Biology subjects

Schneider, A.

Publications and source records attributed to Schneider, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

EXOSOMES FROM CYCLIC MICE MODULATE LIVER TRANSCRIPTOME IN ESTROUPAUSE MICE INDEPENDENT OF AGE

BackgroundExosomes are extracellular vesicles secreted by cells that contain microRNAs (miRNAs). These miRNAs can induce changes in gene expression and function of recipient cells. In different cells exosome content can change with age and physiological state affecting tissues function and health. AimsTherefore, the aim of this study was to characterize the miRNA content and role of exosomes from cyclic female mice in the modulation of liver transcriptome in estropausal mice. Main MethodsTwo-month-old female mice were induced to estropause using 4-vinylcyclohexene diepoxide (VCD). At six months of age VCD-treated mice were divided in control group (VCD) and exosome treated group (VCD+EXO), which received 10 injections at 3-day intervals of exosomes extracted from serum of cyclic female mice (CTL). Key findingsExosome injection in estropausal mice had no effect on body mass, insulin sensitivity or organ weight. We observed ten miRNAs differentially regulated in serum exosomes of VCD compared to CTL mice. In the liver we observed 931 genes differentially expressed in VCD+EXO compared to VCD mice. Interestingly, eight pathways were up-regulated in liver by VCD treatment and down-regulated by exosome treatment, indicating that exosomes from cyclic mice can reverse changes promoted by estropause in liver. Cyp4a12a expression which is male-specific was increased in VCD females and not reversed by exosome treatment. SignificanceOur findings indicate that miRNAs content in exosomes is regulated by estropause in mice independent of age. Additionally, treatment of estropausal mice with exosomes from cyclic mice can partially reverse changes in liver transcriptome.

physiology↗

bioRxiv2024

Genetic and functional adaptations and alcohol-biased signaling in the mediodorsal thalamus of alcohol dependent mice

Alcohol Use Disorder (AUD) is a significant health concern characterized by cognitive dysfunction and an inability to control alcohol intake leading to severe social and health consequences. It is crucial to uncover neuroadaptations and cellular mechanisms responsible for poor decisions surrounding alcohol drinking. Although the mediodorsal thalamus (MD) is an essential brain region for cognitive function and reward-guided choices, the effects of alcohol dependence on MD neuroadaptations and how dependence alters MD activity during choice behaviors for alcohol over natural rewards (i.e., sucrose) are not well understood. Genetic and physiological adaptations in the MD were assessed in mice treated with the chronic intermittent ethanol (CIE) exposure model of dependence, which increased alcohol intake and preference during choice sessions for water or sucrose. Results indicated that CIE exposure induced changes in transcript expression and excitability of MD neurons. Enrichment analysis of alcohol-sensitive genes revealed dysregulation of genes that control glial function and axonal myelination. Fiber photometry was used to record MD calcium signals in CIE mice during choice drinking sessions for alcohol and either water or sucrose. Results demonstrated that MD activity was elevated at the start of and after licking bouts for alcohol, water, or sucrose, although the signal for alcohol was significantly higher than signal for other solutions and this effect persisted after induction of dependence. These findings demonstrate that CIE exposure causes genetic and physiological neuroadaptations in the MD that coincide with alcohol-biased behaviors, with the MD uniquely responsive to alcohol over other solutions.

neuroscience↗

bioRxiv2024

Dysfunction of the episodic memory network in the Alzheimer's disease cascade

Alzheimers disease (AD) is a major cause of dementia and cognitive decline. Here we assessed how episodic memory circuit dysfunction, a hallmark of AD, is related to the longitudinal cascade of AD biomarkers, neurodegeneration and cognition using data from the DZNE Longitudinal Cognitive Impairment and Dementia study. This data set is unique by including over 1000 longitudinal functional magnetic resonance imaging (fMRI) measurements during episodic memory encoding. We leveraged a disease progression model (DPM) to obtain AD progression scores. Voxel-wise analyses revealed widespread loss of deactivation (hyperactivation) and activation (hypoactivation) with increasing disease stage. Hyperactivation trajectories were nonlinear and visually preceded trajectories of cognition. Overall, hyperactivation was independently associated with co-occurrence of amyloid- and tau-positivity and neurodegeneration, suggesting synaptic dysfunction and neurodegeneration as two independent drives of cognitive decline. Our results therefore provide evidence for a critical time window in which pharmacological treatments targeting the synapse may improve cognition.

