Properties of nucleic acid staining dyes used in gel electrophoresis

Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed? was the most sensitive and safest dye to use with UV light excitation, and both GelGreen? and Diamond? Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.     

A high concentration of genistein down-regulates activin A, Smad3 and other TGF-β pathway genes in human uterine leiomyoma cells

Previously, we found that high doses of genistein show an inhibitory effect on uterine leiomyoma (UtLM) cell proliferation. In this study, using microarray analysis and Ingenuity Pathways Analysis™, we identified genes (up- or down-regulated, ≥ 1.5 fold, P ≤ 0.001), functions and signaling pathways that were altered following treatment with an inhibitory concentration of genistein (50 µg/ml) in UtLM cells. Downregulation of TGF-β signaling pathway genes, activin A, activin B, Smad3, TGF-β2 and genes related to cell cycle regulation, with the exception of the upregulation of the CDK inhibitor P15, were identified and validated by real-time RT-PCR studies. Western blot analysis further demonstrated decreased protein expression of activin A and Smad3 in genistein-treated UtLM cells. Moreover, we found that activin A stimulated the growth of UtLM cells, and the inhibitory effect of genistein was partially abrogated in the presence of activin A. Overexpression of activin A and Smad3 were found in tissue samples of leiomyoma compared to matched myometrium, supporting the contribution of activin A and Smad3 in promoting the growth of UtLM cells. Taken together, these results suggest that down-regulation of activin A and Smad3, both members of the TGF-β pathway, may offer a mechanistic explanation for the inhibitory effect of a high-dose of genistein on UtLM cells, and might be potential therapeutic targets for treatment of clinical cases of uterine leiomyomas.     

Energy decompositions according to physical space partitioning schemes: treatments of the density cumulant

This article is a continuation of our previous paper on schemes of energy decompositions of molecular systems in the real space [D. R. Alcoba et al., J. Chem. Phys. 122, 074102 (2005)] now using correlated state functions. We study, according to physical arguments, the appropriate management of the density cumulant arising from the second-order reduced density matrix at correlated level, whose contributions can be assigned to one-center or to two-center terms in the energy partitioning. Our treatments are applied within two physical space partitioning schemes: the Bader partitioning into atomic basins and the fuzzy atom procedure. The results obtained in selected molecules are analyzed and discussed in detail.     

A convenient synthesis of novel pyrido(1′,2′:1,2)imidazo[5,4‐d]‐1,2,3‐triazinones from imidazo[1,2‐a]pyridines

The imidazo[1,2‐a]pyridine system was investigated as a synthon for the building of very attractive fused triazines, a planar, angular tri‐heterocycle with potential biological activity. Thus ethyl 3‐nitroimidazo[1,2‐a]pyridine‐2‐carboxylate was treated with ammonia or with an excess of primary amines to generate the corresponding substituted nitro carboxamidoimidazopyridines. The nitro substituent in the latter products, was reduced to yield 3‐amino‐2‐carboxamidoimidazo[1,2‐a]pyridine derivatives, which in turn were treated with nitrous acid to furnish 1‐oxo‐2‐substituted pyrido(1′,2′:1,2)imidazo[5,4‐d]‐1,2,3‐triazines.     

Quantitative measurement of different ceramide species from crude cellular extracts by normal-phase high-performance liquid chromatography coupled to atmospheric pressure ionization mass spectrometry

Normal-phase high-performance liquid chromatography (NP-HPLC) coupled to atmospheric pressure ionization mass spectrometry (APCI-MS) allows quantitative analysis of endogenous ceramide and dihydroceramide species from crude lipid extracts. Qualitative information for the species comes from observation of differences in chromatographic and mass spectrometric behavior between species (Pettus et al. Rapid Commun. Mass Spectrom. 2003; 17: 1017-1026). Quantitative analysis is achieved by (1) use of a synthetic internal standard as an extraction and injection control, (2) lack of salt adduction, ion suppression, or other matrix effects in APCI mode, and (3) consistent fragmentation and ionization of external standards across the physiologically relevant concentration range found in endogenous lipid samples. Application to the analysis and quantitation of ceramide and dihydroceramide from various cell lines is demonstrated. The results from APCI-MS analysis corroborate and enhance information acquired from use of the diacylglycerol kinase assay for total ceramide measurement. This technique readily allows simultaneous quantitation of ceramide and dihydroceramide species.     

