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1.
Phys Chem Chem Phys ; 21(37): 20678-20692, 2019 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-31508628

RESUMO

In this work we present a high-throughput approach to the computation of absorption UV-Vis spectra tailored to mutagenesis studies. The scheme makes use of a single molecular dynamics trajectory of a reference (non-mutated) species. The shifts in absorption energy caused by a residue mutation are evaluated by building an effective potential of the environment and computing a correction term based on perturbation theory. The sampling is only performed in the phase space of the initial protein. We analyze the robustness of the method by comparing different approximations for the effective potential, the sampling of mutant residue geometries and observing the impact in the prediction of both bathocromic and hypsochromic shifts. As a test subject, we consider a red fluorescent protein variant with potential biotechnological applications.


Assuntos
Testes Genéticos/métodos , Luz , Proteínas/química , Proteínas/genética , Análise Espectral , Raios Ultravioleta , Simulação de Dinâmica Molecular , Mutação
2.
Anticancer Res ; 39(9): 4637-4642, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31519561

RESUMO

AIM: The aim of this study was to characterize the role of Alport syndrome, mental retardation, midface hypoplasia, and elliptocytosis chromosomal region gene 1 (AMMECR1) in human lung cancer cell lines. MATERIALS AND METHODS: AMMECR1 gene expression was evaluated in four lung cell lines, with A549 then selected for further in-depth examination. To characterize the role of AMMECR1, silencing was achieved utilizing lentivirus-mediated RNA interference, and confirmed by quantitative real-time polymerase chain reaction and western blotting. The impact of AMMECR1 silencing on cellular proliferation was assessed using Celigo-based and MTT assays. Apoptosis was determined using the annexin V-allophycocyanin single staining method. Cell-cycle arrest was assessed by flow cytometry. Finally, colony formation was assessed using Giemsa staining. RESULTS: In A549 cells, AMMECR1 silencing was found to significantly suppress cell proliferation, reduce colony formation, promote apoptosis, and arrest cells in the S and G2/M phases. CONCLUSION: AMMECR1 plays a critical role in cell proliferation, cell-cycle progression, and apoptosis of human lung cancer cells, and may serve as a potential therapeutic target for non-small-cell lung cancer.


Assuntos
Apoptose/genética , Ciclo Celular/genética , Neoplasias Pulmonares/genética , Proteínas/genética , Células A549 , Linhagem Celular Tumoral , Expressão Gênica , Técnicas de Inativação de Genes , Humanos , Neoplasias Pulmonares/metabolismo , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/patologia , Proteínas/metabolismo , RNA Mensageiro/genética
3.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(9): 910-913, 2019 Sep 10.
Artigo em Chinês | MEDLINE | ID: mdl-31515788

RESUMO

OBJECTIVE: To explore the genetic basis for an infant featuring developmental delay, hand deformity and hypertonia of extremities. METHODS: Clinical data and peripheral blood samples of the proband and her parents were collected. Following DNA extraction, potential mutations were screened on an Ion PGM platform using a gene panel. Suspected mutation was verified by PCR and Sanger sequencing. RESULTS: A novel heterozygous nonsense mutation, c.2521C>T(p.R841X), was identified in the NIPBL gene. The mutation may cause premature termination of translation of the adhesion protein loading factor at 841st amino acids. The same mutation was not found in her parents and 931 healthy controls, and was absent from public databases including ExAC and 1000G. Bioinformatic analysis suggested the mutation to be disease causing. CONCLUSION: The c.2521C>T (p.R841X) mutation of the NIPBL gene probably underlies the Cornelia De Lange syndrome in the infant. Prenatal diagnosis may be provided to this family upon their subsequent pregnancy.


