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1.
Zhonghua Wai Ke Za Zhi ; 58(1): 37-41, 2020 Jan 01.
Artigo em Chinês | MEDLINE | ID: mdl-31902168

RESUMO

Pancreatic cancer is the most lethal malignancy with an overall 5-year survival rate less than 9%, mainly due to late diagnosis and lack of effective therapeutic options.In the last decade, post-operative survival has been enhanced with advent of neoadjuvant therapy and combined adjuvant therapy.Furthermore, the information gained from the omics data, including next generation sequencing data, hasn't yet begun to affect treatment of pancreatic cancer patients.However, in terms of precision medicine, pancreatic cancer has always lagged behind other tumors.Therefore, combined with practical experience, summary of the latest development and research progress of precise medical treatment of pancreatic cancer, especially from the fields of molecular biology and experimental models, is of critical importance. Further development of precise medicine for pancreatic cancer based on platforms using PDX and organoid model would promisingly help in effective improvement of clinical treatment.


Assuntos
Neoplasias Pancreáticas/terapia , Medicina de Precisão , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Terapia Neoadjuvante
2.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 37(1): 21-24, 2020 Jan 10.
Artigo em Chinês | MEDLINE | ID: mdl-31922589

RESUMO

OBJECTIVE: To identify potential variant in a child diagnosed as infantile neuroaxonal dystrophy. METHODS: Genomic DNA was extracted from peripheral blood samples from the patient and his parents and subjected to next generation sequencing. Suspected variant was verified by PCR and Sanger sequencing. Pathogenicity of the mutation was predicted by using bioinformatic software including SIFT and PolyPhen-2. RESULTS: The child was found to carry compound heterozygous variations c.668C>A (p.Pro223Gln) and c.2266C>T (p.Gln756Ter) of the PLA2G6 gene, which were respectively inherited from his father and mother. c.2266C>T has changed codon 756 (glutamine) into a stop codon, resulting premature termination of peptide chain synthesis. c.2266C>T has not been reported previously and was predicted to be harmful. CONCLUSION: The compound variants of c.668C>A (p.Pro223Gln) and c.2266C>T (p.Gln756Ter) of the PLA2G6 gene probably underlies the disease in the child. Above finding has enriched the variant spectrum of the PLA2G6 gene.


Assuntos
Fosfolipases A2 do Grupo VI , Distrofias Neuroaxonais , Criança , Fosfolipases A2 do Grupo VI/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mutação , Distrofias Neuroaxonais/genética
3.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 37(1): 57-59, 2020 Jan 10.
Artigo em Chinês | MEDLINE | ID: mdl-31922598

RESUMO

OBJECTIVE: To explore the genetic basis of a child with idiopathic mental retardation. METHODS: Clinical data and peripheral blood sample of the child were collected. Genomic DNA was extracted and subjected to copy number analysis using single nucleotide polymrophism array comparative genome hybridization (SNP-aCGH) and targeted capture and next generation sequencing (NGS). RESULTS: No microdeletion/microduplication were detected by SNP-aCGH. NGS has detected homozygous c.722delA (p.Asp241fs) variant of the LISN1 gene, which is known to underlie autosomal recessive mental retardation-27 (MRT 27). Both parents are carriers of the variant, conforming to the autosomal recessive inheritance. CONCLUSION: A novel pathogenic variant of the LINS1 gene has been identified, which probably underlies the MRT 27 in the patient.


Assuntos
Deficiência Intelectual , Proteínas , Criança , Hibridização Genômica Comparativa , Sequenciamento de Nucleotídeos em Larga Escala , Homozigoto , Humanos , Deficiência Intelectual/genética , Proteínas/genética
4.
Anticancer Res ; 40(1): 101-107, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31892558

