Sequence Architecture Research Articles

Effect of molecular architecture on the morphology diversity of the multicompartment micelles: A dissipative particle dynamics simulation study

Dissipative particle dynamics simulation is performed to study the sensitive influence of the molecular architecture and/or segment sequence on the morphology diversity of the multicompartment micelles. The multicompartment micelle morphologies formed by ABC triblock copolymers with various molecular architectures, such as the linear, the pentalinear, the cyclic, the star-like, the tetra-arm, and the π-shape are investigated, and different morphologies of the multicompartment micelles, for example, worm-like, “hamburger”, sheet-like with pores, “sweet potato” with alternating layers, sheet-like with cylinder-inclusion, and three-dimensional network are observed in this work. The density profiles and the radial distribution functions are calculated to characterize the structures of the multicompartment micelles. The preparation of complex multicompartment micelles can be fulfilled by simply changing the segment sequence and molecular architecture such as adding new bonds and grafting points.

Interplay between tectonics and compaction in a rift‐margin, lacustrine delta system: Miocene of the Eger Graben, Czech Republic

AbstractThe Early Miocene Bílina Palaeodelta consists of fluvio‐deltaic and lacustrine clastics deposited along the south‐eastern margin of the extensional Most Basin, part of the Eger Graben in north Bohemia (Czech Republic). The Bílina succession shows evidence of repeated advances of an axial deltaic system across a thick accumulation of organic material and clay in the hangingwall of an active fault. Exposures up to ca 4·5 km long in the Bílina open‐cast mine help bridge the gap between seismic scale and typical outcrop scale of observation and thus allow the relationships between small‐scale and basin‐scale stratal geometries to be evaluated. The Bílina Palaeodelta deposits include sand‐dominated, fluvial channel fills and heterolithic sheets interpreted as delta plain strata, sand‐dominated mouth‐bar wedges and heterolithic sheets of prodeltaic deposits, passing distally into lacustrine clays. The depositional environment is interpreted as a fluvial‐dominated, mixed‐load, lacustrine delta with a high degree of grain‐size segregation at the feeder‐channel mouths. On the largest temporal and spatial scales, variable tectonic subsidence controlled the overall advance and retreat of the delta system. The medium‐term transgressive‐regressive history was probably driven by episodes of increased subsidence rate. However, at this temporal scale, the architecture of the deltaic sequences (deltaic lobes and correlative lacustrine deposits) was strongly affected by: (i) compaction of underlying peat and clay which drove lateral offset stacking of medium‐term sequences; and (ii) growth of a fault‐propagation fold close to the active Bílina Fault. At the smallest scale, the geometries of individual mouth bars and groups of mouth bars (short‐term sequences) reflect the interaction among sediment loading, compaction and growth faulting that produced high‐frequency relative lake‐level fluctuations and created local accommodation at the delta front.

Interactions between upstream and core promoter sequences determine gene expression and nucleosome positioning in tobacco PR-1a promoter

The expression of PR-1a gene in tobacco is accompanied by changes in the chromatin architecture over its promoter region. The transcription initiates when the gene is induced in defense response, a condition that can be simulated experimentally by external application of salicylic acid. Mutagenesis of the core promoter sequence established that the TATA-box was critical to the expression of PR-1a gene. In order to study functional specificity between the core promoter and upstream activator region, the native core promoter was exchanged with that of a heterologous salicylic acid inducible promoter, Pcec. The core promoter and the activator region of PR-1a together determine its tightly regulated expression, slow kinetics of induction by SA and several fold induction of expression. In uninduced state, a single nucleosome was present over the core promoter of PR-1a. It masked both the TATA-box and the transcription initiation region. The transcriptional activation of the promoter by SA was accompanied by shift in the position of this nucleosome. The chimeric promoters failed to show inducibility or gave very low level of induction. They showed failure in shifting the nucleosome from the core promoter region. The promoter Pcec expressed constitutively at a high uninduced level in spite of a nucleosome over the TATA-box region. However, in this case, the nucleosome did not mask the transcript initiation region. The TATA-box nucleosome was shifted as the expression increased further, following induction by SA. A fully induced Pcec had the TATA-box fully exposed, though a weak nucleosome appeared on the +1 region. The results support a close relationship among promoter sequence architecture, nucleosome positioning and PR-1a expression.

