bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of poly(p‐diphenylmethylterephthalamide) from recycled monomers
Authors: Norakankorn C. , Chuayjuljit S. , Pimpan V.
Published: October 2003

Poly(p‐diphenylmethylterephthalamide) or PMA was synthesized from the reaction between recycled terephthalic acid (TPA) and recycled 4,4′‐methylenedianiline (MDA) in the presence of pyridine, triphenyl phosphite, and a solubilizing‐aid agent. The reaction conditions used for this polymerization were determined from a model reaction using pure TPA and pure MDA as reactants. It was found that PMA with the highest % yield and molecular weight was obtained when the mixture of lithium chloride (LiCl) and calcium chloride (CaCl2) were used as solubilizing‐aid agents with a reaction time of 4 h. Recycled TPA with 92% purity was obtained from acid hydrolysis of waste PET bottles using sulfuric acid as a catalyst at 150°C for 5 h. Recycled MDA with 99% purity was obtained from aminolysis of rigid polyurethane foam scrap using diethylenetriamine as a degrading agent at 180°C for 70 min. PMAs prepared from recycled monomers exhibited thermal properties, which were comparable to those of PMA prepared from pure monomers. However, due to a possibility of several isomers present in recycled MDA, PMAs prepared from this monomer had lower melting points and thermal decomposition temperatures than those prepared from pure MDA. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3723–3729, 2003
Recycling of jute textile in phenol formaldehyde–jute composites
Authors: Hassan Mohammad L.
Published: October 2003

Jute textile was recycled into composites using different percents of phenol formaldehyde (PF) resin. The effect of the resin percent, from 12 to 30%, on the flexural strength, tensile strength, water absorption, and thickness swelling of the produced composites was studied. To improve the dimensional stability of the produced composites, jute textile was acetylated or steamed. The effect of steaming and acetylation on the structure and thermal stability of jute fibers was studied using Fourier Transform Infrared (FTIR) spectroscopy and Thermogravimetric analysis (TGA), respectively. The effect of these treatments on the flexural strength, tensile strength, water absorption, and thickness swelling of the produced composites was studied. Steaming of jute textile was superior to acetylation in improving the dimensional stability. Cyclic wetting and drying test of the composites showed that steaming of the jute textile resulted in much less irreversible and reversible thickness swelling than in case of using acetylated or untreated jute textile. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3588–3593, 2003
Polystyrene‐supported polyoxyethylene bound potassium permanganate as a heterogeneous oxidizing agent
Authors: Chacko Asha , Mathew Beena
Published: October 2003

Oxidation behavior of a 2 mol % divinylbenzene (DVB)‐crosslinked polystyrene‐supported permanganate function was investigated toward low molecular weight primary and secondary alcohols and aldehydes. The permanganate function was attached to a polystyrene support through cyclic polyoxyethylene (POE) units immobilized on the support. Contrary to the oxidations catalyzed by low molecular weight permanganate reagents, the oxidation of primary alcohol terminated in the aldehyde stage. The secondary alcohols were converted to the respective ketone and aldehyde to acid. The effect of the variable parameters similar to solvent, temperature, and reagent to substrate ratio was followed. Nonpolar cyclohexane was found to be the best solvent for the present study. Also the reactivity increased with increasing temperature. The oxidizing reagent possesses a long shelf life and could be recycled several times without reduction of capacity and mechanical stability. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3708–3717, 2003
Study on propene polymerization using a novel spherical Ziegler‐Natta catalyst and its kinetics
Authors: Ye Zhao‐Yang , Wang Li , Jiang Shan
Published: October 2003

The effects of the Al/Ti ratio and external donor (ED) on the catalytic activity and kinetics of propene polymerization catalyzed by a spherical Ziegler‐Natta (Z‐N) catalyst were investigated. The preparation conditions of the catalyst play an important role in the polymerization kinetics. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3737–3740, 2003
Effect of aluminum chloride and Pt/ TiO2 on the thermal degradation of poly(vinyl chloride) in solution
Authors: Gupte Sachin L. , Agarwal Nitin , Madras Giridhar , Nagaveni K. , Hegde M.S.
Published: October 2003

The effect of two catalysts, Pt/TiO2 and aluminum chloride, on the degradation of poly (vinyl chloride) (PVC) in solution was investigated at various temperatures. The molecular weight distribution of the polymer was obtained by analyzing the samples by gel permeation chromatography. Experimental data indicated that the catalysts enhanced the degradation rate of PVC compared to the thermal degradation of PVC. Continuous distribution kinetic models were used to evaluate the degradation rate coefficients. The activation energy, calculated from the temperature dependence of rate coefficients, was 26.5, 31.5, and 43.7 kcal/mol for the thermal degradation of PVC in solution, in the presence of Pt/TiO2 and in the presence of AlCl3, respectively. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3532–3535, 2003
Preparation and swelling behavior of biodegradable hydrogels based on α,β‐poly(N‐2‐hydroxyethyl‐DL‐aspartamide)
Authors: Yoon Seung‐Wook , Chung Dong Jun , Kim Ji‐Heung
Published: October 2003

