scholarly journals Global Transcriptome Characterization and Assembly of Thermophilic Ascomycete Chaetomium thermophilum

2019 ◽  
Author(s):  
Amit Singh ◽  
Géza Schermann ◽  
Sven Reislöhner ◽  
Nikola Kellner ◽  
Ed Hurt ◽  
...  
Keyword(s):  
Basic Research ◽  
Industrial Applications ◽  
Open Reading Frames ◽  
Annotation Database ◽  
Go Annotation ◽  
Chaetomium Thermophilum ◽  
Alternatively Spliced ◽  
Comprehensive Search ◽  
R Packages ◽  
Novel Transcripts

A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome Chaetomium thermophilum has been reported previously, but it is limited to open reading frames (ORFs) of genes and contains only a few noncoding transcripts. In this study, we identified and annotated by deep RNA sequencing full-length transcripts of C.thermophilum. We annotated 7044 coding genes and a large number of noncoding genes (n=4567). Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help understanding the gene regulatory landscape in C.thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species. The R packages for gene and GO annotation database can be found under https://www.bzh.uni-heidelberg.de/brunner/Chaetomium_thermophilum.

scholarly journals Global Transcriptome Characterization and Assembly of the Thermophilic Ascomycete Chaetomium thermophilum

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1549
Author(s):  
Amit Singh ◽  
Géza Schermann ◽  
Sven Reislöhner ◽  
Nikola Kellner ◽  
Ed Hurt ◽  
...  
Keyword(s):  
Basic Research ◽  
Industrial Applications ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Chaetomium Thermophilum ◽  
Alternatively Spliced ◽  
Comprehensive Search ◽  
Novel Transcripts ◽  
Gene Regulatory ◽  
Reading Frames

A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome of Chaetomium thermophilum has been reported previously, but it is essentially limited to open reading frames (ORFs) of protein coding genes and contains only a few noncoding transcripts. In this study, we identified and annotated full-length transcripts of C. thermophilum by deep RNA sequencing. We annotated 7044 coding genes and 4567 noncoding genes. Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes as well as 2878 novel noncoding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help to understand the gene regulatory landscape in C. thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species.

scholarly journals The UniProt-GO Annotation database in 2011

2011 ◽  
Vol 40 (D1) ◽  
pp. D565-D570 ◽  
Author(s):  
E. C. Dimmer ◽  
R. P. Huntley ◽  
Y. Alam-Faruque ◽  
T. Sawford ◽  
C. O'Donovan ◽  
...  
Keyword(s):  
Annotation Database ◽  
Go Annotation

Use of Neuroelectric Measures to Assess Cognitive Workload

1984 ◽  
Vol 28 (1) ◽  
pp. 36-36 ◽  
Author(s):  
Alan S. Gevins
Keyword(s):  
Air Force ◽  
Current Knowledge ◽  
Basic Research ◽  
Industrial Applications ◽  
Event Related Potential ◽  
P300 Amplitude ◽  
Naval Research ◽  
Cognitive Workload ◽  
Aerospace Medicine ◽  
Neurocognitive Functions

It would be useful to be able to directly measure the utilization of various brain systems during performance of any choosen task. During the last few years several investigators have been developing paradigms to use the P300 component of the averaged event-related potential (ERP) to assess cognitive workload. Initial results have been encouraging, and it has been suggested that the time may be ripe to transition this type of measure from the laboratory to industrial applications. In this presentation I will discuss the potential advantages and difficulties of the neuroelectric approach to cognitive workload assessment. I will consider current knowledge of the neural origin of P300, as well as its possible neural and psychological significance. Several of the popular paradigms for eliciting P300 will be reviewed, and the permissible inferences about neurocognitive functions obtainable from variations in P300 amplitude or latency will be outlined. The practical problems of transitioning an academic laboratory paradigm to an industrial research setting will be discussed, using the example of a flight simulator. Particular attention will be directed at the contamination of brain electrical recordings by instrumental artifacts, and by head, body and eye movements. The current state-of-the-art in automated detection and filtering of these contaminants will be summarized. Individual differences and the effects of metabolic factors, drugs and fatigue will be discussed, as will techniques for reducing “irrelevant” variance due to these factors. Recent developments in measuring neurocognitve functions will be presented, emphasizing the extraction of more detailed information about multiple, simultaneously- and sequentially-active brain systems. Basic research supported by grants and contracts from the National Science Foundation, The Office of Naval Research, The Air Force Office of Scientific Research, and the Air Force School of Aerospace Medicine.

scholarly journals RNA Expression Analysis Using an AntisenseBacillus subtilis Genome Array

2001 ◽  
Vol 183 (24) ◽  
pp. 7371-7380 ◽  
Author(s):  
Jian-Ming Lee ◽  
Shehui Zhang ◽  
Soumitra Saha ◽  
Sonia Santa Anna ◽  
Can Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dynamic Range ◽  
Expression Patterns ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Biosynthetic Genes ◽  
Coding Regions ◽  
Intergenic Regions ◽  
Differential Gene ◽  
Novel Transcripts

ABSTRACT We have developed an antisense oligonucleotide microarray for the study of gene expression and regulation in Bacillus subtilis by using Affymetrix technology. Quality control tests of the B. subtilis GeneChip were performed to ascertain the quality of the array. These tests included optimization of the labeling and hybridization conditions, determination of the linear dynamic range of gene expression levels, and assessment of differential gene expression patterns of known vitamin biosynthetic genes. In minimal medium, we detected transcripts for approximately 70% of the known open reading frames (ORFs). In addition, we were able to monitor the transcript level of known biosynthetic genes regulated by riboflavin, biotin, or thiamine. Moreover, novel transcripts were also detected within intergenic regions and on the opposite coding strand of known ORFs. Several of these novel transcripts were subsequently correlated to new coding regions.

