Antibiotic research and development: business as usual?

This article contends that poor economic incentives are an important reason for the lack of new drugs and explains how the DRIVE-AB intends to change the landscape by harnessing the expertise, motivation and diversity of its partner

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Evolutionary ecophysiology in subterranean aquatic biotopes : influence of temperature variations on the distribution of Niphargus rhenorhodanensis and Proasellus valdensis

La température est le paramètre abiotique qui influence de façon majoritaire les traits d’histoire de vie des espèces ectothermes. Pour appréhender les relations entre physiologie, environnement et histoire évolutive et leur influence respective sur la délimitation des aires de distribution des espèces, ce travail exploite les caractéristiques thermiques du milieu souterrain. Les résultats réfutent l’hypothèse de sténothermie des deux organismes hypogés étudiés Niphargus rhenorhodanensis et Proasellus valdensis et prouvent que l’histoire évolutive, la dispersion ou la compétition sont des paramètres importants dans l’établissement des aires de distribution des espèces souterraines. En outre, ce travail caractérise pour la première fois chez des organismes souterrains, un gène codant pour des protéines de choc thermique et montre l’importante sensibilité cellulaire de N. rhenorhodanensis face à une augmentation de températureTemperature is the abiotic factor that most influences the life-history traits of ectothermic organisms. In order to study the relationships between physiology, environment and evolutionary history and their respective role in the determination of species distribution areas, this work takes advantage of the thermal caracteristics of subterranean aquatic biotopes. Our results refuted stenothermy in both studied hypogean organisms Niphargus rhenorhodanensis and Proasellus valdensis and they showed that evolutionary history, dispersal and competition are important factors that determine the distribution of subterranean species. Moreover, this work characterized for the first time in subterranean organisms a gene encoding heat shock proteins and demonstrated the high cellular sensitivity of N. rhenorhodanensis to increased water temperatur

Late summer community composition and abundance of photosynthetic picoeukaryotes in Norwegian and Barents Seas

10 pages, 6 figures, 2 tablesWe investigated marine picoeukaryotic diversity (cells ,3 mm) in samples collected in late summer 2002 at the boundary between the Norwegian, Greenland, and Barents Seas. The two main Arctic and Atlantic water masses in this region are separated by the polar front. We combined total counts of picoeukaryotes assemblages by flow cytometry and epifluorescence microscopy with taxa detection by tyramide signal amplification–fluorescent in situ hybridization (TSAFISH) and high performance liquid chromatography (HPLC) pigment analyses. The picoeukaryotic community was primarily composed of photoautotrophs (75% of the cells on average). Members of the division Chlorophyta, in particular the species Micromonas pusilla (Butcher) Manton and Parke, were the major components in truly Arctic waters (32% of the picoeukaryotes, maximum 3,200 cells ml21). M. pusilla was also well represented in coastal waters and at the polar front (25% of the picoeukaryotes, maximum 9,100 cells ml21). Haptophyta were prominent in more typical Atlantic waters (up to 35% of the picoeukaryotes, maximum 4,500 cells ml21). Quantification of haptophyte biomass by HPLC pigment analyses and CHEMTAX, and haptophyte abundances by TSA-FISH were in good agreement. This confirms previous studies, which suggested that M. pusilla is a dominant contributor of picoeukaryotic communities in both coastal and nutrient rich environments, whereas haptophytes seem to be more important in open seawatersPeer reviewe

Omicron Variant Escapes Therapeutic Monoclonal Antibodies (mAbs) Including Recently Released Evusheld®, Contrary to 8 Prior Main Variant of Concern (VOC)

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Female horses spontaneously identify a photograph of their keeper, last seen six months previously

International audienceHorses are capable of identifying individual conspecifics based on olfactory, auditory or visual cues. However, this raises the questions of their ability to recognize human beings and on the basis of what cues. This study investigated whether horses could differentiate between a familiar and unfamiliar human from photographs of faces. Eleven horses were trained on a discrimination task using a computer-controlled screen, on which two photographs were presented simultaneously (32 trials/ session): touching one was rewarded (S+) and the other not (S−). In the training phase, the S+ faces were of four unfamiliar people which gradually became familiar over the trials. The S− faces were novel for each trial. After the training phase, the faces of the horses’ keepers were presented opposite novel faces to test whether the horses could identify the former spontaneously. A reward was given whichever face was touched to avoid any possible learning effect. Horses touched the faces of keepers significantly more than chance, whether it was their current keeper or one they had not seen for six months (t = 3.65; p < 0.004 and t = 6.24; p < 0.0001). Overall, these results show that horses have advanced human facerecognition abilities and a long-term memory of those human faces

Do current environmental conditions explain physiological and metabolic responses of subterranean crustaceans to cold ?

