bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental verification and theoretical analysis of the relationships between hardness, elastic modulus, and the work of indentation
Authors: Yang Rong , Zhang Taihua , Jiang Peng , Bai Yilong
Published: June 2008

The relationship between hardness (H), reduced modulus (Er), unloading work (Wu), and total work (Wt) of indentation is examined in detail experimentally and theoretically. Experimental study verifies the approximate linear relationship. Theoretical analysis confirms it. Furthermore, the solutions to the conical indentation in elastic-perfectly plastic solid, including elastic work (We), H, Wt, and Wu are obtained using Johnson’s expanding cavity model and Lamé solution. Consequently, it is found that the We should be distinguished from Wu, rather than their equivalence as suggested in ISO14577, and (H∕Er)∕(Wu∕Wt) depends mainly on the conical angle, which are also verified with numerical simulations.
All-optical switching using controlled formation of large volume three-dimensional optical matter
Authors: Liu Jin , Dai Qiao-Feng , Meng Zi-Ming , Huang Xu-Guang , Wu Li-Jun , Guo Qi , Hu Wei , Lan Sheng , Gopal Achanta Venu , Trofimov V. A.
Published: June 2008

We demonstrated the creation of large volume three-dimensional optical matter by optically trapping polystyrene spheres in a capillary and the resulting switching operation. The formation of optical matter was confirmed by examining the diffraction pattern of the trap region. Optical switching with an extinction ratio as large as ∼20dB was realized. From the dynamics of the optical matter, it was found that the transition from a disordered state to an ordered one appeared to be quite fast while the recovery of the system to the disordered state took a much longer time.
Contrasting rainforest and savanna ant faunas in monsoonal northern Australia: a rainforest patch in a tropical savanna landscape
Authors: Andersen Alan N. , van Ingen Laura T. , Campos Ricardo I.
Published: June 2008

Rainforest in the tropical savanna landscapes of monsoonal Australia is of high biogeographic interest because it occurs as numerous small and isolated patches, and supports a fauna that contrasts markedly with that of the surrounding savanna. The overall ant fauna of monsoonal rainforest is known reasonably well, but with just one exception (Holmes Jungle in Darwin) the faunas of individual rainforest patches have been only superficially studied. This paper comprehensively documents an ant fauna of a spring-fed rainforest patch at the Territory Wildlife Park (TWP) near Darwin, contrasts it with that of surrounding savanna, and compares it with the Holmes Jungle fauna. Ants were sampled at 21 locations within the TWP rainforest, using Winkler sacs for litter-dwelling species (160 samples), standard pitfall traps for ground-active species (75 traps), and baited pitfall traps taped to trees for arboreal species (75 traps). In total, 43 species were collected, with 35 recorded in leaf litter, 24 in ground pitfall traps and 12 in arboreal pitfall traps. Species of Paratrechina and Pheidole collectively comprised 75% of all individuals recorded. Species richness was far higher in the surrounding savanna, and the rainforest and savanna faunas had markedly different species and functional group composition. The rainforest fauna at TWP was remarkably similar to that at Holmes Jungle. The rainforest/savanna contrast in ant diversity across northern Australia is the reverse of that occurring in Neotropical savanna landscapes.
Evolutionary correlations between microhabitat specialisation and locomotor capabilities in the lizard genus Niveoscincus
Authors: Melville Jane
Published: June 2008

The evolutionary consequences of generalised versus specialised habit is a central issue in organismal biology. Theory predicts that specialist species may have greater capabilities than generalist species in particular habitats but will not be able to maintain this excellence across a broad range of habitats. The evolutionary consequences of ecological specialisation, in terms of functional capabilities, were investigated in the lizard genus Niveoscincus from Tasmania. Breadth of microhabitat occupation and ecologically relevant locomotor capabilities were quantified across the genus. Laboratory performance trials demonstrated that some species excelled in just a few of the five performance traits measured, while other species performed well at all traits but did not excel at any. Results of comparative analyses demonstrate that there is a significant evolutionary correlation between microhabitat breadth and range of locomotor capabilities. These results provide convincing evidence that habitat specialists have a correspondingly limited range of locomotor capabilities.
Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics
Authors: Halskau Øyvind , Perez-Jimenez Raul , Ibarra-Molero Beatriz , Underhaug Jarl , Muñoz Victor , Martinez Aurora , Sanchez-Ruiz Jose M.
Published: June 2008

Protein folding barriers, which range from zero to the tens of
RT
that result in classical two-state kinetics, are primarily determined by protein size and structural topology [Plaxco KW, Simons KT, Baker D (1998)
J Mol Biol
277:985–994]. Here, we investigate the thermodynamic folding barriers of two relatively large proteins of the same size and topology: bovine α-lactalbumin (BLA) and hen-egg-white lysozyme (HEWL). From the analysis of differential scanning calorimetry experiments with the variable-barrier model [Muñoz V, Sanchez-Ruiz JM (2004)
Proc Natl Acad Sci USA
101:17646–17651] we obtain a high barrier for HEWL and a marginal folding barrier for BLA. These results demonstrate a remarkable tuning range of at least 30 kJ/mol (i.e., five to six orders of magnitude in population) within a unique protein scaffold. Experimental and theoretical analyses on these proteins indicate that the surprisingly small thermodynamic folding barrier of BLA arises from the stabilization of partially unfolded conformations by electrostatic interactions. Interestingly, there is clear reciprocity between the barrier height and the biological function of the two proteins, suggesting that the marginal barrier of BLA is a product of natural selection. Electrostatic surface interactions thus emerge as a mechanism for the modulation of folding barriers in response to special functional requirements within a given structural fold.
Casting polymer nets to optimize noisy molecular codes
Authors: Tlusty Tsvi
Published: June 2008

