New peptides under the s(ORF)ace of the genome

Hundreds of previously unidentified functional small peptides could exist in most genomes, but these sequences have been generally overlooked. The discovery of genes encoding small peptides with important functions in different organisms, has ignited the interest in these sequences, and led to an increasing amount of effort towards their identification. Here, we review the advances, both, computational, and biochemical, that are leading the way in the discovery of putatively functional smORFs, as well as the functional studies that have been carried out as a consequence of these searches. The evidence suggests that smORFs form a substantial part of our genomes, and that their encoded peptides could have important functions in a variety of cellular function

Quantitative reconstruction of climatic variations during the Bronze and early Iron ages based on pollen and lake-level data in the NW Alps, France

International audienceVegetation and lake-level data from the archaeological site of Tresserve, on the eastern shore of Lake Le Bourget (Savoie, France), are used to provide quantitative estimates of climatic variables over the period 4000-2300 cal BP in the northern French Pre-Alps, and to examine the possible impact of climatic changes on societies of the Bronze and early Iron Ages. The results obtained indicate that phases of higher lake level at 3500-3100 and 2750-2350 cal BP coincided with major climate reversals in the North Atlantic area. In west-central Europe, they were marked by cooler and wetter conditions. These two successive events may have affected ancient agricultural communities in west-central Europe by provoking harvest failures, more particularly due to increasing precipitation during the growing season. However, archaeological data in the region of Franche-Comté (Jura Mountains, eastern France) show a general expansion of population density from the middle Bronze Age to the early Iron Age. This suggests a relative emancipation of proto-historic societies from climatic conditions, probably in relation to the spread of new modes of social and economic organisation

Revealing the last 13,500 years of environmental history from the multiproxy record of a mountain lake (Lago Enol, northern Iberian Peninsula)

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10933-009-9387-7.We present the Holocene sequence from Lago Enol (43°16′N, 4°59′W, 1,070 m a.s.l.), Cantabrian Mountains, northern Spain. A multiproxy analysis provided comprehensive information about regional humidity and temperature changes. The analysis included sedimentological descriptions, physical properties, organic carbon and carbonate content, mineralogy and geochemical composition together with biological proxies including diatom and ostracod assemblages. A detailed pollen study enabled reconstruction of variations in vegetation cover, which were interpreted in the context of climate changes and human impact. Four distinct stages were recognized for the last 13,500 years: (1) a cold and dry episode that includes the Younger Dryas event (13,500–11,600 cal. year BP); (2) a humid and warmer period characterizing the onset of the Holocene (11,600–8,700 cal. year BP); (3) a tendency toward a drier climate during the middle Holocene (8,700–4,650 cal. year BP); and (4) a return to humid conditions following landscape modification by human activity (pastoral activities, deforestation) in the late Holocene (4,650–2,200 cal. year BP). Superimposed on relatively stable landscape conditions (e.g. maintenance of well established forests), the typical environmental variability of the southern European region is observed at this site.The Spanish Inter-Ministry Commission of Science and Technology (CICYT), the Spanish National Parks agency, the European Commission, the Spanish Ministry of Science, and the European Social Fund

Revealing the last 13,500 years of environmental history from the multiproxy record of a mountain lake (Lago Enol, northern Iberian Peninsula)

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s10933-009-9387-7.We present the Holocene sequence from Lago Enol (43°16′N, 4°59′W, 1,070 m a.s.l.), Cantabrian Mountains, northern Spain. A multiproxy analysis provided comprehensive information about regional humidity and temperature changes. The analysis included sedimentological descriptions, physical properties, organic carbon and carbonate content, mineralogy and geochemical composition together with biological proxies including diatom and ostracod assemblages. A detailed pollen study enabled reconstruction of variations in vegetation cover, which were interpreted in the context of climate changes and human impact. Four distinct stages were recognized for the last 13,500 years: (1) a cold and dry episode that includes the Younger Dryas event (13,500–11,600 cal. year BP); (2) a humid and warmer period characterizing the onset of the Holocene (11,600–8,700 cal. year BP); (3) a tendency toward a drier climate during the middle Holocene (8,700–4,650 cal. year BP); and (4) a return to humid conditions following landscape modification by human activity (pastoral activities, deforestation) in the late Holocene (4,650–2,200 cal. year BP). Superimposed on relatively stable landscape conditions (e.g. maintenance of well established forests), the typical environmental variability of the southern European region is observed at this site.The Spanish Inter-Ministry Commission of Science and Technology (CICYT), the Spanish National Parks agency, the European Commission, the Spanish Ministry of Science, and the European Social Fund

Response of littoral chironomid community and organic matter to late glacial lake level and environmental changes at Lago dell'Accesa (Tuscany, Italy).

International audienceThis study focuses on the response of lacustrine littoral chironomid communities to late glacial changes in limnological, environmental and climate conditions in the Mediterranean context. Late glacial chironomid (Diptera: Chironomidae) assemblages, organic petrography and geochemistry were analysed in a sediment core from the littoral zone of Lago dell'Accesa (Tuscany, Italy), where the lake-level fluctuations and the vegetation history have been previously reconstructed. Comparison of the chironomid stratigraphy to other proxies (pollen assemblages, organic petrography and geochemistry, lake-level) and regional climate reconstruction suggested the predominant influence of lake-level changes on the littoral chironomid fauna. The main lowering events that occurred during the Oldest and the Younger Dryas were followed by higher proportions of taxa typical of littoral habitats. A complementary study of organic matter suggested the indirect impact of lake-level on the chironomids through changes in humic status and habitat characteristics, such as the type of substrate and aquatic macrophyte development. Several chironomid taxa, such as Glyptotendipes, Microtendipes and Cricotopus type patens, were identified as possible indicators of low lake-level in the late glacial records. Nevertheless, this study suggested that parallel analyses of organic matter and chironomid assemblages may be needed to circumvent misinterpretation of littoral chironomid assemblage stratigraphy. There was a weak response of the chironomid assemblages to small lake-level lowerings that corresponded to the Older Dryas and Preboreal oscillations. A higher level of determination, e.g. to the species group level, may be necessary to increase the sensibility of the indicators to lake-level changes

