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ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity
No full textAdsorption of Hyperbranched Arabinogalactan-Proteins from Plant Exudate at the Solid–Liquid Interface
No full textAdsorption of hyperbranched arabinogalactan-proteins (AGPs) from two plant exudates, A. senegal and A. seyal, was thoroughly studied at the solid–liquid interface using quartz crystal microbalance with dissipation monitoring (QCM-D), surface plasmon resonance (SPR), and atomic force microscopy (AFM). Isotherms of the adsorption reveal that 3.3 fold more AGPs from A. seyal (500 ppm) are needed to cover the gold surface compared to A. senegal (150 ppm). The pH and salt concentration of the environment greatly affected the adsorption behavior of both gums, with the surface density ranging from 0.92 to 3.83 mg m−2 using SPR (i.e., “dry” mass) and from 1.16 to 19.07 mg m−2 using QCM-D (wet mass). Surprisingly, the mass adsorbed was the highest in conditions of strong electrostatic repulsions between the gold substrate and AGPs, i.e., pH 7.0, highlighting the contribution of other interactions involved in the adsorption process. Structural changes of AGPs induced by pH would result in swelling of the polysaccharide blocks and conformational changes of the polypeptide backbone, therefore increasing the protein accessibility and hydrophobic interactions and/or hydrogen bonds with the gold substrat
Genome editing reveals reproductive and developmental dependencies on specific types of vitellogenin in zebrafish (Danio rerio)
No full textOviparous vertebrates produce multiple forms of vitellogenin (Vtg), the major source of yolk nutrients, but little is known about their individual contributions to reproduction and development. This study utilized clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) genome editing to assess essentiality and functionality of zebrafish (Danio rerio) type-I and type-III Vtgs. A multiple CRISPR approach was employed to knockout (KO) all genes encoding type-I vtgs (vtg1, 4, 5, 6, and 7) simultaneously (vtg1-KO), and the type-III vtg (vtg3) individually (vtg3-KO). Results of polymerase chain reaction (PCR) genotyping and sequencing, quantitative PCR, liquid chromatography-tandem mass spectrometry, and Western blot analysis showed that only vtg6 and vtg7 escaped Cas9 editing. In fish whose remaining type-I vtgs were incapacitated (vtg1-KO), and in vtg3-KO fish, significant increases in Vtg7 transcript and protein levels occurred in liver and eggs, revealing a heretofore-unknown mechanism of genetic compensation regulating Vtg homeostasis. Egg numbers per spawn were elevated more than 2-fold in vtg1-KO females, and egg fertility was approximately halved in vtg3-KO females. Substantial mortality was evident in vtg3-KO eggs/embryos after only 8 hr of incubation and in vtg1-KO embryos after 5 days. Hatching rate and timing were markedly impaired in embryos from vtg mutant mothers and pericardial and yolk sac/abdominal edema and spinal lordosis were evident in the larvae, with feeding and motor activities also being absent in vtg1-KO larvae. By late larval stages, vtg mutations were either completely lethal (vtg1-KO) or nearly so (vtg3-KO). These novel findings offer the first experimental evidence that different types of vertebrate Vtg are essential and have disparate requisite functions at different times during both reproduction and development
Size and flexibility define the Inhibition of the h3n2 Influenza endonuclease enzyme by calix[n]arenes.
