Next Generation Complex Genome Assembly

Whole genome assembly boosts the discovery of genes and pathways involved in the key metabolites produced in medicinal plants. Many medicinal plants possess large, polyploid and/or heterozygote genomes, thus denovo assembly of these genomes poses a significant challenge both algorithmically and economically. DeNovoMAGIC-2 assembler has successfully reconstructed some of the largest most repetitive, polyploid and heterozygote plant genomes. Using only high coverage of short Illumina reads, DeNovoMAGIC-2 has assembled over 90 % of the genome sequence of the 16 Gb, hexaploid wheat and the 1 Gb, tetraploid and heterozygote mango genome, with N50 of ~7 Mb and ~1 Mb respectively. Assemblies were completed in 14 and 2 days using 1 Tb and 0.512 Tb RAM computers, respectively. BUSCO analysis revealed full intact gene content for over 90 % of the genome, with clear phasing of allelic and paralog genes. Similar employment of DeNovoMAGIC-2 is expected to reconstruct the genome sequences of many medicinal plants, boosting our basic understanding of metabolite production and accumulation, towards industrializing medicine production from plants

Realism in the design process and credibility of a simulation-based virtual laboratory

The credibility of an instructional simulation is a most important issue in distance education, where it may replace hands-on activities. This credibility is based in large part upon verisimilitude, a perception strongly influenced by the simulation’s realism. This paper presents a case study encompassing the design process of a simulation-based virtual laboratory, which was guided by a realism principle, and an investigation of its credibility among potential users. We found that many characteristics of the environment associated with the design principle did favour its credibility, but that others had widely varying, even opposite effects among users. User’s prior experience was shown to play a crucial but intricate role in verisimilitude and credibility judgements

Efficacy of methylsulfonylmethane supplementation on osteoarthritis of the knee: a randomized controlled study

BACKGROUND: Patients with osteoarthritis (OA) take a variety of health supplements in an attempt to reduce pain and improve function. The aim of this study was to determine the efficacy of methylsulfonylmethane (MSM) in treating patients with knee OA. METHODS: This study was a prospective, randomized, double-blind, controlled clinical trial. Forty nine men and women 45-90 (mean 68 ± SD 7.3) years of age with knee OA according to the American College of Rheumatology clinical criteria for OA of the knee and with radiographic confirmed knee OA were enrolled in the study and randomly assigned into 2 groups: One received MSM in doses of 1.125 grams 3 times daily for 12 weeks and the other received a placebo in the same dosing frequency. The primary outcomes were the WOMAC Osteoarthritis Index for pain, stiffness and physical function, the Aggregated Locomotor Function (ALF) test that evaluates each patient's physical function, the SF-36 quality of life health survey and the visual-analogue-scale (VAS) for pain. The secondary outcomes were Knee Society Clinical Rating System for Knee Score (KSKS) and Function Score (KSFS). Patients were assessed at baseline, 6 weeks and 12 weeks. All continuous variables were tested by the Kolmogorov-Smirnov test for Normal distribution. Changes within the groups and differences between the groups were calculated by repeated measures of analysis (ANOVA) with one nested variable. RESULTS: There were significant differences between treatment groups over time in WOMAC physical function (14.6 mm [CI: 4.3, 25.0]; p = 0.04) and in WOMAC total score (15.0 mm [CI: 5.1, 24.9]; p = 0.03). Treatment groups did not differ significantly in WOMAC pain (12.4 mm [CI: 0.0, 24.8]); p = 0.08) or WOMAC stiffness (27.2 mm [CI: 8.2, 46.2]; p = 0.08). There was a non-significant difference in SF-36 total score between treatment groups (11.6 [CI: 1.0, 22.1]; p = 0.54). A significant difference was found between groups in VAS for pain (0.7 s [CI: -0.9, 2.4]; p = 0.05). Secondary outcomes showed non-significant differences between the two groups. CONCLUSIONS: Patients with OA of the knee taking MSM for 12 weeks showed an improvement in pain and physical function. These improvements, however, are small and it is yet to be determined if they are of clinical significance. TRIAL REGISTRATION: ClinicalTrials.gov: NCT0118821

Principal component analysis of IUE galaxy spectra

We analyse the UV spectral energy distribution of a sample of normal galaxies listed in the IUE-INES Guide No. 2-Normal Galaxies (Formiggini & Brosch, 2000) using a Principal Component Analysis. The sample consists of the IUE-SW spectra of the central regions of 118 galaxies, where the IUE aperture included more than 1 per cent of the galaxy size. The principal components are associated with the main components observed in the UV spectra of galaxies. The first component, accounting for the largest source of diversity, can be associated with the UV continuum emission. The second component represents the UV contribution of an underlying evolved stellar population. The third component is sensitive to the amount of activity in the central regions of galaxies and measures the strength of star formation events. In all the samples analysed here the principal component representative of star-forming activity accounts for a significant percentage of the variance. The fractional contribution to the SED by the evolved stars and by the young population are similar. Projecting the SEDs onto their eigenspectra, we find that none of the coefficients of the principal components can outline an internal correlation or can correlate with the optical morphological types. In a sub-sample of 43 galaxies, consisting of almost only compact and BCD galaxies, the third principal component defines a sequence related to the degree of starburst activity of the galaxy.Comment: 13 pages, incl. 14 figures. Accepted by MNRA

Ventilation and outcomes following robotic-assisted abdominal surgery: an international, multicentre observational study

Background: International data on the epidemiology, ventilation practice, and outcomes in patients undergoing abdominal robotic-assisted surgery (RAS) are lacking. The aim of the study was to assess the incidence of postoperative pulmonary complications (PPCs), and to describe ventilator management after abdominal RAS. Methods: This was an international, multicentre, prospective study in 34 centres in nine countries. Patients ≥18 yr of age undergoing abdominal RAS were enrolled between April 2017 and March 2019. The Assess Respiratory Risk in Surgical Patients in Catalonia (ARISCAT) score was used to stratify for higher risk of PPCs (≥26). The primary outcome was the incidence of PPCs. Secondary endpoints included the preoperative risk for PPCs and ventilator management. Results: Of 1167 subjects screened, 905 abdominal RAS patients were included. Overall, 590 (65.2%) patients were at increased risk for PPCs. Meanwhile, 172 (19%) patients sustained PPCs, which occurred more frequently in 132 (22.4%) patients at increased risk, compared with 40 (12.7%) patients at lower risk of PPCs (absolute risk difference: 12.2% [95% confidence intervals (CI), 6.8–17.6%]; P<0.001). Plateau and driving pressures were higher in patients at increased risk, compared with patients at low risk of PPCs, but no ventilatory variables were independently associated with increased occurrence of PPCs. Development of PPCs was associated with a longer hospital stay. Conclusions: One in five patients developed one or more PPCs (chiefly unplanned oxygen requirement), which was associated with a longer hospital stay. No ventilatory variables were independently associated with PPCs. Clinical trial registration: NCT02989415

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Adapting Masculinities: Israeli and American Genres Redefining Mizrahi Masculinity in the TV Series Haborer

The discussion proposed in this article on the Israeli television series Haborer (The Arbitrator, 2007–2014) focuses on the blending of three major genres that characterize and define it: the “masculine” American gangster film, the “feminine” soap opera, and the popular Israeli bourekas movie. I claim that the hybridization of these diverse and contradictory genres allows the series to propose a new and complex representation of Mizrahi masculinity. While the bourekas genre depicted Ashkenazi masculinity as the polar opposite of Mizrahi masculinity, the Mizrahi masculinity off ered in Haborer adopts and contains bourekas Ashkenazi masculinity

Cloning of tangerine from Tomato Reveals a Carotenoid Isomerase Essential for the Production of β-Carotene and Xanthophylls in Plants

Carotenoid biosynthesis in plants has been described at the molecular level for most of the biochemical steps in the pathway. However, the cis-trans isomerization of carotenoids, which is known to occur in vivo, has remained a mystery since its discovery five decades ago. To elucidate the molecular mechanism of carotenoid isomerization, we have taken a genetic map-based approach to clone the tangerine locus from tomato. Fruit of tangerine are orange and accumulate prolycopene (7Z,9Z,7′Z,9′Z-tetra-cis-lycopene) instead of the all-trans-lycopene, which normally is synthesized in the wild type. Our data indicate that the tangerine gene, designated CRTISO, encodes an authentic carotenoid isomerase that is required during carotenoid desaturation. CRTISO is a redox-type enzyme structurally related to the bacterial-type phytoene desaturase CRTI. Two alleles of tangerine have been investigated. In tangerine(mic), loss of function is attributable to a deletion mutation in CRTISO, and in tangerine(3183), expression of this gene is impaired. CRTISO from tomato is expressed in all green tissues but is upregulated during fruit ripening and in flowers. The function of carotene isomerase in plants presumably is to enable carotenoid biosynthesis to occur in the dark and in nonphotosynthetic tissues