RESUMO

BACKGROUND: Mitochondria are energy-producing organelles, and dysfunction in these organelles causes various types of disease. Although several studies have identified mutations in nuclear DNA that are associated with the etiology of ulcerative colitis (UC), information regarding mitochondrial DNA (mtDNA) in UC is limited. This study aimed to investigate the mitochondrial DNA polymorphism underlying the etiology of UC and UC-associated colorectal cancer. MATERIALS AND METHODS: Next-generation sequencing was performed to assess mitochondrial DNA mutations in 12 patients with UC-associated cancer. The mtDNA mutations in the non-neoplastic mucosa, tumor tissues, and healthy controls were compared. RESULTS: The incidence of mutations of nicotinamide adenine dinucleotide phosphate ubiquinone oxidase subunit, ATP synthetase, and tRNA was higher in non-neoplastic mucosa in those with UC compared with the healthy controls. However, no statistically significant differences were observed in mutations between the tumor tissues and non-neoplastic mucosa in UC. CONCLUSION: Significant mutations in mtDNA were observed in the non-neoplastic mucosa of patients with UC-associated cancer.


Assuntos
Colite Ulcerativa/complicações , Colite Ulcerativa/genética , Neoplasias Colorretais/etiologia , Genes Mitocondriais , Polimorfismo Genético , Transformação Celular Neoplásica/genética , Colite Ulcerativa/metabolismo , Colite Ulcerativa/patologia , Neoplasias Colorretais/metabolismo , Neoplasias Colorretais/patologia , Suscetibilidade a Doenças , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Mucosa Intestinal/metabolismo , Mucosa Intestinal/patologia , Masculino , Mutação
5.
Food Microbiol ; 85: 103302, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31500708

RESUMO

This study dealt with the influence of the temperature on the bacterial dynamics of two spontaneously fermented wheat sourdoughs, propagated at 21 ±â€¯1 °C (SD1) and 30 ±â€¯1 °C (SD2), during nine backslopping steps (BS1 to BS9). Proteobacteria was the only phylum found in flour. Escherichia hermannii was predominant, followed by Kosakonia cowanii, besides species belonging to the genera Pantoea and Pseudomonas. After one step of propagation, Clostridium and Bacillus cereus group became predominant. Lactobacillus curvatus was found at low relative abundance. For the second backslopping step, Clostridium was flanked by L. curvatus and Lactobacillus farciminis. From BS4 (6th day) onward, lactic acid bacteria (LAB) became predominant. L. farciminis overcame L. curvatus and remained dominant until the end of propagations for both sourdoughs. At 21 °C, Bacillus, Clostridium, Pseudomonas, and Enterobacteriaceae were gradually inhibited. At the end of propagation, SD1 harbored only LAB. Otherwise, the temperature of 30 °C favored the persistence of atypical bacteria in SD2, as Pseudomonas and Enterobacteriaceae. Therefore, the temperature of 21 °C was more suitable for sourdough propagation in Brazil. This study enhanced the knowledge of temperature's influence on microbial assembly and contributed to the elucidation of sourdough microbial communities in Brazil.


Assuntos
Pão/microbiologia , Fermentação , Metagenoma , Proteobactérias/classificação , Brasil , Contagem de Colônia Microbiana , DNA Bacteriano/genética , Farinha/microbiologia , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota , Proteobactérias/crescimento & desenvolvimento , RNA Ribossômico 16S/genética , Temperatura Ambiente
6.
Sci Total Environ ; 700: 134418, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31629269

RESUMO

Soil pH is an important predictor of bacterial community composition and diversity. Examining the effects of pH on diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soils provide valuable information for knowing potential role of rhizosphere bacteria in crop yield. Here, we collected soils from artificial greenhouses and applied Illumina Miseq sequencing, quantitative PCR techniques, multiple ecological analysis methods, including topological analysis and functional profiling to analyze our data and validate our hypotheses. We found that the soil physicochemical properties, species diversity, and rhizosphere bacterial community composition were significantly affected by the degree of soil acidification (pH < 5.5 and pH > 5.5) but not vegetation type. Additionally, bacterial absolute abundance increased with higher pH. The 18 soil samples were clustered into two distinct groups of pH < 5.5 and pH > 5.5 at the OTU level, and soil pH had more of an effect on bacterial community composition compared to the other physicochemical variables. In addition, rhizosphere bacteria might presented relatively less competition for survival in pH < 5.5 soils, and bacterial community functions, including nutrient (i.e., carbon, nitrogen, phosphorus, and sulphur) cycling-related enzymes and proteins, were downregulated in more acidic soils (pH < 5.5) based on sequence analysis. To our knowledge, this report is the first to show that pH is a key factor affecting the diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soil in artificial greenhouses. Our findings emphasize that community function and structure of rhizosphere bacteria are closely correlated in more acidic soils, and the decreased crop yield may be correlated with attenuation of the function of the rhizosphere bacterial community.


