scholarly journals TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically-oriented application

2017 ◽  
Author(s):  
Thahmina Ali ◽  
Baekdoo Kim ◽  
Carlos Lijeron ◽  
Olorunseun O Ogunwobi ◽  
Raja Mazumder ◽  
...  
Keyword(s):  
Comprehensive Approach ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Data Quality Control ◽  
Biologically Relevant ◽  
Knowledge Database ◽  
Cancer Transcriptome ◽  
The Galaxy ◽  
Sustainable Fashion

In translational medicine, the technology of RNA sequencing (RNA-seq) continues to prove powerful, and transforming the RNA-seq data into biological insights has become increasingly imperative. We present the Transcriptomics profiler for Easy Discovery (TED) toolkit, a comprehensive approach to processing and analyzing RNA-seq data. TED is divided into three major modules: data quality control, transcriptome data analysis, and data discovery, with eleven pipelines in total. These pipelines perform the preliminary steps from assessing and correcting the quality of the RNA-seq data, to the simultaneous analysis of five transcriptomic features (differentially expressed coding, non-coding, novel isoform genes, gene fusions, alternative splicing events, genetic variants of somatic and germline mutations) and ultimately translating the RNA-seq analysis findings into actionable, clinically-relevant reports. TED was evaluated using previously published prostate cancer transcriptome data where we observed previously studied outcomes, and also created a knowledge database of highly-integrated, biologically relevant reports demonstrating that it is well-positioned for clinical applications. TED is implemented on an instance of the Galaxy platform (Galaxy page: http://galaxy.hunter.cuny.edu/u/bioitcore/p/transcriptomics-profiler-for-easy-discovery-ted-toolkit , Documentation Manual: http://ted.readthedocs.io/en/latest/index.html ) as intuitive and reproducible pipelines providing a manageable strategy for conducting substantial transcriptome analysis in a routine and sustainable fashion for bioinformatics researchers and clinicians alike.

scholarly journals TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically-oriented application

2017 ◽  
Author(s):  
Thahmina Ali ◽  
Baekdoo Kim ◽  
Carlos Lijeron ◽  
Olorunseun O Ogunwobi ◽  
Raja Mazumder ◽  
...  
Keyword(s):  
Comprehensive Approach ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Data Quality Control ◽  
Biologically Relevant ◽  
Knowledge Database ◽  
Cancer Transcriptome ◽  
The Galaxy ◽  
Sustainable Fashion

In translational medicine, the technology of RNA sequencing (RNA-seq) continues to prove powerful, and transforming the RNA-seq data into biological insights has become increasingly imperative. We present the Transcriptomics profiler for Easy Discovery (TED) toolkit, a comprehensive approach to processing and analyzing RNA-seq data. TED is divided into three major modules: data quality control, transcriptome data analysis, and data discovery, with eleven pipelines in total. These pipelines perform the preliminary steps from assessing and correcting the quality of the RNA-seq data, to the simultaneous analysis of five transcriptomic features (differentially expressed coding, non-coding, novel isoform genes, gene fusions, alternative splicing events, genetic variants of somatic and germline mutations) and ultimately translating the RNA-seq analysis findings into actionable, clinically-relevant reports. TED was evaluated using previously published prostate cancer transcriptome data where we observed previously studied outcomes, and also created a knowledge database of highly-integrated, biologically relevant reports demonstrating that it is well-positioned for clinical applications. TED is implemented on an instance of the Galaxy platform (Galaxy page: http://galaxy.hunter.cuny.edu/u/bioitcore/p/transcriptomics-profiler-for-easy-discovery-ted-toolkit , Documentation Manual: http://ted.readthedocs.io/en/latest/index.html ) as intuitive and reproducible pipelines providing a manageable strategy for conducting substantial transcriptome analysis in a routine and sustainable fashion for bioinformatics researchers and clinicians alike.

