bluuebunny/crossref_metadata_2025 huggingface dataset:
Defective insulin receptor activation and altered lipid rafts in Niemann–Pick type C disease hepatocytes
Authors: Vainio Saara , Bykov Igor , Hermansson Martin , Jokitalo Eija , Somerharju Pentti , Ikonen Elina
Published: October 2005

Niemann–Pick type C (NPC) disease is a neuro-visceral cholesterol storage disorder caused by mutations in the NPC-1 or NPC-2 gene. In the present paper, we studied IR (insulin receptor) activation and the plasma-membrane lipid assembly in primary hepatocytes from control and NPC1–/– mice. We have previously reported that, in hepatocytes, IR activation is dependent on cholesterol–sphingolipid rafts [Vainio, Heino, Mansson, Fredman, Kuismanen, Vaarala and Ikonen (2002) EMBO Rep. 3, 95–100]. We found that, in NPC hepatocytes, IR levels were up-regulated and the receptor activation was compromised. Defective IR activation was reproduced in isolated NPC plasma-membrane preparations, which displayed an increased cholesterol content and saturation of major phospholipids. The NPC plasma membranes were less fluid than control membranes as indicated by increased DPH (1,6-diphenyl-1,3,5-hexatriene) fluorescence anisotropy values. Both in NPC hepatocytes and plasma-membrane fractions, the association of IR with low-density DRMs (detergent-resistant membranes) was increased. Moreover, the detergent resistance of both cholesterol and phosphatidylcholine were increased in NPC membranes. Finally, cholesterol removal inhibited IR activation in control membranes but restored IR activation in NPC membranes. Taken together, the results reveal a lipid imbalance in the NPC hepatocyte, which increases lipid ordering in the plasma membrane, alters the properties of lipid rafts and interferes with the function of a raft-associated plasma-membrane receptor. Such a mechanism may participate in the pathogenesis of NPC disease and contribute to insulin resistance in other disorders of lipid metabolism.
Ubiquilin regulates presenilin endoproteolysis and modulates γ-secretase components, Pen-2 and nicastrin
Authors: Massey Leann K. , Mah Alex L. , Monteiro Mervyn J.
Published: October 2005

Mutations in presenilin proteins (PS1 and PS2) lead to early-onset Alzheimer's disease. PS proteins are endoproteolytically cleaved into two main fragments: the NTF (PS N-terminal fragment) and the CTF (PS C-terminal fragment). The two fragments are believed to constitute the core catalytic enzyme activity called γ-secretase, which is responsible for cleaving β-amyloid precursor protein to release Aβ. Thus, studying factors that modulate PS fragment levels could provide important information about γ-secretase. Previously, we demonstrated that the protein, ubiquilin-1, interacts both in vivo and in vitro with PS and that overexpression of ubiquilin-1 or -2 leads to increased accumulation of full-length PS proteins. Using wild-type HEK-293 cells (human embryonic kidney 293 cells) and PS-inducible cells, we now show that overexpression of either ubiquilin-1 or -2 decreases the PS NTF and CTF levels. Conversely, siRNA (small interfering RNA)-mediated knockdown of ubiquilin-1 and -2 proteins increased the PS NTF and CTF levels. We considered that ubiquilin might alter PS fragment accumulation by acting as a shuttle factor escorting PS fragments to the proteasome for degradation. However, through proteasome inhibition studies, we show that this does not occur. Instead, our results suggest that ubiquilin regulates PS fragment production. We also examined whether other components of the γ-secretase complex are affected by ubiquilin expression. Interestingly, overexpression of ubiquilin resulted in a decrease in Pen-2 and nicastrin levels, two essential components of the γ-secretase complex. In contrast, knockdown of ubiquilin-1 and -2 protein expression by RNAi (RNA interference) increased Pen-2 and nicastrin levels. Finally, we show that inhibition of the proteasome results in decreased PS fragment production and that reversal of proteasome inhibition restores PS fragment production, suggesting that the proteasome may be involved in PS endoproteolysis. These studies implicate ubiquilin as an important factor in regulating PS biogenesis and metabolism.
Weaning induces NOS-2 expression through NF-κB modulation in the lactating mammary gland: importance of GSH
Authors: Zaragozá Rosa , Miralles Vicente J. , Rus A. Diana , García Concha , Carmena Rafael , García-Trevijano Elena R. , Barber Teresa , Pallardó Federico V. , Torres Luís , Viña Juan R.
Published: October 2005

At the end of lactation the mammary gland undergoes involution, a process characterized by apoptosis of secretory cells and tissue remodelling. To gain insight into this process, we analysed the gene expression profile by oligonucleotide microarrays during lactation and after forced weaning. Up-regulation of inflammatory mediators and acute-phase response genes during weaning was found. Expression of IκBα (inhibitory κBα), a protein known to modulate NF-κB (nuclear factor-κB) nuclear translocation, was significantly up-regulated. On the other hand, there was a time-dependent degradation of IκBα protein levels in response to weaning, suggesting a role for NF-κB. Furthermore, we have demonstrated, using chromatin immunoprecipitation assays, binding of NF-κB to the NOS-2 (inducible nitric oxide synthase) promoter at the early onset of events triggered during weaning. The three isoforms of NOS are constitutively present in the lactating mammary gland; however, while NOS-2 mRNA and protein levels and, consequently, NO production are increased during weaning, NOS-3 protein levels are diminished. Western blot analyses have demonstrated that protein nitration is increased in the mammary gland during weaning, but this is limited to a few specific tyrosine-nitrated proteins. Interestingly, inhibition of GSH synthesis at the peak of lactation partially mimics these findings, highlighting the role of NO production and GSH depletion during involution.
Nitric oxide formation in acutely rejecting cardiac allografts correlates with GTP cyclohydrolase I activity
Authors: Pieper Galen M. , Nilakantan Vani , Halligan Nadine L. N. , Khanna Ashwani K. , Hilton Gail , Vásquez-Vivar Jeannette
Published: October 2005

