Bioinformatic analysis

Cloning, molecular characterization, and expression pattern of FGF5 in Cashmere goat (Capra hircus)

W. L. Bao, Yao, R. Y., He, Q., Guo, Z. X., Bao, C., Wang, Y. F., and Wang, Z. G., “Cloning, molecular characterization, and expression pattern of FGF5 in Cashmere goat (Capra hircus)”, vol. 14, pp. 11154-11161, 2015.

Fibroblast growth factor 5 (FGF5) is a secreted signaling protein that belongs to the FGF family, and was found to be associated with hair growth in humans and other animals. The Inner Mongolia Cashmere goat (Capra hircus) is a goat breed that provides superior cashmere; this breed was formed by spontaneous mutation in China. Here, we report the cloning, molecular characterization, and expression pattern of the Cashmere goat FGF5. The cloned FGF5 cDNA was 813 base pairs (KM596772), including an open reading frame encoding a 270-amino-acid polypeptide.

Bioinformatic analysis of phage AB3, a phiKMV-like virus infecting Acinetobacter baumannii

J. Zhang, Liu, X., and Li, X. - J., “Bioinformatic analysis of phage AB3, a phiKMV-like virus infecting Acinetobacter baumannii”, vol. 14, pp. 190-198, 2015.

The phages of Acinetobacter baumannii has drawn increasing attention because of the multi-drug resistance of A. baumanni. The aim of this study was to sequence Acinetobacter baumannii phage AB3 and conduct bioinformatic analysis to lay a foundation for genome remodeling and phage therapy. We isolated and sequenced A. baumannii phage AB3 and attempted to annotate and analyze its genome. The results showed that the genome is a double-stranded DNA with a total length of 31,185 base pairs (bp) and 97 open reading frames greater than 100 bp.

Identification, molecular characterization, and tissue expression of parathyroid hormone-related protein gene (PTHrP) from water buffalo (Bubalus bubalis)

J. Liu, Qian, L. D., Huo, J. L., Bi, B. L., Li, D. L., Wang, S. F., Chen, T., Li, L. J., Mao, H. M., and Miao, Y. W., “Identification, molecular characterization, and tissue expression of parathyroid hormone-related protein gene (PTHrP) from water buffalo (Bubalus bubalis)”, vol. 14, pp. 2290-2301, 2015.

Parathyroid hormone-related protein (PTHrP) is involved in the deposition of milk calcium in mammal lactation, but its role in buffalo is unclear. In this study, the full-length coding sequence of the water buffalo PTHrP gene was first isolated using reverse transcription-polymerase chain reaction. The protein was then subjected to molecular characterization using bioinformatic methods, and the tissue expression pattern was further assayed by semi-quantitative reverse-transcription polymerase chain reaction.

Molecular cloning and characterization, and prokaryotic expression of the GnRH1 gene obtained from Jinghai yellow chicken

T. Zhang, Zhang, G. X., Han, K. P., Tang, Y., Wang, J. Y., Fan, Q. C., Chen, X. S., Wei, Y., and Wang, Y. J., “Molecular cloning and characterization, and prokaryotic expression of the GnRH1 gene obtained from Jinghai yellow chicken”, vol. 14, pp. 2831-2849, 2015.

The gonadotropin-releasing hormone (GnRH) plays an important role in the control of reproductive functions. Recent studies have reported the occurrence of GnRH molecular variants in numerous species. In this study, the GnRH1 gene from Jinghai yellow chicken was cloned by reverse transcriptase-polymerase chain reaction and transformed into BL21 (DE3) competent cells. The GnRH1 gene and amino acid sequences were subjected to bioinformatic analyses.

Identification of conserved microRNAs and their target genes in Nile tilapia (Oreochromis niloticus) by bioinformatic analysis

X. H. Li, Wu, J. S., Tang, L. H., and Hu, D., “Identification of conserved microRNAs and their target genes in Nile tilapia (Oreochromis niloticus) by bioinformatic analysis”, vol. 14, pp. 2785-2792, 2015.

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in posttranscriptional regulation of target genes. miRNAs are involved in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation in various organisms. Their conserved nature in various organisms makes them a good source of new miRNA discovery using comparative genomic approaches.

