Biology subjects

Young, R.

Publications and source records attributed to Young, R..

At least 19 recordsLinked to original sources

bioRxiv2026

An improved Trypanosoma vivax genome assembly confirms the distinct organisation of its variant antigen repertoire

Trypanosoma vivax is a unicellular parasite spread by biting flies and an important livestock pathogen across sub-Saharan Africa and South America. Alongside its better known relative, T. brucei, it causes animal trypanosomosis. An accurate genome sequence is essential to functional genetics as well as the design of novel diagnostics, drugs and vaccines. However, the existing T. vivax genome sequence is fragmentary, making it difficult to examine genomic features such as the Variant Surface Glycoprotein (VSG) genes that are the basis for antigenic variation, a key phenotype that underpins immune evasion by African trypanosomes. Our aim was to produce a T. vivax genome sequence with improved contiguity to properly characterise the VSG genes. We present a new core genome assembly in 23 scaffolds, forming approximately 10 chromosomes. Many scaffolds are articulated with extensive sub-telomeric domains that, like T. brucei, contain VSG gene arrays but in T. vivax these are near-perfect repeats of intact genes. Using transcriptomic and proteomic analysis of VSG expression during bloodstream infection we show that the active VSG is expressed from a sub-telomeric array while other arrays are silent. We find no evidence for a VSG expression site at the telomeres or elsewhere. Therefore, although monoallelic expression and antigenic switching occur in T. vivax, the familiar regulatory mechanism of T. brucei does not exist in T. vivax. This improved T. vivax genome assembly demonstrates that T. brucei is a poor guide for T. vivax genetics generally and for regulation of antigenic variation specifically.

genomics↗

bioRxiv2026

Long-term liana infestation leaves architectural legacies in host trees

Lianas are an integral component of tropical forests, and their increasing abundance may alter forest structure and function. Whether infested host trees are shorter and smaller-crowned because lianas suppress them, or because lianas preferentially colonise already small trees, has remained unresolved. We used a longitudinal dataset of individual liana infestation histories spanning fourteen years (2011-2025), combined with terrestrial laser scanning (TLS)-derived structural metrics for 251 trees across 67 species on Barro Colorado Island, Panama. Bayesian analyses showed that persistently infested trees were shorter (11.0%), with smaller crown projected area (22.3%) and crown volume (25.9%) than never-infested trees; the 95% credible intervals for these effects excluded zero. Pre-infestation crown architecture did not credibly predict subsequent colonisation. These patterns are more consistent with persistent infestation imposing lasting architectural legacies than with strong pre-existing architectural susceptibility, suggesting rising liana abundance may progressively reduce forest stature and canopy density, with implications for tropical carbon storage projections.

ecology↗

bioRxiv2026

Genetically interacting mutations and mechanical stress affect the stochasticity of developmental eye defects in yap1 mutants

Congenital abnormalities of eye formation show remarkably variable penetrance with phenotypes even varying between left and right eyes. Here we explore this phenomenon through analysis of the mechanistic basis of low penetrance retinal coloboma in zebrafish yap1nl13/nl13 mutants and identification of factors that modify the probability of this phenotype. We find that the low penetrance stochastically occurring coloboma in yap1nl13/nl13 mutants is due to rupture in the ventral retina at the point of apposition of the lips of the closing choroid fissure and that provision of wild-type Yap in the retinal pigment epithelium suppressed this phenotype. Decreasing actomyosin contractility increased the penetrance of coloboma whereas increasing myosin phosphorylation rescued the phenotype suggesting that altered mechanical properties of the RPE sensitize the eye to stochastic failure of choroid fissure closure. Genetic interaction screening revealed enhanced and synthetic eye phenotypes in yap1nl13/nl13mutants upon abrogation of function of genes encoding extracellular matrix and other genes implicated in eye formation. Our data reveal that the variable penetrance of congenital eye abnormalities can be due to genetic and environmental factors impacting the stochastic variability inherent in the developmental processes underlying eye morphogenesis.

developmental biology↗

bioRxiv2026

Lethal permeabilization of host bacteria to small-molecule compounds during phage penetration

