Biology subjects

Schmitt, A.

Publications and source records attributed to Schmitt, A..

At least 19 recordsLinked to original sources

bioRxiv2026

REDD1 Regulates MERCS, Protein Synthesis and NMJ Stability in Fast Myofibers During Dexamethasone-Induced Muscle Wasting

Background: Glucocorticoids cause skeletal muscle atrophy preferentially affecting fast glycolytic fibers, but the mechanisms involved in this fiber selectivity is unclear. REDD1 is a glucocorticoid-induced stress protein that limits muscle protein synthesis inducing atrophy. However, it remains unknown whether REDD1 exerts myofiber type-specific effects and through which precise mechanisms it regulates protein synthesis. We investigated the role of myofiber REDD1 expression in dexamethasone (DEX)-induced muscle atrophy, with a particular focus on its involvement in mitochondria-ER contact sites (MERCS), protein synthesis, and neuromuscular junction (NMJ) integrity. Methods: We generated tamoxifen-inducible, muscle-specific REDD1 knockout mice (REDD1fl/flHSA-CreERT2) and compared them with floxed littermates (WT) in a 2x2 design (WT/KO x PBS/DEX, 7 days). We combined single-nucleus RNA sequencing, RNAscope, immunofluorescence, transmission electron microscopy, proximity ligation assay, SUnSET puromycin labelling, western blot and RT-qPCR, and AdenoFATE1-mediated MERCS disruption in C2C12 myotubes. Results: Glucocorticoid receptor and REDD1 transcripts were co-enriched in fast glycolytic fibers mostly atrophied by DEX (~20%). REDD1 deletion in myofiber drove to lower basal muscle mass and fast fiber volume but protected them from DEX-induced atrophy. DEX inhibited protein synthesis (~70%) in WT mice with no matching change in Akt/mTOR-pathway activity. In REDD1 KO mice, protein synthesis was already low and was not affected by DEX. DEX-induced REDD1 expression remodelled mitochondrial network and MERCS in a subcellular compartment-specific manner. The intermyofibrillar MERCS minimum distance shortened in both genotypes reaching pathological distances only in WT mice (WT ~28 --> ~5 nm; KO ~25 --> ~15 nm). Perinuclear MERCS and mitochondria-nuclei distances increased in WT mice only (~18 --> ~45 nm and ~130 --> ~460 nm). In WT mice only, DEX-induced alteration of the perinuclear mitochondrial network was associated with a loss of myonuclei accumulating mt-RNA and exhibiting an anabolic transcriptomic signature notably enriched in sarcomeric transcripts. These findings suggest that REDD1-dependent MERCS remodelling may regulate muscle anabolism beyond the control of mRNA translation, by shaping the myonuclear transcriptome. Finally, REDD1 localised to the NMJ and reduced endplate area during DEX treatment. Interestingly, MERCS were denser in NMJ than in myofiber body and we showed in vitro that FATE1-mediated MERCS disruption was sufficient to reduce protein synthesis and agrin-induced acetylcholine-receptor clustering demonstrating that REDD1 and MERCS are important for NMJ stabilization. Conclusions: Muscle REDD1 links the glucocorticoid response to compartment-specific mitochondrial network remodelling, protein synthesis as well as NMJ stability in fast glycolytic fibers. Our results also show that REDD1 is important for maintaining basal mitochondrial network and protein synthesis homeostasis.

cell biology↗

bioRxiv2026

Morphologic intratumoral heterogeneity from routine whole-slide histopathology is prognostic for survival in primary central nervous system lymphoma: development in the LOC Network and international external validation