Life relies on the efficient performance of molecular codes, which relate symbols and meanings via error-prone molecular recognition. We describe how optimizing a code to withstand the impact of molecular recognition noise may be understood from the statistics of a two-dimensional network made of polymers. The noisy code is defined by partitioning the space of symbols into regions according to their meanings. The “polymers” are the boundaries between these regions, and their statistics define the cost and the quality of the noisy code. When the parameters that control the cost–quality balance are varied, the polymer network undergoes a transition, where the number of encoded meanings rises discontinuously. Effects of population dynamics on the evolution of molecular codes are discussed.
Transmembrane segment enhanced labeling as a tool for the backbone assignment of α-helical membrane proteins
Authors: Reckel Sina , Sobhanifar Solmaz , Schneider Birgit , Junge Friederike , Schwarz Daniel , Durst Florian , Löhr Frank , Güntert Peter , Bernhard Frank , Dötsch Volker
Published: June 2008

Recent advances in cell-free expression protocols have opened a new avenue toward high-resolution structural investigations of membrane proteins by x-ray crystallography and NMR spectroscopy. One of the biggest challenges for liquid-state NMR-based structural investigations of membrane proteins is the significant peak overlap in the spectra caused by large line widths and limited chemical shift dispersion of α-helical proteins. Contributing to the limited chemical shift dispersion is the fact that ≈60% of the amino acids in transmembrane regions consist of only six different amino acid types. This principle disadvantage, however, can be exploited to aid in the assignment of the backbone resonances of membrane proteins; by
15
N/
13
C-double-labeling of these six amino acid types, sequential connectivities can be obtained for large stretches of the transmembrane segments where number and length of stretches consisting exclusively of these six amino acid types are enhanced compared with the remainder of the protein. We show by experiment as well as by statistical analysis that this labeling scheme provides a large number of sequential connectivities in transmembrane regions and thus constitutes a tool for the efficient assignment of membrane protein backbone resonances.
Continuum percolation of carbon nanotubes in polymeric and colloidal media
Authors: Kyrylyuk Andriy V. , van der Schoot Paul
Published: June 2008

We apply continuum connectedness percolation theory to realistic carbon nanotube systems and predict how bending flexibility, length polydispersity, and attractive interactions between them influence the percolation threshold, demonstrating that it can be used as a predictive tool for designing nanotube-based composite materials. We argue that the host matrix in which the nanotubes are dispersed controls this threshold through the interactions it induces between them during processing and through the degree of connectedness that must be set by the tunneling distance of electrons, at least in the context of conductivity percolation. This provides routes to manipulate the percolation threshold and the level of conductivity in the final product. We find that the percolation threshold of carbon nanotubes is very sensitive to the degree of connectedness, to the presence of small quantities of longer rods, and to very weak attractive interactions between them. Bending flexibility or tortuosity, on the other hand, has only a fairly weak impact on the percolation threshold.
Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor BRI1 and the auxin transporters PIN2 and AUX1
Authors: Robert Stéphanie , Chary S. Narasimha , Drakakaki Georgia , Li Shundai , Yang Zhenbiao , Raikhel Natasha V. , Hicks Glenn R.
Published: June 2008

Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the compartments and pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. To define and dissect specific recycling pathways, chemical effectors of proteins involved in vesicle trafficking, especially through endosomes, would be invaluable. Thus, we identified chemicals affecting essential steps in PM/endosome trafficking, using the intensely localized PM transport at the tips of germinating pollen tubes. The basic mechanisms of this localized growth are likely similar to those of non-tip growing cells in seedlings. The compound endosidin 1 (ES1) interfered selectively with endocytosis in seedlings, providing a unique tool to dissect recycling pathways. ES1 treatment induced the rapid agglomeration of the auxin translocators PIN2 and AUX1 and the brassinosteroid receptor BRI1 into distinct endomembrane compartments termed “endosidin bodies”; however, the markers PIN1, PIN7, and other PM proteins were unaffected. Endosidin bodies were defined by the syntaxin SYP61 and the V-ATPase subunit VHA-a1, two
trans
-Golgi network (TGN)/endosomal proteins. Interestingly, brassinosteroid (BR)-induced gene expression was inhibited by ES1 and treated seedlings displayed a brassinolide (BL)-insensitive phenotype similar to a
bri1
loss-of-function mutant. No effect was detected in auxin signaling. Thus, PIN2, AUX1, and BRI1 use interactive pathways involving an early SYP61/VHA-a1 endosomal compartment.
The contemporary degassing rate of
40
Ar from the solid Earth
Authors: Bender Michael L. , Barnett Bruce , Dreyfus Gabrielle , Jouzel Jean , Porcelli Don
Published: June 2008

