Biology subjects

Herman, A.

Publications and source records attributed to Herman, A..

16 recordsLinked to original sources

bioRxiv2026

Cryo-electron microscopy structure of the bovine ephemeral fever virus RNA-nucleoprotein assembly

Bovine ephemeral fever virus (BEFV), a member of the Rhabdoviridae family, is an arthropod-borne pathogen that causes acute febrile disease in cattle. The structural basis of its genome encapsidation and virion assembly remains unexplored, with the current knowledge largely limited to predictions derived from bioinformatic comparisons with other rhabdoviruses. Furthermore, the structural principles that permit the formation of variable-diameter nucleocapsids resulting in the distinctive bullet-shaped morphology of rhabdoviruses remain poorly understood. Here, we report the cryo-electron microscopy structure of the BEFV nucleoprotein (N) in complex with RNA, in the absence of other viral components. The complex predominantly forms circular decameric oligomers that we propose to act as nucleation intermediates during assembly of the bullet-shaped nucleocapsids. Direct subunit interactions are limited to a small polar surface area, with additional intersubunit links mediated by flexible N- and C-terminal loops. These interfaces generate a structurally plastic oligomeric lattice in which neighbouring N subunits can undergo substantial rigid-body rotations and positional rearrangements while preserving conserved local contacts and continuous RNA encapsidation. Such quasi-equivalent interactions provide a plausible mechanism for accommodating the progressive changes in helical diameter required for the transition from the highly curved bullet tip to the wider cylindrical trunk of rhabdovirus nucleocapsids. The assembly is stabilised by the bound RNA molecule, where nine RNA bases are accommodated by each N subunit. The RNA-binding mechanism is consistent with that of VSV, the closest BEFV homologue characterised structurally, but differs at about half of the RNA-binding residues, demonstrating the versatility of the nucleoprotein scaffold in interacting with ssRNA. Comparative analysis with other rhabdoviruses, as well as negative-sense RNA viruses with constant-diameter nucleocapsids, such as Ebola, further confirms the structural features that enable bullet-shaped versus cylindrical nucleocapsid assembly.

biochemistry↗

bioRxiv2026

Tabular foundation model predicts alternative lengthening of telomeres (ALT) and identifies SMARCAL1 as a target in ALT-driven cancers

Alternative lengthening of telomeres (ALT) is a telomerase-independent pathway used by aggressive cancers to maintain their replicative immortality. Because ALT is absent from normal human cells, it is an appealing target for cancer therapy, but the lack of ability to determine ALT status at scale has hindered discovery. Here, we developed ALTitude, a machine learning method from a tabular foundation model that infers ALT from cell line whole genome sequencing data, without need for paired germline analysis. We deployed ALTitude across the DepMap, doubling the number of known ALT+ cancer models. Systematic integration of ALTitude with CRISPR-Cas9 screens yielded the selective dependency on SMARCAL1 in ALT+ cell lines, where we show it stabilizes the ALT phenotype. Acute depletion of SMARCAL1 leads to G2/M arrest, mitotic catastrophe, and cell death. These data provide a valuable resource for studying ALT-related genomic features and present SMARCAL1 as a therapeutic target for ALT+ malignancies.

cancer biology↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

CD4+ T cells promote fibrosis during metabolic dysfunction-associated steatohepatitis