neuroscience↗

bioRxiv2024

Amyloid Beta Precursor Protein contributes to brain aging and learning decline in short-lived turquoise killifish (Nothobranchius furzeri)

Brain aging is a key risk factor for many neurodegenerative diseases, yet its molecular and cellular mechanisms remain elusive. Amyloid-beta precursor protein (APP) is among the most studied proteins linked to brain pathology; however, its role in non-pathological brain aging remains poorly characterized. Here, we investigate the natural impact of APP on normal brain aging using the short-lived turquoise killifish (Nothobranchius furzeri), which exhibits rapid and spontaneous age-related decline. We found that a pyroglutamated APP derivative (APPpE11) accumulates intra-neuronally in an age-dependent manner, co-localizing with a marker of cell death. We found that intraneuronal APPpE11 is also present in brains from healthy elderly humans, suggesting deep evolutionary conservation. To determine APPs role in spontaneous brain aging, we knock-out "amyloid precursor protein a" (appa) in killifish via CRISPR/Cas9. The lack of appa mitigated brain aging from a proteome-wide perspective, reduced age-related cell death and inflammation, and improved neuronal activity and learning capacity in aged individuals. Our findings show an ancestral and previously unrecognized role of amyloid-beta precursor protein in non-pathological brain aging, making it an ideal target for anti-aging interventions.

neuroscience↗

bioRxiv2024

microbetag: simplifying microbial network interpretation through annotation, enrichment tests and metabolic complementarity analysis

Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to enhance network annotation. Nodes (taxa) are enriched with phenotypic traits, while edges represent metabolic complementarities, highlighting potential cross-feeding relationships. microbetags online version relies on microbetagDB, a database of 34,608 high-quality genomes with detailed annotations. A stand-alone tool allows users to apply microbetag to custom reference genomes/bins/MAGs. Additionally, MGG, a CytoscapeApp, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.

systems biology↗

bioRxiv2024

Molecular characterization of the permanent outer-inner membrane contact site of the mitochondrial genome segregation complex in trypanosomes

The parasitic protozoan Trypanosoma brucei has a single unit mitochondrial genome linked to the basal body of the flagellum via the tripartite attachment complex (TAC). The TAC is crucial for mitochondrial genome segregation during cytokinesis. At the core of the TAC, the outer membrane protein TAC60 binds to the inner membrane protein p166, forming a permanent contact site between the two membranes. Although contact sites between mitochondrial membranes are common and serve various functions, their molecular architecture remains largely unknown. This study elucidates the interaction interface of the TAC60-p166 contact site. Using in silico, in vitro, and mutational in vivo analyses, we identified minimal binding segments between TAC60 and p166. The p166 binding site in TAC60 consists of a short kinked -helix that interacts with the C-terminal - helix of p166. Despite the presence of conserved charged residues in either protein, electrostatic interactions are not necessary for contact site formation. Instead, the TAC60-p166 interaction is driven by the hydrophobic effect, as converting conserved hydrophobic residues in either protein to hydrophilic amino acids disrupts the contact site. Author summaryMitochondria are surrounded by two membranes and essential for nearly all eukaryotes. Contact sites between the two membranes are important for mitochondrial function. However, most contact sites are dynamic making their molecular architecture challenging to study. The tripartite attachment complex (TAC) of parasitic protozoan Trypanosoma brucei connects its compact mitochondrial genome with the basal body of the flagellum. This couples the segregation of the replicated mitochondrial genome to the old and new basal body. The TAC contains permanent contact sites formed by outer membrane protein TAC60 and the intermembrane space-exposed C-terminus of p166 of the inner membrane. We have used it as a model for a prototypical contact site. AlphaFold predictions and in vitro binding assays identified a small region in the intermembrane space region of TAC60 that binds p166 forming contact sites. In vivo expression of various TAC60 and/or p166 mutants followed by immunoprecipitations demonstrates that contact site formation is driven by the hydrophobic effect and independent of the conserved charged amino acids present at the TAC60-p166 interface. The TAC is unique to Kinetoplastids, understanding the molecular architecture of the TAC60-p166 contact site could therefore inform the development of drugs that disrupt this critical interaction.

