Alavian Lab Publications

Sharifi P, Bae H, Gveric D, Gentleman SM, Smith PJS, Tierney TS, Alavian KN: CAV2.3 expression is upregulated in the substantia nigra pars compacta of humans with Parkinson’s disease. Brain Disorders 2022, 5:100031.
Tierney TS, Alavian KN, Altman N, Bhatia S, Duchowny M, Hyslop A, Jayakar P, Resnick T, Wang S, Miller I, Ragheb J: Initial experience with magnetic resonance–guided focused ultrasound stereotactic surgery for central brain lesions in young adults. Journal of Neurosurgery 2022:1-8.
Sandrone S, Alavian KN: Threshold Concepts in Neuroscience: Identification Challenges, Educational Opportunities and Recommendations for Practice. Frontiers in Education 2021, 5.
Niu Y, Moghimyfiroozabad S, Moghimyfiroozabad A, Tierney TS, Alavian KN: The factors for the early and late development of midbrain dopaminergic neurons segregate into two distinct evolutionary clusters. Brain Disorders 2021, 1:100002.
Alavian KN, Yu J-T: Disorders of the brain, paradoxes of the enigma. 1. pp. 100003: Elsevier; 2021:100003.
Weinert M, Millet A, Jonas EA, Alavian KN: The mitochondrial metabolic function of DJ-1 is modulated by 14-3-3beta. FASEB J 2019:fj201802754R.
Mallach A, Weinert M, Arthur J, Gveric D, Tierney TS, Alavian KN: Post mortem examination of Parkinson’s disease brains suggests decline in mitochondrial biomass, reversed by deep brain stimulation of subthalamic nucleus. FASEB J 2019:fj201802628R.
Fang Y, Liu C, Lin J, Li X, Alavian KN, Yang Y, Niu Y: PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. BMC Evol Biol 2019, 19:219.
Chen R, Park HA, Mnatsakanyan N, Niu Y, Licznerski P, Wu J, Miranda P, Graham M, Tang J, Boon AJW, Cossu G, Mandemakers W, Bonifati V, Smith PJS, Alavian KN, Jonas EA: Parkinson’s disease protein DJ-1 regulates ATP synthase protein components to increase neuronal process outgrowth. Cell Death Dis 2019, 10:469.
Park HA, Licznerski P, Mnatsakanyan N, Niu Y, Sacchetti S, Wu J, Polster BM, Alavian KN, Jonas EA: Inhibition of Bcl-xL prevents pro-death actions of DeltaN-Bcl-xL at the mitochondrial inner membrane during glutamate excitotoxicity. Cell Death Differ
Niu Y, Moghimyfiroozabad S, Safaie S, Yang Y, Jonas EA, Alavian KN: Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules. Journal of Molecular Evolution
Niu Y, Liu C, Moghimyfiroozabad S, Yang Y, Alavian KN: PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PeerJ 2017, 5:e3712.
Jonas EA, Porter GA, Beutner G, Mnatsakanyan N, Park H-A, Mehta N, Chen R, Alavian KN: The Mitochondrial Permeability Transition Pore: Molecular Structure and Function in Health and Disease. In Molecular Basis for Mitochondrial Signaling. Edited by Rostovtseva TK. Cham: Springer International Publishing; 2017: 69-105
Beutner G, Alavian KN, Jonas EA, Porter GA, Jr.: The Mitochondrial Permeability Transition Pore and ATP Synthase. Handb Exp Pharmacol 2017, 240:21-46.
Mnatsakanyan N, Beutner G, Porter GA, Alavian KN, Jonas EA: Physiological roles of the mitochondrial permeability transition pore. J Bioenerg Biomembr
