Search bioRxiv⌕ Search

Biology subjects

Baker, C. A.

Publications and source records attributed to Baker, C. A..

8 recordsLinked to original sources

Inferring neural dynamics of memory during naturalistic social communication

Memory processes in complex behaviors like social communication require forming representations of the past that grow with time. The neural mechanisms that support such continually growing memory remain unknown. We address this gap in the context of fly courtship, a natural social behavior involving the production and perception of long, complex song sequences. To study female memory for male song history in unrestrained courtship, we present Natural Continuation (NC)--a general, simulation-based model comparison procedure to evaluate candidate neural codes for complex stimuli using naturalistic behavioral data. Applying NC to fly courtship revealed strong evidence for an adaptive population mechanism for how female auditory neural dynamics could convert long song histories into a rich mnemonic format. Song temporal patterning is continually transformed by heterogeneous nonlinear adaptation dynamics, then integrated into persistent activity, enabling common neural mechanisms to retain continuously unfolding information over long periods and yielding state-of-the-art predictions of female courtship behavior. At a population level this coding model produces multi-dimensional advection-diffusion-like responses that separate songs over a continuum of timescales and can be linearly transformed into flexible output signals, illustrating its potential to create a generic, scalable mnemonic format for extended input signals poised to drive complex behavioral responses. This work thus shows how naturalistic behavior can directly inform neural population coding models, revealing here a novel process for memory formation.

neuroscience↗

The role of fruitless in specifying courtship behaviors differs across Drosophila species

Sex-specific behaviors are critical for reproduction and species survival. The sex-specifically spliced transcription factor fruitless (fru) helps establish male courtship behaviors in invertebrates. Forcing male-specific fru (fruM) splicing in Drosophila melanogaster females produces male-typical behaviors, while disrupting female-specific behaviors. However, whether frus joint role in specifying male and inhibiting female behaviors is conserved across species is unknown. We used CRISPR/Cas9 to force FruM expression in female D. virilis, a species in which males and females produce sex-specific songs. In contrast to D. melanogaster, in which one fruM allele is sufficient to generate male behaviors in females, two alleles are needed in D. virilis females. D. virilis females expressing FruM maintain the ability to sing female-typical song as well as lay eggs, whereas D. melanogaster FruM females cannot lay eggs. These results reveal important differences in fru function between divergent species and underscore the importance of studying diverse behaviors and species for understanding the genetic basis of sex differences.

neuroscience↗

Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator

The ability to optically image cellular transmembrane voltage at millisecond-timescale resolution can offer unprecedented insight into the function of living brains in behaving animals. The chemigenetic voltage indicator Voltron is bright and photostable, making it a favorable choice for long in vivo imaging of neuronal populations at cellular resolution. Improving the voltage sensitivity of Voltron would allow better detection of spiking and subthreshold voltage signals. We performed site saturation mutagenesis at 40 positions in Voltron and screened for increased {Delta}F/F0 in response to action potentials (APs) in neurons. Using a fully automated patch-clamp system, we discovered a Voltron variant (Voltron.A122D) that increased the sensitivity to a single AP by 65% compared to Voltron. This variant (named Voltron2) also exhibited approximately 3-fold higher sensitivity in response to sub-threshold membrane potential changes. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, with lower baseline fluorescence. Introducing the same A122D substitution to other Ace2 opsin-based voltage sensors similarly increased their sensitivity. We show that Voltron2 enables improved sensitivity voltage imaging in mice, zebrafish and fruit flies. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.

neuroscience↗

Alpha satellite insertions and the evolutionary landscape of centromeres

Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by FISH a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by lack of constriction and absence of CENP-A binding. The insertion was associated with a 2.8 kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats (LTRs) and located ~10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20-25 million years ago. Long read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name alpha satellite insertion. It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.

genetics↗

Neural Network Organization for Courtship Song Feature Detection in Drosophila

Animals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in the Drosophila melanogaster brain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons - this represents the first map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes, and that neurons with different song mode preferences are highly interconnected in a network that lacks hierarchical structure. Among this network, frequency tuning is centered on the range of frequencies present in song, whereas pulse rate tuning extends to rates outside of song, suggesting that these neurons form a basis set for downstream processing. Our study provides new insights into the organization of auditory coding within the Drosophila brain.

neuroscience↗

Distribution and strength of interlaminar synaptic connectivity in mouse primary visual cortex revealed by two-photon optogenetic stimulation

The most common synaptic connections between neurons in different cortical layers form the basis of the canonical cortical microcircuit. Understanding of cortical function will require further development and application of methods to efficiently characterize synaptic connections within and outside of the canonical pathway. Accordingly, we measured synaptic inputs onto superficial excitatory neurons in response to sequential two-photon optogenetic stimulation of neurons in deeper layers. Layer 4 excitatory neurons and somatostatin-neurons within layer 2/3 represented the most common sources of input. Although connections from excitatory and somatostatin-neurons in layer 5 were less common, the amplitudes of synaptic responses were equally strong. We examined synaptic strength across all connections, as well as the relationships between the strength of connections diverging from a common presynaptic neuron or converging to a single target. While the overall distribution indicates synaptic weight is concentrated to a few connections, strong excitatory connections are distributed across cells.

neuroscience↗

Multimodal cell type correspondence by intersectional mFISH in intact tissues

Defining a complete set of cell types within the cortex requires reconciling disparate results achieved through diverging methodologies. To address this correspondence problem, multiple methodologies must be applied to the same cells across multiple single-cell experiments. Here we present a new approach applying spatial transcriptomics using multiplexed fluorescence in situ hybridization, (mFISH) to brain tissue previously interrogated through two photon optogenetic mapping of synaptic connectivity. This approach can resolve the anatomical, transcriptomic, connectomic, electrophysiological, and morphological characteristics of single cells within the mouse cortex.

neuroscience↗

Sparse recurrent excitatory connectivity in the cortical microcircuit of the adult mouse and human

Generating a comprehensive description of cortical networks requires a large-scale, systematic approach. To that end, the Allen Institute is engaged in a pipeline project using multipatch electrophysiology, supplemented with 2-photon optogenetics, to characterize connectivity and synaptic signaling between classes of neurons in adult mouse and human cortex. We focus on producing results detailed enough for the generation of computational models and enabling comparison with future studies. Here we report our examination of intralaminar connectivity within each of several classes of excitatory neurons. We find that connections are sparse but present among all excitatory cell types and layers we sampled, with the most sparse connections in layers 5 and 6. Almost all mouse synapses exhibited short-term depression with similar dynamics. Synaptic signaling between a subset of layer 2/3 neurons; however, exhibited facilitation. These results contribute to a body of evidence describing recurrent excitatory connectivity as a conserved feature of cortical microcircuits.

neuroscience↗