scholarly journals Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw155 ◽  
Author(s):  
Marc Feuermann ◽  
Pascale Gaudet ◽  
Huaiyu Mi ◽  
Suzanna E. Lewis ◽  
Paul D. Thomas
Keyword(s):  
Gene Ontology ◽  
Gene Function ◽  
Large Scale ◽  
Cellular Processes

scholarly journals LSTrAP-Cloud: A User-friendly Cloud Computing Pipeline to Infer Co-functional and Regulatory Networks

2020 ◽  
Author(s):  
Qiao Wen Tan ◽  
William Goh ◽  
Marek Mutwil
Keyword(s):  
Rna Sequencing ◽  
Gene Function ◽  
Regulatory Networks ◽  
Large Scale ◽  
Function Prediction ◽  
Sequencing Data ◽  
Gene Function Prediction ◽  
Analysis Pipeline ◽  
User Friendly

AbstractAs genomes become more and more available, gene function prediction presents itself as one of the major hurdles in our quest to extract meaningful information on the biological processes genes participate in. In order to facilitate gene function prediction, we show how our user-friendly pipeline, Large-Scale Transcriptomic Analysis Pipeline in Cloud (LSTrAP-Cloud), can be useful in helping biologists make a shortlist of genes that they might be interested in. LSTrAP-Cloud is based on Google Colaboratory and provides user-friendly tools that process and quality-control RNA sequencing data streamed from the European Sequencing Archive. LSTRAP-Cloud outputs a gene co-expression network that can be used to identify functionally related genes for any organism with a sequenced genome and publicly available RNA sequencing data. Here, we used the biosynthesis pathway of Nicotiana tabacum as a case study to demonstrate how enzymes, transporters and transcription factors involved in the synthesis, transport and regulation of nicotine can be identified using our pipeline.

Identifying the Potential Substrates of the Depalmitoylation Enzyme Acyl-protein Thioesterase 1

2019 ◽  
Vol 19 (5) ◽  
pp. 364-375 ◽  
Author(s):  
Huicong Liu ◽  
Peipei Yan ◽  
Junyan Ren ◽  
Can Wu ◽  
Wei Yuan ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Gene Ontology ◽  
Quantitative Method ◽  
Large Scale ◽  
Biological Pathways ◽  
Protein Enrichment ◽  
Cellular Processes ◽  
Data Independent Acquisition ◽  
Gene Ontology Classification ◽  
Natural Mutation

Background:The homeostasis of palmitoylation and depalmitoylation is involved in various cellular processes, the disruption of which induces severe physiological consequences. Acyl-protein thioesterase (APT) and palmitoyl-protein thioesterases (PPT) catalyze the depalmitoylation process. The natural mutation in human PPT1 caused neurodegenerative disease, yet the understanding of APT1 remains to be elucidated. While the deletion of APT1 in mice turned out to be potentially embryonically lethal, the decoding of its function strictly relied on the identification of its substrates.Objective:To determine the potential substrates of APT1 by using the generated human APT1 knockout cell line.Methods :The combined techniques of palmitoyl-protein enrichment and massspectrometry were used to analyze the different proteins. Palmitoyl-proteins both in HEK293T and APT1-KO cells were extracted by resin-assisted capture (RAC) and data independent acquisition (DIA) quantitative method of proteomics for data collection.Results:In total, 382 proteins were identified. The gene ontology classification segregated these proteins into diverse biological pathways e.g. endoplasmic reticulum process and ubiquitin-mediated proteolysis. A few potential substrates were selected for verification; indeed, major proteins were palmitoylated. Importantly, their levels of palmitoylation were clearly changed in APT1-KO cells. Interestingly, the proliferation of APT1-KO cells escalated dramatically as compared to that of the WT cells, which could be rescued by APT1 overexpression.Conclusion:Our study provides a large scale of potential substrates of APT1, thus facilitating the understanding of its intervened molecular functions.

A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

1996 ◽  
Vol 5 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Chris Halpin ◽  
Barbara Herrmann ◽  
Margaret Whearty
Keyword(s):  
Speech Production ◽  
Hearing Aids ◽  
Role Models ◽  
Speech Intelligibility ◽  
Large Scale ◽  
Speech Language Pathology ◽  
The Family ◽  
Patient Will ◽  
Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

The Boeing 787 Dreamliner--A case study in large-scale design integration

2008 ◽  
Author(s):  
D. L. McMullin ◽  
A. R. Jacobsen ◽  
D. C. Carvan ◽  
R. J. Gardner ◽  
J. A. Goegan ◽  
...  
Keyword(s):  
Large Scale ◽  
Design Integration ◽  
Scale Design

Disruptive innovation and operationalization in local and sustainable food systems: Examining the University of Toronto-Local Food Plus partnership

2019 ◽  
Vol 6 (1) ◽  
pp. 120-139
Author(s):  
Lori Stahlbrand
Keyword(s):  
Food Systems ◽  
Large Scale ◽  
Food System ◽  
Local Food ◽  
Disruptive Innovation ◽  
Government Support ◽  
Sustainable Food ◽  
University Of Toronto ◽  
The University

This paper traces the partnership between the University of Toronto and the non-profit Local Food Plus (LFP) to bring local sustainable food to its St. George campus. At its launch, the partnership represented the largest purchase of local sustainable food at a Canadian university, as well as LFP’s first foray into supporting institutional procurement of local sustainable food. LFP was founded in 2005 with a vision to foster sustainable local food economies. To this end, LFP developed a certification system and a marketing program that matched certified farmers and processors to buyers. LFP emphasized large-scale purchases by public institutions. Using information from in-depth semi-structured key informant interviews, this paper argues that the LFP project was a disruptive innovation that posed a challenge to many dimensions of the established food system. The LFP case study reveals structural obstacles to operationalizing a local and sustainable food system. These include a lack of mid-sized infrastructure serving local farmers, the domination of a rebate system of purchasing controlled by an oligopolistic foodservice sector, and embedded government support of export agriculture. This case study is an example of praxis, as the author was the founder of LFP, as well as an academic researcher and analyst.

Algorithm of combining chromatography mass spectrometry-untargeted profiling and multivariate analysis for identification of marker-substances in samples of complex composition

2020 ◽  
Vol 86 (7) ◽  
pp. 12-19
Author(s):  
I. V. Plyushchenko ◽  
D. G. Shakhmatov ◽  
I. A. Rodin
Keyword(s):  
Mass Spectrometry ◽  
Multivariate Analysis ◽  
Large Scale ◽  
Complex Composition ◽  
Unified Protocol ◽  
Chromatography Mass Spectrometry ◽  
Marker Substances ◽  
Selection Testing ◽  
Untargeted Profiling

A viral development of statistical data processing, computing capabilities, chromatography-mass spectrometry, and omics technologies (technologies based on the achievements of genomics, transcriptomics, proteomics, metabolomics) in recent decades has not led to formation of a unified protocol for untargeted profiling. Systematic errors reduce the reproducibility and reliability of the obtained results, and at the same time hinder consolidation and analysis of data gained in large-scale multi-day experiments. We propose an algorithm for conducting omics profiling to identify potential markers in the samples of complex composition and present the case study of urine samples obtained from different clinical groups of patients. Profiling was carried out by the method of liquid chromatography mass spectrometry. The markers were selected using methods of multivariate analysis including machine learning and feature selection. Testing of the approach was performed using an independent dataset by clustering and projection on principal components.

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