Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency.

Optimizing plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintaining crop yield and reducing environmental pollution. This study aimed at identifying quantitative trait loci (QTLs) and differentially expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterized a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in a greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population. Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven QTLs were detected for three target traits (leaf N content, leaf nitrogen balance index, and petiole NO3- content), 10 and six in the low and high N condition, respectively, while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4752 and 2405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3628 (50.6%) in leaves and 1717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1677 DEGs were shared between organs or tissues. Finally, we integrated DEG and QTL analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding tomato varieties requiring less N input.

Assessment of Non-cultured Autologous Epidermal Cell Grafting Resuspended in Hyaluronic Acid for Repigmenting Vitiligo and Piebaldism Lesions: A Randomized Clinical Trial.

The aim of this study was to assess the efficacy of non-cultured autologous epidermal cell grafting resuspended in hyaluronic acid, performed using a ready-to-use kit, compared with hyaluronic acid alone (neutral comparator) for repigmenting vitiligo and piebaldism lesions at 6 months. Two identified paired lesions per patient were randomized to be treated by either device. Devices with a ready-to-use kit were prepared by separate health professionals, to maintain blinding. A skin biopsy was digested using trypsin, and cells resuspended in hyaluronic acid solution. Among 38 patients screened, 36 (94.7%) patients, corresponding to 72 lesions, were analysed. For difficult-to-treat lesions, defined as those located on the wrist, elbow, and hands (n = 30), no repigmentation ≥ 50% was observed. For all other locations (n = 42), the success rate was significantly higher (p = 0.021) in the ready-to-use kit group (47.6% vs 9.5%) at 6 months and was maintained until 12 months. In conclusion, a single application of non-cultured epidermal cellular grafting using a ready-to-use kit was efficient at 6 months and at 1-year follow-up.

Correction to: Urine cell cycle arrest biomarkers distinguish poorly between transient and persistent AKI in early septic shock: a prospective, multicenter study.

An amendment to this paper has been published and can be accessed via the original article.

Urine cell cycle arrest biomarkers distinguish poorly between transient and persistent AKI in early septic shock: a prospective, multicenter study.

BACKGROUND: The urine biomarkers tissue inhibitor of metalloproteinases-2 (TIMP-2) and insulin-like growth factor-binding protein 7 (IGFBP7) have been validated for predicting and stratifying AKI. In this study, we analyzed the utility of these biomarkers for distinguishing between transient and persistent AKI in the early phase of septic shock. METHODS: We performed a prospective, multicenter study in 11 French ICUs. Patients presenting septic shock, with the development of AKI within the first 6 h, were included. Urine [TIMP-2]*[IGFBP7] was determined at inclusion (0 h), 6 h, 12 h, and 24 h. AKI was considered transient if it resolved within 3 days. Discriminative power was evaluated by receiver operating characteristic (ROC) curve analysis. RESULTS: We included 184 patients, within a median [IQR] time of 1.0 [0.0-3.0] h after norepinephrine (NE) initiation; 100 (54%) patients presented transient and 84 (46%) presented persistent AKI. Median [IQR] baseline urine [TIMP-2]*[IGFBP7] was higher in the persistent AKI group (2.21 [0.81-4.90] (ng/ml)2/1000) than in the transient AKI group (0.75 [0.20-2.12] (ng/ml)2/1000; p < 0.001). Baseline urine [TIMP-2]*[IGFBP7] was poorly discriminant, with an AUROC [95% CI] of 0.67 [0.59-0.73]. The clinical prediction model combining baseline serum creatinine concentration, baseline urine output, baseline NE dose, and baseline extrarenal SOFA performed well for the prediction of persistent AKI, with an AUROC [95% CI] of 0.81 [0.74-0.86]. The addition of urine [TIMP-2]*[IGFBP7] to this model did not improve the predictive performance. CONCLUSIONS: Urine [TIMP-2]*[IGFBP7] measurements in the early phase of septic shock discriminate poorly between transient and persistent AKI and do not improve clinical prediction over that achieved with the usual variables. TRIAL REGISTRATION: NCT02812784.

Chikungunya antibodies detected in non-human primates and rats in three Indian Ocean islands after the 2006 ChikV outbreak.

