bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractA 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

AbstractDetermination 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

AbstractRecent 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

AbstractBackgroundSmall 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.MethodsDifferent electrostatic complexes of HA and PLR (HPs) were formulated: HP101 with 50% (w/w) HA and HP110 with 9% (w/w) HA.ResultsGel 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.ConclusionsHP101 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

AbstractBackgroundA 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.MethodsA 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.ResultsThe 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.ConclusionsThe 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

Abstract
magnified image(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

Abstract
magnified image1‐(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

Abstract
magnified imageInteraction 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

AbstractAcross 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

AbstractDue 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

AbstractMetabolomics 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

AbstractThis 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

AbstractA 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

AbstractIn 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

AbstractThe 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

AbstractThere 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.