bluuebunny/crossref_metadata_2025 huggingface dataset:
Glutamate-64, a newly identified residue of the functionally conserved electron-sharing network contributes to catalysis and structural integrity of glutathione transferases
Authors: Winayanuwattikun Pakorn , Ketterman Albert J.
Published: February 2007

In Anopheles dirus glutathione transferase D3-3, position 64 is occupied by a functionally conserved glutamate residue, which interacts directly with the γ-glutamate moiety of GSH (glutathione) as part of an electron-sharing network present in all soluble GSTs (glutathione transferases). Primary sequence alignment of all GST classes suggests that Glu64 is one of a few residues that is functionally conserved in the GST superfamily. Available crystal structures as well as consideration of the property of the equivalent residue at position 64, acidic or polar, suggest that the GST electron-sharing motif can be divided into two types. Electrostatic interaction between the GSH glutamyl and carboxylic Glu64, as well as with Arg66 and Asp100, was observed to extend the electron-sharing motif identified previously. Glu64 contributes to the catalytic function of this motif and the ‘base-assisted deprotonation’ that are essential for GSH ionization during catalysis. Moreover, this residue also appears to affect multiple steps in the enzyme catalytic strategy, including binding of GSH, nucleophilic attack by thiolate at the electrophilic centre and product formation, probably through active-site packing effects. Replacement with non-functionally-conserved amino acids alters initial packing or folding by favouring aggregation during heterologous expression. Thermodynamic and reactivation in vitro analysis indicated that Glu64 also contributes to the initial folding pathway and overall structural stability. Therefore Glu64 also appears to impact upon catalysis through roles in both initial folding and structural maintenance.
Importin α1 is involved in the nuclear localization of Zac1 and the induction of p21WAF1/CIP1 by Zac1
Authors: Huang Shih-Ming , Huang Sheng-Ping , Wang Sung-Ling , Liu Pei-Yao
Published: February 2007

Zac1, a novel seven-zinc-finger transcription factor, preferentially binds GC-rich DNA elements and has intrinsic transactivation activity. To date, the NLS (nuclear localization signal) of Zac1 has not been empirically determined. We generated a series of EGFP (enhanced green fluorescence protein)-tagged deletion mutants of Zac1 and examined their subcellular localization, from which we defined two NLSs within the DNA-binding (or zinc-finger) domain. Fusion proteins consisting of the two EGFP-tagged zinc-finger clusters (zinc finger motifs 1–3 and 4–7) were located exclusively in the nucleus, demonstrating that each of the zinc-finger clusters is sufficient for nuclear localization. Physical interactions between these two zinc-finger clusters and importin α1 were demonstrated using an in vitro glutathione S-transferase pull-down assay. Finally, our results indicate that the association of Zac1 with importin α1 is also involved in regulating the transactivation activity of Zac1 on the p21WAF1/CIP1 gene and protein expression.
Mitochondria contribute to LPS-induced MAPK activation via uncoupling protein UCP2 in macrophages
Authors: Emre Yalin , Hurtaud Corinne , Nübel Tobias , Criscuolo François , Ricquier Daniel , Cassard-Doulcier Anne-Marie
Published: February 2007

The mitochondrion is a major organelle contributing to energy metabolism but also a main site of ROS (reactive oxygen species) production. LPS (lipopolysaccharide)-induced ROS signalling is a critical event in macrophage activation. In the present paper we report that part of LPS-mediated ROS signalling comes from mitochondria inside a signal amplification loop that enhances MAPK (mitogen-activated protein kinase) activation. More precisely, we have identified the inner mitochondrial membrane UCP2 (uncoupling protein 2) as a physiological brake on ROS signalling. Stimulation of murine bone marrow-derived macrophages by LPS quickly down-regulated UCP2 through the JNK (c-Jun N-terminal kinase) and p38 pathways. UCP2 down-regulation was shown to be necessary to increase mitochondrial ROS production in order to potentiate MAPK activation. Consistent with this, UCP2-deficient macrophages exhibit an enhanced inflammatory state characterized by increased nitric oxide production and elevated migration ability. Additionally, we found that the absence of UCP2 renders macrophages more resistant to nitric oxide-induced apoptosis.
Low variance energy estimators for systems of quantum Drude oscillators: Treating harmonic path integrals with large separations of time scales
Authors: Whitfield Troy W. , Martyna Glenn J.
Published: February 2007

