Application of bioinformatics in the prediction and identifi cation of potential antimicrobial peptides from Curcuma longa

Abstract

Irrigation water has become less available in many regions due to global climate change and an increased competition for water by industry, domestic purposes, and the environment. To confront this challenge, there is an urgent need to develop water-saving irrigation strategies and techniques in order to maximize crop water use effi ciency (WUE). In the other hand over-fertilization of mobile nutrients like nitrogen (N) may lead to leaching beyond root zone under plentiful irrigation, while it may decrease yield under limited irrigation. Thus, fertilizer N needs to be optimized in relation to water availability. In order to determine optimum levels of water and nitrogen of potato, a fi eld experiment was carried out by central composite design (CCD) as Response surface methodology (RSM) as a most popular optimization method, in Dehgolan plain in Kurdistan province, west of Iran, spring season of 2014. The treatments were designed based on low and high levels of water supply (50% and 100% of crop water requirement) and applied nitrogen (250 and 350 kg N ha −1 ) as independent variables. In this study, tuber yield (Y) and WUE were measured as response variables. Optimum levels of N fertilizer and irrigation depth were determined based on three scenarios: availability and nonavailability of water for irrigation. Furthermore, for environmental consideration, effects of minimum rate application of N on surface responses were evaluated also.. The results showed a marked interaction between level of irrigation and nitrogen on potato Y and WUE. The results also revealed that increasing irrigation and fertilizer led to an increase in tuber yield. WUE was decreased with increasing in water supply but N increasing had positive effect on WUE in a certain irrigation depth. Maximum Y was 69200 kg ha ). Based on response surfaces of Y and WUE, the amounts of 552 mm and 349.5 kg N ha −1 was found to be the optimum levels of water and nitrogen for unlimited water conditions. WUE value in this situation was 130 kg ha −1 mm −1. For scarce water condition such as arid and semiarid regions, optimum values of irrigation water and N based on response surfaces were simulated 287 mm and 350 kg N ha −1 , respectively. If the goal of optimization is maximizing Y and WUE simultaneously, then applied water and nitrogen was estimated about 461 mm and 350 kg N ha −1 and corresponding Y and WUE were achieved 62742 kg ha −1 and 143 kg ha −1 mm −1 respectively. For minimizing N application, optimum levels of resources were found 502 mm irrigation and 250 kg N ha-1. In this scenario 50242 kg ha −1 for Y and 105 kg ha −1 mm −1 for WUE were obtained. Comparison of results showed that WUE maximizing strategy resulted in 48% saving in water supply. Simultaneous maximizing of Y and WUE reduced applied irrigation water by 17% and consequently tuber yield reduction rate was 9%. Potato yield reduction in minimum use of N was 27% while irrigation water applied decreased by 9%.

PL‐101‐WK, a novel tryptophan‐ and lysine‐rich peptide with antimicrobial activity against Staphylococcus aureus

“…Regardless of the peptide length, the accuracy of the prediction of these algorithms is between 87% and 93%, and an AMP sequence has a score within 0.5-1.0. [20,38] Since the Lys-substituted sequence had better AMP probability scores than the Arg-substituted one, PL-101-WK was selected for experimental assays. The BLAST searching of the CAMP R3 database displayed that sequence with GI number 914817640 was the most similar one to PL-101-WK with 88% similarity and 63% identity.…”

A Safe and Multitasking Antimicrobial Decapeptide: The Road from De Novo Design to Structural and Functional Characterization

“…Firstly, the removal of two residues and the subsequence single point substitutions were planned in the N-terminal region of 1018-K6 sequence, as it was reported that the substitution of any residues at the positions Val7-Arg12 in the parent peptide (NH2-VRLIVKVRIWRR-CONH2) substantially reduced the antimicrobial activity and were mostly not favorable [21,22]. To this aim, the following criteria were adopted: (i) deletion of a Val residue, as the analysis of amino acid frequency in the AMPs available at CAMP database revealed that this amino acid was less often encountered [23]; (ii) deletion of a further neutral amino acid between Iso or Leu to conserve unaltered the net positive charge, since it is essential for the interactions with the negatively charged membranes of bacteria; (iii) replacement of one neutral amino acid with Trp residue to enhance the total Trp ratio and the hydropathicity, which are key physicochemical parameters influencing the ability of several AMPs to adopt an amphipathic conformation upon binding to the bacterial membrane [24,25]; (iv) conservation of at least an Arg residue, as it has been observed that this amino acid strongly improves the antibacterial activity, due to its enhanced membrane permeability with respect to Lys [26].…”