
Shaner, N. C. et al., “Improved monomeric red, orange and yellow fluorescent proteins derived from
[cited by applicant]
Shaner, N. C. et al., “Improving the photostability of bright monomeric orange and red fluorescent proteins”, Nat. Methods, 5, 2008, 545-51.
[cited by applicant]
Shcherbakova, D. M. , “An orange fluorescent protein with a large Stokes shift for single-excitation multicolor FCCS and FRET imaging”, J. Am. Chem. Soc., 134, 2012, 7913-23.
[cited by applicant]
Shcherbo, D. et al., “Far-red fluorescent tags for protein imaging in living tissues”, Biochem. J., 418, 2009, 567-74.
[cited by applicant]
Sleytr, U. et al., “Heterologous Reattachment of Regular Arrays of Glycoproteins on Bacterial Surfaces”, Nature, vol. 257, 1975, 400-401.
[cited by applicant]
Sleytr, U. et al., “S-Layers Principles and Applications”, FEMS Microbiology Rev., 2014, 1-42.
[cited by applicant]
Sniegowski, J. A. et al., “Maturation efficiency, trypsin sensitivity, and optical properties of Arg96, Glu222, and Gly67 variants of green fluorescent protein”, Biochem. Biophys. Res. Commun., 332, 2005, 657-63.
[cited by applicant]
Steward, O. et al., “Compartmentalized synthesis and degradation of proteins in neurons”, Neuron, vol. 40, 2003, 347-359.
[cited by applicant]
Steward, O. et al., “Synaptic activation causes the mRNA for the leg Arc to localize selectively near activated postsynaptic sites on dendrites”, Neuron, vol. 21, 1998, 741-751.
[cited by applicant]
Strack, R. , “Imaging Bigger is Better for Super-Resolution”, Nature Methods, 12(13), Mar. 1, 2015, 169.
[cited by applicant]
Subach, F. V. et al., “Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells”, J. Am. Chem. Soc., 132, 2010, 6481-91.
[cited by applicant]
Subach, O. M. et al., “An Enhanced Monomeric Blue Fluorescent Protein with the High Chemical Stability of the Chromophore”, PLoS One, 6, 2011, e28674.
[cited by applicant]
Thevenaz, P. et al., “A pyramid approach to subpixel registration based on intensity”. IEEE Trans. Image Process., 7, 1998, 27-41.
[cited by applicant]
Tillberg, P. et al., “Protein-Retention Expansion Microscopy of Cells and Tissues Labeled Using Standard Fluorescent Proteins and Antibodies”, Nature Biotechnology vol. 34(9), 2016, 987-995.
[cited by applicant]
Van Vliet, et al., “The Biomechanics Toolbox: Experimental Approaches for Living Cells and Biomolecules”, Acta Materialia, 51, Aug. 23, 2003, 5881-5905.
[cited by applicant]
Vedaldi, A. et al., Vlfeat. in Proc. Int. Conf. Multimed.—MM '10 1469 (ACM Press, 2010). doi: 10.1145/1873951.1874249.
[cited by applicant]
Wachter, R. M. et al., “Sensitivity of the yellow variant of green fluorescent protein to halides and nitrate”, Curr. Biol., 9, 1999, R628-R629.
[cited by applicant]
Wang, F. et al., “RNAscope: A novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues, Journal of Molecular Diagnostics,” vol. 14(1), 2012, 22-29.
[cited by applicant]
Wu, C. C. et al., “A method for the comprehensive proteomic analysis of membrane proteins”, Nat. Biotechnol., 21, 2003, 532-8.
[cited by applicant]
Xingqi, C. et al., “ATAC-see reveals the accessible genome by transposase-mediated HJ, imaging and sequencing”, Nature Methods, vol. 13, No. 12, Dec. 1, 2016, 1013-1020.
[cited by applicant]
Xu, J. et al., “Bioorthogonally cross-linked hydrogel network with precisely controlled disintegration time over a broad ragne”, J. Am. Chem.Soc., vol. 136, No. 11, Mar. 19, 2014, 4105-4108.
