Estimating vaccine efficacy during open-label follow-up of COVID-19 vaccine trials based on population-level surveillance data

While rapid development and roll out of COVID-19 vaccines is necessary in a pandemic, the process limits the ability of clinical trials to assess longer-term vaccine efficacy. We leveraged COVID-19 surveillance data in the U.S. to evaluate vaccine efficacy in U.S. Government-funded COVID-19 vaccine efficacy trials with a three-step estimation process. First, we used a compartmental epidemiological model informed by county-level surveillance data, a "population model", to estimate SARS-CoV-2 incidence among the unvaccinated. Second, a "cohort model" was used to adjust the population SARS-CoV-2 incidence to the vaccine trial cohort, taking into account individual participant characteristics and the difference between SARS-CoV-2 infection and COVID-19 disease. Third, we fit a regression model estimating the offset between the cohort-model-based COVID-19 incidence in the unvaccinated with the placebo-group COVID-19 incidence in the trial during blinded follow-up. Counterfactual placebo COVID-19 incidence was estimated during open-label follow-up by adjusting the cohort-model-based incidence rate by the estimated offset. Vaccine efficacy during open-label follow-up was estimated by contrasting the vaccine group COVID-19 incidence with the counterfactual placebo COVID-19 incidence. We documented good performance of the methodology in a simulation study. We also applied the methodology to estimate vaccine efficacy for the two-dose AZD1222 COVID-19 vaccine using data from the phase 3 U.S. trial (ClinicalTrials.gov # NCT04516746). We estimated AZD1222 vaccine efficacy of 59.1% (95% uncertainty interval (UI): 40.4%-74.3%) in April, 2021 (mean 106 days post-second dose), which reduced to 35.7% (95% UI: 15.0%-51.7%) in July, 2021 (mean 198 days post-second-dose). We developed and evaluated a methodology for estimating longer-term vaccine efficacy. This methodology could be applied to estimating counterfactual placebo incidence for future placebo-controlled vaccine efficacy trials of emerging pathogens with early termination of blinded follow-up, to active-controlled or uncontrolled COVID-19 vaccine efficacy trials, and to other clinical endpoints influenced by vaccination.

Socio-hydrogeological survey and assessment of organic pollutants to highlight and trace back pollution fluxes threatening a coastal groundwater-dependent ecosystem

Despite being a vector of pollution towards connected ecosystems, groundwater is often underestimated or not taken into account in management frameworks. To fill this gap, we propose to add socio-economic data to hydrogeological investigations to identify past and present pollution sources linked to human activities at watershed scale in order to forecast threats towards groundwater-dependent ecosystems (GDEs). The aim of this paper is to demonstrate, by a cross-disciplinary approach, the added value of socio-hydrogeological investigations to tackle anthropogenic pollution fluxes towards a GDE and to contribute to more sustainable management of groundwater resources. A survey combining chemical compounds analysis, data compilation, land use analysis and field investigations with a questionnaire was carried out on the Biguglia lagoon plain (France). Results show a pollution with a two-fold source, both agricultural and domestic, in all water bodies of the plain. The pesticide analysis reveals the presence of 10 molecules, including domestic compounds, with concentrations exceeding European groundwater quality standards for individual pesticides, as well as pesticides already banned for twenty years. On the basis of both the field survey and the questionnaire, agricultural pollution has been identified as very local highlighting the storage capacity of the aquifer, whereas domestic pollution is diffuse over the plain and attributed to sewage network effluents and septic tanks. Domestic compounds present shorter residence time within the aquifer highlighting continuous inputs, related to consumption habits of the population. Under the Water Framework Directive (WFD), member states are required to preserve the good ecological status, quality and quantity of water bodies. However, for GDEs it is difficult to achieve the 'good status' required without considering the groundwater's pollutant storage capacity and pollution legacy. To help resolve this issue, socio-hydrogeology has proved to be an efficient tool as well as for implementing effective protection measures for Mediterranean GDEs.

The role of groundwater in CO2 production and carbon storage in Mediterranean peatlands: An isotope geochemistry approach

Peatlands are permanent wetlands recognized for ecosystem services such as biodiversity conservation and carbon storage capacity. Little information is available about their response to global change, the reason why most Earth system climate models consider a linear increase in the release of greenhouse gases (GHG), such as CO₂, with increasing temperatures. Nevertheless, numerous studies suggest that an increase in the temperature may not imply a decrease in photosynthesis and carbon storage rates if water availability is sufficient, the latter being under the control of local hydrology mechanisms. Mediterranean peatlands well illustrate this fact. Since they are groundwater-dependent, they are hydrologically resilient to the strong seasonality of hydroclimatic conditions, especially during the summer drought. In the present study, we demonstrate that, even if such peatlands release CO₂ into the atmosphere, they can maintain a carbon storage capacity. To this end, a geochemical study disentangles the origin and fate of carbon within a Mediterranean peatland at the watershed scale. Field parameters, major ions, dissolved organic and inorganic carbon content and associated δ¹³C values allow for characterizing the seasonality of hydrochemical mechanisms and carbon input from an alluvial aquifer (where rain, river, shallow, and deep groundwater flows are mixing) to the peatland. The inorganic and organic content of peat soil and δ¹³C values of total organic matter and CO₂ complete the dataset, making it possible to provide arguments in favour of lower organic matter oxidation compared to primary production. Overall, this study highlights the groundwater role in the fluxes of CO₂ at the peatland-atmosphere interface, and more broadly the need to understand the interactions between the water and carbon cycles to build better models of the future evolution of the global climate.

