This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.journal.chemistrycentral.com/mostviewed/ Most viewed articles in last 30 days from Chemistry Central Journal (ISSN 1752-153X) published by BioMed Central Background: Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.ImplementationPubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem.Results and DiscussionThe program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. http://www.journal.chemistrycentral.com/content/2/1/11 Junguk Hur and David J Wild Chemistry Central Journal 2008, 2:11 Number of accesses: 705 2008-05-15 doi:10.1186/1752-153X-2-11 Chemistry Central Journal 1752-153X 2 11 2008-05-15 Background: A routine method for the quantification of beryllium in biological fluids is essential for the development of a chelation therapy for Chronic Beryllium Disease (CBD). We describe a procedure for the direct determination of beryllium in undigested micro quantities of human blood and serum using graphite furnace atomic absorption spectrometry. Blood and serum samples are prepared respectively by a simple 8-fold and 5-fold dilution with a Nash Reagent. Three experimental setups are compared: using no modifier, using magnesium nitrate and using palladium/citric acid as chemical modifiers. Results: In serum, both modifiers did not improve the method sensitivity, the optimal pyrolysis and atomization temperatures are 1000°C and 2900°C, respectively. In blood, 6 μg of magnesium nitrate was found to improve the method sensitivity. The optimal pyrolysis and atomization temperatures were 800°C and 2800°C respectively. Conclusion: In serum, the method detection limit was 2 ng l-1, the characteristic mass was 0.22 (± 0.07) pg and the accuracy ranged from 95 to 100%. In blood, the detection limit was 7 ng l-1, the characteristic mass was 0.20 (± 0.02) pg and the accuracy ranged from 99 to 101%. http://www.journal.chemistrycentral.com/content/2/1/14 Chadi H Stephan, Michel Fournier, Pauline Brousseau and Sébastien Sauvé Chemistry Central Journal 2008, 2:14 Number of accesses: 496 2008-07-02 doi:10.1186/1752-153X-2-14 Chemistry Central Journal 1752-153X 2 14 2008-07-02 IntroductionIn proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function.DiscussionOptimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. Conclusion: To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today. http://www.journal.chemistrycentral.com/content/2/1/16 Peter R Jungblut, Hermann G Holzhütter, Rolf Apweiler and Hartmut Schlüter Chemistry Central Journal 2008, 2:16 Number of accesses: 365 2008-07-18 doi:10.1186/1752-153X-2-16 Chemistry Central Journal 1752-153X 2 16 2008-07-18 Background: Although the necessity of divalent magnesium and manganese for full activity of sugar nucleotidyltransferases and glycosyltransferases is well known, the role of these metal cations in binding the substrates (uridine 5'-triphosphate, glucose-1-phosphate, N-acetylglucosamine-1-phosphate, and uridine 5'-diphosphate glucose), products (uridine 5'-diphosphate glucose, uridine 5'-diphosphate N-acetylglucosamine, pyrophosphate, and uridine 5'-diphosphate), and/or enzyme is not clearly understood. Results: Using isothermal titration calorimetry we have studied the binding relationship between the divalent metals, magnesium and manganese, and uridine 5'-phosphates to determine the role these metals play in carbohydrate biosynthesis. It was determined from the isothermal titration calorimetry (ITC) data that Mg+2 and Mn+2 are most tightly bound to PPi, Kb = 41,000 ± 2000 M-1 and 28,000 ± 50,000 M-1 respectively, and UTP, Kb = 14,300 ± 700 M-1 and 13,000 ± 2,000 M-1 respectively. Conclusion: Our results indicate that the formal charge state of the phosphate containing substrates determine the binding strength. Divalent metal cations magnesium and manganese showed similar trends in binding to the sugar substrates. Enthalpy of binding values were all determined to be endothermic except for the PPi case. In addition, entropy of binding values were all found to be positive. From this data, we discuss the role of magnesium and manganese in both sugar nucleotidyltransferase and glycosyltransferase reactions, the differences in metal-bound substrates expected under normal physiological metal concentrations and those of hypomagnesaemia, and