bluuebunny/crossref_metadata_2025 huggingface dataset:
The Restructuring of Municipal Services: A Canada—United States Comparison
Authors: Hebdon Robert , Jalette Patrice
Published: February 2008

We examine how cities and towns provide services in the United States and Canada. Comparative analysis focuses on the role of the private sector in service delivery and the factors that affect city managers' decisions to contract out services. Study of the selection of the most effective form of service delivery is particularly instructive at the local level of government because that is where change occurred first and where most research has been focused. Research shows that Canadians have a more coordinated market economy, greater faith in government, and more communitarian values. Thus we hypothesize that Canadian municipalities will offer more services overall but fewer through the private sector than their American counterparts. We provide a comparative view of the forces that motivate city managers to change service-delivery modes. Our data come from the first survey of municipal service delivery in Canadian cities conducted in 2004. We replicated an earlier US survey conducted by the International Cities/Counties Management Association in 2002–03. Privatization plays an important role in the provision of municipal services in both countries. We found support for a view of a more pragmatic city manager than that envisioned in the public choice theory. City managers implement adjustment policies to facilitate restructuring; integrate community voices into the process to accommodate diverse views; and privatize only when contract-monitoring problems can be managed. As expected, Canadian municipalities provided more services than their American counterparts. Contrary to expectations, however, Canadian local governments had higher rates of privatized services and greater numbers of privatization plans. Because of the devolution of services by Canadian provinces to the cities without the necessary funding, it is conceivable that Canadian managers may have been under more pressure to restructure than their American counterparts. There was evidence, for example, that Ontario and Alberta, where pressures have been the highest during the Klein and Harris governments, had significantly higher privatization rates.
Institutional Developments in the Dutch Waste-Collection Market
Authors: Dijkgraaf Elbert , Gradus Raymond H J M
Published: February 2008

We analyse the Dutch waste-collection market for 1998–2005. We show that municipalities with unit-based pricing (UBP) or waste collection by private companies have lower costs. However, this cost advantage decreases over time as competition decreases, because of the introduction of the VAT-compensation fund, and because of contamination of waste streams. The cost advantage of private provision is shown to be much larger in the first years, while a longer duration of private production results in lower efficiency. An important conclusion from this study is that UBP, although its effectiveness deteriorates over time, is more effective in reducing cost than is contracting out. Moreover, we show that the effect of contracting out might have been overestimated in the previous literature because there is a correlation between the use of contracting out and UBP. Low incentive UBP systems, based on volume or frequency, are only effective when the municipality does not collect the waste itself.
Biotechnology, Sound Science, and the Foreign Agricultural Service: A Case Study in Neoliberal Rollout
Authors: Essex Jamey
Published: February 2008

This paper addresses the ways in which policy coordination, and technical assistance and training programs operated by the United States Department of Agriculture's Foreign Agricultural Service (FAS) have helped produce, internationalize, and enforce a neoliberal approach to the regulation of biotechnology, genetically modified crops, and food safety, through the reductionist discourse of sound science. The internationalization of US standards forms a major component of US agrofood trade strategies, while the contentious nature of biotechnology within international trade makes standards harmonization an important political battleground within ongoing processes of neoliberalization. Relying on appeals to sound science that posit US regulations as scientific and objective, and therefore superior to other regulatory models, FAS facilitates the rollout of neoliberal institutions within both the US state and in developing and post-Communist countries to harmonize biotechnology and food safety standards in line with US-led neoliberalization and capitalist internationalization. I examine the political and scientific contours of the sound science discourse, and offer two examples through which FAS has incorporated and deployed sound science in undertaking neoliberal rollout—first by creating a new internal Biotechnology Group, and second through focusing aspects of its Cochran Fellowship Program, a longstanding development and training program for foreign regulators, on biotechnology issues.
Learning Process of Chinese Urban Planning: The Case of Xiamen's City Comprehensive Plan
Authors: Yu Li
Published: February 2008

Devolution, globalisation, and marketisation have made Chinese municipalities key players in urban development and construction, policy makers for increasing competitiveness, and stakeholders in the process of local social and economic development. These changes have greatly affected Chinese urban planning, which was initiated in the centrally planned economy. In this paper I attempt an exploration of the underlying concepts of Chinese planning and its approaches for coping with uncertainties within the new social and economic contexts in practice. Xiamen, one of the special economic zones in China, first confronted the concepts of the market economy in development. I select Xiamen as a case study to assess and to illustrate existing Chinese planning to aid the market economy learning process. I find that different planning approaches have been applied by local politicians and planners to cope with the changes.
Reflecting on Editorial and Publishing Challenges: Government and Policy; The First 25 Years
Authors: Bennett Robert
Published: February 2008

The process of journal publishing is under unprecedented pressure and external scrutiny in Britain. This is in part the result of research assessment exercises for academics, but also the rapid development of e-publishing, and perhaps erosion of the traditional moral suasion that has underpinned peer review. A recent assessment of peer review in the social services and humanities by the British Academy has evidenced some need for improved transparency, timeliness, verifiability, and checks on scholarly malpractice. This paper assesses how the twenty-five year publication history of Government and Policy has responded to these challenges in terms of editorial policy, theme issues, and maintaining its strong focus on internationally resonant and interdisciplinary policy research.
Tax Policy in Emerging Countries
Authors: Bird Richard M , Zolt Eric M
Published: February 2008

