RESUMO
BACKGROUND: Open arthrolysis is used for treating elbow stiffness in adults. This study evaluated the midterm outcomes after open arthrolysis in children and adolescents with posttraumatic elbow stiffness. METHODS: Data of 31 children and adolescents with posttraumatic elbow stiffness following open arthrolysis with or without hinged external fixation from 2010 to 2014 were retrospectively analyzed. Their mean age was 15 (range: 6 to 19) years. At baseline and the follow-up (>4 y), we evaluated the outcomes (range of motion and Mayo Elbow Performance Index) and postoperative complications (pain, ulnar nerve symptoms, infections, and instability) and analyzed the association between outcomes and clinical variables. RESULTS: The Mayo Elbow Performance Index improved from 67.9 (range: 35 to 95 points) to 93.7 points (range: 65 to 100 points; P<0.001). The elbow active flexion/extension arc increased significantly from 49 degrees (range: 0 to 120 degrees) to 108 degrees (range: 0 to 120 degrees; P<0.001), with a mean flexion of 123 degrees (range: 70 to 140 degrees; P<0.001) and mean extension of 15 degrees (range: 0 to 85 degrees; P<0.001) postoperatively. The increasing age at surgery was associated with improved elbow motions (P=0.004). Patients with increased preoperative serum alkaline phosphatase level demonstrated decreased arc of motion (P=0.015). Patients with extra-articular fractures had better outcomes than the other patients. At the final follow-up, 8 patients experienced recurrent contracture in the flexion arc with heterotopic ossification. Two patients had postoperative pain, 1 elbow instability, and 1 ulnar neuropathy. CONCLUSIONS: Most patients showed satisfactory functional outcomes after arthrolysis, indicating that open release with or without hinged external fixation is an effective and maintained technique for children and adolescents with posttraumatic elbow stiffness. The age at surgery, preoperative alkaline phosphatase level, and injury type should be considered to achieve good outcomes. LEVEL OF EVIDENCE: Therapeutic level III.
Assuntos
Contratura/cirurgia , Articulação do Cotovelo/cirurgia , Procedimentos Ortopédicos/estatística & dados numéricos , Complicações Pós-Operatórias/epidemiologia , Adolescente , Criança , Pré-Escolar , China/epidemiologia , Cotovelo/cirurgia , Articulação do Cotovelo/fisiologia , Feminino , Humanos , Instabilidade Articular , Masculino , Procedimentos Ortopédicos/métodos , Ossificação Heterotópica , Dor Pós-Operatória , Amplitude de Movimento Articular , Estudos Retrospectivos , Neuropatias Ulnares , Adulto Jovem , Lesões no CotoveloRESUMO
BACKGROUND Studies have shown inconsistent associations of nitrite and nitrate intake with the risk of gastric cancer or its associated mortality. We performed a meta-analysis of observational studies to evaluate the correlation of nitrite and nitrate intake with the risk of gastric cancer. MATERIAL AND METHODS We searched for studies reporting effect estimates and 95% confidence intervals (CIs) of gastric cancer in PubMed, EMBASE, and the Cochrane Library through November 2018. The summary results of the included studies were pooled using a random-effects model. RESULTS Eighteen case-control and 6 prospective cohort studies recruiting 800 321 participants were included in this study. The summary results indicated that the highest (odds ratio [OR], 1.27; 95%CI, 1.03-1.55; P=0.022) or moderate (OR: 1.12; 95%CI, 1.01-1.26; P=0.037) nitrite intake were associated with a higher risk of gastric cancer. However, we noted that high (OR, 0.81; 95%CI, 0.68-0.97; P=0.021) or moderate (OR, 0.86; 95%CI, 0.75-0.99; P=0.036) nitrate intakes were associated with a reduced risk of gastric cancer. These associations differed when stratified by publication year, study design, country, the percentage of male participants, assessment of exposure, adjusted model, and study quality. CONCLUSIONS High or moderate nitrite intake was associated with higher risk of gastric cancer, whereas high or moderate nitrate intake was correlated with lower risk of gastric cancer.