Assuntos
Rizosfera , Microbiologia do Solo , Solo/química , Bactérias , Biodiversidade , Sequenciamento de Nucleotídeos em Larga Escala , Concentração de Íons de Hidrogênio , Microbiota , Nitrogênio , Fósforo
7.
Gene ; 725: 144164, 2020 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-31639430

RESUMO

Bardet-Biedl syndrome (BBS) is a clinically and genetically heterogeneous ciliopathy with several clinical features including retinitis pigmentosa, obesity, kidney dysfunction, postaxial polydactyly, behavioral dysfunction and hypogonadism with wide spectrum of additional features. With multiple phenotypes and heterogeneous distribution, it is unlikely that BBS is caused by single gene defect. We have performed clinical and genetic diagnosis of two individuals from an Indian family with classical BBS symptoms. Whole exome sequencing identified homozygous missense mutation in BBS10 gene, hemizygous missense AR and homozygous missense PDE6B mutations in the proband and affected sibling with BBS. Identification of BBS10 mutation along with AR and PDE6B gene mutation will expand the genetic and phenotypic spectrum in individuals with BBS.


Assuntos
Síndrome de Bardet-Biedl/genética , Síndrome de Bardet-Biedl/metabolismo , Chaperoninas/genética , Chaperoninas/metabolismo , Nucleotídeo Cíclico Fosfodiesterase do Tipo 6/genética , Análise Mutacional de DNA , Estudos de Associação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Mutação/genética , Linhagem , Fenótipo , Receptores Androgênicos/genética , Retinite Pigmentosa/genética , Sequenciamento Completo do Exoma/métodos , Adulto Jovem
8.
Gene ; 725: 144170, 2020 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-31647996

RESUMO

Caragana korshinskii Kom. is a legume shrub that is widely distributed across desert habitats with gravely, sandy, and saline soils in Asia and Africa. C. korshinskii has highly developed roots and a strong tolerance to abiotic stress. At present, there are few genetic studies of C. korshinskii because of the limited availability of genomic resources. To understand the comprehensive mechanisms that are associated with drought tolerance, we used RNA-seq to survey the differentially expressed genes (DEGs) in comparisons of drought-treated and control plants. After analysing the sequencing results, we found 440 differentially expressed genes existing in drought-treated and control plants. Among the DEGs, 39 unigenes showed up-regulated expression after drought treatment, while 401 unigenes were down-regulated. We used the KEGG database to annotate these drought-induced genes; 126 unigenes were identified by KEGG pathway annotation, and approximately 28% of the unigenes with known function fell into categories related to fatty acid metabolism, starch, sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Finally, we confirmed that one gene has a potential function in drought tolerance. Our study is the first to provide transcriptomic resources for Caragana korshinskii and to determine its digital gene expression profile under conditions of drought stress using the assembled transcriptomic data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic stress conditions.


Assuntos
Caragana/genética , Perfilação da Expressão Gênica/métodos , Estresse Fisiológico/genética , Secas , Fabaceae/genética , Regulação da Expressão Gênica de Plantas/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Anotação de Sequência Molecular , RNA/genética , Transcriptoma/genética
9.
J Clin Pathol ; 73(1): 35-41, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31296605

