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1.
Gene ; 806: 145920, 2022 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-34455026

RESUMO

Depression is deemed a mood disorder characterized by a high rate of relapse. Therefore, overcoming of the recurrent depression is globally expecting. Kososan, a traditional Japanese herbal medicine, has been clinically used for mild depressive mood, and our previous studies have shown some evidence for its antidepressive-like efficacy in experimental animal models of depression. However, it remains unclear whether kososan has beneficial effects on recurrent depression. Here, we examined its effect using a mouse model of modified repeated social defeat stress (SDS) paradigm. Male BALB/c mice were exposed to a 5-min SDS from unfamiliar aggressive CD-1 mice for 5 days. Kososan extract (1.0 kg/kg/day) or an antidepressant milnacipran (60 mg/kg/day) was administered orally for 26 days (days 7-32) to depression-like mice with social avoidant behaviors on day 6. Single 5 min of SDS was subjected to mice recovered from the social avoidance on day 31, and then the recurrence of depression-like behaviors was evaluated on day 32. Hippocampal gene expression patterns were also assayed by DNA microarray analysis. Water- or milnacipran-administered mice resulted in a recurrence of depression-like behaviors by re-exposure of single SDS, whereas kososan-administered mice did not recur depression-like behaviors. Distinct gene expression patterns were also found for treating kososan and milnacipran. Collectively, this finding suggests that kososan exerts a preventive effect on recurrent depression-like behaviors in mice. Pretreatment of kososan is more useful for recurrent depression than that of milnacipran.


Assuntos
Antidepressivos/farmacologia , Depressão/prevenção & controle , Medicamentos de Ervas Chinesas/farmacologia , Proteínas do Tecido Nervoso/genética , Derrota Social , Estresse Psicológico/tratamento farmacológico , Administração Oral , Animais , Depressão/genética , Depressão/fisiopatologia , Depressão/psicologia , Modelos Animais de Doenças , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Ontologia Genética , Hipocampo/efeitos dos fármacos , Hipocampo/metabolismo , Hipocampo/fisiopatologia , Japão , Masculino , Medicina Kampo/métodos , Camundongos , Camundongos Endogâmicos BALB C , Milnaciprano/farmacologia , Anotação de Sequência Molecular , Proteínas do Tecido Nervoso/classificação , Proteínas do Tecido Nervoso/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos , Recidiva , Estresse Psicológico/genética , Estresse Psicológico/fisiopatologia
2.
BMC Res Notes ; 14(1): 352, 2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34496950

RESUMO

OBJECTIVE: Illumina BeadChip arrays are commonly used to generate DNA methylation data for large epidemiological studies. Updates in technology over time create challenges for data harmonization within and between studies, many of which obtained data from the older 450K and newer EPIC platforms. The pre-processing pipeline for DNA methylation is not trivial, and influences the downstream analyses. Incorporating different platforms adds a new level of technical variability that has not yet been taken into account by recommended pipelines. Our study evaluated the performance of various tools on different versions of platform data harmonization at each step of pre-processing pipeline, including quality control (QC), normalization, batch effect adjustment, and genomic inflation. We illustrate our novel approach using 450K and EPIC data from the Diabetes Autoimmunity Study in the Young (DAISY) prospective cohort. RESULTS: We found normalization and probe filtering had the biggest effect on data harmonization. Employing a meta-analysis was an effective and easily executable method for accounting for platform variability. Correcting for genomic inflation also helped with harmonization. We present guidelines for studies seeking to harmonize data from the 450K and EPIC platforms, which includes the use of technical replicates for evaluating numerous pre-processing steps, and employing a meta-analysis.


