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1.
Interdiscip Sci ; 2021 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-34817803

RESUMO

In 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2-T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence.

2.
Database (Oxford) ; 20202020 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-33306800

RESUMO

Essential genes are key elements for organisms to maintain their living. Building databases that store essential genes in the form of homologous clusters, rather than storing them as a singleton, can provide more enlightening information such as the general essentiality of homologous genes in multiple organisms. In 2013, the first database to store prokaryotic essential genes in clusters, CEG (Clusters of Essential Genes), was constructed. Afterward, the amount of available data for essential genes increased by a factor >3 since the last revision. Herein, we updated CEG to version 2, including more prokaryotic essential genes (from 16 gene datasets to 29 gene datasets) and newly added eukaryotic essential genes (nine species), specifically the human essential genes of 12 cancer cell lines. For prokaryotes, information associated with drug targets, such as protein structure, ligand-protein interaction, virulence factor and matched drugs, is also provided. Finally, we provided the service of essential gene prediction for both prokaryotes and eukaryotes. We hope our updated database will benefit more researchers in drug targets and evolutionary genomics. Database URL: http://cefg.uestc.cn/ceg.


Assuntos
Eucariotos , Genes Essenciais , Bases de Dados Factuais , Genes Essenciais/genética , Genômica , Humanos , Proteínas
3.
Brief Bioinform ; 2018 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-30496347

RESUMO

Essential genes have attracted increasing attention in recent years due to the important functions of these genes in organisms. Among the methods used to identify the essential genes, accurate and efficient computational methods can make up for the deficiencies of expensive and time-consuming experimental technologies. In this review, we have collected researches on essential gene predictions in prokaryotes and eukaryotes and summarized the five predominant types of features used in these studies. The five types of features include evolutionary conservation, domain information, network topology, sequence component and expression level. We have described how to implement the useful forms of these features and evaluated their performance based on the data of Escherichia coli MG1655, Bacillus subtilis 168 and human. The prerequisite and applicable range of these features is described. In addition, we have investigated the techniques used to weight features in various models. To facilitate researchers in the field, two available online tools, which are accessible for free and can be directly used to predict gene essentiality in prokaryotes and humans, were referred. This article provides a simple guide for the identification of essential genes in prokaryotes and eukaryotes.

4.
Metab Eng ; 47: 393-400, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29715517

RESUMO

D-glucaric acid is a promising platform compound used to synthesize many other value-added or commodity chemicals. The engineering of Escherichia coli for efficiently converting D-glucose to D-glucaric acid has been attempted for several years, with mixed sugar fermentation recently gaining growing interests due to the increased D-glucaric acid yield. Here, we co-expressed cscB, cscA, cscK, ino1, miox, udh, and suhB in E. coli BL21 (DE3), functionally constructing an unreported route from sucrose to D-glucaric acid. Further deletion of chromosomal zwf, pgi, ptsG, uxaC, gudD, over-expression of glk, and use of a D-fructose-dependent translation control system for pgi enabled the strain to use sucrose as the sole carbon source while achieving a high product titer and yield. The titer of D-glucaric acid in M9 medium containing 10 g/L sucrose reached ~1.42 g/L, with a yield of ~0.142 g/g on sucrose.


Assuntos
Escherichia coli , Ácido Glucárico/metabolismo , Engenharia Metabólica , Microrganismos Geneticamente Modificados , Sacarose/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Microrganismos Geneticamente Modificados/genética , Microrganismos Geneticamente Modificados/metabolismo
5.
Sci Rep ; 5: 16431, 2015 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-26560889

