bluuebunny/crossref_metadata_2025 huggingface dataset:
Fibrillar and microfibrillar structures in poly(p‐phenylene terephthalamide) fibers
Authors: Wang W. , Ruland W. , Cohen Y.
Published: April 2003

The microfibrils and the microfibrillar network in poly(p‐phenylene terephthalamide) (PPTA) fibers formed during the coagulation from a monodomain lyotropic fiber are stabilized by critical point drying and characterized by electron microscopy and small angle X‐ray scattering. The diameter of the microfibrils varies from 20 to 49 nm depending on the PPTA concentration in the lyotropic solution used for the spinning. A formation mechanism for the microfibrils and the microfibrillar network is suggested. During the coagulation, the spinodal decomposition (phase separation) is assumed to occur before the crystallization (phase transition), resulting in the formation of the microfibrils. The formation of the microfibrillar network is considered to be related to the misorientation of macromolecules and the density fluctuation in the cross‐section of the filament during spinodal decomposition.
Modeling sustained oscillations in continuous emulsion polymerization of vinyl chloride
Authors: Tauer K. , Müller I.
Published: April 2003

A simple mathematical model for the continuous emulsion polymerization of vinyl chloride based on nonlinear ordinary differential equations for the variation of particle concentration, total particle volume, and water‐soluble oligomeric products was developed and used to investigate which reactions influence whether or not sustained oscillations of latex properties occur at high conversion steady state. Results of the calculations are in good qualitative agreement with experimental data. Specifically, numerical analysis showed that the occurrence of sustained oscillations depends on particle coalescence as well as on the conversion dependence of both particle volume growth rate and particle coalescence rate. The model makes it possible to calculate the dynamic behavior of continuous emulsion polymerization reactors with regard to latex properties such as particle concentration, mean particle size, latex surface tension, solid content, and degree of coverage of latex surface with emulsifier from the start‐up into a high conversion steady state.
Miscibility behavior of ternary polymethacrylate‐based blends
Authors: Perrin P. , Prud'homme R. E.
Published: April 2003

The miscibility behavior of ternary poly(vinyl chloride)/poly(n‐propyl methacrylate)/poly(n‐amyl methacrylate) (PVC/PPMA/PAMA) and poly(vinyl chloride)/poly(n‐butyl methacrylate)/poly(n‐amyl methacrylate) (PVC/PBMA/PAMA) blends was investigated by differential scanning calorimetry. In both systems, a binary mixture of the two polymethacrylates is totally immiscible (PPMA with PAMA, and PBMA with PAMA). For PVC/PPMA/PAMA blends containing less than 70% PVC, the immiscible phase consists of two coexisting binary PVC/PPMA and PVC/PAMA phases. For an equal amount of the two polymethacrylates in the ternary blend, the PVC/PPMA phase contains 65% of the total weight of PVC and the whole quantity of PPMA; the total amount of PAMA mixes with the remaining 35% PVC to form the PVC/PAMA phase. In contrast, the miscibility zone is predominant in the ternary PVC/PBMA/PAMA system, since blends containing 30% or more of PVC exhibit a single glass transition temperature. In the immiscibe zone, the PVC is distributed equally between PBMA and PAMA, which is in contrast to the 65%‐35% distribution found in the previous system. These results are consistent with the differences of miscibility observed in the binary PVC/polymethacrylate blends discussed.
Free radical copolymerization of electron‐rich vinyl monomers with acrylonitrile complexed to zinc chloride
Authors: Wang H. , Chu G. , Srisiri W. , Padias A. B. , Hall H. K.
Published: April 2003

The spontaneous free radical copolymerizations of a series of electron‐rich olefins with acrylonitrile (AN) complexed to zinc chloride (ZnCl2) have been investigated in solution. With styrene (St) and 2‐vinylnaphthalene, an alternating copolymerization occurred without added initiator at 40°C. Using p‐methylstyrene as the electron‐rich olefin, no‐initiator spontaneous alternating copolymerization was observed at 30°C. Copolymer formed in an amount equal to that of the ZnCl2 used. With p‐methoxystyrene (pMeOSt) and with isobutyl vinyl ether (IBVE), the copolymerizations were conducted in the presence of ethyldiisopropylamine (EDIA) to inhibit cationic homopolymerization of these monomers. The copolymerization with pMeOSt proceeded to high yield, but the copolymers were rich in pMeOSt and the rates were slow presumably due to competitive complexation of ZnCl2 with the methoxy‐substituent. Using IBVE only low yields of a random copolymer were obtained, and again competitive coordination with ZnCl2 appears responsible. The small molecules accompanying these spontaneous copolymerizations were shown by GC/MS to possess cyclobutane and Mayo adduct structures. The mechanism of these spontaneous copolymerizations cannot be decided on the basis of the small molecules formed, but the increases of copolymer molecular weight with time at constant yield speaks for a diradical mechanism.
Synthesis and characterization of copolyamides with rigid and flexible segments
Authors: Fischer H. , Berger W. , Scheller D.
Published: April 2003

