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Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits

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Abstract

Pumpkins are important vegetable crops widely grown worldwide, and seeds are considered a popular nutraceutical food and an excellent source of protein, oil, and vitamins. Seed size is one of the most important targets for commercial breeding in Cucurbita species; studies have shown that pumpkin seed size variation has a similar trend with fruit size, shape, and seed yield. However, few studies have been conducted to identify genetic loci controlling seed-related traits in cultivated pumpkins. This study analyzed the genomic characteristics of pumpkin breeding materials of 321 Cucurbita accessions collected worldwide, including Cucurbita moschata, Cucurbita maxima, and Cucurbita pepo, using extensive single nucleotide polymorphisms obtained from the genotyping-by-sequencing method, significant genetic variations were identified within and between Cucurbita species. Four major cultivar fruit types were further revealed in C. moschata species, and significant differentiation patterns were detected in several chromosomal regions. A total of 15 significant loci associated with pumpkin seed traits were mapped through a genome-wide association approach; 32 genes previously reported to be associated with seed size regulation in Arabidopsis and Oryza sativa were located in the intervals defined by linkage disequilibrium. Through this study, we gained a deep understanding of the genomic variation distribution across Cucurbita species. The available genetic resources and the associated genetic contents could be used in commercial pumpkin breeding and will facilitate molecular marker-assisted selection in pumpkin seed trait improvement.

Identification and characterization of Entyloma eschscholziae, a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.

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Identification and characterization of Entyloma eschscholziae, a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.

The morphology, phylogeny and species boundaries of Entyloma eschscholziae are revisited, and a new species Entyloma dendromeconis is described.


Abstract

Entyloma includes pathogenic and saprobic species that infect or colonize dicotyledonous host plants. Although most Entyloma species are known only from native areas of occurrence, some species were introduced with their host plants and spread outside their natural areas. The identification of introduced species is important for detection and management of invasive species. In this study, the morphology, phylogeny and species boundaries of Entyloma eschscholziae, recently introduced from North America to Europe, are revisited. Morphology was similar among the type and other specimens of E. eschscholziae analysed on Eschscholzia californica. Both asexual and sexual morphs were observed. The rDNA ITS1-5.8S-ITS2 sequences of the E. eschscholziae specimens from Europe and New Zealand and the environmental sequence obtained from grassland soil in California, United States, were identical. Morphological and molecular analyses confirm that the causative agents of white smut on E. californica in native (North America) and introduced (Europe, New Zealand) areas belong to the same species. DNA barcodes obtained in this study (especially ITS sequence from the designated epitype specimen) could be used to facilitate its molecular identification. Specimens on Dendromecon rigida, previously assigned to E. eschscholziae, are morphologically distinct. An attempt to obtain DNA barcode data from degraded holotype material was not successful and no more recent material is available. However, based on the morphological differences and high host specificity found in Entyloma spp., it is appropriate to describe a new species, Entyloma dendromeconis, for this smut pathogen.

The anticancer/cytotoxic effect of a novel gallic acid derivative in non‐small cell lung carcinoma A549 cells and peripheral blood mononuclear cells from healthy individuals and lung cancer patients

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The anticancer/cytotoxic effect of a novel gallic acid derivative in non-small cell lung carcinoma A549 cells and peripheral blood mononuclear cells from healthy individuals and lung cancer patients

This article presents a series of novel derivatives from gallic acid with antioxidant / anticancer properties. These compounds were studied on lymphocytes from healthy individuals and lung cancer patients. Also, gallic acid and its derivatives were examined on non-small cell carcinoma cell line. The anticancer effect of these compounds was revealed which should be confirmed with further future investigations.