biochemistry↗

bioRxiv2024

Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics

Antimicrobial resistance (AMR) is an increasing challenge for therapy of bacterial infections. Currently, patient treatment is guided by antimicrobial susceptibility testing (AST) using phenotypic assays and species identification by MALDI-ToF biotyping. Bacterial phenotype prediction using omics technologies could offer several advantages over current diagnostic methods. It would allow species identification and AST to be combined in a single measurement, it would eliminate the need for secondary cultivation and could enable the prediction of phenotypes beyond AMR, such as virulence. In this study, the potential of proteomics for clinical microbiology was evaluated in an analysis of 126 clinical isolates covering 16 species including all ESKAPE genera and 29 of the most common AMR determinants. For this purpose, a flexible workflow was developed, which enables to report the AMR phenotype and the species of primary cultures within 2h. Proteomics provided high specificity (99.9%) and sensitivity (94.4 %) for AMR detection, while allowing species identification from very large sequence databases with high accuracy. The results show, that proteomics is well suited for phenotyping clinical bacterial isolates and has the potential to become a valuable diagnostic tool for clinical microbiology in the future.

microbiology↗

bioRxiv2024

Fully Automated MRI-based Analysis of the Locus Coeruleus in Aging and Alzheimer's Disease Dementia using ELSI-Net

INTRODUCTIONThe Locus Coeruleus (LC) is linked to the development and pathophysiology of neurodegenerative diseases such as Alzheimers Disease (AD). Magnetic Resonance Imaging based LC features have shown potential to assess LC integrity in vivo. METHODSWe present a Deep Learning based LC segmentation and feature extraction method: ELSI-Net and apply it to healthy aging and AD dementia datasets. Agreement to expert raters and previously published LC atlases were assessed. We aimed to reproduce previously reported differences in LC integrity in aging and AD dementia and correlate extracted features to cerebrospinal fluid (CSF) biomarkers of AD pathology. RESULTSELSI-Net demonstrated high agreement to expert raters and published atlases. Previously reported group differences in LC integrity were detected and correlations to CSF biomarkers were found. DISCUSSIONAlthough we found excellent performance, further evaluations on more diverse datasets from clinical cohorts are required for a conclusive assessment of ELSI-Nets general applicability. HighlightsO_LIthorough evaluation of a fully automatic LC segmentation method termed ELSI-Net in aging and AD dementia C_LIO_LIELSI-Net outperforms previous work and shows high agreement with manual ratings and previously published LC atlases C_LIO_LIELSI-Net replicates previously shown LC group differences in aging and AD C_LIO_LIELSI-Nets LC volume correlates with CSF biomarkers of AD pathology C_LI RESEARCH IN CONTEXTO_LISystematic Review: The authors reviewed the literature using traditional sources (e.g. Pubmed, Google Scholar). Although there are several publications introducing semi-automatic methods for LC segmentation, the application of Deep Learning methods is underexplored. To the best of our knowledge, this is the first paper using a Deep Learning based approach for automated LC segmentation in AD dementia. C_LIO_LIInterpretation: Our work introduces and evaluates an improved automatic, Deep Learning based LC segmentation and analysis approach. The results suggest a very high potential for practical applicability, e.g. in large-scale clinical studies for neurodegenerative diseases. C_LIO_LIFuture Directions: ELSI-Net can be used to assess LC integrity on large- or small-scale studies in Alzheimers Disease dementia. To ensure robust performance, ELSI-Net should be further evaluated in larger, more diverse datasets comprising varying LC MRI protocols and clinical populations. C_LI

bioinformatics↗

bioRxiv2024

Global-scale quantification of responses to anthropogenic stressors in six riverine organism groups

