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1.
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
2.
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
3.
Mem. Inst. Oswaldo Cruz ; 115: e190378, 2020. tab, graf
Article in English | SES-SP, LILACS, SES-SP | ID: biblio-1135284

ABSTRACT

BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium. OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome. METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.


Subject(s)
Humans , Animals , Schistosoma haematobium/genetics , Schistosomiasis/parasitology , Gene Expression Regulation/genetics , Computational Biology/methods , MicroRNAs/genetics , Sequence Analysis, RNA , Transcriptome/genetics
4.
Clin. biomed. res ; 39(1): 89-96, 2019.
Article in Portuguese | LILACS | ID: biblio-1026207

ABSTRACT

A Doença Mista do Tecido Conjuntivo (DMTC) é uma doença autoimune crônica composta por um misto de quatro doenças: Lúpus Eritematoso Sistêmico, Esclerose Sistêmica, Dermatomiosite/Polimiosite e Artrite Reumatoide. Por se tratar de uma combinação de doenças autoimunes o diagnóstico é bastante complexo. Atualmente existem quatro combinações sugeridas por diferentes autores para a realização de um diagnóstico preciso, são eles: Kasukawa, Alarcón-Segovia e Villareal, Kahn e Appeboom e Sharp. Desde a sua descoberta em 1972 por Sharp, passaram-se 46 anos e desta forma o objetivo desta revisão foi verificar a evolução do diagnóstico da DMTC desde a sua descoberta até a atualidade. Para isso utilizou-se sites de busca PUBMED e SCIELO. Por se tratar de uma doença autoimune que leva ao desenvolvimento de um quadro inflamatório crônico utilizou-se a ferramenta STRING que permite a análise da interação de proteínas. Até a presente data, não existe um consenso de qual critério deve ser usado para o diagnóstico correto e eficiente desta doença. A baixa relação de interações observadas a partir da ferramenta STRING demonstra que ainda não existem dados suficientes na literatura para que a ligação entre proteínas marcadoras e a DTMC possa ser estabelecida. (AU)


Mixed connective tissue disease (MCTD) is a chronic autoimmune disorder consisting of a mixture of four diseases: systemic lupus erythematosus, systemic sclerosis, dermatomyositis/polymyositis, and rheumatoid arthritis. Because it is a combination of different autoimmune disorders its diagnosis is quite complex. Currently there are four combinations suggested by the following authors to establish an accurate diagnosis: Kasukawa, Alarcón-Segovia & Villareal, Kahn, and Appeboom & Sharp. It has been 46 years since Sharp reported the disease in 1972 and thus the purpose of this review was to investigate the evolution of the diagnosis of MCTD since then. PubMed and SciELO databases were used for this investigation. Because MCTD is an autoimmune disease that leads to the development of a chronic inflammatory condition, the STRING tool was used to allow the analysis of protein interaction. To date, there is no consensus as to what criterion should be used for a correct and efficient diagnosis of this disease. The low ratio of interactions observed from the STRING tool demonstrates that there is not yet enough data in the literature for establishing the binding between marker proteins and MCTD. (AU)


Subject(s)
Humans , Male , Female , Mixed Connective Tissue Disease/diagnosis , Mixed Connective Tissue Disease/genetics , Antibodies, Antinuclear/genetics , Antibodies, Antinuclear/blood , Computational Biology/methods
5.
Braz. arch. biol. technol ; 62: e19180120, 2019. tab, graf
Article in English | LILACS | ID: biblio-1001422

ABSTRACT

Abstract Root-knot nematodes are a group of endoparasites species that induce the formation of giant cells in the hosts, by which they guarantee their feeding and development. Meloidogyne species infect over 2000 plant species, and are highly destructive, causing damage to many crops around the world. M. enterolobii is considered the most aggressive species in tropical regions, such as Africa and South America. Phytonematodes are able to penetrate and migrate within plant tissues, establishing a sophisticated interaction with their hosts through parasitism factors, which include a series of cell wall degradation enzymes and plant cell modification. Among the parasitism factors documented in the M. enterolobii species, cellulose binding protein (CBP), a nematode excretion protein that appears to be associated with the breakdown of cellulose present in the plant cell wall. In silico analysis can be of great importance for the identification, structural and functional characterization of genomic sequences, besides making possible the prediction of structures and functions of proteins. The present work characterized 12 sequences of the CBP protein of nematodes of the genus Meloidogyne present in genomic databases. The results showed that all CBP sequences had signal peptide and that, after their removal, they had an isoelectric point that characterized them as unstable in an acid medium. The values of the average hydrophilicity demonstrated the hydrophilic character of the analyzed sequences. Phylogenetic analyzes were also consistent with the taxonomic classification of the nematode species of this study. Five motifs were identified, which are present in all sequences analyzed. These results may provide theoretical grounds for future studies of plant resistance to nematode infection.