Biodegradable polymers and the hydrogels have been increasingly applied in a variety of biomedical fields and pharmaceutics. α,β‐Poly(N‐2‐hydroxyethyl‐DL‐aspartamide), PHEA, one of poly(amino acid)s with hydroxyethyl pendants, are known to be biodegradable and biocompatible, and has been studied as an useful biomaterial, especially for drug delivery, via appropriate structural modification. In this work, hydrogels based on PHEA were prepared by two‐step reaction, that is, the crosslinking of polysuccinimide, the precursor polymer, with oligomeric PEG or PEI‐diamines and the following nucleophilic ring‐opening reaction by ethanolamine. Soft hydrogels possessing varying degrees of gel strength could be prepared easily, depending on the amount of different crosslinking reagents. The swelling degrees, which were in the range of 10–40 g–water/dry gel, increased somewhat at higher temperature, and also at alkaline pH of aqueous solution. A typical hydrogel remained almost unchanged for 1 week, at 37°C in phosphate buffer of pH 7.4, and then seemed to degrade slowly as time. A porous scaffold could be fabricated by the freeze drying of water‐swollen gel. The PHEA‐based hydrogels have potential for useful biomaterial applications including current drug delivery system. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3741–3746, 2003
Dielectric properties of aluminum–epoxy composites
Authors: Singh Vishal , Kulkarni A. R. , Rama Mohan T. R.
Published: October 2003

Dielectric properties of Al–epoxy composites were characterized as a function of composition, frequency, and temperature. The dielectric constant increased smoothly with an increase in the concentration of aluminum. An increase in dielectric constant was also observed with an increase in temperature as well as with a decrease in frequency. In general, dissipation factor values for composites with higher concentrations of aluminum were greater than those with lower volume content of aluminum. Also, the dissipation factor showed an increase both with a decrease in frequency and an increase in temperature. The increase in values of dielectric constant and dissipation factor with an increase in concentration of aluminum was attributed to interfacial polarization. The absence of any discontinuity in the plot of dielectric constant versus composition was ascribed to the absence of continuous aluminum chains in the composition range investigated. The increase in dielectric constant with a rise in temperature was attributed to the segmental mobility of the polymer molecules. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3602–3608, 2003
Study on antistatic modification of polyurethane elastomer surfaces by grafting with vinyl acetate and antistatic agent
Authors: Zhou Xiangdong , Liu Pengsheng
Published: October 2003

Under UV light, vinyl acetate (VAc) was grafted onto polyurethane (PU) elastomer membrane, using benzoyl peroxide as photoinitiator. After surface alcoholysis reaction, hydroscopic hydroxyl formed on the surface of PU, and under catalysis of MgCl2, the antistatic agent combined with hydroxyl by chemical linkage, so that the antistatic durability of PU improved. The ATR‐FTIR spectrum, X‐ray photoelectron spectroscopy, and SEM characterized the grafted copolymers and verified the occurrence of grafting copolymerization. The effect of grafting degree of VAc on the antistatic ability of PU surface was also investigated in this study. Experimental results showed that after modification the surface electric resistivity of PU elastomer reached the nearly 108Ω class, with little change in spite of a washing‐fastness experiment, although its mechanical ability was slightly decreased. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3617–3624, 2003
Nanosize polymer latices made by microemulsion copolymerization: Preparation and characterization
Authors: Zhang Yuying , Guo Tianying , Hao Guangjie , Song Maodao , Zhang Banghua
Published: October 2003

Polymer nanoparticles were prepared by a methyl methacrylate/butyl methacrylate/2‐hydroxyethyl methacrylate/acrylate or methyl acrylate microemulsion copolymerization process. A microemulsion copolymerization method was used. With this process high polymer : surfactant weight ratios (≥15 : 1), relatively concentrated (∼ 30 wt %) lattices, and small (∼ 60 nm) particle diameters were obtained. Properties of the latices were characterized in detail by TEM, DSC, dynamic light scattering, spectrophotometry, and tensile strength testing. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3625–3630, 2003
Behavior of poly(methyl methacrylate)–based systems in supercritical CO2 and CO2 plus cosolvent: Solubility measurements and process assessment
Authors: Domingo C. , Vega A. , Fanovich M. A. , Elvira C. , Subra P.
Published: October 2003

Microspheres based on synthetic polymers such as poly(methyl methacrylate) (PMMA) and PMMA blends are known for their medical and optical applications. The development of methods for processing polymeric microspheres using a nontoxic solvent, like supercritical carbon dioxide (SCCO2), is desirable. This work investigates the solubility and behavior of polymers (PMMA and PMMA/polycaprolactone blend) and solutes (cholesterol and albumin) in SCCO2 and SCCO2 + cosolvent (acetone, ethanol, and methylene chloride). The knowledge of solubility behavior of materials in SCCO2 aids in the selection and/or design of the most appropriate technique for materials processing. Processing PMMA‐based polymers with pure SCCO2 leads to polymer swelling. The lack of polymer solubility in pure CO2 precludes their micronization by the RESS (rapid expansion of supercritical solutions) process, but on the other hand allows their impregnation. Polymer plasticization caused by CO2 can be exploited in the PGSS (particles from gas‐saturated solutions) process. Addition of a liquid cosolvent to CO2 enhances the dissolution of solutes and polymers. Precipitation of the studied polymers by antisolvent techniques seems feasible only by use of CO2 + methylene chloride. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3652–3659, 2003
Chemical modification of keratin fibers using 2‐iminothiorane hydrochloride
Authors: Kuzuhara A.
Published: October 2003