RESUMO

AIMS: Precision medicine therapy is remodelling the diagnostic landscape of cancer. The success of these new therapies is often based on the presence or absence of a specific mutation in a tumour. The Idylla platform is designed to determine the mutational status of a tumour as quickly and accurately as possible, as a rapid, accurate diagnosis is of the utmost importance for the treatment of patients. This is the first complete prospective study to investigate the robustness of the Idylla platform for EGFR, KRAS and BRAF mutations in non-small cell lung cancer, metastatic colorectal cancer and metastatic melanoma, respectively. METHODS: We compared prospectively the Idylla platform with the results we obtained from parallel high-throughput next-generation sequencing, which is the current gold standard for mutational testing. Furthermore, we evaluated the benefits and disadvantages of the Idylla platform in clinical practice. Additionally, we reviewed all the published Idylla performance articles. RESULTS: There was an overall agreement of 100%, 94% and 94% between the next-generation panel and the Idylla BRAF, KRAS and EGFR mutation test. Two interesting discordant findings among 48 cases were observed and will be discussed together with the advantages and shortcoming of both techniques. CONCLUSION: Our observations demonstrate that the Idylla cartridge for the EGFR, KRAS and BRAF mutations is highly accurate, rapid and has a limited hands-on time compared with next-generation sequencing.


Assuntos
Biomarcadores Tumorais/genética , Análise Mutacional de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Mutação , Neoplasias/genética , Proteínas Proto-Oncogênicas B-raf/genética , Proteínas Proto-Oncogênicas p21(ras)/genética , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , Receptores ErbB/genética , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Melanoma/genética , Melanoma/secundário , Neoplasias/patologia , Valor Preditivo dos Testes , Estudos Prospectivos , Reprodutibilidade dos Testes , Neoplasias Cutâneas/genética , Neoplasias Cutâneas/patologia , Fluxo de Trabalho
10.
Biosci Biotechnol Biochem ; 84(1): 53-62, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31483222

RESUMO

Large numbers of miRNAs are found in biofluid exosomes. We isolated ~50-200 nm diameter exosomes from four types of porcine biofluid (urine, plasma, semen, and bile) using serial centrifugation and ultracentrifugation procedures. A total of 42.15 M raw data were generated from four small RNA libraries. This produced 40.17 M map-able sequences, of which we identified 204 conserved miRNAs, and 190 novel candidate miRNAs. Furthermore, we identified 34 miRNAs specifically expressed in only one library, all with well-characterized immune-related functions. A set of five universally abundant miRNAs (miR-148a-3p, miR-21-5p, let-7f-5p, let-7i-5p, and miR-99a-5p) across all four biofluids was also found. Function enrichment analysis revealed that the target genes of the five ubiquitous miRNAs are primarily involved in immune and RNA metabolic processes. In summary, our findings suggest that porcine biofluid exosomes contain a large number of miRNAs, many of which may be crucial regulators of the immune system.


Assuntos
Secreções Corporais , Líquidos Corporais , Exossomos/genética , Imunidade Inata , MicroRNAs/genética , MicroRNAs/imunologia , Suínos/genética , Animais , Sequência de Bases/genética , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/imunologia , Sequenciamento de Nucleotídeos em Larga Escala , Microscopia de Força Atômica , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA
11.
Gut ; 69(1): 52-61, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-30971436

RESUMO

OBJECTIVE: Despite improvements in imaging, serum CA19-9 and pathological evaluation, differentiating between benign and malignant bile duct strictures remains a diagnostic conundrum. Recent developments in next-generation sequencing (NGS) have opened new opportunities for early detection and management of cancers but, to date, have not been rigorously applied to biliary specimens. DESIGN: We prospectively evaluated a 28-gene NGS panel (BiliSeq) using endoscopic retrograde cholangiopancreatography-obtained biliary specimens from patients with bile duct strictures. The diagnostic performance of serum CA19-9, pathological evaluation and BiliSeq was assessed on 252 patients (57 trainings and 195 validations) with 346 biliary specimens. RESULTS: The sensitivity and specificity of BiliSeq for malignant strictures was 73% and 100%, respectively. In comparison, an elevated serum CA19-9 and pathological evaluation had sensitivities of 76% and 48%, and specificities of 69% and 99%, respectively. The combination of BiliSeq and pathological evaluation increased the sensitivity to 83% and maintained a specificity of 99%. BiliSeq improved the sensitivity of pathological evaluation for malignancy from 35% to 77% for biliary brushings and from 52% to 83% for biliary biopsies. Among patients with primary sclerosing cholangitis (PSC), BiliSeq had an 83% sensitivity as compared with pathological evaluation with an 8% sensitivity. Therapeutically relevant genomic alterations were identified in 20 (8%) patients. Two patients with ERBB2-amplified cholangiocarcinoma received a trastuzumab-based regimen and had measurable clinicoradiographic response. CONCLUSIONS: The combination of BiliSeq and pathological evaluation of biliary specimens increased the detection of malignant strictures, particularly in patients with PSC. Additionally, BiliSeq identified alterations that may stratify patients for specific anticancer therapies.