Knowledge of the outgassing history of radiogenic
40
Ar, derived over geologic time from the radioactive decay of
40
K, contributes to our understanding of the geodynamic history of the planet and the origin of volatiles on Earth's surface. The
40
Ar inventory of the atmosphere equals total
40
Ar outgassing during Earth history. Here, we report the current rate of
40
Ar outgassing, accessed by measuring the Ar isotope composition of trapped gases in samples of the Vostok and Dome C deep ice cores dating back to almost 800 ka. The modern outgassing rate (1.1 ± 0.1 × 10
8
mol/yr) is in the range of values expected by summing outgassing from the continental crust and the upper mantle, as estimated from simple calculations and models. The measured outgassing rate is also of interest because it allows dating of air trapped in ancient ice core samples of unknown age, although uncertainties are large (±180 kyr for a single sample or ±11% of the calculated age, whichever is greater).
Structure of coronavirus hemagglutinin-esterase offers insight into corona and influenza virus evolution
Authors: Zeng Qinghong , Langereis Martijn A. , van Vliet Arno L. W. , Huizinga Eric G. , de Groot Raoul J.
Published: June 2008

The hemagglutinin-esterases (HEs) are a family of viral envelope glycoproteins that mediate reversible attachment to
O
-acetylated sialic acids by acting both as lectins and as receptor-destroying enzymes (RDEs). Related HEs occur in influenza C, toro-, and coronaviruses, apparently as a result of relatively recent lateral gene transfer events. Here, we report the crystal structure of a coronavirus (CoV) HE in complex with its receptor. We show that CoV HE arose from an influenza C-like HE fusion protein (HEF). In the process, HE was transformed from a trimer into a dimer, whereas remnants of the fusion domain were adapted to establish novel monomer–monomer contacts. Whereas the structural design of the RDE-acetylesterase domain remained unaltered, the HE receptor-binding domain underwent remodeling to such extent that the ligand is now bound in opposite orientation. This is surprising, because the architecture of the HEF site was preserved in influenza A HA over a much larger evolutionary distance, a switch in receptor specificity and extensive antigenic variation notwithstanding. Apparently, HA and HEF are under more stringent selective constraints than HE, limiting their exploration of alternative binding-site topologies. We attribute the plasticity of the CoV HE receptor-binding site to evolutionary flexibility conferred by functional redundancy between HE and its companion spike protein S. Our findings offer unique insights into the structural and functional consequences of independent protein evolution after interviral gene exchange and open potential avenues to broad-spectrum antiviral drug design.
Effect of glycosylation on protein folding: A close look at thermodynamic stabilization
Authors: Shental-Bechor Dalit , Levy Yaakov
Published: June 2008

Glycosylation is one of the most common posttranslational modifications to occur in protein biosynthesis, yet its effect on the thermodynamics and kinetics of proteins is poorly understood. A minimalist model based on the native protein topology, in which each amino acid and sugar ring was represented by a single bead, was used to study the effect of glycosylation on protein folding. We studied
in silico
the folding of 63 engineered SH3 domain variants that had been glycosylated with different numbers of conjugated polysaccharide chains at different sites on the protein's surface. Thermal stabilization of the protein by the polysaccharide chains was observed in proportion to the number of attached chains. Consistent with recent experimental data, the degree of thermal stabilization depended on the position of the glycosylation sites, but only very weakly on the size of the glycans. A thermodynamic analysis showed that the origin of the enhanced protein stabilization by glycosylation is destabilization of the unfolded state rather than stabilization of the folded state. The higher free energy of the unfolded state is enthalpic in origin because the bulky polysaccharide chains force the unfolded ensemble to adopt more extended conformations by prohibiting formation of a residual structure. The thermodynamic stabilization induced by glycosylation is coupled with kinetic stabilization. The effects introduced by the glycans on the biophysical properties of proteins are likely to be relevant to other protein polymeric conjugate systems that regularly occur in the cell as posttranslational modifications or for biotechnological purposes.
NK T cells provide lipid antigen-specific cognate help for B cells
Authors: Leadbetter Elizabeth A. , Brigl Manfred , Illarionov Petr , Cohen Nadia , Luteran Megan C. , Pillai Shiv , Besra Gurdyal S. , Brenner Michael B.
Published: June 2008

The mechanisms of T cell help for production of antilipid antibodies are largely unknown. This study shows that invariant NK T cells (iNK T cells) and B cells cooperate in a model of antilipid antigen-specific antibody responses. We use a model haptenated lipid molecule, 4-hydroxy-3-nitrophenyl-αGalactosylCeramide (NP-αGalCer), to demonstrate that iNK T cells provide cognate help to lipid-antigen-presenting B cells. B cells proliferate and IgG anti-NP is produced fromin vivo-immunized mice andin vitrococultures of B and NK T cells after exposure to NP-αGalCer, but not closely related control glycolipids. This B cell response is absent in CD1d−/−and Jα18−/−mice but not CD4−/−mice. The antibody response to NP-αGalCer is dominated by the IgM, IgG3, and IgG2c isotypes, and marginal zone B cells stimulate betterin vitrolipid antigen-driven proliferation than follicular B cells, suggesting an important role for this B cell subset. iNK T cell help for B cells is shown to involve cognate help from CD1d-instructed lipid-specific iNK T cells, with help provided via CD40L, B7–1/B7–2, and IFN-γ, but not IL-4. This model provides evidence of iNK T cell help for antilipid antibody production, an important aspect of infections, autoimmune diseases, and vaccine development. Our findings also now allow prediction of those microbial antigens that would be expected to elicit cognate iNKT cell help for antibody production, namely those that can stimulate iNKT cells and at the same time have a polar moiety that can be recognized by antibodies.
Rapid recurrent processing gates awareness in primary visual cortex
Authors: Boehler C. N. , Schoenfeld M. A. , Heinze H.-J. , Hopf J.-M.
Published: June 2008

