Biology subjects

Lehmann, J.

Publications and source records attributed to Lehmann, J..

15 recordsLinked to original sources

bioRxiv2026

The Metabolic Scope Theory of Aging: Rising Mitochondrial Impedance Compresses Metabolic Reserve to Constrain Lifespan

Maximum lifespan varies more than 100-fold across vertebrates, yet within each species aging emerges as a coordinated syndrome spanning metabolism, immunity, endocrine signaling, cognition, and regeneration. We propose the Metabolic Scope Theory of Aging (MSTA), which treats longevity as the time required to exhaust mitochondrial bioenergetic reserve rather than as a consequence of resting metabolic rate alone. The framework decomposes lifespan into three physical axes: Scope, the reserve capacity that buffers cumulative damage; Stability, the resistance of mtDNA-linked OXPHOS architecture to erosion; and Pace, the temperature-dependent kinetics of lesion accumulation. Using body mass as a Scope proxy, mtDNA GC content as a Stability proxy, and body temperature as Pace, the resulting Scope-Stability-Pace relation, lnMLS = lnBM + {beta} GC% -{gamma} Tb + c, explains [~]69% of mammalian maximum-lifespan variance across 379 species. Cross-class comparisons reinforce the same constraint structure: birds offset high thermal Pace through elevated mtDNA Stability, and the SSP temperature coefficient derived from mammals matches the temperature dependence of lifespan observed in ectotherms. The framework further connects comparative lifespan scaling to Gompertz-like mortality acceleration through progressive reserve erosion and threshold crossing. Mechanistically, MSTA models cumulative mtDNA-linked damage as rising impedance within OXPHOS. Increasing internal resistance drives mitochondria toward a high-redox-pressure, low-current regime that preserves basal ATP while restricting NAD+ regeneration, CoQ acceptor availability, and {Delta}p-dependent work. The earliest failure is therefore not energetic collapse but loss of regenerative scope: NAD+-gated TCA flux, aspartate and nucleotide synthesis, one-carbon metabolism, and redox-buffered repair become progressively harder to sustain, and diverse age- related pathologies emerge as tissue-specific projections of this shared upstream constraint. MSTA separates a reversible, operational impedance (redox poise, membrane potential, endocrine tone) from a fixed, informational one (accumulated mtDNA damage) that sets the hard ceiling on lifespan. Because the informational layer cannot be reversed by regulatory means, the framework predicts that until therapies can directly restore mitochondrial conductance, interventions will be most effective when they relieve redox pressure or bypass constrained biosynthetic gates.

physiology↗

bioRxiv2026

Effects of age and sex on diet and activities of immature reintroduced western lowland gorillas.

The juvenile life stage is crucial in primates, yet the behavior and diet of juveniles is an understudied area of primatology. Compared with adults, considerably less is known about wild juvenile primate development, particularly that of western lowland gorillas (Gorilla gorilla gorilla). While sex differences in diet and time budgets are well studied in adults, work remains to be done on how age and sex influence juvenile behavior. Here, we use data from nine immature reintroduced western lowland gorillas to fill some of this knowledge gap. We found that the immature gorillas spent most time feeding, followed by resting. Younger juveniles spent less time resting than older individuals, instead spending more time in self-play compared with older juveniles and more time in locomotion than subadults. The group had a varied diet as would be expected for western lowland gorillas; predominantly eating stems, flowers/leaves and fruit, with subadults eating more stems compared to younger individuals. Sex was found to have little influence on either behavior or diet. Additionally, behavioral and dietary diversity were calculated in order to describe the diversity of immature western lowland gorilla behavior. There were no age or sex differences found among this group of individuals, suggesting behavioral repertoire and diet may be influenced by those in their social group. The wider aim of this study is to provide insights into immature western lowland gorilla behavior and diet in the wild while also contributing to understanding of the post-release period for rehabilitated primates.

animal behavior and cognition↗

bioRxiv2025

Non-hydrolyzable acetyllysine analogs to study protein acetylation in vitro and in cells