For the purpose of improving the properties of keratin fibers by chemical modification, we attempted to introduce new disulfide (–SS–) groups into hair using 2‐iminothiorane hydrochloride (2‐IT). After the evaluation of the setting ability of human hair, the waving permanence (66%) of our proposed permanent hair‐setting process clearly improved compared with that of a conventional permanent hair‐setting process (48%). Next, it became clear that new –SS– groups were created in the human hair samples as a result of introducing and then oxidizing new –SH groups. This –SS– content in the hair samples was estimated by employing FT‐Raman spectroscopy. By examining the Raman bands of the treated and untreated hair, it was seen that each band of treated hair did not change, except for the increase of the –SS– groups. This suggests that hair damage does not occur as a result of the investigated treatment. From these experiments, the chemical modification of keratin fibers using 2‐IT was clearly effective for a permanent hair‐setting process. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3646–3651, 2003
Preparation of poly(acrylic acid)–chitosan hydrogels by gamma irradiation and in vitro drug release
Authors: Shim Jae‐Woon , Nho Young‐Chang
Published: October 2003

Biocompatible and biodegradable pH‐responsive hydrogels based on poly(acrylic acid) (AAc) and chitosan were prepared for controlled drug delivery. These interpolymeric hydrogels were synthesized by a gamma irradiation polymerization technique. The degree of gelation was over 96% and increased as the chitosan or acrylic acid content increased. The equilibrium swelling studies of hydrogels prepared in various conditions were carried out in an aqueous solution, and the pH sensitivity in the range of pH 1–12 was investigated. The AAc/chitosan hydrogels showed the highest water content when the 30 vol % AAc and 0.1 wt % chitosan were irradiated with a 30‐kGy radiation dose. Also, an increase of swelling degree with an increase in the pH was noticed and showed the highest value at pH 12. The drug, 5‐fluorouracil, was loaded into these hydrogels and the release studies were carried out in simulated gastric and intestinal fluids. The in vitro release profiles of the drugs showed that more than 90% of the loaded drugs were released in the first 1 h at the intestinal pH and the rest of the drug had been released slowly. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3660–3667, 2003
Intercalary heterochromatin and genetic silencing
Authors: Zhimulev Igor F. , Belyaeva Elena S.
Published: October 2003

We focus here on the intercalary heterochromatin (IH) of Drosophila melanogaster and, in particular, its molecular properties. In the polytene chromosomes of Drosophila, IH is represented by a reproducible set of dense bands scattered along the euchromatic arms. IH contains mainly unique DNA sequences, and shares certain features with other heterochromatin types such as pericentric, telomeric, and PEV‐induced heterochromatin, the inactive mammalian X‐chromosome and the heterochromatized male chromosome set in coccids. These features are transcriptional silencing, chromatin compactness, late DNA replication, underrreplication or elimination in somatic cells, and formation of the heterochromatin state in early embryogenesis. Post‐translational modification of histones and the specific nonhistone protein complexes are shown to participate in the establishment and maintenance of silencing for all heterochromatin types. Many IH regions contain binding sites for HP1 and/or Pc‐G proteins and all the regions are sites of heterochromatin‐associated SuUR protein. Some IH regions are known to contain homeotic genes. Summarizing these data, we suggest that IH regions comprise stable inactivated genes, whose silencing is developmentally programmed. BioEssays 25:1040–1051, 2003. © 2003 Wiley Periodicals, Inc.
DNMT cooperativity—the developing links between methylation, chromatin structure and cancer
Authors: El‐Osta Assam
Published: October 2003

Controversy has reigned for some time over the biological connection between DNA methylation and cancer. For this reason, the methylation mechanism responsible for increased cancer risk has received greater attention in recent years. Tumor suppressor genes are often hypermethylated resulting in gene silencing. Although some have questioned this interpretation of the link between methylation and cancer, it appears that both hypermethylation and hypomethylation events can create epigenetic changes that can contribute to cancer development. Recent studies have shown that the methyltransferases DNMT1 and DNMT3b cooperatively maintain DNA methylation and gene silencing in human cancer cells. Disruption of the human DNMT3b only slightly reduces the overall global DNA methylation; however, demethylation was markedly potentiated when both DNMT1 and DNMT3b were simultaneously deleted. The results to these experiments provide compelling evidence towards a role for DNA methylation in cancer. This review discusses the current understanding of cancer‐epigenetic information and highlights recent studies that connect the methylation machinery and chromatin remodelling with cancer susceptibility. BioEssays 25:1071–1084, 2003. © 2003 Wiley Periodicals, Inc.
TRAF6, a molecular bridge spanning adaptive immunity, innate immunity and osteoimmunology
Authors: Wu Hao , Arron Joseph R.
Published: October 2003

