Papers by Marcelo Brígido
BMC Research Notes, 2017
Background: Anti-CD3 therapy can induce immunosuppression by several non mutually exclusive mecha... more Background: Anti-CD3 therapy can induce immunosuppression by several non mutually exclusive mechanisms that have been proposed to explain the therapeutic effect the administration anti-CD3 mAb, but its immunoregulatory mechanism is still not completely clear. In T cells, microRNAs (miRNAs) regulate several pathways, including those associated with immune tolerance. Here, we report changes in miRNA expression in T cells following treatment with anti-human CD3 antibodies. Peripheral blood mononuclear cells were cultured in the presence of the monoclonal antibody OKT3 or a recombinant fragment of humanized anti-CD3. Following these treatments, the expression profiles of 31 miRNA species were assessed in T cells using TaqMan arrays. Results: Eight of the tested miRNAs (miR-155, miR-21, miR-146a, miR-210, miR-17, miR-590-5p, miR-106b and miR-301a) were statistically significantly up-or down-regulated relative to untreated cells. Conclusions: Stimulation of T cells with anti-human CD3 antibodies alters miRNA expression patterns, including of miRNA species associated with immune regulatory pathways.
BMC bioinformatics, Jan 16, 2018
In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes ... more In phylogenetic reconstruction the result is a tree where all taxa are leaves and internal nodes are hypothetical ancestors. In a live phylogeny, both ancestral and living taxa may coexist, leading to a tree where internal nodes may be living taxa. The well-known Neighbor-Joining heuristic is largely used for phylogenetic reconstruction. We present Live Neighbor-Joining, a heuristic for building a live phylogeny. We have investigated Live Neighbor-Joining on datasets of viral genomes, a plausible scenario for its application, which allowed the construction of alternative hypothesis for the relationships among virus that embrace both ancestral and descending taxa. We also applied Live Neighbor-Joining on a set of bacterial genomes and to sets of images and texts. Non-biological data may be better explored visually when their relationship in terms of content similarity is represented by means of a phylogeny. Our experiments have shown interesting alternative phylogenetic hypothesis fo...
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2007
ABSTRACT Rare minnow (Gobiocypris rarus) is a newly developed aquatic test organism that has been... more ABSTRACT Rare minnow (Gobiocypris rarus) is a newly developed aquatic test organism that has been widely used in a range of studies of toxicological risk assessment by virtue of its higher sensitivity to xenobiotics. To describe extensively the transcripts expressed in the livers of adult rare minnow, we generated 6919 high-quality expressed sequence tags (ESTs) from a non-normalized cDNA library. After processing, a total of 1773 unigenes (unique genes) comprising 771 contigs (consensus sequences) and 1002 singlets were acquired. Based on the analysis by BLAST, 1512 unigenes (85%) had been identified and annotated. The result of functional classification reveals that the genes involved in the processes of general metabolism prevail in liver expressed genes. In addition, we compiled a potentially toxicology-related catalog comprising 262 unigenes that associated with metabolism of xenobiotics and adaptive responses. There are eleven groups referring to diverse functions in the catalog. This report provides the first set of genetic data for rare minnow which is of great value for further exploitation of this species in functional genomics and toxicogenomics, and sets a basis for the discovery of new molecular markers of exposure and for the production of the function-focused microarray.
Brazilian Journal of Oral Sciences, 2010
Aim: This study was developed to compare the morphological, proliferative and immunophenotypic pr... more Aim: This study was developed to compare the morphological, proliferative and immunophenotypic profiles of pulp cells from permanent and primary teeth, obtained by two isolation methods. Methods: Normal human impacted third molars and exfoliated primary teeth were collected and cut around the cementoenamel junction. Pulp cells cultures were established by two approaches: enzyme digestion (3 mg/mL type I colagenase and 4 mg/mL dispase), or culture of the tissue explants in cell culture dishes. Morphological and proliferative analyses, as well as immunophenotype characterization with monoclonal antibodies against CD117, CD34 and CD45 surface receptors were performed. Results: For the permanent teeth, on the 4th day of culture, the cell number was significantly higher for the outgrowth method. By the end of the studied period (14th day), the enzymatic method was more efficient in promoting culture growth. On the other hand, for primary teeth, enzymatic digestion always promoted a highe...