Effects of IL-10 and IL-6 Gene Polymorphisms and Atomic-bomb Radiation Exposure on Gastric Cancer Risk

Cells repair DNA double-strand breaks (DSBs) through a complex set of pathways critical for maintaining genomic integrity. To systematically map these pathways, we developed a high-throughput screening approach called Repair-seq that measures the effects of thousands of genetic perturbations on mutations introduced at targeted DNA lesions. Using Repair-seq, we profiled DSB repair products induced by two programmable nucleases (Cas9 and Cas12a) in the presence or absence of oligonucleotides for homology-directed repair (HDR) after knockdown of 476 genes involved in DSB repair or associated processes. The resulting data enabled principled, data-driven inference of DSB end joining and HDR pathways. Systematic interrogation of this data uncovered unexpected relationships among DSB repair genes and demonstrated that repair outcomes with superficially similar sequence architectures can have markedly different genetic dependencies. This work provides a foundation for mapping DNA repair pathways and for optimizing genome editing across diverse modalities.

Sequence stratigraphy based on high-resolution seismic profiles in the late Pleistocene and Holocene deposits of the Venice area

The sequence-stratigraphic investigation by Very High-Resolution (VHR) seismic profiles allowed recognition of the detailed architecture of the late Pleistocene and Holocene succession of the Venice area. In this way deposits previously known by the analyses of scattered cores, mainly taken along the lagoon margin and the littoral strips, have been correlated at regional scale including the near offshore sector and the result has pointed out the lateral variability of the stratal architecture. Late Pleistocene deposits consist of an aggrading floodplain and fluvial channel fills accumulated during decreasing eustatic sea level, and they are coeval with offlapping forced regressive marine wedges in the Central Adriatic basin. The Holocene sequence is composed of three main seismic units separated by major stratal surfaces. Unit 1 (up to 9 m thick) is formed by channelized deposits separated by areas showing sub-horizontal and hummocky reflectors, and is bounded at the base by a surface that records prolonged conditions of subaerial exposure and at the top by a flatter surface resulting from erosion by marine processes. Deposits of Unit 1 are interpreted as estuarine and distributary channel fills, and back-barrier strata. Unit 2 is well distinguishable from Unit 1 only in the offshore area and at the barrier island bounding the Venice Lagoon, and is composed of a prograding marine wedge (up to 10 m thick) that interacts laterally with ebb tidal deltas. Unit 3 consists of a tidal channel complex and inlet deposits, which testify the evolution of the lagoon area. Tidal channels are entrenched in the lagoon mud flat (coeval with Units 1–2) and cut the Pleistocene–Holocene boundary in several places. Following current sequence-stratigraphic concepts, the Holocene sequence is composed of a paralic transgressive systems tract (TST) (Unit 1) overlying a sequence boundary (the Pleistocene–Holocene boundary) and overlain by a marine highstand systems tract (HST) (Unit 2) in seaward locations and by highstand lagoonal deposits landwards. TST and HST are separated by a downlap surface that is amalgamated with a wave ravinement surface in several places. Unit 3 is coeval with the upper part of Unit 2, and its development has been favoured by human interventions, which led to a transgression limited to the lagoon area. Local factors during the deposition, i.e. subsidence, sediment supply, physiography, and current/wave regimes, led to a significant lateral variability in the architecture of the Holocene sequence, as evidenced by the extreme thickness variation of the TST along both depositional strike and dip. The HST, instead, shows less pronounced strike variations in the stratal architecture. Also, present data clearly evidence that the human impact has a great relevance in influencing the late Holocene sedimentation.