We consider in this paper how emerging countries may in practice best design and develop tax policies, given the complex economic and political environments they face. After an overview of what tax systems look like around the world, we discuss the principal objectives that countries may attempt to achieve through tax policy. We conclude by considering the broad political economy context within which tax policy and development issues must be designed and implemented. Our aim is to set out some of the basic issues facing tax policy in emerging countries and to outline some key elements that should be considered in designing the best feasible tax structure for any particular country at a particular time.
Age-related memory impairment associated with loss of parietal deactivation but preserved hippocampal activation
Authors: Miller Saul L. , Celone Kim , DePeau Kristina , Diamond Eli , Dickerson Bradford C. , Rentz Dorene , Pihlajamäki Maija , Sperling Reisa A.
Published: February 2008

The neural underpinnings of age-related memory impairment remain to be fully elucidated. Using a subsequent memory face–name functional MRI (fMRI) paradigm, young and old adults showed a similar magnitude and extent of hippocampal activation during successful associative encoding. Young adults demonstrated greater deactivation (task-induced decrease in BOLD signal) in medial parietal regions during successful compared with failed encoding, whereas old adults as a group did not demonstrate a differential pattern of deactivation between trial types. The failure of deactivation was particularly evident in old adults who performed poorly on the memory task. These low-performing old adults demonstrated greater hippocampal and prefrontal activation to achieve successful encoding trials, possibly as a compensatory response. Findings suggest that successful encoding requires the coordination of neural activity in hippocampal, prefrontal, and parietal regions, and that age-related memory impairment may be primarily related to a loss of deactivation in medial parietal regions.
Selection for chemical trait remixing in an invasive weed after reassociation with a coevolved specialist
Authors: Zangerl A. R. , Stanley M. C. , Berenbaum M. R.
Published: February 2008

The interaction between
Depressaria pastinacella
(parsnip webworm) and wild parsnip (
Pastinaca sativa
), in its native Europe and in its longstanding nonindigenous range in the midwestern United States, is characterized by chemical phenotype matching, ostensibly mediated by reciprocal selective responses. The first appearance of
D. pastinacella
on
P. sativa
in New Zealand in 2004 provided an opportunity to quantify selective impacts of a coevolved herbivore and calibrate rates of phytochemical response in its host plant. Webworms in 2006 reduced seed production up to 75% in New Zealand populations, and in 2007 infestations increased in severity in all populations except one. Most New Zealand populations fall into a furanocoumarin phenotype cluster distinct from European and U.S. phenotypes, although one heavily attacked population clusters with two U.S. populations and one European population long associated with webworms. Multivariate selection analysis substituting realized fitness (with webworms present) for potential fitness (absent webworms) as the dependent variable revealed that reassociation with a coevolved specialist in a nonindigenous area profoundly altered the selection regime, favoring trait remixing and rapid chemical changes in parsnip populations, as predicted by the geographic mosaic theory. That uninfested populations of New Zealand parsnips contain higher amounts of octyl acetate, a floral volatile used by webworms for orientation, suggests that plants that escape from specialized enemies may also experience selection to increase kairomones, as well as to reduce allomones.
Structure and specificity of lamprey monoclonal antibodies
Authors: Herrin Brantley R. , Alder Matthew N. , Roux Kenneth H. , Sina Christina , Ehrhardt Götz R. A. , Boydston Jeremy A. , Turnbough Charles L. , Cooper Max D.
Published: February 2008

Adaptive immunity in jawless vertebrates (lamprey and hagfish) is mediated by lymphocytes that undergo combinatorial assembly of leucine-rich repeat (LRR) gene segments to create a diverse repertoire of variable lymphocyte receptor (
VLR
) genes. Immunization with particulate antigens induces VLR-B-bearing lymphocytes to secrete antigen-specific VLR-B antibodies. Here, we describe the production of recombinant VLR-B antibodies specific for BclA, a major coat protein of
Bacillus anthracis
spores. The recombinant VLR-B antibodies possess 8–10 uniform subunits that collectively bind antigen with high avidity. Sequence analysis, mutagenesis, and modeling studies show that antigen binding involves residues in the β-sheets lining the VLR-B concave surface. EM visualization reveals tetrameric and pentameric molecules having a central core and highly flexible pairs of stalk-region “arms” with antigen-binding “hands.” Remarkable antigen-binding specificity, avidity, and stability predict that these unusual LRR-based monoclonal antibodies will find many biomedical uses.
Epitope-specific TCRβ repertoire diversity imparts no functional advantage on the CD8+T cell response to cognate viral peptides
Authors: La Gruta Nicole L. , Thomas Paul G. , Webb Andrew I. , Dunstone Michelle A. , Cukalac Tania , Doherty Peter C. , Purcell Anthony W. , Rossjohn Jamie , Turner Stephen J.
Published: February 2008

