bluuebunny/crossref_metadata_2025 huggingface dataset:
Fifteen years of APC/cyclosome: a short and impressive biography
Authors: Simpson-Lavy Kobi J. , Oren Yifat S. , Feine Oren , Sajman Julia , Listovsky Tammy , Brandeis Michael
Published: January 2010

The APC/C (anaphase-promoting complex/cyclosome) discovered exactly 15 years ago by Avram Heshko and Marc Kirschner is by far the most complex ubiquitin ligase discovered so far. The APC/C is composed of roughly a dozen subunits and measures a massive 1.5 MDa. This huge complex, as well as its multiple modes of regulation, boasts impressive evolutionary conservation. One of its most puzzling features is its split personality: regulation of mitotic exit events on the one hand, and its ongoing activity during G1-phase, G0-phase and in terminally differentiated cells. The present short review is intended to provide a basic description of our current understanding of the APC/C, focusing on recent findings concerning its role in G1-phase and in differentiated cells.
Role of ubiquitination in the DNA damage response: proteomic analysis to identify new DNA-damage-induced ubiquitinated proteins
Authors: Selvarajah Jogitha , Moumen Abdeladim
Published: January 2010

The DDR (DNA damage response) is a signalling transduction cascade utilizing many forms of post-translation modification of proteins, including phosphorylation and ubiquitination. The well-known function of ubiquitination is to target proteins for proteasomal degradation; however, it is also involved in the regulation of protein function. The present review describes how ubiquitination regulates the function of certain proteins involved in DDR, in particular FANCD2 (Fanconi's anaemia complementation group D2) and PCNA (proliferating-cell nuclear antigen). Also, the proteomic methods currently used to identify new ubiquitinated proteins in response to DNA damage, including the advantages of using the UBD (ubiquitin-binding domain) beads to purify the ubiquitinated proteins, are considered.
Lessons from interconnected ubiquitylation and acetylation of p53: think metastable networks
Authors: Benkirane Monsef , Sardet Claude , Coux Olivier
Published: January 2010

The critical tumour suppressor p53 plays a major role in response to DNA damage and, more generally, to genotoxic stress. The regulation of its expression and functions is under very tight controls, and involves, in particular, an extremely complex set of post-translational modifications, thanks to a variety of ‘modifiers’, including ubiquitylation E3s and acetyltransferases, that fine-tune the stability and activity of the protein. Work of the last few years has revealed that, in addition to targeting p53, these modifiers also modify each other, forming an intricate network of regulatory molecules and events that must be taken into account to understand p53 regulation. We propose that this network allows a metastable equilibrium that confers both sensitivity and robustness on the p53 pathway, two properties that allow the pathway to respectively answer to a variety of stimuli and return to its initial stage when the stimuli disappear.
Presynaptic targets for acute ethanol sensitivity
Authors: Barclay Jeff W. , Graham Margaret E. , Edwards Mark R. , Johnson James R. , Morgan Alan , Burgoyne Robert D.
Published: January 2010

Acute exposure to ethanol is known to modulate signalling within the nervous system. Physiologically these effects are both presynaptic and postsynaptic in origin; however, considerably more research has focused primarily on postsynaptic targets. Recent research using the model organism Caenorhabditis elegans has determined a role for specific proteins (Munc18-1 and Rab3) and processes (synaptic vesicle recruitment and fusion) in transducing the presynaptic effects of ethanol. In the present paper, we review these results, identifying the proteins and protein interactions involved in ethanol sensitivity and discuss their links with mammalian studies of alcohol abuse.
Molecular mechanism of secretory vesicle docking
Authors: Wit Heidi de
Published: January 2010

Docking, the stable association of secretory vesicles with the plasma membrane, is considered to be the necessary first step before vesicles gain fusion-competence, but it is unclear how vesicles dock. In adrenal medullary chromaffin cells, access of secretory vesicles to docking sites is controlled by dense F-actin (filamentous actin) beneath the plasma membrane. Recently, we found that, in the absence of Munc18-1, the number of docked vesicles and the thickness of cortical F-actin are affected. In the present paper, I discuss the possible mechanism by which Munc18-1 modulates cortical F-actin and how it orchestrates the docking machinery via an interaction with syntaxin-1. Finally, a comparison of Munc18's role in embryonic mouse and adult bovine chromaffin cell model systems will be made to clarify observed differences in cortical F-actin as well as docking phenotypes.
Cell-wide analysis of secretory granule dynamics in three dimensions in living pancreatic β-cells: evidence against a role for AMPK-dependent phosphorylation of KLC1 at Ser517/Ser520 in glucose-stimulated insulin granule movement
Authors: McDonald Angela , Fogarty Sarah , Leclerc Isabelle , Hill Elaine V. , Hardie D. Grahame , Rutter Guy A.
Published: January 2010

