Biology subjects

Wolf, M.

Publications and source records attributed to Wolf, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Quantitative analysis of proteomic changes in monoclonal MDCK cell lines infected with human influenza A virus

AbstractSuspension MDCK cells are a substrate for producing influenza A virus (IAV) and typically show very high virus yields compared to other animal cells. Due to the significant heterogeneity within cell populations, studying and comparing clonal cell lines with regard to specific properties, such as superior growth or higher productivity, could facilitate process optimization. In this study, we analyzed the expressed proteins of clonal cell lines to identify intrinsic characteristics of effective IAV producers. We compared proteome changes in two IAV-infected monoclonal suspension MDCK cell lines: C59, a low-yield IAV producer with fast cell growth and small cell diameter, and C113, a high-yield IAV producer with average cell growth and large cell diameter. We examined growth rate, size, metabolism and IAV production. A total of 5177 host cell proteins were detected in both cell lines using DIA-PASEF mode with a TimsTOFpro mass spectrometer. Analysis of the differentially expressed proteins revealed that fatty acid oxidation and branched-chain amino acid degradation were upregulated in highly productive cells. In contrast, steroid biosynthesis and DNA replication were more active in faster-growing cells. Following infection, 122 proteins were significantly upregulated (p<0.05, log2-fold change [≥]1) in the high-producing cell line. These proteins were associated with membrane trafficking, interactions with the IAV-NS1 protein and virus production. Additionally, 98 proteins associated with antiviral pathways such as the proto-oncogenic receptor tyrosine kinase MET and tumor necrosis factor (TNF) signaling were downregulated (p<0.05, log2-fold change [≤]1). In the cell line that produced lower IAV titers, 77 proteins were downregulated and 57 were upregulated after infection. RNA metabolism appeared to be downregulated, while the tricarboxylic acid (TCA) cycle and the stress response were both upregulated. In the high-yield C113 clone, only proteins associated with apoptosis and the target of rapamycin kinase (TOR) were expressed following infection. This may indicate a more effective release of virus particles. A comparison of intracellular IAV protein levels demonstrated that M1 and NA levels were 4-fold and 8-fold higher, respectively, for the high-yield C113 cell line. These findings again suggest better virus release.

molecular biology↗

bioRxiv2025

Optimization and evaluation of complementary degrader discovery assays for application in screening

Targeted protein degradation (TPD) mediated by molecular glues is an innovative pharmaceutical paradigm. By binding to and modulating the surface of an E3-ligase component, molecular glue degraders can facilitate the recruitment of a specific target protein (or vice versa) and, ultimately, invoke target degradation. This mode of action results in specific challenges for the development of rational discovery strategies, and complex hit validation workflows may be required to reliably eliminate compounds that elicit non-specific effects. With the aim to guide screening efforts, we optimized two orthogonal cell-based, target-centric assays for degrader discovery: (1) a time-resolved FRET assay directly quantifying levels of target protein and its degradation (signal inhibition), and (2) an assay coupling TPD to cell growth (signal rescue). To enable a deeper understanding of the individual assays strengths and limitations, we compared their statistical performance as well as respective hit populations by screening a specifically designed collection of about 1000 compounds containing well annotated reference compounds and known frequent hitters. We found that the signal rescue format reliably and specifically captured active target degraders while it efficiently filtered out interfering or frequent hitter compounds. Importantly, this format achieved to retrieve lower potency hits, which might be desirable in order to confidently include as many diverse chemical starting points as possible at the start of a drug discovery project.

pharmacology and toxicology↗

bioRxiv2025

Wnt-dependent spatiotemporal reprogramming ofbone marrow niches drives fibrosis

Bone marrow fibrosis is the most extensive matrix remodeling of the microenvironment and can include de novo formation of bone (osteosclerosis). Spatiotemporal information on the contribution of distinct bone marrow niche populations to this process is incomplete. We demonstrate that fibrosis-inducing hematopoietic cells cause profibrotic reprogramming of perivascular CXCL12 abundant reticular (CAR) progenitor cells resulting in loss of their hematopoiesis-support and upregulation of osteogenic and pro-apoptotic programs. In turn, peritrabecular osteolineage cells (OLCs) are activated in an injury-specific, Wnt-dependent manner, comparable to skeletal repair. OLCs fuel bone marrow fibrosis through their expansion and skewed differentiation, resulting in osteosclerosis and expansion of Ly6a+ fibroblasts. NCAM1 expression marks peritrabecular OLCs and their expansion into the central marrow is specific for fibrosis in mice and patients. Peritrabecular stromal b-catenin expression is linked to fibrosis in patients and inhibition of Wnt signaling reduces bone marrow fibrosis and osteosclerosis, possibly being a clinically relevant therapeutic target.

