Quantitative high performance liquid chromatography/tandem mass spectrometric analysis of the four classes of F2-isoprostanes in human urine

Isoprostanes (iPs) are free radical catalyzed prostaglandin isomers. Analysis of individual isomers of PGF2α—F2-iPs—in urine has reflected lipid peroxidation in humans. However, up to 64 F2-iPs may be formed, and it is unknown whether coordinate generation, disposition, and excretion of F2-iPs occurs in humans. To address this issue, we developed methods to measure individual members of the four structural classes of F2-iPs, using liquid chromatography/tandem mass spectrometry (LC/MS/MS), in which sample preparation is minimized. Authentic standards of F2-iPs of classes III, IV, V, and VI were used to identify class-specific ions for multiple reaction monitoring. Using iPF2α-VI as a model compound, we demonstrated the reproducibility of the assay in human urine. Urinary levels of all F2-iPs measured were elevated in patients with familial hypercholesterolemia. However, only three of eight F2-iPs were elevated in patients with congestive heart failure, compared with controls. Paired analyses by GC/MS and LC/MS/MS of iPF2α-VI in hypercholesterolemia and of 8,12-iso-iPF2α-VI in congestive heart failure were highly correlated. This approach will permit high throughput analysis of multiple iPs in human disease.

The life sciences Global Image Database (GID)

Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solution to unlock the value of scientific images. The Global Image Database (GID) is a web-based (http://www.g wer.ch/qv/gid/gid.htm) structured central repository for scientific annotated images. The GID was designed to manage images from a wide spectrum of imaging domains ranging from microscopy to automated screening. The annotations in the GID define the source experiment of the images by describing who the authors of the experiment are, when the images were created, the biological origin of the experimental sample and how the sample was processed for visualization. A collection of experimental imaging protocols provides details of the sample preparation, and labeling, or visualization procedures. In addition, the entries in the GID reference these imaging protocols with the probe sequences or antibody names used in labeling experiments. The GID annotations are searchable by field or globally. The query results are first shown as image thumbnail previews, enabling quick browsing prior to original-sized annotated image retrieval. The development of the GID continues, aiming at facilitating the management and exchange of image data in the scientific community, and at creating new query tools for mining image data.

A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy.

Determining the mode-of-binding of a DNA ligand is not always straightforward. Here, we establish a scanning force microscopic assay for mode-of-binding that is (i) direct: lengths of individual DNA-ligand complexes are directly measured; (ii) rapid: there are no requirements for staining or elaborate sample preparation; and (iii) unambiguous: an observed increase in DNA length upon addition of a ligand is definitive evidence for an intercalative mode-of-binding. Mode-of-binding, binding affinity, and site-exclusion number are readily determined from scanning force microscopy measurements of the changes in length of individual drug-DNA complexes as a function of drug concentration. With this assay, we resolve the ambiguity surrounding the mode of binding of 2,5-bis(4-amidinophenyl) furan (APF) to DNA and show that it binds to DNA by nonintercalative modes. APF is a member of an important class of aromatic dicationic drugs that show significant activity in the treatment of Pneumocystis carinii pneumonia, an opportunistic infection that is the leading cause of death in AIDS patients.

Determining RNA solution structure by segmental isotopic labeling and NMR: application to Caenorhabditis elegans spliced leader RNA 1.

Recent developments in multidimensional heteronuclear NMR spectroscopy and large-scale synthesis of uniformly 13C- and 15N-labeled oligonucleotides have greatly improved the prospects for determination of the solution structure of RNA. However, there are circumstances in which it may be advantageous to label only a segment of the entire RNA chain. For example, in a larger RNA molecule the structural question of interest may reside in a localized domain. Labeling only the corresponding nucleotides simplifies the spectrum and resonance assignments because one can filter proton spectra for coupling to 13C and 15N. Another example is in resolving alternative secondary structure models that are indistinguishable in imino proton connectivities. Here we report a general method for enzymatic synthesis of quantities of segmentally labeled RNA molecules required for NMR spectroscopy. We use the method to distinguish definitively two competing secondary structure models for the 5' half of Caenorhabditis elegans spliced leader RNA by comparison of the two-dimensional [15N] 1H heteronuclear multiple quantum correlation spectrum of the uniformly labeled sample with that of a segmentally labeled sample. The method requires relatively small samples; solutions in the 200-300 microM concentration range, with a total of 30 nmol or approximately 40 micrograms of RNA in approximately 150 microliters, give strong NMR signals in a short accumulation time. The method can be adapted to label an internal segment of a larger RNA chain for study of localized structural problems. This definitive approach provides an alternative to the more common enzymatic and chemical footprinting methods for determination of RNA secondary structure.