Exploring disease perception in Behçet's syndrome: combining a quantitative and a qualitative study based on a narrative medicine approach

BACKGROUND

Behçet Syndrome (BS) has a significant psychological and social impact on patients, caregivers and families. The present study aims at exploring disease perception in BS patients, using both a co-designed survey and the narrative medicine (NM) approach.

METHODS

An ad-hoc questionnaire was co-designed by clinicians expert in BS, BS patients and caregivers and BS adult patients were invited to answer the online questionnaires. Cluster analysis was used to analyse data from the survey and to identify groups of patients with diverse disease perception. To further explore real-life perspectives, the stories of illness of a smaller group of adult BS patients were anonymously collected online and analysed by means of text, sentiment and qualitative analysis.

RESULTS

Two hundred and seven patients answered the survey and forty-three stories were collected. The cluster analysis highlighted that accepting or not the disease has a strong impact on the daily life, on how BS patients perceive themselves and in terms of hope for the future. The stories revealed that patients often address common issues, such as the long and complex journey faced from the disease onset until the BS diagnosis, which was strongly connected to the concept of time and perceived as an exhausting period of their lives.

CONCLUSION

To our knowledge, this is the first study that addressed disease perception also applying the NM principles in BS. The current perception that BS patients have of their disease should encourage the BS scientific and patient community in joining forces in order to improve the journey of BS patients.

Projected impact of treatment intensification with statin, ezetimibe, and statin plus ezetimibe fixed-dose combination on MACE across six countries

AIMS

The 2019 European Society of Cardiology/European Atherosclerosis Society (ESC/EAS) dyslipidaemia guidelines recommend achievement of low-density lipoprotein cholestrol (LDL-C) goals based on an individual's risk. We aimed to evaluate the impact of guideline adoption with statin, ezetimibe, and statin plus ezetimibe fixed-dose combination (FDC) on LDL-C goal achievement and incidence of major adverse cardiovascular events (MACE) across six countries.

METHODS AND RESULTS

A simulation model with a five-year horizon (2020-2024) was developed based on Institute for Health Metrics and Evaluation Global Burden of Disease Study database with a business-as-usual (BAU) scenario representing status quo, intervention scenario-1 representing treatment with statin and ezetimibe as separate agents, and intervention scenario-2 representing treatment with statin or statin plus ezetimibe FDC. MACE was defined as the composite of myocardial infarction, ischaemic stroke, and cardiovascular death. The mean population LDL-C was reduced from 4.25 mmol/L in the BAU scenario, to 3.65 mmol/L and 3.59 mmol/L in intervention scenarios-1 and -2, respectively. Compared with BAU, intervention scenarios-1 and-2 resulted in relative reduction of MACE by 5.4% and 6.4% representing ∼3.7 and 4.4 million MACE averted, respectively, across six countries over 5 years. The absolute benefit in terms of MACE averted was highest for China, whereas France had highest relative reduction in MACE with both intervention scenarios compared with BAU.

CONCLUSION

The 2019 ESC/EAS guideline-based treatment intensification with strategies based on statin, ezetimibe, and statin plus ezetimibe FDC is estimated to result in a substantial population-level benefit in terms of MACE averted compared with BAU.

Assessing the hydrogeological resilience of a groundwater-dependent Mediterranean peatland: Impact of global change and role of water management strategies

Mediterranean peatlands remain largely under-documented, except for detailed biological data such as fauna and flora taxa lists, and yet are increasingly threatened by water withdrawal and agriculture practices. This lack of information, particularly on their hydrogeological functioning, makes it impossible to evaluate their response to changing climate conditions. A pilot study on a representative Mediterranean peatland on the island of Corsica (France) was conducted to evaluate recharge modalities in the peatland using a coupled water-level monitoring, geochemical and isotope multi-tracing approach (electric conductivity, major ions, δ¹⁸O, δ²H, ³H, ⁸⁷Sr/⁸⁶Sr). The goal was to understand how water budgets in peatland ecosystems were maintained throughout the year, especially during the summer. Despite the remarkable stability of the peatland water level, the recharge contributions of varied water bodies through an alluvial aquifer vary significantly from one season to another. An end-member mixing analysis (EMMA) indicates that the peatland is mainly recharged by an alluvial aquifer. During fall-winter, the alluvial aquifer on which the peatland depends is recharged by the rainfall, a river, and shallow groundwater (colluvium). During spring-summer, water supply is provided mostly by a river, shallow, and deep groundwater (fractured granite). However, this specific hydrogeological functioning is not taken into account by environmental management policies making peatlands vulnerable to anthropogenic and climatic pressures. Thus, their actual status regarding water and aquatic environment management policies is discussed to provide recommendations for better consideration and preservation.

Temporal offset between precipitation and water uptake of Mediterranean pine trees varies with elevation and season

For climate models that use paleo-environment data to predict future climate change, tree-ring isotope variations are one important archive for the reconstruction of paleo-hydrological conditions. Due to the rather complicated pathway of water, starting from precipitation until its uptake by trees and the final incorporation of its components into tree-ring cellulose, a closer inspection of seasonal variations of tree water uptake is important. In this study, branch and needle samples of two pine species (Pinus pinaster and Pinus nigra subsp. laricio) and several water compartments (precipitation, creek, soil) were sampled over a two-year period and analyzed for the temporal variations of their oxygen and hydrogen stable isotope ratios (δ¹⁸O and δ²H) at five sites over an elevation gradient from sea level to around 1600 m a.s.l. on the Mediterranean island of Corsica (France). A new model was established to disentangle temporal relationships of source water uptake of trees. It uses a calculation method that incorporates the two processes mostly expected to affect source water composition: mixing of waters and evaporation. The model results showed that the temporal offset from precipitation to water uptake is not constant and varies with elevation and season. Overall, seasonal source water origin was shown to be dominated by precipitation from autumn and spring. While autumn precipitation was a more important water source for trees growing at mid- (~800-1000 m a.s.l) and high-elevation (~1600 m a.s.l.) sites, trees at coastal sites mostly took up water from late winter and spring. These findings show that predicted decreases in precipitation amounts during the wet season in the Mediterranean can have strong impacts on water availability for pine trees, especially at higher elevations.