Assuntos
Síndrome de Lange/genética , Diagnóstico Pré-Natal , Proteínas/genética , Síndrome de Lange/diagnóstico , Feminino , Heterozigoto , Humanos , Lactente , Mutação , Gravidez
4.
J Chem Phys ; 151(4): 041101, 2019 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-31370538

RESUMO

We chemically characterize the symmetries underlying the exact solutions of a stochastic negatively self-regulating gene. The breaking of symmetry at a low molecular number causes three effects. Two branches of the solution exist, having high and low switching rates, such that the low switching rate branch approaches deterministic behavior and the high switching rate branch exhibits sub-Fano behavior. The average protein number differs from the deterministically expected value. Bimodal probability distributions appear as the protein number becomes a readout of the ON/OFF state of the gene.


Assuntos
Proteínas/genética , Cinética , Teoria Quântica , Soluções , Processos Estocásticos
5.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 27(4): 1013-1019, 2019 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-31418350

RESUMO

OBJECTIVE: To investigate the effect of silencing LNK gene on the expression of EPO and EPOR in acute myeloid leukemia cells (THP-1). METHODS: THP-1 cells were cultured. The lentivirus was used as a vector to silence the LNK gene stably. After 72 hours of infection, GFP expression level was detected by the fluorescent inverted microscopy. The lentiviral Infection efficiencies were monitored by flow cytometry. The LNK silencing effect was confirmed. The mRNA expressions of EPO and EPOR were detected by RT-PCR. The protein levels of LNK, EPO and EPOR were detected by Western blot. RESULTS: At the time-point of 72 hours after lentivirus infection, the expression level of GFP was above 85% detected by fluorescent inverted microscopy. The infection efficiency was above 99% by flow cytometry. mRNA expressions of LNK, EPO and EPOR in LNK silencing group were signifycantly lower than those in control group (P<0.05). The protein levels of LNK, EPO and EPOR in LNK silencing group were significantly lower than those in the control group (P<0.05). CONCLUSION: THP-1 cell line of LNK gene silencing has been successfully established,the LNK gene has been silenced, the expression of EPO and EPOR decrease, indicating that LNK may participate in the regulation of EPO and EPOR.


Assuntos
Proteínas/genética , Western Blotting , Eritropoetina , Inativação Gênica , Humanos , Receptores da Eritropoetina , Células THP-1
6.
Medicine (Baltimore) ; 98(33): e16899, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31415434

RESUMO

Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive multisystem disorder characterized by oculocutaneous albinism (OCA) and bleeding diathesis, although it displays both genetic and phenotypic heterogeneity. Several genetic subtypes of HPS have been identified in human; however, the characterizations of HPS type 4 (HPS-4) genotype and phenotype remain unclear. This study was aimed to identify gene mutation responsible for HPS-4 with pulmonary fibrosis (PF).Two Chinese siblings in their 50 s afflicted with OCA and progressive dyspnea were recruited and underwent clinical and genetic examinations. In both patients, chest high-resolution computerized tomography showed severe interstitial PF in bilateral lung fields, and the pulmonary function test indicated restrictive lung disease. A novel homozygous frameshift mutation (NM_022081: c.630dupC; p.A211fs) in the HPS4 gene was identified by whole-exome sequencing analysis followed by Sanger DNA sequencing, and it segregated with the phenotypes. The c.630dupC mutation was not found in unaffected healthy controls. The patients were considered as HPS-4 with interstitial PF and eventually died of respiratory failure.This is the first report on the genotype and clinical phenotype of HPS-4 in China. Our results demonstrate the association between a novel frameshift mutation in HPS4 and severe PF with poor prognosis in HPS is presented.


Assuntos
Mutação da Fase de Leitura , Síndrome de Hermanski-Pudlak/genética , Fibrose Pulmonar Idiopática/genética , Proteínas/genética , Adulto , China , Testes Genéticos , Humanos , Fibrose Pulmonar Idiopática/diagnóstico por imagem , Masculino , Pessoa de Meia-Idade , Análise de Sequência de DNA , Irmãos
7.
BMC Bioinformatics ; 20(Suppl 14): 335, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-31266447