Preliminary stratigraphic and structural architecture of Bhutan: Implications for the along strike architecture of the Himalayan system

Preliminary mapping and stratigraphic correlation of Lesser Himalayan rock in eastern Bhutan using field characteristics, U–Pb detrital zircon dating, and ɛNd geochemistry define the first-order stratigraphic architecture of the Indian passive margin sequence in the eastern Himalaya. We use this new image of the lateral and vertical relationships of the original stratigraphy to determine the structural framework of the eastern Himalayan fold-thrust belt in Bhutan. We propose that Lesser Himalayan rock in Bhutan can be divided into lower Lesser Himalayan rocks with a Paleoproterozoic detrital zircon signal, and upper Lesser Himalayan rocks with detrital zircon signals of ∼ 1000–500 Ma. The ∼ 500 Ma detrital grains are from rocks in the frontal portions of the fold-thrust belt north of the Main Boundary thrust as well as directly in the footwall of the Main Central thrust in the hinterland. Our preliminary stratigraphic study coupled with mapping allows us to construct a composite balanced cross-section through the Kuru Chu valley in eastern Bhutan which provides the first image of the geometry and amount of shortening through Bhutan. The Main Frontal thrust tilts a 6 km of thick section of Neogene foreland basin deposits. These deposits are separated from folded and faulted upper Lesser Himalayan rocks by the Main Boundary thrust. North of the Main Boundary thrust, we propose two duplex systems. The southernmost duplex contains 9 repeated sections of upper Lesser Himalayan units, including the Permian Gondwana Sequence and the Cambrian (or younger) Baxa Group. The northernmost duplex is located in the footwall of the Main Central thrust, and is comprised of two repeated sections of the Proterozoic Shumar and Daling Formations. The southern boundary of this northern duplex is the Shumar thrust which acts as a roof thrust for the southern duplex system and may correlate to the Ramgarh thrust in Nepal and India. We propose that the development of the duplex systems passively folded overlying Tethyan and Greater Himalayan rocks. Minimum shortening for this part of the Himalayan fold-thrust belt is 359 km, all of which has occurred from 22 Ma to present defining a long-term shortening rate of 16 mm/yr.

Copy number variations in the NF1 gene region are infrequent and do not predispose to recurrent type-1 deletions

Gross deletions of the NF1 gene at 17q11.2 belong to the group of 'genomic disorders' characterized by local sequence architecture that predisposes to genomic rearrangements. Segmental duplications within regions associated with genomic disorders are prone to non-allelic homologous recombination (NAHR), which mediates gross rearrangements. Copy number variants (CNVs) without obvious phenotypic consequences also occur frequently in regions of genomic disorders. In the NF1 gene region, putative CNVs have been reportedly detected by array comparative genomic hybridization (array CGH). These variants include duplications and deletions within the NF1 gene itself (CNV1) and a duplication that encompasses the SUZ12 gene, the distal NF1-REPc repeat and the RHOT1 gene (CNV2). To explore the possibility that these CNVs could have played a role in promoting deletion mutagenesis in type-1 deletions (the most common type of gross NF1 deletion), non-affected transmitting parents of patients with type-1 NF1 deletions were investigated by multiplex ligation-dependent probe amplification (MLPA). However, neither CNV1 nor CNV2 were detected. This would appear to exclude these variants as frequent mediators of NAHR giving rise to type-1 deletions. Using MLPA, we were also unable to confirm CNV1 in healthy controls as previously reported. We conclude that locus-specific techniques should be used to independently confirm putative CNVs, originally detected by array CGH, to avoid false-positive results. In one patient with an atypical deletion, a duplication in the region of CNV2 was noted. This duplication could have occurred concomitantly with the deletion as part of a complex rearrangement or may alternatively have preceded the deletion.

