PhcrTx2, a new crab-paralyzing peptide toxin from the sea anemone <i>Phymanthus crucifer</i>

Sea anemones produce proteinaceous toxins for predation and defense, including peptide toxins that act on a large variety of ion channels of pharmacological and biomedical interest. Phymanthus crucifer is commonly found in the Caribbean Sea; however, the chemical structure and biological activity of its toxins remain unknown, with the exception of PhcrTx1, an acid-sensing ion channel (ASIC) inhibitor. Therefore, in the present work, we focused on the isolation and characterization of new P. crucifer toxins by chromatographic fractionation, followed by a toxicity screening on crabs, an evaluation of ion channels, and sequence analysis. Five groups of toxic chromatographic fractions were found, and a new paralyzing toxin was purified and named PhcrTx2. The toxin inhibited glutamate-gated currents in snail neurons (maximum inhibition of 35%, IC50 4.7 µM), and displayed little or no influence on voltage-sensitive sodium/potassium channels in snail and rat dorsal root ganglion (DRG) neurons, nor on a variety of cloned voltage-gated ion channels. The toxin sequence was fully elucidated by Edman degradation. PhcrTx2 is a new β-defensin-fold peptide that shares a sequence similarity to type 3 potassium channels toxins. However, its low activity on the evaluated ion channels suggests that its molecular target remains unknown. PhcrTx2 is the first known paralyzing toxin in the family Phymanthidae

Geranium leaf-mediated synthesis of silver nanoparticles and their transcriptomic effects on Candida albicans

Candida albicans is the most predominant fungal species isolated from medical devices, including catheters, heart valves, and dental prostheses. In recent years, it has been demonstrated to be resistant to many antifungals; therefore, silver nanoparticles (AgNPs) have been proposed as an alternative. But only a handful of research is contributed to omic-based studies to study the various impacts of AgNPs on Candida species and other microorganisms. Thus, the study aims to biosynthesize AgNPs using Pelargonium-hortorum leaf and test its antifungal, cytotoxicity, and global gene expression on Candida through transcriptomic profiling. The leaf-assisted AgNPs resulted in spherical shapes with a particle size of 38 nm. The anticandidal effect demonstrated that the Minimum inhibitory concentration was 25 μg·mL−1. Later, the cytotoxicity assay reported a moderate impact on the human gingival fibroblast cells. Finally, the transcriptomic analysis demonstrated the differential gene expression of 3,871 upregulated and 3,902 downregulated genes. Thus, proving the anticandidal effect of AgNPs on Candida through RNA-seq experiments and the regulated genes is highly important to cell wall integrity, adherence, and virulence

De Novo Transcriptome of Safflower and the Identification of Putative Genes for Oleosin and the Biosynthesis of Flavonoids

Safflower (Carthamus tinctorius L.) is one of the most extensively used oil crops in the world. However, little is known about how its compounds are synthesized at the genetic level. In this study, Solexa-based deep sequencing on seed, leaf and petal of safflower produced a de novo transcriptome consisting of 153,769 unigenes. We annotated 82,916 of the unigenes with gene annotation and assigned functional terms and specific pathways to a subset of them. Metabolic pathway analysis revealed that 23 unigenes were predicted to be responsible for the biosynthesis of flavonoids and 8 were characterized as seed-specific oleosins. In addition, a large number of differentially expressed unigenes, for example, those annotated as participating in anthocyanin and chalcone synthesis, were predicted to be involved in flavonoid biosynthesis pathways. In conclusion, the de novo transcriptome investigation of the unique transcripts provided candidate gene resources for studying oleosin-coding genes and for investigating genes related to flavonoid biosynthesis and metabolism in safflower

Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

Background: Cucurbita pepo belongs to the Cucurbitaceae family. The "Zucchini" types rank among the highest-valued vegetables worldwide, and other C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins. A broad range of genomic tools are today available for other cucurbits that have become models for the study of different metabolic processes. However, these tools are still lacking in the Cucurbita genus, thus limiting gene discovery and the process of breeding.Results: We report the generation of a total of 512,751 C. pepo EST sequences, using 454 GS FLX Titanium technology. ESTs were obtained from normalized cDNA libraries (root, leaves, and flower tissue) prepared using two varieties with contrasting phenotypes for plant, flowering and fruit traits, representing the two C. pepo subspecies: subsp. pepo cv. Zucchini and subsp. ovifera cv Scallop. De novo assembling was performed to generate a collection of 49,610 Cucurbita unigenes (average length of 626 bp) that represent the first transcriptome of the species. Over 60% of the unigenes were functionally annotated and assigned to one or more Gene Ontology terms. The distributions of Cucurbita unigenes followed similar tendencies than that reported for Arabidopsis or melon, suggesting that the dataset may represent the whole Cucurbita transcriptome. About 34% unigenes were detected to have known orthologs of Arabidopsis or melon, including genes potentially involved in disease resistance, flowering and fruit quality. Furthermore, a set of 1,882 unigenes with SSR motifs and 9,043 high confidence SNPs between Zucchini and Scallop were identified, of which 3,538 SNPs met criteria for use with high throughput genotyping platforms, and 144 could be detected as CAPS. A set of markers were validated, being 80% of them polymorphic in a set of variable C. pepo and C. moschata accessions.Conclusion: We present the first broad survey of gene sequences and allelic variation in C. pepo, where limited prior genomic information existed. The transcriptome provides an invaluable new tool for biological research. The developed molecular markers are the basis for future genetic linkage and quantitative trait loci analysis, and will be essential to speed up the process of breeding new and better adapted squash varieties. © 2011 Blanca et al; licensee BioMed Central Ltd.Blanca Postigo, JM.; Cañizares Sales, J.; Roig Montaner, MC.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Picó Sirvent, MB. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics. 12:104-117. doi:10.1186/1471-2164-12-104S1041171

The Lingering Effects of NAFTA: An Ethnographic Dialectical Analysis of Neoliberalism, Resistance, and Hegemony in Michoacán and Idaho

As neoliberal policies coincided with increased drug trafficking (Gill 2004), the North American Free Trade Agreement’s (NAFTA) lingering effects are present in Mexico three decades later. Research has shown how people opted to join drug cartels amid limited options or left the country in hopes of better economic opportunities (Sanchez et al., 2018). In Michoacán, the Cartel Jalisco Nuevo Generación runs rampant, people live in poverty, and avocado farmers have formed self-defense groups to combat cartels. Meanwhile, the cartel hosts huge parties providing villages with vast amounts of food, luxury entertainment, and money handout rituals bolo (a Mexican tradition involving throwing money for kids). This project explores the evolving realities in Michoacán. It uses my personal and family experiences as a window into the intimate and collective experiences of migration to the United States due to NAFTA along with the lives of those remaining behind. This article’s qualitative methods combine auto-ethnography of my own experience and fieldwork back in Michoacán, including observation and interviews, to understand evolving conditions in Mexico almost three decades after the trade agreement. It utilizes a regionally-rooted Mexican-American neo-Marxist perspective to reconceptualize Marxism. This research seeks to analyze my family\u27s experience in relation to changing realities in Michoacán and the relationship between global political hegemony and neoliberal economic policy

The Lingering Effects of NAFTA: An Ethnographic Dialectical Analysis of Neoliberalism, Resistance, and Hegemony in Michoacán and Idaho

As neoliberal policies coincided with increased drug trafficking (Gill 2004), the North American Free Trade Agreement’s (NAFTA) lingering effects are present in Mexico three decades later. Research has shown how people opted to join drug cartels amid limited options or left the country in hopes of better economic opportunities (Sanchez et al., 2018). In Michoacán, the Cartel Jalisco Nuevo Generación runs rampant, people live in poverty, and avocado farmers have formed self-defense groups to combat cartels. Meanwhile, the cartel hosts huge parties providing villages with vast amounts of food, luxury entertainment, and money handout rituals bolo (a Mexican tradition involving throwing money for kids). This project explores the evolving realities in Michoacan. It uses my personal and family experiences as a window into the intimate and collective experiences of migration to the United States due to NAFTA along with the lives of those remaining behind. This article’s qualitative methods combine auto-ethnography of my own experience and fieldwork back in Michoacán, including observation and interviews, to understand evolving conditions in Mexico almost three decades after the trade agreement. It utilizes a regionally-rooted Mexican-American neo-Marxist perspective to reconceptualize Marxism. This research seeks to analyze my family\u27s experience in relation to changing realities in Michoacan and the relationship with global political hegemony and neoliberal economic policy

