Lead-up and manifestation of the Oceanic Anoxic Event 2 at the DSDP Site 398 (Vigo Seamount, NW Iberian offshore): palynological and geochemical insights

Extreme climatic conditions, volcanism, and paleogeographical distribution presumably led to the Oceanic Anoxic Event 2 (OAE 2), one of the most disruptive events for Cretaceous ecosystems. Although the terrestrial response to this issue is barely studied, a turnover within the plant communities seems to be linked to the OAE 2, besides the well-known extinction of several marine groups. In this study, palynological and δ13Corg analyses were combined to research the sediments from DSDP Site 398 (Vigo Seamount) cores 398D-58 to 398D-56 (upper Albian to lower Turonian). The δ13Corg curve exhibits a Carbon Isotopic Excursion (CIE) observed between the interval 948,60 and 947,77 m below seafloor (mbsf), corresponding to the OAE 2. Four palynological assemblages were differentiated, ranging from the uppermost Albian to the lower Turonian. These assemblages comprised diverse marine and terrestrial communities with generally excellent preservation. In addition to previous biostratigraphic works, we present a more detailed chronostratigraphy of DSDP Hole 398D based on palynomorphs. The paleoecological reconstruction reveals the significant changes during the OAE 2 period: a decrease in the diversity and abundance of dinoflagellate cysts and a shift to angiosperm-dominated terrestrial communities (i.e., Normapolles) which, unlike other sites, occurs prior to the maximum values of δ13C

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape

BIO2014-57291-R and SAF2017-88908-R from the Spanish Ministry of Economy and Competitivenessgrant PI15/00854 from the FIS“Plataforma de Recursos Biomoleculares y Bioinformáticos” PT17/0009/0006 from the ISCIII, cofunded with European Regional Development FundsFP7-PEOPLE-2012-ITN MLPM2012EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERAT

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome

Spanish Ministry of Economy and Competitiveness grant BIO2014–57291-RSpanish Ministry of Economy and Competitiveness grant SAF2017–88908-R“Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676559)EU FP7-People ITN Marie Curie Project (ref 316861)

Palynological reconstruction of the habitat and diet of Iguanodon bernissartensis in the Lower Cretaceous Morella Formation, NE Iberian Peninsula

The recent discovery of iguanodontid remains from the new Palau-3 site in the Lower Cretaceous Morella Formation is the most complete non-articulated skeleton of Iguanodon bernissartensis on the NE Iberian Peninsula. To elucidate the paleoenvironment of the Palau-3 site, a palynological analysis was carried out on matrix samples collected from around the skeleton. The palynological assemblage is found to correspond to an upper Barremian age. While the assemblage is composed of bryophytes, pteridophytes, gymnosperms, freshwater algae, dinoflagellate cysts and fungal spores, the palynoflora is mostly dominated by the Cheirolepidiaceae conifer (Classopollis) and Anemiaceae fern (mainly Cicatricosisporites) families. The absence of angiosperm pollen in this flora is also noteworthy, as angiosperm remains have been recorded previously elsewhere in the Morella Formation. At the Palau-3 site, the fronds of Cyatheaceae and Anemiaceae ferns, as well as the foliage of the Cheirolepidiaceae conifers, may have been the major sources of nutrition of I. bernissartensis and other herbivorous iguanodontians. The paleobotany of the four major localities bearing I. bernissartensis remains in western Europe was surveyed to determine the habitat and feeding preferences of this styracosternan dinosaur. These localities are Bernissart (Belgium), Isle of Wight (England), Nehden (Germany), and Morella (Spain). In accordance to this survey, the habitat preferences of I. bernissartensis and association with specific plant communities show that this ornithopod species was adapted to a wide variety of paleoenvironments.Xunta de Galicia | Ref. ED431C-2019/28Xunta de Galicia | Ref. ED481A-2020/175Universidade de Vigo/CISU

Paleobotanical and palynological evidence for the age of the Matzitzi Formation, Mexico

This study addresses some of the stratigraphical problems of the Matzitzi Formation of Puebla and Oaxaca States in Mexico. The age assignment for this unit is controversial although most researchers today accept a Leonardian age (Kungurian, 279.3–272.3 Ma) based on the presence of the gigantopterid Lonesomia mexicana Weber. However, after re-examination of the holotype and two paratypes, the absence of diagnostic taxonomic characters prevents the assignment of this fossil type species to the gigantopterid group. Excluding the presence of gigantopterids in this formation, the macroflora seems to be Permian in age. Samples were collected for palynological analysis to determine the age of the formation. Studied palynological assemblages seem to be reworked and are represented by 18 fossil taxa assigned to the following genera: Calamospora, Deltoidospora, Densosporites, Granulatisporites, Laevigatosporites, Latipulvinites, Lophotriletes, Platysaccus, Punctatosporites, Raistrickia, Schopfipollenites, Thymospora, Triquitrites, Verrucosisporites, and Vesicaspora. Described palynomorphs are likely Late Pennsylvanian according to the presence of Latipulvinites kosankii and Thymospora thiessenii. The biostratigraphic and geochronologic age disparities should be solved in the future