Tumor necrosis factor (TNF) receptor associated factor 6 (TRAF6) is a crucial signaling molecule regulating a diverse array of physiological processes, including adaptive immunity, innate immunity, bone metabolism and the development of several tissues including lymph nodes, mammary glands, skin and the central nervous system. It is a member of a group of six closely related TRAF proteins, which serve as adapter molecules, coupling the TNF receptor (TNFR) superfamily to intracellular signaling events. Among the TRAF proteins, TRAF6 is unique in that, in addition to mediating TNFR family signaling, it is also essential for signaling downstream of an unrelated family of receptors, the interleukin‐1 (IL‐1) receptor/Toll‐like receptor (IL‐1R/TLR) superfamily. Gene targeting experiments have identified several indispensable physiological functions of TRAF6, and structural and biochemical studies have revealed the potential mechanisms of its action. By virtue of its many signaling roles, TRAF6 represents an important target in the regulation of many disease processes, including immunity, inflammation and osteoporosis. BioEssays 25:1096–1105, 2003. © 2003 Wiley Periodicals, Inc.
Small GTPases and the evolution of the eukaryotic cell
Authors: Jékely Gáspár
Published: October 2003

The origin of eukaryotes is one of the major challenges of evolutionary cell biology. Other than the endosymbiotic origin of mitochondria and chloroplasts, the steps leading to eukaryotic endomembranes and endoskeleton are poorly understood. Ras‐family small GTPases are key regulators of cytoskeleton dynamics, vesicular trafficking and nuclear function. They are specific for eukaryotes and their expansion probably traces the evolution of core eukaryote features. The phylogeny of small GTPases suggests that the first endomembranes to evolve during eukaryote evolution had secretory, and not phagocytic, function. Based on the reconstruction of putative roles for ancestral small GTPases, a hypothetical scenario on the origins of the first endomembranes, the nucleus, and phagocytosis is presented. BioEssays 25:1129–1138, 2003. © 2003 Wiley Periodicals, Inc.
Pathogenic archaea: do they exist?
Authors: Cavicchioli Ricardo , Curmi Paul M.G. , Saunders Neil , Thomas Torsten
Published: October 2003

Archaea are microorganisms that are distinct from bacteria and eukaryotes. They are prevalent in extreme environments, and yet found in most ecosystems. They are a natural component of the microbiota of most, if not all, humans and other animals. Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified. Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist. This review examines whether this is a good assumption by investigating the potential for archaea to be or become pathogens. This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea. In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis. The view of this report is that, although archaea can presently be described as non‐pathogenic, they have the potential to be (discovered as) pathogens. The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future. BioEssays 25:1119–1128, 2003. © 2003 Wiley Periodicals, Inc.
PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease
Authors: Vossenaar Erik R. , Zendman Albert J.W. , van Venrooij Walther J. , Pruijn Ger J.M.
Published: October 2003

Peptidylarginine deiminase (PAD, EC 3.5.3.15) enzymes catalyze the conversion of protein‐bound arginine to citrulline. This post‐translational modification may have a big impact on the structure and function of the target protein. In this review, we will discuss the effects of citrullination and its involvement in several human diseases, including rheumatoid arthritis and multiple sclerosis. So far, four isotypes of PAD have been described in mammals. We describe the existence of PAD in non‐mammalian vertebrates and the existence of a fifth mammalian PAD. In addition, tissue‐specific expression, genomic organization and evolutionary conservation of the different PAD isotypes will be discussed in detail. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265‐9247/suppmat/2003/25/v25.1106.html. BioEssays 25:1106–1118, 2003. © 2003 Wiley Periodicals, Inc.
Anti‐cancer selection as a source of developmental and evolutionary constraints
Authors: Galis Frietson , Metz Johan A.J.
Published: October 2003

Recently at least two papers1,2have appeared that look at cancer from an evolutionary perspective. That cancer has a negative effect on fitness needs no argument. However, cancer origination is not an isolated process, but the potential for it is linked in diverse ways to other genetically determined developmental events, complicating the way selection acts on it, and through it on the evolution of development. The two papers take a totally different line. Kavanagh argues that anti‐cancer selection has led to developmental constraints. Leroi et al. argue that cancer is a side‐effect of recent evolutionary changes that usually will disappear over time through anti‐cancer selection. Here we place the papers in a wider perspective, and in so doing discuss various alternative developmental links cancer may have together with their evolutionary implications. BioEssays 25:1035–1039, 2003. © 2003 Wiley Periodicals, Inc.
Alternative splicing and evolution
Authors: Boue Stephanie , Letunic Ivica , Bork Peer
Published: October 2003

Alternative splicing is a critical post‐transcriptional event leading to an increase in the transcriptome diversity. Recent bioinformatics studies revealed a high frequency of alternative splicing. Although the extent of AS conservation among mammals is still being discussed, it has been argued that major forms of alternatively spliced transcripts are much better conserved than minor forms.1 It suggests that alternative splicing plays a major role in genome evolution allowing new exons to evolve with less constraint. BioEssays 25:1031–1034, 2003. © 2003 Wiley Periodicals, Inc.
Mechanism‐based protein design: Attempted “nucleation–condensation” approach to a possible minimal helix‐bundle protein
Authors: Mohanraja K. , Dhanasekaran M. , Kundu B. , Durani S.
Published: October 2003

