Biology subjects

Wang, Y.-C.

Publications and source records attributed to Wang, Y.-C..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic microtubules drive yolk-cytoplasm segregation in the syncytial Drosophila embryo

Yolk-cytoplasm segregation is among the earliest spatial organization events in the developing embryo of many oviparous animals. The segregation process is intimately linked to early embryonic cleavage and pattern formation, and exhibits a wide range of spatial and temporal diversity. However, the underlying cytoskeletal mechanism remains largely unknown, except for a small number of species. Using quantitative live imaging, we investigated yolk segregation in the Drosophila embryo during the syncytial nuclear cycles 11-14. We find that the yolk vesicles move progressively inward in spatial and temporal coordination with the inward expanding microtubule networks that are nucleated from centrosomes positioned at the cortex, whereas cortical actin meshwork remains spatially restricted. Using the gnu RNAi embryo to decouple nuclear migration and division from cytoskeletal dynamics, we establish causality with targeted pharmacological disruption and find that microtubule dynamics is required for yolk segregation, while depolymerization of actin has no discernible effect. In support of a mechanism of growth-propelled passive displacement, microtubule plus end comets come in apparent contact with yolk vesicles, and injected, inert microbeads are displaced towards the embryo center presumably by the same pushing force. These findings identify microtubule polymerization as a predominant driver of yolk-cytoplasm segregation in Drosophila and suggest that diverse cytoskeletal mechanisms evolved to accomplish this crucial reorganization process

developmental biology↗

bioRxiv2026

Context-dependent variant interpretation from Mendelian disease to genetic predisposition: a proof-of-concept using LPL

As genomic sequencing evolves beyond rare disease diagnostics toward population screening and precision medicine, clinical variant interpretation is increasingly challenged by variants whose clinical consequences depend on biological context. Current frameworks, including the ACMG/AMP guidelines, generally assign a single classification to each variant regardless of inheritance state or genetic context, potentially failing to communicate context-dependent clinical consequences. Here, we address this issue using loss-of-function variants in LPL as a uniquely informative model system in which residual physiological LPL activity can be directly quantified in vivo. By systematically integrating published biallelic LPL genotypes, physiological measurements, functional studies, and clinical phenotypes, we identified a biologically meaningful transition at approximately 10% residual physiological LPL activity. Activity below this level was predominantly associated with classical childhood-onset familial chylomicronemia syndrome (FCS), whereas higher activity was associated with phenotypic attenuation and modifier-dependent clinical expression. Furthermore, heterozygous loss-of-function variants exhibited an estimated penetrance of 5-7% for severe hypertriglyceridemia. We therefore propose a context-dependent framework in which biallelic complete- or near-complete loss-of-function genotypes are interpreted as causative for FCS, whereas heterozygous variants are interpreted as predisposing to severe hypertriglyceridemia while retaining recognition of FCS carrier status. Together, our findings demonstrate that clinical variant interpretation should integrate available biological context--including, where relevant, allelic configuration, residual biological function, and penetrance--rather than rely on the intrinsic molecular consequence of the variant alone. More broadly, this framework provides a conceptual model for interpreting variants across the continuum from Mendelian disease to genetic predisposition in the era of precision medicine.