Combinations of geoenvironmental data underline coastal aquifer anthropogenic nitrate legacy through groundwater vulnerability mapping methods

Groundwater quality is strongly dependent on land use. Past and current anthropogenic activities can lead to the diffusion of contaminants in aquifers. This diffusion can threaten the resource exploitation for decades, thereby endangering the ecological health of groundwater dependent ecosystems. Thus, groundwater stakeholders need methods for long-term management which integrate groundwater vulnerability. This study was conducted on the shallow alluvial aquifer of the groundwater-dependent Biguglia lagoon on Corsica Island, France. The aquifer is exposed to anthropogenic contamination for many decades with nitrate contamination legacy linked to agricultural activities, uncontrolled urbanization and sewage leakages. In most cases, vulnerability mapping is done in the objective of comparing groundwater situation regarding an on-going contamination process. But the question is still pending for aquifers where contamination is inherited from past practices or contaminations and where anthropogenic influences have changed through time. To propose an effective and innovative method for territorial management in Mediterranean alluvial aquifers, four index-based groundwater vulnerability mapping methods were tested and compared: two intrinsic vulnerability mapping methods (DRASTIC and SINTACS) and two specific vulnerability mapping methods (Modified-DRASTIC and SI), the latter integrating land use in the accuracy of groundwater vulnerability. Novelty is coming from the comparison between vulnerability maps and their application and validation in a hydrosystem affected by nitrate legacy-type contamination. The specific vulnerability mapping methods are more likely to represent the current pressures to which groundwater are subject. Thus, specific vulnerability methods such as the SI one revealed here very relevant to assess groundwater quality and to react retrospectively. The comparison between groundwater nitrate legacy and intrinsic groundwater vulnerability methods appeared also useful to define priority protection areas in long-term territorial management planning (EU Water Framework Direction). In this sense, the SINTACS method seems to be the more appropriate in the Mediterranean and alluvial context of this study.

Riverine carbon dioxide evasion along a high-relief watercourse derived from seasonal dynamics of the water-atmosphere gas exchange

The high-relief catchment of the Tavignanu River (Corsica Island, France) with an elevation range from sea level to 2622 m above sea level was investigated for its riverine carbon budget and stable carbon isotopes. Major riverine dissolved inorganic carbon (DIC or TCO₂) sources depended on seasons and sub-catchment lithology. In winter δ¹³C_DIC values of -2 to -7‰ (VPDB) indicated influences of atmospheric CO₂. δ¹³C_DIC values decreased gradually to values between -9 and -12‰ in July, which indicates elevated soil CO₂ contribution. An observed downstream increase in the total amount of carbon species correlated with inputs from carbonate bearing tributaries and evaporation effects in summer. Main channel partial pressure of CO₂ (pCO₂) was seasonally highly variable in the upper silicate catchment and the lower coastal plain, where summer values exceed up to six times atmospheric levels. During winter, the central section of the Tavignanu River was found to be undersaturated with respect to atmospheric CO₂ levels. The median values for main channel pCO₂ were below atmospheric levels in winter and spring and above in summer and autumn. The annual carbon flux across the air-water boundary (F_CO2) along the Tavignanu River was calculated with (0.77 ± 0.24) Gg C yr^-1, which is about seven times higher than the riverine TCO₂ transport to the sea of about 0.11 Gg C yr^-1. While large sections of the river experienced year-round atmospheric CO₂ uptake or equilibrium, the river as a whole was a small but continuous net source of carbon to the atmosphere. This underlines the important, but so far not well-constrained, contributions of smaller streams and rivers to the terrestrial carbon flux and the need of incorporating them into future global carbon cycle models.

Delayed nitrate dispersion within a coastal aquifer provides constraints on land-use evolution and nitrate contamination in the past

Identifying sources of anthropogenic pollution, and assessing the fate and residence time of pollutants in aquifers is important for the management of groundwater resources, and the ecological health of groundwater dependent ecosystems. This study investigates anthropogenic contamination in the shallow alluvial aquifer of the Marana-Casinca, hydraulically connected to the Biguglia lagoon (Corsica, France). A multi-tracer approach, combining geochemical and environmental isotopic data (δ¹⁸O-H₂O, δ²H-H₂O, ³H, δ¹⁵N-NO₃^-, δ¹⁸O-NO₃^-, δ¹¹B), and groundwater residence-time tracers (³H and CFCs) was carried out in 2016, and integrated with a study of land use evolution in the catchment during the last century. Groundwater NO₃^- concentrations, ranged between 2 mg/L and up to 30 mg/L, displaying the degradation of groundwater quality induced by anthropogenic activities (agricultural activities). Comparatively high δ¹⁵N-NO₃^- values (up to 19.7‰) in combination with δ¹¹B values that were significantly lower (between 23‰ and 26‰) than the seawater background are indicative of sewage contamination. The ongoing deterioration of groundwater quality can be attributed to the uncontrolled urbanization development all over the alluvial plain, with numerous sewage leakages from the sanitation network and private sewage systems. Integration of contaminant and water-residence time data revealed a progressive accumulation of pollutants with time in the groundwater, particularly in areas with major anthropogenic pressure and slow dynamic groundwater flow. Our approach provides time-dependent insight into nitrogen pollution in the studied aquifer over the past decades, revealing a systematic change in the dominant NO₃^- source, from agricultural to sewage contamination. Yet, today's low groundwater quality is to large parts due to legacy pollution from land-use practices several decades ago, underlining the poor self-remediating capacity of this hydrosystem. Our results can be taken as warning that groundwater pollution that happened in the recent past, or today, may have dire impacts on the quality of groundwater-dependent ecosystems in the future.

