bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrochemical Oxidation of ds‐DNA on Polypyrrole Nanofiber Modified Pencil Graphite Electrode
Authors: Özcan Ali , Şahin Yücel , Özsöz Mehmet , Turan Servet
Published: September 2007

Preparation of a polypyrrole nanofiber (PPyNF) modified pencil graphite (PG) electrode and its usage in the electrochemical DNA biosensors was investigated. The electrodes (PPyNF/PG1 and PPyNF/PG2) were prepared from a solution containing 0.1 M pyrrole, 0.1 M Na2CO3 and 0.1 M LiCIO4 by using potentiostatic and potentiodynamic methods. PPyNF/PG2 electrodes which were prepared by potentiostatic procedure showed higher responses for the oxidation of ds‐DNA than the PPyNF/PG1 electrodes prepared by potentiodynamic methods. Immobilization of the ds‐DNA on PG and PPyNF/PG surfaces was performed at a constant potential, +0.5 V, for 300 s in 0.5 M ABS (pH 4.8) containing 15 μg mL−1 ds‐DNA and 20 mM LiCIO4. The oxidation peak potentials of the ds‐DNA bases, guanine and adenine, were shifted to more cathodic values by using PPyNF/PG electrodes. The oxidation signal of the guanine base of ds‐DNA was decreased in the presence of methylene blue.
Bismuth Film Electrode as an Alternative for Mercury Electrodes: Determination of Azo Dyes and Application for Detection in Food Stuffs
Authors: Claux Benoît , Vittori Olivier
Published: September 2007

Bismuth electrodes were investigated and exhibit electrochemical properties similar to mercury electrodes but with much lower toxicity. An electrochemical application of bismuth film modified glassy carbon electrode for azo dyes determination was investigated. The plating step was optimized in order to achieve its analytical efficiency. A plating potential of −0.9 V in a solution of 200 mg/L Bi(NO3)3, 0.5 M HNO3 for 100 s yields to a suitable electrode (in terms of stability and detection). Azo dyes such as azorubine (i.e., carmoisine, E122), amaranth (E123), ponceau 4R (i.e., new coccine, E124) and allura red (E129) were determined by differential pulse voltammetry in a NaCl solution in the concentration range of few ppm to 100 ppm. The reproducibility of the signal, characterized by the relative standard deviation, was found to be less than 5%, the detection and quantification limits were few mg/L. The influence of other food components on the signal was studied and the applicability was tested on real beverages samples.
Preparation of Carbon Nanotubes/Neutral Red Composite Film Modified Electrode and Its Catalysis on Rutin
Authors: Wang Guangfeng , Hu Nianjun , Wang Wen , Li Pengcheng , Gu Haochen , Fang Bin
Published: September 2007

Neutral red was directly electropolymerized onto the carbon nanotubes modified electrode. A polymerized neutral red/carbon nanotubes composite film was characterized by scanning electron micrograph (SEM) and cyclic voltammetry (CV). Well‐defined voltammetric responses are observed for [Fe(CN)6]4−/3− on the composite film modified glassy carbon electrode. And it's found that this modified electrode has good catalysis on the redox of rutin. Differential pulse voltammetry method was used to determinate the concentration of rutin and obtain a linear equation between the current and concentration in a certain range. The modified electrode is satisfied with us for its good sensibility and stability.
A Nanocomposite Chitosan Based on Ferrocene‐Modified Silica Nanoparticles and Carbon Nanotubes for Biosensor Application
Authors: Qiu Jian‐Ding , Guo Jin , Liang Ru‐Ping , Xiong Meng
Published: September 2007

A novel amperometric biosensor for glucose was developed by entrapping glucose oxidase (GOD) in a chitosan composite doped with ferrocene monocarboxylic acid‐aminated silica nanoparticles conjugate (FMC‐ASNPs) and multiwall carbon nanotubes (MWNTs). The entrapped FMC‐ASNPs conjugate performed excellent redox electrochemistry and the presence of MWNTs improved the conductivity of the composite film. This matrix showed a biocompatible microenvironment for retaining the native activity of the entrapped GOD and was in favor of the accessibility of substrate to the active site of GOD, thus the affinity to substrates is improved greatly. Under optimal conditions this biosensor was able to detect glucose with a detection limit of 10 μM (S/N=3) in the linear range of 0.04 to 6.5 mM. The proximity of these three components FMC‐ASNPs, MWNTs and GOD enhanced the electron transfer between the film and electrode. This composite film can be extended to immobilize other enzymes and biomolecules, which will greatly facilitate the development of biosensors and other bioelectrochemical devices.
CE methods applied to the analysis of micronutrients in foods
Authors: Cheung Rodney Hau Fung , Marriott Philip J. , Small Darryl M.
Published: September 2007

This article reviews the applications of CE that are relevant to the analysis of small molecules in foods. CE has been applied to a wide range of important areas of food analysis and is rapidly being established as an alternative technique to chromatographic methods including HPLC and GC within analytical food and research laboratories. In recent years the analysis of food by CE has become more frequent and important and as such a variety of compounds have been separated and quantified. Although many other analytes have been detected by CE, this review will highlight areas relating primarily to the rather broad chemical classes of free amino acids, carbohydrates, organic acids, vitamins and a variety of antioxidants. In addition, information relating to the analyte, sample matrix, mode of CE employed, scope of the methodology and the detection and derivatization of the small molecules are considered and discussed.
CZE for the speciation of arsenic in aqueous soil extracts
Authors: Kutschera Kristin , Schmidt Anne‐Christine , Köhler Stefan , Otto Matthias
Published: September 2007

