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Biology subjects

Ward, J.

Publications and source records attributed to Ward, J..

At least 19 recordsLinked to original sources

Unexpected post-release behaviours of reintroduced kakapo

Translocations are commonly used to reduce the risk of extinction of threatened species, and often to reintroduce animals to their former habitats. If extirpation occurred a long time ago, individuals may be placed into novel environments outside of conditions they have previously experienced, which can affect translocation success. To measure success of translocations, particularly those to novel habitats, it is important to monitor post-release spatial behaviour. In 2023, ten critically endangered k[a]k[a]p[o] (Strigops habroptilus) were released to form a new population at the fenced mainland island of Sanctuary Mountain Maungatautari (hereafter Maungatautari) in the North Island of New Zealand, an area from which they were extirpated approximately a century earlier. The spatial behaviour and habitat selection of these k[a]k[a]p[o] was analysed using dynamic space use and step selection functions with temporally dynamic responses applied to GPS logger data recorded over a seven month period. These showed three unexpected results: k[a]k[a]p[o] were highly mobile and used larger areas compared to other sites; there was synchronicity of movement, with most individuals simultaneously moving toward the perimeter fence in spring; and when near the fence k[a]k[a]p[o] selected for areas of pasture and exotic vegetation more than anticipated. While direct comparisons are difficult due to varying data availability, this unexpected spatial behaviour and habitat selection suggests that k[a]k[a]p[o] behavioural responses were different at Maungatautari compared to other sites. This may indicate that k[a]k[a]p[o] released at Maungatautari had a longer exploratory stage than elsewhere; that there were behavioural effects influenced by conspecific density or the availability of novel and exotic vegetation; or that there were specific breeding habitat requirements not met at the site during the study period. These results highlight the importance of high-resolution spatial monitoring to evaluate the success of translocations, particularly those to novel environments.

animal behavior and cognition↗

Mathematical modelling of a novel bioactive glass treatment for bacterial biofilms

Chronic wounds (principally pressure sores, venous leg ulcers and diabetic foot ulcers) are a drain on global health services and remain a major area of unmet clinical need. Chronic wounds are characterised by a bacterial biofilm (densely aggregated colonies of bacteria encased by a matrix of extracellular polymeric substances), which hinders innate immune response and can prevent wound healing. Bioactive glass (BG) fibres doped with antimicrobial metal ions, such as silver, can offer a promising treatment for chronic wound infections, where silver is well known for its antimicrobial activity against a range of pathogens and is commonly used in wound dressings. We first present a system of non-linear partial differential equations to model the treatment of a chronic wound biofilm infection with BG fibres. The BG fibres are assumed to have two mechanisms of action against the biofilm: physical disruption of the top layers of the biofilm by the BG fibres; and release of antimicrobial silver ions from the BG fibres, which then diffuse into the biofilm and can kill the bacteria. Treatment-associated parameters are estimated from in vitro experimental data using a combination of least-squares minimisation and Approximate Bayesian Computation (ABC). Sensitivity investigations are performed on other parameters that cannot currently be calculated experimentally to investigate their influence on treatment efficacy. We thus predict key parameter regimes that should lead to biofilm eradication, crucially informing the future design of metal-doped BG fibres to maximise treatment efficacy.

microbiology↗

CD56dimCD16dim NK cells are the dominant effector cells against HIV-infected primary T-cells