In the effort to develop atomistic models capable of accurately describing nanoscale systems with complex interfaces, it has become clear that simple treatments with rigid charge distributions and dispersion coefficients selected to generate bulk properties are insufficient to predict important physical properties. The quantum Drude oscillator model, a system of one-electron pseudoatoms whose “pseudoelectrons” are harmonically bound to their respective “pseudonuclei,” is capable of treating many-body polarization and dispersion interactions in molecular systems on an equal footing due to the ability of the pseudoatoms to mimic the long-range interactions that characterize real materials. Using imaginary time path integration, the Drude oscillator model can, in principle, be solved in computer operation counts that scale linearly with the number of atoms in the system. In practice, however, standard expressions for the energy and pressure, including the commonly used virial estimator, have extremely large variances that require untenably long simulation times to generate converged averages. In this paper, low-variance estimators for the internal energy are derived, in which the large zero-point energy of the oscillators does not contribute to the variance. The new estimators are applicable to any system of harmonic oscillators coupled to one another (or to the environment) via an arbitrary set of anharmonic interactions. The variance of the new estimators is found to be much smaller than standard estimators in three example problems, a one-dimensional anharmonic oscillator and quantum Drude models of the xenon dimer and solid (fcc) xenon, respectively, yielding 2–3 orders of magnitude improvement in computational efficiency.
Structures, energetics, and spectra of aqua-cesium (I) complexes: An ab initio and experimental study
Authors: Kołaski Maciej , Lee Han Myoung , Choi Young Cheol , Kim Kwang S. , Tarakeshwar P. , Miller Dorothy J. , Lisy James M.
Published: February 2007

The design of cesium-selective ionophores must include the nature of cesium-water interactions. The authors have carried out extensive ab initio and density functional theory calculations of hydrated cesium cations to obtain reasonably accurate energetics, thermodynamic quantities, and IR spectra. An extensive search was made to find the most stable structures. Since water⋯water interactions are important in the aqua-Cs+ clusters, the authors investigated the vibrational frequency shifts as a function of the number of water molecules and the frequency characteristics with and without the presence of outer-shell water molecules. The predicted vibrational frequencies were then compared with the infrared photodissociation spectra of argon-tagged hydrated cesium cluster ions. This comparison allowed the identification of specific hydrogen-bonding structures present in the experimental spectra.
Monte Carlo simulations of stress relaxation of entanglement-free Fraenkel chains. I. Linear polymer viscoelasticity
Authors: Lin Y.-H. , Das A. K.
Published: February 2007

Shear stress relaxation modulus GS(t) curves of entanglement-free Fraenkel chains have been calculated using Monte Carlo simulations based on the Langevin equation, carrying out both in the equilibrium state and following the application of a step shear deformation. While the fluctuation-dissipation theorem is perfectly demonstrated in the Rouse-chain model, a quasiversion of the fluctuation-dissipation theorem is observed in the Fraenkel-chain model. In both types of simulations on the Fraenkel-chain model, two distinct modes of dynamics emerge in GS(t), giving a line shape similar to that typically observed experimentally. Analyses show that the fast mode arises from the segment-tension fluctuations or reflects the relaxation of the segment tension created by segments being stretched by the applied step strain—an energetic-interactions-driven process—while the slow mode arises from the fluctuations in segmental orientation or represents the randomization of the segmental-orientation anisotropy induced by the step deformation—an entropy-driven process. Furthermore, it is demonstrated that the slow mode is well described by the Rouse theory in all aspects: the magnitude of modulus, the line shape of the relaxation curve, and the number-of-beads (N) dependence of the relaxation times. In other words, one Fraenkel segment substituting for one Rouse segment, it has been shown that the entropic-force constant on each segment is not a required element to give rise to the Rouse modes of motion, which describe the relaxation modulus of an entanglement-free polymer over the long-time region very well. This conclusion provides an explanation resolving a long-standing fundamental paradox in the success of Rouse-segment-based molecular theories for polymer viscoelasticity—namely, the paradox between the Rouse segment size being of the same order of magnitude as that of the Kuhn segment (each Fraenkel segment with a large force constant HF can be regarded as basically equivalent to a Kuhn segment) and the meaning of the Rouse segment as defined in the Rouse-chain model. The general agreement observed in the comparison of the simulation and experimental results indicates that the Fraenkel-chain model, while being still relatively simple, has captured the key element in energetic interactions—the rigidity on the segment—in a polymer system.
K
-leap method for accelerating stochastic simulation of coupled chemical reactions
Authors: Cai Xiaodong , Xu Zhouyi
Published: February 2007

Leap methods are very promising for accelerating stochastic simulation of a well stirred chemically reacting system, while providing acceptable simulation accuracy. In Gillespie’s τ-leap method [D. Gillespie, J. Phys. Chem. 115, 1716 (2001)], the number of firings of each reaction channel during a leap is a Poisson random variable, whose sample values are unbounded. This may cause large changes in the populations of certain molecular species during a leap, thereby violating the leap condition. In this paper, we develop an alternative leap method called the K-leap method, in which we constrain the total number of reactions occurring during a leap to be a number K calculated from the leap condition. As the number of firings of each reaction channel during a leap is upper bounded by a properly chosen number, our K-leap method can better satisfy the leap condition, thereby improving simulation accuracy. Since the exact stochastic simulation algorithm (SSA) is a special case of our K-leap method when K=1, our K-leap method can naturally change from the exact SSA to an approximate leap method during simulation, whenever the leap condition allows to do so.
Accelerating the replica exchange method through an efficient all-pairs exchange
Authors: Brenner Paul , Sweet Christopher R. , VonHandorf Dustin , Izaguirre Jesús A.
Published: February 2007

