Predicting beta-turns in proteins using support vector machines with fractional polynomials

Background

β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino acids in protein structures are situated on them. Their prediction is considered to be one of the crucial problems in bioinformatics and molecular biology, which can provide valuable insights and inputs for the fold recognition and drug design.

Results

We propose an approach that combines support vector machines (SVMs) and logistic regression (LR) in a hybrid prediction method, which we call (H-SVM-LR) to predict β-turns in proteins. Fractional polynomials are used for LR modeling. We utilize position specific scoring matrices (PSSMs) and predicted secondary structure (PSS) as features. Our simulation studies show that H-SVM-LR achieves Qtotal of 82.87%, 82.84%, and 82.32% on the BT426, BT547, and BT823 datasets respectively. These values are the highest among other β-turns prediction methods that are based on PSSMs and secondary structure information. H-SVM-LR also achieves favorable performance in predicting β-turns as measured by the Matthew's correlation coefficient (MCC) on these datasets. Furthermore, H-SVM-LR shows good performance when considering shape strings as additional features.

Conclusions

In this paper, we present a comprehensive approach for β-turns prediction. Experiments show that our proposed approach achieves better performance compared to other competing prediction methods.

     

Vancomycin-Eluting Niosomes: A New Approach to the Inhibition of Staphylococcal Biofilm on Abiotic Surfaces

A new vancomycin (VCM)-eluting mixed bilayer niosome formulation was evaluated for the control of staphylococcal colonization and biofilm formation on abiotic surfaces, a niosome application not explored to date. Cosurfactant niosomes were prepared using a Span 60/Tween 40/cholesterol blend (1: 1: 2). Tween 40, a polyethoxylated amphiphile, was included to enhance VCM entrapment and confer niosomal surface properties precluding bacterial adhesion. VCM-eluting niosomes showed good quality attributes including relatively high entrapment efficiency (～50%), association of Tween 40 with vesicles in a constant proportion (～87%), biphasic release profile suitable for inhibiting early bacterial colonization, and long-term stability at 4°C for a 12-month study period. Niosomes significantly enhanced VCM activity against planktonic bacteria of nine staphylococcal strains. Using microtiter plates as abiotic surface, VCM-eluting niosomes proved superior to VCM in inhibiting biofilm formation, eradicating surface-borne biofilms, inhibiting biofilm growth, and interfering with biofilm induction by VCM subminimal inhibitory concentrations. Data suggest dual functionality of cosurfactant VCM-eluting niosomes as passive colonization inhibiting barrier and active antimicrobial-controlled delivery system, two functions recognized in infection control of abiotic surfaces and medical devices.     

Propylene Glycol Liposomes as a Topical Delivery System for Miconazole Nitrate: Comparison with Conventional Liposomes

Propylene glycol (PG)-phospholipid vesicles have been advocated as flexible lipid vesicles for enhanced skin delivery of drugs. To further characterize the performance of these vesicles and to address some relevant pharmaceutical issues, miconazole nitrate(MN)-loaded PG nanoliposomes were prepared and characterized for vesicle size, entrapment efficiency, in vitro release, and vesicle stability. An issue of pharmaceutical importance is the time-dependent, dilution-driven diffusion of propylene glycol out of the vesicles. This was addressed by assessing propylene glycol using gas chromatography in the separated vesicles and monitoring its buildup in the medium after repeated dispersion of separated vesicles in fresh medium. Further, the antifungal activity of liposomal formulations under study was assessed using Candida albicans, and their in vitro skin permeation and retention were studied using human skin. At all instances, blank and drug-loaded conventional liposomes were included for comparison. The results provided evidence of controlled MN delivery, constant percent PG uptake in the vesicles (≈45.5%) in the PG concentration range 2.5 to 10%, improved vesicle stability, and enhanced skin deposition of MN with minimum skin permeation. These are key issues for different formulation and performance aspects of propylene glycol-phospholipid vesicles.     

Entrapment efficiency of pyridoxine hydrochloride in unilamellar liposomes: experimental versus model-generated data

The present study investigates the effect of the preparation method (four methods) and formulation additives (propylene glycol (PG) and cholesterol (CH)) on the entrapment efficiency (EE) of pyridoxine hydrochloride (vitamin B6 (VB6)), representing hydrophilic water-soluble low permeable vitamins, in unilamellar liposomes. The main aim is to compare determined EE with predicted values generated using a web-published, computational model. Results showed that among the different preparation methods, modified film hydration showed significantly higher EE (p?). With regard to formulation additives, PG (5% w/v) produced smaller vesicles size with narrow size distribution. Agreement between determined and model-generated EE values was more evident in formulae with narrow size distribution (polydispersity index (PdI) below 0.23). Formulae containing PG showed slightly higher determined than predicted EE values indicating vitamin–phospholipid bilayer interaction. Meanwhile, agreement between determined and predicted EE was limited to VB6-to-phospholipid ratio below (1.2:2). The comparison provided further insight into the usefulness of the prediction model factors affecting agreement between determined and predicted EE data.     

