Modeling the neuron as a nanocommunication system to identify spatiotemporal molecular events in neurodegenerative disease

References

• BurnsAIliffeSAlzheimer’s diseaseBMJ2009338b1585
   Google Scholar
• World Health OrganizationDementia Fact Sheet N°362; 2015 Available from: http://www.who.int/mediacentre/factsheets/fs362/en/
   Google Scholar
• Alzheimer’s AssociationChanging the Trajectory of Alzheimer’s Disease: How a Treatment by 2025 Saves Lives and Dollars2009 Available from: https://alz.org/documents_custom/trajectory.pdf
   Google Scholar
• GanKJSilvermanMADendritic and axonal mechanisms of Ca2+ elevation impair BDNF transport in Aβ oligomer-treated hippocampal neuronsMol Biol Cell20152661058107125609087
   PubMed Web of Science ®Google Scholar
• NumakawaTSuzukiSKumamaruEAdachiNRichardsMKunugiHBDNF function and intracellular signaling in neuronsHistopathol2010252237258
   Web of Science ®Google Scholar
• BushSFPaluhJLPiroGP1906.1/D2.1 Recommended Practice for Nanoscale and Molecular Communication FrameworkNew York, NYIEEE Standards Association2015
   Google Scholar
• BarrettABvan RossumMCWOptimal learning rules for discrete synapsesPLoS Comput Biol200841117
   Web of Science ®Google Scholar
• BerridgeMJCalcium hypothesis of Alzheimer’s diseasePflugers Arch2010459344144919795132
   PubMed Web of Science ®Google Scholar
• FerreiraSTKleinWLThe Abeta oligomer hypothesis for synapse failure and memory loss in Alzheimer’s diseaseNeurobiol Learn Mem201196452954321914486
   PubMed Web of Science ®Google Scholar
• DeFeliceFGVelascoPTLambertMPAbeta oligomers induce neuronal oxidative stress through an N-methyl-D-aspartate receptor-dependent mechanism that is blocked by the Alzheimer drug memantineJ Biol Chem2007282115901160117308309
   PubMed Web of Science ®Google Scholar
• AlberdiESánchez-GómezMVCavaliereFAmyloid beta oligomers induce Ca2+ dysregulation and neuronal death through activation of ionotropic glutamate receptorsCell Calcium201047326427220061018
   PubMed Web of Science ®Google Scholar
• Paula-LimaACAdasmeTSanMartinCAmyloid beta-peptide oligomers stimulate RyR-mediated Ca2+ release inducing mitochondrial fragmentation in hippocampal neurons and prevent RyR-mediated dendritic spine remodeling produced by BDNFAntioxid Redox Signal20111471209122320712397
   PubMed Web of Science ®Google Scholar
• ReeseLCTaglialatelaGA role for calcineurin in Alzheimer’s diseaseCurr Neuropharmacol2011968566922654726
   PubMed Web of Science ®Google Scholar
• MorfiniGSzebenyiGElluruRRatnerNBradySTGlycogen synthase kinase 3 phosphorylates kinesin light chains and negatively regulates kinesin-based motilityEmbo J20022128129311823421
   PubMed Web of Science ®Google Scholar
• LashuelHAHartleyDPetreBMWalzTLansburyPTJrAmyloid pores from pathogenic mutationsNature20024186895291
   PubMed Web of Science ®Google Scholar
• DemuroASmithMParkerISingle channel Ca2+ imaging implicates Ab1-42 amyloid pores in Alzheimer’s disease pathologyJ Cell Biol201119551552422024165
   PubMed Web of Science ®Google Scholar
• PrangkioPYuskoECSeptDYangJMayerMMultivariate analyses of amyloid-beta oligomer populations indicate a connection between pore formation and cytotoxicityPLoS One2012710e4726123077580
   PubMed Web of Science ®Google Scholar
• DemuroAMinaEKayedRMiltonSCParkerIGlabeCGCalcium dysregulation and membrane disruption as a ubiquitous neurotoxic mechanism of soluble amyloid oligomersJ Biol Chem2005280172941730015722360
   PubMed Web of Science ®Google Scholar
• SchauerteJAWongPTWisserKCDingHSteelDGGafniASimultaneous single-molecule fluorescence and conductivity studies reveal distinct classes of AB species on lipid bilayersBiochem2010493031303920201586
   PubMed Web of Science ®Google Scholar
• BodeDCBakerMDVilesJHIon channel formation of amloid-β42 oligomers but not amyloid-β40 in cellular membranesJ Biol Chem201729241404141327927987
   PubMed Web of Science ®Google Scholar
• Di ScalaCTroadecJ-DLelivreCGarmyNFantiniJChahinianHMechanism of cholesterol-assisted oligomeric channel formation by a short Alzheimer β-amyloid peptideJ Neurochem2014128118619523919567
   PubMed Web of Science ®Google Scholar
