Biology subjects

Moos, M.

Publications and source records attributed to Moos, M..

14 recordsLinked to original sources

bioRxiv2026

Prenatal e-cigarette exposure induces region- and cell type-specific metabolic and developmental reprogramming

Prenatal e-cigarette exposure (PeCE) is increasingly prevalent and has been associated with adverse neurodevelopmental outcomes, yet how maternal vaping perturbs early brain development remains poorly understood. We integrated spatial transcriptomics, snRNA-seq and lipidomics to define neonatal rat brain responses to PeCE in rats at regional and cellular resolution. PeCE induced pronounced spatial heterogeneity in vulnerability, with the striatum exhibiting the strongest developmental transcriptional disruption. PeCE disrupts lipid metabolic homeostasis and induced molecular signatures suggestive of enhance Ca2+ signaling, dopaminergic responsiveness and region-specific synaptic stress programs. In the striatum, PeCE induced transcriptional programs consistent with altered lipid utilization, silent synapse-like molecular features, suppressed dendritic spine development and delayed D1-medium spiny neuron maturation. PeCE-sensitive genes were enriched in human autism spectrum disorders and neurodevelopment risk loci. Together, these findings identify disrupted metabolic and developmental reprogramming as a central feature of neonatal brain vulnerability to maternal vaping and provide a mechanistic framework linking PeCE to neurodevelopmental disease risk.

neuroscience↗

bioRxiv2026

Host-derived lipids license proliferation of sterol-auxotrophic tick cells and promote flavivirus output

Sterol molecules play indispensable roles in the biology of cells and organisms. Yet, arthropods, including ticks, lack the capacity for de novo sterol biosynthesis and must rely on exogenous sources. How these organisms sense and utilise exogenous lipids at the cellular level remains poorly understood. Here, we show that host cholesterol and linoleic acid act as essential external signals that license proliferation of Ixodes ricinus tick cells. In lipid-depleted conditions, cells fail to proliferate despite retaining intracellular cholesterol, indicating that exogenous lipids function as regulatory cues rather than merely structural components. We further demonstrate that tick cells exhibit a non-canonical intracellular distribution of cholesterol, with predominant accumulation in lysosome-associated compartments, and that lipid availability induces a coordinated transcriptional program involving lipid uptake and trafficking machinery. Importantly, we find that limiting host lipid availability significantly reduces extracellular RNA output of tick-borne encephalitis virus (TBEV) from infected tick cells, indicating that viral production is affected by the metabolic state of the host cell. Together, our findings establish host-derived lipids as key regulators of cellular state in a sterol-auxotrophic organism and identify lipid availability as a determinant of flavivirus output. This work provides a conceptual framework linking nutrient sensing, cell proliferation, and vector-pathogen interactions.

microbiology↗

bioRxiv2025

Comparative analysis of plasma steroid hormone levels reveals lower concentrations in Afrotropical than Palearctic temperate zone passerines

Latitudinal changes in environmental conditions shape the evolution of avian life history traits: tropical bird species typically exhibiting prolonged breeding seasons, a slower pace of life, lower annual investment in reproduction and increased annual survival compared to their temperate counterparts. Major shifts in physiology, reflecting these differences, are expected to be mediated by endocrine regulation, yet comparative data on the sources of inter-specific variation in hormone concentrations remain sparse, especially outside the Nearctic-Neotropic system. We examined variation in two key steroid hormones, corticosterone and testosterone, across 100 passerine species from Europe and the Afrotropics, sampled using standardized field protocols. Baseline levels of both hormones were consistently lower in tropical species, as expected. While stress-induced corticosterone reactivity did not differ between latitudes, it declined with migration distance. Testosterone levels were higher in males than females and declined with migration distance. In tropical species, neither hormone was associated with elevation, another source of environmental variation, but both varied during the breeding cycle, challenging the view of tropical aseasonality. This study broadens the perspective on endocrine correlates of avian life history evolution by testing their generality in an understudied Afrotropical-Palearctic system. The results support the hypothesis that steroid hormone profiles co-evolve with latitude.

ecology↗

bioRxiv2025

Reversal of ATP synthase is a key attribute for cellular differentiation of the Trypanosoma brucei insect forms

