Universidad de Salamanca

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics. The 1000 Genomes Project has sought to comprehensively catalogue human genetic variation across populations, providing a valuable public genomic resource. The data obtained so far have found applications ranging from association studies and fine mapping studies to the filtering of likely neutral variants in rare-disease cohorts. The authors now report on the final phase of the project, phase 3, which covers previously uncharacterized areas of human genetic diversity in terms of the populations sampled and categories of characterized variation. The sample now includes more than 2,500 individuals from 26 global populations, with low coverage whole-genome and deep exome sequencing, as well as dense microarray genotyping. They find that while most common variants are shared across populations, rarer variants are often restricted to closely related populations. The authors also demonstrate the use of the phase 3 dataset as a reference panel for imputation to improve the resolution in genetic association studies.

This paper presents the first cosmological results based on Planck measurements of the cosmic microwave background (CMB) temperature and lensing-potential power spectra. We find that the Planck spectra at high multipoles ( > 40) are extremely well described by the standard spatiallyflat six-parameter CDM cosmology with a power-law spectrum of adiabatic scalar perturbations. Within the context of this cosmology, the Planck data determine the cosmological parameters to high precision: the angular size of the sound horizon at recombination, the physical densities of baryons and cold dark matter, and the scalar spectral index are estimated to be * = (1.04147 0.00062) 10 -2 , b h 2 = 0.02205 0.00028, c h 2 = 0.1199 0.0027, and n s = 0.9603 0.0073, respectively (note that in this abstract we quote 68% errors on measured parameters and 95% upper limits on other parameters). For this cosmology, we find a low value of the Hubble constant, H 0 = (67.3 1.2) km s -1 Mpc -1 , and a high value of the matter density parameter, m = 0.315 0.017. These values are in tension with recent direct measurements of H 0 and the magnituderedshift relation for Type Ia supernovae, but are in excellent agreement with geometrical constraints from baryon acoustic oscillation (BAO) surveys. Including curvature, we find that the Universe is consistent with spatial flatness to percent level precision using Planck CMB data alone. We use high-resolution CMB data together with Planck to provide greater control on extragalactic foreground components in an investigation of extensions to the six-parameter CDM model. We present selected results from a large grid of cosmological models, using a range of additional astrophysical data sets in addition to Planck and high-resolution CMB data. None of these models are favoured over the standard six-parameter CDM cosmology. The deviation of the scalar spectral index from unity is insensitive to the addition of tensor modes and to changes in the matter content of the Universe. We find an upper limit of r 0.002 < 0.11 on the tensor-to-scalar ratio. There is no evidence for additional neutrino-like relativistic particles beyond the three families of neutrinos in the standard model. Using BAO and CMB data, we find N eff = 3.30 0.27 for the effective number of relativistic degrees of freedom, and an upper limit of 0.23 eV for the sum of neutrino masses. Our results are in excellent agreement with big bang nucleosynthesis and the standard value of N eff = 3.046. We find no evidence for dynamical dark energy; using BAO and CMB data, the dark energy equation of state parameter is constrained to be w = -1.13 +0.13 -0.10 . We also use the Planck data to set limits on a possible variation of the fine-structure constant, dark matter annihilation and primordial magnetic fields. Despite the success of the six-parameter CDM model in describing the Planck data at high multipoles, we note that this cosmology does not provide a good fit to the temperature power spectrum at low multipoles. The unusual shape of the spectrum in the multipole range 20 < < 40 was seen previously in the WMAP data and is a real feature of the primordial CMB anisotropies. The poor fit to the spectrum at low multipoles is not of decisive significance, but is an "anomaly" in an otherwise self-consistent analysis of the Planck temperature data.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome). Of the deleted ORFs, 17 percent were essential for viability in rich medium. The phenotypes of more than 500 deletion strains were assayed in parallel. Of the deletion strains, 40 percent showed quantitative growth defects in either rich or minimal medium.

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.

