Biology subjects

Pereira, J.

Publications and source records attributed to Pereira, J..

33 records · Page 2Linked to original sources

bioRxiv2022

Outer membrane beta-barrel structure prediction through the lens of AlphaFold2

Most proteins found in the outer membrane of Gram-negative bacteria share a common domain: the transmembrane {beta}-barrel. These outer membrane {beta}-barrels (OMBBs) occur in multiple sizes, and different families with a wide range of functions evolved independently by amplification from a pool of homologous ancestral {beta}{beta}-hairpins. This is part of the reason why predicting their three-dimensional (3D) structure, especially by homology modeling, is a major challenge. Recently, DeepMinds AlphaFold v2 (AF2) became the first structure prediction method to reach close-to-experimental atomic accuracy in CASP even for difficult targets. However, membrane proteins, especially OMBBs, were not abundant during its training, raising the question of how accurate the predictions are for these families. In this study, we assessed the performance of AF2 in the prediction of OMBBs of various topologies using an in-house-developed tool for the analysis of OMBB 3D structures, barrOs. In agreement with previous studies on other membrane protein classes, our results indicate that AF2 predicts OMBB structures at high accuracy independently of the use of templates, even for novel topologies absent from the training set. These results provide confidence on the models generated by AF2 and open the door to the structural elucidation of novel OMBB topologies identified in high-throughput OMBB annotation studies.

bioinformatics↗

bioRxiv2022

New β-propellers are continuously amplified from single blades in all major lineages of the β-propeller superfamily

{beta}-Propellers are toroidal folds, in which consecutive supersecondary structure units of four anti-parallel {beta}-strands - called blades - are arranged radially around a central axis. Uniquely among toroidal folds, blades span the full range of sequence symmetry, from near identity to complete divergence, indicating an ongoing process of amplification and differentiation. We have proposed that the major lineages of {beta}-propellers arose through this mechanism and that therefore their last common ancestor was a single blade, not a fully formed {beta}-propeller. Here we show that this process of amplification and differentiation is also widespread within individual lineages, yielding {beta}-propellers with blades of more than 60% median pairwise sequence identity in most major {beta}-propeller families. In some cases, the blades are nearly identical, indicating a very recent amplification event, but even in cases where such recently amplified {beta}-propellers have more than 80% overall sequence identity to each other, comparison of their DNA sequence shows that the amplification occurred independently.

bioinformatics↗

bioRxiv2022

Fine-scale survey of intertidal macroalgae reveals recent changes in a cold-water biogeographic stronghold

Global warming has been causing severe impacts on marine ecosystems, a notorious one being shifts in the geographical ranges of species. The north-western coast of the Iberian Peninsula is an especially interesting zone to study distributional shifts as it has a strong latitudinal thermal gradient, is influenced by the Canary upwelling system (which partially cancels coastal warming) and holds some of the most diverse macroalgae communities in Europe. Notably, it is within this region that many cold-water species, common in northern Europe, have their southernmost distribution refuge. Recent studies hypothesize that the environmental conditions may be nonetheless changing and already threatening this biodiversity hotspot. The main goal of this study was to carry out a fine-scale assessment of the distributional limits of several macroalgae in North-western Iberia, as well as identify possible population and range shifts using historical data (2001-2005) as reference. In addition, invasive species were also surveyed. We also assessed if the regions of (i) Galicia, (ii) Northern Portugal, and (iii) Central Portugal displayed distinctive characters regarding macroalgae composition and abundance. We identified an increase in abundance of some invasive macroalgae as well as a decrease in the abundance of some cold-water species. In the most severe cases, cold-water species were extirpated along hundreds of km. The compounded effect of the decrease in the abundance of cold-water species and the increase in the abundance of invasive species is leading to the homogenization of macroalgae communities in north-western Iberia.

