bluuebunny/crossref_metadata_2025 huggingface dataset:
Microfluidic vias enable nested bioarrays and autoregulatory devices in Newtonian fluids
Authors: Kartalov Emil P. , Walker Christopher , Taylor Clive R. , Anderson W. French , Scherer Axel
Published: August 2006

We report on a fundamental technological advance for multilayer polydimethylsiloxane (PDMS) microfluidics. Vertical passages (vias), connecting channels located in different layers, are fabricated monolithically, in parallel, by simple and easy means. The resulting 3D connectivity greatly expands the potential complexity of microfluidic architecture. We apply the vias to printing nested bioarrays and building autoregulatory devices. A current source is demonstrated, while a diode and a rectifier are derived; all are building blocks for analog circuitry in Newtonian fluids. We also describe microfluidic septa and their applications. Vias lay the foundation for a new generation of microfluidic devices.
Convergent evidence that
oligodendrocyte lineage transcription factor 2
(
OLIG2
) and interacting genes influence susceptibility to schizophrenia
Authors: Georgieva Lyudmila , Moskvina Valentina , Peirce Tim , Norton Nadine , Bray Nicholas J. , Jones Lesley , Holmans Peter , MacGregor Stuart , Zammit Stanley , Wilkinson Jennifer , Williams Hywel , Nikolov Ivan , Williams Nigel , Ivanov Dobril , Davis Kenneth L. , Haroutunian Vahram , Buxbaum Joseph D. , Craddock Nick , Kirov George , Owen Michael J. , O’Donovan Michael C.
Published: August 2006

Abnormal oligodendrocyte function has been postulated as a primary etiological event in schizophrenia.
Oligodendrocyte lineage transcription factor 2
(
OLIG2
) encodes a transcription factor central to oligodendrocyte development. Analysis of
OLIG2
in a case-control sample (
n
= ≈1,400) in the U.K. revealed several SNPs to be associated with schizophrenia (minimum
P
= 0.0001, gene-wide
P
= 0.0009). To obtain independent support for this association, we sought evidence for genetic interaction between
OLIG2
and three genes of relevance to oligodendrocyte function for which we have reported evidence for association with schizophrenia:
CNP
,
NRG1
, and
ERBB4
. We found interaction effects on disease risk between
OLIG2
and
CNP
(minimum
P
= 0.0001, corrected
P
= 0.008) for interaction with
ERBB4
(minimum
P
= 0.002, corrected
P
= 0.04) but no evidence for interaction with
NRG1
. To investigate the biological plausibility of the interactions, we sought correlations between the expression of the genes. The results were similar to those of the genetic interaction analysis.
OLIG2
expression significantly correlated in cerebral cortex with
CNP
(
P
< 10
−7
) and
ERBB4
(
P
= 0.002, corrected
P
= 0.038) but not
NRG1
. In mouse striatum,
Olig2
and
Cnp
expression also was correlated, and linkage analysis for trans-effects on gene expression suggests that each locus regulates the other’s expression. Our data provide strong convergent evidence that variation in
OLIG2
confers susceptibility to schizophrenia alone and as part of a network of genes implicated in oligodendrocyte function.
Structure–activity relationships by interligand NOE-based design and synthesis of antiapoptotic compounds targeting Bid
Authors: Becattini Barbara , Culmsee Carsten , Leone Marilisa , Zhai Dayong , Zhang Xiyun , Crowell Kevin J. , Rega Michele F. , Landshamer Stefan , Reed John C. , Plesnila Nikolaus , Pellecchia Maurizio
Published: August 2006

Bcl-2 family proteins play a crucial role in tissue homeostasis and apoptosis (programmed cell death). Bid is a proapoptotic member of the Bcl-2 family, promoting cell death when activated by caspase-8. Following an NMR-based approach (structure–activity relationships by interligand NOE) we were able to identify two chemical fragments that bind on the surface of Bid. Covalent linkage of the two fragments led to high-affinity bidentate derivatives.
In vitro
and in-cell assays demonstrate that the compounds prevent tBid translocation to the mitochondrial membrane and the subsequent release of proapoptotic stimuli and inhibit neuronal apoptosis in the low micromolar range. Therefore, by using a rational chemical–biology approach, we derived antiapoptotic compounds that may have a therapeutic potential for disorders associated with Bid activation, e.g., neurodegenerative diseases, cerebral ischemia, or brain trauma.
Early evolution of animal cell signaling and adhesion genes
Authors: Nichols Scott A. , Dirks William , Pearse John S. , King Nicole
Published: August 2006