Despite being rare among circulating natural killer (NK) cells and expressing 10-fold less CD16 than the predominant CD56dimCD16bright population, CD56dimCD16dim NK cells are expanded in HIV long-term elite controllers, yet their capacity to kill HIV-infected cells remained untested. Here, we show that these rare cells are the dominant effectors against HIV-infected T-cells, mediating approximately 4-fold higher direct cytotoxicity and 3-4-fold higher antibody-dependent cellular cytotoxicity (ADCC) than CD56dimCD16bright cells, and serially engaging multiple targets. This advantage is intrinsic, unexplained by cytotoxic granule content or inhibitory receptors recognizing MHC class I. Direct killing depends on NKG2D recognition of Vpr-induced ligands, with NKG2D elevated on CD56dimCD16dim cells; ADCC requires both NKG2D and ADAM17-mediated CD16 turnover for serial engagement. These findings explain the elite-controller reorganization, reveal that NK effector dominance is target-tuned rather than fixed (CD56dimCD16negative cells dominate against K562 cells), and identify high-NKG2D CD56dimCD16dim cells as the effector population HIV therapies should reproduce. Impact StatementA rare natural killer cell subset that makes up only a few percent of circulating NK cells, yet is enriched in the people who control HIV for years without medication, turns out to be the dominant killer of HIV-infected cells, far outperforming the common subset long assumed to do the job, and this work shows how these cells recognize and repeatedly attack infected targets, pointing to the specific effector that future cell-based therapies might use to help people with HIV stay healthy without lifelong drugs.

immunology↗

Human heart organoids reveal a regenerative strategy for mitochondrial disease

The human heart is among the most complex tissues to replicate in vitro, with vascular, neuronal, and immune elements shaping its development and function. Here we describe cardiomorphs, self-organising human cardiac organoids that recapitulate the cellular diversity, structural organisation, vascularisation, and innervation of the myocardium and mature along a developmental trajectory from early cardiogenesis to adult tissue. Using patient-derived cardiomorphs, we establish the first three-dimensional human tissue model of Kearns-Sayre syndrome (KSS), a rare mitochondrial disorder characterised by large-scale mtDNA deletions. KSS-cardiomorphs faithfully reproduce disease-associated metabolic, contractile, and ultrastructural hallmarks. Leveraging this platform, we identify Betaxolol, an FDA-approved selective {beta}1-adrenergic antagonist, as a modulator of mitochondrial quality control. Betaxolol increases intracellular oxygenation, selectively eliminates dysfunctional mitochondria via mitophagy, and promotes biogenesis of functional organelles, restoring contractility in KSS tissues. This dual-action, mutation-agnostic mechanism suggests a therapeutic principle with broad relevance to mitochondrial disease, cardiac pathology, and age-associated decline.

cell biology↗

Suppression of non-canonical autophagy induces endothelial and cardiac dysfunction

BackgroundWhile roles for canonical autophagy in the pathophysiology of cardiovascular disease have been established, we have limited understanding of the non-canonical functions of autophagy proteins in this context. LC3-asssociated endocytosis (LANDO) is a novel non-canonical function of autophagy proteins, in which LC3 (microtubule-associated protein light chain 3) is conjugated to early endosome membranes using a portion of the canonical autophagy machinery, and functions in the endocytic recycling of several plasma membrane proteins. Here we ask whether perturbation of LANDO can promote cardiovascular pathogenesis. MethodsCardiac and endothelial functions were assessed by echocardiography and flow-mediated dilatation in mice lacking Rubicon (Rubcn-/-) or the WD domain of ATG16L1 (Atg16l1{Delta}WDki), two known effectors of LANDO. Mice with conditional depletion of Rubicon in the endothelial, myeloid and cardiomyocyte compartments were used as well. Three-dimensional murine cardiac vasculature leakiness was investigated by light sheet fluorescence microcopy. Endothelial activation induced by shear stress was characterized in vitro in primary endothelial cells isolated from murine lungs and human aortic endothelial cells. Associations between genetically predicted expression of candidate genes involved in LANDO and human cardiovascular parameters were studied in the Young Finns Study and the UK Biobank. ResultsCompared to littermate controls, young Rubcn-/- and Atg16l1{Delta}WDki mice showed a decrease in cardiac and endothelial functions, as did mice with endothelium-specific deficiency. VEGFR2 recycling to the plasma membrane and nitric oxide pathway during shear stress were disrupted in LANDO-deficient primary murine and human endothelial cells. Proteomic analysis in primary human aortic endothelial cells revealed an upregulation of intracellular hemoglobin subunit alpha (Hb-) upon shear stress, which was blunted when RUBCN was ablated. Genetic expression studies uncovered several candidate genes related to LANDO that correlated with cardiovascular parameters. These included the retromer complex subunit VPS29, disruption of which decreased Hb- expression levels in human endothelial cells. ConclusionsOur data support a pivotal role of non-canonical functions of autophagy proteins in recycling VEGFR2 upon shear stress activation in endothelial cells together with Hb- expression that may contribute to the etiology of cardiovascular diseases.