Sequence architecture within a low-accommodation setting: An example from the Permian of the Galilee and Bowen basins, Queensland, Australia

The coal-bearing, Upper Permian Betts Creek Beds (BCB) of the northeastern intracratonic Galilee Basin in north-central Queensland, Australia, record sedimentation within an alluvial-coastal plain in a low-accommodation basin-margin setting. Six third-order depositional sequences are preserved within the BCB and are characterized by a sequence architecture that is overall relatively thin (15 m; 49 ft), condensed, and top truncated. Sequences have a lowstand systems tract composed of extensive braided fluvial sheet sandstones, a transgressive systems tract characterized by tidally influenced fluvial sheet sandstones and bioturbated estuarine mudrocks, and a highstand systems tract composed of coastal-plain mudrocks and coals. Sequences can be correlated throughout the entire Galilee Basin and related to the lithostratigraphy established in the adjacent Bowen Basin, a foreland basin to the east. The overall Late Permian fill is considered a second-order sequence. The stacking patterns show an overall retrogradational to progradational architecture suggestive of relatively low accommodation space. Sequences show an extremely laterally continuous geometry (1000 km; 600 mi) and are relatively uniform in thickness. Sequences do not show evidence of onlap, toplap, or erosional truncation, but instead are thin in areas of low accommodation and expand into areas of higher accommodation. That these third-order sequences can be traced across basins with differing tectonic regimes, together with the persistent, sheetlike nature of the sequences, suggests that tectonic effects on the sequence architecture were minimal. The basin fill covers a time interval during which two glacial events occurred in the final stages of the late Paleozoic Ice Age, suggesting that changes in glacioeustasy may have been the dominant controls on the sequence architecture of the Late Permian succession in the Galilee Basin of northeastern Australia.

Early Holocene paleoseismic history at the Pakarae locality, eastern North Island, New Zealand, inferred from transgressive marine sequence architecture

Early Holocene transgressive marine deposits infilling the Pakarae River paleovalley are used to extend the paleoseismic history of the Pakarae River locality, East Coast, North Island, New Zealand, back in time prior to eustatic sea level stabilization at ∼7 calibrated (cal) ka B.P. Paleoenvironmental evolution of the Pakarae River paleovalley from 7 to 10 cal ka B.P is reconstructed using sedimentology and biostratigraphy. Two estuarine units display sudden vertical transitions to floodplain sediments implying significant marine regressions and estuary abandonment. These regressions are attributed to coseismic coastal uplift events at ∼9000 and ∼8500 cal years B.P. A third uplift between 8500 and ∼7350 cal years B.P. is inferred from a significant difference between the amount of sediment preserved and the predicted sediment thickness according to the eustatic sea level curve. This study demonstrates the utility of the analysis of transgressive deposits and their paleoenvironmental characteristics for neotectonic investigations on active coasts.

Margin segmentation and volcano-tectonic architecture along the volcanic margin off Argentina/Uruguay, South Atlantic

Some 25,000 kilometers of regional multichannel seismic data, acquired by BGR along the continental margins off Argentina and Uruguay document that the Early Cretaceous South Atlantic continental breakup and initial sea-floor spreading were accompanied by large-scale, transient volcanism emplacing voluminous extrusives, manifested in the seismic data by huge wedges of seaward dipping reflectors (SDRs). The emplacement of the deeply buried, 60–120 km wide SDRs was probably episodic as documented by at least three superimposed SDRs units. Distinct along-margin variations in architecture, volume, and width of the SDRs wedges are probably related to margin segmentation. It is suggested that the margin can be divided, at least, in four compartments bounded by the Falkland Fracture Zone/Falkland transfer, the Colorado transfer, the Ventana transfer and the Salado transfer. The individual margin segments reflect in the distribution and thickness of the post-rift sediments. The individual transfer zones may have acted as rift propagation barriers, selectively directing rift segments in left stepping patterns along the western South Atlantic margin. Although we found extensive variations in the architecture, style, and extent of the seaward dipping reflector sequences, a general trend is that the largest volumes are emplaced close to the proposed transfer zones and the width of the SDRs wedges decreases northward within the individual margin segments. We suggest that mainly adiabatic decompression and melt generation from shallow sources can explain distinct along-margin variations in the volcano-tectonic architecture and volumes of extruded magmas.