RESUMO

BACKGROUND: Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding the relationship between protein structure and function. To this end, several methods have been developed to predict changes in the Gibbs free energy of unfolding (∆∆G) between wild type and variant proteins, using sequence and structure information. Most of the available methods however do not exhibit the anti-symmetric prediction property, which guarantees that the predicted ∆∆G value for a variation is the exact opposite of that predicted for the reverse variation, i.e., ∆∆G(A → B) = -∆∆G(B → A), where A and B are amino acids. RESULTS: Here we introduce simple anti-symmetric features, based on evolutionary information, which are combined to define an untrained method, DDGun (DDG untrained). DDGun is a simple approach based on evolutionary information that predicts the ∆∆G for single and multiple variations from sequence and structure information (DDGun3D). Our method achieves remarkable performance without any training on the experimental datasets, reaching Pearson correlation coefficients between predicted and measured ∆∆G values of ~ 0.5 and ~ 0.4 for single and multiple site variations, respectively. Surprisingly, DDGun performances are comparable with those of state of the art methods. DDGun also naturally predicts multiple site variations, thereby defining a benchmark method for both single site and multiple site predictors. DDGun is anti-symmetric by construction predicting the value of the ∆∆G of a reciprocal variation as almost equal (depending on the sequence profile) to -∆∆G of the direct variation. This is a valuable property that is missing in the majority of the methods. CONCLUSIONS: Evolutionary information alone combined in an untrained method can achieve remarkably high performances in the prediction of ∆∆G upon protein mutation. Non-trained approaches like DDGun represent a valid benchmark both for scoring the predictive power of the individual features and for assessing the learning capability of supervised methods.


Assuntos
Algoritmos , Estabilidade Proteica , Proteínas/química , Sequência de Aminoácidos , Evolução Molecular , Humanos , Mutação Puntual , Proteínas/genética , Termodinâmica
8.
Cancer Immunol Immunother ; 68(8): 1379-1389, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31338557

RESUMO

Squamous cell carcinoma of the head and neck (SCCHN) is the sixth most common cancer worldwide and epidermal growth factor receptor (EGFR) is overexpressed in greater than 90% of patient tumors. Cetuximab is a monoclonal antibody that binds to EGFR and can activate immune cells, such as natural killer (NK) cells, that express receptors for the Fc (constant region) of immunoglobulin G. IL-15 (interleukin-15) is a critical factor for the development, proliferation and activation of effector NK cells. A novel IL-15 compound known as ALT-803 that consists of genetically modified IL-15 plus the IL-15 receptor alpha protein (IL15Rα) fused to the Fc portion of IgG1 has recently been developed. We hypothesized that treatment with ALT-803 would increase NK cell-mediated cytotoxicity of cetuximab-coated head and neck squamous cells. CD56+ NK cells from normal healthy donors were treated overnight with ALT-803 and tested for their ability to lyse cetuximab-coated tumor cells. Cytotoxicity was greater following NK cell ALT-803 activation, as compared to controls. ALT-803-treated NK cells secreted significantly higher levels of IFN-γ than control conditions. Additionally, NK cells showed increased levels of phospho-ERK and phospho-STAT5 when co-cultured with cetuximab-coated tumors and ALT-803. Administration of both cetuximab and ALT-803 to mice harboring Cal27 SCCHN tumors resulted in significantly decreased tumor volume when compared to controls and compared to single-agent treatment alone. Overall, the present data suggest that cetuximab treatment in combination with ALT-803 in patients with EGFR-positive SCCHN may result in significant NK cell activation and have important anti-tumor activity.