The tailed phages (Caudoviricetes) rely on specialized mechanisms to inject their double-stranded linear genomic DNA (gDNA) across the bacterial envelope. During this gDNA entry process, ionic fluxes and membrane depolarization may occur, potentially leading to increased vulnerability to antibiotic molecules. Here, we report that phage gDNA translocation combined with certain small molecules triggers a rapid and phage-specific cell permeabilization leading to growth arrest. Using live-cell fluorescence microscopy, we visualized the accumulation of otherwise excluded compounds such as anthracyclines and propidium iodide. We show that the influx and accumulation of these compounds depend on both the presence of an inner membrane (IM) receptor and persistent membrane depolarization. We further demonstrate that phage-induced permeabilization enhances the efficacy of certain antibiotics, enabling a synergistic elimination of antibiotic-resistant bacteria. Our results provide a mechanistic foundation for combining phages with small-molecule therapeutics and offer new insights into how phage entry relies on and alters host physiology.

microbiology↗

bioRxiv2025

The Lysis Cassette of Jumbophage phiKZ

Pseudomonas jumbophage phiKZ is prominent because of the proteinaceous nuclear structure that is formed during the infection cycle, conferring resistance of the replicating phage DNA to anti-phage resistance systems. Progress has been made in deciphering the molecular basis of nucleus formation and other unique aspects of phiKZ biology, but the understanding of how it causes host lysis remains minimal. Here we present bioinformatic, physiological and molecular evidence for a "lysis cassette", the expression of which is necessary and sufficient for the temporally regulated disruption of the host envelope. This cluster contains genes for the usual components of an MGL (multigene lysis) system, including the holin, endolysin, i-spanin and o-spanin. In addition, a fifth gene in the cluster, encoding a cytoplasmic protein, was found to accelerate the timing of holin-mediated lethality when expressed in trans. Evidence is provided that suggests this lysis regulator protein interacts with the cytoplasmic domain of the phiKZ class III holin. In support of this notion, alpha-fold analysis generated a high-confidence structure of a conserved holin-lysis regulator heterodimer complex. Infections at high multiplicity resulted in slower bulk culture lysis profiles than at low multiplicity, suggesting that phiKZ might have a lysis-inhibition system.

microbiology↗

bioRxiv2025

Chimpanzee culture beyond the conspicuous: Evidence for broad-scale observational social learning in wild individuals

Wild chimpanzees possess diverse cultural repertoires, representing the richest example of non-human animal cultures. However, traditional methods, which investigate culture at the group level, have likely underestimated the full extent of chimpanzee cultural repertoires. In particular, the cultural relevance of everyday behaviors has remained largely unexplored. Here, we investigated evidence for social transmission of everyday behaviors to assess the breadth of individuals cultural repertoires in a population of wild eastern chimpanzees (Pan troglodytes schweinfurthii). First, we validated whether peering (i.e. close-range observation of a conspecific) serves as an indicator of social (i.e., cultural) learning. We then examined the contexts in which chimpanzees engage in peering to determine the range of behaviors that may be culturally transmitted. Finally, we explored potential motivations and additional functions of peering behavior. Our results indicate that chimpanzees use peering for targeted social information seeking in learning-intensive contexts. Peering rate was highest during immaturity, for complex or rare food items, and when observing older, more experienced conspecifics. Overall, wild chimpanzees peered at a wide range of everyday skills, such as feeding and grooming, and directed peering towards various conspecifics from an early age. We found no evidence supporting peering as a begging or submissive "gesture", but our findings indicate that it may function as a signal to initiate affinitive interactions. Our findings suggest that wild chimpanzees use peering to learn a broad variety of skills, thereby highlighting unrecognized cultural potential in everyday skills. Furthermore, our findings suggest that peering may have multiple functions and underlying motivations.

animal behavior and cognition↗

bioRxiv2025

Mesenchymal Stem Cell-Derived Extracellular Vesicles Mitigate Immune Cell Activation in an In Vitro Model of Post-Resuscitation Inflammation