Background: Clinical scores incompletely capture outcomes in primary central nervous system lymphoma (PCNSL). We quantified morphologic heterogeneity in pretreatment hematoxylin and eosin (H\&E) whole slides. Patients and methods: Three independent cohorts of immunocompetent, HIV- and EBV-negative patients treated recently were analyzed: LOC 2023 (122 slides), phase III BLOCAGE-01 (245 slides; NCT02313389), and external Barcelona (BCN; 41 slides). UNI embeddings, prototype learning, spatial metrics, and elastic-net Cox regression defined ITH-C. Results: Models achieved bootstrap-corrected concordance of 0.797--0.834. Age-, sex-, and KPS-adjusted ITH-C HRs were 1.29 (95\% CI 1.01--1.64), 1.27 (1.07--1.51), and 2.13 (1.35--3.37), respectively. Adding ITH-C increased MSKCC C-index from 0.671 to 0.717, 0.560 to 0.593, and 0.588 to 0.706. Spatial transcriptomics linked ITH-C to immune programs. Conclusions: Routine H\&E encodes prognostic spatial heterogeneity in PCNSL. ITH-C complements clinical scores, supporting prospective risk stratification.

bioinformatics↗

bioRxiv2026

Memory T Cells in MHC-Deficient Humanized Mice

Major histocompatibility complexes (MHC) govern antigen presentation and T cell receptor (TCR) selection. Accurate in vivo modeling of human immunity therefore requires physiological human MHC TCR interactions. Humanized NOD scid IL2null (NSG) mice engrafted with human CD34+ hematopoietic stem cells are widely used to provide preclinical platforms for the development of advanced therapies; however, interactions between murine MHC and human TCR can promote xenoreactivity and alter T cell development. Here, we investigated how elimination of murine MHC together with different conditioning regimens shapes human T cell maturation in vivo. CD34+ cells from ten cord blood donors were transplanted into conventional NSG mice or murine MHC deficient NSG derivatives (DKO) following either sublethal irradiation or myeloablative busulfan conditioning. Integrated analyses combining flow cytometry, plasma cytokine profiling, and bulk and single cell TCR sequencing revealed marked differences in T cell differentiation across models. Busulfan conditioned DKO mice developed highly proliferative, activated, and cytotoxic T cells together with clonally expanded TCR repertoires. In contrast, irradiated NSG mice preferentially accumulated naive, NKT, and regulatory T cell populations. Busulfan-conditioned DKO mice showed no evidence of xenogeneic graft versus host disease and represent a refined enabling platform for human T cell development and provide a foundation for future preclinical evaluation of advanced gene and cell therapies.

immunology↗

bioRxiv2026

Alternative exon splicing reveals hidden mitochondrial targeting of PLIN3

Perilipin 3 (PLIN3) is a lipid droplet-associated protein implicated in cellular lipid metabolism. We characterize a previously unrecognized alternative splicing event in human PLIN3. The generated transcript PLIN3B is detectable at the RNA level across human tissues and is modulated by antisense oligonucleotide-mediated splicing. Despite clear evidence for PLIN3B transcript expression, endogenous PLIN3B protein could not be detected using multiple complementary state-of-the-art detection strategies. When expressed exogenously, PLIN3B coding sequence encodes an unstable protein that localizes predominantly within mitochondria, in contrast to canonical PLIN3. Using super-resolution microscopy, correlative light-electron microscopy, and interaction proteomics, we show that PLIN3B accumulates intramitochondrially and engages protein quality control machinery. Mitochondrial targeting depends on residues shared by both isoforms, not altered by alternative splicing, indicating that mitochondrial targeting is normally repressed. Together, these results show that alternative exon splicing in PLIN3 reveals latent mitochondrial targeting without producing detectable endogenous protein, underscoring the need to distinguish transcript diversity from stable protein expression.

cell biology↗

bioRxiv2025

The LINC complex and microtubule motors regulate the number and position of nuclei in the subperineurial glial cells of the Drosophila blood-brain barrier