Journal of immunology (Baltimore, Md. : 1950), Jan 15, 1991
The cDNA for H and L chain V regions of two anti-Z-DNA mAb, Z22 and Z44, were cloned and sequence... more The cDNA for H and L chain V regions of two anti-Z-DNA mAb, Z22 and Z44, were cloned and sequenced. These are the first experimentally induced anti-nucleic acid antibody sequences available for comparison with autoantibody sequences. Z22 and Z44 are IgG2b and IgG2a antibodies from C57BL/6 mice. They recognize different facets of the Z-DNA structure. They both use VH10 family genes and share 95% sequence base sequence identity in the VH and leader sequences; however, they differ in the 5'-untranslated region of the VH mRNA, indicating they arise from different germline genes. Both use JH4 segments. They differ from each other very extensively in the CDR3 of both H and L chains. The most closely related H chains in the current GenBank/EMBL data base are two mouse IgG anti-DNA autoantibodies, one from an MRL-lpr/lpr mouse (MRL-DNA4) and one from an NZB/NZW mouse (BV04-01). Z22 and Z44 share 95% sequence identity with these antibodies in the VH segment. In addition, Z22 is identical...
Lecture Notes in Computer Science, 2012
Z-DNA is an alternative conformation of the DNA molecule implied in regulation of gene expression... more Z-DNA is an alternative conformation of the DNA molecule implied in regulation of gene expression. However, the exact role of this structure in cell metabolism is not yet fully understood. Here we present a novel Z-DNA analysis workflow using the R software environment which aims to investigate Z-DNA forming regions (ZDRs) throughout the genome. It combines thermodynamic analysis of the well-known software Z-Catcher with biological data manipulation capabilities of several Bioconductor packages. We employed our methodology in the human chromosome 14 as a case study. With that, we established a correlation of ZDRs with transcription start sites (TSSs) which is in agreement with previous reports. In addition, our workflow was able to show that ZDRs which are positioned inside genes tend to occur in intronic sequences rather than exonic and that ZDRs upstream to TSSs may have a positive correlation with the up-regulation of RNA polymerase activity.
Cell Technology for Cell Products
In this work the closest human germline sequence was used as the framework on to which to graft m... more In this work the closest human germline sequence was used as the framework on to which to graft murine CDRs. The proposed fully humanized version displays the same staining pattern to different cell subpopulations like CD4, CD8 and memory CD45RO lymphocytes, ...
International Journal of Molecular Sciences, 2012
Since the advent of phage display technology, dating back to 1985, antibody libraries displayed o... more Since the advent of phage display technology, dating back to 1985, antibody libraries displayed on filamentous phage surfaces have been used to identify specific binders for many different purposes, including the recognition of tumors. Phage display represents a high-throughput technique for screening billions of random fusion antibodies against virtually any target on the surface or inside cancer cells, or even soluble markers found in patient serum. Many phage display derived binders targeting important tumor markers have been identified. Selection directed to tumoral cells' surfaces lead to the identification of unknown tumoral markers. Also the improvement of methods that require smaller amounts of cells has opened the possibility to use this approach on patient samples. Robust techniques combining an antibody library displayed on the phage surface and protein microarray allowed the identification of auto antibodies recognized by patient sera. Many Ab molecules directly or indirectly targeting angiogenesis have been identified, and one of them, ramucirumab, has been tested in 27 phase I-III clinical trials in a broad array of cancers. Examples of such antibodies will be discussed here with emphasis on those used as probes for molecular imaging and other clinical trials.
Lecture Notes in Computer Science, 2011
We present a simple method to obtain groups of homologous genes across multiple (k) organisms, ca... more We present a simple method to obtain groups of homologous genes across multiple (k) organisms, called kGC. It takes all-againstall BLASTP comparisons as input and produces groups of homologous sequences as output. The algorithm is based on the identification of maximal cliques in graphs of sequences and paralogous groups. We have used our method on six Actinobacterial complete genomes and investigated the Pfam classification of the homologous groups with respect to the results produced by OrthoMCL. Although kGC is simpler, it presented similar results with respect to Pfam classification in reasonable time.
Infection, Genetics and Evolution, 2009
In 2004, an outbreak of HCPS in Brazil made hantaviruses a national threat to the rural and urban... more In 2004, an outbreak of HCPS in Brazil made hantaviruses a national threat to the rural and urban population. During this outbreak, 164 cases were reported, and 18.3% of them occurred in the Federal District. In this study, hantavirus genomic sequences were amplified from seven patients who resided in Central Brazil and then sequenced and compared to other hantavirus sequences. The complete S segment sequence, which is 1847 bases long and potentially encodes the 428 amino acid nucleocapsid protein, was determined for one patient. Moreover, a 700 base-pair sequence of the S segment was obtained from two other patients, and we analyzed M segment sequences from all samples. It can be inferred by both identity and phylogenetic analysis that the sequences obtained are highly related to Araraquara variant and Maciel virus. Phylogenetic results show that hantaviruses isolated in Central Brazil can be divided into two monophyletic groups: one group that clusters with Araraquara variant and the other group that includes the complete S segment sequence obtained in this study. Therefore, we propose the name Paranoa for this variant that co-exists with the Araraquara-like hantavirus in Central Brazil.
Immunology Letters, 1990
Present-day methods for the definition of antibody binding sites on antigenic polypeptides show a... more Present-day methods for the definition of antibody binding sites on antigenic polypeptides show a strong bias toward identification of sequential epitopes. We have employed anti-sequence monoclonal antibodies raised against short synthetic peptides to screen a random-primed cDNA library constructed in an expression vector. Sequence data analysis performed on three clones thus isolated showed that the clones did not cross-hybridize and that the antigenic peptide sequence was found in none of them. Our findings suggest therefore that sequential epitopes may be preferentially identified because of an inherent bias in commonly used epitope mapping protocols which masks available conformational determinants.
... Márcio R Cruz/++, Daniela M Cerqueira, Waldenor B Cruz, Geni NL Camara*, Marcelo M Brígido, E... more ... Márcio R Cruz/++, Daniela M Cerqueira, Waldenor B Cruz, Geni NL Camara*, Marcelo M Brígido, Evandro O Silva**, Luciano GS Carvalho***, Cláudia RF Martins/+ ... Camara GNL,Cerqueira DM, Oliveira AP, Silva EO, Carvalho LGS, Martins CRF 2003. ...
Biotechnology Letters, 2012
The expression enhancement by cytomegalovirus promoter and different intron A (IA) variants were ... more The expression enhancement by cytomegalovirus promoter and different intron A (IA) variants were evaluated in CHO-K1, HepG2, HEK-293 and COS-7 cells by assessing the levels of luciferase activity. This data along with mRNA levels measurement indicated that the construct harboring an IA variant with a 200-nucleotide deletion (D200) had the greatest impact on increasing luciferase expression among all constructs evaluated. Based on these results, we redesigned pCMV-IA variants and cloned them into plasmids expressing a humanized antibody. These plasmids were then used to transfect CHO-K1 cells. Production of the antibody was not augmented with the D200 promoter variant. The 600-nucleotide deletion (D600) and whole IA promoter variants expressed similar levels of the recombinant protein. These data indicate that the IA-based enhanced expression of transgenes depends on a small region within the intron.
Journal of Bioinformatics and Computational Biology, 2015
Noncoding RNAs (ncRNAs) have been focus of intense research over the last few years. Since charac... more Noncoding RNAs (ncRNAs) have been focus of intense research over the last few years. Since characteristics and signals of ncRNAs are not entirely known, researchers use different computational tools together with their biological knowledge to predict putative ncRNAs. In this context, this work presents ncRNA-Agents, a multi-agent system to annotate ncRNAs based on the output of different tools, using inference rules to simulate biologists’ reasoning. Experiments with data from the fungus Saccharomyces cerevisiae allowed to measure the performance of ncRNA-Agents, with better sensibility, when compared to Infernal, a widely used tool for annotating ncRNA. Besides, data of the Schizosaccharomyces pombe and Paracoccidioides brasiliensis fungi identified novel putative ncRNAs, which demonstrated the usefulness of our approach. NcRNA-Agents can be be found at: http://www.biomol.unb.br/ncrna-agents .
Plos One, 2013
B-cell maturation occurs in several steps and requires constant stimulus for its continuing devel... more B-cell maturation occurs in several steps and requires constant stimulus for its continuing development. From the emergence of the pre-B-cell receptor, signal transduction stimulates and supports B-cell development. Current viewpoints indicate that both positive selection pressure for autoantigens and tonic signaling constitutively stimulate B-cell maturation. In this work, we tested for the presence of a putative DNA binding site in a variable gene segment in a germline configuration, independently of VDJ recombination. After a survey of the public antibody databases, we chose a single mouse heavy variable gene segment that is highly represented in anti-nucleic acid antibodies and tested it for ssDNA binding. A phage display approach was used to search for intrinsic binding to oligo deoxythymidine. The results revealed that binding to an antigen can be influenced by the use of a specific DNA binding V H gene segment. Our data support the idea that some variable genes have intrinsic reactivity towards specific types of endogenous autoantigens, and this property may contribute to the establishment of the immature B-cell repertoire.
Genome announcements, Jan 9, 2014
A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had it... more A Bacillus cereus strain, FT9, isolated from a hot spring in the midwest region of Brazil, had its entire genome sequenced.
Transgenic Research, 2010
The seed-based production of recombinant proteins is an efficient strategy to achieve the accumul... more The seed-based production of recombinant proteins is an efficient strategy to achieve the accumulation, correct folding, and increased stability of these recombinant proteins. Among potential plant molecular farming systems, soybean [Glycine max (L.) Merrill] is a viable option for the production of recombinant proteins due to its high protein content, known regulatory sequences, efficient gene transfer protocols, and a scalable production system under greenhouse conditions. We report here the expression and stable accumulation of human coagulation factor IX (hFIX) in transgenic soybean seeds. A biolistic process was utilised to co-introduce a plasmid carrying the hFIX gene under the transcriptional control of the a 0 subunit of a b-conglycinin seed-specific promoter and an a-Coixin signal peptide in soybean embryonic axes from mature seeds. The 56-kDa hFIX protein was expressed in the transgenic seeds at levels of up to 0.23% (0.8 g kg-1 seed) of the total soluble seed protein as determined by an enzyme-linked immunosorbent assay (ELISA) and western blot. Ultrastructural immunocytochemistry assays indicated that the recombinant hFIX in seed cotyledonary cells was efficiently directed to protein storage vacuoles. Mass spectrometry characterisation confirmed the presence of the hFIX recombinant protein sequence. Protein extracts from transgenic seeds showed a blood-clotting activity of up to 1.4% of normal plasma. Our results demonstrate the correct processing and stable accumulation of functional hFIX in soybean seeds stored for 6 years under room temperature conditions (22 ± 2°C).
Protein Engineering Design and Selection, 2000
The 6.7 murine monoclonal antibody (mAb) recognizes the human CD18 antigen and is therefore of in... more The 6.7 murine monoclonal antibody (mAb) recognizes the human CD18 antigen and is therefore of interest as an anti-inflammatory agent. The 6.7 heavy variable chain (VH) was humanized using the closest human germline sequence as the template on to which to graft the murine complementary determining regions (CDRs). Two versions were proposed, one in which the residue proline 45 of the murine form was maintained and another in which this framework residue was changed to the leucine found in the human sequence. These VH humanized versions were expressed in the yeast Pichia pastoris as hemi-humanized single-chain Fv (scFvs), with the VL from the murine antibody. The scFv from the murine antibody was also expressed. The binding activities of the murine and both hemi-humanized scFvs were determined by flow cytometry analysis. All the constructions were able to recognize human lymphocytes harboring CD18, indicating successful humanization with transfer of the original binding capability. Some differences between the two hemi-humanized versions were observed. The method used was simple and straightforward, with no need for refined structural analyses and could be used for the humanization of other antibodies.
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Papers by Marcelo Brígido