bluuebunny/crossref_metadata_2025_split huggingface dataset:
An automatable screen for the rapid identification of proteins amenable to refolding
Authors: Cowieson Nathan P. , Wensley Beth , Listwan Pawel , Hume David A. , Kobe Bostjan , Martin Jennifer L. 
Published: February 2006

AbstractInsoluble expression of heterologous proteins in Escherichia coli is a major bottleneck of many structural genomics and high‐throughput protein biochemistry projects. Many of these proteins may be amenable to refolding, but their identification is hampered by a lack of high‐throughput methods. We have developed a matrix‐assisted refolding approach in which correctly folded proteins are distinguished from misfolded proteins by their elution from affinity resin under non‐denaturing conditions. Misfolded proteins remain adhered to the resin, presumably via hydrophobic interactions. The assay can be applied to insoluble proteins on an individual basis but is particularly well suited for high‐throughput applications because it is rapid, automatable and has no rigorous sample preparation requirements. The efficacy of the screen is demonstrated on small‐scale expression samples for 15 proteins. Refolding is then validated by large‐scale expressions using SEC and circular dichroism.
Comparative proteome analysis of subcellular fractions from Borrelia burgdorferi by NEPHGE and IPG
Authors: Nowalk Andrew J. , Nolder Christi , Clifton Dawn R. , Carroll James A. 
Published: February 2006

AbstractBorrelia burgdorferi, the cause of Lyme disease, produces excessive amounts of membrane lipoproteins such as outer surface protein A (OspA) when grown in vitro, and consequently many low or moderately abundant proteins are underrepresented when cell lysates are examined by 2‐DE. We analyzed the B. burgdorferi B31 proteome computationally and by IPG or modified NEPHGE after subcellular fractionation into membrane‐associated and soluble proteins. The B. burgdorferi B31 theoretical proteome is comprised of 1623 proteins and has a mean pI of 8.36 and a median pI of 9.03 with 68% of the proteome possessing a pI ≥7.5. Separation of soluble proteins by IPG resulted in 205 individual spots and identification of 78 protein spots by MALDI‐TOF MS. Separation by modified NEPHGE routinely resulted in approximately 185 soluble and 160 membrane protein spots with the identification of 88 individual protein spots combined by MALDI‐TOF MS. Homologues to GroEL and aminopeptidase I were present in greater amounts in the membrane faction, with enolase at nearly equivalent amounts in the soluble and membrane fractions. Identification of proteins isolated and separated by such methods will enable future determination of proteome changes in membrane and soluble protein fractions as spirochetes adapt to their changing environments.
Differential protein expression in hypertrophic heart with and without hypertension in spontaneously hypertensive rats
Authors: Jin Xian , Xia Li , Wang Li‐Shun , Shi Jun‐Zhi , Zheng Ying , Chen Wen‐Li , Zhang Lei , Liu Zhen‐Guo , Chen Guo‐Qiang , Fang Ning‐Yuan 
Published: February 2006

AbstractAlthough cardiac hypertrophy in hypertension has been well recognized, the molecular mechanisms for the development of hypertrophy are still largely unknown. In this study, the protein expression profiles of left ventricular myocardia in spontaneously hypertensive rats (SHR) and Wistar‐Kyoto (WKY) rats at different ages were analyzed using 2‐DE in combination with MALDI‐TOF/TOF MS/MS. The results showed that 20 proteins were modulated in the hypertrophic myocardium. Out of these modulated proteins, 13 proteins presented significant changes in SHR at an early stage prior to the development of sustained hypertension, while the changes of the other 7 protein expressions occurred only at a late stage in SHR when the blood pressure was significantly elevated, and were largely reversible by treatment with rennin‐angiotensin‐aldosterone system inhibitors losartan or enalapril. These data demonstrate that the changes in energy metabolism in the hypertrophied heart favor an increase in glycolysis and a decrease in oxidation of fatty acid and glucose, which occur at an early stage in SHR without hypertension. Our results also provide evidence to support the hypothesis that oxidative stress plays an important role in the development of hypertensive cardiac hypertrophy.
Multiplex detection of surface molecules on colorectal cancers
Authors: Ellmark Peter , Belov Larissa , Huang Pauline , Lee C. Soon , Solomon Michael J. , Morgan Daniel K. , Christopherson Richard I. 
Published: February 2006