[cited by applicant]
Yazici, I. et al., “Spatial Inhomogeneity in Poly(acrylic acid) Hydrogels”, Polymer, vol. 46, 2005, 2595-2602.
[cited by applicant]
Zhang, D. et al., “Dynamic DNA nanotechnology using strand-displacement reactions”, Nature Chemistry, vol. 3, 2011, 103-113.
[cited by applicant]
Zhang, R. et al., “Tools for GPCR Drug Discovery”, Acta Pharmacologica Sinica, 33, 2012, 372-384.
[cited by applicant]
Zhou, C. et al., “Synthesis and characterization of well-defined PAA-PEG multi-responsive hydrogels by ATRP and click chemistry”, RSC ADV., vol. 4, No. 97, Jan. 1, 2014, 54631-54640.
[cited by applicant]
Zimmerman, T. A. et al., “Adapting the stretched sample method from tissue profiling to imaging”, Proteomics, 8, 2008, 3809-3815.
[cited by applicant]
Boutin, J. A. “Myristoylation.” Cell. Signal, 9(1):15-35. (Jan. 1997) doi:10.1016/S0898-6568(96)00100-3.
[cited by applicant]
Bullock, G. R. “The current status of fixation for electron microscopy: A review.” J. Microsc., 133: 1-15. (1984). doi:10.1111/j. 1365-2818.1984.tb00458.x.
[cited by applicant]
Chen, X. et al. [Supplementary material] “AT AC-see reveals the accessible genome by transposase-mediated imaging and sequencing,” Nature Methods, vol. 13, No. 12, Oct. 17, 2016, 1813-1828.
[cited by applicant]
Cochilla, A. J. et al. “Monitoring secretory membrane with FM1-43 flourescence.” Annu, Rev, Neurosci. 22:1-10 (1999). doi:10.1146/annurev.neuro.22.1.1.
[cited by applicant]
Danilczyk, U. G., et al. “Functional relationship between calreticulin, calnexin, and the endoplasmic reticulum luminal domain of calnexin.” J. Biol. Chem. 275(17): 13089-13097 (2000). doi: 10.1074/jbc.275.17.13089.
[cited by applicant]
Duan, C. et al., “Application of antigen retrieval method in hMAM immunohistochemical staining of old paraffin-embedded specimens,” Academy of Military Medical Sciences, vol. 38(12), Dec. 31, 2014, 965-967.
[cited by applicant]
English, A. R. et al. “Endoplasmic reticulum structure and interconnections with other organelles.” Cold Spring Harbor Perspectives in Biology 2013:5:a013227. doi:10.1101/cshperspect.a013227.
[cited by applicant]
Guo A. et al. “The Critical Role of Surface Chemistry In Protein Microarrays” in Functional Protein Microarrays in Drug Discovery, edt. Paul Predki, p. 53-71 (CRC press, Boca Raton, 2007).
[cited by applicant]
Guo, H. et al. “An efficient procedure for protein extraction from formalin-fixed, Paraffin-embedded tissues for reverse phase protein arrays.” Proteome Sci. 10:56 (2012). doi:10.1186/1477-5956-10-56.
[cited by applicant]
Honig, M. G. et al. “DiI and DiO: versatile fluorescent dyes for neuronal labeling and pathway tracing.” Trends Neurosci. 12(9):333-341 (1989). doi:10.1016/0166-2236(89)90040-4.
[cited by applicant]
Honig, M. G. et al. “Fluorescent carbocyanine dyes allow living neurons of identified origin to be studied in long-term cultures.” J. Cell Biol. 103:171-187 (1986). doi: 10.1083/jcb. 103.1.171.
[cited by applicant]
International Search Report and Written Opinion from the International Searching Authority dated Apr. 28. 2020 from corresponding International Patent Application No. PCT/US2020/018789 Filed on Feb. 19, 2020.