In stark contrast to the rapid morphological radiation of eumetazoans during the Cambrian explosion, the simple body plan of sponges (Phylum Porifera) emerged from the Cambrian relatively unchanged. Although the genetic and developmental underpinnings of these disparate evolutionary outcomes are unknown, comparisons between modern sponges and eumetazoans promise to reveal the extent to which critical genetic factors were present in their common ancestors. Two particularly interesting classes of genes in this respect are those involved in cell signaling and adhesion. These genes help guide development and morphogenesis in modern eumetazoans, but the timing and sequence of their origins is unknown. Here, we demonstrate that the spongeOscarella carmela, one of the earliest branching animals, expresses core components of the Wnt, transforming growth factor β, receptor tyrosine kinase, Notch, Hedgehog, and Jak/Stat signaling pathways. Furthermore, we identify sponge homologs of nearly every major eumetazoan cell-adhesion gene family, including those that encode cell-surface receptors, cytoplasmic linkers, and extracellular-matrix proteins. From these data, we infer that key signaling and adhesion genes were in place early in animal evolution, before the divergence of sponge and eumetazoan lineages.
Cortical feedback depolarization waves: A mechanism of top-down influence on early visual areas
Authors: Roland Per E. , Hanazawa Akitoshi , Undeman Calle , Eriksson David , Tompa Tamas , Nakamura Hiroyuki , Valentiniene Sonata , Ahmed Bashir
Published: August 2006

Despite the lack of direct evidence, it is generally believed that top-down signals are mediated by the abundant feedback connections from higher- to lower-order sensory areas. Here we provide direct evidence for a top-down mechanism. We stained the visual cortex of the ferret with a voltage-sensitive dye and presented a short-duration contrast square. This elicited an initial feedforward and lateral spreading depolarization at the square representation in areas 17 and 18. After a delay, a broad feedback wave (FBW) of neuron peak depolarization traveled from areas 21 and 19 toward areas 18 and 17. In areas 18 and 17, the FBW contributed the peak depolarization of dendrites of the neurons representing the square, after which the neurons decreased their depolarization and firing. Thereafter, the peak depolarization surrounded the figure representation over most of areas 17 and 18 representing the background. Thus, the FBW is an example of a well behaved long-range communication from higher-order visual areas to areas 18 and 17, collectively addressing very large populations of neurons representing the visual scene. Through local interaction with feedforward and lateral spreading depolarization, the FBW differentially activates neurons representing the object and neurons representing the background.
Basonuclins 1 and 2, whose genes share a common origin, are proteins with widely different properties and functions
Authors: Vanhoutteghem Amandine , Djian Philippe
Published: August 2006

Basonuclin (bn) 1 possesses three separated pairs of zinc fingers and a nuclear localization signal. It is largely confined to the basal cells of stratified squamous epithelia and to reproductive germ cells. bn1 can shuttle between the nucleus and the cytoplasm, and its location is correlated with the proliferative potential of the cell. The recently discovered bn2 also possesses three separated pairs of zinc fingers and a nuclear localization signal. Conservation of the zinc fingers and the nuclear localization signal by bn1 and bn2 indicates a common origin. However, in contrast to bn1, bn2 is found in virtually every cell type and is confined to the nucleus. Bn2 but not bn1 colocalizes with SC35 in nuclear speckles and, therefore, is likely to have a function in nuclear processing of mRNA.
Involvement of Toll-like receptor 5 in the recognition of flagellated bacteria
Authors: Feuillet Vincent , Medjane Samir , Mondor Isabelle , Demaria Olivier , Pagni Philippe P. , Galán Jorge E. , Flavell Richard A. , Alexopoulou Lena
Published: August 2006

Toll-like receptors (TLRs) are key components of the immune system that detect microbial infection and trigger antimicrobial host defense responses. TLR5 is a sensor for monomeric flagellin, which is a component of bacterial flagella known to be a virulence factor. In this study we generated TLR5-deficient mice and investigated the role of TLR5 signaling in the detection of flagellin and antibacterial immune responses toSalmonella typhimuriumandPseudomonas aeruginosa. We found that TLR5 is essential for the recognition of bacterial flagellin bothin vivoandex vivo. TLR5 contribution to antibacterial host response to i.p. infection withS. typhimuriumor intranasal administration ofP. aeruginosamay be masked by TLR4 or other sensing mechanisms. By using radiation bone marrow chimera, we showed that upon i.p. injection of flagellin immune responses are mediated by lymphoid cells, whereas resident cells are required for the initiation of response upon intranasal flagellin administration. These results suggest that flagellin recognition in different organs is mediated by distinct TLR5-expressing cells and provide insights into the cooperation of the TLR5 and TLR4 signaling pathways used by the innate immune system in the recognition of bacterial pathogens.
Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays
Authors: Liang Fu-Sen , Greenberg William A. , Hammond Jennifer A. , Hoffmann Julia , Head Steven R. , Wong Chi-Huey
Published: August 2006

We have developed methods for using DNA array technology to probe the entire transcriptome to determine the RNA-binding specificity of ligands. Two methods were investigated. In the first method, the RNA-binding aminoglycoside antibiotic tobramycin was covalently linked to magnetic beads. The beads were bound to human liver mRNA and washed, and specifically bound RNA was eluted, amplified, and analyzed with DNA array technology. A small number of genes were found to bind specifically to the tobramycin beads. In the second method, the aminoglycoside ligand was added directly to the array hybridization reaction, and the signal was compared with a control experiment in the absence of ligand. The aminoglycosides were found to interfere with a small percentage of all hybridization events. These methods differ from traditional DNA array experiments in that the readout is a direct measure of the interaction between mRNA and a ligand, rather than an indirect measure of effect on expression. We expect that the results will lead to the discovery of new aminoglycoside-binding RNA motifs and may also have relevance toward understanding and overcoming the side effects observed with these antibiotics in the clinic.
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications
Authors: Gheldof Nele , Tabuchi Tomoko M. , Dekker Job
Published: August 2006