Subject(s)
Parasitic Diseases , Computer Simulation , Cell Wall , Computational Biology/methods , Nematoda
6.
Braz. arch. biol. technol ; 62: e19180715, 2019. tab, graf
Article in English | LILACS | ID: biblio-1019541

ABSTRACT

Abstract Cold stress is one of the limiting factors of plant production that plants use different mechanisms for cold tolerance. CBF genes play critical role to regulate the cold responsive genes. To better understand of CBF gene functions, the tomato-CBFs and Arabidopsis-CBFs were evaluated using bioinformatics tools, and finally the expression patterns of SlCBF1 gene were analyzed under 10 and 4˚C in two contrasting tomato species (Solanum lycopersicum and S. habrochaites). The different cis regulatory elements were observed in promoter region of SlCBF1 and AtCBF1 genes, and ICE1, COR and HOS1 proteins exhibited high interaction with CBFs. The results of Real time PCR of SlCBF1 exhibited that under 10 and 4 ˚C, SlCBF1 was down regulated in cold sensitive tomato genotype while it was slightly up-regulated in cold tolerant genotype at 4 ˚C. The results showed that the SlCBF1 and AtCBF1 genes have differential expression in cold stress.


Subject(s)
Core Binding Factors , Cold-Shock Response , Real-Time Polymerase Chain Reaction/instrumentation , Lycopersicon esculentum , Computational Biology/methods
7.
Braz. j. med. biol. res ; 51(6): e6801, 2018. tab, graf
Article in English | LILACS | ID: biblio-889107

ABSTRACT

Gene networks have been broadly used to predict gene functions based on guilt by association (GBA) principle. Thus, in order to better understand the molecular mechanisms of esophageal squamous cell carcinoma (ESCC), our study was designed to use a network-based GBA method to identify the optimal gene functions for ESCC. To identify genomic bio-signatures for ESCC, microarray data of GSE20347 were first downloaded from a public functional genomics data repository of Gene Expression Omnibus database. Then, differentially expressed genes (DEGs) between ESCC patients and controls were identified using the LIMMA method. Afterwards, construction of differential co-expression network (DCN) was performed relying on DEGs, followed by gene ontology (GO) enrichment analysis based on a known confirmed database and DEGs. Eventually, the optimal gene functions were predicted using GBA algorithm based on the area under the curve (AUC) for each GO term. Overall, 43 DEGs and 67 GO terms were gained for subsequent analysis. GBA predictions demonstrated that 13 GO functions with AUC>0.7 had a good classification ability. Significantly, 6 out of 13 GO terms yielded AUC>0.8, which were determined as the optimal gene functions. Interestingly, there were two GO categories with AUC>0.9, which included cell cycle checkpoint (AUC=0.91648), and mitotic sister chromatid segregation (AUC=0.91597). Our findings highlight the clinical implications of cell cycle checkpoint and mitotic sister chromatid segregation in ESCC progression and provide the molecular foundation for developing therapeutic targets.


Subject(s)
Humans , Carcinoma, Squamous Cell/genetics , Computational Biology/methods , Esophageal Neoplasms/genetics , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic/genetics , Gene Regulatory Networks/genetics , Area Under Curve
8.
Mem. Inst. Oswaldo Cruz ; 113(5): e170393, 2018. tab, graf
Article in English | LILACS | ID: biblio-894924

