Helper T cell immunity in humans with inherited CD4 deficiency

CD4+ T cells are vital for host defense and immune regulation. However, the fundamental role of CD4 itself remains enigmatic. We report seven patients aged 5-61 years from five families of four ancestries with autosomal recessive CD4 deficiency and a range of infections, including recalcitrant warts and Whipple's disease. All patients are homozygous for rare deleterious CD4 variants impacting expression of the canonical CD4 isoform. A shorter expressed isoform that interacts with LCK, but not HLA class II, is affected by only one variant. All patients lack CD4+ T cells and have increased numbers of TCRαβ+CD4-CD8- T cells, which phenotypically and transcriptionally resemble conventional Th cells. Finally, patient CD4-CD8- αβ T cells exhibit intact responses to HLA class II-restricted antigens and promote B cell differentiation in vitro. Thus, compensatory development of Th cells enables patients with inherited CD4 deficiency to acquire effective cellular and humoral immunity against an unexpectedly large range of pathogens. Nevertheless, CD4 is indispensable for protective immunity against at least human papillomaviruses and Trophyrema whipplei.

Non-uniform sampling to enhance the performance of compact NMR for characterizing new psychoactive substances

Efficient and robust analytical methods are needed to improve the identification and subsequent regulation of new psychoactive substances (NPS). NMR spectroscopy is a unique method able to determine the structure of small molecules such as NPS even in mixtures. However, high-field NMR analysis is associated with expensive purchase and maintenance costs. For more than a decade, compact NMR spectrometers have changed this paradigm. It was recently shown that a dedicated analytical workflow combining compact NMR and databases could identify the molecular structure of NPS, in spite of the lower spectral dispersion and sensitivity of compact spectrometers. This approach relies on 1H-13C HSQC to both recognize NPS and elucidate the structure of unknown substances. Still, its performance is limited by the need to compromise between resolution and experiment time. Here, we show that this strategy can be significantly improved by implementing non-uniform sampling (NUS) to improve spectral resolution in the 13C dimension of HSQC at no cost in terms of experiment time. Gains in the range of 3 to 4 in resolution are achieved for pure NPS and for a mixture. Finally, 2D HSQC with NUS was applied to improve the identification of NPS with the assistance of databases. The resulting method appears as a useful tool for the characterization of NPS in mixtures, which is essential for forensic laboratories.

Prospecting for rare earth element (hyper)accumulators in the Paris Herbarium using X-ray fluorescence spectroscopy reveals new distributional and taxon discoveries

BACKGROUND

Rare earth elements (REEs) are increasingly crucial for modern technologies. Plants could be used as a biogeochemical pathfinder and a tool to extract REEs from deposits. However, a paucity of information on suitable plants for these tasks exists.

METHODS

We aimed to discover new REE-(hyper)accumulating plant species by performing an X-ray fluorescence (XRF) survey at the Herbarium of the Muséum national d'Histoire naturelle (MNHN, Paris, France). We selected specific families based on the likelihood of containing REE-hyperaccumulating species, using known taxa that accumulate REEs. A total of 4425 specimens, taken in the two main evolutionary lineages of extant vascular plants, were analysed, including the two fern families Blechnaceae (n = 561) and Gleicheniaceae (n = 1310), and the two flowering plant families Phytolaccaceae (n = 1137) and Juglandaceae (n = 1417).

KEY RESULTS

Yttrium (Y) was used as a proxy for REEs for methodological reasons, and a total of 268 specimens belonging to the genera Blechnopsis (n = 149), Dicranopteris (n = 75), Gleichenella (n = 32), Phytolacca (n = 6), Carya (n = 4), Juglans (n = 1) and Sticherus (n = 1) were identified with Y concentrations ranging from the limit of detection (LOD) >49 µg g-1 up to 1424 µg g-1. Subsequently, analysis of fragments of selected specimens by inductively coupled plasma atomic emission spectroscopy (ICP-AES) revealed that this translated to up to 6423 µg total REEs g-1 in Dicranopteris linearis and up to 4278 µg total REEs g-1 in Blechnopsis orientalis which are among the highest values ever recorded for REE hyperaccumulation in plants. It also proved the validity of Y as an indicator for REEs in XRF analysis of herbarium specimens. The presence of manganese (Mn) and zinc (Zn) was also studied by XRF in the selected specimens. Mn was detected in 1440 specimens ranging from the detection limit at 116 µg g-1 up to 3807 µg g-1 whilst Zn was detected in 345 specimens ranging from the detection limit at 77 µg g-1 up to 938 µg g-1.

CONCLUSIONS AND IMPLICATIONS

This study led to the discovery of REE accumulation in a range of plant species, substantially higher concentrations in species known to be REE hyperaccumulators, and records of REE hyperaccumulators outside of the well-studied populations in China.

Macaque claustrum, pulvinar and putative dorsolateral amygdala support the cross-modal association of social audio-visual stimuli based on meaning

Social communication draws on several cognitive functions such as perception, emotion recognition and attention. The association of audio-visual information is essential to the processing of species-specific communication signals. In this study, we use functional magnetic resonance imaging in order to identify the subcortical areas involved in the cross-modal association of visual and auditory information based on their common social meaning. We identified three subcortical regions involved in audio-visual processing of species-specific communicative signals: the dorsolateral amygdala, the claustrum and the pulvinar. These regions responded to visual, auditory congruent and audio-visual stimulations. However, none of them was significantly activated when the auditory stimuli were semantically incongruent with the visual context, thus showing an influence of visual context on auditory processing. For example, positive vocalization (coos) activated the three subcortical regions when presented in the context of positive facial expression (lipsmacks) but not when presented in the context of negative facial expression (aggressive faces). In addition, the medial pulvinar and the amygdala presented multisensory integration such that audiovisual stimuli resulted in activations that were significantly higher than those observed for the highest unimodal response. Last, the pulvinar responded in a task-dependent manner, along a specific spatial sensory gradient. We propose that the dorsolateral amygdala, the claustrum and the pulvinar belong to a multisensory network that modulates the perception of visual socioemotional information and vocalizations as a function of the relevance of the stimuli in the social context. SIGNIFICANCE STATEMENT: Understanding and correctly associating socioemotional information across sensory modalities, such that happy faces predict laughter and escape scenes predict screams, is essential when living in complex social groups. With the use of functional magnetic imaging in the awake macaque, we identify three subcortical structures-dorsolateral amygdala, claustrum and pulvinar-that only respond to auditory information that matches the ongoing visual socioemotional context, such as hearing positively valenced coo calls and seeing positively valenced mutual grooming monkeys. We additionally describe task-dependent activations in the pulvinar, organizing along a specific spatial sensory gradient, supporting its role as a network regulator.

