Biology subjects

Singer, J.

Publications and source records attributed to Singer, J..

16 recordsLinked to original sources

bioRxiv2026

Ecdysone Antagonizes Growth and Juvenile Hormone-Dependent Soldier Caste Identity in Camponotus floridanus

From tardigrades to lobsters, ecdysone is the critical steroid hormone regulating ecdysis across Panarthropoda. In insects, the sesquiterpenoid hormone called juvenile hormone (JH) prolongs the juvenile state, and together, ecdysone and JH regulate growth and developmental timing. The complex worker caste system in ants has elaborated multiple times and is composed of individuals exhibiting an array of size and allometry variation. While we have accumulated a great deal of knowledge related to the role of JH in influencing size and caste identity in ants, the role of ecdysone in caste development remains poorly understood. Here we show in Camponotus floridanus that ecdysone negatively regulates size, can block soldier determination, and there is an antagonistic relationship between JH and ecdysone. First, we show that during the worker-soldier switchpoint sensitivity window of development, ecdysone is capable of negatively influencing head size, body size, head-to-body allometry, and unexpectedly extends developmental timing. We then show at the molecular level that as expected, developing soldiers upregulate ecdysone degradation, yet surprisingly, developing soldiers also upregulate ecdysone synthesis and the reception of ecdysone signalling. We next investigated the interaction between JH and ecdysone signaling and found that the two hormones antagonize each other at both the molecular and phenotypic levels. Furthermore, in contrast to other insects, we uncovered that ecdysone signaling is negatively regulated by temperature. Beyond its role in size regulation, we also provide preliminary data suggesting that the interaction of JH and ecdysone may have sex inducing properties, generating male-like anomalies. Altogether, our findings show that ecdysone blocks JH-dependent soldier development and we propose that the dynamic regulation of ecdysone synthesis, reception, and degradation may be the basis for the complex sigmoid-like head-to-body allometry found in this species as well as several others across ants. More generally, the evolutionary tinkering of antagonistic growth hormones, their regulation and interaction, and opposing responses to environmental cues, may be a major source for size diversity across developmentally plastic organisms.

developmental biology↗

bioRxiv2026

Eyewire II - A connectomic resource for resolving cell types and circuits of the mouse retina

Comprehensive wiring diagrams from electron microscopy (EM) are a powerful tool to understand the inner workings of the brain. The retina is an easily accessible part of the brain that performs complex visual computations. Its thin, layered structure offers a unique opportunity to decipher neural cell types and map their connectivity. A major obstacle has been the limited size of existing retinal EM datasets, which could not resolve rare cell types and neurons with large dendritic arbors. Here, we describe Eyewire II, a large-scale EM dataset covering nearly 1 mm2 of the adult mouse retina - roughly 10-100 times larger than previous retinal EM volumes. Human proofreading of an automated reconstruction has so far yielded more than 8, 000 bipolar cells, 13, 000 amacrine cells, and 4, 000 retinal ganglion cells. Automated detection is complete for synaptic ribbons and in progress for conventional synapses. Prior to EM imaging, visual responses to diverse stimuli - including natural movies - were recorded in a subset of neurons using two-photon Ca2+ imaging, enabling direct alignment of morphological and functional cell type identity. To enable high-throughput, automatic cell typing, we devised a human-in-the-loop approach that combines deep learning with human expert annotations. As a proof-of-principle, we show that morphological features of reconstructed bipolar cells are sufficient to recover all 15 known bipolar cell types with regular, non-overlapping mosaics. Together, these data and tools establish Eyewire II as a shared resource for the field of retina research. Already now, more than 30 laboratories worldwide are contributing proofreading, expert annotations, and software tools, advancing Eyewire II towards a complete cell type catalog and synaptic wiring diagram of a mammalian retina.

neuroscience↗

bioRxiv2025

Adaptive recruitment of cortex-wide recurrence for visual object recognition

Theories of the neural mechanism underpinning rapid recognition debate whether it relies solely on a feedforward sweep through the ventral stream or instead requires recurrent processing, possibly engaging additional brain regions. Here we directly tested the "adaptive recurrence hypothesis", that attempts to unify these disparate views by proposing that additional recurrent cortical resources beyond the visual stream are recruited when feedforward processing alone is insufficient to solve object recognition. To investigate this hypothesis, we contrasted functional MRI (fMRI) and electroencephalography (EEG) responses to compare neural responses to images that are equally well recognized by humans, but that differ in whether they could be solved by a feedforward deep neural network; a computational proxy for ventral stream feedforward processing. We found that when feedforward processing in the ventral visual stream is insufficient, additional parieto-frontal networks are rapidly and transiently recruited, representationally reconfiguring the ventral visual stream. Our results reveal that object recognition flexibly adapts through fast, cortex-wide recurrence, providing a unifying framework for competing theories of visual recognition.