Jonas EA, Porter GA, Beutner G, Mnatsakanyan N, Alavian KN: The Mitochondrial Permeability Transition Pore, the c-Subunit of the F1Fo ATP Synthase, Cellular Development, and Synaptic Efficiency. In The Functions, Disease-Related Dysfunctions, and Therapeutic Targeting of Neuronal Mitochondria. John Wiley & Sons, Inc; 2016: 31-64
Weinert M, Selvakumar T, Tierney TS, Alavian KN: Isolation, culture and long-term maintenance of primary mesencephalic dopaminergic neurons from embryonic rodent brains. J Vis Exp
Selvakumar T, Alavian KN, Tierney T: Analysis of Gene Expression Changes in the Rat Hippocampus After Deep Brain Stimulation of the Anterior Thalamic Nucleus. J Vis Exp 2015:e52457.
Park HA, Licznerski P, Alavian KN, Shanabrough M, Jonas EA: Bcl-xL is necessary for neurite outgrowth in hippocampal neurons. Antioxid Redox Signal 2015, 22:93-108.
Licznerski P, Duric V, Banasr M, Alavian KN, Ota KT, Kang HJ, Jonas EA, Ursano R, Krystal JH, Duman RS, Traumatic Stress Brain Study G: Decreased SGK1 Expression and Function Contributes to Behavioral Deficits Induced by Traumatic Stress. PLoS Biol 2015, 13:e1002282.
Jonas EA, Porter GA, Jr., Beutner G, Mnatsakanyan N, Alavian KN: Cell death disguised: The mitochondrial permeability transition pore as the c-subunit of the FF ATP synthase. Pharmacol Res
Cotroneo E, Ashek A, Wang L, Wharton J, Dubois OD, Bozorgi SS, Busbridge M, Alavian KN, Wilkins MR, Zhao L: Iron Homeostasis and Pulmonary Hypertension: Iron Deficiency Leads to Pulmonary Vascular Remodeling in the Rat. Circ Res
Alavian KN, Dworetzky SI, Bonanni L, Zhang P, Sacchetti S, Li H, Signore AP, Smith PJ, Gribkoff VK, Jonas EA: The mitochondrial complex V-associated large-conductance inner membrane current is regulated by cyclosporine and dexpramipexole. Mol Pharmacol 2015, 87:1-8.
Jonas EA, Porter GA, Alavian KN: Bcl-xL in neuroprotection and plasticity. Front Physiol 2014, 5:355.
Alavian KN, Jeddi S, Naghipour SI, Nabili P, Licznerski P, Tierney TS: The lifelong maintenance of mesencephalic dopaminergic neurons by Nurr1 and engrailed. J Biomed Sci 2014, 21:27.
Alavian KN, Beutner G, Lazrove E, Sacchetti S, Park HA, Licznerski P, Li H, Nabili P, Hockensmith K, Graham M, Porter GA, Jr., Jonas EA: An uncoupling channel within the c-subunit ring of the F1FO ATP synthase is the mitochondrial permeability transition pore. Proc Natl Acad Sci USA (PNAS) 2014, 111:10580-10585.
Sacchetti S, Alavian KN, Lazrove E, Jonas EA: F1FO ATPase vesicle preparation and technique for performing patch clamp recordings of submitochondrial vesicle membranes. J Vis Exp 2013:e4394.
Li H, Alavian KN, Lazrove E, Mehta N, Jones A, Zhang P, Licznerski P, Graham M, Uo T, Guo J, Rahner C, Duman RS, Morrison RS, Jonas EA: A Bcl-xL-Drp1 complex regulates synaptic vesicle membrane dynamics during endocytosis. Nature Cell Biology 2013, 15:773-785.
Ofengeim D, Chen YB, Miyawaki T, Li H, Sacchetti S, Flannery RJ, Alavian KN, Pontarelli F, Roelofs BA, Hickman JA, Hardwick JM, Zukin RS, Jonas EA: N-terminally cleaved Bcl-xL mediates ischemia-induced neuronal death. Nature Neuroscience 2012, 15:574-580.
Gray JP, Alavian KN, Jonas EA, Heart EA: NAD kinase regulates the size of the NADPH pool and insulin secretion in pancreatic beta-cells. Am J Physiol Endocrinol Metab 2012, 303:E191-199.
Alavian KN, Dworetzky SI, Bonanni L, Zhang P, Sacchetti S, Mariggio MA, Onofrj M, Thomas A, Li H, Mangold JE, Signore AP, Demarco U, Demady DR, Nabili P, Lazrove E, Smith PJ, Gribkoff VK, Jonas EA: Effects of dexpramipexole on brain mitochondrial conductances and cellular bioenergetic efficiency. Brain Res 2012, 1446:1-11.
Sanchez CE, Tierney TS, Gale JT, Alavian KN, Sahin A, Lee JS, Mulligan RC, Carter BS: Recombinant adeno-associated virus type 2 pseudotypes: comparing safety, specificity, and transduction efficiency in the primate striatum. Laboratory investigation. J Neurosurg 2011, 114:672-680.
Chen YB, Aon MA, Hsu YT, Soane L, Teng X, McCaffery JM, Cheng WC, Qi B, Li H, Alavian KN, Dayhoff-Brannigan M, Zou S, Pineda FJ, O’Rourke B, Ko YH, Pedersen PL, Kaczmarek LK, Jonas EA, Hardwick JM: Bcl-xL regulates mitochondrial energetics by stabilizing the inner membrane potential. J Cell Biol 2011, 195:263-276.
Alavian KN, Li H, Collis L, Bonanni L, Zeng L, Sacchetti S, Lazrove E, Nabili P, Flaherty B, Graham M, Chen Y, Messerli SM, Mariggio MA, Rahner C, McNay E, Shore GC, Smith PJ, Hardwick JM, Jonas EA: Bcl-xL regulates metabolic efficiency of neurons through interaction with the mitochondrial F1FO ATP synthase. Nature Cell Biology 2011, 13:1224-1233.
Vahedi S, Rajabian M, Misaghian A, Grbec D, Simon HH, Alavian KN: Parkinson’s disease candidate gene prioritization based on expression profile of midbrain dopaminergic neurons. J Biomed Sci 2010, 17:66.
Chung CY, Licznerski P, Alavian KN, Simeone A, Lin Z, Martin E, Vance J, Isacson O: The transcription factor orthodenticle homeobox 2 influences axonal projections and vulnerability of midbrain dopaminergic neurons. Brain 2010, 133:2022-2031.
Simon HH, Alavian KN: Transcriptional regulation of their survival: the Engrailed homeobox genes. Adv Exp Med Biol 2009, 651:66-72.
Pruszak J, Ludwig W, Blak A, Alavian K, Isacson O: CD15, CD24, and CD29 define a surface biomarker code for neural lineage differentiation of stem cells. Stem Cells 2009, 27:2928-2940.
Alavian KN, Simon HH: Linkage of cDNA expression profiles of mesencephalic dopaminergic neurons to a genome-wide in situ hybridization database. Mol Neurodegener 2009, 4:6.
Alavian KN, Sgado P, Alberi L, Subramaniam S, Simon HH: Elevated P75NTR expression causes death of engrailed-deficient midbrain dopaminergic neurons by Erk1/2 suppression. Neural Dev 2009, 4:11.
Alavian KN, Scholz C, Simon HH: Transcriptional regulation of mesencephalic dopaminergic neurons: the full circle of life and death. Mov Disord 2008, 23:319-328.
Sgado P, Alberi L, Gherbassi D, Galasso SL, Ramakers GM, Alavian KN, Smidt MP, Dyck RH, Simon HH: Slow progressive degeneration of nigral dopaminergic neurons in postnatal Engrailed mutant mice. Proc Natl Acad Sci USA (PNAS) 2006, 103:15242-15247.
Thuret S, Alavian KN, Gassmann M, Lloyd CK, Smits SM, Smidt MP, Klein R, Dyck RH, Simon HH: The neuregulin receptor, ErbB4, is not required for normal development and adult maintenance of the substantia nigra pars compacta. J Neurochem 2004, 91:1302-1311.