ecology↗

bioRxiv2022

Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease

Hexanucleotide G4C2 repeat expansions in the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Dipeptide repeat proteins (DPRs) generated by translation of repeat-containing RNAs show toxic effects in vivo as well as in vitro and are key targets for therapeutic intervention. We generated human antibodies that bind DPRs with high affinity and specificity. Anti-GA antibodies engaged extra- and intracellular poly-GA and reduced aggregate formation in a poly-GA over-expressing human cell line. However, antibody treatment in human neuronal cultures synthesizing exogenous poly-GA resulted in the formation of large extracellular immune complexes and did not affect accumulation of intracellular poly-GA aggregates. Treatment with antibodies was also shown to directly alter the morphological and biochemical properties of poly-GA and to shift poly-GA/antibody complexes to more rapidly sedimenting ones. These alterations were not observed with poly-GP and have important implications for accurate measurement of poly-GA levels including the need to evaluate all centrifugation fractions and disrupt the interaction between treatment antibodies and poly-GA by denaturation. Targeting poly-GA and poly-GP in two mouse models expressing G4C2 repeats by systemic antibody delivery for up to 16 months was well-tolerated and led to measurable brain penetration of antibodies. Long term treatment with anti-GA antibodies produced improvement in an open field movement test in aged C9ORF72450 mice. However, chronic administration of anti-GA antibodies in AAV-(G4C2)149 mice was associated with increased levels of poly-GA detected by immunoassay and did not significantly reduce poly-GA aggregates or alleviate disease progression in this model. SignificanceImmunotherapy has been proposed for neurodegenerative disorders including Alzheimers or Parkinsons diseases. Recent reports using antibodies against poly-GA or active immunization suggested similar immunotherapy in ALS/FTD caused by repeat expansion in the C9ORF72 gene (1, 2). Here, we systematically characterized human antibodies against multiple DPR species and tested the biological effects of antibodies targeting poly-GA in different cellular and mouse models. Target engagement was shown in three independent cellular models. Anti-GA antibodies reduced the number of intracellular poly-GA aggregates in human T98G cells but not in cultured human neurons. Whereas chronic anti-GA treatment in BAC C9ORF72450 mice did not impact poly-GA levels and modestly improved one behavioral phenotype, poly-GA levels detected by immunoassays were increased and disease progression was unaltered in AAV-(G4C2)149 mice.

neuroscience↗

bioRxiv2021

Competition between hematopoietic stem and progenitor cells controls hematopoietic stem cell compartment size.

Cellular competition for limiting hematopoietic factors is a physiologically regulated but poorly understood process. Here, we studied this phenomenon by hampering hematopoietic progenitor access to Leptin receptor+ mesenchymal stem/progenitor cells (MSPCs) and endothelial cells (ECs). We show that HSC numbers increased by 2-fold when multipotent and lineage-restricted progenitors failed to respond to CXCL12 produced by MSPCs and ECs. HSCs were qualitatively normal, and HSC expansion only occurred when early hematopoietic progenitors but not differentiated hematopoietic cells lacked CXCR4. Furthermore, the MSPC and EC transcriptomic heterogeneity was remarkably stable, suggesting that it is impervious to dramatic changes in hematopoietic progenitor interactions. Instead, HSC expansion was caused by increased availability of membrane-bound stem cell factor (mSCF) on MSPCs and ECs due to reduced consumption by cKit-expressing hematopoietic progenitors. These studies revealed an intricate homeostatic balance between HSCs and proximal hematopoietic progenitors regulated by cell competition for limited amounts of mSCF.

immunology↗

bioRxiv2021

Reconstruction and variability of tropical pollination networks in the Brazilian Atlantic Forest