Inducible nitric oxide synthase (iNOS) is a prominent component of the complex array of mediators in acute graft rejection. While NO production is determined by iNOS expression, BH4 (tetrahydrobiopterin), a cofactor of iNOS synthesized by GTP cyclohydrolase I, has been considered critical in sustaining NO production. In the present study, we examined time-dependent changes in iNOS and GTP cyclohydrolase I in rat cardiac allografts. The increase in iNOS protein and mRNA in allografts was similar at POD4 (post-operative day 4) and POD6. However, the peak increase in intragraft NO level at POD4 was not sustained at POD6. This disparity could not be explained by any decrease in iNOS enzyme activity measured ex vivo with optimal amounts of substrate and cofactors. Lower iNOS activity could be explained by changes in total biopterin levels in allografts at POD4 that was decreased to baseline at POD6. Changes in biopterin production correlated with lower GTP cyclohydrolase I protein levels but not by any change in GTP cyclohydrolase I mRNA. Functionally, allografts displayed bradycardia and distended diastolic and systolic dimensions at POD6 but not at POD4. Likewise, histological rejection scores were increased at POD4 but with a secondary increased stage at POD6. It is hypothesized that the dissimilar amounts of NO at early and later stages of rejection is due to uncoupling of iNOS arising from disproportionate synthesis of BH4. These findings provide insight into a potential pathway regulating NO bioactivity in graft rejection. Such knowledge may potentially assist in the design of newer strategies to prevent acute graft rejection.
Kinetic probes for inter-domain co-operation in human somatic angiotensin-converting enzyme
Authors: Skirgello Olga E. , Binevski Peter V. , Pozdnev Vladimir F. , Kost Olga A.
Published: October 2005

s-ACE (the somatic form of angiotensin-converting enzyme) consists of two homologous domains (N- and C-domains), each bearing a catalytic site. Negative co-operativity between the two domains has been demonstrated for cow and pig ACEs. However, for the human enzyme there are conflicting reports in the literature: some suggest possible negative co-operativity between the domains, whereas others indicate independent functions of the domains within s-ACE. We demonstrate here that a 1:1 stoichiometry for the binding of the common ACE inhibitors, captopril and lisinopril, to human s-ACE is enough to abolish enzymatic activity towards FA {N-[3-(2-furyl)acryloyl]}-Phe-GlyGly, Cbz (benzyloxycarbonyl)-Phe-His-Leu or Hip (N-benzoylglycyl)-His-Leu. The kinetic parameters for the hydrolysis of seven tripeptide substrates by human s-ACE appeared to represent average values for parameters obtained for the individual N- and C-domains. Kinetic analysis of the simultaneous hydrolysis of two substrates, Hip-His-Leu (S1) and Cbz-Phe-His-Leu (S2), with a common product (His-Leu) by s-ACE at different values for the ratio of the initial concentrations of these substrates (i.e. σ=[S2]0/[S1]0) demonstrated competition of these substrates for binding to the s-ACE molecule, i.e. binding of a substrate at one active site makes the other site unavailable for either the same or a different substrate. Thus the two domains within human s-ACE exhibit strong negative co-operativity upon binding of common inhibitors and in the hydrolysis reactions of tripeptide substrates.
Conformational changes in dynamin on GTP binding and oligomerization reported by intrinsic and extrinsic fluorescence
Authors: Solomaha Elena , Palfrey H. Clive
Published: October 2005

The effects of guanine nucleotides on the intrinsic and extrinsic fluorescence properties of dynamin were assessed. The intrinsic Trp (tryptophan) fluorescence spectra of purified recombinant dynamin-1 and -2 were very similar, with a maximum at 332 nm. Collisional quenching by KI was weak (∼30%), suggesting that the majority of Trp residues are buried. Binding of guanine nucleotides decreased intrinsic fluorescence by 15–20%. Titration of the effects showed that GTP and GDP bound to a single class of non-interacting sites in dynamin tetramers with apparent dissociation constants (Kd) values of 5.4 and 7.4 μM (dynamin-1) and 13.2 and 7.1 μM (dynamin-2) respectively. Similar dissociation constant values for both nucleotides were obtained by titrating the quenching of IAEDANS [N-iodoacetyl-N′-(5-sulpho-1-naphthyl)ethylenediamine]-labelled dynamin-2. Despite the similar binding affinities, GTP and GDP result in different conformations of the protein, as revealed by sensitivity to proteinase K fragmentation. Dynamins contain five Trp residues, of which four are in the PH domain (pleckstrin homology domain) and one is in the C-terminal PRD (proline/arginine-rich domain). Guanine nucleotides quenched fluorescence emission from a truncated (ΔPRD) mutant dynamin-1 to the same extent as in the full-length protein, suggesting conformational coupling between the G (groove)-domain and the PH domain. Efficient resonance energy transfer from PH domain Trp residues to bound mant-GTP [where mant stands for 2′-(3′)-O-(N-methylanthraniloyl)] suggests that the G-domain and PH domain are in close proximity (5–6 nm). Promotion of dynamin-2 oligomerization, by reduction in ionic strength or increasing protein concentration, had little effect on intrinsic dynamin fluorescence. However, fluorescence emission from IAEDANS·dynamin-2 showed a significant spectral shift on oligomerization. In addition, energy transfer was observed when oligomerization was promoted in mixtures of IAEDANS·dynamin-2 and 4-(4-dimethylaminophenylazo)benzoic acid-coupled dynamin-2, an effect that was counteracted by GTP but not GDP.
Diversification in substrate usage by glutathione synthetases from soya bean (Glycine max), wheat (Triticum aestivum) and maize (Zea mays)
Authors: Skipsey Mark , Davis Benjamin G. , Edwards Robert
Published: October 2005

