2025
Update of the sideroflexin (SLC56) gene family
Katsafadou A, Nebert D, Krupenko S, Thompson D, Vasiliou V. Update of the sideroflexin (SLC56) gene family. Human Genomics 2025, 19: 69. PMID: 40542427, PMCID: PMC12180156, DOI: 10.1186/s40246-025-00779-w.Peer-Reviewed Original ResearchConceptsIron-sulfur cluster assemblyMitochondrial iron-regulatedMitochondrial iron homeostasisMitochondrial serine transporterMitochondrial transmembrane proteinOxidative phosphorylation disordersSolute carrier familyEukaryotic speciesOne-carbon metabolismMitochondrial researchGene familyModel organismsCellular homeostasisEvolutionary trajectoriesMitochondrial metabolismTransmembrane domainCongenital sideroblastic anemiaTransmembrane proteinsCarrier familySideroflexinHeme biosynthesisIron regulationCitrate metabolismMitochondrial functionSerine transport
2024
Large Language Models and Genomics for Summarizing the Role of microRNA in Regulating mRNA Expression
Bhasuran B, Manoharan S, Iyyappan O, Murugesan G, Prabahar A, Raja K. Large Language Models and Genomics for Summarizing the Role of microRNA in Regulating mRNA Expression. Biomedicines 2024, 12: 1535. PMID: 39062108, PMCID: PMC11274411, DOI: 10.3390/biomedicines12071535.Peer-Reviewed Original ResearchMiRNA-mRNA interactionsRegulation of gene expressionMaintenance of cellular homeostasisMicroRNA (miRNA)-messenger RNAGenomic approachesRegulate mRNA expressionCellular homeostasisCellular differentiationGene expressionBiological processesPathogenesis of numerous diseasesMiRNA-mRNAPotential therapeutic targetGenomeDisease mechanismsNumerous diseasesLLM modelTherapeutic targetMetabolic conditionsMRNA expressionExpressionMicroRNAsRNAApoptosisLlamasCellular Dynamics of Fas-Associated Death Domain in the Regulation of Cancer and Inflammation
Ranjan K, Pathak C. Cellular Dynamics of Fas-Associated Death Domain in the Regulation of Cancer and Inflammation. International Journal Of Molecular Sciences 2024, 25: 3228. PMID: 38542202, PMCID: PMC10970579, DOI: 10.3390/ijms25063228.Peer-Reviewed Original ResearchConceptsFas-associated death domainDeath domainDeath receptorsInitiation of apoptotic signalingRegulate programmed cell deathExpression of Fas-associated death domainSignaling pathwayCellular dynamicsRegulator of inflammatory signalingRegulation of cancerAdaptor proteinActivated caspasesApoptotic functionApoptosis signalingSubcellular localizationApoptotic signalingCellular homeostasisCell deathCell survivalCoordinated removalCellular senescenceIntracellular expressionCell proliferationSpatiotemporal mechanismsInflammatory signalingYeast 26S proteasome nuclear import is coupled to nucleus-specific degradation of the karyopherin adaptor protein Sts1
Breckel C, Johnson Z, Hickey C, Hochstrasser M. Yeast 26S proteasome nuclear import is coupled to nucleus-specific degradation of the karyopherin adaptor protein Sts1. Scientific Reports 2024, 14: 2048. PMID: 38267508, PMCID: PMC10808114, DOI: 10.1038/s41598-024-52352-5.Peer-Reviewed Original ResearchConceptsProteasome storage granulesNuclear importUbiquitin-independent proteasomal degradationProteasome degradation in vitroYeast Saccharomyces cerevisiaeProlonged glucose starvationNuclear import factorsUbiquitin-proteasome systemProteasome interactionGlucose starvationKaryopherin proteinsProteasomal degradationNuclear transportCellular homeostasisDegradation in vivoSTS1KaryopherinProtein degradationProteasomeDegradation in vitroGlucose refeedingStorage granulesProteinEukaryotesRanGTP
2023
The active zone protein Clarinet regulates synaptic sorting of ATG-9 and presynaptic autophagy
Xuan Z, Yang S, Clark B, Hill S, Manning L, Colón-Ramos D. The active zone protein Clarinet regulates synaptic sorting of ATG-9 and presynaptic autophagy. PLOS Biology 2023, 21: e3002030. PMID: 37053235, PMCID: PMC10101500, DOI: 10.1371/journal.pbio.3002030.Peer-Reviewed Original ResearchConceptsATG-9Presynaptic autophagyAdaptor protein complexesZone proteinActive zone proteinsC. elegans neuronsSynaptic vesicle proteinsGenetic screenPeriactive zoneAutophagosome biogenesisCellular homeostasisProtein complexesVesicle proteinsGenetic analysisLong isoformNovel roleSynaptic vesiclesAutophagyDistinct mechanismsProteinVesiclesSortingCLA-1Abnormal accumulationActive zone
