Almeida, J. R. | Search bioRxiv

bioRxiv2024

Peroxidasin expression is increased in intratumoural capillaries and in proximal tubular cells adjacent to clear cell renal cell carcinoma.

Peroxidasin (PXDN), is a heme peroxidase with a critical role in the crosslinking of type IV collagen, being essential for basement membrane integrity. In many cancers, PXDN overexpression has been linked with processes associated with poor disease outcomes, namely the impairment of endothelial functions, pathogenesis of vascular diseases, vascular remodelling, apoptosis, and tissue fibrosis. In RCC, almost nothing is so far known. In this work we characterized the expression of PXDN in tumour and non-neoplastic adjacent tissue from clear cell renal cell carcinoma (ccRCC) and renal oncocytoma by immunohistochemistry. Results showed a significant increase of PXDN expression in intratumoural capillaries of ccRCC in comparison with oncocytoma, and an increase in the proximal tubular epithelial cells of non-neoplastic adjacent parenchyma from ccRCC cases, in comparison with the same area from oncocytomas. Overall, our results suggest, for the first time, that PXDN may have a role in tumour angiogenesis that may favour metastases and tumour malignity, being also enrolled in the crosstalk between the tumour and adjacent tissue, that deserves further investigation. HighlightsO_LIPeroxidasin is increased in ccRCC microvasculature comparing to oncocytoma. C_LIO_LIPeroxidasin is increased in proximal tubules of ccRCC kidney adjacent parenchyma. C_LIO_LIIs Peroxidasin a modulator of tumour microenvironment promoting angiogenesis? C_LI

pathology↗

bioRxiv2021

Bacillus sp. RZ2MS9, a tropical PGPR, colonizes maize endophytically and alters the plant's production of volatile organic compounds both independently and when co-inoculated with Azospirillum brasilense Ab-V5

Bacillus spp. are among the most efficient known plant growth-promoting rhizobacteria (PGPR). The PGPR Bacillus sp. strain RZ2MS9 is a multi-trait maize growth promoter previously isolated from guarana plants cultivated in the Amazon rainforest. However, there are several aspects of its interaction with the host that need further investigation. To achieve effective performance of microbial inoculants in crop production, it is necessary to monitor the plants colonization by a PGPR and to assess the potential synergy among beneficial strains. Here, we obtained a stable mutant of RZ2MS9 labelled with green fluorescent protein (RZ2MS9-GFP). We verified that the insertion of the plasmid did not affect either bacterial growth nor its ability to promote maize growth in vitro. Using fluorescent microscopy and qPCR, we demonstrated that RZ2MS9-GFP successfully colonizes maizes roots and leaves endophytically. Subsequently, we evaluated whether RZ2MS9 has a synergistic effect on plant growth promotion when co-inoculated with Azospirillum brasilense Ab-V5, a commercial inoculant for maize. The two strains combined enhanced maizes roots and shoots dry weight by 50.8% and 79.6%, respectively, when compared to the non-inoculated control. In addition, we used co-inoculation experiments in glass chambers to analyze the plants Volatile Organic Compounds (VOCs) production during the maize-RZ2MS9 and maize-RZ2MS9-Ab-V5 interaction. We found that the single and co-inoculation altered maizes VOCs emission profile, with an increase in the production of indoles in the co-inoculation. Collectively, these results increase our knowledge about the interaction between the tropical PGPR Bacillus sp. RZ2MS9 and maize, and provide a new possibility of combined application with the commercial inoculant A. brasilense Ab-V5. ImportanceBacillus sp. RZ2MS9 is a PGPR, previously isolated from guarana plants cultivated in the Brazilian Amazon, which successfully promotes the growth of maize and soybean plants. To improve our knowledge about the interaction between this very promising PGPR and maize, we labelled RZ2MS9 with gfp and monitored its maize colonization. The transformation did not affect either RZ2MS9 growth nor its ability to promote maize growth in vitro. We demonstrated that RZ2MS9 colonizes endophytically maizes roots and leaves. We also verified that the co-inoculation of RZ2MS9 and Azospirillum brasilense Ab-V5, a known commercial maize inoculant enhanced maizes roots and shoots growth. Moreover, the co-inoculation altered the maizes volatile organic compounds, increasing the production of indoles, that is related with decreased upon the reduction of fertilization. Certainly, our research contributed with better Bacillus sp. RZ2MS9 - maize interaction understanding and also provided new information concerning RZ2MS9 activity when applied with A. brasilense Ab-V5.

molecular biology↗

bioRxiv2020

GTO: a toolkit to unify pipelines in genomic and proteomic research

SummaryNext-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics inquiry to students in life sciences. Availability and implementationGTO is implemented in C language and it is available, under the MIT license, at http://bioinformatics.ua.pt/gto. Contactpratas@ua.pt Supplementary informationSupplementary data are available at publishers Web site.

bioinformatics↗