β‐strand recombination in tricalbin evolution and the origin of synaptotagmin‐like C2 domains

Two protein families involved in membrane traffic, tricalbins and synaptotagmins, contain several copies of C2 domains and are related based on their sequence and domain architecture. Paradoxically, tricalbin and synaptotagmin C2 domains belong to different structural types with apparent circular permutation of terminal beta-strands. To understand whether a topological switch took place, we analyzed tricalbin and synaptotagmin-like C2 domains using two-dimensional structural analysis. We found that yeast tricalbins contain five to six C2 domains. One of these C2 domains possesses many features of synaptotagmin-like C2 domains and also carries a conserved C-terminal strand that is similar to its structural equivalent in synaptotagmin-like C2 domains, suggesting a structural permutation event. Indeed, among higher eukaryotes, animal tricalbins have evolved a C2 domain with synaptotagmin-like topology indicating that the structural conversion has taken place. Investigation of plant synaptotagmins, however, proves that they are direct tricalbin orthologs. Our analysis shows that beta-strand recombination is a possible evolutionary mechanism to generate new structural topologies with altered functional properties.

Sequence stratigraphy of the Precambrian

The method of sequence stratigraphy requires the application of the same workflow and principles irrespective of the age of strata under analysis. In that respect, its application to Precambrian successions is similar to the approach used for Phanerozoic case studies. Differences, however, are recorded in terms of the preservation potential and the amount of data available for analysis; the rates and intensities of the allogenic controls on sedimentation; the environmental conditions and related physical processes; and the evolution of competing groups of organisms and associated biogenic processes. The combined effect of these contrasting aspects accounts for differences in the architecture of depositional sequences, particularly with respect to the relative contributions of various systems tracts to the makeup of a sequence. The application of sequence stratigraphy to Precambrian basins has considerably enlarged the perspective on the fundamental principles governing the processes of sedimentary basin formation and the mechanisms controlling stratigraphic cyclicity in the rock record. These first-order principles are perhaps the most important contribution of Precambrian research to sequence stratigraphy. At the broader scale of Earth's geological history, the tectonic regimes governing the formation and evolution of sedimentary basins are shown to have been much more erratic in terms of nature and rates than originally inferred solely from the study of the Phanerozoic record. This provides important clues with respect to the criteria that should be involved in the hierarchy system of classification of stratigraphic sequences and bounding surfaces.

Facies architecture of an isolated carbonate platform in the Hawasina Basin: The Late Triassic Jebel Kawr of Oman

In the oceanic realm of the southern Tethys, carbonate production of isolated platforms ceased after the end-Permian mass extinction and did not recover until the Late Triassic. The Misfah Formation (MF) at Jebel Kawr in the Oman Mountains is interpreted as a relic of such an isolated Late Triassic platform of the Hawasina Ocean, a part of the Neo-Tethys. Correlation of three sections at Jebel Kawr points to a sequence architecture with four third-order sequences (MF1–MF4). The maximum flooding surface (mfs) of MF3 can be correlated to the attached Arabian platform. The shallow-water carbonates of Jebel Kawr comprise a platform rim reef facies and bedded inner-platform facies characterized by stacked high-frequency cycles with subtidal to intertidal carbonate sequences. The depositional profile of this Late Triassic isolated platform evolved during Carnian and Norian time from a low-relief carbonate bank to a high-relief platform rimmed by reefs. The onset of the carbonate sedimentation is characterized by an initial phase with volcaniclastic interruptions, followed by a carbonate bank stage with a shallow subtidal to peritidal interior and marginal oolite shoals. In the Norian vertical accumulation caused an increase of the platform height and developed a relief along the margins that progressively increased through the aggrading reef stage. The possibility that a reef rim existed and was later removed by erosion is suggested by the Sint reef and olistoliths of similar reef limestones in the surrounding areas.