2022
Quantification of Protein Exit at the Trans-Golgi Network
Tran M, Kim Y, von Blume J. Quantification of Protein Exit at the Trans-Golgi Network. Methods In Molecular Biology 2022, 2557: 583-594. PMID: 36512239, DOI: 10.1007/978-1-0716-2639-9_35.Peer-Reviewed Original ResearchConceptsTrans-Golgi networkProtein exportSecretory pathwaySelective hooks (RUSH) systemCell biological approachesProtein of interestPulse-chase experimentsProtein exitProtein sortingExport kineticsCellular homeostasisProtein transportDifferent cargoesLive cellsBiological approachesRUSH systemProteinPathwayTraffickingHomeostasisExportCargoSortingCompartmentsCellsTargeted Deletion of Mitofusin 1 and Mitofusin 2 Causes Female Infertility and Loss of Follicular Reserve
Cozzolino M, Ergun Y, Seli E. Targeted Deletion of Mitofusin 1 and Mitofusin 2 Causes Female Infertility and Loss of Follicular Reserve. Reproductive Sciences 2022, 30: 560-568. PMID: 35739352, DOI: 10.1007/s43032-022-01014-w.Peer-Reviewed Original ResearchConceptsMitofusin 1Mitofusin 2Double deletionFemale reproductive competencePotential functional redundancyDynamic organellesCellular homeostasisFunctional redundancyMitochondrial dynamicsEnvironmental stressMitochondrial functionMitochondrial dysfunctionMfn1Reproductive competenceTargeted deletionMfn2Oocyte maturationDeletionCritical roleReproductive agingFemale infertilityOocytesOocyte qualityFusion mechanismMitofusinsArming a killer: mitochondrial regulation of CD8+ T cell cytotoxicity
Lisci M, Griffiths G. Arming a killer: mitochondrial regulation of CD8+ T cell cytotoxicity. Trends In Cell Biology 2022, 33: 138-147. PMID: 35753961, DOI: 10.1016/j.tcb.2022.05.007.Peer-Reviewed Original ResearchConceptsCD8<sup>+</sup> cytotoxic T lymphocytesCD8+ T cell cytotoxicityRegulation of cellular homeostasisMitochondrial protein synthesisStages of T cell developmentStudy of mitochondriaT cell cytotoxicityCytotoxic T lymphocytesCTL-mediated killingT cell differentiationT cell developmentMitochondrial regulationCellular homeostasisT lymphocytesImmune cellsMitochondriaMitochondrial dysfunctionProtein synthesisImmune systemHomeostatic regulationCellsIntensifying interest
2021
Calcium Signaling Regulates Autophagy and Apoptosis
Sukumaran P, Da Conceicao V, Sun Y, Ahamad N, Saraiva L, Selvaraj S, Singh B. Calcium Signaling Regulates Autophagy and Apoptosis. Cells 2021, 10: 2125. PMID: 34440894, PMCID: PMC8394685, DOI: 10.3390/cells10082125.Peer-Reviewed Original ResearchConceptsCell survivalOpposing functionCell death processMaintenance of cellular functionDepletion of Ca<sup>2+</sup>Pathogenesis of neurodegenerative diseasesPromote cell survivalNon-excitable cellsCytosolic Ca<sup>2+</sup> levelsCellular homeostasisCellular functionsAutophagy machineryER storesHuntington's diseaseDiverse functionsDeath processNeuronal developmentFunctional significanceNeurodegenerative diseasesPhysiological functionsNeurodegenerative conditionsApoptosisCellsHomeostasisImmune regulationCoronavirus Disease (COVID)-19 and Diabetic Kidney Disease
Srivastava SP, Srivastava R, Chand S, Goodwin JE. Coronavirus Disease (COVID)-19 and Diabetic Kidney Disease. Pharmaceuticals 2021, 14: 751. PMID: 34451848, PMCID: PMC8398861, DOI: 10.3390/ph14080751.Peer-Reviewed Original ResearchCell typesDiabetic kidney diseaseCOVID-19 patientsSuppression of AMPProtein kinase activationKidney cellsMAS1 receptorCellular homeostasisKidney diseaseKinase activationCell homeostasisAcute respiratory syndrome coronavirus 2 infectionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectionTransferase 4Diabetic COVID-19 patientsSyndrome coronavirus 2 infectionCoronavirus 2 infectionAMPK levelsDPP-4 levelsCOVID-19 severityCOVID-19-associated cytokine stormTubular epithelial cellsMesenchymal activationOrgan fibrosisNovel drug therapiesNeurodegenerative diseases: a hotbed for splicing defects and the potential therapies
