Search bioRxiv⌕ Search

Biology subjects

Williams, S.

Publications and source records attributed to Williams, S..

At least 19 recordsLinked to original sources

Adult corals enhance juvenile recruitment through cumulative ecological niche construction

Ecosystem engineers are ecological niche constructors: by modifying local environments, they alter the conditions under which organisms establish, persist and interact. Although niche construction is often framed as a population-level evolutionary feedback, it could also operate at the assemblage level when communities collectively shape their environments and filter future recruitment. Reef-building corals provide a perfect system to test this idea because adult colonies form three-dimensional carbonate structures that can persist after colony death, creating an inherited habitat for subsequent coral generations. Here, we tested whether coral recruitment to the juvenile stage was associated with local adult coral abundance, reef structure, and larval settlement supply. Combining spatially explicit coral censuses, photogrammetric reef digital elevation models and data from settlement tiles across 15 reef sites at two time points at Jiigurru, Great Barrier Reef, we found that juvenile abundance increased additively on the log scale with adult abundance and with fractal dimension, a metric of fine-scale structural complexity. Surface rugosity had weaker effects, and interactions between adult abundance and habitat structure were limited, indicating largely additive, rather than synergistic or antagonistic, effects. Our results show that both adult assemblages and the concurrent structural complexity, consistent with assemblage-level niche construction and ecological inheritance theory, shape coral recruitment.

ecology↗

SARS-CoV-2 maturation driven by a mechano-active nucleocapsid-RNA condensate

The nucleocapsid (N) protein, the core component of the SARS-CoV-2 virus, binds to the 30-kb viral genomic RNA (vgRNA) to form ribonucleoprotein assemblies that are packaged into ~100 nm membrane-enclosed virions. In addition to viral assembly, the N protein performs other functions, including roles in viral mRNA transcription, replication, and immune regulation, making it a key target for developing diagnostics and vaccines. Recent studies show that N protein and RNA undergo phase separation to form a biomolecular condensate that constitutes the viral core. However, how this condensate becomes selectively enveloped by a membrane remains unclear. Here, using a minimal reconstituted system, we demonstrate that N protein-vgRNA condensates are spontaneously enveloped by lipid bilayer membranes, whereas condensates formed by N protein alone or with genomic RNA fragments fail to undergo envelopment and instead adhere to or weakly deform membranes. We show that RNA length tunes the material properties of N protein condensates, with vgRNA imparting enhanced elasticity. We propose a physical model for SARS-CoV-2 maturation in which adhesion between the membrane and the N protein-vgRNA condensate drives membrane bending, while condensate elasticity preserves core geometry. These results identify RNA-dependent material properties as an underlying physical principle for selective SARS-CoV-2 maturation.

biophysics↗

PRISM: A Plasmid-based Reporter for Intracellular Spectral Microscopy

Organelles form an interconnected network whose morphology, positioning and interactions reflect cellular state. However, reproducibly quantifying these organelle phenotypes across large cell populations and diverse cell types remains a significant challenge. Here we present PRISM (Plasmid-based Reporter for Intracellular Spectral Microscopy), a PiggyBac-integrable construct encoding five unique fluorescent organelle reporters for spectral microscopy, with an accompanying modular analysis pipeline. PRISM stably labels the Golgi, peroxisomes, endoplasmic reticulum, mitochondria and lysosomes in multiple cell types while remaining compatible with additional molecular or functional probes. The workflow extracts over 500 metrics per cell, describing organelle morphology and distribution alongside pairwise and higher-order contacts. We use PRISM to characterise organelle responses to cytoskeletal perturbation, map PI(4)P redistribution during lysosomal damage, and reveal how Zika virus remodels the organelle landscape during infection. PRISM provides a reproducible approach for investigating organelle network remodelling across biological contexts

cell biology↗

Lineage-specific expansion of a potential novel class of resistance genes in Myrtaceae