Assuntos
Antineoplásicos/uso terapêutico , Carcinoma de Células Escamosas/tratamento farmacológico , Cetuximab/uso terapêutico , Neoplasias de Cabeça e Pescoço/tratamento farmacológico , Imunoterapia/métodos , Células Matadoras Naturais/imunologia , Proteínas/uso terapêutico , Animais , Carcinoma de Células Escamosas/imunologia , Linhagem Celular Tumoral , Citotoxicidade Imunológica , Receptores ErbB/imunologia , Receptores ErbB/metabolismo , Neoplasias de Cabeça e Pescoço/imunologia , Humanos , Interferon gama/metabolismo , Interleucina-15/genética , Células Matadoras Naturais/efeitos dos fármacos , Ativação Linfocitária , Camundongos , Proteínas/genética , Receptores de Interleucina-15/genética , Proteínas Recombinantes de Fusão/genética , Carga Tumoral , Ensaios Antitumorais Modelo de Xenoenxerto
9.
Nat Commun ; 10(1): 2905, 2019 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-31266953

RESUMO

Delivery into mammalian cells remains a significant challenge for many applications of proteins as research tools and therapeutics. We recently reported that the fusion of cargo proteins to a supernegatively charged (-30)GFP enhances encapsulation by cationic lipids and delivery into mammalian cells. To discover polyanionic proteins with optimal delivery properties, we evaluate negatively charged natural human proteins for their ability to deliver proteins into cultured mammalian cells and human primary fibroblasts. Here we discover that ProTα, a small, widely expressed, intrinsically disordered human protein, enables up to ~10-fold more efficient cationic lipid-mediated protein delivery compared to (-30)GFP. ProTα enables efficient delivery at low- to mid-nM concentrations of two unrelated genome editing proteins, Cre recombinase and zinc-finger nucleases, under conditions in which (-30)GFP fusion or cationic lipid alone does not result in substantial activity. ProTα may enable mammalian cell protein delivery applications when delivery potency is limiting.


Assuntos
Edição de Genes/métodos , Lipossomos/química , Proteínas/química , Edição de Genes/instrumentação , Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Células HeLa , Humanos , Integrases/química , Integrases/genética , Integrases/metabolismo , Lipossomos/metabolismo , Transporte Proteico , Proteínas/genética , Proteínas/metabolismo , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Nucleases de Dedos de Zinco/química , Nucleases de Dedos de Zinco/genética , Nucleases de Dedos de Zinco/metabolismo
10.
Cytogenet Genome Res ; 158(3): 121-125, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31315107

RESUMO

VACTERL association is defined by the occurrence of congenital malformations: vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula with esophageal atresia, radial and renal dysplasia, and limb defects. No genetic alterations have been discovered except for some sporadic chromosomal rearrangements and gene mutations. We report a boy with VACTERL association and shawl scrotum with bifid scrotum who presented with a de novo Yq11.223q11.23 microdeletion identified by array CGH. The deletion spans 3.1 Mb and encompasses several genes in the AZFc region, frequently deleted in infertile men with severe oligozoospermia or azoospermia. Herein, we discuss the possible explanation for this unusual genotype-phenotype correlation. We suggest that the deletion of the BPY2 (previously VCY2) gene, located in the AZFc region and involved in spermatogenesis, contributed to the genesis of the phenotype. In fact, BPY2 interacts with a ubiquitin-protein ligase, involved in the SHH pathway which is known to be implicated in the genesis of VACTERL association.


Assuntos
Canal Anal/anormalidades , Deleção Cromossômica , Cromossomos Humanos Y/genética , Esôfago/anormalidades , Cardiopatias Congênitas/genética , Cardiopatias Congênitas/patologia , Rim/anormalidades , Deformidades Congênitas dos Membros/genética , Deformidades Congênitas dos Membros/patologia , Proteínas/genética , Escroto/patologia , Coluna Vertebral/anormalidades , Traqueia/anormalidades , Canal Anal/patologia , Hibridização Genômica Comparativa , Esôfago/patologia , Estudos de Associação Genética , Humanos , Lactente , Rim/patologia , Masculino , Coluna Vertebral/patologia , Traqueia/patologia , Ubiquitina-Proteína Ligases/metabolismo , Incerteza
11.
BMC Bioinformatics ; 20(1): 393, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311505