Anatomia ecológica do lenho de espécies arbustivas e arbóreas que ocorrem naturalmente em bosques com drástico gradiente de precipitação ao Noroeste da Patagônia, Argentina

A utilização de gradientes ambientais no estudo de comunidades vegetais possibilita a eleição de sítios onde há a predominância de um fator abiótico que determina o sucesso ou o fracasso de espécies ao longo de sua extensão. Entre as inúmeras ferramentas utilizadas no estudo de gradientes climáticos, se destaca a anatomia do lenho, pois, é um ramo da ciência que permite analisar, além dos aspectos espaciais, os aspectos temporais dos sítios por meio dos anéis de crescimento. Além disso, a ampla distribuição das plantas lenhosas ao longo do globo possibilita análises em praticamente todos os tipos de biomas e ecossistemas terrestres. Dentro desse contexto estão os bosques andino-patagônicos de Araucaria araucana (Pehuén) ao norte de sua distribuição na Argentina. Esses bosques ocupam territórios caracterizados por um acentuado gradiente de precipitação, que vai de cerca de 3000 a 100 milímetros anuais, entre a cordilheira do Andes e a estepe patagônica, que os define como bosques mésicos e xéricos, com diferenças ecológicas que condicionam a formação vegetal, dinâmica, estrutura, relações com o clima e vulnerabilidade em cenários de mudanças ambientais. O objetivo do projeto foi descrever e analisar comparativamente a estrutura anatômica do lenho de 33 espécies arbóreas e arbustivas ocorrentes ao longo de um gradiente de precipitação, entre a encosta da cordilheira dos Andes e a estepe Patagônica, para verificar possíveis alterações anatômicas que permitam a determinação de tendências e elucidem os limites de distribuição das espécies. Foram coletadas amostras não destrutivas de lenho durante três expedições para a Patagônia entre 2012 e 2014, seguidas de procedimentos laboratoriais de confeccção de lâminas histológicas, preparo de amostras para análises dendrocronológicas, captura de imagens com câmeras acopladas a microscópios óptico e eletrônico de varredura, mensurações, descrições e análises comparativas com o auxílio de softwares. Foram identificados caracteres anatômicos exclusivos de sítios secos e úmidos que permitiram a caracterização, posicionamento ao longo do gradiente de precipitação e grupamento de espécies xerófitas e mesófitas; A ultra-estrutura das pontoações de traqueídeos de Araucaria araucana apresentou diferenças marcantes na frequência e porosidade de suas membranas, sendo maior e menos porosas em sítios xéricos, e menor e mais porosas nos mésicos; a chave dicotômica microscópica permitiu a identificação das 32 espécies arbustivas, as espécies Chuquiraga oppositifolia e Nothofagus antarctica apresentaram potencial dendrocronológico, e foram identificadas tendências anatômicas latitudinais influenciadas pelo clima nos extremos da América do Sul. A anatomia do lenho se mostrou uma ferramenta confiável no estudo de um gradiente de precipitação na Patagônia argentina, e os resultados apontam para riscos de embolismos e morte induzida por falha no sistema hidráulico de Araucaria araucana ao longo de todo o gradiente, em função do atual cenário climático, e suas projeções em médio e longo prazos.

