Biology subjects

Rera, M.

Publications and source records attributed to Rera, M..

5 recordsLinked to original sources

bioRxiv2022

Alignment-based protein mutational landscape prediction: doing more with less

The wealth of genomic data has boosted the development of computational methods predicting the phenotypic outcomes of missense variants. The most accurate ones exploit multiple sequence alignments, which can be costly to generate. Recent efforts for democratizing protein structure prediction have overcome this bottleneck by leveraging the fast homology search of MMseqs2. Here, we show the usefulness of this strategy for mutational outcome prediction through a large-scale assessment of 1.5M missense variants across 72 protein families. Our study demonstrates the feasibility of producing alignment-based mutational landscape predictions that are both high-quality and compute-efficient for entire proteomes. We provide the community with the whole human proteome mutational landscape and simplified access to our predictive pipeline. Significant statementUnderstanding the implications of DNA alterations, particularly missense variants, on our health is paramount. This study introduces a faster and more efficient approach to predict these effects, harnessing vast genomic data resources. The speed-up is possible by establishing that resource-saving multiple sequence alignments suffice even as input to a method fitting few parameters given the alignment. Our results opens the door to discovering how tiny changes in our genes can impact our health. They provide valuable insights into the genotype-phenotype relationship that could lead to new treatments for genetic diseases.

bioinformatics↗

bioRxiv2022

Drosophilid cuticle pigmentation impacts body temperature

Cuticle pigmentation has been clearly demonstrated to impact body temperature for several relatively large species of insects, but it was questioned for small insects. Here we used a thermal camera to assess the impact of drosophilid cuticle pigmentation on body temperature when individuals are exposed to light. We compared mutants of large effects within species (Drosophila melanogaster ebony and yellow mutants). Then we analyzed the impact of naturally occurring pigmentation variation within species complexes (Drosophila americana/Drosophila novamexicana and Drosophila yakuba/Drosophila santomea). Finally we analyzed lines of D. melanogaster with moderate differences in pigmentation. We found significant differences in temperatures for each of the four pairs we analyzed. The temperature differences appeared to be proportional to the differently pigmented area: between Drosophila melanogaster ebony and yellow mutants or between Drosophila americana and Drosophila novamexicana, for which the whole body is differently pigmented, the difference in temperatures was around 0.6{degrees}C {+/-}0.2{degrees}C. By contrast, between D. yakuba and D. santomea or between Drosophila melanogaster Dark and Pale lines, for which only the posterior abdomen is differentially pigmented, we detected a temperature difference of about 0.14{degrees}C {+/-}0.10{degrees}C. This demonstrates that cuticle pigmentation has ecological implications in drosophilids regarding adaptation to environmental temperature.

evolutionary biology↗

bioRxiv2022

Smurfness-based two-phase model of ageing helps deconvolve the ageing transcriptional signature

Ageing is characterised at the molecular level by six transcriptional hallmarks of ageing, that are commonly described as progressively affected as time passes. By contrast, the Smurf assay separates high-and-constant-mortality risk individuals from healthy, zero-mortality risk individuals, based on increased intestinal permeability. Performing whole body total RNA sequencing, we found that Smurfness distinguishes transcriptional changes associated with chronological age from those associated with biological age. We show that transcriptional heterogeneity increases with chronological age in non-Smurf individuals preceding the other five hallmarks of ageing, that are specifically associated with the Smurf state. Using this approach, we also devise targeted pro-longevity genetic interventions delaying entry in the Smurf state. We anticipate that increased attention to the evolutionary conserved Smurf phenotype will bring about significant advances in our understanding of the mechanisms of ageing. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=150 HEIGHT=200 SRC="FIGDIR/small/517330v5_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@37b39org.highwire.dtl.DTLVardef@8ef8f0org.highwire.dtl.DTLVardef@797299org.highwire.dtl.DTLVardef@1529b0d_HPS_FORMAT_FIGEXP M_FIG The two-phase model of ageing allows to study separately the effect of chronological and physiological age. (A) Classic approaches for studying ageing tend to consider it as a black box affecting all individuals progressively from birth to death. Instead, the Smurf phenotype shows that life can be divided into two consecutive phases separated by an abrupt transition. (B) All individuals undergo this transition at a different moment in their life, prior to death. This allows us to switch from population based approaches, comparing bulks of age-matched individuals through time, to individuals-centred approaches relying on direct access to their transition status. (C) Such paradigm shift shows that hallmarks of ageing long thought to progressively change with age are actually mostly affected in a growing proportion of Smurfs, allowing for the identification of the chain of events accompanying ageing and death from natural causes. (D) By studying the behaviour of the ageing transcriptome as a function of chronological age and Smurfness separately, we demonstrate that the progressively changing transcriptional ageing signature, as described in Frenk & Houseley (2018), is in fact the convolution changes accompanying chronological age signature (increased transcriptional noise) and changes associated with Smurfness (or biological age) signature (increased stress response and inflammation, decreased expression of ribosomal and mitochondrial genes). We also identified a hallmark partially associated with only old Smurfs (ATH5), suggesting that chronological age can affect, late in life, the Smurf response. C_FIG

