2021
12 Iron Metabolism and Related Disorders
Ginzburg Y, Finberg K. 12 Iron Metabolism and Related Disorders. 2021, 445-499. DOI: 10.1016/b978-0-12-812535-9.00012-1.ChaptersGene productsNumerous fundamental biological processesFundamental biological processesIron metabolismGenetic defectsSystemic iron balanceSystemic iron regulationMolecular geneticsBiological processesIron regulationIron-refractory iron deficiency anemiaIron homeostasisIron availabilityFriedreich's ataxiaIron movementMajor genetic disordersErythroid precursorsGenetic disordersIron regulatory hormone hepcidinSideroblastic anemiaMetabolismGenetic formsMutationsKey roleHormone hepcidin
2020
Structures of the β‐barrel assembly machine recognizing outer membrane protein substrates
Xiao L, Han L, Li B, Zhang M, Zhou H, Luo Q, Zhang X, Huang Y. Structures of the β‐barrel assembly machine recognizing outer membrane protein substrates. The FASEB Journal 2020, 35: e21207. PMID: 33368572, DOI: 10.1096/fj.202001443rr.Peer-Reviewed Original ResearchConceptsBAM complexFirst β-strandOMP substratesΒ-strandsΒ-barrel outer membrane proteinsΒ-barrel assembly machinery (BAM) complexΒ-barrel assembly machineAssembly machinery complexBamA β-barrelChaperone-bound stateMembrane protein substratesRelated functional analysisLast β-strandFundamental biological processesOuter membrane proteinsDifferent conformational statesOMP biogenesisNutrition acquisitionGram-negative bacteriaProtein substratesMembrane proteinsΒ-barrelFunctional analysisBiological processesConformational statesExtensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D
Kennedy S, Jarboui M, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn M, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko B, Iglesias-Martinez L, Ryan C, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn D, Kolch W. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D. Nature Communications 2020, 11: 499. PMID: 31980649, PMCID: PMC6981206, DOI: 10.1038/s41467-019-14224-9.Peer-Reviewed Original ResearchConceptsEpidermal growth factor receptor (EGFR) networkGrowth factor receptor networkFundamental biological processesColorectal cancer cellsCancer cellsEGFR networkTranscriptional regulationProtein complexesExtensive rewiringCellular phenotypesInteraction networksBiological processesOncogenic mutationsOncogenic KRAS mutationsReceptor networkGenetic alterationsProtein expressionPPInsMutationsCellsInteractorsPhosphorylationRewiringPoor patient outcomesSignal flow
2015
Watching a roundworm develop with a sheet of light
Kumar A, Colón-Ramos D, Shroff H. Watching a roundworm develop with a sheet of light. Physics Today 2015, 68: 58-59. DOI: 10.1063/pt.3.2856.Peer-Reviewed Original ResearchFundamental biological processesLight sheet fluorescence microscopyBiological processesFluorescence microscopySheet of lightRoundwormsNeurobiologists
2014
Generation of transgenic Hydra by embryo microinjection.
