title: Investigation of gene expressions in differentiated cell derived bone marrow stem cells during bone morphogenetic protein-4 treatments with Fourier transform infrared spectroscopy.
abstract: A model was set up to predict the differentiation patterns based on the data extracted from FTIR spectroscopy. For this reason, bone marrow stem cells (BMSCs) were differentiated to primordial germ cells (PGCs). Changes in cellular macromolecules in the time of 0, 24, 48, 72, and 96h of differentiation, as different steps of the differentiation procedure were investigated by using FTIR spectroscopy. Also, the expression of pluripotency (Oct-4, Nanog and c-Myc) and specific genes (Mvh, Stella and Fragilis) were investigated by real-time PCR. However, the expression of genes in five steps of differentiation was predicted by FTIR spectroscopy. FTIR spectra showed changes in the template of band intensities at different differentiation steps. There are increasing changes in the stepwise differentiation procedure for the ratio area of CH2, which is symmetric to CH2 asymmetric stretching. An ensemble of expert methods, including regression tree (RT), boosting algorithm (BA), and generalized regression neural network (GRNN), was the best method to predict the gene expression by FTIR spectroscopy. In conclusion, the model was able to distinguish the pattern of different steps from cell differentiation by using some useful features extracted from FTIR spectra.
authors: Department of Toxicology and Pharmacology, Faculty of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. Electronic address: jaberzafari@yahoo.com.
authors: Jaber
authors: J
authors: Zafari
authors: Department of Microbiology, Islamic Azad University, Tehran North Branch, Tehran, Iran. Electronic address: javani_f@yahoo.com.
authors: Fatemeh Javani
authors: FJ
authors: Jouni
authors: Computer Science and Informatics Department, EMORY University School of Medicine, Atlanta, GA, USA. Electronic address: ali.ahmadvand.66@gmail.com.
authors: Ali
authors: A
authors: Ahmadvand
authors: Department of Microbiology, Islamic Azad University, Tehran North Branch, Tehran, Iran. Electronic address: parviz@modares.ac.ir.
authors: Parviz
authors: P
authors: Abdolmaleki
authors: Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran. Electronic address: soodi@modares.ac.ir.
authors: Malihe
authors: M
authors: Soodi
authors: Environmental and Occupational Hazards control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Occupational Hygiene, School of Public Health, Shahid Beheshti University, Tehran, Iran.. Electronic address: zendehdel76@yahoo.com.
authors: Rezvan
authors: R
authors: Zendehdel
mesh_terms: D000465:Algorithms; D000818:Animals; D001854:Bone Marrow Cells / Q000166:cytology; D055415:Bone Morphogenetic Protein 4 / Q000494:pharmacology*; D002454:Cell Differentiation / Q000187:drug effects / Q000235:genetics; D005786:Gene Expression Regulation / Q000187:drug effects*; D006412:Hematopoietic Stem Cells / Q000166:cytology* / Q000187:drug effects / Q000502:physiology*; D016018:Least-Squares Analysis; D008297:Male; D008962:Models, Theoretical; D000071317:Nanog Homeobox Protein / Q000235:genetics; D016571:Neural Networks, Computer; D050814:Octamer Transcription Factor-3 / Q000235:genetics; D017208:Rats, Wistar; D060888:Real-Time Polymerase Chain Reaction; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*
chemical_list: D055415:Bone Morphogenetic Protein 4; D000071317:Nanog Homeobox Protein; C547030:Nanog protein, rat; D050814:Octamer Transcription Factor-3
keywords: Differentiation; FTIR; Gene expression; Regression models