Visual awareness has been proposed to depend on recurrent processing in early visual cortex areas including the primary visual cortex (V1). Here, we address this hypothesis with high spatiotemporal resolution magnetoencephalographic recordings in subjects performing a substitution masking paradigm. Neural activity reflecting awareness is assessed by directly comparing the neuromagnetic response elicited by effectively and ineffectively masked targets after the proportion of trials leading to masking was individually adjusted to match the proportion of trials without masking. This revealed a modulation of recurrent activity in the primary visual cortex rapidly after the onset of the feedforward sweep of processing in striate and extrastriate areas but significantly before the onset of attention-dependent recurrent modulations in V1. Our data provide direct support for the notion that (
i
) recurrent processing in V1 correlates with visual awareness and (
ii
) that attention and awareness involve distinct recurrent processing operations.
The cyclin-dependent kinase inhibitor p57kip2 is a negative regulator of Schwann cell differentiation and
in vitro
myelination
Authors: Heinen André , Kremer David , Göttle Peter , Kruse Fabian , Hasse Birgit , Lehmann Helmar , Hartung Hans Peter , Küry Patrick
Published: June 2008

The p57kip2 gene encodes a member of the cyclin-dependent kinase inhibitor family, proteins known to block G
1
/S transition during the mammalian cell cycle. We observed that expression of p57kip2 in Schwann cells of the developing and injured adult peripheral nervous system is dynamically regulated. Using gene knockdown by means of vector-based RNA interference in cultured primary Schwann cells we found that reduced levels of p57kip2 lead to cell cycle exit, actin filament stabilization, altered cell morphology and growth, and down-regulation of promyelinating markers as well as induction of myelin genes and proteins. In addition, we could demonstrate that
in vitro
myelination is enhanced by p57kip2-suppressed Schwann cells. Using microarray technology we found that these cellular reactions are specific to lowered p57kip2 expression levels and detected a shift of the transcriptional expression program toward the pattern known from Schwann cells in developing peripheral nerves. Because in the absence of axons primary Schwann cells normally do not display differentiation-associated reactions, we conclude that we have identified a mechanism and an important intrinsic negative regulator of myelinating glia differentiation.
DEAF-1 regulates immunity gene expression in
Drosophila
Authors: Reed Darien E. , Huang Xinhua M. , Wohlschlegel James A. , Levine Michael S. , Senger Kate
Published: June 2008

Immunity genes are activated in the
Drosophila
fat body by Rel and GATA transcription factors. Here, we present evidence that an additional regulatory factor, deformed epidermal autoregulatory factor-1 (DEAF-1), also contributes to the immune response and is specifically important for the induction of two genes encoding antimicrobial peptides, Metchnikowin (
Mtk
) and Drosomycin (
Drs
). The systematic mutagenesis of a minimal
Mtk
5′ enhancer identified a sequence motif essential for both a response to LPS preparations in S2 cells and activation in the larval fat body in response to bacterial infection. Using affinity chromatography coupled to multidimensional protein identification technology (MudPIT), we identified DEAF-1 as a candidate regulator. DEAF-1 activates the expression of
Mtk
and
Drs
promoter-luciferase fusion genes in S2 cells. SELEX assays and footprinting data indicate that DEAF-1 binds to and activates
Mtk
and
Drs
regulatory DNAs via a TTCGGBT motif. The insertion of this motif into the Diptericin (
Dpt
) regulatory region confers DEAF-1 responsiveness to this normally DEAF-1-independent enhancer. The coexpression of DEAF-1 with Dorsal, Dif, and Relish results in the synergistic activation of transcription. We propose that DEAF-1 is a regulator of
Drosophila
immunity.
B cell receptor-mediated uptake of CD1d-restricted antigen augments antibody responses by recruiting invariant NKT cell helpin vivo
Authors: Barral Patricia , Eckl-Dorna Julia , Harwood Naomi E. , De Santo Carmela , Salio Mariolina , Illarionov Petr , Besra Gurdyal S. , Cerundolo Vincenzo , Batista Facundo D.
Published: June 2008

Highly regulated activation of B cells is required for the production of specific antibodies necessary to provide protection from pathogen infection. This process is initiated by specific recognition of antigen through the B cell receptor (BCR), leading to early intracellular signaling followed by the late recruitment of T cell help. In this study we demonstrate that specific BCR uptake of CD1d-restricted antigens represents an effective means of enhancing invariant natural killer T (iNKT)-dependent B cell responsesin vivo. This mechanism is effective over a wide range of antigen affinities but depends on exceeding a tightly regulated avidity threshold necessary for BCR-mediated internalization and CD1d-dependent presentation of particulate antigenic lipid. Subsequently, iNKT cells provide the help required for stimulating B cell proliferation and differentiation. iNKT-stimulated B cells develop within extrafollicular foci and mediate the production of high titers of specific IgM and early class-switched antibodies. Thus, we have demonstrated that in response to particulate antigenic lipids iNKT cells are recruited for the assistance of B cell activation, resulting in the enhancement of specific antibody responses. We propose that such a mechanism may operate to potentiate adaptive immune responses against pathogensin vivo.
Rate-specific synchrony: Using noisy oscillations to detect equally active neurons
Authors: Markowitz David A. , Collman Forrest , Brody Carlos D. , Hopfield John J. , Tank David W.
Published: June 2008

