bluuebunny/crossref_metadata_2025 huggingface dataset:
PUBLIC SCIENCE IN THE ENLIGHTENMENT
Authors: TERRALL MARY
Published: August 2005

Mi Gyung Kim, Affinity, That Elusive Dream: A Genealogy of the Chemical Revolution (Cambridge, MA: MIT Press, 2003)

Guiliano Pancaldi, Volta: Science and Culture in the Age of Enlightenment (Princeton, NJ: Princeton University Press, 2003)

To challenge the presumed isolation of the scientific method from social concerns and forces, to question the inevitability of progress, to explore the ideological and polemical aspects of science—all these are by now goals commonly stated in historical studies of science. In the quest for these desiderata over the past twenty years or so, historians of science have in many cases distanced themselves from intellectual history in its idealist, disembodied form. However, in spite of salutary moves to analyze instruments, laboratory practices, visual representations, instituions and politics, a great deal of the raw material for the history of science remains textual, very often in the form of print. And, as the existence of this journal attests, intellectual history has retooled to take seriously the contexts for ideas and intellectual movements. At the present moment, when intellectual historians and historians of science are allied in the game of contextualizing our subjects, it is worth considering how current scholarship is working to define multi-layered contexts for scientific ideas and the texts in which they appear.
Hydrogen-bond interaction in 1:1 complexes of tetrahydrofuran with water, hydrogen fluoride, and ammonia: A theoretical study
Authors: Sahu Prabhat K. , Lee Shyi-Long
Published: August 2005

Ab initio and density-functional theory electronic structure calculations have been performed for the 1:1 complexes of tetrahydrofuran with water, hydrogen fluoride, and ammonia. Upon hydrogen bonding with H2O and HF, the structure of tetrahydrofuran (THF) remains relatively unchanged with the exception of THF sites involved in hydrogen-bonding interaction. But the similar findings are not true, upon hydrogen bonded with NH3, where the C2 symmetry of THF changed. The hydrogen-bonding strength for the 1:1 complexes of THF with water, HF, and NH3 is found to be in the order HF>H2O>NH3, which is well characterized by the order in bond angles O2H15F14, O2H16O14, and O2H15N14 closer to linearity, respectively, and the redshifted of stretching frequencies of vFH, vOH, and vNH, respectively. This work is an attempt to provide important predictions and to aid in future experimental and theoretical studies towards the understanding of such hydrogen-bonded van der Waals systems.
Intermolecular electrostatic energies using density fitting
Authors: Cisneros G. Andrés , Piquemal Jean-Philip , Darden Thomas A.
Published: August 2005

A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+–H2O, Cu+–H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.
Optical and transient photoconductive properties of pentacene and functionalized pentacene thin films: Dependence on film morphology
Authors: Ostroverkhova Oksana , Shcherbyna Svitlana , Cooke David G. , Egerton Ray F. , Hegmann Frank A. , Tykwinski Rik R. , Parkin Sean R. , Anthony John E.
Published: August 2005

We present a comprehensive study of the optical and transient photoconductive properties of pentacene and functionalized pentacene thin films grown by evaporation or from solution onto a variety of substrates. The transient photoconductivity was studied over picosecond time scales using time-resolved terahertz pulse spectroscopy. The structure and morphology of the films were assessed using x-ray diffraction, atomic force microscopy, and scanning electron microscopy. Regular pentacene films grown by evaporation under similar conditions but on different substrates yielded polycrystalline films with similar morphology and similar optical and transient photoconductive properties. Single exponential or biexponential decay dynamics was observed in all of the regular pentacene films studied. Functionalized pentacene films grown by evaporation at two different substrate temperatures (as well as from solution) yielded significant variations in morphology, resulting in different optical-absorption spectra and transient photoconductivities that could be correlated with film structure. The lower limit of the charge-carrier mobility, estimated from the amplitude of the transient photoconductive response, was ∼0.02–0.04cm2∕Vs in the case of regular pentacene films and ∼0.01–0.06cm2∕Vs in the case of functionalized pentacene films, depending on the film morphology. The best functionalized pentacene films exhibited transient photoconductivity values reaching ∼30%–40% of those obtained in functionalized pentacene single-crystal samples, and showed similar power-law decay dynamics. We also report on terahertz pulse generation from voltage-biased pentacene thin films.
Enhancement of third-order optical nonlinearities by conjugated polymer-bonded carbon nanotubes
Authors: Feng Wei , Yi Wenhui , Wu Hongcai , Ozaki Masanori , Yoshino Katsumi
Published: August 2005

Third-order nonlinear susceptibility χ(3) and second-order hyperpolarizability γ of poly{[3-octylthiophene-2,5-diyl]-[p-aminobenzylidenequinomethane]-bonded multiwalled carbon nanotubes (POTABQ-MWNTs) were measured in chloroform solution using degenerate four-wave mixing at 532nm under nanosecond pulse excitation. Effective nonlinear absorption coefficient βeff and nonlinear refraction index n2 were obtained using open aperture and close aperture Z-scan technique at the same wavelength, respectively. Optical limiting property of the sample was also investigated. The resulting POTABQ-MWNTs exhibited large third-order nonlinear optical responses mainly due to the formation of intramolecular photoinduced charge-transfer system of polymers and carbon nanotubes.
Thermodynamics of coarse-grained models of supercooled liquids
Authors: Chandler David , Garrahan Juan P.
Published: August 2005

