species

The role of endogenous chimeric mRNA encoded GasderminD fusion proteins in immunity

Project Summary: Programmed inflammatory cell death, or pyroptosis, is a crucial innate defense mechanism that protects hosts against infection and orchestrates subsequent immune responses. Central to this process is Gasdermin D (GSDMD), a protein that forms plasma membrane pores upon activation, enabling the release of pro- inflammatory cytokines such as IL-1β and driving cell lysis. Although GSDMD-mediated pyroptosis has been conventionally understood to be controlled mainly at the post-translational level, through proteolytic cleavage by inflammatory caspases, we have discovered compelling evidence that alternative RNA processing may introduce additional, previously unappreciated complexity in GSDMD regulation. Our laboratories have developed and optimized a highly innovative long-read direct RNA sequencing pipeline, which bypasses conventional cDNA synthesis to avoid artifacts and enables unbiased discovery of native chimeric mRNA (chRNA) in mammalian cells. Using this approach, we have uncovered a remarkably diverse repertoire of chRNA species, including over a thousand unique fusions in murine macrophages and more than two thousand in human inflamed tissues. Among the chRNA found in mice, we identified a chRNA joining the effector domain of GSDMD with a novel C-terminal region encoded by Tmem106a, giving rise to the GSDMD:TMEM106A fusion protein. Functional studies demonstrate that GSDMD:TMEM106A is not only produced in response to inflammatory signals in macrophages but is critical for GSDMD-dependent cytokine release and optimal pyroptosis. Genetic loss of GSDMD:TMEM106A in mice results in reduced cytokine secretion and increased susceptibility to bacterial infection, while in vivo delivery of Gsdmd:Tmem106a mRNA is sufficient for protective immunity. Intriguingly, we have also identified a putative human counterpart, GSDMD:S100A6, which is highly inducible in colon biopsies from patients with inflammatory bowel disease. In this application, we propose a comprehensive exploration of this newly defined class of naturally occurring GSDMD fusion proteins. The specific aims are: (1) to elucidate the subcellular localization, protein-protein interactions, and pore-forming function of GSDMD:TMEM106A during canonical and non-canonical inflammasome activation; (2) to determine the transcriptomic, proteomic, and physiological consequences of GSDMD chRNA expression in vivo during infection, sepsis, and inflammatory disease, and to validate and functionally characterize GSDMD:S100A6 in relevant immune and barrier cell populations. Collectively, this work will establish chimeric splicing as a fundamental source of immunoregulatory protein diversity, redefining the landscape of cell death control in the immune system. By revealing new layers of gasdermin regulation and function, our studies have the potential to identify novel therapeutic strategies for infectious, auto-inflammatory, and immune-mediated diseases.

Regulation of neutrophil endoplasmic reticulum stress response by IRE1a

Project Summary/Abstract: The lungs are exposed to pathogens and environmental toxins that trigger stress and cause numerous respiratory diseases. Effective host defenses against lung infection by bacterial pathogens, including methicillin- resistant Staphylococcus aureus (MRSA), rely on innate immune cells including neutrophils, prominent early responders to sites of infection. If host defenses are ineffective, MRSA causes serious lung infection, resulting in severe morbidity and a significant economic burden on healthcare facilities, where it is endemic. MRSA infections have a mortality rate of up to 14% and an estimated $500 million in healthcare costs in the US alone. Increasing resistance to vancomycin, the last resort antibiotic for MRSA infections, underscore the urgent need for innovative treatment approaches. Although directly targeting pathogens with antibiotics has been a successful approach for treating infections, many pathogens, including MRSA, eventually will become resistant to these drugs. As an alternative, immunomodulatory strategies to enhance host defenses, such as those shown to be effective against cancer cells, have the potential for treating drug-resistant pathogen infections. Recently, we showed that the inositol-requiring enzyme 1-α (IRE1α), an endoplasmic reticulum (ER) stress sensor, is required for clearance of MRSA in a murine skin abscess model, where neutrophils are robustly recruited to the site of infection. Further, IRE1α coordinates signaling events upstream of calcium (Ca2+) mobilization, histone citrullination, and production of mitochondrial reactive oxygen species (mitoROS), all of which are important for neutrophil inflammatory responses including the formation of antimicrobial neutrophil extracellular traps (NETs). Because excessive neutrophil activation and NET release can be detrimental to vital organs, it is not clear whether neutrophil IRE1α-mediated stress responses aid or impede the resolution of infection in the lungs. While IRE1α activation has been linked to the development of lung fibrosis through the regulation of alveolar epithelial- to-mesenchymal transition in the context of chronic inflammatory diseases, its role in pulmonary neutrophil defenses is unknown. Thus, there is a gap in our knowledge of how cellular stress responses modulate pulmonary neutrophil defenses and infection outcomes in the lungs. The overarching goal of this proposal is to elucidate the mechanisms by which neutrophil IRE1α signaling influences production of mitoROS and Ca2+ mobilization to drive NET release, injure lungs, and regulate pulmonary host defense against MRSA. We will accomplish the following Aims: (1) Define the molecular mechanisms underlying IRE1α-mediated mitoROS hyperactivation of human and mouse primary neutrophils and excessive NET release, and (2) Elucidate the role of neutrophil IRE1α signaling in excessive NET release, lung injury, and immunity in vivo using a MRSA pneumonia infection mouse model. These studies will yield mechanistic insight into how IRE1α-driven ER stress responses impact pulmonary neutrophil defenses and lung injury revealing potential targets for anti-microbial immunotherapies.

Circulating extracellular vesicles as functional indicators of maternal mental and physical health in pregnancy and postpartum

Women with high levels of adverse childhood experiences (ACEs) are at significantly greater risk for negative health outcomes in pregnancy and postpartum, including gestational diabetes, PTB, and depressed mood. However, we still lack biomarkers or a sufficient understanding of causal mechanisms. Extracellular vesicles (EVs) are one of the most dynamic and abundant biological signals secreted into maternal circulation, largely produced by the placenta – where levels increase 4-5-fold during pregnancy. Similarly, removal of the placenta at delivery produces a dramatic drop in maternal EV concentration. Across species, we and others have identified significant EV changes during pregnancy associated with homeostatic regulation, including glucose and glucocorticoid levels, supporting key roles for EVs in maternal health. However, longitudinal studies in human pregnancy and postpartum have not been conducted. We know little as to the mechanisms controlling EV secretion or the roles for EVs in maternal pregnancy and postpartum health. Our decade’s long work identified the X-linked gene, O-glycosyltransferase (OGT), in mouse and human placenta as a master gage of the maternal milieu, where OGT regulation of annexin A1 (AA1) is key to EV cargo loading and secretion from the placenta. We recently reported that placental OGT levels positively correlate with maternal EV concentration. How this association may contribute toward postpartum health, including regulating maternal stress physiology and mood in humans is not known. We hypothesize that increased ACEs, similar to stress in preclinical models, are negatively associated with a cell’s ability to secrete EVs important to maintain homeostasis in the face of the challenges of pregnancy and postpartum, producing an increasingly unhealthy state. Therefore, the goals of these proposed studies in both mice and humans are as follows: 1) To identify cellular mechanisms involved in EV secretion important to maternal health outcomes utilizing the placenta as a tool to genetically target OGT in mice and examine maternal homeostatic control related to EV concentration and composition during pregnancy; 2) To examine the functional ability for a dynamic elevation in maternal EV concentration to improve homeostatic regulation in pregnancy and postpartum using chemogenetic activation (DREADDs) of placenta trophoblast cells in pregnancy, and by EV transfer by tail vein injection postpartum; and 3) To examine in women changes in maternal EVs in a longitudinal pregnancy and postpartum study in association with maternal glucose and cortisol changes, we will examine markers of physical (glucose challenge test), HPA stress (hair cortisol & stress- stimulated salivary cortisol) and psychological (Hamilton Rating Scale for Depression, Perceived Stress Scale) health across pregnancy and the postpartum period in 150 healthy women with varying degrees of exposure to ACEs as measured using the ACE Questionnaire (ACE-Q).

Response and defense mechanisms of extraintestinal Escherichia coli to reactive oxygen and chlorine species

Members of the Escherichia coli species are remarkably diverse and comprise commensal, probiotic and pathogenic strains. While some pathogenic E. coli cause intestinal diseases, extraintestinal E. coli (ExPEC) can colonize and infect environments outside the gut. For instance, members of this pathotype can inhabit the urinary tract where they are confronted with a multitude of bactericidal host defense strategies, which requires specialized genetic adaption for survival. ExPEC must defend highly toxic antimicrobials such as hypochlorous acid (HOCl), a potent reactive oxygen and chlorine species (RO/CS) generated during neutrophil-mediated phagocytosis and by enzymes in uroepithelial cells to control bacterial colonization. The increasing rate of ExPEC infections in humans due to changing infection dynamics demonstrate the critical need for a better understanding of ExPEC pathogenesis, which is desperately needed to improve approaches for infection prevention and treatment given the rise in antibiotic resistance spreading among E. coli. Our lab has reported that members of the ExPEC pathotype are more resistant to RCS in vitro and to neutrophil-mediated phagocytosis when compared to non-pathogenic and enteropathogenic E. coli. We identified the defense system responsible for these phenotypes and characterized its regulation during RCS stress: the RcrR regulon consisting of the rcrARB genes is controlled by the RCS-sensing transcriptional repressor RcrR, which reversibly loses its repressor activity upon oxidation by RCS, resulting in de-repression of its downstream targets. Induced expression of rcrB contributes significantly to ExPEC’s increased RCS resistance, however, the precise mechanism of RcrB and the role of RcrA (and potentially other defense players) during RCS stress remain enigmatic. Our long-term goal is to increase the efficacy of existing antimicrobial therapies by purposefully and selectively sensitizing ExPEC to clearance by innate immune cells. The overall objective of this application is a comprehensive analysis of ExPEC’s RCS defense with particular focus on the mechanism of the RcrR regulon. We hypothesize that RcrB directly protects cells from HOCl, while RcrA, another member of the RcrR regulon, mediates evasion from HOCl and invasion into host cells. In Aim 1, we will use phenotypic, biochemical, and imaging approaches to investigate the mechanism by which RcrB contributes to ExPEC’s increased RCS resistance. In Aim 2, we will study the role of RcrA for ExPEC motility, biofilm formation, and host cell invasion. In Aim 3, we will use independent unbiased and targeted approaches, including phenotypic characterization of transposon mutants, to fully comprehend ExPEC-specific responses to and defenses against RCS. Identifying, characterizing and targeting ExPEC-specific defense systems has the potential to increase the body’s own capacity to fight UTIs. Overall, we will involve at least four undergraduate students in our research projects, which we believe will provide an excellent training opportunity for the next generation of scientists.

