Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequencing using a two-steps strategy reveals high genetic diversity in the S gene of SARS-CoV-2 after a high transmission period in Tunis, Tunisia

Recent efforts have reported numerous variants that influence SARS-CoV-2 viral characteristics including pathogenicity, transmission rate and ability of detection by molecular tests. Whole genome sequencing based on NGS technologies is the method of choice to identify all viral variants; however, the resources needed to use these techniques for a representative number of specimens remain limited in many low and middle income countries. To decrease sequencing cost, we developed a couple of primers allowing to generate partial sequences in the viral S gene allowing rapid detection of numerous variants of concern (VOCs) and variants of interest (VOIs); whole genome sequencing is then performed on a selection of viruses based on partial sequencing results. Two hundred and one nasopharyngeal specimens collected during the decreasing phase of a high transmission COVID-19 wave in T unisia were analyzed. The results reveal high genetic variability within the sequenced fragment and allowed the detection of first introduction in the country of already known VOCs and VOIs as well as others variants that have interesting genomic mutations and need to be kept under surveillance. Importance The method of choice for SARS-CoV-2 variants detection is whole genome sequencing using NGS technologies. Resources for this technology remain limited in many low and middle income countries where it is not possible to perform whole genome sequencing for representative number of SARS-CoV-2 positive cases. In the present work, we developed a novel strategy based on a first partial sanger screening in the S gene including key mutations of the already known VOCs and VOIs for rapid identification of these VOCs and VOIs and helps to better select specimens that need to be sequenced by NGS technologies. The second step consisting in whole genome sequencing allowed to have a holistic view of all variants within the selected viral strains and confirmed the initial classification of the strains based on partial S gene sequencing.
EcoEvoApps: Interactive apps for theoretical models in ecology and evolutionary biology

The integration of theory and data drives progress in science, but a persistent barrier to such integration in ecology and evolutionary biology (EEB) is that theory is often developed and expressed in the form of mathematical models that can feel daunting and inaccessible for students and empiricists with variable quantitative training and attitudes towards math. A promising way to make mathematical models more approachable is to embed them into interactive tools with which one can visually evaluate model structures and directly explore model outcomes through simulation. To promote such interactive learning of quantitative models, we developed EcoEvoApps, a collection of free, open-source (R/Shiny) apps that include model overviews, interactive model simulations, and code to implement these models directly in R. The package currently focuses on canonical models of population dynamics, species interaction, and landscape ecology. We also outline a vision and approach for growing the collection to include more models from across EEB. These apps help illustrate fundamental results from theoretical ecology and can serve as valuable teaching tools in classroom settings. We present data from student surveys which show that students rate these apps as useful learning tools, and that using interactive apps leads to substantial gains in students’ interest and confidence in mathematical models. This points to the potential for interactive activities to make theoretical models more accessible to a wider audience, and thus facilitate the feedback between theory and data across ecology and evolutionary biology.
How does the brain represent the semantic content of an image?

Using deep neural networks (DNNs) as models to explore the biological brain is controversial, which is mainly due to the impenetrability of DNNs. Inspired by neural style transfer, we circumvented this problem by using deep features that were given a clear meaning—the representation of the semantic content of an image. Using encoding models and the representational similarity analysis, we quantitatively showed that the deep features which represented the semantic content of an image mainly predicted the activity of voxels in the early visual areas (V1, V2, and V3) and these features were essentially depictive but also propositional. This result is in line with the core viewpoint of the grounded cognition to some extent, which suggested that the representation of information in our brain is essentially depictive and can implement symbolic functions naturally.
Computational and experimental assessment of backbone templates for computational protein design

