Timing and depositional environments of a Middle Pleistocene glaciation of northeast England: New evidence from Warren House Gill, County Durham

At various times during the Quaternary, north-eastern England was a zone of confluence between dynamic ice lobes sourced from the Pennines, northern Scotland, the Cheviots, and Scandinavia. The region thus has some of the most complex exposures of Middle to Late Pleistocene sediments in Britain, with both interglacial and glacial sediments deposited in terrestrial and marine settings. We investigated sedimentary sequences exposed on the coastline of County Durham at Warren House Gill, and present a new model of British and Fennoscandian Ice Sheet interaction in the North Sea Basin during the Middle Pleistocene. The stratigraphy at Warren House Gill consists of a lower diamicton and upper estuarine sediments, both part of the Warren House Formation. They are separated from the overlying Weichselian Blackhall and Horden tills by a substantial unconformity. The lower diamicton of the Warren House Formation is re-interpreted here as an MIS 8 to 12 glaciomarine deposit containing ice-rafted lithics from north-eastern Scotland and the northeast North Sea, and is renamed the ‘Ash Gill Member’. It is dated by lithological comparison to the Easington Raised Beach, Middle Pleistocene Amino Acid Racemisation values, and indirectly by optically stimulated luminescence. The overlying shallow subaqueous sediments were deposited in an estuarine environment by suspension settling and bottom current activity. They are named the ‘Whitesides Member’, and form the uppermost member of the Warren House Formation. During glaciation, ice-rafted material was deposited in a marine embayment. There is no evidence of a grounded, onshore Scandinavian ice sheet in County Durham during MIS 6, which has long been held as the accepted stratigraphy. This has major implications for the currently accepted British Quaternary Stratigraphy. Combined with recent work on the Middle Pleistocene North Sea Drift from Norfolk, which is now suggested to have been deposited by a Scottish ice sheet, the presence of a Scandinavian ice sheet in eastern England at any time during the Quaternary is becoming increasingly doubtful.

Archaeofacies Analysis: Using Depositional Attributes to Identify Anthropic Processes of Deposition in a Monumental Shell Mound of Santa Catarina State, Southern Brazil

In the coast of Santa Catarina State (southern Brazil), a large population of monumental shell mounds characterizes a highly dynamic coastal setting. In this paper, sedimentary facies analysis was adapted for description, sampling, and interpretation of shell mound complex and repetitive archaeostratigraphic successions. Archaeofacies identification in the field, according to depositional attributes, is tested by contrasting field description with multi-element chemical analyses, total carbon and nitrogen determinations, and micromorphological descriptions. Two vertical sequences at the black deposit of Jabuticabeira II shell mound were studied and preliminary results showed that: (1) depositional attributes are a reliable base for archaeofacies identification in the field, (2) the formation process of this site involved a sequence of anthropic depositional processes, where burned refuse was redeposited over the shell mound following a ritual construction pattern, and (3) the black deposit includes a double palimpsest that refers to provenance and meaning of mound construction material. (C) 2009 Wiley Periodicals, Inc.

Sedimentary rocks of the Internal Hellenides, Greece: age, source, and depositional setting