Multinucleated cells, or syncytia, provide a unique system in which to understand the mechanisms of cellular organization. The two most dramatic features of syncytial cells are the number of nuclei and the positioning of nuclei within a shared cytoplasm. While the mechanisms that regulate these features have been studied in some syncytial cells, most syncytial cells are uncharacterized. Furthermore, whether the formation of the syncytia and the organization of the syncytia are linked is not known. We have characterized the subperineurial glial cells (SPG) which form the most restrictive layer of the Drosophila blood-brain barrier. We have found that disruption of the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, Kinesin, or cytoplasmic Dynein specifically in SPG cells affected both SPG cell development and general brain development. Specifically, the brains were smaller in each case and the SPG cells were smaller when the LINC complex or cytoplasmic Dynein were disrupted. The number of nuclei per cell was increased when Kinesin was disrupted, decreased when cytoplasmic Dynein was disrupted, and abnormal numbers of nuclei were found when the LINC complex was disrupted. Finally, the positions of nuclei relative to their nearest neighbor was decreased when the expression of each gene was disrupted and nuclei were closer to the cell edge when either Kinesin or cytoplasmic Dynein were disrupted. Finally, the evenness of nuclear spacing was reduced when LINC complex or Kinesin expression was disrupted. Together, these data illustrate that formation of SPG cells and the organization of SPG cells are dependent on microtubule motors and the LINC complex.

cell biology↗

bioRxiv2025

Elucidating the interaction network of one of the largest icosahedral capsids in the virosphere

Giant viruses challenge traditional boundaries of virology with their large particle sizes, complex genomes, and unique replication strategies. Yet, despite its 750 nm diameter and incorporation of dozens of proteins, mimivirus virion retains an icosahedral symmetry, a trait often associated with smaller viruses. The functional roles and interactions of most proteins composing such complex icosahedral particles remain elusive. Here, we dissect the spatial and functional organization of mimivirus morphogenesis by integrating bioinformatics, genetics and interactomics. We performed protein clustering using a structure-informed approach integrating AlphaFold models with sequence information to classify and functionally annotate the ORFan-rich mimivirus proteome. To map the protein-protein interaction network during morphogenesis, we employed endogenous tagging and co-immunoprecipitation coupled to mass spectrometry. This strategy revealed distinct interaction modules associated with the virion membrane, nucleoid and viral factory compartments. Comparative analyses with other icosahedral and non-icosahedral giant viruses uncovered conserved assembly nodes and virion shape-specific adaptations. Our findings shed light on the global organization of mimivirus virion biogenesis and highlight the evolutionary plasticity of viral morphogenetic networks within the Nucleocytoviricota.

microbiology↗

bioRxiv2025

Two Spag6 genes control sperm formation and male fertility in mice

Sperm-associated antigen 6 (SPAG6) is the mammalian orthologue of Chlamydomonas PF16, a central axonemal protein essential for flagellar motility. In mice, two homologous genes have been identified: the ancestral Spag6 on chromosome 2 and the evolutionary derived Spag6l on chromosome 16. Although Spag6 knockout mice (Spag6-/-) are phenotypically normal, the surviving Spag6l-/- males are infertile. To further investigate the roles of SPAG6 and SPAG6L, we generated compound mutants by crossing the two knockout lines. Compound heterozygous Spag6+/-; Spag6l+/- mice are fertile, while all Spag6-/-; Spag6l+/- males are infertile despite grossly normal appearance. Histological and ultrastructural analyses revealed defective spermiogenesis, including abnormal chromatin condensation, malformed acrosome and manchette, and disorganized mitochondrial and fibrous sheath. Both SPAG6 and SPAG6L bind to SPINK2, a key regulator of acrosome function, but SPAG6 has an approximately 10-fold higher binding affinity than SPAG6L. Moreover, SPAG6 modulates testicular AKAP4 and SPAG16L levels, which are critical components of the fibrous sheath and central apparatus respectively. Notably, SPAG6 suppresses tubulin acetylation, whereas SPAG6L enhances this post-translational modification, suggesting antagonistic roles in microtubule assembly. Overall, our findings demonstrate that SPAG6 and SPAG6L coordinately regulate sperm formation and male fertility during evolution.