Fast and flexible inference for joint models of multivariate longitudinal and survival data using integrated nested Laplace approximations

Modeling longitudinal and survival data jointly offers many advantages such as addressing measurement error and missing data in the longitudinal processes, understanding and quantifying the association between the longitudinal markers and the survival events, and predicting the risk of events based on the longitudinal markers. A joint model involves multiple submodels (one for each longitudinal/survival outcome) usually linked together through correlated or shared random effects. Their estimation is computationally expensive (particularly due to a multidimensional integration of the likelihood over the random effects distribution) so that inference methods become rapidly intractable, and restricts applications of joint models to a small number of longitudinal markers and/or random effects. We introduce a Bayesian approximation based on the integrated nested Laplace approximation algorithm implemented in the R package R-INLA to alleviate the computational burden and allow the estimation of multivariate joint models with fewer restrictions. Our simulation studies show that R-INLA substantially reduces the computation time and the variability of the parameter estimates compared with alternative estimation strategies. We further apply the methodology to analyze five longitudinal markers (3 continuous, 1 count, 1 binary, and 16 random effects) and competing risks of death and transplantation in a clinical trial on primary biliary cholangitis. R-INLA provides a fast and reliable inference technique for applying joint models to the complex multivariate data encountered in health research.

Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.

Sharing information across patient subgroups to draw conclusions from sparse treatment networks

Network meta-analysis (NMA) usually provides estimates of the relative effects with the highest possible precision. However, sparse networks with few available studies and limited direct evidence can arise, threatening the robustness and reliability of NMA estimates. In these cases, the limited amount of available information can hamper the formal evaluation of the underlying NMA assumptions of transitivity and consistency. In addition, NMA estimates from sparse networks are expected to be imprecise and possibly biased as they rely on large-sample approximations that are invalid in the absence of sufficient data. We propose a Bayesian framework that allows sharing of information between two networks that pertain to different population subgroups. Specifically, we use the results from a subgroup with a lot of direct evidence (a dense network) to construct informative priors for the relative effects in the target subgroup (a sparse network). This is a two-stage approach where at the first stage, we extrapolate the results of the dense network to those expected from the sparse network. This takes place by using a modified hierarchical NMA model where we add a location parameter that shifts the distribution of the relative effects to make them applicable to the target population. At the second stage, these extrapolated results are used as prior information for the sparse network. We illustrate our approach through a motivating example of psychiatric patients. Our approach results in more precise and robust estimates of the relative effects and can adequately inform clinical practice in presence of sparse networks.

Dimensionless numbers reveal distinct regimes in the structure and dynamics of pedestrian crowds

In fluid mechanics, dimensionless numbers like the Reynolds number help classify flows. We argue that such a classification is also relevant for crowd flows by putting forward the dimensionless Intrusion and Avoidance numbers, which quantify the intrusions into the pedestrians' personal spaces and the imminency of the collisions that they face, respectively. Using an extensive dataset, we show that these numbers delineate regimes where distinct variables characterize the crowd's arrangement, namely, Euclidean distances at low Avoidance number and times-to-collision at low Intrusion number. On the basis of these findings, a perturbative expansion of the individual pedestrian dynamics is carried out around the noninteracting state, in quite general terms. Simulations confirm that this expansion performs well in its expected regime of applicability.

Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites

Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.

Ryanodine receptor dysfunction causes senescence and fibrosis in Duchenne dilated cardiomyopathy

BACKGROUND

Duchenne muscular dystrophy (DMD) is an X-linked disorder characterized by progressive muscle weakness due to the absence of functional dystrophin. DMD patients also develop dilated cardiomyopathy (DCM). We have previously shown that DMD (mdx) mice and a canine DMD model (GRMD) exhibit abnormal intracellular calcium (Ca2+) cycling related to early-stage pathological remodelling of the ryanodine receptor intracellular calcium release channel (RyR2) on the sarcoplasmic reticulum (SR) contributing to age-dependent DCM.

METHODS

Here, we used hiPSC-CMs from DMD patients selected by Speckle-tracking echocardiography and canine DMD cardiac biopsies to assess key early-stage Duchenne DCM features.

RESULTS

Dystrophin deficiency was associated with RyR2 remodelling and SR Ca2+ leak (RyR2 Po of 0.03 ± 0.01 for HC vs. 0.16 ± 0.01 for DMD, P < 0.01), which led to early-stage defects including senescence. We observed higher levels of senescence markers including p15 (2.03 ± 0.75 for HC vs. 13.67 ± 5.49 for DMD, P < 0.05) and p16 (1.86 ± 0.83 for HC vs. 10.71 ± 3.00 for DMD, P < 0.01) in DMD hiPSC-CMs and in the canine DMD model. The fibrosis was increased in DMD hiPSC-CMs. We observed cardiac hypocontractility in DMD hiPSC-CMs. Stabilizing RyR2 pharmacologically by S107 prevented most of these pathological features, including the rescue of the contraction amplitude (1.65 ± 0.06 μm for DMD vs. 2.26 ± 0.08 μm for DMD + S107, P < 0.01). These data were confirmed by proteomic analyses, in particular ECM remodelling and fibrosis.

CONCLUSIONS

We identified key cellular damages that are established earlier than cardiac clinical pathology in DMD patients, with major perturbation of the cardiac ECC. Our results demonstrated that cardiac fibrosis and premature senescence are induced by RyR2 mediated SR Ca2+ leak in DMD cardiomyocytes. We revealed that RyR2 is an early biomarker of DMD-associated cardiac damages in DMD patients. The progressive and later DCM onset could be linked with the RyR2-mediated increased fibrosis and premature senescence, eventually causing cell death and further cardiac fibrosis in a vicious cycle leading to further hypocontractility as a major feature of DCM. The present study provides a novel understanding of the pathophysiological mechanisms of the DMD-induced DCM. By targeting RyR2 channels, it provides a potential pharmacological treatment.

Acoustic levitation as a tool for cell-driven self-organization of human cell spheroids during long-term 3D culture

Acoustic levitation, which allows contactless manipulation of micro-objects with ultrasounds, is a promising technique for spheroids formation and culture. This acoustofluidic technique favors cell-cell interactions, away from the walls of the chip, which leads to the spontaneous self-organization of cells. Using this approach, we generated spheroids of mesenchymal stromal cells, hepatic and endothelial cells, and showed that long-term culture of cells in acoustic levitation is feasible. We also demonstrated that this self-organization and its dynamics depended weakly on the acoustic parameters but were strongly dependent on the levitated cell type. Moreover, spheroid organization was modified by actin cytoskeleton inhibitors or calcium-mediated interaction inhibitors. Our results confirmed that acoustic levitation is a rising technique for fundamental research and biotechnological industrial application in the rapidly growing field of microphysiological systems. It allowed easily obtaining spheroids of specific and predictable shape and size, which could be cultivated over several days, without requiring hydrogels or extracellular matrix.

Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions

A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.

Polysaccharides as a Hydrophilic Building Block of Amphiphilic Block Copolymers for the Conception of Nanocarriers

Polysaccharides are gaining increasing attention for their relevance in the production of sustainable materials. In the domain of biomaterials, polysaccharides play an important role as hydrophilic components in the design of amphiphilic block copolymers for the development of drug delivery systems, in particular nanocarriers due to their outstanding biocompatibility, biodegradability, and structural versatility. The presence of a reducing end in polysaccharide chains allows for the synthesis of polysaccharide-based block copolymers. Compared with polysaccharide-based graft copolymers, the structure of block copolymers can be more precisely controlled. In this review, the synthesis methods of polysaccharide-based amphiphilic block copolymers are discussed in detail, taking into consideration the structural characteristics of polysaccharides. Various synthetic approaches, including reductive amination, oxime ligation, and other chain-end modification reactions, are explored. This review also focuses on the advantages of polysaccharides as hydrophilic blocks in polymeric nanocarriers. The structure and unique properties of different polysaccharides such as cellulose, hyaluronic acid, chitosan, alginate, and dextran are described along with examples of their applications as hydrophilic segments in the synthesis of amphiphilic copolymers to construct nanocarriers for sustained drug delivery.

