bluuebunny/crossref_metadata_2025 huggingface dataset:
The Rising Pulse of the Atmosphere: Variability of the Global Atmospheric Circulation During the Past 100 Years; Monte Verit, Switzerland, 15–20 June 2008
Authors: Brönnimann Stefan , Ewen Tracy , Luterbacher Jürg
Published: December 2008

Understanding atmospheric circulation is fundamental not only to accurate weather prediction. Climate change leads to, proceeds through, and can be detected by changes in atmospheric circulation. Seasonal to interannual prediction means reproducing large‐scale circulation responses. Progress in assessing climate change effects and climate prediction requires documenting and modeling the past variability of atmospheric circulation—and stringently comparing models with observations. The past 100 years, which reflect a range of forcings (both natural and anthropogenic) and different variability timescales, are ideal for testing our understanding.
MAFALDA: An early warning modeling tool to forecast volcanic ash dispersal and deposition
Authors: Barsotti S. , Nannipieri L. , Neri A.
Published: December 2008

Forecasting the dispersal of ash from explosive volcanoes is a scientific challenge to modern volcanology. It also represents a fundamental step in mitigating the potential impact of volcanic ash on urban areas and transport routes near explosive volcanoes. To this end we developed a Web‐based early warning modeling tool named MAFALDA (Modeling and Forecasting Ash Loading and Dispersal in the Atmosphere) able to quantitatively forecast ash concentrations in the air and on the ground. The main features of MAFALDA are the usage of (1) a dispersal model, named VOL‐CALPUFF, that couples the column ascent phase with the ash cloud transport and (2) high‐resolution weather forecasting data, the capability to run and merge multiple scenarios, and the Web‐based structure of the procedure that makes it suitable as an early warning tool. MAFALDA produces plots for a detailed analysis of ash cloud dynamics and ground deposition, as well as synthetic 2‐D maps of areas potentially affected by dangerous concentrations of ash. A first application of MAFALDA to the long‐lasting weak plumes produced at Mt. Etna (Italy) is presented. A similar tool can be useful to civil protection authorities and volcanic observatories in reducing the impact of the eruptive events. MAFALDA can be accessed at http://mafalda.pi.ingv.it.
Depth variation of coseismic stress drop explains bimodal earthquake magnitude‐frequency distribution
Authors: Zielke O. , Arrowsmith J. R.
Published: December 2008

An essential part of seismic hazard analysis is the earthquake size‐frequency relationship, used to estimate earthquake recurrence time, and thus probability. A key feature of those distributions is their bimodal character: small to moderate magnitude earthquakes follow the Gutenberg‐Richter (GR) inverse power‐law relation while large magnitude (characteristic) earthquakes are more frequent than anticipated from GR, following approximately a gaussian distribution around the maximum magnitude limited by fault geometry. Using a numerical earthquake simulator, we show that the temperature dependence of friction behavior and therefore the depth‐variation of coseismic stress drop, derived from laboratory friction experiments, presents a simple and comprehensive explanation for the observed bimodal seismicity distribution. Characteristic earthquakes are the result of an abrupt increase in rupture width at the transition from small to large earthquakes.
Effect of bromine chemistry on the atmospheric mercury cycle
Authors: Seigneur Christian , Lohman Kristen
Published: December 2008

Bromine chemistry is believed to play a major role in the atmospheric oxidation of elemental mercury (Hg0) to divalent mercury (HgII). However, its effect on the speciation of atmospheric mercury (Hg) has been mostly ignored in models of the fate and transport of mercury. We investigate the effect of bromine chemistry on Hg speciation for various reaction kinetics and environmental conditions with a box model. Bromine chemistry was also added to the chemical mechanism of a global chemical transport model, and simulations of the global mercury cycle were conducted with different sets of bromine reaction kinetics. The global model simulations conducted with bromine chemistry lead to Hg0 concentrations that are consistent with observations only if the pressure dependence of the kinetics of the oxidation of Hg0 by Br is taken into account. Bromine chemistry is found to reduce the overall lifetime of Hg by about 10%.
Rock spectral classes observed by the Spirit Rover's Pancam on the Gusev Crater Plains and in the Columbia Hills
Authors: Farrand W. H. , Bell J. F. , Johnson J. R. , Arvidson R. E. , Crumpler L. S. , Hurowitz J. A. , Schröder C.
Published: December 2008

This paper examines the ferrous and ferric iron mineralogy of rocks inferred from 246 visible/near‐infrared (430–1010 nm) multispectral observations made by the Mars Exploration Rover Spirit's Pancam on its traverse from its landing site to its second Winter Haven location. Principal component, correspondence analyses, and a sequential maximum angle convex cone technique were used to identify 14 candidate classes. Spectra from the West Spur of Husband Hill and the Watchtower area had the highest 535 and 601 nm band depths indicating that these areas were more oxidized. Differences in the depth and band center of a near infrared (NIR) absorption feature were observed using 904 nm band depth and 803:904 nm ratio and parameters gauging the 754–864 and 754–1009 nm slopes. Spectra of rocks from the southern flank of Husband Hill had negative 754–1009 nm slopes and a broad NIR absorption consistent with high olivine abundances. Rocks observed on the lower West Spur, at the Cumberland Ridge locale, at the Husband Hill summit, and at the Haskin Ridge locale had deep 904 nm band depths and steep 754–864 nm slopes consistent with greater pyroxene abundances. These observations are consistent with results on iron‐bearing mineralogy from Spirit's Mössbauer spectrometer. Comparisons of these rock spectral classes with a set of terrestrial analog samples found similarities between the West Spur and Watchtower classes and red hematite‐bearing impact melts. Fewer similarities were found in comparisons of the Columbia Hills classes with basaltic hydrovolcanic tephras.
Estimating the uncertainty of hydrological forecasts: A statistical approach
Authors: Montanari Alberto , Grossi Giovanna
Published: December 2008