ABSTRACT

BACKGROUND The genus Flavivirus includes a variety of medically important viruses, including dengue virus (DENV) and Zika virus (ZIKV), which are most prevalent in Brazil. Because the clinical profile of patients affected by different DENV serotypes or ZIKV may be similar, the development of new methods that facilitate a rapid and accurate diagnosis is crucial. OBJECTIVES The current study aimed to develop an improved reverse transcription-polymerase chain reaction (RT-PCR) protocol for universal detection of flaviviruses by using semi-nested primers that discriminate between DENV serotypes and ZIKV. METHODS The bioinformatics workflow adopted for primer design included: (1) alignment of 1,442 flavivirus genome sequences, (2) characterisation of 27 conserved regions, (3) generation of a primer set comprising 77 universal primers, and (4) selection of primer pairs with greatest coverage and specificity. Following primer design, the reaction was validated in vitro. The same approach was applied to the design of primers specific for DENV and ZIKV, using a species-specific sequence database. FINDINGS The new assay amplified an 800-806 nt variable region of the NS5 gene and allowed discrimination of virtually all flavivirus species using reference-sequence comparison. The 800-806 nt fragment was validated as a template for a semi-nested multiplex PCR using five additional primers for the detection of DENV and ZIKV. These primers were designed to generate amplicons of different sizes, allowing differentiation of the four serotypes of DENV, and ZIKV using agarose gel electrophoresis. MAIN CONCLUSIONS The bioinformatics pipeline allowed efficient primer design, making it possible to identify the best targets within the coding region of the NS5 protein. The multiplex system proved effective in differentiation of DENV1-4 and ZIKV on a 2% agarose gel. The possibility of discriminating DENV serotypes and ZIKV in the same reaction provided a faster result consuming less sample. In addition, this simplified approach ensured the reduction of the cost per analysis.


Subject(s)
Viral Nonstructural Proteins , Dengue Virus/genetics , Zika Virus , DNA Primers/genetics , Computational Biology/methods , Reverse Transcriptase Polymerase Chain Reaction
9.
Biol. Res ; 51: 26, 2018. tab, graf
Article in English | LILACS | ID: biblio-950909

ABSTRACT

BACKGROUND: Diffuse intrinsic pontine glioma (DIPG) is the main cause of pediatric brain tumor death. This study was designed to identify key genes associated with DIPG. METHODS: The gene expression profile GSE50021, which consisted of 35 pediatric DIPG samples and 10 normal brain samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified by limma package. Functional and pathway enrichment analyses were performed by the DAVID tool. Protein-protein interaction (PPI) network, and transcription factor (TF)-microRNA (miRNA)-target gene network were constructed using Cytoscape. Moreover, the expression levels of several genes were validated in human glioma cell line U251 and normal glia HEB cells through real-time polymerase chain reaction (PCR). RESULTS: A total of 378 DEGs were screened (74 up-regulated and 304 down-regulated genes). In the PPI network, GRM1, HTR2A, GRM7 and GRM2 had higher degrees. Besides, GRM1 and HTR2A were significantly enriched in the neuroactive ligand-receptor interaction pathway, and calcium signaling pathway. In addition, TFAP2C was a significant down-regulated functional gene and hsa-miR-26b-5p had a higher degree in the TF-miRNA-target gene network. PCR analysis revealed that GRM7 and HTR2A were significantly downregulated while TFAP2C was upregulated in U251 cells compared with that in HEB cells (p < 0.001). GRM2 was not detected in cells. CONCLUSIONS: GRM1 and HTR2A might function in DIPG through the neuroactive ligand-receptor interaction pathway and the calcium signaling pathway. Furthermore, the TFAP2C and hsa-miR-26b-5p might play important roles in the development and progression mechanisms of DIPG.


Subject(s)
Humans , Computational Biology/methods , Brain Stem Neoplasms/genetics , MicroRNAs/genetics , Glioma/genetics , Down-Regulation , Up-Regulation , Microarray Analysis/methods , Real-Time Polymerase Chain Reaction , Transcriptome
10.
Braz. j. microbiol ; 48(1): 9-10, Jan.-Mar. 2017.
Article in English | LILACS | ID: biblio-839335

ABSTRACT

Abstract Bradyrhizobium embrapense CNPSo 2833T is a nitrogen-fixing symbiont of the legume pasture Desmodium. Its draft genome contains 8,267,832 bp and 7876 CDSs. The symbiotic island includes nodulation and nitrogen fixation genes resembling the operon organization of B. japonicum. Several CDSs related to secretion proteins and stress tolerance were also identified.


