The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Background: Brassica carinata (Ethiopian mustard) is an ancient crop from the Ethiopian highlands with remarkable heat and drought tolerance that has potential as a sustainable oil source for biofuel production. The resilience of this species might be due to hybrid vigor, as B. carinata is a species derived from a hybridization between Brassica nigra (black mustard) and Brassica oleracea (kale, broccoli, etc.). Thus, the B. carinata genome is allotetraploid with two parental genomes, or subgenomes, merged in one nucleus. We present a high-quality, chromosome-scale reference assembly of the B. carinata genome, which is the last of six genomes comprising the classic Triangle of U model used to study hybridization and polyploid evolution. Question: Here, we compare B. carinata to the other Triangle of U genomes for insight into the remarkable heat and drought tolerance of this crop. We investigate the evolutionary trajectory of the B. carinata genome as it returns to the diploid state to elucidate the mechanisms that act on duplicated genes, such as functional divergence of gene families and the biased fractionation of one subgenome. Findings: The B. carinata genome is the largest among the Triangle of U with notable expansions in repetitive DNA sequences and gene families related to transcriptional regulation and stress tolerance. We characterized patterns of subgenome bias, finding that the subgenome derived from B. nigra is likely dominant over the subgenome from B. oleracea. Furthermore, we comprehensively characterize subgenomic bias in homoeologous exchanges, or meiotic crossover between subgenomes, in the Triangle of U allotetraploids. Next steps: The presented B. carinata genome is a crucial resource for its expanded use as a biofuel feedstock and insight into polyploid evolution. Unraveling the genomic basis of the stress resilience of B. carinata provides an opportunity to introgress these traits to other cruciferous vegetables, which are used worldwide as vegetable and oil sources.Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.We gratefully acknowledge the support of the Nevada Agricultural Experiment Station (Grant No. NEV00384) and VPRI research funding (University of Nevada, Reno).The Pires lab is funded by the National Science Foundation (NSF IOS 1339156) and the Department of Energy Defense Threat Reduction Agency (HDTRA 1-16-1-0048). The Edger lab is funded by the National Science Foundation (NSF IOS 2029959). The Mason lab is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC 2070 - 390732324). The Alvarez-Ponce lab is funded by the National Science Foundation (NSF MCB 1818288)

Investigation of the Performance of the New Orleans Flood Protection System in Hurricane Katrina on August 29, 2005: Volume 1

This report presents the results of an investigation of the performance of the New Orleans regional flood protection system during and after Hurricane Katrina, which struck the New Orleans region on August 29, 2005. This event resulted in the single most costly catastrophic failure of an engineered system in history. Current damage estimates at the time of this writing are on the order of $100 to$200 billion in the greater New Orleans area, and the official death count in New Orleans and southern Louisiana at the time of this writing stands at 1,293, with an additional 306 deaths in nearby southern Mississippi. An additional approximately 300 people are currently still listed as “missing”; it is expected that some of these missing were temporarily lost in the shuffle of the regional evacuation, but some of these are expected to have been carried out into the swamps and the Gulf of Mexico by the storm’s floodwaters, and some are expected to be recovered in the ongoing sifting through the debris of wrecked homes and businesses, so the current overall regional death count of 1,599 is expected to continue to rise a bit further. More than 450,000 people were initially displaced by this catastrophe, and at the time of this writing more than 200,000 residents of the greater New Orleans metropolitan area continue to be displaced from their homes by the floodwater damages from this storm event. This investigation has targeted three main questions as follow: (1) What happened?, (2) Why?, and (3) What types of changes are necessary to prevent recurrence of a disaster of this scale again in the future? To address these questions, this investigation has involved: (1) an initial field reconnaissance, forensic study and data gathering effort performed quickly after the arrival of Hurricanes Katrina (August 29, 2005) and Rita (September 24, 2005), (2) a review of the history of the regional flood protection system and its development, (3) a review of the challenging regional geology, (4) detailed studies of the events during Hurricanes Katrina and Rita, as well as the causes and mechanisms of the principal failures, (4) studies of the organizational and institutional issues affecting the performance of the flood protection system, (5) observations regarding the emergency repair and ongoing interim levee reconstruction efforts, and (6) development of findings and preliminary recommendations regarding changes that appear warranted in order to prevent recurrence of this type of catastrophe in the future. In the end, it is concluded that many things went wrong with the New Orleans flood protection system during Hurricane Katrina, and that the resulting catastrophe had it roots in three main causes: (1) a major natural disaster (the Hurricane itself), (2) the poor performance of the flood protection system, due to localized engineering failures, questionable judgments, errors, etc. involved in the detailed design, construction, operation and maintenance of the system, and (3) more global “organizational” and institutional problems associated with the governmental and local organizations responsible for the design, construction, operation, maintenance and funding of the overall flood protection system

Measuring the burden of arboviral diseases: the spectrum of morbidity and mortality from four prevalent infections

