2025
Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms
Dai J, Ouyang Y, Gupte R, Liu X, Li Y, Yang F, Chen S, Provin T, Van Schaik E, Samuel J, Jayaraman A, Zhou A, de Figueiredo P, Zhou J, Han A. Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms. Applied And Environmental Microbiology 2025, 91: e01794-24. PMID: 39936906, PMCID: PMC11921321, DOI: 10.1128/aem.01794-24.Peer-Reviewed Original ResearchConceptsSoil microorganismsSoil extractsSoil metabolitesMicroorganism diversityDiversity of soil microorganismsMicroorganism communitiesDownstream functional analysisSoil microorganism communitiesFunctional analysisMicrofluidic dropletsUnique generaUncultured microorganismsDiverse microorganismsNatural habitatsSoilIndividual isolatesCultivation conditionsClonal growthEnvironmental microorganismsHigh-throughput phenotypingBioremediationCulture media formulationsMicroorganismsCultivation methodsMedium formulation
2023
Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery
Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler A, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. Cell Reports Methods 2023, 3: 100511. PMID: 37426761, PMCID: PMC10326451, DOI: 10.1016/j.crmeth.2023.100511.Commentaries, Editorials and LettersMeSH KeywordsAntigens, NeoplasmHistocompatibility Antigens Class IHLA AntigensHumansMass SpectrometryMicrofluidicsNeoplasmsConceptsSingle-cell proteomicsMicrofluidic technologyPotential of microfluidicsMass spectrometrySample preparationDroplet microfluidicsDigital microfluidicsMicrofluidic methodPhysical moleculesMicrofluidicsHigh sensitivityReproducible mannerPillar arraysRecent advancesSpectrometryMoleculesImmunopeptidomicsPowerful toolProteomicsPreparationMSPeptidesSolutionMicrofluidic Immuno‐Serolomic Assay Reveals Systems Level Association with COVID‐19 Pathology and Vaccine Protection
Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan J, Buitrago‐Pocasangre N, Lele N, Asashima H, Racke M, Wilson J, Givens T, Tomayko M, Schulz W, Longbrake E, Hafler D, Halene S, Fan R. Microfluidic Immuno‐Serolomic Assay Reveals Systems Level Association with COVID‐19 Pathology and Vaccine Protection. Small Methods 2023, 7: e2300594. PMID: 37312418, PMCID: PMC10592458, DOI: 10.1002/smtd.202300594.Peer-Reviewed Original ResearchConceptsB cell depletion therapyAcute COVID infectionAnti-spike IgGHigh-risk patientsCoronavirus disease-19COVID-19 pathologyDepletion therapyVaccine protectionAntibody responseCOVID infectionHematologic malignanciesImmune protectionDisease-19Healthy donorsMultiple time pointsSerology assaysBlood samplesSoluble markersB cellsImmunization strategiesPatientsFunctional deficiencySerological analysisTime pointsClonotype diversityNucleic Acid Quantification by Multi-Frequency Impedance Cytometry and Machine Learning
Kokabi M, Sui J, Gandotra N, Khamseh A, Scharfe C, Javanmard M. Nucleic Acid Quantification by Multi-Frequency Impedance Cytometry and Machine Learning. Biosensors 2023, 13: 316. PMID: 36979528, PMCID: PMC10046493, DOI: 10.3390/bios13030316.Peer-Reviewed Original Research
2022
Development of an Open Microfluidic Platform for Oocyte One-Stop Vitrification with Cryotop Method
Miao S, Guo C, Jiang Z, Wei H, Jiang X, Gu J, Hai Z, Wang T, Liu Y. Development of an Open Microfluidic Platform for Oocyte One-Stop Vitrification with Cryotop Method. Biosensors 2022, 12: 766. PMID: 36140151, PMCID: PMC9496857, DOI: 10.3390/bios12090766.Peer-Reviewed Original ResearchConceptsCryotop methodMitochondrial membrane potentialMicrofluidic systemReactive oxygen speciesLevels of oocytesEffect of vitrificationCryoprotective agentsOocyte vitrificationRisk of cell lossOpen microfluidic systemTreated oocytesFertility preservationCell transferCryotopReproductive centerCell lossSurvival rateOpen microfluidic chipOocytesAssisted reproductionSufficient cooling rateMembrane potentialProcessing chipOpen microfluidic platformAutomatic microfluidic system
2021
Multi-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 ResearchMeSH KeywordsBiosensing TechniquesElectric ImpedanceFlow CytometryMicrofluidicsOligodeoxyribonucleotidesConceptsTarget molecule bindsComplex biological samplesElectronic biosensorsNon-target materialsProbe selectivityAnalytical performanceMolecules bindBiological samplesReaction productsDifferent lengthsDNA moleculesDNA detectionMicrofluidic chipNonspecific bindingFmolElectronic signalsParamagnetic beadsImpedance sensorBeadsBiosensorDNA concentrationDNA fragmentsSelectivityProbePolymerase chain reaction products