Rivers globally are impacted by numerous anthropogenic stressors, including water pollution, habitat degradation, and climate change, which collectively stress biodiversity and ecosystem functioning. This study systematically reviews and analyses published and unpublished data to understand how five aquatic organism groups (bacteria, algae, macrophytes, invertebrates, fish) respond to seven common stressors (salinization, oxygen depletion, fine sediment enrichment, temperature increase, flow modifications and nitrogen or phosphorus enrichment). Using an analytical framework that includes Generalized Linear Models (GLMs) and Robust Bayesian Meta Analysis (RoBMA), we extracted data from 143 relevant datasets out of 29,749 screened articles. Our results reveal a negative relationship between invertebrates and salinity, fine sediment enrichment, and temperature increase, while fish respond positively to increased oxygen levels and temperature. Bacteria and algae show variable responses, with algae positively associated with nitrogen. The findings highlight strong variability in stressor-response relations across organism groups and stressor types, and emphasize the need for more targeted studies on underrepresented groups like macrophytes and microorganisms. This analysis enhances the predictive understanding of stressor impacts on riverine biodiversity, informing future river ecosystem management and restoration efforts.

ecology↗

bioRxiv2024

ER-associated biogenesis of PINK1 preprotein for neuronal mitophagy

A central role in mitochondrial quality control is played by the Parkinson-related mitochondrial kinase PINK1, whose mRNA is transported in neurons by mitochondrial hitch- hiking. Using a live-cell imaging assay for the translation of the PINK1 precursor, we show that local translation of PINK1 requires a concerted interplay between mitochondria and the ER in neurons. For efficient translation, the Pink1 mRNA needs to relocate to ribosomes located near endolysosomes and the ER. The ER membrane-tethered chaperone DNAJB6 then shields the PINK1 precursor on transit to mitochondria following the ER-SURF pathway. Loss of DNAJB6 hence leads to persistence of ER/endolysosome-associated PINK1 precursor stores and failure of mitophagy upon mitochondrial damage.

neuroscience↗

bioRxiv2024

The ferroptosis mediator ACSL4 fails to prevent disease progression in mouse models of MASLD

Metabolic dysfunction-associated steatotic liver disease is an increasingly prevalent condition, representing a major risk factor for the development of progressive chronic liver damage. This can potentially give rise to the development of steatohepatitis and hepatocellular carcinoma (HCC). It is already known, that patients with metabolic dysfunction-associated steatotic liver disease (MASLD) show increased systemic and hepatic iron concentrations as well as perturbed lipid metabolism, suggesting involvement of ferroptotic cell death in the development and progression of MASLD. Consequently, inhibition of ferroptosis represents a potential therapeutic option for patients with MASLD. The aim of this study was to determine whether a liver parenchymal cell specific conditional deletion of the pro-ferroptotic gene acyl-CoA synthetase long-chain family member 4 (ACSL4LPC-KO) can ameliorate the onset and progression of MASLD in mice. To this end, ACSL4LPC-KO and floxed wild-type littermates were fed a choline-deficient high-fat diet over the course of 20 and 40 weeks to monitor the progression of metabolic liver injury as well as the development of metabolic syndrome. In contrast to the recently published studies by Duan et al. [1], our results show no significant differences between ACSL4LPC-KO and WT mice with regard to the development of MASLD or the progression of metabolic syndrome. Furthermore, no differences were observed in metabolic parameters (i.e. weight gain, glucose tolerance test, hepatic steatosis) or MASLD-associated inflammatory response. Our analyses therefore suggest that loss of ACSL4 has no effect on the progression of MASLD induced by choline-deficient high fat diet. The discrepancy between our and previously published results could be due to differences in the diets or the influence of a distinct microbiome, so the results obtained with liver parenchymal cell specific ACSL4 null mice should be taken with caution.

