scholarly journals Assessing Host-Pathogen Interaction Networks via RNA-Seq Profiling: A Systems Biology Approach

2021 ◽  
Author(s):  
Sudhesh Dev Sareshma ◽  
Bhassu Subha
Keyword(s):  
Rna Sequencing ◽  
High Throughput Sequencing ◽  
Ribosome Profiling ◽  
Host Pathogen Interaction ◽  
Host Pathogen ◽  
Experimental Approaches ◽  
The Common ◽  
Next Generation Sequencing Ngs ◽  
Potential Use ◽  
Generation Sequencing

RNA sequencing is a valuable tool brought about by advances in next generation sequencing (NGS) technology. Initially used for transcriptome mapping, it has grown to become one of the ‘gold standards’ for studying molecular changes that occur in niche environments or within and across infections. It employs high-throughput sequencing with many advantages over previous methods. In this chapter, we review the experimental approaches of RNA sequencing from isolating samples all the way to data analysis methods. We focus on a number of NGS platforms that offer RNA sequencing with each having their own strengths and drawbacks. The focus will also be on how RNA sequencing has led to developments in the field of host-pathogen interactions using the dual RNA sequencing technique. Besides dual RNA sequencing, this review also explores the application of other RNA sequencing techniques such as single cell RNA sequencing as well as the potential use of newer techniques like ‘spatialomics’ and ribosome-profiling in host-pathogen interaction studies. Finally, we examine the common challenges faced when using RNA sequencing and possible ways to overcome these challenges.

scholarly journals A Transcriptomically Guided Computational Quantification of the SRR8671434 RNA Sequence

2021 ◽  
Author(s):  
Rohan Bhansali
Keyword(s):  
Data Mining ◽  
Rna Sequencing ◽  
Ribosomal Rna ◽  
Biological Sample ◽  
Genomic Library ◽  
Rna Sequence ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Cellular Transcriptome ◽  
Potential Biomarkers

Ribonucleic acid (RNA) is a single strand nucleic acid responsible for genetic coding, decoding, regulation, and expression that consists of phosphate and ribose groups with several purposeful variants, notably messenger, transfer, and ribosomal RNA. RNA sequencing is a next-generation sequencing (NGS) technique capable of continuously analyzing cellular transcriptome and revealing the presence and quantity of RNA within a biological sample. The process entails reverse transcribing the extracted RNA into cDNA; subsequently, the cDNA is fragmented, enabling its input into an NGS workflow, after which adapters are added to both ends of the fragments. RNA sequencing is an expensive and time-consuming process due to its necessitation of an entire genomic library that is often difficult to analyze through traditional methods; however, applying computational methods can overcome these challenges through cutting edge data mining and informatics technologies. In this study, the SRR8671434 RNA sequence is quantified and analyzed for its ability to serve as an indicator for congenital afflictions. The findings in this paper can be applied towards preventing and curing associated diseases, as well as discerning other potential biomarkers within genetic materials.

scholarly journals The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers

Life ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 228
Author(s):  
Soyeon Kim ◽  
Joo Won Lee ◽  
Young-Seok Park
Keyword(s):  
Next Generation Sequencing ◽  
Oral Cancer ◽  
Genetic Alterations ◽  
Eligibility Criterion ◽  
Next Generation ◽  
Novel Biomarkers ◽  
Targeted Gene Therapy ◽  
Next Generation Sequencing Ngs ◽  
Potential Use ◽  
Generation Sequencing

Despite the introduction of next-generation sequencing in the realm of DNA sequencing technology, it is not often used in the investigation of oral squamous cell carcinoma (OSCC). Oral cancer is one of the most frequently occurring malignancies in some parts of the world and has a high mortality rate. Patients with this malignancy are likely to have a poor prognosis and may suffer from severe facial deformity or mastication problems even after successful treatment. Therefore, a thorough understanding of this malignancy is essential to prevent and treat it. This review sought to highlight the contributions of next-generation sequencing (NGS) in unveiling the genetic alterations and differential expressions of miRNAs involved in OSCC progression. By applying an appropriate eligibility criterion, we selected relevant studies for review. Frequently identified mutations in genes such as TP53, NOTCH1, and PIK3CA are discussed. The findings of existing miRNAs (e.g., miR-21) as well as novel discoveries pertaining to OSCC are also covered. Lastly, we briefly mention the latest findings in targeted gene therapy and the potential use of miRNAs as biomarkers. Our goal is to encourage researchers to further adopt NGS in their studies and give an overview of the latest findings of OSCC treatment.

scholarly journals Demystification of RNAseq Quality Control

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Dragana Dudić ◽  
Bojana Banović Đeri ◽  
Vesna Pajić ◽  
Gordana Pavlović-Lažetić
Keyword(s):  
Quality Control ◽  
Next Generation Sequencing ◽  
Rna Sequencing ◽  
Next Generation ◽  
Comprehensive Guidance ◽  
Dna And Rna ◽  
Control Evaluation ◽  
Downstream Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next Generation Sequencing (NGS) analysis has become a widely used method for studying the structure of DNA and RNA, but complexity of the procedure leads to obtaining error-prone datasets which need to be cleansed in order to avoid misinterpretation of data. We address the usage and proper interpretations of characteristic metrics for RNA sequencing (RNAseq) quality control, implemented in and reported by FastQC, and provide a comprehensive guidance for their assessment in the context of total RNAseq quality control of Illumina raw reads. Additionally, we give recommendations how to adequately perform the quality control preprocessing step of raw total RNAseq Illumina reads according to the obtained results of the quality control evaluation step; the aim is to provide the best dataset to downstream analysis, rather than to get better FastQC results. We also tested effects of different preprocessing approaches to the downstream analysis and recommended the most suitable approach.

Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy

2021 ◽  
Vol 21 ◽  
Author(s):  
Simna SP ◽  
Zongchao Han
Keyword(s):  
Gene Therapy ◽  
Genomic Dna ◽  
Insertional Mutagenesis ◽  
Molecular Medicine ◽  
Significant Development ◽  
Complementary Dna ◽  
A Genome ◽  
Next Generation Sequencing Ngs ◽  
Potential Use ◽  
Generation Sequencing

: Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full-length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.

scholarly journals Sequencing your genome: your future is here, but are you sure you want to know it?

2014 ◽  
Vol 96 ◽  
Author(s):  
NIR PILLAR ◽  
OFER ISAKOV ◽  
NOAM SHOMRON
Keyword(s):  
Next Generation Sequencing ◽  
Research Laboratory ◽  
High Throughput Sequencing ◽  
Genomic Research ◽  
Sequencing Technology ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
The Past ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS; also known as deep sequencing or ultra-high throughput sequencing) has probably been the most important tool for genomic research over the past few years. NGS has led to numerous discoveries and scientific breakthroughs in the genetic field. The sequencing technology that has entered the research laboratory in the past decade is now being introduced into the clinical diagnostic laboratory. Consequently, NGS results are becoming available in the medical arena as abundance of clinically relevant variants, conferring predisposition to disease, are being discovered at a growing rate (Stanley, 2014).

scholarly journals High-Throughput Sequencing of Virus-infected Cucurbita pepo Samples Revealed The Presence of Zucchini Shoestring Virus in Zimbabwe

2019 ◽  
Author(s):  
Charles Karavina ◽  
Jacques Davy Ibaba ◽  
Augustine Gubba
Keyword(s):  
South African ◽  
Cucurbita Pepo ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Large Open Reading Frame ◽  
Polya Tail ◽  
Reading Frame ◽  
Growing Seasons ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Objectives: Plant-infecting viruses remain a serious challenge towards achieving food security worldwide. Cucurbits, in Zimbabwe, like in the other parts of the world, are used in various ways. A small-scaled cucurbit virus survey was conducted in Zimbabwe during the 2014 and 2015 growing seasons. Cucurbit leaf samples displaying virus-like symptoms were collected and stored until analysis. The samples were then subjected to next-generation sequencing (NGS). The data generated from NGS were analysed using genomics technologies. Zucchini shoestring virus (ZSSV), a cucurbit-infecting potyvirus previously described in South Africa was one of the viruses identified. The genomes of three ZSSV isolates from Zimbabwe are described in this note. Results: The three ZSSV isolates had the same genome size of 10297 bp excluding the polyA tail with a 43% GC content. The large open reading frame (ORF) was found at positions 69 to 10106 on the genome and encodes a 3345 amino acids long polyprotein which had the same cleavage site sequences as those described on the South African isolates except for the P1-pro site. The smaller ORF, also called the pretty interesting Potyviridae ORF, was located at positions 3611 to 3793 on the genomes for all three ZSSV isolates.

scholarly journals Next-Generation Sequencing Reveals Four Novel Viruses Associated with Calf Diarrhea

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1907
Author(s):  
Qi Wu ◽  
Jizong Li ◽  
Wei Wang ◽  
Jinzhu Zhou ◽  
Dandan Wang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Aichi Virus ◽  
Bovine Coronavirus ◽  
S Gene ◽  
Calf Diarrhea ◽  
The Common ◽  
And Control ◽  
Orf2 Region ◽  
Generation Sequencing

Calf diarrhea is one of the common diseases involved in the process of calf feeding. In this study, a sample of calf diarrhea that tested positive for bovine coronavirus and bovine astrovirus was subjected to high-throughput sequencing. The reassembly revealed the complete genomes of bovine norovirus, bovine astrovirus, bovine kobuvirus, and the S gene of bovine coronavirus. Phylogenetic analysis showed that the ORF2 region of bovine astrovirus had the lowest similarity with other strains and gathered in the Mamastrovirus unclassified genogroup, suggesting a new serotype/genotype could appear. Compared with the most closely related strain, there are six amino acid mutation sites in the S gene of bovine coronavirus, most of which are located in the S1 subunit region. The bovine norovirus identified in our study was BNoV-GIII 2, based on the VP1 sequences. The bovine kobuvirus is distributed in the Aichi virus B genus; the P1 gene shows as highly variable, while the 3D gene is highly conserved. These findings enriched our knowledge of the viruses in the role of calf diarrhea, and help to develop an effective strategy for disease prevention and control.

scholarly journals High-throughput sequencing techniques to flax genetics and breeding

2020 ◽  
Author(s):  
Alena Olegovna Akhmetshina ◽  
Ksenia Vladimirovna Strygina ◽  
Elena Konstantinovna Khlestkina ◽  
Elisaveta Alexandrovna Porokhovinova ◽  
Nina Borisovna Brutch
Keyword(s):  
Stress Responses ◽  
High Throughput Sequencing ◽  
Molecular Genetic ◽  
Stress Factors ◽  
Fundamental Interest ◽  
Genetic Mechanisms ◽  
High Marker Density ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Selection Of

Flax (Lnum usitatssimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS sequencing in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatssimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.

scholarly journals RNA modifications detection by comparative Nanopore direct RNA sequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Adrien Leger ◽  
Paulo P. Amaral ◽  
Luca Pandolfini ◽  
Charlotte Capitanchik ◽  
Federica Capraro ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput Sequencing ◽  
Control Sample ◽  
Analytical Framework ◽  
Rna Modifications ◽  
Rna Molecules ◽  
Oxford Nanopore ◽  
Experimental Approaches

AbstractRNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m6A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.

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