bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the interaction forces between hydrophobic peptides and supported lipid bilayers using AFM
Authors: Andre Guillaume , Brasseur Robert , Dufrêne Yves F. 
Published: September 2007

AbstractDespite the vast body of literature that has accumulated on tilted peptides in the past decade, direct information on the forces that drive their interaction with lipid membranes is lacking. Here, we attempted to use atomic force microscopy (AFM) to explore the interaction forces between the Simian immunodeficiency virus peptide and phase‐separated supported bilayers composed of various lipids, i.e. dipalmitoylphosphatidylcholine, dioleoylphosphatidylcholine, dioleoylphosphatidic acid and dipalmitoylphosphatidylethanolamine. Histidine‐tagged peptides were attached onto AFM tips terminated with nitrilotriacetate and tri(ethylene glycol) groups, an approach expected to ensure optimal exposure of the C‐terminal hydrophobic domain. Force–distance curves recorded between peptide‐tips and the different bilayer domains always showed a long‐range repulsion upon approach and a lack of adhesion upon retraction, in marked contrast with the hydrophobic nature of the peptide. To explain this unexpected behaviour, we suggest a mechanism in which lipids are pulled out from the bilayer due to strong interactions with the peptide‐tip, in agreement with the very low force needed to extract lipids from supported bilayers. Copyright © 2007 John Wiley & Sons, Ltd.
Fast detection of quadruplex structure in DNA by the intrinsic fluorescence of a single‐stranded DNA binding protein
Authors: Zhuang Xin‐ying , Tang Jun , Hao Yu‐hua , Tan Zheng 
Published: September 2007

AbstractSingle‐stranded guanine‐rich (G‐rich) DNA can fold into a four‐stranded G‐quadruplex structure and such structures are implicated in important biological processes and therapeutic applications. So far, bioinformatic analysis has identified up to several hundred thousand of putative quadruplex sequences in the genome of human and other animal. Given such a large number of sequences, a fast assay would be desired to experimentally verify the structure of these sequences. Here we describe a method that identifies the quadruplex structure by a single‐stranded DNA binding protein from a thermoautotrophic archaeon. This protein binds single‐stranded DNA in the unfolded, but not in the folded form. Upon binding to DNA, its fluorescence can be quenched by up to 70%. Formation of quadruplex greatly reduces fluorescence quenching in a K+‐dependent manner. This structure‐dependent quenching provides simple and fast detection of quadruplex in DNA at low concentration without DNA labelling. Copyright © 2007 John Wiley & Sons, Ltd.
Quality of plant products from organic agriculture
Authors: Rembiałkowska Ewa 
Published: September 2007

AbstractDuring the last decade, consumers' trust in food quality has decreased drastically, mainly because of growing ecological awareness and several food scandals (e.g. BSE, dioxins, bacterial contamination). It has been found that intensive conventional agriculture can introduce contaminants into the food chain. Consumers have started to look for safer and better controlled foods produced in more environmentally friendly, authentic and local systems. Organically produced foods are widely believed to satisfy the above demands, leading to lower environmental impacts and higher nutritive values. So far, studies have partly confirmed this opinion. Organic crops contain fewer nitrates, nitrites and pesticide residues but, as a rule, more dry matter, vitamin C, phenolic compounds, essential amino acids and total sugars than conventional crops. Organic crops also contain statistically more mineral compounds and usually have better sensory and long‐term storage qualities. However, there are also some negatives: plants cultivated in organic systems generally have 20% lower yields than conventionally produced crops. Several important problems need to be addressed in the coming years: environmental, bacterial and fungal contamination of organic crops and, the most essential issue, the impact of organic food consumption on animal and human health. Copyright © 2007 Society of Chemical Industry
Furanocoumarins in vegetables: influence of farming system and other factors on levels of toxicants
Authors: Schulzová Věra , Hajšlová Jana , Botek Petr , Peroutka Radek 
Published: September 2007

