Nonclinical safety assessment of an mRNA Covid-19 vaccine candidate following repeated administrations and biodistribution.

Messenger RNA (mRNA) vaccines have demonstrated efficacy against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in humans. mRNA technology holds tremendous potential for rapid control and prevention of emergencies due to its flexibility with respect to production, application, and design for an efficacious and safe use in humans. We assessed the toxicity and biodistribution of MRT5500, an mRNA vaccine encoding for the full-length of the SARS-CoV-2 spike protein and delivered by lipid nanoparticles (LNPs) containing a novel ionizable lipid, Lipid-1 in preclinical animal models. In the repeated dose toxicity study, rabbits received three intramuscular (IM) injections of MRT5500 at 3-week interval followed by a 4-week observation period. In an exploratory biodistribution study in mice receiving a single IM injection of an mRNA encoding luciferase encapsulated in an LNP containing Lipid-1, the expression of the luciferase protein was monitored in vivo and ex vivo at several time points. In the regulatory biodistribution study in rabbits receiving a single IM injection of MRT5500, the quantification of the mRNA and the ionizable Lipid-1 were monitored in the same organs and time points as in the exploratory biodistribution study. MRT5500 was safe and well-tolerated with a transient acute phase response/inflammation and an expected vaccine-related immunological response, typical of those observed following a vaccine administration. The biodistribution data demonstrated that the mRNA and Lipid-1 components of the vaccine formulations were mainly detected at the injection site and in the draining lymph nodes. These results support the use of MRT5500 and its deployment into clinical trials.

Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex.

The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterized a small orphan protein, Q9UZY3 (UniProt ID), conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (proteasome-activating nucleotidase [PAN]) as bait. X-ray crystallography and small-angle X-ray scattering experiments revealed that the protein is monomeric and adopts a ß-barrel core structure with an oligonucleotide/oligosaccharide-binding (OB)-fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays transfer ribonucleic acid (tRNA)-binding properties. Pull-downs, co-immunoprecipitation and isothermal titration calorimetry (ITC) studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi (Pa) cellular extracts. The protein was therefore named Pbp11, for Proteasome-Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA-processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.

IT/QA and Regulatory Aspects of Digital Pathology: Results of the 8th ESTP International Workshop.

Digital toxicologic histopathology has been broadly adopted in preclinical compound development for informal consultation and peer review. There is now increased interest in implementing the technology for good laboratory practice-regulated study evaluations. However, the implementation is not straightforward because systems and work processes require qualification and validation, with consideration also given to security. As a result of the high-throughput, high-volume nature of safety evaluations, computer performance, ergonomics, efficiency, and integration with laboratory information management systems are further key considerations. The European Society of Toxicologic Pathology organized an international expert workshop with participation by toxicologic pathologists, quality assurance/regulatory experts, and information technology experts to discuss qualification and validation of digital histopathology systems in a good laboratory practice environment, and to share the resulting conclusions broadly in the toxicologic pathology community.

RNA processing machineries in Archaea: the 5'-3' exoribonuclease aRNase J of the ß-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery.

A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the ß-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of ß-CASP RNase/helicase complex in archaeal RNA metabolism.

Direct Detection of miR-122 in Hepatotoxicity Using Dynamic Chemical Labeling Overcomes Stability and isomiR Challenges.

Circulating microRNAs are biomarkers reported to be stable and translational across species. MicroRNA-122 (miR-122) is a hepatocyte-specific microRNA biomarker for drug-induced liver injury (DILI). We developed a single molecule, dynamic chemical labeling (DCL) assay to directly detect miR-122 in blood. The DCL assay specifically measured miR-122 directly from 10 µL of serum or plasma without any extraction steps, with a limit of detection of 1.32 pM that enabled the identification of DILI. Testing of 192 human serum samples showed that DCL accurately identified patients at risk of DILI after acetaminophen overdose (area under ROC curve 0.98 (95% CI; 0.96-1), P < 0.0001). The DCL assay also identified liver injury in rats and dogs. The use of specific captured beads had the additional benefit of stabilizing miR-122 after sample collection, with no signal loss after 14 days at room temperature, in contrast to PCR that showed significant loss of signal. RNA sequencing demonstrated the presence of multiple miR-122 isomiRs in the serum of patients with DILI that were at low concentration or not present in healthy individuals. Sample degradation over time produced more isomiRs, particularly rapidly with DILI. PCR was inaccurate when analyzing miR-122 isomiRs, whereas the DCL assay demonstrated accurate quantification. We conclude that the DCL assay can accurately measure miR-122 to diagnose liver injury in humans and other species and can overcome microRNA stability and isomiR challenges.

