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1.
Braz. j. biol ; 83: e243910, 2023. tab, graf
Article in English | MEDLINE, LILACS, VETINDEX | ID: biblio-1278525

ABSTRACT

Abstract Nucleotide excision repair (NER) acts repairing damages in DNA, such as lesions caused by cisplatin. Xeroderma Pigmentosum complementation group C (XPC) protein is involved in recognition of global genome DNA damages during NER (GG-NER) and it has been studied in different organisms due to its importance in other cellular processes. In this work, we studied NER proteins in Trypanosoma cruzi and Trypanosoma evansi, parasites of humans and animals respectively. We performed three-dimensional models of XPC proteins from T. cruzi and T. evansi and observed few structural differences between these proteins. In our tests, insertion of XPC gene from T. evansi (TevXPC) in T. cruzi resulted in slower cell growth under normal conditions. After cisplatin treatment, T. cruzi overexpressing its own XPC gene (TcXPC) was able to recover cell division rates faster than T. cruzi expressing TevXPC gene. Based on these tests, it is suggested that TevXPC (being an exogenous protein in T. cruzi) interferes negatively in cellular processes where TcXPC (the endogenous protein) is involved. This probably occurred due interaction of TevXPC with some endogenous molecules or proteins from T.cruzi but incapacity of interaction with others. This reinforces the importance of correctly XPC functioning within the cell.


Resumo O reparo por excisão de nucleotídeos (NER) atua reparando danos no DNA, como lesões causadas por cisplatina. A proteína Xeroderma Pigmentosum complementation group C (XPC) está envolvida no reconhecimento de danos pela via de reparação global do genoma pelo NER (GG-NER) e tem sido estudada em diferentes organismos devido à sua importância em outros processos celulares. Neste trabalho, estudamos proteínas do NER em Trypanosoma cruzi e Trypanosoma evansi, parasitos de humanos e animais, respectivamente. Modelos tridimensionais das proteínas XPC de T. cruzi e T. evansi foram feitos e observou-se poucas diferenças estruturais entre estas proteínas. Durante testes, a inserção do gene XPC de T. evansi (TevXPC) em T. cruzi resultou em crescimento celular mais lento em condições normais. Após o tratamento com cisplatina, T. cruzi superexpressando seu próprio gene XPC (TcXPC) foi capaz de recuperar as taxas de divisão celular mais rapidamente do que T. cruzi expressando o gene TevXPC. Com base nesses testes, sugere-se que TevXPC (sendo uma proteína exógena em T. cruzi) interfere negativamente nos processos celulares em que TcXPC (a proteína endógena) está envolvida. Isso provavelmente ocorreu pois TevXPC é capaz de interagir com algumas moléculas ou proteínas endógenas de T.cruzi, mas é incapaz de interagir com outras. Isso reforça a importância do correto funcionamento de XPC dentro da célula.


Subject(s)
Humans , Animals , Trypanosoma cruzi/genetics , Xeroderma Pigmentosum , DNA Damage/genetics , Computational Biology , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , DNA Repair/genetics
2.
Medicina (Ribeirão Preto) ; 54(1)jul, 2021. fig.
Article in Portuguese | LILACS | ID: biblio-1353725

ABSTRACT

RESUMO: Modelo do estudo: Trata-se de um estudo experimental in vitro com abordagem computacional. Objetivo: Ana-lisar a existência de interação entre as drogas hidrofóbicas bezafibrato e hidroclorotiazida com a hemoglobina a fim de prever alterações na biodisponibilidade das drogas, bem como na função proteica. Metodologia: Testes de interação in vitro entre a hemoglobina bovina e bezafibrato ou hidroclorotiazida foram realizados por espectrofo-tometria; análises dos sítios de interação e extrapolações para a hemoglobina humana foram feitas por técnicas de bioinformática. Resultados: Os testes in vitro demonstraram diminuição de absorbância (k) em 405 nm igual a 8,75 x 10-4 min-1 para o bezafibrato e 6,25 x 10-4 min--1 para a hidroclorotiazida. A diminuição sugere interação das drogas com a hemoglobina, sendo que o bezafibrato parece interagir com afinidade ligeiramente maior. As análises in silico mostraram que as drogas se ligam à porção proteica da hemoglobina. A constante de afinidade de ligação obtida por ancoragem molecular para o bezafibrato com a hemoglobina bovina (-8,3 kcal/mol) corrobora com o valor experimental de k e com o maior número de interações observadas, em relação à hidroclorotiazida (-6,6 kcal/mol). O mesmo padrão é observado para a interação do bezafibrato (-7,6 kcal/mol) e da hidroclorotiazida (-6,7 kcal/mol) com a hemoglobina humana. Conclusão: As técnicas de espectrofotometria e bioinformática utilizadas sugerem a possibilidade de interação da hemoglobina com drogas de natureza hidrofóbica, como bezafibrato e hi-droclorotiazida, sendo que essa interação pode afetar a função normal da hemoglobina e alterar a farmacodinâmica e farmacocinética das drogas prejudicando sua eficiência terapêutica. (AU)