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Nitratos/efeitos adversos , Nitritos/efeitos adversos , Neoplasias Gástricas/metabolismo , Nitrito de Amila/efeitos adversos , Estudos de Casos e Controles , Humanos , Nitratos/metabolismo , Nitritos/metabolismo , Razão de Chances , Estudos Prospectivos , Fatores de Risco , Neoplasias Gástricas/fisiopatologiaRESUMO
The γ-aminobutyric acid type A (GABAA) receptor is an important pentameric inhibitory neurotransmitter receptor, and the γ2 subunit of this receptor plays a key role in potentiation of the GABAA response. We previously detected that the expression of GABAA receptor in the livers of Carassius auratus gibelio significantly increased after medication (avermectin and difloxacin treatment). In order to better understand the mechanism of action of the GABAA receptor γ2 subunit in the livers of C. auratus gibelio, we constructed a C. auratus gibelio liver cDNA library (the titer value of 1.2 × 106 cfu/mL) and identified the proteins that interact with the GABAA receptor γ2 subunit by using a yeast two-hybrid assay. The yeast two-hybrid screening yielded seven positive clones, namely, prelid3b, cdc42, sgk1, spg21, proteasome, chia.5, and AP-3 complex subunit beta-1, all of which have been annotated by the NCBI database. The functions of these proteins are complex; therefore, additional studies are required to determine the specific interactions of these proteins with the GABAA receptor γ2 subunit in the liver of C. auratus gibelio. Although the interactions identified by the yeast two-hybrid system should be considered as preliminary results, the findings of this study may provide further direction and a foundation for future research focusing on the mechanisms of the GABAA receptor γ2 subunit in C. auratus gibelio livers.
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Carpa Dourada/fisiologia , Fígado/metabolismo , Receptores de GABA-A/metabolismo , Animais , Regulação da Expressão Gênica , Ligação Proteica , Técnicas do Sistema de Duplo-HíbridoRESUMO
Meiotic recombination not only ensures the stability of chromosome numbers during the sexual reproduction in eukaryotes, but also shuffles the maternal and paternal genetic materials to generate genetic diversity in the gametes. Therefore, meiotic recombination is an important pathway for genetic diversity, which has been considered as a major driving force for species evolution and biodiversity in nature. In most eukaryotes, meiotic recombination is strictly limited, despite the large variation of physical genome size and chromosome numbers among species, but the mechanisms suppressing meiotic recombination remain elusive. Recently, several suppressors have been identified through the forward genetics screen, and revealed the functions and regulation pathways of these suppressors. In this review, we summarize the breakthrough discovery of meiotic recombination suppressors in plants based on research in Arabidopsis, with particular focus on the gene function and its regulation network to elucidate the molecular mechanisms of meiotic recombination suppression in plants.
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Meiose , Plantas/genética , Recombinação Genética , Arabidopsis/genéticaRESUMO
UGT2B10 is an important metabolism enzyme in human body and its substrates include multiple amine-containing compounds, especially nicotine, tamoxifen and multiple antidepressants. Multiple common SNPs have been observed in its promoter region, but their role in expression regulation has never been investigated. In this preliminary study, we identified a novel cis-regulatory SNP, rs294775, for UGT2B10 by plasmid construction, mutagenesis, and luciferase assay, whose mechanism was also investigated. Our work provides a basis for further pharmacogenetics study.
