bluuebunny/crossref_metadata_2025 huggingface dataset:
Project will map geological data across Earth
Authors: Zielinski Sarah
Published: April 2007

The One Geology project, which will map geological data across the Earth over the next two years, began the week of 12 March. Scientists from more than 55 countries will provide geological data for an online digital database that will use a new international standard for the data, a geological exchange language called GEOSciML. The project's target scale is 1:1 million. The first test datasets will become available later this year, and data will be added through 2008. The final data will be made available through interactive map browsers and portals such as Google Earth. The OneGeology project is part of the United Nations International Year of Planet Earth 2008. Additional information is available at http://www.onegeology.org
Global change education in the Arctic
Authors: Moore John , Kinnunen Heli , Boone Richard
Published: April 2007

Bird species new to the Arctic call across ancient forests where the buzz is from the super sawmills, not the sound of elk hooves. Oil and gas wells plumb the tundra depths, and the pipelines scarify the surface, pumping fossil wealth south with a return flow measured in dollars and rubles. The eternal ice is going and tourist ships are coming, ironically to see the icy landscape that is disappearing. This is the Arctic today.

Global change has been a fact of life for many indigenous peoples in remote parts of the world for many decades. In Svalbard, Norway, which lies north of Europe in the Arctic Ocean, January 2006 was warmer than any previous April while April was five standard deviations warmer than average. Over the longer term, the Inuit in Nunavut, Canada, have found that hunting for seals—traditionally their major food supply—has become much more difficult as sea pup numbers have declined along with sea ice [Arctic Climate Impact Assessment, 2004]. About 20 Alaskan villages are candidates for relocation because of severe coastal erosion, exacerbated by loss of protective sea ice. For example, the U.S. Army Corps of Engineers estimates that it could cost from $100 million to $400 million to relocate Kivalina, which has only 385 inhabitants [U.S. General Accounting Office, 2003].
Ionospheric challenges of the International Polar Year
Authors: Sojka Jan , Schunk Robert , van Eyken Tony , Kelly John , Heinselman Craig , McCready Mary
Published: April 2007

Fifty years ago, the first International Geophysical Year (IGY) generated a huge step function increase in observations of ionospheric variability associated with the almost continuous geomagnetic activity experienced during the largest solar maximum of the past 100 years. In turn, these observations fueled more than a decade of theoretical advancement of magnetospheric‐ionospheric electrodynamics and geomagnetic storm physics.

In stark contrast, the current International Polar Year (IPY; 2007–2009) is occurring during what may well turn out to be the deepest solar minimum in 100 years. Potentially, it could be a very geomagnetically quiet period, a period during which ionospheric variability will be driven by processes in the troposphere and mesosphere. Since the variability of the ionosphere‐thermosphere system associated with the upward propagating planetary, tidal, and gravity waves from the lower atmosphere is expected to be independent of the solar cycle, the IPY period is an ideal time to study the interchanges between the lower and upper atmospheric regions.
International Space Station supports International Polar Year
Authors: Evans Cynthia A. , Pettit Donald R.
Published: April 2007

The International Space Station (ISS) provides an excellent venue for observing Earth systems. Starting in March 2007 and coinciding with the beginning of the International Polar Year (IPY), NASA's Crew Earth Observations (CEO) payload invites IPY investigators to submit requests for relevant imagery be collected from the ISS.

Every day, ISS astronauts photograph designated sites and dynamic events on the Earth's surface using digital cameras equipped with a variety of lenses. Depending on observation parameters, astronauts can collect high‐resolution (4–6 meter pixel size; see J. Robinson and C. Evans, Eos Trans. AGU, 83(17), 185, 2002) or synopticview (lower resolution but covering very large areas) digital data in three (red‐greenblue) color bands.
Ten recommendations for reducing carbon emissions
Authors: Anonymous
Published: April 2007

Former U.S. Vice President Al Gore testified about possible solutions to mitigate anthropogenic climate change at two 21 March hearings held before committees of the U.S. House of Representatives and the U.S. Senate. His 10 recommendations to reduce U.S. carbon emissions: 1. Immediately freeze carbon dioxide emissions and then begin a program to reduce them by at least 90% by 2050. 2. Replace the payroll tax for Social Security and Medicare with a tax on pollution, particularly carbon dioxide.
On the twilight zone between clouds and aerosols
Authors: Koren Ilan , Remer Lorraine A. , Kaufman Yoram J. , Rudich Yinon , Martins J. Vanderlei
Published: April 2007

Cloud and aerosols interact and form a complex system leading to high uncertainty in understanding climate change. To simplify this non‐linear system it is customary to distinguish between “cloudy” and “cloud‐free” areas and measure them separately. However, we find that clouds are surrounded by a “twilight zone” – a belt of forming and evaporating cloud fragments and hydrated aerosols extending tens of kilometers from the clouds into the so‐called cloud‐free zone. The gradual transition from cloudy to dry atmosphere is proportional to the aerosol loading, suggesting an additional aerosol effect on the composition and radiation fluxes of the atmosphere. Using AERONET data, we find that the measured aerosol optical depth is higher by 13% ± 2% in the visible and 22% ± 2% in the NIR in measurements taken near clouds relative to its value in the measurements taken before or after, and that 30%−60% of the free atmosphere is affected by this phenomenon.
Thermal stability of a nanostructured trilayer synthetic antiferromagnet
Authors: Han J. K. , Shin K. H. , Lim S. H.
Published: April 2007