The authors accelerate the replica exchange method through an efficient all-pairs replica exchange. A proof of detailed balance is shown along with an analytical estimate of the enhanced exchange efficiency. The new method provides asymptotically four fold speedup of conformation traversal for replica counts of 8 and larger with typical exchange rates. Experimental tests using the blocked alanine dipeptide demonstrate the method’s correctness and show an approximate sampling efficiency improvement of 100% according to potential energy cumulative averages and an ergodic measure. An explicitly solvated PIN1 WW domain system of 4958 atoms is sampled using our new method, yielding a cluster sampling rate almost twice that of the single exchange near neighbor implementation. Computational software and scripts along with input and output data sets are available at http:∕∕www.nd.edu∕̃lcls∕APEREM.
Fragmentation in biaxial tension
Authors: Campbell Geoffrey H. , Archbold Gregory C. , Hurricane Omar A. , Miller Paul L.
Published: February 2007

We have carried out an experiment that places a ductile stainless steel in a state of biaxial tension at a high rate of strain. The loading of the ductile metal spherical cap is performed by the detonation of a high-explosive layer with a conforming geometry to expand the metal radially outwards. Simulations of the loading and expansion of the metal predict strain rates that compare well with experimental observations. A high percentage of the high explosives loaded material was recovered through a soft capture process, and characterization of the recovered fragments provided high- quality data, including uniform strain prior to failure and fragment size. These data were used with a modified fragmentation model to determine a fragmentation energy.
Ring-beam driven maser instability for quasiperpendicular shocks
Authors: Yoon Peter H. , Wang C. B. , Wu C. S.
Published: February 2007

The cyclotron maser instability is a well-known radiation emission mechanism responsible for radio emissions in magnetized planets and for laboratory microwave generation devices. The present paper discusses mechanisms and properties of cyclotron maser instability driven by a ring-beam distribution of energetic electrons with application to the quasiperpendicular collisionless shock. It is shown that the fast extraordinary and ordinary electromagnetic waves as well as slow upper-hybrid Z-mode are excited over a wide range of physical parameters. The implications of the present findings for actual applications including the coronal type II radio source are also discussed.
Demixing instability in coil-rod blends undergoing polycondensation reactions
Authors: Teixeira P. I. C. , Read D. J. , McLeish T. C. B.
Published: February 2007

The authors extend their earlier work on the stability of a reacting binary polymer blend with respect to demixing [D. J. Read, Macromolecules 31, 899 (1998); P. I. C. Teixeira et al., Macromolecules 33, 387 (2000)] to the case where one of the polymers is rod-like and may order nematically. As before, the authors combine the random phase approximation for the free energy with a Markov chain model for the chemistry to obtain the spinodal as a function of the relevant degrees of reaction. These are then calculated by assuming a simple second-order chemical kinetics. Results are presented, for linear systems, which illustrate the effects of varying the proportion of coils and rods, their relative sizes, and the strength of the nematic interaction between the rods.
The similarity of shock waves generated by a cone-shaped plasma and by a solid cone in a supersonic airflow
Authors: Kuo Spencer P. , Bivolaru Daniel
Published: February 2007

A truncated 60° cone with a slender central spike, which protrudes to the tip location of a perfect cone, is designed as a wind tunnel model. It generates a bow shock in a supersonic airflow. This model is featured with an on-board discharge arrangement with the central spike and the truncated cone as two electrodes. When the central electrode is designated as the cathode, a dc pulsed discharge produces a hollow cone-shaped plasma that envelops the spike. The results show that this plasma has changed the original bow shock to a conical shock, equivalent to reinstating the model into a perfect cone and to generate a 70% increase in the body aspect ratio. A significant drag reduction in each discharge is inferred from the pressure measurements; at the discharge maximum, the pressure on the frontal surface of the body decreases by more than 30%, the pressure on the cone surface increases by about 5%, while the pressure on the cylinder surface remains unchanged. The energy loss due to wave drag is reduced to make up for the two-thirds of the energy consumed in the electric discharge for plasma generation. The measurements also show that the plasma effect on shock structure lasts much longer than the discharge period.
Partial degeneracy effects in the stopping of relativistic electrons in supercompressed thermonuclear fuels
Authors: Starikov Konstantin V. , Deutsch Claude
Published: February 2007

The effects of supercompressed and partially degenerate electron fluid on projectile energy loss of laser produced relativistic electron beams (REBs) in the MeV range are investigated. Partial degeneracy is shown to affect significantly the REB stopping power for 0.2≤θ=T∕TF≤1 while its variations with beam energy appear much less θ dependent. The latter exhibit a characteristic V-like shape for any target electron density, and θ values.
Spherical silicon-shell photonic band gap structures fabricated by laser-assisted chemical vapor deposition
Authors: Wang H. , Yang Z. Y. , Lu Y. F.
Published: February 2007

Laser-assisted chemical vapor deposition was applied in fabricating three-dimensional (3D) spherical-shell photonic band gap (PBG) structures by depositing silicon shells covering silica particles, which had been self-assembled into 3D colloidal crystals. The colloidal crystals of self-assembled silica particles were formed on silicon substrates using the isothermal heating evaporation approach. A continuous wave Nd:YAG laser (1064nm wavelength) was used to deposit silicon shells by thermally decomposing disilane gas. Periodic silicon-shell∕silica-particle PBG structures were obtained. By removing the silica particles enclosed in the silicon shells using hydrofluoric acid, hollow spherical silicon-shell arrays were produced. This technique is capable of fabricating structures with complete photonic band gaps, which is predicted by simulations with the plane wave method. The techniques developed in this study have the potential to flexibly engineer the positions of the PBGs by varying both the silica particle size and the silicon-shell thickness. Ellipsometry was used to investigate the specific photonic band gaps for both structures.
Challenges in Evaluating Models of Geographic Complexity
Authors: Manson Steven M
Published: February 2007