genetics↗

bioRxiv2026

Sexually dimorphic behavioural signatures of tau toxicity in adult Drosophila

Tau pathology is central to Alzheimers disease and related tauopathies, yet mechanisms driving neuronal dysfunction and degeneration downstream of pathological changes in tau remain poorly understood. Drosophila melanogaster models provide a genetically tractable system with an intact nervous system and short lifespan that allows investigation of mechanisms of many diseases. However, in Drosophila, developmental expression of human tau frequently causes lethality and developmental phenotypes, limiting the study of neurodegenerative disease processes. Further, sex is rarely considered in Drosophila studies of tau pathology despite clear sex differences being observed in many aspects of human tauopathies. Here, we used an inducible, pan-neuronal GeneSwitch system to express human tau isoforms exclusively in adulthood, enabling the dissection of tau toxicity independent of development. We combined longitudinal behavioural monitoring with lifespan and neurodegeneration analyses, and performed a targeted genetic screen to identify modifiers of tau-induced dysfunction. Adult-onset tau expression produced striking, sexually dimorphic effects on survival and behaviour. Neuronal expression of the human tau isoform with 4 microtubule binding repeats and neither alternatively spliced N-terminal exon (0N4R tau) caused pronounced neurodegeneration and reduced lifespan, which was exacerbated in flies expressing the phospho-mimetic 0N4R-TauE14 variant. Tau expression produced sexually dimorphic effects on survival and behaviour, with females exhibiting a greater reduction in lifespan, while the induction-dependent increase in vacuolar neurodegeneration was broadly comparable between sexes. Behaviourally, tau expression induced elevated daytime inactivity in females, whereas males exhibited hyperactivity, revealing opposing functional outcomes between sexes. A targeted genetic screen further identified modifiers of tau-dependent behavioural impairment. APOE2 expression in glia, syndecan overexpression in neurons, and increased global expression of the chaperone heat shock protein 90 all reduced 0N4R-TauE14-induced behavioural changes. Seventeen candidate perturbations enhanced the TauE14-induced behavioural phenotype, including manipulations of APOE3, CLU, INPP5D/INPP5K, BIN1/Amph, synaptogyrin, LRP1, NPC1, and Hsp90 pathways. Together, these findings establish an adult-onset Drosophila model of tauopathy that uncouples neurotoxicity from development, reveals sex as a major determinant of tau-induced behavioural outcomes in flies, and uncovers genetic modulators of tau-induced dysfunction. This work highlights the importance of incorporating sex as a biological variable and provides a platform for mechanistic and translational studies of tauopathy.

neuroscience↗

bioRxiv2026

Abiotic cues modulate exopolysaccharides to influence type VI secretion system-mediated antagonism

The type VI secretion system (T6SS) enables Gram-negative bacteria to inject toxic effectors into neighboring cells, mediating contact-dependent antagonism and interbacterial competition. How the T6SS-mediated attack responds to environmental cues varies and remains unclear among different bacteria. Here, using Agrobacterium fabrum C58, a soil-borne phytopathogenic bacterium, we investigated the impact of osmolarity, moisture, surface stiffness, and glucose on T6SS-mediated antagonism. We show that these abiotic factors influenced the production of two polysaccharides, cyclic-{beta}-(1,2)-glucan (C{beta}G) and succinoglycan (SG), and modulated the T6SS-killing outcome. Mechanistically, high osmolarity inhibits C{beta}G production, thereby enhancing the expression and secretion of the T6SS. In contrast, SG biosynthesis, in response to moisture, surface stiffness, and glucose, does not impact T6SS expression and function but decreases T6SS-mediated killing efficacy. Electron microscopy revealed that SG creates a physical barrier between bacterial cells. Such physical distancing not only hinders the T6SS attack from Agrobacterium, but also confers protection against other competitors at both intra- and inter-species levels. Our results unravel the complexity of how specific environmental factors modulate the contact-dependent antagonism and highlight a balance between offensive and defensive behaviors. Significance StatementBacteria live in polymicrobial communities where they often need to fight off competitors to survive. One well-characterized weapon is the type VI secretion system (T6SS), a nanomachine mediating contact-dependent antagonism. In this study, we aim to study how the T6SS attack is influenced by environmental cues. We discovered that carbon sources, osmolarity, and surface stiffness modulate the T6SS efficacy through the secretion of sugar chains outside the cell. This sugar secretion increases the physical distance between cells, protecting against T6SS-mediated attack. However, such physical distancing also hinders the efficacy of the T6SS attack originating from Agrobacterium itself. Our results reveal a previously understudied offense-defense tradeoff between EPS production and T6SS-mediated attack. This finding underscores the intricate balance between bacterial offense and defense strategies.

microbiology↗

bioRxiv2026

A multi-omics map of diabetic nephropathy links c-Jun activation to tubular injury and metabolic stress