Thermal stability of a nanostructured trilayer synthetic antiferromagnet is investigated in the Worledge model. No or minimal shape anisotropy effect is predicted from the model due to the simplifying assumption that the self-demagnetizing field is equal to the dipole field. A slight relaxation of the assumption causes a large impact on the thermal stability. In the case that the dipole field is 90% of the demagnetizing field, the energy barrier to spin flop is doubled to 80kT in a typical ellipsoid cell (212×106nm2) for high density magnetic random access memory. The thermal stability of half-selected cells in the writing scheme based on the spin flop is also improved by relaxing the assumption over the applied field range relevant to magnetic random access memory applications.
Invariant analytic orthonormalization procedure with an application to coherent states
Authors: Bagarello F. , Triolo S.
Published: April 2007

We discuss a general strategy which produces an orthonormal set of vectors, stable under the action of a given set of unitary operators Aj, j=1,2,…,n, starting from a fixed normalized vector in H and from a set of unitary operators. We discuss several examples of this procedure and, in particular, we show how a set of coherentlike vectors can be produced and in which condition over the lattice spacing this can be done.
Kinetics of ion-beam damage in lithium niobate
Authors: García-Navarro A. , Agulló-López F. , Bianconi M. , Olivares J. , García G.
Published: April 2007

The damage kinetics induced by irradiation with a diversity of swift ions (O at 5MeV; F at 5.1MeV; Si at 5, 7.5, and 41MeV; and Cl at 11 and 46MeV) has been investigated in the range of 1012–1015at.∕cm2. It covers from the initial stage where single damage tracks are isolated and well separated, up to the stage where a full amorphous layer is produced. The damage is characterized by the areal fraction of disorder derived from the Rutherford backscattering∕channeling spectra. The data approximately fit an abrupt Avrami-type dependence with fluence. The fluence value at which 50% of the sample surface becomes disordered shows a clear increasing trend with the electronic stopping power of the ion. The trend is consistent with Monte Carlo simulations based on a recent model for defect creation. Moreover, the quantitative agreement for the defect generation rate appears also reasonable.
Monte Carlo calculation of second and third virial coefficients of small-scale comb polymers on lattice
Authors: Shida Kazuhito , Kasuya Atsuo , Ohno Kaoru , Kawazoe Yoshiyuki , Nakamura Yo
Published: April 2007

This paper reports the first computational estimation of the comb polymers’ third virial coefficients. The number of the chains in the comb polymers range from 5 to 11. An algorithm that counts the contributing terms of the third virial coefficients in an accelerated manner is presented along with its efficiency dependence on the polymers’ size. In addition, the second virial coefficients are estimated for the comb polymers and compared to previously reported results.
Close-coupling study of rotational energy transfer and differential scattering in H2O collisions with He atoms
Authors: Yang Benhui , Stancil P. C.
Published: April 2007

Quantum close-coupling scattering calculations of rotational energy transfer (RET) of rotationally excited H2O due to collisions with He are presented for collision energies between 10−6 and 1000cm−1 with para-H2O initially in levels 11,1, 20,2, 21,1, and 22,0 and ortho-H2O in levels 11,0, 21,2, and 22,1. Quenching cross sections and rate coefficients for state-to-state RET were computed. Both elastic and inelastic differential cross sections are also calculated and compared with relative experimental results giving generally good agreement in all cases, but less so for inelastic results. Significant differences in the computed collisional parameters, obtained on three different potential energy surfaces (PESs), were found particularly in the ultracold regime. In the thermal regime, the rate coefficients calculated on each of the surfaces are generally in better agreement and comparable, but typically larger, than those obtained in a previous calculation. Unfortunately, a lack of absolute differential or integral inelastic experimental data prevents firm determination of a preferred PES.
Thermal conductivity of ordered molecular water
Authors: Evans William , Fish Jacob , Keblinski Pawel
Published: April 2007

The authors use molecular dynamics simulation to investigate the thermal transport characteristics of water with various degree of orientational and translational orders induced by the application of an electric field. The authors observe that the orientational ordering of the water dipole moments has a minor effect on the thermal conductivity. However, electric-field-induced crystallization and associated translational order result in approximately a three fold increase of thermal conductivity with respect to the base water, i.e., to values comparable with those characterizing ice crystal structures.
Engineering the magnetic properties of amorphous (Fe80Co20)80B20 with multilayers of variable anisotropy direction
Authors: González-Guerrero Miguel , Prieto José Luis , Ciudad David , Sánchez Pedro , Aroca Claudio
Published: April 2007

The main goal of this work is to generate a method to control the magnetic properties of magnetostrictive metals (anisotropy and coercive field) without affecting the total magnetostriction. Multilayers of amorphous (Fe80Co20)80B20 are sputtered changing alternatively the anisotropy direction of the successive layers. The hysteresis loops show how the anisotropy field can be controlled by playing with the thickness ratio of the layers. Additionally, a clear decrease of the coercive field when the anisotropy direction rotates 90° from layer to layer is observed. This effect seems to have its origin in the mechanical energy accumulated in each layer.
Scanned micro-Hall microscope for detection of biofunctionalized magnetic beads
Authors: Kazakova Olga , Gallop John , Perkins Garry , Cohen Lesley
Published: April 2007

