Predicting enzymatic function of protein sequences with attention

MOTIVATION

There is a growing number of available protein sequences, but only a limited amount has been manually annotated. For example, only 0.25% of all entries of UniProtKB are reviewed by human annotators. Further developing automatic tools to infer protein function from sequence alone can alleviate part of this gap. In this article, we investigate the potential of Transformer deep neural networks on a specific case of functional sequence annotation: the prediction of enzymatic classes.

RESULTS

We show that our EnzBert transformer models, trained to predict Enzyme Commission (EC) numbers by specialization of a protein language model, outperforms state-of-the-art tools for monofunctional enzyme class prediction based on sequences only. Accuracy is improved from 84% to 95% on the prediction of EC numbers at level two on the EC40 benchmark. To evaluate the prediction quality at level four, the most detailed level of EC numbers, we built two new time-based benchmarks for comparison with state-of-the-art methods ECPred and DeepEC: the macro-F1 score is respectively improved from 41% to 54% and from 20% to 26%. Finally, we also show that using a simple combination of attention maps is on par with, or better than, other classical interpretability methods on the EC prediction task. More specifically, important residues identified by attention maps tend to correspond to known catalytic sites. Quantitatively, we report a max F-Gain score of 96.05%, while classical interpretability methods reach 91.44% at best.

AVAILABILITY AND IMPLEMENTATION

Source code and datasets are respectively available at https://gitlab.inria.fr/nbuton/tfpc and https://doi.org/10.5281/zenodo.7253910.

BayesTICS: Local temporal image correlation spectroscopy and Bayesian simulation technique for sparse estimation of diffusion in fluorescence imaging

The dynamics and fusion of vesicles during the last steps of exocytosis are not well established yet in cell biology. An open issue is the characterization of the diffusion process at the plasma membrane. Total internal reflection fluorescence microscopy (TIRFM) has been successfully used to analyze the coordination of proteins involved in this mechanism. It enables to capture dynamics of proteins with high frame rate and reasonable signal-to-noise values. Nevertheless, methodological approaches that can analyze and estimate diffusion in local small areas at the scale of a single diffusing spot within cells, are still lacking. To address this issue, we propose a novel correlation-based method for local diffusion estimation. As a starting point, we consider Fick's second law of diffusion that relates the diffusive flux to the gradient of the concentration. Then, we derive an explicit parametric model which is further fitted to time-correlation signals computed from regions of interest (ROI) containing individual spots. Our modeling and Bayesian estimation framework are well appropriate to represent isolated diffusion events and are robust to noise, ROI sizes, and localization of spots in ROIs. The performance of BayesTICS is shown on both synthetic and real TIRFM images depicting Transferrin Receptor proteins.

Gut microbiota analysis for prediction of clinical relapse in Crohn's disease

The role of intestinal bacterial microbiota has been described as key in the pathophysiology of Crohn's disease (CD). CD is characterized by frequent relapses after periods of remission which are not entirely understood. In this paper, we investigate whether the heterogeneity in microbiota profiles in CD patients could be a suitable predictor for these relapses. This prospective observational study involved 259 CD patients, in which 41 provided an additional total of 62 consecutive fecal samples, with an average interval of 25 weeks in between each of these samples. Fecal microbiota was analyzed by massive genomic sequencing through 16 S rRNA amplicon sampling. We found that our 259 CD patients could be split into three distinct subgroups of microbiota (G1, G2, G3). From G1 to G3, we noticed a progressive decrease in alpha diversity (p ≤ 0.0001) but no change in the fecal calprotectin (FC) level. Focusing on the 103 consecutive samples from 41 CD patients, we showed that the patients microbiota profiles were remarkably stable over time and associated with increasing symptom severity. Investigating further this microbiota/severity association revealed that the first signs of aggravation are (1) a loss of the main anti-inflammatory Short-Chain Fatty Acids (SCFAs) Roseburia, Eubacterium, Subdoligranumum, Ruminococcus (P < 0.05), (2) an increase in pro-inflammatory pathogens Proteus, Finegoldia (P < 0.05) while (3) an increase of other minor SCFA producers such as Ezakiella, Anaerococcus, Megasphaera, Anaeroglobus, Fenollaria (P < 0.05). Further aggravation of clinical signs is significantly linked to the subsequent loss of these minor SCFAs species and to an increase in other proinflammatory Proteobacteria such as Klebsiella, Pseudomonas, Salmonella, Acinetobacter, Hafnia and proinflammatory Firmicutes such as Staphylococcus, Enterococcus, Streptococcus. (P < 0.05). To our knowledge, this is the first study (1) specifically identifying subgroups of microbiota profiles in CD patients, (2) relating these groups to the evolution of symptoms over time and (3) showing a two-step process in CD symptoms' worsening. This paves the way towards a better understanding of patient-to-patient heterogeneity, as well as providing early warning signals of future aggravation of the symptoms and eventually adapting empirically treatments.