We have analyzed the effects of gene activation on chromatin conformation throughout an ≈170-kb region comprising the human fragile X locus, which includes a single expressed gene, FMR1 (fragile X mental retardation 1). We have applied three approaches: (
i
) chromosome conformation capture, which assesses relative interaction frequencies of chromatin segments; (
ii
) an extension of this approach that identifies domains whose conformation differs from the average, which we developed and named chromosome conformation profiling; and (
iii
) ChIP analysis of histone modifications. We find that, in normal cells where FMR1 is active, the FMR1 promoter is at the center of a large (≈50 kb) domain of reduced intersegment interactions. In contrast, in fragile X cells where FMR1 is inactive, chromatin conformation is uniform across the entire region. We also find that histone modifications that are characteristic of active genes occur tightly localized around the FMR1 promoter in normal cells and are absent in fragile X cells. Therefore, the expression-correlated change in conformation affects a significantly larger domain than that marked by histone modifications. Domain-wide changes in interaction probability could reflect increased chromatin expansion and may also be related to an altered spatial disposition that results in increased intermingling with unrelated loci. The described approaches are widely applicable to the study of conformational changes of any locus of interest.
Vaccination against weight gain
Authors: Zorrilla Eric P. , Iwasaki Shinichi , Moss Jason A. , Chang Jason , Otsuji Jonathan , Inoue Koki , Meijler Michael M. , Janda Kim D.
Published: August 2006

Obesity endangers the lives of millions of people worldwide, through comorbidities such as heart disease, cancers, type 2 diabetes, stroke, arthritis, and major depression. New approaches to control body weight remain a high priority. Vaccines traditionally have been used to protect against infectious diseases and, more recently, for unconventional targets such as drug addiction. Methodologies that could specifically modulate the bioavailability of an endogenous molecule that regulates energy balance might provide a new foundation for treating obesity. Here we show that active vaccination of mature rats with ghrelin immunoconjugates decreases feed efficiency, relative adiposity, and body weight gain in relation to the immune response elicited against ghrelin in its active, acylated form. Three active vaccines based on the 28-aa residue sequence of ghrelin, a gastric endocrine hormone, were used to immunize adult male Wistar rats (
n
= 17). Synthetic ghrelin analogs were prepared that spanned residues 1–10 [ghrelin (
1

–
10
) Ser-3(butanoyl) hapten, Ghr1], 13–28 [ghrelin (
13

–
28
) hapten, Ghr2], and 1–28 [ghrelin(
1

–
28
) Ser-3(butanoyl) hapten, Ghr3], and included
n
-butanoyl esters at Ser-3. Groups immunized with Ghr1 or Ghr3 showed greater and more selective plasma binding capacity for the active, Ser-3-(
n
-octanoyl) form of ghrelin as compared with Ghr2 or keyhole limpet hemocyanin vaccinated controls. Accordingly, they gained less body weight, with sparing of lean mass and preferential reduction of body fat, consistent with reduced circulating leptin levels. The ratio of brain/serum ghrelin levels was lower in rats with strong anti-ghrelin immune responses. Effects were not attributable to nonspecific inflammatory responses. Vaccination against the endogenous hormone ghrelin can slow weight gain in rats by decreasing feed efficiency.
Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: Engineering a recombination-resistant genome
Authors: Yount Boyd , Roberts Rhonda S. , Lindesmith Lisa , Baric Ralph S.
Published: August 2006

Live virus vaccines provide significant protection against many detrimental human and animal diseases, but reversion to virulence by mutation and recombination has reduced appeal. Using severe acute respiratory syndrome coronavirus as a model, we engineered a different transcription regulatory circuit and isolated recombinant viruses. The transcription network allowed for efficient expression of the viral transcripts and proteins, and the recombinant viruses replicated to WT levels. Recombinant genomes were then constructed that contained mixtures of the WT and mutant regulatory circuits, reflecting recombinant viruses that might occur in nature. Although viable viruses could readily be isolated from WT and recombinant genomes containing homogeneous transcription circuits, chimeras that contained mixed regulatory networks were invariantly lethal, because viable chimeric viruses were not isolated. Mechanistically, mixed regulatory circuits promoted inefficient subgenomic transcription from inappropriate start sites, resulting in truncated ORFs and effectively minimize viral structural protein expression. Engineering regulatory transcription circuits of intercommunicating alleles successfully introduces genetic traps into a viral genome that are lethal in RNA recombinant progeny viruses.
Are Residents Willing to Pay for their Community Forests? Results of a Contingent Valuation Survey in Missouri, USA
Authors: Treiman Thomas , Gartner Justine
Published: August 2006

