Biology subjects

Stella, A.

Publications and source records attributed to Stella, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Dynamic membrane organization coordinates protein-O-mannosylation and proteostasis in mycobacteria.

Integral membrane enzymes operate within molecular environments, yet how these are organized remains poorly understood. Using M. smegmatis as a mycobacterial model, we define the membrane environment of the protein O-mannosyltransferase MtPMT through stratified interactomics combining affinity purification-mass spectrometry under four stringencies with a persistence score. This approach resolves a persistent membrane-associated core of 108 proteins from more transient layers, revealing a hierarchically organized landscape enriched in Sec protein translocation, protein biogenesis and envelope proteostasis machineries. Reciprocal affinity purification and in vivo FRET identify YajC and FtsH as neighbors of MtPMT, while structural modelling supports integration within a Sec-associated assembly. Genetic disruption of factors reduces O-mannosylation activity, demonstrating dependence on platform integrity. The MtPMT-associated network is remodelled during growth, indicating an adaptive system. Loss of POM compromises envelope permeability and stress resilience, linking O-mannosylation to fitness. Together, our results establish protein O-mannosylation as an integrated component of a dynamic membrane platform coordinating secretion, membrane protein biogenesis and proteostasis. Our findings support a model in which mycobacterial membranes contain specialized domains dynamically modulated by physiological state.

cell biology↗

bioRxiv2026

A Quality Measure for Repeating Multiple-Unit Spike Patterns

We propose a quality measure for spatio-temporal spike patterns (STPs) in multiple-neuron recordings. In such recordings, repeating STPs or pattern repetitions (PRs) are often found, with many of these generated by chance. To rule those out, statistical tests have been developed to discriminate the unlikely from the more likely PRs. This statistical problem is complicated by the fact that there are several obvious quality criteria for a PR, such as the size (the number of spikes) of the pattern and the number of its occurrences. Here, we propose a canonical way of combining several criteria (which we collect in the so-called signature of the pattern) into a single quality measure, based on the unlikeliness of the pattern. This measure is defined mathematically, and a formula for its computation is derived for stationary spike trains. It can be used to compare PRs. Since spike trains are not stationary in practice, we discuss, for two experimental data sets, how well the stationary formula correlates with the defined quality measure as determined from simulations. The results encourage the use of the stationary formula or also some simpler, related formulas as proxies for the quality, for the comparison of PRs and also for statistical tests that avoid the multiple testing problem incurred by using several quality criteria. Based on our results, we propose a few test statistics, i.e., random variables on the space of multi-unit spike trains with an appropriate null-hypothesis distribution, to evaluate STPs with less computational and sampling efforts.

neuroscience↗

bioRxiv2026

ST8SIA4-mediated polysialylation is critical for CCR2-driven monocyte egress from the bone marrow

Polysialylation is a rare post-translational protein modification essential for brain development and synaptic plasticity, where it fine-tunes cell-cell and cell-matrix interactions to direct neuronal migration, neurite outgrowth and synaptogenesis. Although polysialic acid is also expressed on circulating leukocytes, its functions in the immune system remain largely unexplored. Guided by analysis of publicly available human genomic data showing that naturally occurring variants of ST8SIA4, which encodes one of the two enzymes that mediate polysialylation, associate with reduced circulating monocyte counts, we investigated the in vivo role of this enzyme in monocyte biology. Using St8sia4-deficient mice, we show that ST8SIA4-dependent polysialylation is essential for CCR2-mediated egress of inflammatory monocytes from the bone marrow at steady state and during Mycobacterium tuberculosis infection. We confirm NCAM1 as the principal polysialylated protein in inflammatory monocytes and demonstrate that Ncam1-deficient mice phenocopy the monocyte defects observed in St8sia4-deficient animals. Mechanistically, loss of ST8SIA4-dependent polysialylation impairs engagement and internalization of the CCR2 ligands CCL2 and CCL7, accompanied by disrupted CCR2 surface organization and extensive cytoskeletal remodeling. Together, these findings identify polysialylation as a previously unrecognized regulator of CCR2 function and monocyte mobilization, with broad implications for immune surveillance and inflammatory responses. Highlights- Human ST8SIA4 variants are associated with reduced blood monocyte and lymphocyte counts and increased risk of SLE. - St8sia4-/- mice exhibit monocytopenia with impaired CCR2-mediated egress of inflammatory monocytes from the bone marrow both at steady state and during Mycobacterium tuberculosis infection. - ST8SIA4 polysialylates NCAM1 (CD56) in inflammatory monocytes, and Ncam1-/- - mice phenocopy the monocytopenia observed in St8sia4-/- mice. - Loss of ST8SIA4 and polysialylation impairs CCR2-mediated binding and endocytosis of CCL2 and CCL7 by monocytes. - Polysialic acid itself does not function as a co-receptor for these chemokines, revealing a new paradigm for its role in immune cell trafficking. - Proper CCR2 surface distribution and function, as well as cytoskeletal organization in inflammatory monocytes, depend on ST8SIA4-mediated polysialylation.