Unresolved inflammation and fibrosis are the two key features of metabolic dysfunction-associated steatohepatitis (MASH), a progressive form of steatotic liver disease that can evolve into cirrhosis and liver cancer. Although innate immunity has been well studied in MASH, the role of CD4 T cells remains underexplored despite their potential to coordinate immune responses by providing help to other immune cells, promoting inflammation, or regulating immune activity through effector and regulatory subsets. To better understand the role of CD4+ T cells in the pathogenesis of MASH, we comprehensively characterized hepatic CD4+ T cells in murine and human MASH at a single-cell protein, transcriptional, and functional level. Mass cytometry and CITE-sequencing revealed a marked shift in intrahepatic CD4 T-cell composition in MASH, with enrichment of Th1, regulatory, and cytotoxic CD4 T cells. Similar phenotypic changes were mirrored in the peripheral blood and validated in human MASH samples. Functional assays demonstrated increased production of IFN{gamma} and TNF by hepatic CD4 T cells, highlighting their proinflammatory effector activity. Transcriptomic profiling identified Tnfrsf4 (OX40) upregulation in hepatic CD4 T cells during MASH. Therapeutic blockade of the OX40L-OX40 axis reversed hepatic fibrosis and improved histologic disease scores in mice with established MASH, and also decreased inflammatory markers in a human ex vivo liver model. Together, these studies provide a proteogenomic single-cell atlas for hepatic CD4 T cells and uncover a CD4 T cell-dependent immunopathogenic circuit as a promising immunotherapeutic target to alleviate MASH and liver fibrosis.

immunology↗

bioRxiv2025

Individual differences in sequential decision-making

1People differ widely in how they make decisions in uncertain environments. While many studies leverage this variability to measure differences in specific cognitive processes and parameters, the key dimension(s) of individual variability in uncertain decision-making tasks has not been identified. Here, we analyzed behavioral data from 1001 participants performing a restless three-armed bandit task, where reward probabilities fluctuated unpredictably over time. Using a novel analytical approach that controlled for the stochasticity in this tasks, we identified a dominant nonlinear axis of individual variability. We found that this primary axis of variability was strongly and selectively correlated with the probability of exploration, as inferred by latent state modeling. This suggests that the major factor shaping individual differences in bandit task performance is the tendency to explore (versus exploit), rather than personality characteristics, reinforcement learning model parameters, or low-level strategies. Certain demographic characteristics also predicted variance along this principle axis: participants at the exploratory end tended to be younger than participants at the exploitative end, and self-identified men were overrepresented at both extremes. Together, these findings offer a principled framework for understanding individual differences in task behavior while highlighting the cognitive and demographic factors that shape individual differences in decision-making under uncertainty.

neuroscience↗

bioRxiv2025

Interaction with tumor cell spheroids induces suppression in primary human cytotoxic T cells

Cytotoxic T lymphocytes (CTL) are key effectors in the anti-tumor immune response. However, their function is commonly suppressed in tumors in the form of exhausted CTL. Understanding molecular mechanisms of suppression and of therapeutics to overcome them is of substantial basic and translational importance yet hindered by limited access to large numbers of exhausted CTL in vitro. Here we use three-dimensional tissue culture to generate primary human CTL with suppressed function. Using a 21-antibody flow cytometry panel and determination of calcium signaling and cell couple maintenance, we show that these cells closely resemble exhausted CTL from tumors. For better understanding of in vitro human primary CTL as key tools in therapeutic development, before and after induction of suppression, we have determined the dependence of CTL function on technicalities of in vitro CTL generation, antigen dose and affinity across two T cell receptors and multiple tumor cell lines. We have investigated morphology and subcellular F-actin distributions of CTL as a key regulators of effector function. Primary human CTL formed cell couples with tumor target cells even in the absence of antigen. Yet, gradual stabilization of such cell couples was associated with increasing CTL effector function. Induction of suppression substantially destabilized CTL tumor cell couples. This comprehensive characterization of the phenotype of in vitro primary human CTL, including a suppressed state, should facilitate their wider use in basic and translational research.

immunology↗

bioRxiv2024

Macrophage-derived CCL24 promotes fibrosis and worsens cardiac dysfunction during heart failure