Copolyamides with rigid and flexible chain segments were prepared using the reaction between diacids and diisocyanates. Segmented copolymers of these copolyamides are formed directly and spontaneously. UV‐ and NMR‐spectroscopy exclude the formation of homopolyamides only. The copolyamides with a content of rigid chain units between 20% nd 40% show thermotropic liquid crystalline behavior. Polarization microscopy and X‐ray diffraction investigations indicate the presence of nematic phase.
Preferential wetting of oligomeric ethylene glycol/propylene glycol blends on solid surfaces
Authors: Muniz E.C. , Pellegrini M.C. , Nunes S. Pereira
Published: April 2003

The phase separation of oligomeric ethylene glycol/propylene glycol systems was investigated by light scattering in the presence of a solid surface. Beside the spinodal decomposition in the bulk of the system, a wetting transition was observed when phase separation occurred at conditions near the maxima of these phase diagrams. The transition was detected as a light scattering halo, which is more intense at a composition which does not coincide with the critical one. This composition does not depend on the surface but the halo intensity is higher when glass is used instead of PVC.
Dichroism in photoinduced infrared spectra of polyalkylthiophenes
Authors: Veronelli M. , Gallazzi M.C. , Zerbi G.
Published: April 2003

The photoinduced infrared spectra of stretch‐oriented polyhexylthiophene and polyoctylthiophene are reported as a function of the polarization both of the pump light and of the probe IR beam. There is no change in the intensity of photoinduced IR absorption due to the polarization of the pump; however, the spectra show parallel dichroism when the probe is polarized. The experimental results are analyzed on the basis of the “effective conjugation coordinate” theory (ECC).
Application of a new generation of computerized apparatus for the study of oxygen uptake and production of CO and CO2 during photo‐(thermal) oxidation of polymers
Authors: Czekajewski J. , Nennerfelt L. , Kaczmarek H. , Rabek J. F.
Published: April 2003

In an attempt to measure simultaneously oxygen uptake and CO and CO2 production during photo‐(thermal) oxidation of polymers, an apparatus was constructed for sensitive measurements of changes in oxygen, CO and CO2 concentrations of 5–10 parts per million. The oxygen uptake and CO and CO2 production profiles show first‐order kinetics of observed photooxidative processes in polyethylene, poly(phenylene oxide) and cellulose. The experimental results suggest that this apparatus has a certain potential for the study of photo‐(thermal), bio‐ and environmental oxidation of polymers.
Synthesis of critically cross‐linked microgels by dispersion polymerization
Authors: Antonietti M. , Bremser W. , Pakula T.
Published: April 2003

Microgels with cross‐link densities close to the critical value of gel transition are synthesized via polymerization in microemulsion stabilized with a polymeric surfactant. The resulting structures are characterized by static and dynamic light scattering, viscometry, small angle neutron scattering and dynamic‐mechanical shear experiments.

The proximity of the gel point influences the different properties in a different way. Global properties such as particle shape are closely connected with the gel point whereas the local structure and relaxation show critical behavior even quite far from the gel point.
Electrical noise in aqueous solutions of gelatin containing KCL during the sol–gel transition
Authors: Quadrat O. , Klason C. , Kubát J. , McQueen D. H.
Published: April 2003

Electrical current noise and electrical resistivity as well as viscosity were measured in aqueous solutions of gelatin containing KCl during the sol—gel transition. While the viscosity rises toward infinity at the transition, the current noise power and the resistivity are continuous functions of the time and are therefore potentially useful probes for characterizing polymers undergoing gelation.
Fibers from blends of PBT and thermotropic liquid crystalline copolyester
Authors: Mehta S. , Deopura B. L.
Published: April 2003

Blends of poly(ethylene terephthalate‐co‐p‐oxybenzoate), PET/PHB, with poly(butylene terephthtalate), PBT, have been studied in the form of as‐spun and drawn fibers. DSC melting and crystallization studies of blend fibers show a single melting endotherm, corresponding to PBT crystallites and a decrease in the crystallization of PBT by the addition of LCP in the matrix. X‐ray diffraction patterns of the blends exhibit mainly all the reflections of the homopolymer component (PBT). However, the diffused meridional reflections in the blend fibers show that the crystal structure of the matrix is affected by the addition of LCP and there is possible formation of LCP oriented domains. SEM studies of drawn blend fibers show that the blends up to 10 wt.% LCP content contain the LCP domains in the size range of 0.1‐–0.3 μm and are well distributed in the PBT matrix. Mechanical properties of drawn PBT/LCP blend fibers show an increase in modulus with the increase in LCP content. Values of the modulus are predicted from composite theory by assuming the blend system to consist of LCP domains dispersed in PBT matrix.
Local motions in polymeric and low molar mass supramolecular hydrogen bond assemblies: One‐ and two‐dimensional 2H‐NMR studies, full papers
Authors: Dardin A. , Boeffel C. , Spiess H. W. , Stadler R. , Samulski E. T.
Published: April 2003