Computational protein design has taken big strides over the recent years, however, the tools available are still not at a state where a sequence can be designed to fold into a given protein structure at will and with high probability. We have here applied a recent release of Rosetta Design to redesign a set of structurally very similar proteins belonging to the Thioredoxin fold. We determined design success using a combination of a genetic screening tool to assay folding/stability in E. coli and selecting the best hits from this for further biochemical characterization. We have previously used this set of template proteins for redesign and found that success was highly dependent on template structure, a trait which was also found in this study. Nevertheless, state of the art design software is now able to predict the best template, most likely due to the introduction of the cart_bonded energy term. The template that led to the greatest fraction of successful designs was the same (a Thioredoxin from spinach) as that identified in our previous study. Our previously described redesign of Thioredoxin, which also used the spinach protein as template, however also performed well. In the present study, both these templates yielded proteins with compact folded structures, and enforces the conclusion that any design project must carefully consider different design templates. Fortunately, selecting designs using the cart_bonded energy term appears to correctly identify such templates.
MRP5 and MRP9 play a concerted role in male reproduction and mitochondrial function

Significance Multidrug Resistance Proteins (MRPs) are typically implicated in cancer biology. Here, we show that MRP9 and MRP5 localize to mitochondrial-associated membranes and play a concerted role in maintaining mitochondrial homeostasis and male reproductive fitness. Our work fills in significant gaps in our understanding of MRP9 and MRP5 with wider implications in male fertility. It is plausible that variants in these transporters are associated with male reproductive dysfunction. Multidrug Resistance Proteins (MRPs) are transporters that play critical roles in cancer even though the physiological substrates of these enigmatic transporters are poorly elucidated. In Caenorhabditis elegans, MRP5/ABCC5 is an essential heme exporter because mrp-5 mutants are unviable due to their inability to export heme from the intestine to extraintestinal tissues. Heme supplementation restores viability of these mutants but fails to restore male reproductive deficits. Correspondingly, cell biological studies show that MRP5 regulates heme levels in the mammalian secretory pathway even though MRP5 knockout (KO) mice do not show reproductive phenotypes. The closest homolog of MRP5 is MRP9/ABCC12, which is absent in C. elegans, raising the possibility that MRP9 may genetically compensate for MRP5. Here, we show that MRP5 and MRP9 double KO (DKO) mice are viable but reveal significant male reproductive deficits. Although MRP9 is highly expressed in sperm, MRP9 KO mice show reproductive phenotypes only when MRP5 is absent. Both ABCC transporters localize to mitochondrial-associated membranes, dynamic scaffolds that associate the mitochondria and endoplasmic reticulum. Consequently, DKO mice reveal abnormal sperm mitochondria with reduced mitochondrial membrane potential and fertilization rates. Metabolomics show striking differences in metabolite profiles in the DKO testes, and RNA sequencing shows significant alterations in genes related to mitochondrial function and retinoic acid metabolism. Targeted functional metabolomics reveal lower retinoic acid levels in the DKO testes and higher levels of triglycerides in the mitochondria. These findings establish a model in which MRP5 and MRP9 play a concerted role in regulating male reproductive functions and mitochondrial sufficiency.
Evolutionary plasticity of SH3 domain binding by Nef proteins of the HIV-1/SIVcpz lentiviral lineage

