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Whole exome sequencing from individuals with intellectual disability and (or) multiple congenital abnormalities with regions of homozygosity previously detected by chromosomal microarray analysis
No full textOrientador: Társis Antônio Paiva VieiraDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências MédicasResumo:Técnicas advindas do sequenciamento do genoma humano, tal qual a Análise Cromossômica por Microarray (Chromosomal Microarray Analysis – CMA), melhoraram o diagnóstico de indivíduos com atraso no desenvolvimento neuropsicomotor (ADNMP), deficiência intelectual (DI) e (ou) malformações congênitas. A CMA, quando inclui oligonucleotídeos com polimorfismos de nucleotídeo único (SNP), permite a detecção tanto de variações no número de cópias, quanto o aumento de regiões de homozigose no genoma (Regions of Homozigosity - ROH). As ROH ocorrem em decorrência de dois eventos principais: identidade por descendência e a dissomia uniparental (UPD). Porém, quando detectadas por CMA, é necessária a análise complementar para a identificação de UPD ou variantes de sequência em genes de herança recessiva. Assim, o objetivo deste trabalho foi investigar a causa da deficiência intelectual e (ou) anomalias congênitas múltiplas, em indivíduos nos quais se identificou aumento de ROH no genoma autossômico pela CMA. Chamadas de homozigose de 265 pacientes e 289 controles testados por CMA foram analisados utilizando o programa Chromosome Analysis Suite - ChAS (Affymetrix®) (hg19) com filtros de no mínimo 500 marcadores e 1.500kb. Detectou-se uma única ROH maior ou igual a 10Mb em 1,9% dos pacientes e 0,3% no grupo controle. Além disso, ROH >1% no genoma autossômico foram detectadas em 7,2% dos pacientes e 1,4% no grupo controle. Foi realizado o sequenciamento do exoma de sete indivíduos com porcentagem de ROH aumentada no genoma. Foram detectadas sete variantes de sequência em cinco indivíduos, e cincos dessas apresentam compatibilidade com os fenótipos dos indivíduos. Entre essas, quatro são variantes novas. Com isso, reforçamos a importância da análise e do relato das regiões de homozigose em resultados de CMA, além de demonstrarmos que as análises complementares por meio do sequenciamento do exoma são altamente eficazes para o esclarecimento de fenótipos heterogêneos de causa não esclarecida.Abstract: The sequencing of the human genome has brought new technologies, such as Chromosomal Microarray Analysis (CMA), which has improved the diagnosis of neurodevelopmental delay (NDD), intellectual disability (ID) and multiple congenital malformations. The CMA, when includes oligonucleotides with single nucleotide polymorphism (SNP), allows the detection of both copy number variations and regions of homozygosity (ROH) in the genome. These regions can occur due to two main events: identity by descent, mainly when there is parental consanguinity, and uniparental disomy (UPD). However, the detection of these regions by CMA, demand further analysis for UPD characterization or detection of sequence variants in genes of recessive inheritance. Thus, the aim of this study was to investigate the etiology in individuals with intellectual disabilities and (or) multiple congenital anomalies, in which increased ROH was identified in the autosomal genome by CMA. Homozygosity calls from 265 patients and 289 controls tested with CMA were analyzed using the Chromosome Analysis Suite - ChAS (Affymetrix®) (hg19) with filters set as a minimum of 500 markers and 1,500kb. Single ROH greater than or equal to 10Mb were detected in 1.9% of patients, compared with 0.3% of the control group. In addition, ROH achieving >1% of the autosomal genome were detected in 7.2% of patients, compared with 1.4% of the control group. The Whole exome sequencing (WES) was performed for seven individuals with increased percentage of ROH in the genome. Seven sequence variants were detected by WES, in five patients, and five of these variants were compatible with the patients' phenotypes. Among then, four were novel variants. Thus, we reinforce the importance of analyzing and reporting homozygous regions in CMA results, besides demonstrating that complementary analyzes by WES are highly effective in clarifying heterogeneous phenotypes of unclear etiology.MestradoGenética MédicaMestra em Ciências132494/2019-12018/08890-9CNPQFAPES
Follow-up in researchformation: experiences of collective orientation and narrative writing (self) biographic
