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Variation: Analytical Solutions of Ordinary Differential Equations
Published in Markus W. Covert, Fundamentals of Systems Biology, 2017
A second, related assumption is that a rate for a given system does not change significantly under the conditions that interest us. For example, certain genes are known as housekeeping genes because their protein products are so critical to cellular function that they are essentially always transcribed at a nearly constant rate. These genes are often used as controls in experiments monitoring gene or protein expression. For housekeeping genes, we would replace Ratetranscription with a constant, such as ktrs, with units of concentration over time. This constant is a parameter of the model, which needs to be assigned a value to solve numerically. Ideally, we would measure ktrs for our circuit; if that were not possible, we would need to estimate it.
Naturally Occurring Polymers—Animals
Published in Charles E. Carraher, Carraher's Polymer Chemistry, 2017
Gene expression simply refers to its transcription, resulting subsequently, in most cases, in the synthesis of a protein or protein part. The flow of information typically is DNA → RNA → protein → cell structure and function. Transcription is the term used to describe the transfer of information from the DNA to RNA; the flow of information from the RNA to the protein is called translation. Genes whose product is needed essentially all the time are present at a constant amount in virtually every cell. Genes for enzymes of the central metabolic pathways are of this type and are often called housekeeping genes. Unvarying expression of a gene is called constitutive gene expression.
Laboratory tutorials
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2018
The RT-PCR method can be used not only to detect specific mRNAs but also to semiquantitate their levels. Thus, one can compare levels of transcripts in different samples. This can be done in two different ways. One is to quantify against levels of transcripts from a control, housekeeping gene, such as actin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). (Transcription of housekeeping genes is believed to be unaffected by almost all experimental conditions.) The second method is to add an exogenous, primer-specific PCR template during PCR.
Scaffold geometry and computational fluid dynamics simulation supporting osteogenic differentiation in dynamic culture
Published in Computer Methods in Biomechanics and Biomedical Engineering, 2023
Somruethai Channasanon, Pakkanun Kaewkong, Surapol Chantaweroad, Passakorn Tesavibul, Yotsakorn Pratumwal, Somboon Otarawanna, Soshu Kirihara, Siriporn Tanodekaew
To determine the level of osteoblast-specific gene expression, i.e. type I collagen, osteopontin and osteocalcin, total RNA was extracted from cell-seeded scaffold using TRIZOL reagent (Life Technologies, USA) according to the manufacturer’s instruction. First-strand complementary DNA (cDNA) was synthesized from 1 µg RNA by using RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific, USA). The following amplification primers were used: type I collagen forward primer: 5′- TCTCCACTCTTCTAGTTCCT-3′; reverse primer:5′- TTGGGTCATTTCCACATGC-3′, osteopontin forward primer: 5′-CTTTCACTCCAATCGTCCCTAC-3′; reverse primer:5′-GCTCTCTTTGGAATG CTCAAGT-3′, osteocalcin forward primer: 5′-ATGAGGACCCTCTCTCTGCT-3′; reverse primer: 5′-CCGTAGATGCGTTTGTAGGC-3′, GAPDH forward primer: 5′-GCCATCAACGACCCCTTCATTGAC-3′; reverse primer: 5′-ACGGAAGGCCATGCC AGTGAGCTT-3′. Real-time PCR reactions were prepared by using Fast SYBR® Green Master Mix (Applied Biosystems, USA) and performed by using 7500 Fast Real-Time PCR system (Applied Biosystems). Target gene expression was normalized to the expression level of housekeeping gene GAPDH. The relative amount of each gene was calculated using the comparative 2-ΔΔCt method.
Zearalenone perturbs the circadian clock and inhibits testosterone synthesis in mouse Leydig cells
Published in Journal of Toxicology and Environmental Health, Part A, 2021
Lijia Zhao, Yaoyao Xiao, Cuimei Li, Jing Zhang, Yaojia Zhang, Meina Wu, Tiantian Ma, Luda Yang, Xiaoyu Wang, Haizhen Jiang, Qian Li, Hongcong Zhao, Yiqun Wang, Aihua Wang, Yaping Jin, Huatao Chen
Cells, including those treated with 10 μM ZEA, were harvested at the indicated time points (after DXM synchronization for 24, 30, 36, 42 or 48 hr). For in vivo analysis, testes were collected at the indicated time points (ZT0 and ZT12) after injecting ZEA or corn oil for 1 week. Total RNA was extracted from cells and tissues using TRIZOL reagent (Takara Bio, Dalian, China) and subsequently treated with RNase-free DNase (TianGen, Beijing, China). cDNA was generated using the PrimeScript RT Reagent Kit (TaKaRa Bio). The primer sets used for real time-quantitative PCR (qPCR) are presented in Supplemental Table 1. All qPCR reactions were performed in a final volume of 20 μl containing 10 ng of cDNA, the SYBR Premix Ex Taq II kit (Takara Bio), and 200 nM specific primers. Amplification was performed using the CFX96™ qPCR system (Bio-Rad) as previously described (Chen et al. 2019; Gao et al. 2019). All reactions were performed in triplicate. The relative expression levels of each sample were normalized to the average level of the constitutively expressed housekeeping gene 36b4. The amplitude and phase of gene expression were determined using the single Cosinor method in Timing Series Single 6.3 (Expert Soft Tech., Richelieu, France).
Three dimensionally printed pearl powder/poly-caprolactone composite scaffolds for bone regeneration**
Published in Journal of Biomaterials Science, Polymer Edition, 2018
Xu Zhang, Xiaoyu Du, Dejian Li, Rongguang Ao, Bin Yu, Baoqing Yu
The expression levels of osteogenic genes such as runt-related transcription factor 2 (RUNX2), osteocalcin (OCN), bone sialoprotein (BSP), bone morphogenetic protein-2 (BMP-2), and collagen type I (COL1)) were measured with qRT-PCR. Typically, the MC3T3-E1 cells were seeded at 1 × 105 cells per scaffold and cultured for 7 or 14 days. The cells were then lysed using TRIzol Reagent (Invitrogen Pty Ltd, Australia) to extract the RNA. The RNA was reverse transcribed into complementary DNA (cDNA) using a RevertAid First Strand cDNA Synthesis Kit (Thermo), and the qRT-PCR analysis was performed on an ABI Prism 7300 Thermal Cycler (Applied Biosystems, Australia) using a SYBR Green detection reagent. The relative gene expression was normalized against the housekeeping gene GAPDH. All samples were assayed in triplicate using independent experiments. The mean cycle threshold (Ct) value of each target gene was normalized against the Ct value of GAPDH. The relative expression was calculated using the following formula: P = 2−ΔΔCt.