Inactivation and sub-lethal injury of salmonella typhi, salmonella typhimurium and vibrio cholerae in copper water storage vessels

Background: This study provides information on the antibacterial effect of copper against the water-borne pathogens Salmonella Typhi, Salmonella Typhimurium and Vibrio cholerae. Methods: Suspensions of each pathogen were kept in water within a traditional copper vessel at 30°C for 24 h. Samples were withdrawn, diluted and plated onto suitable growth media. Conventional enumeration of healthy (uninjured) bacteria was carried out using standard aerobic incubation conditions. Additionally, reactive oxygen species-neutralised (ROS-n) conditions were achieved by adding the peroxide scavenger sodium pyruvate to the medium with anaerobic incubation, to enumerate uninjured (ROS-insensitive) and injured (ROS-sensitive) bacteria. Differences between log-transformed means of conventional (aerobic) and ROS-n counts were statistically evaluated using t tests. Results: Overall, all three pathogens were inactivated by storage in copper vessels for 24 h. However, for shorter-term incubation (4-12 h), higher counts were observed under ROS-n conditions than under aerobic conditions, which demonstrate the presence of substantial numbers of sub-lethally injured cells prior to their complete inactivation. Conclusions: The present study has for the first time confirmed that these bacterial pathogens are inactivated by storage in a copper vessel within 24 h. However, it has also demonstrated that it is necessary to account for short-term sub-lethal injury, manifest as ROS-sensitivity, in order to more fully understand the process. This has important practical implications in terms of the time required to store water within a copper vessel to completely inactivate these bacteria and thereby remove the risk of water-borne disease transmission by this route

Climate Change and the Geographic Distribution of Infectious Diseases

Our ability to predict the effects of climate change on the spread of infectious diseases is in its infancy. Numerous, and in some cases conflicting, predictions have been developed, principally based on models of biological processes or mapping of current and historical disease statistics. Current debates on whether climate change, relative to socioeconomic determinants, will be a major influence on human disease distributions are useful to help identify research needs but are probably artificially polarized. We have at least identified many of the critical geophysical constraints, transport opportunities, biotic requirements for some disease systems, and some of the socioeconomic factors that govern the process of migration and establishment of parasites and pathogens. Furthermore, we are beginning to develop a mechanistic understanding of many of these variables at specific sites. Better predictive understanding will emerge in the coming years from analyses regarding how these variables interact with each other

Unraveling the forcings controlling the vegetation and climate of the best orbital analogues for the present interglacial in SW Europe

The suitability of MIS 11c and MIS 19c as analogues of our present interglacial and its natural evolution is still debated. Here we examine the regional expression of the Holocene and its orbital analogues over SW Iberia using a model-data comparison approach. Regional tree fraction and climate based on snapshot and transient experiments using the LOVECLIM model are evaluated against the terrestrial-marine profiles from Site U1385 documenting the regional vegetation and climatic changes. The pollen-based reconstructions show a larger forest optimum during the Holocene compared to MIS 11c and MIS 19c, putting into question their analogy in SW Europe. Pollen-based and model results indicate reduced MIS 11c forest cover compared to the Holocene primarily driven by lower winter precipitation, which is critical for Mediterranean forest development. Decreased precipitation was possibly induced by the amplified MIS 11c latitudinal insolation and temperature gradient that shifted the westerlies northwards. In contrast, the reconstructed lower forest optimum at MIS 19c is not reproduced by the simulations probably due to the lack of Eurasian ice sheets and its related feedbacks in the model. Transient experiments with time-varying insolation and CO2 reveal that the SW Iberian forest dynamics over the interglacials are mostly coupled to changes in winter precipitation mainly controlled by precession, CO2 playing a negligible role. Model simulations reproduce the observed persistent vegetation changes at millennial time scales in SW Iberia and the strong forest reductions marking the end of the interglacial "optimum".SFRH/BD/9079/2012, SFRH/BPD/108712/2015, SFRH/BPD/108600/2015info:eu-repo/semantics/publishedVersio

Chironomid-based palaeotemperature estimates for northeast Finland during Oxygen Isotope Stage 3.

Quantitative palaeotemperature estimates for the earlier part of Oxygen Isotope Stage (OIS-) 3 are inferred from subfossil chironomid remains. The high-latitudinal study site of Sokli, northeast Finland, provides for a unique lacustrine deposit covering the earlier part of OIS-3, and the chironomid remains found in the sediments show that a shallow lake with a diverse fauna was present at the study site throughout the record. Using a Norwegian calibration data set as a modern analogue, mean July air temperatures are reconstructed. The chironomid-inferred July air temperatures are surprisingly high, reaching values similar to the current temperature at the study site. Other proxies that were applied to the sediments included the analysis of botanical and zoological macro-remains, and our results concur with temperature estimates derived from climate indicator taxa. Summer temperatures for interstadial conditions, reconstructed with climate models, are as high as our proxy-based palaeotemperatures