On Methodology for Designing Architectural Lighting of Production Site Interior

2020 ◽  
pp. 10-21 ◽  
Author(s):  
Vladimir V. Voronov ◽  
Nikolay I. Shchepetkov
Keyword(s):  
Architectural Design ◽  
Comprehensive Approach ◽  
Scientific Methodology ◽  
Field Observations ◽  
Production Site ◽  
Artificial Illumination ◽  
Engineering Parameters ◽  
Architectural Lighting ◽  
Candidate Thesis

The article describes content of original and relevant but virtually forgotten thesis of V.V. Voronov on lighting of production site interiors by means of overhead natural (using three types of skylights) and artificial illumination, in order to elaborate scientific methodology for architectural design of more qualitative luminous environment on the basis of comprehensive approach and enhanced criteria framework of its evaluation using light engineering parameters. The thesis is unique in terms of the scope and quality of field and laboratory observations which are reflected not only in the text but also in the graphical attachments, namely photos, figures, schemes, drawings, charts, nomograms, and diagrams accompanied by specific measured or calculated parameters. The first part of the thesis contains theoretical basics and results of field observations conducted by different methods. This second part is the exposition of chapter 3 of the V.V. Voronov’s candidate thesis (1985). It describes the methodology for and the results of the experiments by means of planar and volumetric light simulation using the architectural lighting simulating assembly (chamber) which were conducted in MARKHI in 1970–1985.

scholarly journals Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)

2021 ◽  
Vol 11 (8) ◽  
pp. 3562
Author(s):  
Yong Jin Lee ◽  
Sang Yong Park ◽  
Dae Yeon Kim ◽  
Jae Yoon Kim
Keyword(s):  
Abscisic Acid ◽  
Differential Expression Analysis ◽  
Preharvest Sprouting ◽  
Global Changes ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Global Issue ◽  
End Use ◽  
Transcriptomic Changes

Preharvest sprouting (PHS) is a key global issue in production and end-use quality of cereals, particularly in regions where the rainfall season overlaps the harvest. To investigate transcriptomic changes in genes affected by PHS-induction and ABA-treatment, RNA-seq analysis was performed in two wheat cultivars that differ in PHS tolerance. A total of 123 unigenes related to hormone metabolism and signaling for abscisic acid (ABA), gibberellic acid (GA), indole-3-acetic acid (IAA), and cytokinin were identified and 1862 of differentially expressed genes were identified and divided into 8 groups by transcriptomic analysis. DEG analysis showed the majority of genes were categorized in sugar related processes, which interact with ABA signaling in PHS tolerant cultivar under PHS-induction. Thus, genes related to ABA are key regulators of dormancy and germination. Our results give insight into global changes in expression of plant hormone related genes in response to PHS.

scholarly journals Comparison of Silks from Pseudoips prasinana and Bombyx mori Shows Molecular Convergence in Fibroin Heavy Chains but Large Differences in Other Silk Components

2021 ◽  
Vol 22 (15) ◽  
pp. 8246
Author(s):  
Michal Rindos ◽  
Lucie Kucerova ◽  
Lenka Rouhova ◽  
Hana Sehadova ◽  
Michal Sery ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Silk Gland ◽  
Amino Acid Sequences ◽  
Phylogenetic Distance ◽  
Rna Seq ◽  
Chain Molecules ◽  
Heavy Chains ◽  
Lepidopteran Larvae ◽  
Crystalline Domains

Many lepidopteran larvae produce silk feeding shelters and cocoons to protect themselves and the developing pupa. As caterpillars evolved, the quality of the silk, shape of the cocoon, and techniques in forming and leaving the cocoon underwent a number of changes. The silk of Pseudoips prasinana has previously been studied using X-ray analysis and classified in the same category as that of Bombyx mori, suggesting that silks of both species have similar properties despite their considerable phylogenetic distance. In the present study, we examined P. prasinana silk using ‘omics’ technology, including silk gland RNA sequencing (RNA-seq) and a mass spectrometry-based proteomic analysis of cocoon proteins. We found that although the central repetitive amino acid sequences encoding crystalline domains of fibroin heavy chain molecules are almost identical in both species, the resulting fibers exhibit quite different mechanical properties. Our results suggest that these differences are most probably due to the higher content of fibrohexamerin and fibrohexamerin-like molecules in P. prasinana silk. Furthermore, we show that whilst P. prasinana cocoons are predominantly made of silk similar to that of other Lepidoptera, they also contain a second, minor silk type, which is present only at the escape valve.

scholarly journals TrancriptomeReconstructoR, A Data-Driven Annotation of Complex Transcriptomes

2020 ◽  
Author(s):  
Maxim Ivanov ◽  
Albin Sandelin ◽  
Sebastian Marquardt
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
R Package ◽  
Sequence Information ◽  
Rna Seq ◽  
Sequencing Data ◽  
Gene Model ◽  
Preparation Methods ◽  
Downstream Analysis

Abstract Background: The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data. Results: We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: i) full-length RNA-seq for detection of splicing patterns and ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts.We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the two most commonly used community gene models, TAIR10 and Araport11. In particular, we identify thousands of transient transcripts missing from the existing annotations. Our new annotation promises to improve the quality of A.thaliana genome research.Conclusions: Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.