An Analytical Method for Assessing Recharge Using Groundwater Travel Time in Dupuit-Forchheimer Aquifers

An analytical solution to calculate the recharge of unconfined aquifers with Dupuit-Forchheimer type flow conditions is proposed. This solution is derived from an existing closed-form analytical solution initially developed to determine groundwater travel time when the recharge of the aquifer is known. This existing solution has been modified to determine recharge when groundwater travel time is known. An illustration is given with a field case example for the Bonifacio aquifer of the island of Corsica (France), in the Mediterranean. In this aquifer, previously established differences in groundwater residence time between two water samples were determined from anthropogenic atmospheric gas (chlorofluorocarbons and sulfur hexafluoride) measurements. The time difference is entered into the new analytical solution to determine recharge. The calculations yield a value of average recharge that agrees with the results obtained by several other methods that were presented in previous studies to assess the recharge of the Bonifacio aquifer. Also presented in this study is a sensitivity analysis of the new analytical solution, to quantify the influence of different parameters that control recharge: hydraulic conductivity, effective porosity and the groundwater travel time. This study illustrates how geochemical data can be combined with physical models to measure recharge. Such an approach could be adopted in other homogeneous aquifers worldwide that satisfy Dupuit-Forchheimer type flow conditions.

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber

AIM

To characterize microbial communities present in natural rubber (NR) coagula from Hevea brasiliensis latex during maturation and identify microbial taxa (bacteria and fungi) having an impact on dry NR properties.

METHODS AND RESULTS

Microbial community dynamics in NR coagula maturated under controlled conditions were compared and related with the evolution of dry NR properties. The pyrosequencing of 16S (119 837 effective reads) and 18S (131 879 effective reads) rRNA gene regions was performed on 21 samples covering different maturation times and two aeration conditions. Results showed a relatively high bacterial richness (Chao1 estimates of 200-1000) associated with significant bacterial dynamics. Lactic acid bacteria (LAB) were dominant in the first days of maturation. Then, in aerobic conditions, development of Actinobacteria represented by the family Microbacteriaceae was associated with alkalinization of the samples and a higher sensitivity of NR to thermo-oxidation as evaluated by its plasticity retention index (PRI). In anaerobiosis, the reduced development of bacteria, mostly LAB present, was associated with improved NR properties (higher initial plasticity P₀ and PRI).

CONCLUSIONS

The involvement of micro-organisms in the evolution of dry NR properties during the maturation of NR coagula was confirmed. The importance of the structure and dynamics of microbial communities is specifically highlighted.

SIGNIFICANCE AND IMPACT OF THE STUDY

Natural rubber is a key elastomer for the tyre industry and for a variety of other applications. The majority of raw NR is obtained by natural coagulation of H. brasiliensis latex under the activity of micro-organisms. An improved understanding of the microbial communities involved in the maturation of NR coagula may lead to an improvement in the production process of raw NR to provide a better consistency in NR quality.

Strontium isotopes as tracers of water-rocks interactions, mixing processes and residence time indicator of groundwater within the granite-carbonate coastal aquifer of Bonifacio (Corsica, France)

This study aims at identifying the water-rock interactions and mixing rates within a complex granite-carbonate coastal aquifer under high touristic pressure. Investigations have been carried out within the coastal aquifer of Bonifacio (southern Corsica, France) mainly composed of continental granitic weathering products and marine calcarenite sediments filling a granitic depression. A multi-tracer approach combining physico-chemical parameters, major ions, selected trace elements, stable isotopes of the water molecule and ⁸⁷Sr/⁸⁶Sr ratios measurements is undertaken for 20 groundwater samples during the low water period in November 2014. 5 rock samples of the sedimentary deposits and surrounding granites are also analysed. First, the water-rock interactions processes governing the groundwater mineralization are described in order to fix the hydrogeochemical background. Secondly, the flow conditions are refined through the quantification of inter aquifer levels mixing, and thirdly, the kinetics of water-rock interaction based on groundwater residence time from a previous study using CFCs and SF₆ are quantified for the two main flow lines. A regional contrast in the groundwater recharge altitude allowed the oxygene-18 to be useful combined with the ⁸⁷Sr/⁸⁶Sr ratios to differentiate the groundwater origins and to compute the mixing rates, revealing the real extension of the watershed and the availability of the resource. The results also highlight a very good correlation between the groundwater residence time and the spatial evolution of ⁸⁷Sr/⁸⁶Sr ratios, allowing water-rock interaction kinetics to be defined empirically for the two main flow lines through the calcarenites. These results demonstrate the efficiency of strontium isotopes as tracers of water-rock interaction kinetics and by extension their relevance as a proxy of groundwater residence time, fundamental parameter documenting the long term sustainability of the hydrosystem.

