A proposal to demonstrate production of salad crops in the space station mockup facility with particular attention to space, energy, and labor constraints

A desire for fresh vegetables for consumption during long term space missions has been foreseen. To meet this need in a microgravity environment within the limited space and energy available on Space Station requires highly productive vegetable cultivars of short stature to optimize vegetable production per volume available. Special water and nutrient delivery systems must also be utilized. As a first step towards fresh vegetable production in the microgravity of Space Station, several soil-less capillary action media were evaluated for the ability to support growth of two root crops (radish and carrot) which are under consideration for inclusion in a semi-automated system for production of salad vegetables in a microgravity environment (Salad Machine). In addition, productivity of different cultivars of radish was evaluated as well as the effect of planting density and cultivar on carrot production and size. Red Prince radish was more productive than Cherry Belle and grew best on Jiffy Mix Plus. During greenhouse studies, vermiculite and rock wool supported radish growth to a lesser degree than Jiffy Mix Plus but more than Cellular Rooting Sponge. Comparison of three carrot cultivars (Planet, Short n Sweet, and Goldinhart) and three planting densities revealed that Short n Sweet planted at 25.6 sq cm/plant had the greatest root fresh weight per pot, the shortest mean top length, and intermediate values of root length and top fresh weight per pot. Red Prince radish and Short n Sweet carrot showed potential as productive cultivars for use in a Salad Machine. Results of experiments with solid capillary action media were disappointing. Further research must be done to identify a solid style capillary action media which can productively support growth of root crops such as carrot and radish

DNA-based identification of Lentinula edodes strains with species-specific primers

Lentinula edodes is among the five globally cultivated edible mushrooms, which are wood decaying spore bearing Basidiomycetes possessing separate hyphae. Specific identification of this fungus from others in the division Basidiomycota using specific primers enables a fast and accurate detection through polymerase chain reaction (PCR). As a prelude to additional nutritional and sequence characterization research, we have developed a species specific PCR assay for this fungus after screening four primer-pairs and two universal primer pairs. The primer-pair LE1F/R was specific in amplifications of ATCC-defined L. edodes strains and did not amplify DNA from six medicinally and nutritionally important fungal reference strains, Oyster (Pleurotus ostreatus), Maitake (Grifola frondosa), Enoki (Flammulina velutipes), Baby bella (Agaricus bisporus), Porcini (Boletus edulis), and Chanterelle (Cantharellus cibarius). However, amplifications using the universal primers were positive for all six strains. This assay will therefore serve to validate morphology-based identifications of L. edodes strains.Keywords: Lentinula edodes, LE1F/R, species-specific primer

Genetic Resistance to the Reniform Nematode in Cotton

Among major nematode pests of Upland, cotton production is the reniform nematode, which is a serious threat in various cotton-producing regions. The availability of germplasm lines with tolerance or resistance to this menacing pest is a valued asset. To date, various laboratories and research institutions have collaborated to transfer the reniform nematode resistance from wild gene pools of cotton into widely cultivated Upland cotton, which have led to positive results. This chapter focuses on the current status of these introgressions and resistance mechanisms in cotton. In this overview, four major themes are being pursed: (1) tolerance mechanisms in cotton to the reniform nematode, (2) genotype evaluations, (3) introgression of reniform resistance into Upland cotton, and (4) functional analysis of reniform infection in Upland cotton. Genetic resistance in Upland cotton to the reniform nematode is the only practical solution because conventional control measures are the most cost-effective and environmentally sustainable and therefore have been and will be actively pursued. Resistance genes, if successfully introgressed into crop plants from wild relatives, should complement management of the reniform nematode with traditional methods

Traditional and novel references towards systematic normalization of qRT-PCR data in plants

Abstract The selection of appropriate controls is the key requirement for target gene normalization through quantitative real-time PCR. The consistent control is selected via a gene validation approach that includes several classic and novel housekeeping references. Our aim in this paper is to present major achievements, largely concerned with finding an invariable internal control in different plant species under a range of experimental conditions. The conflicts in gene normalization using classical references and their replacement with novel references are discussed as leading subject. This review also accentuates different methods used for the amplification of reference genes with special importance on ortholog/paralog approaches, and multi-transcript targeting. Some other issues are also discussed such as the use of quantitative real-time PCR in different areas of plant science for target gene normalization, and some areas where it might be a useful technique in unraveling other issues

Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium

Cotton is economically and evolutionarily important crop for its fiber. In order to improve fiber quality and yield, and to exploit the natural genetic potential inherent in genotypes, understanding genome structure and function of cultivated cotton is important. In order to achieve this, a functional understanding of bioinformatics resources such as databases, software solutions, and analysis tools is required. But currently, there are very few unified reports on bioinformatics tools and even fewer repositories to access cotton genomic information. Also, resourceful developers and bioinformatics scientists actively addressing complex genomic challenges in cotton genomes are much in need. The primary goal of this chapter is to provide a review of such tools and resources for analyzing the structure and function of the cotton genome with preferential emphasis on this complex and economically important plant species. This discourse begins with a description of concurrent advances in high‐throughput genome sequencing and bioinformatics analyses and focuses on four major sections covering bioinformatics tools and resources for analysis of: (1) genomes; (2) transcriptomes; (3) small RNAs; and (4) epigenomes. In each section, recent advances in cotton have been discussed. Cotton genome sequencing and annotation efforts are outlined within these sections. This review discusses the availability of genome information of both diploid and tetraploid species that have impelled cotton genome research into the post‐genomics era, opening new avenues for exploring regulatory mechanisms associated with fine‐tuning of gene expression of fiber‐related genes. Finally, the potential impacts of these rapid advances, especially the challenges in handling and analyzing the large datasets are discussed

Comprehensive Evaluation of Corticospinal Tract Metabolites in Amyotrophic Lateral Sclerosis Using Whole-Brain 1H MR Spectroscopy

Changes in the distribution of the proton magnetic resonance spectroscopy (MRS) observed metabolites N-acetyl aspartate (NAA), total-choline (Cho), and total-creatine (Cre) in the entire intracranial corticospinal tract (CST) including the primary motor cortex were evaluated in patients with amyotrophic lateral sclerosis (ALS). The study included 38 sporadic definite-ALS subjects and 70 age-matched control subjects. All received whole-brain MR imaging and spectroscopic imaging scans at 3T and clinical neurological assessments including percentage maximum forced vital capacity (FVC) and upper motor neuron (UMN) function. Differences in each individual metabolite and its ratio distributions were evaluated in the entire intracranial CST and in five segments along the length of the CST (at the levels of precentral gyrus (PCG), centrum semiovale (CS), corona radiata (CR), posterior limb of internal capsule (PLIC) and cerebral peduncle (CP)). Major findings included significantly decreased NAA and increased Cho and Cho/NAA in the entire intracranial CST, with the largest differences for Cho/NAA in all the groups. Significant correlations between Cho/NAA in the entire intracranial CST and the right finger tap rate were noted. Of the ten bilateral CST segments, significantly decreased NAA in 4 segments, increased Cho in 5 segments and increased Cho/NAA in all the segments were found. Significant left versus right CST asymmetries were found only in ALS for Cho/NAA in the CS. Among the significant correlations found between Cho/NAA and the clinical assessments included the left-PCG versus FVC and right finger tap rate, left -CR versus FVC and right finger tap rate, and left PLIC versus FVC and right foot tap rate. These results demonstrate that a significant and bilaterally asymmetric alteration of metabolites occurs along the length of the entire intracranial CST in ALS, and the MRS metrics in the segments correlate with measures of disease severity and UMN function

The GALAH survey: Milky Way disc metallicity and alpha-abundance trends in combined APOGEE-GALAH catalogues

GALAH and APOGEE are two high resolution multi object spectroscopic surveys that provide fundamental stellar parameters and multiple elemental abundance estimates for $>$ 400,000 stars in the Milky Way. They are complimentary in both sky coverage and wavelength regime. Thus combining the two surveys will provide us a large sample to investigate the disc metallicity and alpha abundance trends. We use the Cannon data-driven approach selecting training sets from among $\sim$20,000 stars in common for the two surveys to predict the GALAH scaled stellar parameters from APOGEE spectra as well as APOGEE scaled stellar parameters from GALAH spectra. We provide two combined catalogues with GALAH scaled and APOGEE scaled stellar parameters each having $\sim$500,000 stars after quality cuts. With $\sim$470,000 stars that are common in both these catalogues, we compare the GALAH scaled and APOGEE scaled metallicity distribution functions (MDF), radial and vertical metallicity gradients as well as the variation of [$\alpha$/Fe] vs [Fe/H] trends along and away from the Galactic mid plane. We find mean metallicities of APOGEE scaled sample to be higher compared to that for the GALAH scaled sample. We find similar [$\alpha$/Fe] vs [Fe/H] trends using both samples consistent with previous observational as well as simulation based studies. Radial and vertical metallicity gradients derived using the two survey scaled samples are consistent except in the inner and outer Galactocentric radius bins. Our gradient estimates in the solar neighborhood are also consistent with previous studies and are backed by larger sample size compared to previous works.Comment: 21 pages, 19 figures, submitted to MNRA