In an intended mechanism‐based de novo approach, a 22‐mer peptide was so designed as to make it both a stereochemically nucleatable and hydrophobically condensable minimal globular protein. Framework‐like nucleation of a triple‐helix bundle was targeted by employing as folding nucleators composite β‐turns that could both nucleate helices and place them in close juxtaposition for possible interhelical interaction. To promote the targeted triple‐helix bundle to condense as a globular protein, an amphipathic sequence pattern was adopted for possible hydrophobic interhelical interaction. A predominantly helicogenic 22‐mer amphipathic peptide was thus designed, punctuating it with composite type II′–III and type II–Asx type β‐turns as the helix nucleators cum chain reversal elements. The peptide made by solid‐phase synthesis was shown by NMR and CD to be a nascent and distorted triple‐helix bundle in a trifluoroethanol (TFE)–water mixture, but more or less a random coil in water. A fold nucleation effect is evident in the TFE–water mixture, but apparently the hydrophobic effect cannot sustain the peptide conformational order in water. A lack of synergy between folding nucleation and hydrophobic condensation of the peptide is possible. Indeed, a mismatch between the sequential H,P pattern of the peptide and its nascent‐type globular fold in a TFE–water mixture is evident based on a simulated annealing study guided by NMR. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 355–363, 2003
DNA deformation energetics and protein binding
Authors: Zakrzewska K.
Published: October 2003

The formation of protein‐DNA complexes often involves deformation of the DNA double helix. We have calculated the energy necessary to produce this deformation in 71 crystallographically determined complexes, using internal coordinate energy optimization with the JUMNA program and a generalized Born continuum solvent treatment. An analysis of the data allows deformation energy to be interpreted in terms of both local and global structural changes. We find that, in the majority of complexes, roughly 60% of the deformation energy corresponds to backbone distortion. It is also found that large changes in stacking and pairing energies are often compensated for by other, longer range, stabilizing factors. Some deformations, such as base opening, can be large, but only‐produce local energetic effects. In terms of backbone distortions, the angle α, most often involved in αγ transitions, makes the most significant energetic contribution. This type of transition is twice as costly as those involving β, or coupled εζ changes. Sugar amplitude changes are also energetically significant, in contrast to changes in phase angles. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 414–423, 2003
Binding of copper(II) ions to the polyproline II helices of PEVK modules of the giant elastic protein titin as revealed by ESI‐MS, CD, and NMR
Authors: Ma Kan , Wang Kuan
Published: October 2003

Titin, a family of giant elastic proteins, constitutes an elastic sarcomere matrix in striated muscle. In the I‐band region of the sarcomere, the titin PEVK segment acts as a molecular spring to generate elasticity as well as sites of adhesion with parallel thin filaments. Previously, we reported that PEVK consists of tandem repeats of 28 residue modules and that the “polyproline II‐coil” motif is the fundamental conformational motif of the PEVK module. In order to characterize the factors that may affect and alter the PPII‐coil conformational motifs, we have initiated a systematic study of the interaction with divalent cations (Cu2+, Ca2+, Zn2+, and Ni2+) and a conformational profile of PEVK peptides (a representative 28‐mer peptide PR: PEPPKEVVPEKKAPVAPPKKPEVPPVKV and its subfragments PR1: kvPEPPKEVVPE, PR2: VPEKKAPVAPPK, PR3: KPEVPPVKV). UV‐Vis absorption difference spectra and CD spectra showed that Cu2+ bound to PR1 with high affinity (20 μM), while its binding to PR2 and PR3 as well as the binding of other cations to all four peptides were of lower affinity (>100 μM). Conformational studies by CD revealed that Cu2+ binding to PR1 resulted in a polyproline II to turn transition up to a 1:2 PR1/Cu2+ ratio and a coil to turn transition at higher Cu2+ concentration. ESI‐MS provided the stoichiometry of PEVK peptide‐Cu2+ complexes at both low and high ion strength, confirming the specific high affinity binding of Cu2+ to PR1 and PR. Furthermore, NMR and ESI‐MS/MS fragmentation analysis elucidated the binding sites of the PEVK peptide‐Cu2+ complexes at −2KVPE2, 8VPE10, 13APV15, and 22EVP24. A potential application of Cu2+ binding in peptide sequencing by mass spectrometry was also revealed. We conclude that Cu2+ binds and bends PEVK peptides to a beta‐turn‐like structure at specific sites. The specific targeting of Cu2+ towards PPII is likely to be of significant value in elucidating the roles of PPII in titin elasticity as well as in interactions of proline‐rich proteins. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 297–309, 2003
Spectroscopic investigation on gel‐forming β‐sheet assemblage of peptide derivatives
Authors: Ganesh S. , Prakash S. , Jayakumar R.
Published: October 2003