Assessment of myocardial injuries in ischaemic and non-ischaemic cardiomyopathies using magnetic resonance T1-rho mapping

AIMS

To identify clinical correlates of myocardial T1ρ and to examine how myocardial T1ρ values change under various clinical scenarios.

METHODS AND RESULTS

A total of 66 patients (26% female, median age 57 years [Q1-Q3, 44-65 years]) with known structural heart disease and 44 controls (50% female, median age 47 years [28-57 years]) underwent cardiac magnetic resonance imaging at 1.5 T, including T1ρ mapping, T2 mapping, native T1 mapping, late gadolinium enhancement, and extracellular volume (ECV) imaging. In controls, T1ρ positively related with T2 (P = 0.038) and increased from basal to apical levels (P < 0.001). As compared with controls and remote myocardium, T1ρ significantly increased in all patients' sub-groups and all types of myocardial injuries: acute and chronic injuries, focal and diffuse tissue abnormalities, as well as ischaemic and non-ischaemic aetiologies (P < 0.05). T1ρ was independently associated with T2 in patients with acute injuries (P = 0.004) and with native T1 and ECV in patients with chronic injuries (P < 0.05). Myocardial T1ρ mapping demonstrated good intra- and inter-observer reproducibility (intraclass correlation coefficient = 0.86 and 0.83, respectively).

CONCLUSION

Myocardial T1ρ mapping appears to be reproducible and equally sensitive to acute and chronic myocardial injuries, whether of ischaemic or non-ischaemic origins. It may thus be a contrast-agent-free biomarker for gaining new and quantitative insight into myocardial structural disorders. These findings highlight the need for further studies through prospective and randomized trials.

Turnover Number in Photoinduced Molecular Catalysis of Hydrogen Evolution: a Benchmarking for Catalysts?

Development of devices for production of H2 using light and a sustainable source of electrons may require the design of molecular systems combining a molecular catalyst and a photosensitizer. Evaluation of the efficiency of hydrogen production is commonly performed in homogeneous solution with a sacrificial electron donor and the report of the maximal turnover number vs catalyst (T O N c a t lim ${TON_{cat}^{\lim } }$ ). This figure of merit is strongly dependent on deactivation pathways and does not by itself provide a benchmarking for catalysts. In particular, when the photosensitizer degradation is the primary source of limitation, a kinetic model, rationalizing literature data, shows that a decrease of the catalyst concentration leads to an increase ofT O N c a t lim ${TON_{cat}^{\lim } }$ . It indicates that exceptionally highT O N c a t lim ${TON_{cat}^{\lim } }$ obtained at very low catalyst concentration shall not be considered as an indication of an exceptional catalytic system. We advocate for a systematic kinetic analysis in order to get a quantitative measure of the competitive pathways leading toT O N c a t lim ${TON_{cat}^{\lim } }$ values and to provide keys for performance improvement.

Transport of N-acetylchitooligosaccharides and fluorescent N-acetylchitooligosaccharide analogs into rat liver lysosomes

Free polymannose-type oligosaccharides (fOS) are processed by cytosolic enzymes to generate Man5GlcNAc which is transferred to lysosomes and degraded. Lysosomal fOS import was demonstrated in vitro but is poorly characterized in part due to lack of convenient substrates. As chitooligosaccharides (COS, oligomers β1,4-linked GlcNAc) block [3H]Man5GlcNAc transport into lysosomes, we asked if COS are themselves transported and if so, can they be chemically modified to generate fluorescent substrates. We show that COS are degraded by lysosomal hydrolases to generate GlcNAc, and robust ATP-dependent transport of [3H]COS2/4 di and tetrasaccharides into intact rat liver lysosomes was observed only after blocking lysosomal [3H]GlcNAc efflux with cytochalasin B. As oligosaccharides with unmodified reducing termini are the most efficient inhibitors of [3H]COS2/4 and [3H]Man5GlcNAc transport, the non-reducing GlcNAc residue of COS2-4 was de-N-acetylated using Sinorhizobium meliloti NodB, and the resulting amine substituted with rhodamine B (RB) to yield RB-COS2-4. The fluorescent compounds inhibit [3H]Man5GlcNAc transport and display temperature-sensitive, ATP-dependent transport into a sedimentable compartment that is ruptured with the lysosomotropic agent L-methyl methionine ester. Once in this compartment, RB-COS3 is converted to RB-COS2 further identifying it as the lysosomal compartment. RB-COS2/3 and [3H]Man5GlcNAc transports are blocked similarly by competing sugars, and are partially inhibited by the vacuolar ATPase inhibitor bafilomycin and high concentrations of the P-type ATPase inhibitor orthovanadate. These data show that Man5GlcNAc, COS2/4 and RB-COS2/3 are transported into lysosomes by the same or closely related mechanism and demonstrate the utility of COS modified at their non-reducing terminus to study lysosomal oligosaccharide transport.

Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors

Pediatric high-grade gliomas (pHGG) are devastating and incurable brain tumors with recurrent mutations in histone H3.3. These mutations promote oncogenesis by dysregulating gene expression through alterations of histone modifications. We identify aberrant DNA repair as an independent mechanism, which fosters genome instability in H3.3 mutant pHGG, and opens new therapeutic options. The two most frequent H3.3 mutations in pHGG, K27M and G34R, drive aberrant repair of replication-associated damage by non-homologous end joining (NHEJ). Aberrant NHEJ is mediated by the DNA repair enzyme polynucleotide kinase 3'-phosphatase (PNKP), which shows increased association with mutant H3.3 at damaged replication forks. PNKP sustains the proliferation of cells bearing H3.3 mutations, thus conferring a molecular vulnerability, specific to mutant cells, with potential for therapeutic targeting.

G-quadruplexes control hepatitis B virus replication by promoting cccDNA transcription and phase separation in hepatocytes

Phase separation regulates fundamental processes in gene expression and is mediated by the local concentration of proteins and nucleic acids, as well as nucleic acid secondary structures such as G-quadruplexes (G4s). These structures play fundamental roles in both host gene expression and in viral replication due to their peculiar localisation in regulatory sequences. Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is an episomal minichromosome whose persistence is at the basis of chronic infection. Identifying the mechanisms controlling its transcriptional activity is indispensable to develop new therapeutic strategies against chronic hepatitis B. The aim of this study was to determine whether G4s are formed in cccDNA and regulate viral replication. Combining biochemistry and functional studies, we demonstrate that cccDNA indeed contains ten G4s structures. Furthermore, mutations disrupting two G4s located in the enhancer I HBV regulatory region altered cccDNA transcription and viral replication. Finally, we showed for the first time that cccDNA undergoes phase separation in a G4-dependent manner to promote its transcription in infected hepatocytes. Altogether, our data give new insight in the transcriptional regulation of the HBV minichromosome that might pave the way for the identification of novel targets to destabilize or silence cccDNA.