Publicly owned trees have important environmental and amenity values contributing to the quality of urban life. Community officials charged with managing this resource face a lack of funding and underestimate the value that residents place on street trees. A survey of residents in 44 Missouri, USA, communities included a contingent valuation method item designed to estimate how residents' willingness-to-pay for improved tree care and maintenance varied with community size and location. Residents in communities with a population of 50 000 or more, in the St Louis and Kansas City suburbs, and in St Louis and Kansas City show strong support for a ballot issue establishing a tree fund supported by a tax of between $14 and $16 per household per year. The results of this survey, together with recent surveys of community forestry officials and street tree inventories, are used to make recommendations to state agencies charged with managing community forests.
Making Housing Assistance More Efficient: A Risk Management Approach
Authors: Hall Jon , Berry Mike
Published: August 2006

Housing affordability has declined in a number of countries over the past 20 years. Governments are under increasing pressure to maximise the reach and effectiveness of housing assistance policies to deal with the resulting problems of increasing housing stress. This paper presents a model, based on Monte Carlo simulation, that estimates the expected subsidy costs required for a range of housing assistance policy approaches, assuming that an affordability benchmark is met. The required subsidies reflect and vary with the systematic risk factors characterising different regional housing markets, suggesting that significant subsidy cost savings can be gained by tailoring particular policy mixes to each market. The model is applied to Australia's eight state capital cities.
Collective Action and Community-driven Development in Rural and Urban Indonesia
Authors: Beard Victoria A. , Dasgupta Aniruddha
Published: August 2006

The article analyses differences in collective action in rural and urban communities that participated in a poverty alleviation project in Indonesia. It was found that the main determinants of collective action are relationships among multiscalar social, political and historical factors, internal and external to communities. Two distinct forms of collective action are also identified. The first form is based on community cohesion, stable social relationships and adherence to social hierarchy. The second form is based on a community's perception of an interdependent future and a shared desire for structural change. Both forms of collective action are effective in delivering project resources to beneficiaries; however, only the second form demonstrates potential for social transformation.
Urban Regeneration, Governance and the State: Exploring Notions of Distance and Proximity
Authors: Jones Phil , Evans James
Published: August 2006

Recent debates over how to characterise the governance of urban regeneration are developed in this paper using a detailed case study of Attwood Green in Birmingham, UK. Specifically, the relationship between actors within governance networks and the state is critically reappraised. The case study suggests that actors tend to display highly reflexive understandings of government as multifaceted and multidimensional, simultaneously trying to establish distance and proximity from different aspects of state power. The relationship between those agents regenerating Attwood Green and local and central government is highly strategic, manipulating transfers of financial, political and legal power through new organisational configurations.
Urbanisation and Water Consumption: Influencing Factors in the Metropolitan Region of Barcelona
Authors: Domene Elena , Saurí David
Published: August 2006

This paper is concerned with the relationships between urbanisation and residential water consumption, taking as a case study the Metropolitan Region of Barcelona. More precisely, it investigates the influence of certain demographic, behavioural and housing factors on this consumption using descriptive statistics and a regression analysis. The data are derived from a sample of 532 households in 22 municipalities of the study area. Results show that income, housing type, members per household, the presence of outdoor uses (garden and swimming pool), the kind of species planted in the garden and consumer behaviour towards conservation practices play a significant role in explaining variations in water consumption. It is concluded that, along with prices and incomes, further research is needed on other demographic and housing variables in order to obtain a more comprehensive understanding of the determinants of domestic water consumption in areas periodically affected by water stress.
The Effect of Foreign Direct Investment on the Urban Wage in China: An Empirical Examination
Authors: Ge Ying
Published: August 2006

How does foreign direct investment (FDI) affect the wage levels of cities in a host country? This paper uses a panel dataset of Chinese cities to examine the impact of inward FDI on the urban real wage. The results suggest that the existence of FDI has a significant and positive effect on urban real wages and that this impact remains significant after controlling for other city characteristics. Cross-city variation of FDI intensity is one important factor contributing to intercity wage inequality.
Community and Economic Development: Seeking Common Ground in Discourse and in Practice
Authors: Lejano Raul P. , Taufen Wessells Anne
Published: August 2006

As communities evolve greater capacities for mobilisation and political action, local issues are finding new entry-points into development and land use planning. In this regard, two strong discourses emerge: that of economic development and community. What are the synergies, antagonisms, or other relationships between these two frameworks? Do policy actors reconcile the differing discourses by appealing to a metanarrative, engaging in a pluralistic or agonistic process, or finding compromise solutions? Are there differing narratives within each of these broad frameworks? This article examines the divergences and convergences of these two discourses. It then focuses on Taylor Yard, a vacant brownfield in downtown Los Angeles, California, to study how policy actors reconciled differing visions for the use of the land. It can be seen that attempts to construct a metanarrative, that of a park, served to create a coalition of policy actors that was powerful enough to overturn a strong pro-industrial narrative. However, the weakness of the metanarrative became evident when tested by the need for explicit action, pointing to the need to fashion movements out of real relationships and grounded action. If discourse is conceived as text, then action requires that text encounter and be shaped by context.
The Role and Behaviour of Commercial Property Investors and Developers in French Urban Regeneration: The Experience of the Paris Region
Authors: Nappi-Choulet Ingrid
Published: August 2006