Diabetic nephropathy (DN) is a major cause of end-stage renal disease, yet the molecular mechanisms driving tubular injury and fibrosis remain poorly defined. Here, we integrated single-cell multiplexed protein imaging, spatial transcriptomics, single-nucleus and single-cell RNA sequencing and chromatin accessibility profiling to comprehensively characterize human DN pathology. Our multi-modal analysis precisely maps kidney cell types and their spatial distributions, immune-fibrotic interactions, and key transcriptional regulators. We identified eight distinct cellular neighborhoods defining the immune-fibrotic microenvironment and uncovered molecular networks driving tubular injury and fibrosis. JUN (encoding c-Jun) emerged as a central regulator of transcriptional reprogramming during tubular injury and fibrogenic remodeling. In a diabetic mouse model, c-Jun is activated in injured proximal tubules. Using an inducible c-Jun mouse model, we demonstrated that tubular-specific c-Jun activation alone is sufficient to induce tubular injury, chronic inflammation, progressive fibrosis, and systemic metabolic alterations, including impaired glucose homeostasis. We also observed reduced expression of SLC4A4, a bicarbonate transporter essential for proximal tubular function, in injured tubules. Together, our findings establish a spatially resolved framework for understanding DN pathogenesis and identify c-Jun as a key mediator of tubular injury and fibrosis in diabetic kidney disease.

pathology↗

bioRxiv2026

Cell-intrinsic compliance mechanism enables release of tensile stress to prevent tissue rupture

Contractile forces are necessary to sculpt tissue structures and organ shapes during morphogenesis. In the early embryo, this presents an engineering challenge as the deforming tissue can be relatively large, while the forces thus generated might be poorly compartmentalized, generating tensile stresses that can cause damage if unmitigated. Here we show that during Drosophila gastrulation, the squamous morphogenesis of the extraembryonic amnioserosa functions mechanically to release tensile stresses yielded from the neighboring ectodermal convergent-extension and mesodermal invagination. Amnioserosa master regulator Zen transcriptionally silences shroom to endow it with low junctional actomyosin stresses, thereby ensuring high mechanical compliance. Loss of Zen, or targeted ectopic expression of Shroom in the amnioserosa using a novel optogenetic Gal4 system, leads to increased junctional myosin, thereby causing load-dependent tissue ruptures. Our data establish a previously unknown function for the Drosophila extraembryonic tissue, whereby cell-intrinsic mechanical compliance prevents tissue rupture to mitigate inter-tissue mechanical conflicts.

developmental biology↗

bioRxiv2025

Multi-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening

We profiled developmental-series transcriptome, methylome, and metabolome profiling to reveal extensive epigenetic reprogramming during black raspberry (Rubus occidentalis) fruit ripening. Fruit tissues exhibit globally higher DNA methylation than leaves, particularly in CHG and CHH contexts. Local methylation in all cytosine contexts progressively decreases in promoter regions during ripening, whereas CHG and CHH methylation increase in transposon-rich regions. Two primary methylation transitions--promoter hypomethylation and CHH hypermethylation--govern transcriptional shifts in genes involved in ripening processes. Methyl-binding transcription factors with activation potential likely promote CHH hypermethylation-linked transcriptional activation. Multi-omics integration revealed coordinated anthocyanin accumulation parallels expression of biosynthetic and regulatory genes within coherent networks. Elevated non-CG methylation in heterochromatin coincides with increased transcription of histone variants mediating chromatin compaction, suggesting chromatin remodelers fine-tune accessibility for methyltransferases. Our study highlights both genome-wide and locus-specific epigenetic reprogramming and demonstrates a coordinated interplay between DNA methylation and transcriptional regulation during black raspberry fruit ripening.

genomics↗

bioRxiv2025

Repurpose of Ritlecitinib Reduces Neointima Formation and Enhances Endothelial Recovery Following Vascular Injury