ABSTRACT: Study model: It is an in vitro experimental study with a computational approach. Objective: Analyze the presence of interaction between hydrophobic drugs bezafibrate and hydrochlorothiazide and hemoglobin to predict bioavailability changes as well as in the protein function. Metodology: The in vitro tests to evaluate the interaction between the bovine hemoglobin and bezafibrate and hydrochlorothiazide were perfomed by spectrophotometry; bioinformatic tools made interaction analysis and extrapolation for human hemoglobin. Results: The in vitro tests showed a decrease in the absorbance (k) at 405 nm equal to 8.75 x 10-4 min-1 for bezafibrate and 6.25 x 10-4 min-1 for hydrochlorothiazide. The decrease suggests an interaction between the drugs and hemoglobin, for bezafibrate this interaction seems to be stronger than hydrochlorothiazide. The in silico analysis showed that the drugs bind to the protein portion of the hemoglobin. The binding affinity constant obtained by molecular docking from bezafibrate and bovine hemoglobin (-8.3 Kcal/mol) sustain the experimental value of k and the greater number of interactions observed in relation to hydrochlorothiazide (-6.6 kcal/mol). The same pattern was observed for interaction of bezafibrate (-7.6 kcal/mol) and hydrochlorothiazide (-6.7 kcal/mol) with human hemoglobin. Conclusion: The spectrophotometry and bioinformatic methods suggested the possibility of hemoglobin interaction with hydrophobic drugs such as bezafibrate and hydrochlorothiazide; this interaction could affect the normal function of hemoglobin and change the pharmacodynamics and pharmacokinetics of drugs impairing their therapeutic efficiency. (AU)


Subject(s)
Spectrophotometry , Hemoglobins , Computational Biology , Molecular Docking Simulation
3.
Rev. cuba. inform. méd ; 13(1): e389, ene.-jun. 2021. tab, graf
Article in Spanish | LILACS, CUMED | ID: biblio-1251726

ABSTRACT

El presente trabajo aborda una experiencia en la implementación del aula invertida. Se emplea como estrategia de investigación un estudio de caso efectuado en la Universidad de las Ciencias Informáticas (UCI), de 16 estudiantes de Ingeniería en Bioinformática. En los resultados obtenidos, se confirma la relación entre la interactividad, motivación, trabajo y aprendizaje colaborativo y la evaluación formativa; además, que el diseño de actividades de aprendizaje y su evaluación en el modelo de aula invertida con el desarrollo de estrategias de estudiantes prosumidores de videos contribuye a que estos mejoren sus habilidades comunicativas e informáticas. Se concluye que la evaluación debe estimular el aprendizaje colaborativo, la interactividad, la tolerancia, la motivación y la responsabilidad en los entornos virtuales(AU)


This paper presents an experience in the flipped classroom teaching. A case study conducted at the University of Informatics Science (UCI, acronym in Spanish) with 16 Bioinformatics Engineering students. In the results obtained, the relationship between interactivity, motivation, work and collaborative learning and formative evaluation is confirmed; in addition, the design of learning activities and assessment in the flipped classroom model with the development of strategies for video prosumers students helps them to improve their communication and computer skills. It is concluded that evaluation should stimulate collaborative learning, interactivity, tolerance, motivation and responsibility in virtual environments(AU)


Subject(s)
Software , Computational Biology/methods
4.
Braz. j. med. biol. res ; 54(3): e10152, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153522

ABSTRACT

The goal of this study was to identify potential transcriptomic markers in pediatric septic shock prognosis by an integrative analysis of multiple public microarray datasets. Using the R software and bioconductor packages, we performed a statistical analysis to identify differentially expressed (DE) genes in pediatric septic shock non-survivors, and further performed functional interpretation (enrichment analysis and co-expression network construction) and classification quality evaluation of the DE genes identified. Four microarray datasets (3 training datasets and 1 testing dataset, 252 pediatric patients with septic shock in total) were collected for the integrative analysis. A total of 32 DE genes (18 upregulated genes; 14 downregulated genes) were identified in pediatric septic shock non-survivors. Enrichment analysis revealed that those DE genes were strongly associated with acute inflammatory response to antigenic stimulus, response to yeast, and defense response to bacterium. A support vector machine classifier (non-survivors vs survivors) was also trained based on DE genes. In conclusion, the DE genes identified in this study are suggested as candidate transcriptomic markers for pediatric septic shock prognosis and provide novel insights into the progression of pediatric septic shock.