RESUMO

BACKGROUND: MicroRNAs (miRNAs) are small RNAs that regulate gene expression at a post-transcriptional level and are emerging as potentially important biomarkers for various disease states, including pancreatic cancer. In silico-based functional analysis of miRNAs usually consists of miRNA target prediction and functional enrichment analysis of miRNA targets. Since miRNA target prediction methods generate a large number of false positive target genes, further validation to narrow down interesting candidate miRNA targets is needed. One commonly used method correlates miRNA and mRNA expression to assess the regulatory effect of a particular miRNA. The aim of this study was to build a bioinformatics pipeline in R for miRNA functional analysis including correlation analyses between miRNA expression levels and its targets on mRNA and protein expression levels available from the cancer genome atlas (TCGA) and the cancer proteome atlas (TCPA). TCGA-derived expression data of specific mature miRNA isoforms from pancreatic cancer tissue was used. RESULTS: Fifteen circulating miRNAs with significantly altered expression levels detected in pancreatic cancer patients were queried separately in the pipeline. The pipeline generated predicted miRNA target genes, enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Predicted miRNA targets were evaluated by correlation analyses between each miRNA and its predicted targets. MiRNA functional analysis in combination with Kaplan-Meier survival analysis suggest that hsa-miR-885-5p could act as a tumor suppressor and should be validated as a potential prognostic biomarker in pancreatic cancer. CONCLUSIONS: Our miRNA functional analysis (miRFA) pipeline can serve as a valuable tool in biomarker discovery involving mature miRNAs associated with pancreatic cancer and could be developed to cover additional cancer types. Results for all mature miRNAs in TCGA pancreatic adenocarcinoma dataset can be studied and downloaded through a shiny web application at https://emmbor.shinyapps.io/mirfa/ .


Assuntos
MicroRNAs/metabolismo , Neoplasias Pancreáticas/genética , Proteínas/genética , Interface Usuário-Computador , Automação , Humanos , Estimativa de Kaplan-Meier , MicroRNAs/genética , Neoplasias Pancreáticas/mortalidade , Neoplasias Pancreáticas/patologia , Mapas de Interação de Proteínas , Proteínas/metabolismo , RNA Mensageiro/metabolismo
12.
BMC Evol Biol ; 19(1): 144, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311498

RESUMO

BACKGROUND: Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depends on the analysis of sequence homology at the nucleotide or protein level. RESULTS: We analyzed mRNA GC content, codon usage and divergence of orthologous proteins in 55 vertebrate genomes. Data were visualized in genome-wide landscapes using a sliding window approach. Landscapes of GC content reveal both evolutionary conservation of clustered genes, and lineage-specific changes, so that it was possible to construct a phylogenetic tree that closely matched the classic "tree of life". Landscapes of GC content also strongly correlated to landscapes of amino acid usage: positive correlation with glycine, alanine, arginine and proline and negative correlation with phenylalanine, tyrosine, methionine, isoleucine, asparagine and lysine. Peaks of GC content correlated strongly with increased protein divergence. CONCLUSIONS: Landscapes of base- and amino acid composition of the coding genome opens a new approach in comparative genomics, allowing identification of discrete regions in which protein evolution accelerated over deep evolutionary time. Insight in the evolution of genome structure may spur novel studies assessing the evolutionary benefit of genes in particular genomic regions.


Assuntos
Composição de Bases/genética , Evolução Molecular , Exoma/genética , Proteínas/genética , Vertebrados/genética , Animais , Códon/genética , Genoma , Humanos , Mamíferos/genética , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Répteis/genética
14.
Gene ; 710: 186-192, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31175924

RESUMO

EMT (Epithelial-Mesenchymal Transition) is one of the factors in the pathogenesis of adenomyosis. FMNL2 induced invasion of cancer cell through promoting EMT, but it is unclear the role of FMNL2 in the adenomyosis. By IHC staining, we found the expression level of FMNL2 was significantly higher in the ectopic endometrial stromal cells from women with adenomyosis when compared with normal endometrial stromal cells. Knockdown of FMNL2 inhibited the invasion and migration of ectopic endometrial stromal cells and promoted the protein levels of E-cadherin and Vimentin. Meanwhile, inhibition of FMNL2 could induce the cell membrane localization of E-cadherin. Our findings reveal that the aberrant activation of FMNL2 promotes the pathogenesis of adenomyosis through inducing the EMT process. On the contrary, inhibition of FMNL2 promotes the transition of ectopic endometrial stromal cells to epithelial cells in adenomyosis through a MET-like process.