Subject(s)
Genome, Bacterial , Bradyrhizobium/genetics , Genomics , Root Nodules, Plant/microbiology , Fabaceae/microbiology , Symbiosis , Sequence Analysis, DNA , Computational Biology/methods , Bradyrhizobium/isolation & purification , Bradyrhizobium/metabolism , Genomics/methods , High-Throughput Nucleotide Sequencing , Molecular Sequence Annotation
11.
Braz. j. microbiol ; 48(1): 7-8, Jan.-Mar. 2017. tab
Article in English | LILACS | ID: biblio-839336

ABSTRACT

Abstract Geobacillus thermodenitrificans DSM 101594 was isolated as a producer of extracellular thermostable pectic polysaccharide degrading enzymes. The completely sequenced genome was 3.6 Mb in length with GC content of 48.86%. A number of genes encoding enzymatic active against the high molecular weight polysaccharides of potential biotechnological importance were identified in the genome.


Subject(s)
Genome, Bacterial , Genomics , Geobacillus/genetics , High-Throughput Nucleotide Sequencing , Pectins/metabolism , Computational Biology/methods , Genomics/methods , Geobacillus/metabolism , Molecular Sequence Annotation
12.
Braz. j. microbiol ; 48(1): 11-12, Jan.-Mar. 2017.
Article in English | LILACS | ID: biblio-839337

ABSTRACT

Abstract The draft genome of Pectobacterium carotovorum subsp. brasiliense (Pcb) which causes blackleg of potato was submitted to the NCBI and released with reference number NZ_LGRF00000000.1. The estimated genome size based on the draft genome assembly is 4,820,279 bp from 33 contigs ranging in length from 444 to 1,660,019 nucleotides. The genome annotation showed 4250 putative genes, 4114 CDS and 43 pseudo-genes. Three complete rRNA gene species were detected: nine 5S, one 16S and one 23S. Other partial rRNA gene fragments were also identified, nine 16S rRNA and three 23S rRNA. A total of 69 tRNA genes and one ncRNA gene were also annotated in this genome.


Subject(s)
Genome, Bacterial , Pectobacterium carotovorum/genetics , Genomics , Sequence Analysis, DNA , Computational Biology/methods , Genomics/methods , High-Throughput Nucleotide Sequencing , Molecular Sequence Annotation
13.
Braz. j. microbiol ; 48(1): 5-6, Jan.-Mar. 2017.
Article in English | LILACS | ID: biblio-839345

ABSTRACT

Abstract Prevotella intermedia has long been known to be as the principal etiologic agent of periodontal diseases and associated with various systemic diseases. Previous studies showed that the intra-species difference exists in capacity of biofilm formation, antibiotic resistance, and serological reaction among P. intermedia strains. Here we report the genome sequence of P. intermedia SUNY aB G8-9K-3 (designated ATCC49046) that displays a relatively high antimicrobial resistant and biofilm-forming capacity. Genome sequencing information provides important clues in understanding the genetic bases of phenotypic differences among P. intermedia strains.


Subject(s)
Genome, Bacterial , Prevotella intermedia/drug effects , Prevotella intermedia/physiology , Biofilms , Drug Resistance, Bacterial , High-Throughput Nucleotide Sequencing , Anti-Bacterial Agents/pharmacology , Sequence Analysis, DNA , Computational Biology/methods , Polymorphism, Single Nucleotide , Genomics/methods , Molecular Sequence Annotation
14.
Braz. j. microbiol ; 48(1): 3-4, Jan.-Mar. 2017.
Article in English | LILACS | ID: biblio-839346

ABSTRACT

Abstract Thermococcus thioreducens DSM 14981T, a sulfur-reducing archaeon, was isolated from the rainbow hydrothermal vent site on the Mid-Atlantic Ridge. Herein, we report the draft genome sequence of T. thioreducens DSM 14981T; we obtained 41 contigs with a genome size of 2,052,483 bp and G + C content of 53.5%. This genome sequence will not only help understand how the archaeon adapts to the deep-sea hydrothermal environment but also aid the development of enzymes that are highly stable under extreme conditions for industrial applications.


Subject(s)
Sulfur/metabolism , Thermococcus/genetics , Thermococcus/metabolism , Genome, Archaeal , Genomics , High-Throughput Nucleotide Sequencing , Sequence Analysis, DNA , Computational Biology/methods , Genomics/methods , Molecular Sequence Annotation
15.
Braz. j. microbiol ; 48(1): 1-2, Jan.-Mar. 2017.
Article in English | LILACS | ID: biblio-839362

ABSTRACT

Abstract Pediococcus acidilactici strain K3 is an alcohol-tolerant lactic acid bacterium isolated from nuruk, which is a traditional Korean fermentation starter for makgeolli brewing. Draft genome of this strain was approximately 1,991,399 bp (G+C content, 42.1%) with 1525 protein-coding sequences (CDS), of which 44% were assigned to recognized functional genes. This draft genome sequence data of the strain K3 will provide insights into the genetic basis of its alcohol-tolerance.