Subject(s)
Humans , Child , Shock, Septic/diagnosis , Shock, Septic/genetics , Transcriptome , Biomarkers , Computational Biology , Gene Expression Profiling , Microarray Analysis
5.
Braz. arch. biol. technol ; 64: e21210007, 2021. tab, graf
Article in English | LILACS | ID: biblio-1339314

ABSTRACT

Abstract Improving the accuracy of protein secondary structure prediction has been an important task in bioinformatics since it is not only the starting point in obtaining tertiary structure in hierarchical modeling but also enhances sequence analysis and sequence-structure threading to help determine structure and function. Herein we present a model based on DSPRED classifier, a hybrid method composed of dynamic Bayesian networks and a support vector machine to predict 3-state secondary structure information of proteins. We used the SCOPe (Structural Classification of Proteins-extended) database to train and test the model. The results show that DSPRED reached a Q3 accuracy rate of 82.36% when trained and tested using proteins from all SCOPe classes. We compared our method with the popular PSIPRED on the SCOPe test datasets and found that our method outperformed PSIPRED.


Subject(s)
Protein Structure, Secondary , Support Vector Machine , Artificial Intelligence , Computational Biology/methods
6.
Braz. j. med. biol. res ; 54(11): e11363, 2021. graf
Article in English | LILACS | ID: biblio-1339445

ABSTRACT

Cervical cancer (CC) is the most common malignant tumor in females. Although persistent high-risk human papillomavirus (HPV) infection is a leading factor that causes CC, few women with HPV infection develop CC. Therefore, many mechanisms remain to be explored, such as aberrant expression of oncogenes and tumor suppressor genes. To identify promising prognostic factors and interpret the relevant mechanisms of CC, the RNA sequencing profile of CC was downloaded from the Cancer Genome Atlas and the Gene Expression Omnibus databases. The GSE63514 dataset was analyzed, and differentially expressed genes (DEGs) were obtained by weighted coexpression network analysis and the edgeR package in R. Fifty-three shared genes were mainly enriched in nuclear chromosome segregation and DNA replication signaling pathways. Through a protein-protein interaction network and prognosis analysis, the kinesin family member 14 (KIF14) hub gene was extracted from the set of 53 shared genes, which was overexpressed and associated with poor overall survival (OS) and disease-free survival (DFS) of CC patients. Mechanistically, gene set enrichment analysis showed that KIF14 was mainly enriched in the glycolysis/gluconeogenesis signaling pathway and DNA replication signaling pathway, especially in the cell cycle signaling pathway. RT-PCR and the Human Protein Atlas database confirmed that these genes were significantly increased in CC samples. Therefore, our findings indicated the biological function of KIF14 in cervical cancer and provided new ideas for CC diagnosis and therapies.


Subject(s)
Humans , Female , Uterine Cervical Neoplasms/genetics , Papillomavirus Infections , Gene Expression Regulation, Neoplastic , Cell Cycle/genetics , Kinesin/genetics , Oncogene Proteins , Disease-Free Survival , Computational Biology , Protein Interaction Maps
7.
Mem. Inst. Oswaldo Cruz ; 116: e200634, 2021. graf
Article in English | LILACS | ID: biblio-1154876

ABSTRACT

The availability of Trypanosomatid genomic data in public databases has opened myriad experimental possibilities that have contributed to a more comprehensive understanding of the biology of these parasites and their interactions with hosts. In this review, after brief remarks on the history of the Trypanosoma cruzi and Leishmania genome initiatives, we present an overview of the relevant contributions of genomics, transcriptomics and functional genomics, discussing the primary obstacles, challenges, relevant achievements and future perspectives of these technologies.


