Biology subjects

Meyer, E.

Publications and source records attributed to Meyer, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Bio-inspired chromatophore network model generates dynamic skin patterns akin to those observed in cephalopods

Cephalopod skin exhibits a wide range of dynamic visual displays, including traveling waves, light/dark flashes, and flickering, all generated by muscle-regulated expansion and retraction of pigment-filled elastic sacs known as chromatophores. While central neural control is essential for high-level body-wide pattern coordination, experimental evidence from excised and denervated skin reveals that intricate spatiotemporal patterns can also emerge spontaneously in the skin. This raises questions about the respective roles of central versus peripheral control. To determine the simplest control necessary to generate such patterns, we developed ChromatoNet, a biophysical model of chromatophore arrays that includes mechanical interactions on 1- and 2-dimensional lattices with the excitability properties of radial muscles. With minimal external input, our modified Morris--Lecar model reproduces a rich repertoire of skin dynamics, including spontaneous flickering as well as traveling and spiral waves. Both spontaneous and stimulus-evoked waves emerge at an intrinsic resonant frequency, determined by model parameters. Propagation speeds remain stable across conditions and are consistent with the range observed in denervated skin preparations. The model generates diverse output states in response to local couplings and the time-dependence and shape of the input stimulation, with little top-down direction. The results provide a proof-of-principle that chromatophore/muscle dynamics with minimal central neural driving can produce rich dynamic patterns.

neuroscience↗

bioRxiv2026

Minocycline engages microglia in the midbrain periaqueductal grey to attenuate hypoxia-triggered panic-like behaviour in rats

Panic disorder (PD) is a chronic and highly disabling psychiatric disorder characterised by recurrent and unexpected panic attacks, with underlying neurobiological mechanisms poorly understood. Emerging evidence suggests that inflammatory processes may contribute to the triggering of panic attacks, with a subset of PD patients exhibiting alterations in circulating cytokine levels, while animal studies indicate that an immunoresponsive microglial phenotype may contribute to the disorders pathophysiology. Minocycline, a tetracycline-class antibiotic that crosses the blood-brain barrier, exerts anti-inflammatory effects and has demonstrated therapeutic potential in attenuating panic attacks, supporting its potential as an alternative strategy for reducing PD-related symptoms by modulating microglial activity. In this study, we investigated whether exposure of male Sprague-Dawley rats to a panicogenic stimulus, hypoxia (7% O2), is followed by microglial morphological remodelling in the midbrain periaqueductal grey (PAG), a well-known panic-associated structure, at baseline and after minocycline treatment. The effects of hypoxia on the expression of panic-like jumping behaviour were measured during the respiratory challenge, whereas microglial morphology was assessed at 1, 6, or 24h following the aversive stimulus. In a second experiment, the effects of minocycline (30 mg/kg, i.p., administered once daily for 5 days) on the immediate behavioural responses to hypoxia were compared with those produced by an acute administration of alprazolam (2 mg/kg, i.p.), a benzodiazepine widely used in the clinical management of PD. Minocycline effects on microglial morphology in the PAG were also assessed. Our findings show that hypoxia elicited robust jumping behaviour, without affecting overall locomotion. This panicogenic effect was accompanied by marked and time-dependent microglial morphological changes in the dorsomedial (dmPAG) and ventrolateral (vlPAG) columns of the PAG, consistent with a shift towards an immunoresponsive phenotype. Notably, minocycline, similarly to alprazolam, reduced the number of jumps, indicating a panicolytic effect, while also preventing hypoxia-induced microglial remodelling in the dmPAG. Altogether, these findings suggest a role for microglia in regulating hypoxia-induced panic- like behaviour, indicating that microglial inhibition, as achieved here with minocycline, represents a promising therapeutic strategy for preventing panic attacks.