International audienceSubterranean environments are characterized by the quasi absence of thermal variations (±1°C within a year), and organisms living in these biotopes for several millions of years, such as hypogean crustaceans, can be expected to have adapted to this very stable habitat. As hypogean organisms experience minimal thermal variation in their native biotopes, they should not be able to develop any particular cold adaptations to cope with thermal fluctuations. Indeed, physiological responses of organisms to an environmental stress are proportional to the amplitude of the stress they endure in their habitats. Surprisingly, previous studies have shown that a population of an aquatic hypogean crustacean, Niphargus rhenorhodanensis, exhibited a high level of cold hardiness. Subterranean environments thus appeared not to be following the classical above-mentioned theory. To confirm this counter-example, we studied seven karstic populations of N. rhenorhodanensis living in aquifers at approximately 10°C all year round and we analysed their behavioural, metabolic and biochemical responses during cold exposure (3°C). These seven populations showed reduced activities, and some cryoprotective molecules were accumulated. More surprisingly, the amplitude of the response varied greatly among the seven populations, despite their exposure to similar thermal conditions. Thus, the overall relationship that can be established between the amplitude of thermal variations and cold-hardiness abilities of ectotherm species may be more complex in subterranean crustaceans than in other arthropods

Matrix-Encoding Gene Diversity of 624 Influenza A/H3N2 Genomes Does Not Show Association with Impaired Viral Detection by Commercialized qPCR Assays

As for the case of SARS-CoV-2, genome sequencing of influenza viruses is of potential interest to raise and address virological issues. Recently, false-negativity of real-time reverse transcription-PCR (qPCR) assays that detect influenza A/H3N2 virus RNA were reported and associated with two mutations (A37T and C161T) in the Matrix-encoding (M1) gene located on viral segment 7. This triggered a national alert in France. The present study sought to assess the association between the presence of these mutations and potential false negative results of influenza A/H3N2 virus RNA detection by commercialized qPCR assays at the clinical virology laboratory of our university hospitals in southern France. This study focused on the genetic diversity in the M1 gene and segment 7 of 624 influenza A/H3N2 virus genomes obtained from respiratory samples having tested qPCR-positive with M1 gene-targeting assays in our clinical virology laboratory. A total of 585 among the 624 influenza A/H3N2 virus genomes (93.7%) were of clade 3C.2a1b.2a.2, and 39 (6.3%) were of clade 3C.2a1b.1a. M1 gene substitutions A37T and C161T were both present in 582 (93.3%) genomes, only of clade 3C.2a1b.2a.2. Substitution A37T was present in 621 (99.5%) genomes. Substitution C161T was present in 585 genomes (93.8%), all of clade 3C.2a1b.2a.2. Moreover, 21 other nucleotide positions were mutated in ≥90% of the genomes. The present study shows that A37T/C and C161T mutations, and other mutations in the M1 gene and segment 7, were widely present in influenza A/H3N2 virus genomes recovered from respiratory samples diagnosed qPCR-positive with commercialized assays

Human face recognition in horses: data in favor of a holistic process

International audienceRecent studies have demonstrated that horses can recognize humans based simply on visual information. However, none of these studies have investigated whether this involves the recognition of the face itself, or simply identifying people from non-complex external clues, such as hair color. To go beyond this we wanted to know whether certain features of the face were indispensable for this recognition (e.g., colors, hair or eyes). The 11 horses in this study had previously learned to identify four unfamiliar faces (portrait view and in color) presented repeatedly on a screen. We thus assessed whether they were able to identify these same faces spontaneously when they were presented in four other conditions: profile view, black and white, eyes hidden, changed hairstyle. The horses' performances remained higher than chance level for all the conditions. In a choice test under real conditions, they then approached the people whose face they had learned more often than unknown people. In conclusion, when considering all the individuals studied, no single facial element that we tested appears to be essential for recognition, suggesting holistic processing in face recognition. That means horses do not base their recognition solely on an easy clue such as hair color. They can also link faces from photographs with people in real life, indicating that horses do not process images of faces as simple abstract shapes

Concurrent Nanopore next-generation sequencing of Hepatitis B and Delta Virus genomes directly from patient plasma

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