We developed two separation methods using CZE with UV detection for the determination of the most common inorganic and methylated arsenic species and some phenylarsenic compounds. Based on the separation method for anions using hydrodynamic sample injection the detection limits were 0.52, 0.25, 0.27, 0.12, 0.37, 0.6, 0.6, 1.2 and 1.0 mg As/L for phenylarsine oxide (PAO), p‐aminophenylarsonic acid (p‐APAA), o‐aminophenylarsonic (o‐APAA), phenylarsonic acid (PAA), 4‐hydroxy‐3‐nitrobenzenearsonic acid (roxarsone), monomethylarsonic acid (MMA), dimethylarsinic acid (DMA), arsenite or arsenious acid (AsIII) and arsenate (AsV), respectively. These detection limits were improved by large‐volume sample stacking with polarity switching to 32, 28, 14, 42, 22, 27, 26 and 27 μg As/L for p‐APAA, o‐APAA, PAA, roxarsone, MMA, DMA, AsIII and AsV, respectively. We have applied both methods to the analysis of the arsenic species distribution in aqueous soil extracts. The identification of the arsenic species was validated by means of both standard addition and comparison with standard UV spectra. The comparison of the arsenic species concentrations in the extracts determined by CZE with the total arsenic concentrations measured by inductively coupled plasma‐atomic emission spectroscopy (ICP‐AES) indicated that CZE is suited for the speciation of arsenic in environmental samples with a high arsenic content. The extraction yield of phenylarsenic compounds from soil was derived from the arsenic concentrations of the aqueous soil extracts and the total arsenic content of the soil determined by ICP‐AES after microwave digestion. We found that 6–32% of the total amount of arsenic in the soil was extractable by a one‐step extraction with water in dependence on the type of arsenic species.
Application of CE with novel dynamic coatings and field‐amplified sample injection to the sensitive determination of isomeric benzoic acids in atmospheric aerosols and vehicular emission
Authors: Dabek‐Zlotorzynska Ewa , Piechowski Maria
Published: September 2007

A simple and reliable CE method with direct UV detection has been developed to separate eight isomeric benzoic acids in atmospheric aerosols and vehicular emission without complex sample pretreatment. Optimal electrophoretic conditions, with migration times under 5 min, were obtained by using a 50 mM acetate buffer (pH 4.7) containing a dynamic surface coating EOTrol™ LN (0.005% w/v). The separations were carried out in a cathode to anode direction (−30 kV) allowing the low cathodal EOF (∼1×10−9 m2V−1s−1) to extend the effective separation by slowing the movement of the studied aromatic acids. Moreover, the sensitivity of the method at 200 nm was enhanced by using a field‐amplified sample injection (FASI) with electrokinetic (EK) sample injection (−2 kV, 60 s). Prior to sample injection, a short water plug (3 s at 0.5 psi) was introduced. Under these conditions, the method was capable of detecting the analytes in deionized water with LODs (S/N = 3) as low as 0.1 μg/L for most of the studied acids. In the presence of 10 mg/L of sulphate (added to simulate a sample matrix), LODs ranged from 0.26 to 0.62 μg/L. The validation of the method has proven an excellent separation performance and accuracy for the determination of isomeric benzoic acids in the studied matrices.
CE in anticancer metallodrug research – an update
Authors: Hartinger Christian G. , Keppler Bernhard K.
Published: September 2007

With the current demographic development and the knowledge that the probability to be diagnosed with cancer increases with age, the search for new treatment options in cancer chemotherapy is of utmost importance for the society. Capillary electrophoretic methods have been applied in the last few years for studying the properties of metal‐based drugs and drug candidates. Especially, the elucidation of the mode of action of such compounds could contribute significantly to design new drugs for overcoming the threat of cancer. This review article highlights the developments in metallodrug research applying CE during the last 4 years and follows a review from 2003 (Hartinger, C. G., Timerbaev, A. R., Keppler, B. K., Electrophoresis 2003, 24, 2023–2037). Most importantly the broadening of application areas of CE must be noted: especially the binding studies of metal complexes toward proteins (including the determination of association and rate constants), following redox reactions of metal complexes and their influence on the reactivity toward biotargets, etc. are important development areas of the last few years. In parallel with these new applications goes the usage of new or modified separation methods including microemulsion EKC or ACE, or the advantageous use of equipping the CE system with mass spectrometric detectors such as inductively coupled plasma (ICP) or ESI mass spectrometers (MS) for determining the degree of metallation of a protein or characterizing the adducts. Finally, upcoming requirements for expanding the method's application area are discussed including studies on new targets in the cell, analyzing real‐world samples, methodological development, and contributions to improve the design of new anticancer agents.
Determination of vigabatrin in human plasma by means of CE with LIF detection
Authors: Musenga Alessandro , Mandrioli Roberto , Comin Irene , Kenndler Ernst , Raggi Maria Augusta
Published: September 2007

A method has been developed for the quantitation of the antiepileptic drug vigabatrin (VGB) in human plasma. It is based on CE with LIF detection. The effect of the pH of the buffer and of N‐methylglucamine (GLC) as BGE constituent was investigated. The final BGE consisted of 50 mM borate buffer, pH 9.0, with 100 mM GLC and enabled separation within 12 min at 20 kV voltage. An SPE procedure was used for the pretreatment of biological samples, based on mixed‐mode lipophilic‐cation exchange cartridges, followed by a derivatization step with 6‐carboxyfluorescein‐N‐succinimidyl ester (CFSE). Fluorescence was excited by an Ar‐ion laser (λexc = 488 nm). Linearity was observed in the 10–120 μg/mL plasma concentration range. Extraction yield was >96%, precision (expressed as RSD) <6.7% and accuracy (recovery) was between 97.0 and 101.6%. The method has been successfully applied to the analysis of VGB in plasma of epileptic patients undergoing therapy with the drug.
Fluorinated ethylenepropylene copolymer as a potential capillary material in CE
Authors: Evenhuis Christopher J. , Yang Wen‐Chu , Johns Cameron , Macka Miroslav , Haddad Paul R.
Published: September 2007

