Comparative interactions of withanolides and sterols with two members of sterol glycosyltransferases from Withania somnifera

Background

Sterol glycosyltransferases (SGTs) are ubiquitous but one of the most diverse group of enzymes of glycosyltransferases family. Members of this family modulate physical and chemical properties of secondary plant products important for various physiological processes. The role of SGTs has been demonstrated in the biosynthesis of pharmaceutically important molecules of medicinal plants like Withania somnifera.

Results

Analysis suggested conserved behaviour and high similarity in active sites of WsSGTs with other plant GTs. Substrate specificity of WsSGTs were analysed through docking performance of WsSGTs with different substrates (sterols and withanolides). Best docking results of WsSGTL1 in the form of stable enzyme-substrate complex having lowest binding energies were obtained with brassicasterol, transandrosteron and WsSGTL4 with solasodine, stigmasterol and 24-methylene cholesterol.

Conclusion

This study reveals topological characters and conserved nature of two SGTs from W. somnifera (WsSGTs) i.e. WsSGTL1 and WsSGTL4. However, besides being ubiquitous in nature and with broad substrate specificity, difference between WsSGTL1 and WsSGTL4 is briefly described by difference in stability (binding energy) of enzyme-substrate complexes through comparative docking.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0563-7) contains supplementary material, which is available to authorized users.     

Lignans of Piper clusii

From the petrol extract of Piper clusii five lignans were isolated. One of the lignans (?)-clusin is assigned the structure (?)-2-furanol-4(1,3-benzodioxol-5-ylmethyl) tetrahydro-3(3,4,5-trimethoxyphenyl) methyl. This is the first report of this compound from a natural source. Asaronaldehyde and sitosterol were also present.     

Effects of cover soil stockpiling on plant community development following reclamation of oil sands sites in Alberta

Stockpiling of cover soil can influence vegetation development following reclamation. Cover soil, comprising the upper 15–30 cm of the surface material on sites scheduled for mining, is commonly salvaged prior to mining and used directly or stockpiled for various lengths of time until it is needed. Salvaging and stockpiling causes physical, chemical, and biological changes in cover soils. In particular, stockpiling reduces the availability and vigor of vegetative propagules and seed, and can lead to increases in the abundance of some weedy species. This study uses data from monitoring plots to assess how stockpiling of cover soil impacts plant community development on reclaimed oil sands mine sites in northern Alberta. Development of plant communities differed distinctly between directly placed and stockpiled cover soil treatments even 18 years after reclamation. Direct placement of cover soil resulted in higher percent cover, species richness, and diversity. Nonmetric multidimensional scaling and multiresponse permutation procedure revealed compositional differentiation between the treatments. Indicator species analysis showed that direct placement treatment was dominated by perennial species while grasses and annual forb species dominated sites where stockpiled soil was used. Results indicate that stockpiling leads to slower vegetation recovery while direct placement of cover soil supports more rapid succession (from ruderal and annual communities to perennial communities). In addition, direct placement may be less costly than stockpiling. However, scheduling of salvage and placement remains a challenge.     

Isolation and Symbiotic Characteristics of Two Tn5-Derived Phage-Resistant <Emphasis Type="Italic">Bradyrhizobium japonicum</Emphasis> Strains that Nodulate Soybean

Using transponson Tn5 mutagenesis, two transconjugants of Bradyrhizobium japonicum with the properties of both phage resistance and ability to induce nodulation were isolated at the frequency of 0.02%. These transconjugants were tested for their symbiotic performance on soybean cv. JS335 under greenhouse and field conditions. Both phage-resistant mutants induced nodules (nod (+)), but the transconjugant B. japonicum E13 was ineffective in nitrogen fixation (fix (-)). Rhizobiophage presence in the inoculum of phage-resistant mutants did not influence the symbiotic effectiveness. The mixture of wild strain and phage in the inoculum caused reduced symbiotic performance under controlled conditions, while under a field environment phage (100 and 500 mul of approximately 10(8) particles ml(-1)) presence did not have any recognizable effect on increased nodule dry weight, nitrogenase activity, or foliar N(2) content. On the basis of restriction fragment length polymorphism analysis, phage-sensitive, less effective, homologous bradyrhizobia belonging to B. japonicum were detected in root nodules of both inoculated and uninoculated plants. Inoculation of a higher concentration of phage in the inoculum significantly reduced the symbiotic performance, while the lower concentration of phage did not show any effect on phage-susceptible, less effective, homologous bradyrhizobia or, thus, symbiotic efficiency under field conditions. The phage-resistant mutant B. japonicum A49 showed effective symbiosis as efficient as that of the wild strain. Inoculation of phage-resistant mutants with lytic phage may reduce the occupancy of phage-susceptible, ineffective/less effective/mediocre homologous bradyrhizobia strains under natural complex soil conditions.     