The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant

The location and timing of domestication of the olive tree, a key crop in Early Mediterranean societies, remain hotly debated. Here, we unravel the history of wild olives (oleasters), and then infer the primary origins of the domesticated olive. Phylogeography and Bayesian molecular dating analyses based on plastid genome profiling of 1263 oleasters and 534 cultivated genotypes reveal three main lineages of pre-Quaternary origin. Regional hotspots of plastid diversity, species distribution modelling and macrofossils support the existence of three long-term refugia; namely the Near East (including Cyprus), the Aegean area and the Strait of Gibraltar. These ancestral wild gene pools have provided the essential foundations for cultivated olive breeding. Comparison of the geographical pattern of plastid diversity between wild and cultivated olives indicates the cradle of first domestication in the northern Levant followed by dispersals across the Mediterranean basin in parallel with the expansion of civilizations and human exchanges in this part of the world.

A composite map of expressed sequences in maize

A maize genetic map based mainly on expressed sequences has been constructed. The map incorporates data from four segregating populations. Three recombinant inbred line populations were derived from the nonreciprocal crosses between three inbred lines. A map derived from an independent F2 progeny from one of the crosses was also used. With a total of 521 genotyped individuals, accuracy in gene order is expected. Five sources of markers were used: (i) 109 loci corresponding to 69 genes of known function, (ii) 39 loci controlling protein position shifts revealed by two-dimensional electrophoresis, (iii) 8 isozyme loci, (iv) 17 loci corresponding to 14 sequenced cDNAs for which no homology was found in gene banks, and (v) 102 loci corresponding to 81 anonymous probes. As many loci were common to all maps, we tested heterogeneity between recombination fractions. The comparison of recombination fractions revealed: (i) a good correspondence between the maps derived from the same cross, (ii) few significant differences in interval distances, and (iii) global differences, which can reach 20% of the total map length. A composite map of 275 loci covering 1765 cM has been constructed. Key words : Zea mays L., RFLP, genetic map, molecular markers, proteins.

High throughput analysis of grape genetic diversity as a tool for germplasm collection management

Using 20 SSR markers well scattered across the 19 grape chromosomes, we analyzed 4,370 accessions of the INRA grape repository at Vassal, mostly cultivars of Vitis vinifera subsp. sativa (3,727), but also accessions of V. vinifera subsp. sylvestris (80), interspecific hybrids (364), and rootstocks (199). The analysis revealed 2,836 SSR single profiles: 2,323 sativa cultivars, 72 wild individuals (sylvestris), 306 interspecific hybrids, and 135 rootstocks, corresponding to 2,739 different cultivars in all. A total of 524 alleles were detected, with a mean of 26.20 alleles per locus. For the 2,323 cultivars of V. vinifera, 338 alleles were detected with a mean of 16.9 alleles per locus. The mean genetic diversity (GDI) was 0.797 and the level of heterozygosity was 0.76, with broad variation from 0.20 to 1. Interspecific hybrids and rootstocks were more heterozygous and more diverse (GDI = 0.839 and 0.865, respectively) than V. vinifera cultivars (GDI = 0.769), Vitis vinifera subsp. sylvestris being the least divergent with GDI = 0.708. Principal coordinates analysis distinguished the four groups. Slight clonal polymorphism was detected. The limit between clonal variation and cultivar polymorphism was set at four allelic differences out of 40. SSR markers were useful as a complementary tool to traditional ampelography for cultivar identification. Finally, a set of nine SSR markers was defined that was sufficient to distinguish 99.8% of the analyzed accessions. This set is suitable for routine characterization and will be valuable for germplasm management.

Grinding up wheat: a massive loss of nucleotide diversity since domestication

Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analyzed nucleotide diversity at 21 loci in a sample of 101 individuals representing 4 taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum, and bread wheats) to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify 2 genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms--by 69% in bread wheat and 84% in durum wheat--with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3--giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness--an important trait for end-use quality in wheat.

Lichen biomonitoring of ammonia emission and nitrogen deposition around a pig stockfarm

Effects of high ammonia emissions and nitrogen deposition were investigated on lichens around a pig stockfarm (ca. 7,000 animals) in central Italy. Four sites were selected along a transect at 200, 400, 1000 and 2500 m from the stockfarm, the diversity of epiphytic lichens was measured and transplanted thalli of Xanthoria parietina and Flavoparmelia caperata exposed, together with passive NH3 (diffusion tubes) samplers. Ammonia dramatically decreased from the centre of the stockfarm to the sampled sites, where it was correlated with bark pH. Total lichen diversity was not associated with either NH3 concentrations or bark pH, but the diversity of strictly nitrophytic species was highly correlated with both parameters. Physconia grisea was the best indicator species for NH3 pollution. Total N accumulated in X. parietina and F. caperata was correlated with NH3 concentrations.

Effects of NO2 and NH3 from road traffic on epiphytic lichens

The results of a survey aimed at investigating whether NO2 and NH3 emitted by road traffic can influence lichen diversity, lichen vitality and the accumulation of nitrogen in lichen thalli are reported. For this purpose, distance from a highway in a rural environment of central Italy was regarded as the main parameter to check this hypothesis. The results of the present survey indicated that road traffic is not a relevant source of NH3. On the other hand, NO2 concentrations, although rather low, were negatively correlated with distance from the highway according to a typical logarithmic function. No association between NO2 concentrations and the diversity of epiphytic lichens was found, probably because of the low NO2 values measured. Also bark properties were not influenced by distance from the highway. Accumulation of nitrogen, reduction in the content of chlorophyll a, chlorophyll b and total carotenoids were found in transplanted thalli of Evernia prunastri, but NO2 was not responsible for these changes, which were probably caused by applications of N-based fertilizers.