physiology↗

CRISPRi Screen Identifies a Novel Growth Suppressor lncRNA, INSTAR, in Human Monocytes

Acute myeloid leukemia (AML) is a heterogeneous disease that arises from dysregulated myeloid proliferation. We performed a high-throughput CRISPR interference (CRISPRi) screen in the THP-1 monocytic cancer cell line to identify long noncoding RNAs (lncRNAs) that play a role in contributing to cell proliferation. Our screen identified INSTAR (Intergenic Nuclear Suppressor lncRNA Targeting Adjacent Regulator SFMBT2) as a top candidate. RNA-seq on INSTAR deficient THP-1 cells revealed transcriptional changes in genes involved in cell proliferation as well as other cellular processes. Loss of INSTAR selectively reduced expression of its neighboring gene, SFMBT2. Functional assays confirmed that both genes suppress cell growth, revealing a cis-regulatory mechanism in which INSTAR regulates SFMBT2 expression to control monocyte proliferation. Here, we leverage high-throughput screening to rapidly pinpoint functional lncRNAs providing novel insights into a key regulatory locus consisting of INSTAR and SFMBT2 which could be critical for better understanding dysregulation contributing to acute myeloid leukemia.

immunology↗

Global organisation of structural covariance networks derived from parcellated cortical surface area in atypical populations.

Higher-order features of brain organisation are powerful measures for understanding the relationship between brain and experience. In particular, the global arrangement of structural features of the cortex provides insight into neurodevelopmental processes that underlie individual differences in perception and cognition. Structural covariance networks (SCNs), which capture regional coordination of brain morphometry, are an efficient method to derive global properties of the cortex. However, their interpretation relies on an array of methodological choices that are often inconsistent between studies. Using a hierarchically-clustered version of the Human Connectome Project (HCP) atlas, we constructed SCNs of regional cortical surface area for groups with four different conditions - synaesthesia, autism, early psychosis, and anxiety or depression - and compared global network properties with those of age- and sex-matched controls. SCNs for synaesthesia and autism showed globally stronger connectivity, with specific increases at moderate cortical distances, as well as lower network complexity. Conversely, the SCN for early psychosis showed a globally lower connectivity and a greater complexity, while depression and anxiety showed few differences compared to controls. The results for autism and depression were replicated across two datasets each. These findings support the notion that synaesthesia and autism share neurodevelopmental mechanisms, while psychosis may involve a diverging process. This study is also an important proof of principle for analysing diverse populations under one methodological framework.

neuroscience↗

Design and development of a SARS and MERS Combination Vaccine

This work was conducted during the COVID-19 pandemic prior to the licensing of any vaccines against COVID-19. Although several COVID-19 vaccines are now commercially available, this research on the development of a combination Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV), SARS-coronavirus 2 (SARS-CoV-2), and Middle Eastern Respiratory Syndrome (MERS) is still relevant and shows how a combination vaccine can be designed, produced and rapidly tested in the laboratory. We present the development of a combination vaccine designed to provide immunity against Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV), SARS-coronavirus 2 (SARS-CoV-2), and Middle Eastern Respiratory Syndrome (MERS). The primary objective of this vaccine design is twofold: to mitigate the burden of coronavirus and to address the specific vulnerability of regions prone to recurrent MERS outbreaks. Our combination vaccine incorporates antigenic components from zoonotic sources, specifically SARS-CoV, SARS-CoV-2, and MERS. We assess the impact of combining different Spike proteins S1 subunit antigens, due to its recognised immunogenic potential, and adjuvants on serum antibody titres, virus neutralizing capabilities, and inter-antigen immune responses. We report a robust and broad antibody response against SARS-CoV-2 and related coronaviruses, which was amplified by different adjuvant formulations, including alum, MPLA, CpG, and Squalene-in-Water Emulsion.

