Proteogenomics Reveals Orthologous Alternatively Spliced Proteoforms in the Same Human and Mouse Brain Regions with Differential Abundance in an Alzheimer's Disease Mouse Model.

Alternative splicing (AS) may increase the number of proteoforms produced by a gene. Alzheimer's disease (AD) is a neurodegenerative disease with well-characterized AS proteoforms. In this study, we used a proteogenomics strategy to build a customized protein sequence database and identify orthologous AS proteoforms between humans and mice on publicly available shotgun proteomics (MS/MS) data of the corpus callosum (CC) and olfactory bulb (OB). Identical proteotypic peptides of six orthologous AS proteoforms were found in both species: PKM1 (gene PKM/Pkm), STXBP1a (gene STXBP1/Stxbp1), Isoform 3 (gene HNRNPK/Hnrnpk), LCRMP-1 (gene CRMP1/Crmp1), SP3 (gene CADM1/Cadm1), and PKCßII (gene PRKCB/Prkcb). These AS variants were also detected at the transcript level by publicly available RNA-Seq data and experimentally validated by RT-qPCR. Additionally, PKM1 and STXBP1a were detected at higher abundances in a publicly available MS/MS dataset of the AD mouse model APP/PS1 than its wild type. These data corroborate other reports, which suggest that PKM1 and STXBP1a AS proteoforms might play a role in amyloid-like aggregate formation. To the best of our knowledge, this report is the first to describe PKM1 and STXBP1a overexpression in the OB of an AD mouse model. We hope that our strategy may be of use in future human neurodegenerative studies using mouse models.

Bioactive Male-Produced Volatiles from Anastrepha obliqua and their Role in Attraction of Conspecific Females.

The study of insect semiochemicals, especially pheromones, is of fundamental importance for the development of strategies for controlling agricultural pests. In this study, volatile compounds involved in the communication between males and females of the fruit fly, Anastrepha obliqua (Diptera: Tephritidae), for mating purposes were characterized to develop attractant formulations for females of this species. Extracts containing volatile compounds released by males of A. obliqua were obtained by the dynamic headspace technique and analyzed by gas chromatography coupled with an electroantennographic detector (GC-EAD) and gas chromatography coupled with mass spectrometry (GC-MS). Twenty-one volatile compounds were identified in the aeration extracts of males. Five of them caused EAD responses from the antennae of females: 1-heptanol, linalool, (Z)-3-nonen-1-ol, (E,Z)-3,6-nonadien-1-ol, and (Z,E)-α-farnesene. Six synthetic mixtures of these compounds, including the five-component blend and all possible four-component blends, were formulated in a biopolymer and used in behavioral bioassays conducted in the laboratory arena with conspecific virgin females. One blend of 1-heptanol, linalool, (Z)-3-nonen-1-ol, and (Z,E)-α-farnesene attracted more females than the collection of volatiles from virgin males used as control. The other mixtures were as attractive to A. obliqua females as the control treatment. This study indicates potential for use of these compounds in monitoring and control strategies for this pest.

From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics.

Bioinformatics is a fast-evolving research field, requiring effective educational initiatives to bring computational knowledge to Life Sciences. Since 2017, an organizing committee composed of graduate students and postdoctoral researchers from the Universidade Federal de Minas Gerais (Brazil) promotes a week-long event named Summer Course in Bioinformatics (CVBioinfo). This event aims to diffuse bioinformatic principles, news, and methods mainly focused on audiences of undergraduate students. Furthermore, as the advent of the COVID-19 global pandemic has precluded in-person events, we offered the event in online mode, using free video transmission platforms. Herein, we present and discuss the insights obtained from promoting the Online Workshop in Bioinformatics (WOB) organized in November 2020, comparing it to our experience in previous in-person editions of the same event.

The Challenge to Search for New Nervous System Disease Biomarker Candidates: the Opportunity to Use the Proteogenomics Approach.

