scholarly journals Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum

2015 ◽  
Vol 9 ◽  
pp. BBI.S20751 ◽  
Author(s):  
Stefan Simm ◽  
Sotirios Fragkostefanakis ◽  
Puneet Paul ◽  
Mario Keller ◽  
Jens Einloft ◽  
...  
Keyword(s):  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Ribosome Biogenesis ◽  
Developmental Stages ◽  
Male Gametophyte ◽  
Expression Profiles ◽  
Transcript Abundance ◽  
Rrna Processing ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.

Machine Learning Perspective in Cancer Research

2021 ◽  
pp. 142-163
Author(s):  
Aman Sharma ◽  
Rinkle Rani
Keyword(s):  
Machine Learning ◽  
Cancer Research ◽  
Expression Profiles ◽  
Genetic Diseases ◽  
Cost Effective ◽  
Healthcare Sector ◽  
Diagnosis And Prognosis ◽  
Cost Effective Approach ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Advancement in genome sequencing technology has empowered researchers to think beyond their imagination. Researchers are trying their hard to fight against various genetic diseases like cancer. Artificial intelligence has empowered research in the healthcare sector. Moreover, the availability of opensource healthcare datasets has motivated the researchers to develop applications which can help in early diagnosis and prognosis of diseases. Further, next-generation sequencing (NGS) has helped to look into detailed intricacies of biological systems. It has provided an efficient and cost-effective approach with higher accuracy. The advent of microRNAs also known as small noncoding genes has begun the paradigm shift in oncological research. We are now able to profile expression profiles of RNAs using RNA-seq data. microRNA profiling has helped in uncovering their relationship in various genetic and biological processes. Here in this chapter, the authors present a review of the machine learning perspective in cancer research.

scholarly journals Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia

2020 ◽  
Vol 21 (4) ◽  
pp. 1230
Author(s):  
Gangqiao Kuang ◽  
Wenjing Tao ◽  
Shuqing Zheng ◽  
Xiaoshuang Wang ◽  
Deshou Wang
Keyword(s):  
Ribosomal Proteins ◽  
Nile Tilapia ◽  
Ribosome Biogenesis ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Ribosomal Protein Genes ◽  
Expression Levels ◽  
Sexually Dimorphic Expression ◽  
Complete Set ◽  
Almost All

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates.

scholarly journals In silico gene expression profiling in Cannabis sativa

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 69 ◽  
Author(s):  
Luca Massimino
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Starting Point ◽  
Scientific Papers

The cannabis plant and its active ingredients (i.e., cannabinoids and terpenoids) have been socially stigmatized for half a century. Luckily, with more than 430,000 published scientific papers and about 600 ongoing and completed clinical trials, nowadays cannabis is employed for the treatment of many different medical conditions. Nevertheless, even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills. In this work, publicly available gene expression datasets have been analyzed giving rise to a total of 40,224 gene expression profiles taken from cannabis plant tissue at different developmental stages. The resource presented here will provide researchers with a starting point for future investigations with Cannabis sativa.

scholarly journals A smart polymer for sequence-selective binding, pulldown, and release of DNA targets

2019 ◽  
Author(s):  
Elisha Krieg ◽  
Krishna Gupta ◽  
Andreas Dahl ◽  
Mathias Lesche ◽  
Susanne Boye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Low Cost ◽  
Clinical Diagnostics ◽  
Ease Of Use ◽  
Preparative Scale ◽  
Smart Polymer ◽  
Double Stranded Dna ◽  
Next Generation Sequencing Ngs ◽  
Pure Target ◽  
Generation Sequencing

AbstractSelective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single- as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for the depletion of insulin, glucagon, and transthyretin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets.

scholarly journals Environmental Variations in Mycobacterium ulcerans Transcriptome: Absence of Mycolactone Expression in Suboptimal Environments

Toxins ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 146
Author(s):  
Daniel Sanhueza ◽  
Jean-François Guégan ◽  
Heather Jordan ◽  
Christine Chevillon
Keyword(s):  
Culture Medium ◽  
Expression Profiles ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Virulence Plasmid ◽  
Genomic Expression ◽  
Environmental Variations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Buruli ulcer is a neglected tropical infectious disease, produced by the environmentally persistent pathogen Mycobacterium ulcerans (MU). Neither the ecological niche nor the exact mode of transmission of MU are completely elucidated. However, some environmental factors, such as the concentration in chitin and pH values, were reported to promote MU growth in vitro. We pursued this research using next generation sequencing (NGS) and mRNA sequencing to investigate potential changes in MU genomic expression profiles across in vitro environmental conditions known to be suitable for MU growth. Supplementing the growth culture medium in either chitin alone, calcium alone, or in both chitin and calcium significantly impacted the MU transcriptome and thus several metabolic pathways, such as, for instance, those involved in DNA synthesis or cell wall production. By contrast, some genes carried by the virulence plasmid and necessary for the production of the mycolactone toxin were expressed neither in control nor in any modified environments. We hypothesized that these genes are only expressed in stressful conditions. Our results describe important environmental determinants playing a role in the pathogenicity of MU, helping the understanding of its complex natural life cycle and encouraging further research using genomic approaches.

scholarly journals The Ubiquity and Development-Related Abundance Dynamics of Ophiocordyceps Fungi in Soft Scale Insects