Assuntos
Adenomiose/metabolismo , Células Epiteliais/metabolismo , Proteínas/metabolismo , Células Estromais/metabolismo , Regulação para Cima , Adenomiose/genética , Adulto , Antígenos CD/metabolismo , Caderinas/metabolismo , Movimento Celular , Proliferação de Células , Células Cultivadas , Células Epiteliais/citologia , Transição Epitelial-Mesenquimal , Feminino , Técnicas de Silenciamento de Genes , Humanos , Pessoa de Meia-Idade , Proteínas/genética , Transdução de Sinais , Células Estromais/citologia , Vimentina/metabolismo
15.
Gene ; 710: 240-245, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31181311

RESUMO

Hirschsprung disease (HSCR) is a congenital rare disorder and a kind of developmental neuropathies, characterized by the lack of enteric neurons in variable segments of distal bowel. Our recent genome-wide association study identified a variant (rs13223150) of testis-specific A13 (TSGA13) as a potential risk locus for total colonic aganglionosis (TCA) in HSCR. The aim of this study was to identify the impact of the variant (rs13223150) and potential association of genetic variations of TSGA13 with TCA in HSCR. This study performed a fine mapping and extended analyses in Korean population. A total of 9 single nucleotide polymorphisms (SNPs) of TSGA13 were genotyped in a larger HSCR cohort (187 HSCR patients and 283 unaffected controls), and extended genetic analyses using various genetic modelling, haplotype, and combined analyses were performed. The rs13223150_A allele showed a significant association with TCA (P = 0.003), even after correcting for multiple testing (Pcorr = 0.02). One haplotype (BL1_ht1, G-A-C-C) including rs13223150 also showed a significant association with TCA (P = 0.002, Pcorr = 0.01). Further combined imputation analysis indicated that several single nucleotide polymorphisms of TSGA13 were significantly associated with TCA in HSCR. Although replications in other population cohorts and functional evaluations are needed, our results suggest that TSGA13 genetic variants may affect TCA in HSCR and/or the extent of aganglionosis during enteric nervous system development.


Assuntos
Doença de Hirschsprung/genética , Polimorfismo de Nucleotídeo Único , Proteínas/genética , Estudos de Casos e Controles , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Haplótipos , Humanos , Modelos Genéticos , República da Coreia
16.
BMC Bioinformatics ; 20(1): 338, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208327

RESUMO

BACKGROUND: The advent of high-throughput experimental techniques paved the way to genome-wide computational analysis and predictive annotation studies. When considering the joint annotation of a large set of related entities, like all proteins of a certain genome, many candidate annotations could be inconsistent, or very unlikely, given the existing knowledge. A sound predictive framework capable of accounting for this type of constraints in making predictions could substantially contribute to the quality of machine-generated annotations at a genomic scale. RESULTS: We present OCELOT, a predictive pipeline which simultaneously addresses functional and interaction annotation of all proteins of a given genome. The system combines sequence-based predictors for functional and protein-protein interaction (PPI) prediction with a consistency layer enforcing (soft) constraints as fuzzy logic rules. The enforced rules represent the available prior knowledge about the classification task, including taxonomic constraints over each GO hierarchy (e.g. a protein labeled with a GO term should also be labeled with all ancestor terms) as well as rules combining interaction and function prediction. An extensive experimental evaluation on the Yeast genome shows that the integration of prior knowledge via rules substantially improves the quality of the predictions. The system largely outperforms GoFDR, the only high-ranking system at the last CAFA challenge with a readily available implementation, when GoFDR is given access to intra-genome information only (as OCELOT), and has comparable or better results (depending on the hierarchy and performance measure) when GoFDR is allowed to use information from other genomes. Our system also compares favorably to recent methods based on deep learning.