Inverse association between plasma chlordecone concentrations and progression of alcoholic liver fibrosis: the role of liver metabolism

BACKGROUND AND AIMS

Chlordecone is a persistent organochlorinated insecticide, extensively used in the French West Indies and has been contaminating the population for more than thirty years. Its potentiation effect on hepatotoxic agents has been demonstrated in animal models. We investigated the relationship between environmental exposure to chlordecone and the progression of liver fibrosis.

METHODS

This study included 182 consecutive patients with chronic alcoholic hepatitis whose liver fibrosis was assessed using non-invasive methods. Measured plasma chlordecone concentrations at inclusion were used as surrogate of long-term exposure under steady-state conditions. As the pharmacokinetic processing of chlordecone is largely determined by the liver, we used a human physiologically based pharmacokinetic model to predict plausible changes in the steady-state blood chlordecone concentrations induced by liver fibrosis.

RESULTS

With a median follow-up of 27.1 years after the onset of alcohol consumption, we found a significant decrease in the risk of advanced liver fibrosis with increasing plasma chlordecone concentration (adjusted hazard ratio = 0.56; 95% confidence interval: 0.34-0.95 for the highest vs. lowest tertile, p = 0.04). Changes induced by liver fibrosis influenced the pharmacokinetic processing of chlordecone, resulting in substantial modifications in its steady-state blood concentrations.

CONCLUSION

According to this human model of coexposure to alcohol, reverse causality is the most plausible explanation of this inverse association between plasma chlordecone concentrations and progression of liver fibrosis. This study underlines the importance of considering the pharmacokinetic of environmental contaminants in epidemiological studies when biomarkers of exposure are used to investigate their own impact on the liver.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT03373396.

Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines

In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.

Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS

The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution.

SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space

MOTIVATION

Popular shape-based alignment methods handle molecular flexibility by utilizing conformational ensembles to select the most fitted conformer. However, the initial conformer library generation step is computationally intensive and limiting to the overall alignment process. In this work, we describe a method to perform flexible alignment of two molecular shapes by optimizing the 3D conformation. SENSAAS-Flex, an add-on to the SENSAAS tool, is able to proceed from a limited set of initial conformers through an iterative process where additional conformational optimizations are made at the substructure level and constrained by the target shape.

RESULTS

In self- and cross-alignment experiments, SENSAAS-Flex is able to reproduce the crystal structure geometry of ligands of the AstraZeneca Molecule Overlay Test set and PDBbind refined dataset. Our study shows that the point-based representation of molecular surfaces is appropriate in terms of shape constraint to sample the conformational space and perform flexible molecular alignments.

AVAILABILITY AND IMPLEMENTATION

The documentation and source code are available at https://chemoinfo.ipmc.cnrs.fr/Sensaas-flex/sensaas-flex-main.tar.gz.

Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome

We present the first chromosome-level genome assembly and annotation of the pearly heath Coenonympha arcania, generated with a PacBio HiFi sequencing approach and complemented with Hi-C data. We additionally compare synteny, gene, and repeat content between C. arcania and other Lepidopteran genomes. This reference genome will enable future population genomics studies with Coenonympha butterflies, a species-rich genus that encompasses some of the most highly endangered butterfly taxa in Europe.

HyPedSim: A Multi-Level Crowd-Simulation Framework-Methodology, Calibration, and Validation

Large-scale crowd phenomena are complex to model because the behaviour of pedestrians needs to be described at both strategic, tactical, and operational levels and is impacted by the density of the crowd. Microscopic models manage to mimic the dynamics at low densities, whereas mesoscopic models achieve better performances in dense situations. This paper proposes and evaluates a novel agent-based model to enable agents to dynamically change their operational model based on local density. The ability to combine microscopic and mesoscopic models for multi-scale simulation is studied through a use case of pedestrians at the Festival of Lights, Lyon, France. Pedestrian outflow data are extracted from video recordings of exiting crowds at the festival. The hybrid model is calibrated and validated using a genetic algorithm that optimises the match between simulated and observed outflow data. Additionally, a local sensitivity analysis is then conducted to identify the most sensitive parameters in the model. Finally, the performance of the hybrid model is compared to different models in terms of density map and computation time. The results demonstrate that the hybrid model has the capacity to effectively simulate pedestrians across varied density scenarios while optimising computational performance compared to other models.

Electroactive Bi-Functional Liquid Crystal Elastomer Actuators

Liquid crystal elastomers (LCEs) with promising applications in the field of actuators and soft robotics are reported. However, most of them are activated by external heating or light illumination. The examples of electroactive LCEs are still limited; moreover, they are monofunctional with one type of deformation (bending or contraction). Here, the study reports on trilayer electroactive LCE (eLCE) by intimate combination of LCE and ionic electroactive polymer device (i-EAD). This eLCE is bi-functional and can perform either bending or contractile deformations by the control of the low-voltage stimulation. By applying a voltage of ±2 V at 0.1 Hz, the redox behavior and associated ionic motion provide a bending strain difference of 0.80%. Besides, by applying a voltage of ±6 V at 10 Hz, the ionic current-induced Joule heating triggers the muscle-like linear contraction with 20% strain for eLCE without load. With load, eLCE can lift a weight of 270 times of eLCE-actuator weight, while keeping 20% strain and affording 5.38 kJ·m-3 work capacity. This approach of combining two smart polymer technologies (LCE and i-EAD) in a single device is promising for the development of smart materials with multiple degrees of freedom in soft robotics, electronic devices, and sensors.

Adult rats sired by obese fathers present learning deficits associated with epigenetic and neurochemical alterations linked to impaired brain glutamatergic signaling

AIM

Offspring of obese mothers are at high risk of developing metabolic syndrome and cognitive disabilities. Impaired metabolism has also been reported in the offspring of obese fathers. However, whether brain function can also be affected by paternal obesity has barely been examined. This study aimed to characterize the learning deficits resulting from paternal obesity versus those induced by maternal obesity and to identify the underlying mechanisms.

METHODS

Founder control and obese female and male Wistar rats were mated to constitute three first-generation (F1) experimental groups: control mother/control father, obese mother/control father, and obese father/control mother. All F1 animals were weaned onto standard chow and underwent a learning test at 4 months of age, after which several markers of glutamate-mediated synaptic plasticity together with the expression of miRNAs targeting glutamate receptors and the concentration of kynurenic and quinolinic acids were quantified in the hippocampus and frontal cortex.

RESULTS

Maternal obesity induced a severe learning deficit by impairing memory encoding and memory consolidation. The offspring of obese fathers also showed reduced memory encoding but not impaired long-term memory formation. Memory deficits in offspring of obese fathers and obese mothers were associated with a down-regulation of genes encoding NMDA glutamate receptors subunits and several learning-related genes along with impaired expression of miR-296 and miR-146b and increased concentration of kynurenic acid.

CONCLUSION

Paternal and maternal obesity impair offspring's learning abilities by affecting different processes of memory formation. These cognitive deficits are associated with epigenetic and neurochemical alterations leading to impaired glutamate-mediated synaptic plasticity.