Scientific and Regulatory Policy Committee Points to Consider*: Approaches to the Conduct and Interpretation of Vaccine Safety Studies for Clinical and Anatomic Pathologists.

The design and execution of toxicology studies supporting vaccine development have some unique considerations relative to those supporting traditional small molecules and biologics. A working group of the Society of Toxicologic Pathology Scientific and Regulatory Policy Committee conducted a review of the scientific, technical, and regulatory considerations for veterinary pathologists and toxicologists related to the design and evaluation of regulatory toxicology studies supporting vaccine clinical trials. Much of the information in this document focuses on the development of prophylactic vaccines for infectious agents. Many of these considerations also apply to therapeutic vaccine development (such as vaccines directed against cancer epitopes); important differences will be identified in various sections as appropriate. The topics addressed in this Points to Consider article include regulatory guidelines for nonclinical vaccine studies, study design (including species selection), technical considerations in dosing and injection site collection, study end point evaluation, and data interpretation. The intent of this publication is to share learnings related to nonclinical studies to support vaccine development to help others as they move into this therapeutic area. [Box: see text].

Physical and functional interplay between PCNA DNA clamp and Mre11-Rad50 complex from the archaeon Pyrococcus furiosus.

Several archaeal species prevalent in extreme environments are particularly exposed to factors likely to cause DNA damages. These include hyperthermophilic archaea (HA), living at temperatures >70°C, which arguably have efficient strategies and robust genome guardians to repair DNA damage threatening their genome integrity. In contrast to Eukarya and other archaea, homologous recombination appears to be a vital pathway in HA, and the Mre11-Rad50 complex exerts a broad influence on the initiation of this DNA damage response process. In a previous study, we identified a physical association between the Proliferating Cell Nuclear Antigen (PCNA) and the Mre11-Rad50 (MR) complex. Here, by performing co-immunoprecipitation and SPR analyses, we identified a short motif in the C- terminal portion of Pyrococcus furiosus Mre11 involved in the interaction with PCNA. Through this work, we revealed a PCNA-interaction motif corresponding to a variation on the PIP motif theme which is conserved among Mre11 sequences of Thermococcale species. Additionally, we demonstrated functional interplay in vitro between P. furiosus PCNA and MR enzymatic functions in the DNA end resection process. At physiological ionic strength, PCNA stimulates MR nuclease activities for DNA end resection and promotes an endonucleolytic incision proximal to the 5' strand of double strand DNA break.

Connecting Few-Body Inelastic Decay to Quantum Correlations in a Many-Body System: A Weakly Coupled Impurity in a Resonant Fermi Gas.

We study three-body recombination in an ultracold Bose-Fermi mixture. We first show theoretically that, for weak interspecies coupling, the loss rate is proportional to Tan's contact. Second, using a ^{7}Li/^{6}Li mixture we probe the recombination rate in both the thermal and dual superfluid regimes. We find excellent agreement with our model in the BEC-BCS crossover. At unitarity where the fermion-fermion scattering length diverges, we show that the loss rate is proportional to n_{f}^{4/3}, where n_{f} is the fermionic density. This unusual exponent signals nontrivial two-body correlations in the system. Our results demonstrate that few-body losses can be used as a quantitative probe of quantum correlations in many-body ensembles.

Critical Velocity and Dissipation of an Ultracold Bose-Fermi Counterflow.

We study the dynamics of counterflowing bosonic and fermionic lithium atoms. First, by tuning the interaction strength we measure the critical velocity v(c) of the system in the BEC-BCS crossover in the low temperature regime and we compare it to the recent prediction of Castin et al., C. R. Phys. 16, 241 (2015). Second, raising the temperature of the mixture slightly above the superfluid transitions reveals an unexpected phase locking of the oscillations of the clouds induced by dissipation.

Momentum Distribution of a Dilute Unitary Bose Gas with Three-Body Losses.

Using a combination of Boltzmann's equation and virial expansion, we study the effect of three-body losses and interactions on the momentum distribution of a homogeneous unitary Bose gas in the dilute limit where quantum correlations are negligible. The comparison of our results to the recent measurement made at JILA on a unitary gas of ^{85}Rb allows us to determine an experimental fugacity z=0.5(1).

Development of Mass Spectrometry Imaging on skeletal muscle to characterize the local pro-inflammatory and pro-resolution lipid responses in a vaccination context.