Inflammation is a significant risk factor and contributes to cardiovascular disease by driving both adaptive and maladaptive processes. Macrophages are the most abundant immune cells in the heart and play an important role in the remodeling of cardiac tissue. We have previously shown an overall protective function of resident cardiac macrophages after pressure-overloaded injury. However, a subpopulation of resident macrophages also expresses high levels of the profibrotic CC motif chemokine ligand 24 (CCL24), suggesting a dichotomous role in pressure overload-induced cardiac remodeling. Here, we report that following transverse aortic constriction CCL24 knockout (CCL24 KO) mice have improved systolic function, cardiac wall enlargement, as well as increased myocyte surface area and hypertrophy, suggesting that CCL24 disrupts compensatory hypertrophy. TAC-operated CCL24 KO mice also displayed reduced fibrosis and diminished expression of fibrotic genes, implying a pro-fibrotic role for CCL24. Indeed, CCL24 induced the proliferation and activation of primary mouse fibroblasts in a process that required CCR3, the sole G protein-coupled receptor for CCL24. Correspondingly, selective ablation of CCR3 in fibroblasts improved cardiac function and ameliorated fibrosis following pressure overload. Administration of a CCL24 blocking antibody or a CCR3 antagonist both improved cardiac function in pressure-overloaded mice, highlighting the CCL24-CCR3 axis as a potential therapeutic target for heart failure. Finally, CCL24 deficiency improved cardiac function and ameliorated fibrosis during physiological aging. Overall, these results show that macrophage-derived CCL24 aggravates fibrosis via the CCR3 receptor, leading to impaired cardiac function in acute and chronic heart failure.

immunology↗

bioRxiv2024

Humans forage for reward in reinforcement learning tasks

How do we make good decisions in uncertain environments? In psychology and neuroscience, the classic view is that we calculate the value of each option, compare them, and choose the most rewarding modulo exploratory noise. An ethologist, conversely, would argue that we commit to one option until its value drops below a threshold and then explore alternatives. Because the fields use incompatible methods, it remains unclear which view better describes human decision-making. Here, we found that humans use compare-to-threshold computations in classic compare-alternative tasks. Because compare-alternative computations are central to the reinforcement-learning (RL) models typically used in the cognitive and brain sciences, we developed a novel compare-to-threshold model ("foraging"). Compared to previous RL models, the foraging model better fit participant behavior, better predicted the tendency to repeat choices, and predicted held-out participants that were almost impossible under comparealternative models. These results suggest that humans use compare-to-threshold computations in sequential decision-making.

neuroscience↗

bioRxiv2024

Individual differences in uncertainty evaluation explain opposing exploratory behaviors in anxiety and apathy

Decision-making in uncertain environments often leads to varied outcomes. Understanding how individuals interpret the causes of unexpected feedback is crucial for adaptive behavior and mental well-being. Uncertainty can be broadly categorized into two components: volatility and stochasticity. Volatility is about how quickly conditions change, impacting results. Stochasticity, on the other hand, refers to outcomes affected by random chance or "luck". Understanding these factors enables individuals to have more effective environmental analysis and strategy implementation (explore or exploit) for future decisions. This study investigates how anxiety and apathy, two prevalent affective states, influence the perceptions of uncertainty and exploratory behavior. Participants (N = 1001) completed a restless three-armed bandit task that was analyzed using latent state models. Anxious individuals perceived uncertainty as more volatile, leading to increased exploration and learning rates, especially after reward omission. Conversely, apathetic individuals viewed uncertainty as more stochastic, resulting in decreased exploration and learning rates. The perceived volatility-to-stochasticity ratio mediated the anxiety-exploration relationship post-adverse outcomes. Dimensionality reduction showed exploration and uncertainty estimation to be distinct but related latent factors shaping a manifold of adaptive behavior that is modulated by anxiety and apathy. These findings reveal distinct computational mechanisms for how anxiety and apathy influence decision-making, providing a framework for understanding cognitive and affective processes in neuropsychiatric disorders.

