bluuebunny/crossref_metadata_2025 huggingface dataset:
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions
Authors: Anandakrishnan Ramu , Onufriev Alexey V.
Published: June 2009

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N2) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Stability of the hydration layer of tropocollagen: A QM study
Authors: Pálfi Villő K. , Perczel András
Published: June 2009

Collagen is a triple helical protein, highly hydrated in nature. Bella and Berman (J Mol Biol 1996, 264, 734) have reported the structure of the first hydration layer. Water molecules form bridges of different length around the POG repeats and self assemble into left‐handed helical water threads. To explore the stability of these specifically hydrated places, we have designed suitable QM models: each comprises a triple helix formed by 18 residues surrounded by 8 to 12 explicit waters. Two sets of amino acids were used, one standing for the core structural subunit of tropocollagen (POG‐model) and one for its natural enzyme recognition sites (AAG‐model). We have determined the stability order of the water binding places, the strongest being −8.1 kcal mol−1, while the weakest −6.1 kcal mol−1 per hydrogen bond. In X‐ray structures, each triplet of tropocollagen is shielded by six to nine water molecules. Beside the mandatory six, the “surplus” three water molecules further strengthen the binding of all the others. However, the displacement of selected water molecules turns out to be energy neutral. These water binding places on the surface of the triple helix can provide explanation on how an almost liquid‐like hydration environment exists between the closely packed tropocollagens (Henkelman et al., Magn Reson Med 1994, 32, 592). It seems that these water reservoirs or buffers can provide space for “hole conduction” of water molecules and thus contribute to the elasticity of collagen. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein
Authors: Murata Katsumi , Nagata Naoya , Nakanishi Isao , Kitaura Kazuo
Published: June 2009

Solvent dipole ordering (SDO), introduced by Higo et al. (Proteins Struct Funct Genet 2000, 40, 193), is an entity that captures an aspect of hydration structure. We have studied SDO in the ligand binding site of two proteins (FK506 binding protein and dihydrofolate reductase) and found that the high SDO regions overlap significantly with the 3D structures of known inhibitors bound to the proteins. Thus, the SDO region might be used to predict the preferred molecular shape of ligands that bind to a protein. Based on this finding, we propose a novel docking procedure using model molecules that mimic the shape of the SDO region. To prove the validity of thisapproach, we performed a redocking experiment for p38 mitogen‐activated protein kinase ligands using model molecules for search queries; we succeeded in identifying the binding conformations and binding modes of known inhibitors. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation
Authors: Li Hui , Fedorov Dmitri G. , Nagata Takeshi , Kitaura Kazuo , Jensen Jan H. , Gordon Mark S.
Published: June 2009

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6‐31G* level) is used to optimize the solution structure of the 304‐atom Trp‐cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the α‐helix, β‐turn and the extended form in solution are elucidated for polyalanine. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
A fast method for large‐scale De Novo peptide and miniprotein structure prediction
Authors: Maupetit Julien , Derreumaux Philippe , Tufféry Pierre
Published: June 2009

Although peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large‐scale experiments is still missing. We introduce a new approach—PEP‐FOLD—to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model‐derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse‐grained energy score. On a benchmark of 52 peptides with 9–23 amino acids, PEP‐FOLD generates lowest‐energy conformations within 2.8 and 2.3 Å Cα root‐mean‐square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27–49 amino acids, PEP‐FOLD reaches an accuracy of 3.6 and 4.6 Å Cα root‐mean‐square deviation for the most‐native and lowest‐energy conformations, using the nonflexible regions identified by NMR. PEP‐FOLD simulations are fast—a few minutes only—opening therefore, the door to in silico large‐scale rational design of new bioactive peptides and miniproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity
Authors: Tawari Nilesh R. , Degani Mariam S.
Published: June 2009

A five point pharmacophore was generated using PHASE for a series of nitroaromatic compounds and their congeners as antitubercular agents. The generated pharmacophore yielded significant 3D‐QSAR model with r2 of 0.890 for a training set of 92 molecules. The model also showed excellent predictive power with correlation coefficient Q2 of 0.857 for a test set of 31 compounds. The pharmacophore indicated that presence of a nitro group, a piperazine moiety, one aromatic ring feature and two acceptor features are necessary for potent antitubercular activity. The pharmacophore was supported by electronic property analysis using density functional theory (DFT) at B3LYP/3–21*G level. Molecular electrostatic profile of the compounds was consistent with the generated pharmacophore model, particularly appearance of localized negative potential regions near both the oxygen atoms of nitro group extending laterally to the isoxazole ring system/amide bond in the most active compounds. Calculated data further revealed that all active compounds have smaller LUMO energies located over the nitro group, furan ring, and isoxazole ring/amide bond attached to it. Higher negative values of LUMO energies concentrated over the nitro group are indicative of the electron acceptor capacity of the compounds, suggesting that these compounds are prodrugs and must be activated by TB‐nitroreductase. The results obtained from this study should aid in efficient design and development of nitroaromatic compounds as antitubercular agents. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Validation of a radioimmunoassay for measuring fecal cortisol metabolites in the hystricomorph rodent, Octodon degus
Authors: Soto‐Gamboa Mauricio , Gonzalez Sandra , Hayes Loren D. , Ebensperger Luis A.
Published: June 2009