Assuntos
Metilação de DNA , Ilhas de CpG , Estudos Epidemiológicos , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Estudos Prospectivos
3.
Anticancer Res ; 41(9): 4463-4470, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34475070

RESUMO

BACKGROUND/AIM: The treatment of advanced clear cell renal cell carcinoma (ccRCC) is based on stratification of patients according to prognosis (favorable, intermediate, and poor). The aim of the study was to improve prognostication by biomarkers involved in angiogenesis. PATIENTS AND METHODS: The study group consisted of 20 patients who underwent surgery for ccRCC. Gene expression analysis was peformed on a set of matched (primary tumor, metastasis, n=20+20) FFPE tissue samples. An additional analysis was done on expression data of 606 patients obtained from the TCGA Kidney Clear Cell Carcinoma (KIRC) database. Quantitative estimation of mRNA of selected genes (TaqMan human Angiogenesis Array, 97 genes) was performed by a real-time RT-PCR method with TaqMan® arrays. RESULTS: Using the Cox regression model, 4 genes (PDGFB, FGF4, EPHB2 and BAI1) were identified whose expression was related to progression-free interval (PFI). Further analysis using the Kaplan Meier method conclusively revealed the relationship of BAI1 expression to prognosis (both datasets). Patients with higher BAI1 expression had significantly shorter PFI and overall survival. CONCLUSION: We showed that tumor tissue BAI1 expression level is a prognostic marker in ccRCC. Therefore, this gene might be involved in a prognostic panel to improve scoring systems on which the management of metastatic ccRCC patients is based.


Assuntos
Proteínas Angiogênicas/genética , Biomarcadores Tumorais/genética , Carcinoma de Células Renais/genética , Perfilação da Expressão Gênica/métodos , Neoplasias Renais/genética , Receptores Acoplados a Proteínas G/genética , Regulação para Cima , Carcinoma de Células Renais/mortalidade , Carcinoma de Células Renais/cirurgia , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias Renais/mortalidade , Neoplasias Renais/cirurgia , Masculino , Análise de Sequência com Séries de Oligonucleotídeos , Prognóstico , Análise de Regressão , Análise de Sobrevida
4.
Anticancer Res ; 41(9): 4377-4385, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34475057

RESUMO

BACKGROUND/AIM: Expression of pleckstrin homology-like domain family A member 2 (PHLDA2) has been reported to be suppressed or activated in several cases of malignant tumors. However, its apoptotic regulatory mechanism and role in gastric cancer are not understood. This study examined the role of PHLDA2 in apoptosis in gastric cancer. MATERIALS AND METHODS: We used cell culture, western blotting, semiquantitative reverse transcription polymerase chain reaction, MTT assays, and PHLDA2 knockdown with short hairpin RNA (shRNA). RESULTS: To identify the pathway associated with HGF-induced PHLDA2 up-regulation, the cells were treated with PI3-kinase inhibitor (LY294002), MEK inhibitor (PD098059), or p38 inhibitor (SB203580) and then analyzed by western blotting. HGF-mediated changes in PHLDA2 protein levels were only decreased by LY294002. PHLDA2-shRNA cells showed decreased levels of p53 and increased levels of pAKT. Furthermore, HGF-induced cell proliferation and in vitro invasion were increased in PHLDA2 knockdown cells and HGF-induced cell apoptosis was increased in PHLDA2 knockdown cells. CONCLUSION: PHLDA2 plays a role in gastric cancer tumorigenesis by inhibiting apoptosis through the PI3K/AKT pathway.


Assuntos
Fator de Crescimento de Hepatócito/metabolismo , Proteínas Nucleares/metabolismo , Neoplasias Gástricas/metabolismo , Regulação para Cima , Apoptose , Linhagem Celular Tumoral , Cromonas/farmacologia , Flavonoides/farmacologia , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Técnicas de Silenciamento de Genes , Humanos , Imidazóis , Morfolinas/farmacologia , Proteínas Nucleares/genética , Análise de Sequência com Séries de Oligonucleotídeos , Piridinas
5.
Medicine (Baltimore) ; 100(33): e26964, 2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34414965

