2024
Reliable detection of stochastic epigenetic mutations and associations with cardiovascular aging
Markov Y, Levine M, Higgins-Chen A. Reliable detection of stochastic epigenetic mutations and associations with cardiovascular aging. GeroScience 2024, 46: 5745-5765. PMID: 38736015, PMCID: PMC11493905, DOI: 10.1007/s11357-024-01191-3.Peer-Reviewed Original ResearchStochastic epigenetic mutationsAge-related DNA methylation changesEpigenetic mutationsBlood cell type compositionDNA methylation changesCell type compositionUnmethylated probesPresence of SNPsGenomic locationsMethylation patternsMethylation changesDinucleotide sitesMethylation probesTechnical noiseBlood cell compositionTechnical replicate dataR packageAging phenotypesFramingham Heart StudyMutationsCell compositionAging biomarkersSNPsType compositionProbe
2023
Membrane Tubulation with a Biomembrane Force Probe
Pincet L, Pincet F. Membrane Tubulation with a Biomembrane Force Probe. Membranes 2023, 13: 910. PMID: 38132914, PMCID: PMC10744658, DOI: 10.3390/membranes13120910.Peer-Reviewed Original ResearchBiomembrane force probeOptical tweezersForce probeTweezersGiant unilamellar vesiclesMeasurement of forcesExperimental setupMicromanipulation techniqueUnilamellar vesiclesProbeSimilar tubesMaterial transportLocal geometryHigh curvatureMicromanipulationMolecular interactionsGUVsSetupEnergeticsInteractionMeasurementsFormationTubeNanospringsRecent advances in organelle-specific two-photon small-molecule fluorescent probes for bioanalysis in live tissues
Lee H, Juvekar V, Lee D, Kim H. Recent advances in organelle-specific two-photon small-molecule fluorescent probes for bioanalysis in live tissues. TrAC Trends In Analytical Chemistry 2023, 165: 117128. DOI: 10.1016/j.trac.2023.117128.Peer-Reviewed Original ResearchOrganelle dynamicsEndoplasmic reticulumCellular organellesPlasma membraneTwo-photon probeOrganellesLipid dropletsSmall-molecule fluorescent probesBiological eventsNear-infrared photonsFluorescent probeTwo-photon microscopyExcitation sourceHigh-resolution imagesGolgiLiving samplesMitochondriaReticulumLysosomesProbeLiving tissuesPhoto-physical propertiesPhotons
2022
Two-photon fluorescent probes for quantitative bio-imaging analysis in live tissues
Juvekar V, Lee H, Lee D, Kim H. Two-photon fluorescent probes for quantitative bio-imaging analysis in live tissues. TrAC Trends In Analytical Chemistry 2022, 157: 116787. DOI: 10.1016/j.trac.2022.116787.Peer-Reviewed Original ResearchFluorescent probeTwo-photon fluorescent probeDeep tissue imagingNeutral moleculesLow-energy lightTP fluorescent probesExcitation sourceHigh-resolution fluorescence imagingBio-thiolsTarget analytesMetal ionsEnergy lightReactive speciesMillimeter depthLight scatteringNear-infrared windowLiving systemsScatteringDesign strategyProbe design strategyExcitationTP probesAnalytesProbeBio-imaging analysisSnowmass2021 theory frontier white paper: Astrophysical and cosmological probes of dark matter
Boddy K, Lisanti M, McDermott S, Rodd N, Weniger C, Ali-Haïmoud Y, Buschmann M, Cholis I, Croon D, Erickcek A, Gluscevic V, Leane R, Mishra-Sharma S, Muñoz J, Nadler E, Natarajan P, Price-Whelan A, Vegetti S, Witte S. Snowmass2021 theory frontier white paper: Astrophysical and cosmological probes of dark matter. Journal Of High Energy Astrophysics 2022, 35: 112-138. DOI: 10.1016/j.jheap.2022.06.005.Peer-Reviewed Original ResearchDark matterCosmological probesDark matter discoveryEffective field theoryEarly universeNew observablesCosmological domainField theoryStatistical inferenceSignificant open questionsConsistent pictureTheoretical techniquesGeneral propertiesTheoretical challengesGalaxiesAstrophysicsFundamental natureStarsTheoretical foundationUniversePhysicsObservablesProbeMatterOpen questionFluorogenic DNA-PAINT for faster, low-background super-resolution imaging
Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J. Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Nature Methods 2022, 19: 554-559. PMID: 35501386, PMCID: PMC9133131, DOI: 10.1038/s41592-022-01464-9.Peer-Reviewed Original ResearchConceptsSlow imaging speedSuper-resolution imagingSuper-resolution microscopy methodsDNA-PAINTOptical sectioningImaging speedFast imagingNanometer resolutionDNA-based points accumulationHigh-fidelity imagesUnbound fluorophoresMicroscopy methodsDocking strandsHigh backgroundPoint accumulationNanoscale topographyProbeMultimodal imaging of synaptic vesicles with a single probe
An SJ, Stagi M, Gould TJ, Wu Y, Mlodzianoski M, Rivera-Molina F, Toomre D, Strittmatter SM, De Camilli P, Bewersdorf J, Zenisek D. Multimodal imaging of synaptic vesicles with a single probe. Cell Reports Methods 2022, 2: 100199. PMID: 35497490, PMCID: PMC9046237, DOI: 10.1016/j.crmeth.2022.100199.Peer-Reviewed Original ResearchConceptsC2 domainSynaptic vesiclesSynaptic vesicle recyclingMembrane-binding C2 domainMultiple microscopy methodsEndocytic markersMembrane recyclingVesicle functionVesicle populationsCytosolic phospholipase ACell typesPhospholipase ADetectable tagMicroscopy modalitiesModular probesMultiple microscopy techniquesVesiclesComplete understandingDomainMicroscopy methodsMultiple levelsProbeAvailable probesMicroscopy techniquesPathway
2021
Highly Stable Red-Emissive Ratiometric Probe for Monitoring β‑Galactosidase Activity Using Fluorescence Microscopy and Flow Cytometry
Lee H, Juvekar V, Lee D, Kim S, Kim H. Highly Stable Red-Emissive Ratiometric Probe for Monitoring β‑Galactosidase Activity Using Fluorescence Microscopy and Flow Cytometry. Analytical Chemistry 2021, 93: 14778-14783. PMID: 34705435, DOI: 10.1021/acs.analchem.1c03453.Peer-Reviewed Original ResearchConceptsCell sorting flow cytometryB-galactosidase activitySorting flow cytometryReporter enzymeFluorescence-activated cell sorting flow cytometryB-galFlow cytometryLiving cellsEnzyme activityB-galactosidaseFluorescence microscopyEnzymeRatiometric imagingOvarian cancerRatiometric probeFluorescent probeMinimal cytotoxicityEmission color changeCytometryProbeMulti-frequency impedance sensing for detection and sizing of DNA fragments
Sui J, Gandotra N, Xie P, Lin Z, Scharfe C, Javanmard M. Multi-frequency impedance sensing for detection and sizing of DNA fragments. Scientific Reports 2021, 11: 6490. PMID: 33753781, PMCID: PMC7985362, DOI: 10.1038/s41598-021-85755-9.Peer-Reviewed Original ResearchConceptsTarget molecule bindsComplex biological samplesElectronic biosensorsNon-target materialsProbe selectivityAnalytical performanceMolecules bindBiological samplesReaction productsDifferent lengthsDNA moleculesDNA detectionMicrofluidic chipNonspecific bindingFmolElectronic signalsParamagnetic beadsImpedance sensorBeadsBiosensorDNA concentrationDNA fragmentsSelectivityProbePolymerase chain reaction productsRecent progress in the two-photon fluorescent probes for metal ions