Li D, McIntosh C, Mastaglia F, Wilton S, Aung-Htut M. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Translational Neurodegeneration 2021, 10: 16. PMID: 34016162, PMCID: PMC8136212, DOI: 10.1186/s40035-021-00240-7.Peer-Reviewed Original ResearchConceptsAlternative splicingSplicing patternsSplicing defectsNeurodegenerative diseasesTrans-splicing factorsEukaryotic gene expressionDiversity of proteomesNon-coding regionsPrecursor messenger RNAAntisense oligonucleotide therapeuticsSplice-switching antisense oligonucleotidesRNA splicingMature mRNAGenetic plasticityCellular homeostasisSplicingGene expressionNeuronal differentiationNeuronal migrationNeuronal cellsNeurodegenerative disordersAlzheimer's diseaseSynaptic functionMessenger RNAAntisense oligonucleotidesBasics of Fungal Siderophores: Classification, Iron Transport and Storage, Chemistry and Biosynthesis, Application, and More
Arputhanantham S, Raja K, Shanmugam L, Raman V. Basics of Fungal Siderophores: Classification, Iron Transport and Storage, Chemistry and Biosynthesis, Application, and More. Fungal Biology 2021, 1-12. DOI: 10.1007/978-3-030-53077-8_1.Peer-Reviewed Original ResearchFungal siderophoresEssential proteinsSecrete siderophoresCellular homeostasisCellular functionsSiderophorePublished biomedical literatureOptimal growthIron uptakeIron transportBiosynthesisFungiBacteriaMicroorganismsAccumulation of ironBiomedical literatureIron-chelating agentProteinIntrinsic mechanismHomeostasisHostDefective autophagy in Sf1 neurons perturbs the metabolic response to fasting and causes mitochondrial dysfunction
Coupé B, Leloup C, Asiedu K, Maillard J, Pénicaud L, Horvath TL, Bouret SG. Defective autophagy in Sf1 neurons perturbs the metabolic response to fasting and causes mitochondrial dysfunction. Molecular Metabolism 2021, 47: 101186. PMID: 33571700, PMCID: PMC7907893, DOI: 10.1016/j.molmet.2021.101186.Peer-Reviewed Original ResearchConceptsLoss of Atg7Energy homeostasisCellular homeostasisGene Atg7Defective autophagyMitochondria morphologyPhysiological processesCellular responsesCellular componentsMetabolic responseMitochondrial dysfunctionAutophagyAtg7SF1 neuronsHomeostasisMutant miceNeurons displayLoxP/Energy expenditure regulationImportant roleVMH neuronsVentromedial nucleusLeptin sensitivityStarvationCentral response
2020
Heterogeneity of midgut cells and their differential responses to blood meal ingestion by the mosquito, Aedes aegypti
Cui Y, Franz AWE. Heterogeneity of midgut cells and their differential responses to blood meal ingestion by the mosquito, Aedes aegypti. Insect Biochemistry And Molecular Biology 2020, 127: 103496. PMID: 33188922, PMCID: PMC7739889, DOI: 10.1016/j.ibmb.2020.103496.Peer-Reviewed Original ResearchConceptsIntestinal stem cellsBlood meal ingestionMosquito midgutSingle-nucleus RNA sequencingCell type clustersCell typesVisceral muscle cellsNutrient absorptionCell type compositionHuman pathogenic parasitesNumerous mosquito speciesEC-like cellsBlood meal digestionEnteroendocrine cellsAedes aegyptiBlood-feeding behaviorMeal ingestionCellular homeostasisCellular diversityGenetic compatibilityHematophagous insectsFemale midgutTranscriptional profilesBlood digestionRNA sequencingPolycystin 2 is increased in disease to protect against stress-induced cell death
Brill AL, Fischer TT, Walters JM, Marlier A, Sewanan LR, Wilson PC, Johnson EK, Moeckel G, Cantley LG, Campbell SG, Nerbonne JM, Chung HJ, Robert ME, Ehrlich BE. Polycystin 2 is increased in disease to protect against stress-induced cell death. Scientific Reports 2020, 10: 386. PMID: 31941974, PMCID: PMC6962458, DOI: 10.1038/s41598-019-57286-x.Peer-Reviewed Original ResearchConceptsPolycystin-2General cellular homeostasisCell deathStress-induced cell deathPathological cell deathAutosomal dominant polycystic kidney diseaseEndoplasmic reticulum membraneCellular homeostasisCellular stressPrimary ciliaUbiquitous expressionExpression changesCell stressReticulum membraneTransient receptor potential cation channelHuman diseasesMultiple tissuesEndogenous roleDominant polycystic kidney diseaseTissue typesCation channelsPolycystic kidney diseaseDifferent pathological statesMultiple diseasesKidney disease
2019
Mouse Norovirus Infection Arrests Host Cell Translation Uncoupled from the Stress Granule-PKR-eIF2α Axis