BackgroundSystemic inflammation is a well-established component of post-cardiac arrest syndrome (PCAS), a condition responsible for significant morbidity and mortality in patients who are initially resuscitated from sudden cardiac arrest. Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have emerged as promising immunomodulatory agents in various inflammatory conditions, including after ischemia-reperfusion injury (IRI). Here, we investigated the therapeutic potential of MSC-EVs in porcine peripheral blood mononuclear cells (PBMCs) stimulated with lipopolysaccharide (LPS) or mitochondrial DNA (mtDNA) to mimic immune cell activation in PCAS. MethodsPBMCs were isolated from healthy pigs (Sus scrofa), cultured in vitro, stimulated with LPS or mtDNA, and treated with a range of MSC-EV concentrations. Flow cytometry, quantitative PCR, ELISA, and ROS/RNS measurements were performed to assess PBMC activation. ResultsMSC-EV treatment reduced LPS-induced inflammatory granulocyte activation and selectively modulated cytokine transcripts, including IFN, IL-1{beta}, and TNF-, in a concentration-dependent manner. Similar immunosuppressive effects were observed in mtDNA-stimulated PBMCs, where MSC-EVs attenuated dendritic cell activation and inflammatory cytokine release. Furthermore, higher concentrations of MSC-EVs significantly decreased ROS/RNS production in both LPS- and mtDNA-challenged PBMCs. ConclusionsMSC-EVs exhibit potent immunomodulatory properties against LPS- and mtDNA-induced activation of porcine PBMCs, highlighting their broad capacity to modulate immune responses and mitigate oxidative stress induced by pro-inflammatory stimuli that are relevant to PCAS. These findings provide further support for the administration of MSCs, or MSC-EVs themselves, as a potential therapeutic intervention to target immune activation in PCAS and other disorders characterized by an acute systemic inflammatory state.

immunology↗

bioRxiv2024

High-fidelity in vitro packaging of diverse synthetic cargo into encapsulin protein cages

Cargo-filled protein cages are powerful tools in biotechnology with demonstrated potential as catalytic nanoreactors and vehicles for targeted drug delivery. While endogenous biomolecules can be packaged into protein cages during their expression and self-assembly inside cells, synthetic cargo molecules are typically incompatible with live cells and must be packaged in vitro. Here we report a fusion-based in vitro assembly method for packaging diverse synthetic cargo into encapsulin protein cages that outperforms standard in cellulo assembly, producing cages with superior uniformity and thermal stability. Fluorescent dyes, proteins and cytotoxic drug molecules can all be selectively packaged with high efficiency via a peptide-mediated targeting process. The exceptional fidelity and broad compatibility of our in vitro assembly platform enables generalisable access to cargo-filled protein cages that host novel synthetic functionality for diverse biotechnological applications.

biochemistry↗

bioRxiv2024

ACSS2 regulates ferroptosis in an E2F1-dependent manner in breast cancer brain metastatic cells

Brain metastasis diagnosis in breast cancer patients is considered an end-stage event. The median survival after diagnosis is measured in months, thus there is an urgent need to develop novel treatment strategies. Breast cancers that metastasize to the brain must adapt to the unique brain environment and are highly dependent on acetate metabolism for growth and survival. However, the signaling pathways that regulate survival in breast cancer brain metastatic (BCBM) tumors are not known. Primary brain tumor cells can convert acetate to acetyl-CoA via phosphorylation of acetyl-CoA synthetase 2 (ACSS2) by the cyclin-dependent kinase-5 (CDK5) regulated by the nutrient sensor O-GlcNAc transferase (OGT). Here, we show that breast cancer cells selected to metastasize to the brain contain increased levels of O-GlcNAc, OGT and ACSS2-Ser267 phosphorylation compared to parental breast cancer cells. Moreover, OGT and CDK5 are required for breast cancer cell growth in the brain parenchyma in vivo. Importantly, ACSS2 and ACSS2-S267D phospho-mimetic mutant are critical for in vivo breast cancer growth in the brain but not in the mammary fat pad. Mechanistically, we show that ACSS2 regulates BCBM cell survival by suppressing ferroptosis via regulation of E2F1-mediated expression of anti-ferroptotic proteins SLC7A11 and GPX4. Lastly, we show treatment with a novel brain-permeable small molecule ACSS2 inhibitor induced ferroptosis and reduced BCBM growth ex vivo and in vivo. These results suggest a crucial role for ACSS2 in protecting from ferroptosis in breast cancer brain metastatic cells and suggests that breast cancer brain metastatic cells may be susceptible to ferroptotic inducers.

cancer biology↗

bioRxiv2024

The development of social attention in orangutans: comparing peering behaviour in wild and zoo-housed individuals

