Whole genome de novo assemblies of three divergent strains of rice,Oryza sativa,document novel gene space of aus and indica

The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the ‘pan-genome’ of three divergent rice varieties and document several megabases of each genome absent in the other two. Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.     

Mutational analysis of the oxidoreductase ERp57 reveals the importance of the two central residues in the redox motif

The oxidoreductase ERp57 is involved in the formation and breaking of disulfide bonds in assembling proteins within the environment of the endoplasmic reticulum. Site-directed mutants of the redox-active Cys-Gly-His-Cys motif within an isolated ERp57 sub-domain have been studied. Whereas mutation of either cysteine residue abolished reductase activity, substitution of the central residues resulted in retention of partial activity. Alkylation studies indicated that the central residue mutants retained the normal disulfide bond in the motif, whereas this disulfide bond became more resistant to reduction following addition of a third residue into the redox motif, demonstrating an optimum spacing within the redox-active motif of ERp57.     

First Record of Fusarium Wilt of Tobacco in Greece Imported as Seedborne Inoculum

Leaf yellowing and brown discoloration was observed in tobacco plants cv. Burley TN97 in tobacco fields of central Greece in 2002. Fusarium oxysporum f. sp. nicotianae was isolated from symptomatic plants and Koch's postulates were fulfilled. The pathogenicity of the isolated fungus was examined on five tobacco cultivars (Burley TN97, BurleyB21, VirginiaBE9, Virginia Niki and Anatolika KE26/2). The pathogen was present in tobacco seed batches imported in 2000 and 2001, which indicates that the infected seed is most probably the primary source of the disease in Greece. As Fusarium oxysporum f. sp. vasinfectum can also cause vascular wilt in tobacco, the hypothesis that the isolated F. oxysporum strain belongs to f. sp. vasinfectum was excluded by a pathogenicity test to cotton cv. Acala SJ‐2. This is the first report of F. oxysporum f. sp. nicotianae in Greece and the second in the European Union, although the seedborne nature of the pathogen has not been previously reported in Europe.     

Lack of tyrosine 320 impairs spontaneous endocytosis and enhances release of HLA-B27 molecules

Several lines of evidence suggest that endocytosis of MHC class I molecules requires conserved motifs within the cytoplasmic domain. In this study, we show, in the C58 rat thymoma cell line transfected with HLA-B27 molecules, that replacement of the highly conserved tyrosine (Tyr320) in the cytoplasmic domain of HLA-B27 does not hamper cell surface expression of beta2-microglobulin H chain heterodimers or formation of misfolded molecules. However, Tyr320 replacement markedly impairs spontaneous endocytosis of HLA-B27. Although wild-type molecules are mostly internalized via endosomal compartments, Tyr320-mutated molecules remain at the plasma membrane in which partial colocalization with endogenous transferrin receptors can be observed, also impairing their endocytosis. Finally, we show that Tyr320 substitution enhances release of cleaved forms of HLA-B27 from the cell surface. These studies show for the first time that Tyr320 is most likely part of a cytoplasmic sorting motif involved in spontaneous endocytosis and shedding of MHC class I molecules.     

They are here to stay: the biology and ecology of lionfish (Pterois miles) in the Mediterranean Sea

The lionfish, Pterois miles, is one of the most recent Lessepsian immigrants into the Mediterranean Sea, and it poses a serious threat to marine ecosystems in the region. This study assesses the basic biology and ecology of lionfish in the Mediterranean, examining morphometrics, reproduction and diet as well as population structure and distribution. The population density of lionfish has increased dramatically in Cyprus since the first sighting in late 2012; by 2018 aggregations of up to 70 lionfish were found on rocky grounds with complex reefs and artificial reefs in depths of 0–50 m. Lionfish in Cyprus become mature within a year, and adults are capable of spawning year-round, with peak spawning in summer when the sea-surface temperature reaches 28.4°C. The Cypriot lionfish grow faster and bigger than in their native range, and females are more common than males. Lionfish are generalist predators in these waters, as also found in their native range, consuming a range of teleost and crustacean prey, some of which are of high economic value (e.g., Spicara smaris and Sparisoma cretense) or have an important role in local trophic webs (e.g., Chromis chromis). Overall, the reproductive patterns, the presence of juveniles and adults throughout the year, the rapid growth rates and the generalist diet indicate that lionfish are thriving and are now already well established in the region and could potentially become the serious nuisance that they are in their temperate and tropical western Atlantic–invasive range.     

Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study

Background

Genetic association studies have revealed numerous polymorphisms conferring susceptibility to melanoma. We aimed to replicate previously discovered melanoma-associated single-nucleotide polymorphisms (SNPs) in a Greek case-control population, and examine their predictive value.

