2024
Reading the palimpsest of cell interactions: What questions may we ask of the data?
Pavlicev M, Wagner G. Reading the palimpsest of cell interactions: What questions may we ask of the data? IScience 2024, 27: 109670. PMID: 38665209, PMCID: PMC11043885, DOI: 10.1016/j.isci.2024.109670.Peer-Reviewed Original ResearchCompartmentalization of cellular processesStructure of interaction networksCell interactionsMulticellular organismsIntegrity of cellsCellular processesInteraction networkLevels of structural organizationBiological functionsBiological interpretationCell communicationInteraction dataStructural organizationWealth of dataCellsCoordination of functionsOrganizationHigher levels of structural organizationCompartmentalizationInteraction
2022
Microbial Biofilms at Meat-Processing Plant as Possible Places of Bacteria Survival
Nikolaev Y, Yushina Y, Mardanov A, Gruzdev E, Tikhonova E, El-Registan G, Beletskiy A, Semenova A, Zaiko E, Bataeva D, Polishchuk E. Microbial Biofilms at Meat-Processing Plant as Possible Places of Bacteria Survival. Microorganisms 2022, 10: 1583. PMID: 36014001, PMCID: PMC9415349, DOI: 10.3390/microorganisms10081583.Peer-Reviewed Original ResearchMeat processing plantsSurfaces of technological equipmentSimilarity of cellsHeterogeneity of cellsTaxonomic compositionFood productsMetagenomic analysisFood qualityAnimal pathogensMorphological similarityBacteria survivalBiofilm bacteriaRuthenium red stainingBiofilmMicrobial biofilmsUnique familyStructural organizationFoodCutting tableBacterial infectionsPlantsBacteriaRaw materialsDiversityElectron microscopic studies
2021
MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells
Jeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBreast NeoplasmsCell ProliferationCytoskeletal ProteinsDrug Resistance, NeoplasmEndocytosisFemaleHumansMembrane MicrodomainsMyelin and Lymphocyte-Associated Proteolipid ProteinsPhosphoproteinsPlasma Membrane Calcium-Transporting ATPasesReceptor, ErbB-2Sodium-Hydrogen ExchangersTrastuzumabTumor Cells, CulturedConceptsLipid raft formationBreast cancer cellsLipid raftsLipid raft resident proteinsCancer cellsRaft formationRaft-resident proteinsProximity ligation assayProtein complexesMembrane protrusionsProtein interactionsPlasma membraneLigation assayMAL2Membrane stabilityStructural organizationPotential therapeutic targetPhysical interactionMembrane retentionProteinRaftsTherapeutic targetCellsIntracellular calcium concentrationLow intracellular calcium concentration
2020
Investigation of Formation and Development of Anammox Biofilms by Light, Epifluorescence, and Electron Microscopy
Kallistova A, Nikolaev Y, Mardanov A, Berestovskaya Y, Grachev V, Kostrikina N, Pelevina A, Ravin N, Pimenov N. Investigation of Formation and Development of Anammox Biofilms by Light, Epifluorescence, and Electron Microscopy. Microbiology 2020, 89: 708-719. DOI: 10.1134/s0026261720060077.Peer-Reviewed Original ResearchSequencing batch reactorAnammox bacteriaBiofilm formationExtracellular polymeric substancesLaboratory sequencing batch reactorRRNA gene fragmentsHigh-throughput sequencingElectron microscopyAnaerobic organotrophsRod-shapedGene fragmentsAnammox biofilmPhyla ChloroflexiAnammox bacteria CaAnammox processColony ageBiomass retentionGenus CaBatch reactorEpifluorescence microscopyBiofilmBacteriaSulfate reducersStructural organizationAnammox
2019
The Injectisome, a Complex Nanomachine for Protein Injection into Mammalian Cells
