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  • Hindawi Limited  (8)
  • 1
    Online Resource
    Online Resource
    Whole-Genome Resequencing of Twenty Branchiostoma belcheri Individuals Provides a Brand-New Variant Dataset for Branchiostoma
    Hindawi Limited ; 2020
    In:  BioMed Research International Vol. 2020 ( 2020-01-26), p. 1-15
    Details
    In: BioMed Research International, Hindawi Limited, Vol. 2020 ( 2020-01-26), p. 1-15
    Abstract: As the extant representatives of the basal chordate lineage, amphioxi (including the genera Branchiostoma , Asymmetron and Epigonichthys ) play important roles in tracing the state of chordate ancestry. Previous studies have reported that members of the Branchiostoma species have similar morphological phenotypic characteristics, but in contrast, there are high levels of genetic polymorphisms in the populations. Here, we resequenced 20 Branchiostoma belcheri genomes to an average depth of approximately 12.5X using the Illumina HiSeq 2000 platform. In this study, over 52 million variations (~12% of the total genome) were detected in the B. belcheri population, and an average of 12.8 million variations (~3% of the total genome) were detected in each individual, confirming that Branchiostoma is one of the most genetically diverse species sequenced to date. Demographic inference analysis highlighted the role of historical global temperature in the long-term population dynamics of Branchiostoma , and revealed a population expansion at the Greenlandian stage of the current geological epoch. We detected 594 Single nucleotide polymorphism and 148 Indels in the Branchiostoma mitochondrial genome, and further analyzed their genetic mutations. A recent study found that the epithelial cells of the digestive tract in Branchiostoma can directly phagocytize food particles and convert them into absorbable nontoxic nutrients using powerful digestive and immune gene groups. In this study, we predicted all potential mutations in intracellular digestion-associated genes. The results showed that most “probably damaging” mutations were related to rare variants (MAF  〈  0.05) involved in strengthening or weakening the intracellular digestive capacity of Branchiostoma . Due to the extremely high number of polymorphisms in the Branchiostoma genome, our analysis with a depth of approximately 12.5X can only be considered a preliminary analysis. However, the novel variant dataset provided here is a valuable resource for further investigation of phagocytic intracellular digestion in Branchiostoma and determination of the phenotypic and genotypic features of Branchiostoma .
    Type of Medium: Online Resource
    ISSN: 2314-6133 , 2314-6141
    URL: Article
    DOI: 10.1155/2020/3697342
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2020
    detail.hit.zdb_id: 2698540-8
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  • 2
    Online Resource
    Online Resource
    Next-Generation Sequencing of MicroRNAs for Breast Cancer Detection
    Hindawi Limited ; 2011
    In:  Journal of Biomedicine and Biotechnology Vol. 2011 ( 2011), p. 1-7
    Details
    In: Journal of Biomedicine and Biotechnology, Hindawi Limited, Vol. 2011 ( 2011), p. 1-7
    Abstract: It is reported that different microRNA (miRNA) profiles can be detected in the blood of cancer patients. We investigated that whether the key serum miRNAs could discriminate patients with and without breast cancer. This study was divided into three parts: (1) miRNA marker discovery using SOLiD sequencing-based miRNA profiling on cancerous and adjacent noncancerous breast tissue of one breast cancer patient; (2) marker selection and validation by real-time PCR on a small set of serum; (3) gene ontology analysis of the key miRNA target genes. Of genome-wide tissue miRNA expression analysis, five miRNAs were found to be altered more than fivefold by SOLiD sequencing (i.e., miR-29a, miR-23a, miR-23b, miR-192, and miR-21). All the five miRNAs were validated on the 20 breast cancer patients and 20 controls. miR-29a and miR-21 were significantly increased in the serum of breast cancer patients (). Gene ontology analysis of the target genes revealed enrichment for special biological process categories, that is, signal transduction, development, apoptosis, cell proliferation, and cell adhesion. SOLiD sequencing provides a promising method for cancer-related miRNA profiling. Serum miRNAs may be useful biomarkers for breast cancer detection.