Ziel der vorliegenden Dissertation war die Untersuchung der Liefergebiete und Ablagerungsräume sedimentärer Gesteine aus ausgewählten Gebieten der inneren Helleniden Griechenlands. Die untersuchten Sedimente Nordgriechenlands gehören zu den Pirgadikia und Vertiskos Einheiten des Serbo-Makedonische Massifs, zu den Examili, Melissochori und Prinochori Formationen der östlichen Vardar Zone und zur Makri Einheit und Melia Formation des östlichen Zirkum-Rhodope-Gürtels in Thrakien. In der östlichen Ägäis lag der Schwerpunkt bei den Sedimenten der Insel Chios. Der Metamorphosegrad der untersuchten Gesteine variiert von der untersten Grünschieferfazies bis hin zur Amphibolitfazies. Das stratigraphische Alter reicht vom Ordovizium bis zur Kreide. Zur Charakterisierung der Gesteine und ihrer Liefgebiete wurden Haupt- und Spurenelementgehalte der Gesamtgesteine bestimmt, mineralchemische Analysen durchgeführt und detritische Zirkone mit U–Pb datiert. An ausgewählten Proben wurden außerdem biostratigraphische Untersuchungen zur Bestimmung des Sedimentationsalters durchgeführt. Die Untersuchungsergebnisse dieser Arbeit sind von großer Bedeutung für paläogeographische Rekonstruktionen der Tethys. Die wichtigsten Ergebnisse lassen sich wie folgt zusammenfassen: Die ältesten Sedimente Nordgriechenlands gehören zur Pirgadikia Einheit des Serbo-Makedonischen Massifs. Es sind sehr reife, quarzreiche, siliziklastische Metasedimente, die auf Grund ihrer Maturität und ihrer detritischen Zirkone mit ordovizischen overlap-Sequenzen vom Nordrand Gondwanas korreliert werden können. Die Metasedimente der Vertiskos Einheit besitzen ein ähnliches stratigraphisches Alter, haben aber einen anderen Ablagerungsraum. Das Altersspektrum detritischer Zirkone lässt auf ein Liefergebiet im Raum NW Afrikas (Hun Superterrane) schließen. Die Gesteinsassoziation der Vertiskos Einheit wird als Teil einer aktiven Kontinentalrandabfolge gesehen. Die ältesten biostratigraphisch datierten Sedimente Griechenlands sind silurische bis karbonische Olistolithe aus einer spätpaläozoischen Turbidit-Olistostrom Einheit auf der Insel Chios. Die Alter detritischer Zirkone und die Liefergebietsanalyse der fossilführenden Olistolithe lassen den Schluss zu, dass die klastischen Sedimente von Chios Material vom Sakarya Mikrokontinent in der West-Türkei und faziellen Äquivalenten zu paläozoischen Gesteinen der Istanbul Zone in der Nord-Türkei und der Balkan Region erhalten haben. Während der Permotrias wurde die Examili Formation der östlichen Vardar Zone in einem intrakontinentalen, sedimentären Becken, nahe der Vertiskos Einheit abgelagert. Untergeordnet wurde auch karbonisches Grundgebirgsmaterial eingetragen. Im frühen bis mittleren Jura wurde die Melissochori Formation der östlichen Vardar Zone am Abhang eines karbonatführenden Kontinentalrandes abgelagert. Der Großteil des detritischen Materials kam von permokarbonischem Grundgebirge vulkanischen Ursprungs, vermutlich von der Pelagonischen Zone und/oder der unteren tektonischen Einheit des Rhodope Massifs. Die Makri Einheit in Thrakien besitzt vermutlich ein ähnliches Alter wie die Melissochori Formation. Beide sedimentären Abfolgen ähneln sich sehr. Der Großteil des detritischen Materials für die Makri Einheit kam vom Grundgebirge der Pelagonischen Zone oder äquivalenten Gesteinen. Während der frühen Kreide wurde die Prinochori Formation der östlichen Vardar Zone im Vorfeld eines heterogenen Deckenstapels abgelagert, der ophiolitisches Material sowie Grundgebirge ähnlich zu dem der Vertiskos Einheit enthielt. Ebenfalls während der Kreidezeit wurde in Thrakien, vermutlich im Vorfeld eines metamorphen Deckenstapels mit Affinitäten zum Grundgebirge der Rhodopen die Melia Formation abgelagert. Zusammenfassend kann festgehalten werden, dass die Subduktion eines Teiles der Paläotethys und die anschließende Akkretion vom Nordrand Gondwanas stammender Mikrokontinente (Terranes) nahe dem südlichen aktiven Kontinentalrand Eurasiens den geodynamischen Rahmen für die Schüttung des detritischen Materials der Sedimente der inneren Helleniden im späten Paläozoikum bildeten. Die darauf folgenden frühmesozoischen Riftprozesse leiteten die Bildung von Ozeanbecken der Neotethys ein. Intraozeanische Subduktion und die Obduzierung von Ophioliten prägten die Zeit des Jura. Die spätjurassische und frühkretazische tektonische Phase wurde durch die Ablagerung von mittelkretazischen Kalksteinen besiegelt. Die endgültige Schließung von Ozeanbecken der Neotethys im Bereich der inneren Helleniden erfolgte schließlich in der späten Kreide und im Tertiär.