RESUMO

ABSTRACT: Hepatocellular carcinoma (HCC) is one of the tumors with a higher mortality rate globally, which significantly threatens people's health. Hepatitis C virus (HCV) infection is a major driving factor of HCC. This study aims to determine the key microRNA (miRNA), hub genes, and related pathways, construct potential miRNA-mRNA regulatory networks, and clarify the new molecular mechanism of HCV-related HCC. In this study, 16 differentially expressed miRNAs (DE miRNAs) were identified. The prediction of potential transcription factors and target genes not only found that SP1 and ERG1 may potentially regulate most of the screened DE miRNAs, but it also obtained 2923 and 1782 predicted target genes for the up-regulation and down-regulation of DE miRNAs, respectively. Subsequently, the introduction of differentially expressed genes dataset GSE62232 for target gene verification yielded 98 and 147 potential up-regulation and down-regulation target genes. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes pathway enrichment analysis showed that they were mainly enriched in the cell cycle process, that is, subsequently, 20 hub genes were screened out through the protein-protein interaction network, and related genes were further evaluated using the GEPIA database. Based on the above analysis, the miRNA-hub gene regulatory network was constructed. In short, this research's hub genes and miRNAs closely related to HCV-related HCC were screened and identified through bioinformatics analysis and then built their connection. These results are expected to find potential therapeutic targets for HCV-related HCC.


Assuntos
Carcinoma Hepatocelular/etiologia , Hepatite C/complicações , Neoplasias Hepáticas/etiologia , MicroRNAs/metabolismo , RNA Mensageiro/metabolismo , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/virologia , Biologia Computacional , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Regulação Viral da Expressão Gênica , Hepatite C/metabolismo , Humanos , Neoplasias Hepáticas/metabolismo , Análise de Sequência com Séries de Oligonucleotídeos
6.
Int J Mol Sci ; 22(16)2021 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-34445494

RESUMO

Despite significant advances in treatment of acute coronary syndromes (ACS) many subjects still develop heart failure due to significantly reduced ejection fraction. Currently, there are no commonly available treatment strategies that replace the infarcted/dysfunctional myocardium. Therefore, understanding the mechanisms that control the regeneration of the heart muscle is important. The development of new coronary vessels plays a pivotal role in cardiac regeneration. Employing microarray expression assays and RT-qPCR validation expression pattern of genes in long-term primary cultured cells isolated form the right atrial appendage (RAA) and right atrium (RA) was evaluated. After using DAVID software, it indicated the analysis expression profiles of genes involved in ontological groups such as: "angiogenesis", "blood vessel morphogenesis", "circulatory system development", "regulation of vasculature development", and "vasculature development" associated with the process of creation new blood vessels. The performed transcriptomic comparative analysis between two different compartments of the heart muscle allowed us to indicate the presence of differences in the expression of key transcripts depending on the cell source. Increases in culture intervals significantly increased expression of SFRP2, PRRX1 genes and some other genes involved in inflammatory process, such as: CCL2, IL6, and ROBO1. Moreover, the right atrial appendage gene encoding lysyl oxidase (LOX) showed much higher expression compared to the pre-cultivation state.


Assuntos
Vasos Coronários/crescimento & desenvolvimento , Perfilação da Expressão Gênica/métodos , Desenvolvimento Muscular , Miocárdio/citologia , Animais , Células Cultivadas , Vasos Coronários/química , Regulação da Expressão Gênica no Desenvolvimento , Redes Reguladoras de Genes , Miocárdio/química , Análise de Sequência com Séries de Oligonucleotídeos , Cultura Primária de Células , Suínos , Sequenciamento Completo do Exoma
7.
Int J Mol Sci ; 22(16)2021 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-34445502

RESUMO

Trace amine-associated receptors (TAAR) recognize organic compounds, including primary, secondary, and tertiary amines. The TAAR5 receptor is known to be involved in the olfactory sensing of innate socially relevant odors encoded by volatile amines. However, emerging data point to the involvement of TAAR5 in brain functions, particularly in the emotional behaviors mediated by the limbic system which suggests its potential contribution to the pathogenesis of neuropsychiatric diseases. TAAR5 expression was explored in datasets available in the Gene Expression Omnibus, Allen Brain Atlas, and Human Protein Atlas databases. Transcriptomic data demonstrate ubiquitous low TAAR5 expression in the cortical and limbic brain areas, the amygdala and the hippocampus, the nucleus accumbens, the thalamus, the hypothalamus, the basal ganglia, the cerebellum, the substantia nigra, and the white matter. Altered TAAR5 expression is identified in Down syndrome, major depressive disorder, or HIV-associated encephalitis. Taken together, these data indicate that TAAR5 in humans is expressed not only in the olfactory system but also in certain brain structures, including the limbic regions receiving olfactory input and involved in critical brain functions. Thus, TAAR5 can potentially be involved in the pathogenesis of brain disorders and represents a valuable novel target for neuropsychopharmacology.


