bluuebunny/crossref_metadata_2025 huggingface dataset:
Near-field optical recording using a planar solid immersion mirror
Authors: Peng Chubing , Mihalcea Christophe , Büchel Dorothea , Challener William A. , Gage Edward C.
Published: September 2005

A near-field planar solid immersion mirror (PSIM) has been developed and applied to the writing and reading of marks in a phase-change material. Light focusing of a PSIM is realized by a two-dimensional parabolic reflective surface integrated in a planar waveguide. Using a PSIM fabricated out of a waveguide consisting of a 100nm Ta2O5 core layer and a SiO2 cladding layer on an Al2O3–TiC substrate, we have recorded marks with dimensions of λ∕4.
Direct imaging of quantum antidots in MgO dispersed with Au nanoclusters
Authors: Wang C. M. , Shutthanandan V. , Thevuthasan S. , Duscher G.
Published: September 2005

Formation of quantum antidots at the immediate neighborhood of Au nanocluster has been proposed in order to explain the observed nonlinear optical behavior of magnesium oxide (MgO) when Au nanoclusters were dispersed in it. In this letter, using high-angle annular dark-field imaging in an aberration-corrected scanning transmission electron microscope, we report the direct observation of clustering of vacancies in excess of Au atoms to form quantum antidots at the immediate neighborhood of the Au clusters, leading to a spatially associated Au nanoclusters and the quantum antidots. The antidots show a terraced layer structure and are typically faceted along the MgO{100} planes.
A Spatial Economic Perspective on Language Acquisition: Segregation, Networking, and Assimilation of Immigrants
Authors: Florax Raymond J G M , de Graaff Thomas , Waldorf Brigitte S
Published: September 2005

Immigration and multiculturalism are at the heart of modern Western societies. The issue of language acquisition of immigrants is intrinsically linked to immigration. We formally link language acquisition of immigrants to the relative size of the immigrant stock, employing a microeconomic trading framework. Our model allows for spatial interaction going beyond the immigrant's area of residence, and explicitly incorporates spatial segregation. In addition, behavioral differences of immigrants with respect to their level of assimilation into the host country, as well as differences in networking within their own ethnic community, are accounted for. We test our model for four non-Western immigrant groups in the Netherlands at two different spatial scale levels. The empirical results reveal that there is only ambiguous support for the inverse relationship between size of the immigrant community and language acquisition or language proficiency in The Netherlands. We find instead that there is strong support for language acquisition and understanding being positively influenced by assimilation to the host country's culture.
New Economic Geography: What about the N?
Authors: Ottaviano Gianmarco I P , Thisse Jacques-François
Published: September 2005

Since its very appearance, probably thanks to its provocative name, new economic geography (NEG) has stirred a debate on whether it is economic geography proper or rather geographical economics. In both cases, its real novelty has been questioned. We focus on this last issue. In particular, we argue that many NEG ideas have been around for a long time in the works of economic geographers and location theorists. However, NEG has the fundamental merit of having framed those ideas within a general equilibrium model encompassing most of these ideas. This has drawn economic geography and location theory from the periphery to the center of mainstream economic theory. More importantly, it has made already existing ideas more amenable to empirical scrutiny and policy analysis.
The Role of Multinational Corporations in Metropolitan Innovation Systems: Empirical Evidence from Europe and Southeast Asia
Authors: Diez Javier Revilla , Berger Martin
Published: September 2005

Using firm-level survey data from Barcelona, Stockholm, and Vienna in Europe, and Singapore, Penang (Malaysia), and Bangkok in Southeast Asia, we enquire into the different R&D and innovation behaviour of multinational and local companies in these metropolitan regions. Scrutinizing a set of input, throughput, and output indicators as well as information on cooperation characteristics, we try to evaluate (a) if the spatial pattern of more (intense) innovation activity in Europe when compared with Southeast Asia is still valid; and (b) if there are reasons to believe that R&D units of multinational corporations in Europe are concerned mainly with the enhancement of the knowledge base and the development of future competitiveness by tapping into localized knowledge and using the particular host regions' innovation systems, whereas multinational corporations in Southeast Asia use R&D to support existing production facilities in order to exploit an existing competitive advantage. We are able to show that there is still a major gap in innovation performance between Southeast Asia and Europe and that there are indeed indications that R&D units in Europe are orientated more towards the augmentation of the company's knowledge base.
Spatial Spillovers and Innovation Activity in European Regions
Authors: Moreno Rosina , Paci Raffaele , Usai Stefano
Published: September 2005

This paper explores the spatial distribution of innovative activity and the role of technological spillovers in the process of knowledge creation and diffusion across 175 regions of seventeen countries in Europe (the fifteen members of the pre-2004 European Union plus Switzerland and Norway). The analysis is based on a databank set up by CRENoS on regional patenting at the European Patent Office, spanning 1978–2001 and classified by ISIC sectors. The first step is an exploratory spatial data analysis of the dissemination of innovative activity in Europe. The goal of the rest of the paper is to analyse to what extent externalities that cross regional boundaries can explain the spatial association process detected in the distribution of innovative activity in the European regions. The framework given by the knowledge-production function together with the use of spatial econometrics techniques allow us to look for insights on the mechanics of knowledge interdependences across regions, which are shown to exist. Empirical results point to the relevance of internal regional factors (R&D expenditure and agglomeration economies). Moreover, the production of knowledge appears also to be affected by spatial spillovers due to innovative activity (both patenting and R&D) performed in other regions. Additional results show that spillovers are mostly constrained by national borders within less than 250 km, and that technological similarity between regions also matters.
Growth, Integration, and Regional Disparities in the European Union
Authors: Petrakos George , Rodríguez-Pose Andrés , Rovolis Antonis
Published: September 2005