Geographic complexity—the explicit integration of complexity research with space and place-based research—faces interrelated methodological, conceptual, and policy challenges. The rubric of model evaluation is central both to understanding and to meeting these challenges. They include methodological issues such as sensitivity and complex scaling; the conceptual challenges of conflating pattern and process, and reconciling simplicity and complexity; and policy issues posed by the science–policy gap and postnormal science. The importance of these challenges and the centrality of model evaluation in meeting them are demonstrated through examples drawn from human-environment systems, with particular reference to global environmental change and land-use and land-cover change. Specific model-evaluation strategies are also offered.
Assessing Multiagent Parcelization Performance in the MABEL Simulation Model Using Monte Carlo Replication Experiments
Authors: Alexandridis Konstantinos , Pijanowski Bryan C
Published: February 2007

In this paper we present and test the functionality of a parcelization algorithm, implemented in our spatially explicit, agent-based land-use-change model which we call the Multi Agent-based Behavioral Economic Landscape (MABEL) model. In order to test the best possible spatial configuration of the algorithm and its efficiency compared with historically observed land-use changes, we employed a Monte Carlo simulation approach with a series of replication experiments across time, and compared observed changes between 1970 and 1990, and across two different landscapes in Michigan, USA. We compare the simulated parcel shapes with historically observed land-use changes using the landscape-ecology metric program, FRAGSTATS.
Aquatic macroinvertebrate communities on wood in an Australian lowland river: experimental assessment of the interactions of habitat, substrate complexity and retained organic matter
Authors: Scealy J. A. , Mika S. J. , Boulton A. J.
Published: February 2007

Since European settlement, vast amounts of wood have been removed from Australian rivers. In recognition of its ecological value, including as habitat for aquatic invertebrates, wood is being reintroduced but with little understanding of optimum placement (pools v. riffles) or structural complexity to enhance invertebrate diversity. We hypothesised that complex woody debris would support higher numbers and more macroinvertebrate taxa, especially in riffles. Wood substrates of two complexities but similar surface areas were introduced into pools and riffles at three sites along the Hunter River, Australia. After 30 days, more taxa and individuals occurred on the complex substrates in pools and riffles at all sites. Substrates in riffles usually supported more taxa and individuals but responses were site-specific. Community composition varied among sites, substrates and habitats. Complex substrates, especially in riffles, trapped drifting organic matter that increased abundance and taxa richness but did not alter overall trends among substrates or habitats within sites. However, densities of rheophilic (flow-loving) taxa were reduced by entrained organic matter. Our results indicated that complex woody debris introduced into riffles could enhance diversity and abundance of macroinvertebrates in the Hunter River. However, these conclusions from a short-term, small-scale experiment need validation from longer-term, large-scale river rehabilitation projects.
Potential population and economic consequences of sublethal injuries in the spiny lobster fishery of the Florida Keys
Authors: Parsons D. M. , Eggleston D. B.
Published: February 2007

Animals that interact with but are not retained by fishing gears may later die. The population and economic consequences of these sublethal fishery interactions are seldom known but may be significant. In the present study, a population model was used to quantify potential population and economic consequences of injuries that Caribbean spiny lobsters (Panulirus argus) sustain from fishing activities in the Florida Keys, USA. Injuries generated by the fishery are known to reduce growth and elevate mortality. Simulation modelling results indicated that injuries may reduce adult lobster abundance and associated landings by ≥50% in areas with high recreational fishing effort. When simulated injuries were ~20 times lower (representing areas with lower fishing effort), these injuries were only responsible for a 5 and 8% reduction in the adult lobster population and commercial landings respectively. Important parameters within the model (growth, time in stage and mortality of injured lobsters) were altered by ±10% to assess model sensitivity. Final results changed <10% (with the exception of one 15% change), suggesting that model output was relatively insensitive to variation in key parameters. When the impact of sublethal injuries was applied to the entire spiny lobster fishery in the Florida Keys, adult stock biomass and annual commercial landings were reduced by 900 and 160 t (US$1.6 million) respectively. These results suggest that sublethal fishery interactions can lead to high population and economic losses, and highlight the need to incorporate sublethal injuries into stock assessments and economic models.
Polychaete trunk neuroectoderm converges and extends by mediolateral cell intercalation
Authors: Steinmetz Patrick R. H. , Zelada-Gonzáles Fabiola , Burgtorf Carola , Wittbrodt Joachim , Arendt Detlev
Published: February 2007