neuroscience↗

bioRxiv2026

Targeted depletion of CD38+ autoreactive T cells prevents type 1 diabetes

Type 1 diabetes (T1D) is caused by T cell-mediated autoimmune destruction of insulin-producing islet {beta}-cells. Treatment with T-cell depleting therapies delays the progression of stage 2 and 3 T1D, but these agents exert broad immunosuppressive effects on T cell populations, including T regulatory cells (Tregs), which are key in promoting immune tolerance. We evaluated non-obese diabetic (NOD) mice and recently diagnosed T1D patients and identified CD38 as a marker for pathogenic T cell populations. Using adoptive T-cell transfer in Recombination Activating Gene 1 knockout NOD mice and in a humanized mouse model of autoimmune diabetes, we demonstrated that CD38-expressing autoreactive T cells drive diabetes pathogenesis. Furthermore, we found that selective depletion of CD38+ cells, using an anti-CD38 monoclonal antibody (mAb), prevents insulitis and diabetes onset without depleting CD4+CD25+ Tregs. Administration of anti-CD38 mAb did not adversely affect islet function and may selectively eliminate immunogenic senescent islet {beta}-cells. These results support the strategy of selectively depleting diabetogenic T cells using an anti-CD38 mAb to treat T1D and restore immune tolerance. Therefore, transient depletion of autoreactive T cells using anti-CD38 mAb may provide a novel strategy to prevent or abrogate {beta}-cell autoimmunity in T1D. One sentence summaryPathogenic autoreactive are characterized by CD38 overexpression, and their selective depletion with anti-CD38 monoclonal antibody prevents autoimmune diabetes.

immunology↗

bioRxiv2026

Integrative multi-omic analysis identifies tumor-intrinsic p38 as a driver of immune exclusion in human epithelial cancers

Patients with tumors not responding to immune-checkpoint inhibition (ICI) often harbor a non-T cell-inflamed tumor microenvironment, characterized by the absence of IFN-{gamma}-associated CD8+ T cells and dendritic cell activation. While the role of p38 mitogen-activated protein kinases (MAPKs) in regulating dendritic and myeloid cells is established, the tumor-intrinsic immunomodulatory function of p38 remains underexplored. Here, we identify tumor cell-intrinsic p38 signaling as a target candidate associated with immune exclusion and reduced immunotherapy response. In human papillomavirus-negative head and neck squamous carcinoma (HNSCC), molecular analysis of 395 tumor tissues revealed a p38-centered network enriched in non-T cell-inflamed tumors. Multi-cancer single-cell RNA sequencing analysis of over 200,000 cells further identifies p38 activation as a potential immune-exclusion program across multiple epithelial tumor types, including HNSCC and lung squamous cell carcinoma (LUSC), supported by tissue validation in [~]250 human biospecimens using multispectral imaging and digital spatial profiling. Functional studies demonstrate that p38 knockdown or pharmacologic inhibition in HNSCC and LUSC cell lines increases T cell migration, with CXCL16 identified as a chemokine mediator in vitro; neutralization of CXCL16 attenuated this effect. Together, these findings identify tumor-intrinsic p38 activation as a driver of immune exclusion in epithelial cancers and support its potential as a therapeutic target to overcome immunotherapy resistance.

Cancer Biology↗

bioRxiv2026

Spore-Based Biocomposite Thermoplastic Polyesters with Enhanced Toughness and Programmable Disintegration

Thermoplastic polyesters are widely used in commodity and high-performance applications due to their tunable and exceptional properties, versatile performance, and increasing relevance in sustainable materials. Integrating biological functionality into these polymers offers a promising route to enhance performance and end-of-life behavior beyond what conventional additives can achieve. Here, we report the generalization of an embedded spore-based engineered living material concept to three representative thermoplastic polyesters; polycaprolactone (PCL), polylactic acid (PLA), and poly(butylene adipate-co-terephthalate) (PBAT). Heat-shock-tolerized Bacillus subtilis spores were compounded with each polyester as a living biofiller via hot melt extrusion. The resulting biocomposite polyesters retained high spore viability (>90%) after extrusion and exhibited improved mechanical performance (up to 41% toughness improvement compared to neat polymers). End-of-life behavior was evaluated in a microbially-limited composting environment, where spore-containing PCL exhibited nearly complete disintegration within five months, corresponding to a [~]7-fold increase in degradation kinetics relative to neat PCL. Finally, 3D printing of biocomposite PCL was demonstrated through fused deposition modeling and direct ink writing methodologies. Together, this work demonstrated the successful extension of spore-based engineered living materials from thermoplastic polyurethane to multiple thermoplastic polyesters. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/707801v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@4eaafaorg.highwire.dtl.DTLVardef@bb17c2org.highwire.dtl.DTLVardef@114e4ceorg.highwire.dtl.DTLVardef@b9bd0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Breaking the species barrier: recurrent genomic introgressions from very distant lineages in a ciliate