systems biology↗

bioRxiv2024

Effect of senolytic drugs in young female mice chemically induced to estropause

AimsThis study aimed to assess metabolic responses and senescent cell burden in young female mice induced to estropause and treated with senolytic drugs. Main methodsEstropause was induced by 4-vinylcyclohexene diepoxide (VCD) injection in two-month-old mice. The senolytics dasatinib and quercetin (D+Q) or fisetin were given by oral gavage once a month from five to 11 months of age. Key findingsVCD-induced estropause led to increased body mass and reduced albumin concentrations compared to untreated cyclic mice, without affecting insulin sensitivity, lipid profile, liver enzymes, or total proteins. Estropause decreased catalase activity in adipose tissue but had no significant effect on other redox parameters in adipose and hepatic tissues. Fisetin treatment reduced ROS levels in the hepatic tissue of estropause mice. Estropause did not influence senescence-associated beta-galactosidase activity in adipose and hepatic tissues, but increased senescent cell markers and fibrosis in ovaries. Senolytic treatment did not decrease ovarian cellular senescence induced by estropause. SignificanceOverall, the findings suggest that estropause leads to minor metabolic changes in young females, and senolytics had no protective effects despite increased ovarian senescence.

physiology↗

bioRxiv2024

Chronic abolition of evoked vesicle release from layer 5 projection neurons disrupts the laminar distribution of parvalbumin interneurons in the adult cortex

Establishing precisely built neuronal networks during cortical development requires appropriate proportions of glutamatergic and GABAergic neurons. Developmental disturbances in pyramidal neuron activity can impede the development of GABAergic neurons with long-lasting effects on inhibitory networks. However, the role of deep-layer pyramidal neurons in instructing the development and distribution of GABAergic neurons remains unknown. To unravel the role of deep-layer pyramidal neuron activity in orchestrating the spatial and laminar organisation of parvalbumin neurons, we selectively manipulated the activity of projection neurons in layer 5 of the cortex. By ablating SNAP25 from subsets of glutamatergic L5 projection neurons across the cortical mantle, we abolished Ca2+-dependent vesicle release from Rbp4-Cre+ pyramidal neurons. We explored the local (location of the cell bodies) and the global (subcortical projection sites) effects of chronically silencing cortical L5 neurons on parvalbumin interneurons. We found that the chronic cessation of vesicle release from L5 projection neurons left the density, distribution, and developmental trajectory of cortical and subcortical PV neurons intact during the second and third postnatal week; however, it resulted in the reorganisation of the laminar distribution of cortical PV neurons in layer 4 of S1 in the adult cortex. The abolition of evoked vesicle release from L5 also affected the perineuronal nets in the adult motor cortex and revealed a significant decrease in the density of VVA+ and PV-VVA+ cells in L5 of M1 at 3 months of age. The alterations in the laminar arrangement of VVA+ neurons may imply that Ca2+- dependent synaptic transmission from L5 may control PNN density in adult networks. We also discovered that the absence of L5 activity only had a transient effect on the morphology of striatal PV neurons. The correlation between PV and VVA neurons was contingent on brain regions and cortical layers, therefore the link between the perineuronal net and PV neurons is significantly more intricate than previously believed. The present study will aid our understanding of the bidirectional relationship between deep-layer pyramidal cells and GABAergic neurons while uncovering the long-term effects of chronically disrupting pyramidal neurons on inhibitory networks.

neuroscience↗

bioRxiv2024

T-cell development and activation in humanized mice lacking mouse major histocompatibility complexes

Humanized mice transplanted with CD34+ hematopoietic progenitor cells (HPCs) are used to study human immune responses in vivo. However, the mismatch between the mouse major histocompatibility complexes (MHCs) and the human leukocyte antigens (HLAs) is not optimal for T-cell development and can trigger xenograft reactivity. We evaluated human T-cell development in NOD.Scid.Gamma mice lacking expression of MHC class I and II (NSG-DKO). Human leukocyte engraftment was detectable at 8 weeks post-transplantation. Human CD4+ and CD8+ T-cells were detectable in blood, thymus, bone marrow and spleen of humanized NSG-DKO mice for up to 20 weeks post-transplantation. Further, we evaluated the effects of lentiviral vector (LV) systemic delivery of HLA-A*02:01, HLA-DRB1*04:01, human GM-CSF/IFN- and the human cytomegalovirus gB antigen. LV delivery promoted development and activation of human central memory, {beta} and {gamma}{delta} T-cells with amplifications of the T-cell repertoire. LV administration unleashed multiple reactome pathways such as type-I interferon responses, cell cycle and metabolic processes. In summary, development of human T-cells in humanized mice does not rely on mouse MHCs and can be boosted systemically via LV administration.