Assuntos
Colangiopancreatografia Retrógrada Endoscópica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Neoplasias dos Ductos Biliares/diagnóstico , Neoplasias dos Ductos Biliares/genética , Neoplasias dos Ductos Biliares/patologia , Doenças Biliares/diagnóstico , Doenças Biliares/genética , Doenças Biliares/patologia , Biomarcadores Tumorais/sangue , Antígeno CA-19-9/sangue , Constrição Patológica/diagnóstico , Constrição Patológica/genética , Diagnóstico Diferencial , Feminino , Humanos , Cirrose Hepática Biliar/diagnóstico , Cirrose Hepática Biliar/genética , Cirrose Hepática Biliar/patologia , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Sensibilidade e Especificidade , Manejo de Espécimes/métodos , Adulto Jovem
12.
Equine Vet J ; 52(1): 67-75, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31006119

RESUMO

BACKGROUND: Although, peripheral caries (PC) affects almost half of UK horses, no comprehensive microbiological study has been performed on this disorder. As a high proportion of oral bacteria cannot be conventionally cultured, molecular microbiological techniques such as Next Generation Sequencing are required to examine the complex oral bacteria community. OBJECTIVES: To identify the microbiota involved in equine PC, including comparing microbiota at the more commonly and severely affected three caudal cheek teeth with the less commonly affected three rostral cheek teeth. STUDY DESIGN AND METHODS: Equine dental plaque samples were collected from the palatal aspects of cheek teeth of 63 horses. DNA was isolated and amplified using PCR, targeting the V4 region of the 16S rRNA gene and Next Generation Sequencing of these gene amplicons was performed. The acquired data were processed and analysed using Mothur and R. RESULTS: Streptococcus species was the genus most commonly associated with equine PC, whereas Gemella species was the genus most associated with the control group. In a further analysis where the rostral and caudal cheek teeth were compared with each other and with the control group. Veillonella species was the most commonly associated genus with PC of the rostral cheek teeth, Streptococcus species was the most associated genus with the caudal cheek teeth, and Corynebacterium with the control group. MAIN LIMITATIONS: Some bacteria can have multiple heterogeneous copies of the 16S rRNA gene, which can affect the estimation of their relative abundance. CONCLUSIONS: Similar to caries studies in other species, acidogenic and aciduric microorganisms including Streptococcus species were found to be associated with equine peripheral caries.


Assuntos
Bactérias/genética , Cárie Dentária/veterinária , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Doenças dos Cavalos/microbiologia , Animais , Bactérias/isolamento & purificação , Cárie Dentária/microbiologia , Placa Dentária/microbiologia , Placa Dentária/veterinária , Cavalos
13.
Zhonghua Nei Ke Za Zhi ; 59(1): 35-39, 2020 Jan 01.
Artigo em Chinês | MEDLINE | ID: mdl-31887834

