Recovering circulating extracellular or cell-free RNA from bodily fluids

The presence of extracellular circulating or cell-free RNA in biological fluids is becoming a promising diagnostic tool for non invasive and cost effective cancer detection. Extracellular RNA or miRNA as biological marker could be used either for the early detection and diagnosis of the disease or as a marker of recurrence patterns and surveillance. In this review article, we refer to the origin of the circulating extracellular RNA, we summarise the data on the biological fluids (serum/plasma, saliva, urine, cerebrospinal fluid and bronchial lavage fluid) of patients suffering from various types of malignancies reported to contain a substantial amount of circulating extracellular (or cell-free) RNAs and we discuss the appropriate reagents and methodologies needed to be employed in order to obtain RNA material of high quality and integrity for the majority of the experimental methods used in RNA expression analysis. Furthermore, we discuss the advantages and disadvantages of the RT-PCR or microarray methodology which are the methods more often employed in procedures of extracellular RNA analysis.     

A simple glutathione transferase-based colorimetric endpoint assay for insecticide detection

The natural ability of the detoxification enzymes glutathione transferases (GSTs) to interact with xenobiotics can be used for the production of colorimetric assays. Detection is usually based on the inhibition of the GST-catalysed reaction, with detection achieved spectrophotometrically or electrochemically. Here we have adopted a chromogenic (visual) activity assay for screening GSTs with alkyltransferase activity for iodoalkene substrates for detection of insecticides. We screened a number of GSTs from insecticide resistant mosquito species for their ability to catalyse iodoalkane biotransformation reactions. AaGSTE2 was found to metabolise iodoethane with high turnover, which resulted in a dark blue colour in the enzymatic reaction. Following assay optimisation we exploited the high recognition affinity of the AgGSTE2 for insecticides to develop a novel colorimetric detection assay for organochlorine and pyrethroid quantification. Calibration curves were obtained for permethirn, deltamethrin, λ-cyhalothrin and DDT, with useful concentration ranges of 0–40 μg/ml (0–100 μM), 0–50 μg/ml (0–100 μM), 0–100 μg/ml (0–220 μM), and 0–50 μg/ml (0–140 μM), respectively. The assay was validated with extracts from insecticide sprayed surfaces and found to be reproducible and reliable compared with HPLC. The assay is therefore suitable for monitoring insecticide residues in insecticide treated materials, and therefore has potential for insect vector control operations.     

Rare case of XX/XY mosaicism and trisomy 13 in early prenatal diagnosis

Coexistence of XX/XY sex mosaicism and autosomal trisomy in prenatal diagnosis is particularly rare. Herein, we report the first, to our knowledge, case of a fetus with cyclopia, ambiguous genitalia and a 47,XX,+13,inv9[47]/47,XY,+13[13] karyotype detected at 13 weeks of gestation after chorionic villus sampling. Molecular analysis after prenatal diagnosis suggests that this is a case of sex mosaicism coexisting with trisomy 13, rather than chimera.     

Diversity and annual fluctuations of culturable airborne fungi in Athens, Greece: a 4-year study

The diversity and the abundance of the culturable airborne fungi have been studied by a volumetric method in the city of Athens, for a period of 4 years. A total of 6,600 plates were exposed during 562 calendar days, and 70,583 colonies of fungi have been recovered and studied in detail. One hundred and forty-eight species in fifty-four genera of filamentous fungi were identified. A total of three hundred and twenty strains were isolated and maintained as reference material. The annual mean concentration of the total fungi was 538, 640, 694 and 638 CFU/m³, and the concentration range, 25–2,435, 117–2,822, 122–2,201 and 116–2,590 CFU/m³ for each year, respectively. There is no statistically significant year-to-year variation in the distribution patterns and in the annual mean concentrations of the total fungi. The diversity and the abundance of the total fungi and of the dominant genera Cladosporium, Aspergillus and Alternaria were increased, whereas those of Penicillium decreased during the warm months of each year. The majority of the species are newly reported as airborne from Greece. Also, 19 genera and 93 species are totally new records for this country. The species Acrodontium virellum, Aspergillus aculeatus, A. tubingensis, Circinella minor, C. umbellata, Cladosporium breviramosum, C. malorum, Drechslera tetramera, Paecilomyces crustaceus, Petriella guttulata, Rutola graminis and Sporotrichum pruinosum are reported as airborne for the first time worldwide.     

N-(4-Substituted-benzoyl)-N'-(β-d-glucopyranosyl)ureas as inhibitors of glycogen phosphorylase: Synthesis and evaluation by kinetic, crystallographic, and molecular modelling methods

N-(4-Substituted-benzoyl)-N'-(β-d-glucopyranosyl) ureas (substituents: Me, Ph, Cl, OH, OMe, NO(2), NH(2), COOH, and COOMe) were synthesised by ZnCl(2) catalysed acylation of O-peracetylated β-d-glucopyranosyl urea as well as in reactions of O-peracetylated or O-unprotected glucopyranosylamines and acyl-isocyanates. O-deprotections were carried out by base or acid catalysed transesterifications where necessary. Kinetic studies revealed that most of these compounds were low micromolar inhibitors of rabbit muscle glycogen phosphorylase b (RMGPb). The best inhibitor was the 4-methylbenzoyl compound (K(i)=2.3μM). Crystallographic analyses of complexes of several of the compounds with RMGPb showed that the analogues exploited, together with water molecules, the available space at the β-pocket subsite and induced a more extended shift of the 280s loop compared to RMGPb in complex with the unsubstituted benzoyl urea. The results suggest the key role of the water molecules in ligand binding and structure-based ligand design. Molecular docking study of selected inhibitors was done to show the ability of the binding affinity prediction. The binding affinity of the highest scored docked poses was calculated and correlated with experimentally measured K(i) values. Results show that correlation is high with the R-squared (R(2)) coefficient over 0.9.     