The coordination of spindle-positioning forces during the asymmetric division of the Caenorhabditis elegans zygote

In Caenorhabditis elegans zygote, astral microtubules generate forces essential to position the mitotic spindle, by pushing against and pulling from the cortex. Measuring microtubule dynamics there, we revealed the presence of two populations, corresponding to pulling and pushing events. It offers a unique opportunity to study, under physiological conditions, the variations of both spindle-positioning forces along space and time. We propose a threefold control of pulling force, by polarity, spindle position and mitotic progression. We showed that the sole anteroposterior asymmetry in dynein on-rate, encoding pulling force imbalance, is sufficient to cause posterior spindle displacement. The positional regulation, reflecting the number of microtubule contacts in the posterior-most region, reinforces this imbalance only in late anaphase. Furthermore, we exhibited the first direct proof that dynein processivity increases along mitosis. It reflects the temporal control of pulling forces, which strengthens at anaphase onset following mitotic progression and independently from chromatid separation. In contrast, the pushing force remains constant and symmetric and contributes to maintaining the spindle at the cell centre during metaphase.

Interdisciplinary Research in Artificial Intelligence: Challenges and Opportunities

The use of artificial intelligence (AI) in a variety of research fields is speeding up multiple digital revolutions, from shifting paradigms in healthcare, precision medicine and wearable sensing, to public services and education offered to the masses around the world, to future cities made optimally efficient by autonomous driving. When a revolution happens, the consequences are not obvious straight away, and to date, there is no uniformly adapted framework to guide AI research to ensure a sustainable societal transition. To answer this need, here we analyze three key challenges to interdisciplinary AI research, and deliver three broad conclusions: 1) future development of AI should not only impact other scientific domains but should also take inspiration and benefit from other fields of science, 2) AI research must be accompanied by decision explainability, dataset bias transparency as well as development of evaluation methodologies and creation of regulatory agencies to ensure responsibility, and 3) AI education should receive more attention, efforts and innovation from the educational and scientific communities. Our analysis is of interest not only to AI practitioners but also to other researchers and the general public as it offers ways to guide the emerging collaborations and interactions toward the most fruitful outcomes.

A V0-ATPase-dependent apical trafficking pathway maintains the polarity of the intestinal absorptive membrane

Intestine function relies on the strong polarity of intestinal epithelial cells and the array of microvilli forming a brush border at their luminal pole. Combining a genetic RNA interference (RNAi) screen with in vivo super-resolution imaging in the Caenorhabditis elegans intestine, we found that the V0 sector of the vacuolar ATPase (V0-ATPase) controls a late apical trafficking step, involving Ras-related protein 11 (RAB-11)⁺ endosomes and the N-ethylmaleimide-sensitive factor-attachment protein receptor (SNARE) synaptosome-associated protein 29 (SNAP-29), and is necessary to maintain the polarized localization of both apical polarity modules and brush border proteins. We show that the V0-ATPase pathway also genetically interacts with glycosphingolipids and clathrin in enterocyte polarity maintenance. Finally, we demonstrate that silencing of the V0-ATPase fully recapitulates the severe structural, polarity and trafficking defects observed in enterocytes from individuals with microvillus inclusion disease (MVID) and use this new in vivo MVID model to follow the dynamics of microvillus inclusions. Thus, we describe a new function for V0-ATPase in apical trafficking and epithelial polarity maintenance and the promising use of the C. elegans intestine as an in vivo model to better understand the molecular mechanisms of rare genetic enteropathies.

Reproduction cost reduces demographic stochasticity and enhances inter-individual compatibility

A population׳s survival depends on its ability to adapt to constraints impinging upon it. As such, adaptation is at the heart of an increasing number of theoretical models. In this paper, we propose a bottom-up evolutionary model to explore the relationship between individual evolutionary dynamics and population-level survival. To do so, we extend a well-established model of gene network evolution by introducing a cost for reproduction. As a result population sizes fluctuate and populations can even go extinct. We find that if a population survives a small and critical number of generations, it will reach a quasi-stationary state which ensures long-term survival. In a constant environment, individual adaptation occurs in response to changes in a populations genetic composition. We show that genetic compatibility increases over generations as a by-product of selection for robustness, thus preventing extinction. We also demonstrate that the number of reproductive opportunities per individual, initial population size, and mutation rates all influence population survival. Finally, mixing different populations reveals that individual properties of gene networks co-evolve with the genetic composition of the population in order to maximize an individuals reproductive success.

How evolving heterogeneity distributions of resource allocation strategies shape mortality patterns

It is well established that individuals age differently. Yet the nature of these inter-individual differences is still largely unknown. For humans, two main hypotheses have been recently formulated: individuals may experience differences in aging rate or aging timing. This issue is central because it directly influences predictions for human lifespan and provides strong insights into the biological determinants of aging. In this article, we propose a model which lets population heterogeneity emerge from an evolutionary algorithm. We find that whether individuals differ in (i) aging rate or (ii) timing leads to different emerging population heterogeneity. Yet, in both cases, the same mortality patterns are observed at the population level. These patterns qualitatively reproduce those of yeasts, flies, worms and humans. Such findings, supported by an extensive parameter exploration, suggest that mortality patterns across species and their potential shapes belong to a limited and robust set of possible curves. In addition, we use our model to shed light on the notion of subpopulations, link population heterogeneity with the experimental results of stress induction experiments and provide predictions about the expected mortality patterns. As biology is moving towards the study of the distribution of individual-based measures, the model and framework we propose here paves the way for evolutionary interpretations of empirical and experimental data linking the individual level to the population level.