RESUMO

Objective: To explore the relationship between driver gene mutation (JAK2, MPL and CALR) and disease type in BCR-ABL negative myeloproliferative neoplasms (MPNs) including primary myeloid fibrosis (PMF), essential thrombocytosis (ET) and polycythemia vera (PV). Methods: A total of 32 MPN related genes were detected by high-throughput sequencing in 156 MPN patients. The relationships between disease type and patients' general performance, the characteristics of driver gene mutations, concomitant gene mutations were analyzed. Results: In the population with JAK2 V617F positive mutation, the proportion of patients over 60 years old in PMF was higher than that with ET or PV. By high-throughput sequencing, 22 concomitant gene mutations were detected in 46 patients with JAK2, MPL or CALR mutations, including 4 (8.3%) in PV, 20 (29.4%) in ET, and 22 (55.0%) in PMF. DNMT3A mutation was detected only in patients with PV, while splicing factor related genes including SF3B1, SRSF2 and U2AF1 were only accompanied by PMF. According to the variation allele frequency (VAF) value of JAK2 V617F mutation, the VAF value associated with PV was the highest (68.15%), followed by PMF (37.7%) and ET (23%). However, there were significant differences in the incidence of JAK2 V617F homozygous among 3 different diseases. In patients with JAK2 mutation, the proportion of other gene mutations in PV and ET was significantly lower than that in PMF. Conclusions: Under the condition of common driver gene mutations (JAK2, MPL and CALR), patients' age, VAF value and homozygous state, concomitant gene mutations are closely related to different disease type. These correlations help to improve clinical understanding of disease characteristics and risk assessment.


Assuntos
Calreticulina/genética , Proteínas de Fusão bcr-abl/genética , Janus Quinase 2/genética , Transtornos Mieloproliferativos/genética , Receptores de Trombopoetina/genética , Adolescente , Adulto , Distribuição por Idade , Idoso , Idoso de 80 Anos ou mais , Grupo com Ancestrais do Continente Asiático/genética , Calreticulina/metabolismo , Feminino , Proteínas de Fusão bcr-abl/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Janus Quinase 2/metabolismo , Masculino , Pessoa de Meia-Idade , Mutação , Transtornos Mieloproliferativos/sangue , Transtornos Mieloproliferativos/metabolismo , Policitemia Vera/genética , Mielofibrose Primária/genética , Receptores de Trombopoetina/metabolismo , Trombocitemia Essencial/genética
14.
Chemosphere ; 238: 124661, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31472350

RESUMO

Toxicities of the marine algae Alexandrium minutum and its excreted gonyautoxins (GTXs) to the marine crustacean Artemia salina were investigated. Mortality was observed for neither larvae nor adult A. salina exposed to A. minutum at a density of 5000 cells/mL or 0.5 µM GTX2/3. After exposure, the full transcriptome of adult A. salina was assembled and functionally annotated. A total of 599,286 transcripts were obtained, which were clustered into 515,196 unigenes. Results of the transcriptional effect level index revealed that direct exposure to the toxic algae A. minutum caused greater alterations in the transcriptome than did exposure to the extracellular product GTX2/3. Mechanisms of effects were different between exposure of A. salina to A. minutum cells or GTX2/3. Exposure to A. minutum modulated formation of the ribonucleoprotein complex and metabolism of amino acids and lipids in A. salina. Exposure to GTX2/3 exposure inhibited expression of genes related to metabolism of chitin, which might result in disruption of molting process or disturbed sheath morphogenesis. Overall, effects on transcription observed in this study represent the first report based on application of next generation sequencing techniques to investigate the transcriptomic response of A. salina exposed to an environmentally realistic level of A. minutum or GTX2/3.


Assuntos
Artemia/genética , Saxitoxina/análogos & derivados , Transcriptoma/efeitos dos fármacos , Animais , Artemia/fisiologia , Quitina/genética , Quitina/metabolismo , Dinoflagelados/citologia , Dinoflagelados/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Saxitoxina/farmacologia , Saxitoxina/toxicidade
15.
Sheng Wu Gong Cheng Xue Bao ; 35(12): 2284-2294, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31880136

RESUMO

With the development of liquid biopsy technology, plasma cell-free DNA (cfDNA) becomes one of the research hotspots. Whole-genome bisulfite sequencing of plasma cell-free DNA has shown great potential medical applications such as cancer detection. However, the practical stability evaluation is still lacking. In this study, plasma cell-free DNA samples from two volunteers at different time were collected and prepared for sequencing in multiple laboratories. The library preparation strategies include pre-bisulfite, post-bisulfite and regular whole-genome sequencing. We established a set of quality control references for plasma cell-free DNA sequencing data and evaluated practical stability of blood collection, DNA extraction, and library preparation and sequencing depth. This work provided a technical practice guide for the application of plasma cfDNA methylation sequencing for clinical applications.


