bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative proteomics by fluorescent labeling of cysteine residues using a set of two cyanine‐based or three rhodamine‐based dyes
Authors: Volke Daniela , Hoffmann Ralf 
Published: November 2008

AbstractDespite all remarkable progress in gel‐based proteomics in recent years, there is still need to further improve quantification by decreasing the detection limits and increasing the dynamic range. These criteria are achieved best by fluorescent dyes that specifically stain the proteins either by adsorption after gel electrophoresis (in‐gel staining) or covalent coupling prior to gel electrophoresis (in‐solution staining). Here we report a multiplex analysis of protein samples using maleimide‐activated cyanine‐based (Cy3 and Cy5) and rhodamine‐based dyes (Dy505, Dy535, and Dy635) to permanently label all thiol‐groups of cysteine‐containing proteins. The detection limits in SDS‐PAGE were about 10 ng per band and even 2 ng for BSA due to its high content of cysteine residues. Thus only 5 μg protein of a mouse brain homogenate were analyzed by 2‐DE. Both cyanine‐ and rhodamine‐based dyes also stained proteins that did not contain cysteines, probably by reaction with amino groups. This side reactivity did not limit the method and might even extend its general use to proteins missing cysteine residues, but at a lower sensitivity. The dynamic range was more than two orders of magnitude in SDS‐PAGE and the Dy‐fluorophores did not alter the mobility of the tested proteins. Thus, a mixture of Dy505‐, Dy555‐, and Dy635‐labeled Escherichia coli lysates were separated by 2‐DE in a single gel and the three spot patterns relatively quantified.
Improved conditions for fluorescent staining of proteins with 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid in SDS‐PAGE
Authors: Cong Wei‐Tao , Hwang Sun‐Young , Jin Li‐Tai , Choi Jung‐Kap 
Published: November 2008

AbstractA simple and sensitive fluorescent staining method for the detection of proteins in SDS‐PAGE, namely IB (improved 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid) stain, is described. Non‐covalent hydrophobic probe 4,4′‐dianilino‐1,1′‐binaphthyl‐5,5′‐disulfonic acid was applied as a fluorescent dye, which can bind to hydrophobic sites in proteins non‐specifically. As low as 1 ng of protein band can be detected briefly by 30 min washing followed by 15 min staining without the aiding of stop or destaining step. The sensitivity of the new presented protocol is similar to that of SYPRO Ruby, which has been widely accepted in proteomic research. Comparative analysis of the MS compatibility of IB stain and SYPRO Ruby stain allowed us to address that IB stain is compatible with the downstream of protein identification by PMF.
Enantiomeric separation of glycidyl tosylate by CE: Application to the study of catalytic asymmetric epoxidation of allyl alcohol
Authors: Morante‐Zarcero Sonia , Crego Antonio L. , del Hierro Isabel , Sierra Isabel , Marina Maria Luisa 
Published: November 2008

AbstractA CE method using CDs as chiral selectors was developed and validated to achieve the separation of glycidyl tosylate enantiomers originated by in situ derivatization of glycidol enantiomers obtained in asymmetric epoxidation of allyl alcohol with chiral titanium‐tartrate complexes as catalysts. The effects of the nature, pH and concentration of the buffer, the nature and concentration of chiral selector, the addition of SDS, methanol, ethanol or 2‐propanol, the capillary temperature, the effective capillary length and the applied voltage on the chiral resolution of glycidyl tosylate enantiomers were investigated. The best separation conditions were achieved using a Tris‐borate buffer mixture (50 and 25 mM, respectively) at pH=9.3 with a dual CD system consisting of 2.5% succinyl‐β‐CD and 1.0% β‐CD w/v at 15°C. A baseline separation (resolution∼2.0) of the glycidyl tosylate enantiomers was obtained in a relatively short time (less than 12 min). Satisfactory results were obtained in terms of linearity (r>0.99) and intermediate precision (RSD below 8.5%). The LOD and LOQ were 3.0 and 10.0 mg/L, respectively, and the recoveries ranged from 99.8 to 108.8%. Finally, the method was applied to the determination of the enantiomeric excess and the yield obtained in the asymmetric epoxidation of allyl alcohol employing chiral titanium‐tartrate complexes as catalysts after an in situ derivatization of glycidol enantiomers to glycidyl tosylate.
Pressure‐assisted CEC versus CEC using methacrylate‐based monolithic columns: Influence of the polymerization‐mixture composition
Authors: Tanret Indiana , Mangelings Debby , Vander Heyden Yvan 
Published: November 2008