[cited by applicant]
Jamur, M. C. et al. “Permeabilization of Cell Membranes.” in Immunocytochemical Methods and Protocols 588:63-6 (2010). doi:10.1007/978-1-59745-324-0 9.
[cited by applicant]
Ku, T. et al. “Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues.” Nat. Biotechnol. 34(9): 973-981 (2016). doi:10.1038/nbt 3641.
[cited by applicant]
Lakkaraju, A. K. K. et al. “Palmitoylated calnexin is a key component of the ribosome-translocon complex.” EMBO J. 31, 1823-1835 (2012). doi:10.1038/emboj.2012.15.
[cited by applicant]
Linder, M. E. et al. “Palmitoylation: Policing protein stability and traffic.” Nature Reviews Molecular Cell Biology 8:74-84 (2007). doi:10.1038/nr2084.
[cited by applicant]
Mabrey, S. et al. “Investigation of phase transitions of lipids and lipid mixtures by sensitivity differential scanning calorimetry.” Proc. Natl. Acad. Sci. 73(11): 3862-3866 (1976). doi:10.1073/pnas.73.11.3862.
[cited by applicant]
Menon, A. K. “Lipid modifications of proteins.” in 'Biochemistry of Lipids, Lipoproteins and Membranes' 39-58 (2008). doi: 10.1016/8978-044453219-0.50004-0.
[cited by applicant]
Myhill, N. et al. “The subcellular distribution of calnexin is mediated by PACS-2.” Mol, Biol. Cell 19:2777-2788 (2008). doi: 10.1091/mbc.E07-10-0995.
[cited by applicant]
Revelo, N. H. et al. “A new probe for super-resolution imaging of membranes elucidates trafficking pathways.” J. Cell Biol. 205(4):591-606 (2014). doi:10.1083/jcb.201402066.
[cited by applicant]
Sarrazin, S. et al. “Heparan sulfate proteoglycans.” Cold Spring Harb. Perspect. Biol. 2011;3:a004952. doi: 10.1101/cshperspect.a004952.
[cited by applicant]
Scicchitano, M. S., et al. “Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry.” J. Histochem. Cytochem. 57(9): 849-860 (2009). doi:10.1369/jhc.2009.953…
[cited by applicant]
Seifert U. “Configurations of fluid membranes and vesicles.” Adv. Phys. 46(1):13-137 (1997). doi:10.1080/00018739700101488.
[cited by applicant]
Shen, K., et al. “Comparison of different buffers for protein extraction from formalin-fixed and paraffin-embedded tissue specimens.” PLoS One 10(11): e0142650 (2015). doi:10.1371/journal.pone.0142650.
[cited by applicant]
Shi, S. R., et al. “Antigen retrieval in formalin-fixed, paraffin-embedded tissues: An enhancement method for immunohistochemical staining based on microwave oven heating of tissue sections.” J. Histochem. Cytochem. 39 …
[cited by applicant]
Tanca, A. et al. “Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting.” J. Proteomics 77:561-576 (2012). doi:10.1016/j…
[cited by applicant]
Tanca, A. et al. “Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: Insights from liver tissue.” Clin. Proteomics 11:28 (2014). doi:10.1186…
[cited by applicant]
Testagrossa et al. “Immunohistochemical expression of podocyte markers in the variants of focal segmental glomerulosclerosis.” National Dial Transplant 28: 91-98 (2013).
[cited by applicant]
ThermoFisher Scientific, Epitope Recovery Methods for IHC, Nov. 7, 2015, pp. 1-2.
[cited by applicant]
Valenzuela, J. I. et al. “Diversifying the secretory routes in neurons.” Frontiers in Neuroscience 9:358 (2015). doi:10.3389/fnins.2015.00358.
[cited by applicant]
Van Meer, G., et al. “Membrane lipids: Where they are and how they behave.” Nature Reviews Molecular Cell Biology 9(2): 112-124 (2008). doi:10.1038/nrm2330.