Vaccine reactogenicity is well documented at the clinical level but the mechanism involved at the local or systemic level are still poorly understood. Muscular tissue where most vaccines are administered is the first place of interaction between the vaccine formulation and the host's immune cells. So far, this site of vaccine administration is not well documented from a mechanistic standpoint. The study of early molecular events at the injection site is crucial to understand the local response to vaccines. In this paper, we report a standardized workflow, from the injection of vaccine formulations in rabbit muscle, to the analysis by desorption electrospray ionization and histology staining to understand the role of lipids involved in the inflammation and its resolution on striated muscular tissue. The analysis of lipid mediators was optimized at the site of needle insertion to allow the spatial comparison of cellular infiltrates at the injection site. We showed that lipids were distributed across the spatial tissue morphology in a time-dependent manner. The MS imaging applied to vaccinology could pave the way to a better understanding of vaccine reactogenicity and mechanism of action.

Cooperation between two modes for DNA replication initiation in the archaeon Thermococcus barophilus.

The mechanisms underpinning the replication of genomic DNA have recently been challenged in Archaea. Indeed, the lack of origin of replication has no deleterious effect on growth, suggesting that replication initiation relies on homologous recombination. Recombination-dependent replication (RDR) appears to be based on the recombinase RadA, which is of absolute requirement when no initiation origins are detected. The origin of this flexibility in the initiation of replication and the extent to which it is used in nature are yet to be understood. Here, we followed the process of DNA replication throughout the growth stages of Thermococcus barophilus. We combined deep sequencing and genetics to elucidate the dynamics of oriC utilization according to growth phases. We discovered that in T. barophilus, the use of oriC diminishes from the lag to the middle of the log phase, and subsequently increases gradually upon entering the stationary phase. Although oriC demonstrates no indispensability, RadA does exhibit essentiality. Notably, a knockdown mutant strain provides confirmation of the pivotal role of RadA in RDR for the first time. Thus, we demonstrate the existence of a tight combination between oriC utilization and homologous recombination to initiate DNA replication along the growth phases. Overall, this study demonstrates how diverse physiological states can influence the initiation of DNA replication, offering insights into how environmental sensing might impact this fundamental mechanism of life. IMPORTANCE: Replication of DNA is highly important in all organisms. It initiates at a specific locus called ori, which serves as the binding site for scaffold proteins-either Cdc6 or DnaA-depending on the domain of life. However, recent studies have shown that the Archaea, Haloferax volcanii and Thermococcus kodakarensis could subsist without ori. Recombination-dependent replication (RDR), via the recombinase RadA, is the mechanism that uses homologous recombination to initiate DNA replication. The extent to which ori's use is necessary in natural growth remains to be characterized. In this study, using Thermococcus barophilus, we demonstrated that DNA replication initiation relies on both oriC and RDR throughout its physiological growth, each to varying degrees depending on the phase. Notably, a knockdown RadA mutant confirmed the prominent use of RDR during the log phase. Moreover, the study of ploidy in oriC and radA mutant strains showed that the number of chromosomes per cell is a critical proxy for ensuring proper growth and cell survival.

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

The secretome of Thermococcus barophilus in the presence of carbohydrates and the potential role of the TrmBL4 regulator.

Global transcriptional regulators are crucial for supporting rapid adaptive responses in changing environments. In Thermococcales, the TrmB sugar-sensing regulator family is well represented but knowledge of the functional role/s of each of its members is limited. In this study, we examined the link between TrmBL4 and the degree of protein secretion in different sugar environments in the hyperthermophilic Archaeon Thermococcus barophilus. Although the absence of TrmBL4 did not induce any growth defects, proteomics analysis revealed different secretomes depending on the sugar and/or genetic contexts. Notably, 33 secreted proteins present in the supernatant were differentially detected. Some of these proteins are involved in sugar assimilation and transport, such as the protein encoded by TERMP_01455 (cyclomaltodextrin glucanotransferase), whereas others have intracellular functions, such as the protein encoded by TERMP_01556 (pyruvate: ferredoxin oxidoreductase Δsubunit). Then, using reverse transcription quantitative polymerase chain reaction experiments, we observed effective transcription regulation by TrmBL4 of the genes encoding at least two ABC-type transporters according to sugar availability.

Does the type of anesthesia (regional vs. general) represent an independent predictor for in-hospital complications in operatively treated malleolar fractures? A retrospective analysis of 5262 patients.