AbstractA technique of fluorescence multiplexing is described for analysis of the plasma membrane proteome of colorectal cancer cells from surgically resected specimens, enabling detection and immunophenotyping when the cancer cells are in the minority. A single‐cell suspension was prepared from a colorectal tumour, and the mixed population of cells was captured on a CD antibody microarray. The cancer cells were detected using a fluorescently tagged antibody for carcinoembryonic antigen (CEA‐Alexa647) or epithelial cell adhesion marker (EpCAM‐Alexa488). Using this multiplexing procedure, dot patterns from colorectal cancers were distinct from those of adjacent normal tissue. Subtraction of the expression levels for each antigen from normal tissue from those for the cancer shows differential expression in the cancer of CD66c, CD15s, CD55, CD45, CD71, CD45RO, CD11b and CEA, in descending order. Cells captured on the same microarray were also labelled with fluorescent CD3‐phycoerythrin antibody revealing the presence of tumour‐infiltrating lymphocytes. The immunophenotypes of T lymphocytes from the tumour samples showed differential expression of HLA‐DR, TCR α/β, CD49d, CD52, CD49e, CD5, CD95, CD28, CD38 and CD71, in descending order. Fluorescence multiplexing of mixed cell populations captured on a single antibody microarray enables expression profiling of multiple sub‐populations of cells within a tumour sample.
Optimizing search conditions for the mass fingerprint‐based identification of proteins
Authors: Ossipova Elena , Fenyö David , Eriksson Jan 
Published: February 2006

AbstractThe two central problems in protein identification by searching a protein sequence collection with MS data are the optimal use of experimental information to allow for identification of low abundance proteins and the accurate assignment of the probability that a result is false. For comprehensive MS‐based protein identification, it is necessary to choose an appropriate algorithm and optimal search conditions. We report a systematic study of the quality of PMF‐based protein identifications under different sequence collection search conditions using the Probity algorithm, which assigns the statistical significance to each result. We employed 2244 PMFs from 2‐DE‐separated human blood plasma proteins, and performed identification under various search constraints: mass accuracy (0.01–0.3 Da), maximum number of missed cleavage sites (0–2), and size of the sequence collection searched (5.6×104–1.8×105). By counting the number of significant results (significance levels 0.05, 0.01, and 0.001) for each condition, we demonstrate the search condition impact on the successful outcome of proteome analysis experiments. A mass correction procedure utilizing mass deviations of albumin matching peptides was tested in an attempt to improve the statistical significance of identifications and iterative searching was employed for identification of multiple proteins from each PMF.
On the development of special positive isotactic polypropylene spherulites
Authors: Li Huihui , Sun Xiaoli , Wang Jijun , Yan Shouke , Schultz Jerold M. 
Published: February 2006

AbstractA new type of positive α‐iPP spherulites has been developed by self‐seeding process. The growth process of these positive α‐iPP spherulites is just like “photographic development process,” which is very different from the conventional growth process of polymer spherulites. Scanning electron microscopy (SEM) was used to explore the morphologies of these positive α‐iPP spherulites on a lamellar level. The results show that these spherulites are composed of a large number of lamellae having interwoven structures, which result in different optical character, special melting behavior, and different contrast under SEM as compared with the conventional melt‐crystallized spherulites. The development of these interwoven lamellar structures has been considered because in the sites of the original spherulites, a large number of self‐nuclei are formed because of the incomplete melting of the original spherulites and these induce nearly equal number of radial and tangential lamellae at rather high temperatures. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1114–1121, 2006
Polymer modification using difluoromethane (HFC 32) and carbon dioxide
Authors: Abbott Andrew P. , Brooks Nick , Eltringham Wayne , Hillman A. Robert , Hope Eric G. 
Published: February 2006

AbstractThe infusion of difluoromethane (HFC 32) and CO2 into polystyrene and polyethylene has been characterized using a quartz crystal microbalance technique over a range of temperatures and pressures. The results were adequately modeled by Flory‐Huggins theory. Significant plasticization was observed in the polymeric materials and it is shown that manipulation of the experimental temperature, pressure, and rate of depressurisation can cause significant changes in the morphology of the samples. It is demonstrated for the first time how rate constant data for the kinetics of gas sorption can be extracted quickly and easily from in situ quartz crystal microbalance measurements. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1072–1083, 2006
On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites
Authors: Nayal Murad , Honig Barry 
Published: February 2006