TCR repertoire diversity has been convincingly shown to facilitate responsiveness of CD8+T cell populations to mutant virus peptides, thereby safeguarding against viral escape. However, the impact of repertoire diversity on the functionality of the CD8+T cell response to cognate peptide-MHC class I complex (pMHC) recognition remains unclear. Here, we have compared TCRβ chain repertoires of three influenza A epitope-specific CD8+T cell responses in C57BL/6 (B6) mice: DbNP366–374, DbPA224–233, and a recently described epitope derived from the +1 reading frame of the influenza viral polymerase B subunit (residues 62–70) (DbPB1-F262). Corresponding to the relative antigenicity of the respective pMHCs, and irrespective of the location of prominent residues, the DbPA224- and DbPB1-F262-specific repertoires were similarly diverse, whereas the DbNP366population was substantially narrower. Importantly, parallel analysis of response magnitude, cytotoxicity, TCR avidity, and cytokine production for the three epitope-specific responses revealed no obvious functional advantage conferred by increased T cell repertoire diversity. Thus, whereas a diverse repertoire may be important for recognition of epitope variants, its effect on the response to cognate pMHC recognition appears minimal.
A role for caspase 2 and PIDD in the process of p53-mediated apoptosis
Authors: Baptiste-Okoh Nicole , Barsotti Anthony M. , Prives Carol
Published: February 2008

When treated with some DNA-damaging agents, human tumor-derived H1299 cells expressing inducible versions of wild-type or mutant p53 with inactive transactivation domain I (p53
Q22/S23
) undergo apoptosis as evidenced by cytochrome
c
release, nuclear fragmentation, and sub-G
1
DNA content. Apoptosis induced by p53
Q22/S23
is relatively slow, however, and key downstream effector caspases are not activated. Nevertheless, with either version of p53, caspase 2 activation is required for release of cytochrome
c
and cell death. Remarkably, although p53
Q22/S23
is known to be defective in transcriptional activation of numerous p53 target genes, it can induce expression of proapoptotic targets including PIDD and AIP1 at least to the same extent as wild-type p53. Furthermore, RNAi silencing of PIDD, previously shown to be required for caspase 2 activation, suppresses apoptosis by both wild-type p53 and p53
Q22/S23
. Thus, the initial stage of DNA damage-facilitated, p53-mediated apoptosis occurs by a PIDD- and caspase 2-dependent mechanism, and p53's full transcriptional regulatory functions may be required only for events that are downstream of cytochrome
c
release.
Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete for the same binding surface
Authors: Marintcheva Boriana , Marintchev Assen , Wagner Gerhard , Richardson Charles C.
Published: February 2008

ssDNA-binding proteins are key components of the machinery that mediates replication, recombination, and repair. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft, therefore predicting that the binding of ssDNA and the C-terminal tail is mutually exclusive. Using chemical cross-linking, competition studies, and NMR chemical-shift mapping, we demonstrate that: (
i
) the C-terminal peptide of the gene 2.5 protein cross-links to the core of the protein only in the absence of ssDNA, (
ii
) the cross-linked species fails to bind to ssDNA, and (
iii
) a C-terminal peptide and ssDNA bind to the same overall surface of the protein. We propose that the protection of the DNA-binding cleft by the electrostatic shield of the C-terminal tail observed in prokaryotic ssDNA-binding proteins, ribosomal proteins, and high-mobility group proteins is an evolutionarily conserved mechanism. This mechanism prevents random binding of charged molecules to the nucleic acid-binding pocket and coordinates nucleic acid–protein and protein–protein interactions.
Prophinder: a computational tool for prophage prediction in prokaryotic genomes
Authors: Lima-Mendez Gipsi , Van Helden Jacques , Toussaint Ariane , Leplae Raphaël
Published: February 2008

Summary: Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in the current sparse phage sequence space, which should cover an estimated 100 million species. Systematic and reliable predictions will enable further studies of prophages contribution to the bacteriophage gene pool and to better understand gene shuffling between prophages and phages infecting the same host.

Availability: Softare is available at http://aclame.ulb.ac.be/prophinder

Contact:  gipsi@scmbb.ulb.ac.be

Supplementary information: Supplementary data is available on http://aclame.ulb.ac.be/Tools/Prophinder/evaluations_table.html.
Efficacy and Safety of a Traditional Herbal Medicine, Hochu-ekki-to in the Long‐Term Management of Kikyo (Delicate Constitution) Patients with Atopic Dermatitis: A 6‐Month, Multicenter, Double‐Blind, Randomized, Placebo‐Controlled Study
Authors: Kobayashi Hiromi , Ishii Masamitsu , Takeuchi Satoshi , Tanaka Yoichi , Shintani Takahiro , Yamatodani Atsushi , Kusunoki Tadashi , Furue Masutaka
Published: February 2008