AbstractPressure‐assisted CEC (pCEC) can either be performed on a CE instrument by adding pressure at the column inlet, or by applying voltage on a capillary liquid chromatography system. This study investigates the pressure's added value in pCEC using an LC instrument as well as the influence of the polymerization‐mixture composition on monolithic columns in such experimental circumstances. Two factors of the polymerization mixture, which is used to prepare the monolithic capillary columns, were varied according to an experimental design approach: the pore‐forming solvent/total monomer ratio and the pore‐forming solvents composition. Initially, the effect of the resulting stationary phase on the elution behavior of mainly pharmaceutical compounds was studied. Four responses were used to evaluate the effects on the chromatography: retention time, retention factor, peak asymmetry and number of theoretical plates. After processing the results, the stationary phase composition with the best chromatographic behavior was determined and tested. The advantageous properties of this stationary phase compared with the design center‐point column were demonstrated. Secondly, the results of these pCEC experiments were compared with those generated in an identical experimental setup previously performed using CEC. Chromatographic conditions were chosen so that the center‐point column showed similar retention in CEC and pCEC. The expected advantage (faster analysis) and drawback (decreased efficiency) of pCEC in the analysis of pharmaceuticals was evaluated. Analysis time and efficiency were both found to depend greatly on the porosity of the column. The conclusion of this comparison is that pCEC did not have a significant added value to CEC. However, this was mainly due to the instrument's limitation of the pressure‐driven flow over the column. A clear benefit of the pCEC setup was apparatus‐related, i.e. the presence of a loop injection system on the pCEC instrument, which avoids the injection problems that were occasionally observed in CEC.
Non‐hydrostatic 3D free surface layer‐structured finite volume model for short wave propagation
Authors: Cea L. , Stelling G. , Zijlema M. 
Published: November 2008

AbstractIn this paper a layer‐structured finite volume model for non‐hydrostatic 3D environmental free surface flow is presented and applied to several test cases, which involve the computation of gravity waves. The 3D unsteady momentum and mass conservation equations are solved in a collocated grid made of polyhedrons, which are built from a 2D horizontal unstructured mesh, by just adding several horizontal layers. The mesh built in such a way is unstructured in the horizontal plane, but structured in the vertical direction. This procedure simplifies the mesh generation and at the same time it produces a well‐oriented mesh for stratified flows, which are common in environmental problems. The model reduces to a 2D depth‐averaged shallow water model when one single layer is defined in the mesh. Pressure–velocity coupling is achieved by the Semi‐Implicit Method for Pressure‐Linked Equations algorithm, using Rhie–Chow interpolation to stabilize the pressure field. An attractive property of the model proposed is the ability to compute the propagation of short waves with a rather coarse vertical discretization. Several test cases are solved in order to show the capabilities and numerical stability of the model, including a rectangular free oscillating basin, a radially symmetric wave, short wave propagation over a 1D bar, solitary wave runup on a vertical wall, and short wave refraction over a 2D shoal. In all the cases the numerical results are compared either with analytical or with experimental data. Copyright © 2008 John Wiley & Sons, Ltd.
Pyridine‐4‐thiol and Amphoteric Analogs: Novel Protection of Aryl Bromides in Strong Alkali
Authors: Chen Wei‐Min , Cheng Chao , Li Bing‐Zhou , Ho Tse‐Lok , Cai Zhao‐Shuo , Wang Yuqiang , Sun Ping‐Hua 
Published: November 2008

AbstractThe use of pyridine‐4‐thiol (PT) to preserve certain aryl bromides in strong alkali is reported (Scheme 1). The presence of this additive or of some of its amphoteric analogs such as 3‐hydroxypyridin‐4(1H)‐ones suppresses the replacement of the Br‐substituent by hydroxide and alkoxide ions. A mechanistic interpretation of the effect is proposed.
Two New Endiandric Acid Analogs, a New Benzopyran, and a New Benzenoid from the Root of Beilschmiedia erythrophloia
Authors: Yang Ping‐Shin , Cheng Ming‐Jen , Chen Jih‐Jung , Chen Ih‐Sheng 
Published: November 2008

AbstractPhytochemical investigation of the root of Beilschmiedia erythrophloia led to the isolation and structural elucidation of two new endiandric acid analogs, endiandric acids I and J (1 and 2, resp.), a new benzopyran, dehydrooligandrol methyl ether (3), and a new benzenoid, farnesylol (4), together with six known compounds. Their structures were established on the basis of extensive 1D‐ and 2D‐NMR analyses in combination with HR‐MS experiments.
Phenolic Derivatives from Fruits of Dipteryx lacuniferaDucke and Evaluation of Their Antiradical Activities
Authors: Júnior Gerardo Magela V. , de M. Sousa Cleyton Marcos , Cavalheiro Alberto J. , Lago João Henrique G. , Chaves Mariana H. 
Published: November 2008