immunology↗

bioRxiv2025

Assembly and cell-free expression of a partial genome for the synthetic cell

The de novo design and assembly of a DNA genome represents an important milestone toward the construction of a minimal synthetic cell. The genome must contain all the instructions to enable primary cellular functions, probably comprising over 150 genes with a total size over 200 kb. Here, we designed and built a partial synthetic genome that satisfies the requirements for its expression in PURE system--a minimal transcription-translation machinery reconstituted from purified elements--and its replication by the protein-primed {varphi}29 DNA replication system. The partial minimal synthetic genome (MSG) has a size of 41 kb, was assembled in yeast from 14 fragments, and harbors genes for phospholipid biosynthesis, DNA replication, and cell division. Yeast marker fragments were added between coding fragments to facilitate screening of correct assemblies and a BAC backbone was included to enable transfer from yeast to E. coli for amplification. Synthesis of all MSG-encoded proteins in PURE system was confirmed by liquid chromatography-mass spectrometry and fluorescence measurements. Moreover, we demonstrate successful compartmentalization and expression of the MSG in liposomes, as well as full-length replication of the linearized MSG by the {varphi}29 DNA replication machinery. This work provides proof-of-concept for the bottom-up assembly and cell-free expression of a functional genome for a minimal synthetic cell.

synthetic biology↗

bioRxiv2025

Nucleoside Binding by a Surface Lipoprotein Governs Conjugative ICE Acquisition in Ruminant Mycoplasmas

Integrative and conjugative elements (ICEs) are major mediators of horizontal gene transfer (HGT) in bacteria. However, the role of recipient cells in their acquisition has received little attention. Using the ruminant pathogens Mycoplasma agalactiae and Mycoplasma bovis as minimal models, we combined genome-wide transposon mutagenesis with high-throughput mating assays to identify recipient factors required for ICE acquisition. The surface lipoprotein P48 emerged as the primary determinant of ICE uptake in both species. Structural and functional analyses revealed that P48 is the substrate-binding component of an ABC transporter with nucleoside-binding capacity. A single point mutation that abolished nucleoside binding drastically reduced ICE acquisition, demonstrating that P48-mediated nucleoside recognition is essential for conjugative transfer. However, ICE uptake did not require nucleoside transport, as inactivation of the transporter permease blocked nucleoside analog toxicity but not ICE invasion. Loss of P48 also triggered transcriptional activation of vestigial ICE genes, suggesting that surface recognition affects the intracellular state of the recipient. Remarkably, ICE transmission from recipient-derived donors was unaffected by P48 loss, underscoring its acquisition-specific role. Together, these results reveal a previously unrecognized, surface-exposed recipient factor critical for efficient ICE transfer in mycoplasmas and identify nucleotide binding as a central function in conjugation. By demonstrating that recipient-encoded functions can directly control ICE dissemination, this work challenges the donor-centric paradigm of bacterial conjugation and suggests new strategies to restrict horizontal gene flow in pathogenic and synthetic mycoplasmas. IMPORTANCEIntegrative and conjugative elements (ICEs) are mobile DNA elements that drive bacterial conjugation, a major process by which bacteria exchange genes. Although conjugation has been studied for decades, the focus has been almost exclusively on donor cells and the ICE itself, leaving the role of recipient cells largely overlooked. Using the wall-less ruminant pathogens Mycoplasma agalactiae and Mycoplasma bovis as minimal models, we discovered that a single recipient lipoprotein is required for efficient ICE uptake. Our data show that nucleoside recognition by P48, but not transport, is critical for conjugation, revealing an unexpected mechanistic link between nutrient sensing and gene acquisition. These findings shift the paradigm of conjugation from a donor-driven process to one jointly determined by donor and recipient functions. By identifying a recipient-encoded determinant of ICE transfer, this work opens new avenues to control horizontal gene flow in both pathogenic and engineered bacteria. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/677790v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f7cc15org.highwire.dtl.DTLVardef@77a34eorg.highwire.dtl.DTLVardef@82699corg.highwire.dtl.DTLVardef@1e3be93_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Inferring domestic goat demographic history through ancient genome imputation

