Juan Marcos Alarcón, PhD

Our laboratory explores how experiences change brain function in neurotypical laboratory rodents as well as in animal models of brain disease. My background training in electrophysiology started with ion channels biophysics during my PhD under Dr. Eduardo Rojas (Univ. of Chile), and then with hippocampal synaptic plasticity function during my post-doc under Dr. Eric Kandel (Columbia Univ.).

At SUNY Downstate Health Sciences University (DHSU), I joined an expert and collegial team of scientists that allowed me to expand our investigational scope to explore neurobiological processes at the gene expression level (e.g. RNAseq), synaptic function level (e.g. synaptic and neuronal electrophysiology), neuronal ensemble organization (e.g. activity-dependent immediate early gene tagging), and behavior (e.g. rodent tasks).

Our current research projects test the connection between neurodevelopmental mechanisms and brain function in animal models of autism. Inspired by this and concomitant with DHSU mission, I developed and co-led with Dr. Jenny Libien an R25 summer research course for young under-represented minorities to investigate the neurobiology of autism spectrum disorders. Overall, our lab's main goal is to provide unique and deeper insight on the nature and mechanisms of neurodevelopmental and neurological disorders.

Visit the Alarcon Lab Website

Education

Undergraduate: Bs & Ms in Biology; University of Concepcion, Chile.

Advanced Degree: PhD in Biomedical Sciences, University of Chile.

Post-Graduate: Neurobiology of Memory, Columbia University, NY, USA.

Research Interests:

Neurobiology, Neurodevelopment

Office

Office location: 4-113
Lab Tel: (718) 221-5325

Research Interest Summary

Understanding how the brain changes with experience is a fundamental question in neuroscience. Our research projects attempt to address this question by characterizing how neuronal and synaptic circuit function changes by experience-driven neural activity.

Research Questions

• How are memory experiences organized within neural ensembles and synaptic circuits?
• What processes and mechanisms underlie the organization of a memory?
• How does the organization of a memory evolve over time?
• How do new memory experiences shape an extant memory organization?

Grants

R25 NS120283 01 (Alarcon, Libien, mPI) 01/01/21-12/31/25
NINDS, “REACH pipeline summer research experience for minority and underrepresented high school and undergraduate students.” 
The Research Experience in Autism for College and High School students (REACH) is an eight-week pipeline summer course for minorities and underrepresented students interested in the field of neuroscience. REACH’s long- term goal is to increase access and retention of underrepresented minorities in science and their representation and decision-making influence within our nation.