The process of speciation, through which two reproductively isolated species emerge from an ancestral population, is often gradual, including a period during which gene flow still occurs, and hence speciation remains reversible. However, if isolation persists, the progressive accumulation of genetic incompatibilities ultimately locks the speciation process, reaching the point where hybrid offspring are inviable or sterile. In plants and animals, the establishment of species barriers is quite rapid: beyond a net genetic divergence of 0.02 substitutions per synonymous site, interspecific introgressions become extremely rare. Here we report that in ciliates, species barriers can be broken despite huge genetic divergence. We show that the genome of Paramecium sonneborni contains hundreds of DNA segments that were acquired by recurrent horizontal transfers from multiple very distant lineages (synonymous divergence [~]1 substitution/site). These segments approach the size of full-length chromosomes, which indicates that they were introgressed by inter-specific mating. These data show that in the ancestry of P. sonneborni, hybridization events with highly divergent species occurred repeatedly and led to viable and fertile offspring. We propose that this unexpected promiscuous sexual behavior is made possible by the fact that paramecia separate somatic and germline functions in two types of nuclei: the elimination of non-self DNA fragments during the development of the somatic genome allows individuals of a species to remain phenotypically the same, despite recurrent genetic flow from distant species into their germline. Significance StatementAn important issue in evolutionary biology is to understand the process of speciation, i.e. how two reproductively isolated species emerge from an ancestral population. Various factors can initiate the speciation process, but whatever the initial factor, once two populations become reproductively isolated, they start accumulating genetic incompatibilities. In plants and animals these incompatibilities accumulate rapidly, preventing the formation of viable and fertile hybrids, except between very closely related species. We show here that this rule does not apply to all eukaryotes. We discovered that the unicellular eukaryote Paramecium sonneborni recurrently acquired large DNA segments via hybridization with very distantly related species. This unexpected phenomenon highlights the diversity of factors that affect the delineation of species across eukaryotes.

evolutionary biology↗

bioRxiv2026

Soluble LAG-3 Identifies a Dynamic Early T Cell Activation Window in self-reactivity, Type 1 Diabetes, and Broader Immune Responses.

