Pollen-based reconstruction of Holocene vegetation and climate in Southern Italy: the case of Lago di Trifoglietti

International audienceA high-resolution pollen record from Lago Trifoglietti in Calabria (southern Italy) provides new insights into the paleoenvironmental and palaeoclimatic changes which characterise the Holocene period in the southern Italy. The chronology is based on 11 AMS radiocarbon dates from terrestrial organic material. The Holocene history of the vegetation cover shows the persistence of an important and relatively stable Fagus forest present over that entire period, offering a rare example of a beech woodstand able to withstand climate changes for more than 11 000 yr. Probably in relation with early Holocene dry climate conditions which affected southern Italy, the Trifoglietti pollen record supports a southward delay in thermophyllous forest expansion dated to ca. 13 500 cal BP at Monticchio, ca. 11 000 cal BP at Trifoglietti, and finally ca. 9800 cal BP in Sicily. Regarding the human impact history, the Trifoglietti pollen record shows only poor imprints of agricultural activities and anthopogenic indicators, apart from those indicating pastoralism activities beneath forest cover. The selective exploitation of Abies appears to have been the strongest human impact on the Trifoglietti surroundings. On the basis of (1) a specific ratio between hygrophilous and terrestrial taxa, and (2) the Modern Analogue Technique, the pollen data collected at Lago Trifoglietti led to the establishment of two palaeoclimatic records tracing changes in (1) lake depth and (2) annual precipitation. On a millennial scale, these records give evidence of increasing moisture from ca. 11 000 to ca. 9400 cal BP and maximum humidity from ca. 9400 to ca. 6200 cal BP, prior to a general trend towards the drier climate conditions that have prevailed up to the present. In addition, several successive centennial-scale oscillations appear to have punctuated the entire Holocene. The identification of a cold dry event around 11 300 cal BP, responsible for a marked decline in timberline altitude and possibly equivalent to the PBO, remains to be confirmed by further investigations verifying both chronology and magnitude. Two cold and possibly drier Boreal oscillations developed at ca. 9800 and 9200 cal BP. At Trifoglietti, the 8.2 kyr event corresponds to the onset of cooler and drier climatic conditions which persisted until ca. 7500 cal BP. Finally, the second half of the Holocene was characterised by dry phases at ca. 6100–5200, 4400–3500, and 2500–1800 cal BP, alternating with more humid phases at ca. 5200–4400 and ca. 3500–2500 cal BP. Considered as a whole, these millennial-scale trends and centennial-scale climatic oscillations support contrasting patterns of palaeohydrological changes recognised between the north- and south-central Mediterranean

Orbital changes, variation in solar activity and increased anthropogenic activities: controls on the Holocene flood frequency in the Lake Ledro area, Northern Italy

International audienceTwo lacustrine sediment cores from Lake Ledro in northern Italy were studied to produce chronologies of floodevents for the past 10 000 yr. For this purpose, we have developed an automatic method that objectively identifies the sedimentary imprint of river floods in the downstream lake basin. The method was based on colour data extracted from processed core photographs, and the count data were analysed to capture the flood signal. Flood frequency and reconstructed sedimentary dynamics were compared with lake-level changes and pollen inferred vegetation dynamics. The results suggest a record marked by low flood frequency during the early and middle Holocene (10 000–4500 cal BP). Only modest increases during short intervals are recorded at ca. 8000, 7500, and 7100 cal BP. After 4500–4000 cal BP, the record shows a shift toward increased flood frequency. With the exception of two short intervals around 2900–2500 and 1800–1400 cal BP, which show a slightly reduced number of floods, the trend of increasing flood frequency prevailed until the 20th century, reaching a maximum between the 16th and the 19th centuries. Brief-flood frequency increases recorded during the early and middle Holocene can be attributed to climatic oscillations. On a centennial time scale, major changes in flood frequency, such as those observed after ca. 4500/4000 and 500 cal BP, can be attributed to large-scale climatic changes such as the Neo-glacial and Little Ice Age, which are under orbital and possibly solar control. However, in the Bronze Age and during the Middle Ages and modern times, forest clearing and land use probably partially control the flood activity

Corrigendum to “Pollen-based paleoenvironmental and paleoclimatic change at Lake Ohrid (south-eastern Europe) during the past 500 ka” published in Biogeosciences, 13, 1423–1437, 2016

In this corrigendum we report an updated pollen record from the Lake Ohrid DEEP site spanning the past 500 ka whereby we have reprocessed and re-analyzed 104 samples affected by chemical procedure problems that occurred in one palynological laboratory. Firstly, these samples were affected by the use of wrong containers, causing in- adequate settling of particles at the set centrifuging speed. Secondly, HCl and HF treatments were combined without the prescribed intermediate centrifuging and decanting steps. The inaccuracy in the protocol resulted in the loss of smaller pollen grains and in the overrepresentation of bisaccate ones in most of the re-analyzed samples. We therefore provide an updated set of figures with the new data and have revised the description of the results, discussion and conclusions re- ported in Sadori et al. (2016) where necessary. We stress that the majority of the original results and conclusions remain valid, while the records’ reliability and resolution have improved as 12 samples that had been omitted in the original study because of low count sums are now included in the revised dataset (Sadori et al., 2018)