Ecological status of the Mediterranean Juniperus phoenicea L. Relicts in the desert mountains of North Sinai,Egypt

Juniperus phoenicea L. is listed as threatened tree by IUCN Red List. In Egypt, J. phoenicea L. is the only conifer tree that is restricted to the three mountains of northern Sinai: Gabal El-Halal, Gabal El-Maghara and Gabal Yelleq. As a Mediterranean relict it has been included in a national list as target for conservation and management. To provide baseline information for the development of a conservation strategy, the present study aims at comparing the isolated populations of J. phoenicea and their associated plant composition and diversity at the three mountains. The application of TWINSPAN and DCA analysis techniques has resulted in identifying of four vegetation types associated with juniper, and each could be related to a specific geomorphologic habitat on a topographic gradient. Chiliadenus montanus and Zygophyllum dumosum characterized the slopes of smooth-faced rock outcrops in Wadi Abu Seyal (at 350–470 m altitude of Gabal El-Halal), Deverra tortuosa, Ephedra aphylla and Gymnocarpos decander inhabited together with the target species the soil pockets of north-facing slope in Neqeb Abu Hamam (at 600–700 m altitude of Gabal El-Halal), Stachys aegyptiaca and Moricandia nitens characterized the juniper occurrences in the runnels of Wadi Arar (at 450–560 m altitude of Gabal El-Maghara), and Artemisia herba-alba, Atriplex halimus and Reaumuria hirtella represent the stands on slope runnels (at 900–960 m) of Gabal Yelleq. The two vegetation types recognized at Gabal El-Halal had, on average, the highest species diversity, juniper density and cover. Juniper shows generally poor conditions of vitality at higher elevation (600–960 m) with a higher proportions of old and recent dead trees, and with the predominance of male individuals, as compared with the populations of Gabal El-Maghara and Gabal Yelleq. In contrast, the juniper populations at lower elevation (350–470 m) of Gabal El-Halal proved to be in best condition with mostly living foliage and reproductive branches. The differences in rock types and elevation among the three mountains reflect serious limitation on recruitment of J. phoenicea due to moisture availability. The results of this study showed that J. phoenicea is an endangered species and its conservation in northern Sinai mountains is a priority. For a successful conservation of this community it is highly recommended to preserve in particular the suitable habitats at Gabal El-Halal, but also the other stands merit conservation measures.     

Persistence and competitiveness of threeBradyrhizobium japonicum inoculant strains in clay loam Nile valley soil

The nitrogen contribution from the shoot and root system of symbiotically grown leucaena was evaluated in a field experiment on an Alfisol at IITA in Southern Nigeria. Maize in plots that received prunings from inoculated leucaena contained more N and grain yield was increased by 1.9 t.ha.^–1. Large quantities of nitrogen were harvested with leucaena prunings (300 kg N ha^–1 in six months) but the efficiency of utilization of this nitrogen by maize was low compared to inorganic N fertilizer (ammonium sulphate) at 80 kg N ha^–1. Maize yield data indicated that nitrogen in leucaena prunigs was 34 and 45% as efficient as 80 kg N ha^–1 of (NH₄)₂SO₄ for uninoculated and inoculated plants with Rhizobium IRc 1045, respectively. In plots where the prunings were removed, the leaf litter and decaying roots and nodules contributed N equivalent of 32 kg ha^–1. Twenty-five kg ha^–1 was the inorganic N equivalent from nitrogen fixed symbiotically by leucaena when inoculated with Rhizobium strain IRc 1045. Application of prunings from inoculated leucaena resulted in higher soil ogranic C, total N, pH and available NO₃.     

Development of some lepidopterous cotton pests as affected by exposure to sublethal levels of endotoxins of Bacillus thuringiensis for different periods

Three spore-δ-endotoxin preparations from Bacillus thuringiensis vars. kurstaki and entomocidus including a commercial biological insecticide, Thuricide, were studied with respect to their biological interactions with the lepidopterous cotton pests, Spodoptera littoralis, Spodoptera exigua, and Heliothis armigera. The biological effects of sublethal doses and the length of exposure time to low endotoxin concentrations were assessed during and after removal of toxin from the diet. Retardation in larval development, reduction in egg production of the moths, and fertility of the egg were observed together with significant reduction in pupal weight and appearance of deformities in both pupae and moth populations. The influence of exposure to sublethal toxin concentrations was also manifested in term of decreasing the adult emergence, fecundity reduction, and prolonging the generation period. In the exposed insects, the precentage of larvae that survived and succeeded to pupate increased with the decrease in the toxin concentration and with the decrease in exposure time. The reduction of the pupal weight significantly increased with the increase in either toxin concentration or the duration of exposure. The longevity of the moths was not affected by larval treatment and the data showed no clear correlation with the concentration and time of larval exposure to the toxin.     

Assessment of faba bean (Vicia faba) response to inoculation with Rhizobium leguminosarum in clay loam Nile Delta soil

A field experiment was conducted to assess the response to inoculation with rhizobia in a clay loam soil of the Nile Delta using faba bean (Vicia faba) for two successive winter seasons (1985/6 and 1986/7). Three selected strains of Rhizobium leguminosarum, TAL 634, NRC 65 and TAL 1400, were used singly or in combination as peat-based inocula in 1985/6 winter season. Strain TAL 1400 was replaced by strain F9 in the 1986/7 winter season. A significant seed yield response was obtained only with strain TAL 1400, in the 1985/6 season. In the 1986/7 season, no significant yield response was observed with any of the strains. The serotyping of nodules collected in the 1985/6 season showed that strain TAL 1400 was more competitive than either the indigenous rhizobia or the two inoculant strains. However, the majority of nodules formed in the 1986/7 season were formed from strains other than the inoculant ones.     

Biotransformation of glabratephrin, a rare type of isoprenylated flavonoids, by Aspergillus niger

Microbial transformation of glabratephrin, the major isolated compound from Tephrosia purpurea, afforded pseudosemiglabrin. The formation of the transformed compound seems to be performed via ring opening-closure of a five-membered ring causing transformation from a spiro into a fused system. The structure of the transformed compound was determined by comprehensive NMR studies, including DEPT, COSY, HMQC, NOE and MS.