The mitochondrial FoF1-ATP synthase is a reversible nanomachine responsible for generating the majority of cellular ATP by oxidative phosphorylation. In various pathological contexts associated with mitochondrial dysfunction, this enzyme can reverse its function to maintain essential mitochondrial membrane potential at the expense of ATP. This reversal is regulated by the conserved protein Inhibitory Factor 1 (IF1). Here, we demonstrate that ATP synthase reversal also occurs under physiological conditions during the cellular differentiation of the unicellular parasite Trypanosoma brucei, which transitions between insect and mammalian hosts. Differentiation of the insect forms is marked by upregulation of alternative oxidase (AOX) along with decreased expression of trypanosomal IF1 (TbIF1), collectively creating a metabolic environment conducive to ATP synthase reversal. We show that this reversal is key for proper parasite differentiation: parasites lacking TbIF1 efficiently transitioned into the mammalian-infective form. In these TbIF1 knockout parasites, ATP synthase reversal was associated with an increased ADP/ATP ratio, activation of AMP-activated protein kinase, enhanced cellular respiration driven by elevated proline metabolism, and increased mitochondrial and cellular reactive oxygen species (ROS), known signaling molecules. Conversely, parasites with inducible TbIF1 overexpression failed to reverse ATP synthase activity, showed no AMPK activation or ROS elevation, and remained locked in the initial insect stage. Our findings highlight the critical role of TbIF1 downregulation in enabling life cycle progression and underscore the unique function of the ATP synthase/IF1 axis in cellular signaling.

cell biology↗

bioRxiv2024

SAM transmethylation pathway and adenosine recycling to ATP are essential for systemic regulation and immune response

During parasitoid wasp infection, activated immune cells of Drosophila melanogaster larvae release adenosine to conserve nutrients for immune response. S-adenosylmethionine (SAM) is a methyl group donor for most methylations in the cell and is synthesized from methionine and ATP. After methylation, SAM is converted to S-adenosylhomocysteine, which is further metabolized to adenosine and homocysteine. Here, we show that the SAM transmethylation pathway is up-regulated during immune cell activation and that the adenosine produced by this pathway in immune cells acts as a systemic signal to delay Drosophila larval development and ensure sufficient nutrient supply to the immune system. We further show that the up-regulation of the SAM transmethylation pathway and the efficiency of the immune response also depend on the recycling of adenosine back to ATP by adenosine kinase and adenylate kinase. We therefore hypothesize that adenosine may act as a sensitive sensor of the balance between cell activity, represented by the sum of methylation events in the cell, and nutrient supply. If the supply of nutrients is insufficient for a given activity, adenosine may not be effectively recycled back into ATP and may be pushed out of the cell to serve as a signal to demand more nutrients.

cell biology↗

bioRxiv2024

A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data

Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful tool for cancer research, enabling in-depth characterization of tumor heterogeneity at the single-cell level. Recently, scRNA-seq copy number variation (scCNV) inference methods have been developed, expanding the application of scRNA-seq to study genetic heterogeneity in cancer using transcriptomic data. However, the fidelity of these methods has not been investigated systematically. In this study, we benchmarked five commonly used scCNV inference methods, HoneyBADGER, CopyKAT, CaSpER, inferCNV, and sciCNV. We evaluated their performance across four different scRNA-seq platforms derived data from a multicenter study. We further evaluated the scCNV performance using scRNA-seq datasets derived from mixed samples consisting of five human lung adenocarcinoma cell lines and generated a clinical scRNA-seq dataset from a human small cell lung cancer patient to validate our findings. Our evaluation criteria included sensitivity and specificity of CNV detection, and subclone identification from mixed cancer samples. We found that the sensitivity and specificity of the five scCNV inference methods varied, depending on the selection of reference data, sequencing depths, and read lengths. Overall, CopyKAT and CaSpER exhibited superior performance to other methods, while inferCNV, sciCNV, and CopyKAT outperformed other methods in subclone identification accuracy. Remarkably, inferCNV achieved high accuracy in subclone identification when using data from a "single scRNA-seq protocol", however, when applying these methods to a dataset derived from multiple scRNA-seq platforms from the mixed samples, we found that batch effects significantly affected the performance of subclone identification for most methods, except for HoneyBADGER. Our benchmarking study revealed the strengths and weaknesses of each of the five scCNV inference methods and provided guidance for selecting the optimal CNV inference method using scRNA-seq data.

