Real-time PCR

Establishment of a prediction model for the miRNA-based heading date characteristics of rice in the booting stage

Y. C. Chen, Lin, W. S., Chen, R. K., Chao, Y. Y., Chin, S. W., Chen, F. C., and Lee, C. Y., “Establishment of a prediction model for the miRNA-based heading date characteristics of rice in the booting stage”, vol. 14, pp. 4381-4390, 2015.

Rice (Oryza sativa L.) is one of the most important food crops in the world. In Taiwan, due to the warm climate, there are two harvests annually. However, the yield and quality of rice can vary between each crop season in any given year. Previous reports have shown that microRNAs (miRNAs) play a crucial role in many developmental and physiological processes in plants. In this study, the heading date characteristics of 167 rice cultivars from the second crop season were recorded, and 27 rice cultivars were selected for preliminary microarray analysis.

Salt stress represses production of extracellular proteases in Bacillus pumilus

R. F. Liu, Huang, C. L., and Feng, H., “Salt stress represses production of extracellular proteases in Bacillus pumilus”, vol. 14, pp. 4939-4948, 2015.

Bacillus pumilus is able to secrete subtilisin-like prote­ases, one of which has been purified and characterized biochemically, demonstrating great potential for use in industrial applications. In the current study, the biosynthesis and transcription of extracellular pro­teases in B. pumilus (BA06) under salt stress were investigated using various methods, including a proteolytic assay, zymogram analysis, and real-time PCR.

Physiological quality and gene expression during the development of habanero pepper (Capsicum chinense Jacquin) seeds

H. O. Santos, Von Pinho, E. V. R., Von Pinho, I. V., Dutra, S. M. F., Andrade, T., and Guimarães, R. M., “Physiological quality and gene expression during the development of habanero pepper (Capsicum chinense Jacquin) seeds”, vol. 14, pp. 5085-5098, 2015.

Phytohormones have different characteristics and functions, and they may be subject to changes in their gene expression and synthesis during seed development. In this study, we evaluated the physiological qualities of habanero peppers (Capsicum chinense Jacquin) during seed development and the expression of genes involved in germination. Seeds were obtained from fruits harvested at different stages of development [i.e., 14, 21, 28, 35, 42, 49, 56, 63, and 70 days after anthesis (DAA)].

Validation of two real-time PCRs targeting the PE-PGRS 20 gene and the region of difference 4 for the characterization of Mycobacterium bovis isolates

M. L. Sales, Fonseca, Jr., A. A., Orzil, L., Alencar, A. P., Hodon, M. A., Issa, M. A., Filho, P. M. Soares, Silva, M. R., Lage, A. P., and Heinemann, M. B., “Validation of two real-time PCRs targeting the PE-PGRS 20 gene and the region of difference 4 for the characterization of Mycobacterium bovis isolates”, vol. 13, pp. 4607-4616, 2014.

This study aimed to develop and validate real-time PCR for the diagnosis of Mycobacterium bovis isolates. Two hundred and seventy-four M. bovis isolates and 156 M. tuberculosis isolates were tested. Both qPCRs amplified all of the 274 M. bovis samples, but none of the 156 M. tuberculosis samples. The qPCR for PE-PGRS 20 had 91% efficiency and a detection limit of 0.32 ng (sensitivity and specificity for qPCR “Mbovis.100” were 99.64 and 100%, respectively).

Absolute quantification of free tumor cells in the peripheral blood of gastric cancer patients

N. Bayat, Mokhtari, M. M., Rezaei-Tavirani, M., Baradaran-rafii, A., S. Zadeh, R., Heidari-Keshel, S., and Ghasemvand, F., “Absolute quantification of free tumor cells in the peripheral blood of gastric cancer patients”, vol. 13, pp. 4425-4432, 2014.

RETRACTION of "Absolute quantification of free tumor cells in the peripheral blood of gastric cancer patients" by N. Bayat, M.M. Mokhtari, M. Rezaei-Tavirani, A. Baradaran-Rafii, S. Rahman Zadeh, S. Heidari-Keshel and F. Ghasemvand. Genet. Mol. Res. 13 (2): 4425-4432 (2014)

Devolopmental and growth temperature regulation of omega-3 fatty acid desaturase genes in safflower (Carthamus tinctorius L.)