Determination of fecal steroid metabolites is a noninvasive technique that characterizes the physiological state of organisms without the physiological and psychological stress of handling. Although this technique has many applications in the study of wildlife and/or captive animals without the necessity of capturing individuals, it requires a species‐specific validation before use. A complete validation includes an analytical and a physiological one. In the latter changes in fecal hormone metabolites are induced by previous manipulations of the respective plasma hormones. Here we validated a method for measuring fecal cortisol metabolites (FCM) in the hystricomorph rodent Octodon degus. We extracted feces with 80% ethanol and quantified steroids using a commercial available cortisol radioimmunoassay. We first compared baseline levels of blood cortisol and FCM, and then performed a challenge test with adrenocorticotropic hormone (ACTH) to demonstrate that FCM accurately reflect adrenocortical activity. We found a significantly positive relationship between concentrations of blood cortisol and its fecal metabolites. During the ACTH challenge test, blood cortisol levels peaked 30 min after injection, and FCM mirrored this peak with a delay of about 6 hr. Our successfully validated noninvasive method provides new opportunities for studies assessing the influence of social and ecological factors on degus under natural conditions. J. Exp. Zool. 311A:496–503, 2009. © 2009 Wiley‐Liss, Inc.
Dynamic reticulate evolution in a Daphnia multispecies complex
Authors: Gießler Sabine , Englbrecht Claudia C.
Published: June 2009

Recent genomic data suggest that the role of hybridization in evolution might be more important than previously assumed. Here, we examine species‐specific differentiation and signatures of reticulation in a multi‐species complex of the crustacean genus Daphnia. We did a combined examination of mtDNA, allozymes and ITS1 (a part of the nuclear ribosomal DNA) in the Daphnia longispina group. We focused on the sequence variation of ITS1 in two unambiguous species (D. galeata, D. cucullata) and two ecotypes hyalina and rosea within the recently revised taxon D. longispina (O.F. Müller). We found two ITS1‐types (S, L) and intra‐individual and intra‐specific polymorphisms. Another ITS1‐type (XL) was restricted to the outgroup D. umbra. S was present in all taxa but occurred as only two variants. Surprisingly, D. galeata and D. cucullata, which were well differentiated by mtDNA and allozymes, were virtually indistinguishable with respect to S‐ITS1 (Scg). The two ecotypes of D. longispina shared the second S‐ITS1‐variant (Srh) and were therefore almost indistinguishable for all types of molecular markers surveyed. The L‐type differed between D. galeata and D. longispina samples, but L was absent in D. cucullata. Between hyalina and rosea ecotypes, we found some L‐differentiation. Combined data suggest that reticulate evolution enabled the spread of one S‐ITS1‐variant (Scg) beyond species boundaries and that S‐introgression was species‐specific, despite contemporary hybridization between all species. Our data have implications for phylogenetic as well as phylogeographic surveys. Because of the dynamic impact of gene flow in multi‐species complexes, misinterpretations of presumed species‐specific data should be considered. J. Exp. Zool. 311A:530–548, 2009. © 2009 Wiley‐Liss, Inc.
Hyaluronic acid complexed to biodegradable poly L‐arginine for targeted delivery of siRNAs
Authors: Kim Eun‐Joong , Shim Gayong , Kim Kwangmyeung , Kwon Ick Chan , Oh Yu‐Kyoung , Shim Chang‐Koo
Published: June 2009

Background

Small interfering RNA (siRNA) has been recognized as a new therapeutic drug to treat various diseases by inhibition of oncogene or viral gene expression. Because hyaluronic acid (HA) has been described as a biocompatible biomaterial, we tested the nanoparticles formed by electrostatic complexation of negatively‐charged HA and cationic poly L‐arginine (PLR) for siRNA delivery systems.

Methods

Different electrostatic complexes of HA and PLR (HPs) were formulated: HP101 with 50% (w/w) HA and HP110 with 9% (w/w) HA.

Results

Gel retardation assays showed that HP101 and HP110 could form complexes with siRNAs. The diameters of these complexes were less than 200 nm. Cellular delivery efficiency of siRNAs by HPs depended on cell surface CD44 density. The HP‐mediated delivery of siRNAs was highest in WM266.4 cells followed by B16F10 cells and COS‐7 cells, in parallel with CD44 surface densities of these cell lines. TC50 values (i.e. the HP concentrations at which 50% of cells were viable after treatment) were used as indicators of cytotoxicity. HP101 showed TC50 values that were 2‐fold and 23‐fold higher than those of HP110 and PLR, respectively. After delivery into cells, siRNA exerted target‐specific RNA interference effects on mRNA and protein levels. Three days after treatment of red fluorescent protein (RFP)‐expressing B16F10 cells with RFP‐specific siRNA complexed to HP101, cellular fluorescence signals were reduced. Intratumoral administration of RFP‐specific siRNA via HP101 delivery significantly reduced the expression of RFP in tumor tissues.

