Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi

© Medina et al.Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.

The Rotational Evolution and Magnetospheric Emission of the Magnetic Early B-type Stars

How do the magnetic fields of massive stars evolve over time? Are their gyrochronological ages consistent with ages inferred from evolutionary tracks? Why do most stars predicted to host Centrifugal Magnetospheres (CMs) display no H$\alpha$ emission? Does plasma escape from CMs via centrifugal breakout events, or by a steady-state leakage mechanism? This thesis investigates these questions via a population study with a sample of 51 magnetic early B-type stars. The longitudinal magnetic field \bz~was measured from Least Squares Deconvolution profiles extracted from high-resolution spectropolarimetric data. New rotational periods $P_{\rm rot}$ were determined for 15 stars from \bz, leaving only 3 stars for which $P_{\rm rot}$ is unknown. Projected rotational velocities \vsini~were measured from multiple spectral lines. Effective temperatures and surface gravities were measured via ionization balances and line profile fitting of H Balmer lines. Fundamental physical parameters, \bz, \vsini, and $P_{\rm rot}$ were then used to determine radii, masses, ages, dipole oblique rotator model, stellar wind, magnetospheric, and spindown parameters using a Monte Carlo approach that self-consistently calculates all parameters while accounting for all available constraints on stellar properties. Dipole magnetic field strengths $B_{\rm d}$ follow a log-normal distribution similar to that of Ap stars, and decline over time in a fashion consistent with the expected conservation of fossil magnetic flux. $P_{\rm rot}$ increases with fractional main sequence age, mass, and $B_{\rm d}$, as expected from magnetospheric braking. However, comparison of evolutionary track ages to maximum spindown ages $t_{\rm S,max}$ shows that initial rotation fractions may be far below critical for stars with $M_*>10 M_\odot$. Computing $t_{\rm S,max}$ with different mass-loss prescriptions indicates that the mass-loss rates of B-type stars are likely much lower than expected from extrapolation from O-type stars. Stars with H$\alpha$ in emission and absorption occupy distinct regions in the updated rotation-magnetic confinement diagram: H$\alpha$-bright stars are found to be younger, more rapidly rotating, and more strongly magnetized than the general population. Emission strength is sensitive both to the volume of the CM and to the mass-loss rate, favouring leakage over centrifugal breakout.

Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence.

Over the years, many reviews of different aspects of diatom biology, ecology and evolution have appeared. Since 1993 many molecular trees have been produced to infer diatom phylogeny. In 2004, Medlin & Kaczmarska revised the systematics of the diatoms based on more than 20 years of consistent recovery of two major clades of diatoms that did not correspond to a traditional concept of centrics and pennates and established three classes of diatoms: Clade 1 = Coscinodiscophyceae (radial centrics) and Clade 2 = Mediophyceae (polar centrics + radial Thalassiosirales) and Bacillariophyceae (pennates). However, under certain analytical conditions, an alternative view of diatom evolution, a grades of clades, has been recovered that suggests a gradual evolution from centric to pennate symmetry. These two schemes of diatom evolution are evaluated in terms of whether or not the criteria advocated by Medlin & Kaczmarska that should be met to recover monophyletic classes have been used. The monophyly of the three diatom classes can only be achieved if (1) a secondary structure of the small subunit (SSU) rRNA gene was used to construct the alignment and not an alignment based on primary structure and (2) multiple outgroups were used. These requirements have not been met in each study of diatom evolution; hence, the grade of clades, which is useful in reconstructing the sequence of evolution, is not useful for accepting the new classification of the diatoms. Evidence for how these two factors affect the recovery of the three monophyletic classes is reviewed here. The three classes have been defined by clear morphological differences primarily based on gametangia and auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. New evidence supporting the three clades is reviewed. Other features of the cell are examined to determine whether they can also be used to support the monophyly of the three classes.

Evolution of the diatoms: major steps in their evolution and a review of the supporting molecular and morphological evidence.

