Sedimentology and paleontology of the lower member of the Nogueras Fm (Lower Devonian) at Santa Cruz de Nogueras (Teruel, NE Spain)

An integrated sedimentological and paleontological analysis has been canted out in the lower member (d2a) of the shallow-marine Nogueras Formation (Lower Devonian, Iberian Chains). This formation represents the first carbonate-dominated and fossil-rich sedimentary unit of the Devonian of the Iberian Chains. Nine sedimentary facies, including terrigenous-clastic, mixed and carbonate facies, which are complexly intercalated at bed scale, have been characterized. Based on their sedimentary features and their lateral relationships using Markov chain analysis, two sedimentary models for the lower and upper part of d2a member have been proposed, which represent deposition in a mixed elastic-carbonate shallow marine depositional system. They include terrigenous-clastic intertidal deposits and predominant skeletal, carbonate-dominated and grain-supported facies in the high-energy shallow subtidal zone, whith a clear zonation of the skeletal components (brachiopods, bryozoans and crinoids, from shallow to relatively deep areas). Phosphate nodules, phosphatized fossils, ferruginous crusts and iron ooids, which are frequently associated with the relatively shallower bioclastic brachiopod facies, were probably linked to mineral continental sources and to remobilization in the shallow water high-energy area. The paleontological analysis shows that some of those organisms lived in protected areas of the subtidal zone, including in particular high-diversity communities of brachiopods, adapted to turbid waters with fine terrigenous suspended sediments. Se ha realizado un análisis sedimentológico y paleontológico integrado del miembro inferior (d2a) de la Formación Nogueras, que representa la primera unidad marina somera predominantemente carbonatada del Devónico de las Cadenas Ibéricas. Se han definido nueve facies sedimentarias tcrrígeno-clás ticas, mixtas y carbonatadas, que están complejamente intercaladas a escala de capa, depositadas en un sistema mixto de- trítico-carbonatado de aguas someras. En Junción de sus rasgos sedimentarios y del análisis de sus relaciones laterales mediante cadenas de Markov, se proponen dos modelos sedimentarios para la parte inferior y superior del miembro estudiado. Los dos modelos incluyen depósitos terrígenos en la zona intermareal y facies carbonatadas bioclásticas en la zona submareal somera, con una clara zonación de sus componentes esqueléticos dominantes (braquiópodos, briozoos, crinoides, desde la zona somera a la relativamente profunda). Los nodulos de fosfato, fósiles fósfatizados, costras y ooides ferruginosas frecuentes en las facies bioclasticas de braquiópodos relativamente someras, se relacionaron probablemente con aportes minerales desde el continente y retrabajamiento en la zona marina de alta energía. El análisis paleontológico muestra que algunos de estos organismos vivían en áreas protegidas de la zona submareal, incluyendo particularmente comunidades con alta diversidad de braquiópodos, adaptadas a aguas turbias con elevado sedimento terrígeno fino en suspensión

Weathering events recorded in uppermost Hauterivian-lower Barremian clay-dominated continental successions from the NW Iberian Range: climatic vs. tectonic controls

The facies and clay mineral study of clay/marl-rich levels from the Torrelapaja Formation (latest Hauterivian-early Barremian, NW Iberian Range, NE Spain) allowed to establish the palaeoclimatic and palaeoenvironmental conditions under they were generated. The muddy levels and pisoids contained therein of two logs were sampled and studied by X-ray diffraction and optical and electron microscopy. A similar mineralogical upwards trend is recorded in both logs, with a decrease in calcite coupled with an increase in quartz and orthoclase content and constant proportions in goethite, hematite, diaspore, anatase, rutile, ilmenite, and clay mineral content. The lower muddy levels have higher kaolinite content than the upper levels, where illitic phases are the dominant clay minerals. Smectite and intergrowths of illitic phases and kaolinite are also detected upwards. The kaolinite and smectite textures indicate an authigenic origin, whereas the illitic phases are former phases acting as a substrate for kaolinite crystallization. Pisoids mineralogy and texture show an in-situ origin, but some are fractured, indicating reworking processes. The mineral association found in the muddy levels is characteristic of oxisols formed under warm and humid conditions. The upward decrease in kaolinite content is coeval with an increase in the illitic phases and quartz content, related to siliciclastic input, but is also coeval with the presence of authigenic smectite. This indicates a decrease in chemical weathering, not fully registered due to the siliciclastic contribution, which was possibly associated with a change to colder, drier conditions during the latest Hauterivian-early Barremian in the studied area