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Glucuronosiltransferase/genética , Polimorfismo de Nucleotídeo Único , Glucuronosiltransferase/metabolismo , Células Hep G2 , Humanos , MutagêneseRESUMO
OBJECTIVE: The primary objective of our study was to examine the association between contrast-enhanced ultrasound (CEUS) parameters and established gray-scale ultrasound with color Doppler imaging (CDI) for the determination of disease activity in patients with Crohn disease. Our secondary objective was to develop quantitative time-signal intensity curve thresholds for disease activity. MATERIALS AND METHODS: One hundred twenty-seven patients with Crohn disease underwent ultrasound with CDI and CEUS. Reviewers graded wall thickness, inflammatory fat, and mural blood flow as showing remission or inflammation (mild, moderate, or severe). If both gray-scale ultrasound and CDI predicted equal levels of disease activity, the studies were considered concordant. If ultrasound images suggested active disease not supported by CDI findings, the ultrasound results for disease activity were indeterminate. Time-signal intensity curves from CEUS were acquired with calculation of peak enhancement (PE), and AUCs. Interobserver variation and associations between PE and ultrasound parameters were examined. Multiclass ROC analysis was used to develop CEUS thresholds for activity. RESULTS: Ninety-six (76%) studies were concordant, 19 of which showed severe disease, and 31 (24%) studies were indeterminate. Kappa analyses revealed good interobserver agreement on grades for CDI (κ = 0.76) and ultrasound (κ = 0.80) assessments. PE values on CEUS and wall thickness showed good association with the Spearman rank correlation coefficient for the entire population (ρ = 0.62, p < 0.01) and for the concordant group (ρ = 0.70, p < 0.01). Multiclass ROC analyses of the concordant group using wall thickness alone as the reference standard showed cutoff points of 18.2 dB for differentiating mild versus moderate activity (sensitivity, 89.0% and specificity, 87.0%) and 23.0 dB for differentiating moderate versus severe (sensitivity, 90% and specificity, 86.8%). Almost identical cutoff points were observed when using ultrasound global assessment as the reference standard: using 18.2 dB to differentiate mild versus moderate activity yielded sensitivity of 89.2% and specificity of 90.9% and using 22.9 dB to differentiate moderate versus severe activity yielded sensitivity of 89.5% and specificity of 83.1%. CONCLUSION: Quantitative CEUS parameters integrated into inflammatory assessments with ultrasound reduce indeterminate results and improve disease activity level determinations.
Assuntos
Doença de Crohn/diagnóstico por imagem , Doença de Crohn/fisiopatologia , Ultrassonografia Doppler em Cores/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Meios de Contraste , Estudos Transversais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Sensibilidade e EspecificidadeRESUMO
BACKGROUND The aim of this study was to investigate the association of the polymorphism of folylpolyglutamate synthetase (FPGS) with the dynamic plasma concentration of methotrexate (MTX) in pediatric patients with acute lymphocytic leukemia (ALL), as well as the prognosis. MATERIAL AND METHODS 57 ALL patients and 31 age and sex-matched children (control) were included in this study. Polymerase chain reaction-restriction fragment length polymorphism was performed for the analysis of the genotype of FPGS rs1544105 and high-performance liquid chromatography for measurement of MTX plasma concentration after 24-h and 44-h treatment. Overall survival was analyzed by Kaplan-Meier method. RESULTS No differences were observed between patients and controls regarding the distribution frequency of genotype and alleles of rs1544105. Patients carrying AA genotype had a significantly higher plasma concentration of MTX after 24 h than those carrying GG or GA (P<0.05) and no differences were found after 44 h. Kaplan-Meier survival analysis showed a longer median survival time in patients with AA than other genotypes with significant difference in overall survival. CONCLUSIONS Polymorphism of FPGS rs1544105 might be used as an effective approach for prediction of the treatment outcome of MTX.
Assuntos
Metotrexato/administração & dosagem , Peptídeo Sintases/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/tratamento farmacológico , Leucemia-Linfoma Linfoblástico de Células Precursoras/enzimologia , Alelos , Antimetabólitos Antineoplásicos/administração & dosagem , Antimetabólitos Antineoplásicos/efeitos adversos , Antimetabólitos Antineoplásicos/sangue , Criança , Pré-Escolar , Feminino , Frequência do Gene , Humanos , Masculino , Metotrexato/efeitos adversos , Metotrexato/sangue , Peptídeo Sintases/metabolismo , Polimorfismo de Nucleotídeo Único , Leucemia-Linfoma Linfoblástico de Células Precursoras/sangue , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , PrognósticoRESUMO
At the 4th Guangzhou International Symposium on Oncology, Rui-Hua Xu, Chao-Nan Qian, and Wei Zhang--the chairmen and editors of the Chinese Journal of Cancer--announced and presented awards to 14 authors in recognition of their outstanding contributions to the journal.