• Di ScalaCYahiNBoutemeurSCommon molecular mechanism of amyloid pore formation by Alzheimer’s b-amyloid peptide and alpha-synucleinSci Rep201662878127352802
   PubMedGoogle Scholar
• MatamorosAJBaasPWMicrotubules in health and degenerative disease of the nervous systemBrain Res Bull2016126Pt 321722527365230
   PubMedGoogle Scholar
• AhmadzadehHSmithDHShenoyVBViscoelasticity of Tau proteins leads to strain rate-dependent breaking of microtubules during axonal stretch injury: predictions from a mathematical modelBiophys J201410651123113324606936
   PubMed Web of Science ®Google Scholar
• AhmadzadehHSmithDHShenoyVBMechanical effects of dynamic binding between Tau proteins on microtubules during axonal injuryBiophys J2015109112328233726636944
   PubMed Web of Science ®Google Scholar
• LazarusCSoheilypourMMofradMRKTorsional behaviour of axonal microtubule bundlesBiophy J20151092231239
   PubMed Web of Science ®Google Scholar
• LedderoseJSenciónLSalgadoHArias-CarriónOTreviñoMA software tool for the analysis of neuronal morphology dataInt Archives Med201476
   PubMedGoogle Scholar
• MianISRoseCCommunication theory and multicellular biologyIntegr Biol201134350367
   Google Scholar
• RiehlmanTDOlmstedZTPaluh JanetLMolecular motors (Chapter 4)XieYThe Nanobiotechnology HandbookBoca Raton, FLCRC Press201273111
   Google Scholar
• DupontAGorelashviliMSchüllerVThree-dimensional single-particle tracking in live cells: news from the third dimensionNew J Phys201315117
   Web of Science ®Google Scholar
• GrienbergerCKonnerthAImaging calcium in neuronsNeuron201273586288522405199
   PubMed Web of Science ®Google Scholar
• LyonsDATalbotWSTargeting mechanisms in myelinated axons: not all nodes are created equalDev Cell20122217922264726
   PubMed Web of Science ®Google Scholar
• KnuthDThe Art of Computer Programming3rd edBoston, MAAddion Wesley19972
   Google Scholar
• DonahueBSAbercrombieRFFree diffusion coefficient of ionic calcium in cytoplasmCell Calcium1987864374483435913
   PubMed Web of Science ®Google Scholar
• DubeyJRatnakaranNKoushikaSPNeurodegeneration and micro-tubule dynamics: death by a thousand cutsFront Cell Neurosci20159911525667569
   PubMedGoogle Scholar
• OlmstedZTColliverAGPaluhJLThe kinesin–tubulin complex: considerations in structural and functional complexityCell Health Cytoskelet201578397
   Google Scholar
• BustamanteCChemiaYRFordeNRIzhakyDMechanical processes in biochemistryAnnu Rev Biochem20047370574815189157
   PubMed Web of Science ®Google Scholar
• BushSFNanoscale Communication Networks1st edNorwood, MAArtech House2010
   Google Scholar
• MudrakolaHVZhangKCuiBOptically resolving individual microtubules in live axonsStructure200917111433144119913478
   PubMed Web of Science ®Google Scholar
• KleinrockLQueueing Systems Theory1Hoboken, NJWiley & Sons1975
   Google Scholar
• GavishBHantlerSLAn algorithm for optimal route selection networks in SNA NetworksIEEE Trans Commun1983311011541161
   Web of Science ®Google Scholar
• MiyawakiALlopisJHeimRFluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulinNature199738866458828879278050
   PubMed Web of Science ®Google Scholar
• LaskeCStranskyELeyheTStage-dependent BDNF serum concentrations in Alzheimer’s diseaseJ Neural Transm200611391217122416362629
   PubMed Web of Science ®Google Scholar
• O-BryantSEHobsonVHallJRBrain-derived neurotrophic factor levels in Alzheimer’s DiseaseJ Alzheimers Dis200917233734119363274
   PubMed Web of Science ®Google Scholar
• QinX-YCaoCCawleyNXDecreased peripheral brain-derived neurotrophic factor levels in Alzheimer’s disease: a meta-analysis study (N=7277)Molec Psychiatry201722231232027113997
   PubMed Web of Science ®Google Scholar
• HirokawaNShiomuraYOkabeSTau proteins: the molecular structure and mode of binding on microtubulesJ Cell Biol19881074144914593139677
   PubMed Web of Science ®Google Scholar
• ZhangKOsakadaYVrljicMChenLMudrakolaHVCuiBSingle molecule imaging of NGF axonal tansport in microfluidic devicesLab Chip201010192566257320623041
   PubMed Web of Science ®Google Scholar
• PenazziLBakotaLBrandtRMicrotubule dynamics in neuronal development, plasticity, and neurodegenerationInt Rev Cell Mol Biol20163218916926811287
