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/ The latest articles from Chemistry Central Journal (ISSN 1752-153X) published by BioMed Central 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 1000C and 2900C, respectively. In blood, 6 ug of magnesium nitrate was found to improve the method sensitivity. The optimal pyrolysis and atomization temperatures were 800C and 2800C 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 Sebastien Sauve Chemistry Central Journal 2008, 2:14 2008-07-02 doi:10.1186/1752-153X-2-14 Chemistry Central Journal 1752-153X 2 14 2008-07-02 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 2008-06-25 doi:10.1186/1752-153X-2-13 Chemistry Central Journal 1752-153X 2 13 2008-06-25 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 2008-06-24 doi:10.1186/1752-153X-2-12 Chemistry Central Journal 1752-153X 2 12 2008-06-24 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 2008-05-15 doi:10.1186/1752-153X-2-11 Chemistry Central Journal 1752-153X 2 11 2008-05-15 Background: Occupational exposure to beryllium may cause Chronic Beryllium Disease (CBD), a lung disorder initiated by an electrostatic interaction with the MHC class II human leukocyte antigen (HLA). Molecular studies have found a significant correlation between the electrostatic potential at the HLA-DP surface and disease susceptibility. CBD can therefore be treated by chelation therapy. In this work, we studied the effect of two complexing agents, nitrilotriproprionic acid (NTP) and 4,5-dihydroxy-1,3-benzene disulphonate (Tiron), on the fractionation of beryllium in human serum analysed by graphite furnace atomic absorption spectrometry (GFAAS). Results: We found the average serum beryllium concentration of fourteen non-exposed individuals to be 0.53 (± 0.14) μg l-1, with 21 (± 3)% of the beryllium mass bound to the low molecular weight fraction (LMW), and 79 (± 3)% bound to the high molecular weight fraction (HMW). The addition of Tiron increased the beryllium mass in the HMW fraction, while NTP was not seen to have any influence on the fractionation of beryllium between the two fractions. NTP was, however, shown to complex 94.5% of the Be mass in the LMW fraction. The beryllium GFAAS detection limit, calculated as three times the standard deviation of 10 replicates of the lowest standard (0.05 μg L-1), was 6.0 (± 0.2) ng L-1. Conclusion: The concentration of beryllium or its fractionation in human serum was not affected by sex or smoking habit. On average, three quarters of the beryllium in serum were found in the HMW fraction. Of the two ligands tested, only Tiron was effective in mobilising beryllium under physiological conditions, thus increasing the Be content in the HMW fraction. http://www.journal.chemistrycentral.com/content/2/1/10 Chadi H Stephan, Michel Fournier, Pauline Brousseau and Sébastien Sauvé Chemistry Central Journal 2008, 2:10 2008-05-14 doi:10.1186/1752-153X-2-10 Chemistry Central Journal 1752-153X 2 10 2008-05-14 Background: This work reports the determination of the levels of phthalate esters (dimethyl phthalate (DMP), diethyl phthalate (DEP), dibutyl phthalate (DBP), diethyl hexyl phthalate (DEHP)) and metals (lead, cadmium, manganese, zinc, iron, calcium) in composite soil samples. The soil samples were collected randomly within the Muledane open dump, Thohoyandou, Limpopo province, South Africa. Control samples were collected about 200 m away from the open dump. The phthalate esters were separated and determined by capillary gas chromatography with a flame ionization detector, whilst the metals were determined by atomic absorption spectrophotometry. Results: Open dump values for the phthalate esters and metals to be generally higher in comparison to control samples for DMP, DEP, DBP and DEHP – the mean values calculated were 0.31 ± 0.12, 0.21 ± 0.05, 0.30 ± 0.07, and 0.03 ± 0.01 mg/kg, respectively, for the open dump soil samples. Nonetheless, the mean open dump values for lead, cadmium, manganese, zinc, iron and calcium were 0.07 ± 0.04, 0.003 ± 0.001, 5.02 ± 1.92, 0.31 ± 0.02, 11.62 ± 9.48 and 0.12 ± 0.13 mg/kg, respectively. The results were compared statistically. Conclusion: Our results revealed that the discarding of wastes into the open dump is a potential source of soil contamination in the immediate vicinity and beyond, via dispersal. Increased levels of phthalate esters and metals in the soil pose a risk to public health, plants and animals. Sustained monitoring of these contaminants is recommended, in addition to upgrading the facility to a landfill. http://www.journal.chemistrycentral.com/content/2/1/9 Adeleke Adeniyi, Matthew Dayomi, Pitso Siebe and Olumuyiwa Okedeyi Chemistry Central Journal 2008, 2:9 2008-05-12 doi:10.1186/1752-153X-2-9 Chemistry Central Journal 1752-153X 2 9 2008-05-12 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 2008-05-06 doi:10.1186/1752-153X-2-8 Chemistry Central Journal 1752-153X 2 8 2008-05-06 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 2008-04-14 doi:10.1186/1752-153X-2-7 Chemistry Central Journal 1752-153X 2 7 2008-04-14 Background: The determination of the osmolality of aqueous samples using a freezing point osmometer is a well-established, routine laboratory method. In addition to their use in clinical and pharmaceutical laboratories, freezing point osmometers are also employed in food testing laboratories. One application is the determination of the osmolality of milk. Although cow's milk is a natural product whose water content is approximately 87%, the osmolality of milk is a significant value when the milk is collected from a larger population of animals. This value is used in milk processing to control the water content, based on the German Food Control Regulations for Milk. Results: Measurement of the freezing point and osmolality of milk samples was performed with a Knauer Semi-Micro Freezing Point Osmometer. Osmolality was measured for the untreated milk samples and following their dilution (by volume) with 10% and 50% water. The measurements were made after 1, 4 and 7 days to evaluate changes over time. All measurement values for the undiluted milk were spread over a small interval with an average of 271 mOsmol/kg. After mixing the milk samples with 10% water, the average decreased to 242 mOsmol/kg, while mixing with 50% water resulted in an average osmolality of 129 mOsmol/kg. There was no significant change for the osmolality within the 7 days (measurements from days 1, 4 and 7). Conclusion: The results observed demonstrate clearly that the additional water content of milk can be determined easily using a freezing point osmometer. Milk samples that contain additional water have a significantly decreased osmolality, corresponding to an increased freezing point. The effect on osmolality of ageing the milk samples could not be determined in this study's time-dependent measurements. http://www.journal.chemistrycentral.com/content/2/1/6 Britta Büttel, Markus Fuchs and Birger Holz Chemistry Central Journal 2008, 2:6 2008-03-10 doi:10.1186/1752-153X-2-6 Chemistry Central Journal 1752-153X 2 6 2008-03-10 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 2008-03-09 doi:10.1186/1752-153X-2-5 Chemistry Central Journal 1752-153X 2 5 2008-03-09