Although gamma frequency oscillations are common in the brain, their functional contributions to neural computation are not understood. Here we report
in vitro
electrophysiological recordings to evaluate how noisy gamma frequency oscillatory input interacts with the overall activation level of a neuron to determine the precise timing of its action potentials. The experiments were designed to evaluate spike synchrony in a neural circuit architecture in which a population of neurons receives a common noisy gamma oscillatory synaptic drive while the firing rate of each individual neuron is determined by a slowly varying independent input. We demonstrate that similarity of firing rate is a major determinant of synchrony under common noisy oscillatory input: Near coincidence of spikes at similar rates gives way to substantial desynchronization at larger firing rate differences. Analysis of this rate-specific synchrony phenomenon reveals distinct spike timing “fingerprints” at different firing rates that emerge through a combination of phase shifting and abrupt changes in spike patterns. We further demonstrate that rate-specific synchrony permits robust detection of rate similarity in a population of neurons through synchronous activation of a postsynaptic neuron, supporting the biological plausibility of a Many Are Equal computation. Our results reveal that spatially coherent noisy oscillations, which are common throughout the brain, can generate previously unknown relationships among neural rate codes, noisy interspike intervals, and precise spike synchrony codes. All of these can coexist in a self-consistent manner because of rate-specific synchrony.
Modulation of dendritic cell differentiation by HLA-G and ILT4 requires the IL-6—STAT3 signaling pathway
Authors: Liang Siyuan , Ristich Vladimir , Arase Hisashi , Dausset Jean , Carosella Edgardo D. , Horuzsko Anatolij
Published: June 2008

The expression of Ig-like transcript (ILT) inhibitory receptors is a characteristic of tolerogenic dendritic cells (DCs). However, the mechanisms of modulation of DCs via ILT receptors remain poorly defined. HLA-G is a preferential ligand for several ILTs. Recently, we demonstrated that triggering of ILT4 by HLA-G1 inhibits maturation of human monocyte-derived conventional DCs and murine DCs from ILT4 transgenic mice, resulting in diminished expression of MHC class II molecules, CD80 and CD86 costimulatory molecules, and prolongation of skin allograft survival. Different isoforms of HLA-G have diverse effects on the efficiency to induce ILT-mediated signaling. In this work, we show that HLA-G1 tetrameric complex and HLA-G5 dimer, but not HLA-G5 monomer, induce strong ILT-mediated signaling. We determined that the arrest of maturation of ILT4-positive DCs by HLA-G ligands involves the IL-6 signaling pathway and STAT3 activation. Ligation of ILT4 with HLA-G on DCs results in recruitment of SHP-1 and SHP-2 protein tyrosine phosphatases. We propose a model where SHP-2 and the IL-6–STAT3 signaling pathway play critical roles in the modulation of DC differentiation by ILT4 and HLA-G.
Insulin-like growth factor 1 receptor is a potential therapeutic target for gastrointestinal stromal tumors
Authors: Tarn Chi , Rink Lori , Merkel Erin , Flieder Douglas , Pathak Harsh , Koumbi Daphne , Testa Joseph R. , Eisenberg Burton , von Mehren Margaret , Godwin Andrew K.
Published: June 2008

A subset of gastrointestinal stromal tumors (GISTs) lack gain-of-function mutations in c-
KIT
and
PDGFR
α. These so-called wild-type (WT) GISTs tend to be less responsive to imatinib-based therapies and have a poor prognosis. We identified amplification of
IGF1R
in a SNP analysis of GIST and thus studied its potential as a therapeutic target in WT and mutant GIST. Expression of IGF1R and downstream effectors in clinical GIST samples was examined by using immunoblots and immunohistochemistry. The roles of IGF1R signaling in GIST and viability were analyzed by using NVP-AEW541, an inhibitor of IGF1R, alone and in combination with imatinib, or via siRNA silencing of IGF1R. IGF1R was strongly overexpressed, and
IGF1R
amplification was detected at a significantly higher frequency in WT GISTs, including a pediatric WT GIST, compared with mutant GISTs (
P
= 0.0173 and
P
= 0.0163, respectively). Inhibition of IGF1R activity
in vitro
with NVP-AEW541 or down-regulation of expression with siIGF1R led to cytotoxicity and induced apoptosis in GIST cell lines via AKT and MAPK signaling. Combination of NVP-AEW541 and imatinib in GIST cell lines induced a strong cytotoxicity response. Our results reveal that
IGF1R
is amplified and the protein is overexpressed in WT and pediatric GISTs. We also demonstrate that the aberrant expression of IGF1R may be associated with oncogenesis in WT GISTs and suggest an alternative and/or complementary therapeutic regimen in the clinical management of all GISTs, especially in a subset of tumors that respond less favorably to imatinib-based therapy.
Genetic analysis of CAND1–CUL1 interactions in
Arabidopsis
supports a role for CAND1-mediated cycling of the SCF
TIR1
complex
Authors: Zhang Wenjing , Ito Hironori , Quint Marcel , Huang He , Noël Laurent D. , Gray William M.
Published: June 2008

