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Biology subjects

Machado, M. P.

Publications and source records attributed to Machado, M. P..

5 recordsLinked to original sources

SUSTAINED SYSTEMIC AND NEUROINFLAMMATION IN COGNITIVE DYSFUNCTIONAL FEMALE MICE AFTER NON-SEVERE EXPERIMENTAL MALARIA

Plasmodial infection induces systemic inflammation with great potential to contribute to the development of severe illness and lethality. It is known that the hippocampus and cortex both play a pivotal role in memory processes and are affected by the neuroinflammation associated with cerebral malaria that causes long-lasting cognitive and behavioral sequelae. Since these sequelae are also associated with the non-severe form of malaria, it is important to correlate brain morphology, particularly glial cell involvement, and neuroimmune and neuroinflammatory features with memory acquisition and consolidation processes, in this clinical presentation of malaria, the most frequent worldwide. Here, we aimed to investigate cellular and molecular neuroimmune aspects of non-severe experimental malaria-associated cognitive dysfunction. Female C57BL/6 mice were infected with Plasmodium berghei ANKA and treated with chloroquine before any clinical signs of cerebral malaria emerged. No histopathological alteration, in hematoxylin-eosin staining, or axonal damage, in Bielschowskys silver-impregnated brain sections, was observed. However, morphological alterations in GFAP+ and Iba-1+ cells suggest that: i) astrocytes in the hippocampal dentate gyrus and the cornu Ammonis 1 regions and ii) microglia in the cornu Ammonis 1 region are responding to infection. Curiously, the effect persisted only in Iba-1+ cells up to 22 days post-infection. An increase in pro-inflammatory cytokines levels and expression was observed, in both the prefrontal cortex and the hippocampus. Also, serum and spleen cytokine levels were increased at 4 days post-infection. At 22 days post-infection, infected and treated mice showed an increase in serum cytokine levels that had homeostatic levels at 155 days post-infection. This dynamic points to both an immune stimulus persistence and a cytokine autoregulation post-infection. Infected mice exhibited acquisition and consolidation memory deficits in behavioral tests early after treatment (22 days post-infection). In conclusion, in a context of sustained systemic inflammation, mild neuroinflammatory alterations of glial cells may be involved in cognitive sequelae following a single episode of non-severe experimental malaria.

immunology↗

A novel Mannan-specific chimeric antigen receptor M-CAR redirects T cells to interact with Candida spp. hyphae and Rhizopus oryzae spores

Invasive fungal infections (IFIs) are responsible for elevated rates of morbidity and mortality, causing around of 1.5 million deaths annually worldwide. One of the main causative agents of IFIs is Candida albicans, and non-albicans Candida species have emerged as a spreading global public health concernment. Furthermore, COVID-19 has contributed to a boost in the incidence of IFIs, such as mucormycosis, in which Rhizopus oryzae is the most prevalent causative agent. The effector host immune response against IFIs depends on the activity of T cells, which are susceptible to the regulatory effects triggered by fungal virulence factors. The fungal cell wall plays a crucial role as a virulence factor, and its remodeling compromises the development of a specific T-cell response. The redirection of Jurkat T cells to target Candida spp. by recognizing targets expressed on the fungal cell wall can be facilitated using chimeric antigen receptor (CAR) technology. This study generated an M-CAR that contains an scFv with specificity to -1,6 mannose backbone of fungal mannan, and the expression of M-CAR on the surface of modified Jurkat cells triggered a strong activation against Candida albicans (hyphae form), Candida tropicalis (hyphae form), Candida parapsilosis (pseudohyphal form), and Candida glabrata (yeast form). Moreover, M-CAR Jurkat cells recognized Rhizopus oryzae spores, which induced high expression of cell activation markers. Thus, a novel Mannan-specific CAR enabled strong signal transduction in modified Jurkat cells in the presence of Candida spp. or R. oryzae.

bioengineering↗

DEN-IM: Dengue Virus identification from shotgun and targeted metagenomics

Dengue virus (DENV) represents a public health and economic burden in affected countries. The availability of genomic data is key to understand viral evolution and dynamics, supporting improved control strategies. Currently, the use of High Throughput Sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR amplified viral sequences (targeted metagenomics), is the most informative approach to monitor the viral dissemination and genetic diversity.\n\nDespite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper reproducibility and comparison of results.\n\nHere we present DEN-IM, a one-stop, user-friendly, containerised and reproducible workflow for the analysis of DENV sequencing data, both from shotgun and targeted metagenomics approaches. It is able to infer DENV coding sequence (CDS), identify serotype and genotype, and generate a phylogenetic tree. It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement of extensive bioinformatics expertise.\n\nUsing DEN-IM, we successfully analysed two DENV datasets. The first comprised 25 shotgun metagenomic sequencing samples of varying serotype and genotype, including a spiked sample containing the existing four serotypes. The second dataset consisted of 106 targeted metagenomics samples of DENV 3 genotype III where DEN-IM allowed detection of the intra-genotype diversity.\n\nThe DEN-IM workflow, parameters and execution configuration files, and documentation are freely available at https://github.com/B-UMMI/DEN-IM.

bioinformatics↗

Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in Campylobacter coli

Campylobacter jejuni and Campylobacter coli are the most common cause of bacterial gastroenteritis worldwide. Additionally, C. jejuni is the most common bacterial etiological agent in the autoimmune Guillain-Barre syndrome (GBS). Ganglioside mimicry by C. jejuni lipooligosaccharide (LOS) is the triggering factor of the disease. LOS-associated genes involved in the synthesis (neuABC) and transfer of sialic acid (sialyltranferases) are essential in C. jejuni to synthesize ganglioside-like LOS. Therefore these genes have been identified as GBS markers. So far, scarce genetic evidence supports C. coli as a GBS causative agent despite being isolated from GBS patients. Here we show that genes putatively involved in sialic acid transfer are widely distributed in the C. coli population. Evidence found herein suggests that a small group of C. coli strains are very likely to express ganglioside mimics, implying that C. coli can potentially trigger GBS. C. coli also presents a larger repertoire of sialyltransferases than C. jejuni and loss of functions of some those LOS-associated genes has happened during adaptation to agriculture niche. Nevertheless, the activity of these sialyltransferases and their role in shaping C. coli population is yet to be explored.

microbiology↗

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA or as a docker image at https://hub.docker.com/r/ummidock/chewbbaca/.\n\nDATA SUMMARYO_LIAssembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted as Streptococcus agalactiae taxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare (https://figshare.com/s/9cbe1d422805db54cd52), where a file with the original ftp link for each NCBI directory is also available.\nC_LIO_LICode for the chewBBACA suite is available at https://github.com/B-UMMI/chewBBACA while the tutorial example is found at https://github.com/B-UMMI/chewBBACA_tutorial.\nC_LI\n\nI/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. {boxtimes}\n\nIMPACT STATEMENTThe chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability. The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.

bioinformatics↗