Subject(s)
Trypanosoma cruzi/genetics , Genome, Protozoan/genetics , Leishmania/genetics , Computational Biology , Genomics
8.
Article in English | WPRIM | ID: wpr-880615

ABSTRACT

OBJECTIVES@#To study the gene expression of adipose tissue CD14@*METHODS@#The data of GSE54350 were obtained from the public database of gene expression profiling. The data were pre-processed by Network Analyst, String 11.0, Cytoscape 3.7.1, and other analytical software. The differentially expressed genes were analyzed by gene ontology biological function and kyoto encycopedia of genes and genomes (KEGG) signaling pathway to establish differential gene protein interaction network, transcription factor-gene regulatory network, microRNA-gene regulatory network, environmental factors-gene regulatory network, and other interaction systems.@*RESULTS@#The gene expression pattern of CD14@*CONCLUSIONS@#The gene expression of adipose tissue CD14


Subject(s)
Adipose Tissue , Computational Biology , DNA-Binding Proteins , Diabetes Mellitus, Type 2/genetics , Gene Expression , Gene Expression Profiling , Gene Regulatory Networks , Humans , MicroRNAs/genetics , Muscle Proteins
9.
Article in Chinese | WPRIM | ID: wpr-880178

ABSTRACT

OBJECTIVE@#To analyze and predict the effect of coronavirus infection on hematopoietic system and potential intervention drugs, and explore their significance for coronavirus disease 2019 (COVID-19).@*METHODS@#The gene expression omnibus (GEO) database was used to screen the whole genome expression data related with coronavirus infection. The R language package was used for differential expression analysis and KEGG/GO enrichment analysis. The core genes were screened by PPI network analysis using STRING online analysis website. Then the self-developed apparent precision therapy prediction platform (EpiMed) was used to analyze diseases, drugs and related target genes.@*RESULTS@#A database in accordance with the criteria was found, which was derived from SARS coronavirus. A total of 3606 differential genes were screened, including 2148 expression up-regulated genes and 1458 expression down-regulated genes. GO enrichment mainly related with viral infection, hematopoietic regulation, cell chemotaxis, platelet granule content secretion, immune activation, acute inflammation, etc. KEGG enrichment mainly related with hematopoietic function, coagulation cascade reaction, acute inflammation, immune reaction, etc. Ten core genes such as PTPRC, ICAM1, TIMP1, CXCR5, IL-1B, MYC, CR2, FSTL1, SOX1 and COL3A1 were screened by protein interaction network analysis. Ten drugs with potential intervention effects, including glucocorticoid, TNF-α inhibitor, salvia miltiorrhiza, sirolimus, licorice, red peony, famciclovir, cyclosporine A, houttuynia cordata, fluvastatin, etc. were screened by EpiMed plotform.@*CONCLUSION@#SARS coronavirus infection can affect the hematopoietic system by changing the expression of a series of genes. The potential intervention drugs screened on these grounds are of useful reference significance for the basic and clinical research of COVID-19.


Subject(s)
COVID-19 , Computational Biology , Follistatin-Related Proteins , Hematopoietic System , Humans , Pharmaceutical Preparations , SARS-CoV-2
10.
Article in Chinese | WPRIM | ID: wpr-880142

ABSTRACT

OBJECTIVE@#To analyze gene expression profile of T cell lymphoma Jurkat cell line treated with paclitaxel by computational biology based on next generation sequencing and to explore the possible molecular mechanism of paclitaxel resistance to T cell lymphoma at gene level.@*METHODS@#IC50 of paclitaxel on Jurkat cell line was determined by CCK-8 assay. Gene expression profile of Jurkat cells treated with paclitaxel was acquired by next generation sequencing technology. Gene microarray data related to human T cell lymphoma were screened from Gene Expression Omnibus (GEO) database (including 720 cases of T cell lymphoma and 153 cases of normal tissues). Combined with the sequencing data, differential expression genes (DEGs) were intersected and screened. DAVID database was used for enrichment analysis of GO function and KEGG pathway to determine and visualize functional entries of DEGs, and protein-protein interactions network of DEGs was drawn. The levels of gene expression were detected and verified by RT-qPCR.@*RESULTS@#CCK-8 results showed that the proliferation of Jurkat cells was inhibited by paclitaxel depended on the concentration apparently. Treated by paclitaxel for 48 h, P<0.05 and |log2(FC)|≥1 were used as filter criteria on the results of RNA Sequencing (RNA-Seq) and GeoChip, 351 DEGs were found from Jurkat cells, including 323 up-regulated genes and 28 down-regulated genes. The GO functional annotation and KEGG pathway enrichment analysis showed that the role of paclitaxel was mainly concentrated in protein heterodimerization activity, nucleosome assembly and transcriptional dysregulation in cancer, etc. The results of RT-qPCR were consistent with those of the sequencing analysis, which verified the reliability of this sequencing.@*CONCLUSION@#Paclitaxel can affect the proliferation and apoptosis of T-cell lymphoma by up-regulating JUN gene, orphan nuclear receptor NR4A family genes and histone family genes.