Lysine acetylation plays a prominent regulatory role in eukaryotic cells. Yet, determining the functional consequences of acetylation for a given protein represents a considerable challenge. For instance, lysine residues are subject to various posttranslational modifications, rendering interpretation of mutational studies difficult. The genetic code expansion technology enables site-specific incorporation of acetyllysine (AcK) into proteins, but the applicability of AcK is limited, as within cells, the acetyl group is removed by deacetylases. Here, we show that site-specific incorporation of the non-hydrolyzable AcK analog ketolysine (KeK) into ubiquitin closely resembles the structural and functional effects of AcK incorporation. Furthermore, AcK and KeK can be efficiently incorporated into the tumor suppressor p53 in cells. However, whereas AcK becomes deacetylated, KeK remains stable. Accordingly, incorporation of KeK, but not AcK, affects p53-mediated transcription. Thus, we propose that KeK is the AcK surrogate of choice for studying acetylation of a given protein in cells.

biochemistry↗

bioRxiv2025

HydroMEA: A 3D Hydrogel Based Microfluidic Device to Study Electrophysiology for Myelinated Nerve-on-Chip

Engineered in vitro platforms are powerful systems to study information flow in the nervous system. While existing polydimethylsiloxane (PDMS)-based microfluidic platforms offer precise architectures, the cultured neurons grow on two-dimensional (2D) planar multielectrode arrays (MEA). To mimic the native microenvironment, where neurons grow in three-dimensional (3D) extracellular matrices (ECM), 3D hydrogels can be designed to encapsulate cells and enable physiologically-mimicked behaviors. Here, we describe hydroMEA, a 3D platform fabricated by placing PDMS microstructures on a high-density MEA and filled with a desired hydrogel, to offer controlled topologies, physiologically-relevant microenvironments, and real-time electrophysiological measurements. First, we developed a gelatin methacryloyl (GelMA) hydrogel with incorporated ECM components and tuned the mechanical properties to match those of nerve tissue. The hydrogel was able to support: 1) the growth of iPSC-derived sensory neurons (hSNs) for >100 days; 2) co-cultures of hSN with human embryonic stem cell-derived Schwann cells (hSCs), to enable reliable 3D myelination. Next, hydroMEA were prepared for topologically- defined 3D growth and myelination in designated compartments. Finally, electrophysiological evaluation of hSN-hSCs co-cultures revealed increased conduction speeds indicating functional myelin. This platform is a promising tool to study cell-cell interactions and to functionally evaluate the effect of pharmacological compounds in a more translational manner.

bioengineering↗

bioRxiv2025

Disparate social structures are underpinned by distinct social rules across a primate radiation

Over six decades of research on wild baboons and their close relatives (collectively, the African papionins) have uncovered substantial variation in their behavior and social systems. While most papionins form discrete social groups (single-level societies), a few others form small social units that are nested within larger supergroups (multi-level societies). These two systems are generally thought to be qualitatively distinct, but data from wild populations increasingly suggest that there may be areas of overlap. To quantify this potential gradient in social structure, a more systematic, comparative analysis is needed. Here, we constructed a database of behavioral and demographic records spanning 135 group-years, 28 social groups, 13 long-term field studies, and 11 species to quantify variation in grooming network structure, and identify the individual and dyadic properties (e.g., kinship and social status effects) that underlie this variation. Consistent with accumulating observations in the field, the single-level species could be divided into two categories: cohesive and cliquish. Cohesive single-level networks were dense, kin-biased, and moderately rank-structured, while cliquish single-level networks were more differentiated, slightly more kin-biased, and strongly rank-structured. As expected, multi-level networks were very modular and shaped by females ties to specific dominant males but varied in their kin biases. Taken together, these data suggest that (i) kin and rank biases are widespread but vary in their strength; (ii) male-centered subgroups are exclusive to multi-level systems; and (iii) increases in network modularity can emerge in response to heightened nepotism and male-centered clustering. SIGNIFICANCE STATEMENTWhat forces explain variation in primate societies? While kinship and dominance shape the social lives of many of our close relatives, it is unclear how their effects differ across species. Using a new database comprising decades of field research, we found that baboons and their close relatives fell into three general patterns: one in which groups were cohesive, kin-biased, and moderately rank-biased, another in which groups were more cliquish and nepotistic, and a third in which groups were divided into clusters centered on dominant males. Distinct primate societies may thus reflect differences in the strength of females nepotistic biases and the degree of males social influence.