Aims/hypothesisType 1 diabetes is a complex autoimmune disorder in which autoreactive CD4 and CD8 T cells destroy pancreatic beta-cells, resulting in insulin deficiency and hyperglycemia. Although genetic susceptibility, particularly certain HLA alleles, contributes to disease risk, not all genetically predisposed individuals develop Type 1 diabetes. Screening first degree relatives (FDRs) for islet autoantibodies (GAD65, IAA, IA-2, ZnT8) helps detect autoimmune activity. However, these serum markers arise only after T-helper cell activation, limiting early intervention opportunities. Since protein antigen recognition by B cells requires T-helper cell assistance through linked recognition, T cell activation precedes B cell activation and autoantibody production. Activation of these T cells leads to shedding of the immune-regulatory (activation) surface protein LAG-3 (Lymphocyte Activation Gene-3 or CD223), generating its soluble form, sLAG-3, that is detectable in circulation. We hypothesized that sLAG-3 may serve as an early biomarker of autoimmune activity preceding islet autoantibody development in type 1 diabetes. MethodsPlasma sLAG-3 levels were measured longitudinally in female diabetes-prone NOD mice and analyzed in relation to islet antigen-specific CD4 T cell expansion and diabetes onset. To mechanistically link autoreactive T cell activation to sLAG-3 release. Naive autoreactive C6.6.9 TCR-transgenic (TCR-Tg) CD4 T cells were adoptively transferred into NOD.SCID mice and longitudinal assessment for plasma sLAG-3, beta-cell antigen specific CD4 T cell tetramer profiles, and circulating insulin (Ins2) mRNA to determine ongoing beta-cell stress. In parallel, sLAG-3 levels were analyzed from different human cohorts, including FDRs of individuals with type 1 diabetes, using cross-sectional and longitudinal approaches. ResultsIn murine models, elevated sLAG-3 correlated with expansion of islet-specific CD4 T cells that preceded hyperglycemia and diabetes onset. In the adoptive transfer model, early increases in sLAG-3 and circulating Ins2 mRNA marked immune activation and emerging beta-cell stress prior to overt diabetes. In our human cohorts, sLAG-3 was detectable in autoantibody-negative and single-autoantibody-positive FDRs, with higher levels observed in progressors compared to non-progressors, and associated with high-risk HLA genotypes. Conclusions/interpretationThese findings identify sLAG-3 as a candidate biomarker of early T cell activation in type 1 diabetes that may precede islet autoantibody development. Integration of sLAG-3 with antigen-specific T cell and beta-cell stress markers could improve early risk stratification and inform preventive strategies before substantial loss of beta-cell. Prospective longitudinal studies aligned to seroconversion are required to validate sLAG-3 as a surrogate marker of early disease activity. Research in contextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIBefore the clinical onset of hyperglycemia, type 1 diabetes is characterized by a prolonged preclinical phase in which autoreactive B and T cells mediate progressive beta-cell destruction. C_LIO_LICurrent risk stratification strategies rely mainly on genetic susceptibility (genomic DNA) and the detection of islet autoantibodies in plasma/serum. C_LIO_LIIslet autoantibodies arise only after CD4 T cell activation and therefore do not capture the earliest stages of immune dysregulation. C_LIO_LIConsequently, biomarkers that directly reflect early pathogenic T cell activity prior to, or independent of, seroconversion remain limited and insufficiently validated. C_LI What is the key question?Can plasma sLAG-3 levels, beta-cell antigen-specific CD4 T cell tetramer expression, and circulating Ins2 mRNA serve as very early biomarkers of autoimmune activity in type 1 diabetes and serve to better inform risk stratification, thereby informing preventive intervention strategies for the clinician? What are the new findings?O_LIsLAG-3 increases transiently during early antigen-specific CD4 T cell activation stage, precedes hyperglycemia in mouse models, and is elevated in autoantibody-negative and single-autoantibody-positive first-degree relatives who later progress to type 1 diabetes. C_LIO_LIsLAG-3 was associated with beta-cell antigen-specific CD4 T cell expansion, assessment of stress induced beta cell Ins2 mRNA release and high-risk HLA genotypes, indicating early autoimmune activation rather than established disease. C_LI How might this impact clinical practice in the foreseeable future?These findings support sLAG-3 as a candidate early biomarker of T cell activation, before or at the earliest stages of islet autoantibody development in some at-risk individuals. Integration of plasma sLAG-3 with beta-cell antigen specific CD4 T cell profiling and insulin mRNA measurements could complement current autoantibody-based screening, improve risk stratification, and enable earlier preventive interventions to preserve beta-cell function in patients at-risk for type 1 diabetes.

immunology↗

bioRxiv2025

The tiny germline chromosomes of Paramecium aurelia have anexceptionally high recombination rate and are capped by a new class of Helitrons

BackgroundParamecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual generations. A polyploid transcriptionally active somatic macronucleus (MAC) develops at each sexual generation from a copy of the MIC through programmed DNA elimination (PDE) of > 30% of germline DNA. PDE requires the domesticated PiggyMac (Pgm) transposase. Assembly of Paramecium germline genomes has presented an enormous challenge owing to the difficulty of MIC isolation. ResultsWe report chromosome-scale short-read MIC assemblies for 7 species from the P. aurelia species complex. We discovered a novel clade of Helitrons, with 9-10 kb transposase ORFs under purifying selection, that have remained active in all P. aurelia lineages. A long-read assembly for P. tetraurelia together with a genetic linkage map provided a nearly telomere-to-telomere assembly. Conclusions.The genome consists of tiny (300 kb - 1.2 Mb) and numerous ([~]160) germline chromosomes with the highest recombination rate ever reported for a eukaryote (420 cM/Mb). The ends of the chromosomes consist of Helitrons inserted in telomeric C4A2 repeats, forming a distinct genomic compartment that is eliminated very early during MAC development in a Pgm-independent manner.

genomics↗

bioRxiv2025

Curing autoimmune diabetes with islet and hematopoietic cell transplantation after CD117 antibody-based conditioning

