Biology subjects

Martin, A.

Publications and source records attributed to Martin, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies

The evolution of sexual secondary characteristics necessitates regulatory factors that confer sexual identity to differentiating tissues and cells. In Colias eurytheme butterflies, males exhibit two specialized wing scale types -- UV-iridescent (UVI) and lanceolate scales -- absent in females and likely integral to male courtship behavior. This study investigates the regulatory mechanisms and single-nucleus transcriptomics underlying these two sexually dimorphic cell types during wing development. We show that Doublesex (Dsx) expression is itself dimorphic and required to repress the UVI cell state in females, while unexpectedly, UVI activation in males is independent from Dsx. In the melanic marginal band, Dsx is required in each sex to enforce the presence of lanceolate scales in males, and their absence in females. Single-nucleus RNAseq reveals that UV-iridescent and lanceolate scale cell precursors each show distinctive gene expression profiles at 40% of pupal development, with marker genes that include regulators of transcription, cell signaling, cytoskeletal patterning, and chitin secretion. Both male-specific cell types share a low expression of the Bric-a-brac (Bab) transcription factor, a key repressor of the UVI fate. Bab ChIP-seq profiling suggests that Bab binds the cis-regulatory regions of gene markers associated to UVI fate, including potential effector genes involved in the regulation of cytoskeletal processes and chitin secretion, and loci showing signatures of recent selective sweeps in an UVI-polymorphic population. These findings open new avenues for exploring wing patterning and scale development, shedding light on the mechanisms driving the specification of sex-specific cell states and the differentiation of specialized cell ultrastructures.

developmental biology↗

bioRxiv2024

Autophagy across tissues of aging mice

Autophagy is a waste-disposal pathway that protects against age-related pathology. It is widely accepted that autophagy declines with age, yet the role that sex and diet-related obesity play during aging remain unknown. Here, we present the most comprehensive in vivo study of autophagic flux to date. We employed transgenic mice overexpressing tandem-florescent LC3B (RFP-GFP-LC3B) to measure autophagic flux in the blood (PBMCs), heart, and motor cortex neurons of aging mice that were fed regular chow or a high-fat diet for 6-, 12- or 18-months. In male mice, aging decreased autophagic flux in the heart, increased it in the blood, and had no effect in motor cortex neurons. Age-dependent changes autophagic flux were less pronounced in female mice. High-fat diet influenced autophagic flux in the blood and heart of male but not female mice. Overall, we uncovered sexual dimorphisms that underpin how autophagy changes with age across different tissues and in response to a high-fat diet.

cell biology↗

bioRxiv2024

Protection against Neisseria meningitidis nasopharyngeal colonization relies on antibody opsonization and phagocytosis by neutrophils

Neisseria meningitidis is a human-restricted pathogen that can cause a rapidly progressing invasive meningococcal disease, yet it is also a regular inhabitant of the human nasopharynx. Vaccines that target N. meningitidis aim to prevent invasive disease, but their ability to interfere with nasal colonization could effectively eradicate this bacteria in a population, and so is an important target for meningococcal vaccine design. While protection against invasive meningococcal disease is classically attributed to IgG-dependent complement activation and bacterial killing, there remains no indication of what confers protection against nasopharyngeal colonization, making it impossible to deliberately target this stage during vaccine development. Moreover, without understanding what confers protection in this tissue site, it is impossible to understand the level of susceptibility within a population. To address this, we have taken advantage of the CEACAM1-humanized mouse model to characterize immune effectors that protect against nasal carriage of N. meningitidis. Protection against nasal colonization could be induced by live mucosal infection or by parenteral immunization with heat-killed bacteria. Mice possessing genetic deficiencies in B cells were used to evaluate the role of B cells and a specific antibody response, while neutrophil and complement depletion were used to evaluate their respective contributions to immunization-induced protection against meningococcal nasal carriage. Despite the essential role for complement killing in preventing invasive meningococcal disease, complement was not required for protection against nasal colonization. Instead, N. meningitidis-specific antibodies and neutrophils were both required to protect mice against the nasal infection. Combined, these data suggest that phagocytic bacterial killing is necessary for protection against mucosal colonization by N. meningitidis, indicating that nasal immunoglobulin with the ability to promote opsonophagocytosis must be considered as a correlate of protection against meningococcal carriage. AUTHORS SUMMARYNeisseria meningitidis can cause devastating and often fatal systemic infections including sepsis and meningitis, yet it frequently lives in the throat of healthy individuals. Vaccines developed against some meningococcal strains allow the individual to resist becoming colonized by the bacteria, an effect that protects them from disease and prevents them from spreading the bacteria to others, while other vaccines effectively protect against disease but still allow the individual to carry the bacteria in their throat. The reason for this difference has remained difficult to explain. Here, we use a humanized mouse model that allows N. meningitidis infection in the nasal passages to establish that effective protection against nasal colonization requires that antibodies present within the infected mucosal tissues can coat the bacteria so that they are engulfed by neutrophils, a potent bacteria-killing white blood cell that is recruited to the site of infection. These findings suggest that antibodies with the ability to promote neutrophil recognition and killing of N. meningitidis should be the goal of future vaccines, and the presence of these can be used to consider an individuals resistance against this terrible pathogen.