In this work, a new generation UV‐transparent polymer, fluorinated ethylenepropylene copolymer (FEP) exhibiting a low degree of crystallinity, extruded in dimensions similar to the most commonly used CE capillaries of ∼80 μm id and about 360 μm od was investigated for its use as a CE capillary. FEP is transparent down to the low‐UV region, and as fluorinated polymers in general are good electrical insulators and exhibit reasonable heat conductivity, it has considerable potential as a material for electrodriven analysis in capillary or microchip formats. The FEP capillary has been characterised with regard to some important aspects for its use as a CE capillary, including its profile of EOF versus pH, as well as procedures for manipulating EOF by coating the inner capillary wall with various semipermanent and dynamic layers. The FEP capillaries were tested and compared with fused‐silica capillary for the separation of inorganic and small organic ions using conditions involving direct and indirect detection in the low‐UV region. Finally, advantages of the use of the FEP capillary for simultaneous detection of a mixture containing nine inorganic cations and anions using indirect photometric detection with a movable light‐emitting diode (LED) detector and a novel electrolyte are demonstrated.
Analysis of inorganic and small organic ions by CE with amperometric detection
Authors: Chen Rongsheng , Cheng Han , Wu Wenzhan , Ai Xiaoni , Huang Weihua , Wang Zongli , Cheng Jieke
Published: September 2007

Capillary electrophoresis has become a widely useful analytical technology. Amperometric detection is extensively employed in capillary electrophoresis for its many inherent virtues, such as rapid response, remarkable sensitivity, and low cost of both detectors and instrumentations. Analysis of inorganic and small organic ions by capillary electrophoresis is an important research field. This review focuses on the recent developments of capillary electrophoresis coupled with amperometric detection for analysis of inorganic and small organic ions. Advancements in electrophoresis separation modes, amperometric detection modes, working electrodes, and applications of inorganic ions, amino acids, phenols, and amines are discussed.
Rainfall‐induced consolidation and sealing effects on soil erodibility during concentrated runoff for loess‐derived topsoils
Authors: Knapen A. , Poesen J. , Baets S. De
Published: September 2007

Flume experiments simulating concentrated runoff were carried out on remolded silt loam soil samples (0·36 × 0·09 × 0·09 m3) to measure the effect of rainfall‐induced soil consolidation and soil surface sealing on soil erosion by concentrated flow for loess‐derived soils and to establish a relationship between soil erodibility and soil bulk density. Soil consolidation and sealing were simulated by successive simulated rainfall events (0–600 mm of cumulative rainfall) alternated by periods of drying. Soil detachment measurements were repeated for four different soil moisture contents (0·04, 0·14, 0·20 and 0·31 g g−1). Whereas no effect of soil consolidation and sealing is observed for critical flow shear stress (τcr), soil erodibility (Kc) decreases exponentially with increasing cumulative rainfall depth. The erosion‐reducing effect of soil consolidation and sealing decreases with a decreasing soil moisture content prior to erosion due to slaking effects occurring during rapid wetting of the dry topsoil. After about 100 mm of rainfall, Kc attains its minimum value for all moisture conditions, corresponding to a reduction of about 70% compared with the initial Kc value for the moist soil samples and only a 10% reduction for the driest soil samples. The relationship estimating relative Kc values from soil moisture content and cumulative rainfall depth predicts Kc values measured on a gradually consolidating cropland field in the Belgian Loess Belt reasonably well (MEF = 0·54). Kc is also shown to decrease linearly with increasing soil bulk density for all moisture treatments, suggesting that the compaction of thalwegs where concentrated flow erosion often occurs might be an alternative soil erosion control measure in addition to grassed waterways and double drilling. Copyright © 2007 John Wiley & Sons, Ltd.
The chronology and long term dynamics of a low energy river system: the Kelvin Valley, central Scotland
Authors: Tipping R. , Jones A. P. , Carter S. , Holden T. , Cressey M.
Published: September 2007

The long term (Holocene) channel and floodplain dynamics of a low gradient, low energy, fine grained aggradational fluvial system within a formerly glaciated landscape in central Scotland, the Kelvin Valley, are described from a series of sediment stratigraphic transects and 12 14C assays in a headwater reach between Kirkintilloch and Kilsyth. The 14C assays and dated archaeological sites on the floodplain together suggest that the River Kelvin ceased to aggrade more than 2000 years ago, probably much more, so the 4–6 m of channel and floodplain deposits are almost entirely of early to mid‐Holocene age. The Kelvin Valley is characterized, despite its low flow characteristics, by a highly variable floodplain architecture, in which some transects suggest long term channel stability and strong partitioning of floodplain sedimentation and others indicate high channel mobility. This variation makes the application of general models of fluvial evolution difficult. Copyright © 2007 John Wiley & Sons, Ltd.
A new ultra‐fast contingency screening algorithm without time‐domain simulation for online transient security assessment
Authors: Nam H. K. , Kim Y. H. , Shim K. S. , Choi J. H. , Kwak N. H.
Published: September 2007