animal behavior and cognition↗

bioRxiv2025

From Toxicogenomics Data to Cumulative Assessment Groups: A Mechanistic Framework for Chemical Grouping

The grouping of chemicals based on shared properties or molecular mechanisms of action is pivotal for advancing regulatory toxicology, reducing data gaps, and enabling cumulative risk assessments. This study introduces a novel framework usingChemical-Gene-Phenotype-Disease (CGPD) tetramers derived from the Comparative Toxicogenomics Database (CTDbase). Our approach integrates toxicogenomics data to identify and cluster chemicals with similar molecular and phenotypic effects across diverse categories, including pesticides, pharmaceuticals, and industrial chemicals such as bisphenols and per- and poly-fluoroalkyl substances (PFAS). We validated our method by comparing CGPD Tetramer-based clusters with cumulative assessment groups (CAGs) for pesticides, demonstrating strong overlap with established groupings while identifying additional compounds relevant for risk assessment. Key examples include clusters associated with endocrine disruption and metabolic disorders.By bridging omics-derived molecular data with phenotypic and disease endpoints, this framework provides a comprehensive tool for chemical grouping and supports evidence-based regulatory decision-making, facilitating the transition to next-generation risk assessment methodologies.

pharmacology and toxicology↗

bioRxiv2023

Reply to: Contribution of carbon inputs to soil carbon accumulation cannot be neglected

In the accompanying Comment1, He et al. argue that the determinant role of microbial carbon use efficiency in global soil organic carbon (SOC) storage shown in Tao et al. (2023)2 was overestimated because carbon inputs were neglected in our data analysis while they suggest that our model-based analysis could be biased and model-dependent. Their argument is based on a different choice of independent variables in the data analysis and a sensitivity analysis of two process-based models other than that used in our study. We agree that both carbon inputs and outputs (as mediated by microbial processes) matter when predicting SOC storage - the question is their relative contributions. While we encourage further studies to examine how the evaluation of the relative importance of CUE to global SOC storage may vary with different model structures, He et al.s claims about Tao et al. (2023) need to be taken as an alternative, unproven hypothesis until empirical data support their specific parameterization. Here we show that an additional literature assessment of global data does not support He et al.s argument, in contrast to our study, and that further study on this topic is essential.

ecology↗

bioRxiv2023

Intron retention of an adhesion GPCR generates single transmembrane-helix isoforms to enable 7TM-adhesion GPCR function

Adhesion G protein-coupled receptors (aGPCR) function as metabotropic mechanosensors in the nervous system and other organs. aGPCR are heavily spliced forecasting an extraordinary molecular structural diversity. Many predicted isoforms lack the transmembrane (7TM) signaling subunit, but to what extent these non-GPCR isoforms are produced and what physiological purpose they serve is unknown. Alternative splicing through intron retention of ADGRL/Latrophilin/Cirl mRNA in Drosophila generates transcripts encoding unconventional proteins with an extracellular domain anchored by a single transmembrane helix (Cirl1TM). Here, we show that Cirl1TM transcripts are translated in vivo and that Cirl1TM binds Cirl7TM N-terminal fragment-dependently. This interaction enables mechanosensory neurons to distinguish input intensities through Go-dependent signaling. Similarly, a direct interaction was found for mammalian GPR126/ADGRG6 isoforms. Together, our findings define intron retention and isoform-specific heteromerization as extraordinary molecular strategies to adjust Cirl-dependent mechanosensation and demonstrate physiological relevance of versatile aGPCR isoform repertoire to tune cellular responsiveness.

neuroscience↗

bioRxiv2021

Genetic code degeneracy is established by the decoding center of the ribosome

The degeneracy of the genetic code confers a wide array of properties to coding sequences. Yet, its origin is still unclear. A structural analysis has shown that the stability of the Watson-Crick base pair at the second position of the anticodon-codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. Based on recent cryo-EM analyses, the present work shows that residue A1493 of the decoding center provides a significant contribution to the stability of this base pair, revealing that the ribosome is directly involved in the establishment of degeneracy. Building on existing evolutionary models, we show the evidence that the early appearance of A1493 and A1492 established the basis of degeneracy when an elementary kinetic scheme of translation was prevailing. Logical considerations on the expansion of this kinetic scheme indicate that the acquisition of the peptidyl transferase center was the next major evolutionary step, while the induced-fit mechanism, that enables a sharp selection of the tRNAs, necessarily arose later when G530 was acquired by the decoding center.