microbiology↗

bioRxiv2024

Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution

Tendon ruptures in humans have regularly been studied during the chronic phase of injury. However, the early response to injury remains less investigated. Quadriceps tendons, which require prompt surgical treatment, offer a model to investigate this early response. Therefore, this study aimed to explore the early cellular changes in ruptured compared to healthy human quadriceps tendons. Quadriceps tendon samples were collected from patients undergoing tibial shaft fracture repair (healthy) or tendon repair surgery for complete rupture (collected 7-8 days post-injury). Nuclei were isolated for single-nucleus RNA sequencing, and comprehensive transcriptomic analysis was conducted to profile cellular changes. The transcriptomes of 12,808 nuclei were profiled, including 7,268 nuclei from healthy and 5,540 nuclei from ruptured quadriceps tendons, revealing 12 major cell types and several cell subtypes and states. Rupture samples showed increased expression of genes related to extracellular matrix organisation and cell cycle signalling, and a decrease in expression of genes in lipid metabolism pathways. These changes were driven predominantly by gene expression changes in the fibroblast, vascular endothelial cells (VECs), mural cell, and macrophage populations: fibroblasts shift to an activated phenotype upon rupture and there is an increase in proportion of capillary and dividing VECs, suggesting an angiogenic response. A diverse immune environment was observed, with a shift from homeostatic to activated macrophages following rupture. Cell-cell interactions increased in rupture, both in their number and diversity, and primarily involving fibroblast and endothelial cell populations. Collectively, this transcriptomic analysis suggests that fibroblasts and endothelial cells are key orchestrators of the early injury response within ruptured quadriceps tendon.

genomics↗

bioRxiv2024

Dispersion indices for universal quantification of fluorescently-labelled subcellular structure spatial distributions

Image analysis of subcellular structures and biological processes relies on specific, context-dependent pipelines, which are labor-intensive, constrained by the intricacies of the specific biological system, and inaccessible to broader applications. Here we introduce the application of dispersion indices, a statistical tool traditionally employed by economists, to analyze the spatial distribution and heterogeneity of subcellular structures. This computationally efficient high-throughput approach, termed GRID (Generalized Readout of Image Dispersion), is highly generalizable, compatible with open-source image analysis software, and adaptable to diverse biological scenarios. GRID readily quantifies diverse structures and processes to include autophagic puncta, mitochondrial clustering, and microtubule dynamics. Further, GRID is versatile, applicable to both 2D cell cultures and 3D multicellular organoids, and suitable for high-throughput screening and performance metric measurements, such as half-maximal effective concentration (EC50) values. The approach enables mechanistic analysis of critical subcellular structure processes of relevance for diseases ranging from metabolic and neuronal diseases to cancer as well as a first-pass screening method for identifying biologically active agents for drug discovery. Statement of SignificanceCurrent methods for image analysis in microscopy are tailored to specific biological contexts, which creates challenges in implementation and efficiency for researchers studying a diverse range of subcellular processes. Our application of dispersion indices, traditionally used in economics, offers a universal framework for high throughput quantification of biological structures, enabling easier and more consistent analysis across various biological contexts. By transforming pixel intensity and count into meaningful statistical measures, our method simplifies the quantification of subcellular structures such as autophagic puncta, microtubule dynamics, and mitochondrial clustering. This approach accelerates the quantitative analysis of sub-cellular processes in disease as well as imaged-based drug discovery. Classification: Bioengineering, Cell Biology, Applied Biological Sciences