AbstractFuranocoumarins are toxic chemicals that occur naturally in edible food plants such as celery, parsnip, carrot, etc. belonging to the Apiaceae family. Lower levels of these phytochemicals are also found in citrus fruits and other crops representing the Rutaceae family. Since their presence in the human diet represents a food safety issue of concern, more knowledge is needed to reduce consumer exposure. This paper provides an overview of various factors influencing the levels of furanocoumarins in vegetables and processed commodities. Special attention is paid to the comparison of crops from organic and conventional farming systems with regard to levels of furanocoumarins and their changes during storage and processing. Copyright © 2007 Society of Chemical Industry
A numerical study of a semi‐algebraic multilevel preconditioner for the local discontinuous Galerkin method
Authors: Castillo Paul E. , Velázquez Esov S. 
Published: September 2007

AbstractIn this work, we consider the local discontinuous Galerkin (LDG) method applied to second‐order elliptic problems arising in the modeling of single‐phase flows in porous media. It has been recently proven that the spectral condition number of the stiffness matrix exhibits an asymptotic behavior of 𝒪(h−2) on structured and unstructured meshes, where h is the mesh size. Thus, efficient preconditioners are mandatory. We present a semi‐algebraic multilevel preconditioner for the LDG method using local Lagrange‐type interpolatory basis functions. We show, numerically, that its performance does not degrade, or at least the number of iterations increases very slowly, as the number of unknowns augments. The preconditioner is tested on problems with high jumps in the
coefficients, which is the typical scenario of problems arising in porous media. Copyright © 2007 John Wiley & Sons, Ltd.
Lagrangian finite element treatment of transient vibration/acoustics of biosolids immersed in fluids
Authors: Krysl P. , Cranford T. W. , Hildebrand J. A. 
Published: September 2007

AbstractSuperposition principle is used to separate the incident acoustic wave from the scattered and radiated waves in a displacement‐based finite element model. An absorbing boundary condition is applied to the perturbation part of the displacement. Linear constitutive equation allows for inhomogeneous, anisotropic materials, both fluids and solids. Displacement‐based finite elements are used for all materials in the computational volume. Robust performance for materials with limited compressibility is achieved using assumed‐strain nodally integrated simplex elements or incompatible‐mode brick elements. A centered‐difference time‐stepping algorithm is formulated to handle general damping accurately and efficiently. Verification problems (response of empty steel cylinder immersed in water to a step plane wave, and scattering of harmonic plane waves from an elastic sphere) are discussed for assumed‐strain simplex and for voxel‐based brick finite element models. A voxel‐based modeling scheme for complex biological geometries is described, and two illustrative results are presented from the bioacoustics application domain: reception of sound by the human ear and simulation of biosonar in beaked whales. Copyright © 2007 John Wiley & Sons, Ltd.
Systematic search for the best gene expression markers for melanoma micrometastasis detection
Authors: Soikkeli J , Lukk M , Nummela P , Virolainen S , Jahkola T , Katainen R , Harju L , Ukkonen E , Saksela O , Hölttä E 
Published: September 2007

AbstractMelanoma is notorious for its high tendency to metastasize and its refractoriness to treatment thereafter. Metastasis is believed to occur mostly through the lymphatic system, and the status of sentinel lymph nodes is currently recognized as the best prognostic indicator. Unfortunately, the lymphatic metastatic process is still poorly understood and the occurrence of sentinel node metastases (micrometastases) may be underestimated. We performed genome‐wide gene expression analyses of melanoma lymph node micrometastases and macrometastases, and of primary melanomas and benign naevi, to characterize the early metastatic cells molecularly and to disclose the best diagnostic markers and rational targets for therapy. Significance analysis of microarrays identified 22 over‐ and five under‐expressed genes with ≥ four‐fold changes in the micrometastases. Of these genes, MLANA, TYR, MIA, ERBB3, PRAME, and SPP1 were tested as potential markers by RT‐PCR and immunohistochemistry. In a prospective study of 160 patients, our graded MLANA and TYR RT‐PCR analyses disclosed clinically significant metastases, as assessed by disease recurrence, better than histological and immunohistochemical examinations. These results strongly suggest the clinical implementation of quantifiable RT‐PCR assays to confirm and complement the pathological examination of sentinel node metastases. Furthermore, SPP1 and PRAME proved valuable as melanoma‐specific markers capable of differentiating melanoma cells from benign naevi in the sentinel lymph nodes. Importantly, these two genes may also prove to be ideal targets for drug development and therapy. Most molecular traits of the micrometastases were already present in the primary tumours, suggesting that micrometastasis to sentinel lymph nodes is a fairly non‐selective process. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Glomerular barrier dysfunction in glomerulosclerosis‐resistant Milan rats with experimental diabetes: the role of renal haemodyamics (J Pathol 2007; 213: 210–218)
Authors: Pugliese G , Ricci C , Iacobini C , Menini S , Fioretto P , Ferrandi M , Giardino LA , Armelloni S , Mattinzoli D , Rastaldi MP , Pugliese F 
Published: September 2007