A method for quantifying the uncertainty of hydrological forecasts is proposed. This approach requires the identification and calibration of a statistical model for the forecast error. Accordingly, the probability distribution of the error itself is inferred through a multiple regression, depending on selected explanatory variables. These may include the current forecast issued by the hydrological model, the past forecast error, and the past rainfall. The final goal is to indirectly relate the forecast error to the sources of uncertainty in the forecasting procedure, through a probabilistic link with the explaining variables identified above. Statistical testing for the proposed approach is discussed in detail. An extensive application to a synthetic database is presented, along with a first real‐world implementation that refers to a real‐time flood forecasting system that is currently under development. The results indicate that the uncertainty estimates represent well the statistics of the actual forecast errors for the examined events.
Think locally: control of ubiquitin‐dependent protein degradation in neurons
Authors: Segref Alexandra , Hoppe Thorsten
Published: December 2008

The nervous system coordinates many aspects of body function such as learning, memory, behaviour and locomotion. Therefore, it must develop and maintain an intricate network of differentiated neuronal cells, which communicate efficiently with each other and with non‐neuronal target cells. Unlike most somatic cells, differentiated neurons are post‐mitotic and characterized by a highly polarized morphology that determines the flow of information. Among other post‐translational modifications, the ubiquitination of specific protein substrates was recently shown to have a crucial role in the regulation of neuronal development and differentiation. Here, we review recent findings that illustrate the mechanisms that mediate the temporal and spatial control of neuronal protein turnover by the ubiquitin–proteasome system (UPS), which is crucial for the development and function of the nervous system.
Pendent Drops at Elevated P & T
Authors: Georgiadis Apostolos , Maitland Geoffrey , Trusler Martin , Kazarian Sergei , Bismarck Alexander
Published: December 2008

Within the scope of producing clean fossil fuels by simultaneously tackling greenhouse gas emissions, the interfacial tension of partially miscible phases containing CO~2~ is being investigated with the pendant drop method. Emphasis is given to measurements at elevated pressures and temperatures, analogous to reservoir conditions. A high pressure apparatus consisting of a view cell and high pressure capillary fittings is used for creating pendent drops at the desired conditions. A computer aided Drop Shape Analysis system is used for capturing images of such drops, which are then analysed for the interfacial tension calculation of the two phases with the KRUSS DSA software. The results acquired from the initial measurements conducted for the H~2~O/CO~2~ system are presented in comparison with literature data.
The Physical and Social Environment in Kaiser Permanente’s Research Program in Genes, Environment and Health
Authors: Schaefer Catherine
Published: December 2008

Dr. Catherine Schaefer described Kaiser Permanente's Research Program on Genes, Environment and Health, which will be a large resource facilitating further studies analyzing the influence of genes and the environment. She described both the goals and the processes of the program in detail.To watch Dr. Schaefer’s presentation, please see the Panel 3 "Google Video posting.":http://video.google.com/videoplay?docid=-7775076897136846879&hl=en Panel 3 also features a presentation by Dr. Atul Butte of Stanford University on “Linking the Genome and Envirome.”
Gene-Environment Interaction: Definitions and Study Designs
Authors: Ottman Ruth
Published: December 2008

Dr. Ruth Ottman first discussed different models of gene-environment interactions and then delved into designs of studies attempting to elucidate such interactions. She stressed the importance of using the correct measurement scale, whether additive or multiplicative, noting that the additive measurement scale is more consistent with biological models. Dr. Ottman concluded by reminding the audience of the need for very large sample sizes, and thus collaboration, in gene-environment interaction studies. To watch Dr. Ottman’s presentation, please see the Panel 2 "Google Video posting.":http://video.google.com/videoplay?docid=-8804321603731619003&hl=en
The Undertheorized Environment: Sociological Insights for Behavioral Genetics
Authors: Perrin Andrew
Published: December 2008

Dr. Andrew Perrin discussed the ontological claims and social theory which run beneath ideas of genetic causation of behavioral traits. He outlined five criteria for evaluating and conceptualizing the environment within genetic studies. He concluded by emphasizing complexity and describing gene-environment interaction chains.