Revisión estratigráfica del Sinemuriense-Pliensbachiense inferior de Mallorca

Los nuevos resultados obtenidos en estudios recientes del Sinemuriense-Pliensbachiense inferior (Formación Sóller) en la isla de Mallorca, aconsejan modificar su esquema litoestratigráfico. La nueva propuesta litoestratigráfica para este intervalo elimina la Formación Sóller y eleva sus tres miembros, anteriormente definidos como miembros Es Barraca, Sa Moleta y Es Racó, a la categoría de formación. Esta redefinición se apoya en los nuevos datos estratigráficos, sedimentológicos y bioestratigráficos obtenidos a partir del estudio detallado de la Formación Es Barraca (término recuperado en este artículo), que indican que los miembros de la hasta ahora Formación Sóller no son equivalentes laterales entre sí y representan distintas etapas en la evolución de la cuenca, estando separadas por discontinuidades de carácter regional. La primera unidad (Formación Es Barraca) representa la evolución durante el Sinemuriense de una plataforma carbonatada somera, similar a las plataformas epicontinentales desarrolladas durante el Lías inferior en el ámbito del Tethys más occidental. La segunda y la tercera (Formación Sa Moleta y Formación Es Racó; Pliensbachiense inferior) son unidades disconformes con la anterior, muestran litologías y asociaciones de facies diferenciadas y presentan una distribución y espesores irregulares a favor de surcos intraplataforma. New stratigraphic and bioestratigraphic data from recent studies of the Sinemurian-lower Pliensbachian succession (Soller Formation) of the Mallorca Island demand the modification of the current lithostratigraphic scheme of the Lower Jurassic of Mallorca. The new lithostratigraphic scheme proposed in this work eliminates the Soller Formation and turns into the Formation category its three previous Es Barraca, Sa Moleta and Es Raco members. This new hierarchy for the lithostratigraphic units is based on new stratigraphic, sedimentological and biostratigraphic data obtained from the detailed study of the Es Barraca Formation (new range unit recovered in this work) which indicate that these three new proposed lithostratigraphic formations are not laterally correlatable, they represent different stages in the evolution of the sedimentary basin and are separated by regional unconformities. The first unit (Es Barraca Formation) represents the sedimentary evolution, during the Sinemurian, of a peritidal-shallow subtidal carbonate platform, similar to other epicontinental platforms developed during the Lower Jurassic around the continental margins of the western Tethys. The two others units (Sa Moleta Formation and Es Raco Formation; lower Pliensbachian) are unconformable over the former, showing different lithologies and sedimentary facies and environments, and are disposed with irregular distribution and thicknesses in relation with their deposition in intra-shelf troughs formed during initial stages of platform rifting

X-chromosome tiling path array detection of copy number variants in patients with chromosome X-linked mental retardation

Contiene 3 ficheros adicionales con información suplementaria.-- et al.[Background] Aproximately 5–10% of cases of mental retardation in males are due to copy number variations (CNV) on the X chromosome. Novel technologies, such as array comparative genomic hybridization (aCGH), may help to uncover cryptic rearrangements in X-linked mental retardation (XLMR) patients. We have constructed an X-chromosome tiling path array using bacterial artificial chromosomes (BACs) and validated it using samples with cytogenetically defined copy number changes. We have studied 54 patients with idiopathic mental retardation and 20 controls subjects.[Results] Known genomic aberrations were reliably detected on the array and eight novel submicroscopic imbalances, likely causative for the mental retardation (MR) phenotype, were detected. Putatively pathogenic rearrangements included three deletions and five duplications (ranging between 82 kb to one Mb), all but two affecting genes previously known to be responsible for XLMR. Additionally, we describe different CNV regions with significant different frequencies in XLMR and control subjects (44% vs. 20%).[Conclusion] This tiling path array of the human X chromosome has proven successful for the detection and characterization of known rearrangements and novel CNVs in XLMR patients.The authors thank the "Genoma España" and Genome Canada joint R+D+I projects in human health, plants and aquiculture; the former "Departament d'Universitats i Societat de la Informació" (DURSI) and the "Departament de Salut", from the Catalan Autonomous Government (2005SGR00008 - Generalitat de Catalunya); the Instituto de Salud Carlos III (PI041126, CIBER-ESP), the EU's Sixth Framework Programme [FP6-2005-LIFESCIHEALTH-7; ANEUPLOIDY No. 037627] and Fundación Areces (U-2006-FARECES-O).Peer reviewe

Association of MC1R Variants and host phenotypes with melanoma risk in CDKN2A mutation carriers: a GenoMEL study