Supramolecular structures based on 4‐(3,5‐dioxo‐1,2,4‐triazolidin‐4‐yl) benzoic acid (U4A) units act as effective junction zones in functionalized polybutadienes, resulting in the formation of thermoplastic elastomers. The dynamics on a molecular scale of the phenyl rings have been probed by 2H‐NMR. In the polymeric system, there are three spatially separated environments, which are reflected in the mobility of the polar units. Phenyl rings which are incorporated in the structures are either rigid or undergo 180° phenyl flips. The small fraction of free functional groups move isotropically and their mobility is coupled to the dynamics of the polybutadiene matrix. In two model compounds, where the polymer backbone is replaced by a 1‐butenyl (tBu‐dU4A) or a C12H24‐chain (C12‐dU4A), the packing of the single molecules is more perfect, resulting in better‐defined dynamics of the molecules. The one‐dimensional 2H‐NMR spectra can be described quantitatively assuming a distribution of correlation times over 3 decades for the C12‐dU4A and 2 decades for the tBu‐dU4A, respectively. From the average jump rates the activation energies are determined as 101 kJ/mol and 102 kJ/mol. The geometry of the motional processes is defined by the environment in the clusters up to the order‐disorder transition temperature as determined by DSC. The two‐dimensional spectra of the model compounds show an elliptical exchange pattern, indicating well‐defined slow 180° phenyl flips on a time scale of 100 ms up to 3 s.
Evaluation of equation‐of‐state parameters from PVT data
Authors: Rudolf B. , Kressler J. , Shimomai K. , Ougizawa T. , Inoue T.
Published: April 2003

The characteristic parameters for three different equation‐of‐state (EOS) theories have been determined for polystyrene and low‐molecular weight polyisoprene using pressure‐volume‐temperature (PVT) data. Basically two procedures for the calculation of characteristic parameters were applied. The characteristic parameters were calculated, firstly, from coefficients of expansion, compressibilities and densities, and secondly, by fitting the corresponding EOS to PVT data minimizing the sum of the squares of the differences between experimental and calculated pressures. The characteristic parameters obtained by the two methods are compared with regard to their ability to describe PVT data. A comparison of the three different EOS theories reveals that, for describing polymeric liquids, the modified cell model of Dee and Walsh is superior to the theory of Flory, Orwoll and Vrij as well as to the lattice fluid theory of Sanchez and Lacombe. Finally, formulae are given to convert the characteristic parameters from one theory into those of another.
Complex formation between poly(oxytrimethylene) and cyclodextrins
Authors: Harada A. , Okada M. , Kamachi M.
Published: April 2003

Poly(oxytrimethylene) (POT) has been found to form inclusion complexes with cyclodextrins to give crystalline compounds in high yields. The yields of the complexes of POT with α‐cyclodextrin increased with increase in the molecular weight of POT, reached a maximum at a molecular weight of about 1000, and then decreased with the molecular weight. The stoichiometries are 1:1.5‐2 (CD:monomer unit) when the molecular weight of POT is less than 2000. β‐Cyclodextrin gave complexes with POT in a 1:2‐2.5 ratio when the average molecular weights were less than 2000. When the molecular weight of the polymer was higher than 3000, the ratio of the monomer unit to cyclodextrin increased with increase in the molecular weight. The binding modes are discussed.
Retardation experiments in glass‐forming liquids and their description in terms of the conformon model
Authors: Kilian H. G. , Glöckle W. G.
Published: April 2003

Relaxation in glass‐forming liquids as measured by dielectric, by light‐ and by neutron‐scattering experiments can be described with the aid of the conformon model. Conformons behave like bosons which display a photon statistics. Conformons are excited and can also be annihilated. They show a universal reduced energy density distribution, revealing their thermodynamic roots. Each relaxation mode is assumed to be directly connected with a distinct conformon. The coupling is described by an empirical power law. The actual relaxation time distribution is then obtained by scaling each relaxation mode with the same kinetic factor. The relaxation behavior of liquids is therefore self‐similar, characterized by individual factors such as the relaxation power, the coupling parameter and the temperature of pressure dependence of the kinetic factor (“shift factor”).
Polymerizable dendrimers: 2. Mono‐methacryl modified dendrimers containing up to 16 ester functions via stepwise condensations of L‐aspartic acids
Authors: Niggemann M. , Ritter H.
Published: April 2003

A convergent synthesis of polymerizable dendrimers consisting of one methacrylic function combined with an alkylene spacer and several condensed L‐aspartic acid components is described. The highly functionalized monomers were prepared from N‐methacryloyl amino undecanoic acid (9) via condensation with free amino groups of L‐aspartic acid dimethyl ester (2), α, β‐bis‐(L‐dimethoxyaspartyl)‐L‐aspartic acid hydrobromide (4) and α, β‐bis‐(L‐aspartyl‐α, β‐bis‐(L‐dimethoxyaspartyl))‐L‐aspartic acid hydrobromide (6). The number of ester groups increased from 2 to 4 and 8, up to 16, depending on the dendritic generation of the condensed amino acids. The monomers were homopolymerized and copolymerized with styrene through a free radical mechanism.
Multilayer barrier films on polyethylene polymerized from CF3H/C2H4 plasmas
Authors: Walker M. , Baumgärtner K. M. , Räuchle E.
Published: April 2003

The barrier properties of thin fluorocarbon films toward toluene are studied. Mixtures of trifluoromethane and ethylene are used as monomers in an electron cyclotron resonance plasma discharge. The measured permeation fluxes of toluene through polyethylene show that thin fluorocarbon layers strongly reduce the permeation, e. g. by a factor of about 3000 when an appropriate tapered layer is deposited on polyethylene foils. Different tapering of the barrier layers was investigated with respect to low permeation and good adhesion of the films. The amount of permeated toluene through the untreated and treated polyethylene foils are measured as a function of time using a gas chromatograph with a flame ionization detector.
Degree of branching in hyperbranched polymers. 2. Enhancement of the db: Scope and limitations
Authors: Frey H.
Published: April 2003

