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/
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.
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