Addressing C-F bonds and amyloid-formation in biological systems

The ingestion, pulmonary inhalation, and dermal infiltration of C-F bond-containing compounds, most commonly found in the form of per- and polyfluoroalkyl organic acids, causes oxidative stress, inflammation, DNA damage, and developmental defects in infants and adults. These chemicals accumulate in the brain, disrupt neurological function and compromise cognitive and locomotory behavior. Yet, we lack a high-resolution road-map of the interactions between C-F bonds and biomolecular assemblies driving the trajectory towards neurodegenerative outcomes. This gap constitutes a significant barrier to advancing measures designed to mitigate C-F chemistry-associated neurotoxicity. Emerging experimental and computational data from our laboratory reveals that perfluorooctanoic acid, perfluorodecanoic acid and perfluorosulfonic acid corrupt biomolecular structures through C-F:side-chain interactions in tested soluble, globular proteins found in milk and tissues (matrices where C-F chemistries have been detected). Furthermore, they impaired the physiological function in these proteins through displacement of physiological ligands or by compromising the binding of co-factors. The neuroblastoma-derived SHSY-5Y cell line insulted with the said C-F moieties displayed altered gene expression corresponding to reactive oxygen species (ROS), protein ubiquitination, inflammation along with compromised cytoskeletal integrity. C-F bond ingestion ablated dopaminergic (DA) neurons in the nematode C. elegans and induced locomotory deficits in a manner mimicking paraquat. Based on these findings, we propose to gather data towards our hypothesis that C-F bond exposure perturbs biomolecular, cellular and organismal assemblies to onset neurodegeneration-linked trajectories. In Aim 1, we will determine whether organic fluoroacids alter mRNA levels in differentiated SHSY-5Y cells and in neuroprotective gut bacteria (Lactobacillus rhamnosus, Bifidobacterium lactis and Lactobacillus acidophilus). We will examine whether the neuroblastoma cell line exposed to C-F chemistry displays readouts designed to inform the onset of neurodegeneration-associated trajectories (including α-synuclein aggregation). In Aim 2, we will further address in a preclinical model whether C-F burden induces protein aggregation (α-synuclein, amyloid β, mHTT), interferes with dopaminergic neuronal assembles and induces locomotory deficits. Completion of the proposed work will complement ongoing experimental biophysical, structural (crystallographic, NMR) and computational (docking, molecular dynamics simulations) mapping of the interactions between these anthropogenic “forever” chemicals and amyloid-forming proteins potentially resulting in a soluble-to-toxic transformation. It will prepare the stage for vertebrate testing. The findings from this relatively understudied area likely exposes interventional targets for C-F chemistry associated neurotoxicity, spurs therapeutic efforts and can also guide the development of more biocompatible alternatives.

Overcoming Treatment Resistance by Targeting Polyploid Breast Cancer Cells with AI assisted Single-Cell Analysis

Therapy resistance remains a formidable challenge in breast cancer treatment, with emerging evidence identifying polyploid giant cancer cells (PGCCs) as key drivers. These cells, arising through whole-genome doubling (WGD) events, exhibit enhanced resistance to therapies, contributing to disease relapse. PGCCs are characterized by enlarged cell and nuclear sizes, increased DNA content, and greater resilience compared to non-PGCCs. Their prevalence escalates with disease progression and therapeutic stress, underscoring their critical role in treatment resistance. As such, we hypothesize that inhibiting polyploid cancer cells can effectively reduce therapeutic resistance. Despite this, effective strategies targeting PGCCs are limited, hindered by the lack of high-throughput methods to assess PGCC viability and abundance. Traditional screening assays lack the sensitivity to detect the elimination of small populations of PGCCs, while current detection methods, such as visual inspection and flow cytometry, are not suited for high-throughput compound screening. Our preliminary work has established a high-throughput single-cell morphological analysis pipeline capable of quantifying PGCCs, and we successfully screened 2,726 compounds for their efficacy on PGCCs. Based on the preliminary success, we aim to further improve its robustness and accuracy under diverse staining and imaging conditions, ensuring consistent performance across multiple labs for widespread use in PGCC/WGD studies, with deep learning to accelerate the discovery of therapeutic strategies targeting PGCCs. In addition to empirical screening, our scRNA-Seq analysis of PGCCs has revealed altered gene expression, particularly in genes associated with FOXM1, a transcription factor critical in cell cycle regulation and linked to poor outcomes in various cancers. PGCCs also show altered ferroptosis regulators and elevated reactive oxygen species (ROS), indicating susceptibility to ferroptosis. Here, we propose two independent and complementary aims. Aim 1: We will develop and validate a robust deep learning–based single-cell morphological analysis pipeline for accurate PGCC/non-PGCC discrimination across variable staining, imaging, and lab settings. The model will be benchmarked on independent datasets from external labs and released as open-source, version-controlled software with full documentation to support reproducibility and broad adoption in PGCC/WGD research. Aim 2: Leveraging our screen of 2,726 FDA-approved compounds and mechanistic studies of FOXM1 and ferroptosis, we will prioritize and validate therapies that eradicate PGCCs and reduce treatment resistance. Using patient- derived cells, 3D spheroids, and syngeneic/xenograft models, we will rigorously assess top candidates as monotherapy and in combination with standard-of-care agents. Successful completion of this project will accelerate PGCC/WGD research, advance therapeutic strategies to overcome breast cancer resistance, and especially deliver benefits to patients with high PGCC burden. Given the prevalence of WGD across solid tumors and its induction by standard therapies, our approach holds broad clinical relevance and translational impact.

Multi-modal Micro Electrode Fluidic Array (MEFA) Shells for Brain Organoids

Abstract Brain organoids (BOs) derived from human stem cells bridge the gap between monolayer cell culture studies and animal models, which have well-documented limitations. Monolayer cell culture models fail to accurately replicate the 3D interconnectivity in the brain; animal models, while helpful, are limited due to interspecies differences, with most research focusing on rather phenotypical rather than mechanistic aspects. Concurrent with the advancement of BO models is the urgent need to develop 3D micro instrumentation supporting these organoids to investigate brain development and disease in their accurate physiological environment. Conventional microelectrode arrays (MEAs) used for neuronal cell culture studies are planar, which limits recording access to a small fraction of cells on the bottom side of the organoid. Also, conventional microfluidics is inherently planar, and while recent advances in 3D MEAs and 3D microfluidics have enabled electrical and chemical interrogation in 3D, combining both features with tunability and precision to allow independent and simultaneous control is challenging. Recently, we reported new 3D micro instrumentation in the form of 3D shell MEAs and demonstrated its applicability for electrical recording from BOs. They feature lithographically patterned and chip-integrated electrodes and self-folding polymer shells that can be triggered to wrap around BOs to measure electrical activity from the entire organoid surface. The 3D MEA shell system is modeled on and resembles a miniaturized electroencephalography (EEG) cap; the process used to make them is size-scalable, chip-integrated, and mass- producible. In the research, we aim to develop and validate 3D Micro Electrode Fluidic Array (MEFA) shells with multi-modal electrical recording and biochemical control capabilities, offering high spatiotemporal resolution, tunability, and scalability. Since 3D spatiotemporal patterns of neurochemicals play a critical role in molecular and cellular events of neural development and disease, we propose to apply and validate the MEFA shells in two studies that mimic neurodevelopment and monitor the spatiotemporal effects in neurological disorders and their treatments in vitro. We anticipate that the proposed 3D MEFAs would revolutionize brain sciences by permitting real-time, in-situ studies of electrical and chemical stimulation and interrogation of BOs in a high- throughput manner. The proposed 3D scalable, reproducible, and tunable 3D micro instrumentation for BOs has broad relevance to understanding brain development in utero and the development of anatomically accurate drug and toxicity screening platforms for brain sciences and neurological disorders.

Identifying host-interacting proteins of Sneathia vaginalis

PROJECT SUMMARY AND ABSTRACT Sneathia vaginalis is a member of the human normal flora of the vagina. It is also a human pathogen that is associated with preterm birth and amniotic fluid infections as well as the most common bacterial species associated with HPV infection and cervical cancer. The identification of S. vaginalis as a human pathogen is recent and little is known about how this bacterium interacts with the host in either its commensal or pathogenic lifestyles. With the exception of a single toxin, no additional virulence factors have been identified. Our preliminary data demonstrates that S. vaginalis grows to high cell density in rich media; however, it fails to grow planktonically in other media unless host cells are present indicating that S. vaginalis relies on host cells for nutrients. This is consistent with its reduced genome. In addition, bacterial proliferation requires close proximity with the host cells and previous studies demonstrate that S. vaginalis can bind a variety of host cells. The proteins that mediate contact are unknown. We hypothesize that proteins on the surface of S. vaginalis are critical for host cell adhesion. We will use two Aims to examine this. Aim 1 will use mass spectrometry to identify S. vaginalis surface proteins. Aim 2 generates deletion strains of potential adhesins identified in Aim 1 as well as predicted host-interacting proteins that have already been identified bioinformatically based on those in other bacteria. The mutant bacteria are then tested in host-cell adhesion assays. Together, these aims will identify for the first time the proteins found on the surface of S. vaginalis while identifying proteins that interact with host cells that would be expected to contribute to either its commensal or pathogenic lifestyles or both. Moreover, these studies would be used to inform clinical lab practice as surface-expressed proteins could be used to identify identifying markers of S. vaginalis detection.

