MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I.

The therapeutic targeting of the immune system, for example in vaccinology and cancer treatment, is a challenging task and the subject of active research. Several in silico tools used for predicting immunogenicity are based on the analysis of peptide sequences binding to the Major Histocompatibility Complex (pMHC). However, few of these bioinformatics tools take into account the pMHC three-dimensional structure. Here, we describe a new bioinformatics tool, MatchTope, developed for predicting peptide similarity, which can trigger cross-reactivity events, by computing and analyzing the electrostatic potentials of pMHC complexes. We validated MatchTope by using previously published data from in vitro assays. We thereby demonstrate the strength of MatchTope for similarity prediction between targets derived from several pathogens as well as for indicating possible cross responses between self and tumor peptides. Our results suggest that MatchTope can enhance and speed up future studies in the fields of vaccinology and cancer immunotherapy.

Searching for ancient balanced polymorphisms shared between Neanderthals and Modern Humans

Abstract Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS). We identified a significant excess of trans-SNPs in IMMS (N=547), of which six of these located within genes previously associated with schizophrenia. No excess of trans-SNPs was found in BEHS, but five genes in this system harbor potential signals for balancing selection and are associated with psychiatric or neurodevelopmental disorders. Our approach evidenced recent Homo trans-SNPs that have been previously implicated in psychiatric diseases such as schizophrenia, suggesting that a genetic repertoire common to the immune and behavioral systems could have been maintained by balancing selection starting before the split between archaic and modern humans.

FOXP in Tetrapoda: Intrinsically Disordered Regions, Short Linear Motifs and their evolutionary significance

Abstract The FOXP subfamily is probably the most extensively characterized subfamily of the forkhead superfamily, playing important roles in development and homeostasis in vertebrates. Intrinsically disorder protein regions (IDRs) are protein segments that exhibit multiple physical interactions and play critical roles in various biological processes, including regulation and signaling. IDRs in proteins may play an important role in the evolvability of genetic systems. In this study, we analyzed 77 orthologous FOXP genes/proteins from Tetrapoda, regarding protein disorder content and evolutionary rate. We also predicted the number and type of short linear motifs (SLIMs) in the IDRs. Similar levels of protein disorder (approximately 70%) were found for FOXP1, FOXP2, and FOXP4. However, for FOXP3, which is shorter in length and has a more specific function, the disordered content was lower (30%). Mammals showed higher protein disorders for FOXP1 and FOXP4 than non-mammals. Specific analyses related to linear motifs in the four genes showed also a clear differentiation between FOXPs in mammals and non-mammals. We predicted for the first time the role of IDRs and SLIMs in the FOXP gene family associated with possible adaptive novelties within Tetrapoda. For instance, we found gain and loss of important phosphorylation sites in the Homo sapiens FOXP2 IDR regions, with possible implication for the evolution of human speech.

Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes.

The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.

New evidence for balancing selection at the HLA-G locus in South Amerindians.

HLA-G is a non-classical HLA (Human Leukocyte Antigen) molecule characterized by limited tissue distribution under normal physiological conditions and low variability at both DNA and protein levels. Several studies suggest that HLA-G could play a role, as an immunoregulatory molecule, in situations as diverse as transplantation, cancer, viral infections and inflammatory diseases. A total of 237 individuals from 21 South American tribes speaking nine different linguistic families were studied in relation to the 14 bp insertion/deletion polymorphism at the HLA-G gene. A consistent (seven in nine) excess of heterozygosity in samples classified by language was obtained. Our data supply evidences for balancing selection acting at the HLA-G 14 bp INDEL region. Enhanced fetal survival in a pathogen-rich environment may account for these findings.

LEI0258 microsatellite variability and its relationship to B-F haplotypes in Brazilian (blue-egg Caipira) chickens

A total of 149 chickens from two different sources (one non-commercial, the other commercial) was tested for variability of the LEI0258 microsatellite. Fifty- three genotypes, explainable by 15 alleles, were found. There are clear allele and heterozygosity differences between the two samples. One of them was simultaneously studied for the MHC B-F haplotypes. Strong genetic disequilibrium was observed between the variants of the two systems, therefore providing a cheap alternative for MHC genotyping.

Pathogenesis-related proteins in Brazilian wheat genotypes: protein induction and partial gene sequencing

Leaves from 14 Brazilian genotypes of Triticum aestivum L. were treated with salicylic acid to induce pathogenesis-related (PR) proteins. Inter and intracellular extracts were then obtained and investigated through polyacrilamide gel electrophoresis. Seven bands were observed. Material related to two of them (of 40 and 24 kDa) occurred in intracellular spaces only. DNA from these same genotypes was then amplified through PCR using primers developed from three sequences encoding PR proteins, and compared with previously described sequences. The fragments presented homologies to PR groups 1, 3 (chitinases), and 5 (thaumatin-like). The PR3-like sequence also showed a site characteristic of PRs induced by ethylene and a portion without homology with previous sequences. No variation among genotypes were observed, either for protein extracts or DNA sequences

Saúde pública no Primeiro e Terceiro Mundos: desafios e perspectivas / Public health in the First and Third Worlds: challenges and perspectives

O direito universal à saúde está bem estabelecido, mas entre declarações de propósitos e a realidade existem abismos difíceis de transpor. O desenvolvimento científico-tecnológico desigual tem acentuado as distâncias entre os padrões de vida, e, portanto, o estado sanitário de populações do Primeiro e Terceiro Mundos. Um dos segmentos mais importantes deste desenvolvimento científico-tecnológico é o que se relaciona à genética e à biologia molecular. Os avanços espetaculares nesta área fazem com que nossas vidas sejam cada vez mais "genetizadas". Procurou-se abordar, aqui, as relações entre essas áreas e a da saúde pública no que se refere a (a) doenças infecciosas; (b) enfermidades mendelianas; (c) aberrações cromossômicas; (d) condições multifatoriais; (e) mutagênese, teratogênese, carcinogênese; e (f) hemoglobinopatias e talassemias. O futuro da saúde pública no país está longe de ser promissor, mas deve-se fazer um esforço para a montagem de programas apropriados neste setor que envolvam inversões apropriadas, tanto na infra-estrutura como na formação de recursos humanos; e tais programas não podem se dar ao luxo de ignorar a genética e a biologia molecular.

Comparative study of lactate dehydrogenase in fifteen genera of New World monkeys

Electrophoretic variation of LDH was investigated in 3,200 specimens belonging to 28 species and 15 genera of New World monkeys. A small sample of (Old World) Cercopithecus aethiops was also tested for comparison. Variation was observed in seven species, five alleles being detected for both LDHA and LDHB loci. The frequency of the variant alleles was low in almost all species, the exceptions being Callithrix kuhli and Callithrix jacchus penicillata, in which the LDHA*5 allele showed frequencies of 47 per cent and 60 per cent, respectively. In the monomorphic patterns the B4 and A4 bands were the same in all fifteen genera, but differences were observed in the B3A1, B2A2 and BlA3 hybrid bands. Furthermore, only the B4 band was shared by humans, Old World and New World monkeys. An important marker was found in the genus Cebus, which clearly distinguishes the "tufted" and "untufted" groups.