Molecular cloning and characterization of the pseudorabies virus UL31 gene

M. L. Li, Zhao, Z. Y., Cui, W., Mo, C. C., Wang, J. L., and Cai, M. S., “Molecular cloning and characterization of the pseudorabies virus UL31 gene”, vol. 13, pp. 1832-1847, 2014.

We amplified a 816-bp sequence of the UL31 gene from the pseudorabies virus (PRV) Becker strain genome. Evidence that this was the UL31 gene was confirmed by cloning and sequencing. The PRV UL31 gene encodes a putative protein of 271-amino acid residues, which was designated the UL31 protein. Bioinformatic analysis indicated that PRV UL31 contains a conserved PHA03328 domain, closely related with the herpes virus nuclear egress lamina protein UL31 family and highly conserved among counterparts encoded by herpes UL31 genes.

Molecular characteristics and cloning of two pepper genes AN2 and UPA20

H. X. Chen, Jiang, H., Huo, J. L., Wen, J. F., Zhu, H. S., Ma, C. H., Zhou, H., Lv, J. H., and Deng, M. H., “Molecular characteristics and cloning of two pepper genes AN2 and UPA20”, vol. 13, pp. 2531-2538, 2014.

The complete coding sequences (CDSs) of “Yunnan Purple Pepper No.1” (Capsicum annuum L.) AN2 and UPA20 genes were amplified using the reverse transcriptase polymerase chain reaction on the basis of the conserved sequence information of some Solanaceae plants and known highly homologous pepper expressed sequence tags. The nucleotide sequence analysis of these 2 genes revealed that pepper AN2 gene encoded a protein of 263 amino acids that has high homology with the AN2-like protein of 4 species: tobacco, tomato, potato, and petunia.

Characterization of Riemerella anatipestifer CH-1 gldJ gene and GldJ protein

B. Yuan, Cheng, A. C., and Wang, M. S., “Characterization of Riemerella anatipestifer CH-1 gldJ gene and GldJ protein”, vol. 13, pp. 8329-8341, 2014.

Riemerella anatipestifer (RA) CH-1, a highly virulent field strain, was isolated and identified by our laboratory. The gldJ gene was conserved in RA, and it had a typical TATA promoter region and AU-rich sequence within the 5' untranslated region. The GldJ protein was an outer-membrane lipoprotein with a signal peptide cleavage site between amino acids 20 and 21. GldJ was also a member of proteins involved in gliding motility. The RA GldJ protein had 16 phosphorylation sites and 4 N-glycosylation sites.

Identification and bioinformatic analysis of a putative calcium-dependent protein kinase (CDPK6) from Toxoplasma gondii

N. Z. Zhang, Huang, S. Y., Zhou, D. H., Xu, Y., He, J. J., and Zhu, X. Q., “Identification and bioinformatic analysis of a putative calcium-dependent protein kinase (CDPK6) from Toxoplasma gondii”, vol. 13, pp. 10669-10677, 2014.

Toxoplasma gondii is recognized as an opportunistic human pathogen with a worldwide distribution. Development of effective vaccines is considered the only ideal way to control T. gondii infection. However, only one live vaccine is commercially available for use in sheep and goats. Therefore, the identification of more effective antigenic proteins is very important. In this study, we identified a novel putative calcium-dependent protein kinase of T.

Molecular cloning, sequence characterization, and gene expression profiling of a novel water buffalo (Bubalus bubalis) gene, AGPAT6

S. Song, Huo, J. L., Li, D. L., Yuan, Y. Y., Yuan, F., and Miao, Y. W., “Molecular cloning, sequence characterization, and gene expression profiling of a novel water buffalo (Bubalus bubalis) gene, AGPAT6”, vol. 12, pp. 4116-4126, 2013.

Several 1-acylglycerol-3-phosphate-O-acyltransferases (AGPATs) can acylate lysophosphatidic acid to produce phosphatidic acid. Of the eight AGPAT isoforms, AGPAT6 is a crucial enzyme for glycerolipids and triacylglycerol biosynthesis in some mammalian tissues. We amplified and identified the complete coding sequence (CDS) of the water buffalo AGPAT6 gene by using the reverse transcription-polymerase chain reaction, based on the conversed sequence information of the cattle or expressed sequence tags of other Bovidae species.

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