This paper provides an analysis of the factors underlying private investment decisions concerning property development, with specific reference to urban regeneration in the French context. It is based on the results of a behavioural survey and MCA analysis of the behaviour patterns and motivations of active private investors and developers in the French commercial property markets and their involvement in French urban regeneration initiatives. The pattern of investment and development activity over the 1997-2002 French property market recovery period has been studied and a typology of actors set up, based on their investment policy for these property markets. The findings indicate that property investors in urban regeneration essentially seek speculative developments and short-term investments.
Advantage and Disadvantage across Australia's Extended Metropolitan Regions: A Typology of Socioeconomic Outcomes
Authors: Baum Scott , Haynes Michelle , van Gellecum Yolanda , Han Jung Hoon
Published: August 2006

New national and international economic and social forces have reshaped national geographies in general and the characteristics of cities in particular, resulting in a range of diverse social and spatial outcomes. These outcomes, which include greater differentiation across, within and between cities has become a feature of the economic and social forces associated with post-Fordist social structures. Taking localities across Australia's metropolitan regions, this paper develops a typology of advantage and disadvantage using a model-based approach with clustering of data represented by a parameterised Gaussian mixture model and confidence intervals of the means providing a measure of differences between the clusters. The analysis finds seven clusters of localities that represent different aspects of the socio-spatial structure of the metropolitan regions studied.
Comment: On a Non-appraisal of the 'Jacobs Hypothesis'
Authors: Taylor Peter J.
Published: August 2006

This is a critique of Polese's recent paper entitled 'Cities and national economic growth: a reappraisal' which purports to test the 'Jacobs hypothesis'. It is argued that both main variables used, 'national levels of urbanisation' and 'per capita GDP growth', are misspecified. The critique is related to the state-centric nature of social science and policy.
On the Non-city Foundations of Economic Growth and the Unverifiability of the 'Jacobs Hypothesis': A Reply to Peter Taylor's Comment
Authors: Polese Mario
Published: August 2006

In this reply to Peter Taylor, three points are made: Peter Taylor is correct in stating that I have not tested the 'Jacobs hypothesis'; the 'Jacobs model' (as I understand it) is, I suggest, unverifiable; and, continuing from my original article, I restate the argument that 'cities', independently, are (probably) not sources of economic growth. I end with a few words on the problem of using the term 'city' as an independent variable to explain economic growth.
Systematic approach to the modelling of measurements for uncertainty evaluation
Authors: Sommer K D , Siebert B R L
Published: August 2006

Modern evaluation of measurement uncertainty is based on both the knowledge about the measurement process and the (input) quantities which influence the result of measurement. The knowledge about the input quantities is represented by means of appropriate probability density functions (pdfs), whereas the knowledge about the measurement process is expressed by a so-called model equation which reflects the interrelation between the measurand and the input quantities. The assignment of a pdf for a quantity is based on sound theory but there is no theory on modelling. Neither the Guide to the Expression of Uncertainty in Measurement nor other relevant uncertainty documents provide any guidance on systematic modelling. This paper proposes a systematic and versatile modelling concept that has evolved from the idea of the classical measuring chain. From this concept, a systematic procedure for modelling of measurements has been derived which is structured into five fundamental work steps and requires three types of standard modelling components. The concept utilizes only a few generic model structures which are strongly related to the method of measurement employed. These generic model structures can easily be tailored to any particular measurement task. The paper provides the theoretical reasoning for this concept and derives practical procedures for its application.
ThêoH: a hybrid, high-confidence statistic that improves on the Allan deviation
Authors: Howe D A
Published: August 2006

‘Theo1’ (short terminology for ‘theoretical variance #1’) is derived based on, a variance that separates the Allan variance'saveraging time(τ) from itssampling interval(τs), also called ‘stride’, as applied to normalized fractional-frequencyy(t). The τ-length average ofy(t) is denoted, and every permissible squared difference of-values inis averaged inmτ0segments ofy(t) to compute Theo1(m, τ0). Although biased relative to the Allan variance, Theo1(m, τ0) mimics all statistical properties of the Allan variance and works to very long stride. Its estimatorhas substantially better confidence compared with the best Allan estimator, called ‘Avar’. To make an Allan-compatible statistic, a novel ‘bias-removed’ version ofvariance, called ‘’ variance, yields ThêoH variance (‘H’ to indicate high confidence and/or hybrid Allan andfunctions). ThêoH deviation combines the Allan deviation in short term anddeviation in long term, reporting very long-term frequency stability 50% beyond that possible using the Allan deviation alone and with excellent confidence.
Receptor Signal Output Mediated by the ETR1 N Terminus Is Primarily Subfamily I Receptor Dependent
Authors: Xie Fang , Liu Qian , Wen Chi-Kuang
Published: August 2006