Catalisadores Ni/MgO-SiO2 aplicados na reação de reforma a vapor de glicerol

Catalisadores de Ni (10% em massa) suportado em matrizes mistas MgO-SiO2 foram aplicados na reação de reforma a vapor de glicerol. Os efeitos do teor de MgO como aditivo e do método de preparação foram avaliados frente às propriedades físico-químicas e texturais dos materiais; assim como à atividade, seletividade, estabilidade e formação de carbono na reforma a vapor do glicerol. Os catalisadores foram preparados com diferentes teores mássicos de MgO (10%, 30% e 50%) sobre SiO2 comercial, utilizando processo via seca (mistura física) e via úmida (impregnação sequencial com diferentes solventes: água, etanol e acetona). Foram utilizadas as técnicas de caracterização de espectroscopia de energia dispersiva de raios X, fisissorção de nitrogênio, difratometria de raios X, termogravimetria, difratometria de raios X in situ com O2, redução a temperatura programada com H2, difratometria de raios X in situ com H2, dessorção a temperatura programada com H2 e microscopia eletrônica de varredura. Foi observado que o Ni(II) interage de forma variada com os suportes com diferentes teores de MgO, e que a polaridade do solvente de impregnação utilizado no processo de preparação influencia as propriedades dos catalisadores. A fim de verificar a atividade, seletividade e deposição de carbono; os catalisadores foram testados na reação de reforma a vapor de glicerol a 600oC, por um período de 5h e razão molar água:glicerol de 12:1. Após as reações, os catalisadores foram novamente submetidos às análises de termogravimetria, difratometria de raios X e microscopia eletrônica de varredura, visando a caracterização dos depósitos de carbono obtidos durante o processo catalítico. Os catalisadores de matrizes mistas se mostraram ativos e apresentaram seletividades similares para os produtos gasosos CH4, CO e CO2, além de um alto rendimento em H2. Observou-se que a adição de MgO no suporte, aumentou a dispersão do Ni(II) no material, que por sua vez, influenciou na quantidade de carbono depositado ao longo da reação. A polaridade do solvente de impregnação também teve influência na dispersão metálica, sendo que, quanto menor a polaridade do solvente, maior foi a dispersão obtida no catalisador, e menor a deposição de carbono na reação. O material que apresentou o melhor desempenho catalítico frente ao rendimento de H2 e à deposição de carbono, foi o catalisador preparado com 30% de MgO com etanol como solvente de impregnação.

NaOH and KOH for preparing activated carbons used in energy and environmental applications

Alkaline hydroxides, especially sodium and potassium hydroxides, are multi-million-ton per annum commodities and strong chemical bases that have large scale applications. Some of them are related with their consequent ability to degrade most materials, depending on the temperature used. As an example, these chemicals are involved in the manufacture of pulp and paper, textiles, biodiesels, soaps and detergents, acid gases removal (e.g., SO2) and others, as well as in many organic synthesis processes. Sodium and potassium hydroxides are strong and corrosive bases, but they are also very stable chemicals that can melt without decomposition, NaOH at 318ºC, and KOH at 360ºC. Hence, they can react with most materials, even with relatively inert ones such as carbon materials. Thus, at temperatures higher than 360ºC these melted hydroxides easily react with most types of carbon-containing raw materials (coals, lignocellulosic materials, pitches, etc.), as well as with most pure carbon materials (carbon fibers, carbon nanofibers and carbon nanotubes). This reaction occurs via a solid-liquid redox reaction in which both hydroxides (NaOH or KOH) are converted to the following main products: hydrogen, alkaline metals and alkaline carbonates, as a result of the carbon precursor oxidation. By controlling this reaction, and after a suitable washing process, good quality activated carbons (ACs), a classical type of porous materials, can be prepared. Such carbon activation by hydroxides, known since long time ago, continues to be under research due to the unique properties of the resulting activated carbons. They have promising high porosity developments and interesting pore size distributions. These two properties are important for new applications such as gas storage (e.g., natural gas or hydrogen), capture, storage and transport of carbon dioxide, electricity storage demands (EDLC-supercapacitors-) or pollution control. Because these applications require new and superior quality activated carbons, there is no doubt that among the different existing activating processes, the one based on the chemical reaction between the carbon precursor and the alkaline hydroxide (NaOH or KOH) gives the best activation results. The present article covers different aspects of the activation by hydroxides, including the characteristics of the resulting activated carbons and their performance in some environment-related applications. The following topics are discussed: i) variables of the preparation method, such as the nature of the hydroxide, the type of carbon precursor, the hydroxide/carbon precursor ratio, the mixing procedure of carbon precursor and hydroxide (impregnation of the precursor with a hydroxide solution or mixing both, hydroxide and carbon precursor, as solids), or the temperature and time of the reaction are discussed, analyzing their effect on the resulting porosity; ii) analysis of the main reactions occurring during the activation process, iii) comparative analysis of the porosity development obtained from different activation processes (e.g., CO2, steam, phosphoric acid and hydroxides activation); and iv) performance of the prepared activated carbon materials on a few applications, such as VOC removal, electricity and gas storages.

Intra-population variation and geographic correlation in Canthon humectus hidalgoensis using FTIR-ATR spectroscopy

In some cases external morphology is not sufficient to discern between populations of a species, as occurs in the dung beetle Canthon humectus hidalgoensis Bates; and much less to determine phenotypic distances between them. FTIR-ATR spectroscopy show several advantages over other identification techniques (e.g. morphological, genetic, and cuticular hydrocarbons analysis) due to the non-invasive manner of the sample preparation, the relative speed of sample analysis and the low-cost of this technology. The infrared spectrum obtained is recognized to give a unique ‘fingerprint’ because vibrational spectra are specific and unique to the molecular nature of the sample. In our study, results showed that proteins, amino acids and aromatic ethers of insect exocuticle have promising discriminative power to discern between different populations of C. h. hidalgoensis. Furthermore, the correlation between geographic distances between populations and the chemical distances obtained by proteins + amino acids + aromatic ethers was statistically significant, showing that the spectral and spatial information available of the taxa together with appropriated chemometric methods may help to a better understanding of the identity, structure, dynamics and diversity of insect populations.