Conclusions

HP101 may function as a biocompatible polymeric carrier of siRNAs and have possible application to localized siRNA delivery in vivo. Copyright © 2009 John Wiley & Sons, Ltd.
Intracellular small interfering RNA delivery using genetically engineered double‐stranded RNA binding protein domain
Authors: Kim Juwon , Lee Soo Hyeon , Choe Joonho , Park Tae Gwan
Published: June 2009

Background

A variety of synthetic carriers, such as cationic polymers and lipids, have been used as nonviral carriers for small interfering RNA (siRNA) delivery. Although siRNA polyplexes and lipoplexes exhibited good gene silencing efficiencies, they often showed serious cytotoxicities, which are not useful for clinical applications. A double‐stranded RNA binding cellular protein with highly specific siRNA binding property and noncytotoxicity was used for siRNA delivery.

Methods

A double‐stranded RNA binding domain (dsRBD) of human double‐stranded RNA activated protein kinase R was genetically produced and utilized to complex siRNA for intracellular delivery. For characterization of the siRNA/dsRBD complexes, decomplexation assay and RNase protection assay were performed. Cytotoxicity and target gene inhibition ability were also examined using human carcinoma cell lines.

Results

The recombinantly produced polypeptide dsRBD exhibited its inherent binding activity for siRNA without sequence specificity, and the siRNA/dsRBD complexes protected siRNA from degradation by ribonucleases. Green fluorescent protein (GFP) siRNA/dsRBD complexes showed prominent down‐regulation of a target GFP gene, when an endosomal escape function was supplemented by addition of a fusogenic peptide, KALA, in the formulation.

Conclusions

The results suggest that dsRBD‐based protein carriers could be successfully applied for a wide range of therapeutic siRNAs for intracellular gene inhibition without showing any cytotoxicity. Copyright © 2009 John Wiley & Sons, Ltd.
Dicyanomethylene compounds and heterocyclization of substituted carbohydrazides
Authors: Hassan Alaa A. , Ibrahim Yusria R. , Shawky Ahmed M.
Published: June 2009

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(1,3‐Dioxo‐2,3‐dihydro‐1H‐inden‐2‐ylidene)propanedinitrile (2, in dimethylformamide solution), 3‐(dicyanomethylene)‐2‐indolone (3, in ethanol/piperidine solution) act on substituted carbohydrazides 1a, 1b, 1c, 1d, 1e forming the derivatives of oxadiazolylideneindene‐1,3‐diones 4a, 4b, 4c, 4d, 4e, spiro(indene‐2,2′‐oxadiazole)‐1,3‐dione 5a, 5b, 5c, 5d, 5e, cyloxoindenopyrazolecarbonitriles 6a, 6b, 6c, 6d, 6e, spiro(indoline‐3,2′‐oxadiazol)‐2‐ones 1a, 1b, 1c, 1d, 1e, and acylpyrazoloindoles 13a, 13b, 13c, 13d, 13e. Rational for these conversions involving the nucleophilic addition on the dicyanomethylene carbon atom are presented. J. Heterocyclic Chem., (2009)
Preparation of 5‐nitro‐2‐amino[b]thiophenes and 1‐(2‐amino‐5‐nitrophenyl)ethanones via microwave irradiation
Authors: Rais Afsha , Ankati Haribabu , Biehl Ed
Published: June 2009

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1‐(2‐Chloro‐5‐nitrophenyl)ethanone) reacts with various amines in the presence of sulfur under microwave radiation to give the corresponding 2‐aminobenzo[b]‐thiophenes 3a, 3b, 3c, 3d, 3e, 3f in good yields. The yields of 3a, 3b, 3c, 3d, 3e, 3f are vastly superior to those obtained using conventional heating. Additionally, 1‐(2‐amino‐5‐nitrophenyl)ethanones 4a, 4b, 4c, 4d, 4e, 4f were also obtained. A mechanism is proposed in which 2‐amino thiophenes 3a, 3b, 3c, 3d, 3e, 3f are formed by a SNAr mechanism involving an intramolecular addition of sulfur of the intermediate thioamide to the 2‐substituted carbon to give a Meisenheimer complex, which collapses to 2‐aminothiophenes 3a, 3b, 3c, 3d, 3e, 3f, and 2‐amino ketones (4a, 4b, 4c, 4d, 4e, 4f) are formed by a parallel pathway involving nucleophilic addition amine to the 2‐chloro position of 1 to form a Meisensheimer complex, which collapses to the amino ethanones. J. Heterocyclic Chem., (2009).
Molecular interaction between free base meso‐tetraarylporphyrins and o‐chloranil
Authors: Dehghani Hossein , Farshchian Mahmood
Published: June 2009

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Interaction of meso‐tetraarylporphyrins (H2T(4‐X)PP, X=H, CH3, OCH3, Br) and o‐chloranil (C6Cl4O2) in chloroform at room temperature, with any ratio of the reactants leads to formation of [H2T(4‐X)PP(C6Cl4O2)2] compounds as a sole yield. The significant UV‐vis, 1H NMR, and 13C NMR spectral results suggested distortion of porphyrin core structure in the molecular complexes. Spectral data of the complexes revealed that the lone pair electron of a pyrrolenine nitrogen of porphyrin (σ‐electron donor) occupy π* orbital of a CO group in one o‐chloranil molecule (π‐electron acceptor). J. Heterocyclic Chem., (2009).
Public–public partnerships in Urban water provision: The case of Dar es Salaam
Authors: Dill Brian
Published: June 2009