The conformational studies of peptide derivatives A and B in a gel state were studied by using circular dichroism (CD), Fourier transformed infrared (FTIR), and fluorescence spectroscopic techniques. Birefringence and electron microscopic studies were carried out to characterize the morphological aspects of the fibrils in the gel. The FTIR spectra of the peptides show the absence of free NH in the gel state, implying that the intermolecular hydrogen‐bond formation is the driving force for the aggregation. The CD spectrum of the peptide gels shows the presence of antiparallel and parallel β‐sheet conformation for peptide derivatives A and B, respectively. Electron microscopic studies (EM) of the peptide derivatives A and B reveal that peptide A formed rigid, rod‐like structures without cross‐linking and peptide B formed loose fibrils organized into highly noncovalently cross‐linked mesh‐like structural aggregates. Peptide A was much more soluble in alcoholic solvents than peptide B, and no birefringence was observed with Congo red (CR) staining in the temperature range of 0–80°C. The spectroscopic studies indicate that peptide B consists of domains having a significant amount of β‐sheet structure and exhibiting golden yellow birefringence between 53 and 56°C when stained with Congo red. On the other hand, peptide A gives no evidence of birefringence under polarized light. Fluorescence probe binding studies with pyrene in gel state with peptides A and B indicates the polarity in the interior of the aggregates. The data presented in the present work indicate that peptide B forms fibrils, which is similar to amyloid aggregates that are present in biological systems. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 346–354, 2003
Physicochemical characterization of branched chain polymeric polypeptide carriers based on a poly‐lysine backbone
Authors: Nagy I. B. , Hudecz F. , Alsina M. A. , Reig F.
Published: October 2003

A systematic study is reported on the physicochemical characteristics of two branched chain polymers (based on a poly‐L‐lysine backbone) with a general formula poly[Lys‐(DL‐Alam‐Xi)], where X = Orn (OAK) or N‐acetyl‐Glu (Ac‐EAK) and m ≅ 3, using surface pressure and fluorescence polarization methods. These data are compared with those of the linear poly(L‐Lys) from which OAK and Ac‐EAK are derived. These two polymers show a moderate surface activity, able to form stable monomolecular layers at the air‐water interface. Poly(L‐Lys), the most hydrophilic, has the lowest surface activity. The interaction of these polymers with phospholipid bilayers either neutral or negatively charged was studied with vesicles labeled with two fluorescent probes: ANS and DPH. Results indicate that these polymers are able to accommodate in their internal structure, mainly through electrostatic interactions, a certain amount of ANS marker molecules, but fluorescence increases of the ANS‐polypeptide complexes were so low that its influence in further polarization measurements could be discarded. After interaction with liposomes, these polymers induce an increase in the polarization of the probes, thus indicating a rigidification of the bilayers. Electrostatic forces seem to be very important in this interaction; cationic polymers are clearly more active, with PG‐containing liposomes, than Ac‐EAK. Moreover, in these assays poly(L‐Lys) behaves as the more active compound. This fact is probably due to its major ability to form α‐helical structures that could insert easily in the bilayers. These results indicate that the polymeric structures studied can be used as carriers for biologically active molecules, because their interactions with bilayers remain soft and have a positive effect on the stability of the membranes. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 323–335, 2003
Speed‐up of DNA melting algorithm with complete nearest neighbor properties
Authors: Tøstesen Eivind , Liu Fang , Jenssen Tor‐Kristian , Hovig Eivind
Published: October 2003

We describe an optimized algorithm, which is faster and more accurate compared to previously described algorithms, for computing the statistical mechanics of denaturation of nucleic acid sequences according to the classical Poland‐Scheraga type of model. Nearest neighbor thermodynamics has been included in a complete and general way, by rigorously treating nearest neighbor interactions, helix end interactions, and isolated base‐pairs. This avoids the simplifications of previous approaches and achieves full generality and controllability with respect to thermodynamic modeling. The algorithm computes subchain partition functions by recursion, from which various quantitative aspects of the melting process are easily derived, for example the base‐pairing probability profiles. The algorithm represents an optimization with respect to algorithmic complexity of the partition function algorithm of Yeramian et al. (Biopolymers 1990, 30, 481–497): we reduce the computation time for a base‐pairing probability profile from O(N2) to O(N), where N is the sequence length. This speed‐up comes in addition to the speed‐up due to a multiexponential approximation of the loop entropy factor as introduced by Fixman and Freire22 and applied by Yeramian et al.25 The speed‐up, however, is independent of the multiexponential approximation and reduces time from O(N3) to O(N2) in the exact case. A method for representing very large numbers is described, which avoids numerical overflow in the partition functions for genomic length sequences. In addition to calculating the standard base‐pairing probability profiles, we propose to use the algorithm to calculate various other probabilities (loops, helices, tails) for a more direct view of the melting regions and their positions and sizes. This can provide a better understanding of the physics of denaturation and the biology of genomes. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 364–376, 2003
Structure–activity relationships in the hydrophobic interactions of polyphenols with cellulose and collagen
Authors: Tang H. R. , Covington A. D. , Hancock R. A.
Published: October 2003

