Year: 2015
Type: article
Abstract: The main goal of the present effort is to develop a comprehensive computational and statistical framework for analyzing large scale proteomics data and understand the aging process of Caenorhabditis elegans (C.elegans) nematodes based on the age dependent pattern of the protein expression.Modern numerical methods were used for the analysis, including outlier detection, imputation, entropy and feature selection.Protein expression in C. elegans was found to be highly age dependent.Increased expression in younger nematodes was associated with the activation of metabolic pathways.House-keeping processes, such as proteolysis, protein biogenesis and assembly were found to be important at older age.Network entropy was also found to be age dependent for a significant fraction of proteins.Increased protein expression was associated with reduced entropy.Feature selection analysis further showed that proteins linked to metabolic processes are most predictive of the age of C. elegans nematodes, based on their level of expression. Preparation of NGM plates [Stiernagle 2006]:Equipment and Reagents: NaCl. Agar. Peptone. 5 mg/mL cholesterol in ethanol. 1 M KPO 4 buffer pH 6.0 (108.3 g KH 2 PO 4 , 35.6 g K 2 HPO 4 , H 2 O to 1 liter). 1 M MgSO 4 . Petri plates. Peristaltic pump. Methods: Mix 3 g NaCl, 17 g agar, and 2.5 g peptone in a 2 liter Erlenmeyer flask.Add 975 mL H 2 O. Cover mouth of flask with aluminum foil.Autoclave for 50 min. Cool flask in 55° C water bath for 15 min. Add 1 mL 1 M CaCl 2 , 1 ml 5 mg/mL cholesterol in ethanol, 1 mL 1 M MgSO 4 and 25 mL 1 M KPO 4 buffer.Swirl to mix well. Using sterile procedures, dispense the NGM solution into petri plates using a peristaltic pump.Fill plates 2/3 full of agar. Leave plates at room temperature for 2-3 days before use to allow for detection of contaminants, and to allow excess moisture to evaporate.Plates stored in an airtight container at room temperature will be usable for several weeks.
Author: David Alouani
Institution: Case Western Reserve University
Language: English
Subfield: Aging
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2735605811