AbstractThe original article to which this Erratum refers was published in The Journal of Pathology 2007; 213: 210–218
Fractionation of ethylene/1‐pentene copolymers using a combination of SEC‐FTIR and SEC‐HPer DSC
Authors: Luruli Nyambeni , Pijpers Thijs , Brüll Robert , Grumel Valérie , Pasch Harald , Mathot Vincent 
Published: September 2007

AbstractThe short chain branching distribution (SCBD) and thermal properties of ethylene/1‐pentene copolymers were studied using SEC‐FTIR and SEC‐HPer DSC. The copolymers, synthesized with Cp2ZrCl2/MAO, were fractionated using size exclusion chromatography (SEC). The infrared analysis of the fractions showed that the copolymers had—on average—higher 1‐pentene concentration in the low molecular weight range. Furthermore, the thermal properties of the SEC deposits of these copolymers on a Germanium disc were studied using high performance differential scanning calorimetry (HPer DSC). Single SEC separations were used to accumulate fractions in the microgram range that were directly analyzed with regard to their thermal properties, thus allowing us to study SCBD as well as thermal behavior simultaneously. When these fractions (with masses ranging from 10–80 μg) were analyzed using HPer DSC, good melting and crystallization temperature distributions were obtained, proving that HPer DSC can be used as a complementary method to SEC‐FTIR. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2956–2965, 2007
Crystallization and phase morphology of injection‐molded isotactic polypropylene (iPP)/syndiotactic polypropylene (sPP) blends
Authors: Zou Xiao‐Xuan , Yang Wei , Zheng Guo‐Qiang , Xie Bang‐Hu , Yang Ming‐Bo 
Published: September 2007

AbstractThe crystallization and phase morphology of the injection‐molded isotactic polypropylene (iPP)/syndiotactic polypylenen (sPP) blends were studied, focusing on the difference between the skin layer and core layer. The distribution of crystallinity of PPs in the blends calculated based upon the DSC results shows an adverse situation when compared with that in the neat polymer samples. For 50/50 wt % iPP/sPP blend, the SEM results indicated that a dispersed structure in the skin layer and a cocontinuous structure in the core layer were observed. A migration phenomenon that the sPP component with lower crystallization temperature and viscosity move to the core layer, whereas the iPP component with higher crystallization temperature and viscosity move to the skin layer, occurred in the iPP/sPP blend during injection molding process. The phenomenon of low viscosity content migrate to the low shear zone may be due to the crystallization‐induced demixing based upon the significant difference of crystallization temperature in the sPP and iPP. This migration caused the composition inhomogeneity in the blend and influenced the accuracy of crystallinity calculated based upon the initial composition. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2948–2955, 2007
A monitoring study to assess the acute mortality effects of indoxacarb on honey bees (Apis mellifera L.) in flowering apple orchards
Authors: van der Steen Jozef JM , Dinter Axel 
Published: September 2007