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this we used published high coverage (>8x) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5x genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with [≥]0.5x coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes. SignificancePaleogenomics offers crucial insight into how animals were domesticated, but poor DNA preservation in ancient remains often limits the reach of genetic analyses. We utilise a cutting-edge technique, genotype imputation, to recover missing genetic information from ancient low coverage goat genomes and shine light on their domestication process. Early domestic goats showed low overall runs-of-homozygosity (ROH) and relatedness. We find that during the Neolithic, runs-of-homozygosity (ROH) and relatedness among goats increased, likely a consequence of the movement of herds beyond their natural range by humans. Inbreeding levels decline in more recent periods, potentially due to expanded herd sizes, animal trade networks, or improved husbandry practices. These findings challenge long-standing assumptions about domestication bottlenecks and highlight how ancient DNA can be used to uncover complex evolutionary histories, even from low coverage ancient samples.

genomics↗

bioRxiv2024

Pupillometry and Whole-Brain c-Fos Mapping Uncover Multimodal Mirror Mechanisms in Emotional Contagion Networks of Mice

Emotional contagion (ECo) represents a fundamental form of empathy. In this study, we used pupillometry to quantify ECo by assessing pupil responses of a mouse watching another mouse receive a tail shock. Pupil dilation effectively measured both direct and vicarious emotional response thresholds at the individual level through psychometric curve analysis. The pupillary ECo response diminished when the observer could not see the demonstrator, suggesting a multisensory process involving vision. Viewing videos of tail-shocked mice was sufficient to elicit a pupil response in the observer. Whole-brain c-Fos mapping revealed a broad network of 88 brain regions activated during ECo, with all areas activated in the demonstrator also engaged in the observer. Additionally, in certain brain regions, correlated activation was detected between each observer-demonstrator pair, indicating that ECo promotes a shared neural state. These findings advance our understanding of the neural basis of empathy, with implications for analyzing neuropsychiatric disorder models.

neuroscience↗

bioRxiv2024

SMARTER-database: a tool to explore genomic diversity in small ruminants

Underutilized sheep and goat breeds have the ability to adapt to challenging environments due to their genetic composition. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by important data discrepancies, such as outdated assembly versions or different data formats. Here we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata mainly from SNP chips arrays on global small ruminant populations with a focus on reproducibility. SMARTER-database harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access the genotype data via FTP and interact with the metadata through a web interface or programmatically using their custom scripts, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspects of adaptation and contribute to livestock sustainability, leveraging the rich dataset provided by the SMARTER-database. Availability & ImplementationThe code is available as open source software under the MIT license at https://github.com/cnr-ibba/SMARTER-database.

bioinformatics↗

bioRxiv2024

The human and mouse dendritic cell receptor DCIR binds to LRP1 N-glycans containing terminal galactoses, including the α-Gal antigen

The dendritic cell immunoreceptor (DCIR) is a C-type lectin receptor expressed by myeloid cells that plays a key immunoregulatory role in a wide range of diseases, from inflammation to cancer. However, the ligand(s) of DCIR remain(s) unknown, hampering our understanding of the exact function of this immune receptor. Here, we found that both human DCIR and mouse DCIR1 bind specifically to the low-density lipoprotein receptor-related protein 1 (LRP1), a heavily glycosylated receptor mediating the clearance of various molecules from the extracellular matrix and apoptotic cells. This interaction is mediated by galactose-terminated biantennary complex-type N-glycans, including those carrying the immunogenic -Gal epitope. Our study provides a deeper understanding of the role of DCIR in immune regulation and its potential impact on a range of immune disorders, highlighting its specificity in ligand recognition which is crucial for developing therapeutic strategies.

immunology↗

bioRxiv2024

Integrative in vivo analysis of the ethanolamine utilization bacterial microcompartment in Escherichia coli.

