Minoru Koyama

Assistant Professor

Telephone number

416-208-8182

Building SW 525A

Research Interests

I am interested in understanding the neural circuit mechanisms of behavioural development. Animals develop increasingly sophisticated behaviours after birth. Addressing the underlying mechanisms of circuit maturation in the brain is fundamental to understanding how neural circuits develop, are functionally organized, and operate. In addition, insights gained will provide a platform to aid our understanding of developmental brain disorders. We use zebrafish, an optically and genetically accessible model vertebrate that enables us to examine how circuit elements emerge, form circuitry, and contribute to behaviour across development through powerful combinations of optics, physiology, genetics and behavioural analyses.

Keywords

Neural circuit analysis
Behaviour development
Advanced optics
Genome editing
Lineage tracing
Computational circuit modeling

Research Area

Systems Neuroscience
Developmental Neuroscience
Motor control

Current Research

My lab currently focuses on the circuit mechanisms of the development of sophisticated motor coordination. We are examining the circuit maturation in the hindbrain and the spinal cord that control the executive element of motor behaviours with cutting-edge techniques including two-photon optogenetics circuit mapping, voltage imaging, CRISPR/Cas9-based lineage tracing, photo-inducible cell ablation, and machine-learning-based behavioural analyses.

We are currently recruiting graduate students and postdoctoral fellows. Please inquire via email.

Publications

2022

TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineages

Espinosa-Medina I, Feliciano D, Belmonte-Mateos C, Linda Miyares R, Garcia-Marques J, Foster B, Lindo S, Pujades C, Koyama M, Lee T
2022, Neuron, 10.1016/j.neuron.2022.10.035

2021

In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor

Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL
2021, Cell Reports, 10.1016/j.celrep.2021.109284

Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

Abdelfattah AS, Zheng J, Reep D, Tsegaye G, Tsang A, Arthur BJ, Rehorova M, Olson CV, Huang Y, Shuai Y, Koyama M, Moya MV, Weber TD, Lemire AL, Baker CA, Falco N, Zheng Q, Grimm JB, Yip MC, Walpita D, Forest CR, Chase M, Campagnola L, Murphy G, Wong AM, Mertz J, Economo MN, Turner G, Lin B, Chen T, Novak O, Lavis LD, Svoboda K, Korff W, Schreiter ER, Hasseman JP, Kolb I
2021, , 10.1101/2021.11.09.467909

TEMPO: A system to sequentially label and genetically manipulate vertebrate cell lineages

Espinosa-Medina I, Feliciano D, Belmonte-Mateos C, Garcia-Marques J, Foster B, Miyares RL, Pujades C, Koyama M, Lee T
2021, , 10.1101/2021.10.27.466134

2020

High-throughput cellular-resolution synaptic connectivity mapping in vivo with concurrent two-photon optogenetics and volumetric Ca2+ imaging

McRaven C, Tanese D, Zhang L, Yang C, Ahrens MB, Emiliani V, Koyama M
2020, , 10.1101/2020.02.21.959650

A fast genetically encoded fluorescent sensor for faithful in vivo acetylcholine detection in mice, fish, worms and flies

Borden PM, Zhang P, Shivange AV, Marvin JS, Cichon J, Dan C, Podgorski K, Figueiredo A, Novak O, Tanimoto M, Shigetomi E, Lobas MA, Kim H, Zhu PK, Zhang Y, Zheng WS, Fan C, Wang G, Xiang B, Gan L, Zhang G, Guo K, Lin L, Cai Y, Yee AG, Aggarwal A, Ford CP, Rees DC, Dietrich D, Khakh BS, Dittman JS, Gan W, Koyama M, Jayaraman V, Cheer JF, Lester HA, Zhu JJ, Looger LL
2020, , 10.1101/2020.02.07.939504

A programmable sequence of reporters for lineage analysis

Garcia-Marques J, Espinosa-Medina I, Ku K, Yang C, Koyama M, Yu H, Lee T
2020, Nature Neuroscience, 10.1038/s41593-020-0676-9

A general approach to engineer positive-going eFRET voltage indicators

Abdelfattah AS, Valenti R, Zheng J, Wong A, Podgorski K, Koyama M, Kim DS, Schreiter ER
2020, Nature Communications, 10.1038/s41467-020-17322-1

2019

In vivo glucose imaging in multiple model organisms with an engineered single-wavelength sensor

Keller JP, Marvin JS, Lacin H, Lemon WC, Shea J, Kim S, Lee RT, Koyama M, Keller PJ, Looger LL
2019, , 10.1101/571422

CLADES: a programmable sequence of reporters for lineage analysis

Garcia-Marques J, Yang C, Espinosa-Medina I, Koyama M, Lee T
2019, , 10.1101/655308

A general approach to engineer positive-going eFRET voltage indicators

Abdelfattah AS, Valenti R, Wong A, Koyama M, Kim DS, Schreiter ER
2019, , 10.1101/690925