In this paper we challenge the ability of the conventional methods initiated by Barro and Sala-i-Martin in the early 1990s to detect actual convergence or divergence trends across countries or regions and suggest an alternative dynamic framework of analysis, which allows for a better understanding of the forces in operation. With the use of a SURE model and time-series data for eight European Union (EU) member states, we test directly for the validity of two competing hypotheses: the neoclassical (NC) convergence hypothesis originating in the work of Solow and the cumulative causation hypothesis stemming from Myrdal's theories. We also account for changes in the external environment, such as the role of European integration on the level of regional disparities. Our findings indicate that both short-term divergence and long-term convergence processes coexist. Regional disparities are reported to follow a procyclical pattern, as dynamic and developed regions grow faster in periods of expansion and slower in periods of recession. At the same time, significant spread effects are also in operation, partly offsetting the cumulative impact of growth on space. Similar results are obtained from the estimation of an intra-EU model of disparities at the national level, indicating that the forces in operation are independent of the level of aggregation. Our findings challenge the view of economic growth as the main driver for a reduction of regional disparities and contribute to the growing scientific evidence that points towards the need to rethink current EU-wide regional development policies.
Visual Perception of Writing and Pointing Movements
Authors: Méary David , Chary Catherine , Palluel-Germain Richard , Orliaguet Jean-Pierre
Published: September 2005

Studies of movement production have shown that the relationship between the amplitude of a movement and its duration varies according to the type of gesture. In the case of pointing movements the duration increases as a function of distance and width of the target (Pitts' law), whereas for writing movements the duration tends to remain constant across changes in trajectory length (isochrony principle). We compared the visual perception of these two categories of movement. The participants judged the speed of a light spot that portrayed the motion of the end-point of a hand-held pen (pointing or writing). For the two types of gesture we used 8 stimulus sizes (from 2.5 cm to 20 cm) and 32 durations (from 0.2 s to 1.75 s). Viewing each combination of size and duration, participants had to indicate whether the movement speed seemed “fast”, “slow”, or “correct”. Results showed that the participants' perceptual preferences were in agreement with the rules of movement production. The stimulus size was more influential in the pointing condition than in the writing condition. We consider that this finding reflects the influence of common representational resources for perceptual judgment and movement production.
Menin regulates pancreatic islet growth by promoting histone methylation and expression of genes encoding p27

Kip1

and p18

INK4c
Authors: Karnik Satyajit K. , Hughes Christina M. , Gu Xueying , Rozenblatt-Rosen Orit , McLean Graeme W. , Xiong Yue , Meyerson Matthew , Kim Seung K.
Published: September 2005

Menin, the product of the
Men1
gene mutated in familial multiple endocrine neoplasia type 1 (MEN1), regulates transcription in differentiated cells. Menin associates with and modulates the histone methyltransferase activity of a nuclear protein complex to activate gene expression. However, menin-dependent histone methyltransferase activity in endocrine cells has not been demonstrated, and the mechanism of endocrine tumor suppression by menin remains unclear. Here, we show that menin-dependent histone methylation maintains the
in vivo
expression of cyclin-dependent kinase (CDK) inhibitors to prevent pancreatic islet tumors.
In vivo
expression of CDK inhibitors, including p27 and p18, and other cell cycle regulators is disrupted in mouse islet tumors lacking menin. Chromatin immunoprecipitation studies reveal that menin directly associates with regions of the
p27
and
p18
promoters and increases methylation of lysine 4 (Lys-4) in histone H3 associated with these promoters. Moreover, H3 Lys-4 methylation associated with
p27
and
p18
is reduced in islet tumors from
Men1
mutant mice. Thus, H3 Lys-4 methylation is a crucial function of menin in islet tumor suppression. These studies suggest an epigenetic mechanism of tumor suppression: by promoting histone modifications, menin maintains transcription at multiple loci encoding cell cycle regulators essential for endocrine growth control.
Small RNA genes expressed from
Staphylococcus aureus
genomic and pathogenicity islands with specific expression among pathogenic strains
Authors: Pichon Christophe , Felden Brice
Published: September 2005

Small RNA (sRNA) genes are expressed in all organisms, primarily as regulators of translation and message stability. We have developed comparative genomic approaches to identify sRNAs that are expressed by
Staphylococcus aureus
, the most common cause of hospital-acquired infections. This study represents an in-depth analysis of the RNome of a Gram-positive bacterium. A set of sRNAs candidates were identified
in silico
within intergenic regions, and their expression levels were monitored by using microarrays and confirmed by Northern blot hybridizations. Two sRNAs were also detected directly from purification and RNA sequence determination. In total, at least 12 sRNAs are expressed from the
S. aureus
genome, five from the core genome and seven from pathogenicity islands that confer virulence and antibiotic resistance. Three sRNAs are present in multiple (two to five) copies. For the sRNAs that are conserved throughout the bacterial phylogeny, their secondary structures were inferred by phylogenetic comparative methods.
In vitro
binding assays indicate that one sRNA encoded within a pathogenicity island is a trans-encoded antisense RNA regulating the expression of target genes at the posttranscriptional level. Some of these RNAs show large variations of expression among pathogenic strains, suggesting that they are involved in the regulation of staphylococcal virulence.
Use of gene expression profiling to direct
in vivo
molecular imaging of lung cancer
Authors: Grimm Jan , Kirsch David G. , Windsor Stephen D. , Kim Carla F. Bender , Santiago Philip M. , Ntziachristos Vasilis , Jacks Tyler , Weissleder Ralph
Published: September 2005