[cited by applicant]
Wassie, A. T., et al. “Expansion microscopy: principles and uses in biological research.” Nature Methods 16(1): 33-41 (2019). doi:10.1038/s41592-018-0219-4.
[cited by applicant]
Weber, P. C., et al. “Structural origins of high-affinity biotin binding to streptavidin.” Science 243(4887):85-88 (1989). doi:10.1126/science.2911722.
[cited by applicant]
Wen, G. et al. “Evaluation of direct grafting strategies in Expansion Microscopy.” BioRxiv preprint July 8. 2019. doi: https://doi.org/10.1101/696039 (Jul. 8, 2019).
[cited by applicant]
Wurm, C. A. et al. “Nanoscale distribution of mitochondrial import receptor Tom20 is adjusted to cellular conditions and exhibits an inner-cellular gradient.” Proc. Natl. Acad. Sci. U. S. A. 108(33):13546-13551 (2011). …
[cited by applicant]
Yan, B. X. et al. “Glycine residues provide flexibility for enzyme active sites.” J. Biol. Chem. 272(6): 3190-4 (1997). doi:10.1074/jbc.272.6.3190.
[cited by applicant]
Zhao, Y. et al. “Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy.” Nat. Biotechnol. 35(8): 757-764 (2017). doi:10.1038/nbt.3892.
[cited by applicant]
Zuiderveld, K. “Contrast Limited Adaptive Histogram Equalization.” in Graphics Gems 474-485 (1994). doi:10.1016/b978-0-12-336156-1.50061-6.
[cited by applicant]
Ferri A. (2020). Expansion Microscopy: A New Approach to Microscopic Evaluation. (Master's thesis). Retrieved from https://scholarcommons.sc.edu/etd/6034 (Year: 2020).
[cited by applicant]
Extended European Search Report and search opinion from the European Patent Office dated Oct. 23, 2022 from corresponding International Patent Application PCT/US2020 018789 Filed on Feb. 19, 2020.
[cited by applicant]
Caprette, “Experimental Biosciences: Resources for Introductory & Intermediate level laboratory courses” (2012), available online at https://www.ruf.rice.edu/˜bioslabs/studies/sds-page/denature.html (Year: 2012).
[cited by applicant]
Cho et al., “Expansion Microscopy” (2018), Journal of Microscopy, vol. 271, Issue 2: 123-128. (Year: 2018).
[cited by applicant]
Alon, S. et al. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science 371, 481-+, doi:10.1126/science.aax2656 (2021).
[cited by applicant]
Cahoon, C. K. et al. Superresolution expansion microscopy reveals the three-dimensional organization of the
[cited by applicant]
Campbell, K. R. et al. clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers. Genome Biol 20, 54, doi:10.1186/s13059-019-1645-z (2019).
[cited by applicant]
Chen, G. et al. Reactivity of functional groups on the protein surface: development of epoxide probes for protein labeling. J Am Chem Soc 125, 8130-8133, doi:10.1021/ja034287m (2003).
[cited by applicant]
Cirillo, L. et al. UBAP2L forms distinct cores that act in nucleating stress granules upstream of G3BP1. Curr Biol 30, 698-707 e696, doi:10.1016/j.cub.2019.12.020 (2020).
[cited by applicant]
Cote, A. et al. The spatial distributions of pre-mRNAs suggest post-transcriptional splicing of specific introns within endogenous genes. bioRxiv, doi:10.1101/2020.04.06.028092 (2020).
[cited by applicant]
Cui, Y. et al. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells. Nucleic Acids Res 46, e7, doi:10.1093/nar/gkx874 (201…
[cited by applicant]
Cui, Y. et al. Quantitative mapping of oxidative stress response to lithium cobalt oxide nanoparticles in single cells using multiplexed in situ gene expression analysis. Nano Lett 19, 1990-1997, doi:10.1021/acs.nanolet…
[cited by applicant]
Decarreau, J. et al. Corrigendum: The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat Cell Biol 19, 740, doi:10.1038/ncb3546 (2017).