immunology↗

Characterization of a Novel Transmembrane Activating STING Agonist using Genetically Humanized Mice

STING is a pattern recognition receptor that activates type I interferon and proinflammatory responses in addition to unrelated molecular processes following exposure of DNA to the cytosol. Its pharmacologic stimulation enhances vaccine potency and generates effective antitumor responses but clinical trials evaluating STING agonists have not led to approval for human use. STING activation can occur through ligand engagement of either cytosolic or transmembrane protein domains, processes to which distinct cellular phenotypes are attributed. However, the only transmembrane STING agonist identified is human selective and in vivo testing in conventional models is not feasible. Here we describe synthesis of novel STING agonists efficacious against allelic variants of the protein. We also describe genetically humanized STING mice and demonstrate their suitability as a model to evaluate in vivo responses following exogenous administration of human-selective agonists. Experiments demonstrate that the lead molecule (termed INI3069) functions through binding to the STING transmembrane region and its comparison with conventional agonists reveals significant differences in molecular and immune effects. INI3069 can also enhance antibody responses to co-administered antigens and antitumor responses. This work both represents the first in vivo examination of the effects of transmembrane STING agonism and demonstrates efficacy of a potential novel vaccine adjuvant and oncological therapeutic.

immunology↗

Sensory representations in primary visual cortex are not sufficient for subjective imagery

The contemporary definition of mental imagery is characterized by two aspects: a sensory representation resembling, but not resulting from, perception, and an associated subjective experience. Neuroimaging demonstrated imagery-related sensory representations in primary visual cortex (V1) that show striking parallels to perception. However, it remains unclear whether these representations always reflect subjective experience, or they can be dissociated from it. We addressed this question by comparing sensory representations and subjective imagery among visualizers and aphantasics, the latter with an impaired ability to experience imagery. Importantly, to test for the presence of sensory representations independently of the ability to generate imagery on demand we examined both spontaneous and voluntary imagery forms. Using multivariate fMRI, we tested for decodable sensory representations in V1 and subjective visual imagery reports that occurred either spontaneously (during passive listening of evocative sounds) or in response to the instruction to voluntarily generate imagery of the sound content (always while blindfolded inside the scanner). Among aphantasics, V1 decoding of sound content was at chance during voluntary imagery, and lower than in visualizers, but it succeeded during passive listening, despite them reporting no imagery. In contrast, in visualizers, decoding accuracy in V1 was greater in voluntary than spontaneous imagery (while being positively associated with the reported vividness of both imagery types). Finally, for both conditions, decoding in precuneus was successful in visualizers but at chance for aphantasics. Together, our findings show that V1 representations can be dissociated from subjective imagery, while implicating a key role of precuneus in the latter.

neuroscience↗

Unlocking cellular plasticity: Enhancing human iPSC reprogramming through bromodomain inhibition and extracellular matrix gene expression regulation

The transformation of fibroblasts into epithelial cells is critical for iPSC reprogramming. In this report, we describe studies with PFI-3, a small molecule inhibitor that specifically targets the bromodomains of SMARCA2/4 and PBRM1 subunit of SWI/SNF complex, as an enhancer of iPSC reprogramming efficiency. Our findings revealed that PFI-3 induces cellular plasticity in multiple human dermal fibroblasts, leading to a mesenchymal-epithelial transition (MET) during iPSC formation. This transition was characterized by the upregulation of E-cadherin expression, a key protein involved in epithelial cell adhesion. Additionally, we identified COL11A1 as a reprogramming barrier and demonstrated COL11A1 knockdown increased reprogramming efficiency. Notably, we found that PFI-3 significantly reduced the expression of numerous extracellular matrix (ECM) genes, particularly those involved in collagen assembly. Our research provides key insights into the early stages of iPSC reprogramming, highlighting the crucial role of ECM changes and cellular plasticity in this process.