Using gene expression profiling, we identified cathepsin cysteine proteases as highly up-regulated genes in a mouse model of human lung adenocarcinoma. Overexpression of cathepsin proteases in these lung tumors was confirmed by immunohistochemistry and Western blotting. Therefore, an optical probe activated by cathepsin proteases was selected to detect murine lung tumors
in vivo
as small as 1 mm in diameter and spatially separated. We generated 3D maps of the fluorescence signal and fused them with anatomical computed tomography images to show a close correlation between fluorescence signal and tumor burden. By serially imaging the same mouse, optical imaging was used to follow tumor progression. This study demonstrates the capability for molecular imaging of a primary lung tumor by using endogenous proteases expressed by a tumor. It also highlights the feasibility of using gene expression profiling to identify molecular targets for imaging lung cancer.
Partner-regulated interaction of IFN regulatory factor 8 with chromatin visualized in live macrophages
Authors: Laricchia-Robbio Leopoldo , Tamura Tomohiko , Karpova Tatiana , Sprague Brian L. , McNally James G. , Ozato Keiko
Published: September 2005

IFN regulatory factor (IRF) 8 is a transcription factor that directs macrophage differentiation. By fluorescence recovery after photobleaching, we visualized the movement of IRF8-GFP in differentiating macrophages. Recovery data fitted to mathematical models revealed two binding states for IRF8. The majority of IRF8 was highly mobile and transiently interacted with chromatin, whereas a small fraction of IRF8 bound to chromatin more stably. IRF8 mutants that did not stimulate macrophage differentiation showed a faster recovery, revealing little interaction with chromatin. A macrophage activation signal by IFN-γ/LPS led to a global slowdown of IRF8 movement, leading to increased chromatin binding. In fibroblasts where IRF8 has no known function, WT IRF8 moved as fast as the mutants, indicating that IRF8 does not interact with chromatin in these cells. However, upon introduction of IRF8 binding partners, PU.1 and/or IRF1, the mobility of IRF8 was markedly reduced, producing a more stably bound component. Together, IRF8-chromatin interaction is dynamic in live macrophages and influenced by partner proteins and immunological stimuli.
Apoptosis caused by p53-induced protein with death domain (PIDD) depends on the death adapter protein RAIDD
Authors: Berube Christina , Boucher Louis-Martin , Ma Weili , Wakeham Andrew , Salmena Leonardo , Hakem Razqallah , Yeh Wen-Chen , Mak Tak W. , Benchimol Samuel
Published: September 2005

The p53 tumor suppressor promotes cell cycle arrest or apoptosis in response to diverse stress stimuli. p53-mediated cell death depends in large part on transcriptional up-regulation of target genes. One of these targets, P53-induced protein with a death domain (PIDD), was shown to function as a mediator of p53-dependent apoptosis. Here we show that PIDD is a cytoplasmic protein, and that PIDD-induced apoptosis and growth suppression in embryonic fibroblasts depend on the adaptor protein receptor-interacting protein (RIP)-associated ICH-1/CED-3 homologous protein with a death domain (RAIDD). We provide evidence that PIDD-induced cell death is associated with the early activation of caspase-2 and later activation of caspase-3 and -7. Our results also show that caspase-2
-/-
, in contrast to RAIDD
-/-
, mouse embryonic fibroblasts, are only partially resistant to PIDD. Our findings suggest that caspase-2 contributes to PIDD-mediated cell death, but that it is not the sole effector of this pathway.
An electromechanical material testing system forin situelectron microscopy and applications
Authors: Zhu Yong , Espinosa Horacio D.
Published: September 2005

We report the development of a material testing system forin situelectron microscopy (EM) mechanical testing of nanostructures. The testing system consists of an actuator and a load sensor fabricated by means of surface micromachining. This previously undescribed nanoscale material testing system makes possible continuous observation of the specimen deformation and failure with subnanometer resolution, while simultaneously measuring the applied load electronically with nanonewton resolution. This achievement was made possible by the integration of electromechanical and thermomechanical components based on microelectromechanical system technology. The system capabilities are demonstrated by thein situEM testing of free-standing polysilicon films, metallic nanowires, and carbon nanotubes. In particular, a previously undescribed real-time instrumentedin situtransmission EM observation of carbon nanotubes failure under tensile load is presented here.
Cysteine protease mcII-Pa executes programmed cell death during plant embryogenesis
Authors: Bozhkov Peter V. , Suarez Maria F. , Filonova Lada H. , Daniel Geoffrey , Zamyatnin Andrey A. , Rodriguez-Nieto Salvador , Zhivotovsky Boris , Smertenko Andrei
Published: September 2005