Bacterial microcompartments (BMCs) are self-assembling protein megacomplexes that encapsulate metabolic pathways. Although approximately 20% of sequenced bacterial genomes contain operons encoding putative BMCs, few have been thoroughly characterized, nor any in the most studied Escherichia coli strains. We used an interdisciplinary approach to gain deep molecular and functional insights into the ethanolamine utilization (Eut) BMC system encoded by the eut operon in E. coli K-12. The eut genotype was linked with the ethanolamine utilization phenotype using deletion and overexpression mutants. The subcellular dynamics and morphology of the E. coli Eut BMC were characterized in cellula by fluorescence microscopy and electron (cryo)microscopy. The minimal proteome reorganization required for ethanolamine utilization and the in vivo stochiometric composition of the Eut BMC were determined by quantitative proteomics. Finally, the first flux map connecting the Eut BMC with central metabolism in cellula was obtained by genome scale modelling and 13C-fluxomics. Our results reveal that, contrary to previous suggestions, ethanolamine serves both as a nitrogen and a carbon source in E. coli K-12, while also contributing significant metabolic overflow. Overall, this study provides a quantitative molecular and functional understanding of the BMCs involved in ethanolamine assimilation by E. coli. ImportanceThe properties of BMCs make them an ideal tool to build orthogonal network structures with minimal interactions with native metabolic and regulatory networks. However, this requires an understanding of how BMCs work natively. In this study, we combined genetic manipulation, multi-omics, modelling and microscopy to address this issue for Eut BMCs. We show that the Eut BMC in E. coli turns ethanolamine into usable carbon and nitrogen substrates to sustain growth. These results improve our understanding of compartmentalization in a widely used bacterial chassis.

microbiology↗

bioRxiv2023

The intrinsically disordered region of the E3 ubiquitin ligase TRIP12 induces the formation of chromatin condensates and interferes with DNA damage response.

Chromatin compaction is crucial for the faithful expression and integrity of the genome. Although largely studied, proteins and mechanisms that control the chromatin compaction are not entirely discovered. We previously showed that the nuclear HECT-type E3 ubiquitin ligase Thyroid hormone Receptor Interacting Protein 12 (TRIP12) is tightly associated to chromatin. As TRIP12 is overexpressed in several types of cancers, we explored herein the consequences of a TRIP12 overexpression on chromatin homeostasis. First, we established the TRIP12 proxisome and unveiled its pleiotropic role in chromatin regulation. Second, we demonstrated that TRIP12 overexpression leads to the formation of chromatin condensates enriched in heterochromatin marks via its intrinsically disordered region (IDR). We further discovered that the formation of TRIP12-mediated chromatin condensates is highly dynamic and driven by a mechanism of phase separation. Chromatin condensate formation depends on the TRIP12 concentration, the length of the TRIP12-IDR and relies on electrostatic interactions. We found that the formation of TRIP12 mediated-condensates alters cell cycle progression, genome accessibility, transcription as well as DNA damage response by inhibiting the accumulation of Mediator of DNA Damage Checkpoint 1 (MDC1). Altogether, this study reveals a novel dynamic role for TRIP12 in chromatin compaction independently of its ubiquitin ligase activity with important consequences on cellular homeostasis. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/556486v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@13b3d90org.highwire.dtl.DTLVardef@46b991org.highwire.dtl.DTLVardef@1410bdeorg.highwire.dtl.DTLVardef@1722197_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Model of multiple synfire chains explains cortical spatio-temporal spike patterns