The degree of branching (DB) as well as the ANB (average number of branches) of polymers obtained from polycondensation of AB2 and ABm‐type monomers in general is analyzed in detail on the basis of kinetic considerations. Various possibilities for the enhancement of the DB of hyperbranched polymers beyond the limit for a random ABm polycondensation (0.5 for AB2, 0.44 for AB3) are considered, i.e., (i) enhanced reactivity of linear vs. terminal units; (ii) polymerization of prefabricated, perfect dendritic units and (iii) the slow addition technique. For AB2 monomers, the formation of terminal (T), linear (L) and perfect dendritic (D) units in the course of the random one‐pot polymerization is calculated. Furthermore, the evolution of the DB and ANB with conversion is calculated for ABm monomers. It is shown that the definition of the DB for AB2 systems (DB = 2D/(2D+L)) derived in the first paper on the DB (Acta Polym. 1997, 48, 30) in the case of a random one‐pot polycondensation exhibits the same conversion dependence as the branching parameter α = 1/2PA, defined by Flory for AB2 polycondensations. The dilution principle is introduced, which is based on slow addition of ABm monomers to a core molecule Bf or an ABm‐type hyperbranched molecule with an arbitrary DB. It is shown that the maximum DB value obtainable from such a dilution/slow addition process is 0.67 for AB2 systems. Thus, the DB is considerably higher than in the case of a random one‐step polymerization (0.5). The DB for ABm‐type hyperbranched polymers prepared according to the dilution principle has been calculated to be m/(2m–1).
Pattern formation in the Drosophila wing: The development of the veins
Authors: de Celis Jose F.
Published: April 2003

The veins are cuticular structures that differentiate in precise patterns in insect wings. The genetic and molecular basis of vein pattern formation in Drosophila melanogaster is beginning to be unravelled with the identification and characterisation of the gene products that position the veins and direct their differentiation. Genes affecting the veins fall into two groups: transcriptional regulators that specify individual veins, and members of signalling pathways involved in patterning and differentiation of the veins. The elaboration of the vein pattern is progressive in time and requires the coordinated activities of these signalling pathways and the transcription factors regulated by them. Although the network of genetic interactions that determine vein cell fate is well understood, very little is known about the cellular biology underlying the acquisition of vein histotype. BioEssays 25:443–451, 2003. © 2003 Wiley Periodicals, Inc.
Fine tuning the HIF‐1 ‘global’ O2 sensor for hypobaric hypoxia in Andean high‐altitude natives
Authors: Hochachka Peter W. , Rupert Jim L.
Published: April 2003

Included in the acute response of lowlanders exposed to reduced oxygen availability is an elevated red blood cell count due to increased erythropoietin (Epo) synthesis. According to current thinking, hypoxia is “sensed” by hydroxylases that permit Hypoxia Inducible Factor 1α (HIF‐1α) to complex with HIF‐1β to form a transcriptional activator (HIF‐1) that drives expression of hypoxia‐sensitive genes (such as EPO) under hypoxic conditions. In altitude‐adapted Andean natives, the Epo hypoxic response may be blunted; however, our data indicate that the DNA sequences of the genes encoding Epo (including the 3′ regulatory region) and HIF‐1α appear to be conserved. Hence, adaptive changes in the Andean hypoxic response are not a consequence of changes in the primary sequence of these proteins or of known transcriptional regulatory domains of EPO. These results suggest that the altered erthropoietic response in Andean natives reflects adaptations in hypoxia sensing, rather than hypoxia response, mechanisms. BioEssays 25:515–519, 2003. © 2003 Wiley Periodicals, Inc.
Tumor progression: Small GTPases and loss of cell–cell adhesion
Authors: Lozano Encarnación , Betson Martha , Braga Vania M.M.
Published: April 2003

Tumor progression involves the transition from normal to malignant cells, through a series of cumulative alterations. During this process, invasive and migratory properties are acquired, enabling cells to metastasize (reach and grow in tissues far from their origin). Numerous cellular changes take place during epithelial malignancy, and disruption of E‐cadherin based cell‐cell adhesion is a major event. The small Rho GTPases (Rho, Rac and Cdc42) have been implicated in multiple steps during cellular transformation, including alterations on the adhesion status of the tumor cells. This review focuses on recent in vivo evidence that implicates RhoGTPases in epithelial tumor progression. In addition, we discuss different hypotheses to explain disruption of cadherin‐mediated cell–cell adhesion, directly or indirectly, through activation of Rho GTPases. Understanding the molecular mechanism of how cadherin adhesion and RhoGTPases interplay in normal cells and how this balance is altered during cellular transformation will provide clues as to how to interfere with tumor progression. © 2003 Wiley Periodicals, Inc. BioEssays 25:452–463, 2003. © 2003 Wiley Periodicals, Inc.
A hypothesis for chromatin domain opening
Authors: Xin Li , Liu De‐Pei , Ling Chih‐chuan
Published: April 2003