developmental biology↗

bioRxiv2025

Cranial suture integrity is maintained by Fgfr3 in zebrafish

Cranial suture formation is a dynamic process requiring precise cellular and molecular coordination to regulate bone growth and suture homeostasis. Despite the recognized role of Fibroblast Growth Factor Receptor 3 (FGFR3) in this process and its association with Muenke syndrome, one of the most common syndromic craniosynostoses, its precise function remains undefined. Through analyses of cranial suture formation and maintenance in a fgfr3 LoF zebrafish model displaying abnormal suture morphology, we demonstrate for the first time that Fgfr3 plays a pleiotropic role during these events. Transmission electron microscopy and second harmonic generation imaging revealed that Fgfr3 is involved in the proper organization of the collagen network within the suture. By employing specific transgenic reporter lines and studying gene expression of suture mesenchymal stem cell markers via RNAscope in situ hybridization, we show that Fgfr3 is crucial for regulating osteogenesis within the suture. Specifically, Fgfr3 limits the number of osteoprogenitors at the osteogenic front and promotes osteoblast maturation at the suture edge. Finally, our results reveal that Fgfr3-mediated regulation of osteogenesis involves cross-talk between FGF, canonical Wnt, and potentially BMP signaling pathways. In conclusion, these data position Fgfr3 as a central regulator of cranial suture formation and open new perspectives for understanding suture homeostasis and FGFR3-related craniosynostoses.

developmental biology↗

bioRxiv2024

E-box independent chromatin recruitment turns MYOD into a transcriptional repressor

MYOD is an E-box sequence-specific basic Helix-Loop-Helix (bHLH) transcriptional activator that, when expressed in non-muscle cells, induces nuclear reprogramming toward skeletal myogenesis by promoting chromatin accessibility at previously silent loci. Here, we report on the identification of a previously unrecognized property of MYOD as repressor of gene expression, via E-box-independent chromatin binding within accessible genomic elements, which invariably leads to reduced chromatin accessibility. MYOD-mediated repression requires the integrity of functional domains previously implicated in MYOD-mediated activation of gene expression. Repression of mitogen-and growth factor-responsive genes occurs through promoter binding and requires a highly conserved domain within the first helix. Repression of cell-of-origin/alternative lineage genes occurs via binding and decommissioning of distal regulatory elements, such as super-enhancers (SE), which requires the N-terminal activation domain as well as two chromatin-remodeling domains and leads to reduced strength of CTCF-mediated chromatin interactions. Surprisingly, MYOD-mediated chromatin compaction and repression of transcription do not associate with reduction of H3K27ac, the conventional histone mark of enhancer or promoter activation, but with reduced levels of the recently discovered histone H4 acetyl-methyl lysine modification (Kacme). These results extend MYOD biological properties beyond the current dogma that restricts MYOD function to a monotone transcriptional activator and reveal a previously unrecognized functional versatility arising from an alternative chromatin recruitment through E-box or non-E-box sequences. The E-box independent repression of gene expression by MYOD might provide a promiscuous mechanism to reduce chromatin accessibility and repress cell-of-origin/alternative lineage and growth factor/mitogen-responsive genes to safeguard the integrity of cell identity during muscle progenitor commitment toward the myogenic lineage.

molecular biology↗

bioRxiv2024

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. In future publications, these data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.

genomics↗

bioRxiv2024

Nucleocytoviricota viral factories are transient organelles made by phase separation

Phase separation is a widespread mechanism in viral processes, mediating replication, host manipulation and virion morphogenesis. The phylum Nucleocytoviricota encompasses diverse and ubiquitous viruses, including Poxviridae, the climate-modulating Emiliania huxleyi virus and other so-called Giant Viruses. Cytoplasmic members of this phylum form viral factories but their nature has remained unresolved. Here, we demonstrate that these viral factories are formed by liquid-liquid phase separation. We prove that mimivirus viral factories are formed by multilayered phase separation, orchestrated by at least two scaffold proteins. To extend these findings across the phylum Nucleocytoviricota, we developed a bioinformatic pipeline to predict scaffold proteins based on a conserved molecular grammar, despite major primary sequence variability. Scaffold candidates were validated in Marseilleviridae and Poxviridae, highlighting a role of H5 as a scaffold protein in the vaccinia virus. Finally, we provide a repertoire of client proteins of the nucleus-like viral factory of mimivirus and demonstrate important sub-compartmentalization of functions, including those related to the central dogma. Overall, we reveal a new mechanism for an organelle to deploy nuclear-like functions entirely based on phase separation and re-classified phylum Nucleocytoviricota viral factories as biomolecular condensates.