It has been postulated that information processing in the brain is based on precise temporal correlation of neural activity across populations of neurons. In a recent study we found spatio-temporal spike patterns in experimental recordings from monkey motor cortex, and here we study if those could be explained by a synfire chain (SFC) like model. The model is composed of groups of neurons connected in feed-forward manner from one group to the next with high convergence and divergence. When activated, e.g., by a current pulse to the first group, spiking activity in the SFC is synchronous within neurons of the same group and propagates from group to group. When a few neurons from different groups are recorded from such an SFC, and the SFC is repeatedly activated, we would find a spatio-temporal spike pattern repeating across trials. Here, we take the statistics of the STPs found in the experimental data from 20 sessions as a reference to compare to a simulated network. Distributions of the data we take into account include 1) the pattern sizes, i.e. the number of neurons involved in the patterns, 2) the number of patterns a single neuron is involved in, 3) the durations of the patterns, and 4) the spatial distances of the patterns across the electrode array used to record the data. For the simulations, we embed SFC(s) in an anatomical model of the respective layer of the motor cortex, defined by its height and the density of the neurons. Model parameters are the length of the SFC, the number of neurons per group, the spatial extent of each neuronal group, and the distance between subsequent groups. Given the size and reach of the Utah array electrodes, we derive the probability of recording neurons from the SFC network. An SFC is considered detected if at least two neurons from two different groups are recorded. We find that depending on the model parameters, an embedded SFC can be detected with high probability, despite the massive subsampling of the cortex by the Utah array. Furthermore, to achieve multiple membership of a neuron in different patterns, we embed multiple SFCs that overlap. The fitting of the model to the pattern data constrains the spatial SFC parameters: the chains have to be broadly distributed in space and contain many neurons per group to match the experimental results.

neuroscience↗

bioRxiv2021

Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.

evolutionary biology↗

bioRxiv2021

Generating surrogates for significance estimation ofspatio-temporal spike patterns

The generation of surrogate data, i.e., the modification of original data to destroy a certain feature, is used for the implementation of a null-hypothesis whenever an analytical approach is not feasible. Thus, surrogate data generation has been extensively used to assess the significance of spike correlations in parallel spike trains. In this context, one of the main challenges is to properly construct the desired null-hypothesis distribution and to avoid a bias in the null-hypothesis by altering the spike train statistics. A classical surrogate technique is uniform dithering (UD), which displaces spikes locally and uniformly. In this study, we compare UD against five surrogate techniques (two newly introduced) in the context of the detection of significant spatio-temporal spike patterns. We evaluate the surrogates for their performance, first on spike trains based on point process models with constant firing rate, and second on modeled non-stationary artificial data serving as ground truth to assess the pattern detection in a more complex and realistic setting. We determine which statistical features of the original spike trains are modified and to which extent. Moreover, we find that UD fails as an appropriate surrogate because it leads to a loss of spikes in the context of binning and clipping, and thus to a large number of false-positive patterns. The other surrogates achieve a better performance in detecting precisely timed higher-order correlations. Based on these insights, we analyze experimental data from pre-/motor cortex of macaque monkeys during a reaching-and-grasping task for spatio-temporal spike patterns. Significance statementTemporal jittering or dithering of single spikes or subsections of spike trains is a common method of generating surrogate data for the statistical analysis of temporal spike correlations. We discovered a serious problem with the classical and widely used method of uniform dithering that can lead to an overestimation of significance, i.e., to false positives in the statistical evaluation of spatio-temporal spike patterns. Therefore we consider 5 other dithering methods, compare and evaluate their statistical properties. Finally, we apply a much better method (trial shifting) to the analysis of experimental multiple-unit recordings and find several highly significant patterns that also reflect different experimental situations.

neuroscience↗

bioRxiv2021

Neutralising antibodies against the SARS-CoV-2 Delta variant induced by Alhydroxyquim-II-adjuvanted trimeric spike antigens

Global control of COVID-19 will require the deployment of vaccines capable of inducing long-term protective immunity against SARS-CoV-2 variants. In this report, we describe an adjuvanted subunit candidate vaccine that affords elevated, sustained and cross-variant SARS-CoV-2 neutralising antibodies (NAbs) in multiple animal models. Alhydroxiquim-II is a TLR7/8 small-molecule agonist chemisorbed on aluminium hydroxide. Vaccination with Alhydroxiquim-II combined with a stabilized, trimeric form of the SARS-CoV-2 spike protein (termed CoVac-II) resulted in high-titre NAbs in mice, with no decay in responses over an 8-month period. NAbs from sera of CoVac-II-immunized mice, horses and rabbits were broadly neutralising against SARS-CoV-2 variants. Boosting long-term CoVac-II-immunized mice with adjuvanted spike protein from the Beta variant markedly increased levels of NAb titres against multiple SARS-CoV-2 variants; notably high titres against the Delta variant were observed. These data strongly support the clinical assessment of Alhydroxiquim-II-adjuvanted spike proteins to protect against SARS-CoV-2 variants of concern.