Organic distributed feedback laser to monitor solvent extraction upon thermal annealing in solution-processed polymer films

Solution-processed polymer films are used in multiple technological applications. The presence of residual solvent in the film, as a consequence of the preparation method, affects the material properties, so films are typically subjected to post-deposition thermal annealing treatments aiming at its elimination. Monitoring the amount of solvent eliminated as a function of the annealing parameters is important to design a proper treatment to ensure complete solvent elimination, crucial to obtain reproducible and stable material properties and therefore, device performance. Here we demonstrate, for the first time to our knowledge, the use of an organic distributed feedback (DFB) laser to monitor with high precision the amount of solvent extracted from a spin-coated polymer film as a function of the thermal annealing time. The polymer film of interest, polystyrene in the present work, is doped with a small amount of a laser dye as to constitute the active layer of the laser device and deposited over a reusable DFB resonator. It is shown that solvent elimination translates into shifts in the DFB laser wavelength, as a consequence of changes in film thickness and refractive index. The proposed method is expected to be applicable to other types of annealing treatments, polymer-solvent combinations or film deposition methods, thus constituting a valuable tool to accurately control the quality and reproducibility of solution-processed polymer thin films.

Therapeutic drug monitoring of cefepime with micellar electrokinetic capillary chromatography: Assay improvement, quality assurance, and impact on patient drug levels

The improvement and performance of a micellar electrokinetic capillary chromatography assay for cefepime in human serum and plasma with a 50 μm id fused-silica capillary elongated from 40 to 60 cm is reported. Sample preparation with dodecylsulfate protein precipitation at pH 4.5, the pH 9.1 separation medium and the applied voltage were as reported previously[16]. The change resulted in a significant lower current, higher resolution and increased detection time intervals. The performance of the assay with multi-level internal calibration was assessed with calibration and control samples. Quality assurance data of a two year period assessed under the new conditions demonstrated the robustness of the assay. In serum samples of patients who received both cefepime and sulfamethoxazole, cefepime could not be detected due to the inseparability of the two compounds. The presence of an interference can be recognized by an increased peak width (width > 0.2 min), the appearance of a shoulder or an unresolved double peak. The patient data gathered during a three year period reveal that introduction of therapeutic drug monitoring led to a 50% reduction of the median drug level. The data suggest that therapeutic drug monitoring can help to minimize the risk of major adverse reactions and to increase drug safety on an individual basis. This article is protected by copyright. All rights reserved.

A novel, bedside technique to rapidly identify umbilical cord blood units with high total nucleated cell numbers

BACKGROUND With increasing demand for umbilical cord blood units (CBUs) with total nucleated cell (TNC) counts of more than 150 × 10(7) , preshipping assessment is mandatory. Umbilical cord blood processing requires aseptic techniques and laboratories with specific air quality and cleanliness. Our aim was to establish a fast and efficient method for determining TNC counts at the obstetric ward without exposing the CBU to the environment. STUDY DESIGN AND METHODS Data from a total of 151 cord blood donations at a single procurement site were included in this prospective study. We measured TNC counts in cord blood aliquots taken from the umbilical cord (TNCCord ), from placenta (TNCPlac ), and from a tubing segment of the sterile collection system (TNCTS ). TNC counts were compared to reference TNC counts in the CBU which were ascertained at the cord blood bank (TNCCBU ). RESULTS TNCTS counts (173 ± 33 × 10(7) cells; calculated for 1 unit) correlated fully with the TNCCBU reference counts (166 ± 33 × 10(7) cells, Pearson's r = 0.97, p < 0.0001). In contrast, TNCCord and TNCPlac counts were more disparate from the reference (r = 0.92 and r = 0.87, respectively). CONCLUSIONS A novel method of measuring TNC counts in tubing segments from the sterile cord blood collection system allows rapid and correct identification of CBUs with high cell numbers at the obstetric ward without exposing cells to the environment. This approach may contribute to cost efficacy as only CBUs with satisfactory TNC counts need to be shipped to the cord blood bank.

