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"high throughput sequencing"

Cécile Lorrain, Karen Cristine Gonçalves Dos Santos, Hugo Germain, Arnaud Hecker, Sébastien Duplessis
Rust fungi (Pucciniales) are the largest group of plant pathogens and represent one of the most devastating threats to agricultural crops worldwide. Despite the economic importance of these highly specialized pathogens, many aspects of their biology remain obscure largely because rust fungi are obligate biotrophs. The rise of genomics and advances in high-throughput sequencing technology have presented new options for identifying candidate effector genes involved in pathogenicity mechanisms of rust fungi. Transcriptome analysis and integrated bioinformatics tools have led to the identification of key genetic determinants of host susceptibility to infection by rusts...
December 16, 2018: New Phytologist
Thais Guimarães Martins Nery, Esdras Matheus Silva, Raphael Tavares, Fabio Passetti
Alzheimer's disease, Parkinson's disease, prion diseases, schizophrenia, and multiple sclerosis are the most common nervous system diseases, affecting millions of people worldwide. The current scientific literature associates these pathological conditions to abnormal expression levels of certain proteins, which in turn improved the knowledge concerning normal and affected brains. However, there is no available cure or preventive therapy for any of these disorders. Proteogenomics is a recent approach defined as the data integration of both nucleotide high-throughput sequencing and protein mass spectrometry technologies...
December 15, 2018: Journal of Molecular Neuroscience: MN
Daniel Saucier, Gabriel Wajnberg, Jeremy Roy, Annie-Pier Beauregard, Simi Chacko, Nicolas Crapoulet, Sébastien Fournier, Anirban Ghosh, Stephen M Lewis, Alier Marrero, Colleen O'Connell, Rodney J Ouellette, Pier Jr Morin
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder associated with the progressive death of motor neurons. Mean survival for a patient diagnosed with ALS is between 2 to 5 years. Early and efficient diagnosis of the various forms of ALS remains a significant challenge, resulting in a need to identify clinically-relevant biomarkers in readily accessible body fluids. microRNAs (miRNAs) are short, evolutionarily conserved non-coding RNA molecules involved in post-transcriptional regulation of gene expression that have received interest as disease biomarkers...
December 12, 2018: Brain Research
Yajuan Lin, Scott Gifford, Hugh Ducklow, Oscar Schofield, Nicolas Cassar
An inherent issue of high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxa co-occurrence patterns substantially different from those derived using relative abundances...
December 14, 2018: Applied and Environmental Microbiology
Wei Wang, Jude Juventus Aweya, Su Huimin, Xianliang Zhao, Mingqi Zhong, Yueling Zhang
Tolls and Toll-like receptors (TLRs), as innate immune-recognition receptors that recognize molecular patterns associated with microbial pathogens, play a critical role in antimicrobial immune responses. Here, we report on single nucleotide polymorphisms (SNPs) of Litopenaeus vannamei Toll3 (LvToll3). Multiple sequence alignment of the L. vannamei Toll3 Leucine rich repeat C-terminal domain (LvToll3-LRR-CT) with other L. vannamei Tolls LRR-CT domains showed 39.23 % - 43.96 % homology at the nucleic acid level and 20...
December 11, 2018: Immunology Letters
Xuan Shu, Shenyou Shu, Hongqiu Cheng
BACKGROUND: Increasing evidence indicates that long non-coding RNAs (lncRNAs) play crucial regulatory roles in epithelial-mesenchymal transition (EMT). However, the regulatory mechanisms during EMT of the medial edge epithelium (MEE) remain elusive. The aim of this work is to reveal a novel lncRNA-regulated dysfunction of EMT involved in the development of cleft palate (CP). METHODS: C57BL/6 J mice at embryonic gestation day 14.5 (n = 6, 3 case samples vs. 3 control samples) were used to establish the CP model for lncRNA-mRNA co-expression profile analysis after high-throughput sequencing...
December 12, 2018: Molecular Genetics & Genomic Medicine
Moritz Hebebrand, Georgia Vasileiou, Mandy Krumbiegel, Cornelia Kraus, Steffen Uebe, Arif B Ekici, Christian T Thiel, André Reis, Bernt Popp
Biallelic variants in the AEBP1 gene cause a novel autosomal-recessive connective tissue disorder (CTD) reminiscent of Ehlers-Danlos Syndrome (EDS). The four previously reported individuals show considerable clinical variability. Unbiased high-throughput sequencing enables the rapid identification of additional cases for such rare entities. We identified the homozygous nonsense variant c.917dup, p.Tyr306* in AEBP1 using clinical exome sequencing in a female individual with previously unsolved CTD. Segregation testing confirmed homozygosity in the clinically affected brother and heterozygous carrier status in the healthy mother...
