When comparing gene expression data of different tissues it is often interesting to identify tissue-specific genes or transcripts. Even though there are several metrics to measure tissue-specificity, a user-friendly tool that facilitates this analysis is not available yet. We present tspex, a software that allows easy computation of a comprehensive set of different tissue-specificity metrics from gene expression data. tspex can be used through a web interface, command-line or the Python API. Its package version also provides visualization functions that facilitate inspection of results. The documentation and the source code of tspex are available at https://apcamargo.github.io/tspex/ and the web application can be accessed at https://tspex.lge.ibi.unicamp.br/

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Campomanesia adamantium is an endemic plant of Cerrado biome that has potential for cultivation because its fruits have culinary and medicinal uses. However, genetic diversity studies using molecular markers with Cerrado species are scarce, and the inadequate extractive exploitation of fruits and the expansion of agricultural frontiers may also affect genetic variability. Therefore, studies in this field are of interest as they can provide sources for conservation and breeding programs. In this context, we investigated the genetic diversity of native populations of C. adamantium from different sites and the relationship between genetic variability and the land use and land cover of each site. A total of 207 plants were sampled in seven sites and characterized with seven polymorphic microsatellite markers. The use and coverage of land were mapped based on aerial images, and the land was classified into different categories. The genetic diversity was high in all populations, with low levels of differentiation due to allele sharing, mainly in Mato Grosso do Sul and Paraguay populations. The geographically closest populations were more genetically similar. The use and coverage of land indicated that intense agriculture promotes a significant decrease in genetic variability.

Antimalarial drugs with novel modes of action and wide therapeutic potential are needed to pave the way for malaria eradication. Violacein is a natural compound known for its biological activity against cancer cells and several pathogens, including the malaria parasite, Plasmodium falciparum (Pf). Herein, using chemical genomic profiling (CGP), we found that violacein affects protein homeostasis. Mechanistically, violacein binds Pf chaperones, Pf Hsp90 and Pf Hsp70-1, compromising the latter’s ATPase and chaperone activities. Additionally, violacein-treated parasites exhibited increased protein unfolding and proteasomal degradation. The uncoupling of the parasite stress response reflects the multistage growth inhibitory effect promoted by violacein. Despite evidence of proteotoxic stress, violacein did not inhibit global protein synthesis via UPR activation—a process that is highly dependent on chaperones, in agreement with the notion of a violacein-induced proteostasis collapse. Our data highlight the importance of a functioning chaperone–proteasome system for parasite development and differentiation. Thus, a violacein-like small molecule might provide a good scaffold for development of a novel probe for examining the molecular chaperone network and/or antiplasmodial drug design.

Premise A novel set of nuclear microsatellite markers was developed and characterized for Campomanesia adamantium (Myrtaceae) and tested for cross‐amplification in the related species C. sessiliflora. Methods and Results Forty‐one primer pairs were designed for simple sequence repeat loci, of which 36 successfully amplified and were polymorphic. The number of alleles ranged from two to 14, with an average of 8.14 alleles per locus. Additionally, cross‐amplification was tested in C. sessiliflora; more than 55.5% of the microsatellite loci amplified, confirming the use of these microsatellite markers in a related species. Conclusions We developed a set of microsatellite markers that will be useful for future studies of genetic diversity and population structure of C. adamantium and a closely related species, which will aid in future conservation efforts.

Our library of double transporter deletion strains is a powerful tool for rapid identification of potential drug import and export routes, which can aid in determining the chemical groups necessary for transport via specific carriers. This information may be translated into a better design of drugs for optimal absorption by target tissues and the development of drugs whose utility is less likely to be compromised by the selection of resistant mutants.

Background Plant pathogenesis related-1 (PR-1) proteins belong to the CAP superfamily and have been characterized as markers of induced defense against pathogens. Moniliophthora perniciosa and Moniliophthora roreri are hemibiotrophic fungi that respectively cause the witches’ broom disease and frosty pod rot in Theobroma cacao. Interestingly, a large number of plant PR-1-like genes are present in the genomes of both species and many are up-regulated during the biotrophic interaction. In this study, we investigated the evolution of PR-1 proteins from 22 genomes of Moniliophthora isolates and 16 other Agaricales species, performing genomic investigation, phylogenetic reconstruction, positive selection search and gene expression analysis. Results Phylogenetic analysis revealed conserved PR-1 genes (PR-1a, b, d, j), shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity in Moniliophthora (PR-1f, g, h, i), as well as in recent specialization cases within M. perniciosa biotypes (PR-1c, k, l) and M. roreri (PR-1n). PR-1 families in Moniliophthora with higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host–pathogen arms race. Furthermore, although previous work showed that MpPR-1 can detoxify plant antifungal compounds in yeast, we found that in the presence of eugenol M. perniciosa differentially expresses only MpPR-1e, k, d, of which two are not linked to pathogenicity, suggesting that detoxification might not be the main function of most MpPR-1. Conclusions Based on analyses of genomic and expression data, we provided evidence that the evolution of PR-1 in Moniliophthora was adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Additionally, we also discuss how fungal PR-1 proteins could have adapted from basal conserved functions to possible roles in fungal pathogenesis.

Schinus terebinthifolia is a species native to different ecoregions in the Brazilian Atlantic Forest. The plant is listed on the National Relation of Medicinal Plants and recommended as phytomedicine, however while extractive exploitation prevails as the main route of raw material a significant variation of compounds will be detected. To assure the expansion of productive chain it is important to start by studying population diversity and chemical variations. We used SSR markers for studies of genetic structure among populations from dense ombrophilous forest (ES); the deciduous seasonal forest (SM); the savanna (DOU) and the sandbanks (ITA and MSP), and compared the results to their chemical profiles of essential oil. Genetic structure revealed differences among populations and significant fixation rates. Pairwise studies and Bayesian analysis showed similarities between ITA and SM and between DOU and MSP, proving that the patterns of distribution for the species do not follow the isolation by distance or similarity by environmental conditions. The comparison between PCA of genotypes and chemodiversity reinforces the unique profile for each population despite the environmental similarity observed and genetic analysis. The most divergent genotype and chemical group was found at the ombrophilous forest, strong evidence that we should undertake conservation efforts to prevent losses of biodiversity in that area.