immunology↗

bioRxiv2024

Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924

A growing body of knowledge implicates perturbed RNA homeostasis in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease that currently has no cure and few available treatments. Dysregulation of the multifunctional RNA-binding protein TDP-43 is increasingly regarded as a convergent feature of this disease, evidenced at the neuropathological level by the detection of TDP-43 pathology in most patient tissues, and at the genetic level by the identification of disease-associated mutations in its coding gene TARDBP. To characterize the transcriptional landscape induced by TARDBP mutations, we performed whole-transcriptome profiling of motor neurons differentiated from two knock-in iPSC lines expressing the ALS-linked TDP-43 variants p.A382T or p.G348C. Our results show that the TARDBP mutations significantly altered the expression profiles of mRNAs and microRNAs of the 14q32 cluster in MNs. Using mutation-induced gene signatures and the Connectivity Map database, we identified compounds predicted to restore gene expression toward wild-type levels. Among top-scoring compounds selected for further investigation, the NEDD8-activating enzyme inhibitor MLN4924 effectively improved cell viability and neuronal activity, highlighting a possible role for protein post-translational modification via NEDDylation in the pathobiology of TDP-43 in ALS.

neuroscience↗

bioRxiv2024

Intermembrane space-localized twin Cx9C motif-containing TbTim15 is an essential subunit of the single mitochondrial inner membrane protein translocase of trypanosomes

All mitochondria import >95% of their proteins from the cytosol. This process is mediated by protein translocases in the mitochondrial membranes, whose subunits are generally highly conserved. Most eukaryotes have two inner membrane protein translocases (TIMs) that are specialized to import either presequence-containing or mitochondrial carrier pro-teins. In contrast, the parasitic protozoan Trypanosoma brucei has a single TIM complex consisting of one conserved and five unique subunits. Here, we show that the trypanoso-mal TIM complex contains an additional trypanosomatid-specific subunit, designated TbTim15. TbTim15 is associated with the TIM complex, lacks transmembrane domains and localizes to the intermembrane space. TbTim15 is essential for procyclic and bloodstream forms of trypanosomes. It contains two twin CX9C motifs and mediates import of both, presequence-containing and mitochondrial carrier proteins. While the precise function of TbTim15 in mitochondrial protein import is unknown, our results are consistent with the notion that it may function as an import receptor for the non-canonical trypanosomal TIM complex.

biochemistry↗

bioRxiv2023

Evolutionary repurposing of trypanosomal Pam18 and Pam16 reveals a new regulatory circuit for mitochondrial genome replication

Protein import and genome replication are essential processes for mitochondrial biogenesis and propagation. The J-domain proteins Pam16 and Pam18 regulate the presequence translocase of the mitochondrial inner membrane. In the protozoan Trypanosoma brucei, their counterparts are TbPam16 and TbPam18, which are essential for the procyclic form of the parasite, though not involved in mitochondrial protein import. Here, we show that during evolution, the two proteins have been repurposed to regulate the replication of maxicircles within the intricate kDNA network, the most complex mitochondrial genome known. TbPam18 and TbPam16 have inactive J-domains suggesting a function independent of heat shock proteins. However, their single transmembrane domain is essential for function. Pulldown of TbPam16 identifies a putative client protein, termed MaRF11, the depletion of which causes the selective loss of maxicircles, akin to the effects observed for TbPam18 and TbPam16. Moreover depletion of the mitochondrial proteasome results in increased levels of MaRF11. Thus, we propose a model for a membrane-bound regulatory circuit that controls maxicircle replication in response to an unknown nuclear signal. This model posits that MaRF11 directly mediates maxicircle replication, that its level is controlled by proteasomal digestion, and that it is protected from degradation by binding to the TbPam18/TbPam16 dimer.

biochemistry↗

bioRxiv2023

Four-Core Genotypes mice harbour a 3.2MB X-Y translocation that perturbs Tlr7 dosage

The Four Core Genotypes (FCG) is a mouse model system heavily used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the YSry- chromosome and thus increased the expression of multiple genes including the auto-immune master regulator Tlr7. This previously-unreported X-Y translocation complicates the interpretation of studies reliant on FCG mice.

genetics↗