Hochu-ekki-to is a traditional herbal (Kampo) medicine that has been shown to be effective for patients with Kikyo (delicate, easily fatigable, or hypersensitive) constitution. Previous case reports have suggested that this herbal drug was effective for a certain subgroup of patients with atopic dermatitis (AD). We aimed to evaluate the efficacy and safety of Hochu-ekki-to in the long‐term management of Kikyo patients with AD. In this multicenter, double blind, randomized, placebo‐controlled study, 91 Kikyo patients with AD were enrolled. Kikyo condition was evaluated by a questionnaire scoring system. All patients continued their ordinary treatments (topical steroids, topical tacrolimus, emollients or oral antihistamines) before and after their protocol entry. Hochu-ekki-to or placebo was orally administered twice daily for 24 weeks. The skin severity scores, total equivalent amount (TEA) of topical agents used for AD treatment, prominent efficacy (cases with skin severity score = 0 at the end of the study) rate and aggravated rate (more than 50% increase of TEA of topical agents from the beginning of the study) were monitored and evaluated. Seventy‐seven out of 91 enrolled patients completed the 24‐week treatment course (Hochu-ekki-to: n = 37, placebo: n = 40). The TEA of topical agents (steroids and/or tacrolimus) was significantly (P < 0.05) lower in the Hochu-ekki-to group than in the placebo group, although the overall skin severity scores were not statistically different. The prominent efficacy rate was 19% (7 of 37) in the Hochu-ekki-to group and 5% (2 of 40) in the placebo group (P = 0.06). The aggravated rate was significantly (P < 0.05) lower in the Hochu-ekki-to group (3%; 1 of 37) than in the placebo group (18%; 7 of 39). Only mild adverse events such as nausea and diarrhea were noted in both groups without statistical difference. This placebo‐controlled study demonstrates that Hochu-ekki-to is a useful adjunct to conventional treatments for AD patients with Kikyo constitution. Use of Hochu-ekki-to significantly reduces the dose of topical steroids and/or tacrolimus used for AD treatment without aggravating AD.
Le Cycle de Renart
: From the
Enfances
to the
Jugement
in a Cyclical
Roman de Renart
Manuscript
Authors: Sunderland Luke
Published: February 2008

This article is a reading of a
Roman de Renart
manuscript from the often neglected gamma family, which subsumes the narrative to a broadly biographical (or cyclical) framework. The manuscript studied here therefore opens with an
Enfances
text, which lays the ground for seeing the fox as a radically evil creation, and his crimes as inevitable repetitions of his evil propensities. Whereas the alpha and beta families open with the famous trial (
Le Jugement de Renart
), the gamma family locates it later, after a series of misdeeds by the fox, meaning that this episode now serves less as an attempt to punish Renart for a single sexual crime than to mark the impossibility of holding him to justice for anything he has done. Using an approach to repetition deriving from Lacanian theory, the author argues that the
Jugement
, itself now a rerun of a previous trial, represents the community's failure to confront the Renardian trauma that haunts it, and, by extension, its inability to function effectively. Thwarting the ideological closure of justice allows Renart to become an emblem of the fiction itself.
Death and the Aesthetic of Continuity: Reading Victor Hugo's
Contemplations
Authors: Lunn-Rockliffe Katherine
Published: February 2008

This article addresses the importance of continuity in Victor Hugo's poetry, understood both as connection between author and reader and as sheer length. Arguing that his very prolixity merits analysis, it investigates the relationship between his connective readability and his ability to sustain long verse paragraphs. It uses examples from the long visionary poems in book VI of
Les Contemplations
, which represent death both as a rupture and as a continuity. The first part considers the connection between poet and reader, focusing on Hugo's use of solitude as an experience shared by the dead, the poet and the reader. He plays on the concrete reality that the printed book is read in isolation to draw the reader close to the visionary experience of death. The second part examines how the reader is made to go through this solitary experience line by line, a process that unfolds in time. It shows how Hugo builds verse lines into a continuum and plays on turning points, particularly line-endings, to sustain his long verse paragraphs. Far from being monolithic blocks, these sequences are articulated by a series of transitions which constantly oblige the reader to reconsider the relationship between breaks and joinings, separation and continuity.
The Legacy of the Beast: Patrilinearity and Rupture in Zola's
La Bête humaine
and Freud's
Totem and Taboo
Authors: Counter Andrew
Published: February 2008

This article explores the legacy of primitive violence evoked by Zola and Freud in
La Bête humaine
(1890) and
Totem and Taboo
(1913) respectively, and attempts to show how Zola's and Freud's use of a paradigm of primitive aggression might be ideologically complicit with a violent inclination in their contemporaneous societies. This issue will be considered in its relations with the notions of patrilinearity and rupture, concepts which are integral to both texts, and which, it shall be argued, constitute in some sense the essence of patriarchy. Reading both writers through the prism of Deleuze's theory, patrilinearity itself will begin to appear as a series of ruptures rather than a continuous genealogy, a history of struggle which both perpetuates and conceals the dominance of violence. The ambivalence of Freud's and Zola's rendering of that violence will ultimately appear as an ethical challenge to the reader.
Cdc7-dependent phosphorylation of Mer2 facilitates initiation of yeast meiotic recombination
Authors: Sasanuma Hiroyuki , Hirota Kouji , Fukuda Tomoyuki , Kakusho Naoko , Kugou Kazuto , Kawasaki Yasuo , Shibata Takehiko , Masai Hisao , Ohta Kunihiro
Published: February 2008