Assuntos
Distinções e Prêmios , Oncologia/normas , Publicações Periódicas como Assunto , Pesquisa Biomédica/normas , Congressos como Assunto , HumanosRESUMO
We obtained the allelic frequencies and forensic efficiency data for eight mini short tandem repeat loci including Penta E, D12S391, D6S1043, D2S1338, D19S433, CSF1PO, Penta D and D19S253 loci from a sample of 128 unrelated Uyghur individuals from China. The amplification products of the eight STR loci are <240 bp in size. A total of 94 alleles were observed and the corresponding allelic frequencies ranged from 0.0039 to 0.3438 in the present study. Observed genotype distributions for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. The combined power of discrimination, combined power of exclusion and combined matching probability of the eight STR loci equaled to 0.999999999963373, 0.9997770 and 3.6627 × 10(-11), respectively. Because of the small fragment length of PCR products and the high degree of polymorphisms, the eight STR loci are highly beneficial for the forensic analysis of degraded DNA samples which are commonly observed in forensic cases. The STR data of the Uyghur group were compared with the previously published population STR data of other groups from different ethnic or areas, and significant differences were observed among these groups at some loci.
Assuntos
Povo Asiático/genética , Etnicidade/genética , Genética Forense , Repetições de Microssatélites , Polimorfismo Genético , Alelos , China , Frequência do Gene , Humanos , Desequilíbrio de LigaçãoRESUMO
BACKGROUND: Postpartum depression (PPD) not only affects the psychological and physiological aspects of maternal health but can also affect neonatal growth and development. Partners who are in close contact with parturient women play a key role in communication and emotional support. This study explores the PPD support relationship with partners and its influencing factors, which is believed to establish psychological well-being and improve maternal partner support. AIM: To explore the correlation between PPD and partner support during breastfeeding and its influencing factors. METHODS: Convenience sampling was used to select lactating women (200 women) who underwent postpartum examinations at the Huzhou Maternity and Child Health Care Hospital from July 2022 to December 2022. A cross-sectional survey was conducted on the basic information (general information questionnaire), depression level [edinburgh postnatal depression scale (EPDS)], and partner support score [dyadic coping inventory (DCI)] of the selected subjects. Pearson's correlation analysis was used to analyze the correlation between PPD and DCI in lactating women. Factors affecting PPD levels during lactation were analyzed using multiple linear regression. RESULTS: The total average score of EPDS in 200 lactating women was (9.52 ± 1.53), and the total average score of DCI was (115.78 ± 14.90). Dividing the EPDS, the dimension scores were: emotional loss (1.91 ± 0.52), anxiety (3.84 ± 1.05), and depression (3.76 ± 0.96). Each dimension of the DCI was subdivided into: Pressure communication (26.79±6.71), mutual support (39.76 ± 9.63), negative support (24.97 ± 6.68), agent support (6.87 ± 1.92), and joint support (17.39 ± 4.19). Pearson's correlation analysis demonstrated that the total mean score and individual dimension scores of EPDS during breastfeeding were inversely correlated with the total score of partner support, stress communication, mutual support, and co-support (P < 0.05). The total mean score of the EPDS and its dimensions were positively correlated with negative support (P < 0.05). Multiple linear regression analysis showed that the main factors affecting PPD during breastfeeding were marital harmony, newborn health, stress communication, mutual support, negative support, co-support, and the total score of partner support (P < 0.05). CONCLUSION: PPD during breastfeeding was associated with marital harmony, newborn health, stress communication, mutual support, negative support, joint support, and the total DCI score.