Across the global South, urban residents have come to play a much greater role in the provision of basic public services through a variety of government–community partnerships. Often referred to as public–public partnerships (PuPs), such arrangements are thought to be essential to ensure that services are efficient, equitable, sustainable and responsive to the needs and interests of heterogeneous communities. This paper draws on original research and secondary data to analyse the strengths and limitations of PuPs with respect to water provision in contemporary Dar es Salaam, Tanzania. It explores two ways that community‐based organisations (CBOs) have become partners in the delivery of water and draws attention to the external support received by the most successful community partners. Copyright © 2009 John Wiley & Sons, Ltd.
Accurate molecular weight analysis of histones using FFE and RP‐HPLC on monolithic capillary columns
Authors: Sneekes Evert‐Jan , Han Jun , Elliot Monica , Ausio Juan , Swart Remco , Heck Albert J. R. , Borchers Christoph
Published: June 2009

Due to their large diversity with respect to post‐translational modifications (PTMs), the family of histones provides a major analytical challenge in current proteomics research. Their function has a large impact on the transcription of DNA, and as a result, on the expression of proteins. The variation in PTMs regulates transcription, and, as a result, many methods are being employed for the in‐depth analysis of histones. In this paper, we present a separation strategy for histones based on free‐flow electrophoresis (FFE) followed by an RP separation on capillary monolithic PS‐DVB columns. The capillary columns are directly interfaced with an FT‐ICR MS providing an online system for the detection and accurate molecular weight analysis of intact histones.
Optimization of a GC–MS metabolic fingerprint method and its application in characterizing engineered bacterial metabolic shift
Authors: Tian Jing , Sang Ping , Gao Peng , Fu Ruiyan , Yang Dawei , Zhang Lei , Zhou Jing , Wu Si , Lu Xin , Li Yin , Xu Guowang
Published: June 2009

Metabolomics influences many aspects of life sciences including microbiology. Here, we describe the systematic optimization of metabolic quenching and a sample derivatization method for GC–MS metabolic fingerprint analysis. Methanol, ethanol, acetone, and acetonitrile were selected to evaluate their metabolic quenching ability, and acetonitrile was regarded as the most efficient agent. The optimized derivatization conditions were determined by full factorial design considering temperature, solvent, and time as parameters. The best conditions were attained with N,O‐bis(trimethylsiyl) trifluoroacetamide as derivatization agent and pyridine as solvent at 75°C for 45 min. Method validation ascertained the optimized method to be robust. The above method was applied to metabolomic analysis of six different strains and it is proved that the metabolic trait of an engineered strain can be easily deduced by clustering analysis of metabolic fingerprints.
Fluorimetric determination of intra‐ and extracellular free amino acids in the microalgae Tetraselmis gracilis (Prasinophyceae) using monolithic column in reversed phase mode
Authors: Pires Penteado José Carlo , Rigobello‐Masini Marilda , Wanderlei Liria Cleber , Machini Miranda M. Terêsa , Masini Jorge Cesar
Published: June 2009

This paper describes the development and application of an RP HPLC method using a C18 monolithic stationary phase for the separation and quantification of extra‐ and intracellular amino acids in a batch cultivation of the marine alga Tetraselmis gracilis. Fluorimetric detection was made after separation of the o‐phthaldialdehyde 2‐mercaptoethanol (OPA‐2MCE) derivatives using a binary gradient elution. Separation of 19 amino acids was achieved with resolution >1.5 in about 39 min at a flow rate of 1.5 mL/min. RSD of analyses in seawater medium ranged from 0.36% for Orn (0.50 μmol/L) to 12% for Ile (0.10 μmol/L). The main constituents of the intracellular dissolved free amino acids (DFAAs) in the exponential growth phase were arginine (Arg), asparagine (Asn), alanine (Ala), aspartic acid (Asp), glutamic acid (Glu), serine (Ser), glycine (Gly), glutamine (Gln), and leucine (Leu). The major amino acids excreted to the media were valine (Val), Ala, Ser, and Gly. The monolithic phase facilitates the analysis by shortening the separation time and saving solvents and instrumentation costs (indeed conventional HPLC instrumentation can be used, running at lower pressures than those ones used with packed particle columns).
Profiling of endogenous peptides by multidimensional liquid chromatography: On‐line automated sample cleanup for biomarker discovery in human urine
Authors: Machtejevas Egidijus , Marko‐Varga Gyorgy , Lindberg Claes , Lubda Dieter , Hendriks Robertus , Unger Klaus K.
Published: June 2009