etr1-1 is a dominant ethylene receptor gene in Arabidopsis (Arabidopsis thaliana) and confers ethylene insensitivity. The truncated etr1-1(1-349) protein is capable of repressing ethylene responses, whereas etr1(1-349) is not, lending support to a hypothesis that the dominant etr1-1(1-349) could convert wild-type receptors to an ethylene-insensitive state. Assuming that etr1-1(1-349) and etr1(1-349) would share the same signaling mechanism, we hypothesize that the etr1(1-349) protein is capable of repressing ethylene responses when not bound with ethylene. In this study, we show that both etr1(1-349) and etr1-1(1-349) are capable of receptor signal output, which is primarily dependent on subfamily I receptors. The etr1(1-349) and etr1-1(1-349) clones were individually transformed to mutants and the resulting phenotypes were scored. Each of those transgenes restored the rosette growth and flower fertility of etr1-7 ers1-2 to a similar extent. In contrast, neither etr1(1-349) nor etr1-1(1-349) was capable of signal output in etr1-7 ers1-3. The ERS1 transcript was detectable in ers1-2 but not in ers1-3, implying that ETR1 N-terminal signaling is subfamily I dependent. Loss of the subfamily II receptor genes did not perturb etr1-1(1-349)-mediated ethylene insensitivity. Possible roles of subfamily I receptors and disulfide linkages in ETR1 receptor signal output mediated through the N terminus are discussed.
The Frequency and Efficiency of Endogene Suppression by Transitive Silencing Signals Is Influenced by the Length of Sequence Homology
Authors: Bleys Annick , Vermeersch Leen , Van Houdt Helena , Depicker Anna
Published: August 2006

Transitivity, the spread of RNA silencing along primary target sequences, leads to the degradation of secondary targets that have no sequence homology to the initial silencing trigger. We demonstrate that increasing the distance between direct and adjacent target sequences in a transgenic primary target delays the onset of silencing of a secondary target gene. Silencing can spread in a 3′ to 5′ direction over a distance of at least 500 nucleotides (nt), but this requires consistently more time compared to a distance of 98 nt or 250 nt. The efficiency and frequency of transitive silencing of an endogene depends on the length of its sequence homology with the primary target. With a length of 500 nt, efficient silencing can eventually be established in all plants, whereas lengths of 250 nt and 98 nt homology result in less efficient and less frequent suppression. These results suggest that amplification of secondary small interfering RNAs (siRNAs) is a time-requiring process that gradually expands the population of siRNAs until a steady-state level is reached. Moreover, the length of the sequence homology in the primary target providing secondary siRNAs determines whether this steady-state level readily exceeds the threshold necessary for efficient silencing.
Chimeric Proteins Suggest That the Catalytic and/or C-Terminal Domains Give CesA1 and CesA3 Access to Their Specific Sites in the Cellulose Synthase of Primary Walls
Authors: Wang Jian , Howles Paul A. , Cork Ann H. , Birch Rosemary J. , Williamson Richard E.
Published: August 2006

CesA1 and CesA3 are thought to occupy noninterchangeable sites in the cellulose synthase making primary wall cellulose in Arabidopsis (Arabidopsis thaliana L. Heynh). With domain swaps and deletions, we show that sites C terminal to transmembrane domain 2 give CesAs access to their individual sites and, from dominance and recessive behavior, deduce that certain CesA alleles exclude others from accessing each site. Constructs that swapped or deleted N-terminal domains were stably transformed into the wild type and into the temperature-sensitive mutants rsw1 (Ala-549Val in CesA1) and rsw5 (Pro-1056Ser in CesA3). Dominant-positive behavior was assayed as root elongation at the restrictive temperature and dominant-negative effects were observed at the permissive temperature. A protein with the catalytic and C-terminal domains of CesA1 and the N-terminal domain of CesA3 promoted growth only in rsw1 consistent with it accessing the CesA1 site even though it contained the CesA3 N-terminal domain. A protein having the CesA3 catalytic and C-terminal domains linked to the CesA1 N-terminal domain dramatically affected growth, but only in the CesA3 mutant. This is consistent with the operation of the same access rule taking this chimeric protein to the CesA3 site. In this case, however, the transgene behaved as a genotype-specific dominant negative, causing a 60% death rate in rsw5, but giving no visible phenotype in wild type or rsw1. We therefore hypothesize that possession of CesA3WT protects Columbia and rsw1 from the lethal effects of this chimeric protein, whereas the mutant protein (CesA3rsw5) does not.
Adenosine Kinase Modulates Root Gravitropism and Cap Morphogenesis in Arabidopsis
Authors: Young Li-Sen , Harrison Benjamin R. , U.M. Narayana Murthy , Moffatt Barbara A. , Gilroy Simon , Masson Patrick H.
Published: August 2006

Adenosine kinase (ADK) is a key enzyme that regulates intra- and extracellular levels of adenosine, thereby modulating methyltransferase reactions, production of polyamines and secondary compounds, and cell signaling in animals. Unfortunately, little is known about ADK's contribution to the regulation of plant growth and development. Here, we show that ADK is a modulator of root cap morphogenesis and gravitropism. Upon gravistimulation, soluble ADK levels and activity increase in the root tip. Mutation in one of two Arabidopsis (Arabidopsis thaliana) ADK genes, ADK1, results in cap morphogenesis defects, along with alterations in root sensitivity to gravistimulation and slower kinetics of root gravitropic curvature. The kinetics defect can be partially rescued by adding spermine to the growth medium, whereas the defects in cap morphogenesis and gravitropic sensitivity cannot. The root morphogenesis and gravitropism defects of adk1-1 are accompanied by altered expression of the PIN3 auxin efflux facilitator in the cap and decreased expression of the auxin-responsive DR5-GUS reporter. Furthermore, PIN3 fails to relocalize to the bottom membrane of statocytes upon gravistimulation. Consequently, adk1-1 roots cannot develop a lateral auxin gradient across the cap, necessary for the curvature response. Interestingly, adk1-1 does not affect gravity-induced cytoplasmic alkalinization of the root statocytes, suggesting either that ADK1 functions between cytoplasmic alkalinization and PIN3 relocalization in a linear pathway or that the pH and PIN3-relocalization responses to gravistimulation belong to distinct branches of the pathway. Our data are consistent with a role for ADK and the S-adenosyl-l-methionine pathway in the control of root gravitropism and cap morphogenesis.
Dehydroascorbate Reductase Affects Leaf Growth, Development, and Function
Authors: Chen Zhong , Gallie Daniel R.
Published: August 2006