Genes encoding intracellular nucleotide-binding site leucine-rich repeat (NBS-LRR) receptors represent the largest class of resistance (R) genes in plants, yet their evolutionary trajectory in trees remains poorly understood. Using high-quality long-read genome assemblies from eight Myrtaceae species, we identified 15,792 NBS-encoding genes with threefold variation in gene content across species. To investigate potential decoy domains for effector proteins of pathogens, we parsed the annotated NBS-encoding genes and determined 181 unique non-canonical domains. Notably, we observed frequent integration of Jacalin domains into TIR-NBS proteins. This novel gene family, named TNJ, is hypothesized to represent a new R gene class. Further exploration of TNJ sequence analysis shows up to seven Jacalin domains per protein and forming a monophyletic clade; however, AF3 modelling confirmed only six domains. Conserved residues in the TIR domain and functional motifs within the NB-ARC domain supports TNJs potential role in immune signalling. Most hypervariable sites and positively selected sites detected to be surface-exposed were clustered in the Jacalin region of TNJ, suggesting that surfaces of Jacalin domain may harbour residues determining pathogen recognition specificity. These findings support TNJ as a potentially new class of R genes in Myrtaceae with Jacalin as a replacement for LRR.

evolutionary biology↗

Single cell RNA sequencing of D. pseudoobscura testes reveals transcriptional signatures of heteromorphic spermatogenesis

Sperm heteromorphy, the production of multiple sperm morphs with distinct functions, has evolved repeatedly in animals but its developmental and molecular basis remains poorly understood. In the Drosophila obscura group, males produce fertilising eusperm and non-fertilising parasperm, yet when and how these lineages diverge is unclear. Here, we applied single-cell RNA sequencing to whole testes of D. pseudoobscura to resolve cell-type composition, developmental trajectories, and transcriptional differences between sperm morphs. Analysis of [~]6,500 cells across two replicates identified germline and somatic cell populations and reconstructed spermatogenesis from stem cells to elongated spermatids. We identified a bifurcation in the germline trajectory at the early spermatocyte stage, corresponding to eusperm and parasperm lineages, which was maintained through spermiogenesis. Euspermatocytes, destined to generate longer eusperm, exhibited higher transcriptional activity than paraspermatocytes. Differentially expressed genes included structural sperm tail components, chromatin condensation proteins, post-meiotically transcribed genes and gene duplications resulting in paralogues with reciprocal expression patterns. We also identified markers of somatic cyst cells, including head and tail cyst cells, but found no evidence of morph-specific specialisation within the cyst cell lineage. The transcriptional activities of the distinct germline trajectories corresponded with differential expression of orthologues of critical transcriptional regulators known in D. melanogaster. The transcriptional activator TGIF was enriched in euspermatocytes, while the transcriptional repressor kmg was upregulated in paraspermatocytes. GFP-tagged Kmg showed higher abundance and greater chromatin localisation in paraspermatocytes. These findings demonstrate that sperm morph identity is first apparent in early primary spermatocytes and is largely germline intrinsic. We propose that differential transcriptional provisioning and developmental timing underpin sperm length, providing a framework for understanding the evolution and regulation of sperm heteromorphy.

developmental biology↗

Zinc coordination by the wheat rust effector AvrSr33 provides a structural scaffold required for immune recognition

Abstract/SummaryInteractions between plants and pathogens drive long-term co-evolution through cycles of effector diversification and immune recognition. Effectors play central roles in this molecular interplay, and zinc-binding folds have been identified in a subset of pathogen effectors, yet the contribution of zinc coordination to effector stability and immune recognition remains unclear. Here, we investigated the structure and recognition of the AvrSr33 effector from the wheat stem rust fungus (Puccinia graminis f. sp. tritici, Pgt). Structural and biochemical analyses show that AvrSr33 adopts a fold containing two zinc-binding sites. Transient expression assays in Nicotiana benthamiana show that AvrSr33 directly interacts with Sr33, and comparison of recognised and non-recognised AvrSr33 variants identifies a polymorphic loop associated with recognition. This loop is positioned adjacent to one of the zinc-binding sites with its orientation constrained by zinc coordination. Reciprocal mutations of key surface residues within this region alter recognition, whereas mutation of the zinc-binding site abolishes recognition. Our data suggest that zinc coordination in AvrSr33 provides a structurally constrained scaffold that supports the surface features associated with Sr33 recognition. These findings provide a mechanistic framework for understanding how zinc coordination contributes to effector recognition and may influence the evolutionary trajectories of pathogen effectors.