Utility of Post-Mortem Genetic Testing in Cases of Sudden Arrhythmic Death Syndrome.

BACKGROUND: Sudden arrhythmic death syndrome (SADS) describes a sudden death with negative autopsy and toxicological analysis. Cardiac genetic disease is a likely etiology. OBJECTIVES: This study investigated the clinical utility and combined yield of post-mortem genetic testing (molecular autopsy) in cases of SADS and comprehensive clinical evaluation of surviving relatives. METHODS: We evaluated 302 expertly validated SADS cases with suitable DNA (median age: 24 years; 65% males) who underwent next-generation sequencing using an extended panel of 77 primary electrical disorder and cardiomyopathy genes. Pathogenic and likely pathogenic variants were classified using American College of Medical Genetics (ACMG) consensus guidelines. The yield of combined molecular autopsy and clinical evaluation in 82 surviving families was evaluated. A gene-level rare variant association analysis was conducted in SADS cases versus controls. RESULTS: A clinically actionable pathogenic or likely pathogenic variant was identified in 40 of 302 cases (13%). The main etiologies established were catecholaminergic polymorphic ventricular tachycardia and long QT syndrome (17 [6%] and 11 [4%], respectively). Gene-based rare variants association analysis showed enrichment of rare predicted deleterious variants in RYR2 (p = 5 × 10(-5)). Combining molecular autopsy with clinical evaluation in surviving families increased diagnostic yield from 26% to 39%. CONCLUSIONS: Molecular autopsy for electrical disorder and cardiomyopathy genes, using ACMG guidelines for variant classification, identified a modest but realistic yield in SADS. Our data highlighted the predominant role of catecholaminergic polymorphic ventricular tachycardia and long QT syndrome, especially the RYR2 gene, as well as the minimal yield from other genes. Furthermore, we showed the enhanced utility of combined clinical and genetic evaluation

The GALAH+ Survey : Third Data Release

© 2021 The Author(s) Published by Oxford University Press on behalf of the Royal Astronomical Society. This is the accepted manuscript version of an article which has been published in final form at https://doi.org/10.1093/mnras/stab1242The ensemble of chemical element abundance measurements for stars, along with precision distances and orbit properties, provides high-dimensional data to study the evolution of the Milky Way. With this third data release of the Galactic Archaeology with HERMES (GALAH) survey, we publish 678 423 spectra for 588 571 mostly nearby stars (81.2% of stars are within 75 stellar clusters. We derive stellar parameters $T_\text{eff}$, $\log g$, [Fe/H], $v_\text{mic}$, $v_\text{broad}$ & $v_\text{rad}$ using our modified version of the spectrum synthesis code Spectroscopy Made Easy (SME) and 1D MARCS model atmospheres. We break spectroscopic degeneracies in our spectrum analysis with astrometry from $Gaia$ DR2 and photometry from 2MASS. We report abundance ratios [X/Fe] for 30 different elements (11 of which are based on non-LTE computations) covering five nucleosynthetic pathways. We describe validations for accuracy and precision, flagging of peculiar stars/measurements and recommendations for using our results. Our catalogue comprises 65% dwarfs, 34% giants, and 1% other/unclassified stars. Based on unflagged chemical composition and age, we find 62% young low-$\alpha$, 9% young high-$\alpha$, 27% old high-$\alpha$, and 2% stars with $\mathrm{[Fe/H]} \leq -1$. Based on kinematics, 4% are halo stars. Several Value-Added-Catalogues, including stellar ages and dynamics, updated after $Gaia$ eDR3, accompany this release and allow chrono-chemodynamic analyses, as we showcase.Peer reviewe