bioinformatics↗

bioRxiv2024

Epigenomic, transcriptomic and proteomic characterizations of reference samples

A variety of newly developed next-generation sequencing technologies are making their way rapidly into the research and clinical applications, for which accuracy and cross-lab reproducibility are critical, and reference standards are much needed. Our previous multicenter studies under the SEQC-2 umbrella using a breast cancer cell line with paired B-cell line have produced a large amount of different genomic data including whole genome sequencing (Illumina, PacBio, Nanopore), HiC, and scRNA-seq with detailed analyses on somatic mutations, single-nucleotide variations (SNVs), and structural variations (SVs). However, there is still a lack of well-characterized reference materials which include epigenomic and proteomic data. Here we further performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses and provided a comprehensive catalog of the epigenomic landscape, which overlapped with the transcriptomes and proteomes for the two cell lines. We identified >7,700 peptide isoforms, where the majority (95%) of the genes had a single peptide isoform. Protein expression of the transcripts overlapping CGIs were much higher than the protein expression of the non-CGI transcripts in both cell lines. We further demonstrated the evidence that certain SNVs were incorporated into mutated peptides. We observed that open chromatin regions had low methylation which were largely regulated by CG density, where CG-rich regions had more accessible chromatin, low methylation, and higher gene and protein expression. The CG-poor regions had higher repressive epigenetic regulations (higher DNA methylation) and less open chromatin, resulting in a cell line specific methylation and gene expression patterns. Our studies provide well-defined reference materials consisting of two cell lines with genomic, epigenomic, transcriptomic, scRNA-seq and proteomic characterizations which can serve as standards for validating and benchmarking not only on various omics assays, but also on bioinformatics methods. It will be a valuable resource for both research and clinical communities.

genomics↗

bioRxiv2023

Metabolism of glucose and trehalose by cyclic pentose phosphate pathway is essential for effective immune response in Drosophila

Activation of immune cells requires the remodeling of cell metabolism in order to support immune function. We study these metabolic changes through the infection of Drosophila larvae by parasitoid wasp. Neutralization of the parasitoid egg involves the differentiation of lamellocytes, which encapsulate the egg. A melanization cascade is initiated, producing toxic molecules to destroy the egg; meanwhile the capsule created also protects the host from the toxic reaction. We combine transcriptomics and metabolomics, including 13C-labeled glucose and trehalose tracing, as well as genetic manipulation of sugar metabolism to study changes in metabolism, specifically in Drosophila hemocytes. We found that hemocytes increase the expression of several carbohydrate transporters, and accordingly uptake of sugar during infection. These carbohydrates are metabolized by increased glycolysis, associated with lactate production, and cyclic pentose phosphate pathway (PPP), in which glucose-6-phosphate is re-oxidized to maximize NADPH production. Oxidative PPP is required for lamellocyte differentiation and resistance, as is systemic trehalose metabolism. In addition, fully differentiated lamellocytes use a cytoplasmic form of trehalase to cleave trehalose to glucose, within the cell, to fuel cyclic PPP. Intracellular trehalose metabolism is not required for resistance, but may be associated with host protection from its own toxic response. Thus, our results suggest that sugar metabolism within immune cells, and specifically in cyclic PPP, may be important for not only fighting infection, but also for protecting the host from its own immune response and ensuring sufficient fitness of the survivor.

immunology↗

bioRxiv2023

Trypanosoma brucei bloodstream form mitochondrion is capable of ATP production by substrate phoshorylation

The bloodstream form Trypanosoma brucei maintains essential mitochondrial membrane potential ({Delta}{Psi}m) through the reverse activity of FoF1-ATP synthase. The ATP that drives this activity is thought to be generated by glycolysis and imported from the cytosol via an ATP/ADP carrier (AAC). We have shown that this carrier is the only carrier that can import ATP into the mitochondrial matrix to power the FoF1-ATPase. Contrary to expectations, its deletion has no effect on parasite growth, virulence and levels of {Delta}{Psi}m, suggesting that ATP is produced intramitochondrially by substrate phosphorylation pathways. Therefore, we knocked out the succinyl-CoA synthetase (SCoAS) gene, a key enzyme that produces ATP through substrate phosphorylation. Its absence resulted in changes in the metabolic landscape of the parasite, lower virulence, and reduced mitochondrial ATP content. This minimal mitochondrial ATP pool was maintained by AAC activity as evidenced by the 25- fold increase in sensitivity of the mutant parasites to AAC inhibitor carboxyatractyloside. Under nutrient-limited conditions, suppression of SCoAS expression by RNA interference negatively affected cell growth and levels of {Delta}{Psi}m. We concluded that the bloodstream mitochondrion is capable of generating ATP via substrate phosphorylation pathways, the importance of which depends on environmental conditions.

microbiology↗

bioRxiv2023

The bloodstream form of Trypanosoma brucei displays non-canonical gluconeogenesis