Emotion regulation flexibility and psychosis: A longitudinal study disentangling components of flexibility in psychosis-proneness

OBJECTIVES

Flexibility in self-regulation has emerged as an important component of mental health. Previous findings found that deficits in two components of regulatory flexibility were linked cross-sectionally to psychosis-proneness. We aimed to replicate and extend these findings longitudinally.

METHODS

We measured psychosis-proneness and components of emotion regulation flexibility (i.e. context sensitivity, repertoire and feedback) at two time points with three months in between.

RESULTS

Two flexibility components predicted psychotic-like experiences. The ability to detect the absence of contextual cues was implicated in both positive and negative dimensions but through opposite pathways. Expressive suppression ability-a subcomponent of repertoire-predicted positive symptoms. None of the flexibility components predicted distress related to the symptoms.

CONCLUSIONS

The current study provides further evidence on the implication of emotion regulation flexibility in the longer-term maintenance of psychotic-like experiences. Future studies can advance this work further by evaluating possible bidirectional relationships between psychotic-like experiences and deficits in emotion regulation flexibility.

Occurrence and diversity of stem nodulation in Aeschynomene and Sesbania legumes from wetlands of Madagascar

Legumes have the ability to establish a nitrogen-fixing symbiosis with soil rhizobia that they house in specific organs, the nodules. In most rhizobium-legume interactions, nodulation occurs on the root. However, certain tropical legumes growing in wetlands possess a unique trait: the capacity to form rhizobia-harbouring nodules on the stem. Despite the originality of the stem nodulation process, its occurrence and diversity in waterlogging-tolerant legumes remains underexplored, impeding a comprehensive analysis of its genetics and biology. Here, we aimed at filling this gap by surveying stem nodulation in legume species-rich wetlands of Madagascar. Stem nodulation was readily observed in eight hydrophytic species of the legume genera, Aeschynomene and Sesbania, for which significant variations in stem nodule density and morphology was documented. Among these species, A. evenia, which is used as genetic model to study the rhizobial symbiosis, was found to be frequently stem-nodulated. Two other Aeschynomene species, A. cristata and A. uniflora, were evidenced to display a profuse stem-nodulation as occurs in S. rostrata. These findings extend our knowledge on legumes species that are endowed with stem nodulation and further indicate that A. evenia, A. cristata, A. uniflora and S. rostrata are of special interest for the study of stem nodulation. As such, these legume species represent opportunities to investigate different modalities of the nitrogen-fixing symbiosis and this knowledge could provide cues for the engineering of nitrogen-fixation in non-legume crops.

Pervasive cranial allometry at different anatomical scales and variational levels in extant armadillosAlometría craneal generalizada a diferentes escalas anatómicas y niveles de variación en armadillos actuales

Allometry, i.e., morphological variation correlated with size, is a major pattern in organismal evolution. Since size varies both within and among species, allometry occurs at different variational levels. However, the variability of allometric patterns across levels is poorly known since its evaluation requires extensive comparative studies. Here, we implemented a 3D geometric morphometric approach to investigate cranial allometry at three main variational levels-static, ontogenetic, and evolutionary-and two anatomical scales-entire cranium and cranial subunits-based on a dense intra- and interspecific sampling of extant armadillo diversity. While allometric trajectories differ among distantly related species, they hardly do so among sister families. This suggests that phylogenetic distance plays an important role in explaining allometric divergences. Beyond trajectories, our analyses revealed pervasive allometric shape changes shared across variational levels and anatomical scales. At the entire cranial scale, craniofacial allometry (relative snout elongation and braincase reduction) is accompanied notably by variations of nuchal crests and postorbital constriction. Among cranial subunits, the distribution of allometry was highly heterogeneous, with the frontal and petrosal bones showing the most pervasive shape changes, some of which were undetected at a more global scale. Evidence of widespread and superimposed allometric variations raises questions on their determinants and anatomical correlates and demonstrates the critical role of allometry in morphological evolution.

OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia

Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accommodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signaling pathway that activates 2 coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing intercellular infection and lateral root base nodulation remains elusive. Here, we show that Aeschynomene evenia OROSOMUCOID PROTEIN 1 (AeORM1), a key regulator of sphingolipid biosynthesis, is required for nodule formation. Using A. evenia orm1 mutants, we demonstrate that alterations in AeORM1 function trigger numerous early aborted nodules, defense-like reactions, and shorter lateral roots. Accordingly, AeORM1 is expressed during lateral root initiation and elongation, including at lateral root bases where nodule primordium form in the presence of symbiotic bradyrhizobia. Sphingolipidomics revealed that mutations in AeORM1 lead to sphingolipid overaccumulation in roots relative to the wild type, particularly for very long-chain fatty acid-containing ceramides. Taken together, our findings reveal that AeORM1-regulated sphingolipid homeostasis is essential for rhizobial infection and nodule organogenesis, as well as for lateral root development in A. evenia.

150 Gbps THz Chipscale Topological Photonic Diplexer

Photonic diplexers are being widely investigated for high data transfer rates in on-chip communication. However, dividing the available spectrum into nonoverlapping multicarrier frequency sub-bands has remained a challenge in designing frequency-selective time-invariant channels. Here, an on-chip topological diplexer is reported exhibiting terahertz frequency band filtering through Klein tunneling of topological edge modes. The silicon topological diplexer chip facilitates two high-speed channels with quadrature amplitude modulation (QAM) over a broad bandwidth of 12.5 GHz each. These channels operate at carrier frequencies of 305 and 321.6 GHz, achieving a combined diplexer capacity of 150 Gbit s-1 . To ensure minimal interference between adjacent channels, a guard band is implemented. Topologically protected edge modes suppress the frequency selective fading of the broadband signals and hold promise for diverse integrated photonic applications spanning terahertz and telecommunication realms, including the design of lossless topological multiplexers, interconnects, antennas, and modulators for the sixth to X generation (6G to XG) wireless.

1,3,4,5-Tetrasubstituted Poly(1,2,3-triazolium) Obtained through Metal-Free AA+BB Polyaddition of a Diazide and an Activated Internal Dialkyne

A tetra(ethylene glycol)-based 1,3,4,5-tetrasubstituted poly(1,2,3-triazolium) is synthesized in two steps including: i) the catalyst-free polyaddition of a diazide and an activated internal dialkyne and ii) the N-alkylation of the resulting 1,2,3-triazole groups. In order to provide detailed structure/properties correlations different analogs are also synthesized. First, parent poly(1,2,3-triazole)s are obtained via AA+BB polyaddition using copper(I)-catalyzed alkyne-azide cycloaddition or metal-free thermal alkyne-azide cycloaddition (TAAC). Poly(1,2,3-triazole)s with higher molar masses are obtained in higher yields by TAAC polyaddition. A 1,3,4-trisubstituted poly(1,2,3-triazolium) structural analog obtained by TAAC polyaddition using a terminal activated dialkyne and subsequent N-alkylation of the 1,2,3-triazole groups enables discussing the influence of the methyl group in the C-4 or C-5 position on thermal and ion conducting properties. Obtained polymers are characterized by 1 H, 13 C, and 19 F NMR spectroscopy, differential scanning calorimetry, thermogravimetric analysis, size exclusion chromatography, and broadband dielectric spectroscopy. The targeted 1,3,4,5-tetrasubstituted poly(1,2,3-triazolium) exhibits a glass transition temperature of -23 °C and a direct current ionic conductivity of 2.0 × 10-6 S cm-1 at 30 °C under anhydrous conditions. The developed strategy offers opportunities to further tune the electron delocalization of the 1,2,3-triazolium cation and the properties of poly(1,2,3-triazolium)s using this additional substituent as structural handle.