Polyphenol interactions with both cellulose and collagen in the solid state have been studied by using chromatography on cellulose and by evaluating the hydrothermal stability of the polyphenol treated sheepskin collagen. Twenty‐four polyphenolic compounds were studied, including seven glucose‐based gallotannins, five polyalcohol‐based gallotannins, and twelve ellagitannins. In the cellulose–polyphenols systems, the polyphenol's affinity to cellulose is positively correlated with their molecular masses, the number of galloyl groups, and their hydrophobicity (logP). The polyphenol treatment increased the hydrothermal stability of collagen samples, and such effects are also positively correlated with the molecular masses, total number of galloyl groups and the hydrophobicity of polyphenols. Ellagitannins showed much weaker interactions with both biopolymers than gallotannins having similar molecular mass, the same number of galloyl groups, and the same number of phenolic hydroxyl groups. It is concluded that, for the polyphenol interactions with both cellulose and collagen, (1) the galloyl group of polyphenols is the functional group; (2) the strength of interactions are positively correlated with molecular size, the number of galloyl groups and the hydrophobicity of polyphenols; (3) the hydrophobic interactions are of great significance; and (4) the interactions are strongly dependent on the flexibility of galloyl groups. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 403–413, 2003
The solution structure of frenatin 3, a neuronal nitric oxide synthase inhibitor from the giant tree frog,Litoria infrafrenata
Authors: Brinkworth Craig S. , Carver John A. , Wegener Kate L. , Doyle Jason , Llewellyn Lyndon E. , Bowie John H.
Published: October 2003

The peptide frenatin 3 is a major component of the skin secretion of the Australian giant tree frog,Litoria infrafrenata. Frenatin 3 is 22 amino acids in length, and shows neither antimicrobial nor anticancer activity. It inhibits the production of nitric oxide by the enzyme neuronal nitric oxide synthase at a micromolar concentration by binding to its regulatory protein, Ca2+calmodulin, a protein known to recognize and bind amphipathic α‐helices. The solution structure of frenatin 3 has been investigated using NMR spectroscopy and restrained molecular dynamics calculations. In trifluoroethanol/water mixtures, the peptide forms an amphipathic α‐helix over residues 1–14 while the C‐terminal eight residues are more flexible and less structured. The flexible region may be responsible for the lack of antimicrobial activity. In water, frenatin 3 exhibits some α‐helical character in its N‐terminal region. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 424–434, 2003
Meeting Highlights: Genome Informatics
Authors: Wixon Jo , Ashurst Jennifer
Published: October 2003

We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust ‘Genome Informatics’ Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later. Copyright © 2003 John Wiley & Sons, Ltd.
Post‐normalization quality assessment visualization of microarray data
Authors: McClure John , Wit Ernst
Published: October 2003

Post‐normalization checking of microarrays rarely occurs, despite the problems that using unreliable data for inference can cause. This paper considers a number of different ways to check microarrays after normalization for a variety of potential problems. Four types of problem with microarray data that these checks can identify are: clerical mistakes, array‐wide hybridization problems, problems with normalization and mishandling problems. Any of these can seriously affect the results of any analysis. The three main techniques used to identify these problems are dimension reduction techniques, false array plots and correlograms. None of the techniques are computationally very intensive and all can be carried out in the R statistical package. Once discovered, problems can either be rectified or excluded from the data. Copyright © 2003 John Wiley & Sons, Ltd.
Proteins interacting with Caenorhabditis elegans Gα subunits
Authors: Cuppen Edwin , van der Linden Alexander M. , Jansen Gert , Plasterk Ronald H. A.
Published: October 2003

To identify novel components in heterotrimeric G‐protein signalling, we performed an extensive screen for proteins interacting with Caenorhabditis elegans Gα subunits. The genome of C. elegans contains homologues of each of the four mammalian classes of Gα subunits (Gs, Gi/o, Gq and G12), and 17 other Gα subunits. We tested 19 of the Gα subunits and four constitutively activated Gα subunits in a large‐scale yeast two‐hybrid experiment. This resulted in the identification of 24 clones, representing 11 different proteins that interact with four different Gα subunits. This set includes C. elegans orthologues of known interactors of Gα subunits, such as AGS3 (LGN/PINS), CalNuc and Rap1Gap, but also novel proteins, including two members of the nuclear receptor super family and a homologue of human haspin (germ cell‐specific kinase). All interactions were found to be unique for a specific Gα subunit but variable for the activation status of the Gα subunit. We used expression pattern and RNA interference analysis of the G‐protein interactors in an attempt to substantiate the biological relevance of the observed interactions. Furthermore, by means of a membrane recruitment assay, we found evidence that GPA‐7 and the nuclear receptor NHR‐22 can interact in the animal. Copyright © 2003 John Wiley & Sons, Ltd.
Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition
Authors: Mayers Carl , Duffield Melanie , Rowe Sonya , Miller Julie , Lingard Bryan , Hayward Sarah , Titball Richard W.
Published: October 2003