BackgroundNeointimal hyperplasia after vascular injury reflects excess smooth muscle cell (SMC) proliferation with impaired endothelial recovery. We tested the hypothesis that selective Janus kinase 3 (JAK3) inhibition with the FDA-approved drug Ritlecitinib limits neointima while accelerating reendothelialization. MethodsWe used mouse carotid wire injury and a human internal mammary artery (IMA) xenograft model to evaluate effects of genetic JAK3 loss in SMCs or oral Ritlecitinib in vascular remodeling. Mechanistic studies in SMCs assessed JNK/c-Jun signaling and its regulation of thrombospondin-1 (TSP-1) and vascular endothelial growth factor A (VEGF-A) using RNA-seq and CUT&RUN. Rescue experiments tested whether VEGF-A neutralization or exogenous TSP-1 reversed the antineointimal effects. Patient-derived IMA SMCs were analyzed for variabilities in drug responses. ResultsGenetic JAK3 loss in SMCs or oral Ritlecitinib reduced neointimal area and intima/media ratio and increased luminal CD31+ coverage in both models. In SMCs, Ritlecitinib suppressed JNK/c-Jun signaling, downregulated TSP-1, and restored VEGF-A, shifting the milieu toward endothelial regeneration. RNA-seq and CUT&RUN corroborated JNK/c-Jun- dependent control of TSP-1 and VEGFA. VEGF-A neutralization or exogenous TSP-1 abrogated the anti-neointimal phenotype. In patient-derived IMA SMCs, variable drug response was linked to the JAK3 Pro893Asn variant and a VEGFA promoter SNP. ConclusionSelective JAK3 inhibition by Ritlecitinib simultaneously restrains SMC proliferation and promotes endothelial repair through modulating TSP-1 and VEGF-A activities. Ritlecitinib merits clinical evaluation as a precision therapy to prevent restenosis, with genetic stratification to identify responders.

pathology↗

bioRxiv2025

Floral Stage Optimization and Immune Evasion Enhance Agrobacterium-Mediated Genome Editing in Arabidopsis

O_LIAgrobacterium-mediated transformation via floral inoculation (AMT-FI) enables genetic engineering without tissue culture. It is widely used in the model plant Arabidopsis thaliana, yet its efficiency and broader applicability remain limited. C_LIO_LIHere, we used a dual-reporter system (RUBY and hygromycin resistance) to identify key floral stages and engineered Agrobacterium strains to evade plant immunity, leading to enhanced transient expression and genome editing. C_LIO_LIWe determined that flowers opened at 6 day-post-inoculation (DPI) are optimal for high transformation efficiency, with nearly 100% of siliques harboring transformants. However, Agrobacterium infection induced ovule abortion, particularly in wild-type (Col-0) plants, whereas efr mutants lacking the EF-Tu receptor (EFR)-mediated pattern-triggered immunity (PTI) showed reduced ovule abortion. Notably, efr mutants exhibited more RUBY-positive ovules and significantly enhanced genome editing efficiency. Two engineered stealth Agrobacterium strains (AS201 and AS202) expressing a chimeric EF- Tu for evading recognition by EFR enhanced both transient transformation and genome editing efficiency. Remarkably, genome-edited T1 plants could be recovered based on phenotype or direct sequencing without the need for antibiotic selection when targeting flowers opened at 6 DPI. C_LIO_LIBy integrating floral stage selection, immune evasion, and Agrobacterium engineering, this study provides a practical and versatile platform to advance plant genome engineering. C_LI

plant biology↗

bioRxiv2025

Microbial community characteristics and stable relationships centered on anammox bacteria revealed by global-scale analysis