A dynamic regulatory mechanism controlling bacterial persister formation and resuscitation within biofilms

PROJECT SUMMARY Persisters present a major challenge in clinical infection treatment and recurrent infection management. A continued effort towards a better understanding of the molecular mechanisms of persister formation and resuscitation is needed to provide novel treatment strategies for the control of chronic infections and problems related to persisters. Unlike resistant bacteria, persisters are genetically identical to their susceptible counterparts, and this phenotypic state is inherently transient and shifts in response to environmental conditions. Therefore, it is essential to use an approach tailored to the transient and rare nature of this phenomenon. Pseudomonas aeruginosa (Pa) is an important human pathogen frequently implicated in both acute and chronic infections. Persisters have been identified in both Pa planktonic and biofilm modes of growth, with higher frequencies of persister formation being observed in biofilm, especially in the interior of the mature biofilm structure. In this study, we obtained the first high-resolution single-cell transcriptomes of persister and resuscitated cells isolated directly from the interior of mature biofilms. The results led to the identification of a previously uncharacterized transcriptional regulator that controls persister formation and resuscitation. This regulator, named PriR here, is conserved in Pseudomonas species and has homologs in two critical bacterial pathogens, Acinetobacter baumannii and Enterobacter cloacae. We showed that PriR has a dynamic spatiotemporal gene expression profile, and its expression directly correlates with and causes persister resuscitation. In this application, we propose two specific aims to investigate this novel regulation mechanism of persister formation and resuscitation. Aim 1 will identify the physiological effects of this novel regulatory system on antibiotic tolerance in vitro and in hosts using the Drosophila melanogaster biofilm infection model. Aim 2 will determine its molecular regulatory mechanism via ChIP-seq and RNA-seq, and analyze the putative PriR- controlled genes on persister formation and resuscitation in additional clinically-relevant Pa strains. The insights gained from this proposal will provide crucial new information about the dynamic regulatory mechanism of persister formation and resuscitation. The PriR-controlled resuscitation mechanism could be a promising target for persister eradication approaches by re-sensitizing persister cells to conventional antimicrobials or preventing persister formation. Understanding this novel regulatory system that controls bacterial persister formation and resuscitation could provide new drug targets and/or treatment strategies for persistent infections.

Environmental sampling for the fungal pathogen Coccidioides spp. in New Mexico

PROJECT SUMMARY/ABSTRACT Coccidioidomycosis (also known as Valley fever) is a fungal disease endemic to the arid and semi-arid portions of the United States. Due to its alarming health impacts, it has recently been deemed as one of the fungal diseases of highest concern by the World Health Organization. Disease cases continue to rise, causing increasing concern and warranting further understanding of this disease. Though New Mexico has been considered endemic to the disease since the 1940s, few cases are reported in the state each year, suggesting cases may be going vastly underreported. Indeed, recent epidemiologic models suggest New Mexico is likely underreporting cases, which may be a result of low disease awareness in the state or a lack of understanding what populations are at risk. Meanwhile, the neighboring state of Arizona reports the highest number of cases in the country, despite similarities in climate and ecology to New Mexico. In general, very little is known about the health burden of coccidioidomycosis and the geographical distribution of the causative fungal pathogen, Coccidioides spp., in New Mexico. Interestingly, both species of Coccidioides are likely endemic to New Mexico and hybridization of the species may occur. This, in combination with a variety of different ecosystems across the state, makes New Mexico an ideal location for studying the ecology of Coccidioides spp. The objective of our proposal is to generate preliminary data to gain a better understanding of the geographical distribution of Coccidioides spp. in New Mexico, including any regions where hybridization of the species may be occurring. To achieve this, we will collect soil samples throughout New Mexico to: (1) identify what ecosystems are conducive for the growth of Coccidioides and each Coccidioides species in New Mexico and (2) assess whether locations directly surrounding New Mexico’s five largest population centers (Albuquerque, Las Cruces, Rio Rancho, Santa Fe, and Roswell) are endemic to Coccidioides spp. The positive impacts of our proposal are an understanding of what populations are at risk for contracting this disease, where future disease surveillance efforts should be targeted in the state, and where future soil samples should be collected to further explore the genomics and phenotypes of Coccidioides spp. and potential for hybridization. This will help us achieve our long-term goal: to understand the ecology and endemicity of Coccidioides spp. to increase disease awareness, mitigate the negative health impacts from coccidioidomycosis, and ultimately protect the health of all Americans.

Implementing a New Paradigm for Antifungal Drug Development

About 30% of the drugs currently in clinical use function through covalent modification of their target. Yet, until recently, none of these covalent drugs were specifically designed to utilize this irreversible mode of action. It is our hypothesis that the production of a new class of covalent inactivators, designed to selectively modify new drug targets, will lead to novel agents with efficacy against both native and drug-resistant pathogenic fungal species. Because of their novelty these agents will also offer a greater opportunity to bypass the existing mechanisms of drug resistance. Pathogenic fungal infections remain among the leading causes of human mortality, and this threat is rising due to the increasing prevalence of drug- resistance strains and the paucity of effective antifungal drugs against the more virulent fungal species. Our proposed new drug target is an enzyme that plays a critical role in a uniquely microbial pathway that is essential for the survival of fungal organisms. To test our hypothesis and achieve the goals of this project we plan to complete the following specific aims during the initial R21 phase of this project: (1) Optimization of the potency of novel enzyme inactivators. Our goals here are to use our strong preliminary results to address critical barriers that must be overcome to convert potent enzyme inactivators into advanced drug candidates, thereby achieving higher target selectivity and increasing compound reactivity once bound to the target; (2) Enhance the antifungal capability of these enzyme inactivators. Our strategy for this aim is focused on the incorporation of conjugate partners into this new class of covalent inactivators, enabling them to potentially utilize the existing nutrient uptake systems to achieve toxic levels in Candida species; (3) Examine the target selectivity of our new antifungal agents. Results from fungal growth inhibition and fungal killing assays will be used to evaluate and rank the efficacy of our compounds against both wild-type and drug-resistant Candida strains. Specific milestones are presented to evaluate our achievement of these initial aims. Once accomplished we will immediately proceed to the R33 phase of this project, with the aims of: (4) Pharmacological evaluation of lead candidates, though ranking the drug candidates based on their ADME, pharmacokinetic and toxicity properties; and then (5) Evaluate the efficacy of our candidates against pathogenic fungal infections. A systematic infection animal model will be utilized for candidate screening to identify the best agents against disseminated fungal infections, followed by further efficacy screening in an oral infection model. Completion of these aims will produce, refine and evaluate a new class of antifungal agents with a novel mode of action against an unexplored but essential fungal target. The agents with the most promising drug profiles will then be moved into advanced preclinical trials used to select the most effective new antifungal agents.

Investigating the role of noncoding RNAs in malaria parasites through targeted Cas13-mediated degradation

Project Summary/Abstract One of the most significant sources of morbidity and mortality throughout large regions of the developing world continues to be malaria caused by infection with mosquito-borne parasites of the genus Plasmodium. The parasite species responsible for the most severe form of the disease is P. falciparum. To avoid antibodies produced by their host and thereby maintain lengthy infections, these parasites undergo a process called antigenic variation by which they can extend an infection for over a year. This results from changes in expression of a protein called PfEMP1, the primary antigenic and virulence determinant expressed on the surface of infected red blood cells. A large, multicopy gene family called var encodes different forms of PfEMP1, and switching expression between var genes enables parasites to evade antibody recognition and destruction by the immune system. The process requires precise and coordinated regulation of transcription of each var gene, however how this is accomplished is unknown. It was recently hypothesized that a family of noncoding RNAs (ncRNAs) plays a key role in controlling the expression of each var gene and in determining the likelihood of activation of any given gene. If correct, this would represent a significant advance in our understanding of how P. falciparum controls antigenic variation and avoids immune clearance. To test this hypothesis, we propose to adapt the CRISPR/Cas13 system of targeted RNA degradation for use in P. falciparum. Similar to the extensively used CRISPR/Cas9 system, CRISPR/Cas13 employes guide RNAs to target a nuclease to a sequence-specific target, however Cas13 targets single stranded RNA rather than DNA. By applying this system to the study of var-related ncRNAs, we will degrade specific ncRNAs and determine the effect on var gene expression. Two classes of ncRNAs previously proposed to regulate var gene expression will be targeted, one called ruf6 and a second encoded by the second exon of all var genes. This will enable us to alter ncRNA expression while leaving the underlying genomic DNA untouched, thereby allowing the unambiguous attribution of any resulting phenotypes to the ncRNAs. Aim 1 will optimize the Cas13 system for P. falciparum by testing different variants of the Cas13 endonuclease for their ability to degrade mRNAs encoding fluorescent reporter proteins. We will determine both the efficiency and sequence specificity of the system. Aim 2 will apply the system to var-associated ncRNAs and quantitatively measure changes in var gene expression and transcriptional switching. If successful, the adaptation of the Cas13 system to P. falciparum will provide the malaria research community with a powerful new tool for manipulating gene expression. In addition, we will gain valuable new insights into how malaria parasites regulate var gene expression, antigenic variation and immune evasion.

Astrocytes: From Metabolism to Cognition

Different brain cell types exhibit distinct metabolic signatures that link energy economy to cellular function. Astrocytes and neurons, for instance, diverge dramatically in their reliance on glycolysis versus oxidative phosphorylation, underscoring that metabolic fuel efficiency is not uniform across cell types. A key factor shaping this divergence is the structural organization of the mitochondrial respiratory chain into supercomplexes. Specifically, complexes I (CI) and III (CIII) form a CI–CIII supercomplex, but the degree of this assembly varies by cell type. In neurons, CI is predominantly integrated into supercomplexes, resulting in highly efficient mitochondrial respiration and minimal reactive oxygen species (ROS) generation. Conversely, in astrocytes, a larger fraction of CI remains unassembled, freely existing apart from CIII, leading to reduced respiratory efficiency and elevated mitochondrial ROS production. Despite this apparent inefficiency, astrocytes boast a highly adaptable metabolism capable of responding to diverse stressors. Their looser CI–CIII organization allows for flexible ROS signaling, which activates antioxidant programs via transcription factors like Nrf2. This modular architecture enables astrocytes not only to balance energy production but also to support neuronal health and influence complex organismal behaviors.

