bluuebunny/crossref_metadata_2025 huggingface dataset:
Policy Entrepreneurship and Multilevel Governance: A Comparative Study of European Cross-Border Regions
Authors: Perkmann Markus
Published: November 2007

The author addresses the recent proliferation of cross-border regions, or ‘Euroregions’, in Europe. It is argued that EU multilevel governance patterns generate opportunities for entrepreneurial policy organisations to attract policy tasks and resources. This is conceptualised as policy entrepreneurship and applied to a comparative case-study analysis of three Euroregions: EUREGIO (Germany – Netherlands), Viadrina (Poland – Germany), and Tyrol Euroregion (Austria – Italy). The analysis focuses on the ability of these initiatives to establish themselves as autonomous organisations. It finds considerable variation across the cases in this respect. Following on from this, the paper shows how administrative and institutional environments in different EU member states affect the ability of Euroregions to engage in policy entrepreneurship. It is concluded that it is premature to perceive Euroregions as new types of regional territorial entities; rather, they are part of the policy-innovation scenario enabled by EU multilevel governance.
Surveying seafood consumption - a methodological analysis
Authors: Kronen Mecki , McArdle Brian , Labrosse Pierre
Published: November 2007

This paper addresses the need to establish a fast, effective and reliable method for collecting fish and seafood consumption data at the village level. Two different approaches, a community participatory and a classical survey one were tested and validated against each other. Using fully structured questionnaire surveys also reliability of results obtained from household and individual interviews were compared. Furthermore, taking fresh fish consumption as an example, three different methods were assessed to approximate best per capita consumption. Approaches and methods are validated in terms of time and human resource requirements, and data quality by comparing data sets obtained in Polynesian and Melanesian communities. Adding efficiency criteria, adoption of household average consumption surveys is concluded to
best combine reliable data and least time and financial requirements. Per capita fresh fish consumption was found to best estimated using a simplified WHO system that takes into account gender-age correction factors.
Combined kinetic and thermodynamic analysis of α-helical membrane protein unfolding
Authors: Curnow Paul , Booth Paula J.
Published: November 2007

The analytical toolkit developed for investigations into water-soluble protein folding has yet to be applied in earnest to membrane proteins. A major problem is the difficulty in collecting kinetic data, which are crucial to understanding any reaction. Here, we combine kinetic and thermodynamic studies of the reversible unfolding of an α-helical membrane protein to provide a definitive value for the reaction free energy and a means to probe the transition state. Our analyses show that the major unfolding step in the SDS-induced denaturation of bacteriorhodopsin involves a reduction in α-helical structure and proceeds with a large free-energy change; both our equilibrium and kinetic measurements predict that the free energy of unfolding in the absence of denaturant is +20 kcal·mol
−1
, with an associated
m
-value of 25 kcal·mol
−1
. The rate of unfolding in the absence of denaturant,
k
u

H
2
O

, is surprisingly very slow (≈10
−15
s
−1
). The kinetics also give information on the transition state for this major unfolding step, with a value for β (
m
f
/[
m
f
+
m
u
]) of ≈0.1, indicating that the transition state is close to the unfolded state. We thus present a basis for mapping the structural and energetic properties of membrane protein folding by mutagenesis and classical kinetics.
Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities
Authors: Artyomov Maxim N. , Das Jayajit , Kardar Mehran , Chakraborty Arup K.
Published: November 2007

Detection of different extracellular stimuli leading to functionally distinct outcomes is ubiquitous in cell biology, and is often mediated by differential regulation of positive and negative feedback loops that are a part of the signaling network. In some instances, these cellular responses are stimulated by small numbers of molecules, and so stochastic effects could be important. Therefore, we studied the influence of stochastic fluctuations on a simple signaling model with dueling positive and negative feedback loops. The class of models we have studied is characterized by single deterministic steady states for all parameter values, but the stochastic response is bimodal; a behavior that is distinctly different from models studied in the context of gene regulation. For example, when positive and negative regulation is roughly balanced, a unique deterministic steady state with an intermediate value for the amount of a downstream signaling product is found. However, for small numbers of signaling molecules, stochastic effects result in a bimodal distribution for this quantity, with neither mode corresponding to the deterministic solution; i.e., cells are in “on” or “off” states, not in some intermediate state. For a large number of molecules, the stochastic solution converges to the mean-field result. When fluctuations are important, we find that signal output scales with control parameters “anomalously” compared with mean-field predictions. The necessary and sufficient conditions for the phenomenon we report are quite common. So, our findings are expected to be of broad relevance, and suggest that stochastic effects can enable binary cellular decisions.
Kinetics of DNA-mediated docking reactions between vesicles tethered to supported lipid bilayers
Authors: Chan Yee-Hung M. , Lenz Peter , Boxer Steven G.
Published: November 2007