Over the years, many reviews of different aspects of diatom biology, ecology and evolution have appeared. Since 1993 many molecular trees have been produced to infer diatom phylogeny. In 2004, Medlin & Kaczmarska revised the systematics of the diatoms based on more than 20 years of consistent recovery of two major clades of diatoms that did not correspond to a traditional concept of centrics and pennates and established three classes of diatoms: Clade 1 = Coscinodiscophyceae (radial centrics) and Clade 2 = Mediophyceae (polar centrics + radial Thalassiosirales) and Bacillariophyceae (pennates). However, under certain analytical conditions, an alternative view of diatom evolution, a grades of clades, has been recovered that suggests a gradual evolution from centric to pennate symmetry. These two schemes of diatom evolution are evaluated in terms of whether or not the criteria advocated by Medlin & Kaczmarska that should be met to recover monophyletic classes have been used. The monophyly of the three diatom classes can only be achieved if (1) a secondary structure of the small subunit (SSU) rRNA gene was used to construct the alignment and not an alignment based on primary structure and (2) multiple outgroups were used. These requirements have not been met in each study of diatom evolution; hence, the grade of clades, which is useful in reconstructing the sequence of evolution, is not useful for accepting the new classification of the diatoms. Evidence for how these two factors affect the recovery of the three monophyletic classes is reviewed here. The three classes have been defined by clear morphological differences primarily based on gametangia and auxospore ontogeny and envelope structure, the presence or absence of a structure (tube process or sternum) associated with the annulus and the location of the cribrum in those genera with loculate areolae. New evidence supporting the three clades is reviewed. Other features of the cell are examined to determine whether they can also be used to support the monophyly of the three classes.

The VLT-FLAMES Tarantula Survey: XIX. B-type supergiants: Atmospheric parameters and nitrogen abundances to investigate the role of binarity and the width of the main sequence

Context: Model atmosphere analyses have been previously undertaken for both Galactic and extragalactic B-type supergiants. By contrast, little attention has been given to a comparison of the properties of single supergiants and those that are members of multiple systems. 

Aims: Atmospheric parameters and nitrogen abundances have been estimated for all the B-type supergiants identified in the VLT-FLAMES Tarantula survey. These include both single targets and binary candidates. The results have been analysed to investigate the role of binarity in the evolutionary history of supergiants. 

Methods: tlusty non-local thermodynamic equilibrium (LTE) model atmosphere calculations have been used to determine atmospheric parameters and nitrogen abundances for 34 single and 18 binary supergiants. Effective temperatures were deduced using the silicon balance technique, complemented by the helium ionisation in the hotter spectra. Surface gravities were estimated using Balmer line profiles and microturbulent velocities deduced using the silicon spectrum. Nitrogen abundances or upper limits were estimated from the Nii spectrum. The effects of a flux contribution from an unseen secondary were considered for the binary sample. Results. We present the first systematic study of the incidence of binarity for a sample of B-type supergiants across the theoretical terminal age main sequence (TAMS). To account for the distribution of effective temperatures of the B-type supergiants it may be necessary to extend the TAMS to lower temperatures. This is also consistent with the derived distribution of mass discrepancies, projected rotational velocities and nitrogen abundances, provided that stars cooler than this temperature are post-red supergiant objects. For all the supergiants in the Tarantula and in a previous FLAMES survey, the majority have small projected rotational velocities. The distribution peaks at about 50 km s^-1 with 65% in the range 30 km s^-1 ≤ ν_e sin i ≤ 60 km s^-1. About ten per cent have larger ve sin i (≥100 km s^-1), but surprisingly these show little or no nitrogen enhancement. All the cooler supergiants have low projected rotational velocities of ≤70 km s^-1 and high nitrogen abundance estimates, implying that either bi-stability braking or evolution on a blue loop may be important. Additionally, there is a lack of cooler binaries, possibly reflecting the small sample sizes. Single-star evolutionary models, which include rotation, can account for all of the nitrogen enhancement in both the single and binary samples. The detailed distribution of nitrogen abundances in the single and binary samples may be different, possibly reflecting differences in their evolutionary history. 

Conclusions: The first comparative study of single and binary B-type supergiants has revealed that the main sequence may be significantly wider than previously assumed, extending to T_eff = 20 000 K. Some marginal differences in single and binary atmospheric parameters and abundances have been identified, possibly implying non-standard evolution for some of the sample. This sample as a whole has implications for several aspects of our understanding of the evolutionary status of blue supergiants.