Glucose-stimulated insulin secretion from pancreatic β-cells requires the kinesin-1/Kif5B-mediated transport of insulin granules along microtubules. 5′-AMPK (5′-AMP-activated protein kinase) is a heterotrimeric serine/threonine kinase which is activated in β-cells at low glucose concentrations, but inhibited as glucose levels increase. Active AMPK blocks glucose-stimulated insulin secretion and the recruitment of insulin granules to the cell surface, suggesting motor proteins may be targets for this kinase. While both kinesin-1/Kif5B and KLC1 (kinesin light chain-1) contain consensus AMPK phosphorylation sites (Thr693 and Ser520, respectively) only recombinant GST (glutathione transferase)–KLC1 was phosphorylated by purified AMPK in vitro. To test the hypothesis that phosphorylation at this site may modulate kinesin-1-mediated granule movement, we developed an approach to study the dynamics of all the resolvable granules within a cell in three dimensions. This cell-wide approach revealed that the number of longer excursions (>10 μm) increased significantly in response to elevated glucose concentration (30 versus 3 mM) in control MIN6 β-cells. However, similar changes were seen in cells overexpressing wild-type KLC1, phosphomimetic (S517D/S520D) or non-phosphorylatable (S517A/S520A) mutants of KLC1. Thus, changes in the phosphorylation state of KLC1 at Ser517/Ser520 seem unlikely to affect motor function.
Autoinhibition of SNARE complex assembly by a conformational switch represents a conserved feature of syntaxins
Authors: MacDonald Chris , Munson Mary , Bryant Nia J.
Published: January 2010

Regulation and specificity of membrane trafficking are required to maintain organelle integrity while performing essential cellular transport. Membrane fusion events in all eukaryotic cells are facilitated by the formation of specific SNARE (soluble N-ethylmaleimide-sensitive fusion proteinattachment protein receptor) complexes between proteins on opposing lipid bilayers. Although regulation of SNARE complex assembly is not well understood, it is clear that two conserved protein families, the Sx (syntaxin) and the SM (Sec1p/Munc18) proteins, are central to this process. Sxs are a subfamily of SNARE proteins; in addition to the coiled-coil SNARE motif, Sxs possess an N-terminal, autonomously folded, triple-helical (Habc) domain. For some Sxs, it has been demonstrated that this Habc domain exerts an autoinhibitory effect on SNARE complex assembly by making intramolecular contacts with the SNARE motif. SM proteins regulate membrane fusion through interactions with their cognate Sxs. One hypothesis for SM protein function is that they facilitate a switch of the Sx from a closed to an open conformation, thus lifting the inhibitory action of the Habc domain and freeing the SNARE motif to participate in SNARE complexes. However, whether these regulatory mechanisms are conserved throughout the Sx/SM protein families remains contentious as it is not clear whether the closed conformation represents a universal feature of Sxs.
Role of C2 domain proteins during synaptic vesicle exocytosis
Authors: Martens Sascha
Published: January 2010

Neurotransmitter release is mediated by the fusion of synaptic vesicles with the presynaptic plasma membrane. Fusion is triggered by a rise in the intracellular calcium concentration and is dependent on the neuronal SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) complex. A plethora of molecules such as members of the MUNC13, MUNC18, complexin and synaptotagmin families act along with the SNARE complex to enable calcium-regulated synaptic vesicle exocytosis. The synaptotagmins are localized to synaptic vesicles by an N-terminal transmembrane domain and contain two cytoplasmic C2 domains. Members of the synaptotagmin family are thought to translate the rise in intracellular calcium concentration into synaptic vesicle fusion. The C2 domains of synaptotagmin-1 bind membranes in a calcium-dependent manner and in response induce a high degree of membrane curvature, which is required for its ability to trigger membrane fusion in vitro and in vivo. Furthermore, members of the soluble DOC2 (double-C2 domain) protein family have similar properties. Taken together, these results suggest that C2 domain proteins such as the synaptotagmins and DOC2s promote membrane fusion by the induction of membrane curvature in the vicinity of the SNARE complex. Given the widespread expression of C2 domain proteins in secretory cells, it is proposed that promotion of SNARE-dependent membrane fusion by the induction of membrane curvature is a widespread phenomenon.
Structure and function of mRNA export adaptors
Authors: Walsh Matthew J. , Hautbergue Guillaume M. , Wilson Stuart A.
Published: January 2010

The mRNA export adaptors provide an important link between multiple nuclear mRNA processing events and the mRNA export receptor TAP/NXF1/Mex67p. They are recruited to mRNA through transcriptional and post-transcriptional events, integrating this information to licence mRNA for export. Subsequently they hand mRNA over to TAP and switch TAP to a higher-affinity RNA-binding state, ensuring its stable association with mRNA destined for export. Here we discuss the structure and function of adaptors and how they are recruited to mRNA.
On track with P-bodies
Authors: Kulkarni Meeta , Ozgur Sevim , Stoecklin Georg
Published: January 2010

P-bodies (processing bodies) are cytoplasmic foci visible by light microscopy in somatic cells of vertebrate and invertebrate origin as well as in yeast, plants and trypanosomes. At the molecular level, P-bodies are dynamic aggregates of specific mRNAs and proteins that serve a dual function: first, they harbour mRNAs that are translationally silenced, and such mRNA can exit again from P-bodies to re-engage in translation. Secondly, P-bodies recruit mRNAs that are targeted for deadenylation and degradation by the decapping/Xrn1 pathway. Whereas certain proteins are core constituents of P-bodies, others involved in recognizing short-lived mRNAs can only be trapped in P-bodies when mRNA decay is attenuated. This reflects the very transient interactions by which many proteins associate with P-bodies. In the present review, we summarize recent findings on the function, assembly and motility of P-bodies. An updated list of proteins and RNAs that localize to P-bodies will help in keeping track of this fast-growing field.
HIV protease inhibitors inhibit FACE1/ZMPSTE24: a mechanism for acquired lipodystrophy in patients on highly active antiretroviral therapy?
Authors: Goulbourne Chris N. , Vaux David J.
Published: January 2010

