The long-term dynamics of invasive signal crayfish forcing of fluvial sediment supply via riverbank burrowing

Animals are important drivers of sediment dynamics. Invasive signal crayfish (Pacifastacus leniusculus) have been shown to supply sediment to rivers by burrowing into riverbanks. Burrowing directly transfers excavated sediment into the river and also has an additional indirect affect by promoting riverbank failure. While previous research has isolated burrow densities at a point in time, rates of burrow construction and of burrow loss due to erosion are unknown, which introduces uncertainty into estimates of how much sediment burrows contribute to rivers. Here we report results from a 5-year study that evaluated the temporal dynamics of crayfish populations, rates of burrow loss due to erosion, and the mass of sediment directly supplied to rivers by burrow excavation. At ten reaches across five lowland streams in England, we estimated the mass of sediment displaced by 1861 new and previously constructed burrows. Both crayfish and burrow densities were variable over time, suggesting that burrows contribute temporally variable amounts of fine sediment to riverine systems. 42 % of observed burrows were constructed within the previous 365 days, and individual burrows lasted on average 461 days. Applying this to comparable historical data, an average of 2.0 t km−1 a−1 of sediment was excavated to construct burrows in the study reaches, which is eight times more than estimated in previous studies. Whilst total burrow densities in each year were not consistently correlated with contemporary crayfish densities, the mass of sediment excavated over the prior year was strongly correlated with contemporary crayfish densities. Current fine sediment management practices are largely aimed at controlling fine sediment delivery, predominately from agricultural activities, but biotic burrowing into riverbanks may represent an important and overlooked source of fine sediment supply. Incorporation of biotic processes in sediment dynamics would improve the accuracy of fluvial sediment budgets and enhance the knowledge base underpinning effective fine-sediment management practices

Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor

Faunal Response to Fine Sediment Deposition in Urban Rivers

Fine sediment deposition and infiltration into the bed of lotic ecosystems, such as sedimentation, siltation and colmation, has been widely recognised as one of the most important causes of degradation within lotic ecosystems. The impact of increased fine sediment loading as a result of agricultural practices, urban development and channel management activities for flood defence purposes, have been widely acknowledged but poorly quantified. This chapter quantifies the influence of increasing sediment input that is sediment loading on the benthic invertebrate community inhabiting an artificial channel with an impervious concrete bed. This approach provided highly controlled conditions but also reflected channel and habitat characteristics typical of many highly modified and managed urban streams. Significant advances have been made recently in the development of biomonitoring tools which quantify fine sediment impacts on instream communities and which facilitate identification of vulnerable locations within river channels

Polygenic risk score analysis for amyotrophic lateral sclerosis leveraging cognitive performance, educational attainment and schizophrenia

Amyotrophic Lateral Sclerosis (ALS) is recognised to be a complex neurodegenerative disease involving both genetic and non-genetic risk factors. The underlying causes and risk factors for the majority of cases remain unknown; however, ever-larger genetic data studies and methodologies promise an enhanced understanding. Recent analyses using published summary statistics from the largest ALS genome-wide association study (GWAS) (20,806 ALS cases and 59,804 healthy controls) identified that schizophrenia (SCZ), cognitive performance (CP) and educational attainment (EA) related traits were genetically correlated with ALS. To provide additional evidence for these correlations, we built single and multi-trait genetic predictors using GWAS summary statistics for ALS and these traits, (SCZ, CP, EA) in an independent Australian cohort (846 ALS cases and 665 healthy controls). We compared methods for generating the risk predictors and found that the combination of traits improved the prediction (Nagelkerke-R2) of the case–control logistic regression. The combination of ALS, SCZ, CP, and EA, using the SBayesR predictor method gave the highest prediction (Nagelkerke-R2) of 0.027 (P value = 4.6 × 10−8), with the odds-ratio for estimated disease risk between the highest and lowest deciles of individuals being 3.15 (95% CI 1.96–5.05). These results support the genetic correlation between ALS, SCZ, CP and EA providing a better understanding of the complexity of ALS

Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation–based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions

Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation–based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions

Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Correction to: Nature Genetics https://doi.org/10.1038/s41588-021-00973-1, published online 6 December 2021. In the version of this article initially published, the affiliation for Nazli Başak appeared incorrectly. Nazli Başak is at Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey, and not Bogazici University. The error has been corrected in the HTML and PDF versions of the article