microbiology↗

bioRxiv2024

Genetic analysis of retinal cell types reveals synaptic pathology in schizophrenia

ImportanceAs an accessible part of the central nervous system, the retina provides a unique window to study pathophysiological mechanisms of brain disorders in humans. Imaging and electrophysiological studies have revealed retinal alterations across several neuropsychiatric and neurological disorders. However, it remains largely unclear whether primary disease mechanisms within the retina contribute to the observed retinal alterations and which specific retinal cell types and biological mechanisms are involved. ObjectiveTo determine whether specific retinal cell types are affected by genomic risk for neuropsychiatric and neurological disorders and to explore the mechanisms through which genomic risk converges in these cell types. Design, Setting, and ParticipantsIn this study, we combined findings from genome-wide association studies in schizophrenia, bipolar disorder, major depressive disorder, multiple sclerosis, Parkinson disease, Alzheimer disease, and stroke with retinal single-cell transcriptomic data sets from humans, macaques, and mice. To identify susceptible cell types, we applied MAGMA cell type enrichment analyses and performed subsequent pathway analyses. Furthermore, we translated the cellular top hit to the structural level by using retinal optical coherence tomography and genotyping data in the large population-based UK Biobank cohort (n = 36,349). Main Outcomes and MeasuresCell type-specific enrichment of genetic risk loading for neuropsychiatric and neurological disorder traits in the gene expression profiles of retinal cells. ResultsAmacrine cells (interneurons within the retina) were robustly enriched in schizophrenia genetic risk across mammalian species and in different developmental stages. This enrichment was primarily driven by genes involved in synapse biology. On the structural level, higher polygenic risk for schizophrenia was associated with thinning of the ganglion cell-inner plexiform layer, which contains dendrites and synaptic connections of amacrine cells. Moreover, retinal immune cell populations were enriched in multiple sclerosis genetic risk. No consistent cell type associations were found for bipolar disorder, major depressive disorder, Parkinson and Alzheimer disease, or stroke. Conclusions and RelevanceThis study provides novel insights into the cellular underpinnings of retinal alterations in neuropsychiatric and neurological disorders and highlights the retina as a potential proxy to study synaptic pathology in schizophrenia.

neuroscience↗

bioRxiv2024

Mitochondrial maintenance is involved in the exceptional longevity of reproductive queens of the eusocial ant Lasius niger

Most social insects are characterized by a wide disparity in life-history traits between individuals of the same species. Sterile workers live for months or years while queens may live for decades. Theories of ageing emphasise the importance of metabolism and oxidative stress in explaining longevity, with mitochondrial bioenergetics standing at the crossroads of energy and reactive oxygen species production. Studying mitochondrial functioning therefore takes on its full relevance in determining the nature of the mechanisms that explain the contrasting longevities between insect social castes. We addressed this question in an eusocial species, the black garden ant Lasius niger. We found that caste differences in mitochondrial bioenergetics and oxidative balance only partially match with predictions of the oxidative stress theory of ageing. Long-lived queens were characterized by a lower metabolic rate, lower mitochondrial density yet not necessarily lower levels of mitochondrial oxidative damages. Despite this, queens did not show reduced ATP content; rather, they even possessed a higher energy load in their mitochondria. Converging clues suggested better mitochondrial maintenance in queen ants, with enhanced dynamics of mitochondrial fission and fusion and a more marked expression of mitochondrial enzymes of the Krebs cycle. Overall, our data paves the way for studying deeper into how the rate of ATP production per mitochondria is related to the investment in mitochondrial and somatic cellular maintenance, and whether it has specifically been selected as a key mechanism in defining the still unexplained paradoxical longevity of the queen reproductive caste.

