bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of Cytoplasmic Dynein and LIS1 in Cell Migration
Authors: Vallee R.B. , Dujardin D.L. , Barnhart L.E. , Stehman S.A.
Published: January 2008

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Improvements for HR- and Cryo-SEM by the VCT 100 High-Vacuum Cryo Transfer System and SEM Cooling Stage
Authors: Wepf R. , Richter T. , Sattler M. , Kaech A.
Published: January 2008

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Automated Energy Filtered Most Probable Loss Tomography of Thick Selectively Stained Biological Samples
Authors: Bouwer J.C. , Mackey M. , Lawrence A. , Deerinck T.J. , Jones Y. , Terada M. , Martone M E , Peltier S. , Ellisman M H
Published: January 2008

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Digital Imaging Workflow in Modern Microscopy
Authors: Mackenzie J.
Published: January 2008

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
TEM Investigation of Nanophase Aluminum Powder
Authors: Gertsman Valéry Y. , Kwok Queenie S.M.
Published: January 2008

Nanophase aluminum powder was characterized in a field-emission-gun
transmission electron microscope (TEM). Different techniques were used to
investigate the structure of the particles, including conventional
bright-field and dark-field imaging, scanning transmission electron
microscopy (STEM), high-resolution lattice imaging, diffraction studies,
energy dispersive X-ray spectroscopy (EDS) analysis and mapping, and
electron energy loss spectroscopy (EELS) analysis and mapping. It has been
established that the particle cores consist of aluminum single crystals
that sometimes contain crystal lattice defects. The core is covered by a
passivating layer of aluminum oxide a few nanometers thick. The alumina is
mostly amorphous, but evidences of partial crystallinity of the oxide were
also found. The thickness of this layer was measured using different
techniques, and the results are in good agreement with each other. The
particles are agglomerated in two distinct ways. Some particles were
apparently bonded together during processing before oxidation. These
mostly form dumbbells covered by a joint oxide layer. Also, oxidized
particles are loosely assembled into relatively large clusters.
Cross Talk between Cell–Cell and Cell–Matrix Adhesion Signaling Pathways during Heart Organogenesis: Implications for Cardiac Birth Defects
Authors: Linask Kersti K. , Manisastry Shyam , Han Mingda
Published: January 2008

The anterior–posterior and dorsal–ventral progression of heart organogenesis is well illustrated by the patterning and activity of two members of different families of cell adhesion molecules: the calcium-dependent cadherins, specifically N-cadherin, and the extracellular matrix glycoproteins, fibronectin. N-cadherin by its binding to the intracellular molecule β-catenin and fibronectin by its binding to integrins at focal adhesion sites, are involved in regulation of gene expression by their association with the cytoskeleton and through signal transduction pathways. The ventral precardiac mesoderm cells epithelialize and become stably committed by the activation of these cell–matrix and intracellular signaling transduction pathways. Cross talk between the adhesion signaling pathways initiates the characteristic phenotypic changes associated with cardiomyocyte differentiation: electrical activity and organization of myofibrils. The development of both organ form and function occurs within a short interval thereafter. Mutations in any of the interacting molecules, or environmental insults affecting either of these signaling pathways, can result in embryonic lethality or fetuses born with severe heart defects. As an example, we have defined that exposure of the embryo temporally to lithium during an early sensitive developmental period affects a canonical Wnt pathway leading to β-catenin stabilization. Lithium exposure results in an anterior–posterior progression of severe cardiac defects.
Impaired Intracellular Ca2+Dynamics in Live Cardiomyocytes Revealed by Rapid Line Scan Confocal Microscopy
Authors: Plank David M. , Sussman Mark A.
Published: January 2008

Altered intracellular Ca2+dynamics are characteristically observed in cardiomyocytes from failing hearts. Studies of Ca2+handling in myocytes predominantly use Fluo-3 AM, a visible light excitable Ca2+chelating fluorescent dye in conjunction with rapid line-scanning confocal microscopy. However, Fluo-3 AM does not allow for traditional ratiometric determination of intracellular Ca2+concentration and has required the use of mathematic correction factors with values obtained from separate procedures to convert Fluo-3 AM fluorescence to appropriate Ca2+concentrations. This study describes methodology to directly measure intracellular Ca2+levels using inactivated, Fluo-3-AM-loaded cardiomyocytes equilibrated with Ca2+concentration standards. Titration of Ca2+concentration exhibits a linear relationship to increasing Fluo-3 AM fluorescence intensity. Images obtained from individual myocyte confocal scans were recorded, average pixel intensity values were calculated, and a plot is generated relating the average pixel intensity to known Ca2+concentrations. These standard plots can be used to convert transient Ca2+fluorescence obtained with experimental cells to Ca2+concentrations by linear regression analysis. Standards are determined on the same microscope used for acquisition of unknown Ca2+concentrations, simplifying data interpretation and assuring accuracy of conversion values. This procedure eliminates additional equipment, ratiometric imaging, and mathematic correction factors and should be useful to investigators requiring a straightforward method for measuring Ca2+concentrations in live cells using Ca2+-chelating dyes exhibiting variable fluorescence intensity.
Searching Ultimate Nanometrology for AlOx Thickness in Magnetic
Tunnel Junction by Analytical Electron Microscopy and X-ray
Reflectometry
Authors: Song Se Ahn , Hirano Tatsumi , Park Jong Bong , Kaji Kazutoshi , Kim Ki Hong , Terada Shohei
Published: January 2008