O_LILoss of biodiversity comprehends not only the extinction of individual species, but also the loss of the ecological interactions among them. Survival of species, continuation of ecosystem functioning in nature, and ecosystem services to humans depend on the maintenance of well-functioning networks of species interactions (e.g. plant-pollinator networks and food webs). Analyses of ecological networks often rely on biased and incomplete survey data, especially in species-rich areas, such as the tropics. C_LIO_LIWe used a network inference method to reconstruct pollination data compiled from a large tropical rainforest habitat extent. To gain insight into the characteristics of plant-pollinator interactions across the region, we combined the reconstructed pollination network with species distribution modeling to obtain local pollination networks throughout the area. We explored how global network properties relate to natural forest cover and land cover heterogeneity. C_LIO_LIWe found that some network properties (the sum and evenness of link weights, connectance and nestedness) are positively correlated with forest cover, indicating that networks in sites with more natural habitat have greater diversity of interactions, stability and resilience. Modularity was not related to forest cover, but seemed to reflect habitat heterogeneity, due to the broad spatial scale of the study. C_LIO_LIWe believe that the methodology suggested here can facilitate the use of incomplete network data in a reliable way, and allow us to better understand and protect networks of species interactions in high biodiversity regions of the world. C_LI

ecology↗

bioRxiv2021

Assessing the utility of CASP14 models for molecular replacement

The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real-world application. In CASP7, the metric for molecular replacement assessment involved full likelihood-based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood-based rigid-body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined likelihood (LLG) score. This enabled multi-copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative-expected-LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X-ray, NMR or cryo-EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.

bioinformatics↗

bioRxiv2021

Gram-negative outer membrane proteins with multiple β-barrel domains

Outer membrane beta barrels (OMBBs) are found in the outer membrane of Gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel {beta}-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8-36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers and some function only in this state. Using a combination of sensitive sequence-comparison methods and co-evolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include 8-stranded barrels prevail. These multi-barrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multi-barrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis suggests that their functions are not essential, but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for new functions beyond those of the individual barrels.

biophysics↗

bioRxiv2020

Age-related differences in network structure and dynamic synchrony of cognitive control

Cognitive trajectories vary greatly across older individuals, and the neural mechanisms underlying these differences remain poorly understood. Here, we propose a mechanistic framework of cognitive variability in older adults, linking the influence of white matter microstructure on fast and effective communications between brain regions. Using diffusion tensor imaging and electroencephalography, we show that individual differences in white matter network organization are associated with network clustering and efficiency in the alpha and high-gamma bands, and that functional network dynamics partly explain individual cognitive control performance in older adults. We show that older individuals with high versus low structural network clustering differ in task-related network dynamics and cognitive performance. These findings were corroborated by investigating magnetoencephalography networks in an independent dataset. This multimodal brain connectivity framework of individual differences provides a holistic account of how differences in white matter microstructure underlie age-related variability in dynamic network organization and cognitive performance.

neuroscience↗

bioRxiv2020

The VCBS superfamily, a diverse group of β-propellers that includes tachylectin and integrins

{beta}-Propellers are found in great variety across all kingdoms of life. They assume many cellular roles, primarily as scaffolds for macromolecular interactions and catalysis. Despite their diversity, most {beta}-propeller families clearly originated by amplification from the same ancient peptide - the {beta}-propeller blade. In cluster analyses, {beta}-propellers of the WD40 superfamily always formed the largest group, to which some important families, such as the -integrin, Asp-box, and glycoside hydrolase {beta}-propellers connected weakly. Motivated by the dramatic growth of sequence databases we revisited these connections, with a special focus on VCBS-like {beta}-propellers, which have not been analysed for their evolutionary relationships so far. We found that they form a supercluster with integrin-like {beta}-propellers and tachylectins, clearly delimited from the superclusters formed by WD40 and Asp-Box {beta}-propeller. Connections between the three superclusters are made mainly through PQQ-like {beta}-propeller. Our results present a new, greatly expanded view of the {beta}-propeller classification landscape.