RESUMO
A novel actinomycete strain, designated TRM 46012(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The strain was aerobic and Gram-staining-positive with an optimum NaCl concentration for growth of 0-5% (w/v). The isolate had sparse aerial mycelium and produced bud-shaped spores at the end of the aerial mycelium on ISP medium 4. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid and three unidentified glycolipids. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The major fatty acids were iso-C(16:0), anteiso-C(17:0) and anteiso-C(15:0). The G+C content of the DNA was 74.4 mol%. Phylogenetic analysis showed that strain TRM 46012(T) had 16S rRNA gene sequence similarity of 95.7% with the most closely related species with a validly published name, Streptomyces cheonanensis, and it could be distinguished from all species in the genus Streptomyces by using the data from this polyphasic taxonomic study. On the basis of these data, strain TRM 46012(T) should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces aidingensis sp. nov. is proposed. The type strain is TRM 46012(T) (â=CGMCC 4.5739(T)â=NBRC 108211(T)).
Assuntos
Sedimentos Geológicos/microbiologia , Lagos/microbiologia , Filogenia , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/análise , Glicolipídeos/análise , Dados de Sequência Molecular , Fosfolipídeos/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptomyces/genética , Streptomyces/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/análiseRESUMO
A novel filamentous actinomycete strain, designated TRM 46004(T), was isolated from sediment of Aiding Lake in Tulufan Basin (42° 64' N 89° 26' E), north-west China. The isolate was characterized using a polyphasic approach. The isolate formed abundant aerial mycelium with few branches and vegetative mycelium, occasionally twisted and coiled; spherical sporangia containing one to several spherical spores developed at the ends of short sporangiophores on aerial mycelium. The G+C content of the DNA was 65.2 mol%. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and xylose, galactose and ribose as the major whole-cell sugars. The diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H10). The major fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 46004(T) formed a distinct lineage within the family Pseudonocardiaceae and showed 91.7-96.1 % 16S rRNA gene sequence similarity with members of the family Pseudonocardiaceae. On the basis of the evidence from this polyphasic study, a novel genus and species, Longimycelium tulufanense gen. nov., sp. nov., are proposed. The type strain of Longimycelium tulufanense is TRM 46004(T) (= CGMCC 4.5737(T) = NBRC 107726(T)).
Assuntos
Actinomycetales/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/análise , Lagos/microbiologia , Dados de Sequência Molecular , Fosfolipídeos/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/análiseRESUMO
Lung cancer is a malignant tumor with high rates of mortality and shows significant hereditary predisposition. Previous genome-wide association studies suggest that rs748404, located at promoter of TGM5 (transglutaminase 5), is associated with lung carcinoma. By analysis of 1000 genomes project data for three representative populations in the world, another five SNPs are identified to be in strong linkage disequilibrium with rs748404, thus suggesting that they may also be associated with lung carcinoma risk. However, it is ambiguous about the actually causal SNP(s) and the mechanism for the association. Dual-luciferase assay indicates that the functional SNPs are not rs748404, rs12911132 or rs35535629 but another three SNPs (rs66651343, rs12909095 and rs17779494) in lung cell. By chromosome conformation capture, it is disclosed that the enhancer encompassing the two SNPs, rs66651343 and rs12909095, can interact with the promoter of CCNDBP1 (cyclin D1 binding protein 1). RNA-seq data analysis indicates that CCNDBP1 expression is dependent on the genotype of these two SNPs. Chromatin immunoprecipitation assay suggests that the fragments spanning rs66651343 and rs12909095 can bind with the transcription factors, cut like homeobox 1 and SRY-box transcription factor 9, respectively. Our results establish the connection between genetic variations at this locus and lung cancer susceptibility.