The eukaryotic genome is organized into different domains by cis‐acting elements, such as boundaries/insulators and matrix attachment regions, and is packaged with different degrees of condensation. In the M phase, the chromatin becomes further highly condensed into chromosomes. The first step for transcriptional activation of a given gene, at a particular time during development, in any locus, is the opening of its chromatin domain. This locus needs to be kept in this state in each early G1 phase during every cell cycle. Certain distal enhance elements, including locus control regions (LCRs) and enhancers, are believed to perform this target chromatin domain opening process and several models have been proposed to explain distal enhance action. But they did not explain precisely how a given chromatin domain is opened. Based on various studies, we propose a hypothesis for the mechanism of opening chromatin on a large scale. One important mechanism may involved breaking one or two DNA strands and reducing the linking numbers within chromatin domain. The topological changes can overpass some complexes formed on DNA strands and can be transmitted from specific localized points over a broad region, until boundary elements or insulators are reached. These may initiate downstream events such as propagation of histone acetylation and the binding of transcription factors to proximal promoters and may further augment the action mediated by distal enhancer elements. BioEssays 25:507–514, 2003. © 2003 Wiley Periodicals, Inc.
Renin: from ‘pro’ to promoter
Authors: Morris Brian J.
Published: April 2003

Renin is the rate‐limiting enzyme in a cascade that leads to production of angiotensin II, which is perhaps our most important regulator of salt and water balance and blood pressure. In this personal perspective, I describe how I entered the renin field 33 years ago by discovering that proteases increased the level of renin activity in biological fluids, so revealing the existence of a ‘pro’ form of the molecule. This led me on a journey that encapsulated all of the major milestones in molecular discovery for renin. These included (1) the elucidation of the steps in renin biosynthesis, (2) the cloning of renin cDNA and its gene, (3) demonstration of the structure of the renin protein, (4) using the renin gene in the first genetic studies in hypertension, (5) finding the mechanism by which the major controller, cyclic AMP, regulates the promoter, (6) showing that a strong enhancer and its weak promoter control this physiologically regulatable gene in accord with the variegation (on/off switching) model, and (7) being the first to identify molecules involved in posttranscriptional control. The renin molecule, its gene and molecular control are now very well understood, but more fine details on the topic of renin continue to emerge to delight ‘reninologists’ and others. BioEssays 25:520–527, 2003. © 2003 Wiley Periodicals, Inc.
Subversion of the chemokine world by microbial pathogens
Authors: Liston Adrian , McColl Shaun
Published: April 2003

It is well known that microbial pathogens are able to subvert the host immune system in order to increase microbial replication and propagation. Recent research indicates that another arm of the immune response, that of the chemokine system, is also subject to this sabotage, and is undermined by a range of microbial pathogens, including viruses, bacteria, and parasites. Currently, it is known that the chemokine system is being challenged by a number of mechanisms, and still more are likely to be discovered with further research. Here we first review the general mechanisms by which microbial pathogens bypass mammalian chemokine defences. Broadly, these can be grouped as viral chemokine interacting proteins, microbial manipulation of host chemokine and chemokine receptor expression, microbial blockade of host chemokine receptor signalling, and the largely hypothetical mechanisms of microbial enhancement of host anti‐chemokine networks (including digestion, antagonism, and neutralisation of host chemokines and chemokine receptors). We then discuss the potential results of these interactions in terms of outcome of infection. BioEssays 25:478–488, 2003. © 2003 Wiley Periodicals, Inc.
RNAs templating chromatin structure for dosage compensation in animals
Authors: Wutz Anton
Published: April 2003

The role of RNA as a messenger in the expression of the genome has been long appreciated, but its functions in regulating chromatin and chromosome structure are no less interesting. Recent results have shown that small RNAs guide chromatin‐modifying complexes to chromosomal regions in a sequence‐specific manner to elicit transcriptional repression. However, sequence‐specific targeting by means of base pairing seems to be only one mechanism by which RNA is employed for epigenetic regulation. The focus of this review is on large RNAs that act in the dosage‐compensation pathways of flies and mammals. These RNAs associate with chromatin over the length of whole chromosomes and are crucial for spreading epigenetic changes in chromatin structure. They do not appear to act in a sequence‐specific manner but might provide scaffolds for co‐operative binding of chromatin‐associated complexes that enable spreading of chromatin modifications. BioEssays 25:434–442, 2003. © 2003 Wiley Periodicals, Inc.
NAADP on the up in pancreatic beta cells—a sweet message?
Authors: Patel Sandip
Published: April 2003

Pancreatic beta cells secrete insulin in response to elevated plasma glucose levels in a Ca2+‐dependent fashion. Released insulin may act on the beta cell itself to promote further insulin synthesis and release. Recent studies by Johnson and Misler,1 Masgrau et al.2 and Mitchell et al.3 provide strong evidence (1) for the existence of intracellular Ca2+ stores sensitive to NAADP, a potent Ca2+‐mobilizing messenger, and (2) that these Ca2+ stores are involved in both glucose‐ and insulin‐mediated signal transduction. NAADP may therefore play an important role in controling secretion of insulin from pancreatic beta cells. BioEssays 25:430–433, 2003. © 2003 Wiley Periodicals, Inc.
Playing by pair‐rules?
Authors: Davis Gregory K. , Patel Nipam H.
Published: April 2003