Anaerobic ammonium-oxidizing bacteria (AnAOB) play important roles in both artificial wastewater treatment systems and natural ecosystems. To date, AnAOB pure cultures are not available and they tend to coexist with various microbial species. However, anammox community characteristics including the relationships between AnAOB and their companion bacteria at the global perspective and their impacts on anammox metabolism remain unclear. Here, we systematically analyzed the characteristics of anammox communities and the stable relationships concerning AnAOB using a global dataset containing 619 anammox-related amplicons. Different anammox systems showed significant differences in alpha and beta diversity, but shared some core taxa of interest. A total of 89 and 55 core genera and species were identified respectively across anammox communities worldwide, which formed the backbone of artificial anammox systems. Through the analysis of co-abundance networks derived from four distinct artificial anammox systems--biofilm, granular sludge, flocculent sludge, and planktonic cells--we identified 208 stable and 92 limited stable relationships associated with AnAOB. Functional analysis suggested that stable positively-correlated companion bacteria may provide essential cofactors (e.g., molybdenum cofactor, tetrahydrofolate, and coenzyme A) to AnAOB. The companion bacteria which showed limited stable positive correlations with AnAOB in the anammox attachment-growth systems, may mutualize with AnAOB via type pili. This study deepens the understanding of anammox communities, anammox core microbiome, and AnAOB symbiotic relationships. These (limited) stable companion bacteria and corresponding cofactors can potentially guide the development and application of bioaugmentation methods, synthetic anammox communities, and deterioration biomarkers for engineered anammox systems.

microbiology↗

bioRxiv2024

Rhizobium rhizogenes A4-derived strains mediate hyper-efficient transient gene expression in Nicotiana benthamiana and other solanaceous plants

Agroinfiltration, a method utilizing agrobacteria to transfer DNA into plant cells, is widely used for transient gene expression in plants. Besides the commonly used Agrobacterium strains, Rhizobium rhizogenes can also introduce foreign DNA into host plants for gene expression. While many R. rhizogenes strains have been known for inducing hairy root symptoms, their use for transient expression has not been fully explored. Here, we showed that R. rhizogenes A4 outperformed all other tested agrobacterial strains in agroinfiltration experiments on leaves of Nicotiana benthamiana and other solanaceous plants. By conducting an agroinfiltration screening in N. benthamiana leaves using various agrobacterial strains carrying the RUBY reporter gene cassette, we discovered that A4 mediates the strongest and fastest transient expression. Utilizing the genomic information, we developed a collection of disarmed and modified strains derived from A4. By performing vacuum infiltration assays, we demonstrated that these A4-derived strains efficiently transiently transform 6-week-old N. benthamiana leaves, showing less sensitivity to the age of plants compared to the laboratory strain GV3101. Furthermore, we performed agroinfiltration using AS109, an A4-derived disarmed strain, on the leaves of tomato, pepper, and eggplant. Remarkably, AS109 mediated transient gene expression on tested solanaceous plants more effectively than all the tested commonly used agrobacterial strains. This discovery paves the way for establishing R. rhizogenes A4-derived strains as a new option for enhancing transient expression in N. benthamiana and facilitating the functional study of plant genes in other solanaceous species.

plant biology↗

bioRxiv2024

Drosophila appear resistant to trans-synaptic tau propagation

Alzheimers disease (AD) is the most common cause of dementia in the elderly, prompting extensive efforts to pinpoint novel therapeutic targets for effective intervention. Among the hallmark features of AD is the development of neurofibrillary tangles comprised of hyperphosphorylated tau protein, whose progressive spread throughout the brain is associated with neuronal death. Trans-synaptic propagation of tau has been observed in mouse models and indirect evidence for tau spread via synapses has been observed in human AD. Halting tau propagation is a promising therapeutic target for AD, thus a scalable model system to screen for modifiers of tau spread would be very useful for the field. To this end, we sought to emulate the trans-synaptic spread of human tau (hTau) in Drosophila melanogaster. Employing the trans-Tango circuit mapping technique, we investigated whether tau spreads between synaptically connected neurons. Immunohistochemistry and confocal imaging were used to look for tau propagation. Examination of hundreds of flies expressing 4 different human tau constructs in two distinct neuronal populations reveal a robust resistance in Drosophila to the trans-synaptic spread of hTau. This resistance persisted in lines with concurrent expression of amyloid-{beta}, in lines with global hTau knock-in to provide a template for human tau in downstream neurons, and with manipulations of temperature. These negative data are important for the field as we establish that Drosophila expressing human tau in subsets of neurons are unlikely to be useful to perform screens to find mechanisms to reduce the trans-synaptic spread of tau. The inherent resistance observed in Drosophila may serve as a valuable clue, offering insights into strategies for impeding tau spread in future studies.