Assuntos
Carcinoma , Neoplasias Pulmonares , Humanos , Carcinoma/patologia , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Genótipo , Pulmão/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Strain 211020(T) was isolated from rhizosphere soil of Excoecaria agallocha in a mangrove in Hainan, China. The strain produced longitudinal pair spores branching from aerial hyphae. 16S rRNA gene sequence analysis showed that the isolate belonged to the genus Microbispora, exhibiting the highest 16S rRNA gene sequence similarity (98.75â%) to Microbispora corallina JCM 10267(T) with a low DNA-DNA relatedness value (13 ± 0.6â%). The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid but madurose was not detected. The predominant menaquinones were MK-9(H(4)), MK-9(H(2)) and MK-9(H(0)), and the major fatty acids were iso-C(16â:â0), iso-C(15â:â0) and C(17â:â0). The phospholipid profile of strain 211020(T) comprised phosphatidylinositol mannoside, phosphatidylethanolamine, diphosphatidylglycerol and phospholipids of unknown structure containing glucosamine. The DNA G+C content was 70.8 mol%. On the basis of phenotypic and genotypic data, strain 211020(T) can be distinguished as a novel species of the genus Microbispora, for which the name Microbispora hainanensis sp. nov., is proposed. The type strain is 211020(T) (â=âCGMCC 4.5595(T)â=âDSM 45428(T)).
Assuntos
Actinomycetales/classificação , Euphorbiaceae/microbiologia , Filogenia , Rizosfera , Microbiologia do Solo , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/análise , Ácidos Graxos/análise , Dados de Sequência Molecular , Fosfolipídeos/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
A novel actinomycete strain, designated TRM F103(T), was isolated from a hypersaline habitat of the Tarim basin in Xinjiang province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Amycolatopsis and was most closely related to Amycolatopsis halophila YIM 93223(T) (99.3% 16S rRNA gene sequence similarity). However, DNA-DNA relatedness between these two strains, based on triplicate experiments, was only 31.6%. The isolate contained meso-diaminopimelic acid and ribose, glucose and galactose as the major whole-cell sugars. The predominant menaquinone was MK-8(H(4)). The major fatty acids were iso-C(16:0) and C(16:0). The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and glucosamine-containing phospholipids. The G+C content of the genomic DNA was 66.4 mol%. The phenotypic data clearly distinguished the isolate from its closest relatives. The combined phylogenetic, chemotaxonomic and phenotypic data indicate that the isolate represents a novel species of the genus Amycolatopsis. The proposed name is Amycolatopsis salitolerans sp. nov., with TRM F103(T) (=JCM 15899(T)=CCTCC AB 208326(T)) as the type strain.
Assuntos
Actinomycetales/classificação , Actinomycetales/isolamento & purificação , Microbiologia Ambiental , Actinomycetales/genética , Actinomycetales/fisiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Carboidratos/análise , China , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análiseRESUMO
The next-generation sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is becoming a key technology for the study of transcriptional regulation in the context of functional genomics. Due to the overwhelming amount of data generated from ChIP-seq experiments, the ChIP-seq data processing brings many new challenges in the field of bioinformatics. Considering the development of data processing skills largely behind that of the ChIP-seq experiment techniques, it is urgent to give a review on the ChIP-seq data processing for more and more oncoming researchers to build or improve algorithms. This paper provides a brief overview of the ChIP-seq data processing, highlighting the main prob-lems and methods in detail, to allow scientists to understand rapidly and deeply.
Assuntos
Imunoprecipitação da Cromatina/métodos , Processamento Eletrônico de Dados/métodos , Análise de Sequência de DNA/métodos , Algoritmos , Animais , Biologia Computacional/métodos , HumanosRESUMO
Background: Glioma is one of the central nervous system (CNS) tumors in children, accounting for 80% of malignant brain tumors. Nucleotide excision repair (NER) is a vital pathway during DNA damage repair progression. Xeroderma pigmentosum group D (XPD) or excision repair cross-complementing group 2 (ERCC2) is a critical factor in the NER pathway, playing an indispensable role in the DNA repair process. Therefore, the genetic variants in XPD may be associated with carcinogenesis induced by defects in DNA repair. Methods: We are the first to conduct a multi-center case-control study to investigate the correlation between XPD gene polymorphisms and pediatric glioma risk. We chose three single nucleotide polymorphisms and genotyped them using the TaqMan assay. Results: Although there is no significant association of these genetic variations with glioma susceptibility, the stratified analysis revealed that in the subtype of astrocytic tumors, the rs13181 TG/GG genotype enhanced glioma risk than the TT genotype, and carriers with two to three genotypes also elevated the tumor risk than 0-1 genotypes. Conclusion: In conclusion, our findings provided an insight into the impact of XPD genetic variants on glioma risk.