Although in Drosophila pair‐rule genes play crucial roles in the genetic hierarchy that subdivides the embryo into segments, the extent to which pair‐rule patterning is utilized by different arthropods and other segmented phyla is unknown. Recent data of Dearden et al.1 and Henry et al.,2 however, hint that a pair‐rule mechanism might play a role in the segmentation process of basal arthropods and vertebrates. BioEssays 25:425–429, 2003. © 2003 Wiley Periodicals, Inc.
Idiomatic (gene) expressions
Authors: Rockman Matthew V.
Published: April 2003

Hidden among the myriad nucleotide variants that constitute each species' gene pool are a few variants that contribute to phenotypic variation. Many of these differences that make a difference are non‐coding cis‐regulatory variants, which, unlike coding variants, can only be identified through laborious experimental analysis. Recently, Cowles et al.1 described a screening method that does an end‐run around this problem by searching for genes whose cis regulation varies without having to find the polymorphic nucleotides that influence transcription. While we will continue to require a diverse arsenal of experimental methods, this versatile method will speed the identification of functional genetic variation. BioEssays 25:421–424, 2003. © 2003 Wiley Periodicals, Inc.
The digital origin of human language—a synthesis
Authors: Noll Hans
Published: April 2003

The fact that all languages known are digital poses the question of their origin. The answer developed here treats language as the interface of information theory and molecular development by showing previously unrecognized isomorphisms between the analog and digital features of language and life at the molecular level. Human language is a special case of signal transduction and hence is subject to the coding aspects of Shannon's theorems and the analog aspects of pattern recognition, each represented by genotype and phenotype. Digital language acquisition is late in evolution and postnatal development and requires a neural reorganization by a mechanism of somatic network programming in response to the environment. Such a mechanism would solve the Chomsky conundrum of how children can learn any language without knowing rules of grammar too numerous to be encoded genotypically. BioEssays 25:489–500, 2003. © 2003 Wiley Periodicals, Inc.
Conformational behavior of chondroitin and chondroitin sulfate in relation to their physical properties as inferred by molecular modeling
Authors: Rodríguez‐Carvajal Miguel A. , Imberty Anne , Pérez Serge
Published: April 2003

Chondroitin and chondroitin sulfates belong to the family of glycosaminoglycans. They are most widely distributed in animal tissues, where they are involved in structural functions and in cell–cell communication. Their basic structures consist of a disaccharidic repeating unit of β‐D‐glucuronic acid (GlcA) and 2‐acetamido‐2‐deoxy‐β‐D‐galactose (GalNAc), this latter being sulfated at different positions. Molecular mechanics has been applied to calculate the adiabatic energy maps for each of the constituting disaccharides of chondroitin, chondroitin 4‐sulfate, and chondroitin 6‐sulfate using the MM3 force field. Based on these maps, higher levels of structural organization have been simulated. On one hand, the disordered state is studied through a Metropolis‐based algorithm; the resulting chains present a behavior of semirigid polymers, with an order of stiffness: chondroitin 4‐sulfate > chondroitin > chondroitin 6‐sulfate. On the other hand, the exploration of the stable ordered forms leads to numerous helical conformations of comparable energies. Several of these conformations correspond to the experimentally observed ones. The ability of coordination with cations has also been explored, resulting in a preferential stereospecificity for calcium ions when compared to sodium ions. © 2003 Wiley Periodicals, Inc. Biopolymers 69:15–28, 2003
Conformational preferences of the amylin nucleation site in SDS micelles: An NMR study
Authors: Mascioni Alessandro , Porcelli Fernando , Ilangovan Udayar , Ramamoorthy Ayyalusamy , Veglia Gianluigi
Published: April 2003

Human islet amyloid polypeptide (hIAPP), or amylin, is a 37 amino acid hormone secreted by pancreatic β‐cells. hIAPP constitutes ∼90% of the amyloid deposits found in type II diabetic patients. It has been shown that the central region of the peptide (hIAPP20–29) constitutes the nucleation site for the amyloidogenic process with F23 playing a key role in the formation of the β‐pleated structures. In addition, it has been proposed that an important stage in the cytotoxicity of hIAPP is its interaction with the β‐cell membranes. As a first step toward the characterization of the interaction of hIAPP with cell membranes, we determined conformational preferences of hIAPP20–29in membrane‐mimicking environments. We found that upon interacting with negatively charged micelles, the dominant conformation of hIAPP20–29is a distorted type I β‐turn centered on residues F23 and G24, with F23, A25, and I26 forming a small hydrophobic cluster that may facilitate the interaction of this peptide with the membrane bilayer. Moreover, we were able to elucidate the topological orientation of the peptide that is absorbed on the micelle surface, with the hydrophobic cluster oriented toward the hydrocarbon region of the micelles and both N‐ and C‐termini exposed to the solvent. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 29–41, 2003
Free energy of proton binding in proteins
Authors: Poland Douglas
Published: April 2003