In recent papers, we have argued that kinetically constrained coarse-grained models can be applied to understand dynamic properties of glass-forming materials, and we have used this approach in various applications that appear to validate this view. In one such paper [J. P. Garrahan and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. 100, 9710 (2003)], among other things we argued that this approach also explains why the heat-capacity discontinuity at the glass transition is generally larger for fragile materials than for strong materials. In the preceding article, Biroli, Bouchaud, and Tarjus have objected to our explanation on this point, arguing that the class of models we apply is inconsistent with both the absolute size and the temperature dependence of the experimental specific heat. Their argument, however, neglects parameters associated with the coarse graining. Accounting for these parameters, we show here that our treatment of dynamics is not inconsistent with heat-capacity discontinuities.
Growth and magnetic characterization of epitaxial Fe81Ga19∕MgO (100) thin films
Authors: Butera A. , Gómez J. , Weston J. L. , Barnard J. A.
Published: August 2005

Using magnetization and ferromagnetic resonance techniques, we have characterized Fe81Ga19 (100) thin films (90 nm thick) grown on MgO (100). We have observed that for low sputtering powers (<35W) it is possible to grow films with cubic magnetic symmetry, and that larger powers induce an in-plane magnetic easy axis. Films with cubic symmetry were further characterized using ferromagnetic resonance at frequencies of 34 and 9.7 GHz. From the angular variation of the resonance field we have obtained the cubic magnetocrystalline anisotropy constant, K1=2×105erg∕cm3, and the saturation magnetization, M∼1460G. The magnitude and the angular variation of the linewidth suggest an important contribution of the two-magnon scattering mechanism to the relaxation of the magnetic excitations.
Imbibition of a liquid droplet on a deformable porous substrate
Authors: Anderson Daniel M.
Published: August 2005

We consider the imbibition of a liquid droplet into a deformable porous substrate. The liquid in the droplet is imbibed due to capillary suction in an initially dry and undeformed substrate. Deformation of the substrate occurs as the liquid fills the pore space. In our model, a pressure gradient in the liquid across the developing wet substrate region induces a stress gradient in the solid matrix which in turn leads to an evolving solid fraction and hence deformation. For axisymmetric droplets, we assume that the imbibition and substrate deformation at a given radial position are one-dimensional (in the vertical direction). The coupling to the droplet geometry leads to axisymmetric configurations for the deformed wet substrate. We show that the model chosen to describe the dynamics of the liquid droplet, based in this case on existing models developed for droplet spreading on rigid porous substrates, has little influence on the resultant swelling or shrinking of the substrate—these general trends can be effectively predicted by a one-dimensional imbibition and deformation model—but does strongly influence the details of the wet substrate shape. We characterize these predictions and in some cases can obtain analytical solutions for the evolution.
Nb clusters formation in Nb-doped magnesium hydride
Authors: Checchetto R. , Bazzanella N. , Miotello A. , Maurizio C. , D’Acapito F. , Mengucci P. , Barucca G. , Majni G.
Published: August 2005

Extended x-ray absorption fine structure spectroscopy, x-ray diffraction and transmission electron microscopy were used to analyze the Nb coordination and clustering in Nb-doped (5 at. %) h-Mg film samples deposited by rf magnetron sputtering. Results show that the catalytic effect of the Nb doping in the H2 absorption and desorption kinetics is connected with the formation of Nb nanoclusters dispersed in the host matrix. The H2 desorption from β-MgH2 is favored by local elastic stresses produced by β-NbH0.89 clusters on the MgH2 matrix that reduces the stability of the hydride phase and by preferential paths in the nanocomposite hydride.
Anisotropic thermal properties of monoclinic Yb:KLu(WO4)2 crystals
Authors: Zhang Jianxiu , Wang Kunpeng , Wang Jiyang , Zhang Huaijin , Yu Wentao , Wang Xuping , Wang Zhengping , Lu Qingming , Ba Mingfang , Ran D. G. , Ling Z. C. , Xia H. R.
Published: August 2005

Yb : K Lu ( W O 4 ) 2 (KLuW) crystals with large size and good optical quality have been grown by the top-seeded solution growth (TSSG) method. The melting point and specific heat, anisotropic thermal expansion and thermal conductivity have been measured. The Jackson factor α of a series of observed faces (hkl) on Yb:KLuW crystals have been calculated. In addition, the microhardness has also been measured. We find that the thermal expansion anisotropy of Yb:KLuW is weaker than KGd(WO4)2 (KGW) and KYb(WO4)2 (KYbW) and the thermal conductivity is up to 4.4Wm−1k−1 along [205] directions at 25°C, which is the greatest in their family.
Drosophila
host defense after oral infection by an entomopathogenic
Pseudomonas
species
Authors: Vodovar Nicolas , Vinals Marisa , Liehl Peter , Basset Alan , Degrouard Jeril , Spellman Paul , Boccard Frédéric , Lemaitre Bruno
Published: August 2005