Alzheimer's disease, Parkinson's disease, prion diseases, schizophrenia, and multiple sclerosis are the most common nervous system diseases, affecting millions of people worldwide. The current scientific literature associates these pathological conditions to abnormal expression levels of certain proteins, which in turn improved the knowledge concerning normal and affected brains. However, there is no available cure or preventive therapy for any of these disorders. Proteogenomics is a recent approach defined as the data integration of both nucleotide high-throughput sequencing and protein mass spectrometry technologies. In the last years, proteogenomics studies in distinct diseases have emerged as a strategy for the identification of uncharacterized proteoforms, which are all the different protein forms derived from a single gene. For many of these diseases, at least one protein used as biomarker presents more than one proteoform, which fosters the analysis of publicly available data focusing proteoforms. Given this context, we describe the most important biomarkers for each neurodegenerative disease and how genomics, transcriptomics, and proteomics separately contributed to unveil them. Finally, we present a selection of proteogenomics studies in which the combination of nucleotide and proteome high-throughput data, from cell lines or brain tissue samples, is used to uncover proteoforms not previously described. We believe that this new approach may improve our knowledge about nervous system diseases and brain function and an opportunity to identify new biomarker candidates.

Sobre as práticas tradicionais de cura: subjetividade e objetivação nas propostas terapêuticas contemporâneas / Sur les pratiques traditionnelles de cure: subjectivité et objectivation dans les propositions thérapeutiques contemporaines / Sobre las prácticas tradicionales de cura: subjetividad y objetivación en las propuestas terapéuticas contemporáneas / On traditional healing practices: subjectivity and objectivation in contemporary therapeutics

O presente trabalho constitui uma pesquisa de cunho teórico, na qual é traçado um breve percurso histórico das práticas de cura tradicionais e se faz também uma discussão sobre sua permanência e eficácia na contemporaneidade, apesar dos avanços na área da ciência médica. Tendo em vista a importância crescente da subjetividade na medicina contemporânea, nossa hipótese visa salientar que a objetivação do sujeito doente, operada pelas práticas médicas, condena a subjetividade a um segundo plano e representa uma lacuna importante nas propostas terapêuticas do modelo biomédico. Nosso objetivo é interrogar o lugar das práticas tradicionais de cura nessa lacuna deixada pela medicina e no que tais práticas podem contribuir para o modelo médico.

Ce travail est une recherche théorique où l’on esquisse un bref parcours historique sur les pratiques traditionnelles de cure et on fait aussi un débat sur leur permanence et efficacité dans le monde contemporain, malgré les avancées dans le domaine de la médecine scientifique. En rendant compte l’importance croissante de la subjectivité dans la médecine contemporaine, notre hypothèse souligne que l’objectivation du sujet malade opérée par les pratiques médicales condamne à l’oubli la subjectivité et produit une lacune importante dans les démarches thérapeutiques du modèle biomédical. Notre objectif en est celui d’interroger la place des pratiques traditionnelles de cure dans cette lacune laissée par la médecine et comment ces pratiques peuvent-elles contribuer avec le modèle médical actuel.

Este trabajo esboza un camino histórico por las prácticas tradicionales de cura y, junto a esto, una discusión sobre la permanencia y la eficacia de estas prácticas en el mundo contemporáneo, a pesar de los progresos de la medicina científica. Considerando la importancia creciente de la subjetividad en la medicina contemporánea, nuestra hipótesis destaca que la objetivación del sujeto enfermo operada por las practicas medicales impone un olvido de la subjetividad y produce un vacío importante en las terapéuticas del modelo biomédico. Nuestra meta es investigar el lugar de las prácticas tradicionales de cura en este vacío de sentido de la medicina y se ellas pueden enseñar algo al modelo médico actual.

This article is a theoretical study featuring a brief historical outline of traditional healing practices and also a discussion on their persistence and efficiency in the contemporary world, despite the advances of scientific medicine. Given the increasing relevance of subjectivity in contemporary medicine, our hypothesis aims to emphasize that the objectivation of patients by medical practices eclipses the role of subjectivity and reveals an important deficit in the therapeutics of the biomedical model. Our aim is to understand the role of traditional healing practices and how they may contribute to the medical model.