[cited by applicant]
Decarreau, J. et al. The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat Cell Biol 19, 384-390, doi:10.1038/ncb3486 (2017).
[cited by applicant]
Eirew, P. et al. Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature 518, 422-426, doi:10.1038/nature13952 (2015).
[cited by applicant]
Falahati, H. et al., Thermodynamically driven assemblies and liquid-liquid phase separations in biology. Soft Matter 15, 1135-1154, doi:10.1039/c8sm02285b (2019).
[cited by applicant]
Fecher, C. et al. Cell-type-specific profiling of brain mitochondria reveals functional and molecular diversity. Nat Neurosci 22(10), 1731-1742 doi:10.1038/s41593-019-0479-z (2019).
[cited by applicant]
Gambarotto, D. et al. Imaging cellular ultrastructures using expansion microscopy (U-ExM). Nat Methods 16, 71-74, doi: 10.1038/s41592-018-0238-1 (2019).
[cited by applicant]
Gao, M. et al. Expansion stimulated emission depletion microscopy (ExSTED). ACS Nano 12, 4178-4185, doi:10.1021/acsnano.8b00776 (2018).
[cited by applicant]
Gao, R. et al. A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy. Nat Nanotechnol 16, 698-707, doi: 10.1038/s41565-021-00875-7 (2021).
[cited by applicant]
Gao, R. et al. Cortical col. and whole-brain imaging with molecular contrast and nanoscale resolution. Science 363 (6424), doi:10.1126/science.aau8302 (2019).
[cited by applicant]
Hafner, A. S. et al., Local protein synthesis is a ubiquitous feature of neuronal pre-and postsynaptic compartments. Science 364, doi:10.1126/science.aau3644 (2019).
[cited by applicant]
Halpern, A. R. et al., Hybrid structured illumination expansion microscopy reveals microbial cytoskeleton organization. ACS Nano 11, 12677-12686, doi:10.1021/acsnano.7b07200 (2017).
[cited by applicant]
Hansen, M., Lee, S. J., Cassady, J. M. & Hurley, L. H. Molecular details of the structure of a psorospermin-DNA covalent/intercalation complex and associated DNA sequence selectivity. J Am Chem Soc 118, 5553-5561 (1996).
[cited by applicant]
He, J. et al. Prevalent presence of periodic actin-spectrin-based membrane skeleton in a broad range of neuronal cell types and animal species. Proc Natl Acad Sci U S A 113, 6029-6034, doi:10.1073/pnas.1605707113 (2016).
[cited by applicant]
Invitrogen Corporation, “Proteinase K (solution), RNA Grade”, Cat. No. 25530-049, rev. date: Aug. 25, 2008, 2 pages, accessed from https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.t…
[cited by applicant]
Kao, P. et al., Transcriptional activation of
[cited by applicant]
Karagiannis, E. D. et al. Expansion microscopy of lipid membranes. bioRxiv, 829903, doi:10.1101/829903 (2019).
[cited by applicant]
Keenan et al., “An automated machine vision system for the histological grading of cervical intraepithelial neoplasia (CIN),” Journal of Pathology, J Pathol 2000; 192: pp. 351-362.
[cited by applicant]
Koppers, M. et al. Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons. Elife 8, 1-27 doi:10.7554/eLife.48718 (2019).
[cited by applicant]
Kumar, A. et al. Influenza virus exploits tunneling nanotubes for cell-to-cell spread. Sci Rep 7, 1-14, 40360, doi:10.1038/srep40360 (2017).
[cited by applicant]
Kunz, T. C. et al., Using Expansion Microscopy to Visualize and Characterize the Morphology of Mitochondrial Cristae. Front Cell Dev Biol 8, 617, doi:10.3389/fcell.2020.00617 (2020).
[cited by applicant]
Li, R. et al., Expansion enhanced nanoscopy. Nanoscale 10, 17552-17556, doi:10.1039/c8nr04267e (2018).