molecular biology↗

bioRxiv2020

Src-dependent NM2A tyrosine-phosphorylation regulates actomyosin dynamics

Non-muscle myosin 2A (NM2A) is a key cytoskeletal enzyme that along with actin assembles into actomyosin filaments inside cells. NM2A is fundamental in cellular processes requiring force generation such as cell adhesion, motility and cell division, and plays important functions in different stages of development and during the progression of viral and bacterial infections. We previously identified a novel tyrosine phosphorylation on residue 158 (pTyr158) in the motor domain of NM2A. This phosphorylation is dependent on Src kinase and is promoted by Listeria monocytogenes infection of epithelial cells, however its role is unknown. Here we show that Listeriolysin O (LLO), the pore-forming toxin (PFT) secreted by L. monocytogenes, is sufficient to trigger NM2A pTyr158 by activating Src, an upstream regulator of actomyosin remodeling. We further address the role of NM2A pTyr158 on the organization and dynamics of the actomyosin cytoskeleton and find that, by controlling the activation of the NM2A, the status of the pTyr158 alters cytoskeletal organization, dynamics of focal adhesions and cell motility. In vitro, we observe that non-phosphorylatable and phospho-mimetic versions of NM2A at Tyr158 display motor and ATPase activities similar to the wild-type NM2A, which indicates that the phenotype of these mutants in cells is independent of their ability to translocate actin filaments. Importantly, we find the regulation of this phosphorylation site to be of physiological relevance in Caenorhabditis elegans, in particular in response to intoxication by a PFT and to heat shock. We conclude that the control of the phosphorylation status at NM2A Tyr158 is a conserved trait that contributes to the regulation of actomyosin dynamics and the ability of cells to respond to bacterial infection. We propose Src-dependent NM2A pTyr158 as a novel layer of regulation of the actomyosin cytoskeleton.

cell biology↗

bioRxiv2020

The risk of Xylella fastidiosa outbreaks will decrease in the Mediterranean olive-producing regions

The bacterium Xylella fastidiosa (Xf) is a worldwide distributed invasive insect-borne plant pathogen, which causes lethal diseases to many economically-important crops including olives, citrus, almonds and grapes as well as numerous forest, ornamental, and uncultivated plants. The Mediterranean basin is the top supplier of olive oil with 93% of the world production and is consequently highly concerned about the recent invasion of Xf in Europe. Recently, bioeconomic models estimated putative losses induced by the spread of Xf across the European olive-producing area ranging from 1.9 to 5.2 billion euros over 50 years; however, such models did not take into account the insect vectors, which constitute a key driver of Xf spread. In the present study, we used bioclimatic species distribution models to predict the current and future climate suitability of the Mediterranean area for the main efficient or putative transmitters of Xf to olive (i.e. Philaenus spumarius, Neophilaenus campestris and Aphrophora alni). An important part of the total extent of the Mediterranean olive-producing area, mainly situated in southern Spain, Turkey and Greece, is predicted as currently poorly suitable for these vector species. Moreover, models forecast that nearly the totality of the Mediterranean olive-producing regions will likely become climatically little suitable for these vectors by 2050 due to climate change. In Europe, Xf outbreaks have occurred so far only in localities predicted as climatically suitable for these main vector species (e.g. the Apulia region of Italy) while the areas predicted as poorly suitable are still apparently Xf-free, which suggests that climate tolerances of vectors might play a main role in shaping Xf outbreaks patterns. This pattern highlights the crucial necessity of accounting for vectors when assessing risk of Xf outbreaks, and when considering vector-borne diseases in general. The risk maps presented here will have important practical application for the optimization of current and future strategies to control Xf in the Mediterranean region.

ecology↗

bioRxiv2020

The boundaries of State-Space Granger Causality Analysis applied to BOLD simulated data: a comparative modelling and simulation approach

