bluuebunny/crossref_metadata_2025 huggingface dataset:
Antitumor NK activation induced by the Toll-like receptor 3-TICAM-1 (TRIF) pathway in myeloid dendritic cells
Authors: Akazawa Takashi , Ebihara Takashi , Okuno Manabu , Okuda Yu , Shingai Masashi , Tsujimura Kunio , Takahashi Toshitada , Ikawa Masahito , Okabe Masaru , Inoue Norimitsu , Okamoto-Tanaka Miki , Ishizaki Hiroyoshi , Miyoshi Jun , Matsumoto Misako , Seya Tsukasa
Published: December 2006

Myeloid dendritic cells (mDCs) recognize and respond to polyI:C, an analog of dsRNA, by endosomal Toll-like receptor (TLR) 3 and cytoplasmic receptors. Natural killer (NK) cells are activated
in vivo
by the administration of polyI:C to mice and
in vivo
are reciprocally activated by mDCs, although the molecular mechanisms are as yet undetermined. Here, we show that the TLR adaptor TICAM-1 (TRIF) participates in mDC-derived antitumor NK activation. In a syngeneic mouse tumor implant model (C57BL/6 vs. B16 melanoma with low H-2 expresser), i.p. administration of polyI:C led to the retardation of tumor growth, an effect relied on by NK activation. This NK-dependent tumor regression did not occur in TICAM-1
−/−
or IFNAR
−/−
mice, whereas a normal NK antitumor response was induced in PKR
−/−
, MyD88
−/−
, IFN-β
−/−
, and wild-type mice. IFNAR was a prerequisite for the induction of IFN-α/β and TLR3. The lack of TICAM-1 did not affect IFN production but resulted in unresponsiveness to IL-12 production, mDC maturation, and polyI:C-mediated NK-antitumor activity. This NK activation required NK-mDC contact but not IL-12 function in
in vivo
transwell analysis. Implanted tumor growth in IFNAR
−/−
mice was retarded by adoptively transferring polyI:C-treated TICACM-1-positive mDCs but not TICAM-1
−/−
mDCs. Thus, TICAM-1 in mDCs critically facilitated mDC-NK contact and activation of antitumor NK, resulting in the regression of low MHC-expressing tumors.
Nuclear IKK activity leads to dysregulated Notch-dependent gene expression in colorectal cancer
Authors: Fernández-Majada V. , Aguilera C. , Villanueva A. , Vilardell F. , Robert-Moreno A. , Aytés A. , Real F. X. , Capella G. , Mayo M. W. , Espinosa L. , Bigas A.
Published: December 2006

Nuclear functions for IκB kinase (IKK), including phosphorylation of histone H3 and nuclear corepressors, have been recently described. Here, we show that IKK is activated in colorectal tumors concomitant with the presence of phosphorylated SMRT (silencing mediator of retinoic acid and thyroid hormone receptor) corepressor that is aberrantly localized in the cytoplasm. In these tumors, IKKα associates to the chromatin of specific Notch targets, leading to the release of SMRT. Abrogation of IKK activity by BAY11-7082 or by expressing dominant negative IKKα restores the association of SMRT with Notch target genes, resulting in specific gene repression. Finally, BAY11-7082 significantly reduces tumor size in colorectal cancer xenografts (CRC-Xs) implanted in nude mice.
N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage
Authors: Jiang Tao , Zhou Xinfeng , Taghizadeh Koli , Dong Min , Dedon Peter C.
Published: December 2006

The posttranslational modification of histone and other chromatin proteins has a well recognized but poorly defined role in the physiology of gene expression. With implications for interfering with these epigenetic mechanisms, we now report the existence of a relatively abundant secondary modification of chromatin proteins, the N6-formylation of lysine that appears to be uniquely associated with histone and other nuclear proteins. Using both radiolabeling and sensitive bioanalytical methods, we demonstrate that the formyl moiety of 3′-formylphosphate residues arising from 5′-oxidation of deoxyribose in DNA, caused by the enediyne neocarzinostatin, for example, acylate the N6-amino groups of lysine side chains. A liquid chromatography (LC)–tandem mass spectrometry (MS) method was developed to quantify the resulting N6-formyl-lysine residues, which were observed to be present in unperturbed cells and all sources of histone proteins to the extent of 0.04–0.1% of all lysines in acid-soluble chromatin proteins including histones. Cells treated with neocarzinostatin showed a clear dose–response relationship for the formation of N6-formyl-lysine, with this nucleosome linker-selective DNA-cleaving agent causing selective N6-formylation of the linker histone H1. The N6-formyl-lysine residue appears to represent an endogenous histone secondary modification, one that bears chemical similarity to lysine N6-acetylation recognized as an important determinant of gene expression in mammalian cells. The N6-formyl modification of lysine may interfere with the signaling functions of lysine acetylation and methylation and thus contribute to the pathophysiology of oxidative and nitrosative stress.
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock–lock mechanism
Authors: Nguyen Phuong H. , Li Mai Suan , Stock Gerhard , Straub John E. , Thirumalai D.
Published: December 2006