Plant Biology↗

Aging promotes inflammation and steatosis in alcohol-associated liver disease in mice

Background and AimsAs the older population (aged 65 years and older) continues to expand and more people drink alcohol, aging has been linked to the development of alcohol-associated liver disease (ALD) and to worse disease outcomes. The aim of this study was to explore the mechanisms by which advanced age and alcohol exacerbate alcohol-induced liver injury. MethodsTwo-to-three-month-old and twenty-to-twenty-two-month-old male C57BL/6N mice were subjected to chronic-on-binge alcohol feeding (the Gao-binge model). Serum alanine aminotransferase, aspartate aminotransferase, and triglyceride content were determined using biochemical assays. The levels of lipogenesis, fatty acid-metabolizing proteins, inflammatory markers, mitochondrial and autophagy-related proteins, and senescence-associated proteins were determined by immunoblotting, immunohistochemistry, and real-time quantitative polymerase chain reaction (RT-qPCR). Liver tissues were also subjected to RNA sequencing and metabolomics analyses. Proteomics analysis was performed on serum samples. Tail-vein adenovirus-TFEB was injected to overexpress hepatic TFEB in 22-month-old C57BL/6N male mice, followed by Gao-binge alcohol feeding. ResultsHepatic triglyceride content was significantly increased in aged, alcohol-fed mice, whereas serum ALT and AST levels remained relatively similar between alcohol-fed young and aged mice. Gao-binge alcohol increased the hepatic levels of diacylglycerol and acyl-carnitine species in both aged and young livers. RNA sequencing, proteomic analysis, and serum cytokine array analysis showed that inflammatory cytokines, including Ccr2, Cxcl1, and CCL6, and pro-inflammatory antibody fragments were increased in aged, alcohol-fed mice. Increased gene and protein expression of the senescent markers p21 and p27, along with increased senescent-associated (SA) {beta}-galactosidase activity in ethanol-fed aged mice compared to young mice. Gene and protein expression of TFEB was downregulated in ethanol-fed young and aged animals, along with decreased levels of lysosomal ATPases and hepatic dipeptide content. Overexpression of TFEB in the livers of aged, Gao-binge-fed mice was associated with reduced Ly6G-positive cells, reduced protein levels of the innate immune mediators cGAS, IRF-7, IRF3, and NLRP3, and reduced caspase-1 activity as well as serum ALT levels. ConclusionsOur findings indicate that advanced age perpetuates the detrimental effects of excessive alcohol consumption on various homeostatic processes and promotes steatosis and inflammation in the liver. Modulations in hepatic TFEB could be effective in mitigating pro-inflammatory signaling that occurs due to the synergistic effect of both heavy alcohol consumption and advanced age.

Molecular Biology↗

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

Single cell transcriptomics has transformed our knowledge of reproductive tissues, yet studies remain largely organ-specific and temporally limited, leaving an incomplete picture of how cell types are distributed across the reproductive system over a lifetime. Gynaecological conditions affect more than one in four females and frequently span multiple organs and life stages. To advance our understanding and treatment of these conditions, an integrated cellular reference is essential. Here we present the Human Female Reproductive System Cell Atlas v1: a single-cell transcriptomic resource integrating more than 2M cells across the ovary, fallopian tube, uterus, cervix and vagina over the lifespan and menstrual cycle, further integrated with spatial transcriptomics and chromatin accessibility profiling to define 210 cell types through community-based annotation. Cross-organ integration resolves shared and organ-specific cellular states, identifying uterine-specific perivascular populations lining uterine spiral arteries, hypoxia-sensing type 3 innate lymphoid cells (ILC3s) enriched in the uterus, and lipid-associated macrophages with distinct subsets in each reproductive organ, including a previously undescribed population shared between the uterus and fallopian tube. Cross-organ integration enables detection of ectopic epithelial populations in otherwise healthy donors, including endometrial-like cells within a paediatric ovary consistent with early endometriosis. Integration with genome-wide association studies (GWAS) reveals that risk variants for major gynecological conditions act in mesenchymal cell states defined by specific transcriptional programmes and spatial or temporal context - for instance, heavy menstrual bleeding risk is enriched in basal fibroblasts (SFRP5) of the regenerative endometrial compartment. An integrated chromatin accessibility atlas provides peak-to-gene maps across reproductive cell types, enabling nomination of disease effector genes and providing the first regulatory evidence linking a Polyendocrine Metabolic Ovarian Syndrome (PMOS) risk locus to INHBB in granulosa cells. Together, this resource establishes a cellular and molecular framework for reproductive biology and the pathogenesis of neglected gynaecological conditions.

