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"high throughput sequencing"

Ke Li, Zhen Liu, Libo Xing, Yanhong Wei, Jiangping Mao, Yuan Meng, Lu Bao, Mingyu Han, Caiping Zhao, Dong Zhang
Adventitious root (AR) formation is essential for the vegetative propagation of apple rootstocks. miRNAs play a significant role in regulating AR development, however, large-scale transcriptomic data on miRNA mediated AR formation in apple rootstocks is lacking. Therefore, in order to identify the molecular mechanisms underlying AR formation in 'M9-T337' apple rootstocks, transcriptomic changes occurring during key time points of AR formation (0, 3, and 16 days) were analyzed using high-throughput sequencing with a focus on miRNAs...
March 8, 2019: Plant Physiology and Biochemistry: PPB
Hai Du, Xueshan Wang, Yuhang Zhang, Yan Xu
Many traditional fermented foods and beverages in both eastern and western countries are produced with the addition of starter cultures. Daqu is the undefined starter used for Chinese liquor, which contributed many fermentation functional fungal and bacterial communities to liquor fermentation process. However, the sources of these microbial communities and how these microorganisms formed in Daqu are still unclear. In this study, high-throughput sequencing combined with microbial source tracking analysis were applied to analyze the sources of the microbial communities in Daqu...
February 28, 2019: International Journal of Food Microbiology
Jun Mu, Dongfang Wang, Guangfeng Yang, Xia Cui, Qiao Yang
In this study a preparation strategy was attempted to produce a substitute (BBF) for the Ruditapes philippinarum conglutination mud (RPM), which was newly discovered to be a promising natural bioflocculant resource. A stable yield of 73.77 ± 1.79 g L-1 BBF was established by a sequential batch fermentation under optimized conditions via single factor experiments. BBF attained similar flocculation performance as RPM, showing a maximum flocculation rate of 87.92 ± 0.65%. BBF had significant decolorization efficiency on methylene blue, crystal violet and malachite green by 98...
March 7, 2019: Bioresource Technology
Isabela Tiemy Pereira, Lucia Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya, Bruno Dallagiovanna
BACKGROUND: Cardiac cell fate specification occurs through progressive steps, and its gene expression regulation features are still being defined. There has been an increasing interest in understanding the coordination between transcription and post-transcriptional regulation during the differentiation processes. Here, we took advantage of the polysome profiling technique to isolate and high-throughput sequence ribosome-free and polysome-bound RNAs during cardiomyogenesis. RESULTS: We showed that polysome-bound RNAs exhibit the cardiomyogenic commitment gene expression and that mesoderm-to-cardiac progenitor stages are strongly regulated...
March 15, 2019: BMC Genomics
Nursen Topcuoglu, Arzu Pınar Erdem, Ilker Karacan, Guven Kulekci
PURPOSE: The oral microbiome is maintained by host- and microbe-derived factors. A shift in microbial composition, as a result of diseases related to the immune system, is the most important step in the development of oral and dental diseases. The aim of this study was to investigate the oral microbial composition of patients with Kostmann syndrome, who have severe neutropenia, compared with healthy children. METHODOLOGY: A group of nine Kostmann syndrome patients and a group of nine healthy controls participated...
March 15, 2019: Journal of Medical Microbiology
Jie Liu, Brenna J Hill, Sam Darko, Kaimei Song, Máire F Quigley, Tedi E Asher, Yohei Morita, Hui Y Greenaway, Vanessa Venturi, Daniel C Douek, Miles P Davenport, David A Price, Mario Roederer
The peripheral maturation of human CD1d-restricted natural killer T (NKT) cells has not been well described. In this study, we identified four major subsets of NKT cells in adults, distinguished by the expression of CD4, CD8, and CCR5. Phenotypic analysis suggested a hierarchical pattern of differentiation, whereby immature CD4+ CD8- CCR5- cells progressed to an intermediate CD4+ CD8- CCR5+ stage, which remained less differentiated than the CD4- CD8- and CD4- CD8+ subsets, both of which expressed CCR5. This interpretation was supported by functional data, including clonogenic potential and cytokine secretion profiles, as well as T cell receptor (TCR) excision circle analysis...
March 15, 2019: Immunology and Cell Biology
Renata F Martins, Marie-Louise Kampmann, Daniel W Förster
Efficient methods for building genomic sequencing libraries from degraded DNA have been in place for Illumina sequencing platforms for some years now, but such methods are still lacking for other sequencing platforms. Here, we provide a protocol for building genomic libraries from degraded DNA (archival or ancient sample material) for sequencing on the Ion Torrent™ high-throughput sequencing platforms. In addition to a reduction in time and cost in comparison to commercial kits, this protocol removes purification steps prior to library amplification, an important consideration for work involving historical samples...