RESUMO

Studies had found that bacterial genes are preferentially located on the leading strands. Subsequently, the preferences of essential genes and highly expressed genes were compared by classifying all genes into four groups, which showed that the former has an exclusive influence on orientation. However, only some functional classes of essential genes have this orientation bias. Nevertheless, previous studies only performed comparative analyzes by differentiating the orientation bias extent of two types of genes. Thus, it is unclear whether the influence of essentiality on strand bias works continuously. Herein, we found a significant correlation between essentiality and orientation bias extent in 19 of 21 analyzed bacterial genomes, based on quantitative measurement of gene essentiality (or fitness). The correlation coefficient was much higher than that derived from binary essentiality measures (essential or non-essential). This suggested that genes with relatively lower essentiality, i.e., conditionally essential genes, also have some orientation bias, although it is weaker than that of absolutely essential genes. The results demonstrated the continuous influence of essentiality on orientation bias and provided details on this visible structural feature of bacterial genomes. It also proved that Geptop and IFIM could serve as useful resources of bacterial gene essentiality, particularly for quantitative analysis.


Assuntos
Ordem dos Genes , Genes Bacterianos , Cromossomos Bacterianos , Expressão Gênica , Genes Essenciais , Aptidão Genética , Genoma Bacteriano
6.
Int J Clin Exp Pathol ; 7(5): 2247-55, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24966933

RESUMO

OBJECTIVES: To characterize the exact individual roles of gonadotropins on ovarian epithelial carcinogenesis, an earlier study showed that prohibitin was significantly up-regulated by luteinizing hormone (LH). To further clarify the role of prohibitin in ovarian carcinogenesis and its association with LH, herein we studied the expression of prohibitin in various ovarian tissues including different developmental stages of ovarian epithelial tumors. METHODS: A total of 135 samples were studied by immunohistochemistry. These included benign ovarian cases with follicles, ovarian surface epithelia and ovarian epithelial inclusions (OEI) (n=30), serous cystadenoma (n=14), serous borderline tumor (n=12), serous carcinoma (n=20), mucinous cystadenoma (n=10), mucinous borderline tumor (n=10), mucinous carcinomas (n=10), endometrioid carcinomas (n=12), poorly/undifferentiated carcinomas (n=5), and fallopian tube (n=12). RESULTS: Strong and diffuse staining of prohibitin was detected in luteinized ovarian stromal cells, follicular cells, fallopian tube, and OEI with serous differentiation. A significantly higher prohibitin expression in luteinized stromal cells than in non-luteinized stromal cells was observed (P<.01). Within the ovarian epithelium, the level of prohibitin expression was basically negative in ovarian surface epithelia, but highly expressed in OEI. However, compared to the level of prohibitin expression in OEI, it showed a trend of gradual loss from benign ovarian tumors, to borderline tumors and to carcinomas (P<.0001). Compared to the serous tumors, epithelial tumors with mucinous differentiation showed a significant lower level of prohibitin (P<.0001). An inverse correlation was noted between prohibitin expression and cancer grade. It is interesting to note that a high prohibitin expression level was seen in the fallopian tube, which is similar to OEI. CONCLUSIONS: These data further suggest that prohibitin plays a tumor suppressing role, which is probably associated with LH mediated protection role against ovarian epithelial carcinoma. In addition to the tumor suppressive role of prohibitin, it also plays a role in cellular differentiation, which may be helpful to differentiate ovarian mucinous tumors from the tumors with serous differentiation in clinical settings. More importantly, our findings are supportive that the ovarian epithelial cancers, particularly the serous cancers including those precursors with serous differentiation are likely to be derived from fallopian tube instead of ovarian surface epithelia.


Assuntos
Adenocarcinoma Mucinoso/química , Biomarcadores Tumorais/análise , Carcinoma Endometrioide/química , Cistadenoma Mucinoso/química , Cistadenoma Seroso/química , Neoplasias Epiteliais e Glandulares/química , Neoplasias Ovarianas/química , Proteínas Repressoras/análise , Adenocarcinoma Mucinoso/patologia , Carcinoma Endometrioide/patologia , Carcinoma Epitelial do Ovário , Diferenciação Celular , Linhagem da Célula , Cistadenoma Mucinoso/patologia , Cistadenoma Seroso/patologia , Tubas Uterinas/química , Tubas Uterinas/patologia , Feminino , Humanos , Imuno-Histoquímica , Neoplasias Epiteliais e Glandulares/patologia , Neoplasias Ovarianas/patologia , Células Estromais/química , Células Estromais/patologia
13.
Zhonghua Fu Chan Ke Za Zhi ; 46(7): 516-20, 2011 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-22041444