Cell Biology↗

Two Novel Genes, Stb23 and Stb24, Conferring Multi-stage Resistance to Zymoseptoria tritici: Rapid Deployment in Marker-Assisted Wheat Breeding

The fungal pathogen Zymoseptoria tritici poses a major global threat to wheat production, causing severe yield losses and necessitating intensive and costly fungicide applications. The increasing demand for durable genetic resistance has intensified interest in quantitative resistance loci, particularly those exhibiting multi-stage resistance (MSR), which suppress pathogen development continuously throughout the wheat life cycle. Many previously effective resistance genes are now showing declining efficacy, underscoring the urgent need for novel and long-lasting sources of resistance. In this study, we report the identification and genetic mapping of two quantitative resistance loci that address this need. The first locus, designated Stb23, is a major QTL on chromosome 1DS, with LOD scores exceeding 9 and explaining 6-36% of phenotypic variation at the seedling stage and 2-16% at the adult-plant stage. The second locus, designated Stb24, is a major QTL on chromosome 3DL, with LOD scores of approximately 10 and accounting for 11-30% of seedling-stage variation and 9-23% of adult-plant variation. Furthermore, two tightly linked KASP markers-snp_1D1217527 for Stb23 and snp_3D1077880 for Stb24-were developed and validated across three popular Australian bread wheat cultivars, providing practical tools for deploying these loci in breeding programs targeting improved resistance to Z. tritici. Key messageTwo significant major-effect resistance loci on chromosomes 1DS (proposed as Stb23) and 3DL (proposed as Stb24) were identified and characterized. Two tightly linked KASP markers with these loci were also discovered and validated for molecular-assisted breeding programs.

genetics↗

An Endocytic Checkpoint Controls Macrophage PD-1 Function and Immunotherapy Fate

Responses to PD1 blockade span durable tumor control to hyperprogressive disease (HPD), yet innate immune mechanisms governing these extremes remain undefined. Here we integrate a macrophage systems atlas (>12,500 transcriptomes) with single-cell profiles from >1,000 anti-PD1 treated patients, to identify CCDC88A (GIV) as a macrophage-intrinsic determinant of durable response versus HPD. GIV loss increases PD1 surface retention, suppresses phagocytosis, and accelerates tumor growth across murine models, human macrophages, and patient-derived organoids. Myeloid-specific GIV deletion converts PD1 blockade from tumor-restraining to tumor-accelerating by reprogramming macrophages toward HPD-like states. Mechanistically, GIV engages a conserved TIR-like [TILL] motif within the PD1 cytoplasmic tail to drive dynamin-dependent endocytosis, coupling innate immune signaling logic to checkpoint receptor trafficking. Pharmacologic disruption of this axis phenocopies GIV loss, revealing an endocytic vulnerability that undermines checkpoint efficacy and triggers accelerated growth at relapse. These findings define PD1 routing, rather than ligand-binding, as a macrophage-encoded checkpoint governing antitumor immunity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/718292v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@a8f83aorg.highwire.dtl.DTLVardef@140dc7dorg.highwire.dtl.DTLVardef@14bc366org.highwire.dtl.DTLVardef@1096b8a_HPS_FORMAT_FIGEXP M_FIG GRAPHIC ABSTRACT C_FIG In briefMullick et al. show that PD1 trafficking in tumor associated macrophages (TAMs), controlled by the endocytic adaptor GIV/Girdin, determines the durability of immunotherapy. Disrupting this pathway traps PD1 at the surface, converts checkpoint blockade into hyperprogressive disease, and abolishes therapeutic benefit, revealing PD1 routing as a macrophage-encoded checkpoint of immunotherapy outcome. HighlightsO_LIGIV defines macrophage states that stratify durable response vs hyperprogressive disease C_LIO_LIGIV limits surface checkpoint accumulation by facilitating PD1 endocytosis C_LIO_LILoss of GIV traps PD1 at the membrane and drives hyperprogressive disease C_LIO_LIEndocytic blockade phenocopies GIV loss and abolishes checkpoint efficacy C_LIO_LIPsychotropic drugs disrupt PD1 trafficking and accelerate tumor growth C_LI

cancer biology↗

A NOD2-Encoded Toggle Switch Resolves the Host-Microbe Battle Over Cyclic AMP Control