neuroscience↗

bioRxiv2024

Systematic Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis

Multiple sclerosis (MS) is a complex genetically mediated autoimmune disease of the central nervous system where anti-CD20-mediated B cell depletion is remarkably effective in the treatment of early disease. While previous studies investigated the effect of B cell depletion on select immune cell subsets using flow cytometry-based methods, the therapeutic impact on patient immune landscape is unknown. In this study, we explored how a therapy-driven "in vivo perturbation" modulates the diverse immune landscape by measuring transcriptomic granularity with single-cell RNA sequencing (scRNAseq). We demonstrate that B cell depletion leads to cell type-specific changes in the abundance and function of CSF macrophages and peripheral blood monocytes. Specifically, a CSF-specific macrophage population with an anti-inflammatory transcriptomic signature and peripheral CD16+ monocytes increased in frequency post-B cell depletion. This was accompanied by increases in TNF messenger RNA and protein in monocytes post-B cell depletion, consistent with the finding that anti-TNF treatment exacerbates autoimmune activity in MS. In parallel, B cell depletion induced changes in peripheral CD4+ T cell populations, including increases in the frequency of TIGIT+ regulatory T cells and marked decreases in the frequency of myelin peptide loaded-tetramer binding CD4+ T cells. Collectively, this study provides an exhaustive transcriptomic map of immunological changes, revealing different mechanisms of action contributing to the high efficacy in B cell depletion treatment of MS.

immunology↗

bioRxiv2023

A low dimensional manifold of human exploration and exploitation behavior reveals behavioral states of apathy and anxiety

Exploration-exploitation decision-making is a feature of daily life that is altered in a number of neuropsychiatric conditions. Humans display a range of exploration and exploitation behaviors, which can be affected by apathy and anxiety. It remains unknown how factors underlying decision-making generate the spectrum of observed exploration-exploitation behavior and how they relate to states of anxiety and apathy. Here, we report a latent structure underlying sequential exploration and exploitation decisions that explains variation in anxiety and apathy. 1001 participants in a gender-balanced sample completed a three-armed restless bandit task along with psychiatric symptom surveys. Using dimensionality reduction methods, we found that decision sequences reduced to a low-dimensional manifold. The axes of this manifold explained individual differences in the balance between states of exploration and exploitation and the stability of those states, as determined by a statistical mechanics model of decision-making. Position along the balance axis was correlated with opposing symptoms of behavioral apathy and anxiety, while position along the stability axis correlated with the level of emotional apathy. This result resolves a paradox over how these symptoms can be correlated in samples but have opposite effects on behavior. Furthermore, this work provides a basis for using behavioral manifolds to reveal relationships between behavioral dynamics and affective states, with important implications for behavioral measurement approaches to neuropsychiatric conditions.

neuroscience↗

bioRxiv2021

Strong and opponent contributions of dorsomedial striatal pathways to behavior depends on cognitive demands and task strategy

A classic view of the striatum holds that activity in direct and indirect pathways oppositely modulates motor output. Whether this involves direct control of movement, or reflects a cognitive process underlying movement, remains unresolved. Here we find that strong, opponent control of behavior by the two pathways of the dorsomedial striatum (DMS) depends on the cognitive requirements of a task. Furthermore, a latent state model (a hidden markov model with generalized linear model observations) reveals that--even within a single task--the contribution of the two pathways to behavior is state-dependent. Specifically, the two pathways have large contributions in one of two states associated with a strategy of evidence accumulation, compared to a state associated with a strategy of repeating previous choices. Thus, both the demands imposed by a task, as well as the internal state of mice when performing a task, determine whether DMS pathways provide strong and opponent control of behavior.

neuroscience↗

bioRxiv2020

Patterns of genetic variation in a prairie wildflower, Silphium integrifolium, suggest a non-prairie origin and untapped variation available for improved breeding.