Trypanosoma brucei is a causative agent of the Human and Animal African Trypanosomiases. The mammalian stage parasites infect various tissues and organs including the bloodstream, central nervous system, skin, adipose tissue and lungs. They rely on ATP produced in glycolysis, consuming large amounts of glucose, which is readily available in the mammalian host. In addition to glucose, glycerol can also be used as a source of carbon and ATP and as a substrate for gluconeogenesis. However, the physiological relevance of glycerol-fed gluconeogenesis for the mammalian-infective life cycle forms remains elusive. To demonstrate its (in)dispensability, first we must identify the enzyme(s) of the pathway. Loss of the canonical gluconeogenic enzyme, fructose-1,6-bisphosphatase, does not abolish the process hence at least one other enzyme must participate in gluconeogenesis in trypanosomes. Using a combination of CRISPR/Cas9 gene editing and RNA interference, we generated mutants for four enzymes potentially capable of contributing to gluconeogenesis: fructose-1,6-bisphoshatase, sedoheptulose-1,7-bisphosphatase, phosphofructokinase and transaldolase, alone or in various combinations. Metabolomic analyses revealed that flux through gluconeogenesis was maintained irrespective of which of these genes were lost. Our data render unlikely a previously hypothesised role of a reverse phosphofructokinase reaction in gluconeogenesis and preclude the participation of a novel biochemical pathway involving transaldolase in the process. The sustained metabolic flux in gluconeogenesis in our mutants, including a triple-null strain, indicates the presence of a unique enzyme participating in gluconeogenesis. Additionally, the data provide new insights into gluconeogenesis and the pentose phosphate pathway, and improve the current understanding of carbon metabolism of the mammalian-infective stages of T. brucei. Author SummaryTrypanosoma brucei is a unicellular parasite causing sleeping sickness in humans and nagana disease in cattle. The parasite invades the bloodstream and cerebrospinal fluid and only recently, it has been shown to infect additional tissues such as skin, adipose tissue, or lungs. While the glucose-based metabolism of the bloodstream form is well understood, the parasites metabolism in these secondary tissues has not been sufficiently explored, despite its importance for drug development. One possibility is the use of gluconeogenesis since the mammalian-infective stages can use glycerol as a carbon and ATP source. First, enzymes involved in gluconeogenesis have to be identified, then it can be tested if the pathway is advantageous for the survival of the parasite. We generated mutants in four different enzymes potentially involved in this metabolic pathway. Surprisingly, the flux in gluconeogenesis was maintained in all cell lines tested, implying that another non-canonical enzyme participates in the production of glucose from glycerol in these parasites.

biochemistry↗

bioRxiv2022

Integrative assessment of the transcriptome and virome of the poultry red mite Dermanyssus gallinae.

Dermanyssus gallinae is a blood-feeding mite that parasitises on wild birds and farmed poultry. The D. gallinae mite has a short life cycle of fewer than two weeks from the egg to an egg-laying female. The remarkably swift processing of blood, together with the capacity to blood-feed in most developmental stages, makes this mite a highly debilitating pest. We have constructed developmental stage-specific transcriptomes, through Illumina RNA-seq, to mine the repertoire of protein-encoding mRNA transcripts, products of which participate in key processes that ensure the success of blood digestion, rapid ontogeny, and immunity. As a result of high reproductive capacity, the prevalence of D. gallinae in egg-producing poultry farms globally causes significant economic losses. Acaricides that are used to limit the reproduction of D. gallinae mites target cys-loop ion channels, which are widely shared across the phylogeny of invertebrates. To catalogue a comprehensive list of potential invertebrate-specific ion channels, we have constructed and analysed an additional RNA-seq library of D. gallinae micro-dissected midguts, a tissue with direct exposure to host blood and potential anti-parasitics. We phylogenetically defined groups of cys-loop proteins and probed their sensitivity to selected acaricides. Ultimately, we have catalogued all assembled transcripts and their expression values in a hyper-linked excel sheet with available sequences of individual contigs. The transcriptomic data were complemented by mass-spectrometry (MS)-based metabolite identification and by viability assays using selected inhibitors applied either by microinjection or through artificial membrane feeding. Additionally, we have described the RNA-virome of D. gallinae and identified a novel virus dubbed Red Mite Quaranjavirus 1.

microbiology↗

bioRxiv2021

A mixture of innate cryoprotectants is key for cryopreservation of a drosophilid fly larva.