cell biology↗

Breakthrough: A First-In-Class Virtual Simulator for Dose Optimization of ACE Inhibitors in Veterinary Cardiology

AO_SCPLOWBSTRACTC_SCPLOWThe human and canine renin-angiotensin-aldosterone-systems (RAAS) play a central role in the pathophysiology of congestive heart failure (CHF), justifying the use of angiotensin converting enzyme inhibitors inhibitors (ACEi) in this indication. Seminal studies in canine CHF had suggested that the pharmacological action of benazepril was relatively independent of doses > 0.25 mg/kg P.O, thereby providing a rationale for the European label dose of 0.25 mg/kg P.O q24h in dogs with cardiovascular diseases. However, most of these earlier studies on benazepril pharmacodynamics relied on measures of ACE activity - a sub-optimal endpoint to characterize the effect of benazepril on the RAAS. Nonlinear mixed-effects (NLME) modeling is an established framework for characterizing the effect of therapeutics on complex biological systems, such as the RAAS cascade. Importantly for therapeutic schedule optimization, one can use such a model to predict the outcomes of various hypothetical dosing schedules via simulation. The objectives of this study were (i) to expand on previous NLME modeling efforts of the dose-exposure-response relationship of benazepril on biomarkers of the RAAS which are relevant to CHF pathophysiology and disease prognosis {angiotensins I, II, III, IV, (1-7)} by using a quantitative systems pharmacology (QSP) modeling approach; and (ii) to develop a software implementation of the model capable of simulating clinical trials in benazepril in dogs bedside dose optimization. This study expands on previous modeling efforts to characterize the changes in RAAS pharmacodynamics in response to benazepril administration and showcase how QSP modeling can be used for efficient dose optimization of ACEis at the bedside. Our results suggest that 0.5 mg/kg PO q12h of benazepril produced the most robust reduction in AngII and upregulation of RAAS alternative pathway biomarkers. This model will eventually be expanded to include relevant clinical endpoints, which will be evaluated in an upcoming prospective trial in canine patients with CHF. AO_SCPLOWUTHORC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWCongestive heart failure (CHF) is a disease of the heart, common to both dogs and humans, where the heart is not healthy enough to pump blood around the body efficiently. Because the blood isnt moving around the body as efficiently, it tends to get congested in various areas of the body and increases strain on the heart. Benazepril is a drug for CHF used in both dogs and humans to reduce congestion and improve the functioning of the cardiovascular system. Although benazepril is effective, theres evidence that suggests the dosing could be improved if the therapeutic was further studied. In this experiment, we tested benazepril at several safe dosages in well-cared for and healthy dogs to collect data on the relationship between dose size, dosing frequency, and effect on the cardiovascular system. Using this data, we built computer models of benazepril to simulate many clinical trials. By studying these simulations, we were able to make several predictions about the optimal dosing schedule of benazepril in dogs. Weve also built a web-app version of the computer model for veterinary researchers to use, modify, and study. This work also provides a platform and roadmap for optimizing benazepril dosages in human CHF.

pharmacology and toxicology↗

A Genome-Wide Association Analysis of Happiness: Consistent Genetic Effects Across the Lifespan and Across Genetic Ancestries in Multiple Cohorts.