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPremiseC_ST_ABSUnderstanding the relationship between genetic structure and geography provides information about a species evolutionary history and can be useful to breeders interested in de novo domestication. The North American prairie is especially interesting because of its relatively recent origin and subsequent dramatic fragmentation and degradation. Silphium integrifolium is an iconic perennial American prairie wildflower targeted for domestication as an oilseed crop. Germplasm in the existing breeding program is derived from accessions collected in restricted geographic regions. We present the first application of population genetic data in this species to address the following goals (1) improve breeding programs by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of selection during range expansion. MethodsWe developed a reference transcriptome as a genotyping reference for samples from throughout the species range. Population genetic analyses were used to describe the distribution of genetic variation and demographic modeling was used to characterize potential processes that shaped variation. Outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of selection. Key resultsGenetic variation partitions samples into three geographic clusters. Patterns of variation and demographic modeling suggest that the species origin is in the American southeast. Breeding program accessions are from the region with lowest observed genetic variation. ConclusionsThis iconic prairie species did not originate within the modern prairie. Breeding programs can be improved by including accessions from outside of the germplasm founding region, which has relatively little variation. The geographic structuring coupled with the identified targets and drivers of adaptation can guide collecting efforts towards populations with beneficial agronomic traits.

evolutionary biology↗

bioRxiv2019

In vivo characterisation of endogenous cardiovascular extracellular vesicles in larval and adult zebrafish

ObjectiveExtracellular vesicles (EVs) facilitate molecular transport across extracellular space, allowing local and systemic signalling during homeostasis and in disease. Extensive studies have described functional roles for EV populations, including during cardiovascular disease, but the in vivo characterisation of endogenously produced EVs is still in its infancy. Due to their genetic tractability and opportunities for live imaging, zebrafish represent an ideal but under-used model to investigate endogenous EVs. The overall aim of this study was to establish a transgenic zebrafish model to allow the in vivo identification, tracking and extraction of endogenous EVs produced by different cell types. Approach and ResultsUsing a membrane-tethered fluorophore reporter system, we show that EVs can be fluorescently labelled in larval and adult zebrafish and demonstrate that multiple cell types including endothelial cells and cardiomyocytes actively produce EVs in vivo. Cell-type specific EVs can be tracked by high spatiotemporal resolution light-sheet live imaging and modified flow cytometry methods allow these EVs to be further evaluated. Importantly, we demonstrate the utility of this model by showing that cardiomyocytes, endothelial cells and macrophages exchange EVs in the adult heart and that ischaemic injury models dynamically alter EV production. ConclusionsWe have developed a powerful in vivo zebrafish model for the investigation of endogenous EVs in all aspects of cardiovascular biology and pathology. A cell membrane fluorophore labelling approach allows cell type-specific tracing of EV origin without bias towards the expression of individual protein markers and will allow detailed future examination of their function.

cell biology↗

bioRxiv2019

The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research

The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves, with nearly 450 million years of divergence between zebra mussels and its closest sequenced relative. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate the highest quality molluscan assembly to date. Through comparative analysis and transcriptomics experiments we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.

genomics↗

bioRxiv2018

The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus

Understanding the molecular basis of repeated evolved phenotypes can yield key insights into the evolutionary process. Quantifying the amount of gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture is more common between diverging lineages than previously thought. In this study, we resequenced and analyzed nearly 50 whole genomes of the Mexican tetra from three blind cave populations, two surface populations, and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our dataset. The two lineages likely diverged [~]257k generations ago, which, assuming 1 generation per year, is substantially younger than previous mitochondrial estimates of 5-7mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between [~]161k - 191k generations ago. The favored demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified abundant gene flow between cave and surface fish, between caves, and between separate lineages of cave and surface fish. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite substantial gene flow with surface populations. After incorporating these new demographic estimates, our models support that selection may drive the evolution of cave-derived traits, as opposed to the classic hypothesis of disuse and drift. Finally, we show that a key QTL is enriched for genomic regions with very low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. In sum, our study shows that shared evolutionary history via gene flow must be considered in studies of independent, repeated trait evolution.

evolutionary biology↗