Publications by authors named "Nalvo Franco Almeida"

7 Publications

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Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with : More Is Not Necessarily Better.

J Fungi (Basel) 2020 Nov 24;6(4). Epub 2020 Nov 24.

Laboratory of Molecular Biology of Pathogenic Fungi, Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, DF 70910-900, Brazil.

Most people infected with the fungus spp. do not get sick, but approximately 5% develop paracoccidioidomycosis. Understanding how host immunity determinants influence disease development could lead to novel preventative or therapeutic strategies; hence, we used two mouse strains that are resistant (A/J) or susceptible (B10.A) to to study how dendritic cells (DCs) respond to the infection. RNA sequencing analysis showed that the susceptible strain DCs remodeled their transcriptomes much more intensely than those from the resistant strain, agreeing with a previous model of more intense innate immunity response in the susceptible strain. Contrastingly, these cells also repress genes/processes involved in antigen processing and presentation, such as lysosomal activity and autophagy. After the interaction with , both DCs and macrophages from the susceptible mouse reduced the autophagy marker LC3-II recruitment to the fungal phagosome compared to the resistant strain cells, confirming this pathway's repression. These results suggest that impairment in antigen processing and presentation processes might be partially responsible for the inefficient activation of the adaptive immune response in this model.
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http://dx.doi.org/10.3390/jof6040311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7712260PMC
November 2020

Complete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant.

PLoS One 2020 5;15(11):e0241546. Epub 2020 Nov 5.

Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.

Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0241546PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643998PMC
December 2020

Serratia liquefaciens FG3 isolated from a metallophyte plant sheds light on the evolution and mechanisms of adaptive traits in extreme environments.

Sci Rep 2019 11 29;9(1):18006. Epub 2019 Nov 29.

Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.

Serratia liquefaciens strain FG3 (SlFG3), isolated from the flower of Stachytarpheta glabra in the Brazilian ferruginous fields, has distinctive genomic, adaptive, and biotechnological potential. Herein, using a combination of genomics and molecular approaches, we unlocked the evolution of the adaptive traits acquired by S1FG3, which exhibits the second largest chromosome containing the largest conjugative plasmids described for Serratia. Comparative analysis revealed the presence of 18 genomic islands and 311 unique protein families involved in distinct adaptive features. S1FG3 has a diversified repertoire of genes associated with Nonribosomal peptides (NRPs/PKS), a complete and functional cluster related to cellulose synthesis, and an extensive and functional repertoire of oxidative metabolism genes. In addition, S1FG3 possesses a complete pathway related to protocatecuate and chloroaromatic degradation, and a complete repertoire of genes related to DNA repair and protection that includes mechanisms related to UV light tolerance, redox process resistance, and a laterally acquired capacity to protect DNA using phosphorothioation. These findings summarize that SlFG3 is well-adapted to different biotic and abiotic stress situations imposed by extreme conditions associated with ferruginous fields, unlocking the impact of the lateral gene transfer to adjust the genome for extreme environments, and providing insight into the evolution of prokaryotes.
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http://dx.doi.org/10.1038/s41598-019-54601-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884506PMC
November 2019

Analyses of Seven New Genomes of pv. Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes.

Front Microbiol 2019 11;10:2361. Epub 2019 Oct 11.

Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.

pv. pathotype B (XauB) and pathotype C (XauC) are the causative agents respectively of citrus canker B and C, diseases of citrus plants related to the better-known citrus canker A, caused by pv. . The study of the genomes of strains of these related bacterial species has the potential to bring new understanding to the molecular basis of citrus canker as well as their evolutionary history. Up to now only one genome sequence of XauB and only one genome sequence of XauC have been available, both in draft status. Here we present two new genome sequences of XauB (both complete) and five new genome sequences of XauC (two complete). A phylogenomic analysis of these seven genome sequences along with 24 other related genomes showed that there are two distinct and well-supported major clades, the XauB and XauC clade and the pv. clade. An analysis of 62 Type III Secretion System effector genes showed that there are 42 effectors with variable presence/absence or pseudogene status among the 31 genomes analyzed. A comparative analysis of secretion-system and surface-structure genes showed that the XauB and XauC genomes lack several key genes in pathogenicity-related subsystems. These subsystems, the Types I and IV Secretion Systems, and the Type IV pilus, therefore emerge as important ones in helping explain the aggressiveness of the A type of citrus canker and the apparent dominance in the field of the corresponding strain over the B and C strains.
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http://dx.doi.org/10.3389/fmicb.2019.02361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797930PMC
October 2019

TabPath: interactive tables for metabolic pathway analysis.

Bioinformatics 2018 03;34(6):1040-1042

Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG 35400-000, Brazil.

Motivation: Information about metabolic pathways in a comparative context is one of the most powerful tool to help the understanding of genome-based differences in phenotypes among organisms. Although several platforms exist that provide a wealth of information on metabolic pathways of diverse organisms, the comparison among organisms using metabolic pathways is still a difficult task.

Results: We present TabPath (Tables for Metabolic Pathway), a web-based tool to facilitate comparison of metabolic pathways in genomes based on KEGG. From a selection of pathways and genomes of interest on the menu, TabPath generates user-friendly tables that facilitate analysis of variations in metabolism among the selected organisms.

Availability And Implementation: TabPath is available at http://200.239.132.160:8686.

Contact: [email protected]
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http://dx.doi.org/10.1093/bioinformatics/btx714DOI Listing
March 2018

Draft Genome Sequence of Mycobacterium bovis Strain AN5, Used for Production of Purified Protein Derivative.

Genome Announc 2014 Apr 3;2(2). Epub 2014 Apr 3.

Programa de Pós-Graduação em Ciência Animal, UFMS, Campo Grande, Mato Grosso do Sul, Brazil.

Mycobacterium bovis strain AN5 has been used to produce purified protein derivative (PPD) for the intradermal test for bovine tuberculosis since it was introduced in 1948. This work reports the draft genome sequence of M. bovis AN5, which is used for the production of bovine PPD in Brazil, as well as comparisons to other strains of M. bovis and Mycobacterium tuberculosis.
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http://dx.doi.org/10.1128/genomeA.00277-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974946PMC
April 2014

Draft Genome Sequence of Mycobacterium bovis 04-303, a Highly Virulent Strain from Argentina.

Genome Announc 2013 Nov 27;1(6). Epub 2013 Nov 27.

School of Computing, UFMS, Campo Grande, Mato Grosso do Sul, Brazil.

Mycobacterium bovis strain 04-303 was isolated from a wild boar living in a free-ranging field in Argentina. This work reports the draft genome sequence of this highly virulent strain and the genomic comparison of its major virulence-related genes with those of M. bovis strain AF2122/97 and Mycobacterium tuberculosis strain H37Rv.
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http://dx.doi.org/10.1128/genomeA.00931-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869323PMC
November 2013