Assistant Professor, Department of Biology
Ph.D. University of Oregon
Postdoc, Fred Hutchinson Cancer Research Center
Research Interests: Neural circuit wiring, synapse formation, and electrical synaptogenesis in zebrafish.
Overview: The human brain contains more connections between neurons than the Milky Way has stars! The brain is wired at a gross level into stereotyped neural circuits that underlie sensation, information processing, motor output, and ultimately, consciousness. Disrupted neural circuitry has been linked to many neurodevelopmental disorders, such as autism, epilepsy, and schizophrenia. How do the neurons of the brain connect and wire up into circuits? The goal of the research in the lab is to integrate genetics, biochemistry, cell biology, circuit function, and behavior, to understand how the brain creates functioning neural networks.
Neural circuits are defined by the connections made between neurons, and connections, termed synapses, come in two flavors: chemical, where transmission is mediated by neurotransmitters and receptors, and electrical, where neurons directly communicate with one another through gap junction channels. While the last decade has provided much insight into the developmental genetic mechanisms of building chemical synapses, electrical synapse formation is still not understood. However, it is known that electrical synapses are used by all animals both during development and in adulthood, and are found in sensory, central, and motor circuits. The goal of this project is to unlock the molecular mechanisms underlying electrical synaptogenesis.
Using zebrafish as a model system we have performed a forward genetic screen to identify mutations that cause defects in electrical synapse formation. Mapping mutations from forward genetic screens is challenging, particularly in large vertebrate genomes, but we have developed methods using on next generation sequencing which facilitate the identification of mutated genes (Genome Research). One of the mutations identified in the screen disrupted the autism-associated gene neurobeachin and we found that it was required for both electrical and chemical synapse formation, placing this gene as a critical lynchpin in all of synapse formation (Current Biology). We have also developed a novel CRISPR-based reverse genetic screening method to identify genes required for development – this was the first example that such an approach could be taken in a vertebrate (Nature Methods). The screen identified structural proteins that create the gap junction channel between the neurons and scaffolding that stabilize the synaptic structure. Ongoing work has revealed that electrical synapses can be asymmetric, with unique proteins on each side of the junction. This molecular asymmetry may underlie functional asymmetry and provide differential substrates for altering electrical synapse function.
Current projects focus on several diverse, but related, areas of electrical synaptogenesis:
1) Electrical synapse asymmetry – biochemistry, molecular biology, and genetics
How do the proteins of the synapse function at the molecular level to form the connection? What proteins interact and how do those interactions build the synapse? What other proteins are present at the synapse?
2) Electrical synapse formation – cell biology, development, and genetics
How are proteins trafficked to the synapse? How are they captured and stabilized once present? What are the cytoskeletal structures and motor proteins that facilitate movement? How long do proteins remain at the synapse and are they responsive to neuronal activity?
3) Electrical synapse function – behavior and physiology
Does the composition of the electrical synapse change based on circuit activity? Do molecular asymmetries produce effects on synapse function? How are molecular asymmetries integrated into circuit level function and behavioral output?
4) Electrical and chemical synapse interactions – physiology, development, and genetics
Are early-forming electrical synapses required for subsequent chemical synapse formation? What gap junction channels and scaffolds mediate early circuit activity? How are some early-forming electrical synapses removed as neural circuits mature? How are others retained?
Identification and Characterization of Zebrafish Tlr4 Coreceptor Md-2.
J Immunol. 2021 Jan 20;:
Authors: Loes AN, Hinman MN, Farnsworth DR, Miller AC, Guillemin K, Harms MJ
The zebrafish (Danio rerio) is a powerful model organism for studies of the innate immune system. One apparent difference between human and zebrafish innate immunity is the cellular machinery for LPS sensing. In amniotes, the protein complex formed by TLR4 and myeloid differentiation factor 2 (Tlr4/Md-2) recognizes the bacterial molecule LPS and triggers an inflammatory response. It is believed that zebrafish have neither Md-2 nor Tlr4; Md-2 has not been identified outside of amniotes, whereas the zebrafish tlr4 genes appear to be paralogs, not orthologs, of amniote TLR4s We revisited these conclusions. We identified a zebrafish gene encoding Md-2, ly96 Using single-cell RNA sequencing, we found that ly96 is transcribed in cells that also transcribe genes diagnostic for innate immune cells, including the zebrafish tlr4-like genes. In larval zebrafish, ly96 is expressed in a small number of macrophage-like cells. In a functional assay, zebrafish Md-2 and Tlr4ba form a complex that activates NF-κB signaling in response to LPS. In larval zebrafish ly96 loss-of-function mutations perturbed LPS-induced cytokine production but gave little protection against LPS toxicity. Finally, by analyzing the genomic context of tlr4 genes in 11 jawed vertebrates, we found that tlr4 arose prior to the divergence of teleosts and tetrapods. Thus, an LPS-sensitive Tlr4/Md-2 complex is likely an ancestral feature shared by mammals and zebrafish, rather than a de novo invention on the tetrapod lineage. We hypothesize that zebrafish retain an ancestral, low-sensitivity Tlr4/Md-2 complex that confers LPS responsiveness to a specific subset of innate immune cells.
PMID: 33472906 [PubMed - as supplied by publisher]
Interdependent regulation of stereotyped and stochastic photoreceptor fates in the fly eye.
Dev Biol. 2020 Dec 14;:
Authors: Miller AC, Urban E, Lyons EL, Herman TG, Johnston RJ
Diversification of neuronal subtypes often requires stochastic gene regulatory mechanisms. How stochastically expressed transcription factors interact with other regulators in gene networks to specify cell fates is poorly understood. The random mosaic of color-detecting R7 photoreceptor subtypes in Drosophila is controlled by the stochastic on/off expression of the transcription factor Spineless (Ss). In SsON R7s, Ss induces expression of Rhodopsin 4 (Rh4), whereas in SsOFF R7s, the absence of Ss allows expression of Rhodopsin 3 (Rh3). Here, we find that the transcription factor Runt, which is initially expressed in all R7s, is sufficient to promote stochastic Ss expression. Later, as R7s develop, Ss negatively feeds back onto Runt to prevent repression of Rh4 and ensure proper fate specification. Together, stereotyped and stochastic regulatory inputs are integrated into feedforward and feedback mechanisms to control cell fate.
PMID: 33333066 [PubMed - as supplied by publisher]