Drosophila
has been shown to be a valuable model for the investigation of host–pathogen interactions. Study of the
Drosophila
immune response has been hampered, however, by the lack of true
Drosophila
pathogens. In nearly all studies reported, the bacteria used were directly injected within the body cavity of the insect, bypassing the initial steps of a natural interaction. Here, we report the identification of a previously uncharacterized bacterial species,
Pseudomonas entomophila
(
Pe
), which has the capacity to induce the systemic expression of antimicrobial peptide genes in
Drosophila
after ingestion. In contrast to previously identified bacteria,
Pe
is highly pathogenic to both
Drosophila
larvae and adults, and its persistence in larvae leads to a massive destruction of gut cells. Using this strain, we have analyzed the modulation of the larval transcriptome upon bacterial infection. We found that natural infection by
Pe
induces a dramatic change in larval gene expression. In addition to immunity genes, our study identifies many genes associated with
Pe
pathogenesis that have been previously unreported.
The metal-ion-dependent adhesion site in the Von Willebrand factor-A domain of α
2
δ subunits is key to trafficking voltage-gated Ca
2
+ channels
Authors: Cantí C. , Nieto-Rostro M. , Foucault I. , Heblich F. , Wratten J. , Richards M. W. , Hendrich J. , Douglas L. , Page K. M. , Davies A. , Dolphin A. C.
Published: August 2005

All auxiliary α
2
δ subunits of voltage-gated Ca
2+
(Ca
V
) channels contain an extracellular Von Willebrand factor-A (VWA) domain that, in α
2
δ-1 and -2, has a perfect metal-ion-dependent adhesion site (MIDAS). Modeling of the α
2
δ-2 VWA domain shows it to be highly likely to bind a divalent cation. Mutating the three key MIDAS residues responsible for divalent cation binding resulted in a MIDAS mutant α
2
δ-2 subunit that was still processed and trafficked normally when it was expressed alone. However, unlike WT α
2
δ-2, the MIDAS mutant α
2
δ-2 subunit did not enhance and, in some cases, further diminished Ca
V
1.2, -2.1, and -2.2 currents coexpressed with β1b by using either Ba
2+
or Na
+
as a permeant ion. Furthermore, expression of the MIDAS mutant α
2
δ-2 reduced surface expression and strongly increased the perinuclear retention of Ca
V
α1 subunits at the earliest time at which expression was observed in both Cos-7 and NG108–15 cells. Despite the presence of endogenous α
2
δ subunits, heterologous expression of α
2
δ-2 in differentiated NG108–15 cells further enhanced the endogenous high-threshold Ca
2+
currents, whereas this enhancement was prevented by the MIDAS mutations. Our results indicate that α
2
δ subunits normally interact with the Ca
V
α1 subunit early in their maturation, before the appearance of functional plasma membrane channels, and an intact MIDAS motif in the α
2
δ subunit is required to promote trafficking of the α1 subunit to the plasma membrane by an integrin-like switch. This finding provides evidence for a primary role of a VWA domain in intracellular trafficking of a multimeric complex, in contrast to the more usual roles in binding extracellular ligands in other exofacial VWA domains.
Cardiac repair with intramyocardial injection of allogeneic mesenchymal stem cells after myocardial infarction
Authors: Amado Luciano C. , Saliaris Anastasios P. , Schuleri Karl H. , St. John Marcus , Xie Jin-Sheng , Cattaneo Stephen , Durand Daniel J. , Fitton Torin , Kuang Jin Qiang , Stewart Garrick , Lehrke Stephanie , Baumgartner William W. , Martin Bradley J. , Heldman Alan W. , Hare Joshua M.
Published: August 2005

Although clinical trials of autologous whole bone marrow for cardiac repair demonstrate promising results, many practical and mechanistic issues regarding this therapy remain highly controversial. Here, we report the results of a randomized study of bone-marrow-derived mesenchymal stem cells, administered to pigs, which offer several new insights regarding cellular cardiomyoplasty. First, cells were safely injected by using a percutaneous-injection catheter 3 d after myocardial infarction. Second, cellular transplantation resulted in long-term engraftment, profound reduction in scar formation, and near-normalization of cardiac function. Third, transplanted cells were preprepared from an allogeneic donor and were not rejected, a major practical advance for widespread application of this therapy. Together, these findings demonstrate that the direct injection of cellular grafts into damaged myocardium is safe and effective in the periinfarct period. The direct delivery of cells to necrotic myocardium offers a valuable alternative to intracoronary cell injections, and the use of allogeneic mesenchymal stem cells provides a valuable strategy for cardiac regenerative therapy that avoids the need for preparing autologous cells from the recipient.
The Paleoproterozoic snowball Earth: A climate disaster triggered by the evolution of oxygenic photosynthesis
Authors: Kopp Robert E. , Kirschvink Joseph L. , Hilburn Isaac A. , Nash Cody Z.
Published: August 2005

