Chromosome-Scale Genome Assembly of the Hexaploid Taiwanese Goosefoot “Djulis” (Chenopodium formosanum)

Djulis (Chenopodium formosanum Koidz.) is a crop grown since antiquity in Taiwan. It is a BCD-genome hexaploid (2n=6x = 54) domesticated form of lambsquarters (C. album L.) and a relative of the allotetraploid (AABB) C. quinoa. As with quinoa, djulis seed contains a complete protein profile and many nutritionally important vitamins and minerals. While still sold locally in Taiwanese markets, its traditional culinary uses are being lost as diets of younger generations change. Moreover, indigenous Taiwanese peoples who have long safeguarded djulis are losing their traditional farmlands. We used PacBio sequencing and Hi-C-based scaffolding to produce a chromosome-scale, reference-quality assembly of djulis. The final genome assembly spans 1.63 Gb in 798 scaffolds, with 97.8% of the sequence contained in 27 scaffolds representing the nine haploid chromosomes of each sub-genome of the species. Benchmarking of universal, single-copy orthologs indicated that 98.5% of the conserved orthologous genes for Viridiplantae are complete within the assembled genome, with 92.9% duplicated, as expected for a polyploid. A total of 67.8% of the assembly is repetitive, with the most common repeat being Gypsy long terminal repeat retrotransposons, which had significantly expanded in the B sub-genome. Gene annotation using Iso-Seq data from multiple tissues identified 75,056 putative gene models. Comparisons to quinoa showed strong patterns of synteny which allowed for the identification of homoeologous chromosomes, and sub-genome-specific sequences were used to assign homoeologs to each sub-genome. These results represent the first hexaploid genome assembly and the first assemblies of the C and D genomes of the Chenopodioideae subfamily.BYU Life Sciences BYU DNASC RRID: SCR_01778

InSight Aerothermal Environment Assessment

The Mars Interior Exploration using Seismic Investigations, Geodesy and Heat Transport (InSight) spacecraft, which successfully touched down on the planet surface on November 26, 2018, was proposed as a near build-to-print copy of the Mars Phoenix vehicle to reduce the overall cost and risk of the mission. Since the lander payload and the atmospheric entry trajectory were similar enough to those of the Phoenix mission, it was expected that the Phoenix thermal protection material thickness would be sufficient to withstand the entry heat load. However, allowances were made for increasing the heatshield thickness because the planned spacecraft arrival date coincided with the Mars dust storm season. The aftbody Thermal Protection System (TPS) components were not expected to change. In a first for a US Mars mission, the aerothermal environments for InSight included estimates of radiative heat flux to the aftbody from the wake. The combined convective and radiative heat fluxes were used to determine if the as-flown Phoenix thermal protection system (TPS) design would be sufficient for InSight. Although the radiative heat fluxes on the aftbody were predicted to be comparable to, or even higher than the local convective heat fluxes, all analyses of the aftbody TPS showed that the design would still be adequate. Aerothermal environments were computed for the vehicle from post-flight reconstruction of the atmosphere and trajectory and compared with the design environments. These comparisons showed that the predicted as-flown conditions were less severe than the design conditions

Maternal caloric restriction partially rescues the deleterious effects of advanced maternal age on offspring

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aging Cell 13 (2014): 623–630, doi:10.1111/acel.12217.While many studies have focused on the detrimental effects of advanced maternal age and harmful prenatal environments on progeny, little is known about the role of beneficial non-Mendelian maternal inheritance on aging. Here, we report the effects of maternal age and maternal caloric restriction (CR) on the life span and health span of offspring for a clonal culture of the monogonont rotifer Brachionus manjavacas. Mothers on regimens of chronic CR (CCR) or intermittent fasting (IF) had increased life span compared with mothers fed ad libitum (AL). With increasing maternal age, life span and fecundity of female offspring of AL-fed mothers decreased significantly and life span of male offspring was unchanged, whereas body size of both male and female offspring increased. Maternal CR partially rescued these effects, increasing the mean life span of AL-fed female offspring but not male offspring and increasing the fecundity of AL-fed female offspring compared with offspring of mothers of the same age. Both maternal CR regimens decreased male offspring body size, but only maternal IF decreased body size of female offspring, whereas maternal CCR caused a slight increase. Understanding the genetic and biochemical basis of these different maternal effects on aging may guide effective interventions to improve health span and life span.This work was supported by the National Institute on Aging Division of Aging Biology (R01 AG037960-01), the Ellison Medical Foundation/ American Federation for Aging Research Postdoctoral Fellows in Aging Research Program and a Neil Cornell Career Development Award