Abstract

Gallic acid (GA) is a naturally occurring polyphenol with a strong antioxidant capacity. GA stimulates the apoptosis of cancer cells, thereby suppressing cancer cell invasion. However, the low oral permeability of GA limits its therapeutic use. In order to enhance the antioxidant capacity and oral permeability of GA, a series of compounds analogous to GA were synthesized: 4-methoxybenzenesulfonamide (MBS), 3,4-dimethoxybenzenesulfonamide (DMBS) and 3,4,5-trimethoxybenzenesulfonamide (TMBS). In the new compounds, hydroxyl groups were replaced with various numbers of methoxy groups (stronger electron-donating groups), to increase hydrophobicity and oral permeability compared to GA. In addition, the carboxylic group was replaced with a sulfonyl group (a stronger electron-withdrawing group), to increase the molecular polarity and antioxidative activities of the compounds. The cell counting kit-8 (CCK-8) assay was used to detect the effect of GA, MBS, DMBS, and TMBS on cell proliferation and apoptosis in peripheral blood mononuclear cells (PBMCs) from healthy individuals and non-small cell lung carcinoma A549 cells. Additionally, the comet assay was used to assess the genotoxicity of these compounds in PBMCs from healthy individuals, lung cancer patients, and A549 cells. Compared to untreated cells, TMBS reduced DNA damage more effectively than GA in PBMCs from lung cancer patients and healthy donors. Furthermore, in comparison to GA, TMBS was more cytotoxic in A549 cells. Moreover, TMBS was not cytotoxic in healthy PBMCs, suggesting that TMBS demonstrates therapeutic potential in cancer.

Insights into the antiosteoporotic mechanism of the soy‐derived isoflavone genistein: Modulation of the Wnt/beta‐catenin signaling

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Insights into the antiosteoporotic mechanism of the soy-derived isoflavone genistein: Modulation of the Wnt/beta-catenin signaling

Glucocorticoid-induced osteoporosis (GIO) reduces bone formation, osteoblasts differentiation and function, and accelerates osteoblast and osteocyte apoptosis. Genistein induces bone remodeling through Wnt/β-catenin pathway activation in osteoblast and osteocytes. Genistein could represent an interesting new therapeutic approach for the management of GIO patients.


Abstract

Bone remodeling is a process that involves osteoblasts, osteoclasts, and osteocytes, and different intracellular signaling, such as the canonical Wnt/β-catenin pathway. Dysregulations of this pathway may also occur during secondary osteoporosis, as in the case of glucocorticoid-induced osteoporosis (GIO), which accelerates osteoblast and osteocyte apoptosis by reducing bone formation, osteoblast differentiation and function, accelerates in turn osteoblast, and osteocyte apoptosis. Genistein is a soy-derived nutrient belonging to the class of isoflavones that reduces bone loss in osteopenic menopausal women, inhibiting bone resorption; however, genistein may also favor bone formation. The aim of this study was to investigate whether estrogen receptor stimulation by genistein might promote osteoblast and osteocyte function during glucocorticoid challenge. Primary osteoblasts, collected from C57BL6/J mice, and MLO-A5 osteocyte cell line were used to reproduce an in vitro model of GIO by adding dexamethasone (1 μM) for 24 h. Cells were then treated with genistein for 24 h and quantitative Polymerase Chain Reaction (qPCR) and western blot were performed to study whether genistein activated the Wnt/β-catenin pathway. Dexamethasone challenge reduced bone formation in primary osteoblasts and bone mineralization in osteocytes; moreover, canonical Wnt/β-catenin pathway was reduced following incubation with dexamethasone in both osteoblasts and osteocytes. Genistein reverted these changes and this effect was mediated by both estrogen receptors α and β. These data suggest that genistein could induce bone remodeling through Wnt/β-catenin pathway activation.

Cucurbit chlorotic yellows virus, a crinivirus infecting Cannabis sativa plants

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Cucurbit chlorotic yellows virus, a crinivirus infecting Cannabis sativa plants

Cucurbit chlorotic yellows virus (CCYV-Can), a crinivirus, was transmitted by the whitefly Bemisia tabaci to Cannabis sativa plants causing interveinal chlorosis and leaf yellowing in high-CBD plants.