An unsuspected ecdysteroid/steroid phosphatase activity in the key T‐cell regulator, Sts‐1: Surprising relationship to insect ecdysteroid phosphate phosphatase

The insect enzyme ecdysteroid phosphate phosphatase (EPP) mobilizes active ecdysteroids from an inactive phosphorylated pool. Previously assigned to a novel class, it is shown here that it resides in the large histidine phosphatase superfamily related to cofactor-dependent phosphoglycerate mutase, a superfamily housing notably diverse catalytic activities. Molecular modeling reveals a plausible substrate-binding mode for EPP. Analysis of genomic and transcript data for a number of insect species shows that EPP may exist in both the single domain form previously characterized and in a longer, multidomain form. This latter form bears a quite unexpected relationship in sequence and domain architecture to vertebrate proteins, including Sts-1, characterized as a key regulator of T-cell activity. Long form Drosophila melanogaster EPP, human Sts-1, and a related protein from Caenorhabditis elegans have all been cloned, assayed, and shown to catalyse the hydrolysis of ecdysteroid and steroid phosphates. The surprising relationship described and explored here between EPP and Sts-1 has implications for our understanding of the function(s) of both.

Sedimentology and high-frequency sequence stratigraphy of a forearc extensional basin: The Miocene Caleta Herradura Formation, Mejillones Peninsula, northern Chile

Facies and sequence stratigraphic interpretation for the 380-m-thick Caleta Herradura Formation (Miocene) are presented, based on detailed and comprehensive outcrop data from the Caleta Herradura half-graben, Mejillones Peninsula, northern Chile. The Caleta Herradura Formation contains an array of lithofacies comprising sandstones, sandy mudstones, diatomites and breccio-conglomerates that are interpreted as the products of inner-shelf to non-marine depositional settings. Complete exposure allows for recognition of a number of distinct and laterally persistent key stratal surfaces that permitted the identification of twenty-five high-frequency (meter to tens of meters-scale) sequences. Based on their internal organization, two main motifs of such unconformity-bounded depositional packages can be distinguished: deepening and deepening-to-shallowing upwards. Transgressive and highstand systems tracts were resolved based on such facies stacking patterns. The origin of sequences is difficult to decipher and remains somewhat uncertain. However, several lines of direct and indirect evidence constrain interpretations for both the sequence architecture and bounding unconformities, and help to discriminate between the various mechanisms that may have driven their development. In essence, these demonstrate that neither tectonically driven sea-level oscillations nor climatically induced changes in sediment supply can adequately explain the distinctive features of unconformities and the facies architecture of sediments they delimit. Instead, these high-frequency changes in relative sea level are best explained as a consequence of glacio-eustatic oscillations. The contemporaneous deep-ocean proxy records appear to support a causal link between the observed stratigraphic cyclicity and glacio-eustatic changes in sea level due to modulation of short-term Milankovitch-scale events by longer-period astronomical variations. However, the type of astronomical forcing remains elusive, hindered by lack of adequate age controls and a poor understanding of pacing mechanisms of high-frequency climate changes during the middle to late Miocene.