The role of terrestrial vertebrates in the epidemiology of chikungunya disease is poorly understood. We evaluated their exposure and amplification role during the 2006 chikungunya outbreak in the Indian Ocean. Blood samples were collected from 18 mammalian and reptile species from Reunion Island, Mauritius and Mayotte. Among the 1051 samples serologically tested for chikungunya virus (CHIKV), two crab-eating macaques (Macaca fascicularis) and two ship rats (Rattus rattus) proved to be exposed to CHIKV. CHIKV RNA was not detected in 791 analyzed sera. Our results confirm the preferential infection of simian primates and suggest that other vertebrates played a poor or no role in CHIKV transmission during the 2006 outbreak.

Divergent evolutionary processes associated with colonization of offshore islands.

Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common vole (Microtus arvalis), a species found in continental Europe but not in Britain. Among possible colonization scenarios, our results are most consistent with human introduction at least 5100 bp (confirmed by radiocarbon dating). We used approximate Bayesian computation of population history to infer the coast of Belgium as the possible source and estimated the evolutionary timescale using a Bayesian coalescent approach. We showed substantial morphological divergence of the island populations, including a size increase presumably driven by selection and reduced microsatellite variation likely reflecting founder events and genetic drift. More surprisingly, our results suggest that a recent and widespread cytb replacement event in the continental source area purged cytb variation there, whereas the ancestral diversity is largely retained in the colonized islands as a genetic 'ark'. The replacement event in the continental M. arvalis was probably triggered by anthropogenic causes (land-use change). Our studies illustrate that small offshore islands can act as field laboratories for studying various evolutionary processes over relatively short timescales, informing about the mainland source area as well as the island.

Why has the epidemiology of RSV changed during the COVID-19 pandemic?

The coronavirus disease 2019 (COVID-19) pandemic has drastically perturbed the epidemiology of Respiratory Syncytial Virus (RSV) respiratory tract infections in children. The reasons for this are not clear. In this article, we review the current literature and critically discuss the different theories to explain why the epidemiology of RSV has changed during the COVID-19 pandemic. Proposed mechanisms include decreased viral immunity in vulnerable age groups caused by the prolonged lack of RSV circulation early in the pandemic, potential Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2)-induced immune dysregulation, viral interactions between SARS-CoV-2 and RSV, and modifications in health-seeking behaviors as well as heath systems factors. Research in viral genomics and phylogeny, and more robust immunology research is needed to guide RSV prevention and health care resource planning.

The flying fox Pteropus seychellensis of Mayotte (Comoros): method of capture and blood sampling.

Pteropus seychellensis comorensis is the only Pteropodidae bat species on the island of Mayotte (Comoros Archipelago), and most aspects of its biology are unknown. In order to catch this large bat, we used a simple and low-cost method, consisting of raised mist nets that were set close to foraging sites. Major factors driving catch success were high food availability, good positioning of mist nets, and careful observation of movement patterns to identify foraging sites where the chances of capture are high. Blood was collected from the alar and humeral veins, which appear to be more practical for this purpose than other parts of the venous system.

Parallel assessment of male reproductive function in workers and wild rats exposed to pesticides in banana plantations in Guadeloupe.

BACKGROUND: There is increasing evidence that reproductive abnormalities are increasing in frequency in both human population and among wild fauna. This increase is probably related to exposure to toxic contaminants in the environment. The use of sentinel species to raise alarms relating to human reproductive health has been strongly recommended. However, no simultaneous studies at the same site have been carried out in recent decades to evaluate the utility of wild animals for monitoring human reproductive disorders. We carried out a joint study in Guadeloupe assessing the reproductive function of workers exposed to pesticides in banana plantations and of male wild rats living in these plantations. METHODS: A cross-sectional study was performed to assess semen quality and reproductive hormones in banana workers and in men working in non-agricultural sectors. These reproductive parameters were also assessed in wild rats captured in the plantations and were compared with those in rats from areas not directly polluted by humans. RESULTS: No significant difference in sperm characteristics and/or hormones was found between workers exposed and not exposed to pesticide. By contrast, rats captured in the banana plantations had lower testosterone levels and gonadosomatic indices than control rats. CONCLUSION: Wild rats seem to be more sensitive than humans to the effects of pesticide exposure on reproductive health. We conclude that the concept of sentinel species must be carefully validated as the actual nature of exposure may varies between human and wild species as well as the vulnerable time period of exposure and various ecological factors.

Invasive rodent eradication on islands.