molecular biology↗

bioRxiv2025

Critical Assessment of MetaProteome Investigation 2 (CAMPI-2): Multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

BackgroundFecal samples are widely used as a proxy for studying gut microbiome composition in both human and animal research. Fecal metaproteomics provides valuable insights by tracking changes in the relative abundance of microbial taxa and their protein functions. To ensure reliable results, it is crucial to minimize alterations in the metaproteome occurring from sample collection to protein extraction. Therefore, employing effective stabilization methods is essential to preserve the integrity of the fecal metaproteome from sample collection to laboratory analysis, particularly over long distances or when rapid freezing options are not readily available. In line with these needs, the second edition of the Critical Assessment of MetaProteome Investigation (CAMPI-2) was specifically focused on testing sample stabilization protocols to be applied before metaproteomic analysis. ResultsThis collaborative multicenter study assessed the ability of five different stabilization methods, based on two commercial devices and three specific reagents (acetone, lithium dodecyl sulfate, and an RNAlater-like buffer), respectively, to stabilize the fecal metaproteome during room-temperature storage (14 days) and shipment to mass spectrometry facilities. The five methods were tested simultaneously by eight different laboratories across Europe, using aliquots from the same fecal sample. After protein extraction and digestion, duplicate aliquots of the resulting peptides were analyzed independently by two mass spectrometry facilities at distinct international locations. Analysis of the mass spectrometric data using two different search engines revealed that the fecal metaproteome profile differed considerably depending on the stabilization method used in terms of richness, alpha and beta diversity, reproducibility, and quantitative distribution of main taxa and functions. Although each method showed unique strengths and weaknesses, a commercial swab-based device stood out for its remarkable reproducibility and ranked highest for most of the metrics measured. ConclusionsCAMPI-2 allowed a robust evaluation of five different methods for preserving fecal metaproteome samples. The present investigation provides useful data for the design of metaproteomics and multi-omics studies where fecal sampling cannot be immediately followed by long-term storage at -80{degrees}C. Further optimization of the tested protocols is necessary to improve stabilization efficiency and control bias in the taxonomic and functional profile of the gut microbiome.

microbiology↗

bioRxiv2024

Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites

BackgroundBreast cancer, the most common cancer type among women, was recently found to contain a specific tumor microbiome, but its impact on host biology remains unclear. CD8+ tumor-infiltrating lymphocytes (TILs) are pivotal effectors of anti-tumor immunity that influence cancer prognosis and response to therapy. This study aims to elucidate interactions between CD8+ TILs and the breast tumor microbiome and metabolites, as well as how the breast tumor microbiome may affect the tumor metabolome. MethodsWe investigated the interplay among CD8+ TILs, the tumor microbiome, and the metabolome in a cohort of 46 breast cancer patients with mixed subtypes (Cohort A). We characterized the tumor metabolome by mass spectrometry and CD8+ TILs by immunohistochemistry. Microbiome composition and T cell gene transcript levels were obtained from data from our previous study, which utilized 16S rRNA gene sequencing and a targeted mRNA expression panel. To examine interactions between intratumoral Staphylococcus and specific breast cancer subtypes, we analyzed RNA sequencing data from an independent cohort of 370 breast cancer patients (Cohort B). We explored the functions of the tumor microbiome using mouse models of triple-negative breast cancer (TNBC). ResultsIn tumors from Cohort A, the relative abundance of Staphylococcus positively correlated with the expression of T cell activation genes. The abundances of multiple metabolites exhibited significant correlations with CD8+ TILs, of which NADH, {gamma}-glutamyltryptophan, and {gamma}-glutamylglutamate displayed differential abundance in Staphylococcus-positive versus Staphylococcus-negative breast tumors. In a larger breast cancer cohort (Cohort B), we observed positive correlations between tumoral Staphylococcus and CD8+ TIL activity exclusively in TNBC. Preclinical experiments demonstrated that intratumoral administration of S. aureus, the predominant species of Staphylococcus in human breast tumors, resulted in a depletion of total NAD metabolites, and reduced the growth of TNBC tumors by activating CD8+ TILs. ConclusionsWe identified specific metabolites and microbial taxa associated with CD8+ TILs, delineated interactions between the breast tumor microbiome and metabolome, and demonstrated that intratumoral Staphylococcus influences anti-tumor immunity and TIL-associated metabolites. These findings highlight the role of low-biomass microbes in tumor tissues and provide potential biomarkers and therapeutic agents for breast cancer immunotherapy that merit further investigation.