Subject(s)
Adaptation, Biological/drug effects , Adaptation, Biological/genetics , Genome, Bacterial , Ethanol/pharmacology , Pediococcus acidilactici/drug effects , Pediococcus acidilactici/genetics , Lactic Acid/biosynthesis , Computational Biology/methods , Genomics/methods , Ethanol/metabolism , Fermentation , High-Throughput Nucleotide Sequencing , Molecular Sequence Annotation , Pediococcus acidilactici/isolation & purification , Pediococcus acidilactici/metabolism
16.
Mem. Inst. Oswaldo Cruz ; 111(12): 721-730, Dec. 2016. tab, graf
Article in English | LILACS | ID: biblio-829257

ABSTRACT

The main challenge in the control of malaria has been the emergence of drug-resistant parasites. The presence of drug-resistant Plasmodium sp. has raised the need for new antimalarial drugs. Molecular modelling techniques have been used as tools to develop new drugs. In this study, we employed virtual screening of a pyrazol derivative (Tx001) against four malaria targets: plasmepsin-IV, plasmepsin-II, falcipain-II, and PfATP6. The receiver operating characteristic curves and area under the curve (AUC) were established for each molecular target. The AUC values obtained for plasmepsin-IV, plasmepsin-II, and falcipain-II were 0.64, 0.92, and 0.94, respectively. All docking simulations were carried out using AutoDock Vina software. The ligand Tx001 exhibited a better interaction with PfATP6 than with the reference compound (-12.2 versus -6.8 Kcal/mol). The Tx001-PfATP6 complex was submitted to molecular dynamics simulations in vacuum implemented on an NAMD program. The ligand Tx001 docked at the same binding site as thapsigargin, which is a natural inhibitor of PfATP6. Compound TX001 was evaluated in vitro with a P. falciparum strain (W2) and a human cell line (WI-26VA4). Tx001 was discovered to be active against P. falciparum (IC50 = 8.2 µM) and inactive against WI-26VA4 (IC50 > 200 µM). Further ligand optimisation cycles generated new prospects for docking and biological assays.


Subject(s)
Humans , Antimalarials/chemistry , Aspartic Acid Endopeptidases/chemistry , Cysteine Endopeptidases/chemistry , Molecular Dynamics Simulation , Protozoan Proteins/chemistry , Thapsigargin/chemistry , Computational Biology/methods , Molecular Targeted Therapy/methods
17.
Mem. Inst. Oswaldo Cruz ; 111(3): 200-208, Mar. 2016. tab, graf
Article in English | LILACS | ID: lil-777367

ABSTRACT

Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline.


Subject(s)
Female , Humans , Male , Breast Neoplasms/virology , DNA, Viral/isolation & purification , /genetics , High-Throughput Nucleotide Sequencing/methods , RNA, Viral/isolation & purification , Stomach Neoplasms/virology , Computers , Computational Biology/methods , Computer Simulation/economics , Cost-Benefit Analysis/methods , Mexico , Nucleic Acids/isolation & purification , Polymerase Chain Reaction/methods , Sequence Analysis, DNA/methods , Sequence Analysis, RNA/methods
18.
Braz. j. med. biol. res ; 49(10): e4897, 2016. tab, graf
Article in English | LILACS | ID: biblio-951649

ABSTRACT

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM.


Subject(s)
Humans , Cardiomyopathy, Dilated/genetics , Computational Biology/methods , Gene Expression Profiling/methods , Transcriptome , Reference Values , Transcription Factors/genetics , Signal Transduction/genetics , Receptors, Androgen/genetics , Down-Regulation , Up-Regulation , MicroRNAs
19.
Arch. argent. pediatr ; 113(5): e256-e259, oct. 2015. ilus
Article in Spanish | LILACS | ID: lil-757065