Programmed cell death (PCD) is indispensable for eukaryotic development. In animals, PCD is executed by the caspase family of cysteine proteases. Plants do not have close homologues of caspases but possess a phylogenetically distant family of cysteine proteases named metacaspases. The cellular function of metacaspases in PCD is unknown. Here we show that during plant embryogenesis, metacaspase mcII-Pa translocates from the cytoplasm to nuclei in terminally differentiated cells that are destined for elimination, where it colocalizes with the nuclear pore complex and chromatin, causing nuclear envelope disassembly and DNA fragmentation. The cell-death function of mcII-Pa relies on its cysteine-dependent arginine-specific proteolytic activity. Accordingly, mutation of catalytic cysteine abrogates the proteolytic activity of mcII-Pa and blocks nuclear degradation. These results establish metacaspase as an executioner of PCD during embryo patterning and provide a functional link between PCD and embryogenesis in plants. Although mcII-Pa and metazoan caspases have different substrate specificity, they serve a common function during development, demonstrating the evolutionary parallelism of PCD pathways in plants and animals.
Conservation of spermatogonial stem cell self-renewal signaling between mouse and rat
Authors: Ryu Buom-Yong , Kubota Hiroshi , Avarbock Mary R. , Brinster Ralph L.
Published: September 2005

Self-renewal of spermatogonial stem cells (SSCs) is the foundation for maintenance of spermatogenesis throughout life in males and for continuation of a species. The molecular mechanism underlying stem cell self-renewal is a fundamental question in stem cell biology. Recently, we identified growth factors necessary for self-renewal of mouse SSCs and established a serum-free culture system for their proliferation
in vitro
. To determine whether the stimulatory signals for SSC replication are conserved among different species, we extended the culture system to rat SSCs. Initially, a method to assess
in vitro
expansion of SSCs was developed by using flow cytometric analysis, and, subsequently, we found that a combination of glial cell line-derived neurotrophic factor, soluble glial cell line-derived neurotrophic factor-family receptor α-1 and basic fibroblast growth factor supports proliferation of rat SSCs. When cultured with the three factors, stem cells proliferated continuously for >7 months, and transplantation of the cultured SSCs to recipient rats generated donor stem cell-derived progeny, demonstrating that the cultured stem cells are normal. The growth factor requirement for replication of rat SSCs is identical to that of mouse; therefore, the signaling factors for SSC self-renewal are conserved in these two species. Because SSCs from many mammals, including human, can replicate in mouse seminiferous tubules after transplantation, the growth factors required for SSC self-renewal may be conserved among many different species. Furthermore, development of a long-term culture system for rat SSCs has established a foundation for germ-line modification of the rat by gene targeting technology.
Mapping local Hamiltonians of fermions to local Hamiltonians of spins
Authors: Verstraete F , Cirac J I
Published: September 2005

We show how to map local fermionic problems onto local spin problems on a lattice in any
dimension. The main idea is to introduce auxiliary degrees of freedom, represented by
Majorana fermions, which allow us to extend the Jordan–Wigner transformation to
dimensions higher than one. We also discuss the implications of our results in the numerical
investigation of fermionic systems.
Positivity of quasi-local mass II
Authors: Liu Chiu-Chu Melissa , Yau Shing-Tung
Published: September 2005

We prove the following stronger version of the positivity of quasi-local energy (mass) stated by Liu and Yau: the quasi-local energy of each connected component of the boundary of a compact spacelike hypersurface which satisfies the local energy condition is strictly positive unless the spacetime is flat along the spacelike hypersurface and the boundary of the spacelike hypersurface is connected.
Zeta function of representations of compact 𝑝-adic analytic groups
Authors: Jaikin-Zapirain A.
Published: September 2005

Let

G
G

be an FAb compact

p
p

-adic analytic group and suppose that

p
>
2

p>2

or

p
=
2

p=2

and

G
G

is uniform. We prove that there are natural numbers

n
1

,
…
,

n
k

n_1, \ldots , n_k

and functions

f
1

(

p

−
s

)
,
…
,

f
k

(

p

−
s

)

f_1(p^{-s}),\ldots , f_k(p^{-s})

rational in

p

−
s

p^{-s}

such that
\[
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="zeta Superscript upper G Baseline left-parenthesis s right-parenthesis equals sigma-summation Underscript lamda element-of upper I r r left-parenthesis upper G right-parenthesis Endscripts lamda left-parenthesis 1 right-parenthesis Superscript negative s Baseline equals sigma-summation Underscript i equals 1 Overscript k Endscripts n Subscript i Superscript negative s Baseline f Subscript i Baseline left-parenthesis p Superscript negative s Baseline right-parenthesis period">

ζ
G

(
s
)
=

∑

λ
∈
Irr
⁡
(
G
)

λ
(
1

)

−
s

=

∑

i
=
1

k

n
i

−
s

f
i

(

p

−
s

)
.

\zeta ^G(s)=\sum _{\lambda \in \operatorname {Irr}(G)} \lambda (1) ^{-s}=\sum _{i=1}^kn_i^{-s}f_i(p^{-s}).