Corrigendum to “Pollen-based paleoenvironmental and paleoclimatic change at Lake Ohrid (south-eastern Europe) during the past 500 ka” published in Biogeosciences, 13, 1423–1437, 2016

In this corrigendum we report an updated pollen record from the Lake Ohrid DEEP site spanning the past 500 ka whereby we have reprocessed and re-analyzed 104 samples affected by chemical procedure problems that occurred in one palynological laboratory. Firstly, these samples were affected by the use of wrong containers, causing in- adequate settling of particles at the set centrifuging speed. Secondly, HCl and HF treatments were combined without the prescribed intermediate centrifuging and decanting steps. The inaccuracy in the protocol resulted in the loss of smaller pollen grains and in the overrepresentation of bisaccate ones in most of the re-analyzed samples. We therefore provide an updated set of figures with the new data and have revised the description of the results, discussion and conclusions re- ported in Sadori et al. (2016) where necessary. We stress that the majority of the original results and conclusions remain valid, while the records’ reliability and resolution have improved as 12 samples that had been omitted in the original study because of low count sums are now included in the revised dataset (Sadori et al., 2018)

A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins

<p>Abstract</p> <p>Background</p> <p>The most common substitution matrices currently used (BLOSUM and PAM) are based on protein sequences with average amino acid distributions, thus they do not represent a fully accurate substitution model for proteins characterized by a biased amino acid composition. This problem has been addressed recently by adjusting existing matrices, however, to date, no empirical approach has been taken to build matrices which offer a substitution model for comparing proteins sharing an amino acid compositional bias. Here, we present a novel procedure to construct series of symmetrical substitution matrices to align proteins from similarly biased <it>Plasmodium </it>proteomes.</p> <p>Results</p> <p>We generated substitution matrices by selecting from the BLOCKS database those multiple alignments with a compositional bias similar to that of <it>P. falciparum </it>and <it>P. yoelii </it>proteins. A novel 'fuzzy' clustering method was adopted to group sequences within these alignments, showing that this method retains more complete information on the amino acid substitutions when compared to hierarchical clustering. We assessed the performance against the BLOSUM62 series and showed that the usage of our matrices results in an improvement in the performance of BLAST database searches, greatly reducing the number of false positive hits. We then demonstrated applications of the use of novel matrices to improve the annotation of homologs between the two <it>Plasmodium </it>species and to classify members of the <it>P. falciparum </it>RIFIN/STEVOR family.</p> <p>Conclusion</p> <p>We confirmed that in the case of compositionally biased proteins, standard BLOSUM matrices are not suited for optimal alignments, and specific substitution matrices are required. In addition, we showed that the usage of these matrices leads to a reduction of false positive hits, facilitating the automatic annotation process.</p

Identification of a major rif transcript common to gametocytes and sporozoites of Plasmodium falciparum

Background: The Plasmodium falciparum parasite is transmitted in its sexual gametocyte stage from man to mosquito and as asexual sporozoites from mosquito to man. Developing gametocytes sequester preferentially in the bone marrow, but mature stage gametocytes are released to the bloodstream. Sexual stage parasite surface proteins are of interest as candidate target antigens for transmission blocking vaccines.Methods: In this study, the transcript profiles of rif and var genes, known to encode surface antigens in asexual blood stage parasites, were investigated at different stages of 3D7/NF54 gametocytogenesis and in sporozoites.Results: Gametocytes exhibited a rif transcript profile unlinked to the rif and var transcript profile of the asexual progenitors. At stage V, mature gametocytes produced high levels of a single rif gene, PF13_0006, which also dominated the rif transcript profile of sporozoites. All var genes appeared to be silenced in sporozoites.Conclusions: The most prominent variant surface antigen transcribed in both gametocytes and sporozoites of 3D7/NF54 is a single variant of the RIFIN protein family. This discovery may lead to the identification of the parasites binding ligands responsible for the adhesion during sexual stages and potentially to novel vaccine candidates

DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens

The Plasmodium Export Element Revisited

We performed a bioinformatical analysis of protein export elements (PEXEL) in the putative proteome of the malaria parasite Plasmodium falciparum. A protein family-specific conservation of physicochemical residue profiles was found for PEXEL-flanking sequence regions. We demonstrate that the family members can be clustered based on the flanking regions only and display characteristic hydrophobicity patterns. This raises the possibility that the flanking regions may contain additional information for a family-specific role of PEXEL. We further show that signal peptide cleavage results in a positional alignment of PEXEL from both proteins with, and without, a signal peptide