Nonfibrillar soluble oligomers, which are intermediates in the transition from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. To monitor the early events that direct assembly of amyloidogenic peptides we probe the dynamics of formation of (
A
β
16–22
)

n

by adding a monomer to a preformed (
A
β
16–22
)

n
−1

(
n
= 4–6) oligomer in which the peptides are arranged in an antiparallel β-sheet conformation. All atom molecular dynamics simulations in water and multiple long trajectories, for a cumulative time of 6.9 μs, show that the oligomer grows by a two-stage dock–lock mechanism. The largest conformational change in the added disordered monomer occurs during the rapid (≈50 ns) first dock stage in which the β-strand content of the monomer increases substantially from a low initial value. In the second slow-lock phase, the monomer rearranges to form in register antiparallel structures. Surprisingly, the mobile structured oligomers undergo large conformational changes in order to accommodate the added monomer. The time needed to incorporate the monomer into the fluid-like oligomer grows even when
n
= 6, which suggests that the critical nucleus size must exceed six. Stable antiparallel structure formation exceeds hundreds of nanoseconds even though frequent interpeptide collisions occur at elevated monomer concentrations used in the simulations. The dock–lock mechanism should be a generic mechanism for growth of oligomers of amyloidogenic peptides.
Structure of aspartoacylase, the brain enzyme impaired in Canavan disease
Authors: Bitto Eduard , Bingman Craig A. , Wesenberg Gary E. , McCoy Jason G. , Phillips George N.
Published: December 2006

Aspartoacylase catalyzes hydrolysis of
N
-acetyl-
l
-aspartate to aspartate and acetate in the vertebrate brain. Deficiency in this activity leads to spongiform degeneration of the white matter of the brain and is the established cause of Canavan disease, a fatal progressive leukodystrophy affecting young children. We present crystal structures of recombinant human and rat aspartoacylase refined to 2.8- and 1.8-Å resolution, respectively. The structures revealed that the N-terminal domain of aspartoacylase adopts a protein fold similar to that of zinc-dependent hydrolases related to carboxypeptidases A. The catalytic site of aspartoacylase shows close structural similarity to those of carboxypeptidases despite only 10–13% sequence identity between these proteins. About 100 C-terminal residues of aspartoacylase form a globular domain with a two-stranded β-sheet linker that wraps around the N-terminal domain. The long channel leading to the active site is formed by the interface of the N- and C-terminal domains. The C-terminal domain is positioned in a way that prevents productive binding of polypetides in the active site. The structures revealed that residues 158–164 may undergo a conformational change that results in opening and partial closing of the channel entrance. We hypothesize that the catalytic mechanism of aspartoacylase is closely analogous to that of carboxypeptidases. We identify residues involved in zinc coordination, and propose which residues may be involved in substrate binding and catalysis. The structures also provide a structural framework necessary for understanding the deleterious effects of many missense mutations of human aspartoacylase.
H2A.Z contributes to the unique 3D structure of the centromere
Authors: Greaves Ian K. , Rangasamy Danny , Ridgway Patricia , Tremethick David J.
Published: December 2006

Mammalian centromere function depends upon a specialized chromatin organization where distinct domains of CENP-A and dimethyl K4 histone H3, forming centric chromatin, are uniquely positioned on or near the surface of the chromosome. These distinct domains are embedded in pericentric heterochromatin (characterized by H3 methylated at K9). The mechanisms that underpin this complex spatial organization are unknown. Here, we identify the essential histone variant H2A.Z as a new structural component of the centromere. Along linear chromatin fibers H2A.Z is distributed nonuniformly throughout heterochromatin, and centric chromatin where regions of nucleosomes containing H2A.Z and dimethylated K4 H3 are interspersed between subdomains of CENP-A. At metaphase, using the inactive X chromosome centromere as a model, complex folding of this fiber produces spatially positioned domains where H2A.Z/dimethylated K4 H3 chromatin juxtaposes one side of CENP-A chromatin, whereas a region of H2A/trimethyl K9 H3 borders the other side. A second region of H2A.Z is found, with trimethyl K9 H3 at the inner centromere. We therefore propose that H2A.Z plays an integral role in organizing centromere structure.
A neural basis for inference in perceptual ambiguity
Authors: Sterzer Philipp , Kleinschmidt Andreas
Published: December 2006

When looking at ambiguous visual stimuli, the observer experiences frequent spontaneous transitions between two competing percepts while physical stimulation remains unchanged. Despite recent advances in understanding the neural processes underlying such perceptual rivalry, a key question has remained unresolved: Does perceptual rivalry result merely from local bistability of neural activity patterns in sensory stimulus representations, or do higher-order areas play a causal role by shifting inference and, thus, initiating perceptual changes? We used functional MRI to measure brain activity while human observers reported successive spontaneous changes in perceived direction for an ambiguous apparent motion stimulus. In a control condition, the individual sequences of spontaneous perceptual switches during bistability were replayed by using a disambiguated version of the stimulus. Greater activations during spontaneous compared with stimulus-driven switches were observed in inferior frontal cortex bilaterally. Subsequent chronometric analyses of event-related signal time courses showed that, relative to activations in motion-sensitive extrastriate visual cortex, right inferior frontal cortex activation occurred earlier during spontaneous than during stimulus-driven perceptual changes. The temporal precedence of right inferior frontal activations suggests that this region participates in initiating spontaneous switches in perception during constant physical stimulation. Our findings can thus be seen as a signature of when and where the brain “makes up its mind” about competing perceptual interpretations of a given sensory input pattern.
Eukaryotic operon-like transcription of functionally related genes in
Drosophila
Authors: Ben-Shahar Yehuda , Nannapaneni Kishore , Casavant Thomas L. , Scheetz Todd E. , Welsh Michael J.
Published: December 2006