We present a genome-wide association study of a general happiness measure in 118,851 participants from the UK Biobank. Using BOLT-LMM, we identify 3 significant loci with a heritability estimate of 0.8%. Linkage disequilibrium score regression was performed on the big five personality traits finding significant associations with lower neuroticism and higher extraversion and conscientiousness. Using a novel approach, we construct LDpred-inf polygenic risk scores in the Adolescent Brain Cognitive Development (ABCD) cohort and the Add Health cohort. We detected nominally significant associations with several well-being measures in ABCD and significant correlations with a happiness measure in Add Health. Additionally, we tested for associations with several brain regions in a white British subsample of UK Biobank finding significant associations with several brain structure and integrity phenotypes. We demonstrated a genetic basis for general happiness level and brain structure that appears to remain consistent throughout the lifespan and across multiple ancestral backgrounds. Author summaryAt the genetic level, there has been little investigation into whether people may have a baseline happiness level which varies from person to person. Here we perform a genetic analysis in the UK Biobank to identify three genetic loci that associate with general happiness level and preform genetic correlations of our results with the Big Five personality traits, identifying significant correlations with neuroticism, conscientiousness and extraversion. We use the resulting summary statistics to create LDpred-inf polygenic risk scores in UK biobank identifying several brain metrics and regions associate with genetic loading for general happiness level. We also use a novel method to create LDpred-inf polygenic risk scores in two other cohorts, ABCD and Add Health. We found significant correlations with an independent happiness measure in Add Health and nominally significant correlations with several well-being measures in ABCD in both those of European Ancestry and all other ancestries found in these cohorts. We also attempted to replicate our UK Biobank MRi finding in ABCD. We conclude there is evidence that individuals have a general happiness level that is in part genetic which spans across age and ancestry.

genetics↗

Positive strand RNA viruses differ in the constraints they place on the folding of their negative strand

Genome replication of positive strand RNA viruses requires the production of a complementary negative strand RNA that serves as a template for synthesis of more positive strand progeny. Structural RNA elements are important for genome replication, but while they are readily observed in the positive strand, evidence of their existence in the negative strand is more limited. We hypothesised that this was due to viruses differing in their capacity to allow this latter RNA to adopt structural folds. To investigate this, ribozymes were introduced into the negative strand of different viral constructs; the expectation being that if RNA folding occurred, negative strand cleavage and suppression of replication would be seen. Indeed this was what happened with hepatitis C virus (HCV) and feline calicivirus (FCV) constructs. However, little or no impact was observed for chikungunya virus (CHIKV), human rhinovirus (HRV), hepatitis E virus (HEV) and yellow fever virus (YFV) constructs. Reduced cleavage in the negative strand proved to be due to duplex formation with the positive strand. Interestingly, ribozyme-containing RNAs also remained intact when produced in vitro by the HCV polymerase, again due to duplex formation. Overall, our results show that there are important differences in the conformational constraints imposed on the folding of the negative strand between different positive strand RNA viruses.

microbiology↗

A chemical biology toolbox to investigate in-cell target engagement and specificity of PRMT5-inhibitors

Increasing evidence suggests the protein arginine methyltransferase PRMT5 as a contributor to tumorigenesis in various cancer types and several inhibitors have entered clinical trials. Robust assays to determine cellular target engagement and selectivity are an important asset for the optimisation of inhibitors and the design of relevant in vivo studies. Here we report a suite of chemical biology assays enabling quantitative assessment of PRMT5 inhibitor in-cell target engagement and global selectivity profiling using a representative set of inhibitors. With the help of a bespoke cellular probe, we assess inhibitor target occupancy in cells in relation to biochemical and functional cellular assays. Investigating the influence of SAM, the natural cofactor of PRMT5, our results support the hypothesis that SAM positively contributes to the engagement of substrate-competitive inhibitors via a PRMT5:SAM:inhibitor ternary complex. Extensive proteomic profiling studies by drug affinity chromatography and thermal profiling further indicate high specificity of the clinical PRMT5 inhibitor GSK3326595 (pemrametostat). Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=65 SRC="FIGDIR/small/477145v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@11e448org.highwire.dtl.DTLVardef@a27194org.highwire.dtl.DTLVardef@cec270org.highwire.dtl.DTLVardef@3f76aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

Manipulating the microbiome alters regenerative outcomes in Xenopus laevis tadpoles vis lipopolysaccharide signalling

