Protocol for replacing coding intronic MiMIC and CRIMIC lines with T2A-split-GAL4 lines in Drosophila using genetic crosses.

Here, we present a protocol for generating gene-specific split-GAL4 drivers from coding intronic Minos-mediated integration cassette/CRISPR-mediated integration cassette (MiMIC/CRIMIC) lines in Drosophila. We describe steps for four rounds of in vivo genetic crosses, PCR genotyping, and fluorescence imaging to ensure correct orientation of split-GAL4 integration before establishing stable fly stocks. This protocol offers a cost-effective alternative to traditional microinjection techniques for converting coding intronic MiMIC/CRIMIC lines into gene-specific split-GAL4 lines that are adaptable for fly researchers working on different tissues. For complete details on the use and execution of this protocol, please refer to Chen et al.1.

Using single-cell RNA sequencing to generate predictive cell-type-specific split-GAL4 reagents throughout development.

Cell-type-specific tools facilitate the identification and functional characterization of the distinct cell types that form the complexity of neuronal circuits. A large collection of existing genetic tools in Drosophila relies on enhancer activity to label different subsets of cells and has been extremely useful in analyzing functional circuits in adults. However, these enhancer-based GAL4 lines often do not reflect the expression of nearby gene(s) as they only represent a small portion of the full gene regulatory elements. While genetic intersectional techniques such as the split-GAL4 system further improve cell-type-specificity, it requires significant time and resources to screen through combinations of enhancer expression patterns. Here, we use existing developmental single-cell RNA sequencing (scRNAseq) datasets to select gene pairs for split-GAL4 and provide a highly efficient and predictive pipeline (scMarco) to generate cell-type-specific split-GAL4 lines at any time during development, based on the native gene regulatory elements. These gene-specific split-GAL4 lines can be generated from a large collection of coding intronic MiMIC/CRIMIC lines or by CRISPR knock-in. We use the developing Drosophila visual system as a model to demonstrate the high predictive power of scRNAseq-guided gene-specific split-GAL4 lines in targeting known cell types, annotating clusters in scRNAseq datasets as well as in identifying novel cell types. Lastly, the gene-specific split-GAL4 lines are broadly applicable to any other Drosophila tissue. Our work opens new avenues for generating cell-type-specific tools for the targeted manipulation of distinct cell types throughout development and represents a valuable resource for the Drosophila community.

Using single-cell RNA sequencing to generate cell-type-specific split-GAL4 reagents throughout development.

Cell-type-specific tools facilitate the identification and functional characterization of distinct cell types, which underly the complexity of neuronal circuits. A large collection of existing genetic tools in Drosophila relies on enhancer activity to label different subsets of cells. These enhancer-based GAL4 lines often fail to show a predicable expression pattern to reflect the expression of nearby gene(s), partly due to an incomplete capture of the full gene regulatory elements. While genetic intersectional technique such as the split-GAL4 system further improve cell-type-specificity, it requires significant time and resource to generate and screen through combinations of enhancer expression patterns. In addition, since existing enhancer-based split-GAL4 lines that show cell-type-specific labeling in adult are not necessarily active nor specific in early development, there is a relative lack of tools for the study of neural development. Here, we use an existing single-cell RNA sequencing (scRNAseq) dataset to select gene pairs and provide an efficient pipeline to generate cell-type-specific split-GAL4 lines based on the native genetic regulatory elements. These gene-specific split-GAL4 lines can be generated from a large collection of coding intronic MiMIC/CRIMIC lines either by embryo injection or in vivo cassette swapping crosses and/or CRISPR knock-in at the N or C terminal of the gene. We use the developing Drosophila visual system as a model to demonstrate the high prediction power of scRNAseq-guided gene specific split-GAL4 lines in targeting known cell types. The toolkit allows efficient cluster annotation in scRNAseq datasets but also the identification of novel cell types. Lastly, the gene-specific split-GAL4 lines are broadly applicable to Drosophila tissues. Our work opens new avenues for generating cell-type-specific tools for the targeted manipulation of distinct cell types throughout development and represents a valuable resource to the fly research community. Significance Statement: Understanding the functional role of individual cell types in the nervous systems has remained a major challenge for neuroscience researchers, partly due to incomplete identification and characterization of underlying cell types. To study the development of individual cell types and their functional roles in health and disease, experimental access to a specific cell type is often a prerequisite. Here, we establish an experimental pipeline to generate gene-specific split-GAL4 guided by single-cell RNA sequencing datasets. These lines show high accuracy for labeling targeted cell types from early developmental stages to adulthood and can be applied to any tissues in Drosophila. The collection of gene-speicifc-split-GAL4 will provide a valuable resource to the entire fly research community.