Subject(s)
Computational Biology , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , High-Throughput Nucleotide Sequencing , Humans , Lymphoma, T-Cell , Paclitaxel , Reproducibility of Results
11.
Article in English | WPRIM | ID: wpr-922585

ABSTRACT

OBJECTIVES@#The biomarkers targeting colorectal cancer (CRC) prognosis are short of high accuracy and sensitivity in clinic. Through bioinformatics analysis, we aim to identify and confirm a series of key genes referred to the diagnosis and prognosis of CRC.@*METHODS@#GSE31905, GSE35279, and GSE41657 were selected as complete RNA sequencing data sets of CRC and colorectal mucosa (CRM) tissues from the NCBI-GEO database, and the differentially expressed genes (DEGs) were analyzed. The common DEGs in these 3 data sets were obtained by Venn map, and enriched by STRING network system and Cytoscape software. The Kaplan-Meier plotter website was used to verify the correlation between the enriched genes and the prognosis of CRC.@*RESULTS@#For the whole RNA sequencing data sets of CRC and normal intestinal mucosa samples, the DEGs of CRC and CRM in the 3 data sets (|log@*CONCLUSIONS@#The above 11 genes verified by bioinformatics retrieval and analysis can predict the poor prognosis of CRC to a certain extent, and they provide a possible target for the diagnosis and treatment of CRC.


Subject(s)
Biomarkers, Tumor/metabolism , Colorectal Neoplasms/genetics , Computational Biology , Formins , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Glycoproteins , Humans , Intercellular Signaling Peptides and Proteins , Oncogenes , Prognosis , Protein Interaction Maps
12.
Article in Chinese | WPRIM | ID: wpr-921755

ABSTRACT

Microarray data of hippocampal tissue(HC) of the cognitively intact elderly(60-99 years old) were compared with those of the middle-aged and the young(20-59 years old) by bioinformatics techniques to initially screen out differentially expressed genes(DEGs) and then predict potential effective Chinese medicinals for the treatment of brain aging. The gene expression profile(accession: GSE11882) was downloaded from the Gene Expression Omnibus(GEO) and DEGs were screened based on R package. The key DEGs were identified by STRING, Cytoscape and the plug-in, followed by Gene Ontology(GO) term and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis. Then the key genes and the medical ontology information retrieval platform(Coremine Medical) were mapped against each other to single out the Chinese medicinals for the treatment of brain aging and construct the " Chinese medicinal-active constituent-target" network. Among the resultant 268 DEGs(246 down-regulated and 22 up-regulated), the 15 key genes were mainly involved in biological processes such as leukocyte migration, neutrophil activation, cell chemotaxis, microglia activation and response to external stimulus, and pathways such as inflammatory process, immune response, cytokine-cytokine receptor interaction, PI3 K-Akt signaling pathway, Rap1 signaling pathway, chemokine signaling pathway and Toll-like receptor signaling pathway. The potential effective Chinese medicinals were Notoginseng Radix et Rhizoma, Ginseng Radix et Rhizoma, Salviae Miltiorrhizae Radix et Rhizoma and Astragali Radix. The analysis of DEGs and key genes enhances the understanding of the mechanisms of brain aging. This study provides potential gene targets and ideas for the development of Chinese medicine for brain aging.


Subject(s)
Adult , Aged , Aged, 80 and over , Brain , China , Computational Biology , Gene Expression Profiling , Gene Ontology , Humans , Middle Aged , Transcriptome , Young Adult
13.
Article in Chinese | WPRIM | ID: wpr-921753