December 11, 2018: American Journal of Medical Genetics. Part A
Diana Domanska, Chakravarthi Kanduri, Boris Simovski, Geir Kjetil Sandve
BACKGROUND: The current versions of reference genome assemblies still contain gaps represented by stretches of Ns. Since high throughput sequencing reads cannot be mapped to those gap regions, the regions are depleted of experimental data. Moreover, several technology platforms assay a targeted portion of the genomic sequence, meaning that regions from the unassayed portion of the genomic sequence cannot be detected in those experiments. We here refer to all such regions as inaccessible regions, and hypothesize that ignoring these regions in the null model may increase false findings in statistical testing of colocalization of genomic features...
December 14, 2018: BMC Bioinformatics
Pratiksha Behera, Madhusmita Mohapatra, Ji Yoon Kim, Tapan K Adhya, Ajit K Pattnaik, Gurdeep Rastogi
Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons...
December 13, 2018: Environmental Science and Pollution Research International
Rou-Jun Peng, Bo-Wei Han, Qing-Qing Cai, Xiao-Yu Zuo, Tao Xia, Jie-Rong Chen, Li-Na Feng, Jing Quan Lim, Shu-Wei Chen, Mu-Sheng Zeng, Yun-Miao Guo, Bo Li, Xiao-Jun Xia, Yi Xia, Yurike Laurensia, Burton Kuan Hui Chia, Hui-Qiang Huang, Ken He Young, Soon Thye Lim, Choon Kiat Ong, Yi-Xin Zeng, Jin-Xin Bei
Extranodal natural killer T-cell lymphoma (nasal type; NKTCL) is an aggressive malignancy strongly associated with Epstein-Barr virus (EBV) infection. However, the role of EBV in NKTCL development is unclear, largely due to the lack of information about EBV genome and transcriptome in NKTCL. Here, using high-throughput sequencing, we obtained whole genome (n = 27) and transcriptome datasets (n = 18) of EBV derived from NKTCL tumor biopsies. We assembled 27 EBV genomes and detected an average of 1,152 single nucleotide variants and 44...
December 13, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Fenglin Liu, Tianyu Ma, Yuxiang Zhang
RNA-binding proteins (RBPs) are proteins that bind to the RNA and participate in forming ribonucleoprotein complexes. They have crucial roles in various biological processes such as RNA splicing, editing, transport, maintenance, degradation, intracellular localization and translation. The RBPs bind RNA with different RNA-sequence specificities and affinities, thus, identification of protein binding sites on RNAs (R-PBSs) will deeper our understanding of RNA-protein interactions. Currently, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP, also known as CLIP-Seq) is one of the most powerful methods to map RNA-protein binding sites or RNA modification sites...
December 10, 2018: Biochemical and Biophysical Research Communications
Guijuan Zhang, Bing Li, Jie Liu, Mingqiang Luan, Long Yue, Xiao-Tao Jiang, Ke Yu, Yuntao Guan
BACKGROUND: Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results, suggesting that bacteria can either accelerate or inhibit corrosion. RESULTS: The long-term effects of the bacterial community on cast iron corrosion in reclaimed wastewater distribution systems were investigated from both spatial (yellow layer vs. black layer) and temporal (1-year dynamic process) dimensions of the iron coupon-reclaimed wastewater microcosm using high-throughput sequencing and flow cytometry approaches...
December 13, 2018: Microbiome
Pengfei Wang, Suhua Shi, Junjie Ma, Hui Song, Ye Zhang, Chao Gao, Chuanzhi Zhao, Shuzhen Zhao, Lei Hou, Javier Lopez-Baltazar, Shoujin Fan, Han Xia, Xingjun Wang
BACKGROUND: Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. RESULTS: To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing...