AbstractThe fruits of Dipteryx lacunifera, known as ‘fava de morcego’ and ‘garampara’, comprise pleasant tasting kernels that contain high amounts of fatty acids (mainly oleic acid) and are commonly consumed by inhabitants of the northeast of Brazil. In the present study, the crude EtOH extract of the fruit kernels was separated into hexane‐, Et2O‐, AcOEt‐, and H2O‐soluble fractions. The Et2O fraction was found to exhibit the highest 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical‐scavenging activity in vitro, and was subjected to further fractionation. Column chromatography over silica gel and Sephadex LH‐20, followed by preparative HPLC‐C18, afforded (−)‐eriodictyol (1), (−)‐butin (2), luteolin (3), 3′,4′,7‐trihydroxyflavone (4), butein (5), and sulfuretin (6). The antiradical activities of compounds 1, 2, 4, and 6, together with the positive controls rutin, butylated hydroxy toluene (BHT), and tert‐butylhydroquinone (TBHQ), were evaluated with the DPPH assay and were found to decrease in the order rutin>4>1>6>2>TBHQ>BHT.
CXCL8/IL‐8 and CXCL12/SDF‐1α co‐operatively promote invasiveness and angiogenesis in pancreatic cancer
Authors: Matsuo Yoichi , Ochi Nobuo , Sawai Hirozumi , Yasuda Akira , Takahashi Hiroki , Funahashi Hitoshi , Takeyama Hiromitsu , Tong Zhimin , Guha Sushovan 
Published: November 2008

AbstractCXC‐chemokines are involved in the chemotaxis of neutrophils, lymphocytes and monocytes. However, role of these chemokines in tumorigenesis, especially with regard to interaction between tumor and its microenvironment, has not been clearly elucidated. The purpose of this study was to analyze the co‐operative role of CXCL8 and CXCL12 in the tumor‐stromal interaction in pancreatic cancer (PaCa). Using enzyme‐linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT‐PCR), we initially confirmed the expression of ligands and receptors, respectively, of CXC‐chemokines in PaCa and stromal cells. We examined the co‐operative role of CXCL8 and CXCL12 in proliferation/invasion of PaCa and human umbilical vein endothelial cells (HUVECs), and in HUVEC tube‐formations through tumor‐stromal interaction by MTS, Matrigel invasion, and angiogenesis assays, respectively. We detected expression of CXCR4, but not CXCR2, in all PaCa cells and fibroblasts. PaCa cells secreted CXCL8, and fibroblast cells secreted CXCL12. CXCL8 production in PaCa was significantly enhanced by CXCL12, and CXCL12 production in fibroblasts was significantly enhanced by co‐culturing with PaCa. CXCL8 enhanced proliferation/invasion of HUVECs but did not promote proliferation/invasion of PaCa. Both recombinant and PaCa‐derived CXCL8 enhanced tube formation of HUVECs that were co‐cultured with fibroblast cells. CXCL12 enhanced the proliferation/invasion of HUVECs and the invasion of PaCa cells but had no effect on tube formation of HUVEC. We showed that PaCa‐derived CXCL8 and fibroblast‐derived CXCL12 cooperatively induced angiogenesis in vitro by promoting HUVEC proliferation, invasion, and tube formation. Thus, corresponding receptors CXCR2 and CXCR4 are potential antiangiogenic and antimetastatic therapeutic targets in PaCa. © 2008 Wiley‐Liss, Inc.
Myelodysplastic syndromes and acute myeloid leukemia in cats infected with feline leukemia virus clone33 containing a unique long terminal repeat
Authors: Hisasue Masaharu , Nagashima Naho , Nishigaki Kazuo , Fukuzawa Isao , Ura Shigeyoshi , Katae Hiromi , Tsuchiya Ryo , Yamada Takatsugu , Hasegawa Atsuhiko , Tsujimoto Hajime 
Published: November 2008