Juvekar V, Park S, Yoon J, Kim H. Recent progress in the two-photon fluorescent probes for metal ions. Coordination Chemistry Reviews 2021, 427: 213574. DOI: 10.1016/j.ccr.2020.213574.Peer-Reviewed Original ResearchTwo-photon probeTwo-photon fluorescent probeMetal ionsTwo-photon microscopyIon species distributionDetect metal ionsFluorescent probeAlkali earth metalsTransition metalsEarth metalsMinimal light scatteringIron ionsReduced phototoxicityIonsLight scatteringMetalDeep visualizationDesign strategyScatteringProbeTarget specimen
2020
ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization
Hu M, Yang B, Cheng Y, Radda JSD, Chen Y, Liu M, Wang S. ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. Scientific Reports 2020, 10: 22031. PMID: 33328483, PMCID: PMC7745008, DOI: 10.1038/s41598-020-76439-x.Peer-Reviewed Original ResearchConceptsSingle-molecule RNA FISHSpecific genomic lociSitu hybridizationNucleome architecturesRNA FISHGenomic lociRNA speciesMultiplexed fluorescenceFISH techniqueFishRecent technological advancesMultiplexed imagingHybridizationMultiplexed mannerLociSpeciesFluorescencePowerful methodNotable exampleProbeProbe designTechnological advancesGravitational wave probes of dark matter: challenges and opportunities
Bertone G, Croon D, Amin M, Boddy K, Kavanagh B, Mack K, Natarajan P, Opferkuch T, Schutz K, Takhistov V, Weniger C, Yu T. Gravitational wave probes of dark matter: challenges and opportunities. SciPost Physics Core 2020, 3: 007. DOI: 10.21468/scipostphyscore.3.2.007.Peer-Reviewed Original ResearchGravitational wave probes of dark matter: challenges and opportunities
Bertone G, Croon D, Amin M, Boddy K, Kavanagh B, Mack K, Natarajan P, Opferkuch T, Schutz K, Takhistov V, Weniger C, Yu T. Gravitational wave probes of dark matter: challenges and opportunities. 2020 DOI: 10.21468/scipost.report.1975.Peer-Reviewed Original ResearchNext generation miRNA inhibition using short anti-seed PNAs encapsulated in PLGA nanoparticles
Malik S, Lim J, Slack FJ, Braddock DT, Bahal R. Next generation miRNA inhibition using short anti-seed PNAs encapsulated in PLGA nanoparticles. Journal Of Controlled Release 2020, 327: 406-419. PMID: 32835710, PMCID: PMC7606596, DOI: 10.1016/j.jconrel.2020.08.026.Peer-Reviewed Original ResearchConceptsShort PNA probesPNA probesPLGA nanoparticlesRelease profileNanoparticle formulationNanoparticlesSuperior loadingEfficient transfection efficiencyCationic domainsPotential cancer therapySystemic deliveryTarget proteinsSize distributionProbeTransfection efficiencyMiRNA-155New avenuesPNAUniform distributionProof of conceptCancer therapeuticsCancer therapyReagentsChronic toxicityMicroscopyFluorescent stem peptide mimics: In situ probes for peptidoglycan crosslinking
Gautam S, Kim T, Howell R, Spiegel DA. Fluorescent stem peptide mimics: In situ probes for peptidoglycan crosslinking. Methods In Enzymology 2020, 638: 57-67. PMID: 32416921, DOI: 10.1016/bs.mie.2020.02.016.Peer-Reviewed Case Reports and Technical NotesConceptsBacterial cell wall synthesisSynthetic probesPeptide mimicsPeptidoglycan crosslinkingSynthesisSitu probeKey stepCrosslinkingNumerous classesMechanical strengthNew antibioticsProbeCell wall synthesisPeptidoglycan synthesisSuper-resolution microscopyLive bacteriaWall synthesisReactionCell wallDetailed protocolMicroscopyStaphylococcus aureusHuman pathogens
2019
Wavelength-encoded laser particles for massively multiplexed cell tagging