Abstract

High cannabidiol-containing plants of Cannabis sativa (high-CBD) growing in farms in Israel displayed foliar symptoms of interveinal chlorosis and yellowing, brittleness and occasionally necrosis. These symptoms, which were more apparent in older leaves, resembled those caused by the crinivirus lettuce chlorosis virus (LCV). However, this virus was not detected by reverse transcription (RT)-PCR using specific primer sets. High-throughput sequencing of viral RNA extracted from symptomatic leaves revealed the presence of cucurbit chlorotic yellows virus (CCYV), a crinivirus in the Closteroviridae family. The complete viral genome sequence was obtained using RT-PCR followed by Sanger sequencing. The two CCYV RNA genomic segments shared 99.5%–99.85% nucleotide sequence identity with CCYV isolates from the GenBank. The virus was transmitted from symptomatic cannabis leaves to healthy plants of cannabis and Cucumis sativus ‘King Star’ (cucumber) by the whitefly Bemisia tabaci Middle Eastern Asia Minor 1 (MEAM1) species, causing disease symptoms identical to those of the donor plants. Cannabis-CCYV was also transmitted between infected cucumber plants and cannabis seedlings of unknown genotype. Severe disease symptoms of yellowing and leaf-edge necrosis were observed on high-CBD and high Δ9-tetrahydrocannabinol-containing (high-THC) flowering cannabis plants and were associated with mixed infections of LCV and CCYV. To the best of our knowledge, this is the first report of CCYV infecting C. sativa plants.

QTL mapping and candidate gene analysis of low‐temperature tolerance at the germination stage of soybean

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Abstract

When soybean seeds encounter low temperature during germination, the vigour and germination of soybean seeds are affected, which leads to a lack of seedlings and weak seedlings, resulting in yield reduction. In-depth analysis of the genetic mechanism of soybean seed germination tolerance to low-temperature stress and the cultivation of soybean-tolerant varieties is the key to resisting low-temperature stress at the germination stage. In the present study, a chromosome segment substitution line (CSSL) population constructed by wild soybean ZYD00006 and cultivated soybean SN14 was used to map three quantitative trait loci (QTLs). Five candidate genes were obtained by gene annotation, GO enrichment analysis and protein function prediction. The candidate genes were subjected to bioinformatics analysis, qRT-PCR analysis, trypsin activity analysis and soluble protein content analysis. The results showed that the secondary and tertiary structures of the Glyma.09G162700 proteins were mutated. Within 0–72 h, the expression of Glyma.09G162700 in the two materials with different tolerances was consistent, and the change in trypsin activity was consistent with the change in protein expression. Through haplotype analysis, Glyma.09G162700 produced two haplotypes at −2420 bp. The germination rate (GR) and relative germination rate (RGR) of the two haplotypes were significantly different, indicating that the two haplotypes have wide applicability in soybean resources. In summary, Glyma.09G162700 may be a candidate gene for low-temperature tolerance at the germination stage of soybean. These results provide an important theoretical basis and marker information for analysing the mechanism of low-temperature tolerance in soybean germination stage and cultivating low-temperature-tolerant varieties.

Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research

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Abstract

Complete, gapless telomere-to-telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orientation of genes. Using complementary genomics technologies and assembly algorithms, we developed highly contiguous, nearly gapless, genome assemblies for two economically important soybean [Glycine max (L.) Merr] cultivars (Williams 82 and Lee). The centromeres were distinctly annotated on all the chromosomes of both assemblies. We further found that the canonical telomeric repeats were present at the telomeres of all chromosomes of both Williams 82 and Lee genomes. A total of 10 chromosomes in Williams 82 and eight in Lee were entirely reconstructed in single contigs without any gap. Using the combination of ab initio prediction, protein homology, and transcriptome evidence, we identified 58,287 and 56,725 protein-coding genes in Williams 82 and Lee, respectively. The genome assemblies and annotations will serve as a valuable resource for studying soybean genomics and genetics and accelerating soybean improvement.

A new set of international Leptosphaeria maculans isolates as a resource for elucidation of the basis and evolution of blackleg disease on Brassica napus

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A new set of international Leptosphaeria maculans isolates as a resource for elucidation of the basis and evolution of blackleg disease on Brassica napus

An international collection of Leptosphaeria maculans isolates has been established as a key resource to help understand the interaction between this fungal pathogen and its host, canola (Brassica napus).


Abstract

A collection of isolates of the fungi Leptosphaeria maculans and L. biglobosa, which cause blackleg disease on Brassica napus (canola/oilseed rape) and other Brassicaceae species, was assembled to represent the global diversity of these pathogens and a resource for international research. The collection consists of 226 isolates (205 L. maculans and 21 L. biglobosa) from 11 countries. The genomes of all 205 L. maculans isolates were sequenced, and the distribution and identity of avirulence gene alleles were determined based on genotypic information and phenotypic reactions on B. napus lines that hosted specific resistance genes. Whilst the frequencies of some avirulence alleles were consistent across each of the regions, others differed dramatically, potentially reflecting the canola/oilseed rape cultivars grown in those countries. Analyses of the single-nucleotide polymorphism (SNP) diversity within these L. maculans isolates revealed geographical separation of the populations. This "open access" resource provides a standardized set of isolates that can be used to define the basis for how these fungal pathogens cause disease, and as a tool for discovery of new resistance traits in Brassica species.

Nifuroxazide repurposing for protection from diabetes‐induced retinal injury in rats: Implication of oxidative stress and JAK/STAT3 axis

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Nifuroxazide repurposing for protection from diabetes-induced retinal injury in rats: Implication of oxidative stress and JAK/STAT3 axis

Nifuroxazide (Nifu), the potent STAT3 inhibitor successfully protected the diabetic rats against diabetic retinopathy as it ameliorated the retinal structure deterioration. This effect could be attributed to modulating JAK/STAT3 axis and oxidative stress.


Abstract

The prevalence of diabetes mellitus (DM) is alarmingly increasing worldwide. Diabetic retinopathy (DR) is a prevailing DM microvascular complication, representing the major cause of blindness in working-age population. Inflammation is a crucial player in DR pathogenesis. JAK/STAT3 axis is a pleotropic cascade that modulates diverse inflammatory events. Nifuroxazide (Nifu) is a commonly used oral antibiotic with reported JAK/STAT3 inhibition activity. The present study investigated the potential protective effect of Nifu against diabetes-induced retinal injury. Effect of Nifu on oxidative stress, JAK/STAT3 axis and downstream inflammatory mediators has been also studied. Diabetes was induced in Sprague Dawley rats by single intraperitoneal injection of streptozotocin (50 mg/kg). Animals were assigned into four groups: normal, Nifu control, DM, and DM + Nifu. Nifu was orally administrated at 25 mg/kg/day for 8 weeks. The effects of Nifu on oxidative stress, JAK/STAT3 axis proteins, inflammatory factors, tight junction proteins, histological, and ultrastructural alterations were evaluated using spectrophotometry, gene and protein analyses, and histological studies. Nifu administration to diabetic rats attenuated histopathological and signs of retinal injury. Additionally, Nifu attenuated retinal oxidative stress, inhibited JAK and STAT3 phosphorylation, augmented the expression of STAT3 signaling inhibitor SOCS3, dampened the expression of transcription factor of inflammation NF-κB, and inflammatory cytokine TNF-α. Collectively, the current study indicated that Nifu alleviated DR progression in diabetic rats, suggesting beneficial retino-protective effect. This can be attributed to blocking JAK/STAT3 axis in retinal tissues with subsequent amelioration of oxidative stress and inflammation.