Analysis of superfamily specific profile-profile recognition accuracy

Background  

Annotation of sequences that share little similarity to sequences of known function remains a major obstacle in genome annotation. Some of the best methods of detecting remote relationships between protein sequences are based on matching sequence profiles. We analyse the superfamily specific performance of sequence profile-profile matching. Our benchmark consists of a set of 16 protein superfamilies that are highly diverse at the sequence level. We relate the performance to the number of sequences in the profiles, the profile diversity and the extent of structural conservation in the superfamily.     

Water Balance in Cucumis Plants, Measured by Nuclear Magnetic Resonance, I

In this paper we demonstrate the study of plant water balanceby the non-invasive measurement of tissue water content andwater flow using proton nuclear magnetic resonance (NMR). Sapvelocity and flux were measured independently in the presenceof an excess of stationary tissue water. The instrumentationdescribed allows automated and unattended measurement of flow-and water content-variables in a well-defined region of theplant over periods of several days, with a time resolution betweensuccessive measurements of c. 5 s. Using this apparatus theeffect of changes in light intensity (day/night rhythm) andrelative humidity on stem tissue water content as well as onthe velocity and flux of xylem sap in the stem were investigatedin a cucumber plant. The results are in agreement with predictionsfrom a simple model for plant water balance, which is basedon water potential, flow rate and resistance to flow. As longas only transpiration is varied, flow rate and water content(or potential) are affected in opposite ways as demonstratedin this paper. In contrast, the model predicts that changesin uptake (resulting from changes in, for example, root resistance)will induce changes in water content and flow in the same direction.An experimental verification of this prediction is given ina subsequent paper, where, in addition, the NMR results arecompared to those obtained with a dendrometer. Key words: Water balance model, Cucumis sativus L., flow, water content, NMR, water balance measurement     

<Emphasis Type="Italic">TRAF1/C5</Emphasis>polymorphism is not associated with increased mortality in rheumatoid arthritis: two large longitudinal studies

Introduction  

Recently an association between a genetic variation in TRAF1/C5 and mortality from sepsis or cancer was found in rheumatoid arthritis (RA). The most prevalent cause of death, cardiovascular disease, may have been missed in that study, since patients were enrolled at an advanced disease stage. Therefore, we used an inception cohort of RA patients to investigate the association between TRAF1/C5 and cardiovascular mortality, and replicate the findings on all-cause mortality. As TRAF1/C5 associated mortality may not be restricted to RA, we also studied a large cohort of non-RA patients.     

Spider diagram with greenness evaluation metrics for assessing the new synchronous spectrofluorimetric determination of bicalutamide and resveratrol in human plasma

A simple, selective, and eco-friendly synchronous fluorescence approach was introduced for the first time for the concurrent estimation of the anticancer combination therapy of bicalutamide and resveratrol. The method relies on measuring the synchronous fluorescence spectra of bicalutamide and resveratrol at 269 and 320 nm, respectively, using Δλ of 60 nm with ethanol as a green diluting solvent. The procedure was optimized, and the method was then fully validated. Excellent linearity (R² > 0.999) with very low detection limits (0.044 and 2.001 ng/ml) were obtained for both drugs, allowing for their analysis in human plasma. The green profile of the suggested approach was evaluated using the green solvents selecting tool (GSST), spider diagram for greenness index assessment, green analytical process index (GAPI), and Analytical GREEnness (AGREE) metric tools. These assessment metrics confirmed that the developed approach met the maximum number of green requirements, recommending its application as a green substitute for the regular analysis of the concerned drugs in human plasma. The simplicity of sample measurement enables and substantially accelerates the analysis, resulting in lower costs, enhanced procedure accuracy, and lower environmental effect.     

Reproductive ecology of Rhododendron ponticum (Ericaceae) in relict Mediterranean populations

In the southern Iberian Peninsula, Rhododendron ponticum occurs in restricted and vulnerable populations as a Tertiary relict. Population structure and the main phases of the reproductive process were examined in order to shed light on recruitment patterns and limitations. Rhododendron ponticum flowers are self-compatible and attract a diverse array of insects, which are responsible for a considerable number of seeds set in the populations. Nevertheless, only adults form populations, whilst seedlings are scarce and saplings virtually absent (only two juveniles out of 2489 adults sampled). Non-specialized vegetative multiplication by layering was observed. Recruitment failure seems to depend on the scarcity of safe microsites, which are free from drought, for seedling establishment. The observations contrast with R. ponticum 's reputation as an aggressive invader in temperate Atlantic areas. It is proposed that the species shows a variable balance between sexual reproduction and vegetative multiplication depending on environmental conditions. At present, only the latter seems to be prevailing in relict populations in the Iberian Peninsula. This flexible reproductive strategy is also discussed as a mechanism allowing persistence during geological climatic oscillations.  © The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 297–311.     