Here the authors report a scanned micro-Hall system capable of detecting single micron-sized paramagnetic beads at high scan rates over a wide scan area. Very small changes in local fields (<1μT∕√Hz) are detected in the presence of a large dc polarizing field. The sensor is noninvasive, operates at room temperature, and could be operated in liquids. These attributes make the system particularly suitable for biological applications. For example, it provides the potential for integration of biofunctionalized beads with specific biomarkers for highly sensitive detection.
Low electric-field-induced switching in the B1 bent-core liquid crystal phase
Authors: Kirchhoff J. , Hirst L. S. , Fergusson K. M. , Hird M.
Published: April 2007

The authors observe an electric-field-induced structural transition in the B1 columnar liquid crystalline phase at surprisingly low field strengths in a bent-core liquid crystal material with asymmetric alkyl chains. A possible B1 to B2 transition at applied electric fields of 10V∕μm is observed. After this E-field-induced transition, switching is observed at much lower voltages, down to a fraction of a V∕μm. This study is based on polarized microscopy, electro-optical studies, and differential scanning calorimetry.
Saturated dot density of InAs∕GaAs self-assembled quantum dots grown at high growth rate
Authors: Chia C. K. , Zhang Y. W. , Wong S. S. , Yong A. M. , Chow S. Y. , Chua S. J. , Guo J.
Published: April 2007

The variation in dot density, dot size, and photoluminescence intensity in two series of 1.8 and 2.5 ML InAs quantum dots (QDs) as a function of InAs growth rate has been investigated. As the growth rate increases from 0.14to3.60ML∕s, the average dot lateral size reduces by half, whereas the dot density increases five times. Nonlinear relationships were observed between dot density, dot size, and growth rate. The dot density is found to saturate at a growth rate of 3ML∕s. High dot density of 7.76×1011cm−2 has been demonstrated and is beneficial for applications in high power QD devices.
Monitoring of ZnCdSe layer properties by in situ x-ray diffraction during heteroepitaxy on (001)GaAs substrates
Authors: Benkert A. , Schumacher C. , Brunner K. , Neder R. B.
Published: April 2007

The authors demonstrate in situ high-resolution x-ray diffraction applied during heteroepitaxy on (001)GaAs for instant layer characterization. The current thickness, composition, strain, and relaxation dynamics of pseudomorphic layers are precisely determined from qz scans at the (113) reflection measured at a molecular beam epitaxy chamber with a conventional x-ray tube in static geometry. A simple fitting routine enables real-time in situ x-ray diffraction analysis of layers as thin as 20nm. Critical thicknesses for dislocation formation and plastic relaxation of ZnCdSe layers versus Cd content are determined. The strong influence of substrate temperature on heteroepitaxial nucleation process, deposition rate, composition, and strain relaxation dynamics of ZnCdSe on GaAs is also studied.
Influence of unsymmetrical periodicity on extraordinary transmission through periodic arrays of subwavelength holes
Authors: Ren Xi-Feng , Guo Guo-Ping , Huang Yun-Feng , Wang Zhi-Wei , Guo Guang-Can
Published: April 2007

Quadrate hole array is explored to study the influence of unsymmetrical periodicity on extraordinary optical transmission through periodic arrays of subwavelength holes. It is found that the transmission efficiency of light and the ratio between transmission efficiencies of horizontal and vertical polarized light can be continuously tuned by rotating the quadrate hole array. The authors can calculate out the transmission spectra (including the heights and locations of peaks) for any rotation angle θ with a simple theoretical model.
Pyromorphite formation and stability after quick lime neutralisation in the presence of soil and clay sorbents
Authors: Chappell Mark A. , Scheckel Kirk G.
Published: April 2007

Environmental context. Questions remain regarding the potential risk of human Pb exposure from metal-contaminated soils. Studies show that the risk of human exposure is more accurately linked to the toxicity of the Pb species in soil than the total quantity of Pb. This work explores the practicality of converting Pb to a less toxic, less bioavailable species called pyromorphite in the presence of soil.
Abstract. Soluble Pb is immobilised in pure systems as pyromorphite by adding sources of P, but doubts remain about the effectiveness of this approach in natural soil systems, particularly given the ability of soil humic substances to interfere with Pb-mineral formation. In addition, recent thermodynamic modelling predicts that pyromorphite formed by the addition of phosphoric acid to Pb-contaminated soils, followed by neutralisation with quick lime (Ca(OH)2) will destabilise the mineral, reverting the Pb back to more soluble species such as cerussite or anglesite. In this paper, we describe experiments to form pyromorphite in the presence of two different sorbents: a reference smectite called Panther Creek Bentonite, and a commercially available, organically rich potting mixture. We present X-ray diffraction (XRD) evidence suggestive of pyromorphite formation, yet, like similar studies, the evidence is less than conclusive. Linear combination fits of Pb X-ray absorption fine-structure spectroscopy (XAFS) data collected at the Advanced Photon Source at Argonne National Laboratory show that pyromorphite is the major Pb species formed after the addition of phosphoric acid. Furthermore, XAFS data shows that neutralising with quick lime enhances (as opposed to reducing) pyromorphite content in these systems. These results call into question relying solely on XRD data to confirm or deny the existence of minerals like pyromorphite, whose complex morphology give less intense and more complicated diffraction patterns than some of the simpler Pb minerals.
Borrelia burgdorferi
intercepts host hormonal signals to regulate expression of outer surface protein A
Authors: Scheckelhoff Mark R. , Telford Sam R. , Wesley Mary , Hu Linden T.
Published: April 2007