Practical analyses of the structures of ultrathin multilayers in
tunneling magneto resistance (TMR) and Magnetic Random Access Memory
(MRAM) devices have been a challenging task because layers are very thin,
just 1–2 nm thick. Particularly, the thinness (∼1 nm) and
chemical properties of the AlOx barrier layer are critical to its magnetic
tunneling property. We focused on evaluating the current TEM analytical
methods by measuring the thickness and composition of an AlOx layer using
several TEM instruments, that is, a round robin test, and cross-checked
the thickness results with an X-ray reflectometry (XRR) method. The
thickness measured by using HRTEM, HAADF-STEM, and zero-loss images was
1.1 nm, which agreed with the results from the XRR method. On the other
hand, TEM-EELS measurements showed 1.8 nm for an oxygen 2D-EELS image and
3.0 nm for an oxygen spatially resolved EELS image, whereas the STEM-EDS
line profile showed 2.5 nm in thickness. However, after improving the
TEM-EELS measurements by acquiring time-resolved images, the measured
thickness of the AlOx layer was improved from 1.8 nm to 1.4 nm for the
oxygen 2D-EELS image and from 3.0 nm to 2.0 nm for the spatially resolved
EELS image, respectively. Also the observed thickness from the EDS line
profile was improved to 1.4 nm after more careful optimization of the
experimental parameters. We found that EELS and EDS of one-dimensional
line scans or two-dimensional elemental mapping gave a larger AlOx
thickness even though much care was taken. The reasons for larger measured
values can be found from several factors such as sample drift, beam
damage, probe size, beam delocalization, and multiple scattering for the
EDS images, and chromatic aberration, diffraction limit due to the
aperture, delocalization, alignment between layered direction in samples,
and energy dispersion direction in the EELS instrument for EELS images. In
the case of STEM-EDS mapping with focused nanoprobes, it is always
necessary to reduce beam damage and sample drift while trying to maintain
the signal-to-noise (S/N) ratio as high as possible. Also we confirmed
that the time-resolved TEM-EELS acquisition technique improves S/N
ratios of elemental maps without blurring the images.
Introduction: Frontiers of Electron Microscopy in Materials
Science
Authors: King Wayne
Published: January 2008

The Ninth Frontiers of Electron Microscopy in Materials Science
Conference (FEMMS 2003) was held October 5–10, 2003 at the Claremont
Resort and Spa in Berkeley, CA. Major sponsors for this meeting included
Lawrence Livermore National Laboratory, Argonne National Laboratory,
Lawrence Berkeley National Laboratory, Brookhaven National Laboratory,
Frederick Seitz Materials Research Laboratory, Oak Ridge National
Laboratory, National Science Foundation, and University of California at
Davis. Sponsors also included LEO Electron Microscopy Ltd. (Carl Zeiss
SMT), E. A. Fischione, Inc., Gatan, Inc., Thermo NORAN (Thermo Electron
Corp.), FEI Company, Hitachi-HHTA, JEOL USA, Inc., Seiko Instruments, and
CEOS GmbH.
AUSTRALIAN MICROBEAM ANALYSIS SOCIETY
Authors: Griffin Brendan
Published: January 2008

Message from the President; AMAS calendar of events; and lists of past
AMAS presidents, AMAS executives 2005, and AMAS awards.
Building Rules on Top of Ontologies for the Semantic Web with Inductive Logic Programming
Authors: LISI FRANCESCA A.
Published: January 2008

Building rules on top of ontologies is the ultimate goal of the logical layer of the Semantic Web. To this aim, an ad-hoc markup language for this layer is currently under discussion. It is intended to follow the tradition of hybrid knowledge representation and reasoning systems, such as$\mathcal{AL}$-log that integrates the description logic$\mathcal{ALC}$and the function-free Horn clausal languageDatalog. In this paper, we consider the problem of automating the acquisition of these rules for the Semantic Web. We propose a general framework for rule induction that adopts the methodological apparatus of Inductive Logic Programming and relies on the expressive and deductive power of$\mathcal{AL}$-log. The framework is valid whatever the scope of induction (description versus prediction) is. Yet, for illustrative purposes, we also discuss an instantiation of the framework which aims at description and turns out to be useful in Ontology Refinement.
A record of Antarctic climate and ice sheet history recovered
Authors: Naish Tim , Powell Ross , Levy Richard , Florindo Fabio , Harwood David , Kuhn Gerhard , Niessen Frank , Talarico Franco , Wilson Gary
Published: January 2008

Antarctica's late Cenozoic (the past ∼15 million years) climate history is poorly known from direct evidence, owing to its remoteness, an extensive sea ice apron, and an ice sheet cover over the region for the past 34 million years. Consequently, knowledge about the role of Antarctica's ice sheets in global sea level and climate has relied heavily upon interpretations of oxygen isotope records from deep‐sea cores. Whereas these isotopic records have revolutionized our understanding of climate‐ice‐ocean interactions, questions still remain about the specific role of Antarctic ice sheets in global climate. Such questions can be addressed from geological records at the marine margin of the ice sheets, recovered by drilling from floating ice platforms [e.g., Davey et al., 2001; Harwood et al., 2006; Barrett, 2007].
Toward a new generation of ice sheet models
Authors: Little Christopher M. , Oppenheimer Michael , Alley Richard B. , Balaji Venkatramani , Clarke Garry K. C. , Delworth Thomas L. , Hallberg Robert , Holland David M. , Hulbe Christina L. , Jacobs Stan , Johnson Jesse V. , Levy Hiram , Lipscomb William H. , Marshall Shawn J. , Parizek Byron R. , Payne Antony J. , Schmidt Gavin A. , Stouffer Ronald J. , Vaughan David G. , Winton Michael
Published: January 2008

Large ice sheets, such as those presently covering Greenland and Antarctica, are important in driving changes of global climate and sea level. Yet numerical models developed to predict climate change and ice sheet‐driven sea level fluctuations have substantial limitations: Poorly represented physical processes in the ice sheet component likely lead to an underestimation of sea level rise forced by a warming climate.