This paper proposes a new ultra‐fast contingency screening (CS) method for the transient security assessment (TSA). The method is based on the Single Machine Equivalent (SIME), but computes the critical clearing times (CCT) for given disturbances without the use of time‐domain simulations. All generators and loads are represented by a classical model and constant impedance model, respectively. The critical clustering is done using two stability indices, which are defined as the ratio of the accelerating power to the synchronizing power coefficient and the accelerating area to the decelerating area, respectively. Finally, the CCT is calculated using the equal‐area criterion to the equivalent one‐machine infinite‐bus system with the assumption that the rotor angles of the critical generators increase uniformly and the rotor angles of the non‐critical ones remain constant. The proposed CS method is tested on the 950‐bus, 230‐machine, 60‐Hz KEPCO system. Copyright © 2007 John Wiley & Sons, Ltd.
Optimal measurement placement for security constrained state estimation using hybrid genetic algorithm and simulated annealing
Authors: Kerdchuen T. , Ongsakul W.
Published: September 2007

This paper proposes a hybrid genetic algorithm and simulated annealing (HGS) for solving optimal measurement placement for power system state estimation. Even though the minimum number of measurement pairs is N considering the single measurement loss, their positions are required to make the system observable. HGS algorithm is a genetic algorithm (GA) using the acceptance criterion of simulated annealing (SA) for chromosome selection. The Pδ observable concept is used to check the network observability with and without single measurement pair loss contingency and single branch outage. Test results of 10‐bus, IEEE 14, 30, 57, and 118‐bus systems indicate that HGS is superior to tabu search (TS), GA, and SA in terms of higher frequency of the best hit and faster computational time. Copyright © 2007 John Wiley & Sons, Ltd.
Direct, adjoint and mixed approaches for the computation of Hessian in airfoil design problems
Authors: Papadimitriou D. I. , Giannakoglou K. C.
Published: September 2007

In this paper, four approaches to compute the Hessian matrix of an objective function used often in aerodynamic inverse design problems are presented. The computationally less expensive among them is selected and applied to the reconstruction of cascade airfoils that reproduce a prescribed pressure distribution over their walls, under inviscid and viscous flow considerations. The selected approach is based on the direct sensitivity analysis method for the computation of first derivatives, followed by the discrete adjoint method for the computation of the Hessian matrix. The applications presented in this paper show that the Newton method, based on exact Hessian matrices, outperforms other gradient‐based algorithms such as steepest descent or BFGS algorithm. Copyright © 2007 John Wiley & Sons, Ltd.
Association of human APOBEC3 cytidine deaminases with the generation of hepatitis virus B x antigen mutants and hepatocellular carcinoma
Authors: Xu Rongzhen , Zhang Xuzhao , Zhang Wei , Fang Yongmin , Zheng Shu , Yu Xiao-Fang
Published: September 2007

Human APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3) cytidine deaminases have been shown to be potent inhibitors of diverse retroviruses including Vif-deficient human immunodeficiency virus 1 (HIV-1), hepatitis virus B (HBV), adeno-associated virus, and endogenous retroelements. Despite the fact that these enzymes are known to be potential DNA mutators and to target retroviral DNA for cytidine deamination, the pathological effects of their deregulated expression in human diseases are not yet clear. Mutants of the viral HBx protein have been implicated in the carcinogenesis of hepatocellular carcinoma (HCC); however, little is known about how or why such mutants are generated in the human liver. Here, we report that a number of APOBEC3 deaminases preferentially edit the HBx region of HBV DNA and generate C-terminally truncated HBx mutants. Our functional studies indicated that APOBEC3-mediated HBx mutants, especially the C-terminally truncated mutants, cause a gain of function that enhances the colony-forming ability and proliferative capacity of neoplastic cells. Furthermore, we detected G-to-A hypermutation-mediated HBx mutants in preneoplastic liver tissues of selected patients with active chronic HBV infections. We also observed that the APOBEC3B (A3B) cytidine deaminase was widely up-regulated in HCC tumor tissues; it also promoted the growth of neoplastic human HepG2 liver cells and up-regulated heat shock transcription factor1 (HSF1) expression.

Conclusion:

These findings suggest that some of the APOBEC3 deaminases play a role in the carcinogenesis of HCC through the generation of HBx mutants, providing preneoplastic and neoplastic hepatocytes with a selective clonal growth advantage. Deregulated expression of A3B in liver tissues may also have the potential to promote genetic instability and tumorigenesis. (Hepatology 2007.)
Altered expression of the urokinase receptor homologue, C4.4A, in invasive areas of human esophageal squamous cell carcinoma
Authors: Hansen Line V. , Lærum Ole D. , Illemann Martin , Nielsen Boye S. , Ploug Michael
Published: September 2007