Assuntos
Encéfalo/metabolismo , Transtorno Depressivo Maior/genética , Síndrome de Down/genética , Regulação para Baixo , Encefalite Viral/genética , Infecções por HIV/complicações , Receptores Acoplados a Proteínas G/genética , Bases de Dados Genéticas , Encefalite Viral/etiologia , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Infecções por HIV/genética , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Análise de Sequência de RNA , Distribuição Tecidual
8.
Nutrients ; 13(7)2021 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-34371941

RESUMO

Insulin-like growth factors (IGFs) and insulin-like growth-factor-binding proteins (IGFBPs) regulate cell proliferation and differentiation and may be of importance in obesity development. The aim of the study was to analyze the expression of chosen IGF-axis genes and the concentration of their protein products in 28 obese children (OB) and 34 healthy control (HC), and their correlation with essential parameters associated with childhood obesity. The gene expression of IGFBP7 was higher, and the expression of IGF2 and IGFBP1 genes was lower in the OB. The expression of IGFBP6 tended to be lower in OB. IGFBP4 concentration was significantly higher, and IGFBP3 tended to be higher in the OB compared to the HC, while IGFBP1, IGFBP2, and IGFBP6 were significantly lower, and IGFBP7 tended to be lower in OB. We found numerous correlations between IGFs and IGFBP concentration and obesity metabolic parameters. IGFBP6 correlated positively with apelin, cholecystokinin, glucagone-like peptide-1, and leptin receptor. These peptides were also significantly lower in obese children in our study. The biological role of decreased levels of IGFBP6 in obese children needs further investigation.


Assuntos
Proteínas de Ligação a Fator de Crescimento Semelhante a Insulina/sangue , Fator de Crescimento Insulin-Like II/análise , Fator de Crescimento Insulin-Like I/análise , Obesidade Pediátrica/sangue , Adipocinas/sangue , Adolescente , Biomarcadores/sangue , Estudos de Casos e Controles , Criança , Pré-Escolar , Ensaio de Imunoadsorção Enzimática , Feminino , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Humanos , Proteínas de Ligação a Fator de Crescimento Semelhante a Insulina/genética , Fator de Crescimento Insulin-Like I/genética , Fator de Crescimento Insulin-Like II/genética , Masculino , Análise de Sequência com Séries de Oligonucleotídeos , Obesidade Pediátrica/diagnóstico , Obesidade Pediátrica/genética
9.
Sensors (Basel) ; 21(11)2021 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-34204136

RESUMO

Most existing commercial real-time polymerase chain reaction (RT-PCR) instruments are bulky because they contain expensive fluorescent detection sensors or complex optical structures. In this paper, we propose an RT-PCR system using a camera module for smartphones that is an ultra small, high-performance and low-cost sensor for fluorescence detection. The proposed system provides stable DNA amplification. A quantitative analysis of fluorescence intensity changes shows the camera's performance compared with that of commercial instruments. Changes in the performance between the experiments and the sets were also observed based on the threshold cycle values in a commercial RT-PCR system. The overall difference in the measured threshold cycles between the commercial system and the proposed camera was only 0.76 cycles, verifying the performance of the proposed system. The set calibration even reduced the difference to 0.41 cycles, which was less than the experimental variation in the commercial system, and there was no difference in performance.


Assuntos
Técnicas de Amplificação de Ácido Nucleico , Smartphone , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase em Tempo Real
10.
J Plant Physiol ; 264: 153471, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34315029

RESUMO

During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, likely affecting the global RNA profile of rice genes. Most genes that exhibit sugar-regulation in rice embryos under aerobic conditions are responsive to low energy and anaerobic conditions, indicating that sugar regulation is strongly associated with energy and anaerobic signaling. The interference pattern of sugar regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for altering the expression of sugar-regulated genes. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar regulated gene expression. Anaerobically responsive genes substantially overlap with low energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those provoked by low energy conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It has been noted that abscisic acid (ABA) responsive genes are over representative of genes upregulated under low energy conditions, in contrast to downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.