neuroscience↗

bioRxiv2025

Juvenile Hormone Signalling Underlies the Switchpoint and Differentiation of Soldiers in Camponotus floridanus

Multicellular organisms are composed of various cell types derived from cellular determination and differentiation, which carry out specialized functions in the individual. Ant societies are composed of various castes of individuals derived from caste determination and differentiation, which divide specialized tasks in the colony. From cells to societies, the underlying mechanisms orchestrating determination and differentiation at different biological levels are fundamental in generating biological diversity. While past work has described the developmental process of caste determination and differentiation in ants, the endocrinological and molecular basis for these processes in the genus Camponotus remains unknown. Here we show that minor worker and soldier development is determined by a Juvenile hormone (JH)-mediated minor-soldier switchpoint in C. floridanus. Hormonal treatments identified a sensitivity period when JH can induce bipotential larvae to become soldiers. Induced soldiers phenocopy natural soldiers in size and soldier-specific head-to-body allometry and this is associated with a heterochronic shift in metamorphosis. Furthermore, we molecularly characterize the activity of the JH pathway at the level of synthesis, degradation, reception, and downstream effectors during caste determination and differentiation. Surprisingly, rather than JH synthesis, we found JH reception and JH degradation are the major signalling processes differentially regulated across castes and RNAi of juvenile hormone degradation enzymes generates soldiers. Finally, our data suggests that the hyperdiverse genus Camponotus has independently evolved a JH-mediated minor-soldier switchpoint similar to that known in Pheidole. More generally, the evolution of plastic hormonal regulation may facilitate the origin of developmental determination and differentiation processes underlying complex adaptive phenotypes. Significance StatementAnts live in complex societies like a superorganism where individuals divide reproductive and various non-reproductive labors, which are analogous to the array of functions of germ cells and highly differentiated somatic cells in an organism. While there are over 1500 species of the hyperdiverse genus Camponotus, a genus whose diversity reflects their complex caste system including minor workers and soldiers, the molecular and endocrinological basis for how these castes develop remains unknown. Here we have identified a juvenile hormone (JH) mediated minor-soldier switchpoint during larval development, and have characterized components of the JH signalling pathway that regulate soldier development. This work enables further understanding of how castes are regulated across ants and social insects more broadly.

developmental biology↗

bioRxiv2025

Single-neuron encoding of rapidly learned visual information reshapes human perception

Humans can swiftly learn to recognize visual objects after minimal exposure. Integrating new information with existing knowledge requires forming enduring neuronal representations to enable future recognition. Yet, the neuronal mechanisms in the human brain underlying such rapid perceptual changes remain unclear. We recorded single-neuron activity in occipital (OC) and medial temporal lobe (MTL) regions as participants rapidly learned to recognize degraded images. OC and MTL neurons modulated their activity to encode newly learned visual information and reshape perception. Population decoding revealed that OC neurons required additional processing time to resolve the identity of learned images, delaying neuronal responses in the MTL. Our findings indicate that OC supports recognition after rapid learning via extensive recurrent processing, potentially involving higher-order neocortical areas, without relying on feedback from MTL. These results provide mechanistic constraints for biologically plausible models of visual recognition and few-shot visual learning.

neuroscience↗

bioRxiv2025

Layer-specific spatiotemporal dynamics of feedforward and feedback in human visual object perception

Visual object perception is mediated by information flow between regions of the ventral visual stream along feedforward and feedback anatomical connections. However, feedforward and feedback signals during naturalistic vision are rapid and overlapping, complicating their identification and precise functional specification. Here we recorded human layer-specific fMRI responses to naturalistic object images in early visual cortex (EVC) and lateral occipital complex (LOC) to isolate feedforward and feedback information signals spatially by their cortical layer-specific termination pattern. We combined these layer-specific fMRI responses with electroencephalography (EEG) responses for the same images to segregate feedforward and feedback signals in both time and space. Feedforward signals emerge early in the middle layers of EVC and LOC, followed by feedback signals in the superficial layer of LOC. Comparing the identified dynamics in LOC to a visual deep neural network (DNN), revealed that early feedforward signals in LOC encode medium-to-high complexity features, whereas later feedback signals increase the representational format to high complexity features. Together this specifies the spatiotemporal dynamics and functional role of feedforward and feedback information flow mediating visual object perception.