No full textO presente texto partilha caminhos trilhados com a abordagem narrativa (auto)biográfica, destacando reflexões sobre acompanhamento, vivido por meio da orientação coletiva e da escrita, enquanto dispositivos de viver narrativa e coletivamente a pesquisa e a formação. Tomando o conceito de “acompanhamento em histórias de vida” como caminho de pesquisa que se faz com muitos outros, constituímos um processo de orientação (com)partilhada que envolve estudantes-professoras/es-pesquisadoras/es de cursos de graduação e pós-graduação. Os movimentos coletivos incluem estudo de referenciais teórico-metodológicos, leitura crítico-reflexiva dos textos produzidos pelas pesquisas em andamento e escritos narrativos que se fazem ao longo de todo movi-mento. A experiência que temos vivido nos mobiliza a refletir sobre o potencial dos encontros de orientações coletivas na tessitura da pesquisa narrativa (auto)biográfica, bem como busca compreender os movimentos da escrita narrativa na construção da pesquisa em educação. A abordagem “epistemopolítica” dialoga com au-tores do referido campo, contando ainda com as contribuições de Walter Benjamin, Paul Ricoeur e Bakhtin. A experiência partilhada indica que as orientações coletivas fortalecem e impulsionam a escrita narrativa, gerando aprendizagens na construção do conhecimento científico, possibilitando, ainda, (trans)formações na vida dos sujeitos que participam dos processos formativos mediados pelos encontros, potencializando, assim, a tessitura da “pesquisaformação” narrativa (auto)biográfica em educação e a construção de outras tantas possibilidades de experiências formadoras13Narrativas, docencia universitaria e investigación educativa326343The present text shares paths taken with the (auto) biographical narrative approach, highlighting reflections on accompaniment lived through collective guidance and writing, as devices to live the narrative and collectively research and teachers’ meeting. Taking the concept of “accompaniment in life history” as a research path that is done with many others, we constitute a process of (co) shared orientation that involves students-teachers / researchers of undergraduate and graduate courses. The collective movements include the study of theoretical and methodological references, critical-reflexive reading of texts produced by ongoing research and narrative wri-tings that take place throughout the entire movement. The experience that we have lived mobilizes us to reflect on the potential of collective guidance meetings in the context of (auto) biographical narrative research, as well as the search to understand the movements of narrative writing in the construction of educational research. The “epistemopolitical” approach dialogues with authors in the field, with contributions from Walter Benjamin, Paul Ricoeur and Bakhtin. The shared experience indicates that the collective orientations strengthen and stimulate narrative writing, generating learning in the construction of scientific knowledge, also enabling “(trans)forma-tion” in the lives of individuals who participate in the formative processes mediated by the meetings, thus en-hancing the fabric research narrative (auto) biographical formation in education and the construction of so many possibilities for formative experience
Circulating levels of the angiogenesis mediators endoglin, HB-EGF, BMP-9 and FGF-2 in patients with severe sepsis and septic shock
No full textEndothelial barrier dysfunction is a hallmark of sepsis, and is at least partially mediated by pathways that regulate endothelial barrier assembly during angiogenesis. Not surprisingly, increased levels of key angiogenic proteins such as VEGF-A and Angiopoietin-2 have been described in sepsis. The purpose of this study was to investigate if additional pathways that regulate endothelial barrier integrity during angiogenesis could also be involved in the host response of sepsis. We evaluated circulating levels of four proteins involved in angiogenesis, not previously studied in sepsis, in a cohort of 50 patients with severe sepsis and septic shock. Circulating levels of BMP-9 and FGF-2 were similar in patients and healthy volunteers. In contrast, patients with septic shock presented 1.5-fold higher levels of endoglin (P=0.004), and 2-fold lower levels of Heparin-Binding EGF-like growth factor (HB-EGF) (P=0.002) when compared to healthy individuals. Of note, HB-EGF deficiency has been recently demonstrated to be detrimental to survival in a murine model of sepsis. Endoglin and HB-EGF could be involved in the host response of sepsis. Additional studies are warrant to investigate their role as biomarker or therapeutic targets in sepsis42162167CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP2013/09319-0sem informaçã
Miconia renatogoldenbergii (miconieae, melastomataceae), a new species from savanna enclaves in southern Amazonia, Brazil
No full textA new species of Miconia section Miconia, subsection Seriatiflorae from the Brazilian Amazonian region is described. Miconia renatogoldenbergii has a wide distribution in areas of savanna and forest understory in the states of Pará, Mato Grosso and Rondônia. It is similar to M. punctata as both species have chartaceous leaves with rusty lepidote indument on the abaxial surface. The new species can be distinguished by its mucronate leaf apex, a thyrse with short scorpioid branches, and subulate anthers, with round apex, dehiscent through an apical pore and with cordate connective appendages298218719
Improving organ salvage in testicular torsion: comparative study of patients undergoing vs not undergoing preoperative manual detorsion
No full textPurpose: We compared surgical outcomes between patients undergoing and those not undergoing preoperative manual detorsion for intravaginal testicular torsion.