Unlike animals which accumulate glutathione (γ-glutamyl-L-cysteinyl-glycine) alone as their major thiol antioxidant, several crops synthesize alternative forms of glutathione by varying the carboxy residue. The molecular basis of this variation is not well understood, but the substrate specificity of the respective GSs (glutathione synthetases) has been implicated. To investigate their substrate tolerance, five GS-like cDNAs have been cloned from plants that can accumulate alternative forms of glutathione, notably soya bean [hGSH (homoglutathione or γ-glutamyl-L-cysteinyl-β-alanine)], wheat (hydroxymethylglutathione or γ-glutamyl-L-cysteinyl-serine) and maize (γ-Glu-Cys-Glu). The respective recombinant GSs were then assayed for the incorporation of differing C-termini into γ-Glu-Cys. The soya bean enzyme primarily incorporated β-alanine to form hGSH, whereas the GS enzymes from cereals preferentially catalysed the formation of glutathione. However, when assayed with other substrates, several GSs and one wheat enzyme in particular were able to synthesize a diverse range of glutathione variants by incorporating unusual C-terminal moieties including D-serine, non-natural amino acids and α-amino alcohols. Our results suggest that plant GSs are capable of producing a diverse range of glutathione homologues depending on the availability of the acyl acceptor.
Characterization of a c-Jun-responsive module in the 5′-flank of the human CYP2J2 gene that regulates transactivation
Authors: Marden Nicole Y. , Murray Michael
Published: October 2005

The human cytochrome P450 2J2 (CYP2J2) generates cytoprotective epoxyeicosatrienoic acids from arachidonic acid. Expression of CYP2J2 is decreased in hypoxia, and the resultant decrease in CYP2J2-derived epoxyeicosanoids may contribute to the pathogenesis of cardiac ischaemia. Recent studies have indicated that AP-1 (activator protein-1) regulates CYP2J2 expression in normoxia and hypoxia. Down-regulation of CYP2J2 in hypoxic HepG2 cells was closely associated with the up-regulation of c-fos and transient transfection analysis demonstrated that c-Fos abolishes the activation of CYP2J2 by the AP-1 protein c-Jun. Deletion of the region between nt −122 and −50 upstream of the start codon in CYP2J2 prevented c-Jun transactivation. In this study we demonstrate that the sequence at −105/−95 is a major regulatory element that binds c-Jun and has a prominent role in CYP2J2 gene transactivation. Mutagenesis of both the −105/−95 region and the previously identified element at −56/−63 was required for complete loss of transactivation by c-Jun; separate mutagenesis of the −105/−95 element or, to a lesser extent, the −56/−63 element resulted in a partial loss of gene activation. In contrast to the behaviour of the −56/−63 element, c-Jun homodimers and c-Fos/c-Jun heterodimers bound to the −105/−95 element. These findings demonstrate that the c-Jun-responsive module between −122 and −50 in the CYP2J2 proximal promoter contains an atypical AP-1 element at −105/−95 that has a major role in c-Jun transactivation and acts in conjunction with the −56/−63 element to regulate expression.
Molecular cloning and characterization of PLC-η2
Authors: Zhou Yixing , Wing Michele R. , Sondek John , Harden T. Kendall
Published: October 2005

PLC (phospholipase C) isoenzymes catalyse the conversion of PtdIns(4,5)P2 into the Ca2+-mobilizing second messenger, Ins(1,4,5)P3, and the protein kinase C-activating second messenger, diacylglycerol. With the goal of identifying additional mammalian PLC isoenzymes, we screened the NCBI non-redundant database using a BLAST algorithm for novel sequences with homology with the conserved PLC catalytic core. Two unique sequences corresponding to two unknown PLC isoenzymes were identified, and one of these, designated PLC-η2, was cloned and characterized. Most of the coding sequence of PLC-η2 was constructed from two ESTs (expressed sequence tags), which included an overlapping sequence that was confirmed by multiple ESTs and mRNAs. 5′-RACE (rapid amplification of cDNA ends) also identified an upstream exon not deduced from available EST or mRNA sequences. Sequence analysis of PLC-η2 revealed the canonical domains of a PLC isoenzyme with an additional long C-terminus that contains a class II PDZ-binding motif. Genomic analyses indicated that PLC-η2 is encoded by 23 exons. RT-PCR (reverse transcriptase-PCR) analyses illustrated expression of PLC-η2 in human retina and kidney, as well as in mouse brain, eye and lung. RT-PCR with exon-specific primers also revealed tissue-specific expression of four splice variants in mouse that represent alternative use of sequences in exons 21, 22 and 23. PLC-η2-specific antisera recognized one of these splice variants as an approx. 155 kDa species when expressed in COS-7 cells; PLC-η2 natively expressed in 1321N1 human astrocytoma cells also migrated as an approx. 155 kDa species. PLC activity was observed in vitro and in vivo for three different constructs of PLC-η2, each containing possible alternatively spliced first exons. Co-expression of PLC-η2 with Gβ1γ2 dimers of heterotrimeric G-proteins resulted in marked stimulation of inositol lipid hydrolysis. Thus PLC-η2 may in part function downstream of G-protein-coupled receptors.
Lipopolysaccharide rapidly modifies adenosine receptor transcripts in murine and human macrophages: role of NF-κB in A2A adenosine receptor induction
Authors: Murphree Lauren J. , Sullivan Gail W. , Marshall Melissa A. , Linden Joel
Published: October 2005