Sobre as práticas tradicionais de cura: subjetividade e objetivação nas propostas terapêuticas contemporâneas / Sur les pratiques traditionnelles de cure: subjectivité et objectivation dans les propositions thérapeutiques contemporaines / Sobre las prácticas tradicionales de cura: subjetividad y objetivación en las propuestas terapéuticas contemporáneas / On traditional healing practices: subjectivity and objectivation in contemporary therapeutics

O presente trabalho constitui uma pesquisa de cunho teórico, na qual é traçado um breve percurso histórico das práticas de cura tradicionais e se faz também uma discussão sobre sua permanência e eficácia na contemporaneidade, apesar dos avanços na área da ciência médica. Tendo em vista a importância crescente da subjetividade na medicina contemporânea, nossa hipótese visa salientar que a objetivação do sujeito doente, operada pelas práticas médicas, condena a subjetividade a um segundo plano e representa uma lacuna importante nas propostas terapêuticas do modelo biomédico. Nosso objetivo é interrogar o lugar das práticas tradicionais de cura nessa lacuna deixada pela medicina e no que tais práticas podem contribuir para o modelo médico.

Ce travail est une recherche théorique où l'on esquisse un bref parcours historique sur les pratiques traditionnelles de cure et on fait aussi un débat sur leur permanence et efficacité dans le monde contemporain, malgré les avancées dans le domaine de la médecine scientifique. En rendant compte l'importance croissante de la subjectivité dans la médecine contemporaine, notre hypothèse souligne que l'objectivation du sujet malade opérée par les pratiques médicales condamne à l'oubli la subjectivité et produit une lacune importante dans les démarches thérapeutiques du modèle biomédical. Notre objectif en est celui d'interroger la place des pratiques traditionnelles de cure dans cette lacune laissée par la médecine et comment ces pratiques peuvent-elles contribuer avec le modèle médical actuel.

Este trabajo esboza un camino histórico por las prácticas tradicionales de cura y, junto a esto, una discusión sobre la permanencia y la eficacia de estas prácticas en el mundo contemporáneo, a pesar de los progresos de la medicina científica. Considerando la importancia creciente de la subjetividad en la medicina contemporánea, nuestra hipótesis destaca que la objetivación del sujeto enfermo operada por las practicas medicales impone un olvido de la subjetividad y produce un vacío importante en las terapéuticas del modelo biomédico. Nuestra meta es investigar el lugar de las prácticas tradicionales de cura en este vacío de sentido de la medicina y se ellas pueden enseñar algo al modelo médico actual.

Abstract This article is a theoretical study featuring a brief historical outline of traditional healing practices and also a discussion on their persistence and efficiency in the contemporary world, despite the advances of scientific medicine. Given the increasing relevance of subjectivity in contemporary medicine, our hypothesis aims to emphasize that the objectivation of patients by medical practices eclipses the role of subjectivity and reveals an important deficit in the therapeutics of the biomedical model. Our aim is to understand the role of traditional healing practices and how they may contribute to the medical model.

Unveiling alterative splice diversity from human oligodendrocyte proteome data.

Oligodendrocytes produce and maintain the myelin sheath of axons in the central nervous system. Because misassembled myelin sheaths have been associated with brain disorders such as multiple sclerosis and schizophrenia, recent advances have been made towards the description of the oligodendrocyte proteome. The identification of splice variants represented in the proteome is as important as determining the level of oligodendrocyte-associated proteins. Here, we used an oligodendrocyte proteome dataset deposited in ProteomeXchange to search against a customized protein sequence file containing computationally predicted splice variants. Our approach resulted in the identification of 39 splice variants, including one variant from the GTPase KRAS gene and another from the human glutaminase gene family. We also detected the mRNA expression of five selected splice variants and demonstrated that a fraction of these have their canonical proteins participating in direct protein-protein interactions. In conclusion, we believe our findings contribute to the molecular characterization of oligodendrocytes and may encourage other research groups working with central nervous system disorders to investigate the biological significance of these splice variants. The splice variants identified in this study may encode proteins that could be targeted in novel treatment strategies and diagnostic methods. SIGNIFICANCE: Several disorders of the central nervous system (CNS) are associated with misassembled myelin sheaths, which are produced and maintained by oligodendrocytes (OL). Recently, the OL proteome has been explored to identify key proteins and molecular functions associated with CNS disorders. We developed an innovative approach to select, with a higher level of confidence, a relevant list of splice variants from a proteome dataset and detected the mRNA expression of five selected variants: EEF1D, KRAS, MFF, SDR39U1, and SUGT1. We also described splice variants extracted from OL proteome data. Among the splice variants identified, some are from genes previously linked to CNS and related disorders. Our findings may contribute to oligodendrocyte characterization and encourage other research groups to investigate the biological role of splice variants and to improve current treatments and diagnostic methods for CNS disorders.