ChemInform Abstract: Development of Palladium-Carbene Catalysts for Telomerization and Dimerization of 1,3-Dienes: Form Basic Research to Industrial Applications.

ChemInform ◽  
2008 ◽  
Vol 39 (47) ◽  
Author(s):  
Nicolas D. Clement ◽  
Lucie Routaboul ◽  
Anne Grotevendt ◽  
Ralf Jackstell ◽  
Matthias Beller
Keyword(s):  
Basic Research ◽  
Industrial Applications

scholarly journals Mapping the coevolution, leadership and financing of research on viral vectors, RNAi, CRSPR/Cas9 and other genomic editing technologies

2019 ◽  
Author(s):  
David Fajardo Ortiz ◽  
Annie Shattuck ◽  
Stefan Hornbostel
Keyword(s):  
Viral Vectors ◽  
Basic Research ◽  
The United States ◽  
Industrial Applications ◽  
Incremental Innovation ◽  
Government Agencies ◽  
Network Clustering ◽  
The European Union ◽  
Main Research ◽  
Genomic Editing

AbstractIn the present investigation, we set out to determine and compare the evolution of the research on viral vectors, RNAi and genomic editing platforms as well as determine the profile of the main research institutions and funding agencies. A search of papers on viral vectors RNAi, CRISPR/Cas, TALENs, ZFNs and meganucleases was carried out in the Web of Science. A citation network of 16,746 papers was constructed. An analysis of network clustering combined with text mining was performed. In the case of viral vectors a long term process of incremental innovation in which the clusters of papers are organized around specific improvements of clinical relevance was identified. The most influential investigations on viral vectors were conducted in the United States and the European Union where the main funders were government agencies. The trajectory of RNAi research included clusters related to the study of RNAi as a biological phenomenon and its use in functional genomics, biomedicine and pest control. A British philanthropic organization and a US pharmaceutical company played a key role in the development of basic RNAi research and clinical application respectively, in addition to government agencies and academic institutions. In the case of CRISPR/Cas research, basic science discoveries led to the development of technical improvements, and these two in turn provided the information required for the development of biomedical, agricultural, livestock and industrial applications. The trajectory of CRISPR/Cas research exhibits a geopolitical division of the investigation efforts between the US, as the main producer of basic research and technical improvements, and China increasingly leading the applied research. A set of philanthropic foundations played a key role in specific stages of the CRISPR/Cas research. Our results reflect a change in the model in the financing of science and the emergence of China as a scientific superpower, with implications for the trajectory of development for applications of genomic technologies.

scholarly journals OrBITS: A High-throughput, time-lapse, and label-free drug screening platform for patient-derived 3D organoids

2021 ◽  
Author(s):  
Christophe Deben ◽  
Edgar Cardenas De La Hoz ◽  
Maxim Le Compte ◽  
Paul Van Schil ◽  
Jeroen M. Hendriks ◽  
...  
Keyword(s):  
Personalized Medicine ◽  
High Throughput ◽  
Basic Research ◽  
Automated Analysis ◽  
Time Lapse ◽  
Industrial Applications ◽  
Great Promise ◽  
Label Free ◽  
Current Standard ◽  
Convolutional Network

AbstractPatient-derived organoids are invaluable for fundamental and translational cancer research and holds great promise for personalized medicine. However, the shortage of available analysis methods, which are often single-time point, severely impede the potential and routine use of organoids for basic research, clinical practise, and pharmaceutical and industrial applications. Here, we report the development of a high-throughput automated organoid analysis platform that allows for kinetic monitoring of organoids, named Organoid Brightfield Identification-based Therapy Screening (OrBITS). The combination of computer vision with a convolutional network machine learning approach allowed for the detection and tracking of organoids in routine extracellular matrix domes, advanced Gri3D®-96 well plates, and high-throughput 384-well microplates, solely based on brightfield imaging. We used OrBITS to screen chemotherapeutics and targeted therapies, and incorporation of a fluorescent cell death marker, revealed further insight into the mechanistic action of the drug, a feature not achievable with the current gold standard ATP-assay. This manuscript describes the validation of the OrBITS deep learning analysis approach against current standard assays for kinetic imaging and automated analysis of organoids. OrBITS, as a scalable, high-throughput technology, would facilitate the use of patient-derived organoids for drug development, therapy screening, and guided clinical decisions for personalized medicine. The developed platform also provides a launching point for further brightfield-based assay development to be used for fundamental research.

Sign in / Sign up

Export Citation Format

Share Document