Although biomarker, trace element, and isotopic evidence have been used to claim that oxygenic photosynthesis evolved by 2.8 giga-annum before present (Ga) and perhaps as early as 3.7 Ga, a skeptical examination raises considerable doubt about the presence of oxygen producers at these times. Geological features suggestive of oxygen, such as red beds, lateritic paleosols, and the return of sedimentary sulfate deposits after a ≈900-million year hiatus, occur shortly before the ≈2.3–2.2 Ga Makganyene “snowball Earth” (global glaciation). The massive deposition of Mn, which has a high redox potential, practically requires the presence of environmental oxygen after the snowball. New age constraints from the Transvaal Supergroup of South Africa suggest that all three glaciations in the Huronian Supergroup of Canada predate the Snowball event. A simple cyanobacterial growth model incorporating the range of C, Fe, and P fluxes expected during a partial glaciation in an anoxic world with high-Fe oceans indicates that oxygenic photosynthesis could have destroyed a methane greenhouse and triggered a snowball event on timescales as short as 1 million years. As the geological evidence requiring oxygen does not appear during the Pongola glaciation at 2.9 Ga or during the Huronian glaciations, we argue that oxygenic cyanobacteria evolved and radiated shortly before the Makganyene snowball.
Evolution of carbon sinks in a changing climate
Authors: Fung Inez Y. , Doney Scott C. , Lindsay Keith , John Jasmin
Published: August 2005

Climate change is expected to influence the capacities of the land and oceans to act as repositories for anthropogenic CO
2
and hence provide a feedback to climate change. A series of experiments with the National Center for Atmospheric Research–Climate System Model 1 coupled carbon–climate model shows that carbon sink strengths vary with the rate of fossil fuel emissions, so that carbon storage capacities of the land and oceans decrease and climate warming accelerates with faster CO
2
emissions. Furthermore, there is a positive feedback between the carbon and climate systems, so that climate warming acts to increase the airborne fraction of anthropogenic CO
2
and amplify the climate change itself. Globally, the amplification is small at the end of the 21st century in this model because of its low transient climate response and the near-cancellation between large regional changes in the hydrologic and ecosystem responses. Analysis of our results in the context of comparable models suggests that destabilization of the tropical land sink is qualitatively robust, although its degree is uncertain.
Implications of new petrographic analysis for the Olmec “mother culture” model
Authors: Flannery Kent V. , Balkansky Andrew K. , Feinman Gary M. , Grove David C. , Marcus Joyce , Redmond Elsa M. , Reynolds Robert G. , Sharer Robert J. , Spencer Charles S. , Yaeger Jason
Published: August 2005

Petrographic analysis of Formative Mexican ceramics by J. B. Stoltmanet al.(see the companion piece in this issue of PNAS) refutes a recent model of Olmec “one-way” trade. In this paper, we address the model's more fundamental problems of sampling bias, anthropological implausibility, and logical non sequiturs. No bridging argument exists to link motifs on pottery to the social, political, and religious institutions of the Olmec. In addition, the model of unreciprocated exchange is implausible, given everything that the anthropological and ethnohistoric records tell us about non-Western societies of that general sociopolitical level.
RNase P cleaves transient structures in some riboswitches
Authors: Altman Sidney , Wesolowski Donna , Guerrier-Takada Cecilia , Li Yong
Published: August 2005

RNase P from
Escherichia coli
cleaves the coenzyme B
12
riboswitch from
E. coli
and a similar one from
Bacillus subtilis
. The cleavage sites do not occur in any recognizable structure, as judged from theoretical schemes that have been drawn for these 5′ UTRs. However, it is possible to draw a scheme that is a good representation of the
E. coli
cleavage site for RNase P and for the cleavage site in
B. subtilis
. These data indicate that transient structures are important in RNase P cleavage and in riboswitch function. Coenzyme B
12
has a small inhibitory effect on
E. coli
RNase P cleavage of the
E. coli
riboswitch. Both
E. coli
RNase P and a partially purified RNase P from
Aspergillus nidulans
mycelia succeeded in cleaving a putative arginine riboswitch from
A. nidulans
. The cleavage site may be a representative of another model substrate for eukaryotic RNase P. This 5′ UTR controls splicing of the arginase mRNA in
A. nidulans
. Four other riboswitches in
E. coli
were not cleaved by RNase P under the conditions tested.
Suppression of Huntington's disease pathology in
Drosophila
by human single-chain Fv antibodies
Authors: Wolfgang William J. , Miller Todd W. , Webster Jack M. , Huston James S. , Thompson Leslie M. , Marsh J. Lawrence , Messer Anne
Published: August 2005

Misfolded neuronal proteins have been identified in a number of neurodegenerative disorders and have been implicated in the pathogenesis of diseases that include Alzheimer's disease, Parkinson's disease, prion-based dementia, Huntington's disease (HD), and other polyglutamine diseases. Although underlying mechanisms remain the subject of ongoing research, it is clear that aberrant processing, protein degradation, and aggregate formation or spurious protein association of the abnormal neuronal proteins may be critical factors in disease progression. Recent work in these diseases has demonstrated
in vitro
that specific engineered antibody species, peptides, or other general agents may suppress the formation of aggregates. We have modified an approach with intracellularly expressed single-chain Fv (sFv) antibodies (intrabodies) that bind with unique HD protein epitopes. In cell and tissue culture models of HD, anti-N-terminal huntingtin intrabodies (C4 sFv) reduce aggregation and cellular toxicity. Here, we present the crucial experiment of intrabody-mediated
in vivo
suppression of neuropathology, using a
Drosophila
model of HD. In the presence of the C4 sFv intrabody, the proportion of HD flies surviving to adulthood increases from 23% to 100%, and the mean and maximum lifespan of adult HD flies is significantly prolonged. Neurodegeneration and formation of visible huntingtin aggregates are slowed. We conclude from this investigation that engineered intrabodies are a potential new class of therapeutic agents for the treatment of neurodegenerative diseases. They may also serve as tools for drug discovery and validation of sites on mutant neuronal proteins that could be exploited for rational drug design.
Cilia and Hedgehog responsiveness in the mouse
Authors: Huangfu Danwei , Anderson Kathryn V.
Published: August 2005

