scholarly journals Deep sequencing of small RNA facilitates tissue and sex specific microRNA discovery in zebrafish

2015 ◽  
Author(s):  
Candida Vaz ◽  
Choon Wei Wee ◽  
Serene Gek Ping Lee ◽  
Philip W Ingham ◽  
Vivek Tanavde ◽  
...  
Keyword(s):  
The Novel ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Mirna Expression Data ◽  
Mrna Gene ◽  
Gene Regulatory ◽  
Genomic Resource ◽  
The Brain ◽  
Generation Sequencing

Role of microRNAs in gene regulation has been well established. Though the number of genes appear to be equal between human and zebrafish, miRNAs detected in zebrafish (~247) is significantly low compared to human (~2000; miRBase Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. Using next generation sequencing technology, we sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In few tissues (brain, gut, liver) sequencing was done sex specifically. About 16-62% of the sequenced reads mapped to known miRNAs of zebrafish, with the exceptions of ovary (5.7%) and testis (7.8%). We used miRDeep2, the miRNA predication tool, to discover the novel miRNAs using the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%) that had the largest pool of un-annotated reads. The prediction tool identified a total of 459 novel pre-miRNAs. Comparison of miRNA expression data of the tissues showed the presence of tissue and sex specific miRNAs that could serve as biomarkers. The brain and liver had highest number of tissue specific (36) and sex specific (34) miRNAs, respectively. Taken together, we have made a comprehensive approach to identify tissue and sex specific miRNAs from zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30% homology to human miRNA) as additional genomic resource for zebrafish. This resource can facilitate further investigations to understand miRNA-mRNA gene regulatory network in zebrafish which will have implications to understand human miRNA function.

scholarly journals Alpinia oxyphyllaMiq. Extract Prevents Diabetes in Mice by Modulating Gut Microbiota

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Yiqiang Xie ◽  
Man Xiao ◽  
Yali Ni ◽  
Shangfei Jiang ◽  
Guizhu Feng ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Glucose Levels ◽  
Blood Glucose Levels ◽  
Generation Sequencing ◽  
Administration Protocol ◽  
Gut Microbiota Composition

Recently, the role of gut microbiota in the development of obesity and type 2 diabetes mellitus (T2DM) has been highlighted. We performed an 8-week administration protocol on T2DM (C57BL/6J db-/db-) mice and fecal samples were collected. Comparisons of fecal bacterial communities were performed between db-/db- mice and normal mice (DB/DB) and between the db-/db mice treated and untreated with AOE using next-generation sequencing technology. Our results showed that the db-/db-AOE group had improved glycemic control and renal function compared with the db-/db-H2O group. Compared with the db-/db-H2O group, AOE administration resulted in significantly increased ratio of Bacteroidetes-to-Firmicutes in db-/db- mice. In addition, the abundance ofAkkermansiawas significantly increased, whileHelicobacterwas significantly suppressed in the db-/db-AOE group compared with the db-/db-H2O group. Our data suggest that AOE treatment decreased blood glucose levels and significantly reduced damage of renal pathology in the T2DM mice by modulating gut microbiota composition.

scholarly journals Exome-Wide Analysis of the DiscovEHR Cohort Reveals Novel Candidate Pharmacogenomic Variants for Clinical Pharmacogenomics

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 561
Author(s):  
Maria-Theodora Pandi ◽  
Marc S. Williams ◽  
Peter van der Spek ◽  
Maria Koromina ◽  
George P. Patrinos
Keyword(s):  
Genetic Variation ◽  
Sequence Data ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Exome Sequencing Data ◽  
Whole Exome ◽  
Whole Exome Sequencing Data ◽  
Generation Sequencing

Recent advances in next-generation sequencing technology have led to the production of an unprecedented volume of genomic data, thus further advancing our understanding of the role of genetic variation in clinical pharmacogenomics. In the present study, we used whole exome sequencing data from 50,726 participants, as derived from the DiscovEHR cohort, to identify pharmacogenomic variants of potential clinical relevance, according to their occurrence within the PharmGKB database. We further assessed the distribution of the identified rare and common pharmacogenomics variants amongst different GnomAD subpopulations. Overall, our findings show that the use of publicly available sequence data, such as the DiscovEHR dataset and GnomAD, provides an opportunity for a deeper understanding of genetic variation in pharmacogenes with direct implications in clinical pharmacogenomics.