ABSTRACT

El síndrome de Bazex-Dupré-Christol es una genodermatosis ligada al cromosoma X, la cual se caracteriza por presentar hipotricosis congènita, hipohidrosis, atrofodermia folicular, múltiples quistes de millium y carcinomas basocelulares. Presentamos a una niña y su familia con este síndrome. La paciente y sus hermanos de 5 meses de edad y de 17 años de edad presentaban múltiples quistes de millium e hipotricosis de las cejas y el cuero cabelludo. Su hermano de 8 años presentaba quistes de millium y atrofodermia folicular. Su madre presentaba hipohidrosis, hipotricosis congènita del cuero cabelludo y las cejas, así como también una lesión tumoral en la región paranasal derecha compatible con carcinoma basocelular. Destacamos la importancia del diagnóstico y del seguimiento clínico de estos niños por la posibilidad de desarrollar carcinomas basocelulares.


Bazex-Dupré-Christol syndrome is an X-linked dominantly inherited disorder characterized by congenital hypotrichosis, hypohidrosis, follicular atrophoderma, multiple milia and basal cell carcinomas. We present a girl and her family with this syndrome. Our patient, her 5 month old brother and her 17 year old brother had multiple milia and scalp and eyebrows hypotrichosis. Her 8 year old brother had multiple milia and follicular atrophoderma. Her mother had hypohidrosis and congenital scalp and eyebrows hypotrichosis, as well as a right paranasal lesion suggestive of basal cell carcinoma. We emphasize the importance of precise diagnosis and clinical follow up of these patients due to the possibility of developing basal cell carcinomas.


Subject(s)
Humans , Colitis, Ulcerative/diagnosis , Colitis, Ulcerative/genetics , Crohn Disease/diagnosis , Crohn Disease/genetics , Gene Expression Profiling , Computational Biology/methods , Diagnosis, Differential , Gene Expression Regulation , Gene Regulatory Networks , Genomics/methods , Molecular Sequence Annotation , Protein Interaction Mapping , Protein Interaction Maps
20.
Rev. cuba. invest. bioméd ; 34(1): 54-63, ene.-mar. 2015. ilus
Article in Spanish | LILACS, CUMED | ID: lil-752981

ABSTRACT

INTRODUCCIÓN: las nuevas herramientas informáticas cada vez más influyen en los avances científicos tecnológicos en la esfera de la salud. Una de las áreas de mayor implementación de estas nuevas herramientas de cómputo es sin dudas, la ortopedia, debido en lo fundamental, a la similitud que tiene el cuerpo humano y su estructura ósea con las propiedades de los materiales de ingeniería que permite modelar tejidos y órganos en correspondencia con teorías remodeladoras que predicen su posible comportamiento mecanobiológico. OBJETIVO: describir el comportamiento de una tibia humana ante estímulos externos de torsión. MÉTODOS: se utilizó el Método de los Elementos Finitos implementado en el software profesional ABAQUS/CAE para el cálculo de tensiones y deformaciones presentes en la tibia humana. RESULTADOS: se obtuvo el modelo específico del paciente con síndrome de torsión tibial, a partir de las imágenes médicas de un tomógrafo; las cuales fueron procesadas por ordenador, se utiliza el software de tratamiento de imágenes médicas MIMICS 10.01 para establecer una relación entre la escala de grises (unidades Hounsfield), la densidad ósea y el módulo de Young. CONCLUSIONES: se determinó que el valor correcto de momento torsor estático que debe ser aplicado a este paciente para iniciar el proceso remodelador es de 30 Nm.


INTRODUCTION: new information tools have a growing influence on technological and scientific advances in health care. Orthopedics is one of the areas where new computational tools have been largely implemented, mainly owing to the similarity of the human body and its bone structure to the properties of engineering materials, enabling the modeling of tissues and organs in accordance with remodeling theories predicting their potential mechanobiological behavior. OBJECTIVE: describe the response of a human tibia to external torsion stimuli. METHODS: estimation of tensions and deformities in the human tibia was based on the Finite Element Method incorporated into the professional software Abaqus / CAE. RESULTS: starting from medical tomographic images, a specific model was obtained for a patient with tibial torsion syndrome. The images were computer processed with the medical imaging treatment software MIMICS 10.01 to establish a relationship between the grayscale (Hounsfield units), bone density and Young's modulus. CONCLUSIONS: it was determined that 30 Nm is the correct static torsion moment value to be applied to this patient to start the remodeling process.


Subject(s)
Humans , Tibia , Computational Biology/methods , Finite Element Analysis
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