Xenopus laevis tadpoles can regenerate functional tails, containing spinal cord, notochord, muscle, fin, blood vessels and nerves, except for a brief refractory period at around one week of age. At this stage, amputation of the tadpoles tail may either result in scarless wound healing, or the activation of a regeneration programme, which replaces the lost tissues. We recently demonstrated a link between bacterial lipopolysaccharides and successful tail regeneration in refractory stage tadpoles, and proposed that this could result from lipopolysaccharides binding to Toll-like receptor 4 (TLR4). Here, we have used 16S rRNA sequencing to show that the tadpole skin microbiome is highly variable between sibships and that the community can be altered by raising embryos in the antibiotic gentamicin. Six gram-negative genera, including Delftia and Chryseobacterium, were over-represented in tadpoles that underwent tail regeneration. Lipopolysaccharides purified from a commensal Chryseobacterium spp. XDS4, an exogenous Delftia spp. or Escherichia coli could significantly increase the number of antibiotic-raised tadpoles that attempted regeneration. Conversely, the quality of regeneration was impaired in native-raised tadpoles exposed to the antagonistic lipopolysaccharide of Rhodobacter sphaeroides. Editing TLR4 using CRISPR/Cas9 also reduced regeneration quality, but not quantity, at the level of the cohort. However, we found that the editing level of individual tadpoles was a poor predictor of regenerative outcome. In conclusion, our results suggest that variable regeneration in refractory stage tadpoles depends at least in part on the skin microbiome and lipopolysaccharide signalling, but that signalling via TLR4 cannot account for all of this effect.

developmental biology↗

Light-induced asymmetries in the embryonic retina are mediated by the vascular system and extracellular matrix

Left-right asymmetries in the nervous system (lateralisation) influence a broad range of behaviours, from social responses to navigation and language. The role and pathways of endogenous and environmental mechanisms in the ontogeny of lateralisation remains to be established. The domestic chick is a model of both endogenous and experience-induced lateralisation driven by light exposure. Following the endogenous rightward rotation of the embryo, the asymmetrical position in the egg results in a greater exposure of the right eye to environmental light. To identify the genetic pathways activated by asymmetric light stimulation, and their time course, we exposed embryos to different light regimes: darkness, 6 hours of light and 24 hours of light. We used RNA-seq to compare gene expression in the right and left retinas and telencephalon. As expected, no differential expression between left and right was present in darkness. We detected differential gene expression in right vs left retina after 6 hours of light exposure. This difference disappeared before 24 hours of light exposure, suggesting that light-induced activation is a self-terminating phenomenon. This transient effect of light exposure was associated with a downregulation of the sensitive-period mediator gene DIO2 (iodothyronine deiodinase 2) in the right retina. No differences between genes expressed in the right vs. left telencephalon were detected. Gene networks associated with lateralisation were connected to vascularisation, cell motility, and the extracellular matrix. Interestingly, we know that the extracellular matrix- including the differentially expressed PDGFRB (platelet-derived growth factor receptor {beta}) gene - is involved in both sensitive periods and in the endogenous chiral mechanism of primary cilia, that drives lateralisation. Our data show a similarity between endogenous and experience-driven lateralisation, identifying functional gene networks that affect lateralisation in a specific time window.

neuroscience↗

A prebiotic basis for ATP as the universal energy currency

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires six phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP-equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleotide triphosphates, remains a mystery. Here we show that the deep conservation of ATP reflects its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate, which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that acetyl phosphate can phosphorylate ADP to ATP at nearly 20 % yield in water in the presence of Fe3+ ions. We then show that Fe3+ and acetyl phosphate are surprisingly favoured: a panel of other prebiotically relevant ions and minerals did not catalyze ADP phosphorylation; nor did a number of other potentially prebiotic phosphorylating agents. Only carbamoyl phosphate showed some modest phosphorylating activity. Critically, we show that acetyl phosphate does not phosphorylate other nucleotide diphosphates or free pyrophosphate in water. The phosphorylation of ADP monomers seems to be favoured by the interaction between the N6 amino group on the adenine ring with Fe3+ coupled to acetyl phosphate. Our findings suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.

biochemistry↗