Exploration of the replication of the nanovirus Faba bean necrotic yellows virus using a tagged M-Rep protein

Les nanovirus sont des virus de plantes, multipartites, à ADN simple-brin circulaire, qui se répliquent dans le noyau de cellules infectées par le mécanisme de cercle roulant. Ils dépendent de protéines de leur hôte pour la réplication, seule la protéine M-Rep codée par le virus, est requise pour initier la réplication du génome du nanovirus. Dans le but d élucider les interactions moléculaires entre la protéine M-Rep et des protéines de l hôte, nous avons obtenu plusieurs versions de M-Rep du nanovirus Faba bean necrotic yellows virus (FBNYV) étiquetée avec six histidines, afin de permettre sa purification par chromatographie d affinité. La protéine M-Rep étiquetée est capable d initier, dans les tissus végétaux, la réplication de l ADN qui la code et celle d autres ADN du virus. Le réplicon codant pour cette protéine étiquetée se propage dans Vicia faba infectée par le FBNYV. De plus, il est transmis par l insecte vecteur Aphis craccivora à partir de plantes infectées. L interaction in planta entre les protéines M-Rep étiquetée et M-Rep sauvage a été montrée. D autre part, j ai mis en évidence que la protéine M-Rep étiquetée est phosphorylée in vitro par des kinases de la plante. Enfin, l'infection d Arabidopsis thaliana par le FBNYV, en utilisant l'insecte vecteur A. craccivora a été établie. Nous avons démontré que le FBNYV est capable de se multiplier et d induire des symptômes dans certains écotypes d A. thaliana.Nanoviruses, multipartite single-stranded DNA viruses of plants, multiply in the nucleus of infected cells by rolling circle replication. They rely on host proteins for viral DNA replication, only the viral encoded M-Rep protein is required for initiation of replication of their genome. To enable the study of interactions between M-Rep and viral or host factors involved in replication, we designed oligohistidine-tagged M-Rep protein of the nanovirus Faba bean necrotic yellows virus (FBNYV) that allow its affinity purification from plant tissue. The tagged M-Rep protein is able to initiate replication of its cognate and of other FBNYV DNAs in Nicotiana benthamiana leaf discs and plants. The replicon encoding the tagged M-Rep protein multiplies and moves systemically in FBNYV-infected Vicia faba plants. In addition it is transmitted by the insect vector Aphis craccivora from infected plants. Using the tagged M-Rep protein, the in planta interaction between wild-type M-Rep and its tagged counterpart is demonstrated. Furthermore, I present data showing that a recombinant oligohistidine-tagged M-Rep of FBNYV is phosphorylated in vitro by plant kinases. Finally, infection of Arabidopsis thaliana by FBNYV using the insect vector A. craccivora was established. Susceptibility of several A. thaliana ecotypes to FBNYV was studied.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Identification of an ARGONAUTE for Antiviral RNA Silencing in Nicotiana benthamiana1[C][W][OA]

ARGONAUTE proteins (AGOs) are known to be key components of the RNA silencing mechanism in eukaryotes that, among other functions, serves to protect against viral invaders. Higher plants encode at least 10 individual AGOs yet the role played by many in RNA silencing-related antiviral defense is largely unknown, except for reports that AGO1, AGO2, and AGO7 play an antiviral role in Arabidopsis (Arabidopsis thaliana). In the plant virus model host Nicotiana benthamiana, Tomato bushy stunt virus (TBSV) P19 suppressor mutants are very susceptible to RNA silencing. Here, we report that a N. benthamiana AGO (NbAGO) with similarity to Arabidopsis AGO2, is involved in antiviral defense against TBSV. The activity of this NbAGO2 is shown to be directly associated with anti-TBSV RNA silencing, while its inactivation does not influence silencing of transiently expressed transgenes. Thus, the role of NbAGO2 might be primarily for antiviral defense