The intraflagellar transport (IFT) proteins Ift172/Wimple and Polaris/Ift88 and the anterograde IFT motor kinesin-II are required for the production and maintenance of cilia. These proteins are also required for the activation of targets of the mouse Hedgehog (Hh) pathway by Gli transcription factors. The phenotypes of the IFT mutants, however, are not identical to mutants that lack Smoothened (Smo), an essential activator of the Hh pathway. We show here that mouse embryos that lack both
Ift172
and
Smo
are identical to
Ift172
single mutants, which indicates that Ift172 acts downstream of Smo.
Ift172
mutants have a weaker neural patterning phenotype than
Smo
mutants, because Ift172, but not Smo, is required for proteolytic processing of Gli3 to its repressor form. Dnchc2 and Kif3a, essential subunits of the retrograde and anterograde IFT motors, are also required for both formation of Gli activator and proteolytic processing of Gli3. As a result, IFT mutants display a loss of Hh signaling phenotype in the neural tube, where Gli activators play the major role in pattern formation, and a gain of Hh signaling phenotype in the limb, where Gli3 repressor plays the major role. Because both anterograde and retrograde IFT are essential for positive and negative responses to Hh, and because cilia are present on Hh responsive cells, it is likely that cilia act as organelles that are required for all activity of the mouse Hh pathway.
Mass of the postsynaptic density and enumeration of three key molecules
Authors: Chen Xiaobing , Vinade Lucia , Leapman Richard D. , Petersen Jennifer D. , Nakagawa Terunaga , Phillips Terry M. , Sheng Morgan , Reese Thomas S.
Published: August 2005

The total molecular mass of individual postsynaptic densities (PSDs) isolated from rat forebrain was measured by scanning transmission EM. PSDs had a mean diameter of 360 nm and molecular mass of 1.10 ± 0.36 GDa. Because the mass represents the sum of the molecular masses of all of the molecules comprising a PSD, it becomes possible to derive the number of copies of each protein, once its relative mass contribution is known. Mass contributions of PSD-95, synapse-associated protein (SAP)97, and α-Ca2+/calmodulin-dependent protein kinase II (CaMKII) were determined by quantitative gel electrophoresis of PSD fractions. The number of PSD-95 molecules per average PSD, contributing 2.3% of the mass of the PSD, was calculated to be 300, whereas the number of SAP97 molecules, contributing 0.9% of the mass of the PSD, was 90. The α-CaMKII holoenzymes, which contribute 6% of the mass when brains are homogenized within 2 min of interrupting blood flow, have 80 holoenzymes associated with a typical PSD. When blood flow is interrupted 15 min before homogenization, the average mass of PSDs increases by ≈40%. The additional α-CaMKII associated with PSDs accounts for up to 20% of this mass increase, representing the addition of 100–200 α-CaMKII holoenzymes.
The epidermal barrier function is dependent on the serine protease CAP1/Prss8
Authors: Leyvraz Céline , Charles Roch-Philippe , Rubera Isabelle , Guitard Marjorie , Rotman Samuel , Breiden Bernadette , Sandhoff Konrad , Hummler Edith
Published: August 2005

Serine proteases are proteolytic enzymes that are involved in the regulation of various physiological processes. We generated mice lacking the membrane-anchored channel-activating serine protease (CAP) 1 (also termed protease serine S1 family member 8 [Prss8] and prostasin) in skin, and these mice died within 60 h after birth. They presented a lower body weight and exhibited severe malformation of the stratum corneum (SC). This aberrant skin development was accompanied by an impaired skin barrier function, as evidenced by dehydration and skin permeability assay and transepidermal water loss measurements leading to rapid, fatal dehydration. Analysis of differentiation markers revealed no major alterations in CAP1/Prss8-deficient skin even though the epidermal deficiency of CAP1/Prss8 expression disturbs SC lipid composition, corneocyte morphogenesis, and the processing of profilaggrin. The examination of tight junction proteins revealed an absence of occludin, which did not prevent the diffusion of subcutaneously injected tracer (∼600 D) toward the skin surface. This study shows that CAP1/Prss8 expression in the epidermis is crucial for the epidermal permeability barrier and is, thereby, indispensable for postnatal survival.
Essential role of CIB1 in regulating PAK1 activation and cell migration
Authors: Leisner Tina M. , Liu Mingjuan , Jaffer Zahara M. , Chernoff Jonathan , Parise Leslie V.
Published: August 2005

p21-activated kinases (PAKs) regulate many cellular processes, including cytoskeletal rearrangement and cell migration. In this study, we report a direct and specific interaction of PAK1 with a 22-kD Ca2+-binding protein, CIB1, which results in PAK1 activation both in vitro and in vivo. CIB1 binds to PAK1 within discrete regions surrounding the inhibitory switch domain in a calcium-dependent manner, providing a potential mechanism of CIB1-induced PAK1 activation. CIB1 overexpression significantly decreases cell migration on fibronectin as a result of a PAK1-and LIM kinase–dependent increase in cofilin phosphorylation. Conversely, the RNA interference–mediated depletion of CIB1 increases cell migration and reduces normal adhesion-induced PAK1 activation and cofilin phosphorylation. Together, these results demonstrate that endogenous CIB1 is required for regulated adhesion-induced PAK1 activation and preferentially induces a PAK1-dependent pathway that can negatively regulate cell migration. These results point to CIB1 as a key regulator of PAK1 activation and signaling.
Wnt signaling drives WRM-1/β-catenin asymmetries in early C. elegans embryos
Authors: Nakamura Kuniaki , Kim Soyoung , Ishidate Takao , Bei Yanxia , Pang Kaming , Shirayama Masaki , Trzepacz Chris , Brownell Daniel R. , Mello Craig C.
Published: August 2005