Complex biological processes require coordinated function of many genes. One evolutionary solution to the problem of coordinately expressing functionally related genes in bacteria and nematodes is organization of genes in operons. Surprisingly, eukaryotic operons are considered rare outside the nematode lineage. In
Drosophila melanogaster
, we found
lounge lizard
(
llz
), which encodes a degenerin/ENaC cation channel, cotranscribed with
CheB42a
, a nonhomologous gene of unknown function residing <100 bp upstream. These two genes were transcribed from a single promoter as one primary transcript and were processed posttranscriptionally to generate individual mRNAs. The mechanism did not involve alternative splicing, and it differed from the trans splicing used in nematode operons. Both genes were expressed in the same tissues, and previous work suggested that both may be involved in courtship behavior. A bioinformatic approach identified numerous additional loci as potential
Drosophila
operons. These data reveal eukaryotic operon-like transcription of functionally related genes in
Drosophila
. The results also suggest that operon-based transcription may be more common in eukaryotes than previously appreciated.
Oxidized messenger RNA induces translation errors
Authors: Tanaka Mikiei , Chock P. Boon , Stadtman Earl R.
Published: December 2006

To investigate the effect of RNA oxidation on normal cellular functions, we studied the translation of nonoxidized and oxidized luciferase mRNA in both rabbit reticulocyte lysate and human HEK293 cells. When HEK293 cells transfected with nonoxidized mRNA encoding the firefly luciferase protein were cultured in the presence of paraquat, there was a paraquat concentration-dependent increase in the formation of luciferase short polypeptides (SPs) concomitant with an increase in 8-oxoguanosine. Short polypeptides were also formed when the mRNA was oxidized
in vitro
by the Fe–ascorbate–H
2
O
2
metal-catalyzed oxidation system before its transfection into cells. Translation of the
in vitro
oxidized mRNA in rabbit reticulocyte lysate also led to formation of SPs. The SPs formed by either procedure contained the N-terminal and the C-terminal portions of the tagged luciferase. In addition, the oxidized mRNA was able to associate with ribosomes to form polysomes similar to those formed with nonoxidized mRNA preparations, indicating that the oxidized mRNAs are mostly intact; however, their translation fidelity was significantly reduced. Nevertheless, our results indicate that the SPs were derived from both premature termination of the translation process of the oxidized mRNA and the proteolytic degradation of the modified full-length luciferase resulting from translation errors induced by oxidized mRNA. In light of these findings, the physiological consequences of mRNA oxidation are discussed.
Structural basis for intramembrane proteolysis by rhomboid serine proteases
Authors: Ben-Shem Adam , Fass Deborah , Bibi Eitan
Published: December 2006

Intramembrane proteases catalyze peptide bond cleavage of integral membrane protein substrates. This activity is crucial for many biological and pathological processes. Rhomboids are evolutionarily widespread intramembrane serine proteases. Here, we present the 2.3-Å-resolution crystal structure of a rhomboid from
Escherichia coli
. The enzyme has six transmembrane helices, five of which surround a short TM4, which starts deep within the membrane at the catalytic serine residue. Thus, the catalytic serine is in an externally exposed cavity, which provides a hydrophilic environment for proteolysis. Our results reveal a mechanism to enable water-dependent catalysis at the depth of the hydrophobic milieu of the membrane and suggest how substrates gain access to the sequestered rhomboid active site.
Short wavelength topography on the inner-core boundary
Authors: Cao Aimin , Masson Yder , Romanowicz Barbara
Published: December 2006

Constraining the topography of the inner-core boundary is important for studies of core–mantle coupling and the generation of the geodynamo. We present evidence for significant temporal variability in the amplitude of the inner core reflected phasePKiKPfor an exceptionally high-quality earthquake doublet, observed postcritically at the short-period Yellowknife seismic array (YK), which occurred in the South Sandwich Islands within a 10-year interval (1993/2003). This observation, complemented by data from several other doublets, indicates the presence of topography at the inner-core boundary, with a horizontal wavelength on the order of 10 km. Such topography could be sustained by small-scale convection at the top of the inner core and is compatible with a rate of super rotation of the inner core of ≈0.1–0.15° per year. In the absence of inner-core rotation, decadal scale temporal changes in the inner-core boundary topography would provide an upper bound on the viscosity at the top of the inner core.
Cyclin-dependent kinase 5 modulates nociceptive signaling through direct phosphorylation of transient receptor potential vanilloid 1
Authors: Pareek Tej K. , Keller Jason , Kesavapany Sashi , Agarwal Nitin , Kuner Rohini , Pant Harish C. , Iadarola Michael J. , Brady Roscoe O. , Kulkarni Ashok B.
Published: December 2006

Transient receptor potential vanilloid 1 (TRPV1), a ligand-gated cation channel highly expressed in small-diameter sensory neurons, is activated by heat, protons, and capsaicin. The phosphorylation of TRPV1 provides a versatile regulation of intracellular calcium levels and is critical for TRPV1 function in responding to a pain stimulus. We have previously reported that cyclin-dependent kinase 5 (Cdk5) activity regulates nociceptive signaling. In this article we report that the Cdk5-mediated phosphorylation of TRPV1 at threonine-407 can modulate agonist-induced calcium influx. Inhibition of Cdk5 activity in cultured dorsal root ganglia neurons resulted in a significant reduction of TRPV1-mediated calcium influx, and this effect could be reversed by restoring Cdk5 activity. Primary nociceptor-specific Cdk5 conditional-knockout mice showed reduced TRPV1 phosphorylation, resulting in significant hypoalgesia. Thus, the present study indicates that Cdk5-mediated TRPV1 phosphorylation is important in the regulation of pain signaling.
Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator
Authors: Pierre Valérie C. , Kaiser Jens T. , Barton Jacqueline K.
Published: December 2006