No full textInhibition of H3N2 influenza PA endonuclease activity by a panel of anionic calix[n]arenes and β-cyclodextrin sulfate has been studied. The joint experimental and theoretical results reveal that the larger, more flexible and highly water-soluble sulfonato-calix[n]arenes have high inhibitory activity, with para-sulfonato-calix[8]arene, SC8, having an IC50 value of 6.4 μM. Molecular docking calculations show the SC8 can interact at both the polyanion binding site and also the catalytic site of H3N2 influenza PA endonucleas
Design of a comprehensive microfluidic and microscopic toolbox for the ultra-wide spatio-temporal study of plant protoplasts development and physiology
No full textBackground: Plant protoplasts are basic plant cells units in which the pecto-cellulosic cell wall has been removed, but the plasma membrane is intact. One of the main features of plant cells is their strong plasticity, and their propensity to regenerate an organism from a single cell. Methods and differentiation protocols used in plant physiology and biology usually involve macroscopic vessels and containers that make difficult, for example, to follow the fate of the same protoplast all along its full development cycle, but also to perform continuous studies of the influence of various gradients in this context. These limits have hampered the precise study of regeneration processes. Results: Herein, we present the design of a comprehensive, physiologically relevant, easy-to-use and low-cost microfluidic and microscopic setup for the monitoring of Physcomitrella patens (P. patens) growth and development on a long-term basis. The experimental solution we developed is made of two parts (i) a microfluidic chip composed of a single layer of about a hundred flow-through microfluidic traps for the immobilization of protoplasts, and (ii) a low-cost, light-controlled, custom-made microscope allowing the continuous recording of the moss development in physiological conditions. We validated the experimental setup with three proofs of concepts: (i) the kinetic monitoring of first division steps and cell wall regeneration, (ii) the influence of the photoperiod on growth of the protonemata, and (iii) finally the induction of leafy buds using a phytohormone, cytokinin. Conclusions: We developed the design of a comprehensive, physiologically relevant, easy-to-use and low-cost experimental setup for the study of P. patens development in a microfluidic environment. This setup allows imaging of P. patens development at high resolution and over long time periods
PADI-web corpus: Labeled textual data in animal health domain
No full textMonitoring animal health worldwide, especially the early detec-tion of outbreaks of emerging pathogens, is one of the means ofpreventing the introduction of infectious diseases in countries(Collier et al., 2008)[3]. In this context, we developed PADI-web, aPlatform for Automated extraction of animal Disease Informationfrom the Web (Arsevska et al., 2016, 2018). PADI-web is a text-mining tool that automatically detects, categorizes and extractsdisease outbreak information from Web news articles. PADI-webcurrently monitors the Web forfive emerging animal infectiousdiseases, i.e., African swine fever, avian influenza including highlypathogenic and low pathogenic avian influenza, foot-and-mouthdisease, bluetongue, and Schmallenberg virus infection. PADI-webcollects Web news articles in near-real time through RSS feeds.Currently, PADI-web collects disease information from GoogleNews because of its international and multiple language coverage.We implemented machine learning techniques to identify therelevant disease information in texts (i.e., location and date of anoutbreak, affected hosts, their numbers and clinical signs). In orderto train the model for Information Extraction (IE) from newsarticles, a corpus in English has been manually labeled by domainexperts. This labeled corpus (Rabatel et al., 2017) is presented inthis data paper
Exploring legume-rhizobia symbiotic models for waterlogging tolerance
No full textUnexpected and increasingly frequent extreme precipitation events result in soil flooding or waterlogging. Legumes have the capacity to establish a symbiotic relationship with endosymbiotic atmospheric dinitrogen-fixing rhizobia, thus contributing to natural nitrogen soil enrichment and reducing the need for chemical fertilization. The impact of waterlogging on nitrogen fixation and legume productivity needs to be considered for crop improvement. This review focuses on the legumes-rhizobia symbiotic models. We aim to summarize the mechanisms underlying symbiosis establishment, nodule development and functioning under waterlogging. The mechanisms of oxygen sensing of the host plant and symbiotic partner are considered in view of recent scientific advances
Importance of sugar homeostasis within xylem parenchyma cells to sustain xylem development
No full textThe Arabidopsis floral stem xylem tissue is formed by xylary parenchyma cells and dead cells including xylary fibres and xylary vessels. Especially, these last two cells functions request the presence of an extra-thickened secondary cell wall whose synthesis requires an important amount of carbohydrate skeletons. However, the pathways by which carbon pools, transported as sugars, are supplied to the xylem cells remain unclear. Recently, the SWEET11 and SWEET12 genes coding for sugar transporters located at the plasma membrane of the vascular parenchyma cells were proposed to act in this mechanism. To gain more insights in this process, we analyzed the function of two additional SWEET genes coding for tonoplastic sugar transporters also expressed in the xylem parenchyma cells. We analysed combinations of sweet mutants using microscopy combined with high-throughput image analysis and vibrational spectroscopy techniques. Our analysis reveals defects in the number and the size of the xylary fibres in the sweet16sweet17 mutant, in contrast to the sweet11sweet12 mutant; that has been previously shown to be mostly affected in the xylary vessels (1). Interestingly, the quadruple mutant shows defects in both xylary fibres and vessels, suggesting an additive phenotype. Due to differences in the expression pattern of these genes in different categories of bundles connected or not to axillary buds, we also scrutinized the effects of these mutations depending on the vascular bundle type. Our results suggest that the sugar homeostasis within the xylary parenchyma cells is required to ensure a correct xylem development