Invasive mammals are the greatest threat to island biodiversity and invasive rodents are likely responsible for the greatest number of extinctions and ecosystem changes. Techniques for eradicating rodents from islands were developed over 2 decades ago. Since that time there has been a significant development and application of this conservation tool. We reviewed the literature on invasive rodent eradications to assess its current state and identify actions to make it more effective. Worldwide, 332 successful rodent eradications have been undertaken; we identified 35 failed eradications and 20 campaigns of unknown result. Invasive rodents have been eradicated from 284 islands (47,628 ha). With the exception of two small islands, rodenticides were used in all eradication campaigns. Brodifacoum was used in 71% of campaigns and 91% of the total area treated. The most frequent rodenticide distribution methods (from most to least) are bait stations, hand broadcasting, and aerial broadcasting. Nevertheless, campaigns using aerial broadcast made up 76% of the total area treated. Mortality of native vertebrates due to nontarget poisoning has been documented, but affected species quickly recover to pre-eradication population levels or higher. A variety of methods have been developed to mitigate nontarget impacts, and applied research can further aid in minimizing impacts. Land managers should routinely remove invasive rodents from islands <100 ha that lack vertebrates susceptible to nontarget poisoning. For larger islands and those that require nontarget mitigation, expert consultation and greater planning effort are needed. With the exception of house mice (Mus musculus), island size may no longer be the limiting factor for rodent eradications; rather, social acceptance and funding may be the main challenges. To be successful, large-scale rodent campaigns should be integrated with programs to improve the livelihoods of residents, island biosecurity, and reinvasion response programs.

Population genetics, community of parasites, and resistance to rodenticides in an urban brown rat (Rattus norvegicus) population.

Brown rats are one of the most widespread urban species worldwide. Despite the nuisances they induce and their potential role as a zoonotic reservoir, knowledge on urban rat populations remains scarce. The main purpose of this study was to characterize an urban brown rat population from Chanteraines park (Hauts-de-Seine, France), with regards to haematology, population genetics, immunogenic diversity, resistance to anticoagulant rodenticides, and community of parasites. Haematological parameters were measured. Population genetics was investigated using 13 unlinked microsatellite loci. Immunogenic diversity was assessed for Mhc-Drb. Frequency of the Y139F mutation (conferring resistance to rodenticides) and two linked microsatellites were studied, concurrently with the presence of anticoagulant residues in the liver. Combination of microscopy and molecular methods were used to investigate the occurrence of 25 parasites. Statistical approaches were used to explore multiple parasite relationships and model parasite occurrence. Eighty-six rats were caught. The first haematological data for a wild urban R. norvegicus population was reported. Genetic results suggested high genetic diversity and connectivity between Chanteraines rats and surrounding population(s). We found a high prevalence (55.8%) of the mutation Y139F and presence of rodenticide residues in 47.7% of the sampled individuals. The parasite species richness was high (16). Seven potential zoonotic pathogens were identified, together with a surprisingly high diversity of Leptospira species (4). Chanteraines rat population is not closed, allowing gene flow and making eradication programs challenging, particularly because rodenticide resistance is highly prevalent. Parasitological results showed that co-infection is more a rule than an exception. Furthermore, the presence of several potential zoonotic pathogens, of which four Leptospira species, in this urban rat population raised its role in the maintenance and spread of these pathogens. Our findings should stimulate future discussions about the development of a long-term rat-control management program in Chanteraines urban park.

Eradications as scientific experiments: progress in simultaneous eradications of two major invasive taxa from a Mediterranean island.

BACKGROUND: Black rats, Rattus rattus, and mat-forming iceplants, Carpobrotus aff. acinaciformis and Carpobrotus edulis, are pervasive pests on Mediterranean islands. Their cumulative impacts on native biotas alter the functioning of island ecosystems and threaten biodiversity. A report is given here of the first attempt to eradicate both taxa from a protected nature reserve in south-eastern France (Bagaud Island). In order to minimise unwanted hazardous outcomes and produce scientific knowledge, the operations were embedded in a four-step strategy including initial site assessment, planning, restoration and monitoring. RESULTS: Trapping, which resulted in the removal of 1923 rats in 21 045 trap-nights, made it possible to eliminate a substantial proportion of the resident rat population and to reduce the amount of rodenticide delivered in the second stage of the operation. Forty tons of Carpobrotus spp. were manually uprooted from a total area of 18 000 m(2) ; yet careful monitoring over a decade is still required to prevent germinations from the seed bank. CONCLUSION: Two years after the beginning of the interventions, both eradication operations are still ongoing. Biosecurity measures have been implemented to reduce reinvasion risks of both taxa. With the long-term monitoring of various native plants and animals, Bagaud Island will become a reference study site for scientific purposes.