RESUMO

OBJECTIVE: To evaluate the application of pathological diagnosis by rapid paraffin sections in the diagnosis and treatment of cervical diseases. METHODS: A total of 176 cases from our hospital between September 2009 and January 2010 with abnormal cervical cancer screening (including abnormal cytology result and high-risk HPV continuous positive) were randomly divided into 2 groups. Eighty-seven cases of them whose biopsy were got by Belinson forceps under the direction of colposcopy with rapid paraffin sections by ultrasonic histopathological rapid processor and BT transparent agents were selected as group A, while 89 cases with conventional paraffin sections were selected as group B. The production time and quality for paraffin sections were analyzed in the two groups. Those diagnosed as cervical intraepithelial neoplasia (CIN) II or even worse and some special patients with CINI in the two groups received surgery, including loop electrosurgical procedure (LEEP), cold knife conization (CKC), hysterectomy or radical hysterectomy. Tissue obtained after surgery was sent for routine pathological examination. If the results of postoperative routine pathological examination were inconsistent with the rapid or routine biopsy pathological examination, the heavier results were regard as the final diagnoses. The pathological results and diagnose accordance rates were recorded and compared between group A and group B. RESULTS: The quality of sections in two groups were all satisfied or basically satisfied to meet the diagnostic requirements. There were statistically significant difference in average production time between group A and B (40 minutes vs 24 hours, P<0.05). Thirty patients in group A and 32 patients in group B received surgery. The coincidence rate of biopsy pathological results and final diagnoses were 93% (28/30) for group A and 91% (29/32) for group B, in which there were not statistically significant difference (P>0.05). CONCLUSION: Rapid paraffin sections technology is safe, accurate and economical for rapid pathological diagnosis of cervical diseases, which is worthy for being widely used in hospitals.


Assuntos
Neoplasia Intraepitelial Cervical/diagnóstico , Colo do Útero/patologia , Técnicas Histológicas , Inclusão em Parafina/métodos , Neoplasias do Colo do Útero/diagnóstico , Adulto , Biópsia , Neoplasia Intraepitelial Cervical/patologia , Neoplasia Intraepitelial Cervical/cirurgia , Colo do Útero/cirurgia , Conização , Eletrocirurgia , Feminino , Humanos , Histerectomia , Pessoa de Meia-Idade , Neoplasias do Colo do Útero/patologia , Neoplasias do Colo do Útero/cirurgia , Adulto Jovem
15.
Zhonghua Fu Chan Ke Za Zhi ; 46(10): 729-35, 2011 Oct.
Artigo em Chinês | MEDLINE | ID: mdl-22321344