β-Catenin regulates cell adhesion and cellular differentiation during development, and misregulation of β-catenin contributes to numerous forms of cancer in humans. Here we describe Caenorhabditis elegans conditional alleles of mom-2/Wnt, mom-4/Tak1, and wrm-1/β-catenin. We use these reagents to examine the regulation of WRM-1/β-catenin during a Wnt-signaling-induced asymmetric cell division. While WRM-1 protein initially accumulates in the nuclei of all cells, signaling promotes the retention of WRM-1 in nuclei of responding cells. We show that both PRY-1/Axin and the nuclear exportin homolog IMB-4/CRM-1 antagonize signaling. These findings reveal how Wnt signals direct the asymmetric localization of β-catenin during polarized cell division.
Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression
Authors: Irlbacher Horst , Franke Jacqueline , Manke Thomas , Vingron Martin , Ehrenhofer-Murray Ann E.
Published: August 2005

Heterochromatinization at the silent mating-type loci HMR and HML in Saccharomyces cerevisiae is achieved by targeting the Sir complex to these regions via a set of anchor proteins that bind to the silencers. Here, we have identified a novel heterochromatin-targeting factor for HML, the protein Sum1, a repressor of meiotic genes during vegetative growth. Sum1 bound both in vitro and in vivo to HML via a functional element within the HML-E silencer, and sum1Δ caused HML derepression. Significantly, Sum1 was also required for origin activity of HML-E, demonstrating a role of Sum1 in replication initiation. In a genome-wide search for Sum1-regulated origins, we identified a set of autonomous replicative sequences (ARS elements) that bound both the origin recognition complex and Sum1. Full initiation activity of these origins required Sum1, and their origin activity was decreased upon removal of the Sum1-binding site. Thus, Sum1 constitutes a novel global regulator of replication initiation in yeast.
Mesenchymal stem cells are recruited to striated muscle by NFAT/IL-4-mediated cell fusion
Authors: Schulze Manja , Belema-Bedada Fikru , Technau Antje , Braun Thomas
Published: August 2005

Mesenchymal stem cells (MSCs) or mesenchymal adult stem cells (MASCs) that are present in the stroma of several organs have been proposed to contribute to the regeneration of different tissues including liver, blood, heart, and skeletal muscle. Yet, it remains unclear whether MSCs can be programmed to differentiate cell-autonomously into fully functional cells or whether they are recruited by surrounding cells via fusion and thereby acquire specialized cellular functions. Here, we demonstrate that Wnt signaling molecules activate the expression of distinct sets of genes characteristic for cardiac and skeletal muscle cells in MASCs. However, such cells lack morphological criteria characteristic for functional muscle cells and do not show contractile activity. In contrast, MASCs fuse efficiently with native myotubes in an IL-4-dependent manner to form functional hybrid myotubes. Injection of genetically labeled MSCs into wild-type mouse blastocysts revealed a contribution to skeletal but not cardiac muscle development. Disruption of IL-4 and NFATc2/c3 reduced or prevented a contribution of adult stem cells to the development of Il-4 and NFATc2/c3 mutant embryos, further emphasizing the apparent inability of adult stem cells to differentiate fully into striated muscle in a cell-autonomous manner.
Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations
Authors: Ray Nicolas , Currat Mathias , Berthier Pierre , Excoffier Laurent
Published: August 2005

Most genetic and archeological evidence argue in favor of a recent and unique origin of modern humans in sub-Saharan Africa, but no attempt has ever been made at quantifying the likelihood of this model, relative to alternative hypotheses of human evolution. In this paper, we investigate the possibility of using multilocus genetic data to correctly infer the geographic origin of humans, and to distinguish between a unique origin (UO) and a multiregional evolution (ME) model. We introduce here an approach based on realistic simulations of the genetic diversity expected after an expansion process of modern humans into the Old World from different possible areas and their comparison to observed data. We find that the geographic origin of the expansion can be correctly recovered provided that a large number of independent markers are used, and that precise information on past demography and potential places of origins is available. In that case, it is also possible to unambiguously distinguish between a unique origin and a multiregional model of human evolution. Application to a real human data set of 377 STR markers tested in 22 populations points toward a unique but surprising North African origin of modern humans. We show that this result could be due to ascertainment bias in favor of markers selected to be polymorphic in Europeans. A new estimation modeling this bias explicitly reveals that East Africa is the most likely place of origin for modern humans.
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Authors: Vinson Jade P. , Jaffe David B. , O'Neill Keith , Karlsson Elinor K. , Stange-Thomann Nicole , Anderson Scott , Mesirov Jill P. , Satoh Nori , Satou Yutaka , Nusbaum Chad , Birren Bruce , Galagan James E. , Lander Eric S.
Published: August 2005

Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging for highly polymorphic species. The difficulty arises because two divergent haplotypes are sequenced together, making it difficult to distinguish alleles at the same locus from paralogs at different loci. We present here a method for assembling highly polymorphic diploid genomes that involves assembling the two haplotypes separately and then merging them to obtain a reference sequence. Our method was developed to assemble the genome of the sea squirt Ciona savignyi, which was sequenced to a depth of 12.7× from a single wild individual. By comparing finished clones of the two haplotypes we determined that the sequenced individual had an extremely high heterozygosity rate, averaging 4.6% with significant regional variation and rearrangements at all physical scales. Applied to these data, our method produced a reference assembly covering 157 Mb, with N50 contig and scaffold sizes of 47 kb and 989 kb, respectively. Alignment of ESTs indicates that 88% of loci are present at least once and 81% exactly once in the reference assembly. Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method.
Region-specific detection of neuroblastoma loss of heterozygosity at multiple loci simultaneously using a SNP-based tag-array platform
Authors: Maris John M. , Hii George , Gelfand Craig A. , Varde Shobha , White Peter S. , Rappaport Eric , Surrey Saul , Fortina Paolo
Published: August 2005

Many cancers are characterized by chromosomal aberrations that may be predictive of disease outcome. Human neuroblastomas are characterized by somatically acquired copy number changes, including loss of heterozygosity (LOH) at multiple chromosomal loci, and these aberrations are strongly associated with clinical phenotype including patient outcome. We developed a method to assess region-specific LOH by genotyping multiple SNPs simultaneously in DNA from tumor tissues. We identified informative SNPs at an average 293-kb density across nine regions of recurrent LOH in human neuroblastomas. We also identified SNPs in two copy number neutral regions, as well as two regions of copy number gain. SNPs were PCR-amplified in 12-plex reactions and used in solution-phase single-nucleotide extension incorporating tagged dideoxynucleotides. Each extension primer had 5′ complementarity to one of 2000 oligonucleotides on a commercially available tag-array platform allowing for solid-phase sorting and identification of individual SNPs. This approach allowed for simultaneous detection of multiple regions of LOH in six human neuroblastoma-derived cell lines, and, more importantly, 14 human neuroblastoma primary tumors. Concordance with conventional genotyping was nearly absolute. Detection of LOH in this assay may not require comparison to matched normal DNAs because of the redundancy of informative SNPs in each region. The customized tag-array system for LOH detection described here is rapid, results in parallel assessment of multiple genomic alterations, and may speed identification of and/or assaying prognostically relevant DNA copy number alterations in many human cancers.
Systemic blockade of D2-like dopamine receptors facilitates extinction of conditioned fear in mice
Authors: Ponnusamy Ravikumar , Nissim Helen A. , Barad Mark
Published: August 2005

Extinction of conditioned fear in animals is the explicit model of behavior
therapy for human anxiety disorders, including panic disorder,
obsessive-compulsive disorder, and post-traumatic stress disorder. Based on
previous data indicating that fear extinction in rats is blocked by
quinpirole, an agonist of dopamine D2 receptors, we hypothesized that blockade
of D2 receptors might facilitate extinction in mice, while agonists should
block extinction, as they do in rats. One day after fear conditioning mice
with three pairings of a white noise conditional stimulus (CS) with moderate
footshock, we injected the D2 antagonist, sulpiride, the D2 agonist,
quinpirole, or vehicle, just before repeated CS presentations to generate
extinction. We assayed fear by measuring behavioral freezing during extinction
presentations and then drug-free during CS presentations 1 d later. We found
that sulpiride injections before extinction training facilitated extinction
memory 24 h later, while quinpirole partially blocked extinction memory
compared with vehicle-injected controls. Notably, sulpiride treatment yielded
significant extinction after spaced CS presentations, which yield no
extinction at all in vehicle-treated mice. These findings suggest that
dopamine D2-mediated signaling contributes physiological inhibition of
extinction, and that D2 antagonists may be useful adjuncts to behavior therapy
of human anxiety disorders.
Regulated expression and dynamic changes in subnuclear localization of mammalian Rad18 under normal and genotoxic conditions
Authors: Masuyama Sadaharu , Tateishi Satoshi , Yomogida Kentaro , Nishimune Yoshitake , Suzuki Keiichiro , Sakuraba Yoshiyuki , Inoue Hirokazu , Ogawa Michio , Yamaizumi Masaru
Published: August 2005

Rad18 plays a crucial role in postreplication repair in both lower eukaryotes and higher eukaryotes. However, regulation of the Rad18 expression in higher eukaryotes is largely unknown. We found that the RAD18 transcript is expressed ubiquitously in various tissues and very highly in the testis in mammals. Although human RAD18 (hRAD18) transcription levels fluctuate during the cell cycle, being maximal in the late S and minimal in the early G1, the protein levels remain constant throughout the cell cycle. Following UV‐irradiation, hRAD18 transcription levels decrease significantly, but Rad18 protein levels change little. The protein levels are maintained at least in part by enhanced translation rates. hRad18 localizes in the nucleus in two forms: a diffused form and a condensed form forming nuclear dots. These nuclear dots disperse rapidly in the nucleoplasm after treatments with various genotoxic agents, resulting in an enhancement of the intranuclear Rad18 concentration of the diffused form. No de novo protein synthesis is required for this process. These results suggest that in higher eukaryotes, the maintenance and dynamic translocation of Rad18 protein is important for postreplication repair.
Wnt signaling regulates the sequential onset of neurogenesis and gliogenesis via induction of BMPs
Authors: Kasai Mana , Satoh Kiyotoshi , Akiyama Tetsu
Published: August 2005