Juliano CE, Lin H, Steele RE. Generation of transgenic Hydra by embryo microinjection. Journal Of Visualized Experiments 2014, 51888. PMID: 25285460, PMCID: PMC4828061, DOI: 10.3791/51888.Peer-Reviewed Original ResearchConceptsTransgenic HydraFundamental biological processesEarly stage embryosPatches of tissuePure cell populationsMulticellular animalsStudy of regenerationGene functionMolecular functionsPhylum CnidariaParticular lineageTransgenic linesGene perturbationsSister groupTransgenic tissuesTransgenic methodsPromoter functionAsexual propagationBiological processesEmbryo microinjectionStage embryosLive cellsStem cellsHatchlingsBiochemical analysis
2013
New genes as drivers of phenotypic evolution
Chen S, Krinsky BH, Long M. New genes as drivers of phenotypic evolution. Nature Reviews Genetics 2013, 14: 645-660. PMID: 23949544, PMCID: PMC4236023, DOI: 10.1038/nrg3521.Peer-Reviewed Original ResearchConceptsNew genesPhenotypic evolutionLineage-specific essential genesBiological processesUnexpected genetic diversityEvolution of phenotypesFundamental biological processesGene evolutionGenetic circuitryDrosophila sppEssential genesField of geneticsGenetic diversityGenetic systemBiological diversityMolecular explanationGenesIndispensable roleKey PointsThe studySpeciesDiversityEssential componentEvolutionMammalsCentral importance
2012
The Mechanism of Pre-transfer Editing in Yeast Mitochondrial Threonyl-tRNA Synthetase*
Ling J, Peterson KM, Simonović I, Söll D, Simonović M. The Mechanism of Pre-transfer Editing in Yeast Mitochondrial Threonyl-tRNA Synthetase*. Journal Of Biological Chemistry 2012, 287: 28518-28525. PMID: 22773845, PMCID: PMC3436575, DOI: 10.1074/jbc.m112.372920.Peer-Reviewed Original ResearchConceptsPre-transfer editingThreonyl-tRNA synthetaseHydrolytic water moleculeFundamental biological processesNormal cellular functionAminoacyl-tRNA synthetasesPost-transfer editingPost-transfer editing activityTranslational fidelityAminoacylation siteCellular functionsAminoacylation active siteBiological processesMST1Conformational changesEditing activitySeryl adenylateAmino acidsSpecialized domainsEditingSerineSites 100SynthetaseActive siteAdenylateExploring Biology with Small Organic Molecules
Aberle N, Crews C. Exploring Biology with Small Organic Molecules. 2012, 10-25. DOI: 10.1017/cbo9781139021500.004.Peer-Reviewed Original ResearchChemical geneticsSmall moleculesSmall organic moleculesFundamental biological processesProtein of interestGood target specificityOrganic moleculesSemisynthetic moleculesChemical genomicsBiological processesTarget specificityMoleculesGeneticsBiologyVast arrayActive ingredientsChemistryGenomicsCertain basic elementsHuman medicineTherapeuticsCompoundsPlantsProteinPhenotype
2006
Bayesian error analysis model for reconstructing transcriptional regulatory networks
Sun N, Carroll RJ, Zhao H. Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 7988-7993. PMID: 16702552, PMCID: PMC1472417, DOI: 10.1073/pnas.0600164103.Peer-Reviewed Original ResearchConceptsTranscriptional regulatory networksGene expression dataTranscription regulationRegulatory networksExpression dataProtein-DNA binding dataDNA sequence dataFundamental biological processesYeast cell cycleHigh-throughput technologiesMicroarray gene expression dataBiological experimentsSequence dataGenomic dataBiological processesCell cycleClear biological interpretationThroughput technologiesBiological interpretationMarkov chain Monte CarloBayesian hierarchical model frameworkBiochemical reactionsRegulationLinear system modelHierarchical model framework
2001
Genomics-based identification of targets in pathogenic bacteria for potential therapeutic and diagnostic use
Raczniak G, Ibba M, Söll D. Genomics-based identification of targets in pathogenic bacteria for potential therapeutic and diagnostic use. Toxicology 2001, 160: 181-189. PMID: 11246138, DOI: 10.1016/s0300-483x(00)00454-6.Peer-Reviewed Original ResearchConceptsComplete microbial genome sequencesMicrobial genome sequencesFundamental biological processesPathogen-specific pathwaysAminoacyl-tRNA synthesisGenome sequenceBiochemical approachesMammalian hostsIdentification of targetsBiological processesNumber of pathogensProtein synthesisPharmaceutical exploitationSynthesis pathwayCertain pathwaysNovel targetPathogenic bacteriaEnzyme presentPathwayDiagnostic targetsCell viabilityKey processesGenomicsRecent advancesTargetNucleocytoplasmic mRNA Transport
Huang Y, Carmichael G. Nucleocytoplasmic mRNA Transport. Results And Problems In Cell Differentiation 2001, 34: 139-155. PMID: 11288673, DOI: 10.1007/978-3-540-40025-7_9.Peer-Reviewed Original ResearchConceptsMRNA exportMRNA transportMature mRNA moleculesMRNA nuclear exportViral model systemNuclear pore complexRNA polymerase IIMessenger RNA precursorsFundamental biological processesNucleocytoplasmic mRNA transportRemoval of intronsPolymerase IIPore complexNuclear exportRNA precursorsMRNA moleculesBiological processesProcessing reactionsModel systemCytoplasmDetailed mechanismIntronsPolyadenylationSplicingExport
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