The resultant uncertainty in sea level projections, and the implications for climate policy, have been widely discussed since the publication of the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) [IPCC, 2007]. The assessment report notes that current models do not include “the full effects of changes in ice sheet flow, because a basis in published literature is lacking.” The report also notes that the understanding of rapid dynamical changes in ice flow “is too limited to assess their likelihood or provide a best estimate or an upper bound for sea level rise.”
Tracing the provenance of fine‐grained dust deposited on the central Chinese Loess Plateau
Authors: Sun Youbin , Tada Ryuji , Chen Jun , Liu Qingsong , Toyoda Shin , Tani Atsushi , Ji Junfeng , Isozaki Yuko
Published: January 2008

Eolian dust deposits in north China provide an excellent means of determining past variations in continental paleoclimate and atmospheric circulation. However, debate still exists on which deserts in east Asia are the dominant sources of Chinese loess and whether the dust provenance has shifted significantly at different time scales. Here we present new constraints on the provenance of fine‐grained dust deposited on the central Chinese Loess Plateau (CLP) by combining electron spin resonance signal intensity and crystallinity index of fine‐grained quartz contained in samples from two loess‐paleosol sequences. Our results show that the fine‐grained dust deposits on the CLP originate mainly from the Gobi desert in southern Mongolia and the sandy deserts in northern China (primarily the Badain Juran and Tengger deserts), rather than from the Taklimakan desert in western China, at least during the last climatic cycle. The dominant source of fine‐grained dust varied significantly, from southern Mongolia during cold periods, to northern China during warm periods. The glacial‐interglacial provenance fluctuations are strongly coupled with changes in the intensity of the near‐surface northwesterly winter monsoon.
Selective bias in temporal bisection task by number exposition
Authors: Vicario Carmelo Mario
Published: January 2008

Temporal experience can be modulated by a number of environmental factors such as quantity. Here I show that merely looking at numbers causes a bias in imaginative (but not perceptual) time bisection task that depends on the number’s magnitude. This suggests that automatic shifts of spatial attention to the left and right side, as a result of exposure to numbers, modulates temporal as well as spatial behaviour (2,3,4). This finding suggests that the representation of time and space produce certain patterns in neural maps that are decoded by means of the similar neural mechanisms.
Molecular regulation of T‐cell anergy
Authors: Zheng Yan , Zha Yuanyuan , Gajewski Thomas F
Published: January 2008

The activation of T cells is tightly controlled by many positive and negative regulatory processes. This fine‐tuning allows productive immunity to pathogens while minimizing the risk of autoimmunity. One negative regulatory mechanism is clonal anergy, which is a hyporesponsive state that occurs when T cells are activated through the T‐cell antigen receptor in the absence of appropriate co‐stimulatory signals. Recent studies have confirmed a crucial role for defective Ras activation in mediating this hyporesponsive state. Diminished Ras activation can, in part, be explained by the upregulated expression of diacylglycerol kinases (DGKs), which phosphorylate diacylglycerol and restrict Ras guanyl releasing protein 1 (RasGRP1)‐dependent activation of Ras. Increased expression of DGKs is probably transcriptional and is accompanied by augmented expression of additional negative regulators, including the transcription factors early growth response (Egr) 2 and Egr3, and the E3 ubiquitin ligases known as gene related to anergy in lymphocytes (GRAIL) and Casitas B‐cell lymphoma‐b (Cbl‐b). A model is emerging for how these factors are regulated to control T‐cell responsiveness.
A conserved mechanism for replication origin recognition and binding in archaea
Authors: Majerník Alan I. , Chong James P. J.
Published: January 2008

To date, methanogens are the only group within the archaea where firing DNA replication origins have not been demonstrated in vivo. In the present study we show that a previously identified cluster of ORB (origin recognition box) sequences do indeed function as an origin of replication in vivo in the archaeon Methanothermobacter thermautotrophicus. Although the consensus sequence of ORBs in M. thermautotrophicus is somewhat conserved when compared with ORB sequences in other archaea, the Cdc6-1 protein from M. thermautotrophicus (termed MthCdc6-1) displays sequence-specific binding that is selective for the MthORB sequence and does not recognize ORBs from other archaeal species. Stabilization of in vitro MthORB DNA binding by MthCdc6-1 requires additional conserved sequences 3′ to those originally described for M. thermautotrophicus. By testing synthetic sequences bearing mutations in the MthORB consensus sequence, we show that Cdc6/ORB binding is critically dependent on the presence of an invariant guanine found in all archaeal ORB sequences. Mutation of a universally conserved arginine residue in the recognition helix of the winged helix domain of archaeal Cdc6-1 shows that specific origin sequence recognition is dependent on the interaction of this arginine residue with the invariant guanine. Recognition of a mutated origin sequence can be achieved by mutation of the conserved arginine residue to a lysine or glutamine residue. Thus despite a number of differences in protein and DNA sequences between species, the mechanism of origin recognition and binding appears to be conserved throughout the archaea.
Prototype chicken galectins revisited: characterization of a third protein with distinctive hydrodynamic behaviour and expression pattern in organs of adult animals
Authors: Kaltner Herbert , Solís Dolores , Kopitz Jürgen , Lensch Martin , Lohr Michaela , Manning Joachim C. , Mürnseer Michael , Schnölzer Martina , André Sabine , Sáiz José Luis , Gabius Hans-Joachim
Published: January 2008