neuroscience↗

bioRxiv2025

Transcriptional changes in non-human primate tissues after intrathecal delivery of serotype 9 adeno-associated viral vector: insights into organ toxicities

Adeno associated virus (AAV)-based gene transfer has brought transformative therapeutic benefits to patients with otherwise untreatable genetic diseases. However, treatment-related organ toxicities, particularly for high doses, remain a safety concern in the clinic with some translatability in preclinical species. In the present study, we conducted an RNAseq analysis in non-human primates administered intrathecally with scAAV9-CBA-GFP, empty viral capsid particles, or a Promoterless vector. This analysis revealed a broad and long-lasting (4 weeks after dosing) transcriptional impact of the viral transduction/transgene expression on tissues. Liver and DRG, known to be primary sites of toxicity induced by AAV9, had the highest viral load and the most significant transcriptional changes. Our analysis revealed that most of the differentially expressed genes were upregulated, and common gene signatures belonged to immune pathways (innate and adaptive), demonstrating a persistent low-grade immune response up to four weeks post-dosing. Interestingly and across all tissues considered, the impact of empty capsids or of the Promoterless vector was minimal, suggesting that both the presence of the capsid and of a productive viral genome contributed to the observed changes. This study provides a unique insight into the transcriptional responses to AAV9 in key tissues primarily exposed by the vector.

molecular biology↗

bioRxiv2025

Loss of white matter tracts and persistent microglial activation in the chronic phase of ischemic stroke in female rats and the effect of miR-20a-3p treatment

Our previous studies showed that intravenous injections of the small non-coding RNA mir-20a-3p is neuroprotective for stroke in the acute phase and attenuates long-term cognitive impairment in middle-aged female rats. In this study, we evaluated postmortem brain pathology at 100+d after stroke in a set of behaviorally characterized animals. This included Sham (no stroke) controls or stroke animals that received either mir20a-3p at 4h, 24h and 70d iv post stroke (MCAo+mir20a-3p) or a scrambled oligo (MCAo+Scr). Brain volumetric features were analyzed with T2 weighted and Diffusion Tensor magnetic resonance imaging (MRI) followed by histological analysis. Principal component analysis of Fractional Anisotropy (FA)-diffusion tensor MRI measures showed that MCAo+Scr and MCAo+mir20a-3p groups differed significantly in the volume of white matter but not gray matter. Weil myelin-stained sections confirmed decreased volume of the corpus callosum, internal capsule and the anterior commissure in the ischemic hemisphere of MCAo+Scr animals compared to the non-ischemic hemisphere, while sham and MCAo+Mir-20a-3p showed no hemispheric asymmetries. The MCAo+Scr group also exhibited asymmetry in hemisphere and lateral ventricle volumes, with ventricular enlargement in the ischemic hemisphere as compared to the non-ischemic hemisphere. The numbers of microglia were significantly elevated in white matter tracts in the MCAo+Scr group, with a trend towards increased myelin phagocytic microglia in these tracts. Regression analysis indicated that performance on an episodic memory test (novel object recognition test; NORT) was associated with decreased white matter volume and increased microglial numbers. These data support the hypothesis that stroke-induced cognitive impairment is accompanied by white matter attrition and persistent microglial activation and is consistent with reports that cognitive deterioration resulting from vascular diseases, such as stroke, is associated with secondary neurodegeneration in regions distal from the initial infarction.