microbiology↗

bioRxiv2021

Immunisation of ferrets and mice with recombinant SARS-CoV-2 spike protein formulated with Advax-SM adjuvant protects against COVID-19 infection

The development of a safe and effective vaccine is a key requirement to overcoming the COVID-19 pandemic. Recombinant proteins represent the most reliable and safe vaccine approach but generally require a suitable adjuvant for robust and durable immunity. We used the SARS-CoV-2 genomic sequence and in silico structural modelling to design a recombinant spike protein vaccine (Covax-19). A synthetic gene encoding the spike extracellular domain (ECD) was inserted into a baculovirus backbone to express the protein in insect cell cultures. The spike ECD was formulated with Advax-SM adjuvant and first tested for immunogenicity in C57BL/6 and BALB/c mice. The Advax-SM adjuvanted vaccine induced high titers of binding antibody against spike protein that were able to neutralise the original wildtype virus on which the vaccine was based as well as the variant B.1.1.7 lineage virus. The Covax-19 vaccine also induced potent spike-specific CD4+ and CD8+ memory T-cells with a dominant Th1 phenotype, and this was shown to be associated with cytotoxic T lymphocyte killing of spike labelled target cells in vivo. Ferrets immunised with Covax-19 vaccine intramuscularly twice 2 weeks apart made spike receptor binding domain (RBD) IgG and were protected against an intranasal challenge with SARS-CoV-2 virus 2 weeks after the second immunisation. Notably, ferrets that received two 25 or 50g doses of Covax-19 vaccine had no detectable virus in their lungs or in nasal washes at day 3 post-challenge, suggesting the possibility that Covax-19 vaccine may in addition to protection against lung infection also have the potential to block virus transmission. This data supports advancement of Covax-19 vaccine into human clinical trials.

immunology↗

bioRxiv2020

A single dose, BCG-adjuvanted SARS-CoV-2 vaccine induces Th1-polarized immunity and high-titre neutralizing antibodies in mice

Global control of COVID-19 requires broadly accessible vaccines that are effective against SARS-CoV-2 variants. In this report, we exploit the immunostimulatory properties of bacille Calmette-Guerin (BCG), the existing tuberculosis vaccine, to deliver a vaccination regimen with potent SARS-CoV-2-specific protective immunity. Combination of BCG with a stabilized, trimeric form of SARS-CoV-2 spike antigen promoted rapid development of virus-specific IgG antibodies in the blood of vaccinated mice, that was further augmented by the addition of alum. This vaccine formulation, BCG:CoVac, induced high-titre SARS-CoV-2 neutralizing antibodies (NAbs) and Th1-biased cytokine release by vaccine-specific T cells, which correlated with the early emergence of T follicular helper cells in local lymph nodes and heightened levels of antigen-specific plasma B cells after vaccination. Vaccination of K18-hACE2 mice with a single dose of BCG:CoVac almost completely abrogated disease after SARS-CoV-2 challenge, with minimal inflammation and no detectable virus in the lungs of infected animals. Boosting BCG:CoVac-primed mice with a heterologous vaccine further increased SARS-CoV-2-specific antibody responses, which effectively neutralized B.1.1.7 and B.1.351 SARS-CoV-2 variants of concern. These findings demonstrate the potential for BCG-based vaccination to protect against major SARS-CoV-2 variants circulating globally.

microbiology↗

bioRxiv2020

Distinguishing between recent balancing selection and incomplete sweep using deep neural networks

1Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic data. Specifically, we generated forward-in-time simulations to train and test an artificial neural network (ANN) and a convolutional neural network (CNN). ANN received as input multiple summary statistics calculated on the locus of interest, while CNN was applied directly on the matrix of haplotypes. We found that both architectures have high accuracy to identify loci under recent selection. CNN generally outperformed ANN to distinguish between signals of balancing selection and incomplete sweep and was less affected by incorrect training data. We deployed both trained networks on neutral genomic regions in European populations and demonstrated a lower false positive rate for CNN than ANN. We finally deployed CNN within the MEFV gene region and identified several common variants predicted to be under incomplete sweep in a European population. Notably, two of these variants are functional changes and could modulate susceptibility to Familial Mediterranean Fever, possibly as a consequence of past adaptation to pathogens. In conclusion, deep neural networks were able to characterise signals of selection on intermediate-frequency variants, an analysis currently inaccessible by commonly used strategies.

evolutionary biology↗