During frog and fish development, convergent extension movements transform the spherical gastrula into an elongated neurula. Such transformation of a ball- into a worm-shaped embryo is an ancestral and fundamental feature of bilaterian development, yet this is modified or absent in the protostome model organisms
Caenorhabditis
or
Drosophila
. In the polychaete annelid
Platynereis dumerilii
, early embryonic and larval stages resemble a sphere that subsequently elongates into worm shape. Cellular and molecular mechanisms of polychaete body elongation are yet unknown. Our
in vivo
time-lapse analysis of
Platynereis
axis elongation reveals that the polychaete neuroectoderm converges and extends by mediolateral cell intercalation. This occurs on both sides of the neural midline, the line of fusion of the slit-like blastopore. Convergent extension moves apart mouth and anus that are both derived from the blastopore. Tissue elongation is actin-dependent but microtubule-independent. Dependence on JNK activity and spatially restricted expression of
strabismus
indicates involvement of the noncanonical Wnt pathway. We detect a morphogenetic boundary between the converging and extending trunk neuroectoderm and the anterior
otx
-expressing head neuroectoderm that does not elongate. Our comparative analysis uncovers striking similarities but also differences between convergent extension in the polychaete and in the frog (the classical vertebrate model for convergent extension). Based on these findings, we propose that convergent extension movements of the trunk neuroectoderm represent an ancestral feature of bilaterian development that triggered the separation of mouth and anus along the elongating trunk.
Ultrafast dynamics of protein collapse from single-molecule photon statistics
Authors: Nettels Daniel , Gopich Irina V. , Hoffmann Armin , Schuler Benjamin
Published: February 2007

We use the statistics of photon emission from single molecules to probe the ultrafast dynamics of an unfolded protein via Förster resonance energy transfer. Global reconfiguration of the chain occurs on a time scale of ≈50 ns and slows down concomitant with chain collapse under folding conditions. These diffusive dynamics provide a missing link between the phenomenological chemical kinetics commonly used in protein folding and a physical description in terms of quantitative free energy surfaces. The experiments demonstrate the potential of single-molecule methods in accessing the biologically important nanosecond time scales even in heterogeneous populations.
Establishing the entatic state in folding metallated
Pseudomonas aeruginosa
azurin
Authors: Zong Chenghang , Wilson Corey J. , Shen Tongye , Wittung-Stafshede Pernilla , Mayo Steven L. , Wolynes Peter G.
Published: February 2007

Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting this issue are provided by electron transfer proteins. The environment provided by the folded protein to the cofactor tunes the metal's electron transport capabilities as envisioned in the entatic hypothesis. To see how the entatic state is achieved one must study how the folding landscape affects and in turn is affected by the metal. Here, we develop a coarse-grained functional to explicitly model how the coordination of the metal (which results in a so-called entatic or rack-induced state) modifies the folding of the metallated
Pseudomonas aeruginosa
azurin. Our free-energy functional-based approach directly yields the proper nonlinear extra-thermodynamic free energy relationships for the kinetics of folding the wild type and several point-mutated variants of the metallated protein. The results agree quite well with corresponding laboratory experiments. Moreover, our modified free-energy functional provides a sufficient level of detail to explicitly model how the geometric entatic state of the metal modifies the dynamic folding nucleus of azurin.
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
Authors: Hey Jody , Nielsen Rasmus
Published: February 2007

In 1988, Felsenstein described a framework for assessing the likelihood of a genetic data set in which all of the possible genealogical histories of the data are considered, each in proportion to their probability. Although not analytically solvable, several approaches, including Markov chain Monte Carlo methods, have been developed to find approximate solutions. Here, we describe an approach in which Markov chain Monte Carlo simulations are used to integrate over the space of genealogies, whereas other parameters are integrated out analytically. The result is an approximation to the full joint posterior density of the model parameters. For many purposes, this function can be treated as a likelihood, thereby permitting likelihood-based analyses, including likelihood ratio tests of nested models. Several examples, including an application to the divergence of chimpanzee subspecies, are provided.
Protein kinase A activates protein phosphatase 2A by phosphorylation of the B56δ subunit
Authors: Ahn Jung-Hyuck , McAvoy Thomas , Rakhilin Sergey V. , Nishi Akinori , Greengard Paul , Nairn Angus C.
Published: February 2007

Our previous studies of DARPP-32 in striatal slices have shown that activation of D1 receptors leads to cAMP-dependent dephosphorylation of Thr-75, the Cdk5 site in DARPP-32. In the current study, we have elucidated a mechanism whereby protein phosphatase 2A (PP2A) is activated by a cAMP/PKA-dependent pathway, leading to dephosphorylation of Thr-75. PP2A consists of a catalytic C subunit that associates with the scaffolding A subunit and a variety of B subunits. We have found that the A/C subunits of PP2A, in association with the B56δ (or PPP2R5D) regulatory subunit, is an active DARPP-32 phosphatase. The B56δ subunit expressed in HEK293 cells forms a heterotrimeric assembly that catalyzes PKA-mediated dephosphorylation at Thr-75 in DARPP-32 (also cotransfected into HEK293 cells). The B56δ subunit is phosphorylated by PKA, and this increases the overall activity of PP2A
in vitro
and
in vivo
. Among four PKA-phosphorylation sites identified in B56δ
in vitro
, Ser-566 was found to be critical for the regulation of PP2A activity. Moreover, Ser-566 was phosphorylated by PKA in response to activation of D1 receptors in striatal slices. Based on these studies, we propose that the B56δ/A/C PP2A complex regulates the dephosphorylation of DARPP-32 at Thr-75, thereby helping coordinate the efficacy of dopaminergic neurotransmission in striatal neurons. Moreover, stimulation of protein phosphatase activity by this mechanism may represent an important signaling pathway regulated by cAMP in neurons and other types of cell.
Shugoshin 2 Regulates Localization of the Chromosomal Passenger Proteins in Fission Yeast Mitosis
Authors: Vanoosthuyse Vincent , Prykhozhij Sergey , Hardwick Kevin G.
Published: February 2007