The A2A adenosine receptor (A2AAR) mediates anti-inflammatory actions of adenosine in a variety of cell types. LPS (lipopolysaccharide) was reported to induce a small (<2-fold) increase in the expression of A2AAR mRNA in human monocytes and monocytic cell lines. We investigated the effects of LPS on the expression of adenosine receptor mRNAs in primary mouse IPMΦ (intraperitoneal macrophages), human macrophages and Wehi-3 cells. Treatment with 10 ng/ml LPS for 4 h produced a >100-fold increase in A2AAR mRNA. LPS-induced increases in mRNA for A2AAR and TNFα (tumour necrosis factor α) are reduced by 90% in IPMΦ pretreated with the NF-κB (nuclear factor κB) inhibitor, BAY 11-7082 {(E)3-[(4-methylphenyl)sulphonyl]-2-propenenitrile; 10 μM}. In Wehi-3 cells exposed to LPS, A2AAR and A2BAR transcripts are elevated by 290- and 10-fold respectively, the A1AR transcript is unchanged and the A3AR transcript is decreased by 67%. The induction of A2AAR mRNA by LPS is detectable after 1 h, reaches a peak at 6 h at 600 times control and remains elevated beyond 24 h. The ED50 (effective dose) of LPS is 2.3 ng/ml. A2AAR receptor number, measured by 125I-ZM241385 binding to whole cells, is undetectable in naïve cells and increases linearly at a rate of 23 receptors·cell−1·min−1 to a Bmax of 348 fmol/mg (28000 receptors/cell) in 20 h. The increase in receptor number is correlated with an increase in the potency of an A2A agonist (4-{3-[6-amino-9-(5-ethylcarbamoyl-3,4-dihydroxy-tetrahydro-furan-2-yl)-9H-purin-2-yl]-prop-2-ynyl}-cyclohexanecarboxylic acid methyl ester; referred to as ATL146e) to stimulate cAMP in these cells. After LPS pretreatment, the potency of the A2A agonist, ATL146e, to reduce TNFα release from IPMΦ was increased by 200-fold. The results support the hypothesis that regulation of adenosine receptor expression, especially up-regulation of the A2AAR, is part of a delayed feedback mechanism initiated through NF-κB to terminate the activation of human and mouse macrophages.
New insights into the families of PLC enzymes: looking back and going forward
Authors: Katan Matilda
Published: October 2005

A study in this issue of the Biochemical Journal by Harden and colleagues, in association with one published in the Biochemical Journal very recently [Hwang, Oh, Shin, Kim, Ryu and Suh (2005) Biochem. J. 389, 181–186], have defined a new member of the superfamily of PLC (phosphoinositide-specific phospholipase C) enzymes, PLCη. Two isoforms, PLCη1 and PLCη2, and their splice variants add to the molecular diversity of PLC enzymes. The studies of PLCη regulation suggest that at least some splice variants of PLCη2 could be regulated by the G-protein subunits Gβγ. As two other families, PLCβ and PLCϵ, are also regulated through heterotrimeric G-proteins, this finding reveals further complexity and possible interplay between different PLC families and their regulatory networks. At this point, when it is likely that the PLCη family completes the effort of identifying new members of this related group of PLC enzymes, I also discuss some more general concepts of PLC regulation and catalysis, and challenges awaiting their further studies.
N-Acetylcysteine ameliorates the late phase of liver ischaemia/reperfusion injury in the rabbit with hepatic steatosis
Authors: Fusai Giuseppe , Glantzounis George K. , Hafez Tarek , Yang Wenxuan , Quaglia Alberto , Sheth Hemant , Kanoria Sanjeev , Parkes Harry , Seifalian Alexander , Davidson Brian R.
Published: October 2005

Steatotic livers are highly susceptible to I/R (ischaemia/reperfusion) injury and, therefore, the aim of the present study was to evaluate the in vivo effect of NAC (N-acetylcysteine) on hepatic function in the early and initial late phase of warm liver I/R injury in steatotic rabbits. Twelve New Zealand White rabbits were fed a high-cholesterol (2%) diet. The control group (n=6) underwent lobar liver ischaemia for 1 h, followed by 6 h of reperfusion. In the treated group receiving NAC (n=6), an intravenous infusion of NAC was administered prior to and during the 6 h reperfusion period. Systemic and hepatic haemodynamics were monitored continuously. ALT (alanine aminotransferase) activity and bile production were measured. NMR spectroscopy was used to analyse bile composition. Oxidation of DHR (dihydrorhodamine) to RH (rhodamine) was used as a marker of production of reactive oxygen and nitrogen species. Moderate centrilobular hepatic steatosis was demonstrated by histology. The results showed that NAC administration significantly improved portal flow, hepatic microcirculation, bile composition and bile flow after 5 h of reperfusion. NAC administration was also associated with less hepatocellular injury, as indicated by ALT serum activity, and decreased the oxidation of DHR to RH. In conclusion, NAC administration decreased the extent of I/R injury in the steatotic liver, particularly during the late phase of reperfusion.
Proteomic approach to identify changes in protein expression modified by 17β-oestradiol in bovine vascular smooth muscle cells
Authors: Molero Laura , García-Méndez Antonio , Alonso-Orgaz Sergio , Carrasco Carolina , Macaya Carlos , López Farré Antonio J.
Published: October 2005

