The Oyster River Culvert Analysis Project

Studies have already detected intensification of precipitation events consistent with climate change projections. Communities may have a window of opportunity to prepare, but information sufficiently quantified and localized to support adaptation programs is sparse: published literature is typically characterized by general resilience building or regional vulnerability studies. The Fourth Assessment Report of the IPCC observed that adaptation can no longer be postponed pending the effective elimination of uncertainty. Methods must be developed that manage residual uncertainty, providing community leaders with decision-support information sufficient for implementing infrastructure adaptation programs. This study developed a local-scale and actionable protocol for maintaining historical risk levels for communities facing significant impacts from climate change and population growth. For a coastal watershed, the study assessed the capacity of the present stormwater infrastructure capacity for conveying expected peak flow resulting from climate change and population growth. The project transferred coupled-climate model projections to the culvert system, in a form understandable to planners, resource managers and decision-makers; applied standard civil engineering methods to reverse-engineer culverts to determine existing and required capacities; modeled the potential for LID methods to manage peak flow in lieu of, or combination with, drainage system upsizing; and estimated replacement costs using local and national construction cost data. The mid-21st century, most likely 25-year, 24-hour precipitation is estimated to be 35% greater than the TP-40 precipitation for the SRES A1b trajectory, and 64% greater than the TP-40 value for the SRES A1fi trajectory. 5% of culverts are already undersized for the TP-40 event to which they should have been designed. Under the most likely A1b trajectory, an additional 12% of culverts likely will be undersized, while under the most likely A1fi scenario, an additional 19% likely will be undersized. These conditions place people and property at greater risk than that historically acceptable from the TP-4025-year design storm. This risk level may be maintained by a long-term upgrade program, utilizing existing strategies to manage uncertainty and costs. At the upper-95% confidence limit for the A1fi 25-year event, 65% of culverts are adequately sized, and building the remaining 35%, and planned, culverts to thrice the cross-sectional area specified from TP-40 should provide adequate capacity through this event. Realizable LID methods can mitigate significant impacts from climate change and population growth, however effectiveness is limited for the more pessimistic climate change projections. Results indicate that uncertainty in coupled-climate model projections is not an impediment to adaptation. This study makes a significant contribution toward the generation of reliable and specific estimates of impacts from climate change, in support of programs to adapt civil infrastructures. This study promotes a solution to today\u27s arguably most significant challenge in civil infrastructure adaptation: translating the extensive corpus of adaptation theory and regional-scale impacts analyses into localscale action

Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts

The goal of this paper is to review recent research on copy number variations (CNVs) and their association with complex and rare diseases. In the latter part of this paper, we focus on how large biorepositories such as the electronic medical record and genomics (eMERGE) consortium may be best leveraged to systematically mine for potentially pathogenic CNVs, and we end with a discussion of how such variants might be reported back for inclusion in electronic medical records as part of medical history

Population Dynamics of the Beet Leafhopper in Northeastern Oregon and Incidence of the Beet Leafhopper-Transmitted Virescence Agent Phytoplasma

Beet leafhoppers were collected weekly on yellow sticky traps placed at 36 locations in Morrow and Umatilla Counties in northeastern Oregon in April through November 2007, 2008, and 2009. Insects were counted, collected, and a subset of the insects was tested for the presence of the beet leafhopper-transmitted virescence agent phytoplasma, the causal agent of potato purple top disease in this region. Beet leafhoppers were present throughout the sampling period and the number of insects collected peaked in June of each year with smaller peaks in July and October. Of the 804 insects tested for phytoplasma in 2007, 2008, and 2009, 21, 18, and 22% tested positive for phytoplasma, respectively. Most of the phytoplasma-positive insects were collected from mid-June through July. Positive insects, however, were collected as late as 13 November in 2007 and 2008. These data indicate that a relatively high proportion of the beet leafhoppers in this area are harboring the phytoplasma. Therefore, the potential for development of purple top disease of potatoes from migrating beet leafhoppers in this important potato producing region is quite high and measures to control this pest throughout the growing season are probably necessary in order to reduce disease pressure.Keywords: Plant diseases, BLTVA, Phytoplasm

Incidence of the Beet Leafhopper-Transmitted Virescence Agent Phytoplasma in local Populations of the Beet Leafhopper, Circulifer tenellus, in Washington State

Phytoplasma diseases are increasingly becoming important in vegetable crops in the Pacific Northwest. Recently, growers in the Columbia Basin and Yakima Valley experienced serious outbreaks of potato purple top disease that caused significant yield loss and a reduction in tuber processing quality. It was determined that the beet leafhopper-transmitted virescence agent (BLTVA) phytoplasma was the causal agent of the disease in the area and that this pathogen was transmitted by the beet leafhopper, Circulifer tenellus Baker (Hemiptera: Cicadellidae). To provide the most effective management of phytoplasmas, timing of insecticide applications targeted against insects vectoring these pathogens should be correlated with both insect abundance and infectivity. Beet leafhoppers were collected from a potato field and nearby weeds in Washington throughout the 2005, 2006, and 2007 growing seasons and tested for BLTVA by PCR to determine the incidence of this phytoplasma in the insects. In addition, overwintering beet leafhoppers were collected throughout Columbia Basin and Yakima Valley and tested for BLTVA to investigate if these insects might constitute a source of inoculum for this phytoplasma from one season to the next. Results showed that 29.6% of overwintering leafhoppers collected near potato fields carried the phytoplasma. BLTVA-infected leafhoppers were also found in both potatoes and nearby weedy habitats throughout the growing season. PCR testing indicated that a large proportion of beet leafhoppers invading potatoes were infected with the phytoplasma, with an average of 20.8, 34.8, and 9.2% in 2005, 2006, and 2007, respectively. Similarly, BLTVA infection rate in leafhoppers collected from weeds in the vicinity of potatoes averaged 28.3, 24.5, and 5.6% in 2005, 2006, and 2007, respectively. Information from this study will help develop action thresholds for beet leafhopper control to reduce incidence of purple top disease in potatoes

RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection

Background: Potato virus Y (PVY) is one of the most important plant viruses affecting potato production. The interactions between potato and PVY are complex and the outcome of the interactions depends on the potato genotype, the PVY strain, and the environmental conditions. A potato cultivar can induce resistance to a specific PVY strain, yet be susceptible to another. How a single potato cultivar responds to PVY in both compatible and incompatible interactions is not clear. Results: In this study, we used RNA-sequencing (RNA-Seq) to investigate and compare the transcriptional changes in leaves of potato upon inoculation with PVY. We used two potato varieties: Premier Russet, which is resistant to the PVY strain O (PVYᴼ) but susceptible to the strain NTN (PVYᴺᵀᴺ), and Russet Burbank, which is susceptible to all PVY strains that have been tested. Leaves were inoculated with PVYᴼ or PVYᴺᵀᴺ, and samples were collected 4 and 10 h post inoculation (hpi). A larger number of differentially expressed (DE) genes were found in the compatible reactions compared to the incompatible reaction. For all treatments, the majority of DE genes were down-regulated at 4 hpi and up-regulated at 10 hpi. Gene Ontology enrichment analysis showed enrichment of the biological process GO term “Photosynthesis, light harvesting” specifically in PVYᴼ-inoculated Premier Russet leaves, while the GO term “nucleosome assembly” was largely overrepresented in PVYᴺᵀᴺ-inoculated Premier Russet leaves and PVYᴼ-inoculated Russet Burbank leaves but not in PVYᴼ-inoculated Premier Russet leaves. Fewer genes were DE over 4-fold in the incompatible reaction compared to the compatible reactions. Amongst these, five genes were DE only in PVYᴼ-inoculated Premier Russet leaves, and all five were down-regulated. These genes are predicted to encode for a putative ABC transporter, a MYC2 transcription factor, a VQ-motif containing protein, a non-specific lipid-transfer protein, and a xyloglucan endotransglucosylase-hydroxylase. Conclusions: Our results show that the incompatible and compatible reactions in Premier Russet shared more similarities, in particular during the initial response, than the compatible reactions in the two different hosts. Our results identify potential key processes and genes that determine the fate of the reaction, compatible or incompatible, between PVY and its host

Genetic variation in the HLA region is associated with susceptibility to herpes zoster.

Herpes zoster, commonly referred to as shingles, is caused by the varicella zoster virus (VZV). VZV initially manifests as chicken pox, most commonly in childhood, can remain asymptomatically latent in nerve tissues for many years and often re-emerges as shingles. Although reactivation may be related to immune suppression, aging and female sex, most inter-individual variability in re-emergence risk has not been explained to date. We performed a genome-wide association analyses in 22,981 participants (2280 shingles cases) from the electronic Medical Records and Genomics Network. Using Cox survival and logistic regression, we identified a genomic region in the combined and European ancestry groups that has an age of onset effect reaching genome-wide significance (P>1.0 × 10(-8)). This region tags the non-coding gene HCP5 (HLA Complex P5) in the major histocompatibility complex. This gene is an endogenous retrovirus and likely influences viral activity through regulatory functions. Variants in this genetic region are known to be associated with delay in development of AIDS in people infected by HIV. Our study provides further suggestion that this region may have a critical role in viral suppression and could potentially harbor a clinically actionable variant for the shingles vaccine

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.

Body-fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body-fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF ≥5%) and nine low-frequency or rare (MAF <5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes (DNAH10 and PLXND1). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants

Angiopoietin-Like4 Is a Novel Marker of COVID-19 Severity

IMPORTANCE: Vascular dysfunction and capillary leak are common in critically ill COVID-19 patients, but identification of endothelial pathways involved in COVID-19 pathogenesis has been limited. Angiopoietin-like 4 (ANGPTL4) is a protein secreted in response to hypoxic and nutrient-poor conditions that has a variety of biological effects including vascular injury and capillary leak. OBJECTIVES: To assess the role of ANGPTL4 in COVID-19-related outcomes. DESIGN SETTING AND PARTICIPANTS: Two hundred twenty-five COVID-19 ICU patients were enrolled from April 2020 to May 2021 in a prospective, multicenter cohort study from three different medical centers, University of Washington, University of Southern California and New York University. MAIN OUTCOMES AND MEASURES: Plasma ANGPTL4 was measured on days 1, 7, and 14 after ICU admission. We used previously published tissue proteomic data and lung single nucleus RNA (snRNA) sequencing data from specimens collected from COVID-19 patients to determine the tissues and cells that produce ANGPTL4. RESULTS: Higher plasma ANGPTL4 concentrations were significantly associated with worse hospital mortality (adjusted odds ratio per log CONCLUSIONS AND RELEVANCE: ANGPTL4 is expressed in pulmonary epithelial cells and fibroblasts and is associated with clinical prognosis in critically ill COVID-19 patients

Diversity and evolution of potato mop-top virus

Nearly complete sequences of RNA-CP and 3'-proximal RNA-TGB were determined for 43 samples of potato mop-top virus (PMTV) originating from potato tubers and field soil from Sweden, Denmark and the USA. The results showed limited diversity and no strict geographical grouping, suggesting only a few original introductions of PMTV from the Andes. Two distinguishable types of RNA-CP and RNA-TGB were found in the samples, but no specific combination of them correlated with spraing symptoms in tubers. Lack of positive selection in the coding sequences indicates that there is no specific molecular adaptation of PMTV to new vectors or hosts