Assuntos
Sequenciamento Completo do Genoma , Ácidos Nucleicos Livres , Metilação de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Análise de Sequência de DNA , Sulfitos
16.
Sheng Wu Gong Cheng Xue Bao ; 35(12): 2350-2366, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31880141

RESUMO

Intestinal bacteria interact closely with human health and diseases. With the development of high-throughput sequencing technologies, researchers have discovered the potential of intestinal bacteria in the diagnosis and treatment of diseases. Meanwhile, synthetic biology strategies are applied to engineer these bacteria for clinical applications. These engineered intestinal microbial are constructed by designing editing tools and feedback loops to gain functions of diagnose or targeted therapy. Consequently, these engineered bacteria are capable of sensing, calculating and responding to the environment. In this review, we summarize the recent advances in engineered intestinal bacteria in disease diagnosis and treatment. Furthermore, we also discuss the current status and future prospect of the engineered intestinal bacteria regarding their clinical applications, market, and safety issues.


Assuntos
Bactérias , Biologia Sintética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos
17.
Zhonghua Fu Chan Ke Za Zhi ; 54(12): 797-802, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31874468

RESUMO

Objective: To investigate chromosome abnormality rate and related factors of spontaneous abortion in early pregnancy. Methods: A total of 831 tissue samples of spontaneous abortion in early pregnancy were collected from June 2015 to August 2018 in the First Affiliated Hospital of Nanjing Medical University. Chromosomal copy number was analyzed by next generation sequencing (NGS). The relationships between chromosome abnormality and maternal age, in vitro fertilization-embryo transfer (IVF-ET) pregnancy, number of previous spontaneous abortions, history of live birth were analyzed by statistical methods. Results: Among 831 tissue samples of spontaneous abortion in early pregnancy, 461 (55.5%, 461/831) were found to have chromosome abnormalities. Maternal age (OR=1.107, 95%CI: 1.070- 1.145) and history of live birth (OR=1.909, 95%CI: 1.182-3.083) were the positive correlative factors of chromosome abnormality. Times of previous spontaneous abortion (OR=0.807, 95%CI: 0.702-0.928) and IVF-ET pregnancy (OR=0.554, 95%CI: 0.404-0.760) were the negative correlative factors of chromosome abnormality. Conclusions: Chromosome abnormality is an important cause of spontaneous abortion in early pregnancy. The rate of chromosome abnormality increases with the increase of maternal age and the history of live birth, and decreases with the increase of number of previous spontaneous abortion and IVF-ET pregnancy.


Assuntos
Aborto Espontâneo , Transtornos Cromossômicos/genética , Transferência Embrionária , Fertilização In Vitro , Aborto Espontâneo/genética , Aberrações Cromossômicas , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Idade Materna , Gravidez , Taxa de Gravidez , Primeiro Trimestre da Gravidez
18.
Zhonghua Fu Chan Ke Za Zhi ; 54(12): 808-814, 2019 Dec 25.
Artigo em Chinês | MEDLINE | ID: mdl-31874470

RESUMO

Objective: To evaluate the application of combinatorial probe anchor synthesis (cPAS)-based high-throughput low coverage whole genome sequencing in chromosomal aberration detection in spontaneous miscarriage. Methods: From September 2015 to May 2017, spontaneous miscarriage samples were collected from Inner Mongolia Maternal and Child Health Care Hospital. Those samples were further analyzed with two independent methods, fluorescence in situ hybridization (FISH) and low coverage whole genome sequencing on the BGISEQ-500 high-throughput platform. The performance of low coverage whole genome sequencing was assessed by comparing to FISH results. Results: In 595 spontaneous miscarried specimens, low coverage whole genome sequencing revealed 144 cases (24.2%, 144/595) chromosomal abnormalities, of which a subset of 137 cases (23.0%, 137/595) were detected as aneuploidies, 2 cases (0.3%, 2/595) as mosaicisms and 5 cases (0.8%, 5/595) as copy number variation (≥5 Mb). Conclusion: cPAS-based high-throughput low coverage whole genome sequencing is a reliable method in detecting chromosomal aberrations inspontaneous abortion tissues, including chromosome aneuploidies, mosaicisms and copy number variation (≥5 Mb).