The
Borrelia burgdorferi
infectious cycle requires that the organism adapt to vast differences in environmental conditions found in its tick and mammalian hosts. Previous studies have shown that
B. burgdorferi
accomplishes this accomodation in part by regulating expression of its surface proteins. Outer surface protein A (OspA) is a borrelial protein important in colonization of the tick midgut. OspA is up-regulated when the organism is in its tick host and down-regulated when it is in a mammalian host. However, little is known about how it is up-regulated again in a mammalian host in preparation for entry into a feeding tick. Here, we report that the host neuroendocrine stress hormones, epinephrine and norepinephrine, are specifically bound by
B. burgdorferi
and result in increased expression of OspA. This recognition is specific and blocked by competitive inhibitors of human adrenergic receptors. To determine whether recognition of catecholamines, which are likely to be present at the site of a tick bite, may play a role in preparing the organism for reentry into a tick from a mammalian host, we administered a β-adrenergic blocker, propranolol, to infected mice. Propranolol significantly reduced uptake of
B. burgdorferi
by feeding ticks and decreased expression of OspA in
B. burgdorferi
recovered from ticks that fed on propranolol-treated mice. Our studies suggest that
B. burgdorferi
may co-opt host neuroendocrine signals to inform the organism of local changes that predict the presence of its next host and allow it to prepare for transition to a new environment.
Growth, innovation, scaling, and the pace of life in cities
Authors: Bettencourt Luís M. A. , Lobo José , Helbing Dirk , Kühnert Christian , West Geoffrey B.
Published: April 2007

Humanity has just crossed a major landmark in its history with the majority of people now living in cities. Cities have long been known to be society's predominant engine of innovation and wealth creation, yet they are also its main source of crime, pollution, and disease. The inexorable trend toward urbanization worldwide presents an urgent challenge for developing a predictive, quantitative theory of urban organization and sustainable development. Here we present empirical evidence indicating that the processes relating urbanization to economic development and knowledge creation are very general, being shared by all cities belonging to the same urban system and sustained across different nations and times. Many diverse properties of cities from patent production and personal income to electrical cable length are shown to be power law functions of population size with scaling exponents, β, that fall into distinct universality classes. Quantities reflecting wealth creation and innovation have β ≈1.2 >1 (increasing returns), whereas those accounting for infrastructure display β ≈0.8 <1 (economies of scale). We predict that the pace of social life in the city increases with population size, in quantitative agreement with data, and we discuss how cities are similar to, and differ from, biological organisms, for which β<1. Finally, we explore possible consequences of these scaling relations by deriving growth equations, which quantify the dramatic difference between growth fueled by innovation versus that driven by economies of scale. This difference suggests that, as population grows, major innovation cycles must be generated at a continually accelerating rate to sustain growth and avoid stagnation or collapse.
Specificity of the medaka enteropeptidase serine protease and its usefulness as a biotechnological tool for fusion-protein cleavage
Authors: Ogiwara Katsueki , Takahashi Takayuki
Published: April 2007

We cloned two distinct cDNAs for enteropeptidase (EP) from the intestine of the medaka,
Oryzias latipes
, which is a small freshwater teleost. The mRNAs code for EP-1 (1,036 residues) and EP-2 (1,043 residues), both of which have a unique, conserved domain structure of the N-terminal heavy chain and C-terminal catalytic serine protease light chain. When compared with mammalian EP serine proteases, the medaka enzyme exhibited extremely low amidolytic activity for small synthetic peptide substrates. Twelve mutated forms of the medaka EP protease were produced by site-directed mutagenesis. Among them, one mutant protease, E173A, was found to have considerably reduced nonspecific hydrolytic activities both for synthetic and protein substrates without serious reduction of its Asp-Asp-Asp-Asp-Lys (D
4
K)-cleavage activity. For the cleavage of fusion proteins containing a D
4
K-cleavage site, the medaka EP proteases were shown to have advantages over their mammalian counterparts. Based on our present data, we propose that the E173A mutant is the most appropriate protease to specifically cleave proteins containing the D
4
K cleavage sequence.
The zebrafishcandyflossmutant implicates extracellular matrix adhesion failure in laminin α2-deficient congenital muscular dystrophy
Authors: Hall Thomas E. , Bryson-Richardson Robert J. , Berger Silke , Jacoby Arie S. , Cole Nicholas J. , Hollway Georgina E. , Berger Joachim , Currie Peter D.
Published: April 2007