Mixed hematopoietic chimerism after allogeneic hematopoietic cell transplantation (HCT) promotes tolerance of transplanted donor-matched solid organs, corrects autoimmunity, and could transform therapeutic strategies for autoimmune type 1 diabetes (T1D). However, development of non-toxic bone marrow conditioning protocols is needed to expand clinical use. We developed a chemotherapy-free, non-myeloablative (NMA) conditioning regimen that achieves mixed chimerism and allograft tolerance across MHC barriers in NOD mice. We obtained durable mixed hematopoietic chimerism in prediabetic NOD mice using anti-c-Kit monoclonal antibody, T-cell depleting antibodies, JAK1/2 inhibition, and low-dose total body irradiation prior to transplantation of MHC-mismatched B6 hematopoietic cells, preventing diabetes in 100% of chimeric NOD:B6 mice. In overtly diabetic NOD mice, NMA conditioning followed by combined B6 HCT and islet transplantation durably corrected diabetes in 100% of chimeric mice without chronic immunosuppression or graft-versus-host disease (GVHD). Chimeric mice remained immunocompetent, as assessed by blood count recovery and rejection of 3rd party allogeneic islets. Adoptive transfer studies and analysis of autoreactive T cells confirmed correction of autoimmunity. Analysis of chimeric NOD mice revealed central thymic deletion and peripheral tolerance mechanisms. Thus, with NMA conditioning and cell transplantation, we achieved durable hematopoietic chimerism without GVHD, promoted islet allograft tolerance, and reversed established T1D. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/673576v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@23fcdorg.highwire.dtl.DTLVardef@1aac97borg.highwire.dtl.DTLVardef@191e06forg.highwire.dtl.DTLVardef@25be2b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

The assembly of the membrane arm of mitochondrial complex I follows evolutionarily distinct routes

Complex I is the largest enzyme of the mitochondrial oxidative phosphorylation system. It is composed of core subunits that are conserved across bacteria and eukaryotes and accessory subunits that are lineage-specific. Consequently, the assembly of complex I likely requires lineage-specific assembly machineries. Complex I assembly has been mainly studied in mammals. It follows a modular pathway in which modules are assembled independently and then associated together to form the mature complex. Here, we identify and characterize PAF1 as an assembly factor for the membrane arm of complex I in plants. We show that this protein plays a role in stabilizing a module of the membrane arm prior to its association with the rest of the complex. PAF1 was likely present in the last eukaryotic common ancestor and has been lost in mammals in which the assembly of the membrane arm involves assembly factors not conserved in plants. Altogether, we provide molecular evidence that the assembly of the membrane arm of complex I can be performed by two different machineries.

biochemistry↗

bioRxiv2024

A reference-free algorithm discovers regulation in the plant transcriptome

Most plant genomes and their regulation remain unknown. We used SPLASH - a new, reference-genome free sequence variation detection algorithm - to analyze transcriptional and post-transcriptional regulation from RNA-seq data. We discovered differential homolog expression during maize pollen development, and imbibition-dependent cryptic splicing in Arabidopsis seeds. SPLASH enables discovery of novel regulatory mechanisms, including differential regulation of genes from hybrid parental haplotypes, without the use of alignment to a reference genome.

bioinformatics↗

bioRxiv2023

A Platform for Controlled Template-Independent Enzymatic Synthesis of RNA Oligonucleotides and Therapeutics

Therapeutic RNA oligonucleotides have shown tremendous potential to manage and treat disease, yet current manufacturing methods cannot deliver on this promise. Here, we report the development and optimization of a novel, aqueous-based, template-independent enzymatic RNA oligonucleotide synthesis platform as an alternative to traditional chemical methodologies. Our platform is made possible by reversible terminator nucleoside triphosphates and an enzyme capable of their incorporation. We show that many common therapeutic RNA modifications are compatible with our process and demonstrate the enzymatic synthesis of natural and modified oligonucleotides in both liquid and solid phases. Our platform offers many unique advantages over chemical synthesis, including the realization of a more sustainable process to produce therapeutic RNA oligonucleotides. One-Sentence SummaryAn enzyme and novel nucleotide building blocks are used to synthesize RNA oligonucleotides template independently under aqueous conditions.

synthetic biology↗

bioRxiv2023

Novel regulatory variant in ABO intronic RUNX1 binding site inducing A3 phenotype