Continuous photochemical generation of catalytically active [CpRu]+ complexes from CpRu(η6-C6H6)PF6

Inter- and intramolecular ene-yne coupling reactions catalyzed by a species generated in situ via photolysis of CpRu(η(6)-C(6)H(6))PF(6)--an inexpensive, readily available, and shelf-stable complex--have been demonstrated under conditions of continuous flow. Importantly, the catalyst can be recovered quantitatively at the end of the reaction. Various functional groups are tolerated by the reaction, which affords skipped diene products in high yields.     

Synthesis of Densely Functionalised 5‐Halogen‐1,3‐oxazin‐2‐ones by Halogen‐Mediated Regioselective Cyclisation of N‐Cbz‐Protected Propargylic Amines: A Combined Experimental and Theoretical Study

A very efficient synthesis of 5‐halogen‐1,3‐oxazin‐2‐ones has been accomplished by the halocyclisation reaction of chiral nonracemic N‐carbobenzyloxy (N‐Cbz)‐protected propargylic amines by using I₂, Br₂ and Cl₂ as electrophile sources. The nature of the halogen influences the reaction time and yield. However, in all cases the reaction is totally regioselective taking place through a 6‐endo‐dig process regardless of the nature of the halogen and of the substituents in the starting material. To rationalise the experimental results, theoretical studies at the B3LYP/6‐311G* level have been performed.     

Influence of medium and temperature on the hydrolysis kinetics of propacetamol hydrochloride: determination using derivative spectrophotometry

Propacetamol hydrochloride (PRO) is a water-soluble prodrug of paracetamol (PA) which can be parenterally administered as analgesic for the treatment of postoperative pain, acute trauma, and gastric and/or intestinal disorders where oral administration is not possible. In these circumstances, PRO can be administered in physiologic or glucose solutions since it is rapidly and quantitatively hydrolyzed into PA by plasma estearases. We have studied the degradation kinetics of PRO in 5% glucose and 0.9% saline solutions at 4 degrees C and 25 degrees C (storage and room temperatures, respectively). The analytic technique used to determine PRO and PA quantitatively was first-derivative spectrophotometry. The degradation process of PRO can be best fitted to a second-order kinetics with independence of the medium used (saline or glucose solution). The hydrolysis kinetics of PRO conversion into PA depends on the temperature but not on the assay medium (saline or glucose solution). The degradation rate constants obtained for PRO were approximately 4.5 times higher at 25 degrees C than at 4 degrees C. The values of t(90%) for PRO were 3.17 h and 3.61 h at 25 degrees C, and 13.42 h and 12.36 h at 4 degrees C when the tests were performed in 5% glucose and 0.9% saline solutions, respectively.     

Stability of Plasma Treated Non-vulcanized Polybutadiene Surfaces: Role of Plasma Parameters and Influence of Additives

Surface modification studies of non-vulcanized BR elastomers (butadiene rubber) by low-pressure air plasma treatment and the effect on ageing and adhesion performances are presented in this paper. In particular, the influence of discharge power and distance from the glow discharge, and impact of antioxidant molecules in the BR formulation were examined. To characterize the changes to the BR surface, XPS spectroscopy, contact angle measurements, AFM nanoindentation experiments and tack measurements were utilized. Oxidation and crosslinking were the main mechanisms observed on the polymer chains regardless of the plasma conditions used. Beyond a certain threshold of plasma energy (in our case, discharge power of ~60 W and exposure time of ~30 s), a steady state was reached irrespective of the distance from the glow discharge. The presence of antioxidant molecules considerably reduced crosslinking phenomena while maintaining oxidation processes on polymer chains and increasing the nitrogen content in the near surface region. The mechanisms responsible for these differences have been identified. Interestingly, the COOH/C=O ratio changed according to the balance between oxidation and crosslinking. The hydrophobic recovery rate was mainly driven by temperature-dependent dynamics and varied according to the degree of crosslinking in the surface region. It was found to be lower in air atmosphere in the presence of antioxidant molecules. Finally, the presence of antioxidant molecules in the BR formulation allowed the adhesion performances after plasma exposure to significantly increase.     

Probing vibrational wave packets in molecular excited states

A time-dependent theoretical method is used to describe a UV pump?CUV probe strategy to trace, at a femtosecond time scale, the motion of vibrational wave packets created in excited states of the hydrogen molecule by measuring single ionization probabilities. We use a spectral method to solve the time-dependent Schr?dinger equation in full dimensionality, including correlation and all electronic and vibrational degrees of freedom. A pump pulse initially creates a vibrational wave packet in the intermediate electronic excited states of $\hbox{H}_2$ . The frequency of the probe is chosen to ionize the target leaving the ion in a bound vibrational state. By varying the time delay between pulses, non-dissociative single ionization is enhanced or suppressed. Energy differential ionization probabilities are reported and compared with a model based on the Franck?CCondon approximation.