The changing pace of insular life: 5000 years of microevolution in the Orkney vole (Microtus arvalis orcadensis).

Island evolution may be expected to involve fast initial morphological divergence followed by stasis. We tested this model using the dental phenotype of modern and ancient common voles (Microtus arvalis), introduced onto the Orkney archipelago (Scotland) from continental Europe some 5000 years ago. First, we investigated phenotypic divergence of Orkney and continental European populations and assessed climatic influences. Second, phenotypic differentiation among Orkney populations was tested against geography, time, and neutral genetic patterns. Finally, we examined evolutionary change along a time series for the Orkney Mainland. Molar gigantism and anterior-lobe hypertrophy evolved rapidly in Orkney voles following introduction, without any transitional forms detected. Founder events and adaptation appear to explain this initial rapid evolution. Idiosyncrasy in dental features among different island populations of Orkney voles is also likely the result of local founder events following Neolithic translocation around the archipelago. However, against our initial expectations, a second marked phenotypic shift occurred between the 4th and 12th centuries AD, associated with increased pastoral farming and introduction of competitors (mice and rats) and terrestrial predators (foxes and cats). These results indicate that human agency can generate a more complex pattern of morphological evolution than might be expected in island rodents.

Impacts of biological invasions: what's what and the way forward.

Study of the impacts of biological invasions, a pervasive component of global change, has generated remarkable understanding of the mechanisms and consequences of the spread of introduced populations. The growing field of invasion science, poised at a crossroads where ecology, social sciences, resource management, and public perception meet, is increasingly exposed to critical scrutiny from several perspectives. Although the rate of biological invasions, elucidation of their consequences, and knowledge about mitigation are growing rapidly, the very need for invasion science is disputed. Here, we highlight recent progress in understanding invasion impacts and management, and discuss the challenges that the discipline faces in its science and interactions with society.

Seabird modulations of isotopic nitrogen on islands.

The transport of nutrients by migratory animals across ecosystem boundaries can significantly enrich recipient food webs, thereby shaping the ecosystems' structure and function. To illustrate the potential role of islands in enabling the transfer of matter across ecosystem boundaries to be gauged, we investigated the influence of seabirds on nitrogen input on islands. Basing our study on four widely differing islands in terms of their biogeography and ecological characteristics, sampled at different spatial and temporal intervals, we analyzed the nitrogen isotopic values of the main terrestrial ecosystem compartments (vascular plants, arthropods, lizards and rodents) and their relationship to seabird values. For each island, the isotopic values of the ecosystem were driven by those of seabirds, which ultimately corresponded to changes in their marine prey. First, terrestrial compartments sampled within seabird colonies were the most enriched in δ(15)N compared with those collected at various distances outside colonies. Second, isotopic values of the whole terrestrial ecosystems changed over time, reflecting the values of seabirds and their prey, showing a fast turnover throughout the ecosystems. Our results demonstrate that seabird-derived nutrients not only spread across the terrestrial ecosystems and trophic webs, but also modulate their isotopic values locally and temporally on these islands. The wealth of experimental possibilities in insular ecosystems justifies greater use of these model systems to further our understanding of the modalities of trans-boundary nutrient transfers.

Modeling and using a web-based and tutored portfolio to support certification of professional competence in transfusion medicine.

In order to manage a nationwide assessment program leading to certification of professional competence in blood transfusion throughout France, the National Institute of Blood Transfusion (INTS) and the University of Nice-Sophia Antipolis designed and developed a structured and tutored web-based portfolio. The entire process of certification has been approved by the national healthcare agency (HAS). Eleven assessment programs have been written. The structure of this e-portfolio is based on a matrix of actions defined according to standards of practice. For each action, elements of proof are uploaded by the physician and peer-reviewed by an expert (a tutor) before validation. The electronic portfolio stores all the history of the actions performed by users. This tracking feature generates alerts which are e-mailed to users (physicians and tutors) according to a list of monitored events. After one year of design and development, the application is now being used routinely.

Establishing causes of eradication failure based on genetics: case study of ship rat eradication in Ste. Anne archipelago.