Characterisation of the chemical profiles of Brazilian and Andean morphotypes belonging to the Anastrepha fraterculus complex (Diptera, Tephritidae).

Fruit fly sexual behaviour is directly influenced by chemical and non-chemical cues that play important roles in reproductive isolation. The chemical profiles of pheromones and cuticular hydrocarbons (CHs) of eight fruit fly populations of the Andean, Brazilian-1 and Brazilian-3 morphotypes of the Anastrepha fraterculus cryptic species complex originating from Colombia (four populations) and Brazil (four populations) were analysed using two-dimensional gas chromatography with mass spectrometric detection. The resulting chemical diversity data were studied using principal component analyses. Andean morphotypes could be discriminated from the Brazilian-1 and Brazilian-3 morphotypes by means of male-borne pheromones and/or male and female CH profiles. The Brazilian-1 and Brazilian-3 morphotypes were found to be monophyletic. The use of chemical profiles as species- and sex-specific signatures for cryptic species separations is discussed.

Splice variants in the proteome: a promising and challenging field to targeted drug discovery.

The advent and improvement of high-throughput sequencing over the past decade leveraged the study of whole genomes and transcriptomes of different organisms at lower costs. In transcriptomics, RNA-Seq expands our capacity to understand gene expression in different tissues and pathologies, and how alternative splicing might affect the final protein sequence. Here, we discuss the association of using transcriptome and proteome high-throughput data to foster drug discovery. Using this innovative strategy, some research groups have already identified computationally predicted novel peptides derived from putative splice variants in experimental human proteome data. These discoveries provide new opportunities for targeted drug development.

SpliceProt: a protein sequence repository of predicted human splice variants.

The mechanism of alternative splicing in the transcriptome may increase the proteome diversity in eukaryotes. In proteomics, several studies aim to use protein sequence repositories to annotate MS experiments or to detect differentially expressed proteins. However, the available protein sequence repositories are not designed to fully detect protein isoforms derived from mRNA splice variants. To foster knowledge for the field, here we introduce SpliceProt, a new protein sequence repository of transcriptome experimental data used to investigate for putative splice variants in human proteomes. Current version of SpliceProt contains 159 719 non-redundant putative polypeptide sequences. The assessment of the potential of SpliceProt in detecting new protein isoforms resulting from alternative splicing was performed by using publicly available proteomics data. We detected 173 peptides hypothetically derived from splice variants, which 54 of them are not present in UniprotKB/TrEMBL sequence repository. In comparison to other protein sequence repositories, SpliceProt contains a greater number of unique peptides and is able to detect more splice variants. Therefore, SpliceProt provides a solution for the annotation of proteomics experiments regarding splice isofoms. The repository files containing the translated sequences of the predicted splice variants and a visualization tool are freely available at http://lbbc.inca.gov.br/spliceprot.

Identical sequence patterns in the ends of exons and introns of human protein-coding genes.

Intron splicing is one of the most important steps involved in the maturation process of a pre-mRNA. Although the sequence profiles around the splice sites have been studied extensively, the levels of sequence identity between the exonic sequences preceding the donor sites and the intronic sequences preceding the acceptor sites has not been examined as thoroughly. In this study we investigated identity patterns between the last 15 nucleotides of the exonic sequence preceding the 5' splice site and the intronic sequence preceding the 3' splice site in a set of human protein-coding genes that do not exhibit intron retention. We found that almost 60% of consecutive exons and introns in human protein-coding genes share at least two identical nucleotides at their 3' ends and, on average, the sequence identity length is 2.47 nucleotides. Based on our findings we conclude that the 3' ends of exons and introns tend to have longer identical sequences within a gene than when being taken from different genes. Our results hold even if the pairs are non-consecutive in the transcription order.