Geochemistry of Albian to Santonian black shale sequences on the Demerara Rise, South American margin

Ocean Drilling Program Leg 207 recovered thick sequences of Albian to Santonian organic-carbon-rich claystones at five drill-sites on the Demerara Rise in the western equatorial Atlantic Ocean. Dark-colored, finely laminated, Cenomanian-Santonian black shale sequences contain between 2% and 15% organic carbon and encompass Oceanic Anoxic Events 2 and 3. High Rock-Eval hydrogen indices signify that the bulk of the organic matter in these sequences is marine in origin. However, d13Corg values lie mostly between -30 per mil and -27 per mil, and TOC/TN ratios range from 15 to 42, which both mimic the source signatures of modern C3 land plants. The contradictions in organic matter source indicators provide important implications about the depositional conditions leading to the black shale accumulations. The low d13Corg values, which are actually common in mid-Cretaceous marine organic matter, are consequences of the greenhouse climate prevailing at that time and an associated accelerated hydrologic cycle. The elevated C/N ratios, which are also typical of black shales, indicate depressed organic matter degradation associated with low-oxygen conditions in the water column that favored preservation of carbon-rich forms of marine organic matter over nitrogen-rich components. Underlying the laminated Cenomanian-Santonian sequences are homogeneous, dark-colored, lower to middle Albian siltstones that contain between 0.2% and 9% organic carbon. The organic matter in these rocks is mostly marine in origin, but it occasionally includes large proportions of land-derived material.

Nitrogen isotope ratios of Cretaceous Atlantic sedimentary sequences

At two locations in the Atlantic Ocean (DSDP Sites 367 and 530) early to middle Cretaceous organic-carbon-rich beds (black shales) were found to have significantly lower delta15N values (lower 15N/14N ratios) than adjacent organic-carbon-poor beds (white limestones or green claystones). While these lithologies are of marine origin, the black strata in particular have delta15N values that are significantly lower than those previously found in the marine sediment record and most contemporary marine nitrogen pools. In contrast, black, organic-carbon-rich beds at a third site (DSDP Site 603) contain predominantly terrestrial organic matter and have C- and N-isotopic compositions similar to organic matter of modern terrestrial origin. The recurring 15N depletion in the marine-derived Cretaceous sequences prove that the nitrogen they contain is the end result of an episodic and atypical biogeochemistry. Existing isotopic and other data indicate that the low 15N relative abundance is the consequence of pelagic rather than post-depositional processes. Reduced ocean circulation, increased denitrification, and, hence, reduced euphoric zone nitrate availability may have led to Cretaceous phytoplankton assemblages that were periodically dominated by N2-fixing blue-green algae, a possible source of this sediment 15N-depletion. Lack of parallel isotopic shifts in Cretaceous terrestrially-derived nitrogen (Site 603) argues that the above change in nitrogen cycling during this period did not extend beyond the marine environment.

Description of lithofacies associations and their interpreted settings from sequences of sediment core CRP-1 (Table 2)

Cape Roberts Project drillcore 1 was obtained from Roberts Ridge, a sea-floor high located at 77°S, 16 km offshore from Cape Roberts in western McMurdo Sound, Antarctica. The recovered core is about 147 m long with the upper 43.15 metres below the sea floor (revised figure) being dated as Quarternary and the older part of the sequence being Miocene. The core includes nine facies: sandy diamict, muddy diamict, gravel/conglomerate, mud(stone), clay(stone) and carbonate. These facies occure in associations that are repeated in particulare sequences throughout the core, and are interpreted as representing different depositional environments through time. Seven lithofacies associations are interpreted as representing offshore shelf, ice protected/below wave-base; prodeltaic/offshore shelf; delta front/sandy shelf; ice system; subglacial till/rainout diamict/debris flow diamicts singly or in combination; and a carbonate-rich shelf bank. The facies associations are used to infer that the Quaternary section represents deposition on a polar shelf with perhaps two or three glacial fluctuations. The Quaternary carbonate unit indicates a period of ice sheet retreat, but local glacial activity may have increased with an increase in costal precipitation. The Miocene section represents polythermal glacial systems. The older Miocene section is glacially dominated whereas the younger section is much less so. The glacially dominated section may provide evidence for a major glacial advance thar resulted un a low stand of global eustatic sea level at that time. After the low stand, eustatic sea level was gradually rising during deposition of the younger section dominated more by non-glacial processes.