Sensing and regulation of C and N metabolism - novel features and mechanisms of the TOR and SnRK1 signaling pathways

Carbon (C) and nitrogen (N) metabolisms are tightly integrated to allow proper plant growth and development. Photosynthesis is dependent on N invested in chlorophylls, enzymes, and structural components of the photosynthetic machinery, while N uptake and assimilation rely on ATP, reducing equivalents, and C-skeletons provided by photosynthesis. The direct connection between N availability and photosynthetic efficiency allows the synthesis of precursors for all metabolites and building blocks in plants. Thus, the capacity to sense and respond to sudden changes in C and N availability is crucial for plant survival and is mediated by complex yet efficient signaling pathways such as TARGET OF RAPAMYCIN (TOR) and SUCROSE-NON-FERMENTING-1-RELATED PROTEIN KINASE 1 (SnRK1). In this review, we present recent advances in mechanisms involved in sensing C and N status as well as identifying current gaps in our understanding. We finally attempt to provide new perspectives and hypotheses on the interconnection of diverse signaling pathways that will allow us to understand the integration and orchestration of the major players governing the regulation of the CN balance.

The Minimum Admissible Detuning Efficiency of MRI Receive-Only Surface Coils

BACKGROUND

The minimum admissible detuning efficiency (DE) of a receive coil is an essential parameter for coil designers. A receive coil with inefficient detuning leads to inhomogeneous B1 during excitation. Previously proposed criteria for quantifying the DE rely on indirect measurements and are difficult to implement.

PURPOSE

To present an alternative method to quantify the DE of receive-only surface coils.

STUDY TYPE

Theoretical study supported by simulations and phantom experiments.

PHANTOMS

Uniform spherical (100 mm diameter) and cylindrical (66 mm diameter) phantoms.

FIELD STRENGTH/SEQUENCE

Dual repetition time B1 mapping sequence at 1.5T, and Bloch-Siegert shift B1 mapping sequence at 3.0T.

ASSESSMENT

One non-planar (80 × 43 mm2 ) and two planar (40 and 57 mm diameter) surface coils were built. Theoretical analysis was performed to determine the minimum DE required to avoid B1 distortions. Experimental B1 maps were acquired for the non-planar and planar surface coils at both 1.5T and 3.0T and visually compared with simulated B1 maps to assess the validity of the theoretical analysis.

STATISTICAL TESTS

None.

RESULTS

Based on the theoretical analysis, the proposed minimum admissible DE, defined as DEthr  = 20 Log (Q) + 13 dB, depended only on the quality factor (Q) of the coil and was independent of coil area and field strength. Simulations and phantom experiments showed that when the DE was higher than this minimum threshold level, the B1 field generated by the transmission coil was not modified by the receive coil.

DATA CONCLUSION

The proposed criterion for assessing the DE is simple to measure, and does not depend on the area of the coil or on the magnetic field strength, up to 3T. Experimental and simulated B1 maps confirmed that detuning efficiencies above the theoretically derived minimal admissible DE resulted in a non-distorted B1 field.

EVIDENCE LEVEL

2 TECHNICAL EFFICACY: Stage 1.

A broad-taxa approach as an important concept in ecotoxicological studies and pollution monitoring

Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost-effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long-term effects and ecosystem-wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies. This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad-taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad-taxa approach more feasible, enabling mechanistic studies on non-model organisms. By combining these approaches with in vitro techniques together with the broad-taxa approach, researchers can gain insights into less-explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data-reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem-focused collaboration between diverse scientific disciplines, international standardisation organisations and decision-making bodies, with a focus on transdisciplinary knowledge co-production for the One-Health approach.

A splice donor variant of GAS8 induces structural disorganization of the axoneme in sperm flagella and leads to nonsyndromic male infertility

Motile cilia and flagella are closely related organelles structured around a highly conserved axoneme whose formation and maintenance involve proteins from hundreds of genes. Defects in many of these genes have been described to induce primary ciliary dyskinesia (PCD) mainly characterized by chronic respiratory infections, situs inversus and/or infertility. In men, cilia/flagella-related infertility is usually caused by asthenozoospermia due to multiple morphological abnormalities of the sperm flagella (MMAF). Here, we investigated a cohort of 196 infertile men displaying a typical MMAF phenotype without any other PCD symptoms. Analysis of WES data identified a single case carrying a deleterious homozygous GAS8 variant altering a splice donor consensus site. This gene, also known as DRC4, encodes a subunit of the Nexin-Dynein Regulatory Complex (N-DRC), and has been already associated to male infertility and mild PCD. Confirming the deleterious effect of the candidate variant, GAS8 staining by immunofluorescence did not evidence any signal from the patient's spermatozoa whereas a strong signal was present along the whole flagella length in control cells. Concordant with its role in the N-DRC, transmission electron microscopy evidenced peripheral microtubule doublets misalignments. We confirm here the importance of GAS8 in the N-DRC and observed that its absence induces a typical MMAF phenotype not necessarily accompanied by other PCD symptoms.

Modular Self-Assembling Dendrimer Nanosystems for Magnetic Resonance and Multimodality Imaging of Tumors

Bioimaging is a powerful tool for diagnosing tumors but remains limited in terms of sensitivity and specificity. Nanotechnology-based imaging probes able to accommodate abundant imaging units with different imaging modalities are particularly promising for overcoming these limitations. In addition, the nanosized imaging agents can specifically increase the contrast of tumors by exploiting the enhanced permeability and retention effect. A proof-of-concept study is performed on pancreatic cancer to demonstrate the use of modular amphiphilic dendrimer-based nanoprobes for magnetic resonance (MR) imaging (MRI) or MR/near-infrared fluorescence (NIRF) multimodality imaging. Specifically, the self-assembly of an amphiphilic dendrimer bearing multiple Gd3+ units at its terminals, generates a nanomicellar agent exhibiting favorable relaxivity for MRI with a good safety profile. MRI reveals an up to two-fold higher contrast enhancement in tumors than in normal muscle. Encapsulating the NIRF dye within the core of the nanoprobe yields an MR/NIRF bimodal imaging agent for tumor detection that is efficient both for MRI, at Gd3+ concentrations 1/10 the standard clinical dose, and for NIRF imaging, allowing over two-fold stronger fluorescence intensities. These self-assembling dendrimer nanosystems thus constitute effective probes for MRI and MR/NIRF multimodality imaging, offering a promising nanotechnology platform for elaborating multimodality imaging probes in biomedical applications.

