TMpro web server and web service: transmembrane helix prediction through amino acid property analysis

TMpro is a transmembrane (TM) helix prediction algorithm that uses language processing methodology for TM segment identification. It is primarily based on the analysis of statistical distributions of properties of amino acids in transmembrane segments. This article describes the availability of TMpro on the internet via a web interface. The key features of the interface are: (i) output is generated in multiple formats including a user-interactive graphical chart which allows comparison of TMpro predicted segment locations with other labeled segments input by the user, such as predictions from other methods. (ii) Up to 5000 sequences can be submitted at a time for prediction. (iii) TMpro is available as a web server and is published as a web service so that the method can be accessed by users as well as other services depending on the need for data integration. Availability: http://linzer.blm.cs.cmu.edu/tmpro/ (web server and help), http://blm.sis.pitt.edu:8080/axis/services/TMProFetcherService (web service).     

Building blocks for plant gene assembly

The MultiSite Gateway cloning system, based on site-specific recombination, enables the assembly of multiple DNA fragments in predefined order, orientation, and frame register. To streamline the construction of recombinant genes for functional analysis in plants, we have built a collection of 36 reference Gateway entry clones carrying promoters, terminators, and reporter genes, as well as elements of the LhG4/LhGR two-component system. This collection obeys simple engineering rules. The genetic elements (parts) are designed in a standard format. They are interchangeable, fully documented, and can be combined at will according to the desired output. We also took advantage of the MultiSite Gateway recombination sites to create vectors in which two or three genes can be cloned simultaneously in separate expression cassettes. To illustrate the flexibility of these core resources for the construction of a wide variety of plant transformation vectors, we generated various transgenes encoding fluorescent proteins and tested their activity in plant cells. The structure and sequence of all described plasmids are accessible online at http://www.psb.ugent.be/gateway/. All accessions can be requested via the same Web site.     

Improved effects of polyethylene glycol on the growth,antioxidative enzymes activity and taxanes production in a Taxus baccata L. callus culture

Plant Cell, Tissue and Organ Culture (PCTOC) - Application of abiotic stress-inducing elicitors is one of the effective strategies in order to increase the production of secondary metabolites in...     

In vitro cytotoxicity and DNA/HSA interaction study of triamterene using molecular modelling and multi-spectroscopic methods

The anticancer activity of triamterene on HCT116 and CT26 colon cancer cells lines was investigated. Furthermore, the mechanism of interaction between triamterene and calf thymus DNA (ct-DNA) and also human serum albumin (HSA) was conducted using spectroscopic and molecular docking techniques. In vitro cytotoxicity of triamterene against HCT116 and CT26 cells showed promising anticancer effects with IC50 values of 31.30 and 24.45 μM, respectively. Competitive studies of the triamterene with NR (neutral red) and MB (methylene blue) as intercalator probes showed that triamterene can be replaced by these probes. The viscosity data also confirmed that triamterene binds to calf–thymus DNA through intercalation binding mode. Binding properties of triamterene with HSA in the presence of warfarin and ibuprofen showed that triamterene competes with warfarin for the site I of human serum albumin (HSA). In addition, the binding modes of triamterene with DNA and HSA were verified by molecular docking technique. Abbreviations ct-DNA calf thymus DNA

CV cyclic voltammetry

DNA deoxyribonucleic acid

DPV differential pulse voltammetry

FBS fetal bovine serum

HSA human serum albumin

NR neutral red

MB methylene blue

MTT 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazoliumbromide

Communicated by Ramaswamy H. Sarma     

The role of miRNA-377 as a tumor suppressor in lung cancer by negative regulation of genes belonging to ErbB signaling pathway

Molecular Biology Reports - The ErbB signaling pathway plays important role in the pathogenesis of lung cancer. We explored the role of miRNA-377 as a tumor suppressor in NSCLC through silencing of...     

Fatty acid composition,antioxidant and antibacterial properties of the microwave aqueous extract of three varieties of Labisia pumila Benth

Background

The present study was conducted in order to evaluate the fatty acid profile, anti-oxidant and anti-bacterial activities from the microwave aqueous extract of the leaves of three different varieties of Labisia pumila Benth.

Results

The chemical analysis of the extract showed that fatty acids (palmitic, palmitoleic, stearic, oleic, linoleic and α-linolenic) acid as the main components in three varieties of L. pumila leaves. Furthermore, the obtained results of the anti-oxidant revealed that L. pumila var. alata contained higher anti-oxidative activities compared to var. pumila and var. lanceolata. However, these values were lower than the tested anti-oxidant standards. On the other hand, the aqueous leaf extracts in all three varieties of L. pumila were also found to inhibit a variable degree of antibacterial activities against eight bacteria (four Gram-positive and four Gram-negative bacteria).

Conclusions

In this study, it was observed the leaves of three varieties of L. pumila exhibited variable patterns of fatty acids and the microwave aqueous extraction possess anti-oxidant and anti-bacterial activities.     

Flow injection analysis of riboflavin with chemiluminescence detection using a N-halo compounds-luminol system.

A chemiluminescent method for the determination of riboflavin is described. The method is based on the chemiluminescence (CL) generated during the oxidation of luminol by N-bromosuccinimide (NBS) and N-chlorosuccinimide (NCS) in alkaline medium. It was found that riboflavin could greatly enhance this CL intensity when present in the luminol solution. Based on this observation, a new flow-injection CL method for the determination of riboflavin is proposed in this paper. The detection limits were 7.5 ng/mL and 3.5 ng/mL of riboflavin for the NBS- and NCS-luminol CL systems, respectively. The relative CL intensity was linear, with riboflavin concentration in the range 19-600 ng/mL and 600-2000 ng/mL for the NBS-luminol CL system, and 12-200 ng/mL and 200-2000 ng/mL for the NCS-luminol CL system. The results obtained for the assay of pharmaceutical preparations compared well with those obtained by the official method and demonstrated good accuracy and precision.     

Unfolding of an alpha-helix in water.

We describe a 1 ns molecular dynamics simulation of an 18-residue peptide (corresponding to a portion of the H helix of myoglobin) in water. The initial helical conformation progressively frays to a more disordered structure, with the loss of internal secondary structure generally proceeding from the C-terminus toward the N-terminus. Although a variety of mechanisms are involved in the breaking of helical hydrogen bonds, the formation of transient turn structures, with i----i + 3 hydrogen bonds, and bifurcated hydrogen-bond structures intermediate between alpha and turn or 3(10) structures is a common motif. In some cases a single water molecule is inserted into an internal hydrogen bond, but it is also common to have several water molecules involved in transient intermediates. Overall, the results provide new information about the detailed mechanisms by which helices are made and broken in aqueous solution.     

Desoxyamarogentin ein neuer bitterstoff aus Gentiana pannonica, Scop.

From the roots of Gentiana pannonica, Scop. a new strongly bitter secoiridoid acyl glucoside (amaropanin) was isolated and identified as desoxy amarogentin (sweroside-2′,3″,3?-dihydroxydiphenyl-2-carboxyl acid ester). Amaropanin is chromatographically detectable also in the root of G. purpurea L. and G. punctata L.