Domestication history in the Medicago sativa species complex: inferences from nuclear sequence polymorphism

DNA sequence polymorphism carries genealogical information and allows for testing hypotheses on selection and population history, especially through coalescent-based analysis. Understanding the evolutionary forces at work in plant domestication and subsequent selection is of critical importance for the management of genetic resources. In this study, we surveyed DNA sequence diversity at two assumed neutral nuclear loci in the wild-domesticated species complex of alfalfa (Medicago sativa L.). A high level of polymorphism was detected. The domesticated pool contains on average 31% less diversity than the wild pool, but with a high heterogeneity among loci. Coalescent simulations of the domestication process showed that this result cannot be explained by assuming a constant population size but is rather consistent with a demographic bottleneck during domestication. A very low level of divergence was detected between the wild and the domesticated forms as well as between the related subspecies of the M. sativa species complex. However, the originality of the Spanish wild populations, already observed based on mitochondrial DNA polymorphism, was confirmed. These results, together with patterns of intrapopulation polymorphism, suggest that nuclear sequence polymorphism could be a promising tool, complementary to mitochondrial DNA and phenotypic evaluations, to investigate historical demographic and evolutionary processes.

Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data

Estimation of long-term effective population size (N(e)) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate N(e) because their high mutation rate can be estimated from observed mutations. We used this property to estimate N(e) in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates mu were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter theta = 4N(e)mu. We demonstrated from simulations that the unbiased estimator of theta based on Nei's heterozygosity is the most appropriate for estimating N(e) because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a N(e) of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.

Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa)

The evolutionary history of a wild-cultivated complex is the outcome of different factors, among which are the domestication of the cultivated form, its geographical and demographic expansion, as well as gene flow between natural and cultivated populations. To clarify this history for alfalfa (Medicago sativa), we adopted a phylogeographical approach based on a sample of natural and cultivated populations of the M. sativa species complex. This sample was characterized for mtDNA variation through restriction fragment length polymorphisms. Twenty-two mitotypes were identified in the whole data set (155 individuals). In the wild pool from the presumed area of origin (Near East to Central Asia), the diversity was high but the absence of geographical differentiation hinders a more precise location of the centre of domestication. Within the cultivated alfalfa, the geographical structure suggests strongly the existence of at least two independent routes of dissemination of alfalfa from its centre of origin. In particular, original mitotypes detected in some regions suggest that wild populations not sampled in this study, and located outside the presumed area of domestication, may have contributed to the diversity of the cultivated pool. Finally, analysis of the mtDNA variation shows that natural populations collected in Spain constitute an endemic wild pool now introgressed partially by cultivated alfalfa.

[Appropriateness in the health system: past, present and future]

Nowadays, a health procedure or a clinical pathway are considered appropriate when they appear adequate with respect to scientific knowledge, consistent with the patient's values, safe as to risk management, and convenient with regard to the allocation of resources. This has not always been the case during the course of history, as the different clinical-methodological approaches to the same pathology in different Schools and Universities indicate, even in the same country. A hundred years ago, the difference of approaches could be explained by the limited circulation of ideas, usually based upon weak evidence, if not the personal impressions, of individual physicians. Today, on the contrary, evidence based medicine can represent a useful element in rendering homogeneous different types of behaviour in the same situation, and one of its characterising features is the elaboration of the concept of appropriateness. Appropriateness is a parameter internal to the evolution of health professions, requiring reasoned and shared employment. It originates from the need of health operators to explain why so many different kinds of behaviour exist in the context of the same clinical question. All the issues related to the concepts of clinical judgement and clinical decision-making derive from this and today more and more attention is being dedicated to the idea of appropriateness. The search for appropriateness is a progressive and cyclic process, that may always be improved. At present, strenuous team work is needed to avoid the features of the health system that are more clearly inappropriate, and that emerge from very simple analyses. Doing this is in the interest of the citizens, of health professionals and of the health economy as well.

How mitochondrial DNA diversity can help to understand the dynamics of wild-cultivated complexes. The case of Medicago sativa in Spain

In order to clarify the relationships (genetic exchange and shared ancestry) between natural and cultivated populations of alfalfa (Medicago sativa L.) in Spain, we investigated the patterns of mitochondrial DNA variation (characterized through restriction fragment length polymorphism) for 248 individuals in seven natural and six cultivated populations of this species. Mitochondrial variation was evidenced in both natural and cultivated populations of M. sativa. Among the seven mitotypes identified in the species, two were specific of the natural populations, a result attesting the fact that the Spanish wild form of M. sativa is an original genetic pool compared to the cultivated one. Other mitotypes were observed in both natural and cultivated populations, suggesting the occurrence of gene flow through seeds from cultivated towards natural populations. Comparisons with previously gathered nuclear and phenotypic data give insights into the different evolutionary forces acting on the different kinds of Spanish natural populations examined so far.

Administration of recombinant human growth hormone on alternate days is sufficient to increase whole body protein synthesis and lipolysis in growth hormone deficient adults

OBJECTIVE

At present, the duration of the effect of recombinant human growth hormone (rhGH) on the rates of protein synthesis and lipolysis in GH deficient (GHD) adults is unknown. This study was designed to establish the frequency of rhGH administration necessary to provide the beneficial metabolic effects of the hormone in GHD adults.