Vision for perception versus vision for action: dissociable contributions of visual sensory drives from primary visual cortex and superior colliculus neurons to orienting behaviors

The primary visual cortex (V1) directly projects to the superior colliculus (SC) and is believed to provide sensory drive for eye movements. Consistent with this, a majority of saccade-related SC neurons also exhibit short-latency, stimulus-driven visual responses, which are additionally feature-tuned. However, direct neurophysiological comparisons of the visual response properties of the two anatomically-connected brain areas are surprisingly lacking, especially with respect to active looking behaviors. I will describe a series of experiments characterizing visual response properties in primate V1 and SC neurons, exploring feature dimensions like visual field location, spatial frequency, orientation, contrast, and luminance polarity. The results suggest a substantial, qualitative reformatting of SC visual responses when compared to V1. For example, SC visual response latencies are actively delayed, independent of individual neuron tuning preferences, as a function of increasing spatial frequency, and this phenomenon is directly correlated with saccadic reaction times. Such “coarse-to-fine” rank ordering of SC visual response latencies as a function of spatial frequency is much weaker in V1, suggesting a dissociation of V1 responses from saccade timing. Consistent with this, when we next explored trial-by-trial correlations of individual neurons’ visual response strengths and visual response latencies with saccadic reaction times, we found that most SC neurons exhibited, on a trial-by-trial basis, stronger and earlier visual responses for faster saccadic reaction times. Moreover, these correlations were substantially higher for visual-motor neurons in the intermediate and deep layers than for more superficial visual-only neurons. No such correlations existed systematically in V1. Thus, visual responses in SC and V1 serve fundamentally different roles in active vision: V1 jumpstarts sensing and image analysis, but SC jumpstarts moving. I will finish by demonstrating, using V1 reversible inactivation, that, despite reformatting of signals from V1 to the brainstem, V1 is still a necessary gateway for visually-driven oculomotor responses to occur, even for the most reflexive of eye movement phenomena. This is a fundamental difference from rodent studies demonstrating clear V1-independent processing in afferent visual pathways bypassing the geniculostriate one, and it demonstrates the importance of multi-species comparisons in the study of oculomotor control.

Brain circuits for spatial navigation

In this webinar on spatial navigation circuits, three researchers—Ann Hermundstad, Ila Fiete, and Barbara Webb—discussed how diverse species solve navigation problems using specialized yet evolutionarily conserved brain structures. Hermundstad illustrated the fruit fly’s central complex, focusing on how hardwired circuit motifs (e.g., sinusoidal steering curves) enable rapid, flexible learning of goal-directed navigation. This framework combines internal heading representations with modifiable goal signals, leveraging activity-dependent plasticity to adapt to new environments. Fiete explored the mammalian head-direction system, demonstrating how population recordings reveal a one-dimensional ring attractor underlying continuous integration of angular velocity. She showed that key theoretical predictions—low-dimensional manifold structure, isometry, uniform stability—are experimentally validated, underscoring parallels to insect circuits. Finally, Webb described honeybee navigation, featuring path integration, vector memories, route optimization, and the famous waggle dance. She proposed that allocentric velocity signals and vector manipulation within the central complex can encode and transmit distances and directions, enabling both sophisticated foraging and inter-bee communication via dance-based cues.

The multi-phase plasticity supporting winner effect

Aggression is an innate behavior across animal species. It is essential for competing for food, defending territory, securing mates, and protecting families and oneself. Since initiating an attack requires no explicit learning, the neural circuit underlying aggression is believed to be genetically and developmentally hardwired. Despite being innate, aggression is highly plastic. It is influenced by a wide variety of experiences, particularly winning and losing previous encounters. Numerous studies have shown that winning leads to an increased tendency to fight while losing leads to flight in future encounters. In the talk, I will present our recent findings regarding the neural mechanisms underlying the behavioral changes caused by winning.

Modeling human brain development and disease: the role of primary cilia

Neurodevelopmental disorders (NDDs) impose a global burden, affecting an increasing number of individuals. While some causative genes have been identified, understanding the human-specific mechanisms involved in these disorders remains limited. Traditional gene-driven approaches for modeling brain diseases have failed to capture the diverse and convergent mechanisms at play. Centrosomes and cilia act as intermediaries between environmental and intrinsic signals, regulating cellular behavior. Mutations or dosage variations disrupting their function have been linked to brain formation deficits, highlighting their importance, yet their precise contributions remain largely unknown. Hence, we aim to investigate whether the centrosome/cilia axis is crucial for brain development and serves as a hub for human-specific mechanisms disrupted in NDDs. Towards this direction, we first demonstrated species-specific and cell-type-specific differences in the cilia-genes expression during mouse and human corticogenesis. Then, to dissect their role, we provoked their ectopic overexpression or silencing in the developing mouse cortex or in human brain organoids. Our findings suggest that cilia genes manipulation alters both the numbers and the position of NPCs and neurons in the developing cortex. Interestingly, primary cilium morphology is disrupted, as we find changes in their length, orientation and number that lead to disruption of the apical belt and altered delamination profiles during development. Our results give insight into the role of primary cilia in human cortical development and address fundamental questions regarding the diversity and convergence of gene function in development and disease manifestation. It has the potential to uncover novel pharmacological targets, facilitate personalized medicine, and improve the lives of individuals affected by NDDs through targeted cilia-based therapies.

Cellular and genetic mechanisms of cerebral cortex folding

One of the most prominent features of the human brain is the fabulous size of the cerebral cortex and its intricate folding, both of which emerge during development. Over the last few years, work from my lab has shown that specific cellular and genetic mechanisms play central roles in cortex folding, particularly linked to neural stem and progenitor cells. Key mechanisms include high rates of neurogenesis, high abundance of basal Radial Glia Cells (bRGCs), and neuron migration, all of which are intertwined during development. We have also shown that primary cortical folds follow highly stereotyped patterns, defined by a spatial-temporal protomap of gene expression within germinal layers of the developing cortex. I will present recent findings from my laboratory revealing novel cellular and genetic mechanisms that regulate cortex expansion and folding. We have uncovered the contribution of epigenetic regulation to the establishment of the cortex folding protomap, modulating the expression levels of key transcription factors that control progenitor cell proliferation and cortex folding. At the single cell level, we have identified an unprecedented diversity of cortical progenitor cell classes in the ferret and human embryonic cortex. These are differentially enriched in gyrus versus sulcus regions and establish parallel cell lineages, not observed in mouse. Our findings show that genetic and epigenetic mechanisms in gyrencephalic species diversify cortical progenitor cell types and implement parallel cell linages, driving the expansion of neurogenesis and patterning cerebral cortex folds.

Neural Mechanisms of Subsecond Temporal Encoding in Primary Visual Cortex

Subsecond timing underlies nearly all sensory and motor activities across species and is critical to survival. While subsecond temporal information has been found across cortical and subcortical regions, it is unclear if it is generated locally and intrinsically or if it is a read out of a centralized clock-like mechanism. Indeed, mechanisms of subsecond timing at the circuit level are largely obscure. Primary sensory areas are well-suited to address these question as they have early access to sensory information and provide minimal processing to it: if temporal information is found in these regions, it is likely to be generated intrinsically and locally. We test this hypothesis by training mice to perform an audio-visual temporal pattern sensory discrimination task as we use 2-photon calcium imaging, a technique capable of recording population level activity at single cell resolution, to record activity in primary visual cortex (V1). We have found significant changes in network dynamics through mice’s learning of the task from naive to middle to expert levels. Changes in network dynamics and behavioral performance are well accounted for by an intrinsic model of timing in which the trajectory of q network through high dimensional state space represents temporal sensory information. Conversely, while we found evidence of other temporal encoding models, such as oscillatory activity, we did not find that they accounted for increased performance but were in fact correlated with the intrinsic model itself. These results provide insight into how subsecond temporal information is encoded mechanistically at the circuit level.

Mechanisms of visual diversity: from evolutionary processes to instantaneous responses

Sex hormone regulation of neural gene expression

Gonadal steroid hormones are the principal drivers of sex-variable biology in vertebrates. In the brain, estrogen (17β-estradiol) establishes neural sex differences in many species and modulates mood, behavior, and energy balance in adulthood. To understand the diverse effects of estradiol on the brain, we profiled the genomic binding of estrogen receptor alpha (ERα), providing the first picture of the neural actions of any gonadal hormone receptor. To relate ERα target genes to brain sex differences we assessed gene expression and chromatin accessibility in the posterior bed nucleus of the stria terminalis (BNSTp), a sexually dimorphic node in limbic circuitry that underlies sex-differential social behaviors such as aggression and parenting. In adult animals we observe that levels of ERα are predictive of the extent of sex-variable gene expression, and that these sex differences are a dynamic readout of acute hormonal state. In neonates we find that transient ERα recruitment at birth leads to persistent chromatin opening and male-biased gene expression, demonstrating a true epigenetic mechanism for brain sexual differentiation. Collectively, our findings demonstrate that sex differences in gene expression in the brain are a readout of state-dependent hormone receptor actions, rather than other factors such as sex chromosomes. We anticipate that the ERα targets we have found will contribute to established sex differences in the incidence and etiology of neurological and psychiatric disorders.

Human and Zebrafish retinal circuits: similarities in day and night

Estimating repetitive spatiotemporal patterns from resting-state brain activity data

Repetitive spatiotemporal patterns in resting-state brain activities have been widely observed in various species and regions, such as rat and cat visual cortices. Since they resemble the preceding brain activities during tasks, they are assumed to reflect past experiences embedded in neuronal circuits. Moreover, spatiotemporal patterns involving whole-brain activities may also reflect a process that integrates information distributed over the entire brain, such as motor and visual information. Therefore, revealing such patterns may elucidate how the information is integrated to generate consciousness. In this talk, I will introduce our proposed method to estimate repetitive spatiotemporal patterns from resting-state brain activity data and show the spatiotemporal patterns estimated from human resting-state magnetoencephalography (MEG) and electroencephalography (EEG) data. Our analyses suggest that the patterns involved whole-brain propagating activities that reflected a process to integrate the information distributed over frequencies and networks. I will also introduce our current attempt to reveal signal flows and their roles in the spatiotemporal patterns using a big dataset. - Takeda et al., Estimating repetitive spatiotemporal patterns from resting-state brain activity data. NeuroImage (2016); 133:251-65. - Takeda et al., Whole-brain propagating patterns in human resting-state brain activities. NeuroImage (2021); 245:118711.