2019: Methods in Molecular Biology
Kirstin Henneberger, Axel Barlow, Johanna L A Paijmans
High-throughput sequencing (HTS) allows fast and cost-efficient sequencing of ancient DNA (aDNA) without prior information about what sequences should be targeted. One necessary step for HTS is the preparation of a sequencing library. Commercial kits are available for this purpose, but many of these are not suitable for aDNA or other types of damaged DNA. Here, we outline a protocol for HTS library preparation that is optimized for ancient DNA. We report the library conversion rate for a range of input template and adapter concentrations...
2019: Methods in Molecular Biology
Elizabeth A Regan, Craig P Hersh, Peter J Castaldi, Dawn L DeMeo, Edwin K Silverman, James D Crapo, Russell P Bowler
There is an unmet need for blood biomarkers in diagnosis and prognosis of chronic obstructive pulmonary disease (COPD). The search for these biomarkers has been revolutionized by high throughput sequencing techniques and multiplex platforms which can measure thousands of gene transcripts, proteins, or metabolites. We review COPDGene publications which include DNA methylation, transcriptomics, proteomics, and metabolomic blood biomarkers and discuss their impact on COPD. Key contributions from COPDGene include: identification of DNA methylation effects from smoking and genetic variation; new transcriptomic signatures in the blood; identification of protein biomarkers associated with severity and progression (e...
March 15, 2019: American Journal of Respiratory Cell and Molecular Biology
Lixiong Liang, Yingying Chang, Junqian Lu, Xiaojuan Wu, Qi Liu, Weixi Zhang, Xiaohua Su, Bingyu Zhang
Changes in DNA methylation patterns in different tissues, at various developmental stages, and under environmental stimuli have been investigated in plants. However, the involvement of DNA methylation in daily gene expression regulation and the plant circadian clock have not been reported. Here, we investigated DNA methylomes and mRNA transcriptomes from leaves of P. trichocarpa over 24 h by high-throughput sequencing. We found that approximately 15.63-19.50% of the genomic cytosine positions were methylated in mature poplar leaves, with approximately half being in the form of asymmetric CHH sites...
2019: Frontiers in Plant Science
Lizhi Wang, Kaizhen Liu, Zhisheng Wang, Xue Bai, Quanhui Peng, Lei Jin
The objective of this study was to examine the association between bacterial community structure and the utilization efficiency of nitrogen (UEN) phenotypes by determining the bacterial community in the gastrointestinal tract (GIT) of goats that differ in UEN using high-throughput 16S rRNA gene sequencing. Thirty Nubian goats were selected as experimental animals, and their UEN was determined in a metabolic experiment. Subsequently, eight individuals were grouped into the high nitrogen utilization (HNU) phenotype, and seven were grouped into the low nitrogen utilization (LNU) phenotype...
2019: Frontiers in Microbiology
Xin Li, Meng Wei Li, Yi Nan Zhang, Han Mei Xu
The development of second-generation sequencing (NGS) technology is providing numerous data which shifts the focus of cancer research from the sequencing of multi-species to the analysis and comparison of select data via high-throughput sequencing. The NGS also facilitates the diversity of available genetic data analysis methods, the constant optimization and innovation of analytical approaches for high-throughput genomics as well as the rapid development of genetic data mining and analysis models. The Cancer Genome Atlas (TCGA) database is a direct result of this work...
March 20, 2019: Yi Chuan, Hereditas
Tao Zhang, Chang Liu, Jingliang He, Yanwei Kang, Feng Wang, Shaowei Li
PURPOSE: The aim of this study was to analyze the relevant gene mutations in a Chinese family with special phenotypic variants of granular corneal dystrophy type 2 with cornea guttata. METHODS: A total of 11 individuals from the affected family underwent complete ophthalmic examination. Genomic DNA was extracted from peripheral leukocytes of affected and unaffected family members. High-throughput sequencing was performed to screen for mutations in 290 genes associated with inherited ophthalmic diseases...