cancer biology↗

bioRxiv2024

Better and faster collective decisions by larger fish shoals in the wild

Studies on collective cognition have provided many examples of decision-making benefits in terms of animals sharing information about predators, prey or resources in their environment. It has been shown how the efficient spread of adaptive information within groups can provide benefits which increase with group size. Little is known, however, to which extent groups also amplify maladaptive information such as false alarms and whether such costs reduce or even nullify the above benefits. Here, we investigated fish shoals in the wild that responded collec-tively with escape dives when attacked by birds. We analysed the response of shoals in reac-tion to hard-to-detect bird attacks and similar but harmless flybys as a function of shoal size. With increasing shoal size fish increasingly detected predator attacks (true positives) while their false alarms remained constant. Therefore, larger shoals became better at correctly clas-sifying potentially dangerous stimuli rather than becoming more sensitive to all stimuli poten-tially related to attacks. In addition, decision time decreased with increasing shoal size. Larger shoals were thus able to mitigate two major trade-offs inherent in solitary decision making: the trade-off between true and false positives and the trade-off between speed and accuracy. We report performance increases at shoal sizes of tens of thousands of fish and pose chal-lenges for the modelling of the underlying mechanisms.

animal behavior and cognition↗

bioRxiv2024

The Extracellular Matrix Limits Nanoparticle Diffusion and Cellular Uptake in a Tissue-Specific Manner

Overexpression and remodeling of the extracellular matrix (ECM) in cancer and other diseases may significantly reduce the ability of nanoparticles to reach target sites, preventing effective delivery of therapeutic cargo. Here, we evaluate how tissue-specific properties of the ECM affect nanoparticle diffusion using fluorescence video microscopy and cellular uptake via flow cytometry. In addition, we determined how PEGylation chain size and branching influence the ability of nanoparticles to overcome the ECM barrier from different tissues. We found that purified collagen, in the absence of other ECM proteins and polysaccharides, presented a greater barrier to nanoparticle diffusion as compared to decellularized ECM from the liver, lung, and small intestine submucosa. Nanoparticles with dense PEG coatings achieved up to [~]2000-fold enhancements in diffusion rate and cellular uptake up to [~]5-fold greater than non-PEGylated nanoparticles in the presence of ECM. We also found nanoparticle mobility in the ECM varied significantly between tissue types and the optimal nanoparticle PEGylation strategy to enhance ECM penetration was strongly dependent on ECM concentration. Overall, our data supports the use of low molecular weight PEG coatings which provides an optimal balance of nanoparticle penetration through ECM and uptake in target cells. However, tissue-specific enhancements in ECM penetration and cellular uptake were observed for nanoparticles bearing a branched PEG coating. These studies provide new insight into tissue specific ECM barrier functions which can facilitate the design of nanoparticles that effectively transport through target tissues, improving their therapeutic efficacy.

bioengineering↗

bioRxiv2024

A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations

Synaptic connectivity at the neuronal level is characterized by highly non-random features. Hypotheses about their role can be developed by correlating structural metrics to functional features. But to prove causation, manipula- tions of connectivity would have to be studied. However, the fine-grained scale at which non-random trends are expressed makes this approach challenging to pursue experimentally. Simulations of neuronal networks provide an alternative route to study arbitrarily complex manipulations in morphologically and biophysically detailed models. Here, we present Connectome-Manipulator, a Python framework for rapid connectome manipulations of large- scale network models in SONATA format. In addition to creating or manipulating the connectome of a model, it provides tools to fit parameters of stochastic connectivity models against existing connectomes. This enables rapid replacement of any existing connectome with equivalent connectomes at different levels of complexity, or transplantation of connectivity features from one connectome to another, for systematic study. We employed the framework in a detailed model of rat somatosensory cortex in two exemplary use cases: transplanting interneuron connectivity trends from electron microscopy data and creating simplified connectomes of excitatory connectivity. We ran a series of network simulations and found diverse shifts in the activity of individual neuron populations causally linked to these manipulations.

neuroscience↗

bioRxiv2024

EV-Checklist: A fast documentation tool for enhancing transparency and accessibility in extracellular vesicle research.