neuroscience↗

bioRxiv2024

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing novel insights into domestication and selection in goats and related species. Here, we assembled a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), which included a Y chromosome of 20.9 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrected numerous genome-wide structural and base errors in previous assemblies and added 288.5 Mb of previously unresolved regions (PURs) and 446 newly assembled genes to the reference genome. We sequenced the genomes of five representative goat breeds for PacBio reads, and used T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 SVs (7.41%) in the PURs and 507 overlapping genes significantly enriched (Padj. < 0.05) in the keratin filament pathway. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the PURs. Also, our analyses revealed a set of novel selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

genomics↗

bioRxiv2023

Temporal Transcriptome Analysis Uncovers Regulatory Modules Programming Embryo Development from Embryonic Morphogenesis to Post-Germination

We profiled the soybean seed embryo transcriptome across embryonic development to post-germinative development to understand gene activities and regulatory networks promoting these processes. Transcriptomic landscapes feature highly prevalent transcripts which are categorized into early and late groups with major functions of reserve accumulation and energy generation, respectively, and both functions are dominant during late reserve accumulation as the transitioning stage. During the mid-reserve accumulation, regulatory events simultaneously dominate at the transcriptional and chromatin levels, followed by the emergence of distinct mRNA populations during late reserve accumulation throughout germination. We identified diverse functions conducted by sequentially activated genes across developmental stages. Gene coexpression network analysis reveals modules associated with developmental stages, some of which are enriched in genes with functions involved in specific developmental processes. We identified an early-desiccation-associated gene module, containing most transcription factors responsive to abiotic stress, within which one transcription factor is functionally validated to demonstrate increased drought tolerance in Arabidopsis overexpression lines. Finally, we found that a subset of genes is under purifying selection, surpasses the number of their Arabidopsis germination-specific homologs and most are active before germination from embryonic morphogenesis through dormancy, suggesting a potential role in governing physical dormancy in soybean compared to physiological dormancy in Arabidopsis. Our data represent a step toward identifying genes and regulatory networks in the soybean genome facilitating developmental programs across transition phases to bridge embryonic and germinative development.

plant biology↗

bioRxiv2023

Comparison of Multiple Carbapenemase Tests Based on an Unbiased Colony Selection Method

Carbapenemase-producing organisms (CPOs) present a major threat to public health, demanding precise diagnostic techniques their detection. Discrepancies among CPO tests have raised concerns, partly due to limitations in detecting bacterial diversity within host/specimen. We explored the impact of unbiased colony selection on carbapenemase testing and assessed its relevance on various tests. Based on "FirstAll" for unbiased colony selection to reduce bias, we compared modified carbapenem inactivation method/EDTA-modified carbapenem inactivation method (mCIM/eCIM), Carba5, the CPO panel, and multiplex PCR (M-PCR). Initially, we compared FirstAll to conventional colony selection for mCIM. Second, we used M-PCR as a reference, to evaluate test performance across seven CPO species. The results revealed that FirstAll selection improved carbapenemase detection, revising false-negative in 10.5% of K. pneumoniae isolates. In addition, 12.4% of CPOs tested positive for multiple carbapenemase genes. Both the Carba5 test and CPO panel showed suboptimal performance (sensitivity/specificity: Carba5 75.5%/89.0%, CPO panel 78.1%/74.0%). Carba5 test provided specific carbapenemase class assignments but CPO panel failed in 20.3% of cases. Carba5 test and the CPO panel results correlated well with ceftazidime-avibactam minimal inhibitory concentrations (MICs). Concordance for class A/D with MICs was 88.3% for Carba5 and 92.0% for the CPO panel; whereas for class B, it was 86.5% for Carba5 and 76.2% for the CPO panel. In conclusion, FirstAll as the unbiased colony selection impacted carbapenemase testing. With FirstAll, the diagnostic performance of either Carba5 or the CPO panel was compromised. The utilization of ceftazidime-avibactam guided by either the CPO panel or Carba5 was appropriate. ImportanceThe increasing carbapenemase-producing organisms (CPO) is concerning due to high mortality rates and limited treatment options. Precise testing for CPO is crucial not only for antibiotic treatments but also for infection control. However, discrepant results for an individual overtime or even intra-specimen are found in either phenotypic or genetic testing, posing considerable challenge in clinical management. Based on the colonization-infection model of CPO infections, there would be strain heterogeneity in an individual. On top of the heterogeneity, the single colony selection method in conventional CPO testing would be the source of discrepancy and bias. To test the hypothesis, we proposed FirstAll method as the unbiased colony selection method. We demonstrated that FirstAll corrected around 10% false-negative cases. Lower diagnostic performances of CPO tests were also found in comparison to previous related studies. The study revealed that colony selection would have considerable impacts on CPO testing.

