Le site de la baume Flandin (commune d’Orgnac-l’Aven) : nouvelles données sur ce gisement du Paléolithique moyen

The Baume Flandin, located in the Middle Rhone valley, yielded in the 1950s an archaeological level attributed to the Middle Palaeolithic, with abundant elongated flakes. This feature is rare in southern Europe before MIS 4. The cave was totally excavated and little evidence existed to confirm the date of this level, which was attributed to the ‘Riss–Würm’ according to the fauna remains and the sediments. New fieldwork took place in 2005, in front of the cave entrance, on the terrace. The study of the archaeological level that has been discovered brings new information on the age of the sequence of this site. The human occupation took place in the latest interglacial, at the end of isotopic stage 5e. This date leads us to revive the debate on the first evidence of the laminar debitage between northern and southern Europe.     

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses

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Molecular Reclassification of Crohn’s Disease: A Cautionary Note on Population Stratification

Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn’s disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility to Crohn’s disease is widely acknowledged and has been demonstrated by identification of over 100 CD associated genetic loci. However, relating CD subphenotypes to disease susceptible loci has proven to be a difficult task. In this paper we discuss the use of cluster analysis on genetic markers to identify genetic-based subgroups while taking into account possible confounding by population stratification. We show that it is highly relevant to consider the confounding nature of population stratification in order to avoid that detected clusters are strongly related to population groups instead of disease-specific groups. Therefore, we explain the use of principal components to correct for population stratification while clustering affected individuals into genetic-based subgroups. The principal components are obtained using 30 ancestry informative markers (AIM), and the first two PCs are determined to discriminate between continental origins of the affected individuals. Genotypes on 51 CD associated single nucleotide polymorphisms (SNPs) are used to perform latent class analysis, hierarchical and Partitioning Around Medoids (PAM) cluster analysis within a sample of affected individuals with and without the use of principal components to adjust for population stratification. It is seen that without correction for population stratification clusters seem to be influenced by population stratification while with correction clusters are unrelated to continental origin of individuals.     

Paleomicrobiology to investigate copper resistance in bacteria: isolation and description of Cupriavidus necator B9 in the soil of a medieval foundry

Remains of a medieval foundry were excavated by archaeologists in 2013 in Verdun (France). Ancient workshops specialized in brass and copper alloys were found with an activity between 13th to 16th c. Levels of Cu, Zn and Pb reached 20000, 7000 and 6000 mg kg^?1 (dw), respectively, in several soil horizons. The objective of the present work was to examine the microbial community in this contaminated site. A total of 8–22 10⁶ reads were obtained by shotgun metagenomics in four soil horizons. Bioinformatic analyses suggest the presence of complex bacterial communities dominated by Proteobacteria. The structure of the community was not affected by metals, contrary to the set of metal‐resistance genes. Using selective media, a novel strain of Cupriavidus necator (eutrophus), strain B9, was isolated. Its genome was sequenced and a novel metal resistance gene cluster with Hg resistance genes (merRTPCA) followed by 24 copper‐resistance genes (actP, cusCBAF, silP, copK1, copH4QLOFGJH3IDCBARS, copH2H1, copK2) was found. This cluster is partly homologous to the cop genes of Cupriavidus gilardii CR3 and C. metallidurans CH34. Proteomics indicated that the four copH genes were differentially expressed: CopH1 and CopH2 were mostly induced by Cd while CopH4 was highly expressed by Cu.     

Uropathogenic E. coli induces DNA damage in the bladder

Urinary tract infections (UTIs) are among the most common outpatient infections, with a lifetime incidence of around 60% in women. We analysed urine samples from 223 patients with community-acquired UTIs and report the presence of the cleavage product released during the synthesis of colibactin, a bacterial genotoxin, in 55 of the samples examined. Uropathogenic Escherichia coli strains isolated from these patients, as well as the archetypal E. coli strain UTI89, were found to produce colibactin. In a murine model of UTI, the machinery producing colibactin was expressed during the early hours of the infection, when intracellular bacterial communities form. We observed extensive DNA damage both in umbrella and bladder progenitor cells. To the best of our knowledge this is the first report of colibactin production in UTIs in humans and its genotoxicity in bladder cells.     

Rhesus macaques build new social connections after a natural disaster

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Alpha Reactivity to Complex Sounds Differs during REM Sleep and Wakefulness

We aimed at better understanding the brain mechanisms involved in the processing of alerting meaningful sounds during sleep, investigating alpha activity. During EEG acquisition, subjects were presented with a passive auditory oddball paradigm including rare complex sounds called Novels (the own first name - OWN, and an unfamiliar first name - OTHER) while they were watching a silent movie in the evening or sleeping at night. During the experimental night, the subjects’ quality of sleep was generally preserved. During wakefulness, the decrease in alpha power (8–12 Hz) induced by Novels was significantly larger for OWN than for OTHER at parietal electrodes, between 600 and 900 ms after stimulus onset. Conversely, during REM sleep, Novels induced an increase in alpha power (from 0 to 1200 ms at all electrodes), significantly larger for OWN than for OTHER at several parietal electrodes between 700 and 1200 ms after stimulus onset. These results show that complex sounds have a different effect on the alpha power during wakefulness (decrease) and during REM sleep (increase) and that OWN induce a specific effect in these two states. The increased alpha power induced by Novels during REM sleep may 1) correspond to a short and transient increase in arousal; in this case, our study provides an objective measure of the greater arousing power of OWN over OTHER, 2) indicate a cortical inhibition associated with sleep protection. These results suggest that alpha modulation could participate in the selection of stimuli to be further processed during sleep.     

Fixed vs. Random Temporal Predictability of Predation Risk: An Extension of the Risk Allocation Hypothesis

Predation is a strong selective force acting on prey animals. Predation is by nature highly variable in time; however, this aspect of predation risk has traditionally been overlooked by behavioural ecologists. Lima and Bednekoff proposed the predation risk allocation hypothesis (RAH), predicting how temporal variation in predation risk drives prey antipredator behaviours. This model is based on the concept that prey adaptively allocate their foraging and antipredator efforts across high‐ and low‐risk situations, depending on the duration of high‐ vs. low‐risk situations and the relative risk associated with each of them. An unstudied extension of the RAH is the effect of predictability of predation risk. A predictable risk should lead to prey displaying minimal vigilance behaviours during predictable low‐risk periods and the strongest antipredator behaviours during risky periods. Conversely, an unpredictable predation risk should result in prey displaying constant vigilance behaviour, with suboptimal foraging rates during periods of safety but antipredator behaviours of lower intensity during periods of risk. We tested this extension of the RAH using convict cichlids exposed to high‐risk alarm cues at two frequencies of risk (1× vs. 3×) per day, on either a fixed or random schedule for 5 d. We then tested the fish for a response to high‐risk cues (alarm cues) and to low‐risk cues (disturbance resulting from the introduction of distilled water). Our study supports previous results on the effects of risk frequency and cue intensity on cichlid behaviour. We failed to show an effect of risk predictability on the behavioural responses of cichlids to high‐risk alarm cues, but predictability did influence responses to low‐risk cues. We encourage further studies to test the effect of predictability in other systems.