Many vaccines have been developed from live attenuated forms of bacterial pathogens or from killed bacterial cells. However, an increased awareness of the potential for transient side‐effects following vaccination has prompted an increased emphasis on the use of sub‐unit vaccines, rather than those based on whole bacterial cells. The identification of vaccine sub‐units is often a lengthy process and bioinformatics approaches have recently been used to identify candidate protein vaccine antigens. Such methods ultimately offer the promise of a more rapid advance towards pre‐clinical studies with vaccines. We have compared the properties of known bacterial vaccine antigens against randomly selected proteins and identified differences in the make‐up of these two groups. A computer algorithm that exploits these differences allows the identification of potential vaccine antigen candidates from pathogenic bacteria on the basis of their amino acid composition, a property inherently associated with sub‐cellular location. Copyright © 2003 John Wiley & Sons, Ltd.
Quantitative proteomics of lymphocytes
Authors: Lefkovits Ivan
Published: October 2003

Lymphocytes are the best‐studied higher eukaryote cells. In this report, quantitative relationships of the protein components in resting cell, blast cell and plasma cell types are evaluated. The comparison of these cell types leads to the conclusion that resting cells synthesize about one‐twentieth of the protein species as compared to blast cells. Blast cells seem to be metabolically the most robust lymphocyte type. Plasma cells are geared towards synthesis of one main product (antibody in B plasma cells), while most of the synthesis of other protein species (including those for housekeeping and repair) decreases as the messages decay. Although the data presented in this communication allow a meaningful comparison of three cell populations, they are far from providing a full picture. Both silver staining and radiofluorography depict only proteins of high or intermediate abundance. Silver staining misses most proteins present at <10 000 copies/cell, while radiofluorography misses all those proteins with slow turnover (and those with no methionine residue in their sequence). The detection of 1100 spots in the blast cell‐related radiofluorograph includes visualization of some 97–99% of protein mass, but some 3900 polypeptide species in the remaining 1–3% of protein mass will pass undetected. This protein mass (0.7–2 pg) reflects some 2500–7500 copies of each of those 3900 polypeptide species that are present in the cell below the detection limit. The work emphasizes that full understanding of cellular function can be achieved only if quantitative aspects of cell inventory are considered. Copyright © 2003 John Wiley & Sons, Ltd.
Proposal for a standard representation of two‐dimensional gel electrophoresis data
Authors: Jones Andrew , Wastling Jonathan , Hunt Ela
Published: October 2003

The global analysis of proteins is now feasible due to improvements in techniques such as two‐dimensional gel electrophoresis (2‐DE), mass spectrometry, yeast two‐hybrid systems and the development of bioinformatics applications. The experiments form the basis of proteomics, and present significant challenges in data analysis, storage and querying. We argue that a standard format for proteome data is required to enable the storage, exchange and subsequent re‐analysis of large datasets. We describe the criteria that must be met for the development of a standard for proteomics. We have developed a model to represent data from 2‐DE experiments, including difference gel electrophoresis along with image analysis and statistical analysis across multiple gels. This part of proteomics analysis is not represented in current proposals for proteomics standards. We are working with the Proteomics Standards Initiative to develop a model encompassing biological sample origin, experimental protocols, a number of separation techniques and mass spectrometry. The standard format will facilitate the development of central repositories of data, enabling results to be verified or re‐analysed, and the correlation of results produced by different research groups using a variety of laboratory techniques. Copyright © 2003 John Wiley & Sons, Ltd.
The journey to smORFland
Authors: Davids Wagied , Fuxelius Hans‐Henrik , Andersson Siv G. E.
Published: October 2003

The genome sequences completed so far contain more than 20 000 genes with unknown function and no similarity to genes in other genomes. The origin and evolution of the orphan genes is an enigma. Here, we discuss the suggestion that some orphan genes may represent pseudogenes or short fragments of genes that were functional in the genome of a common ancestor. These may be the remains of unsuccessful duplication or horizontal gene transfer events, in which the acquired sequences have entered the fragmentation process and thereby lost their similarity to genes in other species. This scenario is supported by a recent case study of orphan genes in several closely related species of Rickettsia, where full‐length ancestral genes were reconstructed from sets of short, overlapping orphan genes. One of these was found to display similarity to genes encoding proteins with ankyrin‐repeat domains. Copyright © 2003 John Wiley & Sons, Ltd.
Padlock and proximity probes for in situ and array‐based analyses: tools for the post‐genomic era
Authors: Landegren Ulf , Dahl Fredrik , Nilsson Mats , Fredriksson Simon , Banér Johan , Gullberg Mats , Jarvius Jonas , Gustafsdottir Sigrun , Söderberg Ola , Ericsson Olle , Stenberg Johan , Schallmeiner Edith
Published: October 2003

Highly specific high‐throughput assays will be required to take full advantage of the accumulating information about the macromolecular composition of cells and tissues, in order to characterize biological systems in health and disease. We discuss the general problem of detection specificity and present the approach our group has taken, involving the reformatting of analogue biological information to digital reporter segments of genetic information via a series of DNA ligation assays. The assays enable extensive, coordinated analyses of the numbers and locations of genes, transcripts and protein. Copyright © 2003 John Wiley & Sons, Ltd.