The aim of the present study was to use proteomics to analyse modifications in the level of expression of different proteins in BVSMCs (bovine vascular smooth muscle cells) incubated in the absence and presence of 17β-oestradiol. By using two-dimensional electrophoresis with a pH range of 4–7, we identified several areas on the gels in which the level of expression of proteins were different between control BVSMCs and cells incubated for 24 h with 17β-oestradiol. Changes in several isoforms of α-enolase, HSP60 (heat-shock protein 60), vimentin and PDI (protein disulphide-isomerase) were observed in BVSMCs. The expression of α-enolase isoform 1 was enhanced after 17β-oestradiol treatment. The expression of HSP60 isoform 3, vimentin isoforms 2 and 3 and caldesmon was reduced by 17β-oestradiol. Finally, the expression of PDI isoforms was reduced by 17β-oestradiol. In summary, 17β-oestradiol modified the expression of isoforms of proteins associated with smooth muscle cell proliferation (α-enolase, vimentin and HSP-60), cell contraction (vimentin and caldesmon) and cell redox modulation (PDI). These findings confirm that 17β-oestradiol may modulate a wide range of signalling pathways in vascular smooth muscle cells.
L-Alanine induces changes in metabolic and signal transduction gene expression in a clonal rat pancreatic β-cell line and protects from pro-inflammatory cytokine-induced apoptosis
Authors: Cunningham Grainne A. , Mcclenaghan Neville H. , Flatt Peter R. , Newsholme Philip
Published: October 2005

Acute effects of nutrient stimuli on pancreatic β-cell function are widely reported; however, the chronic effects of insulinotropic amino acids, such as L-alanine, on pancreatic β-cell function and integrity are unknown. In the present study, the effects of prolonged exposure (24 h) to the amino acid L-alanine on insulin secretory function, gene expression and pro-inflammatory cytokine-induced apoptosis were studied using clonal BRIN-BD11 cells. Expression profiling of BRIN-BD11 cells chronically exposed to L-alanine was performed using oligonucleotide microarray analysis. The effect of alanine, the iNOS (inducible nitric oxide synthase) inhibitor NMA (NG-methyl-L-arginine acetate) or the iNOS and NADPH oxidase inhibitor DPI (diphenylene iodonium) on apoptosis induced by a pro-inflammatory cytokine mix [IL-1β (interleukin-1β), TNF-α (tumour necrosis factor-α) and IFN-γ (interferon-γ)] was additionally assessed by flow cytometry. Culture for 24 h with 10 mM L-alanine resulted in desensitization to the subsequent acute insulin stimulatory effects of L-alanine. This was accompanied by substantial changes in gene expression of BRIN-BD11 cells. Sixty-six genes were up-regulated >1.8-fold, including many involved in cellular signalling, metabolism, gene regulation, protein synthesis, apoptosis and the cellular stress response. Subsequent functional experiments confirmed that L-alanine provided protection of BRIN-BD11 cells from pro-inflammatory cytokine-induced apoptosis. Protection from apoptosis was mimicked by NMA or DPI suggesting L-alanine enhances intracellular antioxidant generation. These observations indicate important long-term effects of L-alanine in regulating gene expression, secretory function and the integrity of insulin-secreting cells. Specific amino acids may therefore play a key role in β-cell function in vivo.
Temporal Mitochondrial DNA Variation in the Basque Country: Influence of Post‐Neolithic Events
Authors: Alzualde A. , Izagirre N. , Alonso S. , Alonso A. , De La Rúa C.
Published: October 2005

The Basque population has been considered an outlier in a large number of genetic studies, due to its hypothesized antiquity and greater genetic isolation. The present paper deals with an analysis of the mtDNA variability of the historical population of Aldaieta (VI–VII c. AD; Basque Country) which, together with genetic data existing for other prehistoric populations of the Basque Country (4,500–5,000 YBP), permits an appraisal of the hypotheses proposed for the origin of the genetic differentiation of the Basque population. Given that this is an aDNA study, application has been made both of standard precautions, to avoid contamination, and of authentication criteria (analysis of duplicates, replication in an independent laboratory, quantification of target DNA, sequencing and cloning of PCR products). The variability of the mtDNA haplogroups of the historical population of Aldaieta falls within the range of the present‐day populations of Europe's Atlantic fringe, whereas the prehistoric populations of the Basque Country display clear differentiation in relation to all others. Consequently, we suggest that between 5,000–1,500 YBP approximately, there may have been gene flow amongst the western European populations that homogenised mtDNA lineages.
Nucleation-controlled multiphase transitions
Authors: Ziabicki Andrzej
Published: October 2005

Thermodynamics and kinetics of phase transitions in multiphase systems have been discussed. Thermodynamically admissible transitions have been identified and transition kinetics described in terms of the extended Kolmogoroff-Avrami-Evans model. Different combinations of transitions have been described as directed graphs. Graph nodes represented individual phases, graph edges—transitions. Superposition of parallel transitions in various mother phases, simultaneous transition of the same mother phase into different target phases, and successive (chain) transitions have been analyzed. Detailed solutions for a three-phase system consisting of one liquid phase and two polymorphic solid phases have been presented.
Anomalous dielectric relaxation in strong ac external fields
Authors: Déjardin Jean-Louis , Jadzyn Jan
Published: October 2005