Incised Pleistocene valleys in the Western Belgium coastal plain: Age, origins and implications for the evolution of the Southern North Sea Basin

The Belgian coastal plain occupies a key position as it is located at the transition between the Southern North Sea Basin and the Strait of Dover. It is characterized by thick sequences (> 20 m) of Pleistocene terrestrial and littoral sediments. Yet the wider stratigraphical and palaeo-environmental significance of these sediments received little attention. In this paper we draw on the results of a recent sedimentological study based on > 100 drillings that spans the Pleistocene sequence, and present new biostratigraphical (pollen, foraminifera, ostracods) data, all revealing a complex history of deposition. The record includes evidence of the development of incised-valley systems that were initiated in the late Middle and Late Pleistocene. Five phases of fluvial incision can be identified. The majority of the infills are deposited in an estuarine environment that passes into a fluvial environment land inward, except the Weichselian infill which has a predominant fluvial origin. The greatest part of the most seaward located zone of the western coastal plain was free of valley incisions, there, shallow marine sediments built up the record. Local biostratigraphical investigations provide a timeframe. The result is placed in a regional context.

Phocid seal leptin: tertiary structure and hydrophobic receptor binding site preservation during distinct leptin gene evolution

The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.

Comparative genomic approaches for investigating evolution in the microbial and viral populations of the rumen

The rumen is home to a diverse population of microorganisms encompassing all three domains of life: Bacteria, Archaea, and Eukarya. Viruses have also been documented to be present in large numbers; however, little is currently known about their role in the dynamics of the rumen ecosystem. This research aimed to use a comparative genomics approach in order to assess the potential evolutionary mechanisms at work in the rumen environment. We proposed to do this by first assessing the diversity and potential for horizontal gene transfer (HGT) of multiple strains of the cellulolytic rumen bacterium, Ruminococcus flavefaciens, and then by conducting a survey of rumen viral metagenome (virome) and subsequent comparison of the virome and microbiome sequences to ascertain if there was genetic information shared between these populations. We hypothesize that the bacteriophages play an integral role in the community dynamics of the rumen, as well as driving the evolution of the rumen microbiome through HGT. In our analysis of the Ruminococcus flavefaciens genomes, there were several mobile elements and clustered regularly interspaced short palindromic repeat (CRISPR) sequences detected, both of which indicate interactions with bacteriophages. The rumen virome sequences revealed a great deal of diversity in the viral populations. Additionally, the microbial and viral populations appeared to be closely associated; the dominant viral types were those that infect the dominant microbial phyla. The correlation between the distribution of taxa in the microbiome and virome sequences as well as the presence of CRISPR loci in the R. flavefaciens genomes, suggested that there is a “kill-the-winner” community dynamic between the viral and microbial populations in the rumen. Additionally, upon comparison of the rumen microbiome and rumen virome sequences, we found that there are many sequence similarities between these populations indicating a potential for phage-mediated HGT. These results suggest that the phages represent a gene pool in the rumen that could potentially contain genes that are important for adaptation and survival in the rumen environment, as well as serving as a molecular ‘fingerprint’ of the rumen ecosystem.

An intimate link between antimicrobial peptide sequence diversity and binding to essential components of bacterial membranes

Antimicrobial peptides and proteins (AMPs) are widespread in the living kingdom. They are key effectors of defense reactions and mediators of competitions between organisms. They are often cationic and amphiphilic, which favors their interactions with the anionic membranes of microorganisms. Several AMP families do not directly alter membrane integrity but rather target conserved components of the bacterial membranes in a process that provides them with potent and specific antimicrobial activities. Thus, lipopolysaccharides (LPS), lipoteichoic acids (LTA) or the peptidoglycan precursor Lipid II are targeted by a broad series of AMPs. Studying the functional diversity of immune effectors tells us about the essential residues involved in AMP mechanism of action. Marine invertebrates have been found to produce a remarkable diversity of AMPs. Molluscan defensins and crustacean anti-LPS factors (ALF) are diverse in terms of amino acid sequence and show contrasted phenotypes in terms of antimicrobial activity. Their activity is directed essentially against Gram-positive or Gram-negative bacteria due their specific interactions with Lipid II or Lipid A, respectively. Through those interesting examples, we discuss here how sequence diversity generated throughout evolution informs us on residues required for essential molecular interaction at the bacterial membranes and subsequent antibacterial activity. Through the analysis of molecular variants having lost antibacterial activity or shaped novel functions, we also discuss the molecular bases of functional divergence in AMPs.