HIV-PIs (HIV protease inhibitors) have proved to be of great benefit for the millions of people suffering from AIDS. However, one of the side effects of this component of combined highly active antiretroviral therapy is lipodystrophy, which affects a large number of the patients taking this class of drug. It has been shown that many of these protease inhibitors inhibit the ZMPSTE24 enzyme responsible for removing the farnesylated tail of prelamin A, which is a nuclear lamina component that has been implicated in some of the nuclear laminopathies. Build up of this protein somehow leads to acquired lipodystrophy, possibly through its interaction with a transcription factor called SREBP-1 (sterol-regulatory-element-binding protein-1). The downstream effect of this is altered fatty acid metabolism and sterol synthesis, which may cause lipodystrophy in patients. The build-up of this protein also appears to have morphological consequences on the nucleus and we reveal, by dual-axis electron tomography, a complex nucleoplasmic reticulum that forms after HIV-PI treatment as a result of acute farnesylated prelamin A accumulation. A greater understanding of the molecular mechanisms leading to lipodystrophy will hopefully facilitate the design of improved HIV-PIs that do not cause this debilitating side effect.
CdS enhances Voc and fill factor in CdS/CdTe and CdS/CuInSe2 solar cells
Authors: Böer Karl W.
Published: January 2010

A cover layer of CdS enhances the efficiency of CdTe and CuInSe2 based solar cells. The experimental results are summarized, giving the reasons why a CdS layer causes Voc and the fill factor to increase. Field quenching by Frenkel–Poole excitation in copper doped CdS leads to a negative differential conductivity and a high-field domain with a field of 50 kV/cm, limiting the maximum field in the CdS/CdTe junction. This prevents tunneling through the junction and reducing electron leakage. Other evidence indicates an adjustment of the electron affinity, hence in a shift of the band connection at different bias conditions. A band model of the CdS/CdTe cell is proposed.
Physics design of a 100 keV acceleration grid system for the diagnostic neutral beam for international tokamak experimental reactor
Authors: Singh M. J. , De Esch H. P. L.
Published: January 2010

This paper describes the physics design of a 100 keV, 60 A H− accelerator for the diagnostic neutral beam (DNB) for international tokamak experimental reactor (ITER). The accelerator is a three grid system comprising of 1280 apertures, grouped in 16 groups with 80 apertures per beam group. Several computer codes have been used to optimize the design which follows the same philosophy as the ITER Design Description Document (DDD) 5.3 and the 1 MeV heating and current drive beam line [R. Hemsworth, H. Decamps, J. Graceffa, B. Schunke, M. Tanaka, M. Dremel, A. Tanga, H. P. L. De Esch, F. Geli, J. Milnes, T. Inoue, D. Marcuzzi, P. Sonato, and P. Zaccaria, Nucl. Fusion 49, 045006 (2009)]. The aperture shapes, intergrid distances, and the extractor voltage have been optimized to minimize the beamlet divergence. To suppress the acceleration of coextracted electrons, permanent magnets have been incorporated in the extraction grid, downstream of the cooling water channels. The electron power loads on the extractor and the grounded grids have been calculated assuming 1 coextracted electron per ion. The beamlet divergence is calculated to be 4 mrad. At present the design for the filter field of the RF based ion sources for ITER is not fixed, therefore a few configurations of the same have been considered. Their effect on the transmission of the electrons and beams through the accelerator has been studied. The OPERA-3D code has been used to estimate the aperture offset steering constant of the grounded grid and the extraction grid, the space charge interaction between the beamlets and the kerb design required to compensate for this interaction. All beamlets in the DNB must be focused to a single point in the duct, 20.665 m from the grounded grid, and the required geometrical aimings and aperture offsets have been calculated.
Optimal annealing conditions for Y1Ba2Cu3O7−δ thin films
Authors: Mori Zon , Doi Toshiya , Hakuraku Yoshinori
Published: January 2010

The superconducting current density, Jc, of Y1Ba2Cu3O7−δ (YBCO) is greatly influenced by hole doping levels. Hole doping is mainly dominated by oxygen ordering, so the postannealing process is one of the essential factors for practical applications of YBCO superconductors. However, little research has been reported about the variation in Jc by annealing time. In this study, the optimal annealing conditions were studied using homogeneous c-axis oriented YBCO thin films prepared by the pulsed laser deposition method. As a result, Jc (at 77 K, 0 T) increased from 0.3 to 5.3 MA/cm2 with an annealing time in the range of 0–12 h. This result suggests that annealing for tens of hours is essential for obtaining high Jc samples, even if the film is 250 nm thick. The oxygen diffusion process was examined by applying the one-dimensional diffusion model.
Interchain and intrachain emission branching in polymer light-emitting diode doped by organic molecules
Authors: Krautz D. , Lunedei E. , Puigdollers J. , Badenes G. , Alcubilla R. , Cheylan S.
Published: January 2010