<p><b>Background</b> Carrying the cyclin-dependent kinase inhibitor 2A (CDKN2A) germline mutations is associated with a high risk for melanoma. Penetrance of CDKN2A mutations is modified by pigmentation characteristics, nevus phenotypes, and some variants of the melanocortin-1 receptor gene (MC1R), which is known to have a role in the pigmentation process. However, investigation of the associations of both MC1R variants and host phenotypes with melanoma risk has been limited.</p> <p><b>Methods</b> We included 815 CDKN2A mutation carriers (473 affected, and 342 unaffected, with melanoma) from 186 families from 15 centers in Europe, North America, and Australia who participated in the Melanoma Genetics Consortium. In this family-based study, we assessed the associations of the four most frequent MC1R variants (V60L, V92M, R151C, and R160W) and the number of variants (1, ≥2 variants), alone or jointly with the host phenotypes (hair color, propensity to sunburn, and number of nevi), with melanoma risk in CDKN2A mutation carriers. These associations were estimated and tested using generalized estimating equations. All statistical tests were two-sided.</p> <p><b>Results</b> Carrying any one of the four most frequent MC1R variants (V60L, V92M, R151C, R160W) in CDKN2A mutation carriers was associated with a statistically significantly increased risk for melanoma across all continents (1.24 × 10−6 ≤ P ≤ .0007). A consistent pattern of increase in melanoma risk was also associated with increase in number of MC1R variants. The risk of melanoma associated with at least two MC1R variants was 2.6-fold higher than the risk associated with only one variant (odds ratio = 5.83 [95% confidence interval = 3.60 to 9.46] vs 2.25 [95% confidence interval = 1.44 to 3.52]; Ptrend = 1.86 × 10−8). The joint analysis of MC1R variants and host phenotypes showed statistically significant associations of melanoma risk, together with MC1R variants (.0001 ≤ P ≤ .04), hair color (.006 ≤ P ≤ .06), and number of nevi (6.9 × 10−6 ≤ P ≤ .02).</p> <p><b>Conclusion</b> Results show that MC1R variants, hair color, and number of nevi were jointly associated with melanoma risk in CDKN2A mutation carriers. This joint association may have important consequences for risk assessments in familial settings.</p&gt

Kimmeridgian-Tithonian sea-level fluctuations in the Uljanovsk-Saratov Basin (Russian Platform)

Abstract The Uljanovsk-Saratov Basin, located in the southeast of the Russian Platform, presents an intriguing record of the Kimmeridgian-Tithonian sea-level fluctuations. In the Late Jurassic, this basin was a trough within the Interior Russian Sea. The data available from both outcrops and boreholes have permitted outlining a number of lithostratigraphic units and regional hiatuses in the northeastern segment of the Uljanovsk-Saratov Basin, thus permitting a precise reconstruction of transgressions/regressions and deepenings/shallowings. In total, three transgressive-regressive cycles and two deepening pulses have been established. These regionally documented changes were both related in part to global eustatic changes, and they also corresponded in part to the regional sea-level changes in some basins of Western Europe and Northern Africa, but not to those of the Arabian Platform. Differences observed between the global and regional curves as well as rapid Tithonian sea-level oscillations are explained by the influences of tectonic activity. It is hypothesized that the regional Tithonian oxygen depletion might have been a consequence from the rapid flooding of a densely vegetated land

High Resolution Melt analysis for mutation screening in PKD1 and PKD2

<p>Abstract</p> <p>Background</p> <p>Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disorder. It is characterized by focal development and progressive enlargement of renal cysts leading to end-stage renal disease. <it>PKD1 </it>and <it>PKD2 </it>have been implicated in ADPKD pathogenesis but genetic features and the size of <it>PKD1 </it>make genetic diagnosis tedious.</p> <p>Methods</p> <p>We aim to prove that high resolution melt analysis (HRM), a recent technique in molecular biology, can facilitate molecular diagnosis of ADPKD. We screened for mutations in <it>PKD1 </it>and <it>PKD2 </it>with HRM in 37 unrelated patients with ADPKD.</p> <p>Results</p> <p>We identified 440 sequence variants in the 37 patients. One hundred and thirty eight were different. We found 28 pathogenic mutations (25 in <it>PKD1 </it>and 3 in <it>PKD2 </it>) within 28 different patients, which is a diagnosis rate of 75% consistent with literature mean direct sequencing diagnosis rate. We describe 52 new sequence variants in <it>PKD1 </it>and two in <it>PKD2</it>.</p> <p>Conclusion</p> <p>HRM analysis is a sensitive and specific method for molecular diagnosis of ADPKD. HRM analysis is also costless and time sparing. Thus, this method is efficient and might be used for mutation pre-screening in ADPKD genes.</p