A carnivorous mushroom paralyzes and kills nematodes via a volatile ketone

How a fungus overcomes the defence of C. elegans

Central place foraging: how insects anchor spatial information

Many insect species maintain a nest around which their foraging behaviour is centered, and can use path integration to maintain an accurate estimate of their distance and direction (a vector) to their nest. Some species, such as bees and ants, can also store the vector information for multiple salient locations in the world, such as food sources, in a common coordinate system. They can also use remembered views of the terrain around salient locations or along travelled routes to guide return. Recent modelling of these abilities shows convergence on a small set of algorithms and assumptions that appear sufficient to account for a wide range of behavioural data, and which can be mapped to specific insect brain circuits. Notably, this does not include any significant topological knowledge: the insect does not need to recover the information (implicit in their vector memory) about the relationships between salient places; nor to maintain any connectedness or ordering information between view memories; nor to form any associations between views and vectors. However, there remains some experimental evidence not fully explained by these algorithms that may point towards the existence of a more complex or integrated mental map in insects.

Orientation selectivity in rodent V1: theory vs experiments

Neurons in the primary visual cortex (V1) of rodents are selective to the orientation of the stimulus, as in other mammals such as cats and monkeys. However, in contrast with those species, their neurons display a very different type of spatial organization. Instead of orientation maps they are organized in a “salt and pepper” pattern, where adjacent neurons have completely different preferred orientations. This structure has motivated both experimental and theoretical research with the objective of determining which aspects of the connectivity patterns and intrinsic neuronal responses can explain the observed behavior. These analysis have to take into account also that the neurons of the thalamus that send their outputs to the cortex have more complex responses in rodents than in higher mammals, displaying, for instance, a significant degree of orientation selectivity. In this talk we present work showing that a random feed-forward connectivity pattern, in which the probability of having a connection between a cortical neuron and a thalamic neuron depends only on the relative distance between them is enough explain several aspects of the complex phenomenology found in these systems. Moreover, this approach allows us to evaluate analytically the statistical structure of the thalamic input on the cortex. We find that V1 neurons are orientation selective but the preferred orientation of the stimulus depends on the spatial frequency of the stimulus. We disentangle the effect of the non circular thalamic receptive fields, finding that they control the selectivity of the time-averaged thalamic input, but not the selectivity of the time locked component. We also compare with experiments that use reverse correlation techniques, showing that ON and OFF components of the aggregate thalamic input are spatially segregated in the cortex.

LifePerceives

Life Perceives is a symposium bringing together scientists and artists for an open exploration of how “perception” can be understood as a phenomenon that does not only belong to humans, or even the so-called “higher organisms”, but exists across the entire spectrum of life in a myriad of forms. The symposium invites leading practitioners from the arts and sciences to present unique insights through short talks, open discussions, and artistic interventions that bring us slightly closer to the life worlds of plants and fungi, microbial communities and immune systems, cuttlefish and crows. What do we mean when we talk about perception in other species? Do other organisms have an experience of the world? Or does our human-centred perspective make understanding other forms of life on their own terms an impossible dream? Whatever your answers to these questions may be, we hope to unsettle them, and leave you more curious than when you arrived.

Vision for Predation

Roots of Analogy

Can nonhuman animals perceive the relation-between-relations? This intriguing question has been studied over the last 40 years; nonetheless, the extent to which nonhuman species can do so remains controversial. Here, I review empirical evidence suggesting that pigeons, parrots, crows, and baboons join humans in reliably acquiring and transferring relational matching-to-sample (RMTS). Many theorists consider that RMTS captures the essence of analogy, because basic to analogy is appreciating the ‘relation between relations.’ Factors affecting RMTS performance include: prior training experience, the entropy of the sample stimulus, and whether the items that serve as sample stimuli can also serve as choice stimuli.

Neural circuits for vector processing in the insect brain

Several species of insects have been observed to perform accurate path integration, constantly updating a vector memory of their location relative to a starting position, which they can use to take a direct return path. Foraging insects such as bees and ants are also able to store and recall the vectors to return to food locations, and to take novel shortcuts between these locations. Other insects, such as dung beetles, are observed to integrate multimodal directional cues in a manner well described by vector addition. All these processes appear to be functions of the Central Complex, a highly conserved and strongly structured circuit in the insect brain. Modelling this circuit, at the single neuron level, suggests it has general capabilities for vector encoding, vector memory, vector addition and vector rotation that can support a wide range of directed and navigational behaviours.

Exploring emotion in the expression of ape gesture

Language appears to be the most complex system of animal communication described to date. However, its precursors were present in the communication of our evolutionary ancestors and are likely shared by our modern ape cousins.  All great apes, including humans, employ a rich repertoire of vocalizations, facial expressions, and gestures. Great ape gestural repertoires are particularly elaborate, with ape species employing over 80 different gesture types intentionally: that is towards a recipient with a specific goal in mind. Intentional usage allows us to ask not only what information is encoded in ape gestures, but what do apes mean when they use them. I will discuss recent research on ape gesture, on how we approach the question of decoding meaning, and how with new methods we are starting to integrate long overlooked aspects of ape gesture such as group and individual variation, and expression and emotion into our study of these signals.

Development and evolution of neuronal connectivity

In most animal species including humans, commissural axons connect neurons on the left and right side of the nervous system. In humans, abnormal axon midline crossing during development causes a whole range of neurological disorders ranging from congenital mirror movements, horizontal gaze palsy, scoliosis or binocular vision deficits. The mechanisms which guide axons across the CNS midline were thought to be evolutionary conserved but our recent results suggesting that they differ across vertebrates.  I will discuss the evolution of visual projection laterality during vertebrate evolution.  In most vertebrates, camera-style eyes contain retinal ganglion cell (RGC) neurons projecting to visual centers on both sides of the brain. However, in fish, RGCs are thought to only innervate the contralateral side. Using 3D imaging and tissue clearing we found that bilateral visual projections exist in non-teleost fishes. We also found that the developmental program specifying visual system laterality differs between fishes and mammals. We are currently using various strategies to discover genes controlling the development of visual projections. I will also present ongoing work using 3D imaging techniques to study the development of the visual system in human embryo.

Redox and mitochondrial dysregulation in epilepsy

Epileptic seizures render the brain uniquely dependent on energy producing pathways. Studies in our laboratory have been focused on the role of redox processes and mitochondria in the context of abnormal neuronal excitability associated with epilepsy. We have shown that that status epilepticus (SE) alters mitochondrial and cellular redox status, energetics and function and conversely, that reactive oxygen species and resultant dysfunction can lead to chronic epilepsy. Oxidative stress and neuroinflammatory pathways have considerable crosstalk and targeting redox processes has recently been shown to control neuroinflammation and excitability. Understanding the role of metabolic and redox processes can enable the development of novel therapeutics to control epilepsy and/or its comorbidities.

Epigenome regulation in neocortex expansion and generation of neuronal subtypes

Evolutionarily, the expansion of the human neocortex accounts for many of the unique cognitive abilities of humans. This expansion appears to reflect the increased proliferative potential of basal progenitors (BPs) in mammalian evolution. Further cortical progenitors generate both glutamatergic excitatory neurons (ENs) and GABAergic inhibitory interneurons (INs) in human cortex, whereas they produce exclusively ENs in rodents. The increased proliferative capacity and neuronal subtype generation of cortical progenitors in mammalian evolution may have evolved through epigenetic alterations. However, whether or how the epigenome in cortical progenitors differs between humans and other species is unknown. Here, we report that histone H3 acetylation is a key epigenetic regulation in BP profiling of sorted BPs, we show that H3K9 acetylation is low in murine BPs and high in amplification, neuronal subtype generation and cortical expansion. Through epigenetic profiling of sorted BPs, we show that H3K9 acetylation is low in murine BPs and high in human BPs. Elevated H3K9ac preferentially increases BP proliferation, increasing the size and folding of the normally smooth mouse neocortex. Furthermore, we found that the elevated H3 acetylation activates expression of IN genes in in developing mouse cortex and promote proliferation of IN progenitor-like cells in cortex of Pax6 mutant mouse models. Mechanistically, H3K9ac drives the BP amplification and proliferation of these IN progenitor-like cells by increasing expression of the evolutionarily regulated gene, TRNP1. Our findings demonstrate a previously unknown mechanism that controls neocortex expansion and generation of neuronal subtypes. Keywords: Cortical development, neurogenesis, basal progenitors, cortical size, gyrification, excitatory neuron, inhibitory interneuron, epigenetic profiling, epigenetic regulation, H3 acetylation, H3K9ac, TRNP1, PAX6

On the contributions of retinal direction selectivity to cortical motion processing in mice

Cells preferentially responding to visual motion in a particular direction are said to be direction-selective, and these were first identified in the primary visual cortex. Since then, direction-selective responses have been observed in the retina of several species, including mice, indicating motion analysis begins at the earliest stage of the visual hierarchy. Yet little is known about how retinal direction selectivity contributes to motion processing in the visual cortex. In this talk, I will present our experimental efforts to narrow this gap in our knowledge. To this end, we used genetic approaches to disrupt direction selectivity in the retina and mapped neuronal responses to visual motion in the visual cortex of mice using intrinsic signal optical imaging and two-photon calcium imaging. In essence, our work demonstrates that direction selectivity computed at the level of the retina causally serves to establish specialized motion responses in distinct areas of the mouse visual cortex. This finding thus compels us to revisit our notions of how the brain builds complex visual representations and underscores the importance of the processing performed in the periphery of sensory systems.

Multimodal tracking of motor activity, sleep and mood

This talk will (1) describe patterns and correlates of objectively assessed motor activity (2) present findings on the inter-relationships among motor activity, sleep and circadian rhythms and mood disorders; (3) describe potential of cross species studies of motor activity and related systems to inform human chronobiology research

Reprogramming the nociceptive circuit topology reshapes sexual behavior in C. elegans

In sexually reproducing species, males and females respond to environmental sensory cues and transform the input into sexually dimorphic traits. Yet, how sexually dimorphic behavior is encoded in the nervous system is poorly understood. We characterize the sexually dimorphic nociceptive behavior in C. elegans – hermaphrodites present a lower pain threshold than males in response to aversive stimuli, and study the underlying neuronal circuits, which are composed of the same neurons that are wired differently. By imaging receptor expression, calcium responses and glutamate secretion, we show that sensory transduction is similar in the two sexes, and therefore explore how downstream network topology shapes dimorphic behavior. We generated a computational model that replicates the observed dimorphic behavior, and used this model to predict simple network rewirings that would switch the behavior between the sexes. We then showed experimentally, using genetic manipulations, artificial gap junctions, automated tracking and optogenetics, that these subtle changes to male connectivity result in hermaphrodite-like aversive behavior in-vivo, while hermaphrodite behavior was more robust to perturbations. Strikingly, when presented with aversive cues, rewired males were compromised in finding mating partners, suggesting that the network topology that enables efficient avoidance of noxious cues would have a reproductive "cost". To summarize, we present a deconstruction of a sex-shared neural circuit that affects sexual behavior, and how to reprogram it. More broadly, our results are an example of how common neuronal circuits changed their function during evolution by subtle topological rewirings to account for different environmental and sexual needs.

