Climate emergency summit III:nature-based solutions report

An RSGS & SNH report from the Climate Summit held in April 2020"The Climate Emergency is the result of burning fossils fuels and changes in the way we use the land that short-circuit global carbon and nitrogen cycles. To remain within safe climate limits (1.5-2°C), the remaining carbon budget for all people, and for all time, is now so small that stopping fossil fuel use, while essential, will not by itself address the problem. Changing the way we use the land and sea is now essential. Nature-based solutions are vital to creating a safe operating space for humanity. "Extract from the foreword by Dr Clive Mitchell, Outcome Manager: People and Nature, Scottish Natural Heritage. The report has 45 contributors for a variety of institutions

Ore-forming processes of the daqiao epizonal orogenic gold deposit, west qinling orogen, China: Constraints from textures, trace elements, and sulfur isotopes of pyrite and marcasite, and raman spectroscopy of carbonaceous material

The Daqiao gold deposit is hosted in organic-rich Triassic pumpellyite-actinolite facies metamorphosed turbidites in the West Qinling orogen, central China. Gold mineralization is characterized by high-grade hydraulic breccias (B and C ores) that overprint an earlier tectonic breccia (A ore). A complex paragenesis is defined by four sulfide stages: S1 diagenetic preore pyrite (py), S2 hydrothermal early ore disseminated pyrite and marcasite (mc), S3 main ore pyrite and marcasite aggregates, and S4 late ore coarse-grained marcasite with minor pyrite and stibnite. However, multiple generations of pyrite and marcasite may develop within one individual stage. Ore-related hydrothermal alteration is dominated by intensive silicification, sulfidation, sericitization, and generally distal minor carbonatization. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) trace element analyses show that the stage S1 py1 from the shale interlayers within turbidites contains low gold contents (mean of 0.05 ppm) and other trace elements (Mn, Co, Ni, Cu, Mo, Bi, and Pb), indicating an anoxic to euxinic sedimentary environment. Stage S2 contributed only minimally to the gold endowment with relatively low gold in various sulfides including py2 (mean of 0.09 ppm), py3 (0.84 ppm) to py4 (0.70 ppm), along with mc1 (0.02 ppm) and mc2 (0.14 ppm). Most of the gold was deposited in stage S3, which formed rapidly crystallized, irregular (e.g., framboids, colloform and cyclic zonation) cement-hosted py5a (mean of 27.35 ppm), py5b (9.71 ppm), and mc3 (5.94 ppm) during repeated hydraulic fracturing. Other trace elements (e.g., Ag, As, Sb, Hg, Tl, and W) are also significantly enriched in the main ore-stage pyrite and marcasite. Little or no gold is detected in the S4 py6 and mc4. Sulfur isotopes determined from in situ LA-multicollector (MC)-ICP-MS analyses of hydrothermal pyrite and marcasite from the Daqiao deposit vary significantly from –31.3 to 22.0 (d34S values) but fall mostly between –10 to 10 and provide important information on the source and evolution of sulfur and of the ore-forming fluids. The results show that S2 ore fluids (mean d34Ssulfide = –0.8 to 5.2) were most likely derived from deep-seated Paleozoic carbonaceous sediments during regional metamorphism associated with orogenesis of the West Qinling orogen. Main ore S3 fluids (mean d34Ssulfide = –9.7 to –6.0) are relatively depleted in34S relative to those of S2, presumably due to fluid oxidation associated with hydraulic fracturing caused by the overpressurized fluids. The textural, chemical, and isotopic data indicate two distinct gold-introducing episodes at Daqiao, forming sulfide disseminations during early ore S2 and cement-hosted sulfide aggregates during main ore S3. The S2 mineralization took place in a tectonic breccia beneath low-permeability shale seals that capped the flow of deep-seated metamorphic fluids, facilitating reaction with preexisting carbonaceous material and the host turbidites to form sulfide disseminations and pervasive silicification. Raman spectroscopy analysis suggests that carbonaceous material in the ores is poorly crystallized, with low maturity, giving estimated temperatures of 283° to 355°C that are much higher than those of the ore fluids (100°–240°C). This temperature difference indicates an in situ sedimentary origin modified by the regional pumpellyite-actinolite facies metamorphism for the carbonaceous material in the host rocks, rather than a hydrothermal origin. In S3, continuous flux of hydrothermal fluids caused fluid overpressure and consequent hydraulic fracturing of the competent silicified rocks. Subsequent rapid fluid pressure fluctuations led to phase separation and thus massive oxidation of ore fluids, which triggered fast precipitation of gold and other trace elements within the fine-grained irregular sulfides. Results presented here, in combination with geologic evidences, suggest that the Daqiao gold deposit can be best classified as the shallow-crustal epizonal orogenic type, genetically associated with orogenic deformation and regional metamorphism of the West Qinling orogen

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.