cell biology↗

bioRxiv2024

Dissecting the oncogenic mechanisms of POT1 cancer mutations through deep scanning mutagenesis

Mutations in the shelterin protein POT1 are associated with diverse cancers, but their role in cancer progression remains unclear. To resolve this, we performed deep scanning mutagenesis in POT1 locally haploid human stem cells to assess the impact of POT1 variants on cellular viability and cancer-associated telomeric phenotypes. Though POT1 is essential, frame-shift mutants are rescued by chemical ATR inhibition, indicating that POT1 is not required for telomere replication or lagging strand synthesis. In contrast, a substantial fraction of clinically-validated pathogenic mutations support normal cellular proliferation, but still drive ATR-dependent telomeric DNA damage signaling and ATR-independent telomere elongation. Moreover, this class of cancer-associated POT1 variants elongates telomeres more rapidly than POT1 frame-shifts, indicating they actively drive oncogenesis and are not simple loss-of-function mutations.

cancer biology↗

bioRxiv2024

CRISPR targeting of FOXL2 c.402C>G mutation reduces malignant phenotype in granulosa tumor cells and identifies anti-tumoral compounds

FOXL2 is a transcription factor essential for sex determination and ovary development and maintenance. Mutations in this gene are implicated in syndromes involving premature ovarian failure and granulosa cell tumors (GCTs). This rare cancer accounts for less than 5% of diagnosed ovarian cancers and is causally associated with the FOXL2 c.402C>G, p.C134W mutation in 97% of the adult cases (AGCTs). In this study, we employed CRISPR technology to specifically eliminate the FOXL2 c.402C>G mutation in granulosa tumor cells. Our results show that this Cas9-mediated strategy selectively targets the mutation without affecting the wild-type allele. Granulosa cells lacking the FOXL2 c.402C>G exhibit a reduced malignant phenotype, with significant changes in cell proliferation, invasion, and cell death. Furthermore, these modified cells are more susceptible to Dasatinib and Ketoconazole. Transcriptomic and proteomic analyses reveal that CRISPR-modified granulosa tumor cells shift their expression profiles towards a wild-type like phenotype. Additionally, this altered expression signature has led to the identification of new compounds with antiproliferative and pro-apoptotic effects on granulosa tumor cells. Our findings demonstrate the potential of CRISPR technology for the specific targeting and elimination of a mutation causing granulosa cell tumors, highlighting its therapeutic promise for treating this rare ovarian cancer. Simple SummaryAdult granulosa cell tumors (AGCTs), characterized by a specific point mutation (C134W) in the gene FOXL2, are less than 5% of all the diagnosed ovarian cancers. Surgery is the cornerstone treatment for AGCT even at relapse, with systemic therapy showing poor results. The aim of our study is to explore the potential therapeutic effect of the elimination of the C134W mutation. To achieve our goal, we have eliminated the mutant allele using CRISPR technology. Our results demonstrate that CRISPR-mediated elimination of FOXL2-C134W reduces the malignant phenotype of granulosa tumor cells, which change their transcriptional, proteomic, and cellular phenotype to a wild type like, granulosa type. Moreover, the induced changes allowed us to find new compounds with antitumoral activity. This work highlights the therapeutic potential of CRISPR mediated technology for the treatment of AGCT.

cancer biology↗

bioRxiv2024

Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome

The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system and revealed that Nub1 utilizes FAT10s intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.