The evolution of computation in the brain: Insights from studying the retina

The retina is probably the most accessible part of the vertebrate central nervous system. Its computational logic can be interrogated in a dish, from patterns of lights as the natural input, to spike trains on the optic nerve as the natural output. Consequently, retinal circuits include some of the best understood computational networks in neuroscience. The retina is also ancient, and central to the emergence of neurally complex life on our planet. Alongside new locomotor strategies, the parallel evolution of image forming vision in vertebrate and invertebrate lineages is thought to have driven speciation during the Cambrian. This early investment in sophisticated vision is evident in the fossil record and from comparing the retina’s structural make up in extant species. Animals as diverse as eagles and lampreys share the same retinal make up of five classes of neurons, arranged into three nuclear layers flanking two synaptic layers. Some retina neuron types can be linked across the entire vertebrate tree of life. And yet, the functions that homologous neurons serve in different species, and the circuits that they innervate to do so, are often distinct to acknowledge the vast differences in species-specific visuo-behavioural demands. In the lab, we aim to leverage the vertebrate retina as a discovery platform for understanding the evolution of computation in the nervous system. Working on zebrafish alongside birds, frogs and sharks, we ask: How do synapses, neurons and networks enable ‘function’, and how can they rearrange to meet new sensory and behavioural demands on evolutionary timescales?

Exploring mechanisms of human brain expansion in cerebral organoids

The human brain sets us apart as a species, with its size being one of its most striking features. Brain size is largely determined during development as vast numbers of neurons and supportive glia are generated. In an effort to better understand the events that determine the human brain’s cellular makeup, and its size, we use a human model system in a dish, called cerebral organoids. These 3D tissues are generated from pluripotent stem cells through neural differentiation and a supportive 3D microenvironment to generate organoids with the same tissue architecture as the early human fetal brain. Such organoids are allowing us to tackle questions previously impossible with more traditional approaches. Indeed, our recent findings provide insight into regulation of brain size and neuron number across ape species, identifying key stages of early neural stem cell expansion that set up a larger starting cell number to enable the production of increased numbers of neurons. We are also investigating the role of extrinsic regulators in determining numbers and types of neurons produced in the human cerebral cortex. Overall, our findings are pointing to key, human-specific aspects of brain development and function, that have important implications for neurological disease.

The evolution and development of visual complexity: insights from stomatopod visual anatomy, physiology, behavior, and molecules

Bioluminescence, which is rare on land, is extremely common in the deep sea, being found in 80% of the animals living between 200 and 1000 m. These animals rely on bioluminescence for communication, feeding, and/or defense, so the generation and detection of light is essential to their survival. Our present knowledge of this phenomenon has been limited due to the difficulty in bringing up live deep-sea animals to the surface, and the lack of proper techniques needed to study this complex system. However, new genomic techniques are now available, and a team with extensive experience in deep-sea biology, vision, and genomics has been assembled to lead this project. This project is aimed to study three questions 1) What are the evolutionary patterns of different types of bioluminescence in deep-sea shrimp? 2) How are deep-sea organisms’ eyes adapted to detect bioluminescence? 3) Can bioluminescent organs (called photophores) detect light in addition to emitting light? Findings from this study will provide valuable insight into a complex system vital to communication, defense, camouflage, and species recognition. This study will bring monumental contributions to the fields of deep sea and evolutionary biology, and immediately improve our understanding of bioluminescence and light detection in the marine environment. In addition to scientific advancement, this project will reach K-college aged students through the development and dissemination of educational tools, a series of molecular and organismal-based workshops, museum exhibits, public seminars, and biodiversity initiatives.

The Synaptome Architecture of the Brain: Lifespan, disease, evolution and behavior

The overall aim of my research is to understand how the organisation of the synapse, with particular reference to the postsynaptic proteome (PSP) of excitatory synapses in the brain, informs the fundamental mechanisms of learning, memory and behaviour and how these mechanisms go awry in neurological dysfunction. The PSP indeed bears a remarkable burden of disease, with components being disrupted in disorders (synaptopathies) including schizophrenia, depression, autism and intellectual disability. Our work has been fundamental in revealing and then characterising the unprecedented complexity (>1000 highly conserved proteins) of the PSP in terms of the subsynaptic architecture of postsynaptic proteins such as PSD95 and how these proteins assemble into complexes and supercomplexes in different neurons and regions of the brain. Characterising the PSPs in multiple species, including human and mouse, has revealed differences in key sets of functionally important proteins, correlates with brain imaging and connectome data, and a differential distribution of disease-relevant proteins and pathways. Such studies have also provided important insight into synapse evolution, establishing that vertebrate behavioural complexity is a product of the evolutionary expansion in synapse proteomes that occurred ~500 million years ago. My lab has identified many mutations causing cognitive impairments in mice before they were found to cause human disorders. Our proteomic studies revealed that >130 brain diseases are caused by mutations affecting postsynaptic proteins. We uncovered mechanisms that explain the polygenic basis and age of onset of schizophrenia, with postsynaptic proteins, including PSD95 supercomplexes, carrying much of the polygenic burden. We discovered the “Genetic Lifespan Calendar”, a genomic programme controlling when genes are regulated. We showed that this could explain how schizophrenia susceptibility genes are timed to exert their effects in young adults. The Genes to Cognition programme is the largest genetic study so far undertaken into the synaptic molecular mechanisms underlying behaviour and physiology. We made important conceptual advances that inform how the repertoire of both innate and learned behaviours is built from unique combinations of postsynaptic proteins that either amplify or attenuate the behavioural response. This constitutes a key advance in understanding how the brain decodes information inherent in patterns of nerve impulses, and provides insight into why the PSP has evolved to be so complex, and consequently why the phenotypes of synaptopathies are so diverse. Our most recent work has opened a new phase, and scale, in understanding synapses with the first synaptome maps of the brain. We have developed next-generation methods (SYNMAP) that enable single-synapse resolution molecular mapping across the whole mouse brain and extensive regions of the human brain, revealing the molecular and morphological features of a billion synapses. This has already uncovered unprecedented spatiotemporal synapse diversity organised into an architecture that correlates with the structural and functional connectomes, and shown how mutations that cause cognitive disorders reorganise these synaptome maps; for example, by detecting vulnerable synapse subtypes and synapse loss in Alzheimer’s disease. This innovative synaptome mapping technology has huge potential to help characterise how the brain changes during normal development, including in specific cell types, and with degeneration, facilitating novel pathways to diagnosis and therapy.

Do Capuchin Monkeys, Chimpanzees and Children form Overhypotheses from Minimal Input? A Hierarchical Bayesian Modelling Approach

Abstract concepts are a powerful tool to store information efficiently and to make wide-ranging predictions in new situations based on sparse data. Whereas looking-time studies point towards an early emergence of this ability in human infancy, other paradigms like the relational match to sample task often show a failure to detect abstract concepts like same and different until the late preschool years. Similarly, non-human animals have difficulties solving those tasks and often succeed only after long training regimes. Given the huge influence of small task modifications, there is an ongoing debate about the conclusiveness of these findings for the development and phylogenetic distribution of abstract reasoning abilities. Here, we applied the concept of “overhypotheses” which is well known in the infant and cognitive modeling literature to study the capabilities of 3 to 5-year-old children, chimpanzees, and capuchin monkeys in a unified and more ecologically valid task design. In a series of studies, participants themselves sampled reward items from multiple containers or witnessed the sampling process. Only when they detected the abstract pattern governing the reward distributions within and across containers, they could optimally guide their behavior and maximize the reward outcome in a novel test situation. We compared each species’ performance to the predictions of a probabilistic hierarchical Bayesian model capable of forming overhypotheses at a first and second level of abstraction and adapted to their species-specific reward preferences.

Metabolic spikes: from rogue electrons to Parkinson's

Conventionally, neurons are thought to be cellular units that process synaptic inputs into synaptic spikes. However, it is well known that neurons can also spike spontaneously and display a rich repertoire of firing properties with no apparent functional relevance e.g. in in vitro cortical slice preparations. In this talk, I will propose a hypothesis according to which intrinsic excitability in neurons may be a survival mechanism to minimize toxic byproducts of the cell’s energy metabolism. In neurons, this toxicity can arise when mitochondrial ATP production stalls due to limited ADP. Under these conditions, electrons deviate from the electron transport chain to produce reactive oxygen species, disrupting many cellular processes and challenging cell survival. To mitigate this, neurons may engage in ADP-producing metabolic spikes. I will explore the validity of this hypothesis using computational models that illustrate the implications of synaptic and metabolic spiking, especially in the context of substantia nigra pars compacta dopaminergic neurons and their degeneration in Parkinson's disease.

Synergy of color and motion vision for detecting approaching objects in Drosophila

I am working on color vision in Drosophila, identifying behaviors that involve color vision and understanding the neural circuits supporting them (Longden 2016). I have a long-term interest in understanding how neural computations operate reliably under changing circumstances, be they external changes in the sensory context, or internal changes of state such as hunger and locomotion. On internal state-modulation of sensory processing, I have shown how hunger alters visual motion processing in blowflies (Longden et al. 2014), and identified a role for octopamine in modulating motion vision during locomotion (Longden and Krapp 2009, 2010). On responses to external cues, I have shown how one kind of uncertainty in the motion of the visual scene is resolved by the fly (Saleem, Longden et al. 2012), and I have identified novel cells for processing translation-induced optic flow (Longden et al. 2017). I like working with colleagues who use different model systems, to get at principles of neural operation that might apply in many species (Ding et al. 2016, Dyakova et al. 2015). I like work motivated by computational principles - my background is computational neuroscience, with a PhD on models of memory formation in the hippocampus (Longden and Willshaw, 2007).

Opponent processing in the expanded retinal mosaic of Nymphalid butterflies

In many butterflies, the ancestral trichromatic insect colour vision, based on UV-, blue- and green-sensitive photoreceptors, is extended with red-sensitive cells. Physiological evidence for red receptors has been missing in nymphalid butterflies, although some species can discriminate red hues well. In eight species from genera Archaeoprepona, Argynnis, Charaxes, Danaus, Melitaea, Morpho, Heliconius and Speyeria, we found a novel class of green-sensitive photoreceptors that have hyperpolarizing responses to stimulation with red light. These green-positive, red-negative (G+R–) cells are allocated to positions R1/2, normally occupied by UV and blue-sensitive cells. Spectral sensitivity, polarization sensitivity and temporal dynamics suggest that the red opponent units (R–) are the basal photoreceptors R9, interacting with R1/2 in the same ommatidia via direct inhibitory synapses. We found the G+R– cells exclusively in butterflies with red-shining ommatidia, which contain longitudinal screening pigments. The implementation of the red colour channel with R9 is different from pierid and papilionid butterflies, where cells R5–8 are the red receptors. The nymphalid red-green opponent channel and the potential for tetrachromacy seem to have been switched on several times during evolution, balancing between the cost of neural processing and the value of extended colour information.

Neural representations of space in the hippocampus of a food-caching bird

Spatial memory in vertebrates requires brain regions homologous to the mammalian hippocampus. Between vertebrate clades, however, these regions are anatomically distinct and appear to produce different spatial patterns of neural activity. We asked whether hippocampal activity is fundamentally different even between distant vertebrates that share a strong dependence on spatial memory. We studied tufted titmice – food-caching birds capable of remembering many concealed food locations. We found mammalian-like neural activity in the titmouse hippocampus, including sharp-wave ripples and anatomically organized place cells. In a non-food-caching bird species, spatial firing was less informative and was exhibited by fewer neurons. These findings suggest that hippocampal circuit mechanisms are similar between birds and mammals, but that the resulting patterns of activity may vary quantitatively with species-specific ethological needs.

How do the mammalian complex brains develop?: finding common and species-specific mechanisms

What transcriptomics tells us about retinal development, disease and evolution

Classification of neurons, long viewed as a fairly boring enterprise, has emerged as a major bottleneck in analysis of neural circuits. High throughput single cell RNA-seq has provided a new way to improve the situation. We initially applied this method to mouse retina, showing that its five neuronal classes (photoreceptors, three groups of interneurons, and retinal ganglion cells) can be divided into 130 discrete types. We then applied the method to other species including human, macaque, zebrafish and chick. With the atlases in hand, we are now using them to address questions about how retinal cell types diversify, how they differ in their responses to injury and disease, and the extent to which cell classes and types are conserved among vertebrates.

Adapt or Die: Transgenerational Inheritance of Pathogen Avoidance (or, How getting food poisoning might save your species)

Caenorhabditis elegans must distinguish pathogens from nutritious food sources among the many bacteria to which it is exposed in its environment1. Here we show that a single exposure to purified small RNAs isolated from pathogenic Pseudomonas aeruginosa (PA14) is sufficient to induce pathogen avoidance in the treated worms and in four subsequent generations of progeny. The RNA interference (RNAi) and PIWI-interacting RNA (piRNA) pathways, the germline and the ASI neuron are all required for avoidance behaviour induced by bacterial small RNAs, and for the transgenerational inheritance of this behaviour. A single P. aeruginosa non-coding RNA, P11, is both necessary and sufficient to convey learned avoidance of PA14, and its C. elegans target, maco-1, is required for avoidance. Our results suggest that this non-coding-RNA-dependent mechanism evolved to survey the microbial environment of the worm, use this information to make appropriate behavioural decisions and pass this information on to its progeny.

In vitro bioelectronic models of the gut-brain axis

The human gut microbiome has emerged as a key player in the bidirectional communication of the gut-brain axis, affecting various aspects of homeostasis and pathophysiology. Until recently, the majority of studies that seek to explore the mechanisms underlying the microbiome-gut-brain axis cross-talk relied almost exclusively on animal models, and particularly gnotobiotic mice. Despite the great progress made with these models, various limitations, including ethical considerations and interspecies differences that limit the translatability of data to human systems, pushed researchers to seek for alternatives. Over the past decades, the field of in vitro modelling of tissues has experienced tremendous growth, thanks to advances in 3D cell biology, materials, science and bioengineering, pushing further the borders of our ability to more faithfully emulate the in vivo situation. Organ-on-chip technology and bioengineered tissues have emerged as highly promising alternatives to animal models for a wide range of applications. In this talk I’ll discuss our progress towards generating a complete platform of the human microbiota-gut-brain axis with integrated monitoring and sensing capabilities. Bringing together principles of materials science, tissue engineering, 3D cell biology and bioelectronics, we are building advanced models of the GI and the BBB /NVU, with real-time and label-free monitoring units adapted in the model architecture, towards a robust and more physiologically relevant human in vitro model, aiming to i) elucidate the role of microbiota in the gut-brain axis communication, ii) to study how diet and impaired microbiota profiles affect various (patho-)physiologies, and iii) to test personalised medicine approaches for disease modelling and drug testing.

Predator-prey interactions: the avian visual sensory perspective

My research interests are centered on animal ecology, and more specifically include the following areas: visual ecology, behavioral ecology, and conservation biology, as well as the interactions between them. My research is question-driven. I answer my questions in a comprehensive manner, using a combination of empirical, theoretical, and comparative approaches. My model species are usually birds, but I have also worked with fish, mammals, amphibians, and insects. ​I was fortunate to enrich my education by attending Universities in different parts of the world. I did my undergraduate, specialized in ecology and biodiversity, at the "Universidad Nacional de Cordoba", Argentina. My Ph.D. was in animal ecology and conservation biology at the "Universidad Complutense de Madrid", Spain. My two post-docs were focused on behavioral ecology; the first one at University of Oxford (United Kingdom), and the second one at University of Minnesota (USA). I was an Assistant Professor at California State University Long Beach for almost six years. I am now a Full Professor of Biological Sciences at Purdue University.

Beyond the binding problem: From basic affordances to symbolic thought

Human cognitive abilities seem qualitatively different from the cognitive abilities of other primates, a difference Penn, Holyoak, and Povinelli (2008) attribute to role-based relational reasoning—inferences and generalizations based on the relational roles to which objects (and other relations) are bound, rather than just the features of the objects themselves. Role-based relational reasoning depends on the ability to dynamically bind arguments to relational roles. But dynamic binding cannot be sufficient for relational thinking: Some non-human animals solve the dynamic binding problem, at least in some domains; and many non-human species generalize affordances to completely novel objects and scenes, a kind of universal generalization that likely depends on dynamic binding. If they can solve the dynamic binding problem, then why can they not reason about relations? What are they missing? I will present simulations with the LISA model of analogical reasoning (Hummel & Holyoak, 1997, 2003) suggesting that the missing pieces are multi-role integration (the capacity to combine multiple role bindings into complete relations) and structure mapping (the capacity to map different systems of role bindings onto one another). When LISA is deprived of either of these capacities, it can still generalize affordances universally, but it cannot reason symbolically; granted both abilities, LISA enjoys the full power of relational (symbolic) thought. I speculate that one reason it may have taken relational reasoning so long to evolve is that it required evolution to solve both problems simultaneously, since neither multi-role integration nor structure mapping appears to confer any adaptive advantage over simple role binding on its own.

Themes and Variations: Circuit mechanisms of behavioral evolution

Animals exhibit extraordinary variation in their behavior, yet little is known about the neural mechanisms that generate this diversity. My lab has been taking advantage of the rapid diversification of male courtship behaviors in Drosophila to glean insight into how evolution shapes the nervous system to generate species-specific behaviors. By translating neurogenetic tools from D. melanogaster to closely related Drosophila species, we have begun to directly compare the homologous neural circuits and pinpoint sites of adaptive change. Across species, P1 neurons serve as a conserved node in regulating male courtship: these neurons are selectively activated by the sensory cues indicative of an appropriate mate and their activation triggers enduring courtship displays. We have been examining how different sensory pathways converge onto P1 neurons to regulate a male’s state of arousal, honing his pursuit of a prospective partner. Moreover, by performing cross-species comparison of these circuits, we have begun to gain insight into how reweighting of sensory inputs to P1 neurons underlies species-specific mate recognition. Our results suggest how variation at flexible nodes within the nervous system can serve as a substrate for behavioral evolution, shedding light on the types of changes that are possible and preferable within brain circuits.

Using opsin genes to see through the eyes of a fish

Many animals are highly visual. They view their world through photoreceptors sensitive to different wavelengths of light. Animal survival and optimal behavioral performance may select for varying photoreceptor sensitivities depending on animal habitat or visual tasks. Our goal is to understand what drives visual diversity from both an evolutionary and molecular perspective. The group of more than 2000 cichlid fish species are an ideal system for examining such diversity. Cichlid are a colorful group of fresh water fishes. They have undergone adaptive radiation throughout Africa and the new world and occur in rivers and lakes that vary in water clarity. They are also behaviorally complex, having diverse behaviors for foraging, mate choice and even parental care. As a result, cichlids have highly diverse visual systems with cone sensitivities shifting by 30-90 nm between species. Although this group has seven cone opsin genes, individual species differ in which subset of the cone opsins they express. Some species show developmental shifts in opsin expression, switching from shorter to longer wavelength opsins through ontogeny. Other species modify that developmental program to express just one of the sets, causing the large sensitivity differences. Cichlids are therefore natural mutants for opsin expression. We have used cichlid diversity to explore the relationship between visual sensitivities and ecology. We have also exploited the genomic power of the cichlid system to identify genes and mutations that cause opsin expression shifts. Ultimately, our goal is to learn how different cichlid species see the world and whether differences matter. Behavioral experiments suggest they do indeed use color vision to survive and thrive. Cichlids therefore are a unique model for exploring how visual systems evolve in a changing world.