Social learning is the cornerstone of all cultural processes and plays a pivotal role during the evolution of cognition. To understand how social learning evolved, we have to look at the immediate and developmental conditions affecting individuals tendencies to attend to social information. We compared peering behaviour (i.e., close-range and sustained observation of the activities of conspecifics) in wild and zoo-housed immature Sumatran orangutans (Pongo abelii) by analysing long-term data which included 3101 peering events collected at the Suaq Balimbing research site in Indonesia and at four European zoos on 35 immature individuals. Using Generalized-Additive-Mixed-Models, we tested for age-specific patterns in peering frequency, target, and context selection. We found similar age trajectories of peering in both settings but higher mean frequencies of peering in the zoos, even after controlling for varying social opportunities to peer. Wild immatures preferably peered at their mothers but zoo-housed immatures at non-mother individuals. In both settings, immatures preferred to peer at older individuals, and in learning-intense contexts. Our findings suggest a hard-wired component in the tendency to attend to social information and a considerable degree of ontogenetic plasticity - a combination that was likely foundational for the evolution of complex cultures, including human culture. HighlightsO_LIWe compared attendance to social information in wild and zoo-housed orangutans C_LIO_LIImmature orangutans peer in contexts where learning is expected C_LIO_LIPeering frequency develops similarly over age, suggesting hardwired propensities C_LIO_LIPeering target and context selection differs between the two settings C_LIO_LIOrangutans tendency to attend to social information shows plasticity C_LI

animal behavior and cognition↗

bioRxiv2024

Chemical codes promote selective compartmentalization of proteins

Cells have evolved mechanisms to distribute [~]10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. A protein language model, ProtGPS, was developed that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in targeted subcellular compartments. ProtGPS also identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized code governing their distribution in specific cellular compartments.

biochemistry↗

bioRxiv2024

Integrated analysis and systematic characterization of the regulatory network for human germline development

Primordial germ cells (PGCs) are the precursors of germline that are specified at embryonic stage. Recent studies reveal that humans employ different mechanisms for PGC specification compared with model organisms such as mice. Moreover, the specific regulatory machinery is still largely unexplored, mainly due to the inaccessible nature of this complex biological process. Here, we collect and integrate multi-omics data, including 581 RNA-seq, 54 ATAC-seq, 45 ChIP-seq, and 69 single-cell RNA-seq samples from different stages of human PGC development to recapitulate the precisely controlled and stepwise process, presenting an atlas in the human PGC database (hPGCdb). With these uniformly processed data and integrated analyses, we characterize the potential key transcription factors and regulatory networks governing human germ cell fate. We validate the important roles of some of the key factors in germ cell development by CRISPRi knockdown. We also identify the soma-germline interaction network and discover the involvement of SDC2 and LAMA4 for PGC development, as well as soma-derived NOTCH2 signaling for germ cell differentiation. Taken together, we have built a database for human PGCs and demonstrate that hPGCdb enables the identification of the missing pieces of mechanisms governing germline development, including both intrinsic and extrinsic regulatory programs.

developmental biology↗

bioRxiv2023

Spatial control of the APC/C ensures the rapid degradation of Cyclin B1

The proper control of mitosis depends on the ubiquitin-mediated degradation of the right mitotic regulator at the right time. This is under the control of the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase that is regulated by the Spindle Assembly Checkpoint (SAC). The Checkpoint prevents the APC/C from recognizing Cyclin B1, the essential anaphase and cytokinesis inhibitor, until all chromosomes are attached to the spindle. Once chromosomes are attached, Cyclin B1 is rapidly degraded to enable chromosome segregation and cytokinesis. We have a good understanding of how the SAC inhibits the APC/C, but relatively little is known about how the APC/C recognises Cyclin B1 as soon as the SAC is turned off. Here, by combining live cell imaging, in vitro reconstitution, biochemistry, and structural analysis by cryo-electron microscopy, we provide evidence that the rapid recognition of Cyclin B1 in metaphase requires spatial regulation of the APC/C. Using fluorescence cross correlation spectroscopy, we find that Cyclin B1 and the APC/C primarily interact at the mitotic apparatus. We further show that this is because Cyclin B1, like the APC/C, binds to nucleosomes, and identify an arginine-anchor in the N-terminus as necessary and sufficient for binding to the nucleosome. Mutating the nucleosome binding motif on Cyclin B1 reduces its interaction with APC/C and delays its degradation, and cells with the mutant, non-nucleosome-binding Cyclin B1 become aneuploid, demonstrating the physiological relevance of our findings. Together, our data demonstrate that mitotic chromosomes constitute a platform to promote the efficient interaction between Cyclin B1 and APC/C and ensure the timely degradation of Cyclin B1 and genomic stability.

cell biology↗

bioRxiv2023

Spatial and temporal control of lysis by the lambda holin

The infection cycle of phage {lambda} terminates in lysis mediated by three types of lysis proteins, each disrupting a layer in the bacterial envelope: the S105 holin, the R endolysin, and the Rz/Rz1 spanin complex targeting the inner membrane (IM), cell wall or peptidoglycan (PG), and the outer membrane (OM), respectively. Video microscopy has shown that in most infections lysis occurs as a sudden, explosive event at a cell pole, such that the initial product is a less refractile ghost that retains rod-shaped morphology. Here, we investigate the molecular basis of polar lysis using time lapse fluorescence microscopy. The results indicate that the holin determines the morphology of lysis by suddenly forming two-dimensional rafts at the poles about 100 seconds prior to lysis. Given the physiological and biochemical similarities between the lambda holin and other class I holins, dynamic redistribution and sudden concentration may be common features of holins, probably reflecting the fitness advantage of all-or-nothing lysis regulation.

microbiology↗

bioRxiv2023

Functional analysis of Cdc20 reveals a critical role of CRY box in mitotic checkpoint signaling

Accurate chromosome segregation is coordinated by the spindle assembly checkpoint (SAC) through its effector the mitotic checkpoint complex (MCC), to inhibit the anaphase-promoting complex or cyclosome (APC/C). Cdc20 is an essential mitotic regulator since it promotes mitotic exit through activating the APC/C and monitors kinetochore-microtubule attachment through activating the SAC. The proper functioning of Cdc20 requires multiple interactions with APC/C and MCC subunits. To functionally assess each of these interactions within cells requires efficient depletion of endogenous Cdc20, which is highly difficult to achieve by RNAi. Here we generated Cdc20 RNAi sensitive cell lines by CRISPR/Cas9 which display a penetrant metaphase arrest phenotype by a single RNAi treatment. In this null background, we accurately measured the contribution of each known motif of Cdc20 on APC/C and SAC activation. The CRY box, a previously identified degron was found to be critical for the SAC by promoting the MCC formation and stabilizing the interaction between the MCC and APC/C. These data reveal additional regulatory components within the SAC and establish a novel method to interrogate Cdc20 function.

cell biology↗

bioRxiv2023

Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages {lambda} and P1

Phages are one of the key ecological drivers of microbial community dynamics, function and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor-intensive and are generally phage-specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of non-essential genes. As proof of concept, we use a catalytically inactive Cas12a mediated genome-wide CRISPRi assay to determine the essential genes in the canonical coliphages {lambda} and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification and tracking of phages in diverse applications.

microbiology↗

bioRxiv2023

Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State

Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like "mesenchymal" cell state and a more differentiated sympathetic "adrenergic" cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects a GATA motif in the first intron of LMO1. Here we show that wild-type zebrafish with the GATA genotype develop adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduces the penetrance of MYCN-driven tumors, which are restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrates that TATA/TATA tumors also exhibit a mesenchymal cell state and are low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduces the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that is conserved over 400 million years of evolution separating zebrafish and humans.

cancer biology↗

bioRxiv2022

Enhancer turnover in cancer and species evolution are associated with DNA replication timing

Enhancers are fast-evolving genomic sequences that control spatiotemporal gene expression patterns. By examining enhancer turnover across mammalian species and in multiple tissue types, we uncovered a relationship between the emergence of novel enhancers and genome organization as a function of germline DNA replication time. While enhancers are most abundant in euchromatic regions, new enhancers emerged almost twice as often in late compared to early germline replicating regions, independent of transposable elements. Using a sequence model, we demonstrate that new enhancers are enriched for mutations that alter transcription factor (TF) binding. Recently evolved enhancers appeared to be mostly neutrally evolving and enriched in eQTLs. They also show more tissue specificity than conserved enhancers, and the TFs that bind to these elements, as inferred by binding sequences, also show increased tissue-specific gene expression. We find a similar relationship with DNA replication time in cancer, suggesting that these observations may be time-invariant principles of genome evolution. Our work underscores that genome organization has a profound impact in shaping mammalian gene regulation.

genomics↗