The role of molecular genetics in diagnosing familial hematuria(s)

Familial microscopic hematuria (MH) of glomerular origin represents a heterogeneous group of monogenic conditions involving several genes, some of which remain unknown. Recent advances have increased our understanding and our ability to use molecular genetics for diagnosing such patients, enabling us to study their clinical characteristics over time. Three collagen IV genes, COL4A3, COL4A4, and COL4A5 explain the autosomal and X-linked forms of Alport syndrome (AS), and a subset of thin basement membrane nephropathy (TBMN). A number of X-linked AS patients follow a milder course reminiscent of that of patients with heterozygous COL4A3/COL4A4 mutations and TBMN, while at the same time a significant subset of patients with TBMN and familial MH progress to chronic kidney disease (CKD) or end-stage kidney disease (ESKD). A mutation in CFHR5, a member of the complement factor H family of genes that regulate complement activation, was recently shown to cause isolated C3 glomerulopathy, presenting with MH in childhood and demonstrating a significant risk for CKD/ESKD after 40 years old. Through these results molecular genetics emerges as a powerful tool for a definite diagnosis when all the above conditions enter the differential diagnosis, while in many at-risk related family members, a molecular diagnosis may obviate the need for another renal biopsy

Protein Phosphatase-1α Interacts with and Dephosphorylates Polycystin-1

Polycystin signaling is likely to be regulated by phosphorylation. While a number of potential protein kinases and their target phosphorylation sites on polycystin-1 have been identified, the corresponding phosphatases have not been extensively studied. We have now determined that polycystin-1 is a regulatory subunit for protein phosphatase-1α (PP1α). Sequence analysis has revealed the presence of a highly conserved PP1-interaction motif in the cytosolic, C-terminal tail of polycystin-1; and we have shown that transfected PP1α specifically co-immunoprecipitates with a polycystin-1 C-tail construct. To determine whether PP1α dephosphorylates polycystin-1, a PKA-phosphorylated GST-polycystin-1 fusion protein was shown to be dephosphorylated by PP1α but not by PP2B (calcineurin). Mutations within the PP1-binding motif of polycystin-1, including an autosomal dominant polycystic kidney disease (ADPKD)-associated mutation, significantly reduced PP1α-mediated dephosphorylation of polycystin-1. The results suggest that polycystin-1 forms a holoenzyme complex with PP1α via a conserved PP1-binding motif within the polycystin-1 C-tail, and that PKA-phosphorylated polycystin-1 serves as a substrate for the holoenzyme

A meta-analysis of genome-wide data from five European isolates reveals an association of COL22A1, SYT1, and GABRR2 with serum creatinine level

<p>Abstract</p> <p>Background</p> <p>Serum creatinine (S_CR) is the most important biomarker for a quick and non-invasive assessment of kidney function in population-based surveys. A substantial proportion of the inter-individual variability in S_CRlevel is explicable by genetic factors.</p> <p>Methods</p> <p>We performed a meta-analysis of genome-wide association studies of S_CRundertaken in five population isolates ('discovery cohorts'), all of which are part of the European Special Population Network (EUROSPAN) project. Genes showing the strongest evidence for an association with S_CR(candidate loci) were replicated in two additional population-based samples ('replication cohorts').</p> <p>Results</p> <p>After the discovery meta-analysis, 29 loci were selected for replication. Association between S_CRlevel and polymorphisms in the collagen type XXII alpha 1 (<it>COL22A1</it>) gene, on chromosome 8, and in the synaptotagmin-1 (<it>SYT1</it>) gene, on chromosome 12, were successfully replicated in the replication cohorts (p value = 1.0 × 10^-6and 1.7 × 10^-4, respectively). Evidence of association was also found for polymorphisms in a locus including the gamma-aminobutyric acid receptor rho-2 (<it>GABRR2</it>) gene and the ubiquitin-conjugating enzyme E2-J1 (<it>UBE2J1</it>) gene (replication p value = 3.6 × 10^-3). Previously reported findings, associating glomerular filtration rate with SNPs in the uromodulin (<it>UMOD</it>) gene and in the schroom family member 3 (<it>SCHROOM3</it>) gene were also replicated.</p> <p>Conclusions</p> <p>While confirming earlier results, our study provides new insights in the understanding of the genetic basis of serum creatinine regulatory processes. In particular, the association with the genes <it>SYT1 </it>and <it>GABRR2 </it>corroborate previous findings that highlighted a possible role of the neurotransmitters GABA_Areceptors in the regulation of the glomerular basement membrane and a possible interaction between GABA_Areceptors and synaptotagmin-I at the podocyte level.</p