Lara-tejero M, Galán J. The Injectisome, a Complex Nanomachine for Protein Injection into Mammalian Cells. 2019, 245-259. DOI: 10.1128/9781683670285.ch20.Peer-Reviewed Original ResearchSecretion machineType III protein secretion systemType III secretion machinesProtein secretion systemTarget eukaryotic cellsCell biological processesType III systemMultiprotein nanomachineEukaryotic hostsComplex nanomachinesGram-negative bacteriaPlant pathogensSymbiotic interactionsEukaryotic cellsEffector proteinsSecretion systemMammalian cellsImportant humanBiological processesStructural organizationInjectisomeBacteriaCurrent knowledgeCentral rolePrimary function
2015
HOTAIR Forms an Intricate and Modular Secondary Structure
Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM. HOTAIR Forms an Intricate and Modular Secondary Structure. Molecular Cell 2015, 58: 353-361. PMID: 25866246, PMCID: PMC4406478, DOI: 10.1016/j.molcel.2015.03.006.Peer-Reviewed Original ResearchConceptsFunctional secondary structureFundamental cellular processesSecondary structureProtein-binding motifsProtein-binding domainsGroup II intronsMetastasis suppressor geneSecondary structure elementsCellular processesPhylogenetic analysisLncRNA moleculesEpidermal developmentChemical probingMolecular mechanismsSuppressor geneCancer progressionStructural organizationKey playersLncRNA HOTAIRHOTAIRStructure elementsRNAHomogenous formReceptor activatorIntrons
2011
Lateral assembly of the immunoglobulin protein SynCAM 1 controls its adhesive function and instructs synapse formation
Fogel AI, Stagi M, Perez de Arce K, Biederer T. Lateral assembly of the immunoglobulin protein SynCAM 1 controls its adhesive function and instructs synapse formation. The EMBO Journal 2011, 30: 4728-4738. PMID: 21926970, PMCID: PMC3243608, DOI: 10.1038/emboj.2011.336.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell AdhesionCell Adhesion Molecule-1Cell Adhesion MoleculesCell Adhesion Molecules, NeuronalCell DifferentiationCells, CulturedChlorocebus aethiopsCoculture TechniquesCOS CellsFluorescence Resonance Energy TransferHEK293 CellsHippocampusHumansImmunoglobulinsImmunohistochemistryMiceNeuritesProtein Structure, QuaternarySynapsesConceptsSynCAM 1Specialized adhesion sitesSynapse formationTrans-synaptic interactionsSynaptic cleftCI assemblyProtein complexesSynaptic cell adhesion molecule SynCAM 1Adhesion sitesSynaptogenic activityAdhesive functionSynapse developmentStructural organizationNovel insightsSynapse inductionLateral assemblyAdhesive capacityAdhesion moleculesSynaptic morphologyAdhesive mechanismsOligomerizationAssemblyAxo-dendritic contactsCleftLater stagesAtomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping
Cheng L, Sun J, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J, Zhu P. Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 1373-1378. PMID: 21220303, PMCID: PMC3029759, DOI: 10.1073/pnas.1014995108.Peer-Reviewed Original ResearchConceptsCytoplasmic polyhedrosis virusDeduced amino acid sequenceCryo-EM structureRNA segment 7Amino acid sequenceMechanisms of mRNANascent mRNAEnzymatic domainsAcid sequenceCryoelectron microscopyFamily ReoviridaeProtein VP5Capsid shellPolyhedrosis virusFull atomic modelsAtomic modelStructural organizationGuanylyltransferaseMRNASegment 7ProteinCypovirus
2009
Tertiary architecture of the Oceanobacillus iheyensis group II intron
Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 2009, 16: 57-69. PMID: 19952115, PMCID: PMC2802037, DOI: 10.1261/rna.1844010.Peer-Reviewed Original ResearchConceptsGroup II intronsPotential evolutionary relationshipsGroup II intron structureGroup IIC intronIntron structureEvolutionary relationshipsEukaryotic spliceosomeInteraction networksRNA moleculesIntronsTertiary structural organizationGenetic studiesRibose zipperRNA foldingTertiary interactionsLarge ribozymesInteraction nodesStructural organizationTertiary architectureEukaryotesSpliceosomeGene therapyGenomeZipperFolding