Extracellular vesicle (EV) research has experienced rapid growth in the past decade. While community-driven efforts, such as the MISEV guidelines (2014, 2018, 2023), have aimed to standardize reporting and enhance experimental rigor, these have not yet been universally adopted in daily EV research practices. The complexity and time commitment required by existing reporting tools can deter researchers from fully embracing them, leading to incomplete or inconsistent documentation in EV studies. Therefore, we created EV-checklist, a complementary digital tool to streamline documentation during manuscript submission and increase transparency for the reviewers, editors and readers. Our tool guides researchers through a straightforward checklist covering nomenclature, source, isolation, characterization, and functional studies of EVs. It generates a concise two-page PDF formatted table for easy integration into manuscripts and provides editors, reviewers, and readers with a clear overview of the conducted studies. EV-Checklist intends to complement existing comprehensive registries as a fast-and-easy tool to enhance clarity and accessibility of methodological and functional insights. It may also promote higher adherence to documentation standards and in EV studies. Our tool is available on https://ev-zone.org.

scientific communication and education↗

bioRxiv2023

Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university masters course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 - 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.

genomics↗

bioRxiv2023

Developmental arcs of plasticity in whole movement repertoires of a clonal fish

Developmental plasticity at the behavioral repertoire level allows animals to incrementally adjust their behavioral phenotypes to match their environments through ontogeny, serving as a lynchpin between ecological factors that cue phenotypic adjustments and evolutionary forces that select upon emergent phenotypic variation. Quantifying the continuous arcs of plasticity throughout animals development, however, has often been prohibitively challenging. Here, we leverage recent advancements in high-resolution behavioral tracking and analysis to (i) track the behavior of 45 genetically identical fish clones (Poecilia formosa) reared in near-identical environments during their first four weeks of life at 0.2 s resolution and (ii) quantify the continuous arcs of plasticity across entire behavioral repertoires through development. Doing so, we are able to test one of the most fundamental theoretical predictions from Bayesian models of development that in stable (but initially unknown) environments, behavioral plasticity should gradually decrease from a maximum at the beginning of life. Using two approaches to measure plasticity across ontogeny, we first quantify plasticity in individual behavioral metrics before also developing a novel whole-repertoire approach that calculates plasticity as the degree of behavioral entropy across a multi-dimensional behavioral phenotype space. We robustly find - despite experimentally matching as best as possible the assumptions of models that predict decreasing plasticity - a [~]two-week initial increase in plasticity in movement behaviors before plasticity subsequently decreased. Our results challenge a common intuition about the optimal developmental course of plasticity through early ontogeny, thereby also demonstrating the value of long-term behavioral tracking approaches for testing fundamental predictions on phenotypic development. Significance statementBehavioral plasticity across development may help animals adjust to uncertainty in moderately unpredictable environments. In stable environments, developing animals should gradually decrease this uncertainty through ontogeny, becoming less sensitive to incoming information (and thus less behaviorally plastic) as they age. This intuitive expectation of old dog inflexibility to new tricks, however, has not been adequately tested with the long-term, highresolution datasets that would be ideal. Here, we achieve such a test and emphasize the significance of this study in (1) providing a novel method for quantifying multi-dimensional behavioral plasticity continuously across long-term, high-resolution behavioral timeseries and in (2) testing fundamental theory that links the temporal patterning of environmental conditions to evolved patterns of behavioral plasticity across development.

animal behavior and cognition↗

bioRxiv2023

Perceived predation risk affects the development of among-individual behavioral variation in a naturally clonal freshwater fish

Predation risk is a key driver of natural selection, influencing various aspects of prey behavior. While many studies focus on how predation risk affects average behavior at population level, less attention has been given to its potential impact on behavioral variation within prey populations. Here, we investigate the effect of perceived predation risk on among-individual behavioral variation in naturally clonal Amazon mollies. Juveniles were raised in two groups: one exposed to a predator during feeding (visual cues only) and the other one serving as a control group. We observed activity and feeding behavior (time spent feeding, visits to feeding spot) over a four-week period. (I) Individuals in the predator-exposed group were on average less active but there was no difference in average feeding behavior between the two groups, suggesting individuals strategically respond to threats based on behavior-specific cost-benefit trade-offs. (II) Among-individual behavioral variation was affected by perceived predation risk: in the absence of the predator, individuals developed pronounced differences in the time spent feeding while no such development was observed in the predator-exposed group. This result has the potential of affecting a wide range of fitness-relevant intraspecific interactions if lower among-individual feeding variation translate into reduced sizes differences. The presence of the predator initially reduced among-individual variation in activity and visits to the feeding spot, but these differences did not persist over time. Our findings highlight the importance of considering both population-level and individual-level responses to predation risk for a more comprehensive understanding of its ecological and evolutionary consequences.