Kinetic solubility: Experimental and machine-learning modeling perspectives

Kinetic aqueous or buffer solubility is important parameter measuring suitability of compounds for high throughput assays in early drug discovery while thermodynamic solubility is reserved for later stages of drug discovery and development. Kinetic solubility is also considered to have low inter-laboratory reproducibility because of its sensitivity to protocol parameters [1]. Presumably, this is why little efforts have been put to build QSPR models for kinetic in comparison to thermodynamic aqueous solubility. Here, we investigate the reproducibility and modelability of kinetic solubility assays. We first analyzed the relationship between kinetic and thermodynamic solubility data, and then examined the consistency of data from different kinetic assays. In this contribution, we report differences between kinetic and thermodynamic solubility data that are consistent with those reported by others [1, 2] and good agreement between data from different kinetic solubility campaigns in contrast to general expectations. The latter is confirmed by achieving high performing QSPR models trained on merged kinetic solubility datasets. The poor performance of QSPR model trained on thermodynamic solubility when applied to kinetic solubility dataset reinforces the conclusion that kinetic and thermodynamic solubilities do not correlate: one cannot be used as an ersatz for the other. This encourages for building predictive models for kinetic solubility. The kinetic solubility QSPR model developed in this study is freely accessible through the Predictor web service of the Laboratory of Chemoinformatics (https://chematlas.chimie.unistra.fr/cgi-bin/predictor2.cgi).

Allele-dependent expression and functionality of lipid enzyme phospholipid:diacylglycerol acyltransferase affect diatom carbon storage and growth

In the acyl-CoA-independent pathway of triacylglycerol (TAG) synthesis unique to plants, fungi, and algae, TAG formation is catalyzed by the enzyme phospholipid:diacylglycerol acyltransferase (PDAT). The unique PDAT gene of the model diatom Phaeodactylum tricornutum strain CCMP2561 boasts 47 single nucleotide variants within protein coding regions of the alleles. To deepen our understanding of TAG synthesis, we observed the allele-specific expression of PDAT by the analysis of 87 published RNA-sequencing (RNA-seq) data and experimental validation. The transcription of one of the two PDAT alleles, Allele 2, could be specifically induced by decreasing nitrogen concentrations. Overexpression of Allele 2 in P. tricornutum substantially enhanced the accumulation of TAG by 44% to 74% under nutrient stress; however, overexpression of Allele 1 resulted in little increase of TAG accumulation. Interestingly, a more serious growth inhibition was observed in the PDAT Allele 1 overexpression strains compared with Allele 2 counterparts. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that enzymes encoded by PDAT Allele 2 but not Allele 1 had TAG biosynthetic activity, and 7 N-terminal and 3 C-terminal amino acid variants between the 2 allele-encoded proteins substantially affected enzymatic activity. P. tricornutum PDAT, localized in the innermost chloroplast membrane, used monogalactosyldiacylglycerol and phosphatidylcholine as acyl donors as demonstrated by the increase of the 2 lipids in PDAT knockout lines, which indicated a common origin in evolution with green algal PDATs. Our study reveals unequal roles among allele-encoded PDATs in mediating carbon storage and growth in response to nitrogen stress and suggests an unsuspected strategy toward lipid and biomass improvement for biotechnological purposes.

Emergence of blaNDM-5-harbouring Escherichia coli ST617 in refugee and host communities and their environment

Antimicrobial resistance disproportionately affects displaced and vulnerable populations. Here, we performed an in-depth investigation of blaNDM-5-harbouring Escherichia coli ST617 isolated from disenfranchised Lebanese patients, Syrian refugees, and livestock and the environment of refugee camps. We highlight the need for proactive One Health strategies to combat antimicrobial resistance in vulnerable populations.

Current Knowledge about ActiGraph GT9X Link Activity Monitor Accuracy and Validity in Measuring Steps and Energy Expenditure: A Systematic Review

Over recent decades, wearable inertial sensors have become popular means to quantify physical activity and mobility. However, research assessing measurement accuracy and precision is required, especially before using device-based measures as outcomes in trials. The GT9X Link is a recent activity monitor available from ActiGraph, recognized as a "gold standard" and previously used as a criterion measure to assess the validity of various consumer-based activity monitors. However, the validity of the ActiGraph GT9X Link is not fully elucidated. A systematic review was undertaken to synthesize the current evidence for the criterion validity of the ActiGraph GT9X Link in measuring steps and energy expenditure. This review followed the PRISMA guidelines and eight studies were included with a combined sample size of 558 participants. We found that (1) the ActiGraph GT9X Link generally underestimates steps; (2) the validity and accuracy of the device in measuring steps seem to be influenced by gait speed, device placement, filtering process, and monitoring conditions; and (3) there is a lack of evidence regarding the accuracy of step counting in free-living conditions and regarding energy expenditure estimation. Given the limited number of included studies and their heterogeneity, the present review emphasizes the need for further validation studies of the ActiGraph GT9X Link in various populations and in both controlled and free-living settings.

RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality

RNA is a complex macromolecule that plays central roles in the cell. While it is well known that its structure is directly related to its functions, understanding and predicting RNA structures is challenging. Assessing the real or predictive quality of a structure is also at stake with the complex 3D possible conformations of RNAs. Metrics have been developed to measure model quality while scoring functions aim at assigning quality to guide the discrimination of structures without a known and solved reference. Throughout the years, many metrics and scoring functions have been developed, and no unique assessment is used nowadays. Each developed assessment method has its specificity and might be complementary to understanding structure quality. Therefore, to evaluate RNA 3D structure predictions, it would be important to calculate different metrics and/or scoring functions. For this purpose, we developed RNAdvisor, a comprehensive automated software that integrates and enhances the accessibility of existing metrics and scoring functions. In this paper, we present our RNAdvisor tool, as well as state-of-the-art existing metrics, scoring functions and a set of benchmarks we conducted for evaluating them. Source code is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.

Critical micellar concentration determination of pure phospholipids and lipid-raft and their mixtures with cholesterol

Phospholipids in biological membranes establish a chemical equilibrium between free phospholipids in the aqueous phase (CMC) and self-assembled phospholipids in vesicles, keeping the CMC constant. The CMC is different for each phospholipid, depends on the amount of cholesterol, and, according to the lipid-chaperone hypothesis, controls the interaction between free phospholipids and amyloidogenic proteins (such as amylin, amyloid-β, and α-synuclein, all of which are, respectively, associated with a different proteinopathy), which governs the formation of a toxic complex between free lipids and proteins that leads to membrane destruction. Here, we provide quantitative measurements of CMCs and bilayer stability of pure phospholipids, lipid rafts, and their mixture with cholesterol by fluorescence methods (using pyrene as a probe) and light scattering techniques (resonance Rayleigh scattering and fixed-angle light scattering) performed on LUVs, as well as AFM to measure LUV dimensions. Also, we test the lipid-chaperone hypothesis on human IAPP interacting with different mixture of POPC cholesterol. Stated the importance of CMC in membrane stability and protein aggregation processes, these results could be a starting point for the development of a quantitative kinetic model for the lipid chaperone hypothesis.