Materials and Methods: We retrospectively analyzed consecutive patients treated surgically for testicular torsion who were examined within 24 hours of symptoms at our emergency department between January 2012 and September 2015. Explanatory variables were age, presentation delay (time between symptoms and urological examination), surgical wait time (time from examination to surgery), and whether manual detorsion was attempted and, if attempted, was declared successful. End points were surgical outcome (orchiopexy, orchiectomy) and testicular rotation at surgery. Statistical analysis included nonparametric tests and logistic regression. Statistical significance and confidence intervals were set at p < 0.05 and 0.95, respectively.
Results: Detorsion was attempted in 76 of 133 cases (57.1%) and was successful in 72 (95.1%). Patient age (median 15.6 vs 17.4 years, p = 0.115), presentation delay (6.6 vs 6.3 hours, p = 1.0) and surgical wait time (3.5 vs 3.2 hours, p = 0.412) were comparable between patients who underwent manual detorsion attempt and those who did not. Testicular rotation was less among successfully detorsed patients. Orchiectomy was performed in 2 of 72 successfully detorsed patients (2.8%), compared to 15 of 61 patients (24.6%) in whom detorsion was not attempted or was unsuccessful (OR 11.23, p = 0.0002). Logistic regression indicated that surgical wait time (OR 0.95, p = 0.002) and successful detorsion (OR 17.38, p = 0.001) were independently associated with orchiopexy.
Conclusions: Preoperative manual detorsion was associated with improved surgical salvage in patients with testicular torsion1973811817sem informaçã
Support vector machines in tandem with infrared spectroscopy for geographical classification of green arabica coffee
No full textThe coffee is an important commodity to Brazil. Species, climate, genotypes, cultivation practices and industrialization are critical to final quality of the beverage. Thus, the development of analytical methods for coffee authentication is important to ensure the origin of the bean. The purpose of this study was to develop a methodology for geographical classification of different genotypes of arabica coffee using infrared spectroscopy and support vector machines (SVM). The spectra were collected in the range of near infrared (NIRS) and mid infrared (FTIR). For the data analysis, a SVM was built using radial basis as kernel function and the one-versus-all multiclass approach. The C and gamma parameters of SVM were optimized using the genetic algorithm. With the application of the NIRS-SVM approach all test samples were correctly classified with a sensitivity and specificity of 100%, while FTIR-SVM had a slightly lower performance. Therefore, it was possible to confirm that infrared spectroscopy is a fast and effective method for geographic certification with little sample preparation, and without the production of chemical wastes. Furthermore, the SVM can be a chemometric alternative in tandem with infrared spectroscopy for another classification problems73BSI33033611th Latin American Symposium on Food Science (SLACA)2015-11-08Campinas, Brasilsem informaçã
The first phylogenetic study of Mesembrinellidae (diptera: Oestroidea) based on molecular data: clades and congruence with morphological characters
No full textThe Mesembrinellidae (Diptera: Oestroidea) comprise a small group of strictly Neotropical calyptrate flies, with 36 described species. The group has often been treated as a subfamily of Calliphoridae, but there is growing evidence that it corresponds to a distinct Oestroidea lineage. Internal relationships have so far been addressed based only on morphology, with results lacking resolution and support. This is the first molecular phylogeny for the group, which is based on the analyses of 80 terminal taxa (22 mesembrinellid and 28 outgroup species) and 5 molecular markers (ITS2, 28S, COI, COII and 16S). Maximum-parsimony, maximum-likelihood and Bayesian inference methods were used, the latter two with partitioning strategies considering codon position and secondary structure information. Results corroborate the Mesembrinellidae as a monophyletic lineage inside Oestroidea. Three clades were consistently recovered: (1) (Laneella+Mesembrinella patriciae); (2) (Mesembrinella (excluding M. patriciae) +Eumesembrinella); and (3) (Huascaromusca+Giovanella). Re-examination of the female reproductive tract of M.patriciae revealed a Laneela-type spermatheca, which corroborates the position of the species recovered in the molecular phylogenetic analyses. Mesembrinella and Huascaromusca are in all cases paraphyletic with regards to Eumesembrinella and Giovanella, respectively. These latter two genera should, thus, be seen as subjective junior synonyms332134152CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP309240/2013-12012/23200-2; 2003/10274-
Anticarcinogenic potential of BbTX-II on large lung cell carcinoma (NCI-H460)