We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5′-(dCGG
A
AATT
C
CCG)
2
-3′. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches.
Lung development and repair: Contribution of the ciliated lineage
Authors: Rawlins Emma L. , Ostrowski Lawrence E. , Randell Scott H. , Hogan Brigid L. M.
Published: December 2006

The identity of the endogenous epithelial cells in the adult lung that are responsible for normal turnover and repair after injury is still controversial. In part, this is due to a paucity of highly specific genetic lineage tools to follow efficiently the fate of the major epithelial cell populations: the basal, secretory, ciliated, neuroendocrine, and alveolar cells. As part of a program to address this problem we have used a 1-kb
FOXJ1
promoter to drive
CreER
in the ciliated cells of the embryonic and adult lung. Analysis of
FOXJ1
-
GFP
transgenic lungs shows that labeled cells appear in a proximal-distal pattern during embryogenesis and that the promoter drives expression in all ciliated cells. Using
FOXJ1CreER
adult mice, we have followed the fate of ciliated cells after epithelial injury by naphthalene or sulfur dioxide. From quantitative analysis and confocal microscopy we conclude that ciliated cells transiently change their morphology in response to lung injury but do not proliferate or transdifferentiate as part of the repair process.
The N-terminal domain of Tob55 has a receptor-like function in the biogenesis of mitochondrial β-barrel proteins
Authors: Habib Shukry J. , Waizenegger Thomas , Niewienda Agathe , Paschen Stefan A. , Neupert Walter , Rapaport Doron
Published: December 2006

β-Barrel proteins constitute a distinct class of mitochondrial outer membrane proteins. For import into mitochondria, their precursor forms engage the TOM complex. They are then relayed to the TOB complex, which mediates their insertion into the outer membrane. We studied the structure–function relationships of the core component of the TOB complex, Tob55. Tob55 precursors with deletions in the N-terminal domain were not affected in their targeting to and insertion into the mitochondrial outer membrane. Replacement of wild-type Tob55 by these deletion variants resulted in reduced growth of cells, and mitochondria isolated from such cells were impaired in their capacity to import β-barrel precursors. The purified N-terminal domain was able to bind β-barrel precursors in a specific manner. Collectively, these results demonstrate that the N-terminal domain of Tob55 recognizes precursors of β-barrel proteins. This recognition may contribute to the coupling of the translocation of β-barrel precursors across the TOM complex to their interaction with the TOB complex.
Monocytes give rise to mucosal, but not splenic, conventional dendritic cells
Authors: Varol Chen , Landsman Limor , Fogg Darin K. , Greenshtein Liat , Gildor Boaz , Margalit Raanan , Kalchenko Vyacheslav , Geissmann Frederic , Jung Steffen
Published: December 2006

The mononuclear phagocyte (MP) system is a body-wide macrophage (MΦ) and dendritic cell (DC) network, which contributes to tissue homeostasis, inflammation, and immune defense. The in vivo origins of MPs remain poorly understood. Here, we use an adoptive precursor cell transfer strategy into MP-depleted mice to establish the in vivo differentiation sequence from a recently identified MΦ/DC-restricted bone marrow (BM) precursor (MDP) via BM and blood intermediates to peripheral MΦs and DCs. We show that MDPs are in vivo precursors of BM and blood monocytes. Interestingly, grafted Gr1high “inflammatory” blood monocytes shuttle back to the BM in the absence of inflammation, convert into Gr1low monocytes, and contribute further to MP generation. The grafted monocytes give rise to DCs in the intestinal lamina propria and lung, but not to conventional CD11chigh DCs in the spleen, which develop during homeostasis from MDPs without a monocytic intermediate.
An essential role for RasGRP1 in mast cell function and IgE-mediated allergic response
Authors: Liu Yan , Zhu Minghua , Nishida Keigo , Hirano Toshio , Zhang Weiguo
Published: December 2006

Cross-linking of the FcεRI activates the phosphatidyl inositol 3 kinase (PI3K) and mitogen-activated protein kinase pathways. Previous studies demonstrate that Ras guanyl nucleotide-releasing protein (RasGRP)1 is essential in T cell receptor–mediated Ras-Erk activation. Here, we report that RasGRP1 plays an important role in FcεRI-mediated PI3K activation and mast cell function. RasGRP1-deficient mice failed to mount anaphylactic allergic reactions. RasGRP1−/− mast cells had markedly reduced degranulation and cytokine production. Although FcεRI-mediated Erk activation was normal, PI3K activation was diminished. Consequently, activation of Akt, PIP3-dependent kinase, and protein kinase C δ was defective. Expression of a constitutively active form of N-Ras could rescue the degranulation defect and Akt activation. We further demonstrated that RasGRP1−/− mast cells were defective in granule translocation, microtubule formation, and RhoA activation. Our results identified RasGRP1 as an essential regulator of mast cell function.
Somatic hypermutation: activation-induced deaminase for C/G followed by polymerase η for A/T
Authors: Neuberger Michael S. , Rada Cristina
Published: December 2006