Fission yeast has two members of the Shugoshin family, Sgo1 and Sgo2. Although Sgo1 has clearly been established as a protector of centromere cohesion in meiosis I, the roles of Sgo2 remain elusive. Here we show that Sgo2 is required to ensure proper chromosome biorientation upon recovery from a prolonged spindle checkpoint arrest. Consistent with this, Sgo2 is essential for maintaining the Passenger proteins on centromeres upon checkpoint activation. Interestingly, lack of Sgo2 has a more penetrant effect on the localization of Survivin than on the two other Passenger proteins INCENP and Aurora B, and the Survivin-INCENP complex but not the INCENP-Aurora B complex is destabilized in the absence of Sgo2. Finally we show that the conserved C-terminus of Sgo2 is crucial to maintain Sgo2 and Passenger proteins localization on centromeres upon prolonged checkpoint activation. Taken together, our results demonstrate that Sgo2 is important for chromosome biorientation and that it controls docking of the Passenger proteins on chromosomes in early mitotic cells.
HomologMiner: looking for homologous genomic groups in whole genomes
Authors: Hou Minmei , Berman Piotr , Hsu Chih-Hao , Harris Robert S.
Published: February 2007

Motivation: Complex genomes contain numerous repeated sequences, and genomic duplication is believed to be a main evolutionary mechanism to obtain new functions. Several tools are available for de novo repeat sequence identification, and many approaches exist for clustering homologous protein sequences. We present an efficient new approach to identify and cluster homologous DNA sequences with high accuracy at the level of whole genomes, excluding low-complexity repeats, tandem repeats and annotated interspersed repeats. We also determine the boundaries of each group member so that it closely represents a biological unit, e.g. a complete gene, or a partial gene coding a protein domain.

Results: We developed a program called HomologMiner to identify homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats. We applied it to the whole genomes of human (hg17), macaque (rheMac2) and mouse (mm8). Groups obtained include gene families (e.g. olfactory receptor gene family, zinc finger families), unannotated interspersed repeats and additional homologous groups that resulted from recent segmental duplications. Our program incorporates several new methods: a new abstract definition of consistent duplicate units, a new criterion to remove moderately frequent tandem repeats, and new algorithmic techniques. We also provide preliminary analysis of the output on the three genomes mentioned above, and show several applications including identifying boundaries of tandem gene clusters and novel interspersed repeat families.

Availability: All programs and datasets are downloadable from www.bx.psu.edu/miller_lab

Contact:  mhou@cse.psu.edu
A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies
Authors: Tregouet D. A. , Garelle V.
Published: February 2007

Summary: THESIAS (Testing Haplotype EffectS In Association Studies) is a popular software for carrying haplotype association analysis in unrelated individuals. In addition to the command line interface, a graphical JAVA interface is now proposed allowing one to run THESIAS in a user-friendly manner. Besides, new functionalities have been added to THESIAS including the possibility to analyze polychotomous phenotype and X-linked polymorphisms.

Availability: The software package including documentation and example data files is freely available at http://genecanvas.ecgene.net. The source codes are also available upon request.

Contact:  david.tregouet@chups.jussieu.fr
Postoperative Cognitive Dysfunction in Older Patients with a History of Alcohol Abuse
Authors: Hudetz Judith A. , Iqbal Zafar , Gandhi Sweeta D. , Patterson Kathleen M. , Hyde Trevor F. , Reddy Diane M. , Hudetz Anthony G. , Warltier David C.
Published: February 2007

Background

Postoperative cognitive dysfunction (POCD) affects a significant number of patients and may have serious consequences for quality of life. Although POCD is most frequent after cardiac surgery, the prevalence of POCD after noncardiac surgery in older patients is also significant. The risk factors for POCD after noncardiac surgery include advanced age and preexisting cognitive impairment. Self-reported alcohol abuse is a risk factor for postoperative delirium, but its significance for long-term POCD has not been investigated. The goal of this study was to determine whether neurocognitive function is impaired after noncardiac surgery during general anesthesia in older patients with a history of alcohol abuse.

Methods

Subjects aged 55 yr and older with self-reported alcohol abuse (n = 28) and age-, sex-, education-matched nonalcoholic controls (n = 28) were tested using a neurocognitive battery before and 2 weeks after elective surgery (n = 28) or a corresponding time interval without surgery (n = 28). Verbal memory, visuospatial memory, and executive functions were assessed. A neurologic examination was performed to exclude subjects with potential cerebrovascular damage.

