Functional analysis

Cloning and functional analysis of the promoter of a maize starch synthase III gene (ZmDULL1)

J. D. Wu, Jiang, C. P., Zhu, H. S., Jiang, H. Y., Cheng, B. J., and Zhu, S. W., “Cloning and functional analysis of the promoter of a maize starch synthase III gene (ZmDULL1)”, vol. 14, pp. 5468-5479, 2015.

The ZmDULL1 gene encodes a starch synthase and is a determinant of the structure of endosperm starch in maize (Zea mays L.). However, little is known regarding the regulatory mechanism of the ZmDULL1 gene. In this study, we isolated and characterized the ZmDULL1 promoter (PDULL1), which is the 5' flanking region of ZmDULL1 in maize. Sequence analysis showed that several cis-acting elements important for endosperm expression (GCN4_motif and AACA-element) were located within the promoter.

Screening and functional microarray analysis of differentially expressed genes related to osteoporosis

Y. Chen and Xia, R. G., “Screening and functional microarray analysis of differentially expressed genes related to osteoporosis”, vol. 13, pp. 3228-3236, 2014.

We searched for key genes that could accurately predict bone mineral density. The gene expression profile GSE7429 was downloaded from the Gene Expression Omnibus database, which includes 20 samples, 10 with high and 10 with low bone mineral density. The differentially expressed genes (DEGs) were identified with packages in R language. Further, BLASTX was used to obtain COG function classifications of all the DEGs. The GOTM software was used to find DEGs enriched modules. The functions of genes in the modules was also predicted with the software GENECODIS.

Functional characterization of the Ginkgo biloba chalcone synthase gene promoter in transgenic tobacco

L. L. Li, Cheng, H., Yuan, H. H., Xu, F., Cheng, S. Y., and Cao, F. L., “Functional characterization of the Ginkgo biloba chalcone synthase gene promoter in transgenic tobacco”, vol. 13, pp. 3446-3460, 2014.

The regulative sequence (2273 bp) of the chalcone synthase gene promoter of biloba was cloned by genomic walking. A 2273-bp promoter 5' upstream translation start site of GbCHS was cloned and designated as GbCHSP. pBI121+CHSP:GUS and pBI121-35S:GUS were constructed and transformed into tobacco by LBA4404. We found that GbCHSP could drive transient expression of GUS in tobacco and differentially expressed in root, stem and leaf tissues of this plant.

Functional analysis of differentially expressed genes associated with glaucoma from DNA microarray data

Y. Wu, Zang, W. D., and Jiang, W., “Functional analysis of differentially expressed genes associated with glaucoma from DNA microarray data”, vol. 13, pp. 9421-9428, 2014.

Microarray data of astrocytes extracted from the optic nerves of donors with and without glaucoma were analyzed to screen for differentially expressed genes (DEGs). Functional exploration with bioinformatic tools was then used to understand the roles of the identified DEGs in glaucoma. Microarray data were downloaded from the Gene Expression Omnibus (GEO) database, which contains 13 astrocyte samples, 6 from healthy subjects and 7 from patients suffering from glaucoma. Data were pre-processed, and DEGs were screened out using R software packages.

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