AbstractFeline leukemia virus (FeLV) clone33 was obtained from a domestic cat with acute myeloid leukemia (AML). The long terminal repeat (LTR) of this virus, like the LTRs present in FeLV from other cats with AML, differs from the LTRs of other known FeLV in that it has 3 tandem direct 47‐bp repeats in the upstream region of the enhancer (URE). Here, we injected cats with FeLV clone33 and found 41% developed myelodysplastic syndromes (MDS) characterized by peripheral blood cytopenias and dysplastic changes in the bone marrow. Some of the cats with MDS eventually developed AML. The bone marrow of the majority of cats with FeLV clone33 induced MDS produced fewer erythroid and myeloid colonies upon being cultured with erythropoietin or granulocyte‐macrophage colony‐stimulating factor (GM‐SCF) than bone marrow from normal control cats. Furthermore, the bone marrow of some of the cats expressed high‐levels of the apoptosis‐related genes TNF‐α and survivin. Analysis of the proviral sequences obtained from 13 cats with naturally occurring MDS reveal they also bear the characteristic URE repeats seen in the LTR of FeLV clone33 and other proviruses from cats with AML. Deletions and mutations within the enhancer elements are frequently observed in naturally occurring MDS as well as AML. These results suggest that FeLV variants that bear URE repeats in their LTR strongly associate with the induction of both MDS and AML in cats. © 2008 Wiley‐Liss, Inc.
Putative functional polymorphisms of MMP9 predict survival of NSCLC in a Chinese population
Authors: Jin Guangfu , Miao Ruifen , Hu Zhibin , Xu Lin , Huang Xinen , Chen Yijiang , Tian Tian , Wei Qingyi , Boffetta Paolo , Shen Hongbing 
Published: November 2008

AbstractMatrix metalloproteinases (MMPs) play a crucial role in cancer progression and their over‐expression is often associated with unfavorable survival of non‐small cell lung cancer (NSCLC). Because genetic variants can alter expression level or biological activity of MMPs, we hypothesized that potentially functional single nucleotide polymorphisms (SNPs) in key MMP genes may be associated with the survival of NSCLC patients. We selected and genotyped 14 putative functional SNPs in six MMP genes (MMP1, MMP2, MMP3, MMP7, MMP9 and MMP12) using PCR‐RFLP methods in 561 NSCLC patients. Kaplan‐Meier method with the log‐rank test and Cox proportional hazard models were used for the survival analyses. The C‐1562T, Arg279Gln and Arg668Gln polymorphisms in MMP9 were significantly associated with survival of patients with NSCLC (log‐rank p values = 0.032, 0.038 and 0.036, respectively). The C‐1562T and Arg668Gln loci were in complete linkage disequilibrium (r2 = 1). Patients carrying the 668Gln allele had improved survival with a median survival time (MST) of 51.6 months, compared with 21.8 months for those with the 668Arg/Arg genotype (log‐rank p = 0.010). In contrast, the 279Gln/Gln genotype was associated with a significantly shortened MST (17.3 months, log‐rank p = 0.030) in the recessive model. In the final multivariate Cox regression model, 279Gln/Gln was identified as an independent prognostic factor with an adjusted hazard ratio of 1.60 (95% confidence interval 1.07–2.41). The MMP9 Arg279Gln and Arg668Gln SNPs are potential predictors of survival in NSCLC patients. © 2008 Wiley‐Liss, Inc.
Evidence for the accelerations of sea level on multi‐decade and century timescales
Authors: Woodworth P. L. , White N. J. , Jevrejeva S. , Holgate S. J. , Church J. A. , Gehrels W. R. 
Published: November 2008

AbstractA modification in the rate of change of sea level (i.e. an ‘acceleration’ or ‘nonlinear trend’) is an important climate‐related signal, which requires confirmation and explanation. In this study, the evidence for accelerations in regional and global average sea level on timescales of several decades and longer is reviewed by inter‐comparison of the recent findings of different researchers and by inspection of original tide gauge records. Most sea‐level data originate from Europe and North America, and both the sets display evidence for a positive acceleration, or ‘inflexion’, around 1920–1930 and a negative one around 1960. These inflexions are the main contributors to reported accelerations since the late 19th century, and to decelerations during the mid‐ to late 20th century. However, these characteristic features are not always found in records from other parts of the world. Although some aspects of the sea‐level time series are consistent with changes in rates of globally averaged temperature changes, volcanic eruptions and natural climate variability, modelling undertaken so far has been unable to describe these features adequately. This emphasizes the need for a major enhancement of the sea‐level data set, especially for those parts of the world without long tide gauge records, in order to obtain greater insight into the spatial dependence of accelerations. A number of complementary methods must be employed, of which salt marsh techniques offer the possibility of obtaining time series similar to those that would have been obtained from coastal tide gauges. Copyright © 2008 Royal Meteorological Society
Interannual relations between South American rainfall and tropical sea surface temperature anomalies before and after 1976
Authors: Kayano Mary Toshie , de Oliveira Cristiano Prestrelo , Andreoli Rita Valéria 
Published: November 2008