\]
Critical Role of the Ubiquitin Ligase Activity of UHRF1, a Nuclear RING Finger Protein, in Tumor Cell Growth
Authors: Jenkins Yonchu , Markovtsov Vadim , Lang Wayne , Sharma Poonam , Pearsall Denise , Warner Justin , Franci Christian , Huang Betty , Huang Jianing , Yam George C. , Vistan Joseph P. , Pali Erlina , Vialard Jorge , Janicot Michel , Lorens James B. , Payan Donald G. , Hitoshi Yasumichi
Published: September 2005

Early cellular events associated with tumorigenesis often include loss of cell cycle checkpoints or alteration in growth signaling pathways. Identification of novel genes involved in cellular proliferation may lead to new classes of cancer therapeutics. By screening a tetracycline-inducible cDNA library in A549 cells for genes that interfere with proliferation, we have identified a fragment of UHRF1 (ubiquitin-like protein containing PHD and RING domains 1), a nuclear RING finger protein, that acts as a dominant negative effector of cell growth. Reduction of UHRF1 levels using an UHRF1-specific shRNA decreased growth rates in several tumor cell lines. In addition, treatment of A549 cells with agents that activated different cell cycle checkpoints resulted in down-regulation of UHRF1. The primary sequence of UHRF1 contains a PHD and a RING motif, both of which are structural hallmarks of ubiquitin E3 ligases. We have confirmed using an in vitro autoubiquitination assay that UHRF1 displays RING-dependent E3 ligase activity. Overexpression of a GFP-fused UHRF1 RING mutant that lacks ligase activity sensitizes cells to treatment with various chemotherapeutics. Taken together, our results suggest a general requirement for UHRF1 in tumor cell proliferation and implicate the RING domain of UHRF1 as a functional determinant of growth regulation.
Time-resolved Imaging of HIV-1 Env-mediated Lipid and Content Mixing between a Single Virion and Cell Membrane
Authors: Markosyan Ruben M. , Cohen Fredric S. , Melikyan Grigory B.
Published: September 2005

A method has been developed to follow fusion of individual pseudotyped virus expressing HIV-1 Env to cells by time-resolved fluorescence microscopy. Viral envelopes were labeled with a fluorescent lipid dye (DiD) and virus content was rendered visible by incorporating a Gag-GFP chimera. The Gag-GFP is naturally cleaved to the much smaller NC-GFP fragment in the mature virions. NC-GFP was readily released upon permeabilization of the viral envelope, whereas the capsid was retained. The NC-GFP thus provides a relatively small and mobile aqueous marker to follow viral content transfer. In fusion experiments, virions were bound to cells at low temperature, and fusion was synchronously triggered by a temperature jump. DiD transferred from virions to cells without a significant lag after the temperature jump. Some virions released DiD but retained NC-GFP. Surprisingly, the fraction of lipid mixing events yielding NC-GFP transfer was dependent on the type of target cell: of three infectable cell lines, only one permitted NC-GFP transfer within minutes of raising temperature. NC-GFP release did not correlate with the level of CD4 or coreceptor expression in the target cells. The data indicate that fusion pores formed by HIV-1 Env can remain small for a relatively long time before they enlarge.
Changes in Regulatory Phosphorylation of Cdc25C Ser287 and Wee1 Ser549 during Normal Cell Cycle Progression and Checkpoint Arrests
Authors: Stanford Jennifer S. , Ruderman Joan V.
Published: September 2005

Entry into mitosis is catalyzed by cdc2 kinase. Previous work identified the cdc2-activating phosphatase cdc25C and the cdc2-inhibitory kinase wee1 as targets of the incomplete replication-induced kinase Chk1. Further work led to the model that checkpoint kinases block mitotic entry by inhibiting cdc25C through phosphorylation on Ser287 and activating wee1 through phosphorylation on Ser549. However, almost all conclusions underlying this idea were drawn from work using recombinant proteins. Here, we report that in the early Xenopus egg cell cycles, phosphorylation of endogenous cdc25C Ser287 is normally high during interphase and shows no obvious increase after checkpoint activation. By contrast, endogenous wee1 Ser549 phosphorylation is low during interphase and increases after activation of either the DNA damage or replication checkpoints; this is accompanied by a slight increase in wee1 kinase activity. Blocking mitotic entry by adding the catalytic subunit of PKA also results in increased wee1 Ser549 phosphorylation and maintenance of cdc25C Ser287 phosphorylation. These results argue that in response to checkpoint activation, endogenous wee1 is indeed a critical responder that functions by repressing the cdc2-cdc25C positive feedback loop. Surprisingly, endogenous wee1 Ser549 phosphorylation is highest during mitosis just after the peak of cdc2 activity. Treatments that block inactivation of cdc2 result in further increases in wee1 Ser549 phosphorylation, suggesting a previously unsuspected role for wee1 in mitosis.
Transcriptional Regulation of Cyclooxygenase-2 in Response to Proteasome Inhibitors Involves Reactive Oxygen Species-mediated Signaling Pathway and Recruitment of CCAAT/Enhancer-binding Protein δ and CREB-binding Protein
Authors: Chen Jun-Jie , Huang Wei-Chien , Chen Ching-Chow
Published: September 2005

Inhibition of ubiquitin-proteasome pathway has been shown to be a promising strategy for the treatment of inflammation and cancer. Here, we show that proteasome inhibitors MG132, PSI-1, and lactacystin induce COX-2 expression via enhancing gene transcription rather than preventing protein degradation in the human alveolar NCI-H292 and A549, and gastric AGS epithelial cells. NF-IL6 and CRE, but not NF-κB elements on the COX-2 promoter were involved in the gene transcription event. The binding of CCAAT/enhancer binding protein (C/EBP)β and C/EBPδ to the CRE and NF-IL6 elements, as well as the recruitment of CBP and the enhancement of histone H3 and H4 acetylation on the COX-2 promoter was enhanced by MG132. However, it did not affect the total protein levels of C/EBPβ and C/EBPδ. MG132-induced DNA-binding activity of C/EBPδ, but not C/EBPβ was regulated by p38, PI3K, Src, and protein kinase C. Small interfering RNA of C/EBPδ suppressed COX-2 expression, further strengthening the role of C/EBPδ in COX-2 gene transcription. In addition, the generation of intracellular reactive oxygen species (ROS) in response to MG132 contributed to the activation of MAPKs and Akt. These findings reveal that the induction of COX-2 transcription induced by proteasome inhibitors requires ROS-dependent protein kinases activation and the subsequent recruitments of C/EBPδ and CBP.
Evolutionary conservation of the clk-1-dependent mechanism of longevity: loss of mclk1 increases cellular fitness and lifespan in mice
Authors: Liu Xingxing , Jiang Ning , Hughes Bryan , Bigras Eve , Shoubridge Eric , Hekimi Siegfried
Published: September 2005