Meiosis ensures genetic diversification of gametes and sexual reproduction. For successful meiosis, multiple events such as DNA replication, recombination, and chromosome segregation must occur coordinately in a strict regulated order. We investigated the meiotic roles of Cdc7 kinase in the initiation of meiotic recombination, namely, DNA double-strand breaks (DSBs) mediated by Spo11 and other coactivating proteins. Genetic analysis using bob1-1 cdc7Δ reveals that Cdc7 is essential for meiotic DSBs and meiosis I progression. We also demonstrate that the N-terminal region of Mer2, a Spo11 ancillary protein required for DSB formation and phosphorylated by cyclin-dependent kinase (CDK), contains two types of Cdc7-dependent phosphorylation sites near the CDK site (Ser30): One (Ser29) is essential for meiotic DSB formation, and the others exhibit a cumulative effect to facilitate DSB formation. Importantly, mutations on these sites confer severe defects in DSB formation even when the CDK phosphorylation is present at Ser30. Diploids of cdc7Δ display defects in the chromatin binding of not only Spo11 but also Rec114 and Mei4, other meiotic coactivators that may assist Spo11 binding to DSB hot spots. We thus propose that Cdc7, in concert with CDK, regulates Spo11 loading to DSB sites via Mer2 phosphorylation.
Extracellular matrix protein βig-h3/TGFBI promotes metastasis of colon cancer by enhancing cell extravasation
Authors: Ma Chaoyu , Rong Yu , Radiloff Daniel R. , Datto Michael B. , Centeno Barbara , Bao Shideng , Cheng Anthony Wai Ming , Lin Fumin , Jiang Shibo , Yeatman Timothy J. , Wang Xiao-Fan
Published: February 2008

Metastasis, the major cause of cancer death, is a multistep process that requires interactions between cancer cells and stromal cells and between cancer cells and extracellular matrix. Molecular alterations of the extracellular matrix in the tumor microenvironment have a considerable impact on the metastatic process during tumorigenesis. Here we report that elevated expression of βig-h3/TGFBI (transforming growth factor, β-induced), an extracellular matrix protein secreted by colon cancer cells, is associated with high-grade human colon cancers. Ectopic expression of the βig-h3 protein enhanced the aggressiveness and altered the metastatic properties of colon cancer cells in vivo. Inhibition of βig-h3 expression dramatically reduced metastasis. Mechanistically, βig-h3 appears to promote extravasation, a critical step in the metastatic dissemination of cancer cells, by inducing the dissociation of VE-cadherin junctions between endothelial cells via activation of the integrin αvβ5–Src signaling pathway. Thus, cancers associated with overexpression of βig-h3 may have an increased metastatic potential, leading to poor prognosis in cancer patients.
Overreplication of short DNA regions during S phase in human cells
Authors: Gómez María , Antequera Francisco
Published: February 2008

DNA replication origins (ORI) are regulatory regions from which the genome is replicated once every cell cycle. A widely used method for their identification in mammalian chromosomes relies on quantitative PCR of DNA nascent strands across candidate regions. We developed a new high-resolution PCR strategy to localize ORIs directly on total unfractionated human DNA. The increase in sensitivity provided by this approach has revealed that a short region of ∼200-base-pair overlapping well-characterized replication origins undergoes several rounds of replication, coinciding with their specific time of activation during S phase. This process generates a population of discrete dsDNA fragments detectable as free molecules in preparations of total DNA in normally proliferating cells. Overreplicated regions have precise boundaries at the edge of the nucleosome-free gap that encompasses the transcription initiation sites of CpG island promoters. By itself, active transcription does not induce overreplication but does stimulate it at ORIs associated with promoters. The coincidence in time and space between the overproduction of short DNA fragments and ORI activity predicts the precise localization of thousands of ORIs in the human genome and uncovers a previously unnoticed step in the initiation of DNA replication.
Differential display of DNA-binding proteins reveals heat-shock factor 1 as a circadian transcription factor
Authors: Reinke Hans , Saini Camille , Fleury-Olela Fabienne , Dibner Charna , Benjamin Ivor J. , Schibler Ueli
Published: February 2008

The circadian clock enables the anticipation of daily recurring environmental changes by presetting an organism’s physiology and behavior. Driven and synchronized by a central pacemaker in the brain, circadian output genes fine-tune a wide variety of physiological parameters in peripheral organs. However, only a subset of circadianly transcribed genes seems to be directly regulated by core clock proteins. Assuming that yet unidentified transcription factors may exist in the circadian transcriptional network, we set out to develop a novel technique, differential display of DNA-binding proteins (DDDP), which we used to screen mouse liver nuclear extracts. In addition to several established circadian transcription factors, we found DNA binding of heat-shock factor 1 (HSF1) to be highly rhythmic. HSF1 drives the expression of heat-shock proteins at the onset of the dark phase, when the animals start to be behaviorally active. Furthermore, Hsf1-deficient mice have a longer free-running period than wild-type littermates, suggesting a combined role for HSF1 in the mammalian timekeeping and cytoprotection systems. Our results also suggest that the new screening method DDDP is not limited to the identification of circadian transcription factors but can be applied to discover novel transcriptional regulators in various biological systems.
Qualifying the relationship between sequence conservation and molecular function
Authors: Cooper Gregory M. , Brown Christopher D.
Published: February 2008