Somatic hypermutation (SHM) introduces nucleotide substitutions into immunoglobulin variable (Ig V) region genes at all four bases, but the mutations at C/G and A/T pairs are achieved by distinct mechanisms. Mutations at C/G pairs are a direct consequence of the C→U deamination catalyzed by activation-induced deaminase (AID). Mutations at A/T pairs, however, require a second mutagenic process that occurs during patch repair of the AID-generated U/G mismatch. Several DNA polymerases have been proposed to play a role in SHM, but accumulating evidence indicates that the mutations at A/T are overwhelmingly achieved by recruitment of DNA polymerase η.
The Cullin3 Ubiquitin Ligase Functions as a Nedd8-bound Heterodimer
Authors: Wimuttisuk Wananit , Singer Jeffrey D.
Published: December 2006

Cullins are members of a family of scaffold proteins that assemble multisubunit ubiquitin ligase complexes to confer substrate specificity for the ubiquitination pathway. Cullin3 (Cul3) forms a catalytically inactive BTB-Cul3-Rbx1 (BCR) ubiquitin ligase, which becomes functional upon covalent attachment of the ubiquitin homologue neural-precursor-cell-expressed and developmentally down regulated 8 (Nedd8) near the C terminus of Cul3. Current models suggest that Nedd8 activates cullin complexes by providing a recognition site for a ubiquitin-conjugating enzyme. Based on the following evidence, we propose that Nedd8 activates the BCR ubiquitin ligase by mediating the dimerization of Cul3. First, Cul3 is found as a neddylated heterodimer bound to a BTB domain-containing protein in vivo. Second, the formation of a Cul3 heterodimer is mediated by a Nedd8 molecule, which covalently attaches itself to one Cul3 molecule and binds to the winged-helix B domain at the C terminus of the second Cul3 molecule. Third, complementation experiments revealed that coexpression of two distinct nonfunctional Cul3 mutants can rescue the ubiquitin ligase function of the BCR complex. Likewise, a substrate of the BCR complex binds heterodimeric Cul3, suggesting that the Cul3 complex is active as a dimer. These findings not only provide insight into the architecture of the active BCR complex but also suggest assembly as a regulatory mechanism for activation of all cullin-based ubiquitin ligases.
Nonenzymatic Lipid Peroxidation Reprograms Gene Expression and Activates Defense Markers inArabidopsisTocopherol-Deficient Mutants
Authors: Sattler Scott E. , Mène-Saffrané Laurent , Farmer Edward E. , Krischke Markus , Mueller Martin J. , DellaPenna Dean
Published: December 2006

Tocopherols (vitamin E) are lipophilic antioxidants that are synthesized by all plants and are particularly abundant in seeds. Two tocopherol-deficient mutant loci in Arabidopsis thaliana were used to examine the functions of tocopherols in seedlings: vitamin e1 (vte1), which accumulates the pathway intermediate 2,3-dimethyl-5-phytyl-1,4-benzoquinone (DMPBQ); and vte2, which lacks all tocopherols and pathway intermediates. Only vte2 displayed severe seedling growth defects, which corresponded with massively increased levels of the major classes of nonenzymatic lipid peroxidation products: hydroxy fatty acids, malondialdehyde, and phytoprostanes. In the absence of pathogens, the phytoalexin camalexin accumulated in vte2 seedlings to levels 100-fold higher than in wild-type or vte1 seedlings. Similarly, gene expression profiling in wild-type, vte1, and vte2 seedlings indicated that increased levels of nonenzymatic lipid peroxidation in vte2 corresponded to increased expression of many defense-related genes, which were not induced in vte1. Both biochemical and transcriptional analyses of vte2 seedlings indicate that nonenzymatic lipid peroxidation plays a significant role in modulating plant defense responses. Together, these results establish that tocopherols in wild-type plants or DMPBQ in vte1 plants limit nonenzymatic lipid peroxidation during germination and early seedling development, thereby preventing the inappropriate activation of transcriptional and biochemical defense responses.
Phytotoxicity and Innate Immune Responses Induced by Nep1-Like Proteins
Authors: Qutob Dinah , Kemmerling Birgit , Brunner Frédéric , Küfner Isabell , Engelhardt Stefan , Gust Andrea A. , Luberacki Borries , Seitz Hanns Ulrich , Stahl Dietmar , Rauhut Thomas , Glawischnig Erich , Schween Gabriele , Lacombe Benoit , Watanabe Naohide , Lam Eric , Schlichting Rita , Scheel Dierk , Nau Katja , Dodt Gabriele , Hubert David , Gijzen Mark , Nürnberger Thorsten
Published: December 2006

We show that oomycete-derived Nep1 (for necrosis and ethylene-inducing peptide1)–like proteins (NLPs) trigger a comprehensive immune response in Arabidopsis thaliana, comprising posttranslational activation of mitogen-activated protein kinase activity, deposition of callose, production of nitric oxide, reactive oxygen intermediates, ethylene, and the phytoalexin camalexin, as well as cell death. Transcript profiling experiments revealed that NLPs trigger extensive reprogramming of the Arabidopsis transcriptome closely resembling that evoked by bacteria-derived flagellin. NLP-induced cell death is an active, light-dependent process requiring HSP90 but not caspase activity, salicylic acid, jasmonic acid, ethylene, or functional SGT1a/SGT1b. Studies on animal, yeast, moss, and plant cells revealed that sensitivity to NLPs is not a general characteristic of phospholipid bilayer systems but appears to be restricted to dicot plants. NLP-induced cell death does not require an intact plant cell wall, and ectopic expression of NLP in dicot plants resulted in cell death only when the protein was delivered to the apoplast. Our findings strongly suggest that NLP-induced necrosis requires interaction with a target site that is unique to the extracytoplasmic side of dicot plant plasma membranes. We propose that NLPs play dual roles in plant pathogen interactions as toxin-like virulence factors and as triggers of plant innate immune responses.
MAIGO2 Is Involved in Exit of Seed Storage Proteins from the Endoplasmic Reticulum in Arabidopsis thaliana
Authors: Li Lixin , Shimada Tomoo , Takahashi Hideyuki , Ueda Haruko , Fukao Yoichiro , Kondo Maki , Nishimura Mikio , Hara-Nishimura Ikuko
Published: December 2006