biochemistry↗

bioRxiv2024

Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage

The success of butterflies and moths is tightly linked to the origin of scales within the group. A long-standing hypothesis postulates that scales are homologous to the well-described mechanosensory bristles found in the fruit fly Drosophila melanogaster, where both derive from an epithelial precursor specified by lateral inhibition that then undergoes multiple rounds of division. Previous histological examination and candidate gene approaches identified parallels in genes involved in scale and bristle development. Here, we provide definitive developmental and transcriptomic evidence that the differentiation of lepidopteran scales derives from the canonical cell lineage, known as the Sensory Organ Precursor (SOP). Live imaging in moth and butterfly pupae shows that SOP cells undergo two rounds of asymmetric divisions that first abrogate the neurogenic lineage, and then lead to a differentiated scale precursor and its associated socket cell. Single-nucleus RNA sequencing across a time-series of early pupal development revealed differential gene expression patterns that mirror canonical lineage development, including Notch-Delta signalling components, cell adhesion molecules, cell cycling factors, and terminal cell differentiation markers, suggesting a shared origin of the SOP developmental program. Additionally, we recovered a novel gene, the POU-domain transcription factor pdm3, involved in the proper differentiation of butterfly wing scales. Altogether, these data open up avenues for understanding scale type specification and development, and illustrate how single-cell transcriptomics provide a powerful platform for understanding the evolution of cell types.

developmental biology↗

bioRxiv2024

Combinatorial Wnt Signaling induces Margin Color Elements in Swallowtail Butterfly Ground Plan.

The intricate wing patterns of butterflies are thought to derive from a morphological ground plan that anchors homology relationships between individual color pattern elements and serves as an archetype for comparative analysis. These patterns undergo modifications that drive the diverse morphologies observed in nature. While brush-footed butterflies (Nymphalidae) have been well studied, assigning homologies with other lepidopteran families remains challenging due to substantial divergence. Here, we focus on swallowtails (Papilionidae), an early-diverging butterfly lineage known for its outstanding diversity in wing shapes and patterns but lacking a developmental framework. Through qualitative and phylogenetic analyses, CRISPR perturbation assays, and in situ expression experiments, we investigate homologies between papilionid butterflies, offering phylogenetic and molecular characterization of the Papilionidae wing ground plan. Our results highlight the roles of WntA and Wnt6 in patterning papilionid signature wing elements, such as the glauca and the Submarginal spots. Notably, the nymphalids distinct Central Symmetry System is either reduced or absent in the family, with marginal systems expanding proximally. Our data illuminate a highly adaptable patterning system driven by Wnt signaling pathways in developing butterfly wings.

developmental biology↗

bioRxiv2024

Blended Genome Exome (BGE) as a Cost Efficient Alternative to Deep Whole Genomes or Arrays

Genomic scientists have long been promised cheaper DNA sequencing, but deep whole genomes are still costly, especially when considered for large cohorts in population-level studies. More affordable options include microarrays + imputation, whole exome sequencing (WES), or low-pass whole genome sequencing (WGS) + imputation. WES + array + imputation has recently been shown to yield 99% of association signals detected by WGS. However, a method free from ascertainment biases of arrays or the need for merging different data types that still benefits from deeper exome coverage to enhance novel coding variant detection does not exist. We developed a new, combined, "Blended Genome Exome" (BGE) in which a whole genome library is generated, an aliquot of that genome is amplified by PCR, the exome regions are selected and enriched, and the genome and exome libraries are combined back into a single tube for sequencing (33% exome, 67% genome). This creates a single CRAM with a low-coverage whole genome (2-3x) combined with a higher coverage exome (30-40x). This BGE can be used for imputing common variants throughout the genome as well as for calling rare coding variants. We tested this new method and observed >99% r2 concordance between imputed BGE data and existing 30x WGS data for exome and genome variants. BGE can serve as a useful and cost-efficient alternative sequencing product for genomic researchers, requiring ten-fold less sequencing compared to 30x WGS without the need for complicated harmonization of array and sequencing data.