2021 ◽  
Vol 9 (2) ◽  
pp. 404
Author(s):  
Jun Deng ◽  
Yuhua Yu ◽  
Xu Wang ◽  
Qian Liu ◽  
Xiaolei Huang
Keyword(s):  
Relative Abundance ◽  
Growth And Development ◽  
Developmental Stages ◽  
Scale Insects ◽  
Plant Feeding ◽  
Its Gene ◽  
Next Generation Sequencing Ngs ◽  
New Evidence ◽  
Generation Sequencing

Mutual relationships with symbionts play a crucial role in the evolution and ecology of plant-feeding hemipteran insects. However, there was no specific dominant bacterium observed in soft scales (Coccidae) in the previous studies, it is still unclear whether soft scales have specific primary symbionts. In this study, a nuclear ribosomal internal transcribed spacer (ITS)gene fragment was used to analyze the diversity of fungal communities in 28 Coccidae species based on next-generation sequencing (NGS). Furthermore, samples from different developmental stages of Ceroplastes japonicus were sequenced to illustrate the dynamics of fungal community. Our results showed that Coccidae-associated Ophiocordyceps fungi (COF) were prevalent in all 28 tested species with high relative abundance. Meanwhile, the first and second instars of C. japonicus, two important stages for growth and development, had high relative abundance of COF, while the relative abundances in other stages were low, ranging from 0.68% to 2.07%. The result of fluorescent in situ hybridization showed that the COF were widely present in hemolymph and vertically transmitted from mother to offspring. Our study confirms that the COF have intimate associations with the growth and development of soft scales, and provides new evidence to support that COF are primary fungal symbionts for Coccidae.

scholarly journals Advances in legume research in the genomics era

2019 ◽  
Author(s):  
Ashley N. Egan ◽  
Mohammad Vatanparast
Keyword(s):  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Nitrogen Fixers ◽  
Affected Plant ◽  
Plant Families ◽  
Patterns And Processes ◽  
Next Generation Sequencing Ngs ◽  
Marker Discovery ◽  
Generation Sequencing

Next-generation sequencing (NGS) technologies and applications have enabled numerous critical advances in legume biology, from marker discovery to whole-genome sequencing, and will provide many new avenues for legume research in the future. The past 6 years in particular have seen revolutionary advances in legume science because of the use of high-throughput sequencing, including the development of numerous types of markers and data useful for evolutionary studies above and below the species level that have enabled resolution of relationships that were previously unattainable. Such resolution, in turn, affords opportunities for hypothesis testing and inference to improve our understanding of legume biodiversity and the patterns and processes that have created one of the most diverse plant families on earth. In addition, the genomics era has seen significant advances in our understanding of the ecology of legumes, including their role as nitrogen fixers in global ecosystems. The accumulation of genetic and genomic data in the form of sequenced genomes and gene-expression profiles made possible through NGS platforms has also vastly affected plant-breeding and conservation efforts. Here, we summarise the knowledge gains enabled by NGS methods in legume biology from the perspectives of evolution, ecology, and development of genetic and genomic resources.

scholarly journals Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huangwei Zhang ◽  
Meng Li ◽  
Min Kong ◽  
Jim M. Dunwell ◽  
Yuyan Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Differential Expression ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Fruit Trees ◽  
Rna Seq ◽  
Molecular Process ◽  
Temporal And Spatial ◽  
Generation Sequencing

Abstract Background Pears and apples are both perennial deciduous trees of the Rosaceae family, and both are important economic fruit trees worldwide. The emergence of many varieties in the market has been mostly domesticated from wild to cultivated and regulated by the differential expression of genes. However, the molecular process and pathways underlying this phenomenon remain unclear. Four typical wild and cultivar pear and apple trees at three developmental stages were used in our study to investigate the molecular process at the transcriptome level. Result Physiological observations indicated the obvious differences of size, weight, sugar acid content and peel color in wild and cultivar fruit among each developmental stage. Using next-generation sequencing based RNA-seq expression profiling technology, we produced a transcriptome in procession of a large fraction of annotated pear and apple genes, and provided a molecular basis underlying the phenomenon of wild and cultivar fruit tree differences. 5921 and 5744 differential expression genes were identified in pear and apple at three developmental stages respectively. We performed temporal and spatial differential gene expression profiling in developing fruits. Several key pathways such as signal transduction, photosynthesis, translation and many metabolisms were identified as involved in the differentiation of wild and cultivar fruits. Conclusion In this study, we reported on the next-generation sequencing study of the temporal and spatial mRNA expression profiling of pear and apple fruit trees. Also, we demonstrated that the integrated analysis of pear and apple transcriptome, which strongly revealed the consistent process of domestication in Rosaceae fruit trees. The results will be great influence to the improvement of cultivar species and the utilization of wild resources.

scholarly journals Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum ) population

2017 ◽  
Vol 92 (3) ◽  
pp. 495-508 ◽  
Author(s):  
Prateek Gupta ◽  
Bodanapu Reddaiah ◽  
Hymavathi Salava ◽  
Pallawi Upadhyaya ◽  
Kamal Tyagi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solanum Lycopersicum ◽  
Next Generation ◽  
Induced Mutations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing
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