AbstractIn this article we introduce a new method for the identification and the accurate characterization of protein surface cavities. The method is encoded in the program SCREEN (Surface Cavity REcognition and EvaluatioN). As a first test of the utility of our approach we used SCREEN to locate and analyze the surface cavities of a nonredundant set of 99 proteins cocrystallized with drugs. We find that this set of proteins has on average about 14 distinct cavities per protein. In all cases, a drug is bound at one (and sometimes more than one) of these cavities. Using cavity size alone as a criterion for predicting drug‐binding sites yields a high balanced error rate of 15.7%, with only 71.7% coverage. Here we characterize each surface cavity by computing a comprehensive set of 408 physicochemical, structural, and geometric attributes. By applying modern machine learning techniques (Random Forests) we were able to develop a classifier that can identify drug‐binding cavities with a balanced error rate of 7.2% and coverage of 88.9%. Only 18 of the 408 cavity attributes had a statistically significant role in the prediction. Of these 18 important attributes, almost all involved size and shape rather than physicochemical properties of the surface cavity. The implications of these results are discussed. A SCREEN Web server is available at http://interface.bioc.columbia.edu/screen. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Nearest‐neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side‐chains
Authors: Dwyer Donard S. 
Published: February 2006

AbstractThe electronic properties of amino acid side‐chains are emerging as an important factor in the preference for secondary structure in proteins. These properties have not been fully characterized, nor has their role in the behavior of peptides been explored in any detail. The present studies sought to evaluate several possibilities: 1) that hydrophilicity can be expressed solely in electronic terms, 2) that substituent effects of side‐chains extend across the peptide bond, and (3) nearest‐neighbor effects in dipeptides correlate with secondary structural preferences. Quantum mechanics (QM) calculations were used to define the electronic properties of individual amino acids and dipeptides. It was found that the hydrophilicity of an amino acid side‐chain can be accurately represented as a function of the electron densities of its component atoms. In addition, the nature of an amino acid in the second position of a dipeptide affects the electronic properties (Mulliken populations and electron densities) of the main‐chain atoms of the first residue. Certain electronic features of the dipeptides strongly correlated with propensity for secondary structure. Specifically, Mulliken population data at the Cα atom and N atom predicted preference for α‐helices versus coil and strand conformations, respectively. Analysis of dipeptides arrayed in either helical or extended structures revealed lengthening of main‐chain bonds in the α‐helical conformations. A thorough characterization of the electronic properties of amino acids and short peptide segments may provide a better understanding of the forces that determine secondary structure in proteins. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Phytogrowth‐ and photosynthesis‐inhibiting properties of nostoclide analogues
Authors: Barbosa Luiz CA , Demuner Antônio J , de Alvarenga Elson S , Oliveira Alberto , King‐Diaz Beatriz , Lotina‐Hennsen Blas 
Published: February 2006

AbstractSix nostoclide analogues were synthesised from 3‐benzyl‐2(5H)‐furanone in one step, with yields ranging from 10 to 71%, and subjected to several biological assays. The two most active of these, 5d and 5e, were shown to be phytogrowth inhibitors of the radicle of Lolium multiflorum Lam, while enhancing the root growth of Physalis ixocarpa Brot. Both compounds inhibited electron flow (basal, phosphorylating and uncoupled) from water to methylviologen (MV); both acted as Hill reaction inhibitors, since the synthesis of ATP was prevented. The uncoupled electron transport from photosystem II (PSII) (water to 2,6‐dichlorophenol‐indophenol (DPIP)) and photosystem I (PSI) (2,6‐dichlorophenol‐indophenol reduced (DPIPred) to MV) was inhibited with 500 µM of 5d by 22 and 14% respectively. In addition, 400 µM of 5d inhibited PSI (from tetramethyl‐p‐benzohydroquinone (TMQH2) to MV) by 40%. Thus 5d inhibited electron transport at the b6f complex. Finally, 500 µM of 5e inhibited electron flow (basal and phosphorylating) by 25%, and 300 µM of 5e enhanced light‐activated membrane‐bound Mg2+‐ATPase by 66%. Thus 5e behaved as a weak Hill reaction inhibitor and an uncoupler. In general, the phytotoxicity of the synthetic lactones was only weakly related to inhibition of photosynthesis. Copyright © 2006 Society of Chemical Industry
In vitro selection of an effective fungicide against Armillaria mellea and control of white root rot of grapevine in the field
Authors: Aguín Olga , Mansilla J Pedro , Sainz María J 
Published: February 2006