Mutations in the humanlamininα2(LAMA2) gene result in the most common form of congenital muscular dystrophy (MDC1A). There are currently three models for the molecular basis of cellular pathology in MDC1A: (i) lack of LAMA2 leads to sarcolemmal weakness and failure, followed by cellular necrosis, as is the case in Duchenne muscular dystrophy (DMD); (ii) loss of LAMA2-mediated signaling during the development and maintenance of muscle tissue results in myoblast proliferation and fusion defects; (iii) loss of LAMA2 from the basement membrane of the Schwann cells surrounding the peripheral nerves results in a lack of motor stimulation, leading to effective denervation atrophy. Here we show that the degenerative muscle phenotype in the zebrafish dystrophic mutant,candyfloss(caf) results from mutations in thelamininα2(lama2) gene.In vivotime-lapse analysis of mechanically loaded fibers and membrane permeability assays suggest that, unlike DMD, fiber detachment is not initially associated with sarcolemmal rupture. Early muscle formation and myoblast fusion are normal, indicating that any deficiency in early Lama2 signaling does not lead to muscle pathology. In addition, innervation by the primary motor neurons is unaffected, and fiber detachment stems from muscle contraction, demonstrating that muscle atrophy through lack of motor neuron activity does not contribute to pathology in this system. Using these and other analyses, we present a model of lama2 function where fiber detachment external to the sarcolemma is mechanically induced, and retracted fibers with uncompromised membranes undergo subsequent apoptosis.
Terrestrial-style feeding in a very early aquatic tetrapod is supported by evidence from experimental analysis of suture morphology
Authors: Markey Molly J. , Marshall Charles R.
Published: April 2007

There is no consensus on when in the fish-tetrapod transition suction feeding, the primary method of prey capture in the aquatic realm, evolved into the direct biting on prey typical of terrestrial animals. Here, we show that differences in the morphology of selected cranial sutures between species that span the fish–tetrapod transition (the Devonian osteolepiform fish
Eusthenopteron
, the aquatic Devonian tetrapod
Acanthostega
, and the Permian terrestrial tetrapod
Phonerpeton
) can be used to infer when terrestrial feeding first appeared. Our approach consists of defining a sutural morphospace, assigning functional fields to that morphospace based on our previous measurements of suture function made during feeding in the living fish
Polypterus
, inferring the functions of the fossil sutures based on where they fall in the morphospace, and then using the correlation between feeding mode and the patterns of inferred suture function across the skull roof in taxa where feeding mode is unambiguous to infer the feeding mode practiced by
Acanthostega
. Using this procedure, we find that the suture morphologies of
Acanthostega
are inconsistent with the hypothesis that it captured prey primarily by means of suction, which suggests that it may have bitten directly on prey at or near the water's edge. Thus, our data strongly support the hypothesis that the terrestrial mode of feeding first emerged in aquatic taxa.
Hairpin extensions enhance the efficacy of mycolyl transferase-specific antisense oligonucleotides targeting
Mycobacterium tuberculosis
Authors: Harth Günter , Zamecnik Paul C. , Tabatadze David , Pierson Katherine , Horwitz Marcus A.
Published: April 2007

We have investigated the efficacy of modifying gene-specific antisense phosphorothioate oligodeoxyribonucleotides (PS-ODNs) by the addition of 5′ and 3′ hairpin extensions. As a model system, we have targeted the
Mycobacterium tuberculosis
30/32-kDa mycolyl transferase protein complex genes encoding three highly related enzymes (antigens 85 A, B, and C). Whereas the addition of a hairpin extension at only one end of the PS-ODNs did not improve their inhibitory capacity, the addition of hairpin extensions at both ends enhanced their capacity to inhibit
M. tuberculosis
multiplication in comparison with unmodified PS-ODNs. A combination of three 5′-, 3′-hairpin-modified PS-ODNs (HPS-ODNs) targeting each of the three mycolyl transferase transcripts inhibited bacterial growth in broth culture by ≈1.75 log units (
P
< 0.0001) and in human THP-1 macrophages by ≈0.4 log units (
P
< 0.0001), which to our knowledge has not previously been demonstrated for any PS-ODN; reduced target gene transcription by ≥90%; caused ≈90% reduction in mycolyl transferase expression; and increased bacterial sensitivity to isoniazid by 8-fold. The growth-inhibitory effect of the HPS-ODNs was gene-specific. Mismatched HPS-ODNs had no growth-inhibitory capacity. This study demonstrates that 5′- and 3′-HPS-ODNs are highly efficacious against
M. tuberculosis
and supports the further development of antisense technology as a therapeutic modality against tuberculosis.
Kruppel-like factor 15 is a regulator of cardiomyocyte hypertrophy
Authors: Fisch Sudeshna , Gray Susan , Heymans Stephane , Haldar Saptarsi M. , Wang Baiqiu , Pfister Otmar , Cui Lei , Kumar Ajay , Lin Zhiyong , Sen-Banerjee Sucharita , Das Hiranmoy , Petersen Christine A. , Mende Ulrike , Burleigh Barbara A. , Zhu Yan , Pinto Yigal M. , Liao Ronglih , Jain Mukesh K.
Published: April 2007