A simple and flexible system, employing a column switching technique, has been designed to allow the analysis of peptides and proteins smaller than 15 kDa by molecular weight in filtered urine samples by performing a direct on‐column injection utilising simultaneous sample clean‐up and trace enrichment. The positively charged peptides and small proteins in the sample are attracted to the inner, negatively charged pore structure of the RAM‐SCX column while the larger proteins and uncharged or negatively charged compounds are excluded. After preconditioning with the biological sample, large amounts of sample can be injected. Several important and adjustable parameters for the proper use of a RAM‐SCX column are described and discussed. The main parameters being: i) the column is sensitive to sample overloading, which may result in drastic changes in the adsorption of peptides; ii) adsorption appears to be flow‐rate and concentration dependent, as the sample molecules need time to penetrate into the internal pore structure in order to find complimentary orientated adsorption sites; iii) dilution and pH adjustment of sample during the loading process. The biocompatibility and proof‐of‐principle of this separation platform was demonstrated using human urine samples. Data are presented on repeatability as well as on the reproducibility of different synthesised batches of restricted access material (RAM).
Use of ultra‐high‐pressure liquid chromatography–quadrupole time‐of‐flight MS to discover the presence of pesticide metabolites in food samples
Authors: Hernández Félix , Grimalt Susana , Pozo Óscar J. , Sancho Juan V.
Published: June 2009

In this paper we illustrate the use of two different methodologies to investigate the presence of pesticide metabolites in parent pesticide‐positive food samples, using ultra‐high‐pressure liquid chromatography coupled to hybrid quadrupole time‐of‐flight (UHPLC–QTOF) mass spectrometry. First, a common fragmentation pathway between the parent pesticide and its metabolites has been considered to search for metabolites in two positive market samples (imazalil in lemon, chlorpyrifos in grape). Secondly, olive oil samples from field residue trials were used for automated application of comparative software (MetaboLynx), which was used with treated and untreated samples to search for expected and unexpected metabolites of phosmet. One of the main objectives when using these approaches was to avoid the tedious manual searching for potential metabolites within the huge amount of information contained in the total ion chromatogram acquired by TOF MS. The common fragmentation approach applied to TOF MS full‐acquisition data, considering an enhanced fragmentation in the collision cell, has allowed the discovery of two metabolites of imazalil (1‐[2‐(2,4‐dichlorophenyl)‐2‐hydroxyethyl]‐1H‐imidazole and 1‐[2‐(2,4‐dichlorophenyl)‐2‐oxoethyl]‐1H‐imidazole) in a lemon positive sample, as well as another two metabolites of chlorpyrifos (chlorpyrifos‐oxon and 3,5,6‐trichloro‐2‐pyridinol) in a grape positive sample. Moreover, MetaboLynx application to TOF MS data, without promoting fragmentation, from treated and untreated olive oil samples has been helpful in detecting the metabolite phosmet‐oxon. In both strategies, every metabolite detected by TOF MS was confirmed using QTOF and/or triple quadrupole instruments. Accurate masses given by TOF MS together with the valuable information on product ions given by QTOF MS/MS experiments were crucial for the unambiguous identification of metabolites.
Preparation and characterization of microporous fibers for sample preparation and LC‐MS determination of drugs
Authors: Buszewski Boguslaw , Nowaczyk Jacek , Ligor Tomasz , Olszowy Pawel , Ligor Magdalena , Wasiniak Bartlomiej , Miekisch Wolfram , Schubert Jochen K. , Amann Anton
Published: June 2009

The aim of this study was the preparation of polypyrrole (PPy) fibers for solid phase microextraction (SPME). PPy coatings were obtained during the electrochemical polymerization process. The utility of various metal wires (Fe, Cu, Ag, Cu/Ag, kanthal and medical stainless steel) as a support for polymers was compared. Various experimental conditions of the synthesis process such as scan rate, voltage limits and number of scans and deposition time were applied. The average polymer thickness was in the range of 7–125 μm and its weight was in the scope of 0.65–5.6 mg. Different techniques, mainly elemental analysis, Fourier transform infrared spectroscopy, microscopy, and chromatography were performed for the characterization of obtained fibers with microporous structure. The extraction efficiency of cardiovascular drugs (metoprolol, propranolol, oxprenolol, propafenone and mexiletine) by means of fibers was tested. The concentration of mentioned compounds in standard solution was in the span of 10–150 ng/mL. LC‐MS was employed for determination of drugs in desorption solution. LODs varied from 0.013 to 1.51 ng/mL for metoprolol and mexiletine respectively. The repeatability of extraction was obtained with the RSD values lower than 10%.
Fast GC‐FID based metabolic fingerprinting of Japanese green tea leaf for its quality ranking prediction
Authors: Jumtee Kanokwan , Bamba Takeshi , Fukusaki Eiichiro
Published: June 2009