The accessory protein Nef of human and simian immunodeficiency viruses (HIV and SIV) is an important pathogenicity factor known to interact with cellular protein kinases and other signaling proteins. A canonical SH3 domain binding motif in Nef is required for most of these interactions. For example, HIV-1 Nef activates the tyrosine kinase Hck by tightly binding to its SH3 domain. An archetypal contact between a negatively charged SH3 residue and a highly conserved arginine in Nef (Arg77) plays a key role here. Combining structural analyses with functional assays, we here show that Nef proteins have also developed a distinct structural strategy - termed the “R-clamp” - that favors the formation of this salt bridge via buttressing Arg77. Comparison of evolutionarily diverse Nef proteins revealed that several distinct R-clamps have evolved that are functionally equivalent but differ in the side chain compositions of Nef residues 83 and 120. Whereas a similar R-clamp design is shared by Nef proteins of HIV-1 groups M, O, and P, as well as SIVgor, the Nef proteins of SIV from the Eastern chimpanzee subspecies (SIVcpzP.t.s.) exclusively utilize another type of R-clamp. By contrast, SIV of Central chimpanzees (SIVcpzP.t.t.) and HIV-1 group N strains show more heterogenous R-clamp design principles, including a non-functional evolutionary intermediate of the aforementioned two classes. These data add to our understanding of the structural basis of SH3 binding and kinase deregulation by Nef, and provide an interesting example of primate lentiviral protein evolution. AUTHOR SUMMARY Viral replication depends on interactions with a plethora of host cell proteins. Cellular protein interactions are typically mediated by specialized binding modules, such as the SH3 domain. To gain access to host cell regulation viruses have evolved to contain SH3 domain binding sites in their proteins, a notable example of which is the HIV-1 Nef protein. Here we show that during the primate lentivirus evolution the structural strategy that underlies the avid binding of Nef to cellular SH3 domains, which we have dubbed the R-clamp, has been generated via alternative but functionally interchangeable molecular designs. These patterns of SH3 recognition depend on the amino acid combinations at the positions corresponding to residues 83 and 120 in the consensus HIV-1 Nef sequence, and are distinctly different in Nef proteins from SIVs of Eastern and Central chimpanzees, gorillas, and the four groups of HIV-1 that have independently originated from the latter two. These results highlight the evolutionary plasticity of viral proteins, and have implications on therapeutic development aiming to interfere with SH3 binding of Nef.
Lipid Droplets Protect Human β-Cells From Lipotoxicity-Induced Stress and Cell Identity Changes

Free fatty acids (FFAs) are often stored in lipid droplet (LD) depots for eventual metabolic and/or synthetic use in many cell types, such a muscle, liver, and fat. In pancreatic islets, overt LD accumulation was detected in humans but not mice. LD buildup in islets was principally observed after roughly 11 years of age, increasing throughout adulthood under physiologic conditions, and also enriched in type 2 diabetes. To obtain insight into the role of LDs in human islet β-cell function, the levels of a key LD scaffold protein, perilipin 2 (PLIN2), were manipulated by lentiviral-mediated knockdown (KD) or overexpression (OE) in EndoCβH2-Cre cells, a human cell line with adult islet β-like properties. Glucose-stimulated insulin secretion was blunted in PLIN2KD cells and improved in PLIN2OE cells. An unbiased transcriptomic analysis revealed that limiting LD formation induced effectors of endoplasmic reticulum (ER) stress that compromised the expression of critical β-cell function and identity genes. These changes were essentially reversed by PLIN2OE or using the ER stress inhibitor, tauroursodeoxycholic acid. These results strongly suggest that LDs are essential for adult human islet β-cell activity by preserving FFA homeostasis.
Online Reference Trajectory Adaptation: A Personalized Control Strategy for Lower Limb Exoskeletons

This paper presents a novel method for reference trajectory adaptation in lower limb rehabilitation exoskeletons during walking. Our adaptation rule is extracted from a cost function that penalizes both interaction force and trajectory modification. By adding trajectory modification term into the cost function, we restrict the boundaries of the reference trajectory adaptation according to the patient’s motor capacity. The performance of the proposed adaptation method is studied analytically in terms of convergence and optimality. We also developed a realistic dynamic walking simulator and utilized it in performance analysis of the presented method. The proposed trajectory adaptation technique guarantees convergence to a stable, reliable, and rhythmic reference trajectory with no prior knowledge about the human intended motion. Our simulations demonstrate the convergence of exoskeleton trajectories to those of simulated healthy subjects while the exoskeleton trajectories adapt less to the trajectories of patients with reduced motor capacity (less reliable trajectories). Furthermore, the gait stability and spatiotemporal parameters such as step time symmetry and minimum toe off clearance enhanced by the adaptation in all subjects. The presented mathematical analysis and simulation results show the applicability and effectiveness of the proposed method and its potential to be applied for trajectory adaptation in lower limb rehabilitation exoskeletons.
The ADP-glucose pyrophosphorylase from Melainabacteria: a comparative study between photosynthetic and non-photosynthetic bacterial sources