Quantification of evolutionary constraints via sequence conservation can be leveraged to annotate genomic functional sequences. Recent efforts addressing the converse of this relationship have identified many sites in metazoan genomes with molecular function but without detectable conservation between related species. Here, we discuss explanations and implications for these results considering both practical and theoretical issues. In particular, phylogenetic scope influences the relationship between sequence conservation and function. Comparisons of distantly related species can detect constraint with high specificity due to the loss of conserved neutral sequence, but sensitivity is sacrificed as a result of functional changes related to lineage-specific biology. The strength of natural selection operating on functional sequence is also important. Mutations to functional sequences that result in small fitness effects are subject to weaker constraints. Therefore, particularly when comparing highly divergent species, functional sequences that are degenerate or biologically redundant will be prone to turnover, wherein functional sequences are replaced by effectively equivalent, but nonorthologous counterparts. Finally, considering the size and complexity of metazoan genomes and the fact that many nonconserved sequences are associated with sequence-degenerate, low-level molecular functions, we find it likely that there exist many biochemically functional sequences that are not under constraint. This hypothesis does not lead to the conclusion that huge amounts of vertebrate genomes are functionally important, but rather that such “functionality” represents molecular noise that has weak or no effect on organismal phenotypes.
Drosophila RNA Interference (RNAi) Using a Gal-4 Inducible Transgene Vector: Figure 1.
Authors: Misquitta Leonie , Wei Qin , Paterson Bruce M.
Published: February 2008

INTRODUCTION

RNA interference (RNAi) is a powerful method for determining the role of specific genes during Drosophila embryogenesis. This protocol describes a method for RNAi in vivo using tissue-specific Gal-4 transgenes to induce dsRNA synthesis from an upstream activator sequence (UAS) vector. This vector contains the desired exonic inverted sequences representing the target gene (preferably more than 400 bp) separated by a unique spacer, the first intron of the actin 5C gene. The inverted repeats are stable during cloning in E. coli with this intronic spacer and the intron is spliced out to produce an almost perfect dsRNA target for Dicer cleavage and the production of siRNAs.
PCR Mutagenesis by Overlap Extension and Gene SOE
Authors: Vallejo Abbe N. , Pogulis Robert J. , Pease Larry R.
Published: February 2008

INTRODUCTION

Mutagenesis by PCR is accomplished by incorporating desired genetic changes into custom-made primers used in amplification reactions. Because these mutagenizing primers have terminal complementarity, two separate DNA fragments amplified from a target gene can be fused into a single product by primer extension without relying on restriction endonuclease sites or ligation reactions. Briefly, mutagenesis is achieved by performing PCR with specially designed oligonucleotide primers that include the desired substitutions, insertions, or deletions in their sequence. The two overlapping fragments are fused together in a subsequent extension reaction. The inclusion of outside primers in the extension reaction amplifies the fused product by PCR. Theoretically, the primers can be moved anywhere along the targeted gene to introduce mutations. This method can be exploited further by using DNA fragments from different sources. Such gene splicing by overlap extension (SOE) can be used to rapidly produce chimeras. A limitation of SOE is the difficulty of manipulating large DNA segments (i.e., >1-2 kb). To circumvent this, a cassette system can be targeted, modified by SOE, and reinserted using restriction endonuclease sites designed into the cassette structure. This approach also allows easy shuffling or replacement of gene segments.
Collection of Drosophila Embryos for RNA Interference (RNAi)
Authors: Misquitta Leonie , Wei Qin , Paterson Bruce M.
Published: February 2008

INTRODUCTION

RNA interference (RNAi) is a powerful method for determining the role of specific genes during Drosophila embryogenesis. This protocol describes a method for collection of Drosophila embryos for RNA interference (RNAi) experiments. The embryos are collected in a simple, homemade apparatus, arrayed on prepared glass slides, and readied for injection. It is important to keep the embryos moist and oxygenated. Work expeditiously, because embryos should be injected within 30-60 min after collection.
Labeling Acetylcholine Receptors in Live Cells Using Rhodamine α-Bungarotoxin for Imaging: Figure 1.
Authors: Chazotte Brad
Published: February 2008

INTRODUCTION

The eukaryotic cell has evolved to compartmentalize its functions and transport various metabolites among cellular compartments. Therefore, in cell biology, the study of organization and structure/function relationships is of great importance. Integral membrane protein receptors can be studied using specifically fluoresceinated but still functional hormones or toxins that bind to specific receptors. α-bungarotoxin binds with high affinity to the α-subunit of the nicotinic acetylcholine receptor of the neuromuscular junction. In this article, acetylcholine receptors are labeled with α-bungarotoxin conjugated to rhodamine.
Whole-Mount In Situ Hybridization of RNA Probes to Plant Tissues
Authors: Traas Jan
Published: February 2008