Dielectric relaxation of complex polar fluids is considered in the context of the anomalous diffusion characterized by a fractional parameter α⩽1 (subdiffusion). An infinite hierarchy of three-term differential-recurrence equations governing the time evolution of the electric polarization is established by following a purely phenomenological procedure. The matrix-continued fraction method is used to derive the exact numerical solution of the stationary regime for an assembly of nonelectrically interacting, polar symmetric-top molecules in presence of a strong ac electric field. The results so obtained are valid to any order in the field strength parameter γ1, thus extending previous theories applicable to fields of very small amplitudes only. This is illustrated by Cole-Cole diagrams and three-dimensional relaxation spectra for the first- and third-harmonic components of the electric polarization as a function of α,γ1, and the angular frequency.
Decreasing the hydrogen desorption temperature of LiNH2 through doping: A first-principles study
Authors: Jin H. M. , Wu P.
Published: October 2005

We present a theoretical approach to investigate the possibility of reducing desorption temperature of LiNH2 by partial element substitution. The approach was based on a first-principles study of electronic structure of LiNH2 and (Li,Mg)NH2. Results of the LiNH2 study showed that LiNH2 is nonmetallic, the bonding between Li and N is ionic, and the bonding between N and H is strongly covalent. Results of the (Li,Mg)NH2 study showed that the bonding nature of Li–N and N–H is the same as in LiNH2, but the bond strength of N–H was reduced. In addition, the system becomes metal-like after substitution. These two major differences can be used to explain the experimental observation that the hydrogen desorption temperature was reduced by Mg substitution. More important, they might be used as criteria to predict the behavior of other substitution elements.
The Gardner category and nonlocal conservation laws for N=1 Super KdV
Authors: Andrea S. , Restuccia A. , Sotomayor A.
Published: October 2005

The nonlocal conserved quantities of the N=1 Super KdV are obtained using a Gardner map. A fermionic substitution semigroup and the resulting Gardner category are defined and several propositions concerning their algebraic structure are obtained. This algebraic framework makes it possible to define general transformations between different nonlinear SUSY differential equations. A SUSY ring extension is then introduced to deal with the nonlocal conserved quantities of SKdV. The algebraic version of the nonlocal conserved quantities is solved in terms of the exponential function applied to the D−1 of the local conserved quantities of SKdV. Finally the same formulas are shown to work for rapidly decreasing superfields.
Role of polydispersity in anomalous interactions in electrostatically levitated colloidal systems
Authors: Pangburn Todd O. , Bevan Michael A.
Published: October 2005

In this paper, we investigate the effects of using inverse analyses developed for monodisperse particles to extract particle-particle and particle-surface potentials from simulated interfacial colloidal configurations having finite-size polydispersity. Forward Monte Carlo simulations are used to generate three-dimensional equilibrium configurations of log normal-distributed polydisperse particles confined by gravity near an underlying surface. Particles remain levitated above the substrate and stabilized against aggregation by repulsive electrostatic Derjaguin-Landau-Verwey-Overbeek pair potentials. An inverse Ornstein-Zernike analysis and an inverse Monte Carlo simulation method are used to obtain interactions from simulated distribution functions as a function of polydispersity (σ), relative range of repulsion (κa¯), and projected interfacial concentration (ρ). Both inverse analyses successfully recover input potentials for all monodisperse cases, but fail for polydispersities often encountered in experiments. For different conditions (σ, κa¯, and ρ), our results indicate softened short-range repulsion, anomalous long-range attraction, and apparent particle overlaps, which are similar to commonly reported observations in optical microscopy measurements of quasi-two-dimensional interfacial colloidal ensembles. By demonstrating signatures of, and limitations due to, polydispersity when extracting pair potentials from measured distribution functions, our specific goal is to provide a basis to objectively interpret and resolve the effects of polydispersity in optical microscopy experiments.
Assessment of the attained temperatures and of melting in the nanosecond irradiation of doped poly(methylmethylacrylate) at 308, 248, and 193nm via the examination of dopant reactivity
Authors: Bounos Giannis , Kolloch Andreas , Stergiannakos Taxiarhos , Varatsikou Erene , Georgiou Savas
Published: October 2005

The thermal and structural changes effected to poly(methylmethylacrylate) (PMMA) upon irradiation at 308, 248, and 193nm are assessed via the examination of the formation yields of the products formed by the photolysis of iodoaromatics (iodonaphthalene and iodophenanthrene–ArI–) dopants. Specifically, the main aryl product, the hydrogen-substituted derivative ArH, is formed via a thermally activated process (hydrogen-atom abstraction); thus, its formation efficiency reflects the temperature evolution in the substrate following UV irradiation. In the case of iodonaphthalene dopant, biaryl species (1,1-binaphthalene and perylene) are also formed via diffusion-limited reaction of the aryl radicals; thus, their yield reflects the extent of polymer melting. To this end, laser-induced fluorescence is employed for the quantification of the aryl products formed in the substrate as a function of the irradiation fluence. At all wavelengths, the ArH amount scales linearly with Flaser at low fluences, but at higher fluences, it increases sharply reaching a plateau near the ablation threshold. Only quantitative differences concerning the fluence onset of the ArH increase and the amount of product remaining in the substrate are observed. Simulations accounting for the temporal and spatial evolutions of the temperature reproduce well the observed Flaser dependences. The quantitative differences in the extent of ArH formation are well accounted by the extent of the heat diffusion to the sublayers. Thus, contrary to many previous suggestions, a thermal process is demonstrated to be dominant at the three wavelengths. Concerning the biaryl species, their yield decreases from 308to193nm. The simulation of their formation yield provides semiquantitative information about the polymer viscosity changes (melting) upon irradiation at the three wavelengths. Besides the mechanistic implications, the study also provides insight into the factors affecting the extent of chemical modifications in laser processing of polymers and organic substrates in general. In particular, the reduced extent of chemical modifications upon ablation at strongly absorbed wavelengths is indicated to be crucial for the success of these procedures.
On the structure of the supplementary series of unitary, irreducible representations of the proper, orthochronous Lorentz group
Authors: Kubieniec J.
Published: October 2005