systems biology↗

bioRxiv2022

TRANSCRIPTOMIC SIGNATURES OF TELOMERASE-DEPENDENT AND -INDEPENDENT AGEING, IN THE ZEBRAFISH GUT AND BRAIN

Decreased telomerase expression, telomere shortening, senescence-associated markers and inflammation have all been independently observed in the ageing brain and associated with disease. However, causality between limited telomerase expression and brain senescence and neuro-inflammation in the natural ageing setting is yet to be established. Here, we address these questions using the zebrafish as an ageing model which. Akin to humans, zebrafish display premature ageing and death in the absence of telomerase and where telomere shortening is a driver of cellular senescence. Our work shows for the first time that telomerase deficiency (tert-/-) accelerates key hallmarks of ageing identified in the Wild Type (WT) zebrafish brain at transcriptional, cellular, tissue and functional levels. We show that telomerase depletion accelerates ageing-associated transcriptomic changes associated with dysregulation of stress response and immune genes. These are accompanied by accelerated in situ accumulation of senescence-associated markers and inflammation in the aged brain. Importantly, In vivo, these changes correlate with increased blood-brain barrier permeability and increased anxiety-like behaviour. Of note, the acceleration of senescence-associated markers in the absence of tert occurs not only in the expected proliferative areas but also in non-proliferative ones, where it is unlikely due to telomere-dependent replicative exhaustion, suggesting that non-canonical roles of telomerase may be involved. Together, our work suggests that telomerase has a protective role in the zebrafish brain against the accumulation of senescence and neuro-inflammation and is required for blood-brain barrier integrity. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/493215v4_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@12d3171org.highwire.dtl.DTLVardef@8f45eorg.highwire.dtl.DTLVardef@1e37580org.highwire.dtl.DTLVardef@372777_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract Telomerase depletion accelerates markers of ageing in the zebrafish brain, ranging from dysregulated immune and stress ageing transcriptomic hallmarks to in situ accumulation of senescence-associated markers and inflammation, dysfunction of the blood-brain barrier and increased anxiety behaviour. C_FIG

genomics↗

bioRxiv2022

Positive selection of senescence through increased evolvability: ageing is not a by-product of evolution.

Signs of ageing become apparent only late in life, after organismal development is finalized. Ageing, most notably, decreases an individuals fitness. As such, it is most commonly perceived as a non-adaptive force of evolution and considered a by-product of natural selection. Building upon the evolutionarily conserved age-related Smurf phenotype, we propose a simple mathematical life-history trait model in which an organism is characterized by two core abilities: reproduction and homeostasis. Through the simulation of this model, we observe 1) the convergence of fertilitys end with the onset of senescence, 2) the relative success of ageing populations, as compared to non-ageing populations, and 3) the enhanced evolvability (i.e. the generation of genetic variability) of ageing populations. In addition, we formally demonstrate the mathematical convergence observed in 1). We thus theorize that mechanisms that link the timing of fertility and ageing have been selected and fixed over evolutionary history, which, in turn, explains why ageing populations are more evolvable and therefore more successful. Broadly speaking, our work suggests that ageing is an adaptive force of evolution.

evolutionary biology↗