A blend of the polymer poly[2-(2-ethylhexyloxy)-5-methoxy-1,4-phenylenevinylene] (MEH-PPV) and the electron-transport molecule tris-(8-hydroxyquinoline) aluminum (Alq3) has been investigated by means of electroluminescence and fluorescence spectroscopy, upon variation of the Alq3 content in the blend. A decreased interchain emission is observed upon increasing Alq3 content, due to lower packing of the MEH-PPV chains which leads to a reduction in the interchain interaction, excimer formation, and emission probability. A branching of MEH-PPV interchain and intrachain emissive contributions is clearly time resolved and analyzed as a function of the Alq3 content. At high doping concentration, direct emission from Alq3 molecules is observed.
Three-dimensional shapes and distribution of FePd nanoparticles observed by electron tomography using high-angle annular dark-field scanning transmission electron microscopy
Authors: Sato Kazuhisa , Aoyagi Kenta , Konno Toyohiko J.
Published: January 2010

We have studied three-dimensional shapes and distribution of FePd nanoparticles, prepared by electron beam deposition and postdeposition annealing, by means of single-axis tilt tomography using atomic number contrasts obtained by high-angle annular dark-field scanning transmission electron microscopy. Particle size, shape, and locations were reconstructed by weighted backprojection (WBP), as well as by simultaneous iterative reconstruction technique (SIRT). We have also estimated the particle size by simple extrapolation of tilt-series original data sets, which proved to be quite powerful. The results of the two algorithms for reconstruction have been compared quantitatively with those obtained by the extrapolation method and those independently reported by electron holography. It was found that the reconstructed intensity map by WBP contains a small amount of dotlike artifacts, which do not exist in the results by SIRT, and that the particle surface obtained by WBP is rougher than that by SIRT. We demonstrate, on the other hand, that WBP yields a better estimation of the particle size in the z direction than SIRT does, most likely due to the presence of a “missing wedge” in the original data set.
Exploiting the spatial locality of electron correlation within the parametric two-electron reduced-density-matrix method
Authors: DePrince A. Eugene , Mazziotti David A.
Published: January 2010

The parametric variational two-electron reduced-density-matrix (2-RDM) method is applied to computing electronic correlation energies of medium-to-large molecular systems by exploiting the spatial locality of electron correlation within the framework of the cluster-in-molecule (CIM) approximation [S. Li et al., J. Comput. Chem. 23, 238 (2002); J. Chem. Phys. 125, 074109 (2006)]. The 2-RDMs of individual molecular fragments within a molecule are determined, and selected portions of these 2-RDMs are recombined to yield an accurate approximation to the correlation energy of the entire molecule. In addition to extending CIM to the parametric 2-RDM method, we (i) suggest a more systematic selection of atomic-orbital domains than that presented in previous CIM studies and (ii) generalize the CIM method for open-shell quantum systems. The resulting method is tested with a series of polyacetylene molecules, water clusters, and diazobenzene derivatives in minimal and nonminimal basis sets. Calculations show that the computational cost of the method scales linearly with system size. We also compute hydrogen-abstraction energies for a series of hydroxyurea derivatives. Abstraction of hydrogen from hydroxyurea is thought to be a key step in its treatment of sickle cell anemia; the design of hydroxyurea derivatives that oxidize more rapidly is one approach to devising more effective treatments.
Directed transport as a mechanism for protein foldingin vivo
Authors: González-Candela Ernesto , Romero-Rochín Víctor
Published: January 2010

We propose a model for protein folding in vivo based on a Brownian ratchet mechanism in the multidimensional energy landscape space. The device is able to produce directed transport taking advantage of the assumed intrinsic asymmetric properties of the proteins and employing the consumption of energy provided by an external source. Through such a directed transport phenomenon, the polypeptide finds the native state starting from any initial state in the energy landscape with great efficacy and robustness, even in the presence of different types of obstacles. This model solves Levinthal’s paradox without requiring biased transition probabilities but at the expense of opening the system to an external field.
Chaotic operation by a single transistor circuit in the reverse active region
Authors: Hanias M. P. , Giannis I. L. , Tombras G. S.
Published: January 2010

In this paper, we present an externally triggered experimental chaotic circuit with a bipolar junction transistor operating in its reverse active region in order to investigate for possible control features in its output phase portraits. Nonlinear time series modeling techniques are applied to analyze the circuit’s output voltage oscillations and reveal the presence of chaos, while the chaos itself is achieved by controlling the amplitude of the applied input signal. The phase space, which describes the behavior evolution of a nonlinear system, is reconstructed using the delay embedding theorem suggested by Takens. The time delay used for this reconstruction is chosen after examining the first minimum of the collected data average mutual information, while the sufficient embedding dimension is estimated using the false nearest-neighbor algorithm which has a value of 5. Also the largest Lyapunov exponent is estimated and found equal to 0.020 48. Finally, the phase space embedding based weight predictor algorithm is employed to make a short-term prediction of the chaotic time series for which the system’s governing equations may be unknown.
Comparison of molecular dynamics and moment based methods as tools in the computation of time dependent correlation functions
Authors: Paul Reginald
Published: January 2010

