Abstract
Winters in snow-covered regions have warmed, likely shifting the timing and magnitude of nutrient export, leading to unquantified changes in water quality. Intermittent, seasonal, and ...permanent snow covers more than half of the global land surface. Warming has reduced the cold conditions that limit winter runoff and nutrient transport, while cold season snowmelt, the amount of winter precipitation falling as rain, and rain-on-snow have increased. We used existing geospatial datasets (rain-on-snow frequency overlain on nitrogen and phosphorous inventories) to identify areas of the contiguous United States (US) where water quality could be threatened by this change. Next, to illustrate the potential export impacts of these events, we examined flow and turbidity data from a large regional rain-on-snow event in the United States’ largest river basin, the Mississippi River Basin. We show that rain-on-snow, a major flood-generating mechanism for large areas of the globe (Berghuijs
et al
2019
Water Resour. Res.
55
4582–93; Berghuijs
et al
2016
Geophys. Res. Lett.
43
4382–90), affects 53% of the contiguous US and puts 50% of US nitrogen and phosphorus pools (43% of the contiguous US) at risk of export to groundwater and surface water. Further, the 2019 rain-on-snow event in the Mississippi River Basin demonstrates that these events could have large, cascading impacts on winter nutrient transport. We suggest that the assumption of low wintertime discharge and nutrient transport in historically snow-covered regions no longer holds. Critically, however, we lack sufficient data to accurately measure and predict these episodic and potentially large wintertime nutrient export events at regional to continental scales.
Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of ...infant mortality and ~10% of pediatric hospitalizations. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening to most severe disease genes has hitherto been impractical. Here, we report a preconception carrier screen for 448 severe recessive childhood diseases. Rather than costly, complete sequencing of the human genome, 7717 regions from 437 target genes were enriched by hybrid capture or microdroplet polymerase chain reaction, sequenced by next-generation sequencing (NGS) to a depth of up to 2.7 gigabases, and assessed with stringent bioinformatic filters. At a resultant 160x average target coverage, 93% of nucleotides had at least 20x coverage, and mutation detection/genotyping had ~95% sensitivity and ~100% specificity for substitution, insertion/deletion, splicing, and gross deletion mutations and single-nucleotide polymorphisms. In 104 unrelated DNA samples, the average genomic carrier burden for severe pediatric recessive mutations was 2.8 and ranged from 0 to 7. The distribution of mutations among sequenced samples appeared random. Twenty-seven percent of mutations cited in the literature were found to be common polymorphisms or misannotated, underscoring the need for better mutation databases as part of a comprehensive carrier testing strategy. Given the magnitude of carrier burden and the lower cost of testing compared to treating these conditions, carrier screening by NGS made available to the general population may be an economical way to reduce the incidence of and ameliorate suffering associated with severe recessive childhood disorders.
We used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how ...these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. Total mRNA sequence, gene copy number, and genomic CpG island methylation were carried out using the Illumina Genome Analyzer. Sequences were mapped to the human genome to obtain digitized gene expression data, DNA copy number in reference to the non-tumor cell line (MCF10A), and methylation status of 21,570 CpG islands to identify differentially expressed genes that were correlated with methylation or copy number changes. These were evaluated in a dataset from 129 primary breast tumors. Gene expression in cell lines was dominated by ER-associated genes. ER+ and ER- cell lines formed two distinct, stable clusters, and 1,873 genes were differentially expressed in the two groups. Part of chromosome 8 was deleted in all ER- cells and part of chromosome 17 amplified in all ER+ cells. These loci encoded 30 genes that were overexpressed in ER+ cells; 9 of these genes were overexpressed in ER+ tumors. We identified 149 differentially expressed genes that exhibited differential methylation of one or more CpG islands within 5 kb of the 5' end of the gene and for which mRNA abundance was inversely correlated with CpG island methylation status. In primary tumors we identified 84 genes that appear to be robust components of the methylation signature that we identified in ER+ cell lines. Our analyses reveal a global pattern of differential CpG island methylation that contributes to the transcriptome landscape of ER+ and ER- breast cancer cells and tumors. The role of gene amplification/deletion appears to more modest, although several potentially significant genes appear to be regulated by copy number aberrations.