C4.4A is a glycolipid‐anchored membrane protein with structural homology to the urokinase‐type plasminogen activator receptor (uPAR). Although C4.4A was identified as a metastasis‐associated protein little is known about its actual expression and possible function in malignant disease. In the present study, we have therefore analyzed the expression of C4.4A in 14 esophageal squamous cell carcinomas (ESCC). Normal squamous esophageal epithelium shows a strong cell surface associated C4.4A expression in the suprabasal layers, whereas basal cells are negative. Upon transition to dysplasia and carcinoma in situ the expression of C4.4A is abruptly and coordinately weakened. Double immunofluorescence staining of normal and dysplastic tissue showed that C4.4A colocalizes with the epithelial cell surface marker E‐cadherin in the suprabasal cells and has a complementary expression pattern compared to the proliferation marker Ki‐67. A prominent, but frequently intracellular, C4.4A expression reappeared in tumor cells located at the invasive front and local lymph node metastases. Because C4.4A was reported previously to be a putative laminin‐5 (LN5) ligand, and both proteins are expressed by invasive tumor cells, we analyzed the possible coexpression of C4.4A and the γ2‐chain of LN5 (LN5‐γ2). Although these proteins are indeed expressed by either neighboring cancer cells or in a few cases even coexpressed by the same cells in the tumor front and metastases, we found no evidence for a general colocalization in the extracellular compartment by confocal microscopy. In conclusion, C4.4A is expressed during invasion and metastasis of human ESCC and may thus provide a new histological marker in this disease. © 2007 Wiley‐Liss, Inc.
Transforming growth factor‐β signaling in cancer invasion and metastasis
Authors: Leivonen Suvi‐Katri , Kähäri Veli‐Matti
Published: September 2007

Transforming growth factor‐β (TGF‐β) family members are polypeptides with dual tumor suppressive and oncogenic effects. They signal through serine/threonine kinase receptor complexes, which phosphorylate cytoplasmic mediators, the Smads. Upon phosphorylation, Smads translocate to the nucleus and associate with transcriptional coactivators or corepressors, and regulate the transcriptional activation of various TGF‐β responsive genes. In addition, TGF‐β activates cellular mitogen‐activated protein kinase signaling pathways, which crosstalk with Smad signaling and regulate growth, survival and motility of cells. During tumorigenesis, malignantly transformed cells often lose the response to the tumor suppressive effects of TGF‐β, which, in turn, starts to act as an autocrine tumor promoting factor by enhancing cancer invasion and metastasis. In this review, we summarize current view on the role of TGF‐β signaling in tumorigenesis, with emphasis on cancer invasion and metastasis. On the basis of these recent observations, we discuss new therapeutic strategies targeting TGF‐β signaling at distinct levels as a basis for inhibiting tumor growth, angiogenesis, invasion and metastasis. © 2007 Wiley‐Liss, Inc.
The spatial order of transcription in mammalian cells
Authors: Levsky Jeffrey M. , Shenoy Shailesh M. , Chubb Jonathan R. , Hall Charles B. , Capodieci Paola , Singer Robert H.
Published: September 2007

We have previously developed technology for multiplexing probes for the detection of transcription of many genes simultaneously within single cells. This has allowed us to determine the spatial localization of multiple genes with respect to each other in the nucleus, and ultimately the expression profile of the cell with respect to surrounding cells in a tissue. Six parameters of transcriptional organization in individual cells from culture and tissue were used to characterize significant differences in intracellular and intercellular expression patterns while preserving cellular morphology and histological context. We found that, unlike yeast, mammalian expression is excluded from the periphery and in addition, a subtle but complex organization underlies the transcriptional activity of these cells, both intra‐ and intercellularly. The approach has sufficient spatial resolution to be applied to the detection of chromosomal translocations or the identification of cancer cells. J. Cell. Biochem. 102: 609–617, 2007. © 2007 Wiley‐Liss, Inc.
Reciprocal regulation of Notch and PI3K/Akt signalling in T‐ALL cells In Vitro
Authors: Calzavara Elisabetta , Chiaramonte Raffaella , Cesana Daniela , Basile Andrea , Sherbet Gajanan V. , Comi Paola
Published: September 2007

Notch signalling plays an important role in hematopoiesis and in the pathogenesis of T‐ALL. Notch is known to interact with Ras and PTEN/PI3K (phosphoinositide‐3 kinase)/Akt pathways. We investigated the interaction of Notch with these pathways and the possible reciprocal regulation of these signalling systems in T‐ALL cells in vitro. Our analyses indicate that the PI3K/Akt pathway is constitutively active in the four T‐ALL cell lines tested. Akt phosphorylation was not altered by the sequestration of growth factors, that is, Akt activation seems to be less dependent on but not completely independent of growth factors, possibly being not subject to negative feedback regulation. PTEN expression was not detected in 3/4 cell lines tested, suggesting the loss of PTEN‐mediated Akt activation. Inhibition of the PI3K/Akt pathway arrests growth and enhances apoptosis, but with no modulation of expression of Bax‐α and Bcl‐2 proteins. We analysed the relationship between Notch‐1 and the PI3K/Akt signalling and show that inhibition of the Akt pathway changes Notch expression; Notch‐1 protein decreased in all the cell lines upon treatment with the inhibitor. Our studies strongly suggest that Notch signalling interacts with PI3K/Akt signalling and further that this occurs in the absence of PTEN expression. The consequences of this to the signalling outcome are yet unclear, but we have uncovered a significant inverse relationship between Notch and PI3K/Akt pathway, which leads us to postulate the operation of a reciprocal regulatory loop between Notch and Ras‐PI3K/Akt in the pathogenesis of T‐ALL. J. Cell. Biochem. 103: 1405–1412, 2008. © 2007 Wiley‐Liss, Inc.
cclib: A library for package‐independent computational chemistry algorithms
Authors: O'boyle Noel M. , Tenderholt Adam L. , Langner Karol M.
Published: September 2007

There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package‐independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Rapid acid digestion and simple microplate method for milk iodine determination
Authors: Hedayati Mehdi , Ordookhani Arash , Daneshpour Maryam Sadat , Azizi Fereidoun
Published: September 2007