Fritzlar S, Aktepe TE, Chao YW, Kenney ND, McAllaster MR, Wilen CB, White PA, Mackenzie JM. Mouse Norovirus Infection Arrests Host Cell Translation Uncoupled from the Stress Granule-PKR-eIF2α Axis. MBio 2019, 10: 10.1128/mbio.00960-19. PMID: 31213553, PMCID: PMC6581855, DOI: 10.1128/mbio.00960-19.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaliciviridae InfectionsCytoplasmic GranulesDNA HelicaseseIF-2 KinaseEukaryotic Initiation Factor-2Host-Pathogen InteractionsImmune EvasionImmunity, InnateMicePhosphorylationPoly-ADP-Ribose Binding ProteinsProtein BiosynthesisRNA HelicasesRNA Recognition Motif ProteinsViral ProteinsVirus ReplicationConceptsIntegrated stress responseProtein kinase RStress granulesProtein translationCellular homeostasisProtein G3BP1Host translationCytoplasmic RNA granulesMNV replication complexHijack host machineryPhosphorylation of eIF2αHost protein translationCellular response systemsHost cell translationEukaryotic initiation factorMNV infectionPhosphorylated eukaryotic initiation factorRNA granulesTranslational controlSG formationInitiation factorsSG nucleationTranslational arrestHost machineryVirus replicationSmall open reading frames and cellular stress responses
Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Molecular Omics 2019, 15: 108-116. PMID: 30810554, PMCID: PMC6662920, DOI: 10.1039/c8mo00283e.Peer-Reviewed Original ResearchConceptsSmall open reading framesOpen reading frameUpstream ORFsReading frameStress responseCellular stress responseEukaryotic cellsGenome annotationCellular homeostasisDownstream cistronEvolutionary spaceFunctional polypeptidesAmino acidsEukaryotesSmORFsPolypeptideProkaryotesGenomeCistronGenomicsORFRecent advancesProteomicsFootprintingRegulator
2018
Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins
Panda S, Setia M, Kaur N, Shepal V, Arora V, Singh D, Mondal A, Teli A, Tathode M, Gajula R, Padhy L, Shiras A. Noncoding RNA Ginir functions as an oncogene by associating with centrosomal proteins. PLOS Biology 2018, 16: e2004204. PMID: 30296263, PMCID: PMC6193740, DOI: 10.1371/journal.pbio.2004204.Peer-Reviewed Original ResearchConceptsGenomic stabilityNoncoding RNAsMouse cellsBreast cancer type 1 susceptibility proteinLong intergenic noncoding RNAsIntergenic noncoding RNAsGrowth regulatory signalsLong noncoding RNAHitherto unknown mechanismEukaryotic transcriptomesMitotic regulationCellular homeostasisTranscript pairsCentrosomal proteinsRNA functionMitotic fidelityAntisense transcriptsSusceptibility proteinProtein interactionsEmbryonic developmentFunctional characterisationIndividual transcriptsBRCA1 proteinRegulatory signalsAdult tissuesLso2 is a conserved ribosome-bound protein required for translational recovery in yeast
Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV. Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. PLOS Biology 2018, 16: e2005903. PMID: 30208026, PMCID: PMC6135351, DOI: 10.1371/journal.pbio.2005903.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCodon, InitiatorConserved SequenceGene Expression Regulation, FungalHeLa CellsHumansPeptide Chain Elongation, TranslationalPeptide Chain Termination, TranslationalProtein BiosynthesisRibosomal ProteinsRibosomesRNA, RibosomalRNA, TransferSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsRibosome-binding proteinsRibosome-associated proteinsCodon-specific changesCoiled-coil domainQuantitative mass spectrometryGTPase activation centerRibosome-binding activityMost tRNAsRibosome profilingGene regulationMost genesCellular homeostasisTranslation defectsRibosomal RNATranslational recoveryComplete complementStart codonStop codonLso2Protein synthesisOpen reading frame 2ProteinImportant functionsCodonYeastTargeted protein unfolding uncovers a Golgi-specific transcriptional stress response
Serebrenik YV, Hellerschmied D, Toure M, López-Giráldez F, Brookner D, Crews CM. Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response. Molecular Biology Of The Cell 2018, 29: 1284-1298. PMID: 29851555, PMCID: PMC5994893, DOI: 10.1091/mbc.e17-11-0693.Peer-Reviewed Original ResearchConceptsStress responseTranscriptional stress responseChemical biology strategyStress response mechanismsGolgi structural integrityRNA sequence profilesUncharacterized genesEssential organellesEukaryotic cellsCellular homeostasisMisfolded proteinsGolgi targetingTranscriptional responseProtein substratesOrganelle structureProtein modificationHomeostasis mechanismsGolgi apparatusSecretory systemTargeted proteinsProtein unfoldingFurther revealsMajor siteProteinPrecise processing
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