Methods, such as the continued fractions that are based on the exact moments (Taylor coefficients) provide powerful analytic techniques for calculating approximate dynamic correlation functions of physical properties. Owing to the practical difficulties associated with obtaining higher order exact moments these methods have been largely eclipsed by molecular dynamics. In this paper we develop the formalism for extracting trajectory moments from a molecular dynamics trajectory and compare the performance of the two methods. We begin by using the classical phase space analogs of quantum wave functions to obtain matrix representations (transition matrices) of the Lie group of time displacement operators. The group elements for small time displacements, which correspond to a step of the trajectory, are approximated by using Trotter’s theorem. The method is applied to the linear harmonic oscillator, the Morse oscillator and the Lennard-Jones potential and the resulting moments compared to those obtained by the Taylor expansion of a truncated continued fraction. We find that in the case of the harmonic oscillator the results from the continued fraction are much better than those from molecular dynamics. In the latter two cases, while the truncated fraction performs better than molecular dynamics both methods produce poor quality higher order moments. However, we are able to show the criterion whereby the overall error introduced by the truncated continued fraction is smaller than that introduced by molecular dynamics. From this work we conclude that the moment based methods produce good results, they are analytic in nature rather than numerical and should not be rejected but can be used to complement molecular dynamics.
Mechanism of amyloid plaque formation suggests an intracellular basis of Aβ pathogenicity
Authors: Friedrich Ralf P. , Tepper Katharina , Rönicke Raik , Soom Malle , Westermann Martin , Reymann Klaus , Kaether Christoph , Fändrich Marcus
Published: January 2010

The formation of extracellular amyloid plaques is a common patho-biochemical event underlying several debilitating human conditions, including Alzheimer’s disease (AD). Considerable evidence implies that AD damage arises primarily from small oligomeric amyloid forms of Aβ peptide, but the precise mechanism of pathogenicity remains to be established. Using a cell culture system that reproducibly leads to the formation of Alzheimer’s Aβ amyloid plaques, we show here that the formation of a single amyloid plaque represents a template-dependent process that critically involves the presence of endocytosis- or phagocytosis-competent cells. Internalized Aβ peptide becomes sorted to multivesicular bodies where fibrils grow out, thus penetrating the vesicular membrane. Upon plaque formation, cells undergo cell death and intracellular amyloid structures become released into the extracellular space. These data imply a mechanism where the pathogenic activity of Aβ is attributed, at least in part, to intracellular aggregates.
Bombyx
prothoracicostatic peptides activate the sex peptide receptor to regulate ecdysteroid biosynthesis
Authors: Yamanaka Naoki , Hua Yue-Jin , Roller Ladislav , Spalovská-Valachová Ivana , Mizoguchi Akira , Kataoka Hiroshi , Tanaka Yoshiaki
Published: January 2010

Insect molting and metamorphosis are induced by steroid hormones named ecdysteroids, whose production is regulated by various neuropeptides. We cloned the gene and analyzed the expression of the prothoracicostatic peptide, a unique neuropeptide shown to suppress the production of ecdysteroids in the prothoracic gland of the silkworm,
Bombyx mori
. We also characterized a
Bombyx
G protein-coupled receptor, which has previously been identified as an ortholog of the
Drosophila
sex peptide receptor, as a functional prothoracicostatic peptide receptor. This receptor responded specifically to the prothoracicostatic peptides when examined using a heterologous expression system. The receptor was highly expressed in the prothoracic gland on the day before each larval and pupal ecdysis, when prothoracicostatic peptides are synthesized at a high level in the epiproctodeal glands. These results suggest that the sex peptide receptor functions as a prothoracicostatic peptide receptor in
Bombyx
and that the peripheral neurosecretory cells as well as the central neuroendocrine system play stage-specific roles in regulating ecdysteroidogenesis.
Direct assignment of EPR spectra to structurally defined iron-sulfur clusters in complex I by double electron–electron resonance
Authors: Roessler Maxie M. , King Martin S. , Robinson Alan J. , Armstrong Fraser A. , Harmer Jeffrey , Hirst Judy
Published: January 2010

In oxidative phosphorylation, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. Complex I contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters, in several subunits, to transfer the electrons to quinone. Understanding coupled electron transfer in complex I requires a detailed knowledge of the properties of individual clusters and of the cluster ensemble, and so it requires the correlation of spectroscopic and structural data: This has proved a challenging task. EPR studies on complex I from
Bos taurus
have established that EPR signals N1b, N2 and N3 arise, respectively, from the 2Fe cluster in the 75 kDa subunit, and from 4Fe clusters in the PSST and 51 kDa subunits (positions 2, 7, and 1 along the seven-cluster chain extending from the flavin). The other clusters have either evaded detection or definitive signal assignments have not been established. Here, we combine double electron-electron resonance (DEER) spectroscopy on
B. taurus
complex I with the structure of the hydrophilic domain of
Thermus thermophilus
complex I. By considering the magnetic moments of the clusters and the orientation selectivity of the DEER experiment explicitly, signal N4 is assigned to the first 4Fe cluster in the TYKY subunit (position 5), and N5 to the all-cysteine ligated 4Fe cluster in the 75 kDa subunit (position 3). The implications of our assignment for the mechanisms of electron transfer and energy transduction by complex I are discussed.
Compounded effects of climate change and habitat alteration shift patterns of butterfly diversity
Authors: Forister Matthew L. , McCall Andrew C. , Sanders Nathan J. , Fordyce James A. , Thorne James H. , O’Brien Joshua , Waetjen David P. , Shapiro Arthur M.
Published: January 2010

Climate change and habitat destruction have been linked to global declines in vertebrate biodiversity, including mammals, amphibians, birds, and fishes. However, invertebrates make up the vast majority of global species richness, and the combined effects of climate change and land use on invertebrates remain poorly understood. Here we present 35 years of data on 159 species of butterflies from 10 sites along an elevational gradient spanning 0–2,775 m in a biodiversity hotspot, the Sierra Nevada Mountains of Northern California. Species richness has declined at half of the sites, with the most severe reductions at the lowest elevations, where habitat destruction is greatest. At higher elevations, we observed clear upward shifts in the elevational ranges of species, consistent with the influence of global warming. Taken together, these long-term data reveal the interacting negative effects of human-induced changes on both the climate and habitat available to butterfly species in California. Furthermore, the decline of ruderal, disturbance-associated species indicates that the traditional focus of conservation efforts on more specialized and less dispersive species should be broadened to include entire faunas when estimating and predicting the effects of pervasive stressors.
Full distance-resolved folding energy landscape of one single protein molecule
Authors: Gebhardt J. Christof M. , Bornschlögl Thomas , Rief Matthias
Published: January 2010

Kinetic bulk and single molecule folding experiments characterize barrier properties but the shape of folding landscapes between barrier top and native state is difficult to access. Here, we directly extract the full free energy landscape of a single molecule of the GCN4 leucine zipper using dual beam optical tweezers. To this end, we use deconvolution force spectroscopy to follow an individual molecule’s trajectory with high temporal and spatial resolution. We find a heterogeneous energy landscape of the GCN4 leucine zipper domain. The energy profile is divided into two stable C-terminal heptad repeats and two less stable repeats at the N-terminus. Energies and transition barrier positions were confirmed by single molecule kinetic analysis. We anticipate that deconvolution sampling is a powerful tool for the model-free investigation of protein energy landscapes.
Task2 potassium channels set central respiratory CO
2
and O
2
sensitivity
Authors: Gestreau Christian , Heitzmann Dirk , Thomas Joerg , Dubreuil Véronique , Bandulik Sascha , Reichold Markus , Bendahhou Saïd , Pierson Patricia , Sterner Christina , Peyronnet-Roux Julie , Benfriha Chérif , Tegtmeier Ines , Ehnes Hannah , Georgieff Michael , Lesage Florian , Brunet Jean-Francois , Goridis Christo , Warth Richard , Barhanin Jacques
Published: January 2010

Task2 K
+
channel expression in the central nervous system is surprisingly restricted to a few brainstem nuclei, including the retrotrapezoid (RTN) region. All Task2-positive RTN neurons were lost in mice bearing a Phox2b mutation that causes the human congenital central hypoventilation syndrome. In plethysmography,

Task2
−/−

mice showed disturbed chemosensory function with hypersensitivity to low CO
2
concentrations, leading to hyperventilation. Task2 probably is needed to stabilize the membrane potential of chemoreceptive cells. In addition,

Task2
−/−

mice lost the long-term hypoxia-induced respiratory decrease whereas the acute carotid-body-mediated increase was maintained. The lack of anoxia-induced respiratory depression in the isolated brainstem–spinal cord preparation suggested a central origin of the phenotype. Task2 activation by reactive oxygen species generated during hypoxia could silence RTN neurons, thus contributing to respiratory depression. These data identify Task2 as a determinant of central O
2
chemoreception and demonstrate that this phenomenon is due to the activity of a small number of neurons located at the ventral medullary surface.
Quaternary dynamics and plasticity underlie small heat shock protein chaperone function
Authors: Stengel Florian , Baldwin Andrew J. , Painter Alexander J. , Jaya Nomalie , Basha Eman , Kay Lewis E. , Vierling Elizabeth , Robinson Carol V. , Benesch Justin L. P.
Published: January 2010

Small Heat Shock Proteins (sHSPs) are a diverse family of molecular chaperones that prevent protein aggregation by binding clients destabilized during cellular stress. Here we probe the architecture and dynamics of complexes formed between an oligomeric sHSP and client by employing unique mass spectrometry strategies. We observe over 300 different stoichiometries of interaction, demonstrating that an ensemble of structures underlies the protection these chaperones confer to unfolding clients. This astonishing heterogeneity not only makes the system quite distinct in behavior to ATP-dependent chaperones, but also renders it intractable by conventional structural biology approaches. We find that thermally regulated quaternary dynamics of the sHSP establish and maintain the plasticity of the system. This extends the paradigm that intrinsic dynamics are crucial to protein function to include equilibrium fluctuations in quaternary structure, and suggests they are integral to the sHSPs’ role in the cellular protein homeostasis network.
Kupfer-type immunological synapse characteristics do not predict anti-brain tumor cytolytic T-cell function in vivo
Authors: Yang J. , Sanderson N.S.R. , Wawrowsky K. , Puntel M. , Castro M.G. , Lowenstein P.R.
Published: January 2010