In the mammalian central nervous system, neurogenesis precedes gliogenesis; neurons are primarily generated at the neural stage, whereas most glial cells are generated perinatally and postnatally. However, the signals that regulate this sequence of events remain unclear. Here we show that Wnt signaling induces neuronal and astroglial differentiation but suppresses oligodendroglial differentiation. We observed that precursor cells infected with a retrovirus encoding β‐catenin differentiated into neurons, while astrocytes developed from uninfected precursor cells surrounding infected cells. As neurogenesis proceeded, expression of the bone morphogenetic proteins (BMPs), BMP2, 4 and 7, progressively increased in the cells infected with the retrovirus encoding β‐catenin. Furthermore, treatment of cells with Noggin, a BMP antagonist, completely inhibited astroglial differentiation but partially restored oligodendroglial differentiation. These results suggest that Wnt signaling indirectly regulates gliogenesis by inducing BMPs in neuronal cells. Thus, cooperation between Wnt and BMP signaling may play a key role in determining the sequence of neurogenesis and gliogenesis.
Effects of elevated O3and CO2concentrations on photosynthesis and stomatal conductance in Scots pine
Authors: KELLOMäKI S. , WANG K.‐Y.
Published: August 2005

Naturally regenerated Scots pines (Pinus sylvestrisL.), aged 28–30 years old, were grown in open‐top chambers and subjected insituto three ozone (O3) regimes, two concentrations of CO2, and a combination of O3and CO2treatments From 15 April to 15 September for two growing seasons (1994 and 1995). The gas exchanges of current‐year and 1‐year‐old shoots were measured, along with the nitrogen content of needles. In order to investigate the factors underlying modifications in photosynthesis, five parameters linked to photosynthetic performance and three to stomatal conductance were determined. Elevated O3concentrations led to a significant decline in the CO2compensation point (Г*), maximum RuP2‐saturated rate of carboxylation (Vcmax), maximum rate of electron transport (Jmax), maximum stomatal conductance (gsmax), and sensitivity of stomatal conductance to changes in leaf‐to‐air vapour pressure difference (∂gs/∂Dv) in both shoot‐age classes. However, the effect of elevated O3concentrations on the respiration rate in light (Rd) was dependent on shoot age. Elevated CO2(700 μmol mol−1) significantly decreasedJmaxandgsmaxbut increasedRdin 1‐year‐old shoots and the ∂gs/∂Dvin both shoot‐age classes. The interactive effects of O3and CO2on some key parameters (e.g.VcmaxandJmax) were significant. This may be closely related to regulation of the maximum stomatal conductance and stomatal sensitivity induced by elevated CO2. As a consequence, the injury induced by O3was reduced through decreased ozone uptake in 1‐year‐old shoots, but not in the current‐year shoots. Compared to ambient O3concentration, reduced O3concentrations (charcoal‐filtered air) did not lead to significant changes in any of the measured parameters. Compared to the control treatment, calculations showed that elevated O3concentrations decreased the apparent quantum yield by 15% and by 18%, and the maximum rate of photosynthesis by 21% and by 29% in the current‐year and 1‐year‐old shoots, respectively. Changes in the nitrogen content of needles resulting from the various treatments were associated with modifications in photosynthetic components.
Leaf senescence in a non‐yellowing mutant of Festuca pratensis: implications of the stay‐green mutation for photosynthesis, growth and nitrogen nutrition
Authors: HAUCK B. , GAY A. P. , MACDUFF J. , GRIFFITHS C. M. , THOMAS H.
Published: August 2005

Mutation of the nuclear gene sid disables chlorophyll degradation during leaf senescence in the pasture grass Festuca pratensis. This study investigated the effect of the mutation on photosynthesis and on leaf and whole plant growth under a range of nitrogen regimes. When plants were cultivated in a static hydroponic system, the chlorophyll content of fourth leaves of the stay‐green mutant Bf993 remained virtually unchanged from full expansion to complete senescence, while tissue of the wild‐type (cv. Rossa) became completely yellow. The retention of chlorophyll in Bf993 was not associated with maintenance of photosynthetic activity as shown by rates of light‐saturated CO2 fixation and apparent quantum efficiency. Higher levels of total N in senescing leaves of Bf993 than in Rossa indicated reduced nitrogen remobilization in the mutant. When using a range of [NH4NO3], dry matter production and tillering Mere lower for Bf993 at all but the highest [NH4NO3, which was supra‐optimal for the wild type. In contrast to the static system, where fluctuations in N supply occurred, growth and [NO3−] uptake were similar in mutant and wild type when [NO3−] was continuously maintained by a flowing solution culture system. The results are discussed in relation to the role of N supply and the effect of the stay‐green mutation on N recycling.