SKP1-Cullin1-F-box protein (SCF) ubiquitin-ligases regulate numerous aspects of eukaryotic growth and development. Cullin-Associated and Neddylation-Dissociated (CAND1) modulates SCF function through its interactions with the CUL1 subunit. Although biochemical studies with human CAND1 suggested that CAND1 plays a negative regulatory role by sequestering CUL1 and preventing SCF complex assembly, genetic studies in
Arabidopsis
have shown that
cand1
mutants exhibit reduced SCF activity, demonstrating that
CAND1
is required for optimal SCF function
in vivo
. Together, these genetic and biochemical studies have suggested a model of CAND1-mediated cycles of SCF complex assembly and disassembly. Here, using the SCF
TIR1
complex of the
Arabidopsis
auxin response pathway, we test the SCF cycling model with
Arabidopsis
mutant derivatives of CAND1 and CUL1 that have opposing effects on the CAND1–CUL1 interaction. We find that the disruption of the CAND1–CUL1 interaction results in an increased abundance of assembled SCF
TIR1
complex. In contrast, stabilization of the CAND1–CUL1 interaction diminishes SCF
TIR1
complex abundance. The fact that both decreased and increased CAND1–CUL1 interactions result in reduced SCF
TIR1
activity
in vivo
strongly supports the hypothesis that CAND1-mediated cycling is required for optimal SCF function.
Apoptosome-deficient Cells Lose Cytochromecthrough Proteasomal Degradation but Survive by Autophagy-dependent Glycolysis
Authors: Ferraro Elisabetta , Pulicati Angela , Cencioni Maria Teresa , Cozzolino Mauro , Navoni Francesca , di Martino Simona , Nardacci Roberta , Carrì Maria Teresa , Cecconi Francesco
Published: June 2008

Cytochrome c release from mitochondria promotes apoptosome formation and caspase activation. The question as to whether mitochondrial permeabilization kills cells via a caspase-independent pathway when caspase activation is prevented is still open. Here we report that proneural cells of embryonic origin, when induced to die but rescued by apoptosome inactivation are deprived of cytosolic cytochrome c through proteasomal degradation. We also show that, in this context, those cells keep generating ATP by glycolysis for a long period of time and that they keep their mitochondria in a depolarized state that can be reverted. Moreover, under these conditions, such apoptosome-deficient cells activate a Beclin 1–dependent autophagy pathway to sustain glycolytic-dependent ATP production. Our findings contribute to elucidating what the point-of-no-return in apoptosis is. They also help in clarifying the issue of survival of apoptosome-deficient proneural cells under stress conditions. Unraveling this issue could be highly relevant for pharmacological intervention and for therapies based on neural stem cell transfer in the treatment of neurological disorders.
The Torsin-family AAA+ Protein OOC-5 Contains a Critical Disulfide Adjacent to Sensor-II That Couples Redox State to Nucleotide Binding
Authors: Zhu Li , Wrabl James O. , Hayashi Adam P. , Rose Lesilee S. , Thomas Philip J.
Published: June 2008

A subgroup of the AAA+ proteins that reside in the endoplasmic reticulum and the nuclear envelope including human torsinA, a protein mutated in hereditary dystonia, is called the torsin family of AAA+ proteins. A multiple-sequence alignment of this family with Hsp100 proteins of known structure reveals a conserved cysteine in the C-terminus of torsin proteins within the Sensor-II motif. A structural model predicts this cysteine to be a part of an intramolecular disulfide bond, suggesting that it may function as a redox sensor to regulate ATPase activity. In vitro experiments with OOC-5, a torsinA homolog from Caenorhabditis elegans, demonstrate that redox changes that reduce this disulfide bond affect the binding of ATP and ADP and cause an attendant local conformational change detected by limited proteolysis. Transgenic worms expressing an ooc-5 gene with cysteine-to-serine mutations that disrupt the disulfide bond have a very low embryo hatch rate compared with wild-type controls, indicating these two cysteines are essential for OOC-5 function. We propose that the Sensor-II in torsin family proteins is a redox-regulated sensor. This regulatory mechanism may be central to the function of OOC-5 and human torsinA.
Molecular Mechanisms Controlling GLUT4 Intracellular Retention
Authors: Blot Vincent , McGraw Timothy E.
Published: June 2008

In basal adipocytes, glucose transporter 4 (GLUT4) is sequestered intracellularly by an insulin-reversible retention mechanism. Here, we analyze the roles of three GLUT4 trafficking motifs (FQQI, TELEY, and LL), providing molecular links between insulin signaling, cellular trafficking machinery, and the motifs in the specialized trafficking of GLUT4. Our results support a GLUT4 retention model that involves two linked intracellular cycles: one between endosomes and a retention compartment, and the other between endosomes and specialized GLUT4 transport vesicles. Targeting of GLUT4 to the former is dependent on the FQQI motif and its targeting to the latter is dependent on the TELEY motif. These two motifs act independently in retention, with the TELEY-dependent step being under the control of signaling downstream of the AS160 rab GTPase activating protein. Segregation of GLUT4 from endosomes, although positively correlated with the degree of basal retention, does not completely account for GLUT4 retention or insulin-responsiveness. Mutation of the LL motif slows return to basal intracellular retention after insulin withdrawal. Knockdown of clathrin adaptin protein complex-1 (AP-1) causes a delay in the return to intracellular retention after insulin withdrawal. The effects of mutating the LL motif and knockdown of AP-1 were not additive, establishing that AP-1 regulation of GLUT4 trafficking requires the LL motif.
Exploiting Partial Resistance to Tomato yellow leaf curl virus Derived from Solanum pimpinellifolium UPV16991
Authors: de Castro Ana Pérez , Díez María José , Nuez Fernando
Published: June 2008