Assuntos
Germinação , Oryza/embriologia , Sementes/metabolismo , Metabolismo Energético , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Análise de Sequência com Séries de Oligonucleotídeos , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Oxigênio/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Sementes/crescimento & desenvolvimento , Açúcares/metabolismo
11.
J Neural Eng ; 18(4)2021 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-34280903

RESUMO

The brain is the most complex organ of our body. Such a complexity spans from the single-cell morphology up to the intricate connections that hundreds of thousands of neurons establish to create dense neuronal networks. All these components are involved in the genesis of the rich patterns of electrophysiological activity that characterize the brain. Over the years, researchers coming from different disciplines developedin vitrosimplified experimental models to investigate in a more controllable and observable way how neuronal ensembles generate peculiar firing rhythms, code external stimulations, or respond to chemical drugs. Nowadays, suchin vitromodels are namedbrain-on-a-chippointing out the relevance of the technological counterpart as artificial tool to interact with the brain: multi-electrode arrays are well-used devices to record and stimulate large-scale developing neuronal networks originated from dissociated cultures, brain slices, up to brain organoids. In this review, we will discuss the state of the art of the brain-on-a-chip, highlighting which structural and biological features a realisticin vitrobrain should embed (and how to achieve them). In particular, we identified two topological features, namely modular and three-dimensional connectivity, and a biological one (heterogeneity) that takes into account the huge number of neuronal types existing in the brain. At the end of this travel, we will show how 'far' we are from the goal and how interconnected-brain-regions-on-a-chip is the most appropriate wording to indicate the current state of the art.


Assuntos
Dispositivos Lab-On-A-Chip , Neurônios , Encéfalo , Fenômenos Eletrofisiológicos , Análise de Sequência com Séries de Oligonucleotídeos
12.
Talanta ; 233: 122589, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34215079

RESUMO

Digital bioassays are powerful methods to detect rare analytes from complex mixtures and study the temporal processes of individual entities within biological systems. In digital bioassays, a crucial first step is the discretization of samples into a large number of identical independent partitions. Here, we developed a rapid and facile sample partitioning method for versatile digital bioassays. This method is based on a detachable self-digitization (DSD) chip which couples a reversible assembly configuration and a predegassing-based self-pumping mechanism to achieve an easy, fast, and large-scale sample partitioning. The DSD chip consists of a channel layer used for loading the sample and a microwell layer used for holding the sample partitions. Benefitting from its detachability, the chip avoids a lengthy oil flushing process used to remove the excess sample in loading channels and can compartmentalize a sample into more than 100,000 wells of picoliter volume with densities up to 14,000 wells/cm2 in less than 30 s. We also demonstrated the utility of the proposed method by applying it to digital PCR and digital microbial assays.


Assuntos
Bioensaio , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase
13.
Molecules ; 26(12)2021 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-34207029

RESUMO

The application of micro-Raman spectroscopy was used for characterization of structural features of the high-k stack (h-k) layer of "silicon-on-insulator" (SOI) nanowire (NW) chip (h-k-SOI-NW chip), including Al2O3 and HfO2 in various combinations after heat treatment from 425 to 1000 °C. After that, the NW structures h-k-SOI-NW chip was created using gas plasma etching optical lithography. The stability of the signals from the monocrine phase of HfO2 was shown. Significant differences were found in the elastic stresses of the silicon layers for very thick (>200 nm) Al2O3 layers. In the UV spectra of SOI layers of a silicon substrate with HfO2, shoulders in the Raman spectrum were observed at 480-490 cm-1 of single-phonon scattering. The h-k-SOI-NW chip created in this way has been used for the detection of DNA-oligonucleotide sequences (oDNA), that became a synthetic analog of circular RNA-circ-SHKBP1 associated with the development of glioma at a concentration of 1.1 × 10-16 M. The possibility of using such h-k-SOI NW chips for the detection of circ-SHKBP1 in blood plasma of patients diagnosed with neoplasm of uncertain nature of the brain and central nervous system was shown.