Prototype galectins are versatile modulators of cell adhesion and growth via their reactivity to certain carbohydrate and protein ligands. These functions and the galectins' marked developmental regulation explain their attractiveness as models to dissect divergent evolution after gene duplication. Only two members have so far been assumed to constitute this group in chicken, namely the embryonic muscle/liver form {C-16 or CLL-I [16 kDa; chicken lactose lectin, later named CG-16 (chicken galectin-16)]} and the embryonic skin/intestine form (CLL-II or C-14; later named CG-14). In the present study, we report on the cloning and expression of a third prototype CG. It has deceptively similar electrophoretic mobility compared with recombinant C-14, the protein first isolated from embryonic skin, and turned out to be identical with the intestinal protein. Hydrodynamic properties unusual for a homodimeric galectin and characteristic traits in the proximal promoter region set it apart from the two already known CGs. Their structural vicinity to galectin-1 prompts their classification as CG-1A (CG-16)/CG-1B (CG-14), whereas sequence similarity to mammalian galectin-2 gives reason to refer to the intestinal protein as CG-2. The expression profiling by immunohistochemistry with specific antibodies discerned non-overlapping expression patterns for the three CGs in several organs of adult animals. Overall, the results reveal a network of three prototype galectins in chicken.
Effects of oncogenic p110α subunit mutations on the lipid kinase activity of phosphoinositide 3-kinase
Authors: Carson Jeffrey D. , Van Aller Glenn , Lehr Ruth , Sinnamon Robert H. , Kirkpatrick Robert B. , Auger Kurt R. , Dhanak Dashyant , Copeland Robert A. , Gontarek Richard R. , Tummino Peter J. , Luo Lusong
Published: January 2008

The PIK3CA gene, encoding the p110α catalytic subunit of Class IA PI3Ks (phosphoinositide 3-kinases), is frequently mutated in many human tumours. The three most common tumour-derived alleles of p110α, H1047R, E542K and E545K, were shown to potently activate PI3K signalling in human epithelial cells. In the present study, we examine the biochemical activity of the recombinantly purified PI3K oncogenic mutants. The kinetic characterizations of the wt (wild-type) and the three ‘hot spot’ PI3K mutants show that the mutants all have approx. 2-fold increase in lipid kinase activities. Interestingly, the phosphorylated IRS-1 (insulin receptor substrate-1) protein shows activation of the lipid kinase activity for the wt and H1047R but not E542K and E545K PI3Kα, suggesting that these mutations represent different mechanisms of lipid kinase activation and hence transforming activity in cancer cells.
Activity profiling of human deSUMOylating enzymes (SENPs) with synthetic substrates suggests an unexpected specificity of two newly characterized members of the family
Authors: Drag Marcin , Mikolajczyk Jowita , Krishnakumar I. M. , Huang Ziwei , Salvesen Guy S.
Published: January 2008

SENPs [Sentrin/SUMO (small ubiquitin-related modifier)-specific proteases] include proteases that activate the precursors of SUMOs, or deconjugate SUMOs attached to target proteins. SENPs are usually assayed on protein substrates, and for the first time we demonstrate that synthetic substrates can be convenient tools in determining activity and specificity of these proteases. We synthesized a group of short synthetic peptide fluorogenic molecules based on the cleavage site within SUMOs. We demonstrate the activity of human SENP1, 2, 5, 6, 7 and 8 on these substrates. A parallel positional scanning approach using a fluorogenic tetrapeptide library established preferences of SENPs in the P3 and P4 positions that allowed us to design optimal peptidyl reporter substrates. We show that the specificity of SENP1, 2, 5 and 8 on the optimal peptidyl substrates matches their natural protein substrates, and that the presence of the SUMO domain enhances catalysis by 2–3 orders of magnitude. We also show that SENP6 and 7 have an unexpected specificity that distinguishes them from other members of the family, implying that, in contrast to previous predictions, their natural substrate(s) may not be SUMO conjugates.
Trimerization of collagen IX α-chains does not require the presence of the COL1 and NC1 domains
Authors: Jäälinoja Juha , Ylöstalo Joni , Beckett William , Hulmes David J. S. , Ala-Kokko Leena
Published: January 2008