Geological Evolution of Coastal and Marine Environments off the Campania Continental Shelf Through Marine Geological Mapping - The Example of the Cilento Promontory

The geological evolution of coastal and marine environments offshore the Cilento Promontory through marine geological mapping is discussed here. The marine geological map n. 502 “Agropoli,” located offshore the Cilento Promontory (southern Italy), is described and put in regional geologic setting. The study area covers water depths ranging between 30 and 200 m isobaths. The geologic map has been constructed in the frame of a research program financed by the National Geological Survey of Italy (CARG Project), finalized to the construction of an up-to-date cartography of the Campania region. Geological and geophysical data on the continental shelf and slope offshore the southern Campania region have been acquired in an area bounded northward by the Gulf of Salerno and southward by the Gulf of Policastro. A high-resolution multibeam bathymetry has permitted the construction of a digital elevation model (DEM). Sidescan sonar profiles have also been collected and interpreted, and their merging with bathymetric data has allowed for the realization of the base for the marine geologic cartography. The calibration of geophysical data has been attempted through sea-bottom samples. The morpho-structures and the seismic sequences overlying the outcrops of acoustic basement reported in the cartographic representation have been studied in detail using single-channel seismics. The interpretation of seismic profiles has been a support for the reconstruction of the stratigraphic and structural setting of the Quaternary continental shelf successions and the outcrops of rocky acoustic basement in correspondence to the Licosa Cape morphostructural high. These areas result from the seaward prolongation of the stratigraphic and structural units, widely cropping out in the surrounding emerged sector of the Cilento Promontory. The cartographic approach is based on the recognition of laterally coeval depositional systems, interpreted in the frame of system tracts of the Late Quaternary depositional sequence.

Evolution of genome sequencing techniques

The quality and the speed for genome sequencing has advanced at the same time that technology boundaries are stretched. This advancement has been divided so far in three generations. The first-generation methods enabled sequencing of clonal DNA populations. The second-generation massively increased throughput by parallelizing many reactions while the third-generation methods allow direct sequencing of single DNA molecules. The first techniques to sequence DNA were not developed until the mid-1970s, when two distinct sequencing methods were developed almost simultaneously, one by Alan Maxam and Walter Gilbert, and the other one by Frederick Sanger. The first one is a chemical method to cleave DNA at specific points and the second one uses ddNTPs, which synthesizes a copy from the DNA chain template. Nevertheless, both methods generate fragments of varying lengths that are further electrophoresed. Moreover, it is important to say that until the 1990s, the sequencing of DNA was relatively expensive and it was seen as a long process. Besides, using radiolabeled nucleotides also compounded the problem through safety concerns and prevented the automation. Some advancements within the first generation include the replacement of radioactive labels by fluorescent labeled ddNTPs and cycle sequencing with thermostable DNA polymerase, which allows automation and signal amplification, making the process cheaper, safer and faster. Another method is Pyrosequencing, which is based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation. By the end of the last millennia, parallelization of this method started the Next Generation Sequencing (NGS) with 454 as the first of many methods that can process multiple samples, calling it the 2º generation sequencing. Here electrophoresis was completely eliminated. One of the methods that is sometimes used is SOLiD, based on sequencing by ligation of fluorescently dye-labeled di-base probes which competes to ligate to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction. The widely used Solexa/Illumina method uses modified dNTPs containing so called “reversible terminators” which blocks further polymerization. The terminator also contains a fluorescent label, which can be detected by a camera. Now, the previous step towards the third generation was in charge of Ion Torrent, who developed a technique that is based in a method of “sequencing-by-synthesis”. Its main feature is the detection of hydrogen ions that are released during base incorporation. Likewise, the third generation takes into account nanotechnology advancements for the processing of unique DNA molecules to a real time synthesis sequencing system like PacBio; and finally, the NANOPORE, projected since 1995, also uses Nano-sensors forming channels obtained from bacteria that conducts the sample to a sensor that allows the detection of each nucleotide residue in the DNA strand. The advancements in terms of technology that we have nowadays have been so quick, that it makes wonder: ¿How do we imagine the next generation?