Ascorbic acid (Asc) is a major antioxidant in plants that detoxifies reactive oxygen species (ROS) and maintains photosynthetic function. Expression of dehydroascorbate reductase (DHAR), responsible for regenerating Asc from an oxidized state, regulates the cellular Asc redox state, which in turn affects cell responsiveness and tolerance to environmental ROS. Because of its role in Asc recycling, we examined whether DHAR is important for plant growth. Suppression of DHAR expression resulted in a preferential loss of chlorophyll a, a lower steady state of Rubisco as measured by the amount of the large subunit of Rubisco (RbcL), and a lower rate of CO2 assimilation. As a consequence, a slower rate of leaf expansion and reduced foliar dry weight were observed. In addition, an accelerated rate of loss of chlorophyll, RbcL, light-harvesting complex II, and photosynthetic functioning was observed in mature leaves, resulting in premature leaf aging. Reduced growth rate as measured by plant height and leaf number was consistent with the DHAR-mediated reduction of photosynthetic function. Increasing DHAR expression maintained higher levels of chlorophyll, RbcL, light-harvesting complex II, and photosynthetic functioning, resulting in delayed leaf aging. The effect of DHAR expression on leaf aging inversely correlated with the level of lipid peroxidation, indicating that DHAR functions to protect against ROS-mediated damage. These observations support the conclusion that through its Asc recycling function, DHAR affects the level of foliar ROS and photosynthetic activity during leaf development and as a consequence, influences the rate of plant growth and leaf aging.
Quantitative Profiling of Arabidopsis Polar Glycerolipids in Response to Phosphorus Starvation. Roles of Phospholipases Dζ1 and Dζ2 in Phosphatidylcholine Hydrolysis and Digalactosyldiacylglycerol Accumulation in Phosphorus-Starved Plants
Authors: Li Maoyin , Welti Ruth , Wang Xuemin
Published: August 2006

Phosphorus is an essential macronutrient that often limits plant growth and development. Under phosphorus-limited conditions, plants undergo substantial alterations in membrane lipid composition to cope with phosphorus deficiency. To characterize the changes in lipid species and to identify enzymes involved in plant response to phosphorus starvation, 140 molecular species of polar glycerolipids were quantitatively profiled in rosettes and roots of wild-type Arabidopsis (Arabidopsis thaliana) and phospholipase D knockout mutants pldζ1, pldζ2, and pldζ1pldζ2. In response to phosphorus starvation, the concentration of phospholipids was decreased and that of galactolipids was increased. Phospholipid lost in phosphorus-starved Arabidopsis rosettes was replaced by an equal amount of galactolipid. The concentration of phospholipid lost in roots was much greater than in rosettes. Disruption of both PLDζ1 and PLDζ2 function resulted in a smaller decrease in phosphatidylcholine and a smaller increase in digalactosyldiacylglycerol in phosphorus-starved roots. The results suggest that hydrolysis of phosphatidylcholine by PLDζs during phosphorus starvation contributes to the supply of inorganic phosphorus for cell metabolism and diacylglycerol moieties for galactolipid synthesis.
IMMUTANS Does Not Act as a Stress-Induced Safety Valve in the Protection of the Photosynthetic Apparatus of Arabidopsis during Steady-State Photosynthesis
Authors: Rosso Dominic , Ivanov Alexander G. , Fu Aigen , Geisler-Lee Jane , Hendrickson Luke , Geisler Matt , Stewart Gregory , Krol Marianna , Hurry Vaughan , Rodermel Steven R. , Maxwell Denis P. , Hüner Norman P.A.
Published: August 2006