RESUMO

OBJECTIVE: To investigate the possible origin of ovarian epithelial inclusions and its relationship with the low-grade ovarian serous carcinoma. METHODS: By comparatively evaluating the morphologic (secretory and ciliated cell distribution) and immunophenotypic [using paired box gene 8 (PAX8), tubulin, calretinin, and Ki-67 as first antibodies] attributes of ovarian epithelial inclusions, the normal tubal epithelium, and the ovarian tumors, all adnexal tissues from a total of 198 patients were studied, including 116 adnexae removed for non-neoplastic indications, 53 serous cystadenomas, 44 serous borderline tumors, and 41 low-grade serous carcinomas, which were collected from Qilu Hospital of Shandong University and University of Arizona in USA. Immunohistochemical single staining was used to detect the expressions of PAX8, tubulin, calretinin, and Ki-67 in the two groups, while immunohistochemical double staining of PAX8/calretinin was used to figure out the immunophenotype of various ovarian epithelial inclusions in a more intuitive way. RESULTS: With immunohistochemical single staining of PAX8 and calretinin, the vast majority (90%, 54/60) of ovarian surface epithelia displayed a mesothelial phenotype [calretinin(+), PAX8(-)], whereas 10% (6/60) of the cases displayed foci with tubal phenotype [calretinin(-), PAX8(+)]. In contrast, most (79%, 728/921) of the ovarian epithelial inclusions displayed a tubal phenotype, though 21% (193/921) of the ovarian epithelial inclusions showed a mesothelial phenotype. It was further proved by immunohistochemical double staining of PAX8/calretinin. Secretory and ciliated cells were found in the ovarian epithelial inclusions with tubal phenotype. There was a progressive increase in the secretory/ciliated cells ratio and proliferative index, from ovarian epithelial inclusions/cystadenomas to borderline tumors to low-grade serous carcinoma, according to the expression of tubulin and Ki-67. CONCLUSIONS: The findings make a strong argument that the ovarian epithelial inclusions displaying a tubal phenotype with PAX8(+), calretinin(-) is likely derived from fallopian tube rather than through Mullerian metaplasia from ovarian surface epithelium. The increasing trend of secretory/ciliated cells ratio and proliferative index from ovarian epithelial inclusions/cystadenomas to borderline tumors to low-grade serous carcinoma indicates that the latter is a clonal expansion of secretory cells. Genetic and molecular studies are needed to further confirm these findings.


Assuntos
Cistadenocarcinoma Seroso/patologia , Epitélio/patologia , Corpos de Inclusão/patologia , Neoplasias Ovarianas/patologia , Adulto , Idoso , Calbindina 2 , Transformação Celular Neoplásica/patologia , Cistadenocarcinoma Seroso/etiologia , Cistadenocarcinoma Seroso/metabolismo , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Epitélio/metabolismo , Tubas Uterinas/patologia , Feminino , Humanos , Imuno-Histoquímica , Pessoa de Meia-Idade , Gradação de Tumores , Neoplasias Ovarianas/etiologia , Neoplasias Ovarianas/metabolismo , Ovário/metabolismo , Ovário/patologia , Fator de Transcrição PAX8 , Fatores de Transcrição Box Pareados/metabolismo , Proteína G de Ligação ao Cálcio S100/metabolismo , Tubulina (Proteína)/metabolismo
16.
J Biomol Struct Dyn ; 25(4): 327-36, 2008 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-18092827

RESUMO

The human genome is composed of large sequence segments with fairly homogeneous GC content, namely isochores, which have been linked to many important functions; biological implications of most isochore boundaries, however, remain elusive, partly due to the difficulty in determining these boundaries at high resolution. Using the segmentation algorithm based on the quadratic divergence, we re-determined all 79 boundaries of previously identified human isochores at single-nucleotide resolution, and then compared the boundary coordinates with other genome features. We found that 55.7% of isochore boundaries coincide with termini of repeat elements; 45.6% of isochore boundaries coincide with termini of highly conserved sequences based on alignment of 17 vertebrate genomes, i.e., the highly conserved genome sequence switches to a less or non-conserved one at the isochore boundary; some isochore boundaries coincide with abrupt change of CpG island distribution (note that one boundary can associate with more than one genome feature). In addition, sequences around isochore boundaries are highly conserved. It seems reasonable to deduce that the boundaries of all the isochores studied here would be replication timing sites in the human genome. These results suggest possible key roles of the isochore boundaries and may further our understanding of the human genome organization.