The properties conferred upon triple-helical collagen-mimetic peptides by the presence of cysteine residues

AbstractRecently, the ability of polymeric collagen-like peptides to regulate cell behavior has generated great interest. A triple-helical peptide known as collagen-related peptide (CRP) contains the sequence (Gly-Pro-Hyp)10. With Gly-Pro-Cys triplets appended to both of its termini, designated CRPcys, chemical cross-linking using heterobifunctional reagents generates CRPcys-XL, a potent, widely used, polymeric agonist for platelet Glycoprotein VI, whereas non-cross-linked, monomeric CRPcys antagonizes Glycoprotein VI. Here, we describe how cysteine in these triplets may also undergo random air-induced oxidation, especially upon prolonged storage or repeated freeze–thawing, to form disulphide bonds, resulting in a lesser degree of polymerization than with chemical cross-linking. We investigated the monomeric and polymeric states of these and other cysteine-containing collagen-derived peptides, using gel filtration and dynamic light scattering, allowing the size of a CRP-XL aggregate to be estimated. The effect of cysteine thiols upon peptide adsorption to surfaces and subsequent platelet responses was investigated. This demonstrated that cysteine is required for strong binding to glass coverslips and to plastic plates used in ELISA assays

Open/Closed String Duality for Topological Gravity with Matter

The exact FZZT brane partition function for topological gravity with matter is computed using the dual two-matrix model. We show how the effective theory of open strings on a stack of FZZT branes is described by the generalized Kontsevich matrix integral, extending the earlier result for pure topological gravity. Using the well-known relation between the Kontsevich integral and a certain shift in the closed-string background, we conclude that these models exhibit open/closed string duality explicitly. Just as in pure topological gravity, the unphysical sheets of the classical FZZT moduli space are eliminated in the exact answer. Instead, they contribute small, nonperturbative corrections to the exact answer through Stokes' phenomenon.Comment: 23 pages, 1 figure, harvma

A Prospective Longitudinal Study of the Clinical Outcomes from Cryptococcal Meningitis following Treatment Induction with 800 mg Oral Fluconazole in Blantyre, Malawi

Introduction: Cryptococcal meningitis is the most common neurological infection in HIV infected patients in Sub Saharan Africa, where gold standard treatment with intravenous amphotericin B and 5 flucytosine is often unavailable or difficult to administer. Fluconazole monotherapy is frequently recommended in national guidelines but is a fungistatic drug compromised by uncertainty over optimal dosing and a paucity of clinical end-point outcome data. Methods: From July 2010 until March 2011, HIV infected adults with a first episode of cryptococcal meningitis were recruited at Queen Elizabeth Central Hospital, Blantyre, Malawi. Patients were treated with oral fluconazole monotherapy 800 mg daily, as per national guidelines. ART was started at 4 weeks. Outcomes and factors associated with treatment failure were assessed 4, 10 and 52 weeks after fluconazole initiation. Results: Sixty patients were recruited. 26/60 (43%) died by 4 weeks. 35/60 (58.0%) and 43/56 (77%) died or failed treatment by 10 or 52 weeks respectively. Reduced consciousness (Glasgow Coma Score ,14 of 15), moderate/severe neurological disability (modified Rankin Score .3 of 5) and confusion (Abbreviated Mental Test Score ,8 of 10) were all common at baseline and associated with death or treatment failure. ART prior to recruitment was not associated with better outcomes. Conclusions: Mortality and treatment failure from cryptococcal meningitis following initiation of treatment with 800 mg oral fluconazole is unacceptably high. To improve outcomes, there is an urgent need for better therapeutic strategies and point-of-care diagnostics, allowing earlier diagnosis before development of neurological deficit

Research on atmospheric volcanic emissions: An overview

The project Research on Atmospheric Volcanic Emissions is a unique effort by NASA and university scientists to investigate the detailed chemical nature of plumes from volcanic eruptions. The major goals of the project are to: 1) understand the impact major eruptions will have on atmospheric chemistry processes, 2) understand the importance of volcanic emissions in the atmospheric geochemical cycles of selected species, 3) use knowledge of the plume chemical composition to diagnose and predict magmatic processes. Project RAVE\u27S first mission used the NASA Lockheed Orion P-3 outfitted with equipment to measure concentrations of the gases SO2, OCS, H2S, CS2, NO, O3and trace elements in particles in Mt. St. Helens\u27 plume on September 22, 1980. Measurements of SO2 column densities in the plume permitted calculations of SO2 fluxes. This article is an overview of the first experimental design factors and performance of the initial RAVE experiment