• Transcriptomic signatures of hippocampal active place avoidance memory maintenance. Vingan I, Phatarpekar S, Tung VSK, Hernández AI, Evgrafov OV, Alarcon JM. Front Cell Neurosci. 2026 May 18;20:1769317. doi: 10.3389/fncel.2026.1769317. eCollection 2026. PMID: 42232837 Free PMC article.
• Early-life stress alters adult social and coping behaviors in a sex-specific and domain-dependent manner. Cote E, Kodsi M, Alarcon JM. Stress. 2026 Dec 31;29(1):2611616. doi: 10.1080/10253890.2025.2611616. Epub 2026 Jan 4. PMID: 41486376 Free article.
• Persistently Increased Expression of PKMzeta and Unbiased Gene Expression Profiles Identify Hippocampal Molecular Traces of a Long-Term Active Place Avoidance Memory and "Shadow" Proteins. Han J, Grau-Perales A, Harris RM, Lesburguères E, Kao HY, Pal A, Alarcon JM, Sacktor TC, Martiniani S, Hofmann HA, Fenton AA. Adv Sci (Weinh). 2026 May;13(28):e21254. doi: 10.1002/advs.202521254. Epub 2026 Mar 13. PMID: 41824523 Free PMC article.
• Fingolimod normalizes metabolic signatures associated with synaptic plasticity and memory in APP/PS1 model: Sphingosine-1-phosphate receptor a therapeutic target for Alzheimer's. Kalecký K, Buitrago L, Alarcon JM, Singh A, Bottiglieri T, Kaddurah-Daouk R, Hernández AI. Sci Rep. 2026 Mar 10;16(1):12835. doi: 10.1038/s41598-026-42518-8. PMID: 41803285 Free PMC article.
• Chronic functional deficits following a single closed head injury in mice are prevented by minocycline and N-acetyl cysteine. Lawless SC, Kelley C, Nikulina E, Tahir U, Kaur A, Alarcon JM, Bergold PJ. Mol Cell Neurosci. 2025 Dec;135:104049. doi: 10.1016/j.mcn.2025.104049. Epub 2025 Sep 23. PMID: 40998099
• Dopamine release and dopamine-related gene expression in the amygdala are modulated by the gastrin-releasing peptide in opposite directions during stress-enhanced fear learning and extinction. Morishita Y, Fuentes I, Gonzalez-Salinas S, Favate J, Mejaes J, Zushida K, Nishi A, Hevi C, Goldsmith N, Buyske S, Sillivan SE, Miller CA, Kandel ER, Uchida S, Shah P, Alarcon JM, Barker DJ, Shumyatsky GP. Mol Psychiatry. 2025 Jun;30(6):2381-2394. doi: 10.1038/s41380-024-02843-8. Epub 2024 Nov 23. PMID: 39580604 Free PMC article.
• Spatially resolved transcriptomic signatures of hippocampal subregions and Arc-expressing ensembles in active place avoidance memory. Vingan I, Phatarpekar S, Tung VSK, Hernández AI, Evgrafov OV, Alarcon JM. Front Mol Neurosci. 2024 Oct 31;17:1386239. doi: 10.3389/fnmol.2024.1386239. eCollection 2024. PMID: 39544521 Free PMC article.
• The immunomodulatory effect of oral NaHCO3 is mediated by the splenic nerve: multivariate impact revealed by artificial neural networks. Alvarez MR, Alkaissi H, Rieger AM, Esber GR, Acosta ME, Stephenson SI, Maurice AV, Valencia LMR, Roman CA, Alarcon JM. J Neuroinflammation. 2024 Mar 28;21(1):79. doi: 10.1186/s12974-024-03067-x. PMID: 38549144 Free PMC article.
• Phencyclidine Disrupts Neural Coordination and Cognitive Control by Dysregulating Translation. Park EH, Kao HY, Jourdi H, van Dijk MT, Carrillo-Segura S, Tunnell KW, Gutierrez J, Wallace EJ, Troy-Regier M, Radwan B, Lesburguères E, Alarcon JM, Fenton AA. Biol Psychiatry Glob Open Sci. 2023 May 31;4(1):252-263. doi: 10.1016/j.bpsgos.2023.04.009. eCollection 2024 Jan. PMID: 38298788 Free PMC article.
• Can a basic solution activate the inflammatory reflex? A review of potential mechanisms, opportunities, and challenges. Alvarez MR, Alarcon JM, Roman CA, Lazaro D, Bobrowski-Khoury N, Baena-Caldas GP, Esber GR. Pharmacol Res. 2023 Jan;187:106525. doi: 10.1016/j.phrs.2022.106525. Epub 2022 Oct 28. PMID: 36441036 Free article. Review.
• Persistent increases of PKMζ in memory-activated neurons trace LTP maintenance during spatial long-term memory storage. Hsieh C, Tsokas P, Grau-Perales A, Lesburguères E, Bukai J, Khanna K, Chorny J, Chung A, Jou C, Burghardt NS, Denny CA, Flores-Obando RE, Hartley BR, Rodríguez Valencia LM, Hernández AI, Bergold PJ, Cottrell JE, Alarcon JM, Fenton AA, Sacktor TC. Eur J Neurosci. 2021 Oct;54(8):6795-6814. doi: 10.1111/ejn.15137. Epub 2021 Mar 28. PMID: 33540466 Free PMC article.