To watch Dr. Perrin’s presentation, please see the Panel 2 “Google Video posting.”:http://video.google.com/videoplay?docid=-8804321603731619003&hl=en
The Costs and Benefits of Lousy Measures of the Environment
Authors: Turkheimer Eric
Published: December 2008

Dr. Eric Turkheimer focused on the nonshared environment project and pointed to the nonshared environment and its components as the central problem of human scientific psychology. He described three causal models, applying them to each genetic and environmental causation, and concluded that rough measurements lead to detectable causations, but more precise measurements make the effects harder to detect. To watch Dr. Turkheimer’s presentation, please see the Panel 2 "Google Video posting.":http://video.google.com/videoplay?docid=-8804321603731619003&hl=en
Perspectives on Gene-Environment Interplay in Psychiatry
Authors: Rutter Michael
Published: December 2008

Sir Michael Rutter began the symposium with a broad overview of gene-environment interplay.He described the goals of studying such interactions and pointed to the inherent challenges. He concluded by stressing the need for a variety of strategies for research. To watch Sir Rutter’s presentation, please see the Panel 1 "Google Video posting.":http://video.google.com/videoplay?docid=-3097337289947323438&hl=en Panel 1 also features welcoming remarks by Dr. Mildred Cho and Professor Hank Greely, both of Stanford University.
Neutralization of endomembrane compartments in epithelial MDCK cells affects proteoglycan synthesis in the apical secretory pathway
Authors: Grøndahl Frøy , Tveit Heidi , Prydz Kristian
Published: December 2008

PGs (proteoglycans) are proteins acquiring long, linear and sulfated GAG (glycosaminoglycan) chains during Golgi passage. In MDCK cells (Madin–Darby canine kidney cells), most of the CS (chondroitin sulfate) PGs are secreted apically, whereas most of the HS (heparan sulfate) PGs are secreted basolaterally. The apical and basolateral secretory routes differ in their GAG synthesis, since a protein core that traverses both routes acquires shorter chains, but more sulfate, in the basolateral pathway than in the apical counterpart [Tveit, Dick, Skibeli and Prydz (2005) J. Biol. Chem. 280, 29596–29603]. Golgi cisternae and the trans-Golgi network have slightly acidic lumens. We therefore investigated how neutralization of endomembrane compartments with the vacuolar H+-ATPase inhibitor Baf A1 (bafilomycin A1) affected GAG synthesis and PG sorting in MDCK cells. Baf A1 induced a slight reduction in basolateral secretion of macromolecules, which was compensated by an apical increase. More dramatic changes occurred to PG synthesis in the apical pathway on neutralization. The difference in apical and basolateral PG sulfation levels observed for control cells was abolished, due to enhanced sulfation of apical CS-GAGs. In addition, a large fraction of apical HS-GAGs was elongated to longer chain lengths. The differential sensitivity of the apical and basolateral secretory pathways to Baf A1 indicates that the apical pathway is more acidic than the basolateral counterpart in untreated MDCK cells. Neutralization gave an apical GAG output that was more similar to that of the basolateral pathway, suggesting that neutralization made the luminal environments of the two pathways more similar.
The SR protein family of splicing factors: master regulators of gene expression
Authors: Long Jennifer C. , Caceres Javier F.
Published: December 2008

The SR protein family comprises a number of phylogenetically conserved and structurally related proteins with a characteristic domain rich in arginine and serine residues, known as the RS domain. They play significant roles in constitutive pre-mRNA splicing and are also important regulators of alternative splicing. In addition they participate in post-splicing activities, such as mRNA nuclear export, nonsense-mediated mRNA decay and mRNA translation. These wide-ranging roles of SR proteins highlight their importance as pivotal regulators of mRNA metabolism, and if these functions are disrupted, developmental defects or disease may result. Furthermore, animal models have shown a highly specific, non-redundant role for individual SR proteins in the regulation of developmental processes. Here, we will review the current literature to demonstrate how SR proteins are emerging as one of the master regulators of gene expression.
Signal transduction by vascular endothelial growth factor receptors
Authors: Claesson-Welsh L.
Published: December 2008

Vascular endothelial growth factor (VEGF)/vascular permeability factor is the prototype for a growing family of dimeric growth factors, which exert their effects on vascular and lymphatic endothelial cells, as well as on a wide range of other cell types. Gene targeting shows that most, if not all, of the factors and receptors in this family serve critical functions during vascular development or in adult physiological and pathological angiogenesis. Growing tumours produce VEGF, and many different strategies for inhibiting tumour growth by inhibiting VEGF production are being tested in clinical trials at present. This review focuses on the signal transduction properties of VEGF receptor-1 and VEGF receptor-2.
Agonist binding to peptide hormone receptors
Authors: Wheatley M. , Hawtin S.R. , Wesley V.J. , Howard H.C. , Simms J. , Miles A. , McEwan K. , Parslow R.A.
Published: December 2008

A fundamental issue in molecular pharmacology is to define how agonist–receptor interaction differs from that of antagonist–receptor interaction. The V1a vasopressin receptor (V1aR) is a member of a family of related G-protein-coupled receptors (GPCRs) that are activated by vasopressin, oxytocin (OT) and related peptides. A segment of the N-terminus that was required for agonist binding, but not antagonist binding, was identified by characterizing truncated V1aR constructs. Site-directed mutagenesis revealed that a single residue (Arg46) was critical for agonist binding and receptor activation. The N-terminus of the related OT receptor (OTR) could recover agonist binding in a chimaeric OTRN–V1aR construct. Furthermore, Arg34 of the human OTR, which corresponds to Arg46 of the rat V1aR, provided agonist-specific binding epitopes in the OTR, indicating a conserved function of this locus throughout this GPCR subfamily. Mutation of Arg46 revealed that high-affinity agonist binding had an absolute requirement for arginine at this position.
The complex matter of DNA double-strand break detection
Authors: Bradbury J.M. , Jackson S.P.
Published: December 2008