AbstractArmillaria mellea (Vahl ex Fr) Kummer is an aggressive pathogen which causes white root rot in a wide range of hosts. Most chemicals tested so far against Armillaria, both in vitro and in the field, have not been effective in reducing fungal growth and/or preventing plant decline and mortality. In the present work the effects of four DMI (sterol demethylation inhibitor) fungicides, cyproconazole, hexaconazole, propiconazole and tetraconazole, and another six downwardly mobile systemic chemicals, azoxystrobin, cubiet (copper bis(ethoxy‐dihydroxy‐diethylamino)sulfate), fosetyl‐Al, potassium phosphite, sodium tetrathiocarbonate (STTC) and 2‐(thiocyanomethylthio)benzothiazole (TCMTB), on the mycelial growth of A. mellea were compared and evaluated; the product yielding the best results in in vitro experiments was selected to determine its efficacy in preventing decline and mortality of grapevines in the field. Best results on in vitro fungal growth reduction were obtained with the four azoles tested, in particular with cyproconazole and hexaconazole, achieving 67–72% mycelial growth inhibition at the lowest dose. Results obtained in the field showed that a dose of 50 mg AI litre−1 of cyproconazole once or twice a year was efficient in controlling the disease even in vines seriously affected by the pathogen. However, further research is required to study minimum effective doses, residual effects and the convenience of the application of annual dressings in damaged vineyards, so as to gradually reduce the pathogen inoculum potential in soil and control the disease while reducing chemical residues in the plant and preventing development of fungal resistance. Copyright © 2006 Society of Chemical Industry
Acaricidal activity against Panonychus citri of a ginkgolic acid from the external seed coat of Ginkgo biloba
Authors: Pan Weigao , Luo Peng , Fu Ruobin , Gao Ping , Long Zhangfu , Xu Feiyi , Xiao Haibo , Liu Shigui 
Published: February 2006

AbstractAn acaricidal substance extracted from the external seed coat of Ginkgo biloba L. was identified by UV (ultraviolet), IR (infrared), EI‐MS (electron impact ion source mass spectrometry), 1H NMR (nuclear magnetic resonance) and 13C NMR as 6‐[(Z)‐10‐heptadecenyl]‐2‐hydroxybenzoic acid (compound 1). Laboratory bioassay on citrus red mite, Panonychus citri (Mcg), showed that compound 1 possessed the following properties. (i) Powerful contact toxicity with an LC50 of 5.2 mg litre−1 after 24 h that was similar to that of pyridaben (LC50 = 3.4 mg litre−1) and significantly superior to that of omethoate (LC50 = 122 mg litre−1). Furthermore, its LC90 was 13.4 mg litre−1 after 24 h, which is significantly superior to both pyridaben (LC90 = 69.6 mg litre−1) and omethoate (LC90 = 453 mg litre−1). (ii) Quick‐acting acaricidal activity. At identical concentrations, compound 1 was much faster‐acting than pyridaben or omethoate. (iii) Compound 1 had strong corrosive action on the cuticle of P. citri but no phytotoxicity to plants. Copyright © 2006 Society of Chemical Industry
Baylis–Hillman adducts with molluscicidal activity against Biomphalaria glabrata
Authors: Vasconcellos Mário LAA , Silva Tania MS , Camara Celso A , Martins Rodrigo M , Lacerda Kelly M , Lopes Horacimone M , Pereira Vera LP , de Souza Rodrigo OMA , Crespo Lívia TC 
Published: February 2006

AbstractThe molluscicidal activities of ten Baylis–Hillman adducts against Biomphalaria glabrata (Say) snails, the intermediate host of schistosomiasis, have been determined. Nine of these compounds showed significant molluscicidal activity against B. glabrata, falling below the threshold of 100 µg ml−1 set for potential molluscicidal activity by the World Health Organisation. Among these compounds, 3‐hydroxy‐2‐methylene‐3‐(4‐nitrophenyl)propanenitrile had the highest activity, with LC50 = 6.64 µg ml−1. Copyright © 2006 Society of Chemical Industry
Fumigant distribution in forest nursery soils under water seal and plastic film after application of dazomet, metam‐sodium and chloropicrin
Authors: Wang Dong , Fraedrich Stephen W , Juzwik Jennifer , Spokas Kurt , Zhang Yi , Koskinen William C 
Published: February 2006