AbstractThe differences between 1948–1976 and 1977–2002 periods in the interannual relationships of South American precipitation with sea surface temperature (SST) indices in selected oceanic sectors are documented using correlation analyses. For the total correlation between the eastern equatorial Pacific (EEP) and tropical South Atlantic (TSA) indices and the precipitation, the differences between the two periods reflect, in part, the El Niño‐Southern Oscillation (ENSO) teleconnections over South America, with the Pacific decadal oscillation (PDO) background acting to enhance (weaken) the correlations when ENSO and PDO are in the same (opposite) phase. For the total correlation between the tropical North Atlantic (TNA) and southwest South Atlantic (SWA) indices and precipitation, the results here suggest that the differences between the two periods might be reflected as variations in the Bolivian high‐pressure system. Both the TNA and TSA indices may act to weaken the positive ENSO relations with precipitation over central and eastern Brazil during the cold PDO phase. These analyses provide indications that the ENSO relationship with the TSA shows differences between the two analysed periods. Copyright © 2008 Royal Meteorological Society
CE determination of quinolones in the presence of bovine serum albumin
Authors: Qin Weidong , Liu Qingchun , Fan Yongxia 
Published: November 2008

AbstractThis article describes the influence of bovine serum albumin (BSA) as an additive on the capillary electrophoresis–potential gradient determination of five quinolones, enoxacin, norfloxacin, ofloxacin, fleroxacin, and pazufloxacin. With 10 mg/L of BSA present in the buffer of 30 mM Tris and 3 mM phosphoric acid at pH 9, the detection limits of the five quinolones were in the range of 0.24–0.68 mg/L, i. e. 5.8–16.5‐fold lower than those obtained with the buffer devoid of BSA, and the analysis time was shortened. We suggest that the inner wall‐adsorbed BSA suppresses the adsorption of quinolones and simultaneously enhances the electroosmotic flow rate. Our experiments indicated that adopting the potential gradient detection technique could eliminate the interference of the UV‐active proteins on the detection of quinolones that would occur with conventional optical detection, and therefore offer high detection sensitivity. As a demonstration, the method was applied to the determination of QNs in fortified chicken muscle sample with satisfactory results.
Optimizing capillary column backflush to improve cycle time and reduce column contamination
Authors: Klee Matthew S. 
Published: November 2008

AbstractInterest in decreasing cycle times in capillary GC analyses has driven much of the instrumental developments of the last decade. Recent developments in GC instrumentation now make it reasonable to consider backflushing capillary columns on a routine basis. Significant reduction in analysis and total cycle times (typically 15–50% depending on the application) are readily achieved for analyses that currently require an extended temperature program and bakeout period to remove retained sample components and column contaminants. Setup and optimization of backflush conditions are relatively straight forward as long as some basic concepts are well understood. The parameters affecting capillary column backflushing are described. Examples are shown that help visualize what happens during backflush. The relationship between oven ramp rate and flow turns out to be an important variable that dictates minimum backflush times in temperature programmed CGC. Backflush times corresponding to 2–5 void volumes in the reversed direction are usually sufficient for backflushing, if performed after each temperature programmed run.
Sol–gel polydimethylsiloxane/poly(vinylalcohol)‐coated stir bar sorptive extraction of organophosphorus pesticides in honey and their determination by large volume injection GC
Authors: Yu Chunhe , Hu Bin 
Published: November 2008

AbstractA PDMS/poly(vinylalcohol) (PDMS/PVA) film prepared through a sol–gel process was coated on stir bars for sorptive extraction, followed by liquid desorption and large volume injection–GC–flame photometric detector (LVI–GC–FPD) for the determination of five organophosphorus pesticides (OPPs) (phorate, fenitrothion, malathion, parathion, and quinalphos) in honey. The preparation reproducibility of PDMS/PVA‐coated stir bar ranged from 4.3 to 13.4% (n = 4) in one batch, and from 6.0 to 12.6% (n = 4) in batch to batch. And one prepared stir bar can be used for more than 50 times without apparent coating loss. The significant parameters affecting stir bar sorptive extraction (SBSE) were investigated and optimized. The LODs for five OPPs ranged from 0.013 (parathion) to 0.081 μg/L (phorate) with the RSDs ranging from 5.3 to 14.2% (c = 1 μg/L, n = 6). The proposed method was successfully applied to the analysis of five OPPs in honey.