Results

Significant three-way interactions (analysis of variance) for Visual Immediate Recall, Visual Delayed Recall, Semantic Fluency, Phonemic Fluency, and the Color-Word Stroop Test implied that cognitive performance in the alcoholic group decreased after surgery more than it did in the other three groups.

Conclusions

The results suggest that a history of alcohol abuse in older patients presents a risk for postoperative cognitive impairment in the domains of visuospatial abilities and executive functions that may have important implications for quality of life and health risks.
Postoperative Impairment of Cognitive Function in Rats
Authors: Wan Yanjie , Xu Jing , Ma Daqing , Zeng Yinming , Cibelli Mario , Maze Mervyn
Published: February 2007

Background

Postoperative cognitive dysfunction is being increasingly reported as a complication. The authors investigated the role of cytokine-mediated inflammation within the central nervous system in the development of cognitive dysfunction in a rat model.

Methods

Adult rats were subjected to neuroleptic anesthesia (20 microg/kg fentanyl plus 500 microg/kg droperidol, intraperitoneal) for splenectomy or no surgery. On postanesthetic days 1, 3, and 7, cognitive function was assessed in a Y maze. To evaluate the immune response in the hippocampus, the authors measured glial activation, as well as transcription and expression of key proinflammatory cytokines interleukin 1beta and tumor necrosis factor alpha. To determine propensity for apoptosis, they measured expression of Bax and Bcl-2.

Results

Cognitive function in splenectomized animals was impaired at days 1 and 3 after surgery compared with cognitive function in nonanesthetized rats. At all times, anesthetized rats that were not subjected to surgery were no different from control rats. Glial activation was observed in the hippocampus only in splenectomized rats at postsurgery days 1 and 3. Interleukin-1beta messenger RNA (mRNA) was significantly increased at postsurgery days 1 and 3, with an increase in protein expression detected on day 1. There was a significant increase in tumor necrosis factor-alpha mRNA on day 1 after surgery, although this was not associated with an increase in protein expression. The ratio of Bcl-2:Bax was significantly decreased in the splenectomized animals.

Conclusion

These results suggest that splenectomy performed during neuroleptic anesthesia triggers a cognitive decline that is associated with a hippocampal inflammatory response that seems to be due to proinflammatory cytokine-dependent activation of glial cells.
Multicenter Randomized Comparison of Xenon and Isoflurane on Left Ventricular Function in Patients Undergoing Elective Surgery
Authors: Wappler Frank , Rossaint Rolf , Baumert Jan , Scholz Jens , Tonner Peter H. , van Aken Hugo , Berendes Elmar , Klein Jan , Gommers Diederik , Hammerle Alfons , Franke Andreas , Hofmann Thomas , Schulte am Esch Jochen
Published: February 2007

Background

Volatile anesthetics are commonly used for general anesthesia. However, these can induce profound cardiovascular alterations. Xenon is a noble gas with potent anesthetic and analgesic properties. However, it is uncertain whether xenon alters myocardial function. The aim of this study was therefore to investigate left ventricular function during anesthesia with xenon compared with isoflurane.

Methods

The authors performed a randomized multicenter trial to compare xenon with isoflurane with respect to cardiovascular stability and adverse effects in patients without cardiac diseases scheduled for elective surgery. Two hundred fifty-nine patients were enrolled in this trial, of which 252 completed the study according to the protocol. Patients were anesthetized with xenon or isoflurane, respectively. Before administration of the study drugs and at four time points, the effects of both anesthetics on left ventricular function were investigated using transesophageal echocardiography.

Results

Global hemodynamic parameters were significantly altered using isoflurane (P < 0.05 vs. baseline), whereas xenon only decreased heart rate (P < 0.05 vs. baseline). In contrast to xenon, left ventricular end-systolic wall stress decreased significantly in the isoflurane group (P < 0.05 vs. baseline). Velocity of circumferential fiber shortening was decreased significantly in the xenon group but showed a more pronounced reduction during isoflurane administration (P < 0.05 vs. baseline). The contractile index (difference between expected and actually measured velocity of circumferential fiber shortening) as an independent parameter for left ventricular function was significantly decreased after isoflurane (P < 0.0001) but unchanged using xenon.

Conclusions

Xenon did not reduce contractility, whereas isoflurane decreased the contractile index, indicating that xenon enables favorable cardiovascular stability in patients without cardiac diseases.
Fluorescence Dilution Technique for Measurement of Cardiac Output and Circulating Blood Volume in Healthy Human Subjects
Authors: Maarek Jean-Michel I. , Holschneider Daniel P. , Rubinstein Eduardo H.
Published: February 2007

Background

The authors previously validated in an animal model a new indicator dilution technique for measuring cardiac output and circulating blood volume by recording transcutaneously the fluorescence of circulating indocyanine green with an optical probe placed on the skin surface. The current study compared fluorescence dilution recordings recorded from several locations on the human face in terms of signal intensity and stability and estimated the subjects' cardiac output and circulating blood volume from the recordings.

Methods

Fluorescence dilution traces were recorded transcutaneously in six healthy human volunteers after rapid intravenous injection of 1 mg indocyanine green. Three placements of the optical probe were tested: the nose ala, the ear lobe, and the temple area. In three subjects, the recordings were calibrated in terms of circulating indocyanine green concentration to estimate cardiac output and circulating blood volume.