Cardiac hypertrophy is a common response to injury and hemodynamic stress and an important harbinger of heart failure and death. Herein, we identify the Kruppel-like factor 15 (KLF15) as an inhibitor of cardiac hypertrophy. Myocardial expression of KLF15 is reduced in rodent models of hypertrophy and in biopsy samples from patients with pressure-overload induced by chronic valvular aortic stenosis. Overexpression of KLF15 in neonatal rat ventricular cardiomyocytes inhibits cell size, protein synthesis and hypertrophic gene expression. KLF15-null mice are viable but, in response to pressure overload, develop an eccentric form of cardiac hypertrophy characterized by increased heart weight, exaggerated expression of hypertrophic genes, left ventricular cavity dilatation with increased myocyte size, and reduced left ventricular systolic function. Mechanistically, a combination of promoter analyses and gel-shift studies suggest that KLF15 can inhibit GATA4 and myocyte enhancer factor 2 function. These studies identify KLF15 as part of a heretofore unrecognized pathway regulating the cardiac response to hemodynamic stress.
Recruitment of an inhibitory hippocampal network after bursting in a single granule cell
Authors: Mori Masahiro , Gähwiler Beat H. , Gerber Urs
Published: April 2007

The hippocampal CA3 area, an associational network implicated in memory function, receives monosynaptic excitatory as well as disynaptic inhibitory input through the mossy-fiber axons of the dentate granule cells. Synapses made by mossy fibers exhibit low release probability, resulting in high failure rates at resting discharge frequencies of 0.1 Hz. In recordings from functionally connected pairs of neurons, burst firing of a granule cell increased the probability of glutamate release onto both CA3 pyramidal cells and inhibitory interneurons, such that subsequent low-frequency stimulation evoked biphasic excitatory/inhibitory responses in a CA3 pyramidal cell, an effect lasting for minutes. Analysis of the unitary connections in the circuit revealed that granule cell bursting caused powerful activation of an inhibitory network, thereby transiently suppressing excitatory input to CA3 pyramidal cells. This phenomenon reflects the high incidence of spike-to-spike transmission at granule cell to interneuron synapses, the numerically much greater targeting by mossy fibers of inhibitory interneurons versus principal cells, and the extensively divergent output of interneurons targeting CA3 pyramidal cells. Thus, mossy-fiber input to CA3 pyramidal cells appears to function in three distinct modes: a resting mode, in which synaptic transmission is ineffectual because of high failure rates; a bursting mode, in which excitation predominates; and a postbursting mode, in which inhibitory input to the CA3 pyramidal cells is greatly enhanced. A mechanism allowing the transient recruitment of inhibitory input may be important for controlling network activity in the highly interconnected CA3 pyramidal cell region.
Using theory and computation to model nanoscale properties
Authors: Schatz George C.
Published: April 2007

This article provides an overview of the use of theory and computation to describe the structural, thermodynamic, mechanical, and optical properties of nanoscale materials. Nanoscience provides important opportunities for theory and computation to lead in the discovery process because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial to understanding what is being measured. However, there are important challenges to using theory as well, as the systems of interest are usually too large, and the time scales too long, for a purely atomistic level theory to be useful. At the same time, continuum theories that are appropriate for describing larger-scale (micrometer) phenomena are often not accurate for describing the nanoscale. Despite these challenges, there has been important progress in a number of areas, and there are exciting opportunities that we can look forward to as the capabilities of computational facilities continue to expand. Some specific applications that are discussed in this paper include: self-assembly of supramolecular structures, the thermal properties of nanoscale molecular systems (DNA melting and nanoscale water meniscus formation), the mechanical properties of carbon nanotubes and diamond crystals, and the optical properties of silver and gold nanoparticles.
Gene expression
in vivo
shows that
Helicobacter pylori
colonizes an acidic niche on the gastric surface
Authors: Scott David R. , Marcus Elizabeth A. , Wen Yi , Oh Jane , Sachs George
Published: April 2007

Helicobacter pylori
is a gastric-dwelling pathogen responsible, with acid secretion, for peptic ulcer and a 20-fold increase in the risk of gastric cancer. Several transcriptomes have been described after short-term exposure to acidity
in vitro
, but there are no data identifying the effects of chronic gastric exposure on bacterial gene expression. Comparison of the
in vivo
to the
in vitro
transcriptome at pH 7.4 identified several groups of genes of known function that increased expression >2-fold, and three of these respond both to acidity
in vitro
and to gastric infection. Almost all known acid acclimation genes are highly up-regulated. These include
ureA
,
ureB
, and
rocF
and the pH-gated urea channel,
ureI
. There is also up-regulation of two groups of motility and chemotaxis genes and for pathogenicity island genes, especially
cagA
, a predictor for pathogenicity. Most of these genes interact with
HP0166
, the response element of the pH-sensing two-component histidine kinase,
HP0165
/
HP0166
, ArsRS. Based on the pH profile of survival of
ureI
deletion mutants
in vitro
and their inability to survive in gastric acidity, the habitat of the organism at the gastric surface is acidic with a pH ≤ 4.0. Hence, the pH of the habitat of
H. pylori
on the surface of the stomach largely determines the regulation of these specific groups of genes.
The UNC-45 chaperone mediates sarcomere assembly through myosin degradation inCaenorhabditis elegans
Authors: Landsverk Megan L. , Li Shumin , Hutagalung Alex H. , Najafov Ayaz , Hoppe Thorsten , Barral José M. , Epstein Henry F.
Published: April 2007