(Table 1) Carbon and isotopic composition of organic carbon in sediments from DSDP Leg 56 Holes

We have analyzed inorganic and organic carbons and determined the isotopic composition of both sedimentary organic carbon and inorganic carbon in carbonates contained in sediments recovered from Holes 434, 434A, 434B, 435, and 435A in the landward slope of Japan and from Hole 436 in the oceanic slope of the Japan Trench. Both inorganic and organic carbons were assayed at the P. P. Shirshov Institute of Oceanology, in the same sample, using the Knopp technique and measuring evolved CO2 gravimetrically. Each sample was analyzed twice in parallel. Measurements were of a ±0.05 per cent accuracy and a probability level of 0.95. Carbon isotopic analysis was carried out on a MI-1305 mass spectrometer at the I. M. Gubkin Institute of Petrochemical and Gas Industry and the results presented as dC13 values related to the PDB standard. The procedure for preparing samples for organic carbon isotopic analysis involved (1) drying damp sediments at 60°C; (2) treating samples, while heating, with 10 N HCl to remove carbonate carbon; and (3) evaporating surplus HCl at 60°C. The organic substance was turned to CO2 by oxidizing it in an oxygen atmosphere. To prepare samples for inorganic carbon isotopic analysis we decomposed the carbonates with orthophosphoric acid and refined the gas evolved. The dC13 measurements, including a full cycle of sample preparation, were of a ±0.5 per cent accuracy and a probability level of 0.95.

(Table T1) Age determination of seven ODP Leg 201 sites

As part of a wider paleoclimate and paleoceanographic study of Holocene-upper Pleistocene laminated sediments from the eastern equatorial Pacific and Peru continental margin, we completed 32 accelerator mass spectrometry (AMS) 14C dates from cores recovered during Ocean Drilling Program (ODP) Leg 201. Sample preparation and measurement were carried out at the ANTARES AMS facility, Australian Nuclear Science and Technology Organisation (ANSTO), in Sydney, Australia (Lawson et al., 2000, doi:10.1016/S0168-583X(00)00276-7; Fink et al., 2004, doi:10.1016/j.nimb.2004.04.025). Although the sediments are predominantly diatomaceous oozes (D'Hondt, Jørgensen, Miller, et al., 2003, doi:10.2973/odp.proc.ir.201.2003), they contain sufficient inorganic (e.g., foraminifer tests and nannofossil plates) and organic (Meister et al., 2005, doi:10.2973/odp.proc.sr.201.105.2005) carbon to allow 14C dating. These dates permitted us to reconstruct a history of sediment accumulation over the past 20 k.y., particularly on the Peru continental margin. In this report we present 14C AMS dates and other pertinent data from cores from Sites 1227, 1228, and 1229 collected during Leg 201 at the Peru continental margin.

Chemical analysis of powdered metallurgical slags by X-ray fluorescence spectrometry

Slag composition determines the physical and chemical properties as well as the application performance of molten oxide mixtures. Therefore, it is necessary to establish a routine instrumental technique to produce accurate and precise analytical results for better process and production control. In the present paper, a multi-component analysis technique of powdered metallurgical slag samples by X-ray Fluorescence Spectrometer (XRFS) has been demonstrated. This technique provides rapid and accurate results, with minimum sample preparation. It eliminates the requirement for a fused disc, using briquetted samples protected by a layer of Borax(R). While the use of theoretical alpha coefficients has allowed accurate calibrations to be made using fewer standard samples, the application of pseudo-Voight function to curve fitting makes it possible to resolve overlapped peaks in X-ray spectra that cannot be physically separated. The analytical results of both certified reference materials and industrial slag samples measured using the present technique are comparable to those of the same samples obtained by conventional fused disc measurements.

Aluminium phosphide as a eutectic grain nucleus in hypoeutectic Al-Si alloys

Aluminium phosphide (AlP) particles arc often suggested to be the nucleation site for eutectic silicon in Al-Si alloys, since both the crystal structure and lattice parameter of AlP (crystal structure: cubic K(4) over bar m; lattice parameter: 5.421 Angstrom) are close to that of silicon (cubic Fd3m, 5.431 Angstrom), and the melting point is higher than the Al-Si eutectic temperature. However, the crystallographic relationships between AlP particles and the surrounding eutectic silicon are seldom reported due to the difficulty in analysing the AlP particles, which react with water during sample preparation for polishing. in this study, the orientation relationships between AlP and Si are analysed by transmission electron microscopy using focused ion-beam milling for sample preparation to investigate the nucleation mechanism of eutectic silicon on AlP. The results show a clear and direct lattice relationship between centrally located AlP particles and the surrounding silicon in the hypoeutectic Al-Si alloy.