The Southern Ischia canyon system: examples of deep sea depositional systems on the continental slope off Campania (Italy)

The Southern Ischia canyon system has been investigated in detail through Multibeam bathymetry and Sparker seismic data and has been put in the geological framework of the deep sea depositional systems off the Campania region. The geological and geomorphological characteristics of the canyon system have been also compared with the characters of the Mediterranean submarine canyons and with the deep sea depositional systems of the Tyrrhenian sea. The Southern Ischia canyon system engraves a narrow continental shelf from Punta Imperatore to Punta San Pancrazio, being limited southwestwards from the relict volcanic edifice of the Ischia Bank. It consists of twenty-two drainage axes, whose planimetric trending has been reconstructed in a sketch morphological map realized through the geological interpretation of Multibeam bathymetry. While the eastern boundary of the canyon system is controlled by extensional tectonics, being limited by a NE-SW trending (anti-Apenninic) normal fault, its western boundary is controlled by volcanism, due to the growth of the Ischia volcanic bank. Submarine gravitational instabilities also acted in relationships to the canyon system, allowing for the individuation of large-scale creeping at the sea bottom and hummocky deposits already interpreted as debris avalanche deposits. Quaternary marine seismic sequences have been reconstructed through a densely spaced seismic grid recorded through a Sparker multitip seismic source, allowing for a detailed observation of steep erosional slopes occurring on the southern flank of the island and related deep sea depositional systems. Important implications of this study will regard the coastal monitoring and beach nourishment of the southern flank of the island, being involved by a strong erosion of marine and coastal systems.

Phylogenetic analyses of Cladophora vagabunda (L.) C. Hoek (Cladophorales, Chlorophyta) from Brazil based on SSU rDNA sequences

The complete SSU rDNA was sequenced for 10 individuals of Cladophora vagabunda collected along the coast of Brazil. For C. rupestris (L.) Kütz. a partial SSU rDNA sequence (1634 bp) was obtained. Phylogenetic trees indicate that Cladophora is paraphyletic, but the section Glomeratae sensu lato including C. vagabunda from Brazil, Japan and France, C. albida (Nees) Kütz., C. sericea (Hudson) Kütz., and C. glomerata (L.) Kütz. is monophyletic. Within this group C. vagabunda is paraphyletic. The sequence identity for the SSU rDNA varied from 98.9% to 100% for the Brazilian C. vagabunda, and from 98.3% to 99.7% comparing the Brazilian individuals to the ones from France and Japan. Sequence identity of the Brazilian C. vagabunda to C. albida and C. sericea vary from 98.0% to 98.6%. The SSU rDNA phylogeny support partially the morphological characteristics presented by Brazilian populations of C. vagabunda. On the other hand, C. rupestris from Brazil does not group with C. rupestris from France, both sequences presenting only 96.9% of identity. The inclusion of sequences of individuals from Brazil reinforces the need of taxonomical revision for the genus Cladophora and for the complex C. vagabunda.

Analysis of mangrove forest succession, using sediment cores: a case study in the Cananéia -Iguape coastal system, São Paulo Brazil

Sediment cores are an essential tool for the analysis of the dynamics of mangrove succession. Coring was used to correlate changes in depositional environments and lateral sedimentary facies with discrete stages of forest succession at the Cananéia-Iguape Coastal System in southeastern Brazil. A local level successional pattern was examined based on four core series T1) a sediment bank; T2) a smooth cordgrass Spartina alterniflora bank; T3) an active mangrove progradation fringe dominated by Laguncularia racemosa, and; T4) a mature mangrove forest dominated by Avicennia schaueriana. Cores were macroscopically described in terms of color, texture, sedimentary structure and organic components. The base of all cores exhibited a similar pattern suggesting common vertical progressive changes in depositional conditions and subsequent successional colonization pattern throughout the forest. The progradation zone is an exposed bank, colonized by S. alterniflora. L. racemosa, replaces S. alterniflora as progradation takes place. As the substrate consolidates A. schaueriana replaces L. racemosa and attains the greatest structural development in the mature forest. Cores collected within the A. schaueriana dominated stand contained S. alterniflora fragments near the base, confirming that a smooth cordgrass habitat characterized the establishment and early seral stages. Cores provide a reliable approach to describe local-level successional sequences in dynamic settings subject to drivers operating on multiple temporal and spatial scales where spatial heterogeneity can lead to multiple equilibria and where similar successional end-points may be reached through convergent paths.