In this article we use literature data on the titration of denatured ribonuclease to test the accuracy of proton‐binding distributions obtained using our recent approach employing moments. We find that using only the local slope of the titration curve at a small number of points (five, for example) we can reproduce the detailed proton‐binding distribution at all pH values. Our method gives the complete proton‐binding polynomial for a given protein and each coefficient in this polynomial in turn yields the free energy for binding a given number of protons in all ways to the protein. Using these net free energies, we can then compute the average proton‐binding free energy per proton as a function of the fraction of protons bound. We find that this function is remarkably similar for different proteins, even for proteins that exhibit quite different titration behavior. For the special case of binding to independent sites, we obtain simple relations for the first and last terms in the free energy per‐proton function. For this special case we also can calculate the distribution functions giving the probability that a molecule has a given number of positive or negative charges and the joint distribution that a molecule simultaneously has a given number of positive and negative charge. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 60–71, 2003
Surprising roles of electrostatic interactions in DNA–ligand complexes
Authors: Howerton Shelley B. , Nagpal Akankasha , Dean Williams Loren
Published: April 2003

The positions of cations in x‐ray structures are modulated by sequence, conformation, and ligand interactions. The goal here is to use x‐ray diffraction to help resolve structural and thermodynamic roles of specifically localized cations in DNA–anthracycline complexes. We describe a 1.34 A˚ resolution structure of a CGATCG2–adriamycin2 complex obtained from crystals grown in the presence of thallium (I) ions. Tl+ can substitute for biological monovalent cations, but is readily detected by distinctive x‐ray scattering, obviating analysis of subtle differences in coordination geometry and x‐ray scattering of water, sodium, potassium, and ammonium. Six localized Tl+ sites are observable adjacent to each CGATCG2–adriamycin2 complex. Each of these localized monovalent cations are found within the G‐tract major groove of the intercalated DNA–drug complex. Adriamycin appears to be designed by nature to interact favorably with the electrostatic landscape of DNA, and to conserve the distribution of localized cationic charge. Localized inorganic cations in the major groove are conserved upon binding of adriamycin. In the minor groove, inorganic cations are substituted by a cationic functional group of adriamycin. This partitioning of cationic charge by adriamycin into the major groove of CG base pairs and the minor groove of AT base pairs may be a general feature of sequence‐specific DNA–small molecule interactions and a potentially useful important factor in ligand design. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 87–99, 2003
Binding of Europium(III) ions to RNA stem loops: Role of the primary hydration sphere in complex formation
Authors: Mundoma Claudius , Greenbaum Nancy L.
Published: April 2003

Understanding the process by which RNA molecules fold into stable structures includes study of the role of site‐bound metal ions. Because the alkaline earth metal ions typically associated with RNA structure [most often Mg(II)] do not provide convenient spectroscopic signals, replacement with metal ions having spectroscopically useful properties has been a valuable approach. The luminescence properties of the lanthanide(III) series, in particular europium(III), have made them useful in the study of complexation with biomolecules. We review the physical, chemical, and spectroscopic characteristics of Eu(III) that contribute to its value as a probe of RNA–metal ion interactions, and examples of information obtained from studies of Eu(III) bound to small RNA stem loops. Although Eu(III) has similar site preference to Mg(II), luminescence and isothermal titration calorimetry measurements indicate that Ln(III) loses water molecules from the inner hydration sphere more readily than does Mg(II), resulting in more direct coordination between RNA and the metal ion and very different energetics of binding. In some cases, e.g., a GAAA tetraloop, binding appears to occur by a lock and key process; in the same base sequence containing certain deoxynucleoside substitutions that alter loop structure, binding appears to occur by an induced fit process. © 2003 Wiley Periodicals, Inc. Biopolymers 69:100–109, 2003
Reflections on apparent DNA bending by charge variants of bZIP proteins
Authors: Hardwidge Philip R. , Parkhurst Kay M. , Parkhurst Lawrence J. , Maher L. James
Published: April 2003

Basic‐leucine zipper (bZIP) proteins have been studied intensely as transcription factors. It has been proposed that the bZIP domain might modulate transcription activation through the induction of conformational changes in the DNA binding site. We have been interested in using bZIP peptides as convenient models with which to study the role of asymmetric phosphate neutralization in DNA bending. DNA bending experiments have yielded discordant results for bZIP peptides studied by electrophoretic‐ vs solution‐based assays. We review the history of DNA bending assays involving bZIP peptides and introduce the reader to examples of discordant results. Our recent published experiments designed to clarify this field of study will then be reviewed. The engineering of protein fusions has established that electrophoretic phasing assays are relatively insensitive to precise protein structure/conformation and instead appear to report DNA bending, as influenced by protein charge. New applications of time‐resolved fluorescence resonance energy transfer (FRET) have allowed for the first time corroboration of electrophoretic phasing assays with solution‐based FRET measurements. We report that two conventional DNA bending assays that rely on DNA ligation cannot be applied to analysis of the bZIP peptides we studied due to ligation inhibition. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 110–117, 2003
The solution structures and activity of caerin 1.1 and caerin 1.4 in aqueous trifluoroethanol and dodecylphosphocholine micelles
Authors: Wegener Kate L. , Carver John A. , Bowie John H.
Published: April 2003