Seed storage proteins are synthesized on the endoplasmic reticulum (ER) as precursors and then transported to protein storage vacuoles, where they are processed into mature forms. Here, we isolated an Arabidopsis thaliana mutant, maigo2 (mag2), that accumulated the precursors of two major storage proteins, 2S albumin and 12S globulin, in dry seeds. mag2 seed cells contained many novel structures, with an electron-dense core that was composed of the precursor forms of 2S albumin. 12S globulins were segregated from 2S albumin and were localized in the matrix region of the structures together with the ER chaperones lumenal binding protein and protein disulfide isomerase, which were more abundant in mag2 seeds. The MAG2 gene was identified as At3g47700, and the MAG2 protein had a RINT-1/TIP20 domain in the C-terminal region. We found that some MAG2 molecules were peripherally associated with the ER membrane. MAG2 had an ability to bind to two ER-localized t-SNAREs (for target-soluble NSF [N-ethylmaleimide–sensitive fusion protein] attachment protein receptor; At Sec20 and At Ufe1). Our findings suggest that MAG2 functions in the transport of storage protein precursors between the ER and Golgi complex in plants.
Reduction of Benzenoid Synthesis in Petunia Flowers Reveals Multiple Pathways to Benzoic Acid and Enhancement in Auxin Transport
Authors: Orlova Irina , Marshall-Colón Amy , Schnepp Jennifer , Wood Barbara , Varbanova Marina , Fridman Eyal , Blakeslee Joshua J. , Peer Wendy Ann , Murphy Angus S. , Rhodes David , Pichersky Eran , Dudareva Natalia
Published: December 2006

In plants, benzoic acid (BA) is believed to be synthesized from Phe through shortening of the propyl side chain by two carbons. It is hypothesized that this chain shortening occurs via either a β-oxidative or non-β-oxidative pathway. Previous in vivo isotope labeling and metabolic flux analysis of the benzenoid network in petunia (Petunia hybrida) flowers revealed that both pathways yield benzenoid compounds and that benzylbenzoate is an intermediate between l-Phe and BA. To test this hypothesis, we generated transgenic petunia plants in which the expression of BPBT, the gene encoding the enzyme that uses benzoyl-CoA and benzyl alcohol to make benzylbenzoate, was reduced or eliminated. Elimination of benzylbenzoate formation decreased the endogenous pool of BA and methylbenzoate emission but increased emission of benzyl alcohol and benzylaldehyde, confirming the contribution of benzylbenzoate to BA formation. Labeling experiments with 2H5-Phe revealed a dilution of isotopic abundance in most measured compounds in the dark, suggesting an alternative pathway from a precursor other than Phe, possibly phenylpyruvate. Suppression of BPBT activity also affected the overall morphology of petunia plants, resulting in larger flowers and leaves, thicker stems, and longer internodes, which was consistent with the increased auxin transport in transgenic plants. This suggests that BPBT is involved in metabolic processes in vegetative tissues as well.
KEEP ON GOING, a RING E3 Ligase Essential for Arabidopsis Growth and Development, Is Involved in Abscisic Acid Signaling
Authors: Stone Sophia L. , Williams Luis A. , Farmer Lisa M. , Vierstra Richard D. , Callis Judy
Published: December 2006

Analysis of the Arabidopsis thaliana RING-ANK (for Really Interesting New Gene-Ankyrin) family, a subgroup of RING-type E3 ligases, identified KEEP ON GOING (KEG) as essential for growth and development. In addition to the RING-HCa and ankyrin repeats, KEG contains a kinase domain and 12 HERC2-like repeats. The RING-HCa and kinase domains were functional in in vitro ubiquitylation and phosphorylation assays, respectively. Seedlings homozygous for T-DNA insertions in KEG undergo growth arrest immediately after germination, suggestive of increased abscisic acid (ABA) signaling, a major phytohormone that plays a key role in plant development and survival under unfavorable conditions. Here, we show that KEG is a negative regulator of ABA signaling. keg roots are extremely sensitive to the inhibitory effects of ABA and exhibit hypersensitivity to exogenous glucose, consistent with the known interaction between glucose and ABA signaling. The observations that KEG accumulates high levels of ABSCISIC ACID-INSENSITIVE5 (ABI5) without exogenous ABA, interacts with ABI5 in vitro, and that loss of ABI5 rescues the growth-arrest phenotype of keg mutant seedlings indicate that KEG is required for ABI5 degradation. In this capacity, KEG is central to ABA signaling by maintaining low levels of ABI5 in the absence of stress.
Genetic Characterization and Functional Analysis of the GID1 Gibberellin Receptors inArabidopsis
Authors: Griffiths Jayne , Murase Kohji , Rieu Ivo , Zentella Rodolfo , Zhang Zhong-Lin , Powers Stephen J. , Gong Fan , Phillips Andrew L. , Hedden Peter , Sun Tai-ping , Thomas Stephen G.
Published: December 2006