Assuntos
Glioma/genética , Nanofios/química , RNA Circular/química , RNA Circular/genética , Silício/química , Idoso , Técnicas Biossensoriais/métodos , Encéfalo/efeitos dos fármacos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Análise Espectral Raman/métodos
14.
Trop Anim Health Prod ; 53(3): 395, 2021 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-34245361

RESUMO

BACKGROUND: Assigning animals to their corresponding breeds through breed informative single-nucleotide polymorphisms (SNPs) is required in many fields. For instance, it is used in the traceability and the authentication of meat and other livestock products. SNPs' information for several pork breeds are now accessible thanks to the availability of dense SNP chips. These SNP chips cover a large number of molecular markers distributed across the entire genome. To identify the pork breed from a sample of industrial meat, one must analyze a large panel of genetic markers depending on the SNP chip used. The analysis of such large datasets requires intensive work. This leads to the idea of creating less dense chips of breed informative markers based on a reduced number of SNPs. Therefore, the analysis of the data emanating from the genotyping of these reduced chips will require less time and effort. AIM: The objective of this study is to find the most informative SNPs for the discrimination between four pig breeds, namely Duroc, Landrace, Large White, and Pietrain. METHOD: The Illumina Porcine 60 k SNP chip was used to genotype SNPs distributed all over the individuals' genomes. Firstly, we used three different statistical approaches for feature selection: (i) principal component analysis (PCA), (ii) least absolute shrinkage and selection operator (LASSO), and (iii) random forest (RF). These three approaches identified three sets of SNPs; each set corresponds to one approach. Then, we combined the results of the three methods by setting up a final panel containing the SNPs which appear on the three sets altogether. RESULTS: Separately, each method resulted in a panel with the corresponding most discriminating SNPs. The PCA, the LASSO, and the random forest with Boruta algorithm highlighted 28,816, 50, and 286 SNPs, respectively. The number of SNPs selected by PCA is high compared to Boruta and LASSO because PCA chooses the variables while preserving as much information about the data as possible. The only downside of LASSO regression is that among a group of correlated variables, LASSO tends to select only one variable and ignore the others regardless of their importance. Contrarily to LASSO, the Boruta algorithm considers the interdependence between SNPs and selects informative variables even if they are correlated and have the same effect. The three panels shared 23 SNPs; the distribution of the individuals according to these SNPs showed a grouping of individuals of each breed in well-defined clusters without any overlapping. CONCLUSIONS: The biological pathways represented by 23 breed informative SNPs resulted by the combination of PCA, LASSO, and Boruta should be explored in further analysis. The results provided by our study are promising for further applications of this method in other livestock animals.


Assuntos
Genética Populacional , Polimorfismo de Nucleotídeo Único , Animais , Marcadores Genéticos , Genótipo , Análise de Sequência com Séries de Oligonucleotídeos/veterinária , Suínos/genética
15.
Lab Chip ; 21(15): 2857-2868, 2021 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-34251386

RESUMO

Organ on chip (OoC) devices represent the cutting edge of biotechnologies, combining advanced cell and tissue culture with microengineering. OoC is accelerating innovation in the life sciences and has the potential to revolutionise many fields including biomedical research, drug development and chemical risk assessment. In order to gain acceptance by end-users of OoC based methods and the data derived from them, and to establish OoC approaches as credible alternatives to animal testing, OoC devices need to go through an extensive qualification process. In this context, standardisation can play a key role in ensuring proper characterisation of individual devices, benchmarking against appropriate reference elements and aiding efficient communication among stakeholders. The development of standards for OoC will address several important issues such as basic terminology, device classification, and technical and biological performance. An analysis of technical and biological aspects related to OoC is presented here to identify standardisation areas specific for OoC, focusing on needs and opportunities. About 90 standards are already available from related fields including microtechnologies, medical devices and in vitro cell culture, laying the basis for future work in the OoC domain. Finally, two priority areas for OoC are identified that could be addressed with standards, namely, characterisation of small molecule absorption and measurement of microfluidic parameters.