No full textThe presence of antitumor enzymes in snake venoms were first mentioned during the mid-1960s. Different phospholipases A2 (PLA2s) have been studied for their antitumor properties, among them acidic and basic PLA2s, as well as synthetic peptides derived from K49 PLA2s homologues. Thus, the PLA2 isolated from Naja naja venom caused the death of the human neuroblastoma SK-N-SH cell line, similarly the PLA2 isolated from the venom Bothrops neuweidi, produced cytotoxic activity in murine melanoma B16F10. BbTX-II is a K49 PLA2 homologous isolated from Bothrops brazili snake venom, consists of 121 amino acid residues and has a molecular mass of 13,699 Da. In vivo, it induces local myotoxicity and edematogenic activity, these biological effects occur in the absence of catalytic activity. This work describes the cytotoxic activity of BbTX-II on the large lung carcinoma (NCI-H460) cell line. After formation of the cell monolayer, they were transferred onto plates containing RPMI-1640 medium and 10% FBS, then different concentrations of BbTX-II ranging from 0.008 to 0.5 mg/mL were added. The plates were incubated for 24 and 48 hours in a 5% CO2 oven at 37°C. After each incubation time, the cell viability assay was performed by neutral red staining. The results showed that after 24 and 48 hours of treatment, there was a decrease in cell viability in relation to the control. Thus, after 24 hours from 0.5 mg/mL to 0.15625 mg/mL, between 40 and 50% of the tumor cells were viable. At 48 hours, at the same range of concentrations of BbTX-II, approximately 30% of the cells were viable. This demonstrates the cytotoxic effects of BbTX-II, with approximately 70% dead cells. Both treatment times were statistically significant against the control. We conclude that BbTX-II has antitumor potential, reducing up to 70% the viability of the cells analyzed during 48 hours1774
Anti-inflammatory and antimicrobial effects of Zingiber officinale mouthwash on patients with fixed orthodontic appliances
No full textThis study aimed to assess the anti-inflammatory and antimicrobial effects of mouthwashes with 0.12% chlorhexidine (CLX) and 0.5% Zingiber officinale essential oil (ZOEO). The gas chromatography-mass spectrometry of ZOEO was developed, and the mouthwash was prepared. Thirty-one adult subjects of both sexes with fixed orthodontic appliances were selected. For 7 days, the mouthwashes with CLX, ZOEO, and flavored sterile water placebo were used randomly, with a 15-day interval between each solution. Saliva was collected before the first mouthwash, 1 minute and 15 minutes after it, and on the seventh day. The patients were subjected to clinical examinations of the bonded bracket index proposed by Ciancio, bleeding on probing, and sensory analysis (flavor). Generalized linear models were used to assess in vitro cell viability. The GENMOD procedure was used to assess the changes of bleeding on probing, and Friedman and Wilcoxon tests were used for data on colony-forming units per milliliter (CFU/mL), bonded bracket index, and flavor, at the 5% significance level.In the microbiologic analysis, the ZOEO mouthwash presented antimicrobial effectiveness for Streptococcus mutans as well as the CLX mouthwash, but it did not show the same substantivity. The ZOEO was efficient in controlling dental biofilm and reducing gingival bleeding. The sensory analyses showed that the flavor for ZOEO and CLX solutions presented low acceptability.The ZOEO mouthwash has an anti-inflammatory property with an effect on reducing gingival bleeding. However, it requires adjustments to the formulation to improve flavor quality159212
Hypertension and functional capacities in community-dwelling older women: a cross-sectional study
No full textThe present study aimed to investigate the association between hypertension and physical/functional capacities in community-dwelling older females. Older female volunteers were dichotomized in two groups: hypertensive (n=134) and normotensive (n=244). Volunteers had their medical records reviewed and underwent evaluations of anthropometric data (weight, height and body mass index) and of physical and functional capacities. The results showed that hypertensive older females presented higher values for age, weight, body mass index, and resting diastolic blood pressure than normotensive older females. Normotensive older females showed a higher performance in the one-leg stand test and six-minute walk test compared with hypertensive older females. Age, body mass index, maximal walking speed, performance in the Time Up and Go and six-minute walk test, and diagnosis of diabetes mellitus type II were factors associated with hypertension using the chi-square test. However, the multivariate regression analysis indicated that performance in the six-minute walk test was the only factor associated with hypertension. The patients with higher scores in the six-minute walk test, which is associated with aerobic capacity, show less odds to have clinical diagnosis of hypertension. However, hypertension was not associated with poor physical and functional capacity263156165CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPES