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1.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 27(4): 1220-1226, 2019 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-31418383

RESUMO

OBJECTIVE: To evaluate the diagnostic value of high-throughput sequencing (NGS) in screening the thalassemia genes. METHODS: The peripheral blood of 2 858 cases of pre-pregnancy and pregnancy from October 2014 to October 2016 randomly were collected in department of obstetrics, the third people's hospital in Dongguan city. Peripheral blood was used for the blood routine examination, hemoglobin electrophoresis, traditional thalassaemia gene screening and NGS. RESULTS: The rate of missed diagnosis for α-thalassemia and ß-thalassemia using NGS was 0.87% and 1.59%, respectively. Meanwhile, the missed rate of screening for α-thalassemia and ß-thalassemia by traditional screening models was 26.77% and 2.38%, respectively. The area under the ROC curve of α-thalassemia and ß-thalassemia screened by NGS was 0.994 and 0.991, respectively, however, the area under the ROC curve of screening for α-thalassemia and ß-thalassemia by the traditional screening model was 0.866 and 0.988, respectively. The sensitivity, rate of missed diagnosis, Youden index and negative predictive value of screening for α-thalassemia and ß-thalassemia using NGS all were superior to those using traditional screening. CONCLUSION: Compared with the traditional screening model, the NGS screening for thalassemia genes shows a high accuracy, moreover can avoid missed diagnosis resulted from screening by conventional method, suggesting that the NCS possesses the accurate and diagnostic value for screening of thalassemia and can widely apply to clinical practise so as to provid the guarantee for early diagnosis of thalassemia.


Assuntos
Talassemia alfa , Talassemia beta , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Programas de Rastreamento , Gravidez , Curva ROC
2.
Lancet ; 394(10198): 604-610, 2019 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-31395443

RESUMO

Human genomic sequencing has potential diagnostic, prognostic, and therapeutic value across a wide breadth of clinical disciplines. One barrier to widespread adoption is the paucity of evidence for improved outcomes in patients who do not already have an indication for more focused testing. In this Series paper, we review clinical outcome studies in genomic medicine and discuss the important features and key challenges to building evidence for next generation sequencing in the context of routine patient care.


Assuntos
Genômica/métodos , Medicina de Precisão/métodos , Testes Diagnósticos de Rotina , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Avaliação de Resultados da Assistência ao Paciente , Padrão de Cuidado
3.
Ying Yong Sheng Tai Xue Bao ; 30(7): 2345-2351, 2019 Jul.
Artigo em Chinês | MEDLINE | ID: mdl-31418238

RESUMO

Clubroot, caused by the soil-borne obligate pathogen Plasmodiophora brassicae, is one of the most severe disease in cruciferous crops. Previous studies showed that when oilseed rape was planted after soybean (namely soybean-oilseed rotation), the incidence and severity of clubroot of oilseed rape could be significantly reduced, compared with that with oilseed rape-oilseed rape conti-nuous cropping. Therefore, the soybean-oilseed rape rotation is a good way to suppress clubroot of oilseed rape. In this study, we compared the rhizosphere microbiome of soybean and oilseed rape rhizosphere soil collected from the field by 16S rRNA (for identification of prokaryotes) and the internal transcribed spacer (ITS) (for identification of fungi) sequencing. The results showed that both soybean and oilseed rape rhizosphere soils had Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota. Many microbial genera (e.g., Flavobacterium, Sphingomonas, Bacillus, Streptomyces, Pseudomonas, Trichoderma and Coniothyrium) with activities of biological control and plant growth promotion were more abundant in soybean rhizosphere soil than in the oilseed rape rhizosphere soil. The abundance of plant pathogenic bacteria and fungi was higher in the oilseed rape rhizosphere soil than in the soybean rhizosphere soil. Moreover, the soybean rhizosphere soil was enriched with Rhizobium, Bradyrhizobium (both for nitrogen fixation), and arbuscular mycorrhizal fungus (Glomus). These results indicated that soybean rhizosphere soil could promote the growth and proliferation of beneficial microorga-nisms, but inhibit that of plant pathogens. Our results provide evidence for explanation of the effectiveness of soybean-oilseed rape rotation to control clubroot of oilseed rape and provide potential bio-control resources for clubroot prevention.


Assuntos
Microbiota , Rizosfera , Microbiologia do Solo , Brassica rapa/crescimento & desenvolvimento , Brassica rapa/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , RNA Ribossômico 16S , Soja/crescimento & desenvolvimento , Soja/microbiologia
4.
Stud Health Technol Inform ; 264: 1845-1846, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31438372

RESUMO

Next-generation sequencing has prompted the development of numerous -omics applications. Along with experimental procedures, various computational pipelines became available to address the inherent complexities concerning the volume and quality of data. These pipelines are effective and routinely applied; however, interpreting their outcomes into actionable evidence is still poorly addressed. In this context, this work proposes a method for translating patient genomic profiles to drug response aberrations by integrating pharmacogenomic data into sequencing data analysis pipelines.


Assuntos
Biologia Computacional , Exoma , Relação Dose-Resposta a Droga , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos
5.
BMC Plant Biol ; 19(1): 340, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382873

RESUMO

BACKGROUND: Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (Oryza sativa L.), little is known about the biological roles of circRNAs in the fertility transition of the PTGMS rice line. RESULTS: In the present study, RNA-sequencing libraries were constructed from the young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at three development stages with three biological replicates. A total of 9994 circRNAs were obtained in WXS rice based on high-throughput strand-specific RNA sequencing and bioinformatic approaches, of which 5305 were known circRNAs and 4689 were novel in rice. And 14 of 16 randomly selected circRNAs were experimentally validated with divergent primers. Our results showed that 186 circRNAs were significantly differentially expressed in WXS (F) compared with WXS (S), of which 97, 87 and 60 circRNAs were differentially expressed at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3) and the microspore formation stage (P4), respectively. Fertility specific expression patterns of eight circRNAs were analysis by qRT-PCR. Gene ontology (GO) and KEGG pathway analysis of the parental genes of differentially expressed circRNAs (DECs) revealed that they mainly participated in various biological processes such as development, response to stimulation, hormonal regulation, and reproduction. Furthermore, 15 DECs were found to act as putative miRNA sponges to involved in fertility transition in PTGMS rice line. CONCLUSION: In the present study, the abundance and characteristics of circRNAs were investigated in the PTGMS rice line using bioinformatic approaches. Moreover, the expression patterns of circRNAs were different between WXS (F) and WXS (S). Our findings primarily revealed that circRNAs might be endogenous noncoding regulators of flower and pollen development, and were involved in the fertility transition in the PTGMS rice line, and guide the production and application of two-line hybrid rice.


Assuntos
Oryza/genética , RNA/genética , Fertilidade/genética , Fertilidade/fisiologia , Flores/crescimento & desenvolvimento , Genes de Plantas/genética , Genes de Plantas/fisiologia , Resposta ao Choque Térmico , Sequenciamento de Nucleotídeos em Larga Escala , Oryza/fisiologia , Pólen/crescimento & desenvolvimento , RNA/fisiologia
6.
J Cancer Res Clin Oncol ; 145(9): 2325-2333, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31317326

RESUMO

PURPOSE: Nodal positive lung adenocarcinoma includes wide range of survival. Several methods for the classification of nodal-positive lung cancer have been proposed. However, classification considering the impact of targetable genetic variants are lacking. The possibility of genetic variants for the better stratification of nodal positive lung adenocarcinoma was estimated. METHODS: Mutations of 36 genes between primary sites and metastatic lymph nodes (LNs) were compared using next-generation sequencing. Subsequently, mutations in EGFR and BRAF, rearrangements in ALK and ROS1 were evaluated in 69 resected pN1-2M0 adenocarcinoma cases. Recurrence-free survival (RFS), post-recurrence survival (PRS), and overall survival (OS) were evaluated with respect to targetable variants and tyrosine kinase inhibitor (TKI) therapy after recurrence. RESULTS: About 90% of variants were shared and allele frequencies were similar between primary and metastatic sites. In 69 pN1-2M0 cases, EGFR/ALK were positive in primary sites of 39 cases and same EGFR/ALK variants were confirmed in metastatic LNs of 96.7% tissue-available cases. Multivariate analyses indicated positive EGFR/ALK status was associated with worse RFS (HR 2.366; 95% CI 1.244-4.500; P = 0.009), and PRS was prolonged in cases receiving TKI therapy (no post-recurrence TKI therapies, HR 3.740; 95% CI 1.449-9.650; P = 0.006). OS did not differ with respect to targetable variants or TKI therapy. CONCLUSIONS: Cases harbouring targetable genetic variants had a higher risk of recurrence, but PRS was prolonged by TKI therapy. Classification according to the targetable genetic status provides a basis for predicting recurrence and determining treatment strategies after recurrence.


Assuntos
Adenocarcinoma de Pulmão/diagnóstico , Neoplasias Pulmonares/diagnóstico , Pulmão/metabolismo , Linfonodos/metabolismo , Mutação , Transcriptoma/genética , Adenocarcinoma de Pulmão/genética , Adenocarcinoma de Pulmão/patologia , Idoso , Idoso de 80 Anos ou mais , Análise Mutacional de DNA/métodos , Feminino , Regulação Neoplásica da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Pulmão/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Linfonodos/patologia , Metástase Linfática , Masculino , Análise em Microsséries/métodos , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/genética , Prognóstico , Estudos Retrospectivos
7.
BMC Bioinformatics ; 20(Suppl 13): 384, 2019 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-31337332

RESUMO

BACKGROUND: The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. MAIN BODY: Here, we developed a web-application, "Soybean-VCF2Genomes", http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix. CONCLUSION: The information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.


Assuntos
Genoma de Planta , Soja/genética , Interface Usuário-Computador , Análise por Conglomerados , Bases de Dados Factuais , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Aprendizado de Máquina , Fenótipo , Filogenia , Análise de Componente Principal , Sementes/genética , Soja/classificação , Soja/crescimento & desenvolvimento
8.
Zhonghua Er Ke Za Zhi ; 57(8): 603-607, 2019 Aug 02.
Artigo em Chinês | MEDLINE | ID: mdl-31352745

RESUMO

Objective: To summarize the clinical characteristics of Listeria monocytogenes meningitis (LMM) with complications, and analyze the outcomes of next generation sequencing. Methods: Clinical characteristics, laboratory findings, imaging features, antibiotics treatment, and next generation sequencing of cerebrospinal fluid were analyzed in 3 LMM patients who were hospitalized in the Department of Infectious Diseases of Beijing Children's Hospital Affiliated to Capital Medical University from July 2015 to November 2017. Results: The three patients were 1-year-old girl, 2-year-old girl, and 9-year-old boy, with normal immune function. They had eaten refrigerated food, milk or dairy products before onset. Symptoms included fever, headache, abdominal pain, diarrhea, vomiting, and convulsions, etc. The complications of two cases (case 2 and 3) were appendicitis and Meckel's diverticulitis. The other one (case 1) was with sepsis and pneumonia. Leukocyte counts in cerebrospinal fluid were elevated in all the three cases, and cranial magnetic resonance imaging showed meningeal or periventricular involvement. All the children were diagnosed with LMM by positive CSF culture. CSF for next generation sequencing was sent after carbapenem antibiotics using, yet all the results were positive. The positive results were returned 2, 9, and 9 days earlier than culture results, respectively. The gene coverage was 5.00%, 7.00%, 0.04%, and the reads was 2 561, 1 011 and 8, respectively. All the three children had recurrent fever despite using cephalosporin. Levels of leukocytes in the blood and CSF further elevated. After using carbapenem antibiotics, patients improved eventually and were discharged from hospital. Conclusions: LMM can occur in children with normal immune function and is usually associated with digestive system symptoms. Listeria monocytogenes can be detected quickly and accurately by the next generation sequencing technology, without being limited to sampling time and antibiotics application.


Assuntos
Listeria monocytogenes/genética , Meningite por Listeria/líquido cefalorraquidiano , Antibacterianos/uso terapêutico , Criança , Pré-Escolar , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Lactente , Listeria monocytogenes/isolamento & purificação , Imagem por Ressonância Magnética , Masculino , Meningite por Listeria/tratamento farmacológico
9.
Ann Hematol ; 98(9): 2151-2162, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31312927

RESUMO

Somatic mutations in patients with myelodysplastic syndromes (MDS) undergoing allogeneic hematopoietic stem cell transplantation (HSTC) are associated with adverse outcome, but the role of chronic graft-versus-host disease (cGVHD) in this subset of patients remains unknown. We analyzed bone marrow samples from 115 patients with MDS collected prior to HSCT using next-generation sequencing. Seventy-one patients (61%) had at least one mutated gene. We found that patients with a higher number of mutated genes (more than 2) had a worse outcome (2 years overall survival [OS] 54.8% vs. 31.1%, p = 0.035). The only two significant variables in the multivariate analysis for OS were TET2 mutations (p = 0.046) and the development of cGVHD, considered as a time-dependent variable (p < 0.001), correlated with a worse and a better outcome, respectively. TP53 mutations also demonstrated impact on the cumulative incidence of relapse (CIR) (1 year CIR 47.1% vs. 9.8%, p = 0.006) and were related with complex karyotype (p = 0.003). cGVHD improved the outcome even among patients with more than 2 mutated genes (1-year OS 88.9% at 1 year vs. 31.3%, p = 0.02) and patients with TP53 mutations (1-year CIR 20% vs. 42.9%, p = 0.553). These results confirm that cGVHD could ameliorate the adverse impact of somatic mutations in patients with MDS with HSCT.


Assuntos
Aberrações Cromossômicas , Doença Enxerto-Hospedeiro/genética , Transplante de Células-Tronco Hematopoéticas , Síndromes Mielodisplásicas/genética , Aloenxertos , Medula Óssea/patologia , Doença Crônica , Feminino , Doença Enxerto-Hospedeiro/patologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Síndromes Mielodisplásicas/patologia , Síndromes Mielodisplásicas/terapia , Estudos Retrospectivos
10.
Rinsho Ketsueki ; 60(6): 620-625, 2019.
Artigo em Japonês | MEDLINE | ID: mdl-31281154

RESUMO

Since the introduction of hematopoietic stem cell transplantation (HSCT), matching the HLA with the donor and recipient is the most important factor in improving the outcome. Currently, we are getting familiar with cord blood transplantation and haplo-identical stem cell transplantation which are beyond HLA disparity. However, even in this era, the significance of HLA for HSCT has not changed, and new technology provides knowledge regarding HLA and HSCT. Usually, HLA typing methods only estimate the allele, but next generation sequencing (NGS) can detect the whole sequence of the HLA gene. Moreover, because the NGS method can be used for quantitative analysis, we can also detect 6pLOH in some disease conditions. Furthermore, a previous report showed that HLA epitope mismatch also influenced the outcome of HSCT. This review shows this new technology and findings on HLA and HSCT.


Assuntos
Genômica/tendências , Antígenos HLA/genética , Sequenciamento de Nucleotídeos em Larga Escala , Teste de Histocompatibilidade , Transplante de Células-Tronco Hematopoéticas , Humanos
11.
Virol J ; 16(1): 89, 2019 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-31277670

RESUMO

A tenuivirus, referred to here as JKI 29327, was isolated from a black medic (Medicago lupulina) plant collected in Austria. The virus was mechanically transmitted to Nicotiana benthamiana, M. lupulina, M. sativa, Pisum sativum and Vicia faba. The complete genome was determined by high throughput sequencing. The genome of JKI 29327 consists of eight RNA segments closely related to those of melon chlorotic spot virus (MeCSV) isolate E11-018 from France. Since segments RNA 7 and 8 of JKI 29327 are shorter, its genome is slightly smaller (by 247 nts) than that of E11-018. Pairwise comparisons between the predicted virus proteins of JKI 29327 and their homologues in E11-018 showed aa identities ranging from 80.6 to 97.2%. Plants infected with E11-081 gave intermediate DAS-ELISA reactions with polyclonal antibodies to JKI 29327. Since JKI 29327 and E11-018 appear to be closely related both serologically and genetically, we propose to regard JKI 29327 as the black medic strain of MeCSV. To our knowledge, JKI 29327 represents the second tenuivirus identified from a dicotyledonous plant. Serological and molecular diagnostic methods were developed for future detection.


Assuntos
Cucurbitaceae/virologia , Doenças das Plantas/virologia , Tenuivirus/genética , Tenuivirus/isolamento & purificação , Áustria , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Ervilhas/virologia , Filogenia , RNA Viral/genética , Tabaco/virologia , Vicia faba/virologia , Proteínas Virais/genética
12.
Gene ; 712: 143962, 2019 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-31288057

RESUMO

Veratrum nigrum is protected plant of Melanthiaceae family, able to synthetize unique steroidal alkaloids important for pharmacy. Transcriptomes from leaves, stems and rhizomes of in vitro maintained V. nigrum plants were sequenced and annotated for genes and markers discovery. Sequencing of samples derived from the different organs resulted in a total of 108,511 contigs with a mean length of 596 bp. Transcripts derived from leaf and stalk were annotated at 28%, and 38% in Nr nucleotide database, respectively. The sequencing revealed 949 unigenes related with lipid metabolism, including 73 transcripts involved in steroids and genus-specific steroid alkaloids biosynthesis. Additionally, 3203 candidate SSRs markers we identified in unigenes with average density of one SSR locus every 6.2 kb sequence. Unraveling of biochemical machinery of the pathway responsible for steroidal alkaloids will open possibility to design and optimize biotechnological process. The transcriptomic data provide valuable resources for biochemical, molecular genetics, comparative transcriptomics, functional genomics, ecological and evolutionary studies of V. nigrum.


Assuntos
Alcaloides/biossíntese , Regulação da Expressão Gênica de Plantas , Esteroides/biossíntese , Transcriptoma , Veratrum/metabolismo , Mapeamento de Sequências Contíguas , DNA Complementar/metabolismo , Biblioteca Gênica , Ontologia Genética , Marcadores Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites , Anotação de Sequência Molecular , Análise de Sequência com Séries de Oligonucleotídeos , Folhas de Planta/metabolismo , Proteínas de Plantas/metabolismo , Raízes de Plantas/metabolismo , Análise de Sequência de RNA
13.
Plant Mol Biol ; 101(1-2): 163-182, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31273589

RESUMO

KEY MESSAGE: Deeper insights into the resistance response of Cajanus platycarpus were obtained based on comparative transcriptomics under Helicoverpa armigera infestation. Devastation by pod borer, Helicoverpa armigera is one of the major factors for stagnated productivity in Pigeonpea. Despite possessing a multitude of desirable traits including pod borer resistance, wild relatives of Cajanus spp. have remained under-utilized due to linkage drag and cross-incompatibility. Discovery and deployment of genes from them can provide means to tackle key pests like H. armigera. Transcriptomic differences between Cajanus platycarpus and Cajanus cajan during different time points (0, 18, 38, 96 h) of pod borer infestation were elucidated in this study. For the first ever time, we demonstrated captivating variations in their response; C. platycarpus apparently being reasonably agile with effectual transcriptomic reprogramming to deter the insect. Deeper insights into the differential response were obtained by identification of significant GO-terms related to herbivory followed by combined KEGG and ontology analyses. C. platycarpus portrayed a multilevel response with cardinal involvement of SAR, redox homeostasis and reconfiguration of primary metabolites leading to a comprehensive defense response. The credibility of RNA-seq analyses was ascertained by transient expression of selected putative insect resistance genes from C. platycarpus viz., chitinase (CHI4), Alpha-amylase/subtilisin inhibitor (IAAS) and Flavonoid 3_5 hydroxylase (C75A1) in Nicotiana benthamiana followed by efficacy analysis against H. armigera. qPCR validated results of the study provided innovative insights and useful leads for development of durable pod borer resistance.


Assuntos
Cajanus/genética , Resistência à Doença/genética , Mariposas/fisiologia , Doenças das Plantas/imunologia , Transcriptoma , Animais , Cajanus/imunologia , Cajanus/parasitologia , Perfilação da Expressão Gênica , Genômica , Herbivoria , Sequenciamento de Nucleotídeos em Larga Escala , Doenças das Plantas/parasitologia , Análise de Sequência de RNA
14.
Nan Fang Yi Ke Da Xue Xue Bao ; 39(6): 692-698, 2019 Jun 30.
Artigo em Chinês | MEDLINE | ID: mdl-31270048

RESUMO

OBJECTIVE: To optimize DNA library construction in non-crosslinked chromatin immunoprecipitation coupled with next-generation sequencing (Native ChIP-seq) to obtain high-quality Native ChIP-seq data. METHODS: Human nasopharyngeal carcinoma HONE1 cell lysate was digested with MNase for release of the nucleosomes, and the histone-DNA complexes were immunoprecipitated with specific antibodies. The protein component in the precipitate was digested with proteinase K followed by DNA purification; the DNA library was constructed for sequence analysis. RESULTS: Compared with the conventional DNA library construction, Tn5 transposase method allowed direct enrichment of the target DNA after Tn5 fragmentation, which was simple, time-saving and more efficient. The IGV visualized map showed that the information obtained by the two library construction methods was consistent. The sequencing data obtained by the two methods revealed more signal enrichment with Tn5 transposase library construction than with the conventional approach. H3K4me3 ChIP results showed a good reproducibility after Tn5 transposase library construction with a signal-to-noise ratio above 50%. CONCLUSIONS: Tn5 transposase method improves the efficiency of DNA library construction and the results of subsequent sequence analysis, and is especially suitable for detecting histone modification in the DNA to provide a better technical option for epigenetic studies.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Imunoprecipitação da Cromatina , DNA , Biblioteca Gênica , Humanos , Reprodutibilidade dos Testes , Análise de Sequência de DNA
15.
Bull Environ Contam Toxicol ; 103(1): 56-63, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31256201

RESUMO

MicroRNAs (miRNAs) differentially expressed in plasma were identified using microRNA sequencing (miRNA-seq), and five miRNAs were selected for validation. Potential target genes of these five miRNAs were predicted using the miRWalk3.0 database, and the overlapping portions were analyzed using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Comparison of the cases and controls revealed 127 known differentially expressed miRNAs. A total of 44 and 83 miRNAs were upregulated and downregulated, respectively. Through target gene prediction of five miRNAs, we obtained 1360 target genes. GO enrichment analysis showed that the target genes of these dysregulated miRNAs were related with secretion, protein binding, and cell growth. The KEGG pathway analysis showed that pathways in cancer, calcium signaling, and rat sarcoma (Ras) signaling, etc. were likely regulated by these five miRNAs. These findings highlight the distinct expression patterns of miRNAs in coal-burning endemic fluorosis.


Assuntos
Carvão Mineral , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , MicroRNAs , Regulação para Cima
16.
World J Microbiol Biotechnol ; 35(8): 123, 2019 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-31346774

RESUMO

Constituents of the seed microbiota and initial changes in the microbiota in fermentations are important in fermentation progression. To identify the origin of indigo-reducing bacteria and understand the initial changes in the microbiota that occur concomitantly with the initiation of indigo reduction during indigo fermentation, we analysed the initial changes in the microbiota. The proportions of the reported indigo-reducing taxa Alkalibacterium, Amphibacillus and Polygonibacillus increased to 24.0% on the 5th day, to 15.2% on the 7th day and to 42.8% at 4.5 months, and the relative abundances of these taxa were 0.048%, 0.14% and 0.02%, respectively, in sukumo (composted Japanese indigo plant material used for fermentation). In the early phase of the microbiota transition, two substantial changes were observed. The first change may be attributed to the substantial environmental changes caused by the introduction of heated wood ash extract (pH ≥ 10.5, temperature ≥ 60 °C). This change increased the proportions of Alkalibacterium and the family Bacillaceae. The second change in microbiota might be initiated by the consumption of oxygen by aerobic microorganisms until the 5th day followed by an increase in the abundance of the obligate anaerobe Anaerobranca and the aerotolerant Amphibacillus and a decrease in the abundance of Bacillaceae. This experiment demonstrated that the 0.048% Alkalibacterium in the original material was augmented to 23.6% of the microbiological community within 5 days. This means that using the appropriate material and performing appropriate pretreatment and adjustment of fermentation conditions are important to increase the abundance of the taxa that reduce indigo.


Assuntos
DNA Bacteriano/isolamento & purificação , Fermentação , Índigo Carmim/metabolismo , Microbiota , Bacillaceae/classificação , Bacillaceae/isolamento & purificação , Bacillaceae/metabolismo , DNA Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Concentração de Íons de Hidrogênio , RNA Ribossômico 16S , Análise de Sequência de DNA
17.
J Cancer Res Clin Oncol ; 145(8): 1977-1986, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31309300

RESUMO

CONTEXT: Parathyroid carcinoma (PC) is a rare endocrine malignancy with no approved systemic therapies for unresectable locally invasive or distant metastatic disease. Understanding the molecular changes in advanced PC can provide better understanding of this disease and potentially help directing targeted therapy. OBJECTIVE: To evaluate tumor-specific genetic changes using next-generation sequencing (NGS) panels. DESIGN: All patients with advanced PC were tested for hot-spot panels using NGS panels including a 50-gene panel, a 409-gene panel if the standard 50-gene panel (Ion Torrent, Life Technology) was negative or a FoundationOne panel. SETTING: The University of Texas MD Anderson Cancer Center, Houston, Texas, USA. PATIENTS OR OTHER PARTICIPANTS: 11 patients with advanced PC were selected to undergo molecular testing. MAIN OUTCOME MEASURE(S): Genetic profiles of advanced PC. RESULTS: Among the 11 patients, 4 patients had the 50-gene panel only, 6 had 409-gene panel after a negative 50-gene panel and 1 had FoundationOne. One patient who had 50-gene panel only also had his metastatic site (esophagus) of his tumor tested with FoundationOne. The most common mutations identified were in the PI3 K (PIK3CA, TSC1 and ATM) (4/11 patients) and TP53 (3/11) pathways. Genes not previously reported to be mutated in PC included: SDHA, TERT promoter and DICER1. Actionable mutations were found in 54% (6/11) of the patients. CONCLUSIONS: Mutational profiling using NGS panels in advanced PC has yielded important potentially targetable genetic alterations. Larger studies are needed to identify commonly mutated genes in advanced PC patients. Development of novel therapies targeting these cellular pathways should be considered.


Assuntos
Carcinoma/genética , Perfilação da Expressão Gênica , Técnicas de Diagnóstico Molecular/métodos , Monitorização Fisiológica/métodos , Neoplasias das Paratireoides/genética , Adulto , Idoso , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Carcinoma/diagnóstico , Carcinoma/patologia , Carcinoma/terapia , Análise Mutacional de DNA/métodos , Progressão da Doença , Feminino , Seguimentos , Perfilação da Expressão Gênica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/tendências , Terapia de Alvo Molecular/métodos , Terapia de Alvo Molecular/tendências , Neoplasias das Paratireoides/diagnóstico , Neoplasias das Paratireoides/patologia , Neoplasias das Paratireoides/terapia
18.
Anticancer Res ; 39(6): 2883-2889, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31177126

RESUMO

BACKGROUND/AIM: High-grade serous carcinoma (HGSC) is the most common histological subtype of ovarian carcinoma. Somatic mutation of tumor protein 53 (TP53) is a hallmark of tubo-ovarian HGSC and is observed in almost all such cases. Highly sensitive targeted genomic sequencing can be used to identify novel mutations that may become potential druggable targets and aid in therapeutic decisions. The aim of this study was to describe the clinicopathological and molecular characteristics of HGSCs with novel somatic TP53 mutations identified by next-generation sequencing (NGS). MATERIALS AND METHODS: A commercial NGS panel comprising 170 genes, including TP53, was used to analyze the genetic profiles of 132 ovarian carcinoma cases. The clinicopathological characteristics and p53 immunostaining results of two HGSCs exhibiting novel TP53 mutations were investigated. RESULTS: Eighty-eight (66.7%) out of 132 ovarian carcinoma cases were diagnosed as HGSC. Novel TP53 in-frame deletion mutations c.719_727delGTTCCTGCA (p53 p.Ser240_Cys242del) and c.634_642delTTTCGACAT (p53 p.F212_H214del) were detected in a single case of HGSC each. Both patients were postmenopausal women. Imaging and laboratory studies revealed peritoneal carcinomatosis and elevated levels of serum tumor markers. The patients underwent primary debulking surgery and were diagnosed as having stage IIIC HGSC. In both cases, p53 immunostaining revealed uniform nuclear immunoreactivity in 90% or more of tumor cells at a very strong intensity. CONCLUSION: Targeted genomic sequencing revealed novel in-frame deletion mutations of TP53 leading to p53 overexpression in tubo-ovarian HGSC. This discovery of previously unreported somatic TP53 mutations provides insight into the translation of NGS technology into personalized medicine and identifies new potential targets for therapeutic applications.


Assuntos
Cistadenocarcinoma Seroso/cirurgia , Neoplasias das Tubas Uterinas/cirurgia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias Ovarianas/cirurgia , Neoplasias Peritoneais/cirurgia , Deleção de Sequência , Proteína Supressora de Tumor p53/genética , Regulação para Cima , Núcleo Celular/metabolismo , Cistadenocarcinoma Seroso/genética , Cistadenocarcinoma Seroso/metabolismo , Cistadenocarcinoma Seroso/patologia , Procedimentos Cirúrgicos de Citorredução , Neoplasias das Tubas Uterinas/genética , Neoplasias das Tubas Uterinas/metabolismo , Neoplasias das Tubas Uterinas/patologia , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Pessoa de Meia-Idade , Mutação , Gradação de Tumores , Neoplasias Ovarianas/genética , Neoplasias Ovarianas/metabolismo , Neoplasias Ovarianas/patologia , Neoplasias Peritoneais/genética , Neoplasias Peritoneais/metabolismo , Neoplasias Peritoneais/patologia , Pós-Menopausa , Medicina de Precisão , Análise de Sequência de DNA , Proteína Supressora de Tumor p53/metabolismo
19.
BMC Plant Biol ; 19(1): 227, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146695

RESUMO

BACKGROUND: Persimmon (Diospyros kaki) is the most economically cultivated species belonging to the genus Diospyros. However, little is known about the interspecific diversity and mechanism of domestication, partly due to the lack of genomic information that is available for closely related species of D. kaki (DK). Here, we performed transcriptome sequencing on nine samples, including DK, a variety of DK and seven closely related species, to evaluate the interspecific genetic divergence and to identify candidate genes involved in persimmon domestication. RESULTS: We obtained a total of 483,421 unigenes with N50 at 1490 bp in the nine Diospyros samples and identified 2603 orthogroups that were shared among all the samples using OrthoMCL analysis. A phylogenetic tree was established based on the tandem 2603 one-to-one single copy gene alignments, showing that DK was closely related to D. kaki var. silvestris (DKV) and that it clustered with the clade of D. deyangnsis (DD) and was farthest from the D. cathayensis (DC) species. The nonsynonymous substitutions (Ka), via synonymous substitution (Ks) ratios, was directly proportional to the genetic relationship of the different species. The higher the Ka/Ks ratios, the longer the distance was. Moreover, 31 positively selected genes (PSGs) involved in carbohydrate metabolism and phenolic metabolism were identified and isolated, and nearly all PSGs except the MATE gene had a high expression in the DK or DKV species. It was hypothesized that these genes might contribute to the domestication of the DK species. Finally, we developed the expressed sequence tag-simple sequence repeat (EST-SSR) and identified 2 unique amplicons DKSSR10 and DKSSR39: the former was absent in the DC species but was present in the other species, the latter had a long amplification product in the DJ species. CONCLUSION: This study presents the first transcriptome resources for the closely related species of persimmon and reveals interspecific genetic divergence. It is speculated that DK is derived from the hybridization of DD and DO species. Furthermore, our analysis suggests candidate PSGs that may be crucial for the adaptation, domestication, and speciation of persimmon relatives and suggests that DKSSR10 and DKSSSR39 could potentially serve as species-specific molecular markers.


Assuntos
Diospyros/genética , Domesticação , Variação Genética , Transcriptoma , Etiquetas de Sequências Expressas , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites
20.
BMC Plant Biol ; 19(1): 232, 2019 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-31159725

RESUMO

BACKGROUND: Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known. RESULTS: In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target ibSPL in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in Arabidopsis. Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of SPL and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic Arabidopsis plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed. CONCLUSIONS: The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.


Assuntos
Antocianinas/biossíntese , Regulação da Expressão Gênica de Plantas , Ipomoea batatas/genética , MicroRNAs/genética , RNA de Plantas/genética , Antocianinas/genética , Sequenciamento de Nucleotídeos em Larga Escala , Ipomoea batatas/metabolismo , MicroRNAs/metabolismo , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , RNA de Plantas/metabolismo , Análise de Sequência de RNA
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