Convergent evolution of PICIs-mediated phage interference

Staphylococcal pathogenicity islands (SaPIs), the prototype members of the family of phage inducible chromosomal islands (PICIs), are extremely mobile phage satellites, which are transferred between bacterial hosts after their induction by a helper phage. The intimate relationship between SaPIs and their helper phages is one of the most studied examples of virus satellite interactions in prokaryotic cells. SaPIs encode and disseminate virulence and fitness factors, representing a driving force for bacterial adaptation and pathogenesis. Many SaPIs encode a conserved morphogenetic operon, including a core set of genes whose function allows them to parasitize and exploit the phage life cycle. One of the central mechanisms of this molecular piracy is the specific packaging of the SaPI genomes into reduced sized capsid structures derived from phage proteins. Pac phages were classically thought to be the only phages involved in the mobilisation of phage-mediated virulence genes, including the transfer of SaPIs within related and non-related bacteria. This study presents the involvement of S. aureus cos phages in the intra- and intergeneric transfer of cos SaPIs for the first time. A novel example of molecular parasitism is shown, by which this newly characterised group of cos SaPIs uses two distinct and complementary mechanisms to take over the helper phage packaging machinery for their own reproduction. SaPIbov5, the prototype of the cos SaPIs, does not encode the characteristic morphogenetic operon found in pac SaPIs. However, cos SaPIs features both pac and cos phage cleavage sequences in their genome, ensuring SaPI packaging in small- and full-sized phage particles, depending on the helper phage. Moreover, cos-site packaging in S. aureus was shown to require the activity of a phage HNH nuclease. The HNH protein functions together with the large terminase subunit, triggering cleavage and melting of the cos-site sequence. In addition, a novel piracy strategy, severely interfering with the helper phage reproduction, was identified in cos SaPIs and characterised. This mechanism of piracy depends on the cos SaPI-encoded ccm gene, which encodes a capsid protein involved in the formation of small phage particles, modifying the assembling process via a scaffolding mechanism. This strategy resembles the ones described for pac SaPIs and represents a remarkable example of convergent evolution. A further convergent mechanism of capsid size-reduction was identified and characterised for the Enterococcus faecalis EfCIV583 pathogenicity island, another member of the PICI family. In this case, the self-encoded CpmE conducts this molecular piracy through a putative scaffolding function. Similar to cos SaPIs, EfCIV583 carries the helper phage cleavage sequence in its genome enabling its mobilisation by the phage terminase complex. The results presented in this thesis show how two examples of non-related members of the PICI family follow the same evolutionary convergent strategy to interfere with their helper phage. These findings could indicate that the described strategies might be widespread among PICIs and implicate a significant impact of PICIs mediated-virulence gene transfer in bacterial evolution and the emergence of pathogenic bacteria.

NEW DATA ON THE CHRONOLOGY OF THE VALE DO FORNO SEDIMENTARY SEQUENCE (LOWER TAGUS RIVER TERRACE STAIRCASE) AND ITS RELEVANCE AS FLUVIAL ARCHIVE OF THE MIDDLE PLEISTOCENE IN WESTERN IBERIA