Biased cell adhesion organizes a circuit for visual motion integration.

Layer specific computations in the brain rely on neuronal processes establishing synaptic connections with specific partners in distinct laminae. In the Drosophila lobula plate neuropile, the axons of the four subtypes of T4 and T5 visual motion direction-selective neurons segregate into four layers, based on their directional preference, and form synapses with distinct subsets of postsynaptic neurons. Four bi-stratified inhibitory lobula plate intrinsic cells exhibit a consistent synaptic pattern, receiving excitatory T4/T5 inputs in one layer, and conveying inhibitory signals to an adjacent layer. This layered arrangement establishes motion opponency. Here, we identify layer-specific expression of different receptor-ligand pairs belonging to the Beat and Side families of Cell Adhesion Molecules (CAMs) between T4/T5 neurons and their postsynaptic partners. Genetic analysis reveals that Beat/Side mediated interactions are required to restrict T4/T5 axonal innervation to a single layer. We propose that Beat/Side contribute to synaptic specificity by biasing adhesion between synaptic partners before synaptogenesis.

Control of sugar and amino acid feeding via pharyngeal taste neurons.

Insect gustatory systems comprise multiple taste organs for detecting chemicals that signal palatable or noxious quality. Although much is known about how taste neurons sense various chemicals, many questions remain about how individual taste neurons in each taste organ control feeding. Here, we use the Drosophila pharynx as a model to investigate how taste information is encoded at the cellular level to regulate consumption of sugars and amino acids. We first generate taste-blind animals and establish a critical role for pharyngeal input in food selection. We then investigate feeding behavior of both male and female flies in which only selected classes of pharyngeal neurons are restored via binary choice feeding preference assays as well as Fly Liquid-Food Interaction Counter (FLIC) assays. We find instances of integration as well as redundancy in how pharyngeal neurons control behavioral responses to sugars and amino acids. Additionally, we find that pharyngeal neurons drive sugar feeding preference based on sweet taste but not on nutritional value. Finally, we demonstrate functional specialization of pharyngeal and external neurons using optogenetic activation. Overall, our genetic taste neuron protection system in a taste-blind background provides a powerful approach to elucidate principles of pharyngeal taste coding and demonstrates functional overlap and subdivision among taste neurons.SIGNIFICANCE STATEMENTDietary intake of nutritious chemicals such as sugars and amino acids is essential for an animal's survival. In insects, distinct classes of taste neurons control acceptance or rejection of food sources. Here we develop a genetic system to investigate how individual taste neurons in the Drosophila pharynx encode specific tastants, focusing on sugars and amino acids. By examining flies in which only a single class of taste neurons is active, we find evidence for functional overlap as well as redundancy in responses to sugars and amino acids. We also uncover functional subdivision between pharyngeal and external neurons in driving feeding responses. Overall, we find that different pharyngeal neurons act together to control intake of the two categories of appetitive tastants.

Building a circuit through correlated spontaneous neuronal activity in the developing vertebrate and invertebrate visual systems.

During the development of the vertebrate nervous systems, genetic programs assemble an immature circuit that is subsequently refined by neuronal activity evoked by external stimuli. However, prior to sensory experience, the intrinsic property of the developing nervous system also triggers correlated network-level neuronal activity, with retinal waves in the developing vertebrate retina being the best documented example. Spontaneous activity has also been found in the visual system of Drosophila Here, we compare the spontaneous activity of the developing visual system between mammalian and Drosophila and suggest that Drosophila is an emerging model for mechanistic and functional studies of correlated spontaneous activity.

Recent advances in the genetic basis of taste detection in Drosophila.

The insect gustatory system senses taste information from environmental food substrates and processes it to control feeding behaviors. Drosophila melanogaster has been a powerful genetic model for investigating how various chemical cues are detected at the molecular and cellular levels. In addition to an understanding of how tastants belonging to five historically described taste modalities (sweet, bitter, acid, salt, and amino acid) are sensed, recent findings have identified taste neurons and receptors that recognize tastants of non-canonical modalities, including fatty acids, carbonated water, polyamines, H2O2, bacterial lipopolysaccharide (LPS), ammonia, and calcium. Analyses of response profiles of taste neurons expressing different suites of chemosensory receptors have allowed exploration of taste coding mechanisms in primary sensory neurons. In this review, we present the current knowledge of the molecular and cellular basis of taste detection of various categories of tastants. We also summarize evidence for organotopic and multimodal functions of the taste system. Functional characterization of peripheral taste neurons in different organs has greatly increased our understanding of how insect behavior is regulated by the gustatory system, which may inform development of novel insect pest control strategies.

