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Effects of hypoxia on mRNA expression of housekeeping genes in rat brain tissue and primary cultured neural cells

Frontiers of Medicine 2008年第3期2卷 239-243页

作者： Yingzhong YANG Wenhong FAN Lingling ZHU Tong ZHAO Lan MA Yan WU Rili GE Ming FAN Research Center of High Altitude Medical Sciences Qinghai University School of MedicineXining 810001China Institute of Basic Medical Sciences The Academy of Military Medical SciencesBeijing 100850China

Internal standards are critical for quantitative RNA *** genes are often used as internal standards with the assumption that their express-ion levels remain relatively constant in different experi-mental *** this study,four commonly used housekeeping genes,Glyceraldehyde-3-phosphate dehy-drogenase(GAPDH),β-actin,28S rRNA and 18S rRNA were selected to test whether this assumption is tenable under hypoxic *** tested the RNA expression level of these four genes in different hypoxic *** subjected to acute hypoxia for 2 hours were used for tissue *** cultured neural stem cells from E13 fetal rats were treated with 3%O_(2) or 10%O_(2) for 24 hours for in vitro *** both experiments,expression levels of 28S rRNA and 18S rRNA were constant,independent of hypoxia ***,expression levels of GAPDH and b-actin were all changed in all kinds of hypoxic *** particu-lar,the mRNA expression level of GAPDH was increased by 43.4%under 3%O_(2) hypoxic *** results suggest that 18S rRNA and 28S rRNA are reliable internal controls for comparative analyses of transcrip-tion under *** appears particularly unfa-vorable for this purpose in hypoxic conditions.

关键词： housekeeping genes hypoxia gene express-ion standardization

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Validation of Zebrafish (Danio rerio) Reference genes for Quantitative Real-time RT-PCR Normalization

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Acta Biochimica et Biophysica Sinica 2007年第5期39卷 384-390页

作者： Andrew DODD Daniel LA Warren C. MCNABB Donald R. LOVE School of Biological Sciences University of Auckland Private Bag 92019 Auckland 1142 New Zealand Food and Health Group AgResearch Grasslands Private Bag 11008 Tennant Drive Palmerston North New Zealand

The normalization of quantitative real time RT-PCR (qRT-PCR) is important to obtain accurate gene expression data. The most common method for qRT-PCR normalization is to use reference, or house- keeping genes. However, there is emerging evidence that even reference genes can be regulated under different conditions, qRT-PCR has only recently been used in terms of zebrafish gene expression studies and there is no validated set of reference genes. This study characterizes the expression of nine possible reference genes during zebrafish embryonic development and in a zebrafish tissue panel. All nine reference genes exhibited variable expression. The β-actin, EF1α and Rp113α genes comprise a validated reference gene panel for zebrafish developmental time course studies, and the EF1α, Rp113α and 18S rRNA genes are more suitable as a reference gene panel for zebrafish tissue analysis. Importantly, the zebrafish GAPDH gene appears unsuitable as reference gene for both types of studies.

关键词： zebrafish quantitative real-time RT-PCR housekeeping genes GAPDH gene GeNorm

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Identification of potential internal control genes for real-time PCR analysis during stress response in Pyropia haitanensis

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Chinese Journal of Oceanology and Limnology 2017年第6期35卷 1432-1441页

作者：王霞冯建华黄爱优何林文牛建峰王广策 Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology University of Chinese Academy of Sciences Nantong Branch Institute of Oceanology Chinese Academy of Sciences

Pyropia haitanensis has prominent stress-resistance characteristics and is endemic to China. Studies into the stress responses in these algae could provide valuable information on the stress-response mechanisms in the intertidal Rhodophyta. Here, the effects of salinity and light intensity on the quantum yield of photosystem II in Py. haitanensis were investigated using pulse-amplitude-modulation fluorometry. Total RNA and genomic DNA of the samples under different stress conditions were isolated. By normalizing to the genomic DNA quantity, the RNA content in each sample was evaluated. The cDNA was synthesized and the expression levels of seven potential internal control genes were evaluated using qRT-PCR method. Then, we used geNorm, a common statistical algorithm, to analyze the qRT-PCR data of seven reference genes. Potential genes that may constantly be expressed under different conditions were selected, and these genes showed stable expression levels in samples under a salinity treatment, while tubulin, glyceraldehyde- 3-phosphate dehydrogenase and actin showed stability in samples stressed by strong light. Based on the results of the pulse amplitude-modulation fluorometry, an absolute quantification was performed to obtain gene copy numbers in certain stress-treated samples. The stably expressed genes as determined by the absolute quantification in certain samples conformed to the results of the geNorm screening. Based on the results of the software analysis and absolute quantification, we proposed that elongation factor 3 and 18S ribosomal RNA could be used as internal control genes when the Py. haitanensis blades were subjected to salinity stress, and that a-tubulin and 18S ribosomal RNA could be used as the internal control genes when the stress was from strong light. In general, our findings provide a convenient reference for the selection of internal control genes when designing experiments related to stress responses in Py. haitanensis.