INTRODUCTION

The labeling of entire plantlets (whole-mount labeling) is very easy, but it can cause substantial artifacts. Because whole plants are labeled, certain tissues are not readily accessible to the probes, whereas others can often stain nonspecifically. In the hands of the author, for instance, the elongation zone of the root is labeled even in negative controls, whereas mature parts of the roots and hypocotyl tend to be more resistant to probe penetration. Whole-mount labeling should therefore only be used to monitor gene expression in a limited number of organs and tissues--in particular, root meristems, embryos, and very young primordia--and the results should be interpreted with care. A protocol for whole-mount labeling is described here. Positive (e.g., constitutive probe) and negative controls should be included systematically.
Outcome of ETV6/RUNX1‐positive childhood acute lymphoblastic leukaemia in the NOPHO‐ALL‐1992 protocol: frequent late relapses but good overall survival
Authors: Forestier Erik , Heyman Mats , Andersen Mette K , Autio Kirsi , Blennow Elisabeth , Borgström Georg , Golovleva Irina , Heim Sverre , Heinonen Kristina , Hovland Randi , Johannsson Johann H , Kerndrup Gitte , Nordgren Ann , Rosenquist Richard , Swolin Birgitta , Johansson Bertil ,   the Nordic Society of Paediatric Haematology, Oncology (NOPHO), the Swedish Cytogenetic Leukaemia Study Group (SCLSG) and the NOPHO Leukaemia Cytogenetic Study Group (NLCSG)
Published: February 2008

The prognostic impact of t(12;21)(p13;q22) [ETV6/RUNX1 fusion] in paediatric acute lymphoblastic leukaemia (ALL) has been extensively debated, particularly with regard to the frequency of late relapses and appropriate treatment regimens. We have retrospectively collected 679 ALLs with known ETV6/RUNX1 status, as ascertained by fluorescence in situ hybridization or reverse‐transcription polymerase chain reaction, treated according to the Nordic Society of Paediatric Haematology and Oncology ‐ALL‐1992 protocol. The assigned risk groups/treatment modalities for the 171 (25%) patients with t(12;21)‐positive ALLs were 74 (43%) standard risk, 71 (42%) intermediate risk and 26 (15%) high risk. The 5‐ and 10‐year event‐free survival (EFS) of the 171 patients was 80% and 75% respectively, with no significant differences among the three risk groups. Most of the relapses occurred in boys and were late, with almost 50% of all relapses occurring ≥5 years after diagnosis. Of all relapses after 6 years, 80% occurred in the t(12;21)‐positive group. The overall survival was 94% at 5 years and 88% at 10 years; thus, the treatment of patients in second or later remission is usually successful. As yet, there is no reliable plateau in the EFS curve, a fact that raises the question as to when the prognostic ramifications of ALLs harbouring ETV6/RUNX1 should be evaluated.
Is adequate parenting compatible with maternal drug use? A 5‐year follow‐up
Authors: Street K. , Whitlingum G. , Gibson P. , Cairns P. , Ellis M.
Published: February 2008

Introduction  This prospective, cohort study compares child protection outcomes over the first 5 years of life in a group of children born to self‐declared drug‐using mothers recruited during pregnancy (cases) and a group of children matched for gestational age, chronological age, maternal neighbourhood and place of delivery whose mothers made no such declaration of problematic drug use (controls).

Methodology  We monitored local child protection registers to identify cohort members who came to the attention of the local authority.

Results  Of the 71 original cases and 142 original controls, 55 (77%) and 96 (68%) remained in the area enrolled in local schools at 5 years of age. In total, 26 (47.3%) of the case children were subject to child protection procedures compared with 18 (18.8%) of the control children. This risk difference of 28.5% (95% CI 13.2% to 43.9%) has increased marginally since our previous report in this journal of child protection outcomes at 18 months of age (32% vs. 7%). However, the level of intervention deemed necessary to protect the child has increased significantly with six cases (compared with one control child) taken into the care of the local authority.

Conclusions  Despite early maternal intentions and multiple supportive interventions, 27% of children born to women with significant substance abuse problems in our area required child protection during the pre‐school years. Child protection risk assessment procedures need to weigh problematic maternal drug use heavily. Intervention studies with child welfare outcomes are needed to identify the most effective harm reduction strategies and inform public debate on how we can minimize child abuse related to substance misuse.
Discrepancy between expected and actual child support payments: predicting the health and health‐related quality of life of children living in low‐income, single‐parent families
Authors: Cook K. , Davis E. , Davies B.
Published: February 2008

Objective  Although the amount and frequency of child support payments received by single parents are often erratic and fluctuate, no study to date has quantitatively explored how the discrepancy between expected and actual payments relates to child health. This study aims to examine whether the discrepancy between expected and actual child support payments predicts a range of child health outcomes, including global health, health‐related quality of life, involvement in activities and parental psychological distress.

Methods  This study used results from the Longitudinal Study of Australian Children, which included a sample of parents of children aged 4–5 years (n = 4983). The questionnaire was completed by the parent who spent the most time with the child and knew the child best. From the 4983 families, 332 low‐income single parents reliant on welfare with a formal or informal child support order in place were identified.

Results  After controlling for income, the discrepancy between expected and actual child support predicted school functioning, conduct problems, total mental health problems and involvement in activities. Discrepancy between expected and actual child support payments did not predict the remaining health‐related quality of life domains, mental health domains, global child health or parental psychosocial distress.