AbstractAdequate concentration, exposure time and distribution uniformity of activated fumigant gases are prerequisites for successful soil fumigation. Field experiments were conducted to evaluate gas phase distributions of methyl isothiocyanate (MITC) and chloropicrin (CP) in two forest‐tree nurseries. Concentrations of MITC and CP in soil air were measured from replicated microplots that received dazomet, metam‐sodium and CP. Half of the plots were covered with high‐density polyethylene tarp immediately after fumigation; the other half were not covered but received daily sprinkler irrigation for 1 week to create and maintain a water seal. The magnitude of MITC concentrations was similar between nurseries for metam‐sodium in both tarp and water seal treatments and for dazomet in the tarp treatment. Consistently greater MITC and CP concentrations were found in the upper 30 cm of soil in the tarped plots compared with the water‐sealed plots. Despite potential environmental and economic benefits with the water seal method, tarp covers were more reliable for achieving and maintaining higher MITC and CP concentrations and less prone to variations due to irrigation/rain, soil bulk density and other environmental conditions. Copyright © 2006 Society of Chemical Industry
Threading dislocation density reduction in two‐stage growth of GaN layers
Authors: Bougrov V. E. , Odnoblyudov M. A. , Romanov A. E. , Lang T. , Konstantinov O. V. 
Published: February 2006

AbstractA theoretical approach is proposed to reduce the density of threading dislocations (TDs) in (0001) oriented growth of GaN layers. The approach can be realized by repeated stages of growth surface roughening (stage I) and flattening (stage II). Fundamentals of the approach include the formation of a dislocation redirection layer with inclined TDs at stage I and enhanced reactivity among inclined TDs in a dislocation reaction layer at stage II. A reaction‐kinetics model is applied for the quantitative prediction of TD density reduction which can be achieved as a result of the two‐stage growth technique. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Partition Coefficient Kow of Benzene, Ethanol and Aniline in Benzene‐ethanol and Aniline‐benzene Mixtures and Coefficient of Distribution Kmix of these Mixtures
Authors: Rucki M. , Tichý M. 
Published: February 2006

AbstractThe study related to partition coefficients between n‐octanol and water Kow of compounds in binary mixtures benzene‐ethanol and benzene‐aniline was carried out. Partition coefficients of benzene, aniline and ethanol for different values of molar ratio of benzene and different total concentration of compounds in the mixtures benzene‐ethanol and benzene‐aniline were determined. Coefficient of distribution Kmix was determined for both mixtures. In benzene‐ethanol mixture collected results show statistically significant deviations the Kow of benzene from values for pure compound. For ethanol, there are no statistically significant deviations from values for pure compound. But also there are some trends of changes of Kow. In benzene‐aniline mixture collected results show statistically significant deviations of the Kow of benzene and aniline from values for pure compounds. Changes of Kow were used for explanation of acute toxicity of binary mixtures benzene‐ethanol and aniline‐benzene.
Robust locally testable codes and products of codes
Authors: Ben‐Sasson Eli , Sudan Madhu 
Published: February 2006

AbstractWe continue the investigation of locally testable codes, i.e., error‐correcting codes for which membership of a given word in the code can be tested probabilistically by examining it in very few locations. We give two general results on local testability: First, motivated by the recently proposed notion of robust probabilistically checkable proofs, we introduce the notion of robust local testability of codes. We relate this notion to a product of codes introduced by Tanner and show a very simple composition lemma for this notion. Next, we show that codes built by tensor products can be tested robustly and somewhat locally by applying a variant of a test and proof technique introduced by Raz and Safra in the context of testing low‐degree multivariate polynomials (which are a special case of tensor codes). Combining these two results gives us a generic construction of codes of inverse polynomial rate that are testable with poly‐logarithmically many queries. We note that these locally testable tensor codes can be obtained from any linear error correcting code with good distance. Previous results on local testability, albeit much stronger quantitatively, rely heavily on algebraic properties of the underlying codes. © 2006 Wiley Periodicals, Inc. Random Struct. Alg., 2006