Results

Fluorescence dilution traces had the same duration for the three locations, but the recordings obtained from the nose ala and the ear lobe were twice as intense as those from the temple. The fluorescence intensity at each site was linearly related to the local laser Doppler perfusion index. The coefficient of variation for the area under the first pass curve (inversely proportional to cardiac output) was approximately 6% for triplicate measurements at the same location. Cardiac output and circulating blood volume derived from the fluorescence recordings were in the normal range.

Conclusions

The study demonstrates that intense and reproducible fluorescence dilution signals can be measured transcutaneously in healthy humans and could potentially be used to measure cardiac output and circulating blood volume minimally invasively.
Combined Spinal and General Anesthesia Attenuates Liver Metastasis by Preserving Th1/Th2 Cytokine Balance
Authors: Wada Hiroki , Seki Shuhji , Takahashi Tetsuya , Kawarabayashi Nobuaki , Higuchi Hideyuki , Habu Yoshiko , Sugahara Shinya , Kazama Tomiei
Published: February 2007

Background

Many studies have shown that regional anesthesia improves postoperative outcome and particularly lessens infection by attenuating perioperative immunosuppression related to the stress response to surgery and general anesthesia. However, it remains to be determined whether regional anesthesia improves oncologic outcome after surgery.

Methods

C57BL/6 mice were subjected to laparotomy during sevoflurane general anesthesia alone or combined with spinal block achieved with bupivacaine (5 microg) and morphine (1.25 microg). Control groups were anesthetized only or were untreated. Liver was removed 5 h after surgery to assess antitumor killer cell activity and production of interferon gamma and interleukin 4 by liver mononuclear cells, or mice were inoculated intravenously with liver-metastatic EL4 cells and hepatic metastases were counted 12 days later.

Results

Laparotomy during sevoflurane anesthesia significantly increased the number (+/- SD) of liver metastases from 15.5 +/- 8.7 (control) and 19.4 +/- 5.4 (sevoflurane alone) to 33.7 +/- 8.9. Sevoflurane anesthesia plus spinal block significantly reduced this increase to 19.8 +/- 9. The in vitro killer activity of liver mononuclear cells against EL4 cells decreased from 32.7% (control) and 29.4% (sevoflurane alone) to 18.5% after sevoflurane plus laparotomy, and the addition of spinal block increased activity to 26.6%. The interferon-gamma/interleukin-4 ratio decreased from 89.3 (control) and 95.7 (anesthesia alone) to 15.7 after sevoflurane plus laparotomy, and the addition of spinal block increased the ratio to 46.5.

Conclusions

The addition of spinal block to sevoflurane general anesthesia accompanying surgery attenuates the suppression of tumoricidal function of liver mononuclear cells, presumably by preserving the T helper 1/T helper 2 (Th1/Th2) balance, and thereby reduces the promotion of tumor metastasis.
Differential Effects of Etomidate and Midazolam on Vascular Adenosine Triphosphate–sensitive Potassium Channels
Authors: Nakamura Akiyo , Kawahito Shinji , Kawano Takashi , Nazari Hossein , Takahashi Akira , Kitahata Hiroshi , Nakaya Yutaka , Oshita Shuzo
Published: February 2007

Background

The aim of this study was to investigate the effects of two imidazoline-derived intravenous anesthetics, etomidate and midazolam, on vascular adenosine triphosphate-sensitive potassium (KATP) channel activity.

Methods

In isolated rat aorta, isometric tension was recorded to examine the anesthetic effects on vasodilator response to levcromakalim, a selective KATP channel opener. Using the patch clamp method, the anesthetic effects were also examined on the currents through (1) native vascular KATP channels, (2) recombinant KATP channels with different combinations of various types of inwardly rectifying potassium channel (Kir6.0 family: Kir6.1, 6.2) and sulfonylurea receptor (SUR1, 2A, 2B) subunits, (3) SUR-deficient channels derived from a truncated isoform of Kir6.2 subunit (Kir6.2DeltaC36 channels), and (4) mutant Kir6.2DeltaC36 channels with reduced sensitivity to adenosine triphosphate (Kir6.2DeltaC36-K185Q channels).

Results

Etomidate (> or = 10 m), but not midazolam (up to 10 m), inhibited the levcromakalim-induced vasodilation, which was sensitive to glibenclamide (IC50: 7.21 x 10 m; maximum inhibitory concentration: 1.22 x 10 m). Etomidate (> or = 3 x 10 m), but not midazolam (up to 10 m), inhibited the native KATP channel activity in both cell-attached and inside-out configurations with IC50 values of 1.68 x 10 m and 1.52 x 10 m, respectively. Etomidate (10 m) also inhibited the activity of various types of recombinant SUR/Kir6.0KATP channels, Kir6.2DeltaC36 channels, and Kir6.2DeltaC36-K185Q channels with equivalent potency.

Conclusions

Clinical concentrations of etomidate, but not midazolam, inhibit the KATP channel activity in vascular smooth muscle cells. The inhibition is presumably through its effects on the Kir6.0 subunit, but not on the SUR subunit, with the binding site different from adenosine triphosphate at the amino acid level.