The classification of myeloid neoplasms and acute leukemias was last updated in 2016 within a collaboration between the World Health Organization (WHO), the Society for Hematopathology, and the European Association for Haematopathology. This collaboration was primarily based on input from a clinical advisory committees (CACs) composed of pathologists, hematologists, oncologists, geneticists, and bioinformaticians from around the world. The recent advances in our understanding of the biology of hematologic malignancies, the experience with the use of the 2016 WHO classification in clinical practice, and the results of clinical trials have indicated the need for further revising and updating the classification. As a continuation of this CAC-based process, the authors, a group with expertise in the clinical, pathologic, and genetic aspects of these disorders, developed the International Consensus Classification (ICC) of myeloid neoplasms and acute leukemias. Using a multiparameter approach, the main objective of the consensus process was the definition of real disease entities, including the introduction of new entities and refined criteria for existing diagnostic categories, based on accumulated data. The ICC is aimed at facilitating diagnosis and prognostication of these neoplasms, improving treatment of affected patients, and allowing the design of innovative clinical trials.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Cholangiocarcinoma (CCA) includes a cluster of highly heterogeneous biliary malignant tumours that can arise at any point of the biliary tree. Their incidence is increasing globally, currently accounting for ~15% of all primary liver cancers and ~3% of gastrointestinal malignancies. The silent presentation of these tumours combined with their highly aggressive nature and refractoriness to chemotherapy contribute to their alarming mortality, representing ~2% of all cancer-related deaths worldwide yearly. The current diagnosis of CCA by non-invasive approaches is not accurate enough, and histological confirmation is necessary. Furthermore, the high heterogeneity of CCAs at the genomic, epigenetic and molecular levels severely compromises the efficacy of the available therapies. In the past decade, increasing efforts have been made to understand the complexity of these tumours and to develop new diagnostic tools and therapies that might help to improve patient outcomes. In this expert Consensus Statement, which is endorsed by the European Network for the Study of Cholangiocarcinoma, we aim to summarize and critically discuss the latest advances in CCA, mostly focusing on classification, cells of origin, genetic and epigenetic abnormalities, molecular alterations, biomarker discovery and treatments. Furthermore, the horizon of CCA for the next decade from 2020 onwards is highlighted.

High-harmonic generation (HHG) traditionally combines ~100 near-infrared laser photons to generate bright, phase-matched, extreme ultraviolet beams when the emission from many atoms adds constructively. Here, we show that by guiding a mid-infrared femtosecond laser in a high-pressure gas, ultrahigh harmonics can be generated, up to orders greater than 5000, that emerge as a bright supercontinuum that spans the entire electromagnetic spectrum from the ultraviolet to more than 1.6 kilo-electron volts, allowing, in principle, the generation of pulses as short as 2.5 attoseconds. The multiatmosphere gas pressures required for bright, phase-matched emission also support laser beam self-confinement, further enhancing the x-ray yield. Finally, the x-ray beam exhibits high spatial coherence, even though at high gas density the recolliding electrons responsible for HHG encounter other atoms during the emission process.

We present the first nucleon-nucleon potential at next-to-next-to-next-to-leading order (fourth order) of chiral perturbation theory. Charge dependence is included up to next-to-leading order of the isospin-violation scheme. The accuracy for the reproduction of the nucleon-nucleon $(NN)$ data below $290\text{\ensuremath{-}}\text{MeV}$ lab energy is comparable to the one of phenomenological high-precision potentials. Since $NN$ potentials of order three and less are known to be deficient in quantitative terms, the present work shows that the fourth order is necessary and sufficient for a $NN$ potential reliable up to $290\phantom{\rule{0.3em}{0ex}}\text{MeV}$. The new potential provides a promising starting point for exact few-body calculations and microscopic nuclear structure theory (including chiral many-body forces derived on the same footing).

Since the publication of the Revised European-American Classification of Lymphoid Neoplasms in 1994, subsequent updates of the classification of lymphoid neoplasms have been generated through iterative international efforts to achieve broad consensus among hematopathologists, geneticists, molecular scientists, and clinicians. Significant progress has recently been made in the characterization of malignancies of the immune system, with many new insights provided by genomic studies. They have led to this proposal. We have followed the same process that was successfully used for the third and fourth editions of the World Health Organization Classification of Hematologic Neoplasms. The definition, recommended studies, and criteria for the diagnosis of many entities have been extensively refined. Some categories considered provisional have now been upgraded to definite entities. Terminology for some diseases has been revised to adapt nomenclature to the current knowledge of their biology, but these modifications have been restricted to well-justified situations. Major findings from recent genomic studies have impacted the conceptual framework and diagnostic criteria for many disease entities. These changes will have an impact on optimal clinical management. The conclusions of this work are summarized in this report as the proposed International Consensus Classification of mature lymphoid, histiocytic, and dendritic cell tumors.