[cited by applicant]
Lim, Y. et al. Mechanically resolved imaging of bacteria using expansion microscopy. PLoS Biol 17, e3000268, doi:10.1371/journal.pbio.3000268 (2019).
[cited by applicant]
Martinez, G. F. et al. Quantitative expansion microscopy for the characterization of the spectrin periodic skeleton of axons using fluorescence microscopy. Sci Rep 10, 2917, doi:10.1038/s41598-020-59856-w (2020).
[cited by applicant]
Mosca, T. J. et al., Presynaptic LRP4 promotes synapse number and function of excitatory CNS neurons. Elife 6, doi:10.7554/eLife.27347 (2017).
[cited by applicant]
M'Saad, O. et al., Light microscopy of proteins in their ultrastructural context. Nat Commun 11, 3850, doi:10.1038/s41467-020-17523-8 (2020).
[cited by applicant]
Park, Y. G. et al. Protection of tissue physicochemical properties using polyfunctional crosslinkers. Nat Biotechnol 37, 73-83 , doi:10.1038/nbt.4281 (2019).
[cited by applicant]
Richter, S. et al. Clerocidin alkylates DNA through its epoxide function: evidence for a fine tuned mechanism of action. Nucleic Acids Res 31, 5149-5156, doi:10.1093/nar/gkg696 (2003).
[cited by applicant]
Sahl, S. J. et al., Fluorescence nanoscopy in cell biology. Nat Rev Mol Cell Biol 18(11), 685-701, doi:10.1038/nrm.2017.71 (2017).
[cited by applicant]
Sarkar, D. et al. Expansion revealing: decrowding proteins to unmask invisible brain nanostructures. bioRxiv, doi:10.1101/2020.08.29.273540 (2020).
[cited by applicant]
Shen, F. Y. et al. Light microscopy based approach for mapping connectivity with molecular specificity. Nat Commun 11, 4632, doi:10.1038/s41467-020-18422-8 (2020).
[cited by applicant]
Shurer, C. R. et al. Physical principles of membrane shape regulation by the glycocalyx. Cell 177, 1757-1770 e1721, doi:10.1016/j.cell.2019.04.017 (2019).
[cited by applicant]
Sidenstein, S. C. et al. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. Sci Rep 6, 26725, doi:10.1038/srep26725 (2016).
[cited by applicant]
So, C. et al. A liquid-like spindle domain promotes acentrosomal spindle assembly in mammalian oocytes. Science 364, doi:10.1126/science.aat9557 (2019).
[cited by applicant]
Suofu, Y. et al. Dual role of mitochondria in producing melatonin and driving GPCR signaling to block cytochrome c release. Proc Natl Acad Sci U S A 114, E7997-E8006, doi:10.1073/pnas.1705768114 (2017).
[cited by applicant]
Thevathasan, J. V. et al. Nuclear pores as versatile reference standards for quantitative superresolution microscopy. Nat Methods 16, 1045-1053, doi:10.1038/s41592-019-0574-9 (2019).
[cited by applicant]
Tillberg, P. W. et al. Expansion microscopy: scalable and convenient super-resolution microscopy. Annu Rev Cell Dev Biol 35, 683-701, doi:10.1146/annurev-cellbio-100818-125320 (2019).
[cited by applicant]
Truckenbrodt et al., A practical guide to optimization in X10 expansion microscopy. Nat Protoc 14, 832-863, doi:10.1038/s41596-018-0117-3 (2019).
[cited by applicant]
Valdes, P. A. et al. Decrowding expansion pathology: unmasking previously invisible nanostructures and cells in intact human brain pathology specimens. bioRxiv, doi:10.1101/2021.12.05.471271 (2021).
[cited by applicant]
Wang, G. et al., Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. Sci Rep 8(4847), 1-13 doi:10.1038/s41598-018-22297-7 (2018).