Computational modeling of novel inhibitory peptides targeting proteoglycan like region of carbonic anhydrase IX and in vitro validation in HeLa cells

Abstract

Carbonic anhydrase IX (CAIX) is a tumour-associated, hypoxia-induced, membrane-bound metallo-enzyme which catalyzes the reversible hydration of carbon dioxide (CO₂) to bicarbonate (HCO₃^?) and proton (H⁺) ions. Over expression of CAIX is observed in cancers of colon, lung, kidney, breast, etc. CAIX plays a vital role in maintaining favourable intracellular pH for tumour cell growth and extracellular acidification which in-turn leads to drug resistance and spread of factors influencing tumour invasion. The N-terminal proteoglycan (PG) – like fragment of CAIX is unique to this isoform and is considered as potential druggable hotspot. Recently, M75 monoclonal antibody targeting the LPGEEDLPG epitope of PG like region has been proposed to reduce cellular adhesion in cancer cells. LPGEEDLPG fragment in complex with M75 has been crystallized and it serves as a strong base for development of peptide inhibitors based on interacting interfaces. Thus, in this study, an in-depth analysis of intermolecular interactions in LPGEEDLPG-M75 complex was carried out by implementing extensive molecular dynamics simulations, binding free energy calculations so as to infer the major determinant fragments of M75 that can be used as peptide inhibitors targeting PG region. Based on these analyses, 3 peptides (Pep1, Pep2 and Pep3) were synthesized and validated by in vitro assays involving cytotoxicity assessment, CAIX inhibition analysis through Direct and Indirect functional assays, and inhibition of Cell adhesion in HeLa cells. The results reveal Pep1 to be a promising inhibitor as it could efficiently modulate CAIX mediated pH homeostasis and cell adhesion in cancer cells.

Communicated by Ramaswamy H. Sarma     

Polymerase chain reaction optimization for amplification of Guanine-Cytosine rich templates using buccal cell DNA

CONTEXT:

Amplification of Guanine-Cytosine (GC) -rich sequences becomes important in screening and diagnosis of certain genetic diseases such as diseases arising due to expansion of GC-rich trinucleotide repeat regions. However, GC-rich sequences in the genome are refractory to standard polymerase chain reaction (PCR) amplification and require a special reaction conditions and/or modified PCR cycle parameters.

AIM:

Optimize a cost effective PCR assay to amplify the GC-rich DNA templates.

SETTINGS AND DESIGN:

Fragile X mental retardation gene (FMR 1) is an ideal candidate for PCR optimization as its GC content is more than 80%. Primers designed to amplify the GC rich 5’ untranslated region of the FMR 1 gene, was selected for the optimization of amplification using DNA extracted from buccal mucosal cells.

MATERIALS AND METHODS:

A simple and rapid protocol was used to extract DNA from buccal cells. PCR optimization was carried out using three methods, (a) substituting a substrate analog 7-deaza-dGTP to dGTP (b) in the presence of a single PCR additive and (c) using a combination of PCR additives. All PCR amplifications were carried out using a low-cost thermostable polymerase.

RESULTS:

Optimum PCR conditions were achieved when a combination of 1M betaine and 5% dimethyl sulfoxide (DMSO) was used.

CONCLUSIONS:

It was possible to amplify the GC rich region of FMR 1 gene with reproducibility in the presence of betaine and DMSO as additives without the use of commercially available kits for DNA extraction and the expensive thermostable polymerases.     

Effect of thyroxine on the hepatic glycogen and glucose-6-phosphatase activity of developing rats

The influence of exogenous thyroxine was studied on the hepatic glycogen content and glucose-6-phosphatase activity of rats of different age groups. The glycogen content and glucose-6-phosphatase activity were found to be decreased in the livers of 5, 15, 30 and 60-day-old rats after thyroxine treatment. In normal rats of 5, 15, 30 and 60-day-old, a gradual rise in both the hepatic glycogen content and glucose-6-phosphatase activity was noted as the age advanced from immature to adult.