microbiology↗

bioRxiv2023

Divergent evolutionary strategies preempt tissue collision in fly gastrulation

Metazoan development proceeds through a series of morphogenetic events that sculpt body plans and organ structures. In the early embryonic stages, morphogenetic processes involving growth and deformation occur concurrently. Forces generated in one tissue can thus increase mechanical stress in the neighboring tissue, potentially disrupting spatial patterning, morphological robustness, and consequently decreasing organismal fitness. How organisms evolved mechanisms to reduce or release inter-tissue stresses remains poorly understood. Here we combined phylogenetic survey across a whole insect order (Diptera), quantitative live imaging, and functional mechanical perturbation to investigate the evolution of mechanical stress management during epithelial expansions in the gastrulating fly embryos. We find that two distinct cellular mechanisms exist in Diptera to prevent the accumulation of compressive stress that can arise when the expanding head and trunk tissues collide. In Cyclorrhapha, a monophyletic dipteran subgroup including the fruit fly Drosophila melanogaster, the head-trunk boundary undergoes active out-of-plane deformation to form a transient epithelial fold, called the cephalic furrow (CF), which acts as a mechanical sink to preempt head-trunk collision. Genetic or optogenetic elimination of the CF leads to tissue buckling, yielding deleterious effects of axial distortion that likely results from unmitigated release of compressive stress. Non-cyclorrhaphan flies, by contrast, lack CF formation and instead display widespread out-of-plane division in the head, which shortens the duration of its expansion and reduces surface area increase. Reorienting head mitosis in Drosophila from in-plane to out-of-plane partially suppresses the need for epithelial out-of-plane deformation, suggesting that out-of-plane division can act as an alternative mechanical sink to prevent tissue collision. Our data suggest that programs of mechanical stress management can emerge abruptly under selective pressure of inter-tissue mechanical conflict in early embryonic development.

developmental biology↗

bioRxiv2023

Differential regulation of the proteome and phosphosproteome along the dorso-ventral axis of the early Drosophila embryo

The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3399 and 3433 respectively, were differentially regulated. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo.

developmental biology↗

bioRxiv2023

Genetic dysregulation of an endothelial Ras signaling network in vein of Galen malformations

To elucidate the pathogenesis of vein of Galen malformations (VOGMs), the most common and severe congenital brain arteriovenous malformation, we performed an integrated analysis of 310 VOGM proband-family exomes and 336,326 human cerebrovasculature single-cell transcriptomes. We found the Ras suppressor p120 RasGAP (RASA1) harbored a genome-wide significant burden of loss-of-function de novo variants (p=4.79x10-7). Rare, damaging transmitted variants were enriched in Ephrin receptor-B4 (EPHB4) (p=1.22x10-5), which cooperates with p120 RasGAP to limit Ras activation. Other probands had pathogenic variants in ACVRL1, NOTCH1, ITGB1, and PTPN11. ACVRL1 variants were also identified in a multi-generational VOGM pedigree. Integrative genomics defined developing endothelial cells as a key spatio-temporal locus of VOGM pathophysiology. Mice expressing a VOGM-specific EPHB4 kinase-domain missense variant exhibited constitutive endothelial Ras/ERK/MAPK activation and impaired hierarchical development of angiogenesis-regulated arterial-capillary-venous networks, but only when carrying a "second-hit" allele. These results illuminate human arterio-venous development and VOGM pathobiology and have clinical implications.

genomics↗