Molecular modelling and cytotoxicity of substituted anthraquinones as inhibitors of human telomerase

Molecular modelling has been carried out for a number of amine-functionalised anthraquinone derivatives to determine their extent of binding to G-tetraplex DNA and their ability to inhibit the enzymes telomerase and Taq polymerase. The results are compared to data obtained from a modified TRAP assay and show good correlation between the two methods. The findings suggest that anthraquinone derivatives of this type inhibit telomerase by stabilisation of four-stranded tetraplex structures associated with guanine-rich telomeric DNA regions.     

Structural model and functional characterization of the Bemisia tabaci CYP6CM1vQ, a cytochrome P450 associated with high levels of imidacloprid resistance

The neonicotinoid imidacloprid is one of the most important insecticides worldwide. It is used extensively against the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae), an insect pest of eminent importance globally, which was also the first pest to develop high levels of resistance against imidacloprid and other neonicotinoids in the field. Recent reports indicated that in both the B and Q biotypes of B. tabaci, the resistant phenotype is associated with over-expression of the cytochrome P450 gene CYP6CM1. In this study, molecular docking and dynamic simulations were used to analyze interactions of imidacloprid with the biotype Q variant of the CYP6CM1 enzyme (CYP6CM1vQ). The binding mode with the lowest energy in the enzyme active site, the key amino acids involved (i.e. Phe-130 and Phe-226), and the putative hydroxylation site (lowest distance to carbon 5 of the imidazolidine ring system of imidacloprid) were predicted. Heterologous expression of the CYP6CM1vQ confirmed the accuracy of our predictions and demonstrated that the enzyme catalyses the hydroxylation of imidacloprid to its less toxic 5-hydroxy form (K_cat = 3.2 pmol/min/pmol P450, K_m = 36 μM). The data identify CYP6CM1vQ as a principle target for inhibitor design, aimed at inactivating insecticide-metabolizing P450s in natural insect pest populations.     

Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Many important protein–protein interactions are mediated by the binding of a short peptide stretch in one protein to a large globular segment in another. Recent efforts have provided hundreds of examples of new peptides binding to proteins for which a three-dimensional structure is available (either known experimentally or readily modeled) but where no structure of the protein–peptide complex is known. To address this gap, we present an approach that can accurately predict peptide binding sites on protein surfaces. For peptides known to bind a particular protein, the method predicts binding sites with great accuracy, and the specificity of the approach means that it can also be used to predict whether or not a putative or predicted peptide partner will bind. We used known protein–peptide complexes to derive preferences, in the form of spatial position specific scoring matrices, which describe the binding-site environment in globular proteins for each type of amino acid in bound peptides. We then scan the surface of a putative binding protein for sites for each of the amino acids present in a peptide partner and search for combinations of high-scoring amino acid sites that satisfy constraints deduced from the peptide sequence. The method performed well in a benchmark and largely agreed with experimental data mapping binding sites for several recently discovered interactions mediated by peptides, including RG-rich proteins with SMN domains, Epstein-Barr virus LMP1 with TRADD domains, DBC1 with Sir2, and the Ago hook with Argonaute PIWI domain. The method, and associated statistics, is an excellent tool for predicting and studying binding sites for newly discovered peptides mediating critical events in biology.     

A role for the lymphotoxin/LIGHT axis in the pathogenesis of murine collagen-induced arthritis

A lymphotoxin-beta (LTbeta) receptor-Ig fusion protein (LTbetaR-Ig) was used to evaluate the importance of the lymphotoxin/LIGHT axis in the development and perpetuation of arthritis. Prophylactic treatment with the inhibitor protein LTbetaR-Ig blocked the induction of collagen-induced arthritis in mice and adjuvant arthritis in Lewis rats. Treatment of mice with established collagen-induced arthritis reduced the severity of arthritic symptoms and joint tissue damage. However, in a passive model of anti-collagen Ab-triggered arthritis, joint inflammation was not affected by LTbetaR-Ig treatment precluding LT/LIGHT involvement in the very terminal immune complex/complement/FcR-mediated effector phase. Collagen-II and Mycobacterium-specific T cell responses were not impaired, yet there was evidence that the overall response to the mycobacterium was blunted. Serum titers of anti-collagen-II Abs were reduced especially during the late phase of disease. Treatment with LTbetaR-Ig ablated follicular dendritic cell networks in the draining lymph nodes, suggesting that impaired class switching and affinity maturation may have led to a decreased level of pathological autoantibodies. These data are consistent with a model in which the LT/LIGHT axis controls microenvironments in the draining lymph nodes. These environments are critical in shaping the adjuvant-driven initiating events that impact the subsequent quality of the anti-collagen response in the later phases. Consequently, blockade of the LT/LIGHT axis may represent a novel approach to the treatment of autoimmune diseases such as rheumatoid arthritis that involve both T cell and Ab components.