PURPOSE: The impact of the type of anesthesia (regional vs. general anesthesia) on in-hospital complications in ankle fractures has not been thoroughly studied yet. Identifying factors that place patients at risk for complications following ankle fractures may help reduce their occurrence. The primary goal of this study was (1) to describe the cohort of patients and (2) to evaluate independent risk factors for complications during hospitalization. METHODS: We analyzed patients from 2005 to 2019 with an operatively treated isolated fracture of the medial or lateral malleolus using a prospective national quality measurement database. Patients were selected based on international classifications (ICD) and national procedural codes (CHOP). Uni- and multivariate analysis were applied. RESULTS: In total, we analyzed 5262 patients who suffered a fracture of the malleolus; 3003 patients (57%) had regional and 2259 (43%) general anesthesia. Patients with regional anesthesia were significantly older (51 vs. 46 years), but healthier (23 vs. 28% comorbidities) than patients who received general anesthesia. The in-hospital complication rate was not significantly lower in regional anesthesia (2.2% vs 3.0%). The type of anesthesia was not an independent predictor for complications while controlling for confounders. CONCLUSION: Type of anesthesia was not an independent predictor of complications; however, higher ASA class, age over 70 years, fracture of the medial versus lateral malleolus, longer preoperative stay, and duration of surgery were significant predictors of complications. Patient and procedure characteristics, as well as changes in medical care and epidemiological changes along with patient requests, influenced the choice of the type of anesthesia.

DNA-binding mechanism and evolution of replication protein A.

Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.

Interaction between pedestrians and automated vehicles: Perceived safety of yielding behaviors and benefits of an external human-machine interface for elderly people.

This study focuses on Automated Vehicles (AVs) interactions with pedestrians during road crossing situations. A dual-phase experiment was designed: one from the pedestrian's perspective and the other one from the AV passenger's point of view. Eight AV behaviors to yield were investigated. Participants' task was to assess the safety of each one of these yielding behaviors. Moreover, an external HMI (eHMI) was designed to support them in these interactions. 40 participants were involved in this experiment (50% females, 20 young versus 20 elderly). Results obtained show significant differences between old and young participants: elderly people have not the same way to perceive and assess the safety of the yielding behaviors from "the inside" and from "the outside" of the car. Conversely, young participants assessed AV behaviors similarly whether as pedestrians or as AV passengers. When considering benefits introduced by the eHMI, it significantly reduces differences between old and young participants and tends to harmonize their safety assessments: with to the eHMI, elderly people are more able to adequately perceive and assess the safety/dangerousness of the AV braking manoeuvers, and their safety judgments become at last quite similar to those of young participants. Moreover, the eHMI increases participants' Acceptance of AV and reduces their concerns about their future interactions with AV as a pedestrian, especially for elderly people.

Opto-electrochemical nanosensor array for remote DNA detection.

A high-density array of opto-electrochemical nanosensors is presented for remote DNA detection. It was fabricated by chemical etching of a coherent optical fibre bundle to produce a nanotip array. The surface of the etched bundle was sputter-coated with a thin ITO layer which was eventually insulated by an electrophoretic paint. The fabrication steps produced a high-density array of electrochemical nanosensors which retains the optical fibre bundle architecture and its imaging properties. A DNA probe was then immobilized on the nanosensor array surface in a polypyrrole film by electropolymerisation. After hybridisation with the complementary sequence, detection of the strepavidin-R-phycoerythrin label is performed by fluorescence imaging through the optical fibre bundle itself. Control experiments and regeneration steps have also been successfully demonstrated on this nanostructured opto-electrochemical platform.

Cortical Activity Linked to Clocking in Deaf Adults: fNIRS Insights with Static and Animated Stimuli Presentation.

The question of the possible impact of deafness on temporal processing remains unanswered. Different findings, based on behavioral measures, show contradictory results. The goal of the present study is to analyze the brain activity underlying time estimation by using functional near infrared spectroscopy (fNIRS) techniques, which allow examination of the frontal, central and occipital cortical areas. A total of 37 participants (19 deaf) were recruited. The experimental task involved processing a road scene to determine whether the driver had time to safely execute a driving task, such as overtaking. The road scenes were presented in animated format, or in sequences of 3 static images showing the beginning, mid-point, and end of a situation. The latter presentation required a clocking mechanism to estimate the time between the samples to evaluate vehicle speed. The results show greater frontal region activity in deaf people, which suggests that more cognitive effort is needed to process these scenes. The central region, which is involved in clocking according to several studies, is particularly activated by the static presentation in deaf people during the estimation of time lapses. Exploration of the occipital region yielded no conclusive results. Our results on the frontal and central regions encourage further study of the neural basis of time processing and its links with auditory capacity.

Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase.

Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.