We investigated the physiological function of three Arabidopsis thaliana homologs of the gibberellin (GA) receptor GIBBERELLIN-INSENSITIVE DWARF1 (GID1) by determining the developmental consequences of GID1 inactivation in insertion mutants. Although single mutants developed normally, gid1a gid1c and gid1a gid1b displayed reduced stem height and lower male fertility, respectively, indicating some functional specificity. The triple mutant displayed a dwarf phenotype more severe than that of the extreme GA-deficient mutant ga1-3. Flower formation occurred in long days but was delayed, with severe defects in floral organ development. The triple mutant did not respond to applied GA. All three GID1 homologs were expressed in most tissues throughout development but differed in expression level. GA treatment reduced transcript abundance for all three GID1 genes, suggesting feedback regulation. The DELLA protein REPRESSOR OF ga1-3 (RGA) accumulated in the triple mutant, whose phenotype could be partially rescued by loss of RGA function. Yeast two-hybrid and in vitro pull-down assays confirmed that GA enhances the interaction between GID1 and DELLA proteins. In addition, the N-terminal sequence containing the DELLA domain is necessary for GID1 binding. Furthermore, yeast three-hybrid assays showed that the GA-GID1 complex promotes the interaction between RGA and the F-box protein SLY1, a component of the SCFSLY1 E3 ubiquitin ligase that targets the DELLA protein for degradation.
Proteolytic Enzyme Activity During Storage of Radiation‐ Stabilized Raw Beef and Its Significance to Flavora
Authors: DRAKE MAURICE P. , GERNON GERALD D. , KRAUS FRED J.
Published: December 2006

This study has attempted to define the relationship of proteolysis to flavor during storage of irradiated raw beef. The data presented show that a decrease in consumer‐type taste‐panel preference during unrefrigerated storage of irradiated (4.5 megarad) raw ground beef correlates to some extent with the action of endocellular tissue proteolytic enzymes (cathepsins). The effective control of proteolytic activity using refrigerated storage is demonstrated. In the experiment cited, raw beef round steaks irradiated at a pasteurizing dose of 0.5 megarad were stable both microbiologically and enzymically, and the preference rating did not decline during six months at 3°C. The limited control of proteolysis during unrefrigerated storage using high‐pH beef is shown. The use of high‐pH beef for a limited extension of unrefrigerated storage life without significant decrease in preference rating is suggested. A need for further studies is indicated.
Continuity and Change in British Thinking about Nuclear Weapons
Authors: Croft Stuart
Published: December 2006

For almost fifty years there has been constant argument between those who have supported the development and possession of nuclear weapons by Britain and those opposed to those policies. This article argues that there has been a continuity in the arguments made by policy-makers and their critics, both operating within an unchanging series of linked assumptions forming a paradigm or mind-set. This article sets out the character of the assumptions of the orthodox and alternative thinkers, as they are termed in the article, examining their coherence and differences, particularly during the cold war. It concludes by attempting to draw out some implications for the British security policy debate in the post-cold war period.
The Wild and the Sublime: Lyotard's Post-Modern Politics
Authors: Drolet Michael
Published: December 2006

This paper examines the thought of Jean-François Lyotard in relation to the problems of justice and the constitution of a post-modern politics. It argues that Lyotard is highly influenced by Kant's aesthetics and specifically by the idea of indeterminate judgement in the formulation of a conception of justice that, in an age of social variegation and fragmentation, underlies a politics which strives to promote different ways of looking at, and living in, the world. The text concludes that Lyotard's conception of justice and its resultant politics are founded upon a skewed reading of Kant's work such that claims of truth and morality are separated from those of judgement. The result is a politics marked by radical individualism which poses the threat of social atomization.
Pluralism and Liberalism
Authors: Crowder George
Published: December 2006

Meta-ethical pluralism, as developed in the work of writers like Isaiah Berlin, is the idea that ethical values cannot be reduced to a single hierarchy or system but are irreducibly multiple. It has often been argued that simply to recognize this fact is to have a reason to favour liberal institutions. On the contrary, the plurality of values in itself gives us no reason to support liberalism, indeed no reason to prefer any particular political arrangement to any other. If pluralism is true, the liberal's best defence may lie in appealing, in the manner of writers like Walzer and Rorty, to the de facto limitations on moral commitments imposed by the existing political culture.
ON HOMOGENEOUS ANTIGENS AND ANTIBODIES. III. THE PREPARATION AND PROPERTIES OF THE UNIVALENT HAPTEN‐PROTEIN CONJUGATE PAPAIN‐S‐DNPL*
Authors: Brenneman L. , Singer S. J.
Published: December 2006

Karl Landsteiner's introduction of the systematic study of hapten‐protein conjugates and antihapten antibodies was a great milestone in immunology and immunochemistry. His work, and the work of others following his lead, have illuminated the character of the antigen‐antibody interaction, and have provided antibodies whose specificities could be systematically varied and used in a wide variety of structural studies. It is important to recognize, however, that while conventionally prepared hapten‐protein conjugates are extraordinarily useful as model antigens for certain types of immunochemical studies, they may not be as simple immunogens as has generally been assumed. An adequate appreciation of the two structural considerations: a) that antibody‐combining sites are, generally, considerably larger than simple haptenic groups; and b) that hydrophobic haptens will tend to be immobilized on patches of the surface of the carrier molecule, leads to the realization that from an antigenic point of view, hapten‐protein conjugates may be, in fact, at least as complex and heterogeneous as are protein antigens themselves. Studies with such conjugates that ignore their complexities may come to erroneous conclusions about important immunological phenomena. The use of less heterogeneous or homogeneous hapten conjugates in these experiments may avoid, or at least minimize, such difficulties, and may also lead to the production of homogeneous antibodies useful for detailed chemical and structural studies.
Is Ω*– {u} Absolutely Countably Compact?
Authors: VAN MILL JAN , VAUGHAN JERRY E.
Published: December 2006