physiology↗

bioRxiv2024

How to measure functional connectivity using resting-state fMRI? A comprehensive empirical exploration of different connectivity metrics

BackgroundFunctional connectivity in the context of functional magnetic resonance imaging is typically quantified by Pearso[n]s or partial correlation between regional time series of the blood oxygenation level dependent signal. However, a recent interdisciplinary methodological work proposes more than 230 different metrics to measure similarity between different types of time series. ObjectiveHence, we systematically evaluated how the results of typical research approaches in functional neuroimaging vary depending on the functional connectivity metric of choice. We further explored which metrics most accurately detect neural decline induced by age and malignant brain tumors, aiming to initiate a debate on how best assessing brain connectivity in functional neuroimaging research. MethodsWe addressed both research questions using four independent neuroimaging datasets, comprising multimodal data from a total of 1187 individuals. We analyzed resting-state functional sequences to calculate functional connectivity using 20 representative metrics from four distinct mathematical domains. We further used T1- and T2-weighted images to compute regional brain volumes, diffusion-weighted imaging data to build structural connectomes, and pseudo-continuous arterial spin labeling to measure regional brain perfusion. ResultsFirst, our results demonstrate that the results of typical functional neuroimaging approaches differ fundamentally depending on the functional connectivity metric of choice. Second, we show that correlational and distance metrics are most appropriate to cover neural decline induced by age. In this context, partial correlation performs worse than other correlational metrics. Third, our findings suggest that the FC metric of choice depends on the utilized scanning parameters, the regions of interest, and the individual investigated. Lastly, beyond the major objective of this study, we provide evidence in favor of brain perfusion measured via pseudo-continuous arterial spin labeling as a robust neural entity mirroring age-related neural and cognitive decline. ConclusionOur empirical evaluation supports a recent theoretical functional connectivity framework. Future functional imaging studies need to comprehensively define the study-specific theoretical property of interest, the methodological property to assess the theoretical property, and the confounding property that may bias the conclusions.

neuroscience↗

bioRxiv2024

Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment

Schizophrenia (SCZ) is a genetically heterogenous psychiatric disorder of highly polygenic nature. Correlative evidence from genetic studies indicate that the aggregated effects of distinct genetic risk factor combinations found in each patient converge onto common molecular mechanisms. To prove this on a functional level, we employed a reductionistic cellular model system for polygenic risk by differentiating induced pluripotent stem cells (iPSCs) from 104 individuals with high polygenic risk load and controls into cortical glutamatergic neurons (iNs). Multi-omics profiling identified widespread differences in alternative polyadenylation (APA) in the 3 untranslated region of many synaptic transcripts between iNs from SCZ patients and healthy donors. On the cellular level, 3APA was associated with a reduction in synaptic density of iNs. Importantly, differential APA was largely conserved between postmortem human prefrontal cortex from SCZ patients and healthy donors, and strongly enriched for transcripts related to synapse biology. 3APA was highly correlated with SCZ polygenic risk and affected genes were significantly enriched for SCZ associated common genetic variation. Integrative functional genomic analysis identified the RNA binding protein and SCZ GWAS risk gene PTBP2 as a critical trans-acting factor mediating 3APA of synaptic genes in SCZ subjects. Functional characterization of PTBP2 in iNs confirmed its key role in 3APA of synaptic transcripts and regulation of synapse density. Jointly, our findings show that the aggregated effects of polygenic risk converge on 3APA as one common molecular mechanism that underlies synaptic impairments in SCZ.