Assuntos
Genoma Fúngico , Genômica/métodos , Anotação de Sequência Molecular , Proteínas/genética , Saccharomyces cerevisiae/genética , Algoritmos , Tomada de Decisões , Ontologia Genética
17.
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi ; 35(5): 412-418, 2019 May.
Artigo em Chinês | MEDLINE | ID: mdl-31223110

RESUMO

Objective To measure the effect of duck viperin protein on the proliferation of duck Tembusu virus (DTMUV). Methods We analyzed the duck viperin gene using a bioinformatics. Plasmids pGEX-6P-viperin and pEGFP-N1-viperin were constructed and transformed into Rosseta and transfected into BHK-21 cells, respectively. BHK-21 cells transfected with plasmid pEGFP-N1-viperin and empty vector were infected with DTMUV. The content of DTMUV in cell precipitation and supernatant was analyzed by real-time fluorescent quantitative PCR. Finally, the effect of viperin on DTMUV proliferation and the binding proteins captured by EGFP monoclonal antibody were evaluated using mass spectrometry. Results Significant differences were observed between the expression levels of viperin gene in duck compared to other species. Duck viperin was found to inhibit the budding of DTMUV in BHK-21 cells. Further, we identified six proteins that might be involved in the inhibition of the proliferation and budding of DTMUV, possibly indicative of the viperin anti-Tembusu virus pathway in ducks. Conclusion Expression patterns of duck viperin reveal how the budding of duck Tembusu virus is inhibited.


Assuntos
Patos , Flavivirus/fisiologia , Doenças das Aves Domésticas/virologia , Proteínas/metabolismo , Liberação de Vírus , Animais , Anticorpos Monoclonais , Linhagem Celular , Cricetinae , Proteínas/genética , Transfecção
18.
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi ; 35(5): 425-433, 2019 May.
Artigo em Chinês | MEDLINE | ID: mdl-31223112

RESUMO

Objective To investigate the expression and clinical significance of whey acidic protein (WAP) 4-disulfide core domain 2/human epididymis protein 4 (WFDC2/HE4) in lung adenocarcinoma. Methods The expression of WFDC2 in normal lung tissues and lung adenocarcinoma tissues, the correlation between WFDC2 and the prognosis survival in patients with lung adenocarcinoma were analyzed using the BioGPS database, GEPIA database, Oncomine database and Kaplan-Meier Plotter databases. The expression of WFDC2 in cancer tissue T cells and B cells was analyzed using the Cancer Cell Line Encyclopedia (CCLE). The WFDC2-related genes and functional annotations of their gene ontology (GO), the pathway enrichment of Kyoto Gene and Genomic Encyclopedia (KEGG) were analyzed using the STRING database. The co-expression relationship, correlation and significance of WFDC2-related genes in lung adenocarcinoma were analyzed using the cBioPortal database. The expression of WFDC2 in immune infiltrates and its implication to survival prognosis in the patients with lung adenocarcinoma were analyzed using the Tumor Immune Estimation Resource (TIMER) database. Results BioGPS database analysis showed that the expression of WFDC2 was low in normal lung tissues, but none in T cells and B cells of normal human tissues. GEPIA database analysis showed that the expression of WFDC2 was higher in lung adenocarcinoma compared with normal lung tissues. Four hundred and fourteen samples of differential expression of WFDC2 were obtained from Oncomine database. Nineteen of them had increased WFDC2 expression with four in lung adenocarcinoma; fifteen of them had decreased WFDC2 expression with one in lung adenocarcinoma. Meta-analysis of 4 studies meeting the setting conditions showed that the expression level of WFDC2 was high in lung adenocarcinoma tissues. Kaplan-Meier Plotter database results showed that the overall survival (OS) time of patients with lung adenocarcinoma in the high WFDC2 expression group was significantly longer than that in the low WFDC2 expression group. CCLE analysis showed that the expression of WFDC2 in cancer tissue T cells and B cells was significantly higher than that in normal tissues. String database analysis showed that there were 30 genes associated with WFDC2, which were involved in 4 signaling pathways. The classification results from GO annotation indicated the enrichment in 4 cell components, 8 molecular functions, and 27 biological processes. The cBioPortal database showed that the correlation and difference between secretory leukocyte protease inhibitor (SLPI) and WFDC2 in lung adenocarcinoma were markedly significant (Pearson=0.26; Spearman=0.46; P=6.20E-28). TIMER database analysis showed that B cells with high expression of WFDC2 in the immune microenvironment significantly prolonged the survival prognosis of patients with lung adenocarcinoma for 1 year, 3 years, 5 years and 10 years. Conclusion WFDC2 is highly expressed in lung adenocarcinoma tissues with the anti-tumor immunosuppressive effect, which can significantly prolong OS of lung adenocarcinoma patients and be used as a candidate marker for investigating clinical prognosis of lung adenocarcinoma.