AbstractTo evaluate the effect of the indoxacarb 300 g kg−1 WG, Steward 30WDG™, on the honey bee (Apis mellifera L.) in apple orchards, a monitoring study was conducted in Dutch apple orchards in April/May 2004. Before apple flowering began, two honey bee colonies were placed in each orchard to investigate honey bee mortality. Each hive was provided with a Münster dead bee trap to collect dead honey bees. The numbers of dead bees found in these Münster dead traps were counted every 3–4 days for about 2 weeks before and after the period of the insecticide treatment. In nine flowering orchards no indoxacarb was applied during the flowering period, which served as control sites. In 30 flowering orchards indoxacarb was sprayed by the fruit growers according to local practice at 170–260 g formulated product ha−1 (51–78 g AI ha−1). In the control orchards the average mortality was 8 honey bees colony−1 day−1. The average daily honey bee mortality before and after indoxacarb application was 8 and 10 honey bees colony−1 day−1 respectively. At one test site, indoxacarb was mixed with other plant protection products plus plant nutrients, and in this orchard a slight but biologically non‐significant increase in acute honey bee mortality was recorded. It was concluded that the application of indoxacarb caused no effects on honey bee mortality, and that the number of dead honey bees counted in the Münster traps in the orchard treated with indoxacarb was comparable with those determined in control orchards. Copyright © 2007 Society of Chemical Industry
A partially structured region of a largely unstructured protein, Plasmodium falciparum merozoite surface protein 2 (MSP2), forms amyloid‐like fibrils
Authors: Yang Xiaodong , Adda Christopher G. , Keizer David W. , Murphy Vince J. , Rizkalla Michael M. , Perugini Matthew A. , Jackson David C. , Anders Robin F. , Norton Raymond S. 
Published: September 2007

AbstractMerozoite surface protein 2 (MSP2) from the human malaria parasite Plasmodium falciparum is expressed as a GPI‐anchored protein on the merozoite surface. It has been implicated in the process of erythrocyte invasion and is a leading vaccine candidate. MSP2 is an intrinsically unstructured protein (IUP), and recombinant MSP2 forms amyloid‐like fibrils upon storage. We have examined synthetic peptides corresponding to sequences in the conserved N‐terminal region of MSP2 for the presence of local structure and the ability to form fibrils related to those formed by full‐length MSP2. In a 25‐residue peptide corresponding to the entire N‐terminal region of mature MSP2, structures calculated from NMR data show the presence of nascent helical and turn‐like structures. An 8‐residue peptide from the central region of the N‐terminal domain (residues 8–15) also formed a turn‐like structure. Both peptides formed fibrils that were similar but not identical to the amyloid‐like fibrils formed by full‐length MSP2. Notably, the fibrils formed by the peptides bound both Congo Red and Thioflavin T, whereas the fibrils formed by full‐length MSP2 bound only Congo Red. The propensity of peptides from the N‐terminal conserved region of MSP2 to form amyloid‐like fibrils makes it likely that this region contributes to fibril formation by the full‐length protein. Thus, in contrast to the more common pathway of amyloid formation by structured proteins, which proceeds via partially unfolded intermediates that then undergo β‐aggregation, MSP2 is an example of a largely unstructured protein with at least one small structured region that has an important role in fibril formation. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Effect of positive charge in VIP 16γ‐glutamyl diamino derivatives on hVPAC1 and hVPAC2 receptor function
Authors: de Maria Salvatore , Metafora Vittoria , Metafora Salvatore , Ravagnan Gianpietro , Cartení Maria , Pontoni Gabriele , Facchiano Angelo , Lepretti Marilena , Severino Beatrice , Caliendo Giuseppe , Santagada Vincenzo , Langer Ingrid , Robberecht Patrick 
Published: September 2007

AbstractIncrease of VPAC receptor s binding to the 16γ‐glutamyl diaminopropane vasoactive intestinal peptide (VIP‐DAP) agonist, a vasoactive intestinal polypeptide (VIP) structural analogue containing a positive charge at position 16, has confirmed the importance of a positive charge at this site. By investigating the effect of distance from the peptide backbone Cα of a positive charge in position 16, data are reported here concerning: (i) a novel chemical method used for the synthesis of a new family of 16γ‐glutamyl diamine VIP derivatives differing among them for single carbon atoms and including diaminoethane (VIP‐DAE2), diaminopropane (VIP‐DAP3), diaminobutane (VIP‐DAB4), diaminopentane (VIP‐DAP5), and diaminohexane (VIP‐DAH6); (ii) functional characterization of these compounds on human VPAC1 and VPAC2 receptors. In more detail, the EC50 and IC50 values, when measured as a function of the alkylic chain length, show in more detail, that the use of VIP‐DAB4 derivative changes the IC50 but not the EC50, thus indicating on hVPAC2 receptor an unexpected relationship between binding and activity that differs from that obtained on hVPAC1. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Characterization of monohydroxylated derivatives of the anticancer agent flavone‐8‐acetic acid by liquid chromatography with on‐line UV and mass spectrometry
Authors: Pham Minh Hien , Menet Marie‐Claude , Dugay Annabelle , Regazzetti Anne , Dauzonne Daniel , Auzeil Nicolas , Scherman Daniel , Chabot Guy G. 
Published: September 2007