To maintain genomic stability, despite constant exposure to agents that damage DNA, eukaryotic cells have developed elaborate and highly conserved pathways of DNA damage sensing, signalling and repair. In this review, we concentrate mainly on what we know about DNA damage sensing with particular reference to Lcd1p, a yeast protein that functions early in DNA damage signalling, and MDC1 (mediator of DNA damage checkpoint 1), a recently identified human protein that may be involved in recruiting the MRE11 complex to radiation-induced nuclear foci. We describe a model for the DNA damage response in which factors are recruited sequentially to sites of DNA damage to form complexes that can amplify the original signal and propagate it to the multitude of response pathways necessary for genome stability.
Cross-coupling between the oestrogen receptor and phosphoinositide 3-kinase
Authors: Liao J.K.
Published: December 2008

Gender differences in cardiovascular mortality are well documented and oestrogen replacement therapy in post-menopausal women is associated with improved outcomes from cardiovascular events. Indeed, oestrogen therapy has been shown to restore endothelial function in post-menopausal women and reduce the development of atherosclerotic lesions. Despite extensive evidence on the beneficial effect of oestrogen, relatively little is known regarding the molecular signalling mechanism(s) by which oestrogen exerts some of its vascular effects. While the nuclear function of the oestrogen receptor is clearly established, previous studies regarding the membrane and cytoplasmic actions of oestrogen remain inconclusive. Cross-coupling of the oestrogen receptor to phosphoinositide 3-kinase signalling suggests a potentially critical non-nuclear action of the oestrogen receptor and considerably broadens our understanding of the cellular effects of oestrogen.
A-kinase-anchoring proteins and cytoskeletal signalling events
Authors: Scott J.D.
Published: December 2008

Targeting of protein kinases and phosphatases to the cytoskeleton enhances the regulation of many signalling events. Cytoskeletal signalling complexes facilitate this process by optimizing the relay of messages from membrane receptors to specific sites on the actin cytoskeleton. These signals influence fundamental cell properties such as shape, movement and division. Targeting of the cAMP-dependent kinase (protein kinase A) and other enzymes to this compartment is achieved through interaction with A-kinase-anchoring proteins (AKAPs). The present paper discusses recent progress on dissecting the biological role of WAVE1 (Wiskott–Alrich syndrome protein family verprolin homology protein 1), an AKAP that assembles a cytoskeletal transduction complex in response to signals that emanate from the low-molecular-mass GTPase, Rac.
Plant stress signalling: understanding and exploiting plant–plant interactions
Authors: Pickett J.A. , Rasmussen H.B. , Woodcock C.M. , Matthes M. , Napier J.A.
Published: December 2008

When plants are attacked by insects, volatile chemical signals can be released, not only from the damaged parts, but also systemically from other parts of the plant and this continues after cessation of feeding by the insect. These signals are perceived by olfactory sensory mechanisms in both the herbivorous insects and their parasites. Molecular structures involved can be characterized by means of electrophysiological assays, using the insect sensory system linked to chemical analysis. Evidence is mounting that such signals can also affect neighbouring intact plants, which initiate defence by the induction of further signalling systems, such as those that increase parasitoid foraging. Furthermore, insect electrophysiology can be used in the identification of plant compounds having effects on the plants themselves. It has been found recently that certain plants can release stress signals even when undamaged, and that these can cause defence responses in intact plants. These discoveries provide the basis for new crop protection strategies, that are either delivered by genetic modification of plants or by conventionally produced plants to which the signal is externally applied. Delivery can also be made by means of mixed seed strategies in which the provoking and recipient plants are grown together. Related signalling discoveries within the rhizosphere seem set to extend these approaches into new ways of controlling weeds, by exploiting the elusive potential of allelopathy, but through signalling rather than by direct physiological effects.
Towards an understanding of the pregnancy-blocking urinary chemosignals of mice
Authors: Brennan P.A. , Peele P.
Published: December 2008

Male mouse urine contains a pregnancy-blocking chemosignal that causes pre-implantation pregnancy failure in recently mated female mice. However, females are able to recognize the chemosignal of the male with which they mated, preventing it from aborting his own offspring. The individuality of the pregnancy-blocking chemosignal is influenced by genes of the major histocompatibility complex (MHC), although the chemical nature of the signal remains unclear. Possible candidates include fragments of MHC proteins, the highly polymorphic major urinary proteins (MUPs) and the profile of low-molecular-mass volatiles, which possess male pheromonal activity in other contexts. A recent study has found a high-molecular-mass fraction of male urine containing MUPs to be ineffective in eliciting pregnancy block. Moreover, both the pregnancy-blocking activity and the individuality of the signal were associated with the low-molecular-mass fraction of male urine.
Communication: from neurons to people; from present to future
Authors: Rose S.P.R.
Published: December 2008