molecular biology↗

bioRxiv2021

Autoantibodies against Progranulin and IL-1 receptor antagonist in critically ill COVID-19

STRUCTURED ABSTRACTHyperinflammation is frequently observed in patients with severe COVID-19. Inadequate and defective IFN type I responses against SARS-CoV-2, associated with autoantibodies in a proportion of patients, lead to severe courses of disease. In addition, hyperactive responses of the humoral immune system have been described. In the current study we investigated a possible role of neutralizing autoantibodies against antiinflammatory mediators. Plasma from adult patients with severe and critical COVID-19 was screened by ELISA for antibodies against PGRN, IL-1-Ra, IL-10, IL-18BP, IL-22BP, IL-36-Ra, CD40, IFN-2, IFN-{gamma}, IFN-{omega} and serpinB1. Autoantibodies were characterized and the antigens were analyzed for immunogenic alterations. In a discovery cohort with severe to critical COVID-19 high titers of PGRN-autoantibodies were detected in 11 of 30 (36.7%), and of IL-1-Ra-autoantibodies in 14 of 30 (46.7%) patients. In a validation cohort of 64 patients with critical COVID-19 high-titer PGRN-Abs were detected in 25 (39%) and IL-1-Ra-Abs in 32 of 64 patients (50%). PGRN-Abs and IL-1-Ra-Abs belonged to IgM and several IgG subclasses. In separate cohorts with non-critical COVID-19, PGRN-Abs and IL-1-Ra-Abs were detected in low frequency (i.e. in < 5% of patients) and at low titers. Neither PGRN-nor IL-1-Ra-Abs were found in 40 healthy controls vaccinated against SARS-CoV-2 or 188 unvaccinated healthy controls. PGRN-Abs were not cross-reactive against SARS-CoV-2 structural proteins nor against IL-1-Ra. Plasma levels of both free PGRN and free IL-1-Ra were significantly decreased in autoantibody-positive patients compared to Ab-negative and non-COVID-19 controls. In vitro PGRN-Abs from patients functionally reduced PGRN-dependent inhibition of TNF- signaling, and IL-1-Ra-Abs from patients reduced IL-1-Ra- or anakinra-dependent inhibition of IL-1{beta} signaling. The pSer81 hyperphosphorylated PGRN isoform was exclusively detected in patients with high-titer PGRN-Abs; likewise, a hyperphosphorylated IL-1-Ra isoform was only found in patients with high-titer IL-1-Ra-Abs. Thr111 was identified as the hyperphophorylated amino acid of IL-1-Ra. In longitudinally collected samples hyperphosphorylated isoforms of both PGRN and IL-1-Ra emerged transiently, and preceded the appearance of autoantibodies. In hospitalized patients, the presence of IL-1-Ra-Abs or IL-1-Ra-Abs in combination with PGRN-Abs was associated with a higher morbidity and mortality. To conclude, neutralizing autoantibodies to IL-1-Ra and PGRN occur in a significant portion of patients with critical COVID-19, with a concomitant decrease in circulating free PGRN and IL-1-Ra, indicative of a misdirected, proinflammatory autoimmune response. The break of self-tolerance is likely caused by atypical hyperphosphorylated isoforms of both antigens, whose appearances precede autoantibody induction. Our data suggest that these immunogenic secondary modifications are induced by the SARS-CoV-2-infection itself or the inflammatory environment evoked by the infection and predispose for a critical course of COVID-19.

immunology↗

bioRxiv2020

CLEP: A Hybrid Data- and Knowledge- Driven Framework for Generating Patient Representations

