Biology subjects

Gruber, J.

Publications and source records attributed to Gruber, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Old worms, new tricks: dynamical instability explains late-life rejuvenation in C. elegans

How is it possible to double the lifespan of an organism already close to death? Many biological theories of aging fail to explain this phenomenon. At the Physics of Aging workshop, we presented and discussed late-life lifespan extension in Caenorhabditis elegans to illustrate how a simple stochastic dynamical systems model can account for dramatic geriatric interventions. We build on a Langevin-type instability framework in which aging is a manifestation of dynamical instability-a scenario where stochastic fluctuations amplify over time, driving the system toward a failure thresh-old at which death occurs as a first-passage event. The instability rate (equivalently, the inverse of the mortality-rate doubling time) quantifies the speed of this divergence: a larger means faster exponential growth of z, a steeper Gompertz slope, and a shorter lifespan. The failure threshold zmax{approx} /g, where g is the strength of nonlinear feedback, marks the point beyond which the system diverges irreversibly--physiologically, the saturation of metabolic and regulatory capacity. Within this dynamical-systems framework, auxin-induced degradation of the insulin/IGF-1 receptor DAF-2 in very old animals is naturally interpreted as a late shift in stability parameters that nearly doubles remaining lifespan without resetting accumulated structural damage. This interpretation reconciles the persistence of many senescent pathologies with restored proteostasis and stress resilience, and it shows that targeting the dynamical instability of the regulatory network-rather than reversing damage--can strongly reshape survival trajectories in unstable animals. More broadly, our work exemplifies how physics-inspired low-dimensional stochastic models can capture key features of aging, and we hope it will inspire more collaborations between biologists and physicists to work on late-life interventions.

biochemistry↗

bioRxiv2025

A Minimal Model Explains Aging Regimes and Guides Intervention Strategies

Aging varies widely across species yet converges on uni-versal laws such as Gompertzian mortality. We propose a minimal framework that reduces this complexity to three macroscopic variables: the leading stress response (z0), cumulative entropic damage (Z), and regulatory noise strength (D0). The model predicts two regimes. In unstable species such as flies and mice, intrinsic instability drives exponential divergence of biomarkers and mortality. In stable species such as humans, linear damage accumulation steadily erodes the leading stress response, producing a hyperbolic trajectory toward a finite maximum lifespan. The framework reproduces survival curves and methylation dynamics across taxa and organizes intervention strategies into three levels: modulating stress responses, reducing noise, and slowing entropic damage, offering a roadmap for extending human healthspan and lifespan.

systems biology↗

bioRxiv2024

Discovery of Thermodynamic Control Variables that Independently Regulate Healthspan and Maximum Lifespan

The question, "Can aging be modified, delayed, or reversed?" has profound social and economic implications for rapidly aging societies today. Interventions, ideally, would intercept functional decline and extend healthspan by delaying late-life morbidity (known as "squaring the curve"). These have proven elusive, but examples of differential aging in the animal world abound, suggesting aging itself is a malleable process. We present a novel multi-scale theoretical framework for entropic aging, and apply it to recently published DNA methylation data from 348 evolutionarily distant mammalian species. Our analysis identified modules or correlated DNA methylation changes associated with reversible pathway activation in key biological processes. We discovered a single species-dependent scaling factor controlling the magnitude of fluctuations across biological pathways. It acts as the organisms "effective temperature", quantifying intrinsic biological noise within networks and is unrelated to physical body temperature. Furthermore, we find a distinct stochastic damage signature and an associated extreme value (Gumbel) distribution of activation barriers controlling site-specific damage rates of individual CpG sites. This implies that aging is driven by rare, high-energy transitions on rugged energy landscape, most likely simultaneous and hence practically irreversible failures in highly redundant systems. While the overall rate of damage accumulation and hence the maximum lifespan does not depend on the effective temperature driving the noise in leading pathways, effective temperature does influence both initial mortality rate and the mortality rate doubling time - thereby shaping the survival curve. Lowering effective temperature must, therefore, be a promising Geroscience strategy, aimed directly at squaring the curve of aging. The example shows that targeting the thermodynamic forces driving mammalian aging may provide powerful strategies for the development of truly meaningful interventions to combat aging in humans.