Until recently, all members of the cyanobacterial phylum were considered capable of performing oxygenic photosynthesis. This view has been questioned after the discovery of a group of presumed non-photosynthetic cyanobacteria named Melainabacteria. Using metagenomic data, we identified sequences encoding putative ADP-glucose pyrophosphorylase (EC 2.7.7.27, ADP-GlcPPase) from free-living and intestinal Melainabacteria. These genes were de novo synthesized and overexpressed in Escherichia coli. The purified recombinant proteins from the free-living and the intestinal Melainabacteria showed ADP-GlcPPase activity, with Vmax values of 2.3 and 7.1 U/mg, respectively. Both enzymes had similar affinities towards ATP (S0.5 ∼0.3 mM) although the one from the intestinal source displayed a 6-fold higher affinity for glucose-1P. Both recombinant ADP-GlcPPases were sensitive to allosteric activation by glucose-6P (A0.5 ∼0.3 mM), and to inhibition by Pi and ADP (I0.5 between 0.2 to 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. To the best of our knowledge, this is the first biochemical characterization of an active enzyme from Melainabacteria, offering further data to discussions regarding their phylogenetic position. This work contributes to a better understanding regarding the evolution of allosteric mechanisms in ADP-GlcPPases, an essential enzyme for the synthesis of glycogen in prokaryotes and starch in plants.
A genotype independent DMP-HI system in dicot crops

Doubled haploid (DH) technology is used to obtain homozygous lines in a single generation, which significantly accelerates the crop breeding trajectory. Traditionally, in vitro culture is used to generate DHs, but is limited by species and genotype recalcitrance. In vivo haploid induction (HI) through seed is been widely and efficiently used in maize and was recently extended to several monocot crops. However, a similar generic and efficient HI system is still lacking in dicot crops. Here we show that genotype-independent in vivo HI can be triggered by mutation of DMP genes in tomato, rapeseed and tobacco with HI rates of ~1.9%, 2.4% and 1.2%, respectively. The DMP-HI system offers a robust DH technology to facilitate variety improvement in these crops. The success of this approach and the conservation of DMP genes paves the way for a generic and efficient genotype-independent HI system in other dicot crops.
Parameter identifiability and model selection for sigmoid population growth models

Sigmoid growth models, such as the logistic, Gompertz and Richards’ models, are widely used to study population dynamics ranging from microscopic populations of cancer cells, to continental-scale human populations. Fundamental questions about model selection and parameter estimation are critical if these models are to be used to make practical inferences. However, the question of parameter identifiability – whether a data set contains sufficient information to give unique or sufficiently precise parameter estimates – is often overlooked. We use a profile-likelihood approach to explore practical parameter identifiability using data describing the re-growth of hard coral. With this approach, we explore the relationship between parameter identifiability and model misspecification, finding that the logistic growth model does not suffer identifiability issues for the type of data we consider whereas the Gompertz and Richards’ models encounter practical non-identifiability issues. This analysis of parameter identifiability and model selection is important because different growth models are used within areas of the biological modelling literature without necessarily considering whether parameters are identifiable, or checking statistical assumptions underlying model adequacy. Standard practices that do not consider parameter identifiability can lead to unreliable or imprecise parameter estimates and potentially misleading mechanistic interpretations. While tools developed here focus on three standard sigmoid growth models only, our theoretical developments are applicable to any sigmoid growth model and any relevant data set. MATLAB implementations of all software are available on GitHub.
Synergistic information in the frontal cortex-striatal pathway