ABSTRACT

The present study explored the potential mechanism of Jingfang Granules in relieving alcohol and protecting liver by network pharmacology and molecular docking and verified the effects and related pathways by animal experiments. The active components of Jingfang Granules were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). Targets of drugs and diseases were obtained from PubChem, Swiss Target Prediction and CTD. The common targets were uploaded to STRING to plot the protein-protein interaction(PPI) network. The core targets were screened out and the target organs were identified by Bio GPS and Metascape, followed by Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis of common targets. The acute drunk mouse model was established and the effects of Jingfang Granules on serum ethanol level and the expression of proteins related to the phosphatidylinositol 3-kinase(PI3 K)/protein kinase B(Akt) signaling pathway in the liver tissue of mice were observed. A total of 187 active components of Jingfang Granules were obtained, including 47 common targets with alcoholic liver injury. GO enrichment analysis and KEGG pathway analysis showed that Jingfang Granules might play the role of relieving alcohol and protecting liver through the PI3 K-Akt signaling pathway. The drug-component-target and component-target-pathway networks revealed that the important active components of Jingfang Granules in relieving alcohol and protecting liver included quercetin, 5-O-methylvisamminol, glyasperin M, glyasperin B and hederagenin. Molecular docking showed that the active components had a good affinity with AKT1, EGFR, ESR1 and PTGS2. Experimental results showed that Jingfang Granules(15 and 10. 5 g·kg-1) could significantly reduce the content of serum ethanol in mice and up-regulate the protein expression ratios of p-PI3 K/PI3 K and p-Akt/Akt in the liver tissue. Jingfang Granules could relieve alcohol and protect liver through multi-component and multitarget, and the mechanism may be related to the activation of the PI3 K-Akt signaling pathway.


Subject(s)
Animals , Computational Biology , Drugs, Chinese Herbal/pharmacology , Ethanol , Liver , Medicine, Chinese Traditional , Mice , Molecular Docking Simulation , Technology
14.
Article in English | WPRIM | ID: wpr-921385

ABSTRACT

OBJECTIVES@#To identify the differentially expressed genes (DEGs) during the pathogenesis of periodontitis by bioinformatics analysis.@*METHODS@#GEO2R was used to screen DEGs in GSE10334 and GSE16134. Then, the overlapped DEGs were used for further analysis. g:Profiler was used to perform Gene Ontology analysis and pathway analysis for upregulated and downregulated DEGs. The STRING database was used to construct the protein-protein interaction (PPI) network, which was further visua-lized and analyzed by Cytoscape software. Hub genes and key modules were identified by cytoHubba and MCODE plug-ins, respectively. Finally, transcription factors were predicted via iRegulon plug-in.@*RESULTS@#A total of 196 DEGs were identified, including 139 upregulated and 57 downregulated DEGs. Functional enrichment analysis showed that the upregulated DEGs were mainly enriched in immune-related pathways including immune system, viral protein interaction with cytokine and cytokine receptor, cytokine-cytokine receptor interaction, leukocyte transendothelial migration, and chemokine receptors bind chemokines. On the contrary, the downregulated DEGs were mainly related to the formation of the cornified envelope and keratinization. The identified hub genes in the PPI network were CXCL8, CXCL1, CXCR4, SEL, CD19, and IKZF1. The top three modules were involved in chemokine response, B cell receptor signaling pathway, and interleukin response, respectively. iRegulon analysis revealed that IRF4 scored the highest.@*CONCLUSIONS@#The pathogenesis of periodontitis was closely associated with the expression levels of the identified hub genes including CXCL8, CXCL1, CXCR4, SELL, CD19, and IKZF1. IRF4, the predicted transcription factor, might serve as a dominant upstream regulator.


Subject(s)
Computational Biology , Gene Expression Profiling , Humans , Microarray Analysis , Periodontitis , Protein Interaction Maps
15.
Chinese Medical Journal ; (24): 2465-2474, 2021.
Article in English | WPRIM | ID: wpr-921151