Collagen IX is a heterotrimer of three α-chains, which consists of three COL domains (collagenous domains) (COL1–COL3) and four NC domains (non-collagenous domains) (NC1–NC4), numbered from the C-terminus. Although collagen IX chains have been shown to associate via their C-terminal NC1 domains and form a triple helix starting from the COL1 domain, it is not known whether chain association can occur at other sites and whether other collagenous and non-collagenous regions are involved. To address this question, we prepared five constructs, two long variants (beginning at the NC4 domain) and three short variants (beginning at the COL2 domain), all ending at the NC2 domain (or NC2 replaced by NC1), to study association and selection of collagen IX α-chains. Both long variants were able to associate with NC1 or NC2 at the C-terminus and form various disulfide-bonded trimers, but the specificity of chain selection was diminished compared with full-length chains. Trimers of the long variant ending at NC2 were shown to be triple helical by CD. Short variants were not able to assemble into disulfide-bonded trimers even in the presence of both conserved cysteine residues from the COL1–NC1 junction. Our results demonstrate that collagen IX α-chains can associate in the absence of COL1 and NC1 domains to form a triple helix, but the COL2–NC2 region alone is not sufficient for trimerization. The results suggest that folding of collagen IX is a co-operative process involving multiple COL and NC domains and that the COL1–NC1 region is important for chain specificity.
The role of loop and β-turn residues as structural and functional determinants for the lipoyl domain from the Escherichia coli 2-oxoglutarate dehydrogenase complex
Authors: Jones D. Dafydd , Perham Richard N.
Published: January 2008

The lipoyl domain of the dihydrolipoyl succinyltransferase (E2o) component of the 2OGDH (2-oxoglutarate dehydrogenase) multienzyme complex houses the lipoic acid cofactor through covalent attachment to a specific lysine side chain residing at the tip of a β-turn. Residues within the lipoyl-lysine β-turn and a nearby prominent loop have been implicated as determinants of lipoyl domain structure and function. Protein engineering of the Escherichia coli E2o lipoyl domain (E2olip) revealed that removal of residues from the loop caused a major structural change in the protein, which rendered the domain incapable of reductive succinylation by 2-oxoglutarate decarboxylase (E1o) and reduced the lipoylation efficiency. Insertion of a new loop corresponding to that of the E. coli pyruvate dehydrogenase lipoyl domain (E2plip) restored lipoylation efficiency and the capacity to undergo reductive succinylation returned, albeit at a lower rate. Exchange of the E2olip loop sequence significantly improved the ability of the domain to be reductively acetylated by pyruvate decarboxylase (E1p), retaining approx. 10-fold more acetyl groups after 25 min than wild-type E2olip. Exchange of the β-turn residue on the N-terminal side of the E2o lipoyl-lysine DKA/V motif to the equivalent residue in E2plip (T42G), both singly and in conjunction with the loop exchange, reduced the ability of the domain to be reductively succinylated, but led to an increased capacity to be reductively acetylated by the non-cognate E1p. The T42G mutation also slightly enhanced the lipoylation rate of the domain. The surface loop is important to the structural integrity of the protein and together with Thr42 plays an important role in specifying the interaction of the lipoyl domain with its partner E1o in the E. coli 2OGDH complex.
High rates of superoxide production in skeletal-muscle mitochondria respiring on both complex I- and complex II-linked substrates
Authors: Muller Florian L. , Liu Yuhong , Abdul-Ghani Muhammad A. , Lustgarten Michael S. , Bhattacharya Arunabh , Jang Youngmok C. , Van Remmen Holly
Published: January 2008

Despite the considerable interest in superoxide as a potential cause of pathology, the mechanisms of its deleterious production by mitochondria remain poorly understood. Previous studies in purified mitochondria have found that the highest rates of superoxide production are observed with succinate-driven reverse-electron transfer through complex I, although the physiological importance of this pathway is disputed because it necessitates high concentrations of succinate and is thought not to occur when NAD is in the reduced state. However, very few studies have examined the rates of superoxide production with mitochondria respiring on both NADH-linked (e.g. glutamate) and complex II-linked substrates. In the present study, we find that the rates of superoxide production (measured indirectly as H2O2) with glutamate+succinate (∼1100 pmol of H2O2·min−1·mg−1) were unexpectedly much higher than with succinate (∼400 pmol of H2O2·min−1·mg−1) or glutamate (∼80 pmol of H2O2·min−1·mg−1) alone. Superoxide production with glutamate+succinate remained high even at low substrate concentrations (<1 mM), was decreased by rotenone and was completely eliminated by FCCP (carbonyl cyanide p-trifluoromethoxyphenylhydrazone), indicating that it must in large part originate from reverse-electron transfer through complex I. Similar results were obtained when glutamate was replaced with pyruvate, α-ketoglutarate or palmitoyl carnitine. In contrast, superoxide production was consistently lowered by the addition of malate (malate+succinate ∼30 pmol of H2O2·min−1·mg−1). We propose that the inhibitory action of malate on superoxide production can be explained by oxaloacetate inhibition of complex II. In summary, the present results indicate that reverse-electron transfer-mediated superoxide production can occur under physiologically realistic substrate conditions and suggest that oxaloacetate inhibition of complex II may be an adaptive mechanism to minimize this.
Function of the N-terminus of zizimin1: autoinhibition and membrane targeting
Authors: Meller Nahum , Westbrook M. Jody , Shannon John D. , Guda Chittibabu , Schwartz Martin A.
Published: January 2008