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

This work is supported by grants BIO2014- 57291-R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007 from the ISCIII, both co-funded with European Regional Development Funds (ERDF); PROMETEOII/2014/025 from the Generalitat Valenciana (GVA-FEDER); Fundació la Marató TV3 (ref. 20133134); and EU H2020- INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676559) and EU FP7-People ITN Marie Curie Project (ref 316861)

Paleobotanical and palynological evidence for the age of the Matzitzi Formation, Mexico

This study addresses some of the stratigraphical problems of the Matzitzi Formation of Puebla and Oaxaca States in Mexico. The age assignment for this unit is controversial although most researchers today accept a Leonardian age (Kungurian, 279.3–272.3 Ma) based on the presence of the gigantopterid Lonesomia mexicana Weber. However, after re-examination of the holotype and two paratypes, the absence of diagnostic taxonomic characters prevents the assignment of this fossil type species to the gigantopterid group. Excluding the presence of gigantopterids in this formation, the macroflora seems to be Permian in age. Samples were collected for palynological analysis to determine the age of the formation. Studied palynological assemblages seem to be reworked and are represented by 18 fossil taxa assigned to the following genera: Calamospora, Deltoidospora, Densosporites, Granulatisporites, Laevigatosporites, Latipulvinites, Lophotriletes, Platysaccus, Punctatosporites, Raistrickia, Schopfipollenites, Thymospora, Triquitrites, Verrucosisporites, and Vesicaspora. Described palynomorphs are likely Late Pennsylvanian according to the presence of Latipulvinites kosankii and Thymospora thiessenii. The biostratigraphic and geochronologic age disparities should be solved in the future

The Jurassic – Cretaceous transition in the West Cameros Basin (Tera Group, Burgos, Spain): Sedimentological and palynostratigraphical insights

The Jurassic–Cretaceous boundary transition is widely distributed within the West Cameros Basin. This horizon is constituted by the Tera Group, consisting of two depositional sequences (DS1 and DS2) comprising four geological formations spanning the Tithonian to the Berriasian. Here, a combined sedimentological and palynostratigraphic study was made covering the Tera Group. The sedimentological results for the DS 1 differentiate three facies associations (FA 1-1, 1-2 and 1-3) corresponding to floodplains and braided channels of a distributive fluvial system shifting to shallow lacustrine facies in a semi-arid climate. For the DS 2, three FA were also differentiated (FA 2-1, 2-2, and 2-3), corresponding to tidal-influenced meandering channels and floodplains in a distal fluvial to a delta-plain system that shifts to shallow lacustrine facies. The palynological results were only productive in samples from the Jaramillo Formation. The palynological record shows an assemblage dominated by spores including Concavissimisporites, Leptolepidites and Taurocusporites, as well as Classopollis pollen. According to the stratigraphic ranges of some selected taxa, the suggested chronostratigraphic assignment is lower Berriasian for the Jaramillo Fm. A comparison of the microfloras from the Tithonian–Berriasian recorded in the Iberian Peninsula was carried out. The following observations can be concluded: 1) the change in the plant communities, already observed since the Late Jurassic onwards, became more pronounced between the Tithonian–Berriasian boundary and the late Berriasian; and 2) a noteworthy occurrence of some biostratigraphically important taxa, specifically for the Tithonian–Berriasian interval

The poly-omics of ageing through individual-based metabolic modelling

Abstract Background Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomic) ageing is defined by how time and the environment affect an individual in comparison to other individuals of the same chronological age. Recent research studies have shown that transcriptomic age is associated with certain genes, and that each of those genes has an effect size. Using these effect sizes we can calculate the transcriptomic age of an individual from their age-associated gene expression levels. The limitation of this approach is that it does not consider how these changes in gene expression affect the metabolism of individuals and hence their observable cellular phenotype. Results We propose a method based on poly-omic constraint-based models and machine learning in order to further the understanding of transcriptomic ageing. We use normalised CD4 T-cell gene expression data from peripheral blood mononuclear cells in 499 healthy individuals to create individual metabolic models. These models are then combined with a transcriptomic age predictor and chronological age to provide new insights into the differences between transcriptomic and chronological ageing. As a result, we propose a novel metabolic age predictor. Conclusions We show that our poly-omic predictors provide a more detailed analysis of transcriptomic ageing compared to gene-based approaches, and represent a basis for furthering our knowledge of the ageing mechanisms in human cells

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.Peer reviewe