ABSTRACT

BACKGROUND@#Ubiquitin-conjugating enzyme E2C (UBE2C) has been shown to be associated with the occurrence of various cancers and involved in many tumorigenic processes. This study aimed to investigate the specific molecular mechanism through which UBE2C affects breast cancer (BC) proliferation.@*METHODS@#BC-related datasets were screened according to filter criteria in the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. Then differentially expressed genes (DEGs) were identified using Venn diagram analysis. By using DEGs, we conducted the following analyses including Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI), and survival analysis, and then validated the function of the hub gene UBE2C using quantitative reverse transcription-polymerase chain reaction (RT-qPCR), cell counting kit-8 (CCK-8) assay, transwell assay, and Western blot assay.@*RESULTS@#In total, 151 DEGs were identified from the GEO and TCGA databases. The results of GO analysis demonstrated that the DEGs were significantly enriched with mitotic nuclear division, lipid droplet, and organic acid-binding. KEGG analysis showed that the peroxisome proliferators-activated receptor (PPAR) signaling pathway, regulation of lipolysis in adipocytes, and proximal tubule bicarbonate reclamation were significantly enriched in the signal transduction pathway category. The top three hub genes that resulted from the PPI network were FOXM1, UBE2C, and CDKN3. The results of survival analysis showed a close relationship between UBE2C and BC. The results of CCK-8 and transwell assays suggested that the proliferation and invasion of UBE2C knockdown cells were significantly inhibited (P < 0.050). The results of Western blot assay showed that the level of phosphorylated phosphatase and tensin homology deleted on chromosome 10 (p-PTEN) was obviously increased (P < 0.050), whereas the levels of phosphorylated protein kinase B (p-AKT), phosphorylated mammalian target of rapamycin (p-mTOR), and hypoxia-inducible factor-1 alpha (HIF-1α) were dramatically decreased (P < 0.050) in the UBE2C knockdown cell.@*CONCLUSION@#UBE2C can promote BC proliferation by activating the AKT/mTOR signaling pathway.


Subject(s)
Biomarkers, Tumor , Breast Neoplasms/pathology , Cell Proliferation/genetics , Computational Biology , Female , Gene Expression Regulation, Neoplastic , Humans , Proto-Oncogene Proteins c-akt/genetics , Signal Transduction/genetics , TOR Serine-Threonine Kinases/genetics , Ubiquitin-Conjugating Enzymes/metabolism
16.
J. venom. anim. toxins incl. trop. dis ; 27: e20200173, 2021. tab, graf
Article in English | LILACS, VETINDEX | ID: biblio-1279403

ABSTRACT

Background: Scorpions are widely known for the neurotoxic effects of their venoms, which contain peptides affecting ionic channels. Although Colombia is recognized for its scorpion diversity, only a few studies are available describing the venom content. Methods: In this descriptive study, we analyzed the MS/MS sequence, electrophoretic and chromatographic profile linked to a bioinformatics analysis of the scorpions Chactas reticulatus (Chactidae), Opisthacanthus elatus (Hormuridae), Centruroides edwardsii (Buthidae) and Tityus asthenes (Buthidae) from Colombia. Results: Each scorpion showed a specific electrophoretic and chromatographic profile. The electrophoretic profiles indicate the presence of high molecular mass compounds in all venoms, with a predominance of low molecular mass compounds in the Buthidae species. Chromatographic profiles showed a similar pattern as the electrophoretic profiles. From the MS/MS analysis of the chromatographic collected fractions, we obtained internal peptide sequences corresponding to proteins reported in scorpions from the respective family of the analyzed samples. Some of these proteins correspond to neurotoxins affecting ionic channels, antimicrobial peptides and metalloproteinase-like fragments. In the venom of Tityus asthenes, the MSn analysis allowed the detection of two toxins affecting sodium channels covering 50% and 84% of the sequence respectively, showing 100% sequence similarity. Two sequences from Tityus asthenes showed sequence similarity with a phospholipase from Opisthacanthus cayaporum indicating the presence of this type of toxin in this species for the first time. One sequence matching a hypothetical secreted protein from Hottentotta judaicus was found in three of the studied venoms. We found that this protein is common in the Buthidae family whereas it has been reported in other families - such as Scorpionidae - and may be part of the evolutionary puzzle of venoms in these arachnids. Conclusion: Buthidae venoms from Colombia can be considered an important source of peptides similar to toxins affecting ionic channels. An interesting predicted antimicrobial peptide was detected in three of the analyzed venoms.(AU)


Subject(s)
Animals , Scorpion Venoms , Sodium/analysis , Computational Biology , Neurotoxins
17.
Frontiers of Medicine ; (4): 438-447, 2021.
Article in English | WPRIM | ID: wpr-888752

ABSTRACT

Thoracic aortic dissection (TAD) without familial clustering or syndromic features is known as sporadic TAD (STAD). So far, the genetic basis of STAD remains unknown. Whole exome sequencing was performed in 223 STAD patients and 414 healthy controls from the Chinese Han population (N = 637). After population structure and genetic relationship and ancestry analyses, we used the optimal sequence kernel association test to identify the candidate genes or variants of STAD. We found that COL3A1 was significantly relevant to STAD (P = 7.35 × 10