genomics↗

bioRxiv2024

Development of BODIPY-based fluorescent probes for highly selective amino acid identification

Amino acid sensing is a powerful tool for intra- and extra-cellular assays. We report herein the generation and optimization of bioconjugatable fluorescent reporter for pan-amino acid sensing, the OMNI probe, that through inductive electronics produces a unique photophysical response upon coupling to the -amino group of an amino acid depending on the identity of the adjacent side chain. Using an auto-photocatalyzed Meerwein arylation reaction, we created a library of bis-arylated 8-methylthio-BODIPY dye derivatives exhibiting improved spectral variation, brightness, dynamic range, robustness, water solubility, and reactivity. Aryl groups with optimal photophysical behaviors were combined to create asymmetric versions conferring high spectral range, brightness, and water solubility. Combining aryl group modifications yielded a set of engineered asymmetric probes that achieved complete spectral resolution in a multi-variable analysis (fluorescent emission, lifetime, brightness) for all twenty native amino acid-dye conjugates while increasing reactivity toward amino acids in aqueous buffer. With our robust OMNI probe design, pan-amino acid resolution and identification through high sensitivity fluorescence down to single molecules is now routinely possible for diverse potential applications including protein sequencing.

biochemistry↗

bioRxiv2024

Effect of 10 days of unilateral lower limb suspension on knee extensors neuromuscular function and spinal excitability

The reduction in mechanical loading applied on the lower limb has numerous detrimental consequences on neuromuscular function. The current study aimed to investigate the changes in knee extensors strength and spinal excitability induced by unilateral lower limb suspension (ULLS), providing new insights into the neuromuscular adaptations to muscle hypoactivity. Ten young healthy males (19-28 years old) underwent 10 days of ULLS to simulate muscle disuse. Modulation by unloading of knee extensors function (muscle morphology and strength, activation capacity and contractile properties) and spinal reflexes were explored before and after the ULLS. The knee extensors anatomical cross-sectional area (-4%, p = 0.007), maximal strength (-27%, p < 0.001) and central activation ratio (-3%, p = 0.006) were reduced after 10 days of ULLS. Vastus medialis H-reflex amplitude was enhanced both at rest (+33%, p = 0.038) and during a low-intensity contraction set at 10% of maximal strength (+103%, p = 0.038). No changes in muscle contractility and nerve conduction velocity were observed after the ULLS. The present study suggests that neural impairments mainly contribute to the decrease in knee extensors strength induced by short-term ULLS. The decrease in muscle activation after a short period of ULLS was accompanied by an increase in spinal excitability. However, the latter adaptation did not counterbalance the reduction in activation capacity and thus in maximal strength resulting from ULLS. These adaptations to short-term ULLS should be considered when aiming at improving the neuromuscular function of people experiencing muscle hypoactivity. NEW & NOTEWORTHYThis study provides new insights into the effects of muscle hypoactivity on neuromuscular function and spinal excitability in the major antigravity muscle group of the lower limb. Neural impairments primarily contribute to maximal strength loss after short-term unilateral lower limb suspension, while spinal excitability increased. These findings are crucial as they offer valuable understanding for developing effective interventions to improve health outcomes for individuals experiencing muscle inactivity.

physiology↗

bioRxiv2024

Mean exercise torque is a critical factor influencing neuromuscular fatigability induced by exhausting contractions

PURPOSETo get a more detailed description of neuromuscular fatigability, maximal torque sustainability (i.e., the ability to maintain a high torque level) can be assessed in addition to the classically used maximal voluntary contraction (MVC). Since this parameter appears to be affected by mean exercise torque (MET), the present study aims to examine the relationship between MET and neuromuscular fatigability induced by exhausting contractions. METHODSThirteen participants sustained a plantar flexors MVC for 1 min (MVC1- MIN) before and after exhausting exercises designed to produce a similar MET (30% MVC), and following a 10-min rest period. Exercises consisted of intermittent (INT), continuous (CON) or variable (continuous contraction alternating between moderate and low intensity, VAR) contractions performed until task failure. RESULTSAlthough the INT resulted in greater exercise duration and torque-time integral than CON and VAR, MVC similarly decreased after all exercises due to neural and muscular impairments. The torque loss during the MVC1-MIN increased after all exercises to a similar extent, mainly because of neural alterations. Contrary to MVC, the torque loss during the MVC1-MIN returned to baseline value after the recovery period. CONCLUSIONBy considering both maximal torque production and sustainability, INT, CON and VAR exercises, performed with identical mean torque and until exhaustion, led to a similar neuromuscular fatigability. Results confirm the independence of maximal torque production from the contraction pattern and support the impact of MET on maximal torque sustainability. The present findings are crucial to consider for the management of neuromuscular fatigability in both athletes and patients.