Myosin motors are central to diverse cellular processes in eukaryotes. Homologues of the myosin chaperone UNC-45 have been implicated in the assembly and function of myosin-containing structures in organisms from fungi to humans. In muscle, the assembly of sarcomeric myosin is regulated to produce stable, uniform thick filaments. Loss-of-function mutations in Caenorhabditis elegans UNC-45 lead to decreased muscle myosin accumulation and defective thick filament assembly, resulting in paralyzed animals. We report that transgenic worms overexpressing UNC-45 also display defects in myosin assembly, with decreased myosin content and a mild paralysis phenotype. We find that the reduced myosin accumulation is the result of degradation through the ubiquitin/proteasome system. Partial proteasome inhibition is able to restore myosin protein and worm motility to nearly wild-type levels. These findings suggest a mechanism in which UNC-45–related proteins may contribute to the degradation of myosin in conditions such as heart failure and muscle wasting.
Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks
Authors: Uematsu Naoya , Weterings Eric , Yano Ken-ichi , Morotomi-Yano Keiko , Jakob Burkhard , Taucher-Scholz Gisela , Mari Pierre-Olivier , van Gent Dik C. , Chen Benjamin P.C. , Chen David J.
Published: April 2007

The DNA-dependent protein kinase catalytic subunit (DNA-PKCS) plays an important role during the repair of DNA double-strand breaks (DSBs). It is recruited to DNA ends in the early stages of the nonhomologous end-joining (NHEJ) process, which mediates DSB repair. To study DNA-PKCS recruitment in vivo, we used a laser system to introduce DSBs in a specified region of the cell nucleus. We show that DNA-PKCS accumulates at DSB sites in a Ku80-dependent manner, and that neither the kinase activity nor the phosphorylation status of DNA-PKCS influences its initial accumulation. However, impairment of both of these functions results in deficient DSB repair and the maintained presence of DNA-PKCS at unrepaired DSBs. The use of photobleaching techniques allowed us to determine that the kinase activity and phosphorylation status of DNA-PKCS influence the stability of its binding to DNA ends. We suggest a model in which DNA-PKCS phosphorylation/autophosphorylation facilitates NHEJ by destabilizing the interaction of DNA-PKCS with the DNA ends.
In macrophages, HIV-1 assembles into an intracellular plasma membrane domain containing the tetraspanins CD81, CD9, and CD53
Authors: Deneka Magdalena , Pelchen-Matthews Annegret , Byland Rahel , Ruiz-Mateos Ezequiel , Marsh Mark
Published: April 2007

In macrophages, HIV-1 has been shown to bud into intracellular structures that contain the late endosome marker CD63. We show that these organelles are not endosomes, but an internally sequestered plasma membrane domain. Using immunofluorescence microscopy and immunoelectron microscopy, we find that HIV-1 buds into a compartment that contains the tetraspanins CD81, CD9, and CD53. On uninfected macrophages, these proteins are seen at the cell surface and in intracellular vacuole-like structures with a complex content of vesicles and interconnected membranes that lack endosome markers, including CD63. Significantly, these structures are accessible to small tracers (horseradish peroxidase or ruthenium red) applied to cells at 4°C, indicating that they are connected to the cell surface. HIV assembles on, and accumulates within, these intracellular compartments. Furthermore, CD63 is recruited to the virus-containing structures and incorporated into virions. These results indicate that, in macrophages, HIV-1 exploits a previously undescribed intracellular plasma membrane domain to assemble infectious particles.
Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells
Authors: Tan Jing , Yang Xiaojing , Zhuang Li , Jiang Xia , Chen Wei , Lee Puay Leng , Karuturi R.K. Murthy , Tan Patrick Boon Ooi , Liu Edison T. , Yu Qiang
Published: April 2007

Polycomb-repressive complex 2 (PRC2)-mediated histone methylation plays an important role in aberrant cancer gene silencing and is a potential target for cancer therapy. Here we show that S-adenosylhomocysteine hydrolase inhibitor 3-Deazaneplanocin A (DZNep) induces efficient apoptotic cell death in cancer cells but not in normal cells. We found that DZNep effectively depleted cellular levels of PRC2 components EZH2, SUZ12, and EED and inhibited associated histone H3 Lys 27 methylation (but not H3 Lys 9 methylation). By integrating RNA interference (RNAi), genome-wide expression analysis, and chromatin immunoprecipitation (ChIP) studies, we have identified a prominent set of genes selectively repressed by PRC2 in breast cancer that can be reactivated by DZNep. We further demonstrate that the preferential reactivation of a set of these genes by DZNep, including a novel apoptosis affector, FBXO32, contributes to DZNep-induced apoptosis in breast cancer cells. Our results demonstrate the unique feature of DZNep as a novel chromatin remodeling compound and suggest that pharmacologic reversal of PRC2-mediated gene repression by DZNep may constitute a novel approach for cancer therapy.
The transcription factor HIF-1α plays a critical role in the growth factor-dependent regulation of both aerobic and anaerobic glycolysis
Authors: Lum Julian J. , Bui Thi , Gruber Michaela , Gordan John D. , DeBerardinis Ralph J. , Covello Kelly L. , Simon M. Celeste , Thompson Craig B.
Published: April 2007