NEW DATA ON THE CHRONOLOGY OF THE VALE DO FORNO SEDIMENTARY SEQUENCE (LOWER TAGUS RIVER TERRACE STAIRCASE) AND ITS RELEVANCE AS FLUVIAL ARCHIVE OF THE MIDDLE PLEISTOCENE IN WESTERN IBERIA Pedro P. Cunha 1, António A. Martins 2, Jan-Pieter Buylaert 3,4, Andrew S. Murray 4, Luis Raposo 5, Paolo Mozzi 6, Martin Stokes 7 1 MARE - Marine and Environmental Sciences Centre, Department of Earth Sciences, University of Coimbra, Portugal: pcunha@dct.uc.pt 2 MARE - Marine and Environmental Sciences Centre, Dep. Geociências, University of Évora, Portugal; aam@uevora.pt 3 Centre for Nuclear Technologies, Technical University of Denmark, Risø Campus, Denmark; jabu@dtu.dk 4 Nordic Laboratory for Luminescence Dating, Aarhus University, Risø DTU, Denmark; anmu@dtu.dk 5 Museu Nacional de Arqueologia, Lisboa, Portugal; 3raposos@sapo.pt 6 Department of Geosciences, University of Padova, Italy; paolo.mozzi@unipd.it 7 School of Geography, Earth and Environmental Sciences, University of Plymouth, UK; m.stokes@plymouth.ac.uk The stratigraphic units that record the evolution of the Tagus River in Portugal (study area between Vila Velha de Ródão and Porto Alto villages; Fig. 1) have different sedimentary characteristics and lithic industries (Cunha et al., 2012): - a culminant sedimentary unit (the ancestral Tagus, before the drainage network entrenchment) – SLD13 (+142 to 262 m above river bed – a.r.b.; with probable age ca. 3,6 to 1,8 Ma), without artefacts; - T1 terrace (+84 to 180 m; ca. 1000? to 900 ka), without artefacts; - T2 terrace (+57 to 150 m; top deposits with a probable age ca. 600 ka), without artefacts; - T3 terrace (+43 to 113 m; ca. 460 to 360? ka), without artefacts; - T4 terrace (+26 to 55 m; ca. 335 a 155 ka), Lower Paleolithic (Acheulian) at basal and middle levels but early Middle Paleolithic at top levels; - T5 terrace (+5 to 34 m; 135 to 73 ka), Middle Paleolithic (Mousterian; Levallois technique); - T6 terrace (+3 to 14 m; 62 to 32 ka), late Middle Paleolithic (late Mousterian); - Carregueira Sands (aeolian sands) and colluvium (+3 a ca. 100 m; 32 to 12 ka), Upper Paleolithic to Epipaleolithic; - alluvial plain (+0 to 8 m; ca. 12 ka to present), Mesolithic and more recent industries. The differences in elevation (a.r.b.) of the several terrace staircases results from differential uplift due to active faults. Longitudinal correlation with the terrace levels indicates that a graded profile ca. 200 km long was achieved during terrace formation periods and a strong control by sea base level was determinant for terrace formation. The Neogene sedimentary units constituted the main source of sediments for the fluvial terraces (Fig. 2). Geomorphological mapping, coupled with lithostratigraphy, sedimentology and luminescence dating (quartz-OSL and K-feldspar post-IRIR290) were used in this study focused on the T4 terrace, which comprises a Lower Gravels (LG) unit and an Upper Sand (US) unit. The thick, coarse and dominantly massive gravels of the LG unit indicate deposition by a coarse bed-load braided river, with strong sediment supply, high gradient and fluvial competence, during conditions of rapidly rising sea level. Luminescence dating only provided minimum ages but it is probable that the LG unit corresponds to the earlier part of the MIS9 (ca. 335 to 325 ka), immediately postdating the incision promoted by the very low sea level (reaching ca. -140 m) during MIS10 (362 to 337 ka), a period of relatively cold climate conditions with weak vegetation cover on slopes and low sea level. Fig. 1. Main Portuguese reaches in which the Tagus River can be divided (Lower Tagus Basin): I – from the Spanish border to Arneiro (a general E–W trend, mainly consisting of polygonal segments); II – from Arneiro to Gavião (NE–SW); III – from Gavião to Arripiado (E–W); IV – from Arripiado to Vila Franca de Xira (NNE-SSW); V – from Vila Franca de Xira to the Atlantic shoreline. The faults considered to be the limit of the referred fluvial sectors are: F1 – Ponsul-Arneiro fault (WSW-ENE); F2 – Gavião fault (NW-SE); F3 – Ortiga fault (NW-SE); F4 – Vila Nova da Barquinha fault (W-E); F5 – Arripiado-Chamusca fault (NNE-SSW). 1 – estuary; 2 – terraces; 3 – faults; 4 – Tagus main channel. The main Iberian drainage basins are also represented (inset). The lower and middle parts of the US unit, comprising an alternation of clayish silts with paleosols and minor sands to the east (flood-plain deposits) and sand deposits to the west (channel belt), have a probable age of ca. 325 to 200 ka. This points to formation during MIS9 to MIS7, under conditions of high to medium sea levels and warm to mild conditions. The upper part of the US unit, dominated by sand facies and with OSL ages of ca. 200 to 154 ka, correlates with the early part of the MIS6. During this period, progradation resulted from climate deterioration and relative depletion of vegetation that promoted enhanced sediment production in the catchment, coupled with initiation of sea-level lowering that increased the longitudinal slope. The Vale do Forno and Vale da Atela archaeological sites (Alpiarça, central Portugal) document the earliest human occupation in the Lower Tagus River, well established in geomorphological and environmental terms, within the Middle Pleistocene. The Lower Palaeolithic sites were found on the T4 terrace (+26 m, a.r.b.). The oldest artefacts previously found in the LG unit, display crude bifacial forms that can be attributed to the Acheulian, with a probable age of ca. 335 to 325 ka. The T4 US unit has archaeological sites stratigraphically documenting successive phases of an evolved Acheulian, that probably date ca. 325 to 300 ka. Notably, these Lower Palaeolithic artisans were able to produce tools with different sophistication levels, simply by applying different strategies: more elaborated reduction sequences in case of bifaces and simple reduction sequences to obtain cleavers. Fig. 2. . Simplified geologic map of the Lower Tagus Cenozoic basin, adapted from the Carta Geológica de Portugal, 1/500000, 1992). The study area (comprising the Vale do Forno and Vale de Atela sites) is located on the more upstream sector of the Lower Tagus River reach IV, between Arripiado and Chamusca villages. 1 – alluvium (Holocene); 2 – terraces (Pleistocene); 3 – sands, silts and gravels (Paleogene to Pliocene); 4 – Sintra Massif (Cretaceous); 5 – limestones, marls, silts and sandstones (Mesozoic); 6 – quartzites (Ordovician); 7 – basement (Proterozoic to Palaeozoic); 8 – main fault. The main Portuguese reaches of the Tagus River are identified (I to V). The VF3 site (Milharós), containing a Final Acheulian industry, with fine and elaborated bifaces) found in a stratigraphic level located between the T4 terrace deposits and a colluvium associated with Late Pleistocene aeolian sands (32 to 12 ka), has an age younger than ca. 154 ka but much older than 32 ka. In the study area, the sedimentary units of the T4 terrace seem to record the river response to sea-level changes and climatically-driven fluctuations in sediment supply. REFERENCES Cunha P. P., Almeida N. A. C., Aubry T., Martins A. A., Murray A. S., Buylaert J.-P., Sohbati R., Raposo L., Rocha L., 2012, Records of human occupation from Pleistocene river terrace and aeolian sediments in the Arneiro depression (Lower Tejo River, central eastern Portugal). Geomorphology, vol. 165-166, pp. 78-90.