Analysis of the genomes of four patients with chronic lymphocytic leukaemia, and validation in more than 300 patients, has identified four genes — NOTCH1, MYD88, XPO1 and KLHL6 — that are recurrently mutated in the condition. Mutations in NOTCH1, MYD88 and XPO1 are thought to contribute to the clinical evolution of the disease. Evidence that NOTCH1 and MYD88 mutations are activating events highlights them as potential therapeutic targets. Chronic lymphocytic leukaemia (CLL), the most frequent leukaemia in adults in Western countries, is a heterogeneous disease with variable clinical presentation and evolution1,2. Two major molecular subtypes can be distinguished, characterized respectively by a high or low number of somatic hypermutations in the variable region of immunoglobulin genes3,4. The molecular changes leading to the pathogenesis of the disease are still poorly understood. Here we performed whole-genome sequencing of four cases of CLL and identified 46 somatic mutations that potentially affect gene function. Further analysis of these mutations in 363 patients with CLL identified four genes that are recurrently mutated: notch 1 (NOTCH1), exportin 1 (XPO1), myeloid differentiation primary response gene 88 (MYD88) and kelch-like 6 (KLHL6). Mutations in MYD88 and KLHL6 are predominant in cases of CLL with mutated immunoglobulin genes, whereas NOTCH1 and XPO1 mutations are mainly detected in patients with unmutated immunoglobulins. The patterns of somatic mutation, supported by functional and clinical analyses, strongly indicate that the recurrent NOTCH1, MYD88 and XPO1 mutations are oncogenic changes that contribute to the clinical evolution of the disease. To our knowledge, this is the first comprehensive analysis of CLL combining whole-genome sequencing with clinical characteristics and clinical outcomes. It highlights the usefulness of this approach for the identification of clinically relevant mutations in cancer.

The European Space Agency's Planck satellite, dedicated to studying the early Universe and its subsequent evolution, was launched 14 May 2009 and has been scanning the microwave and submillimetre sky continuously since 12 August 2009. In March 2013, ESA and the Planck Collaboration released the initial cosmology products based on the first 15.5 months of Planck data, along with a set of scientific and technical papers and a web-based explanatory supplement. This paper gives an overview of the mission and its performance, the processing, analysis, and characteristics of the data, the scientific results, and the science data products and papers in the release. The science products include maps of the cosmic microwave background (CMB) and diffuse extragalactic foregrounds, a catalogue of compact Galactic and extragalactic sources, and a list of sources detected through the Sunyaev-Zeldovich effect. The likelihood code used to assess cosmological models against the Planck data and a lensing likelihood are described. Scientific results include robust support for the standard six-parameter ΛCDM model of cosmology and improved measurements of its parameters, including a highly significant deviation from scale invariance of the primordial power spectrum. The Planck values for these parameters and others derived from them are significantly different from those previously determined. Several large-scale anomalies in the temperature distribution of the CMB, first detected by WMAP, are confirmed with higher confidence. Planck sets new limits on the number and mass of neutrinos, and has measured gravitational lensing of CMB anisotropies at greater than 25σ. Planck finds no evidence for non-Gaussianity in the CMB. Planck's results agree well with results from the measurements of baryon acoustic oscillations. Planck finds a lower Hubble constant than found in some more local measures. Some tension is also present between the amplitude of matter fluctuations (σ8) derived from CMB data and that derived from Sunyaev-Zeldovich data. The Planck and WMAP power spectra are offset from each other by an average level of about 2% around the first acoustic peak. Analysis of Planck polarization data is not yet mature, therefore polarization results are not released, although the robust detection of E-mode polarization around CMB hot and cold spots is shown graphically.

Proanthocyanidins (syn condensed tannins) are complex flavonoid polymers naturally present in cereals, legume seeds and particularly abundant in some fruits and fruit juices. They share some common structural features—phenolic nature and high molecular weight—with phenolic polymers found in black tea and red wine (called here tannin-like compounds). The polymeric nature of proanthocyanidins makes their analysis and estimation in food difficult. For this reason, little is known about their consumption, although they likely contribute a large part of the daily polyphenol intake. They also share common physicochemical properties: they form stable complexes with metal ions and with proteins and are, like other polyphenols, good reducing agents. Many of their biological effects of nutritional interest derive from these properties. As metal ion chelators, they influence the bioavailability of several minerals. The nutritional significance of the non-specific complexation of proteins is less clear. As reducing agents, they may participate in the prevention of cancers, both of the digestive tract and inner organs. They may also protect LDLs against oxidation and inhibit platelet aggregation and therefore prevent cardiovascular diseases. In vitro, animal and human studies on the prevention of these chronic diseases are reviewed with particular attention to wine and tea polyphenols. The lack of data on their bioavailability and the paucity of human studies are emphasised. © 2000 Society of Chemical Industry