animal behavior and cognition↗

bioRxiv2023

Resolving the pharmacological redox-sensitivity of SARS-CoV-2 PLpro in drug repurposing screening enabled identification of the competitive GRL-0617 binding site inhibitor CPI-169

The SARS CoV-2 Papain-Like protease has multiple roles in the viral replication cycle, related to both its polypeptide cleavage function and its capacity to antagonize host immune response. Targeting PLpro function is recognized as a promising mechanism to modulate viral replication whilst supporting host immune responses. However, development of PLpro specific inhibitors remains challenging. Upcoming studies revealed the limitation of reported inhibitors by profiling them through a pipeline of enzymatic, binding and cellular activity assays showing unspecific activity. GRL-0617 remained the only validated molecule with demonstrated anti-viral activity in cells. In this study we refer to the pitfalls of redox-sensitivity of PLpro. Using a screening-based approach to identify inhibitors of PLpro proteolytic activity, we made extensive efforts to validate the active compounds over a range of conditions and readouts, emphasising the need for comprehensive orthogonal data when profiling putative PLpro inhibitors. The remaining active compound CPI-169, showed to compete with GRL-0617 in NMR-based experiments, suggesting to share a similar binding mode, opening novel design opportunities for further developments as antiviral agents. Author summaryThe increasing knowledge about SARS-CoV-2 allowed the development of multiple strategies to contain the spread of COVID-19 infection. Nevertheless, effective antiviral pharmacological treatments are still rare and viral evolution allowed a fast adaptation and escape from available containment methods. The papain like protease (PLpro) has now become the next most promising SARS-CoV-2 therapeutic due to its multiple functions in virus replication cycle and antagonization of host immune response. However, due to inherent flexibility and sensitivity of this enzyme specific inhibitors are rare. Here we report on a screening strategy using repurposing of known drugs that takes into account PLpro characteristics to identify new inhibitors, showing the success of the approach by identifying CPI-169 that competitive targets the well described GRL-0617 inhibitor binding pocket of PLpro and helping to design further antiviral agents.

molecular biology↗

bioRxiv2023

Extracellular matrix scaffold-assisted tumor vaccines induce tumor regression and long-term immune memory

Injectable scaffold delivery is an immune engineering strategy to enhance the efficacy and reliability of cancer vaccine immunotherapy. The composition and structure of the biomaterial scaffold determines both vaccine release kinetics and inherent immune stimulation via the scaffold host response. Extracellular matrix (ECM) scaffolds prepared from decellularized tissues initiate an acute alternative inflammatory response following implantation, which facilitates wound healing following tumor resection and promotes local cancer immune surveillance. However, it remains unknown whether this environment is compatible with generating protective anti-tumor cytotoxic immunity with local immunotherapy delivery. Here, we engineered an ECM scaffold-assisted therapeutic cancer vaccine that maintained an immune microenvironment consistent with tissue reconstruction. Immune adjuvants MPLA, GM-CSF, and CDA were screened in a cancer vaccine formulated for decellularized small intestinal submucosa (SIS) ECM scaffold co-delivery. Though MPLA and GM-CSF showed the greatest increase in local myeloid cell infiltration, we found that the STING pathway adjuvant CDA was the most potent inducer of cytotoxic immunity with SIS-ECM scaffold delivery. Further, CDA did not diminish hallmark ECM immune responses needed in wound healing such as high Il4 cytokine expression. SIS scaffold delivery enhanced therapeutic vaccine efficacy using CDA and the antigen ovalbumin, curing greater than 50% of established EG.7 tumors in young mice and 75% in 24-week-old mature mice, compared to soluble components alone (0% cured). SIS-ECM scaffold assisted vaccination extended antigen exposure, was dependent on CD8+ cytotoxic T cells, and generated long term anti-tumor memory at least 7 months post-vaccination in both young and mature-aged mice. This study shows that an ECM scaffold is a promising delivery vehicle to enhance cancer vaccine efficacy while being orthogonal to characteristics of pro-healing immune hallmarks.