There is a need of reliable, rapid, and cost‐effective analysis technique to evaluate food and crop compositions, which are important to improve their qualities and quantities. Prior to fast GC‐FID development, metabolic fingerprints, and predictive models obtained from a conventional GC‐FID were evaluated by comparison to those derived from GC‐TOF‐MS. A similar chromatographic pattern with higher sensitivity of polyphenol compounds including epicatechin gallate (ECg) and epigallocatechin gallate (EGCg) had been achieved by using conventional GC‐FID. Fast gas chromatograph coupled with flame ionization detector (GC‐FID) has been carried out with 10 m×0.18 mm id×0.20 μm df capillary column. The analysis time per sample was reduced to less than 14 min compared to those of a conventional GC‐FID (38 min) and GC‐TOF‐MS (28 min). The fast GC‐FID also offered reliable retention time reproducibility without significant loss of peak resolution. Projections to latent structures by means of partial least squares (PLS) with orthogonal signal correction filtering (OSC) was applied to the fast GC‐FID data. The predictive model showed good model fit and predictability with RMSEP of 3.464, suggesting that fast GC‐FID based metabolic fingerprinting could be an alternative method for the prediction of Japanese green tea quality.
The detection and quantification of lorazepam and its 3‐O‐glucuronide in fingerprint deposits by LC‐MS/MS
Authors: Goucher Edward , Kicman Andrew , Smith Norman , Jickells Sue
Published: June 2009

The use of fingerprints as an alternative biological matrix to test for the presence of drugs and/or their metabolites is a novel area of research in analytical toxicology. This investigation describes quantitative analysis for the benzodiazepine lorazepam and its 3‐O‐glucuronide conjugate in fingerprints following the oral administration of a single 2 mg dose of lorazepam to five volunteers. Creatinine was also measured to investigate whether the amount of drug relative to that of creatinine would help to account for the variable amount of secretory material deposited. Fingerprints were deposited on glass cover slips and extracted by dissolving them in a solution of dichloromethane/methanol, containing tetradeuterated lorazepam as an internal standard. The samples were evaporated, reconstituted with mobile phase and analysed by LC‐MS/MS. Chromatography was achieved using an RP (C18) column for the analysis of lorazapem and its glucuronide, and a hydrophilic interaction column (HILIC) for the analysis of creatinine. Lorazepam and its glucuronide were only detected where ten prints had been combined, up to 12 h following drug administration. In every case, the amount of lorazepam glucuronide exceeded that of lorazepam, the peak amounts being 210 and 11 pg, respectively. Adjusting for creatinine smoothed the elimination profile. To our knowledge, this represents the first time a drug glucuronide has been detected in deposited fingerprints.
General unknown screening procedure for the characterization of human drug metabolites: Application to loratadine phase I metabolism
Authors: Picard Nicolas , Dridi Dorra , Sauvage François‐Ludovic , Boughattas Naceur A. , Marquet Pierre
Published: June 2009

This article describes the application of a recently developed general unknown screening (GUS) strategy based on LC coupled to a hybrid linear IT‐triple quadrupole mass spectrometer (LC‐MS/MS‐LIT) for the simultaneous detection and identification of drug metabolites following in vitro incubation with human liver microsomes. The histamine H1 receptor antagonist loratadine was chosen as a model compound to demonstrate the interest of such approach, because of its previously described complex and extensive metabolism. Detection and mass spectral characterization were based on data‐dependent acquisition, switching between a survey scan acquired in the ion‐trapping Q3 scan mode with dynamic subtraction of background noise, and a dependent scan in the ion‐trapping product ion scan mode of automatically selected parent ions. In addition, the MS3 mode was used in a second step to confirm the structure of a few fragment ions. The sensitivity of the ion‐trapping modes combined with the selectivity of the triple quadrupole modes allowed, with only one injection, the detection and identification of 17 phase I metabolites of loratadine. The GUS procedure used in this study may be applicable as a generic technique for the characterization of drug metabolites after in vitro incubation, as well as probably in vivo experiments.
Separation and sensitive detection of D‐amino acids in biological matrices
Authors: Kirschner Daniel L. , Green Thomas K.
Published: June 2009

The increase in our understanding of D‐amino acid function and distribution in mammals is in many ways a result of the initial development of sensitive enantioselective separation strategies that allow for quantification in real biological samples. This article reviews progress on the development of chiral selective separation and detection of D‐amino acids including enzyme‐based microbiosensors, GC/MS, HPLC/fluorescence, HPLC/MS‐MS, cEKC/fluorescence, and MEKC/fluorescence. Only methods capable of analyzing D‐isomers in biological matrices are given here and significant effort is made to highlight approaches that offer speed, resolution, high sensitivity, and versatility.
Non‐targeted metabolite fingerprinting of oriental folk medicine Angelica acutiloba roots by ultra performance liquid chromatography time‐of‐flight mass spectrometry
Authors: Tianniam Sukanda , Bamba Takeshi , Fukusaki Eiichiro
Published: June 2009

The potential of ultra‐performance (UP)LC‐TOF‐MS based metabolite fingerprinting was explored in the attempt to establish a standard methodology for the quality control of dried angelica roots (Angelica acutiloba) in commercial markets. Accurate mass chromatographic fingerprints of positive and negative ion modes were collected simultaneously at a high‐throughput manner with high resolution and sensitivity, where analysis of hydrophobic, low molecular weight compounds, which includes secondary metabolites, could be achieved. The comparison of various metabolite profiles was performed through the use of chemometric technique, in which distinct partitioning of root samples was effectively achieved by principal component analysis. The discrimination was illustrated to have been subjective to cultivation area and was reported to be an important influential factor for quality determination. Further insights to the chemical constituents in relation to quality were attained where some ion markers significantly linked to dissociation of angelica roots were tentatively identified as some secondary metabolites. Reliable classification models by partial least square discriminant analysis gave good capability in categorizing test set samples. Overall, through the utilization of UPLC‐TOF‐MS, analysis could be attained with great sufficiency and accuracy for angelica root discrimination.
Fast liquid chromatography separation and multiple‐reaction monitoring mass spectrometric detection of neurotransmitters
Authors: Hammad Loubna A. , Neely Matthew , Bridge Bob , Mechref Yehia
Published: June 2009