From its emergence out of organic chemistry and physiology a century ago, the history of biochemistry is one of shifting research agendas. For organic chemists, the questions were those of structure and composition, while for physiologists, they were questions of function. The dynamic biochemistry of the mid-20th century centred on catalysis, energy flow and metabolism. The emergence of molecular biology (‘practising biochemistry without a licence’) introduced information in place of energy as an organizing cellular principle, but in doing so forgot dynamics. For Crick's Central Dogma, information – signals – flowed in one direction only. Now, proteomics is enabling molecular biologists to rediscover biochemistry once more. Signalling – the processes of communication across space and time – occurs at all biological levels. I will review them, and their potential future. Will the metaphor of signalling provide a new organizing principle, one that recognizes the essentially interactive nature of information flow within metabolic webs?: I discuss first, the conservation of signalling molecules at the cellular level over evolutionary time; secondly, the supracellular level of physiological signalling in multicellular organisms – hormones and neurons; thirdly, supraorganismic signalling and communication – from pheromones to speech; and finally, signalling and reception within and outside the biochemical community – how do we/can we communicate with one another and the rest of the world?
AMP-activated protein kinase, super metabolic regulator
Authors: Kemp B.E. , Stapleton D. , Campbell D.J. , Chen Z.-P. , Murthy S. , Walter M. , Gupta A. , Adams J.J. , Katsis F. , van Denderen B. , Jennings I.G. , Iseli T. , Michell B.J. , Witters L.A.
Published: December 2008

The AMP-activated protein kinase (AMPK) is a metabolic-stress-sensing protein kinase that regulates metabolism in response to energy demand and supply by directly phosphorylating rate-limiting enzymes in metabolic pathways as well as controlling gene expression.
Role of the yeast Snf1 protein kinase in invasive growth
Authors: Kuchin S. , Vyas V.K. , Carlson M.
Published: December 2008

The sucrose non-fermenting 1 (Snf1) protein kinase of Saccharomyces cerevisiae is important for transcriptional, metabolic and developmental responses to glucose limitation. Here we discuss the role of the Snf1 kinase in regulating filamentous invasive growth. Haploid invasive growth occurs in response to glucose limitation and requires FLO11, a gene encoding a cell-surface adhesin. Snf1 regulates transcription of FLO11 by antagonizing the function of two repressors, Nrg1 and Nrg2. Snf1 and the Nrg repressors also affect diploid pseudohyphal differentiation, which is a response to nitrogen limitation, suggesting an unexpected signalling role for the Snf1 kinase.
Snf1 protein kinase: a key player in the response to cellular stress in yeast
Authors: Sanz P.
Published: December 2008

Sucrose non-fermenting 1 (Snf1) protein kinase, a yeast homologue of mammalian AMP-activated protein kinase, plays a main role in transcriptional activation and repression of gene expression. In addition, Snf1 kinase has a broad role in the cellular response to several forms of stress, such as nutrient limitation, salt stress and heat shock.
Long-term regulation of AMP-activated protein kinase and acetyl-CoA carboxylase in skeletal muscle
Authors: Winder W.W. , Hardie D.G. , Mustard K.J. , Greenwood L.J. , Paxton B.E. , Park S.H. , Rubink D.S. , Taylor E.B.
Published: December 2008

Evidence is accumulating for roles of AMP-activated protein kinase (AMPK) in controlling glucose uptake, fatty acid oxidation and gene expression in skeletal muscle. Relatively little is known, however, about the control of expression of the AMPK subunit isoforms. Marked differences are noted in subunit expression as a function of muscle fibre type. Expression of the γ3 subunit isoform increases in fast-twitch red fibres of the rat in response to training. All subunit isoforms are expressed to a lesser extent in rats treated with propylthiouracil (PTU; an inhibitor of thyroid hormone synthesis) for 3 weeks compared with rats given excess thyroid hormones for 3 weeks. An approx. 2-fold increase in acetyl-CoA carboxylase was observed in gastrocnemius of hyperthyroid rats compared with experimentally hypothyroid rats. Thyroid state therefore appears to be one important factor controlling expression of these proteins in skeletal muscle.
AMP-activated protein kinase regulates gene expression by direct phosphorylation of nuclear proteins
Authors: Leff T.
Published: December 2008

One of the primary functions of AMP-activated protein kinase (AMPK) is to regulate the metabolic pathways in response to reduced cellular energy charge. Most of the known targets of the kinase are cytoplasmic enzymes involved in both catabolic and anabolic metabolism. In addition, activation of AMPK in many cells results in changes in the pattern of gene expression. Although some of these effects are undoubtedly secondary responses to modified cellular metabolism, it is possible that in addition to its well-characterized function in the cytoplasm, AMPK also directly phosphorylates and regulates proteins involved in gene transcription. There are now several examples of transcription factors, cofactors and components of the transcriptional core machinery that are directly phosphorylated and regulated by AMPK. Here I review these examples and discuss the significance of AMPK activity in the nucleus.
Selective suppression of AMP-activated protein kinase in skeletal muscle: update on ‘lazy mice’
Authors: Mu J. , Barton E.R. , Birnbaum M.J.
Published: December 2008

AMP-activated protein kinase (AMPK) is becoming recognized as a critical regulator of energy metabolism in cells. Using a mouse model in which we specifically blocked AMPK activity in muscles, we have demonstrated that activation of AMPK is necessary for the effects of 5-aminoimidazole-4-carboxamide riboside (‘AICAR’) and hypoxia, and is possibly required for a portion of exercise-induced glucose uptake. These same mice could not maintain sufficient glycogen in their skeletal muscle and it was rapidly depleted when the animals were subjected to mild exercise. Using isolated strips, we observed muscle hypertrophy and increased tiredness in the AMPK-deficient muscle. We also performed microarray analysis and showed dramatic changes of transcription profile in muscles of the lazy mice. These could have a significant impact on muscle function and may contribute to the observed phenotype.
Role of the Saccharomyces cerevisiae Rad9 protein in sensing and responding to DNA damage
Authors: Toh G.W.-L. , Lowndes N.F.
Published: December 2008