Tomato yellow leaf curl disease (TYLCD) causes great economic losses in tomato crops worldwide. Despite efforts undertaken by different research groups, there are no immune commercial plant materials available. Recently, our group reported partial resistance to TYLCD in line L102, derived from Solanum pimpinellifolium UPV16991. Resistance in this line is monogenic, with partial recessiveness and incomplete penetrance. Even though the resistance gene in L102 is not dominant, we also proved that levels of resistance were high in hybrids with different tomato lines. The objective of this work was to evaluate the level of resistance in plants which combined UPV16991-derived resistance and the Ty-1 gene, both in heterozygosis. Most of the hybrids between S. pimpinellifolium- and S. chilense-derived resistant lines exhibited milder symptoms than heterozygotes for either S. pimpinellifolium- or S. chilense-derived resistance. In some of the hybrids, viral accumulation was also lower than in respective heterozygotes. Our results support the utility of resistance derived from UPV16991 combined with the Ty-1 gene in increasing levels of resistance to TYLCD in tomato hybrids. This is the most practical approach to exploiting resistance derived from UPV16991, because it allows the development of hybrids without the need of fixing the resistance gene in both parents.
Optimizing Fungicide Timing for the Control of Rhizoctonia Crown and Root Rot of Sugar Beet Using Soil Temperature and Plant Growth Stages
Authors: Kirk W. W. , Wharton P. S. , Schafer R. L. , Tumbalam P. , Poindexter S. , Guza C. , Fogg R. , Schlatter T. , Stewart J. , Hubbell L. , Ruppal D.
Published: June 2008

Azoxystrobin is applied early in the sugar beet growing season in north-central United States for control of Rhizoctonia damping-off and Rhizoctonia crown and root rot caused by Rhizoctonia solani anastomoses groups (AGs) 4 and 2-2, respectively. Fungicide application timings based on crop growth stage and soil temperature thresholds were evaluated in inoculated small-scale trials and in commercial fields with a history of Rhizoctonia crown and root rot. Soil temperature thresholds of 10, 15, and 20°C were selected for fungicide application timings and used to test whether soil temperature could be used to better time applications of azoxystrobin. In both small- and large-plot trials, timing applications after attainment of specific soil temperature thresholds did not improve efficacy of azoxystrobin in controlling damping-off or Rhizoctonia crown and root rot compared with application timings based on either planting date, seedling development, or leaf stage in a susceptible (E-17) and a resistant (RH-5) cultivar. Application rate and split application timings of azoxystrobin had no significant effect on severity of crown and root rot. Other environmental factors such as soil moisture may interact with soil temperature to influence disease development. Cv. RH-5 had higher sugar yield attributes than the susceptible cultivar (E-17) in seasons conducive and nonconducive to crown and root rot development. All isolates recovered from both small- and large-plot trials in all years were AG 2-2. R. solani AG 4 was not identified in any samples from any year.
Occurrence and Detection of the DMI Resistance-Associated Genetic Element ‘Mona’ in Monilinia fructicola
Authors: Luo Chao-Xi , Cox Kerik D. , Amiri Achour , Schnabel Guido
Published: June 2008

Sterol demethylation inhibitor (DMI) fungicide resistance in isolates of Monilinia fructicola from Georgia has been linked to overexpression of the MfCYP51 gene and a corresponding 65-bp genetic element ‘Mona’ inserted in the upstream region of MfCYP51. In this study, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was developed to detect the Mona element. Fourteen DMI fungicide-resistant (DMI-R) and six DMI fungicide-sensitive (DMI-S) isolates from Georgia, six DMI-R and 11 DMI-S isolates from South Carolina, seven DMI-R and nine DMI-S isolates from New York, and two DMI-R and three DMI-S isolates from Ohio were used in this study. The isolates from the southeastern United States and Ohio were collected from peach, whereas isolates from New York were collected from cherry. A 376-bp fragment containing the Mona element was consistently amplified with primer pair INS65-F and INS65-R from DMI-R isolates, and either a 311-bp or 1,815-bp fragment was amplified from DMI-S isolates. The primer pair did not amplify DNA fragments of similar sizes from isolates of five other common fruit rot pathogens of peach, including Alternaria alternata, Colletotrichum acutatum, Gilbertella persicaria, Penicillium expansum, and Rhizopus stolonifer. Gel electrophoresis of the PCR amplicon can distinguish between DMI-R and DMI-S isolates based on the 65-bp size difference of the amplicon; however, the restriction digestion assay can verify questionable results, especially in the absence of a positive control. Only the 376-bp fragment containing the Mona element was digestable with endonuclease BsrBI, resulting in two restriction fragments of 236 and 140 bp in size. In this study, a protocol for Mona detection from aerial fungal structures was developed that can yield results within a few hours of sampling. This study confirms that the Mona element is strongly linked to the DMI-resistance phenotype and reveals that overexpression of the MfCYP51 gene is a common DMI fungicide resistance mechanism in M. fructicola, not only in Georgia but throughout the eastern United States.
Crown Rot of Zucchini Squash Caused by Fusarium solani f. sp. cucurbitae in Almería Province, Spain
Authors: Gómez J. , Guerra-Sanz J. M. , Sánchez-Guerrero M. C. , Serrano Y. , Melero-Vara J. M.
Published: June 2008