2020
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 2020, 183: 1665-1681.e18. PMID: 33188776, PMCID: PMC7736559, DOI: 10.1016/j.cell.2020.10.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutomationBrainCluster AnalysisDNA Barcoding, TaxonomicDNA, ComplementaryEmbryo, MammalianEyeFemaleGene Expression Regulation, DevelopmentalGenomicsHuman Umbilical Vein Endothelial CellsHumansMice, Inbred C57BLMicrofluidicsOrgan SpecificityReproducibility of ResultsRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsDeterministic barcodingNext-generation sequencingSingle-cell transcriptomesGene expression profilesMajor tissue typesDBiT-seqDNA barcodesDevelopmental biologyExpression profilesEarly organogenesisCancer biologyCell typesBarcodingTissue typesSequencingBarcodesBiologyRapid identificationSets of barcodesTranscriptomeParallel microfluidic channelsOrganogenesisEmbryosProteinTissue pixelsForce and phosphate release from Arp2/3 complex promote dissociation of actin filament branches
Pandit NG, Cao W, Bibeau J, Johnson-Chavarria EM, Taylor EW, Pollard TD, De La Cruz EM. Force and phosphate release from Arp2/3 complex promote dissociation of actin filament branches. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 13519-13528. PMID: 32461373, PMCID: PMC7306818, DOI: 10.1073/pnas.1911183117.Peer-Reviewed Original ResearchConceptsActin filament branchesArp2/3 complexMother filamentFilament branchesTotal internal reflection fluorescence microscopyEssential cellular functionsMechanical forcesActin filament networkReflection fluorescence microscopyCellular functionsActin networkCell motilityComplex generatesActin filamentsArp2/3Filament networkFluorescence microscopyState 1Branch junctionsState 2FilamentsComplexesPhosphate releaseMuscle actinADPAn Integrated Dielectrophoresis-Trapping and Nanowell Transfer Approach to Enable Double-Sub-Poisson Single-Cell RNA Sequencing
Bai Z, Deng Y, Kim D, Chen Z, Xiao Y, Fan R. An Integrated Dielectrophoresis-Trapping and Nanowell Transfer Approach to Enable Double-Sub-Poisson Single-Cell RNA Sequencing. ACS Nano 2020, 14: 7412-7424. PMID: 32437127, DOI: 10.1021/acsnano.0c02953.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsHigh-Throughput Nucleotide SequencingMiceMicrofluidicsSequence Analysis, RNASingle-Cell AnalysisConceptsBead loadingLoading rateLoadingTransfer efficiencyHigh-yield loadingCell trappingNanowell arraysVersatile designSubsequent encapsulationDevicesMicrowell arrayTransfer approachCurrent technologyFundamental limitationsBeadsActive manipulationSingle cellsWellsArrayDielectrophoresisMicrofluidicsStochastic pairing
2019
Highly Reproducible Physiological Asymmetric Membrane with Freely Diffusing Embedded Proteins in a 3D‐Printed Microfluidic Setup
Heo P, Ramakrishnan S, Coleman J, Rothman JE, Fleury J, Pincet F. Highly Reproducible Physiological Asymmetric Membrane with Freely Diffusing Embedded Proteins in a 3D‐Printed Microfluidic Setup. Small 2019, 15: e1900725. PMID: 30977975, DOI: 10.1002/smll.201900725.Peer-Reviewed Original ResearchMeSH KeywordsDimethylpolysiloxanesFluorescence Recovery After PhotobleachingLipid BilayersMicrofluidicsPrinting, Three-DimensionalConceptsMost biological processesLipid leafletAreas of biologyEmbedded proteinsBiological processesRelevant lipidsProteinAsymmetric bilayersPhysiological conditionsModel membranesPlanar bilayersBilayer formation processInvaluable insightsBilayersConfocal microscopeMembraneLipidsTransmembraneBiologyLeafletsMicrofluidic setupRecapitulationMicrofluidic platform enables live-cell imaging of signaling and transcription combined with multiplexed secretion measurements in the same single cells
Ramji R, Alexander AF, Muñoz-Rojas AR, Kellman LN, Miller-Jensen K. Microfluidic platform enables live-cell imaging of signaling and transcription combined with multiplexed secretion measurements in the same single cells. Integrative Biology 2019, 11: 142-153. PMID: 31242304, PMCID: PMC8672722, DOI: 10.1093/intbio/zyz013.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodiesCell CommunicationChemokine CCL2Chemokine CCL3Chemokine CCL5Equipment DesignLab-On-A-Chip DevicesLipopolysaccharidesMacrophagesMiceMice, Inbred C57BLMicrofluidicsRAW 264.7 CellsSignal TransductionTranscription Factor RelATranscription, GeneticTumor Necrosis Factor-alphaConceptsLive-cell imagingCell variabilitySame single cellSingle-cell assaysTranscription dynamicsBacterial component lipopolysaccharideDownstream responsesPathogenic assaultFluorescent reportersProtein secretionSingle cellsCell processesBiological sourcesCCL3 secretionRelative levelsCellsInnate immune cellsTranslocation dynamicsBiological stepC secretionTranscriptionSecretionCCL5 secretionRelAReporter