Conclusion  This was the first study to examine how the discrepancy between expected and actual child support payments relates to child health, providing important data on the effectiveness of the child support system for children's well‐being. These findings highlight the potential impact of the discrepancy on school functioning, conduct problems, total mental health problems and involvement in activities.
Objective measurement of levels and patterns of physical activity
Authors: Reading Richard
Published: February 2008

.
 
Riddoch C.J.,
Mattocks C.,
Deere K.,
Saunders J.,
Kirkby J.,
Tilling K.,
Leary S.D.,
Blair S.N. &
Ness A.R.
(
2007
)

,
92
,
963
–
969
.
DOI: 10.1136/adc.2006.112136.

Objective  To measure the levels and patterns of physical activity, using accelerometers, of 11‐year‐old children participating in the Avon Longitudinal Study of Parents and Children (ALSPAC).

Design  Cross‐sectional analysis.

Setting  The ALSPAC is a birth cohort study located in the former county of Avon, in the south‐west of England. This study used data collected when the children were 11 years old.

Participants  A total of 5595 children (2662 boys, 2933 girls). The children are the offspring of women recruited to a birth cohort study during 1991–1992. The median age (95% CI) of the children is now 11.8 (11.6–11.9) years.

Methods  Physical activity was measured over a maximum of seven consecutive days using the MTI Actigraph accelerometer.

Main outcome measures  Level and pattern of physical activity.

Results  The median physical activity level was 580 counts/min. Boys were more active than girls [median (IQR) 644 (528–772) counts/min vs. 529 (444–638) counts/min, respectively]. Only 2.5% (95% CI 2.1% to 2.9%) of children [boys 5.1% (95% CI 4.3% to 6.0%), girls 0.4% (95% CI 0.2% to 0.7%)] met current internationally recognized recommendations for physical activity. Children were most active in summer and least active in winter (difference = 108 counts/min). Both the mother and partner's education level were inversely associated with activity level [P for trend <0.001 (both mother and partner)]. The association was lost for mother's education (P for trend = 0.07) and attenuated for partner's education (P for trend = 0.02), after adjustment for age, sex, season, maternal age and social class.

Conclusions  A large majority of children are insufficiently active, according to current recommended levels for health.
Diagnosing abuse: a systematic review of torn frenum and other intra‐oral injuries
Authors: Reading Richard
Published: February 2008

.
 
Maguire S.,
Hunter B.,
Hunter L.,
Sibert J.R.,
Mann M.,
Kemp A.M.
, for the

. (
2007
)

,
92
,
1113
–
1117
.

DOI: 10.1136/adc.2006.113001.

Introduction  A torn labial frenum is widely regarded as pathognomonic of abuse.

Methods  We systematically reviewed the evidence for this, and to define other intra‐oral injuries found in physical abuse. Nine studies documented abusive torn labial frena in 30 children and 27 were fatally abused: 22 were less than 5 years old. Only a direct blow to the face was substantiated as a mechanism of injury.

Results  Two studies noted accidentally torn labial frena, both from intubation. Abusive intra‐oral injuries were widely distributed to the lips, gums, tongue and palate and included fractures, intrusion and extraction of the dentition, bites and contusions.

Conclusions  Current literature does not support the diagnosis of abuse based on a torn labial frenum in isolation. The intra‐oral hard and soft tissue should be examined in all suspected abuse cases, and a dental opinion sought where abnormalities are found.
The relationship between cortisol, muscle mass and muscle strength in older persons and the role of genetic variations in the glucocorticoid receptor
Authors: Peeters G. M. E. E. , Van Schoor N. M. , Van Rossum E. F. C. , Visser M. , Lips P.
Published: February 2008

Objective  Cortisol levels increase with age and hypercortisolism is associated with muscle weakness. This study examines the relationship between cortisol, muscle mass and muscle strength in community‐dwelling older persons and the role of genetic variations in the glucocorticoid receptor (GR).

Design/patients  The study was conducted within the Longitudinal Ageing Study Amsterdam (LASA, 1992‐ongoing), a cohort study in a population‐based sample of older persons in the Netherlands. Data were used from 1196 and 1046 participants in the second (1995–1996) and fourth (2001–2002) cycle, respectively.

Measurements  Total serum cortisol and free cortisol were measured in the mornings of the second cycle while salivary cortisol sampled early in the morning and late at night were measured in the fourth cycle. The GR gene polymorphisms (ER22/23EK, N363SS, 9β and BclI) were genotyped by Taqman. Appendicular skeletal muscle mass (ASMM) was measured using DXA in the second cycle and 3 years later (third cycle). Grip strength was assessed using a handgrip dynamometer in the second, third, fourth and fifth cycle.

Results  A relationship was found between both morning and evening salivary cortisol, and loss of grip strength: participants in the highest quartile of cortisol concentration had a twofold higher risk of loss of grip strength than participants in the lowest quartile (P < 0·05). No relationships were found between serum cortisol (loss of) ASMM, and (loss of) grip strength. The ER22/23EK and N363S‐polymorphisms modified the relationships between serum cortisol, ASMM and grip strength, respectively. Due to limited power, these relationships were not significant after stratification for the polymorphisms.

Conclusion  High salivary cortisol is associated with a higher risk of loss of grip strength in older persons. GR genotypes modify the relationship between muscle mass and muscle strength.