the implications for drug design. http://www.journal.chemistrycentral.com/content/2/1/15 Corbin J Zea, Gulden Camci-Unal and Nicola L Pohl Chemistry Central Journal 2008, 2:15 Number of accesses: 360 2008-07-15 doi:10.1186/1752-153X-2-15 Chemistry Central Journal 1752-153X 2 15 2008-07-15 Background: Etodolac (ETD) is a non-steroidal anti-inflamatory antirheumatic drug. A survey of the literature reveals that there is no method available for the determination of ETD in pure form and pharmaceutical formulations by oxidation-reduction reactions. Results: We describe three simple, sensitive and reproducible spectrophotometric assays (A-C) for the determination of etodolac in pure form and in pharmaceutical formulations. Methods A and B are based on the oxidation of etodolac by Fe3+ in the presence of o-phenanthroline (o-phen) or bipyridyl (bipy). The formation of the tris-complex on reaction with Fe3+-o-phen and/or Fe3+-bipy mixtures in acetate buffer solution at optimum pH was demonstrated at 510 and 520 nm with o-phen and bipy. Method C is based on the oxidation of etodolac by Fe3+ in acidic medium, and the subsequent interaction of iron(II) with ferricyanide to form Prussian blue, with the product exhibiting an absorption maximum at 726 nm. The concentration ranges are 0.5–8, 1.0–10 and 2–18 μg mL-1 respectively for methods A, B and C. For more accurate analysis, Ringbom optimum concentration ranges were calculated, in addition to molar absorptivity, Sandell sensitivity, detection and quantification limits. Conclusion: Our methods were successfully applied to the determination of etodolac in bulk and pharmaceutical formulations without any interference from common excipients. The relative standard deviations were ≤ 0.76 %, with recoveries of 99.87 % – 100.21 %. http://www.journal.chemistrycentral.com/content/2/1/7 Ayman A Gouda and Wafaa S Hassan Chemistry Central Journal 2008, 2:7 Number of accesses: 331 2008-04-14 doi:10.1186/1752-153X-2-7 Chemistry Central Journal 1752-153X 2 7 2008-04-14 Background: Considerable research has been directed towards the roles of metal ions in nutrition with metal ion toxicity attracting particular attention. The aim of this study is to measure the levels of metal ions found in selected beverages (red wine, stout and apple juice) and to determine their potential detrimental effects via calculation of the Target Hazard Quotients (THQ) for 250 mL daily consumption. Results: The levels (mean ± SEM) and diversity of metals determined by ICP-MS were highest for red wine samples (30 metals totalling 5620.54 ± 123.86 ppb) followed by apple juice (15 metals totalling 1339.87 ± 10.84 ppb) and stout (14 metals totalling 464.85 ± 46.74 ppb). The combined THQ values were determined based upon levels of V, Cr, Mn, Ni, Cu, Zn and Pb which gave red wine samples the highest value (5100.96 ± 118.93 ppb) followed by apple juice (666.44 ± 7.67 ppb) and stout (328.41 ± 42.36 ppb). The THQ values were as follows: apple juice (male 3.11, female 3.87), stout (male 1.84, female 2.19), red wine (male 126.52, female 157.22) and ultra-filtered red wine (male 110.48, female 137.29). Conclusion: This study reports relatively high levels of metal ions in red wine, which give a very high THQ value suggesting potential hazardous exposure over a lifetime for those who consume at least 250 mL daily. In addition to the known hazardous metals (e.g. Pb), many metals (e.g. Rb) have not had their biological effects systematically investigated and hence the impact of sustained ingestion is not known. http://www.journal.chemistrycentral.com/content/2/1/13 Theresa Hague, Andrea Petroczi, Paul LR Andrews, James Barker and Declan P Naughton Chemistry Central Journal 2008, 2:13 Number of accesses: 310 2008-06-25 doi:10.1186/1752-153X-2-13 Chemistry Central Journal 1752-153X 2 13 2008-06-25 Background: Propolis is widely used in apitherapy, preparations, and food and beverage additives. Various extraction techniques were applied in the extraction of the biologically active constituents of poplar type propolis in order to compare their efficiency. The methods employed were: traditional maceration extraction, ultrasound extraction (UE), and microwave assisted extraction (MAE). Results: The total amounts of extracted phenolics and flavonoids were