2017
Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms
Nadell CD, Ricaurte D, Yan J, Drescher K, Bassler BL. Flow environment and matrix structure interact to determine spatial competition in Pseudomonas aeruginosa biofilms. ELife 2017, 6: e21855. PMID: 28084994, PMCID: PMC5283829, DOI: 10.7554/elife.21855.Peer-Reviewed Original ResearchConceptsMatrix mutantsWild-type cellsMicrobial communitiesMatrix producersEvolutionary stabilityNon-producing strainsMatrix organizationRelative abundanceExtracellular matrixMatrix secretionMatrix productionMutantsSimple flow regimesInitial frequencyBacteriaNatural environmentBiofilmsPseudomonas aeruginosaAbundanceCompetitive dynamicsPseudomonasSpatial competitionSpatial structureCompetitionPotential explanation
2016
Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers
Jiao J, Rebane AA, Ma L, Zhang Y. Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers. Methods In Molecular Biology 2016, 1486: 357-390. PMID: 27844436, PMCID: PMC5508109, DOI: 10.1007/978-1-4939-6421-5_14.Peer-Reviewed Original ResearchConceptsOptical tweezersProtein complexesHigh-resolution optical tweezersSingle-molecule manipulationFolding of proteinsFundamental biological problemOptical trapSingle-molecule measurementsUnprecedented spatiotemporal resolutionThree-dimensional structureTweezersSingle proteinSpontaneous foldingDetailed protocolAmino acidsMolecule proteinProteinBiological problemsPowerful approachMechanical forcesFoldingSpatiotemporal resolutionEnergyTransition kineticsLinear chainsA generic, cost-effective, and scalable cell lineage analysis platform
Biezuner T, Spiro A, Raz O, Amir S, Milo L, Adar R, Chapal-Ilani N, Berman V, Fried Y, Ainbinder E, Cohen G, Barr H, Halaban R, Shapiro E. A generic, cost-effective, and scalable cell lineage analysis platform. Genome Research 2016, 26: 1588-1599. PMID: 27558250, PMCID: PMC5088600, DOI: 10.1101/gr.202903.115.Peer-Reviewed Original ResearchConceptsLineage analysisSingle cell lineage analysisSingle-cell sequencing dataSingle-cell genomicsCurrent sequencing-based methodsIndividual cellsCell lineage analysisSingle-cell sequencingSequencing-based methodsLineage treesSequencing dataLineage relationsCellsTreesGenomicsAnalysis platformInput cellsSequencingBulk analysisVivoDiscoveryLandscape
2015
Synthesis of [18F]FMISO in a flow-through microfluidic reactor: Development and clinical application
Zheng MQ, Collier L, Bois F, Kelada OJ, Hammond K, Ropchan J, Akula MR, Carlson DJ, Kabalka GW, Huang Y. Synthesis of [18F]FMISO in a flow-through microfluidic reactor: Development and clinical application. Nuclear Medicine And Biology 2015, 42: 578-584. PMID: 25779036, DOI: 10.1016/j.nucmedbio.2015.01.010.Peer-Reviewed Original Research
2014
First Human Use of a Radiopharmaceutical Prepared by Continuous-Flow Microfluidic Radiofluorination: Proof of Concept with the Tau Imaging Agent [18F]T807
Liang S, Yokell D, Normandin M, Rice P, Jackson R, Shoup T, Brady T, Fakhri G, Collier T, Vasdev N. First Human Use of a Radiopharmaceutical Prepared by Continuous-Flow Microfluidic Radiofluorination: Proof of Concept with the Tau Imaging Agent [18F]T807. Molecular Imaging 2014, 13: 7290.2014.00025. PMID: 25248283, DOI: 10.2310/7290.2014.00025.Peer-Reviewed Original Research
2004
Mechanosensory function of microvilli of the kidney proximal tubule
Du Z, Duan Y, Yan Q, Weinstein A, Weinbaum S, Wang T. Mechanosensory function of microvilli of the kidney proximal tubule. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 13068-13073. PMID: 15319475, PMCID: PMC516518, DOI: 10.1073/pnas.0405179101.Peer-Reviewed Original ResearchConceptsKidney proximal tubulesProximal tubulesNa+ reabsorptionNa+ transportNa+-H+ exchange activityProximal tubule Na+ reabsorptionNa+-H+ exchangeLuminal cell membraneMechanosensory functionNa+ absorptionTubular diameterLuminal diameterMouse kidneyEpithelial microvilliReabsorptionTubulesKidneyAutoregulatory mechanismNa+ uptakeHormonal systemsMiceActin cytoskeletonCell membraneTerminal webBending moment
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