Inactivation of the Caenorhabditis elegans gene clk-1, which is required for ubiquinone biosynthesis, increases lifespan by an insulin signaling-independent mechanism. We find that homozygous inactivation of mclk1, the mouse ortholog of clk-1, yields ES cells that are protected from oxidative stress and damage to DNA. Moreover, in the livers of old mclk1+/- mice, hepatocytes that have lost mclk1 expression by loss of heterozygosity undergo clonal expansion, suggesting that their resistance to stress allows them to outcompete cells that still express the gene. mclk1+/- mice, whose growth and fertility are normal, also display a substantial increase in lifespan in each of three different genetic backgrounds. These observations indicate that the distinct mechanism by which clk-1/mclk1 affects lifespan is evolutionarily conserved from nematodes to mammals and is not tied to a particular anatomy or physiology.
The Strigolactone Germination Stimulants of the Plant-ParasiticStrigaandOrobanchespp. Are Derived from the Carotenoid Pathway
Authors: Matusova Radoslava , Rani Kumkum , Verstappen Francel W.A. , Franssen Maurice C.R. , Beale Michael H. , Bouwmeester Harro J.
Published: September 2005

The seeds of parasitic plants of the genera Striga and Orobanche will only germinate after induction by a chemical signal exuded from the roots of their host. Up to now, several of these germination stimulants have been isolated and identified in the root exudates of a series of host plants of both Orobanche and Striga spp. In most cases, the compounds were shown to be isoprenoid and belong to one chemical class, collectively called the strigolactones, and suggested by many authors to be sesquiterpene lactones. However, this classification was never proven; hence, the biosynthetic pathways of the germination stimulants are unknown. We have used carotenoid mutants of maize (Zea mays) and inhibitors of isoprenoid pathways on maize, cowpea (Vigna unguiculata), and sorghum (Sorghum bicolor) and assessed the effects on the root exudate-induced germination of Striga hermonthica and Orobanche crenata. Here, we show that for these three host and two parasitic plant species, the strigolactone germination stimulants are derived from the carotenoid pathway. Furthermore, we hypothesize how the germination stimulants are formed. We also discuss this finding as an explanation for some phenomena that have been observed for the host-parasitic plant interaction, such as the effect of mycorrhiza on S. hermonthica infestation.
Nod Factors Induce Nod Factor Cleaving Enzymes in Pea Roots. Genetic and Pharmacological Approaches Indicate Different Activation Mechanisms
Authors: Ovtsyna Alexandra O. , Dolgikh Elena A. , Kilanova Alexandra S. , Tsyganov Viktor E. , Borisov Alexey Y. , Tikhonovich Igor A. , Staehelin Christian
Published: September 2005

Establishment of symbiosis between legumes and rhizobia requires bacterial Nod factors (NFs). The concentration of these lipochitooligosaccharides in the rhizosphere is influenced by plant enzymes. NFs induce on pea (Pisum sativum) a particular extracellular NF hydrolase that releases lipodisaccharides from NFs from Sinorhizobium meliloti. Here, we investigated the ability of non-nodulating pea mutants to respond to NodRlv factors (NFs from Rhizobium leguminosarum bv viciae) with enhanced NF hydrolase activity. Mutants defective in the symbiotic genes sym10, sym8, sym19, and sym9/sym30 did not exhibit any stimulation of the NF hydrolase, indicating that the enzyme is induced via an NF signal transduction pathway that includes calcium spiking (transient increases in intracellular Ca2+ levels). Interestingly, the NF hydrolase activity in these sym mutants was even lower than in wild-type peas, which were not pretreated with NodRlv factors. Activation of the NF hydrolase in wild-type plants was a specific response to NodRlv factors. The induction of the NF hydrolase was blocked by α-amanitin, cycloheximide, tunicamycin, EGTA, U73122, and calyculin A. Inhibitory effects, albeit weaker, were also found for brefeldin A, BHQ and ethephon. In addition to this NF hydrolase, NFs and stress-related signals (ethylene and salicylic acid) stimulated a pea chitinase that released lipotrisaccharides from pentameric NFs from S. meliloti. NodRlv factors failed to stimulate the chitinase in mutants defective in the sym10 and sym8 genes, whereas other mutants (e.g. mutated in the sym19 gene) retained their ability to increase the chitinase activity. These findings indicate that calcium spiking is not implicated in stimulation of the chitinase. We suggest that downstream of Sym8, a stress-related signal transduction pathway branches off from the NF signal transduction pathway.
Allelic Series of Four Powdery Mildew Resistance Genes at the Pm3 Locus in Hexaploid Bread Wheat
Authors: Srichumpa Payorm , Brunner Susanne , Keller Beat , Yahiaoui Nabila
Published: September 2005