DESIGN AND PATIENTS

Two different studies (A and B) were performed in two groups of five GHD men. In study A, whole body protein and lipid kinetics was determined in the basal state (Bas), 12 (GH12h) and 36 (GH36h) h after the last of seven injections of rhGH (3.3 microg/kg), given at bedtime on alternate days. In study B, the same parameters were determined in the basal state (Bas), 60 (GH60h) and 84 (GH84h) h after the last of seven injections of rhGH (3.3 microg/kg), given at bedtime at 3 day intervals.

MEASUREMENTS

The rates of protein metabolism were estimated by infusing [1-13C]leucine, and those of lipolysis by infusing [1,1,2,3, 3-D5]glycerol.

RESULTS

Leucine oxidation decreased (P < 0.01) by approximately 30% after GH12h and GH36h but did not change after GH60h and GH84h. Non-oxidative leucine disposal increased after GH12h and GH36h by approximately 13% (P < 0.05) whereas it did not change after GH60h and GH84h. Glycerol appearance increased (P < 0. 01) by approximately 45% after GH12h and GH36h but did not change after GH60h and GH84h.

CONCLUSIONS

The effects on protein and lipid metabolism following the injection of rhGH last longer than 36 and less than 60 h. In fact, rhGH administration on alternate days induced a sustained increase in the rates of protein synthesis and lipolysis of GHD adults, whereas a longer interval of administration (3 days) had no effect by 60 h.

A dose-response study of growth hormone (GH) replacement on whole body protein and lipid kinetics in GH-deficient adults

This study was designed to establish the lower dose of effective GH replacement therapy in severe GH-deficient (GHD) adults. Whole body protein and lipid kinetics were determined in six GHD men in the basal state (B) and after 1 week of treatment with placebo (PL) or 3.3 (GH3.3) or 2 (GH2) micrograms/kg.day recombinant human GH (rhGH). The rates of whole body proteolysis, oxidation, and synthesis were estimated by infusing [1-13C]leucine (prime, 1 mg/kg; infusion rate, 1 mg/kg.h); those of lipolysis (measured in four of the six patients) were estimated by infusing [1,1,2,3,3-D5]glycerol (prime, 1.8 mumol/kg; infusion rate, 0.06 mumol/kg.min). Serum insulin-like growth factor I (IGF-I) concentrations (picograms per mL; mean +/- SE) similarly increased from the basal level (39 +/- 7) after 3.3 (108 +/- 18) or 2 (109 +/- 24) microgram/kg.day rhGH (P < 0.001 vs. basal), whereas they did not change with placebo (41 +/- 8). Leucine Ra was unaffected by the treatments. GH3.3 reduced by 30% the rate of leucine oxidation (P = 0.0069 vs. basal) and increased by 11% nonoxidative leucine disposal (P = 0.0095 vs. basal) and by 21% glycerol Ra (0.0035 vs. basal); GH2 and placebo had no significant effect. In conclusion, 1) at least 3.3 micrograms/ kg.day rhGH are required to increase whole body protein synthesis and lipolysis in male GHD adults; 2) 2 micrograms/kg.day rhGH normalize serum IGF-I concentrations, but do not modify protein and lipid metabolism; and 3) a normal serum IGF-I concentration does not guarantee that rhGH treatment is also effective on intermediate metabolism.

Moderate and large doses of ethanol differentially affect hepatic protein metabolism in humans

The intake of approximately 70 g of alcohol impairs liver protein metabolism in healthy humans. To establish the threshold at which alcohol impairs hepatic protein metabolism in humans we compared the effects of 500 mL of water (control study), 300 (28.4 g ethanol) or 750 mL (71 g ethanol) of table wine on hepatic protein metabolism in three groups of healthy nonalcoholic volunteers. Hepatic protein metabolism was estimated (L-[1-14C]leucine infusion) by measuring the fractional secretory rates of albumin and fibrinogen during the overnight postabsorptive state (basal) and the subsequent administration of water or two different amounts of wine (300 or 750 mL) given with a liquid glucose-lipid-amino acid meal. During the meal, water did not affect fibrinogen fractional secretory rate and increased albumin fractional secretory rate by approximately 50% (P < 0.01). The 300 mL of wine increased albumin secretory rate by only approximately 20% (P < 0.01 vs. basal, P < 0.04 vs. water) and did not affect fibrinogen secretory rate. The 750 mL of wine profoundly impaired hepatic protein metabolism, decreasing the fractional secretory rates of albumin (P < 0.01 vs. water and 300 mL wine) and fibrinogen (P < 0.04 vs. water and 300 mL of wine) below the postabsorptive values. These results demonstrate that a moderate dose of alcohol (28 g, approximately 2 drinks) slightly affects postprandial hepatic protein metabolism by blunting the meal-induced increase in albumin synthesis, whereas it does not interfere with fibrinogen synthesis as do higher doses.

Two different satellite DNAs in Beta vulgaris L.: evolution, quantification and distribution in the genus

Two highly repeated EcoRI (0.45 × 10(6)) and BamHI (0.17 × 10(6)) fragments per haploid genome were found in sugar beet genomic DNA. Both fragments were located by 6% acrylamide-gel electrophoresis, purified and cloned in pUC18. Four of the inserts corresponding to each family were chosen for further study. Both fragment families display the main characteristics of the satellite DNA of animals and plants. The EcoRI and BamHI fragment families are arranged in long tandem arrays. Fragments of the EcoRI family (pBVE) were analyzed. They vary both in sequence and in length (158-160 nt) in comparison with the consensus sequence of 159nt. Both families are A-T rich; pBVE is 59% rich while pBVB is 69% rich. The BVESAT family is present in all the members of the section Vulgares. It is conserved in the section Procumbentes with 80% homology and the same length, but is not detectable in the Corollinae. The sequence variation rate and the variation in length (330±5 nt) are of the same order in comparison with those of the BVESAT family. However, the BVBSAT family is present in species of the section Vulgares only. As regards other plant satellite DNAs, the BVESAT family shares homology with Allium cepa satellite DNA, with three of the yeast centromeric sequences, and with three Arabidopsis thaliana sequences. The BVBSAT family is unique to the Vulgares and does not share any homology with other plant or animal satellite DNAs sequences so far.