We describe here the fast LC‐MS/MS separation of a mixture of neurotransmitters consisting of dopamine, epinephrine, norepinephrine, 3,4‐dihydroxybenzylamine (DHBA), salsolinol, serotonin, and γ‐aminobutyric acid (GABA). The new UltiMate® 3000 Rapid Separation system (RSLC) was successfully coupled to the 4000 QTRAP mass spectrometer operating in multiple‐reaction monitoring (MRM) mode. The separation was attained using a 100 mm length, 2.2 μm particle size Acclaim column at a flow rate of 0.5 mL/min. The column back pressure was 350 bar, while the total run time including column re‐equilibration was 5.2 min. The peak resolution was minimally affected by the fast separation. The RSLC‐MRM separation was found to have a precision range based on peak area for 50 replicate runs of 2–5% CV for all analytes, and the reproducibility of the retention time for all analytes was found to range from 0–2% CV. The described method represents an almost seven times shorter analysis time of neurotransmitters using LC/MRM which is very useful in screening large quantities of biological samples for various neurotransmitters.
Suitability of silica hydride stationary phase, aqueous normal phase chromatography for untargeted metabolomic profiling of Enterococcus faecium and Staphylococcus aureus
Authors: Weisenberg Scott A. , Butterfield Tiffany R. , Fischer Steven M. , Rhee Kyu Y.
Published: June 2009

We report the robustness of silica hydride stationary phase, aqueous normal phase (ANP) chromatography to the chemical complexity of the intracellular metabolomes of Staphylococcus aureus and Enterococcus faecium. We specifically demonstrate that the chromatographic behavior of known metabolites is unaffected by the intracellular chemical matrix of these microbes and that this method enables untargeted profiling of their intracellular metabolites using accurate mass‐retention time (AMRT) identifiers. We further demonstrate the ability of AMRT‐based metabolite profiling to differentiate bacteria along genetic and phenotypic lines. Overall, these data commend the utility of ANP‐based chromatography for untargeted metabolomics‐based studies of microbial physiology and antibiotic resistance.
Analysis of hydrophilic metabolites in physiological fluids by HPLC‐MS using a silica hydride‐based stationary phase
Authors: Pesek Joseph J. , Matyska Maria T. , Loo Joseph A. , Fischer Steven M. , Sana Theodore R.
Published: June 2009

Aqueous normal‐phase chromatography was used for the analysis of metabolites in human saliva and urine samples. The column was packed with a silica hydride type separation material. Several gradients were tested with different mobile phase additives in order to produce retention for amino acids, small organic acids, and carbohydrates. Detection was done by TOF MS. In some cases the relative concentration levels of various metabolites in human saliva were compared for normal patients and patients with pancreatic cancer or pancreatitis. The reproducibility of retention of individual metabolites in these complex matrices was tested for several compounds.
Post‐fire land degradation of Pinus sylvestris L. woodlands after 14 years
Authors: Pérez‐Cabello F. , Ibarra P. , Echeverría M. T. , de la Riva J.
Published: June 2009

This study analysed medium‐term degradation in Pinus sylvestris L. woodland affected by wildfire. To investigate recovery, a range of pedological (including thickness of the organic horizon, soil structure and texture, organic matter content, pH and the percentage of carbonates), geomorphological and vegetation parameters were assessed in comparable burnt and control plots. Main findings suggest that fire in the medium‐term leads to severe degradation of P. sylvestris L. woodland ecosystems. The main consequences of the passage of fire are: (1) transformation of P. sylvestris L. woodlands into shrublands dominated by Genista scorpius (L.) DC, Buxus sempervirens L. and herbaceous species; (2) decrease in the thickness of the O horizon and its degradation and (3) increase in soil erosion features, due to the detachment of soil particles by rain‐splash or overland flow and their transport downslope. These results could help to provide guidelines for the restoration of burnt areas to minimise the effects of wildfires. Copyright © 2009 John Wiley & Sons, Ltd.
Edaphic indicators for assesment of soil erosion in karst regions, province of Havana, Cuba
Authors: Febles J. M. , Tolón A. , Vega M. B.
Published: June 2009

No sustainability indicator reports have as yet been published reflecting the dynamics of morphogenetic processes in red ferralitic soils (Ferralsol Rhodic in the World Reference Base) in the karstic regions of Havana Province, which have led to sequential degradation of the most productive soils of Cuba. This article proposes an edaphic indicator system, through which the sustainability threshold of these soils are specified for reference localities based on research carried out over more than two decades by means of a combination of qualitative and quantitative data in three key time periods of Cuban agriculture. These indicators generally show a trend towards degradation of soil properties, especially in 1980s, due to the indiscriminate use of agricultural machinery, overgrazing and intensive farming practices that have led to dense compaction with thresholds of apparent density exceeding 1·34 Mg m−3, at 0–30 cm levels in soil. Copyright © 2009 John Wiley & Sons, Ltd.
Gully erosion, land use and topographical thresholds during the last 60 years in a small rangeland catchment in SW Spain
Authors: Gutiérrez Álvaro Gómez , Schnabel Susanne , Contador Francisco Lavado
Published: June 2009

