2024
13. AmpliconSuite: Analyzing focal amplifications in cancer genomes
Luebeck J, Huang E, Dameracharla B, Kim F, Liefeld T, Ahuja R, Prasad D, Prasad G, Kim S, Kim H, Bailey P, Verhaak R, Deshpande V, Reich M, Mischel P, Mesirov J, Bafna V. 13. AmpliconSuite: Analyzing focal amplifications in cancer genomes. Cancer Genetics 2024, 286: s5. DOI: 10.1016/j.cancergen.2024.08.015.Peer-Reviewed Original ResearchWhole-genome sequencingWhole-genome sequencing dataFocal amplificationCancer genomesStructural variationsAmplification of oncogenesExtrachromosomal DNACopy numberEcDNAGenomeOncogene amplificationAmpliconArchitectCancer progressionAmplificationAmplification typeTumor samplesBiocondaNextflowPCAWGGenePatternRobust identificationDNACCLESequenceOncogeneGlycolysis in hepatic stellate cells coordinates fibrogenic extracellular vesicle release spatially to amplify liver fibrosis
Khanal S, Liu Y, Bamidele A, Wixom A, Washington A, Jalan-Sakrikar N, Cooper S, Vuckovic I, Zhang S, Zhong J, Johnson K, Charlesworth M, Kim I, Yeon Y, Yoon S, Noh Y, Meroueh C, Timbilla A, Yaqoob U, Gao J, Kim Y, Lucien F, Huebert R, Hay N, Simons M, Shah V, Kostallari E. Glycolysis in hepatic stellate cells coordinates fibrogenic extracellular vesicle release spatially to amplify liver fibrosis. Science Advances 2024, 10: eadn5228. PMID: 38941469, PMCID: PMC11212729, DOI: 10.1126/sciadv.adn5228.Peer-Reviewed Original ResearchConceptsHepatic stellate cellsLiver fibrosisExtracellular vesiclesEV releaseHistone 3 lysine 9 acetylationExtracellular vesicle releaseIncreased EV releaseFibrotic gene expressionNanosized extracellular vesiclesPromoter regionVesicle releasePotential therapeutic targetGene expressionGenetic inhibitionSpatial transcriptomicsStellate cellsGlycolysisUp-regulatedFibrosisTherapeutic targetPericentral zoneLiverPathwayAmplificationExpressionDefining the Role of Extrachromosomal DNA Amplifications in Medulloblastoma.
Zhao D, Verhaak R. Defining the Role of Extrachromosomal DNA Amplifications in Medulloblastoma. Cancer Research 2024, 84: 515-516. PMID: 38175761, DOI: 10.1158/0008-5472.can-23-4025.Peer-Reviewed Original ResearchConceptsCell-to-cell variabilityWhole-genome sequencingCircular extrachromosomal DNACRISPRi experimentsRewiring eventsExtrachromosomal DNAMultiomics sequencingExtrachromosomal DNA amplificationsCopy numberEcDNADNA amplificationAssociated with worse survivalOncogene amplificationSequenceAmplificationWorse survivalPatient cohortTumor heterogeneityIntratumoral heterogeneityCRISPRiMedulloblastomaPatient outcomesDNA
2023
Megahertz Sampling of Prestin (SLC26a5) Voltage-Sensor Charge Movements in Outer Hair Cell Membranes Reveals Ultrasonic Activity that May Support Electromotility and Cochlear Amplification
Santos-Sacchi J, Bai J, Navaratnam D. Megahertz Sampling of Prestin (SLC26a5) Voltage-Sensor Charge Movements in Outer Hair Cell Membranes Reveals Ultrasonic Activity that May Support Electromotility and Cochlear Amplification. Journal Of Neuroscience 2023, 43: 2460-2468. PMID: 36868859, PMCID: PMC10082455, DOI: 10.1523/jneurosci.2033-22.2023.Peer-Reviewed Original ResearchConceptsConformational switchingMammalian hearingMembrane motor proteinCochlear amplificationMotor protein prestinVoltage-sensor charge movementOuter hair cell electromotilityHair cell electromotilityProtein prestinMotor proteinsConformation switchingCharge movementPrestinPrestin activityCell membraneOHC electromotilityHair cell membraneElectromotilityTransmembrane voltageOrgan of CortiAmplificationMammalsMembrane capacitanceProtein
2022
Extrachromosomal DNA amplifications in cancer
Yi E, Chamorro González R, Henssen A, Verhaak R. Extrachromosomal DNA amplifications in cancer. Nature Reviews Genetics 2022, 23: 760-771. PMID: 35953594, PMCID: PMC9671848, DOI: 10.1038/s41576-022-00521-5.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA amplificationsNew therapeutic vulnerabilitiesCopy number heterogeneityEpigenetic architectureDNA amplificationCell divisionNuclear bodiesMost cancer typesNumber heterogeneityRegulatory landscapeTherapeutic vulnerabilitiesFunctional impactCancer typesDriver alterationsCircular structureEcDNAsChromatinizationChromosomesGenesAmplificationEcDNARecent investigationsEnhancerDeregulationCancer
2021
Mechanical stretch scales centriole number to apical area via Piezo1 in multiciliated cells