bioengineering↗

bioRxiv2023

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part II: Physiology and Experimentation

Cortical dynamics underlie many cognitive processes and emerge from complex multi-scale interactions, which are challenging to study in vivo. Large-scale, biophysically detailed models offer a tool which can complement laboratory approaches. We present a model comprising eight somatosensory cortex subregions, 4.2 million morphological and electrically-detailed neurons, and 13.2 billion local and mid-range synapses. In silico tools enabled reproduction and extension of complex laboratory experiments under a single parameterization, providing strong validation. The model reproduced millisecond-precise stimulus-responses, stimulus-encoding under targeted optogenetic activation, and selective propagation of stimulus-evoked activity to downstream areas. The models direct correspondence with biology generated predictions about how multiscale organization shapes activity; for example, how cortical activity is shaped by high-dimensional connectivity motifs in local and mid-range connectivity, and spatial targeting rules by inhibitory subpopulations. The latter was facilitated using a rewired connectome which included specific targeting rules observed for different inhibitory neuron types in electron microscopy. The model also predicted the role of inhibitory interneuron types and different layers in stimulus encoding. Simulation tools and a large subvolume of the model are made available to enable further community-driven improvement, validation and investigation.

neuroscience↗

bioRxiv2023

Reproductive individuality of clonal fish raised in identical environments and its link to early-life behavioural individuality

Recent studies have documented among-individual variation that is unexplained by genetic or apparent environmental differences, but it remains an open question whether such seemingly stochastic variation has fitness consequences. We perform a life-history experiment with naturally clonal fish (Poecilia formosa), separated directly after birth into near-identical (i.e., highly standardized) environments, quantifying 2522 offspring from 152 broods over 280 days. We find that (i) individuals differ consistently in the size of offspring and broods produced over consecutive broods, (ii) these differences are observed even when controlling for trade-offs between brood size, offspring size and reproductive onset, indicating individual differences in life-history productivity and (iii) early-life behavioral individuality in activity and feeding patterns, with among-individual differences in feeding being predictive of growth, and consequently offspring size. In this work, we provide experimental evidence that processes unexplained by genetic and apparent environmental differences translate into predictable differences in life-history measures and ultimately fitness.

animal behavior and cognition↗

bioRxiv2023

Conserved Chamber-Specific Polyploidy Maintains Heart Function in Drosophila

Developmentally programmed polyploidy (whole-genome-duplication) of cardiomyocytes is common across evolution. Functions of such polyploidy are essentially unknown. Here, we reveal roles for precise polyploidy levels in cardiac tissue. We highlight a conserved asymmetry in polyploidy level between cardiac chambers in Drosophila larvae and humans. In Drosophila, differential Insulin Receptor (InR) sensitivity leads the heart chamber to reach a higher ploidy/cell size relative to the aorta chamber. Cardiac ploidy-reduced animals exhibit reduced heart chamber size, stroke volume, cardiac output, and acceleration of circulating hemocytes. These Drosophila phenotypes mimic systemic human heart failure. Using human donor hearts, we reveal asymmetry in nuclear volume (ploidy) and insulin signaling between the left ventricle and atrium. Our results identify productive and likely conserved roles for polyploidy in cardiac chambers and suggest precise ploidy levels sculpt many developing tissues. These findings of productive cardiomyocyte polyploidy impact efforts to block developmental polyploidy to improve heart injury recovery.

developmental biology↗

bioRxiv2022

Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, interregional connectivity. We present a data-driven computational model of the anatomy of non-barrel primary somatosensory cortex of juvenile rat, integrating whole-brain scale data while providing cellular and subcellular specificity. The model consists of 4.2 million morphologically detailed neurons, placed in a digital brain atlas. They are connected by 14.2 billion synapses, comprising local, mid-range and extrinsic connectivity. We delineated the limits of determining connectivity from neuron morphology and placement, finding that it reproduces targeting by Sst+ neurons, but requires additional specificity to reproduce targeting by PV+ and VIP+ interneurons. Globally, connectivity was characterized by local clusters tied together through hub neurons in layer 5, demonstrating how local and interegional connectivity are complicit, inseparable networks. The model is suitable for simulation-based studies, and a 211,712 neuron subvolume is made openly available to the community.

neuroscience↗