<p>Abstract</p> <p>Background</p> <p>Globally, arthropod-borne virus infections are increasingly common causes of severe febrile disease that can progress to long-term physical or cognitive impairment or result in early death. Because of the large populations at risk, it has been suggested that these outcomes represent a substantial health deficit not captured by current global disease burden assessments.</p> <p>Methods</p> <p>We reviewed newly available data on disease incidence and outcomes to critically evaluate the disease burden (as measured by disability-adjusted life years, or DALYs) caused by yellow fever virus (YFV), Japanese encephalitis virus (JEV), chikungunya virus (CHIKV), and Rift Valley fever virus (RVFV). We searched available literature and official reports on these viruses combined with the terms "outbreak(s)," "complication(s)," "disability," "quality of life," "DALY," and "QALY," focusing on reports since 2000. We screened 210 published studies, with 38 selected for inclusion. Data on average incidence, duration, age at onset, mortality, and severity of acute and chronic outcomes were used to create DALY estimates for 2005, using the approach of the current Global Burden of Disease framework.</p> <p>Results</p> <p>Given the limitations of available data, nondiscounted, unweighted DALYs attributable to YFV, JEV, CHIKV, and RVFV were estimated to fall between 300,000 and 5,000,000 for 2005. YFV was the most prevalent infection of the four viruses evaluated, although a higher proportion of the world's population lives in countries at risk for CHIKV and JEV. Early mortality and long-term, related chronic conditions provided the largest DALY components for each disease. The better known, short-term viral febrile syndromes caused by these viruses contributed relatively lower proportions of the overall DALY scores.</p> <p>Conclusions</p> <p>Limitations in health systems in endemic areas undoubtedly lead to underestimation of arbovirus incidence and related complications. However, improving diagnostics and better understanding of the late secondary results of infection now give a first approximation of the current disease burden from these widespread serious infections. Arbovirus control and prevention remains a high priority, both because of the current disease burden and the significant threat of the re-emergence of these viruses among much larger groups of susceptible populations.</p

Ageing, adipose tissue, fatty acids and inflammation

A common feature of ageing is the alteration in tissue distribution and composition, with a shift in fat away from lower body and subcutaneous depots to visceral and ectopic sites. Redistribution of adipose tissue towards an ectopic site can have dramatic effects on metabolic function. In skeletal muscle, increased ectopic adiposity is linked to insulin resistance through lipid mediators such as ceramide or DAG, inhibiting the insulin receptor signalling pathway. Additionally, the risk of developing cardiovascular disease is increased with elevated visceral adipose distribution. In ageing, adipose tissue becomes dysfunctional, with the pathway of differentiation of preadipocytes to mature adipocytes becoming impaired; this results in dysfunctional adipocytes less able to store fat and subsequent fat redistribution to ectopic sites. Low grade systemic inflammation is commonly observed in ageing, and may drive the adipose tissue dysfunction, as proinflammatory cytokines are capable of inhibiting adipocyte differentiation. Beyond increased ectopic adiposity, the effect of impaired adipose tissue function is an elevation in systemic free fatty acids (FFA), a common feature of many metabolic disorders. Saturated fatty acids can be regarded as the most detrimental of FFA, being capable of inducing insulin resistance and inflammation through lipid mediators such as ceramide, which can increase risk of developing atherosclerosis. Elevated FFA, in particular saturated fatty acids, maybe a driving factor for both the increased insulin resistance, cardiovascular disease risk and inflammation in older adults

OMAE 2003 -37004 AN INDEPENDENT-FLOW-FIELD MODEL FOR A SDOF NONLINEAR STRUCTURAL SYSTEM, PART I: IDENTIFICATION AND COMPARISONS

ABSTRACT An independent-flow-field (IFF) model selected in this study to investigate the nonlinear response behavior of a medium-scale, experimental, submerged, moored structure is validated via parametric studies. Bifurcations in experimental responses are frequently observed and the associated nonlinear primary and secondary resonances are identified in frequency response diagrams. Distinct from previous investigations, this study intends to identify a set of &quot;best-fit&quot; constant coefficients for predictions and comparisons over the entire wave frequencies examined. It is concluded that the small-body, IFF model predicts reasonably well the nonlinear, moored and submerged structural response subjected to regular waves

A Unique Large-Scale, Multidirectional Basin for Collaborative Tsunami and Coastal Research

This paper describes a unique laboratory for the tsunami and coastal engineering communities. Under the Network for Earthquake Engineering Simulation (NEES) program, the US National Science Foundation is funding the expansion of Oregon State University’s multidirectional wave basin to create a next-generation experimental testing facility for research and practicing engineers. The new facility addresses the unique requirements posed by tsunami research, with basin dimensions and wave generation capabilities closely matching the community’s vision of the “ideal basin.” When completed in 2004, the basin will support high resolution, unprecedented-scale experiments with very dense instrumentation. Researchers will be able to test and validate advanced analytical and numerical models of general environmental fluid mechanics issues in coastal science and engineering including tsunami phenomena induced by sub-sea earthquakes, spanning a full range of ocean, coastal, and harbor studies. An integral part of the upgraded facility is the exploitation of advanced network technologies to allow researchers located at distant sites to play active roles in experiments at the facility, viewing data and images in real time and participating in decision-making. The broader research community will benefit from this large long-wave experiment facility, a comprehensive experiment databank, with specialized interfaces for experiment re-play, searching and browsing archives of past experiments, extraction of experimental data for use in validating numerical models, and a community repository for numerical simulation codes