Kulkarni S, Marquez J, Date P, Ventrella R, Mitchell B, Khokha M. Mechanical stretch scales centriole number to apical area via Piezo1 in multiciliated cells. ELife 2021, 10: e66076. PMID: 34184636, PMCID: PMC8270640, DOI: 10.7554/elife.66076.Peer-Reviewed Original ResearchConceptsCentriole numberMulticiliated cellsCentriole amplificationHundreds of centriolesOptimal cell functionTension-dependent mannerMechanosensitive ion channelsEmbryonic elongationOrganelle numberCell biologyNumber controlIon channelsCentriolesMost cellsPiezo1Multiple ciliaCell functionMCC functionMechanical forcesApical areaCiliaCellsPotential roleAmplificationFundamental questions
2019
Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice
Kojima M, de Rooij D, Page D. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice. ELife 2019, 8: e43738. PMID: 30810530, PMCID: PMC6392498, DOI: 10.7554/elife.43738.Peer-Reviewed Original ResearchConceptsInitiation of meiosisMeiotic cell cycleMeiotic initiationTranscriptional programsCell cycleGerm cell-specific genesG1-S cell cycle transitionCell-specific genesCell cycle transitionGene expression programsMulticellular organismsTranscriptional networksDNA replicationGerm lineRobust amplificationMeiosis I.G1-SGenesExpression programsMeiosisStra8GermAmplificationMiceCells
2018
Visualizing Chemoreceptor Arrays in Bacterial Minicells by Cryo-Electron Tomography and Subtomogram Analysis
Qin Z, Hu B, Liu J. Visualizing Chemoreceptor Arrays in Bacterial Minicells by Cryo-Electron Tomography and Subtomogram Analysis. Methods In Molecular Biology 2018, 1729: 187-199. PMID: 29429093, DOI: 10.1007/978-1-4939-7577-8_17.Peer-Reviewed Original ResearchConceptsCryo-electron tomographyChemoreceptor arraysCheW coupling proteinLarge macromolecular assembliesChemotaxis arraysSubtomogram analysisCheA kinaseBacterial chemoreceptorsCellular contextCoupling proteinMacromolecular assembliesChemotaxis signalingMolecular levelSitu structurePrecise architectureBacterial minicellsMinicellsUnique toolKinaseSignalingProteinSubtomogramsAssemblyConcertAmplification
2015
Sequencing of 279 cancer genes in ampullary carcinoma reveals trends relating to histologic subtypes and frequent amplification and overexpression of ERBB2 (HER2)
Hechtman J, Liu W, Sadowska J, Zhen L, Borsu L, Arcila M, Won H, Shah R, Berger M, Vakiani E, Shia J, Klimstra D. Sequencing of 279 cancer genes in ampullary carcinoma reveals trends relating to histologic subtypes and frequent amplification and overexpression of ERBB2 (HER2). Modern Pathology 2015, 28: 1123-1129. PMID: 25975284, PMCID: PMC4977532, DOI: 10.1038/modpathol.2015.57.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAmpulla of VaterBiomarkers, TumorCarcinomaCommon Bile Duct NeoplasmsCyclin-Dependent Kinase Inhibitor p16DNA Mutational AnalysisFemaleGene AmplificationGene DeletionGene Expression ProfilingGene Expression Regulation, NeoplasticGenetic Predisposition to DiseaseGTP PhosphohydrolasesHumansImmunohistochemistryIn Situ HybridizationMaleMembrane ProteinsMiddle AgedMutationOligonucleotide Array Sequence AnalysisPhenotypePredictive Value of TestsProto-Oncogene Proteins p21(ras)Receptor, ErbB-2Tumor Suppressor Protein p53Up-RegulationConceptsOverexpression of ErbB2Next-generation sequencingCancer-associated genesAmpullary carcinomaResistant to inhibitionERBB2-amplified tumorsAmplified genesDownstream mutationsERBB2 amplificationFrequent amplificationCancer genesHistological subtypesMutated genesGenomic alterationsGenesFrequent mutationsEGFR family membersBiological relevanceGene amplificationMutationsAnti-HER2 therapySubtypes of ampullary carcinomasAmplificationDriver mutationsErbB2
2014
Embryonic Cerebrospinal Fluid Nanovesicles Carry Evolutionarily Conserved Molecules and Promote Neural Stem Cell Amplification
Feliciano DM, Zhang S, Nasrallah CM, Lisgo SN, Bordey A. Embryonic Cerebrospinal Fluid Nanovesicles Carry Evolutionarily Conserved Molecules and Promote Neural Stem Cell Amplification. PLOS ONE 2014, 9: e88810. PMID: 24533152, PMCID: PMC3923048, DOI: 10.1371/journal.pone.0088810.Peer-Reviewed Original ResearchConceptsNeural stem cellsRapamycin complex 1 (mTORC1) pathwayIntracellular pathwaysStem cell amplificationInsulin-like growth factorCoordinated regulationGenetic programMicroRNA componentsExosome NanovesiclesEmbryonic CSFCell amplificationStem cellsENSCsPathwayCoordinated transferGrowth factorHuman embryosBrain developmentNanovesiclesMixed cultureAmplificationMoleculesEmbryosProteinExosomes
2013
Real Time Measures of Prestin Charge and Fluorescence during Plasma Membrane Trafficking Reveal Sub-Tetrameric Activity
Bian S, Navaratnam D, Santos-Sacchi J. Real Time Measures of Prestin Charge and Fluorescence during Plasma Membrane Trafficking Reveal Sub-Tetrameric Activity. PLOS ONE 2013, 8: e66078. PMID: 23762468, PMCID: PMC3677934, DOI: 10.1371/journal.pone.0066078.Peer-Reviewed Original ResearchConceptsObligate tetramerPlasma membraneMembrane motor proteinIntegral membrane proteinsTetracycline-inducible cell lineMembrane proteinsMotor proteinsPrestin densityTemperature blockPrestinFluorescence measuresMembrane fluorescenceCell linesNonlinear capacitanceCochlear amplificationProteinTetramerMembraneFluorescencePrevious observationsVoltage clampFluorescence methodCellsAmplification
2008
In Vitro Selection and Characterization of Cellulose-Binding RNA Aptamers Using isothermal Amplification
Boese B, Corbino K, Breaker R. In Vitro Selection and Characterization of Cellulose-Binding RNA Aptamers Using isothermal Amplification. Nucleosides Nucleotides & Nucleic Acids 2008, 27: 949-966. PMID: 18696364, PMCID: PMC5360192, DOI: 10.1080/15257770802257903.Peer-Reviewed Original ResearchConceptsRNA aptamersRibozyme cleavage productsCellulose affinity chromatographyIsolation of RNARapid amplificationVitro SelectionRibozyme functionRibozyme sequenceFunctional nucleic acidsNucleic acid amplification protocolsRNARobust bindingAffinity chromatographyCleavage productsNucleic acidsSequence replicationBindingSignificant bindingAptamerAmplification protocolAmplification
2007
A connector of two-component regulatory systems promotes signal amplification and persistence of expression
Kato A, Mitrophanov AY, Groisman EA. A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 12063-12068. PMID: 17615238, PMCID: PMC1924540, DOI: 10.1073/pnas.0704462104.Peer-Reviewed Original ResearchConceptsTwo-component regulatory systemBacterial signal transductionRegulatory systemPersistence of expressionSignal transductionGene transcriptionRegulatory architectureSmall proteinsSalmonella entericaPathwayFunctional characteristicsPmrDExpressionFunctional propertiesPhoP.AmplificationTranscriptionSignal amplificationTransductionGenesDominant formOrganismsProteinPersistenceEnterica
2003
New tunes from Corti’s organ: the outer hair cell boogie rules
Santos-Sacchi J. New tunes from Corti’s organ: the outer hair cell boogie rules. Current Opinion In Neurobiology 2003, 13: 459-468. PMID: 12965294, DOI: 10.1016/s0959-4388(03)00100-4.Peer-Reviewed Original ResearchConceptsSpecial cell typesHair cellsOuter hair cell electromotilityHair cell electromotilityMolecular identificationCell typesMammalsMechanism of actionOuter hair cellsAdditional mechanismVertebratesCellsAmplificationMechanismKnockoutElectromotilityOrgansSuch amplificationCorti's organAcoustic stimuliRemarkable progressCl− flux through a non‐selective, stretch‐sensitive conductance influences the outer hair cell motor of the guinea‐pig
Rybalchenko V, Santos‐Sacchi J. Cl− flux through a non‐selective, stretch‐sensitive conductance influences the outer hair cell motor of the guinea‐pig. The Journal Of Physiology 2003, 547: 873-891. PMID: 12562920, PMCID: PMC2342734, DOI: 10.1111/j.1469-7793.2003.00873.x.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCarbenoxoloneCell MembraneChloride ChannelsChloridesCyclooxygenase InhibitorsElectric CapacitanceElectric ConductivityGadoliniumGuinea PigsHair Cells, Auditory, OuterIon Channel GatingMechanotransduction, CellularMembrane PotentialsMercuric ChlorideMicrodialysisNiflumic AcidOctanolsProteinsSulfonic AcidsConceptsOuter hair cell motorLateral membranesVoltage-dependent conformational changesLateral plasma membranePlasma membraneMotor proteinsCell motorProtein transitionsConformational changesRecent identificationPrestinSomatic motilityAllosteric modulationCL sensitivityAnion fluxHair cellsCochlear amplificationAcoustic ratesOuter hair cellsAlternative mechanismComplicated roleMembranePronounced shiftCellsAmplification
1979
Simple method for identification of plasmid-coded proteins
Sancar A, Hack AM, Rupp WD. Simple method for identification of plasmid-coded proteins. Journal Of Bacteriology 1979, 137: 692-693. PMID: 368040, PMCID: PMC218506, DOI: 10.1128/jb.137.1.692-693.1979.Peer-Reviewed Original Research
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