Subject(s)
Aneurysm, Dissecting/genetics , Case-Control Studies , Cluster Analysis , Cohort Studies , Collagen Type III/genetics , Computational Biology , Genetic Predisposition to Disease , Humans
18.
Journal of Experimental Hematology ; (6): 1101-1108, 2021.
Article in Chinese | WPRIM | ID: wpr-888524

ABSTRACT

OBJECTIVE@#To screen the core genes of Philadelphia chromosome positive/Ph like T-cell acute lymphoblastic leukemia (Ph@*METHODS@#The WES/RNA-seq examination results of Ph@*RESULTS@#For Ph@*CONCLUSION@#There are obviously abnormal DNA damage repair pathways in children with Ph


Subject(s)
Child , Computational Biology , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Signal Transduction , Software
19.
Journal of Experimental Hematology ; (6): 1039-1049, 2021.
Article in Chinese | WPRIM | ID: wpr-888516

ABSTRACT

OBJECTIVE@#To analyze the hub genes affecting the solely bone marrow relapse of childish acute B-cell lymphoblastic leukemia (B-ALL).@*METHODS@#The high-throughput RNA sequencing data were downloaded from TCGA database, the differentially expressed genes were screened by DESeq2 package of R, and the differentially expressed genes were grouped by GO function enrichment analysis and KEGG pathway enrichment analysis. Further, the data of STRING database and Cytoscape software were used to construct protein interaction network, screen hub genes and highly interaction protein sub network, perform GO and KEGG analysis of the hub genes and protein sub network respectively. JASPAR database was used to screen the upstream transcription factor of the hub gene promoter. Survival analysis based on the expression of hub genes was performed with clinical information attached to TCGA database. The bone marrow samples and clinical data of the patients were collected, the analysis results of hub genes were verified through clinical samples.@*RESULTS@#847 differentially expressed genes were collected, including 813 up-regulated genes, 34 down-regulated genes, 11 hub genes were screened out. The results of survival analysis showed that RPS5、RPS15、RPL23、RPL35、RPS8、RPS27A、RPS3、RPL9、RPS21、RPS7 and RPL38 showed significant effect on the survival of the children, and ZNF460 might be involved in their regulation. The high expressions of RPS3, RPS15, RPS8, RPS27A, and RPS21 had been verified in clinical samples of solely bone marrow relapsed patients.@*CONCLUSION@#RPS3, RPS15, RPS8, RPS27A, RPS21 can be used as biomarkers to indicate the malignant event of solely bone marrow relapse, which may be regulated by ZNF460.


Subject(s)
Bone Marrow , Child , Computational Biology , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Leukemia, B-Cell , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Recurrence
20.
Article in Chinese | WPRIM | ID: wpr-888106

ABSTRACT

The longevity mechanism of ginseng(Panax ginseng) is related to its strong meristematic ability. In this paper, this study used bioinformatic methods to identify the members of the ginseng TCP gene family in the whole genome and analyzed their sequence characteristics. Then, quantitative real-time fluorescent PCR was performed to analyze the TCP genes containing elements rela-ted to meristem expression in the taproots, fibrous roots, stems, and leaves. According to the data, this study further explored the expression specificity of TCP genes in ginseng tissues, which facilitated the dissection of the longevity mechanism of ginseng. The ginseng TCP members were identified and analyzed using PlantTFDB, ExPASy, MEME, PLANTCARE, TBtools, MEGA and DNAMAN. The results demonstrated that there were 60 TCP gene family members in ginseng, and they could be divided into two classes: Class Ⅰ and Class Ⅱ, in which the Class Ⅱ possessed two subclasses: CYC-TCP and CIN-TCP. The deduced TCP proteins in ginseng had the length of 128-793 aa, the isoelectric point of 4.49-9.84 and the relative molecular mass of 14.2-89.3 kDa. They all contained the basic helix-loop-helix(bHLH) domain. There are a variety of stress response-related cis-acting elements in the promoter regions of ginseng TCP genes, and PgTCP20-PgTCP24 contained the elements associated with meristematic expression. The transcription levels of PgTCP20-PgTCP24 were high in fibrous roots and leaves, but low in stems, indicating the tissue-specific expression of ginseng TCP genes. The Class Ⅰ TCP members which contained PgTCP20-PgTCP23, may be important regulators for the growth and development of ginseng roots.


Subject(s)
Computational Biology , Gene Expression Regulation, Plant , Multigene Family , Panax/metabolism , Phylogeny , Plant Proteins/metabolism , Transcription Factors/metabolism
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