To analyze the in vivo structure of antigen-specific immunological synapses during an effective immune response, we established brain tumors expressing the surrogate tumor antigen ovalbumin and labeled antigen-specific anti-glioma T cells using specific tetramers. Using these techniques, we determined that a significant number of antigen-specific T cells were localized to the brain tumor and surrounding brain tissue and a large percentage could be induced to express IFNγ when exposed to the specific ovalbumin-derived peptide epitope SIINFEKL. Detailed morphological analysis of T cells immunoreactive for tetramers in direct physical contact with tumor cells expressing ovalbumin indicated that the interface between T cells and target tumor cells displayed various morphologies, including Kupfer-type immunological synapses. Quantitative analysis of adjacent confocal optical sections was performed to determine if the higher frequency of antigen-specific antiglioma T cells present in animals that developed an effective antitumor immune response could be correlated with a specific immunological synaptic morphology. Detailed in vivo quantitative analysis failed to detect an increased proportion of immunological synapses displaying the characteristic Kupfer-type morphology in animals mounting a strong and effective antitumor immune response as compared with those experiencing a clinically ineffective response. We conclude that an effective cytolytic immune response is not dependent on an increased frequency of Kupfer-type immunological synapses between T cells and tumor cells.
Running enhances spatial pattern separation in mice
Authors: Creer David J. , Romberg Carola , Saksida Lisa M. , van Praag Henriette , Bussey Timothy J.
Published: January 2010

Increasing evidence suggests that regular exercise improves brain health and promotes synaptic plasticity and hippocampal neurogenesis. Exercise improves learning, but specific mechanisms of information processing influenced by physical activity are unknown. Here, we report that voluntary running enhanced the ability of adult (3 months old) male C57BL/6 mice to discriminate between the locations of two adjacent identical stimuli. Improved spatial pattern separation in adult runners was tightly correlated with increased neurogenesis. In contrast, very aged (22 months old) mice had impaired spatial discrimination and low basal cell genesis that was refractory to running. These findings suggest that the addition of newly born neurons may bolster dentate gyrus-mediated encoding of fine spatial distinctions.
A dinoflagellate exploits toxins to immobilize prey prior to ingestion
Authors: Sheng Jian , Malkiel Edwin , Katz Joseph , Adolf Jason E. , Place Allen R.
Published: January 2010

Toxins produced by the harmful algal bloom (HAB) forming, mixotrophic dinoflagellate
Karlodinium veneficum
have long been associated with fish kills. To date, the perceived ecological role for toxins has been relief from grazing pressures. Here, we demonstrate that karlotoxins also serve as a predation instrument. Using high-speed holographic microscopy, we measure the swimming behavior of several toxic and nontoxic strains of
K. veneficum
and their prey,
Storeatula major
, within dense suspensions. The selected strains produce toxins with varying potency and dosages, including a nontoxic one. Results clearly show that mixing the prey with the predatory, toxic strains causes prey immobilization at rates that are consistent with the karlotoxins’ potency and dosage. Even prey cells that continue swimming slow down after exposure to toxic predators. The swimming characteristics of predators vary substantially in pure suspensions, as quantified by their velocity, radii of helical trajectories, and direction of helical rotation. When mixed with prey, all toxic strains that are involved in predation slow down. Furthermore, they substantially reduced their predominantly vertical migration, presumably to remain in the vicinity of their prey. Conversely, the nontoxic control strain does not alter its swimming and does not affect prey behavior. In separate experiments, we show that exposing prey to exogenous toxins also causes prey immobilization at rates consistent with potency. Clearly, the toxic predatory strains use karlotoxins as a means of stunning their prey, before ingesting it. These findings add a substantiated critical understanding for why some HAB species produce such complex toxin molecules.
ABC transporter AtABCG25 is involved in abscisic acid transport and responses
Authors: Kuromori Takashi , Miyaji Takaaki , Yabuuchi Hikaru , Shimizu Hidetada , Sugimoto Eriko , Kamiya Asako , Moriyama Yoshinori , Shinozaki Kazuo
Published: January 2010

Abscisic acid (ABA) is one of the most important phytohormones involved in abiotic stress responses, seed maturation, germination, and senescence. ABA is predominantly produced in vascular tissues and exerts hormonal responses in various cells, including guard cells. Although ABA responses require extrusion of ABA from ABA-producing cells in an intercellular ABA signaling pathway, the transport mechanisms of ABA through the plasma membrane remain unknown. Here we isolated an ATP-binding cassette (ABC) transporter gene,
AtABCG25
, from
Arabidopsis
by genetically screening for ABA sensitivity.
AtABCG25
was expressed mainly in vascular tissues. The fluorescent protein-fused AtABCG25 was localized at the plasma membrane in plant cells. In membrane vesicles derived from AtABCG25-expressing insect cells, AtABCG25 exhibited ATP-dependent ABA transport. The
AtABCG25
-overexpressing plants showed higher leaf temperatures, implying an influence on stomatal regulation. These results strongly suggest that AtABCG25 is an exporter of ABA and is involved in the intercellular ABA signaling pathway. The presence of the ABA transport mechanism sheds light on the active control of multicellular ABA responses to environmental stresses among plant cells.
Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod
Authors: Yao Haimin , Dao Ming , Imholt Timothy , Huang Jamie , Wheeler Kevin , Bonilla Alejandro , Suresh Subra , Ortiz Christine
Published: January 2010

Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of
Crysomallon squamiferum
, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications.
Plants cause ecosystem nutrient depletion via the interruption of bird-derived spatial subsidies
Authors: Young Hillary S. , McCauley Douglas J. , Dunbar Robert B. , Dirzo Rodolfo
Published: January 2010

Plant introductions and subsequent community shifts are known to affect nutrient cycling, but most such studies have focused on nutrient enrichment effects. The nature of plant-driven nutrient depletions and the mechanisms by which these might occur are relatively poorly understood. In this study we demonstrate that the proliferation of the commonly introduced coconut palm,
Cocos nucifera
, interrupts the flow of allochthonous marine subsidies to terrestrial ecosystems via an indirect effect: impact on birds. Birds avoid nesting or roosting in
C. nucifera
, thus reducing the critical nutrient inputs they bring from the marine environment. These decreases in marine subsidies then lead to reductions in available soil nutrients, decreases in leaf nutrient quality, diminished leaf palatability, and reduced herbivory. This nutrient depletion pathway contrasts the more typical patterns of nutrient enrichment that follow plant species introductions. Research on the effects of spatial subsidy disruptions on ecosystems has not yet examined interruptions driven by changes within the recipient community, such as plant community shifts. The ubiquity of coconut palm introductions across the tropics and subtropics makes these observations particularly noteworthy. Equally important, the case of
C. nucifera
provides a strong demonstration of how plant community changes can dramatically impact the supply of allochthonous nutrients and thereby reshape energy flow in ecosystems.
Transforming Growth Factor-β1 Induces Transdifferentiation of Myoblasts into Myofibroblasts via Up-Regulation of Sphingosine Kinase-1/S1P3 Axis
Authors: Cencetti Francesca , Bernacchioni Caterina , Nincheri Paola , Donati Chiara , Bruni Paola
Published: January 2010

The pleiotropic cytokine transforming growth factor (TGF)-β1 is a key player in the onset of skeletal muscle fibrosis, which hampers tissue repair. However, the molecular mechanisms implicated in TGFβ1-dependent transdifferentiation of myoblasts into myofibroblasts are presently unknown. Here, we show that TGFβ1 up-regulates sphingosine kinase (SK)-1 in C2C12 myoblasts in a Smad-dependent manner, and concomitantly modifies the expression of sphingosine 1-phosphate (S1P) receptors (S1PRs). Notably, pharmacological or short interfering RNA-mediated inhibition of SK1 prevented the induction of fibrotic markers by TGFβ1. Moreover, inhibition of S1P3, which became the highest expressed S1PR after TGFβ1 challenge, strongly attenuated the profibrotic response to TGFβ1. Furthermore, downstream of S1P3, Rho/Rho kinase signaling was found critically implicated in the profibrotic action of TGFβ1. Importantly, we demonstrate that SK/S1P axis, known to play a key role in myogenesis via S1P2, consequently to TGFβ1-dependent S1PR pattern remodeling, becomes responsible for transmitting a profibrotic, antidifferentiating action. This study provides new compelling information on the mechanism by which TGFβ1 gives rise to fibrosis in skeletal muscle, opening new perspectives for its pharmacological treatment. Moreover, it highlights the pleiotropic role of SK/S1P axis in skeletal myoblasts that, depending on the expressed S1PR pattern, seems capable of eliciting multiple, even contrasting biological responses.
Introduction: What Is Music Theater?
Authors: Salzman Eric , Desi Thomas
Published: January 2010

What is music theater? This is a fairly recent coinage in English, which can function as an “inclusive” term for all forms of theater based in music or music-and-dance (in which case opera is only a specialized historical form of music theater) and sometimes (as we use it here) as an “exclusive” term to refer to recent developments outside of traditional opera, operetta, and musicals. The crisis of opera is, at least in part, a reflection of the fact that opera is no longer at the apex of the arts, a role that has been taken over by new media. The “return” of music theater and its involvement with new media and new technologies is both the revival of something old, but also something new and ongoing.
Chapter 4 Cultural Narratives and Performance Institutions
Authors: Salzman Eric , Desi Thomas
Published: January 2010

This chapter discusses the cultural narratives inside and outside of opera and music theater as well as structural models for operatic and music theater companies. Issues of storytelling and highbrow/lowbrow art are followed by discussions of new roles for performers and subject matter. The chapter ends with a consideration of “loudspeaker culture”.
Chapter 9 Music Theater as Musiktheater
Authors: Salzman Eric , Desi Thomas
Published: January 2010

Music theater is a coinage taken from the German musiktheater, originally applied to the chamber opera or zeitoper of the '20s and '30s. After World War II, new music in Germany became experimental, almost exclusively instrumental and highly abstract (non-theatrical) as a reaction to fascism and the devastation of the war. This movement was focused on the Darmstadt Summer Courses. The return of the human voice and the influence of Cage can be noted in the works of Stockhausen, Ligeti, Schnebel, and others. Darmstadt began to lose its influence; the events of 1968 and the subsequent collapse of the East German regime created new concerns. Popular and social subjects began to influence younger German and Austrian composers. New technologies, multi-media and cross-over works began to appear. The founding of the Munich Biennale (by Henze) and the establishment of festivals and smaller companies provided platforms for new works of opera and music theater.