Mammalian cells are believed to have a cell-intrinsic ability to increase glucose metabolism in response to hypoxia. Here we show that the ability of hematopoietic cells to up-regulate anaerobic glycolysis in response to hypoxia is dependent on receptor-mediated signal transduction. In the absence of growth factor signaling, hematopoietic cells fail to express hypoxia-inducible transcription factor (Hif-1α) mRNA. Growth factor-deprived hematopoietic cells do not engage in glucose-dependent anabolic synthesis and neither expressHif-1α mRNA nor require HIF-1α protein to regulate cell survival in response to hypoxia. However, HIF-1α is adaptive for the survival of growth factor-stimulated cells, as suppression of HIF-1α results in death when growing cells are exposed to hypoxia. Growth factor-dependent HIF-1α expression reprograms the intracellular fate of glucose, resulting in decreased glucose-dependent anabolic synthesis and increased lactate production, an effect that is enhanced when HIF-1α protein is stabilized by hypoxia. Together, these data suggest that HIF-1α contributes to the regulation of growth factor-stimulated glucose metabolism even in the absence of hypoxia.
Monitoring of neuronal and glial calcium activity using a novel direct‐contact probe
Authors: DUBAJ V. , MAZZOLINI A. , WOOD A.
Published: April 2007

In vivo neuronal and glial calcium activity was monitored using a novel direct‐contact probe that was designed for fluorescence detection deep within biological tissue. A small diameter fibre bundle direct‐contact probe was employed with a laser scanning confocal microscope to detect evoked neuronal and glial activity in the posteromedial barrel subfield of the rat somatosensory cortex in vivo. Resolution of the probe allowed discrimination of single cells, and calcium dynamics spanning milliseconds to several seconds were observed. Initial results indicate that the probe has useful practical applications in the imaging of individual cells and monitoring rapid calcium fluctuations within their cell body and large processes.
The Zoraptera problem: evidence for Zoraptera + Embiodea from the wing base
Authors: YOSHIZAWA KAZUNORI
Published: April 2007

Abstract The order Zoraptera is one of the most enigmatic insect groups. Its phylogenetic position is far from settled, and more than ten different placements have been discussed since the insects were first discovered. This problem is also difficult to resolve with molecular studies because of the unusual characteristics of zorapteran 18S rDNA sequences, which are the most widely used genetic markers for the estimation of the deep phylogeny of insects. In this study, the wing base structures of Zoraptera and various potential sister taxa were examined. Numbers of unique modifications were detected in the wing base structure of Zoraptera, and six were also observed in the wing base of Embiodea (Embioptera, Embiidina; webspinners). No possible synapomorphies supporting the other relationships were detected. This is the second unambiguous morphological synapomorphy providing strong evidence for the phylogenetic position of Zoraptera.
Securing and retaining a mental health workforce in Far Western New South Wales
Authors: Perkins David , Larsen Karen , Lyle David , Burns Pippa
Published: April 2007

Objective:  To identify strategies local managers can use to optimise recruitment and retention of mental health staff in rural locations.

Design:  Forty‐one staff were interviewed about factors that attracted them to work in remote locations, their initial intentions and factors that encourage them to stay.

Setting:  The former Far West Health Area of New South Wales.

Results:  Overall job satisfaction was high (68%). Key attractors were rural lifestyle and environment. Family reasons, the field of work and the rural lifestyle were factors that keep staff in their positions. Some mentioned the desire to achieve professional goals and see projects completed. Many staff reported that their initial intentions to stay had remained the same (43.9%). Reasons for extended intention to stay were: greater career opportunities; a desire to complete professional goals; extension of positions; and personal factors. The most common reason for leaving was better career opportunities. Other reasons included: changes to personal commitments; heavy workloads or burnout; service management; and workplace politics. A large number of respondents mentioned key differences when comparing rural and metropolitan areas: more travel (greater distances); less service options for referral; greater spectrum of illnesses and conditions; more autonomy and responsibility.

Conclusions:  Strategies to recruit and retain staff must take account of personal needs and aspirations. While there is room for state strategies to improve employment incentives, there is also considerable scope for local managers to improve the design and attractiveness of jobs.
Use of social network analysis to describe service links for farmers' mental health
Authors: Fuller Jeffrey , Kelly Brian , Sartore Gina , Fragar Lynne , Tonna Anne , Pollard Georgia , Hazell Trevor
Published: April 2007

Objective:  The primary mental health care needs of farmers require that service innovations incorporate rural support workers into a local service network. This component of the FarmLink pilot sought to develop a social network analysis method that would describe local mental health‐related human service networks. The purpose is to inform improvements in this network and to serve as a baseline against which such improvements can be evaluated.

Design:  A pilot survey of rural human service providers who deal with mental health‐related issues among farmers about their self‐reported links between each other.

Setting:  Service delivery agencies associated with a small rural town in New South Wales.

Participants:  Twenty‐five agents from a range of human services involved in rural human support services to farmers, such as from agricultural and drought support, welfare, primary health care and education.

Intervention:  Telephone interview prior to the conduct of a Mental Health First Aid seminar and a Farmers Mental Health and Wellbeing workshop.

Main outcome measures:  Agent self‐reported service links over the past three months for information exchange, client referrals and working together in relation to helping farmers for mental health, emotional health or stress‐related problems. Analysis trialled on the ‘made referrals’ link shows the network influence, prominence and intermediary status of the rural financial counsellor.

Conclusions:  Within the limitations of recalled self‐report data, social network analysis provides a useful network description for informing and evaluating service network improvements.