Across the cortico-basal ganglia circuit, the medial frontal cortex (MFC) communicates with the dorsal striatum (DS) during learning and planning. How these two brain regions communicate with each other is, however, not fully understood. Here we report the presence of synergistic information during information transfer across the frontal cortex-striatal pathway. Synergistic information emerges from the positive interaction of DS and MFC neurons and provides the DS with additional cortical information. This information is held latent in neuronal signals. To reveal it, we simultaneously record neuronal activities from the MFC and DS of rats trained on an outcome-based decision-making task and determined whether past neuronal activities of the DS positively influence communication rates. We detect a neuronal synergy that enables the MFC to boost its communication rate to the DS. Our results suggest that past neuronal activities of the DS help decode MFC signals. This ability is not attributed to the inherent autocorrelation of DS spiking activities.
Assembled Cell-Decorated Collagen (AC-DC) bioprinted implants mimic musculoskeletal tissue properties and promote functional recovery

Musculoskeletal tissue injuries, including the damage and rupture of ligaments and tendons, and volumetric muscle loss (VML), are exceptionally commonplace and often lead to permanent disability and deformation. We developed an advanced biomanufacturing platform producing cellularized collagen microfiber implants to facilitate functional repair and regeneration of musculoskeletal soft tissues. This Assembled Cell-Decorated Collagen (AC-DC) bioprinting process rapidly and reproducibly forms 3D implants using clinically relevant cells and strong, microfluidic extruded collagen fibers. Quantitative analysis showed that the directionality and distribution of cells throughout AC-DC implants mimic the cellular properties of native musculoskeletal tissue. AC-DC bioprinted implants further approximate or exceed the strength and stiffness of human tendons and ligaments and exceeded the properties of commonplace collagen hydrogels by orders of magnitude. The regenerative potential of AC-DC implants was also assessed in vivo in a rodent VML model. A critically sized muscle injury in the hindlimb was created and repaired, and limb torque generation potential was measured over 12 weeks. Both acellular and cellular implants were found to promote functional recovery compared to the unrepaired group, with AC-DC implants containing therapeutic muscle progenitor cells promoting the highest degree of recovery. Histological analysis and automated image processing of explanted muscle cross-sections revealed increased total muscle fiber count, median muscle fiber size, and increased cellularization for injuries repaired with cellularized implants. These studies introduce the tremendous potential of an advanced bioprinting method for generating tissue analogs with near-native biological and biomechanical properties with the potential to repair numerous challenging musculoskeletal injuries. One Sentence Summary Bioprinted collagen microfiber-based implants mimic musculoskeletal tissue properties in vitro and promote functional recovery in vivo.
Claustral Projections to Anterior Cingulate Cortex Modulate Engagement with the External World

Engagement is a major determinant of performance. Hyper-engagement risks impulsivity and is fatiguing over time, while hypo-engagement could lead to missed opportunities. Even in sleep, when engagement levels are minimal, sensory responsiveness varies. Thus, maintaining an optimal engagement level with the environment is a fundamental cognitive ability. The claustrum, and in particular its reciprocal connectivity with executive regions in the frontal cortex, has been associated with salience, attention and sleep. These apparently disparate roles can be consolidated within the context of engagement. Here we describe the activity of claustro-frontal circuits in a task imposing a tradeoff between response inhibition and sensory acuity (‘ENGAGE’). Recording calcium fiber photometry during >80,000 trials, we characterize claustrum recruitment during salient behavioral events, and find that a moderate level of activity in claustro-cingulate projections defines optimal engagement. Low activity of this pathway is associated with impulsive actions, while high activity is associated with behavioral lapses. Chemogenetic activation of cingulate-projecting claustrum neurons suppressed impulsive behavior and reduced the engagement of mice in the task. This relationship became even clearer upon addressing individual variability in the strategy mice employed during the ENGAGE task. Furthermore, this association of claustrum activity and engagement extends into sleep. Using simultaneous EEG and photometry recordings in the claustrum, we find that cingulate projecting claustrum neurons are most active during deep unresponsive slow-wave sleep, when mice are less prone to awakening by sensory stimuli.