At the Pm3 locus in hexaploid wheat (Triticum aestivum), 10 alleles conferring race-specific resistance to powdery mildew (Blumeria graminis f. sp. tritici) are known. A cluster of genes encoding coiled-coil–nucleotide-binding site–leucine-rich repeat proteins spans the Pm3 locus on wheat chromosome 1A, and one member of this gene family has recently been identified as the Pm3b resistance gene. Using molecular markers closely linked to Pm3b, we performed haplotype analysis of 10 lines carrying different Pm3 alleles. All these lines have a conserved genomic region delimited by markers cosegregating with Pm3b and including a structurally conserved Pm3b-like gene. A polymerase chain reaction–based strategy allowed the amplification of one Pm3b-like sequence from lines carrying Pm3a, Pm3d, and Pm3f alleles. These candidate genes for Pm3a, Pm3d, and Pm3f conferred AvrPm3a-, AvrPm3d-, and AvrPm3f-dependent resistance, respectively, to wheat powdery mildew in a single cell transient transformation assay. A high level of amino acid similarity (97.8%) was found between the PM3A, PM3B, PM3D, and PM3F proteins. The coiled-coil domain was 100% conserved, whereas, in the nucleotide binding site region, sequence exchange was detected, indicating intragenic recombination or gene conversion between alleles. All these results indicate that Pm3a, Pm3b, Pm3d, and Pm3f form a true allelic series. The low level of sequence divergence between the four characterized alleles as well as the finding of a conserved Pm3 haplotype are in agreement with the hypothesis of a recent evolution of Pm3-based resistance, suggesting that some or most of the diversity found at the Pm3 locus in modern wheat has evolved after wheat domestication.
Genetic and Physiological Architecture of Early Vigor in Aegilops tauschii, the D-Genome Donor of Hexaploid Wheat. A Quantitative Trait Loci Analysis
Authors: ter Steege Margreet W. , den Ouden Franka M. , Lambers Hans , Stam Piet , Peeters Anton J.M.
Published: September 2005

Plant growth can be studied at different organizational levels, varying from cell, leaf, and shoot to the whole plant. The early growth of seedlings is important for the plant's establishment and its eventual success. Wheat (Triticum aestivum, genome AABBDD) seedlings exhibit a low early growth rate or early vigor. The germplasm of wheat is limited. Wild relatives constitute a source of genetic variation. We explored the physiological and genetic relationships among a range of early vigor traits in Aegilops tauschii, the D-genome donor. A genetic map was constructed with amplified fragment-length polymorphism and simple sequence repeat markers, and quantitative trait loci (QTL) analysis was performed on the F4 population of recombinant inbred lines derived from a cross between contrasting accessions. The genetic map consisted of 10 linkage groups, which were assigned to the seven chromosomes and covered 68% of the D genome. QTL analysis revealed 87 mapped QTLs (log of the odds >2.65) in clusters, 3.1 QTLs per trait, explaining 32% of the phenotypic variance. Chromosomes 1D, 4D, and 7D harbored QTLs for relative growth rate, biomass allocation, specific leaf area, leaf area ratio, and unit leaf rate. Chromosome 2D covered QTLs for rate and duration of leaf elongation, cell production rate, and cell length. Chromosome 5D harbored QTLs for the total leaf mass and area and growth rate of the number of leaves and tillers. The results show that several physiological correlations between growth traits have a genetic basis. Genetic links between traits are not absolute, opening perspectives for identification of favorable alleles in A. tauschii to improve early vigor in wheat.
Changes in Transcriptional Profiles Are Associated with Early Fruit Tissue Specialization in Tomato
Authors: Lemaire-Chamley Martine , Petit Johann , Garcia Virginie , Just Daniel , Baldet Pierre , Germain Véronique , Fagard Mathilde , Mouassite Mariam , Cheniclet Catherine , Rothan Christophe
Published: September 2005

The cell expansion phase contributes in determining the major characteristics of a fleshy fruit and represents two-thirds of the total fruit development in tomato (Solanum lycopersicum). So far, it has received very little attention. To evaluate the interest of a genomic scale approach, we performed an initial sequencing of approximately 1,200 cell expansion stage-related sequence tags from tomato fruit at 8, 12, and 15 d post anthesis. Interestingly, up to approximately 35% of the expressed sequence tags showed no homology with available tomato expressed sequence tags and up to approximately 21% with any known gene. Microarrays spotted with expansion phase-related cDNAs and other fruit cDNAs involved in various developmental processes were used (1) to profile gene expression in developing fruit and other plant organs and (2) to compare two growing fruit tissues engaged mostly in cell division (exocarp) or in cell expansion (locular tissue surrounding the seeds). Reverse transcription-polymerase chain reaction analysis was further used to confirm microarray results and to specify expression profiles of selected genes (24) in various tissues from expanding fruit. The wide range of genes expressed in the exocarp is consistent with a protective function and with a high metabolic activity of this tissue. In addition, our data show that the expansion of locular cells is concomitant with the expression of genes controlling water flow, organic acid synthesis, sugar storage, and photosynthesis and suggest that hormones (auxin and gibberellin) regulate this process. The data presented provide a basis for tissue-specific analyses of gene function in growing tomato fruit.
Early Effects of Salinity on Water Transport in Arabidopsis Roots. Molecular and Cellular Features of Aquaporin Expression
Authors: Boursiac Yann , Chen Sheng , Luu Doan-Trung , Sorieul Mathias , van den Dries Niels , Maurel Christophe
Published: September 2005