[cited by applicant]
Wang, Y. et al. EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization. Cell 184, 6361-6377 e6324, doi:10.1016/j.cell.2021.11.024 (2021).
[cited by applicant]
Xu, H. et al. Molecular organization of mammalian meiotic chromosome axis revealed by expansion STORM microscopy. Proc Natl Acad Sci U S A 116, 18423-18428, doi:10.1073/pnas.1902440116 (2019).
[cited by applicant]
Xu, K. et al., Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science 339, 452-456, doi:10.1126/science.1232251 (2013).
[cited by applicant]
Abcam, “IHC-Paraffin Protocol (IHC-P)”, 13 pages, published: Jun. 15, 1999, online webpage: www.abcam.com/ps/pdf/protocols/ihc_p.pdf. (Year: 1999).
[cited by applicant]
Abbasi et al., Palmitic Acid-Modified Poly-L-Lysine for Non-Viral Delivery of Plasmid DNA to Skin Fibroblasts, 2007, Biomacromolecules 2007, 8, 1059-1063 (Year: 2007).
[cited by applicant]
Ahearn et al., Posttranslational Modifications of RAS Proteins, Cold Spring Harb Perspect Med 2018;8:a031484 (Year: 2018).
[cited by applicant]
Bensimon, A. et al., “Alignment and Sensitive Detection of DNA by a Moving Interface.” Alignment and Sensitive Detection of DNA by a Moving Interface.
[cited by applicant]
Cheeseman, Kevin, et al. “A Diagnostic Genetic Test for the Physical Mapping of Germline Rearrangements of the Susceptibility Breast Cancer Genes BRCA1 and BRCA2.” Human Mutation, vol. 33, No. 6, 998-1009, 2012.
[cited by applicant]
Diggle Ma et al., A novel method for preparing single-stranded DNA for pyrosequencing, 2003, Molecular Biotechnology, 24(2) :221-224.
[cited by applicant]
Dong, Huimin et al. “Preparation of photodeformable azobenzene polymer fibers by post-crosslinking strategy: Understanding the structure-property relationship”, European Polymer Journal, Pergamon Pressltd Oxford, GB, vo…
[cited by applicant]
Gad, Sophie, et al. “Identification of a large rearrangement of the BRCA1 gene using colour bar code on combed DNA in an American breast/ovarian cancer family previously studied by direct sequencing.” F. Med Genet 2001,…
[cited by applicant]
Guan et al., Understanding Protein Palmitoylation: Biological Significance and Enzymology, 2011, Sci China Chem. Dec. 2011; 54( 12): 1888-1897 (Year: 2011).
[cited by applicant]
Hamano et al., ϵ-Poly-L-Lysine Peptide Chain Length Regulated by the Linkers Connecting the Transmembrane Domains of £-Poly-L-Lysine Synthetase, Aug. 2014, Applied and Environmental Microbiology, vol. 80 Number 16, p. 4…
[cited by applicant]
Hodson, Robert E et al. “In Situ PCR for Visualization of Microscale Distribution of Specific Genes and Gene Products in Prokaryotic Communities.” Applied and Environmental Microbiology, Nov. 1995, p. 4074-4082.
[cited by applicant]
Jain, Miten et al. “Nanopore sequencing and assembly of a human genome with ultra-long reads.” Nature Biotechnology, vol. 36, No. 4, Apr. 2018.
[cited by applicant]
Kaykov, A., et al. “Molecular Combing of Single DNA Molecules on the 10 Megabase Scale.” Sci. Rep. 6, 19636, 2016, p. 1-9.
[cited by applicant]
Kleuss et al., Galphas is palmitoylated at the N-terminal glycine, The EMBO Journal vol. 22 No. 4 pp. 826-832, 2003 (Year: 2003).
[cited by applicant]
Kondo, N. et al. “DNA Damage Induced by Alkylating Agents and Repair Pathways.” Journal of Nucleic Acids, vol. 2010, Article ID 543531, 7 pages.