关键词： real-time quantitative PCR housekeeping genes internal control genes stress responding Pyropia haitanensis

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Identification of Rhizobia Isolated from Nodules of Mexican Commercial Soybean Varieties

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American Journal of Plant Sciences 2024年第1期15卷 29-45页

作者： Cecilia Vázquez Rodríguez Lourdes Vital López Jesús Gerardo García Olivares Homar Rene Gill Langarica Laboratorio de Biotecnología Vegetal Centro de Biotecnología Genómica Instituto Politécnico Nacional Reynosa México Carrera de Mantenimiento Industrial Universidad Tecnológica de Tamaulipas Norte Universidad Tecnológica Reynosa México

Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybean varieties in high-production regions. Multilocus sequence analysis (MLSA) was employed for enhanced species resolution. The study identified six Bradyrhizobium species: Bradyrhizobium japonicum USDA 110, Bradyrhizobium japonicum USDA 6, Bradyrhizobium elkanii USDA 76, Bradyrhizobium neotropicale, Bradyrhizobium lablabi, and Bradyrhizobium icense. Bradyrhizobium japonicum USDA 110 predominated in the soils, displaying symbiotic preference for the Huasteca 400 variety. However, phylogenetic analysis didn't reveal a clear association between strains, soil, and soybean variety. This research sheds light on the diversity of rhizobia in Mexican soybean cultivation, contributing to the understanding of symbiotic relationships in soybean production systems.

关键词： Nodules Soybean housekeeping genes MLSA Rhizobia Bradyrhizobium Nitrogen Fixation Symbiosis Phylogenetic Analysis

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The Gene Expression Patterns Indicate Tissue Development and Functions

The Gene Expression Patterns Indicate Tissue Development and...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者：潘建波 Shi-Chang Hu Xian-Ying Cheng Mei-Chun Cai Quan Zou Zhi-Liang Ji Department of Chemical Biology College of Chemistry and Chemical EngineeringThe Key Laboratory for Chemical Biology of Fujian Province School of Information Science and Technology Xiamen University State Key Laboratory of Stress Cell Biology School of Life Sciences

Background:Spatiotemporal variation of gene expression can happen extensively. Thanks to current applications of high throughput technologies,***,SAGE and next generation sequencing,gene differential expressions could be motored simultaneously in large scale. Methods:Here,we developed a method to identify housekeeping genes,tissue-specific/ selective genes and tissue-repressed genes using three novel statistical parameters:Specificity Measure(SPM),Contribution Measure(CTM) and Dispersion Measure(DPM).Accordingly, a number of pattern genes were thus identified from several microarray *** these pattern genes,a systematic and genome-wide exploration of these pattern genes were demonstrated in various aspects of chromosomal locus,sub-cellular distribution,physiological function,and association with tissue functions. Results:It is observed that many housekeeping genes are non-evenly expressed across tissues in normal physiological state or under experimental *** tend to lie in intracellular organelles,especially in nucleus and ribosome,and their products function in aspects of nucleic acid binding,nucleic acid metabolic process,transcription and translation. To the contrast,products of tissue-specific genes are normally extracellular,*** plasma membrane or in plasma,in the form of secreted proteins or *** often play roles in receptor binding,homeostasis,organ development and signal ***,tissueselective genes may serve as a bridge between *** even provide clues of tissue development. Conclusions:In summary,our study provides an easier,more sensitive and robust way in quantitative detection of gene expression patterns and further better understanding of tissue function and development.

关键词： Specific/Selective genes housekeeping genes Tissue Function

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