Representations from the supplementary series of unitary, irreducible representations of the proper, orthochronous Lorentz group are classified according to the parameter z, 0<z<1. The representations with 0<z<1∕2 are qualitatively different from those with 1∕2<z<1. This is shown in the form of the following theorem: the Casimir operator of the little group of a spacelike vector has for 0<z<1∕2 a single bound state, i.e., a single normalizable eigenstate which disappears for 1∕2<z<1. To this end the scalar product for the supplementary series is explicitly calculated in both regions, 0<z<1∕2 and 1∕2<z<1 in a coordinate system provided by common eigenfunctions of the Casimir operator of the little group of a spacelike vector and the commuting generator of a parabolic rotation. The choice of this coordinate system allows to use the well established properties of the Kontorovich-Lebedev pair of integral transforms.
The UV photodissociation dynamics of ClO radical using velocity map ion imaging
Authors: Kim Hahkjoon , Park Jiho , Niday Tracy C. , North Simon W.
Published: October 2005

We have studied the wavelength-dependent photodissociation dynamics of jet-cooled ClO radical from 235to291nm using velocity map ion imaging. We find that Cl(P3∕22)+O(D21) is the dominant channel above the O(D21) threshold with minor contributions from the Cl(PJ2)+O(PJ3) and Cl(P1∕22)+O(D21) channels. We have measured the photofragment angular distributions for each dissociation channel and find that the AΠ2 state reached via a parallel transition carries most of the oscillator strength above the O(D21) threshold. The formation of O(PJ3) fragments with positive anisotropy is evidence of curve crossing from the AΠ2 state to one of several dissociative states. The curve crossing probability increases with wavelength in good agreement with previous theoretical calculations. We have directly determined the O(D21) threshold to be 38050±20cm−1 by measuring O(D21) quantum yield in the wavelength range of 260–270nm. We also report on the predissociation dynamics of ClO below the O(D21) threshold. We find that the branching ratio of Cl(P3∕22)∕Cl(P1∕22) is 1.5±0.1 at both 266 and 291nm. The rotational depolarization of the anisotropy parameters of the Cl(P3∕22) fragments provides predissociation lifetimes of 1.5±0.2ps for the 9-0 band and 1.0±0.4ps for the 8-0 band, in reasonable agreement with previous spectroscopic and theoretical studies.
Signatures of the fast dynamics in glassy polystyrene: First evidence by high-field Electron Paramagnetic Resonance of molecular guests
Authors: Bercu V. , Martinelli M. , Massa C. A. , Pardi L. A , Leporini D.
Published: October 2005

The reorientation of one small paramagnetic molecule (spin probe) in glassy polystyrene (PS) is studied by high-field electron paramagnetic resonance spectroscopy at two different Larmor frequencies (190 and 285 GHz). Two different regimes separated by a crossover region are evidenced. Below 180 K the rotational times are nearly temperature independent with no apparent distribution. In the temperature range of 180-220 K a large increase of the rotational mobility is observed with the widening of the distribution of correlation times which exhibits two components: (i) a deltalike, temperature-independent component representing the fraction of spin probes w which persist in the low-temperature dynamics; (ii) a strongly temperature-dependent component, to be described by a power distribution, representing the fraction of spin probes 1−w undergoing activated motion over an exponential distribution of barrier heights g(E). Above 180 K a steep decrease of w is evidenced. The shape and the width of g(E) do not differ from the reported ones for PS within the errors. For the first time the large increase of the rotational mobility of the spin probe at 180 K is ascribed to the onset of the fast dynamics detected by neutron scattering at Tf=175±25K.
Shear stress relaxation and physical aging study on simple glass-forming materials
Authors: Shi Xiangfu , Mandanici Andrea , McKenna Gregory B.
Published: October 2005

Relaxation and aging behaviors in three supercooled liquids: m-toluidine, glycerol, and sucrose benzoate have been studied by shear stress relaxation experiments in the time domain above and below their nominal glass transition temperatures. For the equilibrium state, the current study provides new data on the behavior of organic complex fluids. The shape of the relaxation function as characterized by the stretching exponent β is discussed considering that a time-temperature master curve can be constructed even though the β’s for the individual response curves at each temperature vary systematically. In the nonequilibrium state, isothermal physical aging experiments at different glassy structures reveal that the effect of the aging process on the mechanical shear relaxation in these simple glass formers is similar to that observed in polymeric and other systems. Departure from the Vogel-Fulcher-Tamman behavior after the samples have aged back to equilibrium in the glassy state is observed for m-toluidine and, less strongly, for glycerol but not for sucrose benzoate. An inherent structure-based energy landscape concept is briefly discussed to account for the slow dynamics during the physical aging process.
Direct determination of phase behavior of square-well fluids
Authors: Liu Hongjun , Garde Shekhar , Kumar Sanat
Published: October 2005

We have combined Gibbs ensemble Monte Carlo simulations with the aggregation volume-biased method in conjunction with the Gibbs-Duhem method to provide the first direct estimates for the vapor-solid, vapor-liquid, and liquid-solid phase coexistences of square-well fluids with three different ranges of attraction. Our results are consistent with the previous simulations and verify the notion that the vapor-liquid coexistence behavior becomes metastable for cases where the attraction well becomes smaller than 1.25 times the particle diameter. In these cases no triple point is found.
Rotational excitation cross sections of para-H2+para-H2 collisions. A full-dimensional wave-packet propagation study using an exact form of the kinetic energy
Authors: Gatti Fabien , Otto Frank , Sukiasyan Suren , Meyer Hans-Dieter
Published: October 2005