L. - L. Guan, Wu, W., Hu, B., Li, D., Chen, J. - W., Hou, K., and Wang, L., “Devolopmental and growth temperature regulation of omega-3 fatty acid desaturase genes in safflower (Carthamus tinctorius L.)”, vol. 13, pp. 6623-6637, 2014.

Three ω-3 fatty acid desaturase genes (CtFAD3, CtFAD7, and CtFAD8) were isolated from safflower (Carthamus tinctorius L.). Transcript analysis showed that the highest transcript levels were detected for CtFAD3 and the low transcript levels were detected for CtFAD7 and CtFAD8 in flowers. This result indicates that CtFAD3 enzyme activity is important for fatty acid desaturation in flowers.

Prevalence of Plasmodium falciparum and P. vivax in an area of transmission located in Pará State, Brazil, determined by amplification of mtDNA using a real-time PCR assay

C. R. T. Souza, Carvalho, T. A. A., Amaral, R. C. G., Cunha, L. S., Cunha, M. G., and Guerreiro, J. F., “Prevalence of Plasmodium falciparum and P. vivax in an area of transmission located in Pará State, Brazil, determined by amplification of mtDNA using a real-time PCR assay”, vol. 11, pp. 3409-3413, 2012.

The need for a more sensitive and time-efficient assay for malaria has led to the development of molecular assays involving real-time PCR (qPCR), a procedure that has the potential to detect low levels of parasitemia, identify mixed infections, and allow for precise differentiation of species via melting curve analysis or TaqMan fluorescence-labeled probes. Since the first study published in 2001 at least 17 assays have been developed, most of them using SSUrRNA as the target gene. We used qPCR to detect Plasmodium falciparum and P.

Cloning of a phosphatidylinositol 4-kinase gene based on fiber strength transcriptome QTL mapping in the cotton species Gossypium barbadense

H. W. Liu, Shi, R. F., Wang, X. F., Pan, Y. X., Zang, G. Y., and Ma, Z. Y., “Cloning of a phosphatidylinositol 4-kinase gene based on fiber strength transcriptome QTL mapping in the cotton species Gossypium barbadense”, vol. 11, pp. 3367-3378, 2012.

Sea Island cotton (Gossypium barbadense) is highly valued for its superior fiber qualities, especially fiber strength. Based on a transcript-derived fragment originated from transcriptome QTL mapping, a fiber strength related candidate gene of phosphatidylinositol 4-kinase cDNA, designated as GbPI4K, was first cloned, and its expression was characterized in the secondary cell wall thickening stage of G. barbadense fibers. The ORF of GbPI4K was found to be 1926 bp in length and encoded a predicted protein of 641 amino acid residues.

NPRL2 gene expression in the progression of colon tumors

B. Yogurtcu, Hatemi, I., Aydin, I., and Buyru, N., “NPRL2 gene expression in the progression of colon tumors”, vol. 11, pp. 4810-4816, 2013.

Genetic and epigenetic factors affecting DNA methylation and gene expression are known to be involved in the development of colon cancer, but the full range of genetic alterations and many key genes involved in the pathogenesis of colon cancer remain to be identified. NPRL2 is a candidate tumor suppressor gene identified in the human chromosome 3p21.3 region. We evaluated the role of this gene in the pathogenesis of colorectal cancer by investigating NPRL2 mRNA expression in 55 matched normal and tumor colon tissue samples using quantitative RT-PCR analysis.

Analysis of differential gene expression during floral bud abortion in radish (Raphanus sativus L.)

J. Zhang, Sun, X. L., Zhang, L. G., Hui, M. X., and Zhang, M. K., “Analysis of differential gene expression during floral bud abortion in radish (Raphanus sativus L.)”, vol. 12, pp. 2507-2516, 2013.

Radish floral bud abortion (FBA) is an adverse biological phenomenon that occurs during reproduction. Although FBA occurs frequently, its mechanism remains unknown. To elucidate the molecular mechanism underlying FBA, we detected gene expression differences between aborted and normal buds of radish using cDNA-amplified fragment length polymorphism (AFLP) and real-time polymerase chain reaction (real-time PCR).

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