The neural mechanisms for song evaluation in fruit flies

How does the brain decode the meaning of sound signals, such as music and courtship songs? We believe that the fruit fly Drosophila melanogaster is an ideal model for answering this question, as it offers a comprehensive range of tools and assays which allow us to dissect the mechanisms underlying sound perception and evaluation in the brain. During the courtship behavior, male fruit flies emit “courtship songs” by vibrating their wings. Interestingly, the fly song has a species-specific rhythm, which indeed increases the female’s receptivity for copulation as well as male’s courtship behavior itself. How song signals, especially the species-specific sound rhythm, are evaluated in the fly brain? To tackle this question, we are exploring the features of the fly auditory system systematically. In this lecture, I will talk about our recent findings on the neural basis for song evaluation in fruit flies.

As soon as there was life there was danger

Organisms face challenges to survival throughout life. When we freeze or flee in danger, we often feel fear. Tracing the deep history of danger gives a different perspective. The first cells living billions of years ago had to detect and respond to danger in order to survive. Life is about not being dead, and behavior is a major way that organisms hold death off. Although behavior does not require a nervous system, complex organisms have brain circuits for detecting and responding to danger, the deep roots of which go back to the first cells. But these circuits do not make fear, and fear is not the cause of why we freeze or flee. Fear a human invention; a construct we use to account for what happens in our minds when we become aware that we are in harm’s way. This requires a brain that can personally know that it existed in the past, that it is the entity that might be harmed in the present, and that it will cease to exist it the future. If other animals have conscious experiences, they cannot have the kinds of conscious experiences we have because they do not have the kinds of brains we have. This is not meant as a denial of animal consciousness; it is simply a statement about the fact that every species has a different brain. Nor is it a declaration about the wonders of the human brain, since we have done some wonderful, but also horrific, things with our brains. In fact, we are on the way to a climatic disaster that will not, as some suggest, destroy the Earth. But it will make it inhabitable for our kind, and other organisms with high energy demands. Bacteria have made it for billions of years and will likely be fine. The rest is up for grabs, and, in a very real sense, up to us.

Evolving Neural Networks

Evolution has shaped neural circuits in a very specific manner, slowly and aimlessly incorporating computational innovations that increased the chances to survive and reproduce of the newly born species. The discoveries done by the Evolutionary Developmental (Evo-Devo) biology field during the last decades have been crucial for our understanding of the gradual emergence of such innovations. In turn, Computational Neuroscience practitioners modeling the brain are becoming increasingly aware of the need to build models that incorporate these innovations to replicate the computational strategies used by the brain to solve a given task. The goal of this workshop is to bring together experts from Systems and Computational Neuroscience, Machine Learning and the Evo-Devo field to discuss if and how knowing the evolutionary history of neural circuits can help us understand the way the brain works, as well as the relative importance of learned VS innate neural mechanisms.

Causal coupling between neural activity, metabolism, and behavior across the Drosophila brain

Coordinated activity across networks of neurons is a hallmark of both resting and active behavioral states in many species, including worms, flies, fish, mice and humans. These global patterns alter energy metabolism in the brain over seconds to hours, making oxygen consumption and glucose uptake widely used proxies of neural activity. However, whether changes in neural activity are causally related to changes in metabolic flux in intact circuits on the sub-second timescales associated with behavior, is unclear. Moreover, it is unclear whether differences between rest and action are associated with spatiotemporally structured changes in neuronal energy metabolism at the subcellular level. My work combines two-photon microscopy across the fruit fly brain with sensors that allow simultaneous measurements of neural activity and metabolic flux, across both resting and active behavioral states. It demonstrates that neural activity drives changes in metabolic flux, creating a tight coupling between these signals that can be measured across large-scale brain networks. Further, using local optogenetic perturbation, I show that even transient increases in neural activity result in rapid and persistent increases in cytosolic ATP, suggesting that neuronal metabolism predictively allocates resources to meet the energy demands of future neural activity. Finally, these studies reveal that the initiation of even minimal behavioral movements causes large-scale changes in the pattern of neural activity and energy metabolism, revealing unexpectedly widespread engagement of the central brain.

Representations of abstract relations in infancy

Abstract relations are considered the pinnacle of human cognition, allowing analogical and logical reasoning, and possibly setting humans apart from other animal species. Such relations cannot be represented in a perceptual code but can easily be represented in a propositional language of thought, where relations between objects are represented by abstract discrete symbols. Focusing on the abstract relations same and different, I will show that (1) there is a discontinuity along ontogeny with respect to the representations of abstract relations, but (2) young infants already possess representations of same and different. Finally, (3) I will investigate the format of representation of abstract relations in young infants, arguing that those representations are not discrete, but rather built by juxtaposing abstract representations of entities.

Co-tuned, balanced excitation and inhibition in olfactory memory networks

Odor memories are exceptionally robust and essential for the survival of many species. In rodents, the olfactory cortex shows features of an autoassociative memory network and plays a key role in the retrieval of olfactory memories (Meissner-Bernard et al., 2019). Interestingly, the telencephalic area Dp, the zebrafish homolog of olfactory cortex, transiently enters a state of precise balance during the presentation of an odor (Rupprecht and Friedrich, 2018). This state is characterized by large synaptic conductances (relative to the resting conductance) and by co-tuning of excitation and inhibition in odor space and in time at the level of individual neurons. Our aim is to understand how this precise synaptic balance affects memory function. For this purpose, we build a simplified, yet biologically plausible spiking neural network model of Dp using experimental observations as constraints: besides precise balance, key features of Dp dynamics include low firing rates, odor-specific population activity and a dominance of recurrent inputs from Dp neurons relative to afferent inputs from neurons in the olfactory bulb. To achieve co-tuning of excitation and inhibition, we introduce structured connectivity by increasing connection probabilities and/or strength among ensembles of excitatory and inhibitory neurons. These ensembles are therefore structural memories of activity patterns representing specific odors. They form functional inhibitory-stabilized subnetworks, as identified by the “paradoxical effect” signature (Tsodyks et al., 1997): inhibition of inhibitory “memory” neurons leads to an increase of their activity. We investigate the benefits of co-tuning for olfactory and memory processing, by comparing inhibitory-stabilized networks with and without co-tuning. We find that co-tuned excitation and inhibition improves robustness to noise, pattern completion and pattern separation. In other words, retrieval of stored information from partial or degraded sensory inputs is enhanced, which is relevant in light of the instability of the olfactory environment. Furthermore, in co-tuned networks, odor-evoked activation of stored patterns does not persist after removal of the stimulus and may therefore subserve fast pattern classification. These findings provide valuable insights into the computations performed by the olfactory cortex, and into general effects of balanced state dynamics in associative memory networks.

Lessons from the cockpit of a fly

Flies represent nearly 10% of all species described by science and are arguably unmatched among flying organisms in their aerial agility. The flight trajectory of flies often consists of crisp straight flight segments interspersed with rapid changes in course called body saccades. Recent advances in genetic tools have made it possible to explore the neurobiological circuitry underlying these two distinct modes of fly flight behavior.

Neural Population Geometry across model scale: A tool for cross-species functional comparison of visual brain regions

COSYNE 2023

Thoughtful faces: Using facial features to infer naturalistic cognitive processing across species

COSYNE 2023

Information-preserving modulation as a principle of sensory coding during locomotion across species

COSYNE 2025

Invariant synaptic density across species links functional stability and wiring optimization principles

COSYNE 2025

Structural organization of inhibitory neurons is preserved across species and cortical areas

COSYNE 2025

Cell numbers in the reflected blade of CA3 and their relation to other hippocampal principal cell populations across nine species

Comparative analysis of the distribution, structure and innervation of Pacinian corpuscles across different mammalian species

Comparing the anatomy of the antennal lobe across bumblebee species

Cross species metabolomic study in Parkinson’s disease: Brain mitochondrial reprogramming as a biomarker and therapeutic target

Functional effects of human LGI1 autoantibodies on CA3 pyramidal neurons: a species-specific in vitro study in human hippocampal slice cultures

The heterogeneity of synaptic NMDA receptor responses within individual lamina I pain processing neurons is conserved across sex and species

Quantification of Regional and Interspecies Astrocyte Involvement in Synapses

Tracking developmental connectopathy in 22q11.2 deletion syndrome with cross-species fMRI

Variability in escape behaviour is conserved across species and explained by an active inference process

A visual pathway for vocal learning in a songbird species

www.humous.org: friendly and interactive single-cell transcriptomic online resource for comparison of gene expression in different species and conditions across corticogenesis

Awake rat MRI scanning - A contribution to the AwakeRodent multi-center, multi-species, multi-modality study

FENS Forum 2024

Circadian regulation in non-mammalian species - A third-eye view from the bearded dragon

FENS Forum 2024

Context-guided sequence memory across species

FENS Forum 2024

Cross species single-cell/nucleus RNA-seq uncovers the evolutionarily conserved pathological mechanisms of vascular contribution to Alzheimer’s disease

FENS Forum 2024

Hippocampus basal radial glia morphotypes across different mammalian species

FENS Forum 2024

Histological, cellular, and molecular changes induced by chronic exposure to the (neuro)endocrine disruptor tributyltin in a widely used invertebrate model species

FENS Forum 2024

A machine learning toolbox to detect and compare sharp-wave ripples across species

FENS Forum 2024

Mapping neural recovery: Comparative molecular insights into spinal cord injury across species

FENS Forum 2024

Molecular and cellular evolution of the amygdala across species analyzed by single-nucleus transcriptome profiling

FENS Forum 2024

Morphological and volumetric analyses of the brain of two pinniped species – do they show parallels with cetacean brains?

FENS Forum 2024

Pose-guided transformers for non-invasive re-identification methods of unmarked species

FENS Forum 2024

Quenching mitochondrial reactive oxygen species in oligodendrocytes protects axonal function in aging and neuroinflammatory disease

FENS Forum 2024

Screening AAV delivery routes, capsids, and promoters for cortex-wide functional and long-term stable access to brain function in large-brain species

FENS Forum 2024

Sharing the spotlight: Uncovering common attentional dynamics across species

FENS Forum 2024

Species-specific properties of parkinsonian beta oscillations suggest diverging generation mechanisms

FENS Forum 2024

Subcortical and cortical inputs to anterior insula and claustrum in macaque and mouse suggest possible species-specific implications for the role of interoceptive inference in consciousness

FENS Forum 2024

Tactile perception and memory in rats and humans: A general framework across tasks and species

FENS Forum 2024

Deep Reinforcement Learning for anatomically accurate musculoskeletal models to investigate neural control of movement across animal species

Neuromatch 5