A full-dimensional quantum dynamical study of the rotational excitation in para-para H2+H2 collisions using the potential-energy surface of Boothroyd et al. [J. Chem. Phys. 116, 666 (2002)] is reported. The multiconfiguration time-dependent Hartree algorithm is utilized to propagate wave packets and the cross sections for collision energies up to 1.2 eV are determined by a flux analysis through the interaction of the wave packet with a complex absorbing potential. Calculations for a collection of total angular momenta up to J=70 are performed; the missing channels are obtained with a J-interpolation algorithm.
State-resolved collisional quenching of vibrationally excited pyrazine (Evib=37900cm−1) by D35Cl(v=)
Authors: Li Ziman , Korobkova Ekaterina , Werner Kathryn , Shum Lawrence , Mullin Amy S.
Published: October 2005

Supercollision relaxation of highly vibrationally excited pyrazine (Evib=37900cm−1) with D35Cl is investigated using high-resolution transient IR diode laser absorption spectroscopy at 4.4μm. Highly excited pyrazine is prepared by pulsed UV excitation at 266nm, followed by rapid radiationless decay to the ground electronic state. The rotational energy distribution of the scattered DCl (v=0,J) molecules with J=15–21 is characterized by Trot=755±90K. The relative translational energy increases as a function of rotational quantum number for DCl with Trel=710±190K for J=15 and Trel=1270±240K for J=21. The average change in recoil velocity correlates with the change in rotational angular momentum quantum number and highlights the role of angular momentum in energy gain partitioning. The integrated energy-transfer rate for appearance of DCl (v=0,J=15–21) is k2int=7.1×10−11cm3molecule−1s−1, approximately one-eighth the Lennard-Jones collision rate. The results are compared to earlier energy gain measurements of CO2 and H2O.
Thermal conductivity of ethanol
Authors: Petravic Janka
Published: October 2005

We present a factorization of the Ewald sum permitting efficient computation of the reciprocal space part of the molecular representation for the heat flux vector. We use the derived expression to evaluate thermal conductivity of a model of ethanol at several near-ambient state points.
Structure of highly asymmetric hard-sphere mixtures: An efficient closure of the Ornstein-Zernike equations
Authors: Amokrane S. , Ayadim A. , Malherbe J. G.
Published: October 2005

A simple modification of the reference hypernetted chain (RHNC) closure of the multicomponent Ornstein-Zernike equations with bridge functions taken from Rosenfeld’s hard-sphere bridge functional is proposed. Its main effect is to remedy the major limitation of the RHNC closure in the case of highly asymmetric mixtures—the wide domain of packing fractions in which it has no solution. The modified closure is also much faster, while being of similar complexity. This is achieved with a limited loss of accuracy, mainly for the contact value of the big sphere correlation functions. Comparison with simulation shows that inside the RHNC no-solution domain, it provides a good description of the structure, while being clearly superior to all the other closures used so far to study highly asymmetric mixtures. The generic nature of this closure and its good accuracy combined with a reduced no-solution domain open up the possibility to study the phase diagram of complex fluids beyond the hard-sphere model.
Spiral pattern in chlorite-iodide-malonic acid reaction: A theoretical and numerical study
Authors: Riaz Syed Shahed , Ray Deb Shankar
Published: October 2005

The development of spiral pattern in a model representing chlorite-iodide-malonic acid reaction is investigated theoretically and numerically. We have carried out a multiple scale analysis of the model to identify the experimentally admissible parameter range and the appropriate perturbation for shifting Hopf bifurcation boundary towards the oscillating region. Our theoretical analysis is corroborated by numerical simulation.
Efficient Monte Carlo trial moves for polypeptide simulations
Authors: Betancourt Marcos R.
Published: October 2005

A new move set for the Monte Carlo simulations of polypeptide chains is introduced. It consists of a rigid rotation along the (Cα) ends of an arbitrary long segment of the backbone in such a way that the atoms outside this segment remain fixed. This fixed end move, or FEM, alters only the backbone dihedral angles ϕ and ψ and the Cα bond angles of the segment ends. Rotations are restricted to those who keep the α bond angles within their maximum natural range of approximately ±10°. The equations for the angular intervals (τ) of the allowed rigid rotations and the equations required for satisfying the detailed balance condition are presented in detail. One appealing property of the FEM is that the required number of calculations is minimal, as it is evident from the simplicity of the equations. In addition, the moving backbone atoms undergo considerable but limited displacements of up to 3Å. These properties, combined with the small number of backbone angles changed, lead to high acceptance rates for the new conformations and make the algorithm very efficient for sampling the conformational space. The FEMs, combined with pivot moves, are used in a test to fold a group of coarse-grained proteins with lengths of up to 200 residues.
Mass-analyzed threshold ionization study of vinyl bromide cation in the first excited electronic state using vacuum-ultraviolet radiation generated by four-wave mixing in Hg
Authors: Lee Mina , Kim Myung Soo
Published: October 2005

The vibrational spectrum of the vinyl bromide cation in the first excited electronic state ÃA′2 was obtained by one-photon mass-analyzed threshold ionization (MATI) spectroscopy. The use of an improved vacuum-ultraviolet radiation source based on four-wave sum frequency mixing in Hg resulted in excellent sensitivity for MATI signals. From the MATI spectrum, the ionization energy to the ÃA′2 state of the cation was determined to be 10.9150±0.0006eV. Nearly complete vibrational assignments for the MATI peaks were possible by utilizing the vibrational frequencies and Franck-Condon factors calculated at the density-functional theory (DFT) and time-dependent DFT/B3LYP levels with the 6-311+G(df,p) basis set.