IMMUTANS (IM) encodes a thylakoid membrane protein that has been hypothesized to act as a terminal oxidase that couples the reduction of O2 to the oxidation of the plastoquinone (PQ) pool of the photosynthetic electron transport chain. Because IM shares sequence similarity to the stress-induced mitochondrial alternative oxidase (AOX), it has been suggested that the protein encoded by IM acts as a safety valve during the generation of excess photosynthetically generated electrons. We combined in vivo chlorophyll fluorescence quenching analyses with measurements of the redox state of P  700 to assess the capacity of IM to compete with photosystem I for intersystem electrons during steady-state photosynthesis in Arabidopsis (Arabidopsis thaliana). Comparisons were made between wild-type plants, im mutant plants, as well as transgenics in which IM protein levels had been overexpressed six (OE-6×) and 16 (OE-16×) times. Immunoblots indicated that IM abundance was the only major variant that we could detect between these genotypes. Overexpression of IM did not result in increased capacity to keep the PQ pool oxidized compared to either the wild type or im grown under control conditions (25°C and photosynthetic photon flux density of 150 μmol photons m−2 s−1). Similar results were observed either after 3-d cold stress at 5°C or after full-leaf expansion at 5°C and photosynthetic photon flux density of 150 μmol photons m−2 s−1. Furthermore, IM abundance did not enhance protection of either photosystem II or photosystem I from photoinhibition at either 25°C or 5°C. Our in vivo data indicate that modulation of IM expression and polypeptide accumulation does not alter the flux of intersystem electrons to P  700  + during steady-state photosynthesis and does not provide any significant photoprotection. In contrast to AOX1a, meta-analyses of published Arabidopsis microarray data indicated that IM expression exhibited minimal modulation in response to myriad abiotic stresses, which is consistent with our functional data. However, IM exhibited significant modulation in response to development in concert with changes in AOX1a expression. Thus, neither our functional analyses of the IM knockout and overexpression lines nor meta-analyses of gene expression support the model that IM acts as a safety valve to regulate the redox state of the PQ pool during stress and acclimation. Rather, IM appears to be strongly regulated by developmental stage of Arabidopsis.
Rice NTRC Is a High-Efficiency Redox System for Chloroplast Protection against Oxidative Damage
Authors: Pérez-Ruiz Juan Manuel , Spínola María Cristina , Kirchsteiger Kerstin , Moreno Javier , Sahrawy Mariam , Cejudo Francisco Javier
Published: August 2006

One of the mechanisms plants have developed for chloroplast protection against oxidative damage involves a 2-Cys peroxiredoxin, which has been proposed to be reduced by ferredoxin and plastid thioredoxins, Trx x and CDSP32, the FTR/Trx pathway. We show that rice (Oryza sativa) chloroplast NADPH THIOREDOXIN REDUCTASE (NTRC), with a thioredoxin domain, uses NADPH to reduce the chloroplast 2-Cys peroxiredoxin BAS1, which then reduces hydrogen peroxide. The presence of both NTR and Trx-like domains in a single polypeptide is absolutely required for the high catalytic efficiency of NTRC. An Arabidopsis thaliana knockout mutant for NTRC shows irregular mesophyll cell shape, abnormal chloroplast structure, and unbalanced BAS1 redox state, resulting in impaired photosynthesis rate under low light. Constitutive expression of wild-type NTRC in mutant transgenic lines rescued this phenotype. Moreover, prolonged darkness followed by light/dark incubation produced an increase in hydrogen peroxide and lipid peroxidation in leaves and accelerated senescence of NTRC-deficient plants. We propose that NTRC constitutes an alternative system for chloroplast protection against oxidative damage, using NADPH as the source of reducing power. Since no light-driven reduced ferredoxin is produced at night, the NTRC-BAS1 pathway may be a key detoxification system during darkness, with NADPH produced by the oxidative pentose phosphate pathway as the source of reducing power.
Functional Profiling Reveals That Only a Small Number of Phytochrome-Regulated Early-Response Genes inArabidopsisAre Necessary for Optimal Deetiolation
Authors: Khanna Rajnish , Shen Yu , Toledo-Ortiz Gabriela , Kikis Elise A. , Johannesson Henrik , Hwang Yong-Sic , Quail Peter H.
Published: August 2006

In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor–encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.
Marijuana use and depression among adults: testing for causal associations
Authors: Harder Valerie S. , Morral Andrew R. , Arkes Jeremy
Published: August 2006

Aim  To determine whether marijuana use predicts later development of depression after accounting for differences between users and non‐users of marijuana.

Design  An ongoing longitudinal survey of 12 686 men and women beginning in 1979.

Setting  The National Longitudinal Survey of Youth of 1979, a nationally representative sample from the United States.

Participants  A total of 8759 adults (age range 29–37 years) interviewed in 1994 had complete data on past‐year marijuana use and current depression.

Measurements  Self‐reported past‐year marijuana use was tested as an independent predictor of later adult depression using the Center for Epidemiologic Studies—Depression questionnaire. Individual’s propensity to use marijuana was calculated using over 50 baseline covariates.

Findings  Before adjusting for group differences, the odds of current depression among past‐year marijuana users is 1.4 times higher (95% CI: 1.1, 1.9) than the odds of depression among the non‐using comparison group. After adjustment, the odds of current depression among past‐year marijuana users is only 1.1 times higher than the comparison group (95% CI: 0.8, 1.7). Similarly, adjustment eliminates significant associations between marijuana use and depression in four additional analyses: heavy marijuana use as the risk factor, stratifying by either gender or age, and using a 4‐year lag‐time between marijuana use and depression.

Conclusions  After adjusting for differences in baseline risk factors of marijuana use and depression, past‐year marijuana use does not significantly predict later development of depression. These findings are discussed in terms of their relevance for understanding possible causal effects of marijuana use on depression.