Modeling of sequence geometry north of Gargano Peninsula by changing sediment pathways in the Adriatic Sea

Sea level changes can reorganize sediment pathways on continental shelves in ways that can alter sediment supply and the resulting sedimentary deposits. The Adriatic Sea is one place where changing sediment pathways and along-strike currents have a major impact on sequence architecture. The Adriatic Sea, the marine portion of the Apenninic and Dinaric–Hellenic foreland basins, is being filled longitudinally, similar to other active forelands, and sediment transport patterns dramatically reorganized during Quaternary sea level cycles. We investigate the dynamics of sequence formation in the central Adriatic near the Gargano Promontory and the Mid-Adriatic Deep (MAD), where four depositional sequences each recording 100-kyr glacio-eustatic cycles have been mapped. These sequences are composed primarily of progradational units separated by regional unconformities. The geometry of the units is such that the constitutive clinoforms flatten out at their seaward termination into relatively planar strata, particularly in the upper parts of each sequence. Attempts to numerically simulate the sequences using the modeling software Sequence4 were frustrated by the difficulty of flattening the clinoforms seaward of the rollover (or depositional shelf break). The clinoform flattening observed in the Adriatic sequences contrasts with clinoform and depositional shelf break development that is characteristic of both conceptual and numerical models of sequences, including the one used here. We, therefore, modified the numerical model to account for the changes in sediment pathways that occur in the Adriatic Sea. During times with high sea level, such as the present, sediment from the Po and smaller Apennine Rivers is transported southwards along the coast by marine coastal currents and storms. At times of low sea level, fluvial transport of an enlarged Po River, in which the Apennine Rivers are likely captured as tributaries, discharges directly into the MAD basin. This produces a reciprocal sediment supply pattern where the coastal dispersal at high sea level produces prograding clinoforms, but cuts off as the exposure of the northern shelf at low sea level switches supply to the fluvial system, which discharges into the 260-m deep MAD. When the model is adapted for the shift in supply, the clinoforms flatten as nearshore sediment supply decreases and is replaced by deposition in the MAD during sea level lowstands. Including these sediment supply changes as a function of sea level enabled us to obtain a good fit to the overall stratigraphic architecture, supporting conceptual depositional models based on seismic stratigraphy. Similar dramatic shifts in sediment supply and sequence architecture may also occur at other settings, such as where canyons capture fluvial systems and bypass the terrigenous sediment supply to the deep basin. The paucity of observations of the unusual geometry seen at the Adriatic margin suggests that only rarely does the shore and fluvial sediment discharge overreach the shelf edge and cut off along-strike sediment transport to continental margins.

Relationship between phosphogenesis and sequence architecture: Sequence stratigraphy and biostratigraphy in the Middle Ordovician of the Armorican Massif (NW France)

In the Armorican Massif (NW France), the Middle Ordovician formations contain abundant phosphatic (P) beds associated with terrigenous sediments laid down on a storm-dominated shelf. Facies analysis and sequence stratigraphy carried out on sections located in the Crozon Peninsula (W Armorican Massif) allow us to distinguish four P-facies: (1) beds with P-nodules and crusts, contained within sediments laid down on the distal and median parts of the inner shelf; (2) amalgamated beds with P-nodules and crusts and (3) beds with lingulid brachiopods, heavy minerals and P-clasts associated with retrogradation phases; (4) P-clast-bearing conglomerates, associated with progradation phases. The genesis of these facies and their location in the depositional sequences are controlled by the fluctuation of terrigenous inputs during sea-level changes (“sediment volume partitioning”). We propose a genetic model integrating the superposition of very-high-frequency (VHF) and high-frequency (HF) eustatic signals. In this model, the amalgamated beds and beds with lingulid brachiopods, heavy minerals and P-clasts result from the superposition of several sea-level rise episodes of VHF cycles, occurring within the retrogradation phase of a HF cycle. The lateral extension of P-facies was investigated in the eastern part of the Armorican Massif (Bénioc, Domfront/Les Tanneries and St Aubin-du-Cormier sections). Several early Darriwilian transgressive events associated with phosphogenesis episodes are dated through high-resolution chitinozoan studies. Some of these transgressive events are at least of regional scale (e.g., ornensis and protocalix transgressive events). The topmost calix transgressive event is clearly identified over the northern Gondwanan and Avalonian domains, and may reflect a global eustatic signature.