Cucumber, melon, watermelon, and zucchini are intensively cropped in the southern part of Spain where approximately 20,000 ha of the crops are grown in greenhouses. In the spring of 2007, zucchini plants (Cucurbita pepo) at the fruit-bearing stage in three commercial plastichouses in Almería exhibited necrosis on the basal stem, wilt, and death. The incidence of dead plants was 20 to 30%. Fusarium solani was consistently isolated from the basal stems of symptomatic plants on potato dextrose agar (PDA). Cultures of six single-hyphal transfers were identified on the basis of molecular sequences and morphological characteristics (2). Sequences of ribosomal DNA from ITS1 region, 5.8S rDNA, and ITS2 were identical for all six isolates of F. solani. The rDNA sequence of isolate Fscl-3 of F. solani was deposited as GenBank Accession No. AM940070. The pathogenicity of these six isolates of F. solani was tested in two experiments conducted in one plastichouse in Almería. Pregerminated seeds of zucchini cv. Consul were sown in 1-liter containers filled with vermiculite on 21 May and 22 June, 2007 (experiments 1 and 2, respectively). Plants at the one- to two-true-leaf stage or younger were inoculated with a soil drench of 2.0 to 8.4 × 105 propagules per ml). One colonized PDA petri plate of each isolate was blended and homogenized in 500 ml of distilled water. Inoculum (50 ml per plant) was poured around the stem of zucchini plants growing in vermiculite. The experimental design was a randomized complete block with three replicates with each plot comprising four plants (one plant per container). In both experiments, 12 uninoculated plants of the same cultivar served as controls. Plants were maintained for 1 month following inoculation in a greenhouse with mean temperatures ranging between 20.7 and 24.6°C and 23.3 to 29.8°C for experiments 1 and 2, respectively. Wilting first occurred 9 days after inoculation, and 14 days later, all plants inoculated with the F. solani isolates died. Inoculated plants exhibited lesions on the stem base without rot of secondary roots. At the end of the experiment, the uninoculated plants remained asymptomatic. Results of experiment 2, with higher temperatures, were similar. The pathogen was consistently recovered from symptomatic plants in both experiments, fulfilling Koch's postulates. Although F. solani f. sp. cucurbitae race 1 was reported in field squash (C. maxima) in the province of Valencia of east-central Spain (1), to our knowledge, this is the first report of F. solani as the causal agent of crown rot of zucchini plants in plastichouses in the Almería Province of Spain, one of the world's largest concentrations of greenhouses.

References: (1) J. García-Jiménez et al. Plant Dis. 81:1216, 1997. (2) C. M. Messiaen and R. Cassini. Taxonomy of Fusarium. Page 427 in: Fusarium: Diseases, Biology, and Taxonomy. P. E. Nelson et al., eds. Pennsylvania State University, University Park, 1981.
Nonhost Versus Host Resistance to the Grapevine Downy Mildew, Plasmopara viticola, Studied at the Tissue Level
Authors: Díez-Navajas A. M. , Wiedemann-Merdinoglu S. , Greif C. , Merdinoglu D.
Published: June 2008

Following inoculation of host and nonhost plants with Plasmopara viticola, the grapevine downy mildew, a histological survey was undertaken to identify the stage where its development is contained in nonhosts and in resistant host plants. Three herbaceous nonhost species, Beta vulgaris, Lactuca sativa, and Capsicum annuum, and three grapevine species displaying different level of resistance (Vitis vinifera [susceptible], Vitis riparia [partially resistant] and Muscadinia rotundifolia [totally resistant]) where inoculated by P. viticola using a controlled leaf disk inoculation bioassay. During the early steps of infection, defined as encystment of zoospores on stomata, penetration of the germ tube, and production of the vesicle with the primary hypha, there was no evidence of a clear-cut preference to grapevine tissues that could attest to host specificity. The main difference between host grapevine species and nonhosts was observed during the haustorium formation stage. In nonhost tissues, the infection was stopped by cell wall-associated defense responses before any mature haustorium could appear. Defense responses in resistant grapevines were triggered when haustoria were fully visible and corresponded to hypersensitive responses. These observations illustrate that, for P. viticola, haustorium formation is not only a key stage for the establishment of biotrophy but also for the host specificity and the recognition by grapevine resistance factors.
Worms by number
Authors: Glasby C.J , Glasby S.P , Pleijel F
Published: June 2008

This paper investigates alternation patterns in length, shape and orientation of dorsal cirri (fleshy segmental appendages) of phyllodocidans, a large group of polychaete worms (Annelida). We document the alternation patterns in several families of Phyllodocida (Syllidae, Hesionidae, Sigalionidae, Polynoidae, Aphroditidae and Acoetidae) and identify the simple mathematical rule bases that describe the progression of these sequences. Two fundamentally different binary alternation patterns were found on the first four segments: 1011 for nereidiform families and 1010 for aphroditiform families. The alternation pattern in all aphroditiform families matches a simple one-dimensional cellular automaton and that for Syllidae (nereidiform) matches the Fibonacci string sequence. Hesionidae (nereidiform) showed the greatest variation in alternation patterns, but all corresponded to various known substitution rules. Comparison of binary patterns of the first 22 segments using a distance measure supports the current ideas on phylogeny within Phyllodocida. These results suggest that gene(s) involved in post-larval segmental growth employ a switching sequence that corresponds to simple mathematical substitution rules.