Chronology-based architecture of descending circuits that underlie the development of locomotor repertoire after birth

Pujala A, Koyama M
2019, eLife, 10.7554/elife.42135

Dynamic super-resolution structured illumination imaging in the living brain

Turcotte R, Liang Y, Tanimoto M, Zhang Q, Li Z, Koyama M, Betzig E, Ji N
2019, Proceedings of the National Academy of Sciences, 10.1073/pnas.1819965116

Unlimited Genetic Switches for Cell-Type-Specific Manipulation

Garcia-Marques J, Yang C, Espinosa-Medina I, Mok K, Koyama M, Lee T
2019, Neuron, 10.1016/j.neuron.2019.07.005

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang Y, Campagnola L, Seeman SC, Yu J, Zheng J, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Murphy GJ, Podgorski K, Lin B, Chen T, Turner GC, Liu Z, Koyama M, Svoboda K, Ahrens MB, Lavis LD, Schreiter ER
2019, Science, 10.1126/science.aav6416

2018

Unlimited genetic switches for cell-type specific manipulation

Garcia-Marques J, Yang C, Espinosa-Medina I, Mok K, Koyama M, Lee T
2018, , 10.1101/470443

Chronology-based architecture of descending circuits that underlie the development of locomotor repertoire after birth

Pujala A, Koyama M
2018, , 10.1101/425587

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging

Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang Y, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Podgorski K, Lin B, Chen T, Turner GC, Liu Z, Koyama M, Svoboda K, Ahrens MB, Lavis LD, Schreiter ER
2018, , 10.1101/436840

Mutual inhibition of lateral inhibition: a network motif for an elementary computation in the brain

Koyama M, Pujala A
2018, Current Opinion in Neurobiology, 10.1016/j.conb.2017.12.019

50 Hz volumetric functional imaging with continuously adjustable depth of focus

Lu R, Tanimoto M, Koyama M, Ji N
2018, Biomedical Optics Express, 10.1364/boe.9.001964

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

Liu T, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E
2018, Science, 10.1126/science.aaq1392

Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function

Vladimirov N, Wang C, Höckendorf B, Pujala A, Tanimoto M, Mu Y, Yang C, Wittenbach JD, Freeman J, Preibisch S, Koyama M, Keller PJ, Ahrens MB
2018, Nature Methods, 10.1038/s41592-018-0221-x

A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578

Shen Y, Dana H, Abdelfattah AS, Patel R, Shea J, Molina RS, Rawal B, Rancic V, Chang Y, Wu L, Chen Y, Qian Y, Wiens MD, Hambleton N, Ballanyi K, Hughes TE, Drobizhev M, Kim DS, Koyama M, Schreiter ER, Campbell RE
2018, BMC Biology, 10.1186/s12915-018-0480-0

2017

Video-rate volumetric functional imaging of the brain at synaptic resolution

Lu R, Sun W, Liang Y, Kerlin A, Bierfeld J, Seelig JD, Wilson DE, Scholl B, Mohar B, Tanimoto M, Koyama M, Fitzpatrick D, Orger MB, Ji N
2017, Nature Neuroscience, 10.1038/nn.4516

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling

Liu H, Dong P, Ioannou MS, Li L, Shea J, Pasolli HA, Grimm JB, Rivlin PK, Lavis LD, Koyama M, Liu Z
2017, Proceedings of the National Academy of Sciences, 10.1073/pnas.1713895115

2016

A circuit motif in the zebrafish hindbrain for a two alternative behavioral choice to turn left or right

Koyama M, Minale F, Shum J, Nishimura N, Schaffer CB, Fetcho JR
2016, eLife, 10.7554/elife.16808

2011

Mapping a sensory-motor network onto a structural and functional ground plan in the hindbrain

Koyama M, Kinkhabwala A, Satou C, Higashijima S, Fetcho J
2011, Proceedings of the National Academy of Sciences, 10.1073/pnas.1012189108

A structural and functional ground plan for neurons in the hindbrain of zebrafish

Kinkhabwala A, Riley M, Koyama M, Monen J, Satou C, Kimura Y, Higashijima S, Fetcho J
2011, Proceedings of the National Academy of Sciences, 10.1073/pnas.1012185108

2006

MRI-based localization of electrophysiological recording sites within the cerebral cortex at single-voxel accuracy

Matsui T, Koyano KW, Koyama M, Nakahara K, Takeda M, Ohashi Y, Naya Y, Miyashita Y
2006, Nature Methods, 10.1038/nmeth987

2004

Functional Magnetic Resonance Imaging of Macaque Monkeys Performing Visually Guided Saccade Tasks

Koyama M, Hasegawa I, Osada T, Adachi Y, Nakahara K, Miyashita Y
2004, Neuron, 10.1016/s0896-6273(04)00047-9