Sedimentology and stratigraphic architecture of the Late Permian Betts Creek Beds, Queensland, Australia

The Late Permian Betts Creek Beds form a succession of coal-bearing alluvial-coastal plain sediments in a basin marginal setting within the northeastern Galilee Basin, Queensland, Australia. The unit is ∼ 50–60 m in thickness at Porcupine Creek National Park where outcrop is laterally continuous for several kilometers. Eight facies have been identified within the formation and can be grouped into 2 facies associations: (A) channel deposits and (B) floodbasin deposits. The channel association consists of conglomerate (A1) and trough cross-bedded multistorey sandstone facies (A2), both interpreted as deposits of low-sinuosity river systems, tidally influenced fluvial channels (A3), interbedded sandstone and siltstone (A4) interpreted as the abandonment fill of the alluvial systems, and diamictite (A5) interpreted as debris flows. The floodbasin facies association is composed of sandy siltstone (B1; proximal–distal floodbasin), carbonaceous siltstone (B2; mire), and bioturbated siltstone (B3; estuarine) facies. The overall sediment body architecture can be resolved into 6 unconformity-bounded cycles interpreted as sequences in the genetic sense, which are sheet-like in geometry and, in general, consist of amalgamated multistorey, multilateral braided fluvial deposits at the base overlain by extensive sheet-like overbank mudstones, carbonaceous shales, and coals. Sea-level change is interpreted as the primary control on the sequence architecture of the formation, while the internal stratigraphic architecture, however, varies between sequences and is a function of a combination of sea level, tectonic, and autogenic controls.

The ring between ring fingers (RBR) protein family

An overview of the large and functionally diverse RBR protein family that mediates protein-protein interactions of various kinds in development and disease.

Interaction of tectonics, eustasy, climate and carbonate production on the sedimentary evolution of an early/middle Jurassic extensional basin (Southern Provence Sub‐basin, SE France)

ABSTRACTThis paper describes the evolution of an extensional basin in regard to the nature and sequence stratigraphic arrangement of its carbonate deposits. The purpose of this study is to evaluate the respective effects of tectonism, eustasy, climate and oceanography on a carbonate sedimentary record. The case study is the early to mid‐Jurassic age carbonate succession of the Southern Provence Sub‐basin (SE France), located within the southern part of the extensional Western European Tethyan Margin. This work is based on sedimentologic, biostratigraphic (using ammonites and brachiopods) and sequence stratigraphic analysis of the carbonate facies of the Cherty Reddish Limestone Formation (late Sinemurian to earliest Bajocian). These strata were deposited in shoreface to lower offshore depositional environments. The succession of the various environments together with the recognition of key stratigraphic surfaces allow us to define four second‐order depositional sequences; of late Sinemurian to earliest Pliensbachian, early Pliensbachian to late Pliensbachian, earliest Toarcian to middle Aalenian and late Aalenian to early Bathonian ages. The architecture of the depositional sequences (thickness and facies variations within the systems tracts, wedge‐shaped geometries) reflects a strong tectonic control. The sub‐basin was structured by extensional faults (oriented approximately 070–090/250–270). Sea‐level variations, fluctuations in carbonate production and preservation, and environmental changes were also significant controlling factors of the carbonate deposition. The interplay of the tectonic control with the other factors resulted in five main phases in the sedimentary evolution of the sub‐basin: (1) dominant tectonic control during the initial rifting stage (late Sinemurian to early Pliensbachian); (2) increasing extensional tectonics (mid‐Pliensbachian); (3) global climato‐eustatic sea‐level fall (latest Pliensbachian) and global climato‐eustatic sea‐level rise plus hypoxia/anoxia (early Toarcian); (4) relative sea‐level fall linked to tectonic uplift related to the ‘Mid‐Cimmerian phase’ (mid‐Aalenian) and (5) oceanographic events (upwelling) and reduction in carbonate production (hypoxia/anoxia) plus tectonic downwarping (late Aalenian/earliest Bajocian).