    Type of Medium: Online Resource
    ISSN: 1110-7243 , 1110-7251
    URL: Article
    DOI: 10.1155/2011/597145
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2011
    detail.hit.zdb_id: 2698540-8
    detail.hit.zdb_id: 2512507-2
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing
    Hindawi Limited ; 2017
    In:  BioMed Research International Vol. 2017 ( 2017), p. 1-12
    Details
    In: BioMed Research International, Hindawi Limited, Vol. 2017 ( 2017), p. 1-12
    Abstract: The characteristics of tongue coating are very important symbols for disease diagnosis in traditional Chinese medicine (TCM) theory. As a habitat of oral microbiota, bacteria on the tongue dorsum have been proved to be the cause of many oral diseases. The high-throughput next-generation sequencing (NGS) platforms have been widely applied in the analysis of bacterial 16S rRNA gene. We developed a methodology based on genus-specific multiprimer amplification and ligation-based sequencing for microbiota analysis. In order to validate the efficiency of the approach, we thoroughly analyzed six tongue coating samples from lung cancer patients with different TCM types, and more than 600 genera of bacteria were detected by this platform. The results showed that ligation-based parallel sequencing combined with enzyme digestion and multiamplification could expand the effective length of sequencing reads and could be applied in the microbiota analysis.
    Type of Medium: Online Resource
    ISSN: 2314-6133 , 2314-6141
    URL: Article
    DOI: 10.1155/2017/8184160
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2017
    detail.hit.zdb_id: 2698540-8
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  • 4
    Online Resource
    Online Resource
    Genome-Wide miRNA Seeds Prediction in Archaea
    Hindawi Limited ; 2014
    In:  Archaea Vol. 2014 ( 2014), p. 1-6
    Details
    In: Archaea, Hindawi Limited, Vol. 2014 ( 2014), p. 1-6
    Abstract: Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2–8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation signal. Eleven of 29 unique seeds from previous study support our result ( P value 〈 0.01 ), which demonstrates that the pipeline is suitable to predict experimentally detectable miRNA seeds. The statistical significance of the overlap between the detected archaeal seeds and known eukaryotic seeds shows that the miRNA may evolve before the divergence of these two domains of cellular life. In addition, miRNA targets are enriched for genes involved in transcriptional regulation, which is consistent with the situation in eukaryote. Our research will enhance the regulatory network analysis in Archaea.
    Type of Medium: Online Resource
    ISSN: 1472-3646 , 1472-3654
    URL: Article
    DOI: 10.1155/2014/671059
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2014
    detail.hit.zdb_id: 2133011-6
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  • 5
    Online Resource
    Online Resource
    High-Throughput Sequencing of MicroRNAs in Adenovirus Type 3 Infected Human Laryngeal Epithelial Cells
    Hindawi Limited ; 2010
    In:  Journal of Biomedicine and Biotechnology Vol. 2010 ( 2010), p. 1-8
    Details
    In: Journal of Biomedicine and Biotechnology, Hindawi Limited, Vol. 2010 ( 2010), p. 1-8
    Abstract: Adenovirus infection can cause various illnesses depending on the infecting serotype, such as gastroenteritis, conjunctivitis, cystitis, and rash illness, but the infection mechanism is still unknown. MicroRNAs (miRNA) have been reported to play essential roles in cell proliferation, cell differentiation, and pathogenesis of human diseases including viral infections. We analyzed the miRNA expression profiles from adenovirus type 3 (AD3) infected Human laryngeal epithelial (Hep2) cells using a SOLiD deep sequencing. 492 precursor miRNAs were identified in the AD3 infected Hep2 cells, and 540 precursor miRNAs were identified in the control. A total of 44 miRNAs demonstrated high expression and 36 miRNAs showed lower expression in the AD3 infected cells than control. The biogenesis of miRNAs has been analyzed, and some of the SOLiD results were confirmed by Quantitative PCR analysis. The present studies may provide a useful clue for the biological function research into AD3 infection.