Gully erosion plays an important role in degradation processes of Mediterranean environments. In this paper aerial orthophotographs were used for (i) analysing the evolution of a valley bottom gully and its relation with land use and vegetation cover, (ii) exploring the role of land use and vegetation cover on the coefficients of the equation S = aA −b (where S is slope at the headcut and A is drainage area), which is based on the topographical threshold concept and is commonly used to predict gully initiation. The study was carried out in a small catchment (99·5 ha) located in the southwest of the Iberian Peninsula. Gullies and headcuts were mapped together with land use and vegetation cover using aerial photographs for the years 1945, 1956, 1989, 1998, 2002 and 2006, which had to be digitized and orthorectified in advance. The results showed an increase of the area affected by gullying from 695 m2 in 1945–1009 m2 in 2006, reaching a maximum of 1560 m2 in 1956. Gullying was closely related with land use, especially with the amount of cultivated areas within the catchment and also with grazing intensity. No clear relationship was found between the evolution of the gullied area and rainfall amounts. Finally, the values of the exponent b obtained for different headcuts and different dates (close to 0·4) were similar to those proposed by other authors for gully erosion caused by Hortonian overland flow in semiarid environments. Copyright © 2009 John Wiley & Sons, Ltd.
Community participation in the rehabilitation of a sand dune environment in Kenya
Authors: Olukoye G. A. , Kinyamario J. I.
Published: June 2009

This study aims to document various community efforts in land rehabilitation and assess their potential. Data were captured using interviews and focus group with 150 community members. A public participation index was used to establish the extent of community efforts in land rehabilitation. The study revealed that in the absence of proper management and dune stabilisation, large areas covered with mobile sand dunes continue to be a threat to grazing lands in northern Kenya. In recognition of this threat, the people of North Horr have launched several initiatives to contain the problem. Environmental and non‐environmental group members scored participation rates (PP) of 87·5 and 50%, respectively. These include tree planting on both communal and individual plots and the management of Suaeda monoica through natural regeneration. Although the survival rates of most planted trees on group plots were low, Azadirachta indica that were planted on individual homesteads appeared to be performing comparatively well. Natural regeneration of indigenous plant species such as Suaeda monoica has the potential to perform important economic and ecological functions. The study concludes that in order to effectively arrest the process of desertification on the pastoral drylands of northern Kenya and to restore productivity and biodiversity, it is important to take actions that incorporate both biophysical and human considerations. Linking sociology to ecology is thus paramount in any sustainable dune stabilisation (SDS) programme. Copyright © 2009 John Wiley & Sons, Ltd.
Deserts and desertification: Challenges but also opportunities
Authors: Safriel Uriel
Published: June 2009

The UN decision to couple ‘deserts’ and ‘desertification’ in addressing the year 2006 (as well as the following decade) as ‘Year (or Decade) of Deserts and Desertification’ sends several wrong messages regarding both the nature of deserts as natural ecosystems and of desertification as a human‐driven process that reduces the provision of ecosystem services of soil conservation and of biological productivity, specifically in non‐desert areas, more than in desert ones. A new approach to addressing sustainable development in the drylands was presented in an international conference that took place at the end of the ‘International Year’ and hosted by the Blaustein Institutes for Desert Research in Sede Boqer, Israel. This approach (a) qualifies drylands as ecosystems whose biological productivity is constrained by water and hence it is naturally low compared to that of most other terrestrial ecosystems; (b) qualifies desertification as a further persistent reduction of productivity in the drylands brought about mainly through human impact mostly driven by population increase; (c) observes that within the drylands natural productivity linearly declines with aridity, and suggests that sensitivity to impact linearly increases with aridity; (d) further suggests that population density generates the impact, and observes that population density in drylands increases exponentially as aridity declines; and (e) suggests that the product of the linear sensitivity and the exponential impact generates a desertification peak at the transition between non‐desert drylands (where desertification and poverty are high) and the desert drylands (where both are very low). Given these, the Sede Boqer approach suggests that (a) rather than be construed as an adversity, desert drylands offer opportunities to their inhabitants since their environmental conditions are conducive for livelihoods mostly independent of the desert's very low productivity; this includes solar energy development and tourism, but also (counterintuitively!) desert aquaculture; (b) non‐desert drylands, on the other hand, face a serious challenge of becoming desertified, mainly due to increasing population; and (c) global climate change further increases the success of alternative livelihoods in deserts, may create opportunities in some of the non‐desert drylands too, but amplifies the challenges facing non‐desert drylands people. Caution and prudence are required to meet these challenges, especially since currently socio‐political measures are in shorter supply than technological fixes. Copyright © 2009 John Wiley & Sons, Ltd.