neuroscience↗

bioRxiv2023

Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV

Older individuals and people with HIV (PWH) were prioritized for COVID-19 vaccination, yet comprehensive studies of the immunogenicity of these vaccines and their effects on HIV reservoirs are not available. We followed 68 PWH aged 55 and older and 23 age-matched HIV-negative individuals for 48 weeks from the first vaccine dose, after the total of three doses. All PWH were on antiretroviral therapy (cART) and had different immune status, including immune responders (IR), immune non-responders (INR), and PWH with low-level viremia (LLV). We measured total and neutralizing Ab responses to SARS-CoV-2 spike and RBD in sera, total anti-spike Abs in saliva, frequency of anti-RBD/NTD B cells, changes in frequency of anti-spike, HIV gag/nef-specific T cells, and HIV reservoirs in peripheral CD4+ T cells. The resulting datasets were used to create a mathematical model for within-host immunization. Various regimens of BNT162b2, mRNA-1273, and ChAdOx1 vaccines elicited equally strong anti-spike IgG responses in PWH and HIV- participants in serum and saliva at all timepoints. These responses had similar kinetics in both cohorts and peaked at 4 weeks post-booster (third dose), while half-lives of plasma IgG also dramatically increased post-booster in both groups. Salivary spike IgA responses were low, especially in INRs. PWH had diminished live virus neutralizing titers after two vaccine doses which were rescued after a booster. Anti-spike T cell immunity was enhanced in IRs even in comparison to HIV- participants, suggesting Th1 imprinting from HIV, while in INRs it was the lowest. Increased frequency of viral blips in PWH were seen post-vaccination, but vaccines did not affect the size of the intact HIV reservoir in CD4+ T cells in most PWH, except in LLVs. Thus, older PWH require three doses of COVID-19 vaccine to maximize neutralizing responses against SARS-CoV-2, although vaccines may increase HIV reservoirs in PWH with persistent viremia.

immunology↗

bioRxiv2022

Temporal dynamics of oscillatory brain activity during the observation of communicative interactions between point-light agents

Predicting actions from nonverbal cues and using them to optimize ones response behavior (i.e., interpersonal predictive coding) is essential in everyday social interactions. We aimed to investigate the neural correlates of different cognitive processes evolving over time during interpersonal predictive coding. Thirty-nine participants watched two agents depicted by moving point-light stimuli while an electroencephalogram (EEG) was recorded. One well-recognizable agent performed either a communicative or an individual action. The second agent either was blended into a cluster of noise dots (i.e., present), or was entirely replaced by noise dots (i.e., absent), which participants had to differentiate. EEG amplitude and coherence analyses for theta, alpha and beta frequency bands revealed a dynamic pattern unfolding over time: Watching communicative actions was associated with enhanced coupling within medial anterior regions involved in social and mentalizing processes and with dorsolateral prefrontal activation indicating a higher deployment of cognitive resources. Trying to detect the agent in the cluster of noise dots without having seen communicative cues was related to enhanced coupling in posterior regions for social perception and visual processing. Observing an expected outcome was modulated by motor system activation. Finally, when the agent was detected correctly, activation in posterior areas for visual processing of socially-relevant features was increased. Taken together, our results demonstrate that it is crucial to consider the temporal dynamics of social interactions and of their neural correlates to better understand interpersonal predictive coding. This could lead to optimized treatment approaches for individuals with problems in social interactions.

neuroscience↗

bioRxiv2022

Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence

Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patients tumour composition and evolutionary history is key for personalised therapies. Single-cell sequencing now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the uncertainty of the underlying evolutionary process. By modelling the noise processes and allowing mutations to be lost or to reoccur during tumour evolution, we present a method to jointly call mutations in each cell, reconstruct the phylogenetic relationship between cells, and determine the locations of mutational losses and recurrences. Our Bayesian approach allows us to accurately call mutations as well as to quantify our certainty in such predictions. We show the advantages of allowing mutational loss or recurrence with simulated data and present its application to tumour single-cell sequencing data.

genomics↗

bioRxiv2021

Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus; however, the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods, for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 73 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, and areas of persistence and transmission, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as we work towards eliminating dog-mediated rabies, as well as having potential for broad application to the surveillance of other viruses. Author SummaryThe importance of the ability to track the diversity and spread of viruses in a universal way that can be clearly communicated has been highlighted during the SARS-CoV-2 pandemic. This, accompanied with the increase in the availability and use of pathogen sequence data, means the development of new genomic tools and classification systems can strengthen outbreak response and disease control. Here, we present an easy-to-use objective and transferable classification tool for tracking viruses at high resolution. We use rabies virus, a neglected zoonotic disease that causes around 59,000 human deaths each year, as an example use case of this tool. Applying our tool to a global clade of rabies virus, we find an over 200% increase in the definition at which we can classify the virus, allowing us to identify areas of persistence and transmission that were not previously apparent, and patterns of virus spread. Insights from the application of this tool should prove valuable in targeting vaccination campaigns and improving surveillance as countries work towards the elimination of dog-mediated rabies.