Discovery of two novel miRNAs from the Ovis aries by a combinatorial approach of experiments and bioinformatics

2017 ◽  
Author(s):  
Weihua Chang ◽  
Juanhong Wang ◽  
Yong Zhang ◽  
Junyuan Wu
Keyword(s):  
Northern Blotting ◽  
Ovis Aries ◽  
Chromosome 15 ◽  
The Novel ◽  
Sequencing Technology ◽  
Stem Loop ◽  
Next Generation Sequencing Technology ◽  
Stem Loop Structure ◽  
Fine Regulation ◽  
Generation Sequencing

n the study, we successful constructed a library from the ovine testis using next-generation sequencing technology, and identified 219 novel miRNAs by bioinformatics. Two of the novel miRNAs (ovis_aries_testis-m0052_5p and ovis_aries_testis-m0165_5p), which were expressed in the sheep testis and ovary, and were confirmed by real-time PCR and northern blotting. Ovis_aries_testis-m0052_5p was 23 nucleotides in length, was located on chromosome 15, and had 100% similarity to mmu-miR-34c-5p, hsa-miR-34c-5p, gga-miR-34c-5p, and cfa-miR-34c. Ovis_aries_testis-m0165_5p was 21 nucleotides in length, located on chromosome 5, and had 100% similarity to mmu-miR-145a-5p, hsa-miR-145-5p, ssc-miR-145-5p, and bta-miR-145. The pre-miRNAs for Ovis_aries_testis-m0052_5p and Ovis_aries_testis-m0165_5p were 75 and 81 nucleotides in length, and both had a standard hairpin stem-loop structure. From the consistency of the sequence and structure, we speculated that ovis_aries_testis-m0052_5p had a function similar to hsa-miR-34c-5p, mmu-miR-34c-5p, and ovis_aries_testis-m0165_5p had a function similar to hsa-miR-145-5p, which were involved in the fine regulation of cell survival, spermatozoon generate, breeding activities. Therefore, we defined the identified miRNAs as oar-miR-34c-5p and oar-miR-145-5p. The results will enrich the miRNA database, and provide the basis for research into the regulatory mechanisms of miRNA in relation to breeding activities.

scholarly journals Identification of a Novel SARS-CoV-2 Strain with Truncated Protein in ORF8 Gene by Next Generation Sequencing

2021 ◽  
Author(s):  
Stephanie DeRonde ◽  
Hannah Deuling ◽  
Jayme Parker ◽  
Jack Chen
Keyword(s):  
Next Generation Sequencing ◽  
Stop Codon ◽  
Washington State ◽  
The Novel ◽  
Next Generation ◽  
Sequencing Technology ◽  
Truncated Protein ◽  
Next Generation Sequencing Technology ◽  
Protein Mutation ◽  
Generation Sequencing

Abstract Using next generation sequencing technology, we identified a truncated protein mutation located in the ORF8 gene which is near the end of the genome from nucleotides 27,878 to 27,958. The mutation in this novel strain created a stop codon and translates to the novel truncated ORF8 protein, creating a much smaller protein than most other strains of SARS-CoV-2. The novel truncated mutation is most closely related to nine SARS-CoV-2 strains found in Washington state. Our results show a novel strain of SARS-CoV-2 with a truncated ORF8 gene. This shortens the translated ORF8 protein. The effects of ORF8 protein and its functions are still uncertain but a truncated ORF8 could affect antibody response, severity of infection and inflammatory response.

scholarly journals Identification of a Novel Papillomavirus Type (MfoiPV1) Associated with Acrochordon in a Stone Marten (Martes foina)

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 539
Author(s):  
Urška Kuhar ◽  
Diana Žele Vengušt ◽  
Urška Jamnikar-Ciglenečki ◽  
Gorazd Vengušt
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Manifestation ◽  
Skin Tumor ◽  
Wild Animals ◽  
Stone Marten ◽  
Sequencing Technology ◽  
Martes Foina ◽  
Tumor Sample ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

scholarly journals Novel TTLL5 Variants Associated with Cone-Rod Dystrophy and Early-Onset Severe Retinal Dystrophy

2021 ◽  
Vol 22 (12) ◽  
pp. 6410
Author(s):  
Vasily Smirnov ◽  
Olivier Grunewald ◽  
Jean Muller ◽  
Christina Zeitz ◽  
Carolin D. Obermaier ◽  
...  
Keyword(s):  
Early Onset ◽  
Retinal Dystrophy ◽  
Copy Number Variants ◽  
Cone Dystrophy ◽  
The Novel ◽  
Targeted Next Generation Sequencing ◽  
Large Deletions ◽  
Gene Panels ◽  
Generation Sequencing

Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.

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