Assuntos
Dispositivos Lab-On-A-Chip , Microfluídica , Animais , Técnicas de Cultura de Células , Análise de Sequência com Séries de Oligonucleotídeos
16.
Aging (Albany NY) ; 13(13): 17328-17336, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34198263

RESUMO

BACKGROUND: Circular RNAs (circRNAs) have recently emerged as a new class of RNAs, highly enriched in the human tissues and very stable within cells, exosomes and body fluids. In this study, we aimed to screen the plasma cell-free derived circRNAs in laryngeal squamous cell carcinoma (LSCC) and investigate whether these circRNAs could predicted LSCC as potential biomarkers. METHODS: The circRNA microarray was employed with three samples in each group to screen the dysregulated circRNAs isolated from plasma samples. The top 20 circRNAs were first selected as candidates with the upregulated level in the plasma of LSCC. RESULTS: Further validation found that only circ_0019201, circ_0011773 and circ_0122790 was consistent with training set. The ROC curve also revealed a high diagnostic ability an area under ROC curve value (AUC) for single circRNA and combined. The AUC for circ_0019201, circ_0011773 and circ_0122790 and the combined was 0.933, 0.908, 0.965 and 0.990 in training set. For the validation set, the AUC was 0.766, 0.864, 0.908 and 0.951. The three circRNAs were further investigated with stable expression in human plasma samples. CONCLUSIONS: The plasma derived circ_0019201, circ_0011773 and circ_0122790 might be the potential biomarker for predicting the LSCC.


Assuntos
Carcinoma de Células Escamosas/genética , Impressões Digitais de DNA/métodos , Neoplasias Laríngeas/genética , RNA Circular/genética , Adulto , Idoso , Biomarcadores Tumorais , Estudos de Casos e Controles , Ácidos Nucleicos Livres , Feminino , Humanos , Masculino , Análise em Microsséries , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos , Valor Preditivo dos Testes , Curva ROC , Reprodutibilidade dos Testes , Estudos Retrospectivos
17.
Sheng Wu Gong Cheng Xue Bao ; 37(7): 2543-2553, 2021 Jul 25.
Artigo em Chinês | MEDLINE | ID: mdl-34327919

RESUMO

We designed and fabricated a novel high throughput brain-on-chip with three dimensional structure with the aim to simulate the in vivo three-dimensional growth environment for brain tissues. The chip consists of a porous filter and 3D brain cell particles, and is loaded into a conventional 96-well plate for use. The filter and the particle molds were fabricated by using computer modeling, 3D printing of positive mold and agarose-PDMS double reversal mold. The 3D cell particles were made by pouring and solidifying a suspension of mouse embryonic brain cells with sodium alginate into a cell particle mold, and then cutting the resulting hydrogel into pieces. The loaded brain-on-chip was used to determine the neurotoxicity of pesticides. The cell particles were exposed to 0, 10, 30, 50, 100 and 200 µmol/L of chlorpyrifos or imidacloprid, separated conveniently from the medium by removing the porous filter after cultivation. Subsequently, cell proliferation, acetylcholinesterase activity and lactate dehydrogenase release were determined for toxicity evaluation. The embryonic brain cells were able to grow and proliferate normally in the hydrogel particles loaded into the filter in a 96-well plate. Pesticide neurotoxicity test showed that both chlorpyrifos and imidacloprid presented dose-dependent inhibition on cell growth and proliferation. Moreover, the pesticides showed inhibition on acetylcholinesterase activity and increase release of lactate dehydrogenase. However, the effect of imidacloprid was significantly weaker than that of chlorpyrifos. In conclusion, a novel brain-on-chip was developed in this study, which can be used to efficiently assess the drug neurotoxicity, pharmacodynamics, and disease mechanism by combining with a microtiterplate reader.


Assuntos
Clorpirifos , Praguicidas , Animais , Encéfalo , Clorpirifos/toxicidade , Meios de Cultura , Camundongos , Análise de Sequência com Séries de Oligonucleotídeos , Praguicidas/toxicidade
18.
Medicine (Baltimore) ; 100(25): e26499, 2021 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-34160465