In vitro antifungal activity of lactic acid bacteria low molecular peptides against spoilage fungi of bakery products

Bio-preservation, a promising preservation method that involves the use of “friendly” microorganisms such as lactic acid bacteria, has recently become a topic of considerable interest. In the present study, 16 lactic acid bacteria isolates were evaluated for antifungal activity against six fungi commonly associated with bread spoilage. The antifungal compounds were heat stable at 121 °C, and only four isolates, DU15, IT10, TE10, and IS10, showed partial loss of activity when supernatants were treated with proteolytic enzymes. The four isolates showed high inhibition activity at pH 3 and were identified using 16S rDNA sequencing as belonging to Leuconostoc mesenteroides DU15, Lactobacillus plantarum TE10, Lactobacillus plantarum IT10, and Lactobacillus plantarum IS10. The minimum germination inhibitions were 30 mg, 50 mg, 40 mg, and 50 mg for TE10, IT10, DU15, and IS10 respectively. The optimum conditions for the strains to produce antifungal compounds were 37 °C for 48 h for IT10, IS10, and TE10, and 30 °C for 24 h for DU15. Antifungal activity was increased threefold when supernatants were filtered using 10 KDa membranes. These findings demonstrate the potential of using lactic acid bacteria antifungal peptides as natural preservatives in bakery products to control the growth of spoilage fungi.     

Surface modification of lipid nanoparticles for gene therapy

Gene therapies have the potential to target and effectively treat a variety of diseases including cancer as well as genetic, neurological, and autoimmune disorders. Although we have made significant advances in identifying non-viral strategies to deliver genetic cargo, certain limitations remain. In general, gene delivery is challenging for several reasons including the instabilities of nucleic acids to enzymatic and chemical degradation and the presence of restrictive biological barriers such as cell, endosomal and nuclear membranes. The emergence of lipid nanoparticles (LNPs) helped overcome many of these challenges. Despite its success, further optimization is required for LNPs to yield efficient gene delivery to extrahepatic tissues, as LNPs favor accumulation in the liver after systemic administration. In this mini-review, we provide an overview of current preclinical approaches in that LNP surface modification was leveraged for cell and tissue targeting by conjugating aptamers, antibodies, and peptides among others. In addition to their cell uptake and efficiency-enhancing effects, we outline the (dis-)advantages of the different targeting moieties and commonly used conjugation strategies.     

Nematicidal activity of silver nanoparticles of botanical products against root-knot nematode,Meloidogyne incognita

Current study investigated the nematicidal activity of leaf extracts of Conyza dioscoridis, Melia azedarach, and Moringa oleifera that were prepared as silver nanoparticles (Ag-NP). The characterisation and size confirmation of the Ag-NP were done by UV–vis spectrophotometry and the scanning electron microscopy (SEM). The phytochemical contents of crude extracts and the nano formulations were analysed using gas chromatography-mass spectroscopy (GC-MS). Results revealed that silver nanoparticles of C. dioscoridis extractives had great nematicidal activity against the 2^nd stage juvenile (J2) and eggs of Meloidogyne incognita. Also, the Ag-NP showed similar nematicidal effect to the reference nematicide; rugby. The GC-MS analysis revealed the increase of certain metabolites due to the formulation of the Ag-NPs. Aromadendrene, 1-hydroxy-1,7-dimethyl-4-isopropyl-2,7-cyclodecdiene, 6-epi-shyobunol, 4-hexylacetophenone, β-isocomene, caryophyllene, β- and α-selinene, α-cadinol, berkheyaradulen, and bis-(2-ethylhexyl)phthalate were increased more than 2.5-folds in the Ag-NP compared the extract. Therefore, the green synthesis of metal nanoparticles might be a safe, effective and affordable nematicide alternatives.