scholarly journals Nuclear pores as versatile reference standards for quantitative superresolution microscopy

2019 ◽  
Author(s):  
Jervis Vermal Thevathasan ◽  
Maurice Kahnwald ◽  
Konstanty Cieśliński ◽  
Philipp Hoess ◽  
Sudheer Kumar Peneti ◽  
...  
Keyword(s):  
Cell Lines ◽  
Fluorescent Protein ◽  
Reference Standards ◽  
Nuclear Pore ◽  
Biologically Relevant ◽  
Superresolution Microscopy ◽  
Absolute Measurements ◽  
Quantitative Fluorescence

AbstractQuantitative fluorescence and superresolution microscopy are often limited by insufficient data quality or artifacts. In this context, it is essential to have biologically relevant control samples to benchmark and optimize the quality of microscopes, labels and imaging conditions.Here we exploit the stereotypic arrangement of proteins in the nuclear pore complex as in situ reference structures to characterize the performance of a variety of microscopy modalities. We created four genome edited cell lines in which we endogenously labeled the nucleoporin Nup96 with mEGFP, SNAP-tag or HaloTag or the photoconvertible fluorescent protein mMaple. We demonstrate their use a) as 3D resolution standards for calibration and quality control, b) to quantify absolute labeling efficiencies and c) as precise reference standards for molecular counting.These cell lines will enable the broad community to assess the quality of their microscopes and labels, and to perform quantitative, absolute measurements.

scholarly journals Cosmic biology in perspective

2019 ◽  
Vol 364 (11) ◽  
Author(s):  
N. C. Wickramasinghe ◽  
Dayal T. Wickramasinghe ◽  
Christopher A. Tout ◽  
John C. Lattanzio ◽  
Edward J. Steele
Keyword(s):  
Infrared Spectra ◽  
Building Blocks ◽  
Mid Infrared ◽  
Interstellar Clouds ◽  
Astronomical Observations ◽  
Habitable Planets ◽  
Biologically Relevant ◽  
The Galaxy ◽  
Terrestrial Life ◽  
Biologically Relevant Molecules

AbstractA series of astronomical observations obtained over the period 1986 to 2018 supports the idea that life is a cosmic rather than a purely terrestrial or planetary phenomenon. These include (1) the detection of biologically relevant molecules in interstellar clouds and in comets, (2) mid-infrared spectra of interstellar grains and the dust from comets, (3) a diverse set of data from comets including the Rosetta mission showing consistency with biology and (4) the frequency of Earth-like or habitable planets in the Galaxy. We argue that the conjunction of all the available data suggests the operation of cometary biology and interstellar panspermia rather than the much weaker hypothesis of comets being only the source of the chemical building blocks of life. We conclude with specific predictions on the properties expected of extra-terrestrial life if it is discovered on Enceladus, Europa or beyond. A radically different biochemistry elsewhere can be considered as a falsification of the theory of interstellar panspermia.

scholarly journals Review—Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis

2020 ◽  
Vol 21 (3) ◽  
pp. 699 ◽  
Author(s):  
Julius Schwingen ◽  
Mustafa Kaplan ◽  
Florian C. Kurschus
Keyword(s):  
Skin Diseases ◽  
Basic Research ◽  
Bioinformatic Analysis ◽  
Classification Systems ◽  
Rna Seq ◽  
Inflammatory Skin Diseases ◽  
Biologically Relevant ◽  
Depth Analysis ◽  
Inflammatory Skin ◽  
Review Current

During the last decades, high-throughput assessment of gene expression in patient tissues using microarray technology or RNA-Seq took center stage in clinical research. Insights into the diversity and frequency of transcripts in healthy and diseased conditions provide valuable information on the cellular status in the respective tissues. Growing with the technique, the bioinformatic analysis toolkit reveals biologically relevant pathways which assist in understanding basic pathophysiological mechanisms. Conventional classification systems of inflammatory skin diseases rely on descriptive assessments by pathologists. In contrast to this, molecular profiling may uncover previously unknown disease classifying features. Thereby, treatments and prognostics of patients may be improved. Furthermore, disease models in basic research in comparison to the human disease can be directly validated. The aim of this article is not only to provide the reader with information on the opportunities of these techniques, but to outline potential pitfalls and technical limitations as well. Major published findings are briefly discussed to provide a broad overview on the current findings in transcriptomics in inflammatory skin diseases.

Sign in / Sign up

Export Citation Format

Share Document