systems biology↗

bioRxiv2024

Loss of neuropeptidergic regulation of cholinergic transmission induces CaV1-mediated homeostatic compensation in muscle cells

Chemical synaptic transmission at the neuromuscular junction (NMJ) is regulated by electrical activity of the motor circuit, but may also be affected by neuromodulation. Here, we assess the role of neuropeptide signaling in the plasticity of NMJ function in Caenorhabditis elegans. We show that the CAPS (Ca2+-dependent activator protein for secretion) ortholog UNC-31, which regulates the exocytosis of dense core vesicles (DCVs), affects both pre- and post-synaptic functional properties, as well as NMJ-mediated locomotion. Despite reduced evoked acetylcholine transmission, the loss of unc-31 results in a more vigorous response to presynaptic stimulation, i.e., enhanced muscle contraction and Ca2+ transients. Based on expression profiles, we identified neuropeptides involved in both cholinergic (FLP-6, NLP-9, NLP-21 and NLP-38) and GABAergic motor neurons (FLP-15, NLP-15), that mediate normal transmission at the NMJ. In the absence of these peptides, neurons fail to upregulate their transmitter output in response to increased cAMP signaling. We also identified proprotein convertases encoded by aex-5/kpc-3 and egl-3/kpc-2 that act synergistically to generate these neuropeptides. We propose that postsynaptic homeostatic scaling, mediated by increased muscle excitability, could compensate for the reduced cholinergic transmission in mutants affected for neuropeptide signaling, thus maintaining net synaptic strength. We show that in the absence of UNC-31 muscle excitability is modulated by upregulating the expression of the muscular L-type voltage gated Ca2+ channel EGL-19 (CaV1). Collectively, our results unveil a role for neuropeptidergic regulation in synaptic plasticity, linking changes in presynaptic transmission to compensatory changes in muscle excitability.

neuroscience↗

bioRxiv2024

A lipidome Aging Clock shows Age Acceleration in individuals with Autism

Aging is a multifaceted process influenced by intrinsic and extrinsic factors, with lipid alterations playing a critical role in brain aging and neurological disorders. This study introduces DoliClock, a lipid-based biological aging clock designed to predict the age of the prefrontal cortex using post-mortem lipidomic data. Significant age acceleration was observed in samples with autism, schizophrenia, and Down syndrome, with autism showing the most pronounced effects in aging-rate. An increase in entropy around age 40, suggests dysregulation of the mevalonate pathway and dolichol accumulation. Dolichol, a lipid integral to N-glycosylation and intracellular transport, emerged as a potential aging biomarker, with specific variants such as dolichol-19 and dolichol-20 showing unique age-related associations. These findings suggest that lipidomics can provide valuable insights into the molecular mechanisms of brain aging and neurological disorders. By linking dolichol levels and entropy changes to aging, this study highlights the potential of lipid-based biomarkers for understanding and predicting biological age, especially in conditions associated with premature aging.

neuroscience↗

bioRxiv2023

Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CKN, 488,390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entrypoint for plant stress response investigations and the related growth tradeoffs. SKM provides interactive exploration of current knowledge. PSS is also formulated as qualitative and quantitative models for systems biology, and thus represents a starting point of a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation, design of validation experiments, or to gain new insights into experimental observations in plant biology.

plant biology↗

bioRxiv2023

The impact of short-lived controls on the interpretation of lifespan experiments and progress in geroscience

Although lifespan extension remains the gold standard for assessing interventions hypothesized to impact the biology of aging, there are important limitations to this approach. Our reanalysis of lifespan studies from multiple sources suggests that the use of short-lived control cohorts tends to exaggerate the relative efficacy of putative longevity interventions. Moreover, due to the high cost and long timeframes of mouse studies, it is rare that a particular longevity intervention will be independently replicated by multiple groups. To facilitate identification of successful interventions, we propose an alternative approach. The level of confidence we can have in an intervention is proportional to the degree of lifespan extension above the strain- and species-specific upper limit of lifespan, which we can estimate from comparison to historical controls. In the absence of independent replication, a putative mouse longevity intervention should only be considered with high confidence when control lifespans are close to 900 days or if the final lifespan of the treated group is considerably above 900 days. Using this "900-day rule" we identified several candidate interventions from the literature that merit follow-up studies.

physiology↗

bioRxiv2023

Evaluating the transmission risk of amyloid beta peptide via ingestion

BackgroundRecent reports suggest that amyloid beta (A{beta}) peptides can exhibit prion-like pathogenic properties. Transmission of A{beta} peptide and the development of associated pathologies after surgeries with contaminated instruments and intravenous or intracerebral inoculations have now been reported across fish, rodents, primates, and humans. This raises a worrying prospect of A{beta} peptides also having other characteristics typical of prions, such as evasion of the digestive process. We asked if such transmission of A{beta} aggregates via ingestion was possible. MethodsWe made use of a transgenic Drosophila melanogaster line expressing human A{beta} peptide prone to aggregation. Fly larvae were fed to adult zebrafish under two feeding schemes. The first was a short-term, high-intensity scheme over 48 hours to determine transmission and retention in the gut. The second, long-term scheme specifically examined retention and accumulation in the brain. The gut and brain tissues were examined by histology, western blotting, and mass spectrometric analyses. ResultsNone of the analyses could detect A{beta} aggregates in the guts of zebrafish following ingestion, despite being easily detectable in the feed. Additionally, there was no detectable accumulation of A{beta} in the brain tissue or development of associated pathologies after prolonged feeding. ConclusionsWhile human A{beta} aggregates do not appear to be readily transmissible by ingestion across species, two prospects remain open. First, this mode of transmission, if occurring, may stay below a detectable threshold and may take much longer to manifest. A second possibility is that the human A{beta} peptide may not be able to trigger self-propagation or aggregation in other species. Either possibility requires further investigation, taking into account the possibility of such transmission from agricultural species used in the food industry.

neuroscience↗

bioRxiv2023

Genetic differentiation at extreme latitudes in the socially plastic sweat bee Halictus rubicundus

The sweat bee Halictus rubicundus is an important pollinator with a large latitudinal range and many potential barriers to gene flow. Alongside typical physical barriers, including mountain ranges and oceans, the climate may also impose restrictions on gene flow in this species. The climate influences voltinism and sociality in H. rubicundus, which is bivoltine and can nest socially at lower latitudes but can be univoltine and solitary in the north of its range and at higher altitudes where the climate is cooler. Variation in voltinism due to the climate may result in differences in phenology between populations across this species geographical range. Differences in phenology could limit gene flow, rendering populations at extreme latitudes genetically isolated and potentially more vulnerable to environmental stressors. A previous study found that the Irish Sea restricts gene flow in this species, but there was no evidence that differences in phenology had a similar effect as there was no genetic differentiation between H. rubicundus populations on mainland Britain. Here we extend the previous study to consider populations of H. rubicundus at extreme northern and southern latitudes in the UK. Using 12 microsatellite markers for genotyping, we found that bees from a population in the far north of Scotland were genetically differentiated from bees collected in Cornwall in the south-west of England. In contrast, bees collected across the Irish Sea in Northern Ireland showed genetic overlap with both the Scottish and Cornish bees. Our results suggest that when populations at extreme latitudes are considered, phenology and the climate may act alongside physical barriers such as the Scottish Highlands and the Irish Sea to restrict gene flow in H. rubicundus. We discuss the implications of our results for local adaptation in the face of rapidly changing selection pressures which are likely under climate change.

genetics↗

bioRxiv2022

A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence

Aging and senescence are characterized by pervasive transcriptional dysfunction, including increased expression of transposons and introns. Our aim was to elucidate mechanisms behind this increased expression. Most transposons are found within genes and introns, with a large minority being close to genes. This raises the possibility that transcriptional readthrough and intron retention are responsible for age-related changes in transposon expression rather than expression of autonomous transposons. To test this, we compiled public RNA-seq datasets from aged human fibroblasts, replicative and drug-induced senescence in human cells and RNA-seq from aging mice and senescent mouse cells. Indeed, our reanalysis revealed a correlation between transposons expression, intron retention and transcriptional readthrough across samples and within samples. Both intron retention and readthrough increased with aging or cellular senescence and these transcriptional defects were more pronounced in human samples as compared to those of mice. In support of a causal connection between readthrough and transposon expression, analysis of models showing induced transcriptional readthrough confirmed that they also show elevated transposon expression. Taken together, our data suggests that elevated transposon reads during aging seen in various RNA-seq dataset are concomitant with multiple transcriptional defects. Intron retention and transcriptional readthrough are the most likely explanation for the expression of transposable elements that lack a functional promoter.

bioinformatics↗

bioRxiv2022

Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan

Why biological age is a major risk factor for many of the most important human diseases remains mysterious. We know that as organisms age, stem cell pools are exhausted while senescent cells progressively accumulate. Independently, induction of pluripotency via expression of Yamanaka factors (Oct4, Klf4, Sox2, c-Myc; OKSM) and clearance of senescent cells have each been shown to ameliorate cellular and physiological aspects of aging, suggesting that both processes are drivers of organismal aging. However, stem cell exhaustion and cellular senescence likely interact in the etiology and progression of age-dependent diseases because both undermine tissue and organ homeostasis in different if not complementary ways. Here, we combine transient cellular reprogramming (stem cell rejuvenation) with targeted removal of senescent cells to test the hypothesis that simultaneously targeting both cell-fate based aging mechanisms will maximize life and health span benefits. We show that these interventions protect the intestinal stem cell pool, lower inflammation, activate pro-stem cell signaling pathways, and synergistically improve health and lifespan. Our findings suggest that a combination therapy, simultaneously replacing lost stem cells and removing senescent cells, shows synergistic potential for anti-aging treatments. Our finding that transient expression of both is the most effective suggests that drug-based treatments in non-genetically tractable organisms will likely be the most translatable.

developmental biology↗

bioRxiv2021

Reprogramming the neuroblastoma epigenome with a mitochondrial uncoupler

Dysregulated DNA methylation is associated with poor prognosis in cancer patients, promoting tumorigenesis and therapeutic resistance1. DNA methyltransferase inhibitors (DNMTi) reduce DNA methylation and promote cancer cell differentiation, with two DNMTi already approved for cancer treatment2. However, these drugs rely on cell division to dilute existing methylation, thus the demethylation effects are achieved in a passive manner, limiting their application in slow-proliferating tumor cells. In this study we use a mitochondrial uncoupler, niclosamide ethanolamine (NEN), to actively achieve global DNA demethylation. NEN treatment promotes DNA demethylation by activating electron transport chain (ETC) to produce -ketoglutarate (-KG), a substrate for the DNA demethylase TET. In addition, NEN inhibits reductive carboxylation, a key metabolic pathway to support growth of cancer cells with defective mitochondria or under hypoxia. Importantly, NEN treatment reduces 2-hydroxyglutarate (2-HG) generation and blocks DNA hypermethylation under hypoxia. Together, these metabolic reprogramming effects of NEN actively alter the global DNA methylation landscape and promote neuroblastoma differentiation. These results not only support Warburgs original hypothesis that inhibition of ETC causes cell de-differentiation and tumorigenesis, but also suggest that mitochondrial uncoupling is an effective metabolic and epigenetic intervention that remodels the tumor epigenome for better prognosis.