   PubMed Web of Science ®Google Scholar
• SmithMAZhangLXLyonsWEMamounasLAAnterograde transport of endogenous brain-derived neurotrophic factor in hippocampal mossy fibersNeuroreport199788182918349223060
   PubMed Web of Science ®Google Scholar
• Del PreteDCheclerFChamiMRyanodine receptors: physiological function and deregulation in Alzheimer’s diseaseMol Neurodegener20149213624902695
   PubMed Web of Science ®Google Scholar
• KayadRPensalfiniAMargolLAnnular protofibrils are a structurally and functionally distinct type of amyloid oligomerJ Biol Chem200928474230423719098006
   PubMed Web of Science ®Google Scholar
• VermaMVatsATanejaVToxic species in amyloid disorders: oligomers or mature fibrilsAnn Indian Acad Neurol201518213814526019408
   PubMed Web of Science ®Google Scholar
• PrangkioPYuskoECSeptDYangJMayerMMultivariate analyses of amyloid-beta oligomer populations indicate a connection between pore formation and cytotoxicityPLoS One2012710e4726123077580
   PubMed Web of Science ®Google Scholar
• BushSFPaluhJLPiroGRaoVPrasadRVEckfordADefining communication at the bottomIEEE Trans Mol, Biol Multi-Scale Commun2015119097
   Google Scholar
• YuWBaasPWChanges in microtubule number and length during axon differentiationJ Neurosci1994145281828298182441
   PubMed Web of Science ®Google Scholar
• ShengZCaiQMitochondrial transport in neurons: impact on synaptic homeostasis and neurodegenerationNat Rev Neurosci2012132779322218207
   PubMed Web of Science ®Google Scholar
• SimonsTBCalcium and neuronal functionNeurosurg Rev1998119129
   Google Scholar
• DebanneDInformation processing in the axonNat Rev200454304316
   Google Scholar
• LedderoseJSenciónLSalgadoHArias-CarriónOTreviñoMA software tool for the analysis of neuronal morphology dataInt Arch Med2014761924387244
   PubMedGoogle Scholar
• FeinermanOElishaMTransport of information along unidimensional layered networks of dissociated hippocampal neurons and implications for rate codingJ Neurosci200626174526453416641232
   PubMed Web of Science ®Google Scholar
• AmritaTNeeruAFinite-volume method to study calcium diffusion in neuron involving JRyR, JSERCA and JLEAKJ Comput20113114147
   Google Scholar
• FogelsonALZuckerRSPresynaptic calcium diffusion from various arrays of single channelsBiophys J1985486100310172418887
   PubMed Web of Science ®Google Scholar
• BerridgeMJNeuronal calcium signalling reviewNeuron199821713269697848
   PubMedGoogle Scholar
• PierobonMAkyildizIFA physical end-to-end model for molecular communication in nanonetworksIEEE JSAC2010284602611
   Google Scholar
• NakanoTSudaTMooreMEgashiraREnomotoAArimaKMolecular communication for nanomachines using intercellular calcium signalingFifth IEEE Conference on NanomachinesJuly 15, 2005Japan
   Google Scholar
• MooreMEnomotoANakanoTSudaTSimulation of a molecular motor based communication networkProceedings of the 1st International Conference on Bio-Inspired Models of Network, Information and Computing SystemsCavalese, ItalyDecember 11–13, 2006
   Google Scholar
• NittaTTanahashiAHiranoMHessHSimulating molecular shuttle movements: Towards computer-aided design of nanoscale transport systemsLab Chip2006688188516804592
   PubMed Web of Science ®Google Scholar
• PierobonMAkyildizIFNoise analysis in ligand-binding reception for molecular communication in nanonetworksIEEE Trans Sig Process201159941684182
   Web of Science ®Google Scholar
• KuranMSYilmazHBTugcuTModulation techniques for communication via diffusion in nanonetworks2011 IEEE Conference on Computer Communications WorkshopsKyoto, JapanJune 5–9, 2011
   Google Scholar
• MasashiUBergerAJProperties and function of low- and high-voltage-activated Ca2+ channels in hypoglossal motoneuronsJ Neurosci1994149565256608083761
   PubMed Web of Science ®Google Scholar
• TempiaFKanoMSchneggenburgerRFractional calcium current through neuronal AMPA-receptor channels with a low calcium permeabilityJ Neurosci1996762456466
   Google Scholar
• LodishHBerkAZipurskySLMicrotubule structures (Section 19.1)Molecular Cell Biology4th edNew York, NYW. H. Freeman2000
   Google Scholar
• GitHub, Inc Available from: https://github.com/Gaurav111195/nano_com
   Google Scholar