Publications

Sharifi P, Bae H, Gveric D, Gentleman SM, Smith PJS, Tierney TS, Alavian KN: CAV2.3 expression is upregulated in the substantia nigra pars compacta of humans with Parkinson’s disease. Brain Disorders 2022, 5:100031.

Tierney TS, Alavian KN, Altman N, Bhatia S, Duchowny M, Hyslop A, Jayakar P, Resnick T, Wang S, Miller I, Ragheb J: Initial experience with magnetic resonance–guided focused ultrasound stereotactic surgery for central brain lesions in young adults. Journal of Neurosurgery 2022:1-8.

Sandrone S, Alavian KN: Threshold Concepts in Neuroscience: Identification Challenges, Educational Opportunities and Recommendations for Practice. Frontiers in Education 2021, 5.

Niu Y, Moghimyfiroozabad S, Moghimyfiroozabad A, Tierney TS, Alavian KN: The factors for the early and late development of midbrain dopaminergic neurons segregate into two distinct evolutionary clusters. Brain Disorders 2021, 1:100002.

Alavian KN, Yu J-T: Disorders of the brain, paradoxes of the enigma. 1. pp. 100003: Elsevier; 2021:100003.

Weinert M, Millet A, Jonas EA, Alavian KN: The mitochondrial metabolic function of DJ-1 is modulated by 14-3-3beta. FASEB J 2019:fj201802754R.

Mallach A, Weinert M, Arthur J, Gveric D, Tierney TS, Alavian KN: Post mortem examination of Parkinson’s disease brains suggests decline in mitochondrial biomass, reversed by deep brain stimulation of subthalamic nucleus. FASEB J 2019:fj201802628R.

Fang Y, Liu C, Lin J, Li X, Alavian KN, Yang Y, Niu Y: PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. BMC Evol Biol 2019, 19:219.

Park HA, Licznerski P, Mnatsakanyan N, Niu Y, Sacchetti S, Wu J, Polster BM, Alavian KN, Jonas EA: Inhibition of Bcl-xL prevents pro-death actions of DeltaN-Bcl-xL at the mitochondrial inner membrane during glutamate excitotoxicity. Cell Death Differ

Niu Y, Moghimyfiroozabad S, Safaie S, Yang Y, Jonas EA, Alavian KN: Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules. Journal of Molecular Evolution

Niu Y, Liu C, Moghimyfiroozabad S, Yang Y, Alavian KN: PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PeerJ 2017, 5:e3712.

Beutner G, Alavian KN, Jonas EA, Porter GA, Jr.: The Mitochondrial Permeability Transition Pore and ATP Synthase. Handb Exp Pharmacol 2017, 240:21-46.

Mnatsakanyan N, Beutner G, Porter GA, Alavian KN, Jonas EA: Physiological roles of the mitochondrial permeability transition pore. J Bioenerg Biomembr

Weinert M, Selvakumar T, Tierney TS, Alavian KN: Isolation, culture and long-term maintenance of primary mesencephalic dopaminergic neurons from embryonic rodent brains. J Vis Exp

Selvakumar T, Alavian KN, Tierney T: Analysis of Gene Expression Changes in the Rat Hippocampus After Deep Brain Stimulation of the Anterior Thalamic Nucleus. J Vis Exp 2015:e52457.

Park HA, Licznerski P, Alavian KN, Shanabrough M, Jonas EA: Bcl-xL is necessary for neurite outgrowth in hippocampal neurons. Antioxid Redox Signal 2015, 22:93-108.

Licznerski P, Duric V, Banasr M, Alavian KN, Ota KT, Kang HJ, Jonas EA, Ursano R, Krystal JH, Duman RS, Traumatic Stress Brain Study G: Decreased SGK1 Expression and Function Contributes to Behavioral Deficits Induced by Traumatic Stress. PLoS Biol 2015, 13:e1002282.

Jonas EA, Porter GA, Jr., Beutner G, Mnatsakanyan N, Alavian KN: Cell death disguised: The mitochondrial permeability transition pore as the c-subunit of the FF ATP synthase. Pharmacol Res

Cotroneo E, Ashek A, Wang L, Wharton J, Dubois OD, Bozorgi SS, Busbridge M, Alavian KN, Wilkins MR, Zhao L: Iron Homeostasis and Pulmonary Hypertension: Iron Deficiency Leads to Pulmonary Vascular Remodeling in the Rat. Circ Res

Alavian KN, Dworetzky SI, Bonanni L, Zhang P, Sacchetti S, Li H, Signore AP, Smith PJ, Gribkoff VK, Jonas EA: The mitochondrial complex V-associated large-conductance inner membrane current is regulated by cyclosporine and dexpramipexole. Mol Pharmacol 2015, 87:1-8.

