Microarray analysis of transcriptional data for the detection of molecular mechanisms of aging after lipofuscin treatment in the model organism Caenorhabditis elegans

Postgraduate Thesis uoadl:2882540 365 Read counter

Unit:
Κατεύθυνση Βιοπληροφορική
Library of the School of Science
Deposit date:
2019-10-14
Year:
2019
Author:
Aktypi Foteini
Supervisors info:
Οικονομίδου Βασιλική, Επίκουρη Καθηγήτρια, Τμήμα Βιολογίας, ΕΚΠΑ
Τρουγκάκος Ιωάννης, Καθηγητής, Τμήμα Βιολογίας, ΕΚΠΑ
Χονδρογιάννη Νίκη, Ερευνήτρια Β' Βαθμίδας, Ινστιτούτο Χημικής Βιολογίας, Εθνικό Ίδρυμα Ερευνών
Original Title:
Βιοπληροφορική ανάλυση μεταγραφικών δεδομένων μικροσυστοιχιών για τη μελέτη μοριακών μηχανισμών γήρανσης στο μοντέλο οργανισμό Caenorhabditis elegans κατά την επίδραση με λιποφουσκίνη
Languages:
Greek
Translated title:
Microarray analysis of transcriptional data for the detection of molecular mechanisms of aging after lipofuscin treatment in the model organism Caenorhabditis elegans
Summary:
Aging is a process that leads to many harmful functional and structural changes in organisms. Delaying or reversing these degenerative changes is a crucial and important purpose of aging research. To achieve this, the identification of the genetic and environmental factors responsible for the progression of the phenomenon is key. The model organism Caenorhabditis elegans is widely used for the study of molecular mechanisms of aging by utilizing mutant strains and measuring the impact of various substances on its lifespan. On the one hand, the similarity of metabolic pathways to humans and on the other hand the ease of genetic manipulation and low cost of maintenance make it a great model organism.
Lipofuscin is a polymeric substance mainly of lipid and protein composition, derived from the oxidation of cellular components in the lysosomal compartment. As the aging of cells progresses, the accumulation of lipofuscin in their lysosomes increases, while the exact composition of the substance remains unknown. The presence of lipofuscin inside cells is an indicator of cellular aging and appears to have an important role in aging and other pathological conditions. Using lipofuscin to treat human cell cultures or to supplement the diet of the model organism Drosophila melanogaster has adverse effects on both lifespan and healthspan. On the contrary, this is not the case with the Nematode Caenorhabditis elegans, where lipofuscin supplementation leads to lifespan extension.
In the present study, the aim is to investigate the transcriptional profile of the organism Caenorhabditis elegans, after supplementing its diet with lipofuscin, by analyzing transcriptional data in order to discover the biochemical pathways involved in this process.
An Affymetrix DNA oligonucleotide microarray experiment, for the generation of the transciptional data, was designed and performed at the Molecular and Cellular Aging Laboratory of the Institute of Chemical Biology of the National Hellenic Research Institute. A total of 22 samples distributed under the two conditions with and without lipofuscin supplementation, and also of 4 different timepoints (days) of C. elegans lifespan were analyzed.
For the analysis, R programming language was used along with R-Bioconductor packages especially developed to process transcriptional data. Furthermore, for the functional analysis of differentially expressed genes the online platforms of BioInfoMiner, DAVID and Pathview were utilized. This analysis lead to the identification of both, the essential biological pathways that are implicated in the phenomenon and the most important key genes that are targets for further research.
Main subject category:
Science
Keywords:
bioinformatics, microarrays, transcriptomics, Caenorhabditis elegans, lipofuscin, aging, lifespan extension
Index:
Yes
Number of index pages:
0
Contains images:
No
Number of references:
274
Number of pages:
154
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