Assuntos
Aborto Espontâneo/genética , Aberrações Cromossômicas/estatística & dados numéricos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Criança , China , Aberrações Cromossômicas/embriologia , Cromossomos/genética , DNA/genética , Variações do Número de Cópias de DNA/genética , Feminino , Humanos , Hibridização in Situ Fluorescente , Gravidez , Sequenciamento Completo do Genoma/métodos
19.
Zhong Nan Da Xue Xue Bao Yi Xue Ban ; 44(10): 1089-1098, 2019 Oct 28.
Artigo em Chinês | MEDLINE | ID: mdl-31857501

RESUMO

OBJECTIVE: To analyze the differential expression of RAW264.7 macrophage-derived exosomes miRNA stimulated by free silicon dioxide (SiO2).
 Methods: RAW264.7 was stimulated with SiO2 (200 mg/L) for 48 h (exo_48 h group), and the supernatant was collected. The exosomes in the supernatant were extracted by ultracentrifugation. Transmission microscopy, nanoparticle tracking analysis (NTA) and Western blotting were used to identify exosomes. High-throughput sequencing was performed to compare the differential expression of exosome miRNAs between the exo_control group (RAW264.7 cultured for 48 h without SiO2) and the exo_48 h group; miRanda, TargetScan and starBase were used to predict target genes of differential miRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed on target genes to further analyze the biological functions of genes.
 Results: The transmission microscopy showed that the exosomes were lipid membrane coated vesicles, which were heterogeneously distributed, with a diameter ranging from 30 to 100 nm, and the shape was round or elliptical. The volume kurtosis was concentrated between 40 and 100 nm and the exosome marker protein TSG101 was positive. High-throughput sequencing screened 148 differentially expressed exosomal miRNAs. MiR-219c-3p, let-7d-3p, let-7a-1-3p, miR-328-3p, miR-365-3p, and miR-7219-3p were significantly up-regulated, and miR-378d and miR-5106 were significantly down-regulated compared with the control group. Target genes were mainly enriched in mTOR signaling pathway, Wnt signaling pathway, TGF-ß signaling pathway, and so on.
 Conclusion: The exosomes secreted by SiO2-induced macrophages contain abundant miRNAs, and their expressions are significantly different. These differential miRNAs may be involved in the activation of lung fibroblasts and epithelial-mesenchymal transition.


Assuntos
Exossomos , Macrófagos , Animais , Linhagem Celular , Sequenciamento de Nucleotídeos em Larga Escala , Camundongos , MicroRNAs , Dióxido de Silício
20.
BMC Bioinformatics ; 20(Suppl 24): 596, 2019 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-31861975

RESUMO

BACKGROUND: Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have developed several new pipelines and software packages to identify RNA editing sites with a focus on downstream statistical analysis and functional interpretation. RESULTS: Here, we developed a user-friendly public webserver named MIRIA that integrates statistics and visualization techniques to facilitate the comprehensive analysis of RNA editing sites data identified by the pipelines and software packages. MIRIA is unique in that provides several analytical functions, including RNA editing type statistics, genomic feature annotations, editing level statistics, genome-wide distribution of RNA editing sites, tissue-specific analysis and conservation analysis. We collected high-throughput RNA sequencing (RNA-seq) data from eight tissues across seven species as the experimental data for MIRIA and constructed an example result page. CONCLUSION: MIRIA provides both visualization and analysis of mammal RNA editing data for experimental biologists who are interested in revealing the functions of RNA editing sites. MIRIA is freely available at https://mammal.deepomics.org.


Assuntos
Mamíferos , Edição de RNA , Análise de Sequência de RNA , Transcriptoma , Animais , Genoma , Genômica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mamíferos/genética , RNA/genética , Análise de Sequência de RNA/métodos
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