Blood pressure is a heritable trait influenced by several biological pathways and responsive to environmental stimuli. Over one billion people worldwide have hypertension (≥140 mm Hg systolic blood pressure or  ≥90 mm Hg diastolic blood pressure). Even small increments in blood pressure are associated with an increased risk of cardiovascular events. This genome-wide association study of systolic and diastolic blood pressure, which used a multi-stage design in 200,000 individuals of European descent, identified sixteen novel loci: six of these loci contain genes previously known or suspected to regulate blood pressure (GUCY1A3-GUCY1B3, NPR3-C5orf23, ADM, FURIN-FES, GOSR2, GNAS-EDN3); the other ten provide new clues to blood pressure physiology. A genetic risk score based on 29 genome-wide significant variants was associated with hypertension, left ventricular wall thickness, stroke and coronary artery disease, but not kidney disease or kidney function. We also observed associations with blood pressure in East Asian, South Asian and African ancestry individuals. Our findings provide new insights into the genetics and biology of blood pressure, and suggest potential novel therapeutic pathways for cardiovascular disease prevention

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

Numerous genetic loci have been associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N = 74,064) and follow-up studies (N = 48,607), we identified at genome-wide significance (P = 2.7 × 10(-8) to P = 2.3 × 10(-13)) four new PP loci (at 4q12 near CHIC2, 7q22.3 near PIK3CG, 8q24.12 in NOV and 11q24.3 near ADAMTS8), two new MAP loci (3p21.31 in MAP4 and 10q25.3 near ADRB1) and one locus associated with both of these traits (2q24.3 near FIGN) that has also recently been associated with SBP in east Asians. For three of the new PP loci, the estimated effect for SBP was opposite of that for DBP, in contrast to the majority of common SBP- and DBP-associated variants, which show concordant effects on both traits. These findings suggest new genetic pathways underlying blood pressure variation, some of which may differentially influence SBP and DBP

Analysis of shared heritability in common disorders of the brain

ience, this issue p. eaap8757 Structured Abstract INTRODUCTION Brain disorders may exhibit shared symptoms and substantial epidemiological comorbidity, inciting debate about their etiologic overlap. However, detailed study of phenotypes with different ages of onset, severity, and presentation poses a considerable challenge. Recently developed heritability methods allow us to accurately measure correlation of genome-wide common variant risk between two phenotypes from pools of different individuals and assess how connected they, or at least their genetic risks, are on the genomic level. We used genome-wide association data for 265,218 patients and 784,643 control participants, as well as 17 phenotypes from a total of 1,191,588 individuals, to quantify the degree of overlap for genetic risk factors of 25 common brain disorders. RATIONALE Over the past century, the classification of brain disorders has evolved to reflect the medical and scientific communities' assessments of the presumed root causes of clinical phenomena such as behavioral change, loss of motor function, or alterations of consciousness. Directly observable phenomena (such as the presence of emboli, protein tangles, or unusual electrical activity patterns) generally define and separate neurological disorders from psychiatric disorders. Understanding the genetic underpinnings and categorical distinctions for brain disorders and related phenotypes may inform the search for their biological mechanisms. RESULTS Common variant risk for psychiatric disorders was shown to correlate significantly, especially among attention deficit hyperactivity disorder (ADHD), bipolar disorder, major depressive disorder (MDD), and schizophrenia. By contrast, neurological disorders appear more distinct from one another and from the psychiatric disorders, except for migraine, which was significantly correlated to ADHD, MDD, and Tourette syndrome. We demonstrate that, in the general population, the personality trait neuroticism is significantly correlated with almost every psychiatric disorder and migraine. We also identify significant genetic sharing between disorders and early life cognitive measures (e.g., years of education and college attainment) in the general population, demonstrating positive correlation with several psychiatric disorders (e.g., anorexia nervosa and bipolar disorder) and negative correlation with several neurological phenotypes (e.g., Alzheimer's disease and ischemic stroke), even though the latter are considered to result from specific processes that occur later in life. Extensive simulations were also performed to inform how statistical power, diagnostic misclassification, and phenotypic heterogeneity influence genetic correlations. CONCLUSION The high degree of genetic correlation among many of the psychiatric disorders adds further evidence that their current clinical boundaries do not reflect distinct underlying pathogenic processes, at least on the genetic level. This suggests a deeply interconnected nature for psychiatric disorders, in contrast to neurological disorders, and underscores the need to refine psychiatric diagnostics. Genetically informed analyses may provide important "scaffolding" to support such restructuring of psychiatric nosology, which likely requires incorporating many levels of information. By contrast, we find limited evidence for widespread common genetic risk sharing among neurological disorders or across neurological and psychiatric disorders. We show that both psychiatric and neurological disorders have robust correlations with cognitive and personality measures. Further study is needed to evaluate whether overlapping genetic contributions to psychiatric pathology may influence treatment choices. Ultimately, such developments may pave the way toward reduced heterogeneity and improved diagnosis and treatment of psychiatric disorders

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe