Project description:<h4> </h4>Here, we present Viola, a Python package that provides structural variant (SV; large scale genome DNA variations that can result in disease, e.g., cancer) signature analytical functions and utilities for custom SV classification, merging multi-SV-caller output files, and SV annotation. We demonstrate that Viola can extract biologically meaningful SV signatures from publicly available SV data for cancer and we evaluate the computational time necessary for annotation of the data.<h4>Availability</h4>Viola is available on pip (https://pypi.org/project/Viola-SV/) and the source code is on GitHub (https://github.com/dermasugita/Viola-SV).<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.
Project description:The Hawaiian endemic Viola kauaensis A. Gray has a broad distribution in bogs of Kaua`i and a limited distribution on mesic ridges in the Ko`olau Mountains of O`ahu. Based on differences in scale, the O`ahu populations of Viola kauaensis had previously been described as a distinct taxon. The taxonomic status of the O`ahu populations was reevaluated through a morphometric analysis of all varieties of Viola kauaensis and the morphologically similar Viola vanroyenii. Morphological features of historic and freshly collected specimens of all varieties of Viola kauaensis were analyzed with a principal components analysis. Populations from O`ahu represent a distinct cluster that slightly overlaps with Viola kauaensis var. kauaensis. Lamina width, apex angle, and base angles contribute to the separation of the O`ahu populations from other varieties of Viola kauaensis. Due to differences in scale, the O`ahu populations are described as Viola kauaensis var. hosakae, a new critically endangered taxon.
Project description:Heartsease (Viola tricolor L.), a member of the Violaceae family, has a long history as a medicinal plant and has been documented in the Pharmacopoeia of Europe. Due to its anti-inflammatory properties it is regarded as a traditional remedy against skin diseases, for example for the treatment of scabs, itching, ulcers, eczema or psoriasis, and it is also used in the treatment of inflammation of the lungs and chest such as bronchitis or asthma. Because T-cells play an important role in the pathological process of inflammatory diseases we investigated the effect of an aqueous Viola extract on lymphocyte functions and explored the 'active' principle of the extract using bioactivity-guided fractionation.An aqueous Viola extract was prepared by C18 solid-phase extraction. Effects on proliferation of activated lymphocytes (using the cell membrane permeable fluorescein dye CFSE), apoptosis and necrosis (using annexin V and propidium iodide staining), interleukin-2 (IL-2) receptor expression (using fluorochrome-conjugated antibodies) and IL-2 cytokine secretion (using an ELISA-based bead array system) were measured by flow cytometry. Influence on lymphocyte polyfunctionality was characterized by Viola extract-induced production of IFN-? and TNF-?, as well as its influence on lymphocyte degranulation activity. Fractionation and phytochemical analysis of the extract were performed by RP-HPLC and mass spectrometry.The aqueous Viola extract inhibited proliferation of activated lymphocytes by reducing IL-2 cytokine secretion without affecting IL-2 receptor expression. Similarly, effector functions were affected as indicated by the reduction of IFN-? and TNF-? production; degranulation capacity of activated lymphocytes remained unaffected. Bioassay-guided fractionation and phytochemical analysis of the extract led to identification of circular plant peptides, so called cyclotides, as bioactive components.An aqueous Viola extract contains bioactive cyclotides, which inhibit proliferation of activated lymphocytes in an IL-2 dependent manner. The findings provide a rationale for use of herbal Viola preparations in the therapy of disorders related to an overactive immune system. However, further studies to evaluate its clinical potency and potential risks have to be performed.
Project description:<i>Viola verecunda</i> is a perennial plant native to the mountainous areas of Northeast Asia. Here the complete chloroplast genome of <i>V. verecunda</i> and its phylogenetic relationships to other species within the genus <i>Viola</i> are reported. The complete chloroplast genome of <i>V. verecunda</i> is 157,843 bp in length and circular in structure with four regions: a large single-copy region (86,345 bp), a small single-copy region (17,292 bp), and a pair of inverted repeat regions (27,103 bp each). The chloroplast genome contains 111 unique genes comprising 77 protein-coding, 30 unique tRNA, and 4 unique rRNA genes. Based on the protein-coding gene sequences from eight <i>Viola</i> chloroplast genomes, with <i>Balanops balansae</i> designated as the outgroup, maximum likelihood tree analysis indicates that <i>V. verecunda</i> is more closely related to <i>V. raddeana</i> than to other <i>Viola</i> species. The complete chloroplast genome of <i>V. verecunda</i> contributes to a better understanding of the phylogenetic relationships among <i>Viola</i> species.
Project description:<i>Viola selkirkii</i>, belonging to the genus <i>Viola</i>, has heart-shaped leaves and pale purple flowers, and it is widely distributed in the Northern Hemisphere, including Europe, North America, and Asia. In this study, the plastid genome of <i>V. selkirkii</i> was sequenced and phylogenetic analysis was performed on 11 <i>Viola</i> plastid genomes. The length of the plastid genome length of <i>V. selkirkii</i> was 156,774 bp, and it was identified as having a typical quadripartite structure with a large single-copy region (85,930 bp), a small single-copy region (17,982 bp), and two inverted repeat regions (26,431 bp each). A phylogenetic analysis was conducted with 77 protein-coding genes from the complete plastid genomes of 11 <i>Viola</i> and nine Salicaceae species; the complete plastid genome of <i>Erythroxylum novogranatense</i> was used as an outgroup. <i>Viola</i> formed a monophyletic clade, and <i>V. selkirkii</i> was closely related to <i>V. ulleungdoensis</i>. These results contribute to the clear identification of the phylogenetic position of <i>V. selkirkii</i> in <i>Viola.</i>
Project description:The genus Viola is represented by four related species in Brazil belonging to section Leptidium, one of the most primitive sections in the genus. Floral biology and pollination by bees were studied in Viola cerasifolia and V. subdimidiata in high-altitude areas in south-eastern Brazil. Flowers are zygomorphic and spurred. The five stamens are arranged in a cuff around the ovary, and pollen is released by means of apical connective projections, which form a cone surrounding the base of the style. The connective projections of the inferior stamens are elongated and curved to form a hook-shaped structure. Nectar-secreting tissue can occur in the basal connective appendages of the inferior stamens, which project into the spur. Flowers of V. subdimidiata secreted a mean volume of 0.14 micro l nectar over a 24-h period; approx. 40 % of flowers did not secrete any nectar. The main pollinators of these Viola species are female bees belonging to the genus Anthrenoides (Andrenidae), which search mainly for pollen. These bees seem to be oligolectic and obtain large amounts of pollen from Viola by vibrating the flowers or by moving the hook repeatedly back and forth. Males of Anthrenoides patrol Viola clusters and also feed on nectar, acting as secondary pollinators. The basic floral structure in the genus Viola fits that of 'nectar flowers'. The uncommon hook-shaped projections, scanty nectar production, and behaviour of pollinators suggest that V. cerasifolia and V. subdimidiata are shifting their reward for pollinators from nectar to pollen. Based on floral morphology, this shift may be widespread in Viola sect. Leptidium.
Project description:The complete chloroplast genome of <i>Viola philippica</i> was sequenced, assembled, and annotated. It is a circular form of 156,469 bp in length, which was separated into four distinct regions, a large single-copy (LSC) of 85,668 bp, a small single-copy region (SSC) of 18,001 bp, and two inverted repeats (IR) of 26,400 bp. After annotation, a total of 129 genes were predicted, of which, 84 encode proteins, 8 rRNA, and 37 tRNA. The evolutionary history, inferred using maximum likelihood (ML) method, indicates that <i>V. philippica</i> was grouped within Violaceae, and comprised a clade with <i>Viola seoulensis</i> with 100% Bootstrap value.