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp aurantifolii

Background: Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. Results: We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. Conclusion: We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

Registration of temporal sequences of coronal and sagittal MR images through respiratory patterns

This work discusses the determination of the breathing patterns in time sequence of images obtained from magnetic resonance (MR) and their use in the temporal registration of coronal and sagittal images. The registration is made without the use of any triggering information and any special gas to enhance the contrast. The temporal sequences of images are acquired in free breathing. The real movement of the lung has never been seen directly, as it is totally dependent on its surrounding muscles and collapses without them. The visualization of the lung in motion is an actual topic of research in medicine. The lung movement is not periodic and it is susceptible to variations in the degree of respiration. Compared to computerized tomography (CT), MR imaging involves longer acquisition times and it is preferable because it does not involve radiation. As coronal and sagittal sequences of images are orthogonal to each other, their intersection corresponds to a segment in the three-dimensional space. The registration is based on the analysis of this intersection segment. A time sequence of this intersection segment can be stacked, defining a two-dimension spatio-temporal (2DST) image. The algorithm proposed in this work can detect asynchronous movements of the internal lung structures and lung surrounding organs. It is assumed that the diaphragmatic movement is the principal movement and all the lung structures move almost synchronously. The synchronization is performed through a pattern named respiratory function. This pattern is obtained by processing a 2DST image. An interval Hough transform algorithm searches for synchronized movements with the respiratory function. A greedy active contour algorithm adjusts small discrepancies originated by asynchronous movements in the respiratory patterns. The output is a set of respiratory patterns. Finally, the composition of coronal and sagittal image pairs that are in the same breathing phase is realized by comparing of respiratory patterns originated from diaphragmatic and upper boundary surfaces. When available, the respiratory patterns associated to lung internal structures are also used. The results of the proposed method are compared with the pixel-by-pixel comparison method. The proposed method increases the number of registered pairs representing composed images and allows an easy check of the breathing phase. (C) 2010 Elsevier Ltd. All rights reserved.

DNA sequences generated by BCH codes over GF(4)

The question raised by researchers in the field of mathematical biology regarding the existence of error-correcting codes in the structure of the DNA sequences is answered positively. It is shown, for the first time, that DNA sequences such as proteins, targeting sequences and internal sequences are identified as codewords of BCH codes over Galois fields.

A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Molecular phylogeny of Wolbachia endosymbionts in southeast asian mosquitoes (Diptera: Culicidae) based on wsp gene sequences

Wolbachia are maternally inherited intracellular bacteria that infect a wide range of arthropods and nematodes and are associated with various reproductive abnormalities in their hosts. Insect-associated Wolbachia form a monophyletic clade in the α-Proteobacteria and recently have been separated into two supergroups (A and B) and 19 groups. Our recent polymerase chain reaction (PCR) survey using wsp specific primers indicated that various strains of Wolbachia were present in mosquitoes collected from Southeast Asia. Here, we report the phylogenetic relationship of the Wolbachia strains found in these mosquitoes using wsp gene sequences. Our phylogenetic analysis revealed eight new Wolbachia strains, five in the A supergroup and three in the B supergroup. Most of the Wolbachia strains present in Southeast Asian mosquitoes belong to the established Mors, Con, and Pip groups.

wsp Gene sequences from the Wolbachia of filarial nematodes

Wolbachia endosymbiotic bacteria are widespread in arthropods and are also present in filarial nematodes. Almost all filarial species so far examined have been found to harbor these endosymbionts. The sequences of only three genes have been published for nematode Wolbachia (i.e., the genes coding for the proteins FtsZ and catalase and for 16S rRNA). Here we present the sequences of the genes coding for the Wolbachia surface protein (WSP) from the endosymbionts of eight species of filaria. Complete gene sequences were obtained from the endosymbionts of two different species, Dirofilaria immitis and Brugia malayi. These sequences allowed us to design general primers for amplification of the wsp gene from the Wolbachia of all filarial species examined. For these species, partial WSP sequences (about 600 base pairs) were obtained with these primers. Phylogenetic analysis groups these nematode wsp sequences into a coherent cluster. Within the nematode cluster, wsp-based Wolbachia phylogeny matches a previous phylogeny obtained with ftsZ gene sequences, with a good consistency of the phylogeny of hosts (nematodes) and symbionts (Wolbachia). In addition, different individuals of the same host species (Dirofilaria immitis and Wuchereria bancrofti) show identical wsp gene sequences.