March 14, 2019: European Journal of Ophthalmology
Liping Guo, Yujiao Wang, Jaime A Teixeira da Silva, Yongming Fan, Xiaonan Yu
The flower color of Paeonia 'Coral Sunset' and 'Pink Hawaiian Coral' changes from coral to pink to pale yellow during flowering, which confers high ornamental value to these two cultivars. However, the molecular mechanism underlying flower color change is still unclear. In this study, flavonoids in petals of Paeonia 'Coral Sunset' and 'Pink Hawaiian Coral' at seven flowering stages were analyzed to explore the effects of the flavonoid component on changes in flower color. In addition, four cDNA libraries of 'Coral Sunset' during the critical blooming stages were constructed and the transcriptome was sequenced to investigate the molecular mechanism underlying changes to flower color...
March 4, 2019: Plant Physiology and Biochemistry: PPB
Nadine G Assis, Rodolfo A Ribeiro, Larissa G da Silva, Alexandre M Vicente, Isabelle Hug, Marilis V Marques
Small RNAs are important for post-transcriptional regulation of gene expression, affecting stability and activity of their target mRNAs. The bacterial Sm-like protein Hfq is required to promote pairing between both RNAs when their sequence complementarity is limited. To provide a first global view on the post-transcriptional landscape of the α-proteobacterium Caulobacter crescentus, we have identified the Hfq-binding RNAs employing High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP)...
March 14, 2019: RNA Biology
Qi-Hao Wang, Ji-Hai Gao, Hai-Mei Chen, Xiao-Fang Xie, Cheng Peng
In this study,transcriptomics technique was used to investigate the mechanism of action of Aconiti Lateralis Radix Praeparata on acute heart failure rats induced by propafenone hydrochloride.First,rats were randomly divided into normal group,model group and administration group(1.25,2.5,5 g·kg-1).A rat with acute heart failure was constructed by intravenous femoral administration of proparone hydrochloride.The changes of heart rate,+dp/dtmaxand-dp/dtmaxat 5,10,20,30 and 60 min were recorded.Then another group of rats were given the same drug delivery method...
January 2019: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Zhi-Xiang Liu, Jiang Xu, Wei Sun, Yu-Hua Shi, Shi-Lin Chen
DNA metabarcoding,one rapid and robust method using specific standard DNA fragments,has been widely used for rapid species identification of a bulk sample through high-throughput sequencing technologies.While it has been widely used in the studies of metagenomics,animal and plant biodiversity,it has gradually come to be used as a profitable method in species identification of mixed Chinese herbal medicines.In this paper,we mainly summarize the current studies of the application of DNA metabarcoding in species identification of mixed Chinese herbal medicines...
January 2019: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Ludmila Rodrigues Pinto Ferreira
MicroRNAs (miRNAs) are a class of small noncoding RNAs (typically 19-23 nucleotides) which act by annealing to partially complementary binding sites present on the 3' untranslated regions (UTR) of messenger RNAs (mRNAs) leading to inhibition of protein translation or by inducing mRNA decay. Since their discovery, miRNAs have come to be recognized as master regulators of gene expression in plant and mammals, controlling tissue-specific protein expression. Up to one-third of mammalian mRNAs are susceptible to miRNA-mediated regulation...
2019: Methods in Molecular Biology
Jean-Fabrice Nsota Mbango, Charles Coutton, Christophe Arnoult, Pierre F Ray, Aminata Touré
Male infertility due to Multiple Morphological Abnormalities of the sperm Flagella (MMAF), is characterized by nearly total asthenozoospermia due to the presence of a mosaic of sperm flagellar anomalies, which corresponds to short, angulated, absent flagella and flagella of irregular calibre. In the last four years, 7 novel genes whose mutations account for 45% of a cohort of 78 MMAF individuals were identified: DNAH1 , CFAP43 , CFAP44 , CFAP69 , FSIP2 , WDR66 (CFAP251), AK7 . This successful outcome results from the efficient combination of high-throughput sequencing technologies together with robust and complementary approaches for functional validation, in vitro, and in vivo using the mouse and unicellular model organisms such as the flagellated parasite T...
2019: Basic and Clinical Andrology
Liusheng Lai, Xianqing Zhou, Huaizhou Chen, Yadan Luo, Weiguo Sui, Jiaxing Zhang, Donge Tang, Qiang Yan, Yong Dai
The aim of the present study was to assess the genetic diversity of the B-cell receptor (BCR) in kidney transplant recipients with acute rejection. A total of three patients with acute rejection after kidney transplantation were examined by performing a composition and diversity analysis of the BCR immunoglobulin heavy chain (IGH) complementarity-determining region 3 (H-CDR3) repertoire. The peripheral blood mononuclear cells of patients were collected at 1 day prior to (Pre1), as well as 1 day (Post1) and 7 days (Post7) after the transplantation, and DNA was extracted...
March 2019: Experimental and Therapeutic Medicine
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