Insects that naturally tolerate internal freezing produce complex mixtures of multiple cryoprotectants (CPs). Better knowledge on composition of these mixtures, and on mechanisms of how the individual CPs interact, could inspire development of laboratory CP formulations optimized for cryopreservation of cells and other biological material. Here we identify and quantify (using high resolution mass spectrometry) a range of putative CPs in larval tissues of a subarctic fly, Chymomyza costata that survives long-term cryopreservation in liquid nitrogen. The CPs (proline, trehalose, glutamine, asparagine, glycine betaine, glycerophosphoethanolamine, glycerophosphocholine, and sarcosine) accumulate in hemolymph in a ratio of 313:108:55:26:6:4:3:0.5 mmol.L-1. Using calorimetry, we show that the artificial mixtures, mimicking the concentrations of major CPs in hemolymph of freeze-tolerant larvae, suppress the melting point of water and significantly reduce the ice fraction. We demonstrate in a bioassay that mixtures of CPs administered through the diet act synergistically rather than additively to enable cryopreservation of otherwise freeze-sensitive larvae. Using MALDI-MSI, we show that during slow extracellular freezing trehalose becomes concentrated in partially dehydrated hemolymph where it stimulates transition to the amorphous glass phase. In contrast, proline moves to the boundary between extracellular ice and dehydrated hemolymph and tissues where it likely forms a layer of dense viscoelastic liquid. We propose that amorphous glass and viscoelastic liquids may protect macromolecules and cells from thermomechanical shocks associated with freezing and transfer into and out of liquid nitrogen. Summary statementThe composition of natural cryoprotectant mixture of the extremely freeze-tolerant insect is revealed. Components of the mixture work in synergy and behave differently during organismal freezing and cryopreservation.

physiology↗

bioRxiv2020

A Multi-center Cross-platform Single-cell RNA Sequencing Reference Dataset

Single-cell RNA sequencing (scRNA-seq) is developing rapidly, and investigators seeking to use this technology are left with a variety of options for both experimental platform and bioinformatics methods. There is an urgent need for scRNA-seq reference datasets for benchmarking of different scRNA-seq platforms and bioinformatics methods. To be broadly applicable, these should be generated from renewable, well characterized reference samples and processed in multiple centers across different platforms. Here we present a benchmarking scRNA-seq dataset that includes 20 scRNA-seq datasets acquired either as a mixtures or as individual samples from two biologically distinct cell lines for which a large amount of multi-platform whole genome sequencing data are also available. These scRNA-seq datasets were generated from multiple popular platforms across four sequencing centers. Our benchmark datasets provide a resource that we believe will have great value for the single-cell community by serving as a reference dataset for evaluating various bioinformatics methods for scRNA-seq analyses, including but not limited to data preprocessing, imputation, normalization, clustering, batch correction, and differential analysis.

bioinformatics↗

bioRxiv2020

A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples

Single-cell RNA sequencing (scRNA-seq) has become a very powerful technology for biomedical research and is becoming much more affordable as methods continue to evolve, but it is unknown how reproducible different platforms are using different bioinformatics pipelines, particularly the recently developed scRNA-seq batch correction algorithms. We carried out a comprehensive multi-center cross-platform comparison on different scRNA-seq platforms using standard reference samples. We compared six pre-processing pipelines, seven bioinformatics normalization procedures, and seven batch effect correction methods including CCA, MNN, Scanorama, BBKNN, Harmony, limma and ComBat to evaluate the performance and reproducibility of 20 scRNA-seq data sets derived from four different platforms and centers. We benchmarked scRNA-seq performance across different platforms and testing sites using global gene expression profiles as well as some cell-type specific marker genes. We showed that there were large batch effects; and the reproducibility of scRNA-seq across platforms was dictated both by the expression level of genes selected and the batch correction methods used. We found that CCA, MNN, and BBKNN all corrected the batch variations fairly well for the scRNA-seq data derived from biologically similar samples across platforms/sites. However, for the scRNA-seq data derived from or consisting of biologically distinct samples, limma and ComBat failed to correct batch effects, whereas CCA over-corrected the batch effect and misclassified the cell types and samples. In contrast, MNN, Harmony and BBKNN separated biologically different samples/cell types into correspondingly distinct dimensional subspaces; however, consistent with this algorithms logic, MNN required that the samples evaluated each contain a shared portion of highly similar cells. In summary, we found a great cross-platform consistency in separating two distinct samples when an appropriate batch correction method was used. We hope this large cross-platform/site scRNA-seq data set will provide a valuable resource, and that our findings will offer useful advice for the single-cell sequencing community.

genomics↗