Characterization of the nuclear ribosomal DNA units and phylogeny of Beta L. wild forms and cultivated beets

The nuclear rDNA units of species belonging to the genus Beta were characterized using heterologous probes of flax (entire unit and 25S) and sunflower (6.1-kb Eco fragment containing the 18S, the entire intergenic spacer (IGS) and a small piece of the 25S). The physical maps of one species from each section of the genus was constructed by localization of the EcoRI, BamHI, HindIII, KpnI and SacI restriction sites. For each species a single individual was used to obtain total DNA. The major unit length is 11 kb, but variant length units at 10.4, 10.7 and 11.3 kb were found as minor forms. However, some individuals carried the 10.4-kb or the 10.7-kb variant length unit as the major form. For the variant length units of one species the restriction sites were conserved, so that the variation in length occurred in the IGS. The EcoRI fragment corresponding to the intergenic spacer appeared to be the best indicator of variation. The variable sequence in the IGS sometimes generated new restriction sites for the Corollinae and mainly, did so, for the Vulgares relative to the Procumbentes. The variable sites were able, to differentiate the three sections and species within the sections. Corollinae species belong to two different groups according to the absence or the presence of the BamHI (B4) site. The Vulgares species contain several unit types. We proposed that all the unit types derived from a unique unit, V-11-2.3, by unequal crossing-overs or conversion. We also supposed a homogenization mechanism because we found individuals homogeneous for every unit type. Among the cultivated beets, all the root beets contain only one rDNA unit type, V-11-2.9. Thus, we supposed that the common unit type of cultivated beets either brings a physiological advantage or is strictly linked to a favorable allele. It is likely that the rDNA unit of B. maritima were eliminated from sugar beet by the breeding process since they were not recovered. Whatever the process, we deduced that all the cultivated forms of beets likely originated in a unique plant ascendant.A phylogenic tree of the genus is proposed, based on the nuclear rDNA maps, and subsequently discussed relative to the systematic tree and other molecular phylogenies.

Rapid control of purity for the cytoplasm of male-sterile seed stocks by means of a dot hybridization assay

To produce hybrids, one member of the parental line is genetically made male-sterile. This male-sterile trait is encoded by mitochondria so that it is maternally inherited. Consequently, the progeny of a male-sterile plant is fully sterile. Nevertheless, during the handling of cytoplasmic male-sterile seed stocks, some mixture with seeds of the maintainer lines can occur. Up to the present time, the only way to check the homogeneity of the cytoplasmic male-sterile seed stock was to grow the plants until flowering time. We have developed a method which can be used immediately after the harvest, allowing us to check samples from both sunflower and sugar beet. We used the mitochondrial plasmid, present only in the maintainer lines, as a probe for the total nucleic acids prepared from the cytoplasmic male-sterile seed stocks which might be contaminated. The signals compared to those of samples artificially contaminated allow us to measure as few as one male-fertile seed in 1000 seeds in a rapid and accurate manner.

[Metadoxine in alcohol-related pathology]

Metadoxine is an active drug for treatment of acute and chronic alcohol intoxication, affecting both liver and brain function. The authors reviewed the international pharmacological and clinical literature on the drug which shows the potential usefulness of metadoxine in the treatment of alcohol-induced diseases. The case report concerns the results in 20 chronic alcoholics, admitted to the hospital for acute alcohol intake treated with metadoxine (one 500 mg tablet twice daily). Biohumoral hepatopathy parameters and clinical parameters of neuropsychic behaviour were examined simultaneously. Compared with a control group of patients undergoing traditional therapy (sedative and multi-vitamin drugs), metadoxine showed a significant improvement of the values of gamma-GT, GPT, blood ammonia, blood alcohol and of neuropsychic and behavioural parameters such as agitation, tremor, asterixis, sopor and depression. No side-effects or unfavourable reactions occurred during metadoxine treatment, which confirms the safety of this molecule.

[Attenuation of post-ischaemic reactive hyperemia during lifting of the lower limbs]

With a view to determining to what extent changes in the position of the lower limbs influence post-ischaemic reactive hyperaemia, an ischaemic test was run on a group of normal subjects and patients with peripheral obliterative arteriopathy. Reactive hyperaemia was induced both in the usual supine position and then with the leg raised at 60 degrees to the horizontal. Raising of the leg significantly reduced the amplitude and duration of hyperaemia in both groups, though the differences between them with regard to the hyperaemic flow pattern were not affected. Various explanations of the results are offered. Raising of the limb appears to act more on local mechanisms controlling the peripheral arterial flow than on factors responsible for the genesis of RH. In particular, over and above the reduction of hydrostatic pressure, importance may be ascribed to the disequilibrium created by raising the limb on the component of vasal transparietal pressure. In arteriopaths, these factors are made more potent by obstruction of the main limb artery and arteriosclerotic impairment of the colateral circulation. Lastly, emphasis is placed on the possibility that the apparent metabolic deficiency created by ischaemia and remedied by RH is at least partly greater than the real deficiency and the tissues actual metabolic requirements.