December 13, 2018: BMC Plant Biology
Xue-Wen Li, Hui-Ping Chen, Ying-Yan He, Wei-Li Chen, Jian-Wen Chen, Lu Gao, Hai-Yan Hu, Jun Wang
Dendrobium is a traditional Chinese herb with anti-diabetic effects and has diverse bibenzyls as well as phenanthrenes. Little is known about Dendrobium polyphenols anti-diabetic activities, so, a rich-polyphenols extract of D. loddigesii (DJP) was used for treatment of diabetic db/db mice; the serum biochemical index and tissue appearance were evaluated. In order to gain an insight into the anti-diabetic mechanism, the oxidative stress index, tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and gut microbiota modulation were determined by ELISA, immunohistochemistry or high throughput sequencing 16S rRNA gene...
December 7, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Xiao Yang, Dongliang Zhu, Hongguo Zhang, Yuting Jiang, Xiaonan Hu, Dongfeng Geng, Ruixue Wang, Ruizhi Liu
Genetic abnormalities could account for 10% to 15% of male infertility cases, so increasing attention is being paid to gene mutations in this context. DNAH1 gene polymorphisms are highly correlated with astheno-teratozoospermia, but limited information has been reported on pathogenic variations in DNAH1 in the Chinese population. We explored 4 novel variations of the DNAH1 gene in Chinese infertile patients. Mutation screening of the DNAH1 gene was performed on 87 cases of asthenozoospermia with targeted high-throughput sequencing technology; another 200 nonobstructive azoospermia cases were further analyzed to investigate the prevalence of DNAH1 variations...
December 2018: Medicine (Baltimore)
Diane A Lima, Samuel P Cibulski, Caroline Tochetto, Ana Paula M Varela, Fabrine Finkler, Thais F Teixeira, Márcia R Loiko, Cristine Cerva, Dennis M Junqueira, Fabiana Q Mayer, Paulo M Roehe
Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated...
December 10, 2018: Virus Research
Robert Söderlund, Mikhayil Hakhverdyan, Anna Aspán, Eva Jansson
The pathogen Flavobacterium psychrophilum is a major problem for the expanding salmonid fish farming industry in Sweden as well as worldwide. A better understanding of the phylogeography and infection routes of F. psychrophilum outbreaks could help to improve aquaculture profitability and the welfare of farmed fish while reducing the need for antibiotics. In the present study, high-throughput genome sequencing was applied to a collection of F. psychrophilum isolates (n=38) from outbreaks on fish farms in different regions of Sweden between 1988 and 2016...
December 13, 2018: Microbial Genomics
Kathryn A O'Donnell, Yabin Guo, Shruthy Suresh, Barrett L Updegraff, Xiaorong Zhou
Transposon mutagenesis has emerged as a powerful methodology for functionally annotating cancer genomes. Although in vivo transposon-mediated forward genetic screens have proven to be valuable for cancer gene identification, they are also time consuming and resource intensive. To facilitate the rapid and cost-effective identification of genes that regulate tumor-promoting pathways, we developed a complementary ex vivo transposon mutagenesis approach wherein human or mouse cells growing in culture are mutagenized and screened for the acquisition of specific phenotypes in vitro or in vivo, such as growth factor independence or tumor-forming ability...
2019: Methods in Molecular Biology
Charles H Adelmann, Tim Wang, David M Sabatini, Eric S Lander
In this protocol, pooled sgRNA libraries targeting thousands of genes are computationally designed, generated using microarray-based synthesis techniques, and packaged into lentiviral particles. Target cells of interest are transduced with the lentiviral sgRNA pools to generate a collection of knockout mutants-via Cas9-mediated genomic cleavage-and screened for a phenotype of interest. The relative abundance of each mutant in the population can be monitored over time through high-throughput sequencing of the integrated sgRNA expression cassettes...
2019: Methods in Molecular Biology
Diego Valenzuela-Miranda, Cristian Gallardo-Escárate
High-throughput sequencing technologies have offered the possibility to understand the complexity of the transcriptomic responses of an organism during a wide variety of biological scenarios, such as the case of pathogenic infections. Recently, the simultaneous sequencing of both pathogen and host transcriptomes (dual RNA-seq) during the infection has become a promising approach to uncover the complexity of the host-pathogen interactions. In this study, through a double rRNA depletion and RNA sequencing protocols, we simultaneously analyzed the transcriptome of the intracellular bacterium Piscirickettsia salmonis and its host the Atlantic salmon ( Salmo salar ) during the course of the infection...
2018: Frontiers in Microbiology
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