Pathogens hijack macrophages by triggering pathological cAMP surges that block phagolysosomal killing--a defect mirrored in phagocytes from refractory colitis. We identify a host-encoded, pathogen-specific surge-protector comprised of a three-protein toggle: The innate sensor NOD2 binds and masks an evolutionarily conserved motif in GIV that activates trimeric-GTPase Gi, enforcing a biphasic surge-to-plunge cAMP-program: early, NOD2*GIV assembly permits a brief, tolerogenic cAMP rise, whereas subsequent GIV*Gi engagement collapses cAMP to drive phagolysosomal fusion and microbial clearance. Structural, biochemical, and ultrastructural analyses reveal how molecular toggling imposes precise spatial and temporal control. Pharmacogenomic perturbations pinpoint cAMP-PKA hyperactivation as the defining lesion in GIV-deficient macrophages. Functional studies in primary macrophages and human gut organoid co-cultures show that toggling the NOD2*GIV*Gi-axis is necessary and sufficient to convert tolerant macrophages into microbicidal machines that preserve mucosal barrier integrity. These findings uncover a druggable cAMP-control pathway with therapeutic promise in colitis. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/715116v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@53cd40org.highwire.dtl.DTLVardef@1c83c82org.highwire.dtl.DTLVardef@fcbc58org.highwire.dtl.DTLVardef@b14f8e_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC BlurbPathogens hijack macrophages by inducing cAMP surges that help them evade clearance. Anandachar et al. identify a host "toggle switch" in which NOD2 and G proteins compete for GIV, driving a rapid and robust surge-to-plunge transition in cAMP. This temporal switch limits tolerogenic signaling, restores microbial clearance and barrier integrity, and unveils a targetable host pathway in infection and IBD. HighlightsO_LIPathogens exploit cAMP surges in macrophages to block phagolysosomal killing of microbes C_LIO_LIGIV acts as a molecular "toggle" linking NOD2 sensing to Gi-mediated cAMP control C_LIO_LIStructural and mutagenesis studies reveal mutually exclusive binding of NOD2 and Gi to GIV C_LIO_LIPharmacogenomic perturbations pinpoint PKA, not EPAC, as the critical downstream effector C_LIO_LIOrganoid co-cultures show NOD2-GIV-PKA crosstalk safeguards microbial clearance and gut barrier integrity C_LI

immunology↗

Persistent neuroimmune alterations in children who are HIV-exposed but uninfected at age 6-7 years: Associations with language development in a South African birth cohort

BackgroundChildren who are HIV-exposed but uninfected (HEU) are at increased risk of neurodevelopmental delays, yet neuroimmune pathways linking perinatal HIV exposure to school readiness remain unclear. MethodsIn the Drakenstein Child Health Study, 268 children (94 HEU, 174 HIV-unexposed [HU]) underwent magnetic resonance spectroscopy in midline parietal grey and left parietal white matter regions at 6-7 years. Peripheral blood serum immune markers were measured in pregnancy and in children at 6 weeks, 2, 3, and 5 years. Linear mixed-effects models characterised child immune trajectories and linear regressions tested associations with creatine-referenced neurometabolite ratios and school readiness scores. ResultsMothers living with HIV had higher sCD14 and lower MMP-9, NGAL, and GM-CSF than mothers without HIV (p<0.05). Perinatal HIV exposure was associated with altered trajectories of child sCD14, GM-CSF, IL-1{beta}, IL-5, IL-10, and YKL-40. At 6-7 years, children who were HEU had lower parietal grey matter glutamate ratios and lower left parietal white matter choline ratios. By school entry, immune-neurometabolite associations were predominantly driven by child serum markers; IL-8 emerged as a consistent correlate across developmental stages. Children who were HEU had lower language scores than HU peers. Left parietal white matter choline ratios were positively associated with language and overall school readiness in HU children, but not HEU. ConclusionsPerinatal HIV exposure was associated with alterations in immune development, neurometabolites reflecting both white matter maturation and neuronal health, and school readiness. Our findings highlight potential neuroimmune pathways contributing to neurodevelopmental risks in children who are HEU.

neuroscience↗

Acid sphingomyelinase inhibition restores RPE homeostasis and photoreceptor function in preclinical Stargardt macular degeneration models