    Type of Medium: Online Resource
    ISSN: 1110-7243 , 1110-7251
    URL: Article
    DOI: 10.1155/2010/915980
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2010
    detail.hit.zdb_id: 2698540-8
    detail.hit.zdb_id: 2512507-2
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Single nucleotide variation detection by ligation of universal probes on a 3D poyacrylamide gel DNA microarray
    Hindawi Limited ; 2009
    In:  Human Mutation Vol. 30, No. 10 ( 2009-10), p. 1460-1468
    Details
    In: Human Mutation, Hindawi Limited, Vol. 30, No. 10 ( 2009-10), p. 1460-1468
    Type of Medium: Online Resource
    ISSN: 1059-7794 , 1098-1004
    URL: Issue
    URL: Article
    DOI: 10.1002/humu.v30:10
    DOI: 10.1002/humu.21080
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2009
    detail.hit.zdb_id: 1498165-8
    SSG: 12
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  • 7
    Online Resource
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    Maternal Plasma miRNAs Expression in Preeclamptic Pregnancies
    Hindawi Limited ; 2013
    In:  BioMed Research International Vol. 2013 ( 2013), p. 1-9
    Details
    In: BioMed Research International, Hindawi Limited, Vol. 2013 ( 2013), p. 1-9
    Abstract: Objective . Preeclampsia (PE) is a pregnancy-specific syndrome and one of the leading causes of maternal and fetal morbidity and mortality. The pathophysiological mechanisms of PE remain poorly known. Recently, circulating miRNAs are considered as potential useful noninvasive biomarkers. The aim of this study was to identify differentially expressed plasma miRNAs in preeclamptic pregnancies compared with normal pregnancies. Methods . Maternal plasma miRNA expression profiles were detected by SOLiD sequencing. Differential expressions between mPE/sPE and control group were found. Next, four differentially expressed plasma miRNAs were chosen to validate their expression in other large scale samples by real-time PCR. Results . In terms of sequencing results, we identified that 51 miRNAs were differentially expressed. Four differentially expressed plasma miRNAs (miR-141, miR-144, miR-221, and miR-29a) were selected to validate the sequencing results. RT-PCR data confirmed the reliability of sequencing results. The further statistical analysis showed that maternal plasma miR-141 and miR-29a are significantly overexpressed in mPE ( P 〈 0.05 ). Maternal plasma miR-144 is significantly underexpressed in mPE and sPE ( P 〈 0.05 ). Conclusions . Results showed that there were differentially expressed maternal plasma miRNAs in patients with preeclampsia. These plasma miRNAs might be used as notable biomarkers for diagnosis of preeclampsia.
    Type of Medium: Online Resource
    ISSN: 2314-6133 , 2314-6141
    URL: Article
    DOI: 10.1155/2013/970265
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2013
    detail.hit.zdb_id: 2698540-8
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  • 8
    Online Resource
    Online Resource
    Global Egr1-miRNAs Binding Analysis in PMA-Induced K562 Cells Using ChIP-Seq
    Hindawi Limited ; 2010
    In:  Journal of Biomedicine and Biotechnology Vol. 2010 ( 2010), p. 1-11
    Details
    In: Journal of Biomedicine and Biotechnology, Hindawi Limited, Vol. 2010 ( 2010), p. 1-11
    Abstract: Although much is known about microRNAs' regulation in gene expression and their contributions in cell fate, to date, globally lineage-(cell-) specific identification of the binding events between a transcription factor and its targeting microRNA genes is still waiting for elucidation. In this paper, we performed a ChIP-Seq experiment to find the targeting microRNA genes of a transcription factor, Egr1, in human erythroleukemia cell line K562. We found Egr1 binding sites near the promoters of 124 distinct microRNA genes, accounting for about 42% of the miRNAs which have high-confidence predicted promoters (294). We also found EGR1 bind to another 63 pre-miRNAs. We chose 12 of the 187 microRNAs with Egr1 binding sites to perform ChIP-PCR assays and the positive binding signal from ChIP-PCR confirmed the ChIP-Seq results. Our experiments provide the first global binding profile between Egr1 and its targeting microRNA genes in PMA-treated K562 cells, which may facilitate the understanding of pathways controlling microRNA biology in this specific cell line.
    Type of Medium: Online Resource
    ISSN: 1110-7243 , 1110-7251
    URL: Article
    DOI: 10.1155/2010/867517
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2010
    detail.hit.zdb_id: 2698540-8
    detail.hit.zdb_id: 2512507-2
    SSG: 12
    Location Call Number Limitation Availability
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