Rho family small GTPases are critical regulators of multiple cellular functions. Dbl-homology-domain-containing proteins are the classical GEFs (guanine nucleotide exchange factors) responsible for activation of Rho proteins. Zizimin1 is a Cdc42-specific GEF that belongs to a second family of mammalian Rho-GEFs, CZH [CDM (Ced-5/DOCK180/Myoblast city)-zizimin homology] proteins, which possess a novel type of GEF domain. CZH proteins can be divided into a subfamily related to DOCK 180 and a subfamily related to zizimin1. The two groups share two conserved regions named the CZH1 (or DHR1) domain and the CZH2 (DHR2 or DOCKER) domains, the latter exhibiting GEF activity. We now show that limited proteolysis of zizimin1 suggests the existence of structural domains that do not correspond to those identified on the basis of homologies. We demonstrate that the N-terminal half binds to the GEF domain through three distinct areas, including the CZH1, to inhibit the interaction with Cdc42. The N-terminal PH (pleckstrin homology) domain binds phosphoinositides and mediates zizimin1 membrane targeting. These results define two novel functions for the N-terminal region of zizimin1.
SPAK and OSR1: STE20 kinases involved in the regulation of ion homoeostasis and volume control in mammalian cells
Authors: Delpire Eric , Gagnon Kenneth B. E.
Published: January 2008

Since the discovery of an interaction between membrane transport proteins and the mammalian STE20 (sterile 20)-like kinases SPAK (STE20/SPS1-related proline/alanine-rich kinase) and OSR1 (oxidative stress-responsive kinase-1), a significant body of work has been performed probing the molecular physiology of these two kinases. To date, the function of SPAK and OSR1 is probably the best known of all mammalian kinases of the STE20 family. As they regulate by direct phosphorylation key ion transport mechanisms involved in fluid and ion homoeostasis, SPAK and OSR1 constitute key end-of-pathway effectors. Their significance in such fundamental functions as ion homoeostasis and cell volume control is evidenced by the evolutionary pressure that resulted in the duplication of the OSR1 gene in higher vertebrates. This review examines the distribution of these two kinases in the animal kingdom and tissue expression within a single organism. It also describes the main molecular features of these two kinases with emphasis on the interacting domain located at their extreme C-terminus. A large portion of the present review is devoted to the extensive biochemical and physiological studies that have resulted in our current understanding of SPAK/OSR1 function. Finally, as our understanding is a work in progress, we also identify unresolved questions and controversies that warrant further investigation.
Nobel Prize to Rubbia and van der Meer for Finding W and Z
Authors: Lubkin Gloria B.
Published: January 2008

Carlo Rubbia and Simon van der Meer of CERN share the 1984 Nobel prize in physics for “their decisive contributions to the large project which led to the discovery of the field particles W and Z, communicators of weak interaction.” In 1976 Rubbia and his collaborators had the idea of converting the Super Proton Synchrotron at CERN into a proton-antiproton collider, where the W and Z particles could be created. In 1968 van der Meer had invented the method of stochastic cooling, which allowed the dense packing and storage of enough antiprotons to make the W and Z in pp̄ collisions. The CERN pp̄ collider project, the largest ever to appear in the context of the Nobel prize, yielded its first collisions in 1981. Two year later, in 1983, both the W and Z were observed by the UA1 detector group led by Rubbia and by the UA2 detector group. The Royal Swedish Academy of Sciences, in announcing the award, said, “Two persons in the CERN project are outstanding—Carlo Rubbia, who had and developed the idea, and Simon van der Meer, whose invention made it feasible.” This year's prize, which is worth about $193 000, is the first to honor work done at CERN.
Heterogeneous directional mobility in the early stages of polymer crystallization
Authors: Lacevic Naida , Fried Laurence E. , Gee Richard H.
Published: January 2008

Recently, we demonstrated via large-scale molecular dynamics simulations a “coexistence period” in polymer melt ordering before crystallization, where nucleation and growth mechanisms coexist with a phase-separation mechanism [Gee et al., Nat. Mater. 5, 39 (2006)]. Here, we present an extension of this work, where we analyze the directional displacements as a measure of the mobility of monomers as they order during crystallization over more than 100ns of simulation time. It is found that the polymer melt, after quenching, rapidly separates into many ordered hexagonal domains separated by amorphous regions, where surprisingly, the magnitude of the monomer’s displacement in the ordered state, parallel to the domain axial direction, is similar to its magnitude in the melt. The monomer displacements in the domain’s lateral direction are found to decrease during the time of the simulation. The ordered hexagonal domains do not align into uniform lamellar structures during the timescales of our simulations.
On the doubly ionized states of Ar2 and their intra- and interatomic decay to Ar23+
Authors: Stoychev Spas D. , Kuleff Alexander I. , Tarantelli Francesco , Cederbaum Lorenz S.
Published: January 2008

Potential energy curves of the Auger state Ar+(2p−1)–Ar, the different one- and two-site dicationic states Ar2++ (with energies in the range of 32–77eV), and the lowest two-site tricationic states Ar++–Ar+ (with energies in the range of 64–76eV) computed using elaborated ab initio methods are reported. The accessible relaxation channels of the electronic states of Ar++–Ar populated by Auger decay are studied. In particular, we study in detail the interatomic Coulombic decay following the population of one-site satellite states of Ar++(3s−13p−1)–Ar recently observed experimentally. Other relaxation pathways of Ar++–Ar, including radiative charge transfer, nuclear dynamics through curve crossing, and intra-atomic decay processes are also investigated.
High-Resolution Photo of Protoplanetary Disk Orbiting Star
Authors: Schwarzschild Bertram
Published: January 2008

Before the summer of 1983 we had no serious evidence of nonstellar, solid material orbiting any star other than our own. As far as we knew, our solar system might be a rare—perhaps even unique—curiosity in the Galaxy. But in the last 18 months we've learned a lot. Infrared investigations by the Infrared Astronomy Satellite (IRAS) and several ground-based telescopes have provided strong evidence for aggregates of small particles orbiting as many as 40 stars in our extended neighborhood (PHYSICS TODAY, May 1984, page 17).
New Hadron Naming Scheme Proposed
Authors: Schwarzschild Bertram
Published: January 2008