genomics↗

bioRxiv2021

Prediction of Whole-Cell Transcriptional Response with Machine Learning

Applications in synthetic and systems biology can benefit from measuring whole-cell response to biochemical perturbations. Execution of experiments to cover all possible combinations of perturbations is infeasible. In this paper, we present the host response model (HRM), a machine learning approach that takes the cell response to single perturbations as the input and predicts the whole cell transcriptional response to the combination of inducers. We find that the HRM is able to qualitatively predict the directionality of dysregulation to a combination of inducers with an accuracy of >90% using data from single inducers. We further find that the use of known prior, known cell regulatory networks doubles the predictive performance of the HRM (an R2 from 0.3 to 0.65). This tool will significantly reduce the number of high-throughput sequencing experiments that need to be run to characterize the transcriptional impact of the combination of perturbations on the host.

bioinformatics↗

bioRxiv2019

Growth Factor Independence (GFI) 1B-mediated transcriptional repression and lineage allocation require Lysine Specific Demethylase (LSD)1-dependent recruitment of the BHC complex

Growth Factor Independence (GFI)1B coordinates assembly of transcriptional repressor complexes comprised of co-repressors and histone modifying enzymes to control gene expression programs governing lineage allocation in hematopoiesis. Enforced expression of GFI1B in K562 erythroleukemia cells favors erythroid over megakaryocytic differentiation, providing a platform to define molecular determinants of binary fate decisions triggered by GFI1B. We deployed proteome-wide proximity labeling to identify factors whose inclusion in GFI1B complexes depends upon GFI1Bs obligate effector, Lysine Specific Demethylase (LSD)1. We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1, ZMYM2 and ZNF217) in an LSD1-dependent manner to control erythroid fate specification. Among these, depletion of both HMG20A and HMG20B, or GSE1 block GFI1B-mediated erythroid differentiation, phenocopying impaired differentiation brought on by LSD1 depletion or disruption of GFI1B--LSD1 binding. These findings demonstrate the central role of the GFI1B--LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.

molecular biology↗

bioRxiv2018

Intra-tumor heterogeneity and clonal exclusivity in renal cell carcinoma

Intra-tumour heterogeneity is the molecular hallmark of renal cancer, and the molecular tumour composition determines the treatment outcome of renal cancer patients. In renal cancer tumourigenesis, in general, different tumour clones evolve over time. We analysed intra-tumour heterogeneity and subclonal mutation patterns in 178 tumour samples obtained from 89 clear cell renal cell carcinoma patients. In an initial discovery phase, whole-exome and transcriptome sequencing data from paired tumour biopsies from 16 ccRCC patients were used to design a gene panel for follow-up analysis. In this second phase, 826 selected genes were targeted at deep coverage in an extended cohort of 89 patients for a detailed analysis of tumour heterogeneity. On average, we found 22 mutations per patient. Pairwise comparison of the two biopsies from the same tumour revealed that on average 62% of the mutations in a patient were detected in one of the two samples. In addition to commonly mutated genes (VHL, PBRM1, SETD2 and BAP1), frequent subclonal mutations with low variant allele frequency (<10%) were observed in TP53 and in mucin coding genes MUC6, MUC16, and MUC3A. Of the 89 ccRCC tumours, 87 (~98%) harboured private mutations, occurring in only one of the paired tumour samples. Clonally exclusive pathway pairs were identified using the WES data set from 16 ccRCC patients. Our findings imply that shared and private mutations significantly contribute to the complexity of differential gene expression and pathway interaction, and might explain clonal evolution of different molecular renal cancer subgroups. Multi-regional sequencing is central for the identification of subclones within ccRCC.

cancer biology↗

bioRxiv2018

SCIΦ: Single-cell mutation identification via phylogenetic inference

Understanding the evolution of cancer is important for the development of appropriate cancer therapies. The task is challenging because tumors evolve as heterogeneous cell populations with an unknown number of genetically distinct subclones of varying frequencies. Conventional approaches based on bulk sequencing are limited in addressing this challenge as clones cannot be observed directly. Single-cell sequencing holds the promise of resolving the heterogeneity of tumors; however, it has its own challenges including elevated error rates, allelic dropout, and uneven coverage. Here, we develop a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells. Our method, called SCI{Phi}, jointly calls mutations in individual cells and estimates the tumor phylogeny among these cells. Employing a Markov Chain Monte Carlo scheme we robustly account for the various sources of noise in single-cell sequencing data. Our approach enables us to reliably call mutations in each single cell even in experiments with high dropout rates and missing data. We show that SCI{Phi} outperforms existing methods on simulated data and applied it to different real-world datasets, namely a whole exome breast cancer as well as a panel acute lymphoblastic leukemia dataset. Availability: https://github.com/cbg-ethz/SCIPhI

bioinformatics↗