Vascular and haematopoietic cells organize into specialized tissues during early embryogenesis to supply essential nutrients to all organs and thus play critical roles in development and disease. At ...the top of the haemato-vascular specification cascade lies cloche, a gene that when mutated in zebrafish leads to the striking phenotype of loss of most endothelial and haematopoietic cells and a significant increase in cardiomyocyte numbers. Although this mutant has been analysed extensively to investigate mesoderm diversification and differentiation and continues to be broadly used as a unique avascular model, the isolation of the cloche gene has been challenging due to its telomeric location. Here we used a deletion allele of cloche to identify several new cloche candidate genes within this genomic region, and systematically genome-edited each candidate. Through this comprehensive interrogation, we succeeded in isolating the cloche gene and discovered that it encodes a PAS-domain-containing bHLH transcription factor, and that it is expressed in a highly specific spatiotemporal pattern starting during late gastrulation. Gain-of-function experiments show that it can potently induce endothelial gene expression. Epistasis experiments reveal that it functions upstream of etv2 and tal1, the earliest expressed endothelial and haematopoietic transcription factor genes identified to date. A mammalian cloche orthologue can also rescue blood vessel formation in zebrafish cloche mutants, indicating a highly conserved role in vertebrate vasculogenesis and haematopoiesis. The identification of this master regulator of endothelial and haematopoietic fate enhances our understanding of early mesoderm diversification and may lead to improved protocols for the generation of endothelial and haematopoietic cells in vivo and in vitro.
This paper presents a transdisciplinary multiplecase study, set in Switzerland, that was part of the European Fifth Framework Program project VISULANDs—Visualization Tools for Public Participation in ...Managing Landscape Change (2003-2005). The project sought production of new visualization tools enabling public participation in landscape management. In cooperation with workshop participants, researchers constructed three-dimensional (3-D) landscape visualizations to represent various scenarios of landscape change. The planning objective was to develop sustainable solutions for landscape-related planning problems in tourism, agriculture, and forestry. Two of the case studies produced implemented results. The research objective was to analyze the effectiveness of landscape visualization as a tool in transdisciplinary workshops with external researchers and local stakeholders. The research illustrates how the interactive construction of different types of landscape visualization may contribute to solutions for planning problems on local to regional scales through transdisciplinary knowledge construction, dialogue, and consensus building.
In response to historical criticism, evolving accreditation standards, and recent reports on curricula, medical educators and medical schools have been eagerly pursuing integration as a goal of ...curricular reform. The general education literature broadly considers integration to be the deliberate unification of separate areas of knowledge, and it provides support for the concept that integration better meets the needs of adult learners in professional education. The use of integration as a curricular goal is not without its critics, however, nor is it free of difficulties in implementation. In this perspective, the authors propose that most of these difficulties arise from a failure to recognize that integration is a strategy for curricular development rather than a goal in itself, and they argue that adopting a systematic approach to integration offers many potential benefits. They articulate the conceptual and practical issues that they believe are critical to consider in order to achieve successful curricular integration, and they suggest that integration should be approached as a subset of broader curriculum development decisions. They propose a three-level framework for applying integration as a guiding curricular strategy, in which decisions about integration must follow curricular decisions made at the program level, the course level, and then the individual session level.