AbstractThe experimental anticancer agent flavone‐8‐acetic acid (FAA) is metabolized into several monohydroxylated derivatives using mouse microsomes. Because these metabolites could be involved in the biological effects of FAA, the aim of this study was to characterize all its possible monohydroxylated derivatives. To do so, we have developed a methodology using reversed‐phase high‐performance liquid chromatography (RP‐HPLC) coupled with ultraviolet (UV) detection and mass spectrometry (MS) to analyze and identify FAA derivatives hydroxylated at the 2′, 3′, 4′, 3, 5, 6, or 7 position. In RP‐HPLC, 4′‐, 3′‐, 2′‐, 6‐, and 7‐OH‐FAA eluted before FAA, whereas 3‐ and 5‐OH‐FAA eluted after FAA. UV spectra showed a bathochromic shift of band I for all derivatives and of band II for 5‐ and 6‐OH‐FAA. In addition, the position of the OH group could be determined by the presence of certain product ions in MS. Ions atm/z133 and 151 were specific for 2′‐, 3′‐, 4′‐, and 3‐OH‐FAA, whereas the ion atm/z177 was specific for 3‐OH‐FAA only. The ionsm/z133, 151 and 167 were specific for 2′‐OH‐FAA. Ions atm/z149 were specific for the presence of the OH group on cycle A only (i.e., 5‐, 6‐ or 7‐OH‐FAA). The presence of both product ionsm/z149 and 179 were specific for 7‐OH‐FAA. Finally, ions atm/z149 and several product ions of evenm/zvalues were specific for 5‐OH‐FAA. In conclusion, the methodology described can be used to identify all possible monohydroxylated FAA derivatives. Copyright © 2007 John Wiley & Sons, Ltd.
Targeted mass spectrometric strategy for global mapping of ubiquitination on proteins
Authors: Mollah Sahana , Wertz Ingrid E. , Phung Qui , Arnott David , Dixit Vishva M. , Lill Jennie R. 
Published: September 2007

AbstractPost‐translational modifications of proteins including phosphorylation, glycosylation, acetylation and ubiquitination facilitate the regulation of many cellular processes and intracellular signaling events. Ubiquitination plays a key role in the functional regulation and degradation of many classes of proteins, and the study of ubiquitination and poly‐ubiquitination has emerged as one of the most active areas in proteomic research. A variety of mass spectrometric methods have been described for the identification of ubiquitination sites, the study of poly‐ubiquitin topology and the identification of ubiquitin substrates. The most popular workflow for both ubiquitination site mapping and poly‐ubiquitination chain topology characterization is to take advantage of the Gly‐Gly signature on the substrate's lysine residue observed after tryptic digestion. Although a number of protocols have been described for the mapping of ubiquitination sites, one major challenge is that ubiquitination is typically heterogeneous, and several lysine residues may be ubiquitinated within a protein. When multiple ubiquitination sites are present, multiple analyses are often required to cover all of the potential modification sites which in turn can necessitate the usage of larger quantities of material. In addition, the level of ubiquitination on endogenous and recombinant proteins may be of low intensity, adding further analytical challenges in the identification of this modification. The use of the multiple reaction monitoring (MRM)‐initiated detection and sequencing workflow (MIDAS™) for the identification of phosphorylation sites has previously been described. Here, we explore the use of an MRM workflow for ubiquitination site mapping on the substrate protein, receptor interacting protein (RIP). Copyright © 2007 John Wiley & Sons, Ltd.