Background and ObjectivesMixed-field agglutination in ABO phenotyping (A3, B3) has been linked to genetically different blood cell populations like in chimerism, or to rare variants in either ABO exon 7 or regulatory regions. Clarification of such cases is challenging and would greatly benefit from sequencing technologies that allow resolving full-gene haplotypes at high resolution. Materials and MethodsWe used long-read sequencing by Oxford Nanopore Technologies to sequence the entire ABO gene, amplified in two overlapping long-range PCR fragments, in a blood donor presented with A3B phenotype. Confirmation analyses were carried out by Sanger sequencing and included samples from other family members. ResultsOur data revealed a novel heterozygous g.10924C>A variant on the ABO*A-allele located in the transcription factor binding site for RUNX1 in intron 1 (+5.8 kb site). Inheritance was shown by the results of the donors mother, who shared the novel variant and the anti-A specific mixed-field agglutination. ConclusionWe discovered a regulatory variant in the 8-bp RUNX1 motif of ABO, which extends current knowledge of three other variants affecting the same motif and also leading to A3 or B3 phenotypes. Overall, long-range PCR combined with nanopore sequencing proved powerful and showed great potential as emerging strategy for resolving cases with cryptic ABO phenotypes.

genetics↗

bioRxiv2022

Brain injuries and complex motor learning suppress Olig2 in a subpopulation of oligodendrocyte precursor cells

Oligodendrocyte precursor cells (OPCs) are uniformly distributed in the mammalian brain, however their function is rather heterogeneous in respect to their origin, location, receptor/channel expression and age. The basic helix-loop-helix transcription factor Olig2 is expressed in all OPCs as a pivotal determinant of their differentiation. Here, we identified a subset (2-26%) of OPCs lacking Olig2 in various brain regions including cortex, corpus callosum, CA1 and dentate gyrus. These Olig2 negative (Olig2neg) OPCs were enriched in the juvenile brain and decreased subsequently with age, being rarely detectable in the adult brain. However, the loss of this population was not due to apoptosis or microglia-dependent phagocytosis. Unlike Olig2pos OPCs, these subset cells could not be labelled for the mitotic marker Ki67. And, accordingly, BrdU was incorporated only by a three-day long-term labeling but not by a two-hour short pulse, suggesting these cells do not proliferate any more but were derived from proliferating OPCs. The Olig2neg OPCs exhibited a less complex morphology than Olig2pos ones. Olig2neg OPCs preferentially remain in a precursor stage rather than differentiating into highly branched oligodendrocytes. Changing the adjacent brain environment, e.g. by acute injuries or by complex motor learning tasks stimulated the transition of Olig2pos OPCs to Olig2neg cells in the adult. Taken together, our results demonstrate that OPCs transiently suppress Olig2 upon changes of the brain activity. Table of Contents Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/496631v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1f8bc79org.highwire.dtl.DTLVardef@11dd807org.highwire.dtl.DTLVardef@51d2e9org.highwire.dtl.DTLVardef@1edf9a1_HPS_FORMAT_FIGEXP M_FIG C_FIG Main points: A subset of OPCs do not express Olig2, of which population peaks in the juvenile brain while wanes with age. Plastic changes of the brain by acute injuries or complex motor learning stop the expression of Olig2 in OPCs.

neuroscience↗

bioRxiv2022

Time-lapse Imaging of Microglial Activity and Astrocytic Calcium Signaling Reveals a Neuroprotective Effect of Cannabidiol in the Subacute Phase of Stroke