• Pharmacological inhibition of the primary endocannabinoid producing enzyme, DGL-α, induces autism spectrum disorder-like and co-morbid phenotypes in adult C57BL/J mice. Fyke W, Alarcon JM, Velinov M, Chadman KK. Autism Res. 2021 Jul;14(7):1375-1389. PMID: 33886158
• Pharmacological inhibition of BKCa channels induces a specific social deficit in adult C57BL6/J mice. Fyke W, Alarcon JM, Velinov M, Chadman KK. Behav Neurosci. 2021 Aug;135(4):462-468. PMID: 33734729
• Persistent increases of PKMζ in memory-activated neurons trace LTP maintenance during spatial long-term memory storage. Hsieh C, Tsokas P, Grau-Perales A, Lesburguères E, Bukai J, Khanna K, Chorny J, Chung A, Jou C, Burghardt NS, Denny CA, Flores-Obando RE, Hartley BR, Rodríguez Valencia LM, Hernández AI, Bergold PJ, Cottrell JE, Alarcon JM, Fenton AA, Sacktor TC. Eur J Neurosci. 2021 Oct;54(8):6795-6814. PMID: 33540466
• Noncanonical cytoplasmic poly(A) polymerases regulate RNA levels, alternative RNA processing, and synaptic plasticity but not hippocampal-dependent behaviours. Mansur F, Alarcon JM, Stackpole EE, Wang R, Richter JD. RNA Biol. 2021 Jul;18(7):962-971. doi: 10.1080/15476286.2020.1824061. Epub 2020 Oct 12. PMID: 32954964 Free PMC article.
• Hippocampal transcriptomic responses to enzyme-mediated cellular dissociation. Harris RM, Kao HY, Alarcon JM, Hofmann HA, Fenton AA. (2019) Hippocampus. doi: 10.1002/hipo.23095. PMID: 31087609
• Neuropathology of vitamin B12 deficiency in the Cd320-/- mouse. Arora K, Sequeira JM, Alarcon JM, Wasek B, Arning E, Bottiglieri T, Quadros EV. (2019) FASEB Journal. 33(2):2563-2573. doi: 10.1096/fj.201800754RR. PMID: 30303736
• Normal CA1 Place Fields but Discoordinated Network Discharge in a Fmr1-Null Mouse Model of Fragile X Syndrome. Talbot ZN, Sparks FT, Dvorak D, Curran BM, Alarcon JM, Fenton AA. (2018) Neuron;97(3):684-697. doi: 10.1016/j.neuron.2017.12.043. PMID 29358017.
• Effects of regulatory BC1 RNA deletion on synaptic plasticity, learning, and memory. Chung A, Dahan N, Alarcon JM, Fenton AA. (2017) Learning & Memory;24(12):646-649. doi: 10.1101/lm.045617.117. PMID:29142061.
• Behavioral alterations are associated with vitamin B12 deficiency in the transcobalamin receptor/CD320 KO mouse. Arora K, Sequeira JM, Hernández AI, Alarcon JM, Quadros EV. (2017) PLoS One. e0177156. PMID: 28545069 PMCID: PMC5436650 DOI: 10.1371/journal.pone.0177156
• Persistent modifications of hippocampal synaptic function during remote spatial memory. Pavlowsky A, Wallace E, Fenton AA, Alarcon JM. (2017) Neurobiology of Learning and Memory. PubMed PMID: 27568918.
• Nucleolar integrity is required for the maintenance of long-term synaptic plasticity. Allen KD, Gourov AV, Harte C, Gao P, Lee C, Sylvain D, Splett JM, Oxberry WC, van de Nes PS, Troy-Regier MJ, Wolk J, Alarcon JM, Hernández AI. (2014) PLoS One. (8):e104364. doi: 10.1371/journal.pone.0104364. PMID: 25089620 PMCID: PMC4121280
• Relative contributions of CA3 and medial entorhinal cortex to memory in rats. O'Reilly KC, Alarcon JM, Ferbinteanu J. (2014) Frontiers Behavioral Neuroscience. 28;8:292. doi: 10.3389/fnbeh.2014.00292. PMID: 25221487 PMCID: PMC4148030
• Genetic and acute CPEB1 depletion ameliorate fragile X pathophysiology. Udagawa T, Farny NG, Jakovcevski M, Kaphzan H, Alarcon JM, Anilkumar S, Ivshina M, Hurt JA, Nagaoka K, Nalavadi VC, Lorenz LJ, Bassell GJ, Akbarian S, Chattarji S, Klann E, Richter JD. (2013) Nature Medicine. doi: 10.1038/nm.3353. PMID: 24141422 PMCID: PMC3823751
• Interaction between Long-Term Potentiation and Depression in CA1 Synapses: Temporal Constrains, Functional Compartmentalization and Protein Synthesis. Pavlowsky and Alarcon, J.M. (2012) PLoS One. 7(1):e29865. PMID: 22272255 PMCID: PMC3260185