Methods

Based on a field synopsis of genetic variants of melanoma (MelGene), we genotyped 284 patients and 284 controls at 34 melanoma-associated SNPs of which 19 derived from GWAS. We tested each one of the 33 SNPs passing quality control for association with melanoma both with and without accounting for the presence of well-established phenotypic risk factors. We compared the risk allele frequencies between the Greek population and the HapMap CEU sample. Finally, we evaluated the predictive ability of the replicated SNPs.

Results

Risk allele frequencies were significantly lower compared to the HapMap CEU for eight SNPs (rs16891982 – SLC45A2, rs12203592 – IRF4, rs258322 – CDK10, rs1805007 – MC1R, rs1805008 - MC1R, rs910873 - PIGU, rs17305573- PIGU, and rs1885120 - MTAP) and higher for one SNP (rs6001027 – PLA2G6) indicating a different profile of genetic susceptibility in the studied population. Previously identified effect estimates modestly correlated with those found in our population (r = 0.72, P<0.0001). The strongest associations were observed for rs401681-T in CLPTM1L (odds ratio [OR] 1.60, 95% CI 1.22–2.10; P = 0.001), rs16891982-C in SCL45A2 (OR 0.51, 95% CI 0.34–0.76; P = 0.001), and rs1805007-T in MC1R (OR 4.38, 95% CI 2.03–9.43; P = 2×10⁻⁵). Nominally statistically significant associations were seen also for another 5 variants (rs258322-T in CDK10, rs1805005-T in MC1R, rs1885120-C in MYH7B, rs2218220-T in MTAP and rs4911442-G in the ASIP region). The addition of all SNPs with nominal significance to a clinical non-genetic model did not substantially improve melanoma risk prediction (AUC for clinical model 83.3% versus 83.9%, p = 0.66).

Conclusion

Overall, our study has validated genetic variants that are likely to contribute to melanoma susceptibility in the Greek population.     

Developmental stage- and concentration-specific sodium nitroprusside application results in nitrate reductase regulation and the modification of nitrate metabolism in leaves of Medicago truncatula plants

Nitric oxide (NO) is a bioactive molecule involved in numerous biological events that has been reported to display both pro-oxidant and antioxidant properties in plants. Several reports exist which demonstrate the protective action of sodium nitroprusside (SNP), a widely used NO donor, which acts as a signal molecule in plants responsible for the expression regulation of many antioxidant enzymes. This study attempts to provide a novel insight into the effect of application of low (100 μΜ) and high (2.5 mM) concentrations of SNP on the nitrosative status and nitrate metabolism of mature (40 d) and senescing (65 d) Medicago truncatula plants. Higher concentrations of SNP resulted in increased NO content, cellular damage levels and reactive oxygen species (ROS) concentration, further induced in older tissues. Senescing M. truncatula plants demonstrated greater sensitivity to SNP-induced oxidative and nitrosative damage, suggesting a developmental stage-dependent suppression in the plant’s capacity to cope with free oxygen and nitrogen radicals. In addition, measurements of the activity of nitrate reductase (NR), a key enzyme involved in the generation of NO in plants, indicated a differential regulation in a dose and time-dependent manner. Furthermore, expression levels of NO-responsive genes (NR, nitrate/nitrite transporters) involved in nitrogen assimilation and NO production revealed significant induction of NR and nitrate transporter during long-term 2.5 mM SNP application in mature plants and overall gene suppression in senescing plants, supporting the differential nitrosative response of M. truncatula plants treated with different concentrations of SNP.     

Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: the case of C3 inhibition by compstatin

The peptide compstatin and its derivatives inhibit the complement-component protein C3 in primate mammals and are potential therapeutic agents against the unregulated activation of complement in humans, but are inactive against C3 from lower mammals. Recent molecular dynamics (MD) simulations showed that the most potent compstatin analog comprised entirely of natural amino acids (W4A9) had a smaller affinity for rat C3, due to reproducible changes in the rat protein structure with respect to the human protein, which eliminated or weakened specific protein-ligand interactions seen in the human C3:W4A9 complex. Here, we study by MD simulations three W4A9 complexes with the mouse C3 protein, and two "transgenic" mouse derivatives, containing a small number (6-9) of human C3 substitutions. The mouse complex experiences the conformational changes and affinity reduction of the rat complex. In the "transgenic" complexes, the conformation remains closer to that of the human complex, the protein-ligand interactions are improved, and the affinity for compstatin becomes "human-like." The present work creates new avenues for a compstatin-sensitive animal model. A similar strategy, involving the comparison of a series of complexes by MD simulations, could be used to design "transgenic" sequences in other systems.