Combinatorial Pharyngeal Taste Coding for Feeding Avoidance in Adult Drosophila.

Taste drives appropriate food preference and intake. In Drosophila, taste neurons are housed in both external and internal organs, but the latter have been relatively underexplored. Here, we report that Poxn mutants with a minimal taste system of pharyngeal neurons can avoid many aversive tastants, including bitter compounds, acid, and salt, suggesting that pharyngeal taste is sufficient for rejecting intake of aversive compounds. Optogenetic activation of selected pharyngeal bitter neurons during feeding events elicits changes in feeding parameters that can suppress intake. Functional dissection experiments indicate that multiple classes of pharyngeal neurons are involved in achieving behavioral avoidance, by virtue of being inhibited or activated by aversive tastants. Tracing second-order pharyngeal circuits reveals two main relay centers for processing pharyngeal taste inputs. Together, our results suggest that the pharynx can control the ingestion of harmful compounds by integrating taste input from different classes of pharyngeal neurons.

A subset of brain neurons controls regurgitation in adult Drosophila melanogaster.

Taste is essential for animals to evaluate food quality and make important decisions about food choice and intake. How complex brains process sensory information to produce behavior is an essential question in the field of sensory neurobiology. Currently, little is known about higher-order taste circuits in the brain as compared with those of other sensory systems. Here, we used the common vinegar fly, Drosophila melanogaster, to screen for candidate neurons labeled by different transgenic GAL4 lines in controlling feeding behaviors. We found that activation of one line (VT041723-GAL4) produces 'proboscis holding' behavior (extrusion of the mouthpart without withdrawal). Further analysis showed that the proboscis holding phenotype indicates an aversive response, as flies pre-fed with either sucrose or water prior to neuronal activation exhibited regurgitation. Anatomical characterization of VT041723-GAL4-labeled neurons suggests that they receive sensory input from peripheral taste neurons. Overall, our study identifies a subset of brain neurons labeled by VT041723-GAL4 that may be involved in a taste circuit that controls regurgitation.

Using Pox-Neuro (Poxn) Mutants in Drosophila Gustation Research: A Double-Edged Sword.

In Drosophila, Pox-neuro (Poxn) is a member of the Paired box (Pax) gene family that encodes transcription factors with characteristic paired DNA-binding domains. During embryonic development, Poxn is expressed in sensory organ precursor (SOP) cells of poly-innervated external sensory (p-es) organs and is important for specifying p-es organ identity (chemosensory) as opposed to mono-innervated external sensory (m-es) organs (mechanosensory). In Poxn mutants, there is a transformation of chemosensory bristles into mechanosensory bristles. As a result, these mutants have often been considered to be entirely taste-blind, and researchers have used them in this capacity to investigate physiological and behavioral functions that act in a taste-independent manner. However, recent studies show that only external taste bristles are transformed in Poxn mutants whereas all internal pharyngeal taste neurons remain intact, raising concerns about interpretations of experimental results using Poxn mutants as taste-blind flies. In this review, we summarize the value of Poxn mutants in advancing our knowledge of taste-enriched genes and feeding behaviors, and encourage revisiting some of the conclusions about taste-independent nutrient-sensing mechanisms derived from these mutants. Lastly, we highlight that Poxn mutant flies remain a valuable tool for probing the function of the relatively understudied pharyngeal taste neurons in sensing meal properties and regulating feeding behaviors.

Molecular and Cellular Organization of Taste Neurons in Adult Drosophila Pharynx.

The Drosophila pharyngeal taste organs are poorly characterized despite their location at important sites for monitoring food quality. Functional analysis of pharyngeal neurons has been hindered by the paucity of molecular tools to manipulate them, as well as their relative inaccessibility for neurophysiological investigations. Here, we generate receptor-to-neuron maps of all three pharyngeal taste organs by performing a comprehensive chemoreceptor-GAL4/LexA expression analysis. The organization of pharyngeal neurons reveals similarities and distinctions in receptor repertoires and neuronal groupings compared to external taste neurons. We validate the mapping results by pinpointing a single pharyngeal neuron required for feeding avoidance of L-canavanine. Inducible activation of pharyngeal taste neurons reveals functional differences between external and internal taste neurons and functional subdivision within pharyngeal sweet neurons. Our results provide roadmaps of pharyngeal taste organs in an insect model system for probing the role of these understudied neurons in controlling feeding behaviors.