2004
Visualization of plasma membrane compartmentalization with patterned lipid bilayers
Wu M, Holowka D, Craighead HG, Baird B. Visualization of plasma membrane compartmentalization with patterned lipid bilayers. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 13798-13803. PMID: 15356342, PMCID: PMC518836, DOI: 10.1073/pnas.0403835101.Peer-Reviewed Original ResearchConceptsLipid raftsLeaflet componentsPlasma membrane compartmentalizationReceptor clustersMembrane structural organizationLipid bilayersFcepsilon receptor ITyrosine phosphorylation activityMembrane compartmentalizationLyn kinaseInner leafletPhosphorylation activityActin polymerizationCellular componentsStructural organizationCell receptorRaftsCell activationReceptor IMast cell receptorsStructural reorganizationKinaseUnique insightsBilayersProtein
2000
The major and a minor class II β-chain (B-LB ) gene flank the Tapasin gene in the B-F /B-L region of the chicken major histocompatibility complex
Jacob J, Milne S, Beck S, Kaufman J. The major and a minor class II β-chain (B-LB ) gene flank the Tapasin gene in the B-F /B-L region of the chicken major histocompatibility complex. Immunogenetics 2000, 51: 138-147. PMID: 10663576, DOI: 10.1007/s002510050022.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Inbred StrainsAntiportersBase SequenceChickensExonsGene DosageGenes, DominantGenes, MHC Class IIGenetic LinkageHaplotypesHistocompatibility Antigens Class IIHLA-B AntigensImmunoglobulinsIntronsMembrane Transport ProteinsMolecular Sequence DataPhysical Chromosome MappingPolymorphism, GeneticSequence Homology, Nucleic AcidConceptsB-F/B-L regionChicken major histocompatibility complexAdjacent genesB chain genesWell-characterized linesDNA sequencesLines of chickensTapasin geneGenesB12 haplotypeHaplotypesMajor histocompatibility complexB-chainStructural organizationChickenHistocompatibility complexB complexResponse to vaccinationThe kelch repeat superfamily of proteins: propellers of cell function
Adams J, Kelso R, Cooley L, Adams J, Kelso R, Cooley L. The kelch repeat superfamily of proteins: propellers of cell function. Trends In Cell Biology 2000, 10: 17-24. PMID: 10603472, DOI: 10.1016/s0962-8924(99)01673-6.Peer-Reviewed Original ResearchConceptsKelch motifsKelch repeat proteinProtein-protein contact sitesRepeat proteinsTandem elementsMolecular basisORF1 proteinBiological roleContact sitesPolypeptide contextsTertiary structureStructural organizationProteinCell functionMotifDiverse activitiesKelchCurrent informationSequenceCellsMembers
1992
The molecular architecture of an insect midgut brush border cytoskeleton.
Bonfanti P, Colombo A, Heintzelman M, Mooseker M, Camatini M. The molecular architecture of an insect midgut brush border cytoskeleton. European Journal Of Cell Biology 1992, 57: 298-307. PMID: 1511705.Peer-Reviewed Original ResearchConceptsTwo-dimensional gel analysisMolecular architectureMultiple isoelectric variantsBrush border cytoskeletonLepidopteran larvaeBB myosin IVertebrate intestineBrush borderMyosin IOrganelle exclusionHeavy meromyosin decorationCytoskeletal apparatusMyosin IINonmuscle cellsActin filamentsCytoskeletonIsoelectric variantsGel analysisInstar larvaeMajor isoformsStructural organizationRhodamine phalloidinCore proteinIntestinal brush borderMidgut
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