Stargardt disease, which destroys central high-resolution vision in over 2 million people globally, lacks effective therapies. The primary site of damage in Stargardt disease is the retinal pigment epithelium (RPE), which safeguards photoreceptor health and function. Progressive loss of RPE integrity precedes visual deficits, yet insight into mechanisms driving RPE dysfunction and how this influences disease pathogenesis remains elusive. Here, we addressed this in cell-based and pigmented Abca4-/- Stargardt mice models using super-resolution imaging, bioinformatics, and biochemical approaches. We show that ceramide accumulation induced by bisretinoid-mediated overactivation of acid sphingomyelinase (ASM) in Abca4-/- RPE selectively disrupts Rab GTPases and ESCRT machinery involved in apical membrane trafficking and small extracellular vesicle (EV) biogenesis. Consequently, connexin 43 (Cx43) is misrouted from cell-cell junctions into EVs that are released apically by the RPE. This compromises RPE integrity and promotes subretinal immune cell recruitment, leading to photoreceptor dysfunction. Pharmacological ASM inhibition normalizes EV biogenesis and restores Cx43 localization. Decreasing RPE ceramide safeguards RPE structural integrity, limits subretinal microglia, and improves visual function in Abca4-/- mice. This study underscores the importance of the RPE as a communication hub in the retina and identifies ASM as a potential therapeutic target to prevent progressive vision loss.

neuroscience↗

Longitudinal magnetic resonance imaging and spectroscopy in a mouse model of cuprizone-induced demyelination

The cuprizone (CPZ) lesioned mouse is a widely used model of demyelination and remyelination, but most studies rely on histology at terminal timepoints, limiting understanding of disease dynamics. Here, we present a longitudinal multimodal magnetic resonance imaging and spectroscopy (MRI/MRS) study of CPZ-induced pathology, pooling control arms from three independent experiments (n = 40). Mice were imaged at baseline, then exposed to 0.2% cuprizone for 5 weeks and repeatedly imaged at days 24, 35, 49, 63 and 77 after the start of CPZ. Imaging included multiparametric mapping (MPM), diffusion tensor imaging (DTI), tensor-based morphometry (TBM), and single-voxel MRS in the corpus callosum. Histology (MBP, silver, GFAP, Iba1) was performed at selected timepoints for validation. An additional group of 18 CPZ-lesioned mice were imaged ex vivo using a different higher resolution MRI protocol and compared against 19 non-CPZ controls. MPM-derived MTsat{delta} and R1 reductions indicated robust demyelination in the corpus callosum and deep cerebellar nuclei by day 24, expanding to cortex and hippocampus by day 35. Partial recovery was observed by day 77 but changes persisted, consistent with histological evidence. TBM revealed dynamic volumetric alterations, including hippocampal and cerebellar expansion alongside cortical and subcortical shrinkage, persisting beyond CPZ cessation. DTI demonstrated early (days 24-35) decreases in FA and MD, followed by complex trajectories consistent with microstructural disruption and partial repair. MRS detected early increases in GABA, glutamine, taurine, and glutathione, with corresponding decreases in NAA, while inositol showed a biphasic decrease-increase profile, likely reflecting acute astrocytic dysfunction followed by gliosis - neuroinflammatory processes that were corroborated by immunohistochemistry. Together, these results demonstrate that multimodal MRI/MRS sensitively captures widespread, dynamic, and only partially reversible pathology in CPZ-treated mice. Longitudinal imaging provides a non-invasive, translational approach to characterising demyelination, gliosis, and remyelination, offering a powerful alternative to histology for preclinical studies and longitudinal therapeutic screening.

neuroscience↗

PTMOverlay: A Proteomic Tool to Visualize Post-Translational Modifications Across Evolution

Evolutionary conservation has been considered a hallmark of essential basic functions in cells. Therefore, the study of evolutionarily conserved post-translational modifications (PTMs) can provide insight into their role in protein function. In this context, mass spectrometry can identify and quantify thousands of PTM sites. However, a major bottleneck lies in analyzing the large amounts of data collected by the mass spectrometer. Here we address the need for a protein sequence alignment tool for multiple PTMs across several species. We developed a tool named PTMOverlay that takes peptide identification output files and overlays PTM sites onto multiple protein sequence alignments. Examining 31 bacteria isolates, we combined their protein sequences with select PTM types, including acetylation, phosphorylation, monomethylation, dimethylation, and trimethylation. The tool revealed a variety of conserved modification sites on the bacterial central carbon metabolism. Further structural analysis revealed possible interactions between methylated arginine and lysine residues with phosphothreonine/serine sites on the homodimer interface of enolase. Overall, this tool can parse large amounts of mass spectrometry data and allows for more informed and efficient selection of sites for future studies of protein function.