Preliminary in vitro and in vivo studies with valproic acid (VPA) in cell lines and patients with spinal muscular atrophy (SMA) demonstrate increased expression of SMN, supporting the possibility of ...therapeutic benefit. We performed an open label trial of VPA in 42 subjects with SMA to assess safety and explore potential outcome measures to help guide design of future controlled clinical trials. Subjects included 2 SMA type I ages 2-3 years, 29 SMA type II ages 2-14 years and 11 type III ages 2-31 years, recruited from a natural history study. VPA was well-tolerated and without evident hepatotoxicity. Carnitine depletion was frequent and temporally associated with increased weakness in two subjects. Exploratory outcome measures included assessment of gross motor function via the modified Hammersmith Functional Motor Scale (MHFMS), electrophysiologic measures of innervation including maximum ulnar compound muscle action potential (CMAP) amplitudes and motor unit number estimation (MUNE), body composition and bone density via dual-energy X-ray absorptiometry (DEXA), and quantitative blood SMN mRNA levels. Clear decline in motor function occurred in several subjects in association with weight gain; mean fat mass increased without a corresponding increase in lean mass. We observed an increased mean score on the MHFMS scale in 27 subjects with SMA type II (p<or=0.001); however, significant improvement was almost entirely restricted to participants <5 years of age. Full length SMN levels were unchanged and Delta7SMN levels were significantly reduced for 2 of 3 treatment visits. In contrast, bone mineral density (p<or=0.0036) and maximum ulnar CMAP scores (p<or=0.0001) increased significantly.
While VPA appears safe and well-tolerated in this initial pilot trial, these data suggest that weight gain and carnitine depletion are likely to be significant confounding factors in clinical trials. This study highlights potential strengths and limitations of various candidate outcome measures and underscores the need for additional controlled clinical trials with VPA targeting more restricted cohorts of subjects.
ClinicalTrials.gov.
Background: The role of prophylactic factor VIII (FVIII) to decrease hemophilic bleeding and arthropathy is well established. The rationale for this strategy is to convert patients with severe ...hemophilia A to a moderate clinical phenotype by reducing time spent with a FVIII level <1 IU dL−1. Studies to date, however, have not demonstrated a strong link between FVIII level and the bleeding rate. Objectives: To assess the effect of FVIII level on break‐through bleeding in patients with severe hemophilia A on prophylaxis. Patients/methods: This study analysed data from 44 patients aged 1–6 and 99 patients aged 10–65 years with severe hemophilia A (FVIII <1 IU dL−1) who were treated with prophylactic FVIII as part of clinical studies assessing pharmacokinetics, safety and efficacy of a recombinant FVIII (Advate®). Each patient had pharmacokinetic measurements and FVIII infusions recorded, and these were used to calculate time spent with a FVIII below 1, 2 and 5 IU dL−1. Results: The data demonstrate that increasing time with a FVIII below 1 IU dL−1 is associated with increased total bleeds and hemarthroses. Lack of adherence to the intended frequency of FVIII infusion was the most important determinant of low FVIII and increased bleeding. In children aged 1–6 years, the rate of bleeding was also influenced by FVIII half‐life and clearance. Conclusions: These data have important implications for the management of patients with severe hemophilia.
Soluble nutrient flux is increasingly implicated in the degradation of receiving water quality. With high-frequency sensors, river discharge along with nitrate and orthophosphate concentrations were ...collected over 2 years. We examined how storms (16 events) affected the dissolved nutrient flux in two watersheds with contrasting landcover—urban and agricultural. The adjacent watersheds, both < 7km², had very similar soil, slope, relief, and physiography. Wastewater is conveyed outside of the watersheds minimizing this nutrient source. Cumulative nitrate and orthophosphate fluxes in the agricultural watershed were substantially higher than the urban watershed. In both watersheds, a disproportionate amount of discharge, higher orthophosphate concentrations and flux occurred during the highest flow events—approximately 50–70% of flux occurring in the highest 5% of daily discharge. The nitrate flux was dampened compared to discharge during storm events. Baseflow accounted for 66% of the nitrate flux and had higher or comparable concentrations than storm events. The pattern of flux and concentration within storm events also differed for the two solutes. Nitrate exhibited positive hysteresis (higher concentrations on the rising limb of the hydrograph) and magnification of flux during the first flush of storm runoff. In contrast, orthophosphate concentrations were lower on the rising limb and flux during the first flush of storm runoff was dampened. In addition to targeting source reductions, orthophosphate flux may require runoff reducing strategies (i.e., enhanced infiltration) from large runoff events. First flush stormwater management practices combined with enhancement/protection of groundwater nitrate sinks (e.g., riparian wetlands) may help reduce nitrate fluxes.
Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) ...Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.
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