In the early 1950s, when the proliferation of “elementary” particles was still quite benign, Enrico Fermi is alleged to have complained, “If I could remember all those names, I would have been a botanist.” A decade after Fermi's untimely death in 1954, when the population explosion had engendered a nomenclatural anarchy, Murray Gell-Mann (Caltech) and Arthur Rosenfeld (Berkeley), two of Fermi's former students, set out to impose some order—at least to the naming of baryons.
Reaching Ignition in the Tokamak
Authors: Furth Harold P.
Published: January 2008

During the early 1930s, the study of nuclear fusion reactions was at the forefront of high-energy physics. Fifty years later, the particle energies of interest in high-energy research have outstripped those used in controlled fusion research by about eight orders of magnitude. on the other hand, frontline magnetic-fusion devices such as the Tokamak Fusion Test Reactor at Princeton, shown in figure 1, and the Joint European Torus at Culham, England, will have luminosities of 1042 particles/cm2sec—some ten orders of magnitude beyond present-day highenergy particle colliders. these numerical contrasts serve to highlight the very different goals of high-energy physics and fusion research.
Quasiperiodic Oscillations Probe Galactic X-Ray Sources
Authors: Schechter Bruce
Published: January 2008

“It's very frustrating,” says William Priedhorsky, an x-ray astronomer at Los Alamos, “that the brightest x-ray sources in the sky are the ones we have had to be most speculative about.” The sources of Priedhorsky's lament are the so-called galactic bulge sources, energetic enigmas found primarily in the galaxy's central bulge. Theorists had long speculated that the x-ray emissions of a bulge source originate from hot gas falling from a low-mass star onto the surface of its rapidly rotating neutron star companion. Unfortunately, evidence for this model had been indirect; the purported neutron star lies hidden beneath a plasma shroud. But recently the situation changed dramatically when a collaboration of researchers from the Max Planck Institute for Extraterrestrial Physics, the University of Amsterdam and MIT reported observations of rapid, quasiperiodic x-ray oscillations from the bright bulge source GX5—1. Subsequent observations of other bulge sources by Günter Hasinger (Max Planck Institute, Garching) and collaborators, and by Priedhorsky and John Middleditch (Los Alamos) have uncovered five more quasiperiodic oscillators. The existence of QPOs may provide astronomers with their first handle on the bulge source's neutron star. As a bonus they may also offer solutions to a few long-standing puzzles of galactic astronomy.
Magnetic Fields Induce Superconductivity
Authors: Schechter Bruce
Published: January 2008

In 1911 Kammerlingh Onnes made the astonishing discovery that lead loses the last vestige of its electrical resistance when cooled below 7.2 K; a current flowing through a ring of lead in its superconducting state could go on flowing forever. Only a few months later Onnes discovered that this happy state has a natural enemy—magnetism. Until recently every new superconductor discovered was prey to an external magnetic field. The existence of a critical field that destroys superconductivity could be neatly explained in terms of the microscopic theory of superconductivity proposed by John Bardeen, Leon Cooper and J. Robert Schrieffer in 1957. Nevertheless a pair of theorists speculated that, given the right set of conditions, a magnetic field could actually induce a superconducting state. Such speculation was greeted with widespread skepticism, but last year a group of researchers from the University of Geneva and the Max Planck Institute in Grenoble found a substance that apparently exhibits precisely the behavior predicted by the theorists. More recently a group from Temple University, Boston University and Los Alamos reported the discovery of a material that apparently exhibits, in addition to a host of other exotic properties, magnetic-field-induced superconductivity.
First Proton-Antiproton Collisions at Tevatron
Authors: Schwarzschild Bertram
Published: January 2008

In the small hours of Sunday morning, 13 October, the first proton-antiproton collisions produced by the Tevatron p̄p collider at Fermilab were observed by the CDF detector, which surrounds the intersection point where the two countercirculating beams repeatedly crash into one another (see cover). As its name implies, the 4-mile-circumference Tevatron ring of superconducting magnets is designed to accelerate the countercirculating protons and antiprotons to 1 TeV (1012 electron volts). The engineering test run that provided these first recorded collisions achieved beam energies of 800 GeV, giving us p̄p collision energies of 1.6 TeV in the center of mass, about three times the collision energy available at the CERN p̄p collider. One expects to be doing p̄p collider physics with 1-TeV beams next fall, when the CDF detector and a second experimental hall (which will eventually accommodate the D-zero detector system) are completed.
The low-lying electronic states of ArXe+ and their potential energy functions
Authors: Zehnder O. , Merkt F.
Published: January 2008

Photoionization and pulsed-field-ionization zero-kinetic-energy (PFI-ZEKE) photoelectron spectra of ArXe have been recorded between 96 400 and 108200cm−1 following resonance-enhanced two-photon excitation via selected vibrational levels of the C1 and D0+ Rydberg states. The PFI-ZEKE photoelectron spectra consist of three vibrational progressions corresponding to the X1∕2←X0+, A13∕2←X0+, and A21∕2←X0+ transitions. From these progressions, adiabatic ionization energies, equilibrium internuclear distances, and vibrational constants have been derived for the lowest three electronic states of ArXe+. The photoionization spectra reveal long progressions of autoionizing Rydberg states converging to the lowest vibrational levels of the A13∕2 state. A potential model has been developed that enables a global description of the low-lying electronic states of the heteronuclear rare gas dimer ions. The model explicitly treats the effects of the spin-orbit, charge-exchange, and long-range interactions. This model was used to obtain potential energy functions for all six low-lying electronic states of ArXe+ from the experimental positions of the vibrational levels of the X1∕2, A13∕2, and A21∕2 states relative to the ground neutral state and existing spectroscopic data on the B1∕2, C13∕2, and C21∕2 states.
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electroluminescence from Si/Si0.2Ge0.8 type II heterojunctions
Authors: Liao M. H. , Cheng T.-H. , Liu C. W. , Yeh Lingyen , Lee T.-L. , Liang M.-S.
Published: January 2008

A metal-oxide-semiconductor tunneling diode is used to emit electroluminescence from a Si/Si0.2Ge0.8 heterojunction. Besides the 1.1 μm and 1.6 μm infrared emission from the band edges of Si and SiGe, respectively, 2 μm infrared emission is also observed due to the radiative recombination between the electrons in the Si conduction band and the holes in the SiGe valence band. This type II recombination can emit photons whose energy is below the SiGe band gap to extend the emission range of Si/Ge-based light-emitting devices. The emission line shape can be fitted by the electron-hole-plasma recombination model.
Microstructural origin of switching field distribution in patterned Co∕Pd multilayer nanodots
Authors: Lau J. W. , McMichael R. D. , Chung S. H. , Rantschler J. O. , Parekh V. , Litvinov D.
Published: January 2008

We have identified an important microstructural origin of the switching field distribution (SFD) in patterned Co∕Pd multilayer nanodots. In this study, we patterned a marked array of 115nm Co∕Pd nanodots on 50-nm-thick Si3N4 substrate. We identified the dots with unusually small and large (>2 standard deviations of the mean) switching fields with magnetic force microscopy, followed by microstructural characterization of the same dots with transmission electron microscopy (TEM). From electron diffraction, we found that most nanodots with small switching fields have strong (200) spots, whereas those with large switching fields lack these spots. While bright-field TEM images reveal an average grain size of 7nm, dark-field images of the (200) spots reveal on average, a single grain of >10nm in lateral dimensions. Since we observed a direct correlation between strong (200) reflections and small reversal fields, we conclude that the largest grain in each nanodot, with an in-plane [001] is the likely cause for premature switching, which in turn defines the SFD of this array.
Growth of stoichiometric subnanometer silica films
Authors: Stacchiola D. J. , Baron M. , Kaya S. , Weissenrieder J. , Shaikhutdinov S. , Freund H.-J.
Published: January 2008

We present a method to grow stoichiometric SiO2 films of only ∼0.6–0.9nm in thickness on a metal substrate. Based on photoelectron and infrared spectroscopy studies, we conclude that the ∼0.6-nm-thick silica films exhibit characteristics only observed for >2.0-nm-thick films grown on conventional Si substrates. The films can be used as model oxides for fundamental studies and may have implications on the further miniaturization of metal-oxide-semiconductor transistors.
Electric surface potential and frozen-in field direct measurements in thermally poled silica
Authors: Yudistira D. , Faccio D. , Corbari C. , Kazansky P. G. , Benchabane S. , Pruneri V.
Published: January 2008

We report measurements of the electric surface potential (SP) and its temporal evolution in thermally poled silica samples, thus, providing a direct quantitative evidence of the frozen-in voltage. The SP value is found to be directly related to the voltage across the depletion layer and there is a clear link between frozen-in electric field and nonlinear optical coefficient, inferred from SP and second harmonic generation measurements respectively. Our studies also show the presence of screening surface charge layers. We have calculated the space charge distribution making evident that the thinner the sample, the larger the screening surface charge density.
Fine tuning of quantum-dot pillar microcavities by focused ion beam milling
Authors: Lohmeyer H. , Kalden J. , Sebald K. , Kruse C. , Hommel D. , Gutowski J.
Published: January 2008

The targeted fine tuning of semiconductor pillar microcavities by postfabrication focused ion beam milling is described for the example of ZnSe-based structures with CdSe quantum dots embedded. Using the sensitive dependence of the spectral position of the modes on the cavity diameter, the modes are precisely blueshifted by a reduction of the pillar diameter with an accuracy below 100nm. The microcavities can be tuned to match the emission energy of individual quantum dots at a certain temperature, which results in a strongly enhanced luminescence intensity of the dots.
Intense relativistic electron beam generation and prepulse effect in high power cylindrical diode
Authors: Roy Amitava , Menon R. , Mitra S. , Kumar D. D. P. , Kumar Senthil , Sharma Archana , Mittal K. C. , Nagesh K. V. , Chakravarthy D. P.
Published: January 2008

Intense gigawatt relativistic electron beam has been generated in a high power cylindrical diode in the presence of prepulse. A bipolar prepulse voltage, recorded at the diode, varies both in amplitude and time duration with the Marx generator voltage. It was found that only at the accelerating gap ⩽1.65cm there is some shot to shot variation in the diode voltage and current for the same Marx generator voltage. The anode and cathode plasma expansion velocities were calculated using the perveance data. The plasma expands at 5cm∕μs for 1.85cm radial anode-cathode gap and the plasma velocity decreases for smaller gap. It was found that the effect of the prepulse is less pronounced in the cylindrical diode as compared to planar diode that allows one operation of the cylindrical diode with the gap ⩽1.85cm.