systems biology↗

DIVERGENT TRAJECTORIES FOR ANAEROBIC MITOCHONDRIAL EVOLUTION IN BREVIATE PROTISTS

Mitochondrion-related organelles (MROs) have evolved as adaptations to low oxygen conditions multiple times in the eukaryote tree of life. However, the evolutionary steps by which aerobic mitochondrial functions were replaced by anaerobic pathways are still poorly understood. The breviate Pygsuia biforma is particularly interesting because it is the only protist known to have replaced the canonical mitochondrial iron-sulfur cluster (ISC) system with a horizontally acquired SUF-like minimal system (SMS) protein. This functions within an MRO possessing a uniquely configured electron transport chain (ETC). To investigate the evolutionary path by which the P. biforma MRO evolved these features, we conducted a comparative transcriptomic study of eight diverse marine breviate species and predicted their MRO proteomes. We found three distinct patterns of iron-sulfur cluster biosynthesis machinery across the breviates where organisms would encode: the canonical ISC system alone, the ISC system and cytoplasmic SMS system, and a cytoplasmic and MRO-localized SMS system. Phylogenetic analyses suggests that the SMS system was acquired via lateral gene transfer in an ancestor of all breviates and later duplicated, with one copy gaining mitochondrial targeting and replacing the ISC system in a subset of breviates. We observed similarly divergent evolutionary trajectories for quinone-utilizing proteins. Two species have completely lost the ETC while the remaining lineages retain a partial ETC and mitochondrial contact site and cristae organizing system (MICOS), previously thought to be absent in breviates. These patterns reflect divergent biochemical configurations of MROs shaped by gene transfer, loss, and duplication within a single eukaryotic lineage and underscores dynamic remodeling of organellar metabolism in response to marine hypoxic environments.

evolutionary biology↗

The Nematostella synaptonemal complex mediates divergent and sex-specific meiotic programs

Throughout eukaryotes, the synaptonemal complex (SC) is a supramolecular structure essential for meiotic chromosome dynamics and sexual reproduction. While metazoan SC proteins display significant sequence divergence, the lack of functional analyses beyond bilaterian models has obscured a mechanistic understanding of SC evolution. Here we report that the sea anemone Nematostella vectensis exhibits synapsis of homologous chromosomes in a classic zipper-like manner and expresses eight orthologs of ten known vertebrate SC proteins. Surprisingly, mutagenesis of the core SC components sycp1, syce2, and sycp3 resulted in divergent and sexually dimorphic phenotypes, indicating the functional diversification of these conserved factors. Combined, these findings challenge the assumption that the conservation of protein sequence or ultrastructure implies mechanistic homology.

evolutionary biology↗

An integrated synthetic biology and robotics approach for neutralising landmines in post-war communities

Unexploded ordnances (UX.Os) and landmines endanger lives and hinder the economic progress of communities living in post-conflict zones. Currently, the primary method for clearing UX.Os relies on metal detection and manual removal of UX.Os - an expensive, time-consuming, and hazardous process. This study, derived from the 2024 EPFL iGEM project SYNPLODE, presents a new approach that integrates synthetic biology and aerial drone robotics, proposing a novel, end-to-end, safe, and efficient solution to address UX.Os. Starting from bacteria engineered to detect and degrade 2,4,6-trinitrotoluene (TNT), a common explosive in landmines, our solution is designed for three main tasks: detecting TNT and RDX, breaking these compounds down into non-explosive byproducts, and confirming explosive neutralisation. To deploy this solution safely in UXO-contaminated areas, we designed, built, and tested an aerial drone capable of spraying explosive-degrading bacteria. Combining synthetic biology, robotics, mathematical modelling, and affected community engagement, our solution aims to improve UXO and landmine clearance by offering a scalable and cost-effective approach for deactivating UX.Os without risking human lives.

synthetic biology↗