Prognostic Value Of Dna And Mrna E6/e7 Of Human Papillomavirus In The Evolution Of Cervical Intraepithelial Neoplasia Grade 2.

This study aimed at evaluating whether human papillomavirus (HPV) groups and E6/E7 mRNA of HPV 16, 18, 31, 33, and 45 are prognostic of cervical intraepithelial neoplasia (CIN) 2 outcome in women with a cervical smear showing a low-grade squamous intraepithelial lesion (LSIL). This cohort study included women with biopsy-confirmed CIN 2 who were followed up for 12 months, with cervical smear and colposcopy performed every three months. Women with a negative or low-risk HPV status showed 100% CIN 2 regression. The CIN 2 regression rates at the 12-month follow-up were 69.4% for women with alpha-9 HPV versus 91.7% for other HPV species or HPV-negative status (P < 0.05). For women with HPV 16, the CIN 2 regression rate at the 12-month follow-up was 61.4% versus 89.5% for other HPV types or HPV-negative status (P < 0.05). The CIN 2 regression rate was 68.3% for women who tested positive for HPV E6/E7 mRNA versus 82.0% for the negative results, but this difference was not statistically significant. The expectant management for women with biopsy-confirmed CIN 2 and previous cytological tests showing LSIL exhibited a very high rate of spontaneous regression. HPV 16 is associated with a higher CIN 2 progression rate than other HPV infections. HPV E6/E7 mRNA is not a prognostic marker of the CIN 2 clinical outcome, although this analysis cannot be considered conclusive. Given the small sample size, this study could be considered a pilot for future larger studies on the role of predictive markers of CIN 2 evolution.