Determining the causes of a failed eradication of a pest species is important because it enables an argued adjustment of the methodologies used and the improvement of the protocols for future attempts. We examined how molecular monitoring can help distinguish between the two main reasons for an eradication failure (i.e., survival of some individuals vs. recolonization after eradication). We investigated genetic variation in seven microsatellite loci in ship rat (Rattus rattus) populations from four islets off the Martinique coast (French Caribbean). In 1999 an eradication attempt was conducted on the four islets. Three years later rats were observed again on two of them. We compared the genetic signatures of the populations before and after the eradication attempt. On one of the islands, the new rat population was likely a subset of the pre-eradication population. A weak genetic differentiation was found between them, with almost no new alleles observed in the new population and moderate F(ST) values (0.15). Moreover, assignment procedures clustered the two populations together. In contrast, on the other islet, many new alleles were observed after the eradication attempt, resulting in an increase in genetic diversity (from 2.57 to 3.57 mean number of alleles per locus) and strong F(ST) values (0.39). Moreover, genetic clustering clearly separated the two samples (i.e., before and after the eradication attempt) in two different populations. Thus, to achieve long-term eradication on these islets, it seems necessary to redevelop the eradication procedure to avoid individuals surviving and to prevent reinvasion, probably from the mainland, by installing permanent trapping and poisoning devices and conducting regular monitoring. We strongly encourage wildlife managers conducting eradication campaigns to integrate molecular biological tools in their protocols, which can be done easily for most common invasive species.

Genetic divergence in the small Indian mongoose (Herpestes auropunctatus), a widely distributed invasive species.

The combination of founder events, random drift and new selective forces experienced by introduced species typically lowers genetic variation and induces differentiation from the ancestral population. Here, we investigate microsatellite differentiation between introduced and native populations of the small Indian mongoose (Herpestes auropunctatus). Many expectations based on introduction history, such as loss of alleles and relationships among populations, are confirmed. Nevertheless, when applying population assignment methods to our data, we observe a few specimens that are incorrectly assigned and/or appear to have a mixed ancestry, despite estimates of substantial population differentiation. Thus, we suggest that population assignments of individuals should be viewed as tentative and that there should be agreement among different algorithms before assignments are applied in conservation or management. Further, we find no congruence between previously reported morphological differentiation and the sorting of microsatellite variation. Some introduced populations have retained much genetic variation while others have not, irrespective of morphology. Finally, we find alleles from the sympatric grey mongoose (Herpestes edwardsii) in one small Indian mongoose within the native range, suggesting an alternative explanation for morphological differentiation involving a shift in female preferences in allopatry.

Mammal invaders on islands: impact, control and control impact.

The invasion of ecosystems by exotic species is currently viewed as one of the most important sources of biodiversity loss. The largest part of this loss occurs on islands, where indigenous species have often evolved in the absence of strong competition, herbivory, parasitism or predation. As a result, introduced species thrive in those optimal insular ecosystems affecting their plant food, competitors or animal prey. As islands are characterised by a high rate of endemism, the impacted populations often correspond to local subspecies or even unique species. One of the most important taxa concerning biological invasions on islands is mammals. A small number of mammal species is responsible for most of the damage to invaded insular ecosystems: rats, cats, goats, rabbits, pigs and a few others. The effect of alien invasive species may be simple or very complex, especially since a large array of invasive species, mammals and others, can be present simultaneously and interact among themselves as well as with the indigenous species. In most cases, introduced species generally have a strong impact and they often are responsible for the impoverishment of the local flora and fauna. The best response to these effects is almost always to control the alien population, either by regularly reducing their numbers, or better still, by eradicating the population as a whole from the island. Several types of methods are currently used: physical (trapping, shooting), chemical (poisoning) and biological (e.g. directed use of diseases). Each has its own set of advantages and disadvantages, depending on the mammal species targeted. The best strategy is almost always to combine several methods. Whatever the strategy used, its long-term success is critically dependent on solid support from several different areas, including financial support, staff commitment, and public support, to name only a few. In many cases, the elimination of the alien invasive species is followed by a rapid and often spectacular recovery of the impacted local populations. However, in other cases, the removal of the alien is not sufficient for the damaged ecosystem to revert to its former state, and complementary actions, such as species re-introduction, are required. A third situation may be widespread: the sudden removal of the alien species may generate a further disequilibrium, resulting in further or greater damage to the ecosystem. Given the numerous and complex population interactions among island species, it is difficult to predict the outcome of the removal of key species, such as a top predator. This justifies careful pre-control study and preparation prior to initiating the eradication of an alien species, in order to avoid an ecological catastrophe. In addition, long-term monitoring ofthe post-eradication ecosystem is crucial to assess success and prevent reinvasion.