physiology↗

bioRxiv2024

Skeletal muscle effects of antisense oligonucleotides targeting glycogen synthase 1 in a mouse model of Pompe disease

Pompe disease (PD) is a progressive myopathy caused by the aberrant accumulation of glycogen in skeletal and cardiac muscle resulting from the deficiency of the enzyme acid alpha-glucosidase (GAA). Administration of recombinant human GAA as enzyme replacement therapy (ERT) works well in alleviating the cardiac manifestations of PD but loses sustained benefit in ameliorating the skeletal muscle pathology. The limited efficacy of ERT in skeletal muscle is partially attributable to its inability to curb the accumulation of new glycogen produced by the muscle enzyme glycogen synthase 1 (GYS1). Substrate reduction therapies aimed at knocking down GYS1 expression represent a promising avenue to improve Pompe myopathy. However, finding specific inhibitors for GYS1 is challenging given the presence of the highly homologous GYS2 in the liver. Antisense oligonucleotides (ASOs) are chemically modified oligomers that hybridize to their complementary target RNA to induce their degradation with exquisite specificity. In the present study, we show that ASO-mediated Gys1 knockdown in the Gaa-/- mouse model of PD led to a robust reduction in glycogen accumulation in skeletal and cardiac muscle. In addition, combining Gys1 ASO with ERT further reduced glycogen content in muscle, eliminated autophagic buildup and lysosomal dysfunction, and improved motor function in Gaa-/- mice. Our results provide a strong foundation for further validation of the use of Gys1 ASO, alone or in combination with ERT, as a therapy for PD. We propose that early administration of Gys1 ASO in combination with ERT may be the key to preventative treatment options in PD.

molecular biology↗

bioRxiv2024

iSCORE-PD: an isogenic stem cell collection to research Parkinson Disease

Parkinsons disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer a unique experimental platform to advance our understanding of PD etiology by enabling the generation of disease-relevant cell types carrying patient mutations along with isogenic control cells. To facilitate this approach, we generated a collection of 65 human stem cell lines genetically engineered to harbor high risk or causal variants in genes associated with PD (SNCA A53T, SNCA A30P, PRKN Ex3del, PINK1 Q129X, DJ1/PARK7 Ex1-5del, LRRK2 G2019S, ATP13A2 FS, FBXO7 R498X/FS, DNAJC6 c.801 A>G/FS, SYNJ1 R258Q/FS, VPS13C A444P/FS, VPS13C W395C/FS, GBA1 IVS2+1/FS). All mutations were introduced into a fully characterized and sequenced female human embryonic stem cell (hESC) line (WIBR3; NIH approval number NIHhESC-10-0079) using different genome editing techniques. To ensure the genetic integrity of these cell lines, we implemented rigorous quality controls, including whole-genome sequencing of each line. Our analysis of the genetic variation in this cell line collection revealed that while genome editing, particularly using CRISPR/Cas9, can introduce rare off-target mutations, the predominant source of genetic variants arises from routine cell culture and are fixed in cell lines during clonal isolation. The observed genetic variation was minimal compared to that typically found in patient-derived iPSC experiments and predominantly affected non-coding regions of the genome. Importantly, our analysis outlines strategies for effectively managing genetic variation through stringent quality control measures and careful experimental design. This systematic approach ensures the high quality of our stem cell collection, highlights advantages of prime editing over conventional CRISPR/Cas9 methods and provides a roadmap for the generation of gene-edited hPSC collections at scale in an academic setting. Our iSCORE-PD collection represents an easily accessible and valuable platform to study PD, which can be used by investigators to understand the molecular pathophysiology of PD in a human cellular setting.