Women's subsistence networks scaffold cultural transmission among BaYaka foragers in the Congo Basin

In hunter-gatherer societies, women's subsistence activities are crucial for food provisioning and children's social learning but are understudied relative to men's activities. To understand the structure of women's foraging networks, we present 230 days of focal-follow data in a BaYaka community. To analyze these data, we develop a stochastic blockmodel for repeat observations with uneven sampling. We find that women's subsistence networks are characterized by cooperation between kin, gender homophily, and mixed age-group composition. During early childhood, individuals preferentially coforage with adult kin, but those in middle childhood and adolescence are likely to coforage with nonkin peers, providing opportunities for horizontal learning. By quantifying the probability of coforaging ties across age classes and relatedness levels, our findings provide insights into the scope for social learning during women's subsistence activities in a real-world foraging population and provide ground-truth values for key parameters used in formal models of cumulative culture.

Screening for Dyslexia in University Students: a Standardized Procedure Based on Conditional Inference Trees

OBJECTIVE

The focus of this study is on providing tools to enable researchers and practitioners to screen for dyslexia in adults entering university. The first aim is to validate and provide diagnostic properties for a set of seven tests including a 1-min word reading test, a 2-min pseudoword reading test, a phonemic awareness test, a spelling test, the Alouette reading fluency test, a connected-text reading fluency test, and the self-report Adult Reading History Questionnaire (ARHQ). The second, more general, aim of this study was to devise a standardized and confirmatory procedure for dyslexia screening from a subset of the initial seven tests. We used conditional inference tree analysis, a supervised machine learning approach to identify the most relevant tests, cut-off scores, and optimal order of test administration.

METHOD

A combined sample of 60 university students with dyslexia (clinical validation group) and 65 university students without dyslexia (normative group) provided data to determine the diagnostic properties of these tests including sensitivity, specificity, and cut-off scores.

RESULTS

Results showed that combinations of four tests (ARHQ, text reading fluency, phonemic awareness, pseudoword reading) and their relative conditional cut-off scores optimize powerful discriminatory screening procedures for dyslexia, with an overall classification accuracy of approximately 90%.

CONCLUSIONS

The novel use of the conditional inference tree methodology explored in the present study offered a way of moving toward a more efficient screening battery using only a subset of the seven tests examined. Both clinical and theoretical implications of these findings are discussed.

QTL mapping reveals novel genes and mechanisms underlying variations in H2S production during alcoholic fermentation in Saccharomyces cerevisiae

Saccharomyces cerevisiae requirement for reduced sulfur to synthesize methionine and cysteine during alcoholic fermentation, is mainly fulfilled through the sulfur assimilation pathway. Saccharomyces cerevisiae reduces sulfate into sulfur dioxide (SO2) and sulfide (H2S), whose overproduction is a major issue in winemaking, due to its negative impact on wine aroma. The amount of H2S produced is highly strain-specific and also depends on SO2 concentration, often added to grape must. Applying a bulk segregant analysis to a 96-strain-progeny derived from two strains with different abilities to produce H2S, and comparing allelic frequencies along the genome of pools of segregants producing contrasting H2S quantities, we identified two causative regions involved in H2S production in the presence of SO2. A functional genetic analysis allowed the identification of variants in four genes able to impact H2S formation, viz; ZWF1, ZRT2, SNR2, and YLR125W, and involved in functions and pathways not associated with sulfur metabolism until now. These data point out that, in wine fermentation conditions, redox status, and zinc homeostasis are linked to H2S formation while providing new insights into the regulation of H2S production, and a new vision of the interplay between the sulfur assimilation pathway and cell metabolism.

M2OR: a database of olfactory receptor-odorant pairs for understanding the molecular mechanisms of olfaction

Mammalian sense of smell is triggered by interaction between odorant molecules and a class of proteins, called olfactory receptors (ORs). These receptors, expressed at the surface of olfactory sensory neurons, encode myriad of distinct odors via a sophisticated activation pattern. However, determining the molecular recognition spectrum of ORs remains a major challenge. The Molecule to Olfactory Receptor database (M2OR, https://m2or.chemsensim.fr/) provides curated data that allows an easy exploration of the current state of the research on OR-molecule interaction. We have gathered a database of 75,050 bioassay experiments for 51 395 distinct OR-molecule pairs. Drawn from published literature and public databases, M2OR contains information about OR responses to molecules and their mixtures, receptor sequences and experimental details. Users can obtain information on the activity of a chosen molecule or a group of molecules, or search for agonists for a specific OR or a group of ORs. Advanced search allows for fine-grained queries using various metadata such as species or experimental assay system, and the database can be queried by multiple inputs via a batch search. Finally, for a given search query, users can access and download a curated aggregation of the experimental data into a binarized combinatorial code of olfaction.

ATLAS: protein flexibility description from atomistic molecular dynamics simulations

Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances in the field of protein structure resolution and prediction, analysis and prediction of protein dynamic properties remains a major challenge, mostly due to the low accessibility of data and its diversity and heterogeneity. To address this issue, we present ATLAS, a database of standardised all-atom molecular dynamics simulations, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. ATLAS offers a large-scale view and valuable insights on protein dynamics for a large and representative set of proteins, by combining data obtained through molecular dynamics simulations with information extracted from experimental structures. Users can easily analyse dynamic properties of functional protein regions, such as domain limits (hinge positions) and residues involved in interaction with other biological molecules. Additionally, the database enables exploration of proteins with uncommon dynamic properties conditioned by their environment such as chameleon subsequences and Dual Personality Fragments. The ATLAS database is freely available at https://www.dsimb.inserm.fr/ATLAS.

Electrochemical Investigations of Sulfur-Decorated Organic Materials as Cathodes for Alkali Batteries

Alkali metal-sulfur batteries (particularly, lithium/sodium- sulfur (Li/Na-S)) have attracted much attention because of their high energy density, the natural abundance of sulfur, and environmental friendliness. However, Li/Na-S batteries still face big challenges, such as limited cycle life, poor conductivity, large volume changes, and the "shuttle effect" caused by the high solubility of Li/Na-polysulfides. Herein, novel organosulfur-containing materials, i.e., bis(4-hydroxy-2,2,6,6-tetramethylpiperidin-1-yl)disulfide (BiTEMPS-OH) and 2,4-thiophene/arene copolymer (TAC) are proposed as cathode materials for Li and Na batteries. BiTEMPS-OH shows an initial discharge/charge capacity of 353/192 mAh g-1 and a capacity of 62 mAh g-1 after 200 cycles at 100 mA g-1 in ether-based Li-ion electrolyte. Meanwhile, TAC has an initial discharge/charge capacity of 270/248 mAh g-1 and better cycling performance (106 mAh g-1 after 200 cycles) than BiTEMPS-OH in the same electrolyte. However, the rate capability of TAC is limited by the slow diffusion of Li-ions. Both materials show inferior electrochemical performances in Na battery cells compared to the Li analogs. X-ray powder diffraction reveals that BiTEMPS-OH loses its crystalline structure permanently upon cycling in Li battery cells. X-ray photoelectron spectroscopy demonstrates the cleavage and partially reversible formation of S-S bonds in BiTEMPS-OH and the formation/decomposition of thick solid electrolyte interphase on the electrode surface of TAC.