Assuntos
Genoma Humano , Isocoros/genética , Composição de Bases/genética , Sequência de Bases , Sequência Conservada/genética , Sequência Rica em GC/genética , Humanos , Isocoros/fisiologia , Sequências Repetitivas de Ácido Nucleico/genética
18.
Zhong Yao Cai ; 29(3): 242-5, 2006 Mar.
Artigo em Chinês | MEDLINE | ID: mdl-16850722

RESUMO

OBJECTIVE: A HPLC method was first established to determine artemisinin in Artemisia annuna by HPLC-ELSD. Artemisinin in Herba of Artemisia annuna from different places was determined by this new method. METHODS: The method utilized MeOH-H2O (75: 25) as mobile phase with flow rate of 1 ml/min, C18 (250 x 4.6 mm, 5 microm) column. The temperature of detector was 40 degrees C, the pressure of N2 was 3.5 bar, and gain value was 9. RESULTS: The calibration curves were linear within the range of 1 - 5 microg, and the average recovery was 99.33% (RSD = 1.97%). CONCLUSION: The method was rapid, convenient, and accurate. It can be used for the quality control of this herbal medicine.


Assuntos
Artemisia annua/química , Artemisininas/análise , Cromatografia Líquida de Alta Pressão/métodos , Plantas Medicinais/química , Sesquiterpenos/análise , Antimaláricos/química , Artemisia annua/classificação , Medicamentos de Ervas Chinesas/química , Controle de Qualidade , Reprodutibilidade dos Testes , Espalhamento de Radiação , Estações do Ano
19.
Mol Phylogenet Evol ; 36(2): 224-32, 2005 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-15890535

RESUMO

A novel coronavirus has been identified as the cause of the outbreak of severe acute respiratory syndrome (SARS). Previous phylogenetic analyses based on sequence alignments show that SARS-CoVs form a new group distantly related to the other three groups of previously characterized coronaviruses. In this paper, a geometric approach based on the Z-curve representation of the whole genome sequence is proposed to analyze the phylogenetic relationships of coronaviruses. The evolutionary distances are obtained through measuring the differences among the three-dimensional Z-curves. The Z-curve is approximately described by its geometric center and the associated three eigenvectors, which indicate the center position and the trend of the Z-curve, respectively. Although some information is lost due to the approximate description of the Z-curve, the phylogenetic tree constructed based on these parameters is consistent with those of previous analyses. The present method has the merits of simplicity and intuitiveness, but it is still in its premature stage. Because the phylogenetic relationships are inferred from the whole genome, instead of some individual genes, the present method represents a new direction of phylogeny study in the post-genome era.


Assuntos
Algoritmos , Coronavirus/genética , Filogenia , Animais , Coronavirus/classificação , Evolução Molecular , Genoma Viral , Humanos , Vírus da SARS/genética
20.
FEBS Lett ; 553(3): 451-6, 2003 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-14572668

RESUMO

Recently, we have developed a coronavirus-specific gene-finding system, ZCURVE_CoV 1.0. In this paper, the system is further improved by taking the prediction of cleavage sites of viral proteinases in polyproteins into account. The cleavage sites of the 3C-like proteinase and papain-like proteinase are highly conserved. Based on the method of traditional positional weight matrix trained by the peptides around cleavage sites, the present method also sufficiently considers the length conservation of non-structural proteins cleaved by the 3C-like proteinase and papain-like proteinase to reduce the false positive prediction rate. The improved system, ZCURVE_CoV 2.0, has been run for each of the 24 completely sequenced coronavirus genomes in GenBank. Consequently, all the non-structural proteins in the 24 genomes are accurately predicted. Compared with known annotations, the performance of the present method is satisfactory. The software ZCURVE_CoV 2.0 is freely available at http://tubic.tju.edu.cn/sars/.


Assuntos
Coronavirus/enzimologia , Coronavirus/genética , Endopeptidases/metabolismo , Genoma Viral , Poliproteínas/metabolismo , Vírus da SARS/genética , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Animais , Sítios de Ligação , Aves , Bovinos , Coronavirus/química , Bases de Dados Genéticas , Endopeptidases/química , Humanos , Camundongos , Dados de Sequência Molecular , Poliproteínas/química , Poliproteínas/genética , Alinhamento de Sequência , Software , Suínos , Proteínas Virais/genética
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