The caerin 1 peptides are among the most powerful of the broad‐spectrum antibiotic amphibian peptides. Caerin 1.1 has previously been shown to form an amphipathic helix–bend–helix structure in aqueous trifluoroethanol (H. Wong, J. H. Bowie, and J. A. Carver European Journal Biochemistry, 1997, Vol. 247, pp. 545–557) and structure–activity relationship studies indicate that both helices are required for activity, as well as flexibility in the bend region connecting the two. The structure of caerin 1.1 in dodecylphosphocholine micelles was investigated and shown to be very similar to that determined in aqueous trifluoroethanol. Caerin 1.4, which is identical to caerin 1.1, but with serine residues replacing Val5 and Gly7, is less active than caerin 1.1 against most bacterial species but has improved activity against Escherichia coli and Micrococcus luteus. The solution NMR structure of caerin 1.4 was determined in both aqueous trifluoroethanol and dodecylphosphocholine micelles, and was shown to be similar to caerin 1.1. It was concluded that differences in the hydrophobicity and hydrophilic angle of the first helix are probably responsible for the different spectra of antibacterial activity. The similarity of the structures calculated in aqueous trifluoroethanol and dodecylphosphocholine micelles suggests that, for caerin 1.1 and 1.4, these solvent systems are equally as good at representing a membrane environment. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 42–59, 2003
The Ac–RGD–NH2 peptide as a probe of slow conformational exchange of short linear peptides in DMSO
Authors: Biris Nikolaos , Stavrakoudis Athanassios , Politou Anastasia S. , Mikros Emmanuel , Sakarellos‐Daitsiotis Maria , Sakarellos Constantinos , Tsikaris Vassilios
Published: April 2003

According to general belief, the conformational information on short linear peptides in solution derived at ambient temperature from NMR spectrometry represents a population‐weighted average over all members of an ensemble of rapidly interconverting conformations. Usually the search for discrete conformations is concentrated at low temperatures especially when sharp NMR resonances are detected at room temperature. Using the peptide Ac–RGD–NH2 (Ac–Arg–Gly–Asp–NH2, Ac: acetyl) as a model system and following a new approach, we have been able to demonstrate that short linear peptides can adopt discrete conformational states in DMSO‐d6 (DMSO: dimethylsulfoxide) which vary in a way critically dependent on the reconstitution conditions used before their dissolution in DMSO‐d6. The conformers are stabilized by intramolecular hydrogen bonds, which persist at high temperatures and undergo a very slow exchange with their extended structures in the NMR chemical shift time scale. The reported findings provide clear evidence for the occurrence of solvent‐induced conformational exchange and point to DMSO as a valuable medium for folding studies of short linear peptides. © 2003 Wiley Periodicals, Inc. Biopolymers 69:72–86, 2003
Modeling the dynamics of the solvated SL1 domain of HIV‐1 genomic RNA
Authors: La Penna G. , Genest D. , Perico A.
Published: April 2003

A mode‐coupling solution of the Smoluchowski diffusion equation (MCD theory), designed to describe the dynamics of wobbling macromolecules in water, is applied to a macromolecular bead model including water beads in the nearest layers. The necessary statistical averages are evaluated by time averaging along a molecular dynamics (MD) trajectory where both solute and water are introduced as atomistic models. The cross peaks in 1H nuclear Overhauser effect spectroscopy (NOESY) NMR spectra that are routinely measured to determine biological structures are here calculated for the mutated 23 nucleotides stem‐loop fragment of the SL1 domain in the HIV‐1Lai genomic RNA. The calculations are in acceptable agreement with experiments without requiring any screening of the hydrodynamic interactions. The screening of hydrodynamics was necessary in previous MCD calculations obtained by using the same full atomistic MD trajectory, but a nonsolvated frictional model. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 1–14, 2003
A thermodynamic framework for the magnesium‐dependent folding of RNA
Authors: Misra Vinod K. , Shiman Ross , Draper David E.
Published: April 2003

The goal of this review is to present a unified picture of the relationship between ion binding and RNA folding based on recent theoretical and computational advances. In particular, we present a model describing how the association of magnesium ions is coupled to the tertiary structure folding of several well‐characterized RNA molecules. This model is developed in terms of the nonlinear Poisson–Boltzmann (NLPB) equation, which provides a rigorous electrostatic description of the interaction between Mg2+ and specific RNA structures. In our description, most of the ions surrounding an RNA behave as a thermally fluctuating ensemble distributed according to a Boltzmann weighted average of the mean electrostatic potential around the RNA. In some cases, however, individual ions near the RNA may shed some of their surrounding waters to optimize their Coulombic interactions with the negatively charged ligands on the RNA. These chelated ions are energetically distinct from the surrounding ensemble and must be treated explicitly. This model is used to explore several different RNA systems that interact differently with Mg2+. In each case, the NLPB equation accurately describes the stoichiometric and energetic linkage between Mg2+ binding and RNA folding without requiring any fitted parameters in the calculation. Based on this model, we present a physical description of how Mg2+ binds and stabilizes specific RNA structures to promote the folding reaction. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 118–136, 2003
Comments on selected aspects of nucleic acid electrostatics
Authors: Manning Gerald S.
Published: April 2003

Recent experimental, theoretical, and computational developments in the field of nucleic acid electrostatics have brought interesting concepts to the fore. The phosphate charge on the double helix apparently influences its structure. When the charge is neutralized asymmetrically, the resulting force imbalance drives bending toward the neutralized side. When the charge is uniformly neutralized, the force imbalance acts to buckle the helical axis, resulting in a compact tertiary conformation. Sharing of condensed counterions by single strands is a stabilizing factor for formation of the double helix. Sharing of condensed counterions by two double helices causes clustering of DNA and may be a factor in RNA folding. Support for these statements is reviewed. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 137–143, 2003