neuroscience↗

bioRxiv2023

Neurophysiological correlates of Somatosensory tinnitus modulation

Tinnitus is the subjective perception of a sound in absence of corresponding external acoustic stimuli. Research highlights the influence of the sensorimotor system on tinnitus perception. Associated neuronal processes, however, are insufficiently understood and it remains unclear how and at which hierarchical level the sensorimotor system interacts with the tinnitus-processing auditory system. We therefore asked 23 patients suffering from chronic tinnitus (11 males) to perform specific exercises, aimed at relaxing or tensing the jaw area, which temporarily modulated tinnitus perception. Associated neuronal processes were assessed using Magnetencephalography. Results show that chronic tinnitus patients experienced their tinnitus as weaker and less annoying after completion of relaxing compared to tensing exercises. Furthermore, (1) sensorimotor alpha power and alpha-band connectivity directed from the somatosensory to the auditory cortex increased, and (2) gamma power in the auditory cortex, reduced, which (3) related to reduced tinnitus annoyance perception on a trial-by-trial basis in the relaxed state. No effects were revealed for 23 control participants without tinnitus (6 males) performing the same experiment. We conclude that the increase in directed alpha-band connectivity from somatosensory to auditory cortex is most likely reflecting the transmission of inhibition from somatosensory to auditory cortex during relaxation, where concurrently tinnitus-related gamma power reduces. We suggest that revealed neuronal processes are transferable to other tinnitus modulating systems beyond the sensorimotor one that are e.g. involved in attentional or emotional tinnitus modulation and provide deeper mechanistic insights into how and through which channels phantom sound perception might be modulated on a neuronal level. Significance StatementTinnitus describes the perception of auditory phantom sounds. Research suggests that the sensorimotor system impacts on tinnitus perception, associated neuronal mechanisms, however, have remained unclear. Here, chronic tinnitus patients performed exercises with the jaw temporarily reducing (versus increasing) tinnitus perception. Tinnitus reduction was accompanied by an increase of alpha-band connectivity directed from the somatosensory to the auditory cortex and gamma power reduction in the auditory cortex. We suggest that the increase in alpha-band connectivity, when tinnitus is reduced, reflects the transmission of inhibition from somatosensory to auditory cortex, where, in parallel, probably tinnitus related, gamma power reduces. The findings have important implications both for the understanding of phantom sound perception and, more generally, of top-down modulation in healthy and impaired cognition.

neuroscience↗

bioRxiv2023

Knockout of GMC-oxidoreductase genes reveals functional redundancy in mimivirus

The mimivirus 1.2Mb genome was shown to be organized into a nucleocapsid-like genomic fiber encased in the nucleoid compartment inside the icosahedral capsid (1). The genomic fiber protein shell is composed of a mixture of two GMC-oxidoreductase paralogs, one of them being the main component of the glycosylated layer of fibrils at the surface of the virion (2). In this study, we determined the effect of the deletion of each of the corresponding genes on the genomic fiber and the layer of surface fibrils. First, we deleted the GMC-oxidoreductase the most abundant in the genomic fiber, and determined its structure and composition in the mutant. As expected, it was composed of the second GMC-oxidoreductase and contained 5- and 6-start helices similar to the wild-type fiber. This result led us to propose a model explaining their coexistence. Then, we deleted the GMC-oxidoreductase the most abundant in the layer of fibrils to analyze its protein composition in the mutant. Second, we showed that the fitness of single mutants and the double mutant were not decreased compared to the wild-type viruses in laboratory conditions. Third, we determined that deleting the GMC-oxidoreductase genes did not impact the glycosylation or the glycan composition of the layer of surface fibrils, despite modifying their protein composition. Since the glycosylation machinery and glycan composition of members of different clades are different (3, 4), we expanded the analysis of the protein composition of the layer of fibrils to members of the B and C clades and showed that it was different among the three clades and even among isolates within the same clade. Taken together, the results obtained on two distinct central processes (genome packaging and virion coating) illustrate an unexpected functional redundancy in members of the family Mimiviridae, suggesting this may be the major evolutionary force behind their giant genomes. One-Sentence SummaryFunctional redundancy preserves mimivirus genomic fiber and layer of fibrils formation.

microbiology↗

bioRxiv2023

Evolutionary history of the transposon-invaded Pithoviridae genomes

Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-y-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here we report the isolation and genome sequencing of two Pithoviridae from soil samples, in addition to three other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomics study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a non-uniform genome organization in two main regions: one concentrating core genes, and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events and genomic rearrangements, that contribute to their evolution.

genomics↗