We analyse the implications of the Planck data for cosmic inflation. The Planck nominal mission temperature anisotropy measurements, combined with the WMAP large-angle polarization, constrain the scalar spectral index to be ns = 0.9603 ± 0.0073, ruling out exact scale invariance at over 5σ.Planck establishes an upper bound on the tensor-to-scalar ratio of r&lt; 0.11 (95% CL). The Planck data thus shrink the space of allowed standard inflationary models, preferring potentials with V′′&lt; 0. Exponential potential models, the simplest hybrid inflationary models, and monomial potential models of degree n ≥ 2 do not provide a good fit to the data. Planck does not find statistically significant running of the scalar spectral index, obtaining dns/ dlnk = − 0.0134 ± 0.0090. We verify these conclusions through a numerical analysis, which makes no slow-roll approximation, and carry out a Bayesian parameter estimation and model-selection analysis for a number of inflationary models including monomial, natural, and hilltop potentials. For each model, we present the Planck constraints on the parameters of the potential and explore several possibilities for the post-inflationary entropy generation epoch, thus obtaining nontrivial data-driven constraints. We also present a direct reconstruction of the observable range of the inflaton potential. Unless a quartic term is allowed in the potential, we find results consistent with second-order slow-roll predictions. We also investigate whether the primordial power spectrum contains any features. We find that models with a parameterized oscillatory feature improve the fit by Δχ2eff ≈ 10; however, Bayesian evidence does not prefer these models. We constrain several single-field inflation models with generalized Lagrangians by combining power spectrum data with Planck bounds on fNL. Planck constrains with unprecedented accuracy the amplitude and possible correlation (with the adiabatic mode) of non-decaying isocurvature fluctuations. The fractional primordial contributions of cold dark matter (CDM) isocurvature modes of the types expected in the curvaton and axion scenarios have upper bounds of 0.25% and 3.9% (95% CL), respectively. In models with arbitrarily correlated CDM or neutrino isocurvature modes, an anticorrelated isocurvature component can improve the χ2eff by approximately 4 as a result of slightly lowering the theoretical prediction for the ℓ ≲ 40 multipoles relative to the higher multipoles. Nonetheless, the data are consistent with adiabatic initial conditions.

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.

Richard O'Connell and colleagues report the genomes and transcriptomes of two Colletotrichum plant fungal pathogens. C. higginsianum infects Arabidopsis thaliana, and C. graminicola infects maize (Zea mays); comparative genomics in both species lead to molecular insights into the transition from biotrophic to necrotrophic life stages. Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.

Trichoderma (teleomorph Hypocrea) is a fungal genus found in many ecosystems. Trichoderma spp. can reduce the severity of plant diseases by inhibiting plant pathogens in the soil through their highly potent antagonistic and mycoparasitic activity. Moreover, as revealed by research in recent decades, some Trichoderma strains can interact directly with roots, increasing plant growth potential, resistance to disease and tolerance to abiotic stresses. This mini-review summarizes the main findings concerning the Trichoderma-plant interaction, the molecular dialogue between the two organisms, and the dramatic changes induced by the beneficial fungus in the plant. Efforts to enhance plant resistance and tolerance to a broad range of stresses by expressing Trichoderma genes in the plant genome are also addressed.

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

The metric-affine variational principle is applied to generate teleparallel and symmetric teleparallel theories of gravity. From the latter we discover an exceptional class which is consistent with a vanishing affine connection. Based on this remarkable property, this work proposes a simpler geometrical formulation of general relativity that is oblivious to the affine spacetime structure, thus fundamentally depriving gravity of any inertial character. The resulting theory is described by the Hilbert action purged from the boundary term and is more robustly underpinned by the spin-2 field theory, where an extra symmetry is now manifest, possibly related to the double-copy structure of the gravity amplitudes. This construction also provides a novel starting point for modified gravity theories, and the paper presents new and simple generalizations where analytical self-accelerating cosmological solutions arise naturally in the early- and late-time Universe.