RESUMO

BACKGROUND: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple organ damage and the production of a variety of autoantibodies. The pathogenesis of SLE has not been fully defined, and it is difficult to treat. Our study aimed to identify candidate genes that may be used as biomarkers for the screening, diagnosis, and treatment of SLE. METHODS: We used the GEO2R tool to identify the differentially expressed genes (DEGs) in SLE-related datasets retrieved from the Gene Expression Omnibus (GEO). In addition, we also identified the biological functions of the DEGs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Additionally, we constructed protein-protein interaction (PPI) networks to identify hub genes, as well as the regulatory network of transcription factors related to DEGs. RESULTS: Two datasets were identified for use from the GEO (GSE50772, GSE4588), and 34 up-regulated genes and 4 down-regulated genes were identified by GEO2R. Pathway analysis of the DEGs revealed enrichment of the interferon alpha/beta signaling pathway; GO analysis was mainly enriched in response to interferon alpha, regulation of ribonuclease activity. PPIs were constructed through the STRING database and 14 hub genes were selected and 1 significant module (score = 12.923) was obtained from the PPI network. Additionally, 11 key transcription factors that interacted closely with the 14 hub DEGs were identified from the gene transcription factor network. CONCLUSIONS: Bioinformatic analysis is an effective tool for screening the original genomic data in the GEO database, and a large number of SLE-related DEGs were identified. The identified hub DEGs may be potential biomarkers of SLE.


Assuntos
Regulação da Expressão Gênica/imunologia , Redes Reguladoras de Genes , Lúpus Eritematoso Sistêmico/genética , Fatores de Transcrição/metabolismo , Biomarcadores/análise , Biologia Computacional , Conjuntos de Dados como Assunto , Perfilação da Expressão Gênica , Humanos , Lúpus Eritematoso Sistêmico/imunologia , Análise de Sequência com Séries de Oligonucleotídeos , Mapeamento de Interação de Proteínas , Mapas de Interação de Proteínas/genética , Transdução de Sinais/genética , Transdução de Sinais/imunologia
19.
Anim Genet ; 52(4): 560-564, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34096079

RESUMO

Qira black sheep is a famous indigenous sheep breed in China. The objectives of this study are to identify candidate genes related to body size, and to estimate the level of inbreeding depression on body size based on runs of homozygosity in Qira black sheep. Here, 188 adult Qira black sheep were genotyped with a high density (630 K) SNP chip and genome-wide association study for body weight and body size traits (including withers height, body slanting length, tail length, chest girth, chest width, and chest depth) were performed using an additive linear model. In consequence, 12 genome- and chromosome-wide significant SNPs and, accordingly, six candidate genes involved in muscle differentiation, metabolism and cell processes were identified. Of them, ZNF704 (zinc finger protein 704) was identified for body weight; AK2 (adenylate kinase 2) and PARK2 (parkin RBR E3 ubiquitin protein ligase) for tail length; MOCOS (molybdenum cofactor sulfurase) and ELP2 (elongator acetyltransferase complex subunit 2) for chest width; and MFAP1 (microfibril associated protein 1) for chest girth. Additionally, inbreeding depressions on body size were observed in the current herd. These results will provide insightful understandings into the genetic mechanisms of adult body size, and into the conservation and utilization of Qira black sheep.


Assuntos
Tamanho Corporal/genética , Estudo de Associação Genômica Ampla/veterinária , Depressão por Endogamia/genética , Polimorfismo de Nucleotídeo Único , Carneiro Doméstico/fisiologia , Animais , Feminino , Genótipo , Análise de Sequência com Séries de Oligonucleotídeos/veterinária , Carneiro Doméstico/genética
20.
Methods Mol Biol ; 2348: 45-53, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34160798

RESUMO

Despite the fact that next-generation sequencing approaches, in particular RNA sequencing, provide deep genome-wide expression data that allow both careful annotations/mapping of long noncoding RNA (lncRNA) molecules and de-novo sequencing, lncRNA expression studies by microarray is a still cost-effective procedure that could allow to have a landscape of the most characterized lncRNA species. However, microarray design does not always correctly address the overlap between coding and noncoding samples to discriminate between the original transcript source. In order to overcome this issue, in this chapter we present a bioinformatics pipeline that enables accurate annotation of GeneChip® microarrays, to date the most commonly adopted among the commercial solutions. Overall, this approach holds two main advantages, a gain in specificity of transcript detection and the adaptability to the whole panel of GeneChip® arrays.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica , Análise de Sequência com Séries de Oligonucleotídeos , RNA Longo não Codificante , Transcriptoma , Algoritmos , Bases de Dados Genéticas , Perfilação da Expressão Gênica/métodos , Estudo de Associação Genômica Ampla/métodos , Humanos , Anotação de Sequência Molecular , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Software , Interface Usuário-Computador
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