Protein molecular modeling of genetic markers for thyroid cancer / Modelagem molecular proteica dos marcadores genéticos do câncer de tireoide

ABSTRACT Introduction: The advances in thyroid molecular biology studies provide not only insight into thyroid diseases but accurate diagnosis of thyroid cancer. Objective: Design a tutorial on protein molecular modeling of genetic markers for thyroid cancer. Methods: The proteins were selected using the Protein Data Bank sequence and the basic local alignment search tool (BLAST) algorithm. The obtained sequences were aligned with the Clustal W multiple alignment algorithms. For the molecular modeling, three-dimensional structures were generated from this set of constraints with the SWISS-MODEL, which is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server. Results: We demonstrated protein analysis, projection of the molecular structure and protein homology of the following molecular markers of thyroid cancer: receptor tyrosine kinase (RET) proto-oncogene; neurotrophic tyrosine kinase receptor 1 (NTRK1) proto-oncogene; phosphatase and tensin homolog (PTEN); tumor protein p53 (TP53) gene; phosphoinositide 3-kinase/threonine protein kinase (PI3K/AKT); catenin beta 1 (CTNNB1); paired box 8-peroxisome proliferator-activated receptor gamma (PAX8-PPARG); rat sarcoma viral oncogene (RAS); B-raf proto-oncogene, serine/threonine kinase (BRAF); and thyroid-stimulating hormone receptor (TSHR). Conclusion: This study shows the importance of understanding the molecular structure of the markers for thyroid cancer through bioinformatics, and consequently, the development of more effective new molecules as alternative tools for thyroid cancer treatment.

RESUMO Introdução: Os avanços nos estudos de biologia molecular da tireoide não fornecem apenas uma visão sobre as doenças tireoidianas, mas um diagnóstico preciso do câncer de tireoide. Objetivo: Realizar um tutorial sobre modelagem molecular proteica dos marcadores genéticos do câncer de tireoide. Métodos: As proteínas foram selecionadas utilizando sequência do Banco de Dados de Proteínas e algoritmo basic local alignment search tool (BLAST). As sequências obtidas foram alinhadas com os algoritmos de alinhamento múltiplo Clustal W. Para a modelagem molecular, as estruturas tridimensionais foram geradas a partir deste conjunto com o SWISS-MODEL, um servidor de homologia de modelagem de estrutura proteica totalmente automatizado, acessível por meio do servidor web ExPASy. Resultados: Demonstramos a análise das proteínas, a projeção da estrutura molecular e a homologia proteica dos seguintes marcadores moleculares de câncer de tireoide: proto-oncogene receptor tyrosine kinase (RET); proto-oncogene neurotrophic tyrosine kinase receptor 1 (NTRK1); phosphatase and tensin homolog (PTEN); gene tumor protein p53 (TP53); phosphoinositide 3-kinase/threonine protein kinase (PI3K/AKT); catenina beta 1 (CTNNB1); paired box 8-peroxisome proliferator-activated receptor gamma (PAX8-PPARG); rat sarcoma viral oncogene (RAS); B-raf proto-oncogene, serine/threonine kinase (BRAF) e thyroid-stimulating hormone receptor (TSHR). Conclusão: Este estudo mostra a importância do conhecimento da estrutura molecular dos marcadores de câncer da tireoide por meio da bioinformática e, consequentemente, o desenvolvimento de novas moléculas mais eficazes como ferramentas alternativas para o seu tratamento.

Rapid Detection and Identification of Pathogenic Fungi of Some Deep Fungal Infections by PCR in Combination with Genescan Analysis / 中华皮肤科杂志

Objective To rapidly detect and identify pathogenic fungi of some deep fungal infections by PCR.Methods The suspensions of22pathogenic fungi(23strains)were amplified by PCR with fungal universal primers ITS86and ITS4which were labeled by FAM.The precise length of amplified fragments was determined by ABI PRISM TM 377Sequencer and Genescan analysis software,then compared with that of am-plicons of corresponding fungal DNA which were previously extracted.Results(1)Amplification of17pathogenic fungi with ITS4,ITS86resulted in a unique fragment length(except for A.nidulans and A.niger,C.albicans and C.stellatoidea,F.pedrosoi and E.dermatitidis).(2)No significant difference of the length of am-plicons was found between the fungal suspension and control organisms,based on the results of Genescan analysis.(3)The whole process took only6h to complete the detection.Conclusion The combination of fun-gal suspension PCR with ITS fungal universal primers and Genescan analysis might provide an accurate,spe-cific,sensitive,and rapid approach to detect and identify22pathogenic fungi causing deep fungal infections,and hold promise to be applied for the diagnosis of deep fungal infection.

The study of common sequence motif on auto-reactive T cell receptors of patients with rheumatoid arthritis / 中华风湿病学杂志

Objective To study the CDR3 characteristics of T cell receptor carried by auto- reactive Tcells from patients with rheumatoid arthritis. Methods BV14 and BV16 of the beta chain of TCR were ampli-fied by realtime PCR. The length of CDR3 was identified by gene scanning. The sequences of CDR3 were ana-lyzied by sequencing. Results The T cells infiltrated in the synovium of patients with rheumatoid arthritisshowed oligo clonal expansion. The beta chain carried by infiltrated T cells was encoded by different VDJ genefragments. The CDR3 had 15 bp, 21 bp and 24 bp length respectively. There were common motif among CDR3area in infiltrated T cells. Conclusion The auto- reactive T cells infiltrated in the synovium are drived byspecific antigens and therefore result restricted BV usage and common sequence motif among the T cells. Thecharacteristics of the specific antigens that drive auto- reactive T cells need further investigation.