Clinical Prognostic Implications of Wnt Hub Genes Expression in Medulloblastoma.

Medulloblastoma is the most common type of pediatric malignant primary brain tumor, and about one-third of patients die due to disease recurrence and most survivors suffer from long-term side effects. MB is clinically, genetically, and epigenetically heterogeneous and subdivided into at least four molecular subgroups: WNT, SHH, Group 3, and Group 4. We evaluated common differentially expressed genes between a Brazilian RNA-seq GSE181293 dataset and microarray GSE85217 dataset cohort of pediatric MB samples using bioinformatics methodology in order to identify hub genes of the molecular subgroups based on PPI network construction, survival and functional analysis. The main finding was the identification of five hub genes from the WNT subgroup that are tumor suppressors, and whose lower expression is related to a worse prognosis for MB patients. Furthermore, the common genes correlated with the five tumor suppressors participate in important pathways and processes for tumor initiation and progression, as well as development and differentiation, and some of them control cell stemness and pluripotency. These genes have not yet been studied within the context of MB, representing new important elements for investigation in the search for therapeutic targets, prognostic markers or for understanding of MB biology.

New PEPTIR-2.0 Peptide Designed for Use as Recognition Element in Electrochemical Biosensors with Improved Specificity towards E. coli O157:H7.

The detection of pathogens through alternative methodologies based on electrochemical biosensors is being studied. These devices exhibit remarkable properties, such as simplicity, specificity, and high sensitivity in monitoring pathogens. However, it is necessary to continue conducting studies that adequately improve these characteristics, especially the recognition molecule. This work aims to design and evaluate a new peptide, named PEPTIR-2.0, as a recognition molecule in electrochemical biosensors to detect E. coli O157:H7 in water. PEPTIR-2.0 was obtained from modifications of the PEPTIR-1.0 peptide sequence, which was previously reported and exhibited excellent properties for detecting and quantifying this pathogenic microorganism. PEPTIR-1.0 is a peptide analogous to the TIR (Translocated Intimin Receptor) protein capable of interacting with the Intimin outer membrane. The basis of this study was to obtain, by using bioinformatics tools, a molecule analogous to PEPTIR-1.0 that maintains its three-dimensional structure but increases the hydrophobic interactions between it and Intimin, since these intermolecular forces are the predominant ones. The designed PEPTIR-2.0 peptide was immobilized on screen-printed electrodes modified with gold nanoparticles. The detection capacity of E. coli O157:H7 in water was evaluated using electrochemical impedance spectroscopy in the presence of other microorganisms, such as P. aeruginosa, S. aureus, and non-pathogenic E. coli. The results showed that PEPTIR-2.0 confers remarkable specificity to the biosensor towards detecting E. coli, even higher than PEPTIR-1.0.

Cloning and biochemical characterization of three glucose­6­phosphate dehydrogenase mutants presents in the Mexican population.

The deficiency of glucose­6­phosphate dehydrogenase (G6PD) is one of the most common inborn errors of metabolism worldwide. This congenital disorder generally results from mutations that are spread throughout the entire gene of G6PD. Three single-point mutations for G6PD have been reported in the Mexican population and named Veracruz (Arg365His), G6PD Seattle (Asp282His), and G6PD Mexico DF (Thr65Ala), whose biochemical characterization have not yet been studied. For this reason, in this work we analyzed the putative role of the three mutations to uncover the functional consequences on G6PD activity. To this end, was developed a method to clone, overexpress, and purify recombinant human G6PD. The results obtained from all variants showed a loss of catalysis by 80 to 97% and had a decrease in affinity for both physiological substrates with respect to the wild type (WT) G6PD. Our results also showed that the three mutations affected three-dimensional structure and protein stability, suggesting an unstable structure with low conformational stability that affected its G6PD functionality. Finally, based on the biochemical characterization of the unclassified G6PD Mexico DF, we suggest that this variant could be grouped as a Class I variant, because biochemical data are similar with other Class I G6PDs.

MELC Genomics: A Framework for De Novo Genome Assembly.

The development of next-generation sequencing platforms increased substantially the capacity of data generation. In addition, in the past years, the costs for whole genome sequencing have been reduced that made it easier to access this technology. As a result, the storage and analysis of the data generated became a challenge, ushering in the development of bioinformatic tools, such as programs and programming languages, able to store, process, and analyze this huge amount of information. In this article, we present MELC genomics, a framework for genome assembly in a simple and fast workflow.

Evaluation of a hypothetical protein for serodiagnosis and as a potential marker for post-treatment serological evaluation of tegumentary leishmaniasis patients.

The serodiagnosis for tegumentary leishmaniasis (TL) presents problems related to the sensitivity and/or specificity of the tests. In the present study, an enzyme-linked immunosorbent assay (ELISA) technique was used to evaluate the performance from a Leishmania braziliensis hypothetical protein, LbHyM, in an attempt to compare its serological reactivity with a soluble Leishmania antigenic preparation (SLA) for the serodiagnosis of cutaneous (CL) and mucosal (ML) leishmaniasis. LbHyM was predicted to be a kinesin-like protein by bioinformatics tools. Serum samples were collected from both CL and ML patients, as well as from those with Chagas disease and from healthy subjects living in endemic or non-endemic areas of TL. Also, sera were collected from patients before and after the treatments, seeking to evaluate their serological follow-up in relation to the anti-protein and anti-parasite antibody levels. When an ELISA-rLbHyM assay was performed, it proved to be significantly more sensitive than ELISA-L. braziliensis SLA in detecting both CL and ML patients. Also, when using sera from Chagas disease patients, the ELISA-rLbHyM proved to be more specific than ELISA-SLA. The anti-protein and anti-parasite antibody levels were also evaluated 6 months after the treatments, and treated patients showed significantly lower levels of specific-rLbHyM antibodies, when compared to the anti-parasite antibody levels. In conclusion, the ELISA-rLbHyM assay can be considered a confirmatory serological technique for the serodiagnosis of L. braziliensis infection and can also be used in the serological follow-up of treated patients, aiming to correlate the low anti-protein antibody levels with the improvement of the healthy state of the patients.

Mapping of microRNAs related to cervical cancer in Latin American human genomic variants.

Background: MicroRNAs are related to human cancers, including cervical cancer (CC) caused by HPV. In 2018, approximately 56.075 cases and 28.252 deaths from this cancer were registered in Latin America and the Caribbean according to GLOBOCAN reports. The main molecular mechanism of HPV in CC is related to integration of viral DNA into the hosts' genome. However, the different variants in the human genome can result in different integration mechanisms, specifically involving microRNAs (miRNAs). Methods: The miRNAs associated with CC were obtained from literature, the miRNA sequences and four human genome variants (HGV) from Latin American populations were obtained from miRBase and 1000 Genomes Browser, respectively. HPV integration sites near cell cycle regulatory genes were identified. miRNAs were mapped on HGV. miRSNPs were identified in the miRNA sequences located at HPV integration sites on the Latin American HGV.  Results: Two hundred seventy-two miRNAs associated with CC were identified in 139 reports from different geographic locations. By mapping with Blast-Like Alignment Tool (BLAT), 2028 binding sites were identified from these miRNAs on the human genome (version GRCh38/hg38); 42 miRNAs were located on unique integration sites; and miR-5095, miR-548c-5p and miR-548d-5p were involved with multiple genes related to the cell cycle. Thirty-seven miRNAs were mapped on the Latin American HGV (PUR, MXL, CLM and PEL), but only miR-11-3p, miR-31-3p, miR-107, miR-133a-3p, miR-133a-5p, miR-133b, miR-215-5p, miR-491-3p, miR-548d-5p and miR-944 were conserved. Conclusions: Ten miRNAs were conserved in the four HGV. In the remaining 27 miRNAs, substitutions, deletions or insertions were observed. These variation patterns can imply differentiated mechanisms towards each genomic variant in human populations because of specific genomic patterns and geographic features. These findings may help in determining susceptibility for CC development. Further identification of cellular genes and signalling pathways involved in CC progression could lead new therapeutic strategies based on miRNAs.

In-silico design and molecular docking evaluation of peptides derivatives from bacteriocins and porcine beta defensin-2 as inhibitors of Hepatitis E virus capsid protein.

Hepatitis E virus (HEV) is considered the main etiological agent that causes acute hepatitis. It is estimated that 20 million cases occur annually worldwide, reaching mortality rates of 28% in pregnant women. To date, available treatments and vaccines have not been entirely effective. In this study, six antiviral peptides derived from the sequences of porcine Beta-Defensin-2 and bacteriocins Nisin and Subtilosin were generate using in silico tools in order to propose new antiviral agents. Through the use of molecular docking, interactions between the HEV capsid protein and the six new antiviral peptide candidates were evaluated. A peptide of 15 residues derived from Subtilosin showed the best docking energy (-7.0 kcal/mol) with the capsid protein. This is the first report to our knowledge involving a non-well study viral protein interacting with peptides susceptibles to being synthesized, and that could be subsequently evaluated in vitro; moreover, this study provide novel information on the nature of the dimerization pocket of the HEV capsid protein, and could help to understand the first steps in the viral replication cycle, needed for the virus entry to the host cell.

Glucose-6-Phosphate Dehydrogenase: Update and Analysis of New Mutations around the World.

Glucose-6-phosphate dehydrogenase (G6PD) is a key regulatory enzyme in the pentose phosphate pathway which produces nicotinamide adenine dinucleotide phosphate (NADPH) to maintain an adequate reducing environment in the cells and is especially important in red blood cells (RBC). Given its central role in the regulation of redox state, it is understandable that mutations in the gene encoding G6PD can cause deficiency of the protein activity leading to clinical manifestations such as neonatal jaundice and acute hemolytic anemia. Recently, an extensive review has been published about variants in the g6pd gene; recognizing 186 mutations. In this work, we review the state of the art in G6PD deficiency, describing 217 mutations in the g6pd gene; we also compile information about 31 new mutations, 16 that were not recognized and 15 more that have recently been reported. In order to get a better picture of the effects of new described mutations in g6pd gene, we locate the point mutations in the solved three-dimensional structure of the human G6PD protein. We found that class I mutations have the most deleterious effects on the structure and stability of the protein.

Strategies to avoid drowning in the deep sequencing data flood

The enormous technological progress in the field of functional genomics during the last 15 years had a significant impact on animal sciences. With the development of Next Generation Sequencing it became feasible to analyze genomes and transcriptomes within short time frames and affordable costs. One major challenge of this rapid development is to manage the data flood and to perform data analysis and integration in an optimal manner. This review provides some information about a typical analysis pipeline for RNASequencing (RNA-Seq) data and a strategy for the analysis of small RNA-Seq data derived from species with poor annotation for non-coding RNA genes. Furthermore, problems regarding gene annotation in livestock species and their possible implications for data analysis and interpretation are discussed. Despite of not yet solved problems and challenges with respect to data analysis and integration the approaches in the field of functional genome analysis opened up new ways to try to understand the complex trait fertility.(AU)

Strategies to avoid drowning in the deep sequencing data flood

The enormous technological progress in the field of functional genomics during the last 15 years had a significant impact on animal sciences. With the development of Next Generation Sequencing it became feasible to analyze genomes and transcriptomes within short time frames and affordable costs. One major challenge of this rapid development is to manage the data flood and to perform data analysis and integration in an optimal manner. This review provides some information about a typical analysis pipeline for RNASequencing (RNA-Seq) data and a strategy for the analysis of small RNA-Seq data derived from species with poor annotation for non-coding RNA genes. Furthermore, problems regarding gene annotation in livestock species and their possible implications for data analysis and interpretation are discussed. Despite of not yet solved problems and challenges with respect to data analysis and integration the approaches in the field of functional genome analysis opened up new ways to try to understand the complex trait fertility.

Comparative modeling of proteins: a method for engaging students' interest in bioinformatics tools.

The huge increase in data being produced in the genomic era has produced a need to incorporate computers into the research process. Sequence generation, its subsequent storage, interpretation, and analysis are now entirely computer-dependent tasks. Universities from all over the world have been challenged to seek a way of encouraging students to incorporate computational and bioinformatics skills since undergraduation in order to understand biological processes. The aim of this article is to report the experience of awakening students' interest in bioinformatics tools during a course focused on comparative modeling of proteins. The authors start by giving a full description of the course environmental context and students' backgrounds. Then they detail each class and present a general overview of the protein modeling protocol. The positive and negative aspects of the course are also reported, and some of the results generated in class and in projects outside the classroom are discussed. In the last section of the article, general perspectives about the course from students' point of view are given. This work can serve as a guide for professors who teach subjects for which bioinformatics tools are useful and for universities that plan to incorporate bioinformatics into the curriculum.