RESUMO
To further disclose the underlying mechanisms of protein ß-sheet formation, studies were made on the rules of ß-strands alignment forming ß-sheet structure using statistical and machine learning approaches. Firstly, statistical analysis was performed on the sum of ß-strands between each ß-strand pairs in protein sequences. The results showed a propensity of near-neighbor pairing (or called "first come first pair") in the ß-strand pairs. Secondly, based on the same dataset, the pairwise cross-combinations of real ß-strand pairs and four pseudo-ß-strand contained pairs were classified by support vector machine (SVM). A novel feature extracting approach was designed for classification using the average amino acid pairing encoding matrix (APEM). Analytical results of the classification indicated that a segment of ß-strand had the ability to distinguish ß-strands from segments of α-helix and coil. However, the result also showed that a ß-strand was not strongly conserved to choose its real partner from all the alternative ß-strand partners, which was corresponding with the ordination results of the statistical analysis each other. Thus, the rules of "first come first pair" propensity and the non-conservative ability to choose real partner, were possible important factors affecting the ß-strands alignment forming ß-sheet structures.
Assuntos
Modelos Químicos , Estrutura Secundária de Proteína , Proteínas/química , Algoritmos , Inteligência Artificial , Bases de Dados de Proteínas , Dobramento de Proteína , Alinhamento de SequênciaRESUMO
A novel strain, 219820(T), whose metabolites were found to be active against tumour cells, was isolated and characterized. The isolate belonged to the genus Streptomyces and had white to grey aerial mycelium and long chains of smooth spores in the aerial mycelium. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 219820(T) had highest similarity to members of the genus Streptomyces and was most closely, albeit loosely, associated with Streptomyces crystallinus NBRC 15401(T) (98.624â% similarity), Streptomyces melanogenes NBRC 12890(T) (98.565â%) and Streptomyces noboritoensis NBRC 13065(T) (98.564â%). However, DNA-DNA relatedness and phenotypic data readily distinguished strain 219820(T) from these phylogenetically related type strains. It is evident from the combination of genotypic and phenotypic data that strain 219820(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces sanyensis sp. nov. is proposed; the type strain is 219820(T) (â=âCGMCC 4.5626(T) â=âDSM 42014(T)).
Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Microbiologia do Solo , Streptomyces/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Streptomyces/genética , Streptomyces/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
Strain 210417(T), which forms highly branched substrate and aerial mycelia, is a Gram-positive, aerobic and non-motile actinomycete isolated from mangrove rhizosphere soil. 16S rRNA gene sequence analysis showed that the strain should be classified in the genus Nonomuraea, being most closely related to the type strains of Nonomuraea coxensis (99.6 %) and Nonomuraea bangladeshensis (99.3 %). Chemotaxonomic properties [madurose as the major sugar in the cell wall; meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan; MK-9(H(4)) as the major menaquinone; iso-C(16 : 0) (24.1 %) as major fatty acid; and phospholipid pattern type IV] are consistent with the assignment of strain 210417(T) to the genus Nonomuraea. Strain 210417(T) could be differentiated from the closely related species N. coxensis and N. bangladeshensis by morphological, physiological, biochemical and chemotaxonomic properties, 16S rRNA gene sequence analysis and DNA-DNA hybridization results. It is therefore proposed that strain 210417(T) represents a novel species of the genus Nonomuraea, for which the name Nonomuraea wenchangensis sp. nov. is given; the type strain is 210417(T) (â=âCGMCC 4.5598(T) â=âDSM 45477(T)).