Iyer Laboratory Rice University

We are cell biologists, neurobiologists, and evolutionary developmental biologists.

We study the cross talk between the nervous and immune systems, using zebrafish and cavefish to ask how microglia and macrophages build and maintain the brain and body across evolution, development, and aging.

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Research

What we study.

Full research
Disease

Microglia as contributors to neurological disease

Using large-scale CRISPR screens to define new contributions of microglia to neurodevelopmental disorders, beyond their known roles in neurodegeneration.

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Microglia as contributors to neurological diseaseHomeostatic microglia undergo aberrant activation. In neurodegenerative diseases such as Alzheimer’s disease, activated microglia, prolonged inflammation, and neuronal death and damage reinforce one another, alongside amyloid plaques. In neurodevelopmental disorders such as lysosomal storage disorders, marked by metabolite accumulation and distended lysosomes, the role of microglia is still undefined.Neurodegenerative diseasese.g., Alzheimer’s diseaseNeurodevelopmental disorderse.g., lysosomal storage disordersKnown rolesUnknown rolesprolongedinflammationneuronal deathand damageamyloid plaques?metabolite accumulationand distended lysosomesHomeostatic microgliaaberrant activationAberrantly activatedmicroglia?roleundefined
Evolution

Evolution of microglia and macrophages

Comparing surface and cave populations of the Mexican tetra to uncover naturally evolved differences in microglia and other tissue-resident macrophages.

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Evolution of microglia and macrophagesSurface fish and cavefish forms of the Mexican tetra, compared with each other and with zebrafish. Cavefish larvae have fewer macrophages in the tail; cavefish have more microglia in the brain, and their microglia have lower lysosomal pH and larger proteolytic compartments.ZebrafishSurface fishCavefishMacrophages in larvaeMicroglia in the brainSurface fishCavefishfewer macrophagesmore microglialower lysosomal pHand larger proteolytic compartments
Cell biology

Cell biology of microglia and macrophages

How microglia and macrophages remodel their organelles, from lysosomes and peroxisomes to the ER, Golgi, and mitochondria, when they face stress.

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Cell biology of microglia and macrophagesA phagocyte at rest beside the same cell under extracellular stress, such as injury or infection. Each cell holds a nucleus, endoplasmic reticulum, Golgi apparatus, mitochondria, lysosomes, and peroxisomes. Under stress, the transcription factors Tfeb and Tfe3 move into the nucleus, lysosomes become more numerous and more acidic, mitochondria fragment, the ER swells, the Golgi breaks into scattered mini-stacks, and peroxisomes increase in number.At restUnder stressextracellular stressorganellesremodelERGolgimitochondrialysosomesperoxisomesTfeb / Tfe3
Physiology & behavior

Impact of microglia on animal physiology and behavior

Asking which circuits microglia shape during early development, and how those early events have lasting consequences for animal physiology and behavior.

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Impact of microglia on animal physiology and behaviorEarly in development, microglia sit beside connected neurons and help shape their synapses. When microglia are disrupted, circuits are altered, with surplus synapses. This leads to behavioral changes, measured in a learning and memory maze: two square chambers joined by a narrow hallway, the left outlined in red for sensory enrichment and the right outlined in green for negative reinforcement, which the fish learn to avoid.Early developmentDisrupted microgliaaltered circuitsbehavioral changesSensory enrichmentNegative reinforcement
Recent work

Selected papers and preprints.

All publications
2026 Preprint A comparative brain atlas of Mexican cavefish identifies naturally-occurring changes in cellular composition and gene expression A cell-by-cell map of the cavefish brain shows how its cellular makeup and gene expression changed as the fish adapted to life in caves. 2026 Evolved differences in microglial cell biology between surface and cave populations of Astyanax mexicanus Cavefish have more microglia than their surface relatives, and those microglia have more acidic lysosomes and expanded protein-degrading compartments. 2025 Systems Neuroimmunology: Current Bottlenecks, Research Priorities and Future Directions A perspective from across the field on what is holding neuroimmunology back, and where it should go next. 2024 Chloride transporter ClC-7 is essential for phagocytic clearance by microglia Microglia need the lysosomal chloride transporter ClC-7 to digest the dying neurons they engulf. 2022 A lysosomal regulatory circuit essential for the development and function of microglia Microglia depend on a lysosomal signaling circuit to develop and to function normally in the brain.
The shoal

Who we are.

Meet the team
Harini Iyer Harini Iyer Principal Investigator Emilio Méndez Scolari Emilio Méndez Scolari Graduate Student Tanushree Chakraborty Tanushree Chakraborty Research Technician Brandon Martz Brandon Martz Undergraduate Student Arya Arya Lab Dog
From the lab

News & happenings.

All news
Photo from Oct 17, 2026

Harini co-organizes the Aquatic Models of Human Disease conference at the Marine Biological Laboratory in Woods Hole. And it was a huge success!

 Photo from Oct 10, 2026

Tanushree organizes the Mantra Pearland Durga Puja, and we join her for a night of music, dance, and festive food.

 Photo from Oct 8, 2026

We raise a glass to Emilio’s first paper, accepted in the Journal of Experimental Biology!

Curious about microglia? Join our shoal.

We take rotation students from Rice’s BCB and SSPB graduate programs, and welcome inquiries from prospective trainees.

How to join