Antimicrobial peptides (AMPs) are a valuable source of antimicrobial agents and a potential solution to the multi-drug resistance problem. In particular, short-length AMPs have been shown to have enhanced antimicrobial activities, higher stability, and lower toxicity to human cells. We present a shortlength (%30 aa) AMP prediction method, Deep-AmPEP30, developed based on an optimal feature set of PseKRAAC reduced amino acids composition and convolutional neural network. On a balanced benchmark dataset of 188 samples, Deep-AmPEP30 yields an improved performance of 77% in accuracy, 85% in the area under the receiver operating characteristic curve (AUC-ROC), and 85% in area under the precisionrecall curve (AUC-PR) over existing machine learning-based methods. To demonstrate its power, we screened the genome sequence of Candida glabrata-a gut commensal fungus expected to interact with and/or inhibit other microbes in the gut-for potential AMPs and identified a peptide of 20 aa (P3, FWELWKFLKSLWSIFPRRRP) with strong anti-bacteria activity against Bacillus subtilis and Vibrio parahaemolyticus. The potency of the peptide is remarkably comparable to that of ampicillin. Therefore, Deep-AmPEP30 is a promising prediction tool to identify short-length AMPs from genomic sequences for drug discovery. Our method is available at https://cbbio.cis.um.edu.mo/AxPEP for both individual sequence prediction and genome screening for AMPs.
Cao Q.-H., Tang J., Li A., Gruneberg W., Huamani K., Ma D. (2014): Ploidy level and molecular phylogenic relationship among novel Ipomoea interspecific hybrids. Czech J. Genet. Plant Breed., 50: 32-38.Interspecific hybridization can be used to broaden the genetic base, generate novel species, postulate genetic relationships, and to introgress elite alien genes. However, interspecific hybridizations using wild parents outside the Ipomoea section Batatas are very difficult and have not been much studied. We used an improved hybridization technology to generate three novel interspecific hybrids by crossing Ipomoea batatas (L.) Lam. × I. hederacea Jacq., I. batatas (L.) Lam. × I. muricata (L.) Jacq., and I. batatas (L.) Lam. × I. lonchophylla J.M. Black. The ploidy level of the interspecific hybrids was determined by flow cytometry. The cross, I. batatas × I. hederacea, yielded the first artificial pentaploid Ipomoea hybrid ever. The other two hybrids, I. batatas × I. hederacea and I. batatas × I. muricata were tetraploid. The first two hybrids showed normal storage roots, a significant improvement in the storage roots of currently existing interspecific Ipomoea hybrids. AFLP (Amplified Fragment Length Polymorphism) molecular markers were used to explore the genetic relationship of these three novel interspecific hybrids with three other natural diploid, tetraploid, and hexaploid species of the Ipomoea section Batatas. Cluster analysis of AFLP bands showed that these three new interspecific hybrids were closely related to cultivated sweet potato (I. batatas/L./Lam.), which indicated that these novel hybrids can be used as an interspecific bridge to transfer alien genes from wild to cultivated species.
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