cancer biology↗

bioRxiv2020

iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome

While human induced pluripotent stem cells (iPSCs) offer fascinating prospects for research and clinics, evaluating their genomic stability before applications is of utmost importance. During reprogramming, clonal hiPSC lines derived from the same parental cell population were observed to harbor different mitochondrial DNA (mtDNA) variants and variant heteroplasmy levels. It is unknown to date to which extent this unequal segregation of heteroplasmies between cells arises from mosaicism in the parental cell population, selection on mutated mtDNA molecules on the cellular or organelle level, genetic drift during reduction of mtDNA during reprogramming (genetic bottleneck), or de novo mutations. We analyzed mtDNA variants in 26 clonal iPSC lines by mtDNA sequencing. We did not observe a strong bottleneck or any selection for cells with specific mtDNA variants (clonal eliteness) during reprogramming. iPSC culture expansion, however, selects against putatively actionable mutations in the mitochondrial genome that may affect mitochondrial function and cell metabolism. In contrast, heteroplasmy levels of neutral variants remained stable or increased within clonal iPSC lines during culture expansion. Interestingly, the mtDNA copy number per cell got transiently reduced during targeted differentiation of iPSCs into cardiomyocytes, but mtDNA heteroplasmy levels were not affected. Altogether, our results point towards a scenario in which intra-cellular selection on mtDNA during culture expansion, but not during reprogramming or differentiation, pivotally shapes the mutational landscape of the mitochondrial genome in iPSCs. Other mechanisms such as inter-cellular selection, genetic bottleneck, and genetic drift exert minor impact.

genomics↗

bioRxiv2020

Inhibition of mTOR decreases insoluble protein burden by reducing translation in C. elegans

Aging animals accumulate insoluble protein as a consequence of a decline of proteostatic maintenance with age. In Caenorhabditis elegans, for instance, levels of detergent-insoluble protein increase with age. In longer-lived strains of C. elegans, this accumulation occurs more slowly, implying a link to lifespan determination. We further explored this link, and found that detergent-insoluble protein accumulates more rapidly at higher temperatures, a condition where lifespan is short. We employed a C. elegans strain carrying a GFP transcriptional reporter under the control of a heat shock (hsp-16.2) promoter to investigate the dynamics of proteostatic failure in individual nematodes. We found that early, sporadic activation of hsp-16.2 was predictive of shorter remaining lifespan in individual nematodes. Exposure to rapamycin, resulting in reduced mTOR signaling, delayed spurious expression, extended lifespan, and delayed accumulation of insoluble protein, suggesting that targets downstream of the mTOR pathway regulate the accumulation of insoluble protein. We specifically explored ribosomal S6 kinase (rsks-1) as one such candidate and found that RNAi against rsks-1 also resulted in less age-dependent accumulation of insoluble protein and extended lifespan. Our results demonstrate that inhibition of protein translation via reduced mTOR signaling resulted in slower accumulation of insoluble protein, delayed proteostatic crisis and extended lifespan in C. elegans.

biochemistry↗

bioRxiv2019

Application of Optogenetic Amyloid-β Distinguishes Between Metabolic and Physical Damage in Neurodegeneration

The brains of Alzheimers Disease patients show a decrease in brain mass and a preponderance of extracellular Amyloid-{beta} plaques. These plaques are formed by aggregation of polypeptides that are derived from Amyloid Precursor Protein (APP). Amyloid-{beta} plaques are thought to play either a direct or an indirect role in disease progression, however the exact role of aggregation and plaque formation in the ethology of Alzheimers Disease is subject to debate, not least because the biological effects of soluble and aggregated Amyloid-{beta} peptides are difficult to separate in vivo. To investigate the consequences of formation of Amyloid-{beta} oligomers in living tissues, we developed a fluorescently tagged, optogenetic Amyloid-{beta} peptide that oligomerizes rapidly in the presence of blue light. We applied this system to the crucial question of how intracellular Amyloid-{beta} oligomers underlie the pathologies of Alzheimers Disease. We show that, although both expression and induced oligomerization of Amyloid-{beta} were detrimental to lifespan and healthspan, we were able to separate the metabolic and physical damage caused by light-induced Amyloid-{beta} oligomerization from Amyloid-{beta} expression alone. The physical damage caused by Amyloid-{beta} oligomers also recapitulated the catastrophic tissue loss that is a hallmark of late AD. We show that the lifespan deficit induced by Amyloid-{beta} oligomers was reduced with Li+ treatment. Our results present the first model to separate different aspects of disease progression.

developmental biology↗

bioRxiv2019

Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing neuronal human amyloid-β

Alzheimers disease (AD) is the most common neurodegenerative disease affecting the elderly worldwide. Mitochondrial dysfunction has been proposed as a key event in the etiology of AD. We have previously modeled amyloid-beta (A{beta})-induced mitochondrial dysfunction in a transgenic Caenorhabditis elegans strain by expressing human A{beta} peptide specifically in neurons (GRU102). Here, we focus on a deeper analysis of these metabolic changes associated with A{beta}-induced mitochondrial dysfunction. Integrating metabolomics, transcriptomics, biochemical studies and computational modeling, we identify alterations in Tricarboxylic Acid (TCA) cycle metabolism following even low-level A{beta} expression. In particular, GRU102 show reduced activity of a rate-limiting TCA cycle enzyme, alpha-ketoglutarate dehydrogenase. These defects are associated with elevation of protein carbonyl content specifically in mitochondria. Importantly, metabolic failure occurs before any significant increase in global protein aggregate is detectable. Treatment with an antidiabetes drug, Metformin, reverses A{beta}-induced metabolic defects, reduces protein aggregation and normalizes the lifespan of GRU102. Our results point to metabolic dysfunction as an early and causative event in AD pathology and a promising target for intervention.

neuroscience↗

bioRxiv2018

Clonal expansion of mitochondrial DNA deletions is a private mechanism of ageing in long-lived animals

Disruption of mitochondrial metabolism and loss of mitochondrial DNA (mtDNA) integrity are widely considered as evolutionarily conserved (public) mechanisms of ageing (Lopez-Otin et al. 2013). Human ageing is associated with loss in skeletal muscle mass and function (Sarcopenia), contributing significantly to morbidity and mortality. Muscle ageing is associated with loss of mtDNA integrity. In humans, clonally expanded mtDNA deletions co-localize with sites of fiber-breakage and atrophy in skeletal muscle. mtDNA deletions may therefore play an important, possibly causal role in sarcopenia. The nematode Caenorhabditis elegans also exhibits age-dependent decline in mitochondrial function and a form of sarcopenia. However, it is unclear if mtDNA deletions play a role in C. elegans ageing. Here we report identification of 266 novel mtDNA deletions in ageing nematodes. Analysis of the mtDNA mutation spectrum and quantification of mutation burden indicates that (1) mtDNA deletions in nematode is extremely rare, (2) there is no significant age-dependent increase in mtDNA deletions and (3) there is little evidence for clonal expansion driving mtDNA deletion dynamics. Thus, mtDNA deletions are unlikely to drive the age-dependent functional decline commonly observed in C. elegans. Computational modelling of mtDNA dynamics in C. elegans indicates that the lifespan of short-lived animals such as C. elegans is likely too short to allow for significant clonal expansion of mtDNA deletions. Together, these findings suggest that clonal expansion of mtDNA deletions is likely a private mechanism of ageing predominantly relevant in long-lived animals such as humans and rhesus monkey and possibly in rodents.

genetics↗

bioRxiv2018

Thermodynamic analysis of mitochondrial DNA breakpoints reveals mechanistic details of deletion mutagenesis

Broad evidence support double-strand breaks (DSBs) as initiators of mitochondrial DNA (mtDNA) deletion mutations. But the mechanism of DSB-induced deletions, including the DSB repair pathway(s) involved, remains to be established. Here, we used DNA hybridization thermodynamics to analyze misalignment lengths surrounding deletion breakpoints. Our analysis of 9,655 previously reported mammalian mtDNA deletions and 1,307 novel Caenorhabditis elegans mtDNA deletions, indicates a significant role of 0-25bp misalignments, supporting the role of erroneous non-homologous and micro-homology dependent DSB repair in deletion formation. Based on these insights we propose that DSB-induced mtDNA deletions occur via the misjoining of DSB ends and/or strand invasion of open mtDNA regions by DSB ends.

systems biology↗