[cited by applicant]
Larsson, Chatarina et al. “In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes.” Nature Methods, vol. 1, No. 3, Dec. 2004.
[cited by applicant]
Lunzer, Markus et al. “A Modular Approach to Sensitized Two-Photon Patterning of Photodegradable Hydrogels”, Angewandte Chemie, Wiley—V CH Verlaggmbh & Co. KGAA, DE, vol. 130, No. 46, (Oct. 18, 2018), pp. 15342-15347, X…
[cited by applicant]
Marie, R., et al. “Concentrating and labeling genomic DNA in a nanofluidic array.” Nanoscale. 10 (2018), pp. 1376-1382.
[cited by applicant]
Maxam, A. M., and Gilbert W., “A new method for sequencing DNA.” Proc. Natl. Acad. Sci. U.S.A., 74, 560-564, 1977.
[cited by applicant]
Nyren, Pal, et al. “Solid Phase DNA Minisequencing by an Enzymatic Luminometric Inorganic Pyrophosphate Detection Assay.” Analytical Biochemistry 208, 171-175 (1993).
[cited by applicant]
Rapp, Teresa L. et al. “Visible Light-Responsive Dynamic Biomaterials: Going Deeper and Triggering More”, Advanced Healthcare Materials, Wiley—V CH Verlag GmbH & Co. KGAA, DE, vol. 9, No. 7, Feb. 25, 2020, page n/a, XP0…
[cited by applicant]
Salaun et al., The intracellular dynamic of protein palmitoylation, 2010, J. Cell Biol. Vol. 191 No. 7 1229-1238 (Year: 2010).
[cited by applicant]
Schirmer, M., et al. “Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.” Nucleic Acids Research, vol. 43, Issue 6, Mar. 31, 2015, e37, pp. 1-16.
[cited by applicant]
Schonhuber, Wilhelm, et al. “Improved Sensitivity of Whole-Cell Hybridization by the Combination of Horseradish Peroxidase-Labeled Oligonucleotides and Tyramide Signal Amplification.” Applied and Environmental Microbiol…
[cited by applicant]
Shendure, J., et al. “DNA sequencing at 40: past, present, and future.” Nature 2017, Oct. 19;550(7676): 345-353.
[cited by applicant]
Sikdar, Partha et al. “Recent advances in the synthesis of smart hydrogels”, Materials Advances, vol. 2, No. 14, Jan. 1, 2021, pp. 4532-4573, XP093067739,DOI: 10.1039/D1MA00193K.
[cited by applicant]
Singh, Anirudha et al. “Photomodulation of Cellular Gene Expression in Hydrogels”, ACS Macro Letters, vol. 2, No. 3, (Mar. 8, 2013), pp. 269-272, XP093109803, ISSN: 2161-1653, DOI: 10.1021/mz30059lm.
[cited by applicant]
Stankova, Helena, et al. “BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.” Plant Biotechnology Journal (2016) 14, pp. 1523-1531 doi: 10.1111/pbi…
[cited by applicant]
Strick, T., et al. “Twisting and stretching single DNA molecules.” Progress in Biophysics & Molecular Biology 74 (2000) 115-140.
[cited by applicant]
Ueda H.R., et al. “Tissue clearing and its applications in neuroscience.” Nature Reviews, Neuroscience, vol. 21, Feb. 2020.
[cited by applicant]
Varapula et al., A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules, 2019, Scientific Reports, 9, 15059.
[cited by applicant]
Wages JM, Polymerase Chain Reaction, 2005, Encyclopedia of Analytical Science, (2): 243-250.
[cited by applicant]
Wang, X., et al., “Characterization of denaturation and renaturation of DNA for DNA hybridization.” Environ. Health Toxicol, 29, e2014007, 2014.
[cited by applicant]
Wen et al., Specific antibody immobilization with biotin-poly(L-lysine)-g-poly(ethylene glycol) and protein A on microfluidic chips, Journal of Immunological Methods 350 (2009) 97-105 (Year: 2009).
[cited by applicant]