Iodine deficiency leads to deficiency of thyroid hormones, which causes mental retardation in infant. Laboratory confirmation is important in its diagnosis. The major problems associated with the existing methods for iodine determination in milk samples are: 1) nonsafe alkaline solution; 2) harsh thermal condition; and 3) extra time required to complete various steps. In this study, a simple and rapid colorimetric method was investigated, which used acid digestion in combination with a rapid microplate reading format method to determine the total iodine content in milk. Sample digestion was done on 50 µL milk in metavanadate/perchloric, at 230°C for 10 min. After digestion, iodine determination was based on the Sandell‐Kolthoff reaction. The reaction results were read in 96‐well microplates by an enzyme‐linked immunosorbent assay (ELISA) reader. The determination range of the assay was between 2 and 40 µg/dL. The within‐run coefficient of variation percent in three levels (3, 12, and 36 µg/dL) ranged from 6.7 to 9.3 and between‐run coefficients of variation ranged from 8.6 to 12.3%. The results obtained (n=70) by the optimized method have good correlation with the results of alkaline incineration as a reference method (n=70; r2=0.907; y=0.952x+1.77). Recovery tests for accuracy assessment in six levels from 6.2 to 34.2 µg/dL) were between 91.3 and 113%. This method has enabled us to achieve 0.12 µg/dL sensitivity. The results of this study show that a quick acid digestion combined with mild thermal and low sample volume with a quick reading of assay results were the main advantages of the acid digestion and microplate reading format. J. Clin. Lab. Anal. 21:286–292, 2007. © 2007 Wiley‐Liss, Inc.
Influence of sample matrix and storage on BNP measurement on the Bayer Advia Centaur
Authors: Lippi Giuseppe , Fortunato Antonio , Salvagno Gian Luca , Montagnana Martina , Soffiati Giuliano , Guidi Gian Cesare
Published: September 2007

The assessment and management of congestive heart failure relies increasingly on the measurement of B‐type natriuretic peptide (BNP). However, the effective contribution of this biochemical test in the clinical decision making is influenced by reliability of the measure, which also depends on several preanalytical issues. Since there is controversy on the influence of the matrix and the storage conditions on BNP measurement, we compared results of BNP in serum, K2 ethylene diamine tetra‐acetic acid (EDTA) plasma and lithium heparin plasma fresh samples and in matching samples stored at −20 and −80°C for 1 week. BNP measured on the Bayer Advia Centaur was systematically underestimated in heparin plasma (−47%) and serum (−62%) when compared to K2 EDTA plasma. According to the established 100 ng/L cutoff value, 25% and 37% of the fresh samples collected in heparin plasma or serum were misclassified from the reference K2 EDTA fresh specimen, respectively. When compared to the fresh specimens, the mean and interindividual bias observed for samples stored at either −20°C or −80°C was, overall, modest for K2 EDTA plasma (−2%) and heparin plasma (+6% and −4%, respectively), though it appeared clinically meaningful in serum (+47% and +28%, respectively). Although we can not rule out that other BNP assays using different antibodies may be not affected from degradation during storage to the same extent, results of our investigation demonstrate that K2 EDTA plasma is the most suitable specimens for BNP testing on fresh and frozen samples stored at either −20°C or −80°C for up to 1 week. J. Clin. Lab. Anal. 21:293–297, 2007. © 2007 Wiley‐Liss, Inc.
Transcription‐mediated amplification linked to line probe assay as a routine tool for HCV typing in clinical laboratories
Authors: Ross R.S. , Viazov S. , Kpakiwa S.S. , Roggendorf M.
Published: September 2007

Typing of hepatitis C virus (HCV) isolates is currently a prerequisite for adequate tailoring of antiviral combination therapy. In many diagnostic laboratories, there seems to be a tendency toward convenient and time‐saving procedures utilizing amplification products, which are already available from preceding qualitative or quantitative HCV ribonucleic acid (RNA) assays. In this context, we evaluated the performance characteristics of a combination of techniques, i.e., transcription‐mediated amplification‐line probe assay (TMA‐LiPA), which links highly sensitive TMA of HCV RNA to the VERSANT HCV Genotype Assay (version 1). A total of 100 clinical samples were genotyped by TMA‐LiPA. The obtained results were compared to those recorded by the original, nested reverse transcription (RT)‐polymerase chain reaction (PCR)‐based VERSANT assay, the core‐related GEN‐ETI‐K DEIA, and phylogenetic analyses of partial sequences from the HCV core and NS5B regions. TMA‐LiPA assigned the correct genotype to all 100 HCV isolates. For subtyping of genotype 1 and 2 isolates, TMA‐LiPA only showed discriminatory powers of 82% and 53%, respectively. Thus, TMA‐LiPA in our hands turned out as a convenient and time‐saving routine procedure for HCV typing which currently provides sufficient information for clinical purposes. Like all 5′untranslated region (UTR)‐based assays, the technique is limited, however, in its potentials to resolve the complexity of existing HCV subtypes. J. Clin. Lab. Anal. 21:340–347, 2007. © 2007 Wiley‐Liss, Inc.
Short dysfunctional telomeres impair the repair of arsenite‐induced oxidative damage in mouse cells
Authors: Newman Jennifer P.A. , Banerjee Birendranath , Fang Wanru , Poonepalli Anuradha , Balakrishnan Lakshmidevi , Low Grace Kah Mun , Bhattacharjee Rabindra N. , Akira Shizuo , Jayapal Manikandan , Melendez Alirio J. , Baskar Rajamanickam , Lee Han‐Woong , Hande M. Prakash
Published: September 2007

Telomeres and telomerase appear to participate in the repair of broken DNA ends produced by oxidative damage. Arsenite is an environmental contaminant and a potent human carcinogen, which induces oxidative stress on cells via the generation of reactive oxygen species affecting cell viability and chromosome stability. It promotes telomere attrition and reduces cell survival by apoptosis. In this study, we used mouse embryonic fibroblasts (MEFs) from mice lacking telomerase RNA component (mTERC−/− mice) with long (early passage or EP) and short (late passage or LP) telomeres to investigate the extent of oxidative damage by comparing the differences in DNA damage, chromosome instability, and cell survival at 24 and 48 h of exposure to sodium arsenite (As3+; NaAsO2). There was significantly high level of DNA damage in mTERC−/− cells with short telomeres as determined by alkaline comet assay. Consistent with elevated DNA damage, increased micronuclei (MN) induction reflecting gross genomic instability was also observed. Fluorescence in situ hybridization (FISH) analysis revealed that increasing doses of arsenite augmented the chromosome aberrations, which contributes to genomic instability leading to possibly apoptotic cell death and cell cycle arrest. Microarray analysis has revealed that As3+ treatment altered the expression of 456 genes of which 20% of them have known functions in cell cycle and DNA damage signaling and response, cell growth, and/or maintenance. Results from our studies imply that short dysfunctional telomeres impair the repair of oxidative damage caused by arsenite. The results will have implications in risk estimation as well as cancer chemotherapy. J. Cell. Physiol. 214: 796–809, 2008. © 2007 Wiley‐Liss, Inc.
Confocal imaging of chromatographic fouling under flow conditions
Authors: Siu Sun Chau , Boushaba Rihab , Liau Jonathan , Hjorth Rolf , Titchener‐Hooker Nigel J
Published: September 2007

BACKGROUND: The fouling impact of selected fouling species was assessed by utilising confocal scanning laser microscopy (CSLM) to image a packed chromatographic bed during operation. A custom‐made flow cell was packed with Q Sepharose FF and loaded with partially clarified E. coli homogenate. Selective, multicoloured fluorescent dyes were used to label a bovine serum albumin (BSA) test protein (Cy5.5), dsDNA (PicoGreen) and host cell proteins (HCPs) (Cy3). The fouling caused by the various fluorescently labelled components was visualised as a result of the fluorescence emitted by the PicoGreen‐labelled dsDNA and the Cy3‐labelled protein in the foulant stream, and by testing the adsorptive capacity of a test protein (BSA) onto the resin prior to and post‐fouling as well as following the application of a common CIP procedure.

RESULTS: Values for the effective diffusivity of BSA (De) were derived from the confocal images and the fouling impact was assessed by comparing De values obtained from different fouling scenarios. Under the most extreme conditions examined, fouling caused a 20% reduction in capacity compared to a fresh bed. BSA diffusivity did not appear to be affected by the fouling conditions studied. Sequential CIP using 15 CVs of 1 mol L−1 NaCl then 15 CVs of 1 mol L−1 NaOH was shown to be effective in removing nucleic acids and HCPs. Subsequent BSA adsorption showed that the CIP regime successfully restored the column capacity to its original value. In contrast, 15 CVs of 1 mol L−1 NaCl were ineffective in removing dsDNA but substantially removed HCPs.

CONCLUSION: CSLM was demonstrated to be a useful tool for visualising fouling mechanisms. Comparing the results obtained by this technique using different modes of chromatographic operation provided insights into the fouling characteristics of finite baths versus packed beds. Copyright © 2007 Society of Chemical Industry
Enhancement of activity and selectivity in lipase‐catalyzed transesterification in ionic liquids by the use of additives
Authors: Hernández‐Fernández Francisco J , de los Ríos Antonia P , Rubio Manuel , Gómez Demetrio , Víllora Gloria
Published: September 2007

BACKGROUND: Seven ionic liquids (ILs) based on 1‐alkyl‐3‐methylimidazolium cation in combination with hexafluorophosphate and bis{(trifluoromethyl)sulfonyl}imide anions were tested as reaction media for lipase‐catalyzed transesterification in low water conditions. With the aim of improving the activity and/or selectivity of the lipase, various treatments were applied to ionic liquid media such as equilibration with aqueous solutions of salts, NaHCO3 or Na2CO3, or the addition of a catalytic amount of a non‐reactive organic base to the reaction mixture, triethylamine.

RESULTS: The treated ionic liquids were shown to be excellent media for lipase‐catalyzed ester synthesis by transesterification compared with conventional organic solvents, such as n‐hexane. All treatments were found to enhance the synthetic activity of the enzyme, the best results being achieved with the addition of triethylamine. The addition of a catalytic amount of this base to the ILs resulted in a significant increase in both the synthetic activity and selectivity values. For instance, the synthetic activity in [emim+][TfN2−] was enhanced more than 12 times and the selectivity increased from 86% to 95% when triethylamine was used.

CONCLUSION: These treatments could be easy‐to‐use approaches to improve the efficiency of enzymatic reactions in ionic liquids when the reaction does not proceed smoothly. Copyright © 2007 Society of Chemical Industry
Fish fingers: digit homologues in sarcopterygian fish fins
Authors: Johanson Zerina , Joss Jean , Boisvert Catherine A. , Ericsson Rolf , Sutija Margareta , Ahlberg Per E.
Published: September 2007

A defining feature of tetrapod evolutionary origins is the transition from fish fins to tetrapod limbs. A major change during this transition is the appearance of the autopod (hands, feet), which comprises two distinct regions, the wrist/ankle and the digits. When the autopod first appeared in Late Devonian fossil tetrapods, it was incomplete: digits evolved before the full complement of wrist/ankle bones. Early tetrapod wrists/ankles, including those with a full complement of bones, also show a sharp pattern discontinuity between proximal elements and distal elements. This suggests the presence of a discontinuity in the proximal‐distal sequence of development. Such a discontinuity occurs in living urodeles, where digits form before completion of the wrist/ankle, implying developmental independence of the digits from wrist/ankle elements. We have observed comparable independent development of pectoral fin radials in the lungfish Neoceratodus (Osteichthyes: Sarcopterygii), relative to homologues of the tetrapod limb and proximal wrist elements in the main fin axis. Moreover, in the Neoceratodus fin, expression of Hoxd13 closely matches late expression patterns observed in the tetrapod autopod. This evidence suggests that Neoceratodus fin radials and tetrapod digits may be patterned by shared mechanisms distinct from those patterning the proximal fin/limb elements, and in that sense are homologous. The presence of independently developing radials in the distal part of the pectoral (and pelvic) fin may be a general feature of the Sarcopterygii. J. Exp. Zool. (Mol. Dev. Evol.) 308B:757–768, 2007. © 2007 Wiley‐Liss, Inc.
Hamilton cycles in prisms
Authors: Kaiser Tomáš , Ryjáček Zdeněk , Král Daniel , Rosenfeld Moshe , Voss Heinz‐Jürgen
Published: September 2007

The prism over a graph G is the Cartesian product G □ K2 of G with the complete graph K2. If G is hamiltonian, then G□K2 is also hamiltonian but the converse does not hold in general. Having a hamiltonian prism is shown to be an interesting relaxation of being hamiltonian. In this article, we examine classical problems on hamiltonicity of graphs in the context of having a hamiltonian prism. © 2007 Wiley Periodicals, Inc. J Graph Theory 56: 249–269, 2007
Constructing trees in graphs with no K2,s
Authors: Balasubramanian Suman , Dobson Edward
Published: September 2007

Let s ≥ 2 be an integer and k > 12(s − 1) an integer. We give a necessary and sufficient condition for a graph G containing no K2,s with $\delta(G)\ge{k}/2$ and $\Delta(G)\ge k$ to contain every tree T of order k + 1. We then show that every graph G with no K2,s and average degree greater than k − 1 satisfies this condition, improving a result of Haxell, and verifying a special case of the Erdős—Sós conjecture, which states that every graph of average degree greater than k − 1 contains every tree of order k + 1. © 2007 Wiley Periodicals, Inc. J Graph Theory 56: 301–310, 2007
N‐2‐(4‐N‐(4‐[18F]Fluorobenzamido)phenyl)‐propyl‐2‐propanesulphonamide: synthesis and radiofluorination of a putative AMPA receptor ligand
Authors: Kronenberg Ute B. , Drewes Birte , Sihver Wiebke , Coenen Heinz H.
Published: September 2007

Arylpropylsulphonamides are in the focus of research asα‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolpropionic acid (AMPA) receptor ligands. A new fluorine‐18‐labelled potentiator of AMPA receptors was synthesized as a potential radiotracer for cerebral imaging with positron emission tomography. UsingN‐2‐(4‐N‐(4‐nitrobenzamido)phenyl)‐propyl‐2‐propanesulphonamide (7) as labelling precursor for a Kryptofix 2.2.2®/K2CO3‐activated nucleophilic radiofluorination, the putative AMPA receptor ligandN‐2‐(4‐N‐(4‐[18F]fluorobenzamido)phenyl)‐propyl‐2‐propanesulphonamide [18F]8was obtained in one step. Optimization of the reaction parameters time, temperature, solvent and concentration gave a radiochemical yield of 38±8% at 180°C in dimethylsulphoxide within 30‐min reaction time. After a solid‐phase extraction followed by a high‐performance liquid chromatography separation, the product could be obtained in radiochemical yields of 5±1.5%. Radiochemical purity was higher than 95% and the specific activity amounted to 77±40 GBq/µmol. Firstin vitroassays with rat brain slices revealed a high non‐specific binding and a uniform distribution of [18F]8not lending it forin vivoimaging purposes. Copyright © 2007 John Wiley & Sons, Ltd.
Effects of partial substitution of concentrates with maize silage in organic dairy cow rations on performance and feed efficiency
Authors: Velik Margit , Baumung Roswitha , Zollitsch Werner , Knaus Wilhelm F.
Published: September 2007

BACKGROUND: The general goal of organic dairy farming is to minimize purchased concentrate use and focus on milk production from forages. The aim of the present paper is to examine the influence of a partial substitution of purchased concentrates with home‐grown maize silage on feed intake, milk production and feed efficiency in rations for organic dairy cows. In the experimental treatment group (E), two‐thirds of average herd concentrate intake was replaced with 2.7 kg maize silage on a dry matter (DM) basis.

RESULTS: In treatment E, total DM, energy and protein intake were significantly reduced compared to the control treatment group (C). Daily milk yield decreased in E by 11% and milk urea content was significantly lower. Calculated milk production from forage was significantly higher (91 versus 71%) in treatment E. Efficiency of dietary nitrogen (N) utilization (calculated as milk N as a percentage of N intake) was slightly improved in E and protein and energy balance (calculated as intake as a percentage of requirements) were closer to zero than in C.

CONCLUSION: The present study indicates a potential to reduce levels of concentrates and substitute them with maize silage in organic dairy cow rations at least in the second half of lactation. Copyright © 2007 Society of Chemical Industry