As machine learning and artificial intelligence become more useful in the interpretation of biomedical data, their utility depends on the data used to train them. Due to the complexity and high dimensionality of biomedical data, there is a need for approaches that combine prior knowledge around known biological interactions with patient data. Here, we present CLEP, a novel approach that generates new patient representations by leveraging both prior knowledge and patient-level data. First, given a patient-level dataset and a knowledge graph containing relations across features that can be mapped to the dataset, CLEP incorporates patients into the knowledge graph as new nodes connected to their most characteristic features. Next, CLEP employs knowledge graph embedding models to generate new patient representations that can ultimately be used for a variety of downstream tasks, ranging from clustering to classification. We demonstrate how using new patient representations generated by CLEP significantly improves performance in classifying between patients and healthy controls for a variety of machine learning models, as compared to the use of the original transcriptomics data. Furthermore, we also show how incorporating patients into a knowledge graph can foster the interpretation and identification of biological features characteristic of a specific disease or patient subgroup. Finally, we released CLEP as an open source Python package together with examples and documentation.

bioinformatics↗

bioRxiv2020

Microbial community shifts reflect losses of native soil carbon with pyrogenic and fresh organic matter additions and are greatest in low-carbon soils

Soil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the US and 13C-labelled 350{degrees}C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO2 emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their response to PyOM and OM. We found that the effects of amendments on nSOC-derived CO2 reflected the unamended soil C status, where amendments increased C mineralization the most in low-C soils. OM additions produced much greater effects on nSOC-CO2 emissions than PyOM additions. Furthermore, the magnitude of microbial community composition change mirrored the magnitude of increases in nSOC-CO2, indicating a specific subset of microbes were likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common "charosphere". Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions. ImportanceSoil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected, or "pyrogenic" organic matter (PyOM) affects existing SOM stocks has become increasingly important, both due to changing fire regimes, and to interest in "biochar" - pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions, and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss, and that a subset of the soil microbial community is likely responsible for these effects.

microbiology↗

bioRxiv2020

Highly reproducible characterization of Escherichia coli tRNA epitranscriptome with a simple method of library preparation for deep sequencing

In conventional RNA high-throughput sequencing, modified bases prevent a large fraction of tRNA transcripts to be converted into cDNA libraries. Recent proposals aiming at resolving this issue take advantage of the interference of base modifications with RT enzymes to detect and identify them by establishing signals from aborted cDNA transcripts. Because some modifications, such as methyl groups, do almost not allow RT bypassing, demethylation and highly processive RT enzymes have been used to overcome these obstacles. Working with Escherichia coli as a model system, we show that with a conventional (albeit still engineered) RT enzyme and key optimizations in library preparation, all RT-impairing modifications can be highlighted along the entire tRNA length without a demethylation procedure. This is achieved by combining deep-sequencing samples, which allows to establish aborted transcription signal of higher accuracy and reproducibility, with the potential for differentiating tiny differences in the state of modification of all cellular tRNAs. In addition, our protocol provides estimates of the relative tRNA abundance.

genomics↗

bioRxiv2020

Suppressing peatland methane production by electron snorkeling through pyrogenic carbon

Northern peatlands are experiencing more frequent fire events as a result of changing climate conditions. Forest fires naturally result in a direct and negative climate impact by emitting large amounts of carbon into the atmosphere. Recent studies show that this extensive emission may shift the soil carbon regime from a sink to a source. However, the fires also convert parts of the burnt biomass into pyrogenic carbon. Here, we show an indirect, but positive, climate impact induced by fire-derived pyrogenic carbon. We found that the accumulation of pyrogenic carbon reduced post-fire methane production from peatland soils by 13-24%. The conductive, capacitive, and redox-cycling electron transfer mechanisms enabled pyrogenic carbon to function as an electron snorkel, which redirected soil electron fluxes to facilitate alternative microbial respiration and reduced the rate of methane production by 50%. Given the fact that methane has a 34-fold greater warming potential than carbon dioxide, we estimate that global greenhouse gas emissions are reduced by 35 Tg CO2e annually through the electron snorkeling of pyrogenic carbon in peatlands. Our results highlight an important, but overlooked, function of pyrogenic carbon in neutralizing forest fire emissions and call for its consideration in the global carbon budget estimation.

microbiology↗

bioRxiv2018

BioKEEN: A library for learning and evaluating biological knowledge graph embeddings

Knowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programming and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies.\n\nAvailabilityBioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https://github.com/SmartDataAnalytics/BioKEEN and https://github.com/SmartDataAnalytics/PyKEEN as well as through PyPI.

bioinformatics↗