determined, and the effectiveness of the methods compared. MAE was very rapid but led to the extraction of a large amount of non-phenolic and non-flavonoid material. UE gave the highest percentage of extracted phenolics. Conclusion: Compared to the maceration extraction, MAE and UE methods provided high extraction yield, requiring short timeframes and less labour. UE was shown to be the most efficient method based on yield, extraction time and selectivity. http://www.journal.chemistrycentral.com/content/1/1/13 Boryana Trusheva, Dorina Trunkova and Vassya Bankova Chemistry Central Journal 2007, 1:13 Number of accesses: 287 2007-06-07 doi:10.1186/1752-153X-1-13 Chemistry Central Journal 1752-153X 1 13 2007-06-07 Background: In soils contaminated by hydrophobic organic compounds, the concentrations are less indicative of potential exposure and distribution than are the associated chemical activities, fugacities and freely dissolved concentrations. The latter can be measured by diffusive sampling into thin layers of polymer, as in, for example, solid phase micro-extraction. Such measurements require equilibrium partitioning of analytes into the polymer while ensuring that the sample is not depleted. We introduce the validation of these requirements based on parallel sampling into polymer layers of different thicknesses. Results: Equilibrium sampling devices were made by coating glass vials internally with 3–12 μm thick layers of polydimethylsiloxane (PDMS). These were filled with slurries of a polluted soil and gently agitated for 5 days. The concentrations of 7 polycyclic aromatic hydrocarbons (PAHs) in the PDMS were measured. Validation confirmed fulfilment of the equilibrium sampling requirements and high measurement precision. Finally, chemical activities of the PAHs in the soil were determined from their concentrations and activity coefficients in the PDMS. Conclusion: PAHs' thermodynamic activities in a soil test material were determined via a method of uptake into PDMS. This can be used to assess chemical exposure and predict diffusion and partitioning processes. http://www.journal.chemistrycentral.com/content/2/1/8 Fredrik Reichenberg, Foppe Smedes, Jan-Åke Jönsson and Philipp Mayer Chemistry Central Journal 2008, 2:8 Number of accesses: 276 2008-05-06 doi:10.1186/1752-153X-2-8 Chemistry Central Journal 1752-153X 2 8 2008-05-06 Background: The Hedgehog signaling pathway is essential for embryogenesis and for tissue homeostasis in the adult. However, it may induce malignancies in a number of tissues when constitutively activated, and it may also have a role in other forms of normal and maladaptive growth. Cyclopamine, a naturally occurring steroidal alkaloid, specifically inhibits the Hedgehog pathway by binding directly to Smoothened, an important Hedgehog response element. To use cyclopamine as a tool to explore and/or inhibit the Hedgehog pathway in vivo, a substantial quantity is required, and as a practical matter cyclopamine has been effectively unavailable for usage in animals larger than mice. Results: In this paper, we report a rapid and efficient isolation and purification of large quantities of cyclopamine from the roots and rhizomes of Veratrum californicum Dur. (the Corn Lily or Western false hellebore). We also provide unambiguous assignments of the carbon and proton resonances by using the multinuclear spectra and the spin coupling networks. Conclusion: This method could meet a very real need within diverse scientific communities by allowing cyclopamine to become more readily available. http://www.journal.chemistrycentral.com/content/2/1/12 John E Oatis, Pam Brunsfeld, James W Rushing, Peter D Moeller, Daniel W Bearden, Thomas N Gallien and George Cooper Chemistry Central Journal 2008, 2:12 Number of accesses: 270 2008-06-24 doi:10.1186/1752-153X-2-12 Chemistry Central Journal 1752-153X 2 12 2008-06-24 Background: Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results: Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion: Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. http://www.journal.chemistrycentral.com/content/2/1/5 Noel M O'Boyle, Chris Morley and Geoffrey R Hutchison Chemistry Central Journal 2008, 2:5 Number of accesses: 250 2008-03-09 doi:10.1186/1752-153X-2-5 Chemistry Central Journal 1752-153X 2 5 2008-03-09