Pharmacological agents that limit secondary tissue loss and/or improve functional outcomes after stroke are still limited. Cannabidiol, the major non-psychoactive component of Cannabis sativa, has been proposed as a neuroprotective agent against experimental focal cerebral ischemia. The effects of cannabidiol have generally been related to the modulation of neuroinflammation, including the control of glial activation and the toxicity exerted by pro-inflammatory mediators. However, so far, most information concerning cannabidiol neuroprotective effects was obtained from histological and biochemical post-mortem assays. To test whether the effects of cannabidiol on glial cells could be also detected in vivo, we performed time-lapse imaging of microglial activity and astrocytic calcium signaling in the subacute phase of stroke using two-photon laser-scanning microscopy. First, C57BL/6N wild-type mice underwent either sham or transient middle cerebral artery occlusion surgery. The animals received intraperitoneal injection of vehicle or cannabidiol (10 mg/kg) 30 min, 24 h, and 48 h after surgery. One day later the neurological score test was performed. Brain tissue was processed to evaluate the neuronal loss and microglial activation. Transgenic mice with microglial expression of the enhanced green fluorescent protein and astrocyte-specific expression of the calcium sensor GCaMP3 were used to access in vivo microglial activity and astrocytic calcium signaling, respectively. The animals were submitted to the same experimental design described above and to imaging sessions before, 30 min, 24 h and, 48 h after surgery. Astrocytic calcium signaling was also assessed in acutely isolated slices 5 h after transient middle cerebral artery occlusion surgery in the presence of perfusion or cannabidiol solution. Cannabidiol prevented ischemia-induced neurological impairments as well as protected against neuronal loss in ischemic mice. Cannabidiol also reduced ischemia-induced microglial activation, as demonstrated in fixed tissue as well in in vivo conditions. No difference in the amplitude and duration of astrocytic calcium signals was detected before and after the middle cerebral artery occlusion in vivo. Similarly, no significant difference was found in the astrocytic calcium signals between contra and ipsilateral side of acutely isolated brain slices. The present results suggest that the neuroprotective effects of cannabidiol after stroke may occur in the subacute phase of ischemia and reinforce the strong anti-inflammatory property of this compound.

neuroscience↗

bioRxiv2021

ReadZS detects developmentally regulated RNA processing programs in single cell RNA-seq and defines subpopulations independent of gene expression

RNA processing (RNAP), including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNAP from single-cell RNA sequencing data are limited by reliance on pre-existing annotations, peak-calling heuristics, and collapsing measurements by cell type. We introduce ReadZS, the first annotation-free statistical approach to identify regulated RNAP in single cells. ReadZS discovers cell type-specific RNAP in the human lung and conserved, developmentally regulated RNAP in mammalian spermatogenesis - including global 3 UTR shortening in human spermatogenesis. ReadZS also discovers global 3 UTR lengthening in Arabidopsis root development, highlighting the usefulness of this method in under-annotated transcriptomes.

bioinformatics↗

bioRxiv2020

Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences, called Internal Eliminated Sequences (IESs), that have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of nine Paramecium species (from [~]100 Mb in P. aurelia species to > 1.5 Gb in P. caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single-copy in present-day genomes, we identified several families of mobile IESs, including non-autonomous elements acquired via horizontal transfer, that generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.

genomics↗

bioRxiv2020

Genetic variation in heat tolerance of the coral Platygyra daedalea offers the potential for adaptation to ocean warming

Climate change induced increases in global ocean temperature represent the greatest threat to the persistence of reef ecosystems and most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is necessary if corals are to persist in a warming future. While many aspects of heat stress have been well studied, few data are available for predicting the capacity for adaptive cross-generational responses in corals. Consistent sets of heat tolerant genomic markers that reliably predict thermal tolerance have yet to be identified. To address this knowledge gap, we quantified the heritability and genetic variation associated with heat tolerance in Platygyra daedalea from the Great Barrier Reef. We tracked the survival of quantitative genetic crosses of larvae in a heat tolerance selection experiment. We also identified allelic shifts in heat-selected survivors compared with paired, non-selected controls. The narrow-sense heritability of survival under heat stress was 0.66 and a total of 1,069 single nucleotide polymorphisms (SNPs) were associated with different survival probabilities. While 148 SNPs were shared between several experimental crosses, no common SNPs were identified for all crosses suggesting that specific combinations of many markers are responsible for heat tolerance. However, we found two regions that overlap with previously identified loci associated with heat tolerance in Persian Gulf populations of P. daedalea reinforcing the importance of these markers for heat tolerance. These results illustrate the importance of high heritability and the complexity of the genomic architecture underpinning host heat tolerance. These findings suggest that this P. daedalea population has the genetic prerequisites for adaptation to increasing temperatures. This study also provides knowledge for the development of high throughput genomic tools to screen for variation within and across populations to enhance adaptation through assisted gene flow and assisted migration.

evolutionary biology↗