neuroscience↗

bioRxiv2024

A long non-coding RNA at the cortex locus controls adaptive colouration in butterflies

Evolutionary variation in the wing pigmentation of butterflies and moths offers striking examples of adaptation by crypsis and mimicry. The cortex locus has been independently mapped as the locus controlling colour polymorphisms in 14 lepidopteran species, suggesting it acts as a genomic hotspot for the diversification of wing patterns, but functional validation through protein-coding knockouts has proven difficult to obtain. Our study unveils the role of a novel long non-coding RNA (lncRNA) which we name ivory, transcribed from the cortex locus, in modulating colour patterning in butterflies. Strikingly, ivory expression prefigures most melanic patterns during pupal development, suggesting an early developmental role in specifying scale identity. To test this, we generated CRISPR mosaic knock-outs in five nymphalid butterfly species and show that ivory mutagenesis yields transformations of dark pigmented scales into white or light-coloured scales. Genotyping of Vanessa cardui germline mutants associates these phenotypes to small on-target deletions at the conserved first exon of ivory. In contrast, cortex germline mutant butterflies with confirmed null alleles lack any wing phenotype, and exclude a colour patterning role for this adjacent gene. Overall, these results show that a lncRNA acts as a master switch of colour pattern specification, and played key roles in the adaptive diversification of colour patterns in butterflies. Significance statementDeciphering the genetic underpinnings of adaptive variation is fundamental for a comprehensive understanding of evolutionary processes. Long non-coding RNAs (lncRNAs) represent an emerging category of genetic modulators within the genome, yet they have been overlooked as a source of phenotypic diversity. In this study, we unveil the pivotal role of a lncRNA in orchestrating colour transitions between dark and light patterns during butterfly wing development. Remarkably, this lncRNA gene is nested within the cortex locus, a genetic region known to control multiple cases of adaptive variation in butterflies and moths, including iconic examples of natural selection. These findings highlight the significant influence of lncRNAs in developmental regulation, and also underscore their potential as key genetic players in the evolutionary process itself.

evolutionary biology↗

bioRxiv2024

Visually Induced Involuntary Movements

Looking at a virtual 3D environment with structural features rotating at 60{degrees}/s in a head-mounted display soon elicits an illusion of self-rotation and displacement in the opposite direction. We explored in 75 s long trials the effects of visually induced self-rotation on the head, torso, and horizontally extended right arm of standing subjects. The degree of body and limb movement was contingent on whether the arm was extended out freely or pointing at a briefly proprioceptively specified target position, but did not depend on whether the hand held a rod or not. Most subjects in the Free condition showed significant unintentional arm deviations, which averaged approximately 55{degrees} in the direction opposite the induced illusory self-motion, and were more than 150{degrees} in some cases. In contrast, on average, the deviations in the Pointing condition were a quarter of those in the Free condition. Deviations of head and torso positions also occurred in all conditions. Total arm and head deviations were the sum of deviations of the arm and head with respect to the torso plus deviations of the torso with respect to space. When given a pointing target, subjects were largely able to detect and correct for arm and head deviations with respect to the torso but not for the parts of arm and head deviation that were due to deviations of the torso with respect to space. In all conditions, the arm, head, and torso deviations occurred before subjects began to experience compelling self-rotation and displacement. This is contrasted with the compensations for expected but absent Coriolis forces that are made when stationary subjects make reaching movements to targets during exposure to structured moving visual scenes. These compensations do not occur until subjects experience self-rotation and spatial displacement. These results have implications for vehicle control and maneuvering in environments that induce illusory motion and displacement, and in situations where there is motion in a large area of the visual field. The impact of these effects on joystick control is described and discussed. We also describe the subjective sense of ownership attributed to hand-held objects when experiencing illusory self-motion and displacement.

neuroscience↗