Eukaryotic cells have evolved surveillance mechanisms, known as DNA-damage checkpoints, that sense and respond to genome damage. DNA-damage checkpoint pathways ensure co-ordinated cellular responses to DNA damage, including cell cycle delays and activation of repair mechanisms. RAD9, from Saccharomyces cerevisiae, was the first damage checkpoint gene to be identified, although its biochemical function remained unknown until recently. This review examines briefly work that provides significant insight into how Rad9 activates the checkpoint signalling kinase Rad53.
Sister chromatid cohesion and genome stability in vertebrate cells
Authors: Morrison C. , Vagnarelli P. , Sonoda E. , Takeda S. , Earnshaw W.C.
Published: December 2008

For successful eukaryotic mitosis, sister chromatid pairs remain linked after replication until their kinetochores have been attached to opposite spindle poles by microtubules. This linkage is broken at the metaphase–anaphase transition and the sisters separate. In budding yeast, this sister chromatid cohesion requires a multi-protein complex called cohesin. A key component of cohesin is Scc1/Mcd1 (Rad21 in fission yeast). Disruption of the chicken orthologue of Scc1 by gene targeting in DT40 cells causes premature sister chromatid separation. Cohesion between sister chromatids is likely to provide a substrate for post-replicative DNA repair by homologous recombination. In keeping with this role of cohesion, Scc1 mutants also show defects in the repair of spontaneous and induced DNA damage. Scc1-deficient cells frequently fail to complete metaphase chromosome alignment and show chromosome segregation defects, suggesting aberrant kinetochore function. Consistent with this, the chromosomal passenger protein, INCENP (inner centromere protein) fails to localize to centromeres. Survivin, another passenger protein and one which interacts with INCENP, also fails to localize to centromeres in Scc1-deficient cells. These results show that cohesin maintains genomic stability by ensuring appropriate DNA repair and equal chromosome segregation at mitosis.
Phosphoinositide 3-kinase γ: a key modulator in inflammation and allergy
Authors: Wymann M.P. , Björklöf K. , Calvez R. , Finan P. , Thomast M. , Trifilieff A. , Barbier M. , Altruda F. , Hirsch E. , Laffargue M.
Published: December 2008

Chronic inflammation and allergy involve the activation of tissue-resident cells and, later on, the invasion of effector cells. We have previously shown that the loss of phosphoinositide 3-kinase (PI3K) γ impairs chemokine-dependent migration of neutrophils and macrophages both in vitro and in vivo. On the other hand, PI3Kγ is not required either during phagocytic processes or in the activation of bactericidal activities like granule secretion and particle-mediated respiratory burst in neutrophils. Tissue mast cells are key regulators in allergy and inflammation and release histamine upon clustering of their IgE receptors. We have demonstrated that murine mast cell responses are exacerbated in vitro and in vivo by autocrine signals, and require functional PI3Kγ. Adenosine, acting through the A3 adenosine receptor, as well as other agonists of Gαi-coupled receptors, transiently increased PtdIns(3,4,5)P3 exclusively via PI3Kγ. PI3Kγ-derived PtdIns(3,4,5)P3 was instrumental for initiation of a sustained influx of external Ca2+ and degranulation. Mice that lacked PI3Kγ did not form oedema when challenged by passive systemic anaphylaxis. PI3Kγ thus relays inflammatory signals through various GPCRs, and is thus central to mast cell function. Taken together, this suggests that pharmaceutical targeting of PI3Kγ might alleviate inflammation at both early and late stages of the allergic response.
Archaeal DNA repair: paradigms and puzzles
Authors: White M.F.
Published: December 2008

It is now generally accepted that the Archaea share many similarities in their information-processing pathways with eukarya. Archaeal and eukaryal DNA replication and transcriptional machineries show particularly striking similarities, and the archaeal processes have been used extensively as simpler models of the much more complex eukaryal ones. Archaeal DNA-repair pathways are not yet well characterized, and their relationship with repair pathways in bacteria and eukarya are still open to question. There are also strong distinctions between the major subdivisions crenarchaea and euryarchaea within the archaeal domain. This review highlights some of these similarities and differences using specific examples arising from our studies of the double-stranded and single-stranded DNA-binding proteins and the repair endonuclease XPF in the crenarchaeote Sulfolobus solfataricus.
Taste, Smell, and Anorexia in the Aged: What Can We Do To Help the Patients? An Initial Primer
Authors: Henkin Robert I.
Published: December 2008

What is the etiology of anorexia in the aged? Can it be corrected? How is this accomplished? These questions reflect a complex set of phenomena made more complex since there is no standard formula to either define or correct anorexia. There is also no established group of physicians or other caretakers to whom to turn for help to evaluate or treat these problems. This leaves you with the difficult task of offering advice to others who are called upon to deal with these issues but who may feel insecure in their knowledge about caring for anorexia of the elderly or nursing home residents. This may place you in a difficult diagnostic as well as therapeutic quandary. You may be forced to be the leaders to evaluate anorexia and to assist in overcoming its multiple clinical consequences. This paper will attempt to inform you of some helpful strategies which may be effective in assisting you to evaluate and treat one aspect of the complex phenomena which affects the many patients with anorexia.
Cognitive Impairment, Wayfinding, and the Long-Term Care Environment
Authors: Brush Jennifer A. , Calkins Margaret P.
Published: December 2008

Research has shown that the environment affects cognition and communication, and that modifications appear to improve functioning in individuals with dementia. Unfortunately, poorly designed environmental features often contribute to unsatisfactory responses or behaviors in individuals with cognitive impairment. This article will discuss the impact of the environment on orientation and wayfinding and provide some suggestions for effective modification in long-term care facilities.
Dynamics and efficiency of Brownian rotors
Authors: Bauer Wolfgang R. , Nadler Walter
Published: December 2008

Brownian rotors play an important role in biological systems and in future nanotechnological applications. However the mechanisms determining their dynamics, efficiency, and performance remain to be characterized. Here the F0 portion of the F-ATP synthase is considered as a paradigm of the Brownian rotor. In a generic analytical model we analyze the stochastic rotation of F0-like motors as a function of the driving free energy difference and of the free energy profile the rotor is subjected to. The latter is composed of the rotor interaction with its surroundings, of the free energy of chemical transitions, and of the workload. The dynamics and mechanical efficiency of the rotor depend on the magnitude of its stochastic motion driven by the free energy difference and its rectification on the reaction-diffusion path. We analyze which free energy profiles provide maximum flow and how their arrangement on the underlying reaction-diffusion path affects rectification and—by this—the efficiency.
Interfacial superconductivity in bilayer and multilayer IV–VI semiconductor heterostructures
Authors: Yuzephovich O. I. , Mikhailov M. Yu. , Bengus S. V. , Aladyshkin A. Yu. , Pestov E. E. , Nozdrin Yu. N. , Sipatov A. Yu. , Buchstab E. I. , Fogel N. Ya.
Published: December 2008

A comprehensive investigation and comparison of the superconducting properties of bilayer and multilayer epitaxial heterostructures of IV–VI semiconductors exhibiting superconductivity at critical temperatures Tc⩽6.5K is carried out. The superconductivity of these systems is due to inversion of the bands in the narrow-gap semiconductors on account of the nonuniform stresses created by the grids of misfit dislocations arising at the interfaces during the epitaxial growth. It is found that Tc and the character of the superconducting transition of bilayer PbTe∕PbS heterostructures depend on the thickness d of the semiconductor layers and are directly related to the quality of the grids of misfit dislocations at the interfaces (the number and type of structural defects in the grids). Substantial differences in the behavior of bilayer sandwiches and superlattices are found. The minimum thickness d at which superconductivity appears is several times larger for bilayer than for multilayer systems. The upper critical magnetic fields Hc2 of the bilayer systems are more anisotropic. For superlattices 3D behavior is observed in the temperature region close to Tc, and with decreasing temperature a 3D–2D crossover occurs. For the bilayer structures 2D behavior starts immediately from Tc, and a 2D–1D crossover is observed, with the sharp divergence of Hc2 that is characteristic of superconducting nets.
On the particularities of Bose–Einstein condensation of quasiparticles
Authors: Bugrij A. I. , Loktev V. M.
Published: December 2008

An attempt is made to determine the difference between Bose–Einstein condensation of particles and quasiparticles. An equation is obtained for the number of particles in a Bose–Einstein condensate as a function of the total number of particles in the system. This equation is also written for quasiparticles taking account of their creation by external pumping and the presence of equilibrium thermal excitations in the system. Analyzing both equations, the chemical potential of the pumped quasiparticles and their number in the condensate are found as a function of the pumping intensity. A condition under which the Bose–Einstein condensation of low-energy quasiparticle excitations starts and occurs at any, including quite high, temperatures is found.
Structure and stability of nonlinear excitations in magnets in the presence of a local rf field and dissipation
Authors: Kovalev A. S. , Prilepsky Y. E. , Peretyatko A. A.
Published: December 2008

Solitonlike excitations localized around a point of pumping of an easy-axis ferromagnet by a circular rf magnetic field are investigated in the framework of the one-dimensional nonlinear Schrödinger equation and its discrete analog. The influence of damping on the character of the localized excitations and the stability of various types of such states are analyzed in a simplified piecewise-nonlinear model.
Luminescence investigations of hybrids of carbon nanotubes with DNA in a water suspension and film at 5–290K
Authors: Glamazda A. Yu. , Leont’ev V. S. , Linnik A. S. , Karachevtsev V. A.
Published: December 2008

The high-energy part of the luminescence spectrum (1.15–1.5eV) of films of semiconductor, single-wall, carbon nanotubes (SWCN) in a DNA environment at 5–290K were studied. Five luminescence bands of individual nanotubes of definite chirality were observed in the spectrum. Comparing the luminescence spectrum of a water suspension of SWCN:DNA with a film obtained when such a suspension is deposited on a substrate showed that broadening of the bands and a shift of their peaks into the low-energy region relative to the spectrum of a suspension are observed in the luminescence spectrum of the film at 290K. As the temperature of the film decreases, the intensity of the luminescence increases, the width of the spectral bands decreases, and the bands shift into the high-energy region. The temperature dependence of the luminescence of the strongest band in the spectrum lying at 1.229eV and due to the luminescence of nanotubes with chirality (6, 5) was obtained. The possible reasons for the observed temperature changes in the emission spectrum of the nanotubes are discussed.
Efficient solution of Poisson’s equation using discrete variable representation basis sets for Car–Parrinello ab initio molecular dynamics simulations with cluster boundary conditions
Authors: Lee Hee-Seung , Tuckerman Mark E.
Published: December 2008

An efficient computational approach to perform Car–Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn–Sham orbitals and electron density. Poisson’s equation is solved in order to calculate the Hartree potential via an integral representation of the 1∕r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N4∕3)] of the computational cost with respect to the system size (N) for the solution of Poisson’s equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N2 and a water dimer.
Stereoselective isomerization of an ensemble of adsorbed molecules with multiple orientations: Stochastic laser pulse optimization for selective switching between achiral and chiral atropisomers
Authors: Klamroth Tillmann , Kröner Dominik
Published: December 2008

We present quantum dynamical simulations for the laser driven isomerization of an ensemble of surface mounted stereoisomers with multiple orientations. The model system 1-(2-cis-fluoroethenyl)-2-fluorobenzene supports two chiral and one achiral atropisomers upon torsion around the C–C single bond connecting phenyl ring and ethylene group. An infrared picosecond pulse is used to excite the internal rotation around the chiral axis, thereby controlling the chirality of the molecule. In order to selectively switch the molecules—independent of their orientation on a surface—from their achiral to either their left- or right-handed form, a stochastic pulse optimization algorithm is applied. The stochastic pulse optimization is performed for different sets of defined orientations of adsorbates corresponding to the rotational symmetry of the surface. The obtained nonlinearly polarized laser pulses are highly enantioselective for each orientation.
Imaging microflows and nanopore structures using hydrodynamic force microscopy
Authors: Ulrich Elaine S. , Limbach Christopher M. , Manne Srinivas
Published: December 2008

We report the three-dimensional profilometry of gas microflows and the two-dimensional mapping of fluid permeability through nanoporous substrates using hydrodynamic force microscopy (HFM). Using fluid drag from external flows as a contrast mechanism, HFM has mapped Poiseuille flow through ∼100nm pores and has identified subsurface fouling unresolvable by conventional force microscopy. HFM demonstrates nanoscale spatial resolution and flow velocity resolution on the order of 1cm∕s, making it an attractive investigative tool for applications in separation science, microfluidics, and nanoporous materials.
Coherent control of magnetization precession in ferromagnetic semiconductor (Ga,Mn)As
Authors: Rozkotová E. , Němec P. , Tesařová N. , Malý P. , Novák V. , Olejník K. , Cukr M. , Jungwirth T.
Published: December 2008

We report single-color, time-resolved magneto-optical measurements in ferromagnetic semiconductor (Ga,Mn)As. We demonstrate coherent optical control of the magnetization precession by applying two successive ultrashort laser pulses. The magnetic field and temperature dependent experiments reveal the collective Mn-moment nature of the oscillatory part of the time-dependent Kerr rotation, as well as contributions to the magneto-optical signal that are not connected with the magnetization dynamics.
Vertically aligned liquid crystals on a γ-Al2O3 alignment film using ion-beam irradiation
Authors: Park Hong-Gyu , Kim Young-Hwan , Oh Byeong-Yun , Lee Won-Kyu , Kim Byoung-Yong , Seo Dae-Shik , Hwang Jeong-Yeon
Published: December 2008

Using ion-beam (IB) irradiation, liquid crystals (LCs) were vertically aligned (VA) on a γ-Al2O3 alignment film. Atomic-layer deposition was used to orient the LCs on high-quality γ-Al2O3 alignment films. The LC molecule orientation indicates the vertical direction of the atomic-layer-deposited γ-Al2O3 alignment films. X-ray photoelectron spectroscopy showed that IB irradiation changed the chemical structure, shifting the Al–O binding energy and altering the Al–O bonding intensity. The low-voltage transmittance characteristics of the VA LC displays on the γ-Al2O3 alignment films were also measured, showing reduced voltage and power requirements.
Strain relaxation dependent island nucleation rates during the Stranski–Krastanow growth of GaN on AlN by molecular beam epitaxy
Authors: Koblmüller G. , Averbeck R. , Riechert H. , Hyun Y.-J. , Pongratz P.
Published: December 2008

This study reports on the correlation between strain relaxation and nucleation kinetics during the Stranski–Krastanow growth of GaN on (0001)AlN by plasma-assisted molecular beam epitaxy. Using reflection high-energy electron diffraction and real-time desorption mass spectrometry, the strain-related Ga adatom detachment and desorption rates were determined, giving information about the average GaN island nucleation rate. Two different regimes were found: one at low-temperature growth (690<TS<720 °C), where strain relaxation occurred slowly, yielding impeded island nucleation rates and small island sizes (diameter ∼8–12 nm and height ∼2.3–2.7 nm). In the other, i.e., high-temperature growth regime (TS>720 °C), islands showed an abrupt relaxation mode, accompanied by a fast nucleation rate toward island sizes twice as large.