Martino N, Kwok S, Liapis A, Forward S, Jang H, Kim H, Wu S, Wu J, Dannenberg P, Jang S, Lee Y, Yun S. Wavelength-encoded laser particles for massively multiplexed cell tagging. Nature Photonics 2019, 13: 720-727. PMID: 32231707, PMCID: PMC7104740, DOI: 10.1038/s41566-019-0489-0.Peer-Reviewed Original ResearchLaser particleSingle-mode emissionCoherent laser lightCell taggingSemiconductor microcavitiesLaser lightLarge-scale single-cell analysisSpectral multiplexingOptical imagingSpectral crosstalkConventional fluorophoresWavelengthCharacteristic wavelengthFluorescence-based approachParticlesMicrocavitiesLinewidthProbeBiological systemsEmissionReal-time trackingComplex biological systemsMultiplexingLightFluorophoresFunctionalised iron oxide nanoparticles for multimodal optoacoustic and magnetic resonance imaging
Bell G, Balasundaram G, Attia A, Mandino F, Olivo M, Parkin I. Functionalised iron oxide nanoparticles for multimodal optoacoustic and magnetic resonance imaging. Journal Of Materials Chemistry B 2019, 7: 2212-2219. PMID: 32073580, DOI: 10.1039/c8tb02299b.Peer-Reviewed Original ResearchConceptsIron oxide nanoparticlesIron oxide coreOxide nanoparticlesOxide coreFacile synthesisRelaxivity coefficientCoordination chemistryNear-IR wavelengthsDye modificationDye attachmentNanoparticlesMultispectral optoacoustic tomography (MSOT) imagingOA analysisMRI contrastEndogenous contrastIR wavelengthsFlammaSynthesisWavelengthLiterature valuesOptoacousticsChemistryDyeProbeMultimodal characteristics
2018
Activity-Based Protein Profiling at the Host–Pathogen Interface
Kovalyova Y, Hatzios SK. Activity-Based Protein Profiling at the Host–Pathogen Interface. Current Topics In Microbiology And Immunology 2018, 420: 73-91. PMID: 30203396, DOI: 10.1007/82_2018_129.BooksConceptsActivity-based protein profilingHost-pathogen interfaceProtein profilingFunctional proteomePathogen interactionsMicrobial pathogenicityComplex proteomesEnzyme-mediated mechanismReactive amino acidsActive enzymeChemical probesAmino acidsMetabolic adaptationProteomeMicrobial infectionsCo-culture systemBiological systemsHost immunityEnzymeProfilingPathogenicityHostProbeAnimal modelsAdaptation
2017
HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution
Thompson AD, Bewersdorf J, Toomre D, Schepartz A. HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution. Biochemistry 2017, 56: 5194-5201. PMID: 28792749, PMCID: PMC5854879, DOI: 10.1021/acs.biochem.7b00545.Peer-Reviewed Original ResearchConceptsLive cellsOrganelle dynamicsDiscrete organellesMultiple organellesLive-cell nanoscopyPlasma membraneDiverse processesEndoplasmic reticulumDynamic assemblyLiving cellsDynamic reorganizationOrganellesSingle-molecule switchingMembrane probeCellsMembraneMitochondriaReticulumRegulationHigh densityProbeAssemblyNew toolkitLong time periodsDivisionMiniature spectral imaging device for wide-field quantitative functional imaging of the morphological landscape of breast tumor margins
Nichols B, Llopis A, Palmer G, McCachren S, Senlik O, Miller D, Brooke M, Jokerst N, Geradts J, Greenup R, Ramanujam N. Miniature spectral imaging device for wide-field quantitative functional imaging of the morphological landscape of breast tumor margins. Journal Of Biomedical Optics 2017, 22: 026007-026007. PMID: 28241273, PMCID: PMC5321165, DOI: 10.1117/1.jbo.22.2.026007.Peer-Reviewed Original ResearchConceptsBreast tumor marginsDiffuse optical spectroscopyVisible spectral rangeSpectral imaging deviceDiffuse reflectance spectraOptical spectroscopySpectral rangeImaging arrayMorphological landscapeRaster scanningOptical surrogatesImaging devicesQuantitative functional imagingReflectance spectraImaging platformImaging probeMonte CarloCompressive sensingInverse modelContent ratioWavelengthProbeFunctional imagingSpectroscopySpectra
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