Assuntos
Adenocarcinoma de Pulmão/genética , Linfócitos B/metabolismo , Neoplasias Pulmonares/genética , Proteínas/genética , Taxa de Sobrevida , Humanos , Prognóstico , Linfócitos T , Microambiente Tumoral
19.
Chem Commun (Camb) ; 55(52): 7510-7513, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31187817

RESUMO

Self-assembly of protein nanocages into two-dimensional superlattices can be achieved by disulfide-mediated modular interactions, which can be carried out by introducing single point mutation on the exterior surfaces of the protein nanocages nearby the symmetry rotation axes. As designed, the protein cages arrange in an on-axis alignment pattern.


Assuntos
Dissulfetos/química , Nanoestruturas/química , Proteínas/metabolismo , Cisteína/química , Ferritinas/genética , Ferritinas/metabolismo , Humanos , Oxirredução , Mutação Puntual , Proteínas/genética
20.
Gen Physiol Biophys ; 38(4): 295-304, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31241046

RESUMO

Glioma is a serious malignant tumor without effective therapies till now. lncRNA PEG10 was reported to have some biological activities in cancers. Hence, we explored the effects of PEG10 on the human glioma cell line U251 cells. U251 cells were transfected with sh-PEG10 and/or miR-506 inhibitor. The expression of PEG10 and miR-506 was measured by qRT-PCR. Cell viability, cell apoptosis, cell migration and invasion were detected by CCK-8 assay, flow cytometry and Transwell chamber assay, respectively. The cell proliferation and apoptosis related p16, p53, Bcl-2, Bax, and pro-/Cleaved-Caspase-3/9, migration and invasion related-protein: matrix metalloproteinases MMP-2, MMP-9 and vimentin, and Raf/MEK/ERK and JAK1/STAT3 pathways-related proteins were accessed by Western blot. Transfection with sh-PEG10 inhibited cell viability, migration and invasion, and increased cell apoptosis. Meanwhile, PEG10 silence upregulated the expression of p16 and p53, Bax, cleaved-Caspase-3/9 expression, and downregulated Bcl-2 expression. PEG10 silence upregulated miR-506 expression. Co-transfection with sh-PEG10 and miR-506 inhibitor impaired the tumor suppressive effects. PEG10 knockdown decreased the phosphorylation of Raf/MEK/ERK and JAK1/STAT3-related proteins Raf, MEK, ERK, JAK1 and STAT3. PEG10 knockdown inhibited cell viability, migration and invasion, induced cell apoptosis through miR-506 upregulation, as well as inactivation of Raf/MEK/ERK and JAK1/STAT3 signal pathways.


Assuntos
Movimento Celular/genética , Regulação Neoplásica da Expressão Gênica , Técnicas de Silenciamento de Genes , Glioma/patologia , MicroRNAs/genética , Invasividade Neoplásica/genética , Proteínas/genética , RNA Longo não Codificante/genética , Linhagem Celular Tumoral , Proliferação de Células/genética , Glioma/genética , Humanos , MicroRNAs/biossíntese
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