Jonas EA, Porter GA, Alavian KN: Bcl-xL in neuroprotection and plasticity. Front Physiol 2014, 5:355.

Alavian KN, Jeddi S, Naghipour SI, Nabili P, Licznerski P, Tierney TS: The lifelong maintenance of mesencephalic dopaminergic neurons by Nurr1 and engrailed. J Biomed Sci 2014, 21:27.

Sacchetti S, Alavian KN, Lazrove E, Jonas EA: F1FO ATPase vesicle preparation and technique for performing patch clamp recordings of submitochondrial vesicle membranes. J Vis Exp 2013:e4394.

Li H, Alavian KN, Lazrove E, Mehta N, Jones A, Zhang P, Licznerski P, Graham M, Uo T, Guo J, Rahner C, Duman RS, Morrison RS, Jonas EA: A Bcl-xL-Drp1 complex regulates synaptic vesicle membrane dynamics during endocytosis. Nature Cell Biology 2013, 15:773-785.

Ofengeim D, Chen YB, Miyawaki T, Li H, Sacchetti S, Flannery RJ, Alavian KN, Pontarelli F, Roelofs BA, Hickman JA, Hardwick JM, Zukin RS, Jonas EA: N-terminally cleaved Bcl-xL mediates ischemia-induced neuronal death. Nature Neuroscience 2012, 15:574-580.

Gray JP, Alavian KN, Jonas EA, Heart EA: NAD kinase regulates the size of the NADPH pool and insulin secretion in pancreatic beta-cells. Am J Physiol Endocrinol Metab 2012, 303:E191-199.

Sanchez CE, Tierney TS, Gale JT, Alavian KN, Sahin A, Lee JS, Mulligan RC, Carter BS: Recombinant adeno-associated virus type 2 pseudotypes: comparing safety, specificity, and transduction efficiency in the primate striatum. Laboratory investigation. J Neurosurg 2011, 114:672-680.

Vahedi S, Rajabian M, Misaghian A, Grbec D, Simon HH, Alavian KN: Parkinson’s disease candidate gene prioritization based on expression profile of midbrain dopaminergic neurons. J Biomed Sci 2010, 17:66.

Chung CY, Licznerski P, Alavian KN, Simeone A, Lin Z, Martin E, Vance J, Isacson O: The transcription factor orthodenticle homeobox 2 influences axonal projections and vulnerability of midbrain dopaminergic neurons. Brain 2010, 133:2022-2031.

Simon HH, Alavian KN: Transcriptional regulation of their survival: the Engrailed homeobox genes. Adv Exp Med Biol 2009, 651:66-72.

Pruszak J, Ludwig W, Blak A, Alavian K, Isacson O: CD15, CD24, and CD29 define a surface biomarker code for neural lineage differentiation of stem cells. Stem Cells 2009, 27:2928-2940.

Alavian KN, Simon HH: Linkage of cDNA expression profiles of mesencephalic dopaminergic neurons to a genome-wide in situ hybridization database. Mol Neurodegener 2009, 4:6.

Alavian KN, Sgado P, Alberi L, Subramaniam S, Simon HH: Elevated P75NTR expression causes death of engrailed-deficient midbrain dopaminergic neurons by Erk1/2 suppression. Neural Dev 2009, 4:11.

Alavian KN, Scholz C, Simon HH: Transcriptional regulation of mesencephalic dopaminergic neurons: the full circle of life and death. Mov Disord 2008, 23:319-328.

Sgado P, Alberi L, Gherbassi D, Galasso SL, Ramakers GM, Alavian KN, Smidt MP, Dyck RH, Simon HH: Slow progressive degeneration of nigral dopaminergic neurons in postnatal Engrailed mutant mice. Proc Natl Acad Sci USA (PNAS) 2006, 103:15242-15247.

Thuret S, Alavian KN, Gassmann M, Lloyd CK, Smits SM, Smidt MP, Klein R, Dyck RH, Simon HH: The neuregulin receptor, ErbB4, is not required for normal development and adult maintenance of the substantia nigra pars compacta. J Neurochem 2004, 91:1302-1311.