Aquaporins facilitate the uptake of soil water and mediate the regulation of root hydraulic conductivity (Lpr) in response to a large variety of environmental stresses. Here, we use Arabidopsis (Arabidopsis thaliana) plants to dissect the effects of salt on both Lpr and aquaporin expression and investigate possible molecular and cellular mechanisms of aquaporin regulation in plant roots under stress. Treatment of plants by 100 mm NaCl was perceived as an osmotic stimulus and induced a rapid (half-time, 45 min) and significant (70%) decrease in Lpr, which was maintained for at least 24 h. Macroarray experiments with gene-specific tags were performed to investigate the expression of all 35 genes of the Arabidopsis aquaporin family. Transcripts from 20 individual aquaporin genes, most of which encoded members of the plasma membrane intrinsic protein (PIP) and tonoplast intrinsic protein (TIP) subfamilies, were detected in nontreated roots. All PIP and TIP aquaporin transcripts with a strong expression signal showed a 60% to 75% decrease in their abundance between 2 and 4 h following exposure to salt. The use of antipeptide antibodies that cross-reacted with isoforms of specific aquaporin subclasses revealed that the abundance of PIP1s decreased by 40% as early as 30 min after salt exposure, whereas PIP2 and TIP1 homologs showed a 20% to 40% decrease in abundance after 6 h of treatment. Expression in transgenic plants of aquaporins fused to the green fluorescent protein revealed that the subcellular localization of TIP2;1 and PIP1 and PIP2 homologs was unchanged after 45 min of exposure to salt, whereas a TIP1;1-green fluorescent protein fusion was relocalized into intracellular spherical structures tentatively identified as intravacuolar invaginations. The appearance of intracellular structures containing PIP1 and PIP2 homologs was occasionally observed after 2 h of salt treatment. In conclusion, this work shows that exposure of roots to salt induces changes in aquaporin expression at multiple levels. These changes include a coordinated transcriptional down-regulation and subcellular relocalization of both PIPs and TIPs. These mechanisms may act in concert to regulate root water transport, mostly in the long term (≥6 h).
Mating-Induced Shedding of Cell Walls, Removal of Walls from Vegetative Cells, and Osmotic Stress Induce Presumed Cell Wall Genes in Chlamydomonas
Authors: Hoffmann Xenia-Katharina , Beck Christoph F.
Published: September 2005

The first step in sexual differentiation of the unicellular green alga Chlamydomonas reinhardtii is the formation of gametes. Three genes, GAS28, GAS30, and GAS31, encoding Hyp-rich glycoproteins that presumably are cell wall constituents, are expressed in the late phase of gametogenesis. These genes, in addition, are activated by zygote formation and cell wall removal and by the application of osmotic stress. The induction by zygote formation could be traced to cell wall shedding prior to gamete fusion since it was seen in mutants defective in cell fusion. However, it was absent in mutants defective in the initial steps of mating, i.e. in flagellar agglutination and in accumulation of adenosine 3′,5′-cyclic monophosphate in response to this agglutination. Induction of the three GAS genes was also observed when cultures were exposed to hypoosmotic or hyperosmotic stress. To address the question whether the induction seen upon cell wall removal from both gametes and vegetative cells was elicited by osmotic stress, cell wall removal was performed under isosmotic conditions. Also under such conditions an activation of the genes was observed, suggesting that the signaling pathway(s) is (are) activated by wall removal itself.
Protein Geranylgeranyltransferase I Is Involved in Specific Aspects of Abscisic Acid and Auxin Signaling in Arabidopsis
Authors: Johnson Cynthia D. , Chary S. Narasimha , Chernoff Ellen A. , Zeng Qin , Running Mark P. , Crowell Dring N.
Published: September 2005

Arabidopsis (Arabidopsis thaliana) mutants lacking a functional ERA1 gene, which encodes the β-subunit of protein farnesyltransferase (PFT), exhibit pleiotropic effects that establish roles for protein prenylation in abscisic acid (ABA) signaling and meristem development. Here, we report the effects of T-DNA insertion mutations in the Arabidopsis GGB gene, which encodes the β-subunit of protein geranylgeranyltransferase type I (PGGT I). Stomatal apertures of ggb plants were smaller than those of wild-type plants at all concentrations of ABA tested, suggesting that PGGT I negatively regulates ABA signaling in guard cells. However, germination of ggb seeds in response to ABA was similar to the wild type. Lateral root formation in response to exogenous auxin was increased in ggb seedlings compared to the wild type, but no change in auxin inhibition of primary root growth was observed, suggesting that PGGT I is specifically involved in negative regulation of auxin-induced lateral root initiation. Unlike era1 mutants, ggb mutants exhibited no obvious developmental phenotypes. However, era1 ggb double mutants exhibited more severe developmental phenotypes than era1 mutants and were indistinguishable from plp mutants lacking the shared α-subunit of PFT and PGGT I. Furthermore, overexpression of GGB in transgenic era1 plants partially suppressed the era1 phenotype, suggesting that the relatively weak phenotype of era1 plants is due to partial redundancy between PFT and PGGT I. These results are discussed in the context of Arabidopsis proteins that are putative substrates of PGGT I.