ABSTRACT: We construct an ultrafilter u∞Ω*=βω−ω such that the subspace ω*− {u} is not absolutely countably compact, and we show that under the continuum hypothesis, for every u∞βω−ω, the subspace ω*− {u} is not absolutely countably compact.
The Uniformizable Spaces Are Generated by the Real Numbersa
Authors: OOSTRAV ARNOLD
Published: December 2006

ABSTRACT: A topological space X is generated by a space M if it has the weak topology induced by the collection of continuous functions from X to M. Some properties of this relation are discussed and an interesting example is shown: spaces generated by the real numbers are precisely the uniformizable spaces.
Maximal Feebly Compact Expansions
Authors: PORTER JACK R. , STEPHENSON ROBERT M. , WOODS R. GRANT
Published: December 2006

ABSTRACT: Conditions under which a given topological space does, or does not, possess a stronger maximal feebly compact topology are given. Procedures are developed which can be used, for certain feebly compact spaces, to obtain stronger maximal feebly compact spaces. Several examples are constructed.
Duality between Locally m‐Convex Algebras and Completely Regular Spaces
Authors: ROSA DOMENICO
Published: December 2006

ABSTRACT:It is well known that, for the categoryBof commutative Banach algebras and the categoryCHof compact Hausdorff spaces, the contravariant functorsM:B→CHandC:CH→Bare adjoint on the right. This adjoint situation is extended to the category of completely regular spaces and the subcategory consisting of all locallym‐convex algebrasAwhose Gelfand mapA→CM(A)(compact‐open topology) is continuous. An analogous extension is obtained for the dual equivalence (Gelfand duality) betweenB*‐algebras and compact Hausdorff spaces.
Linearly Ordered Topologies and Quasi‐metrization
Authors: SALBANY SERGIO
Published: December 2006

ABSTRACT: We are concerned with spaces where the specialization order is linear. For this class of spaces, a characterization is given for those that admit a compatible quasi‐pseudometric, as well as for those that admit additive compatible quasi‐pseudometrics.
A Note on Locally ℰτ‐compact Spaces
Authors: ŠKOSTAK A.P. , GVAZAVA M.V.
Published: December 2006

ABSTRACT: The local version of the concept of ℰτ‐compactness (where ℰ is a class of Hausdorff spaces and ℰ is a cardinal) introduced by the first author as a generalization of Her‐rlich's concept of ℰ‐compactness (and hence, also of Mrowka's E‐compactness) is defined and the corresponding theory is initiated. An essential part of the theory is developed under the additional assumption that all spaces from ℰ are absolute extensors for spaces under consideration. The theory contains as a special case the classical theory of local compactness.
Disappearance Conditions of Stress Singularities for Anisotropic Bimaterial Half-Plane Wedges Under Antiplane Shear
Authors: Liu Chuan-I , Chue Ching-Hwei
Published: December 2006

Based on the anisotropic elasticity theory and Lekhnitskii’s complex potential functions, the analytical eigenequations of anisotropic bimaterial half-plane wedges under antiplane shear are derived in brief forms. The boundary surfaces of half-plane wedges can be combinations of free and/or clamped edges. The disappearance conditions of stress singularities can be obtained directly from the derived eigenequations, which can be applied to improve the safety of the structures. The interesting phenomenon on the periodic appearance of the singularity orders is proposed and discussed as well.
Local Contact Compliance Relations at Compaction of Composite Powders
Authors: Skrinjar Olle , Larsson Per-Lennart , Storåkers Bertil
Published: December 2006

Local contact behavior of composite powders has been investigated by using the finite element method. In previous analyses of such problems it has in general been assumed that one of the powder materials is rigid while the other deforms at loading as in such a case self-similarity prevails. This is a very good approximation for ceramic/metallic composites but may not be so when the composite consists of two materials of roughly equal hardness. An approximate compliance formula for describing this feature is proposed showing good agreement with corresponding finite element results for representative cases.
Localized Bending Waves in a Rib-Reinforced Elastic Orthotropic Plate
Authors: Belubekyan M. , Ghazaryan K. , Marzocca P. , Cormier C.
Published: December 2006

Localized bending waves in a thin elastic orthotropic cantilever plate reinforced by a rigid rib are studied. A condition under which the edge waves can be eliminated is determined. The condition requires that the rib have a certain minimal stiffness. Such waves are time-varying, and have spatially nonuniform bending perturbations that are localized in the proximity of free surface and are quickly decaying to zero. A general solution is presented and the particular case of an isotropic reinforced plate is shown. An inverse method is described for identifying the elastic properties of the rib.
On the Surface Stability of a Spherical Void Embedded in a Stressed Matrix
Authors: Colin Jérôme
Published: December 2006

The linear stability analysis of the shape of a spherical cavity embedded in an infinite-size matrix under stress has been performed when infinitesimal perturbation from sphericity of the rod is assumed to appear by surface diffusion. Developing the perturbation on a basis of complete spherical harmonics, the growth rate of each harmonic Ylm(θ,φ) has been determined and the conditions for the development of the different fluctuations have been discussed as a function of the applied stress and the order l of the perturbation.