BackgroundThe analysis of connectivity has become a fundamental tool in human neuroscience. Granger Causality Mapping is a data-driven method that uses Granger Causality (GC) to assess the existence and direction of influence between signals, based on temporal precedence of information. More recently, a theory of Granger causality has been developed for state-space (SS-GC) processes, but little is known about its statistical validation and application on functional magnetic resonance imaging (fMRI) data. New MethodWe implemented a new heuristic, focusing on the application of SS-GC with a distinct statistical validation technique - Time Reversed Testing - to generative synthetic models and compare it to classical multivariate computational frameworks. We also test a range of experimental parameters, including block structure, sampling frequency, noise and system mean pairwise correlation, using a statistical framework of binary classification. ResultsWe found that SS-GC with time reversed testing outperforms other frameworks. The results validate the application of SS-GC to generative models. When estimating reliable causal relations, SS-GC returns promising results, especially when considering synthetic data with an high impact of noise and sampling rate. ConclusionsSS-GC with time reversed testing offers a possible framework for future analysis of fMRI data in the context of data-driven causality analysis. HighlightsO_LIState-Space GC was combined with a statistical validation step, using a Time Reversed Testing. C_LIO_LIThis novel heuristic overpowers classical GC, when applied to generative models. C_LIO_LICorrectly identified connections between variables increase with the increase of number of blocks and number of points per block. C_LIO_LISNR and subsampling have a significant impact on the results. C_LI

neuroscience↗

bioRxiv2020

Whole-chromosome fusions in the karyotype evolution of Sceloporus (Iguania, Reptilia) are more intense in sex chromosomes than autosomes

There is a growing body of evidence that the common ancestor of vertebrates had a bimodal karyotype, i.e. consisting of large macrochromosomes and small microchromosomes. This type of karyotype organization is preserved in most reptiles. However, certain species independently experience microchromosome fusions. The evolutionary forces behind this are unclear. We investigated the karyotype of the green spiny lizard, Sceloporus malachiticus, an iguana species which has 2n=22, whereas the ancestral karyotype of iguanas had 2n=36. We obtained and sequenced flow-sorted chromosome-specific DNA samples and found that most of the microchromosome fusions in this species involved sex chromosomes. We found that certain ancestral squamate chromosomes, such as the homologue of the Anolis carolinensis chromosome 11, are repeatedly involved in sex chromosome formation in different species. To test the hypothesis that the karyotypic shift could be associated with changes in recombination patterns, and to study sex chromosome synapsis and recombination in meiosis, we performed synaptonemal complex analysis in this species and in S. variabilis, a related species with 2n=34. We found that in the species studied the recombination patterns correlate more with phylogeny than with the structure of the karyotype. The sex chromosomes had two distal pseudoautosomal regions and a medial differentiated region.

genomics↗

bioRxiv2018

Comprehensive analysis of small RNA profile by massive parallel sequencing in HTLV-1 asymptomatic subjects with monoclonal and polyclonal rearrangement of the T-cell antigen receptor γ-chain

IntroductionIn this study, we used a massive parallel sequencing technology to investigate the cellular small RNA (sRNA) operating in peripheral blood mononuclear cells (PBMCs) of the Human T-lymphotropic virus type I (HTLV-I) infected asymptomatic subjects with a monoclonal and polyclonal rearrangement of the T-cell antigen receptor {gamma}-chain.\n\nMaterials and MethodsBlood samples from 15 HTLV-1 asymptomatic carriers who were tested for clonal TCR-{gamma} gene (seven and eight subjects presented monoclonal and polyclonal expansion of HTLV-1 infected cells, respectively), and were submitted to Illumina for small RNA library construction. sRNA libraries were prepared from cryoperserved PBMCs using TrueSeq Small RNA Library Preparation Kit (Illumina). The sRNA-Seq reads were aligned, annotated, and profiled by different bioinformatics tools.\n\nResultsThrough bioinformatics analysis, we identified a total of 494 known sRNAs and 120 putative novel sRNAs. Twenty-two known and 15 novel sRNA showed a different expression (>2-fold) between the asymptomatic monoclonal (ASM) and asymptomatic polyclonal carriers (ASP). The hsa-mir-196a-5p was the most abundantly upregulated micro RNA (miRNA) and the hsa-mir-133a followed by hsa-mir-509-3p were significantly downregulated miRNAs with more than a three-fold difference in the ASM than ASP group. The target genes predicted to be regulated by the differentially expressed miRNAs play essential roles in diverse biological processes including cell proliferation, differentiation, and/or apoptosis.\n\nDiscussionOur results provide an opportunity for a further understanding of sRNA regulation and function in HTLV-1 infected subjects with monoclonality evidence.

microbiology↗