Membrane–membrane recognition and binding are crucial in many biological processes. We report an approach to studying the dynamics of such reactions by using DNA-tethered vesicles as a general scaffold for displaying membrane components. This system was used to characterize the docking reaction between two populations of tethered vesicles that display complementary DNA. Deposition of vesicles onto a supported lipid bilayer was performed by using a microfluidic device to prevent mixing of the vesicles in bulk during sample preparation. Once tethered onto the surface, vesicles mixed via two-dimensional diffusion. DNA-mediated docking of two reacting vesicles results in their colocalization after collision and their subsequent tandem motion. Individual docking events and population kinetics were observed via epifluorescence microscopy. A lattice-diffusion simulation was implemented to extract from experimental data the probability,
P
dock
, that a collision leads to docking. For individual vesicles displaying small numbers of docking DNA,
P
dock
shows a first-order relationship with copy number as well as a strong dependence on the DNA sequence. Both trends are explained by a model that includes both tethered vesicle diffusion on the supported bilayer and docking DNA diffusion over each vesicle's surface. These results provide the basis for the application of tethered vesicles to study other membrane reactions including protein-mediated docking and fusion.
Phenotypic variability of growing cellular populations
Authors: Lu Ting , Shen Tongye , Bennett Matthew R. , Wolynes Peter G. , Hasty Jeff
Published: November 2007

The dynamics and diversity of proliferating cellular populations are governed by the interplay between the growth and death rates among the various phenotypes within a colony. In addition, epigenetic multistability can cause cells to spontaneously switch from one phenotype to another. By examining a generalized form of the relative variance of populations and classifying it into intracolony and cross-colony contributions, we study the origins and consequences of cellular population variability. We find that the variability can depend highly on the initial conditions and the constraints placed on the population by the growth environment. We construct a two-phenotype model system and examine, analytically and numerically, its time-dependent variability in both unbounded and population-limited growth environments. We find that in unbounded growth environments the overall variability is strictly governed by the initial conditions. In contrast, when the overall population is limited by the environment, the system eventually relaxes to a unique fixed point regardless of the initial conditions. However, the transient decay to the fixed point depends highly on initial conditions, and the time scale over which the variability decays can be very long, depending on the intrinsic time scales of the system. These results provide insights into the origins of population variability and suggest mechanisms in which variability can arise in commonly used experimental approaches.
Determination of virus burst size
in vivo
using a single-cycle SIV in rhesus macaques
Authors: Chen Hannah Yuan , Di Mascio Michele , Perelson Alan S. , Ho David D. , Zhang Linqi
Published: November 2007

A single-cycle simian immunodeficiency virus (scSIV) that undergoes only one round of infection and replication was constructed to calculate the total number of virons produced by an SIV-infected cell
in vivo
. Four Mamu-A*01 rhesus macaques were inoculated on two occasions 11 weeks apart with the scSIV by
ex vivo
infection and i.v. reinfusion of autologous cells. After each inoculation, plasma viral loads peaked between 1 and 2.5 days and then declined exponentially in one or two phases to below detection limits within 2 weeks. Although higher levels of SIV-specific cytotoxic T lymphocytes and modest increases in antibody responses were observed for each animal after the second inoculation, decay rates of the infected cells were only minimally affected. Analyzing the viral load data with a mathematical model, the
in vivo
viral burst size averaged 4.0 × 10
4
and 5.5 × 10
4
virions per cell for the first and second inoculations, respectively, with no significant difference between the two inoculations. This estimate, in conjunction with our prior understanding of other quantitative viral and cellular parameters during SIV and HIV infection, provides critical insights into the dynamic process of viral production and its interplay with the infected host
in vivo
.
Virus movement maintains local virus population diversity
Authors: Snyder Jamie C. , Wiedenheft Blake , Lavin Matthew , Roberto Francisco F. , Spuhler Josh , Ortmann Alice C. , Douglas Trevor , Young Mark
Published: November 2007

Viruses are the largest reservoir of genetic material on the planet, yet little is known about the population dynamics of any virus within its natural environment. Over a 2-year period, we monitored the diversity of two archaeal viruses found in hot springs within Yellowstone National Park (YNP). Both temporal phylogeny and neutral biodiversity models reveal that virus diversity in these local environments is not being maintained by mutation but rather by high rates of immigration from a globally distributed metacommunity. These results indicate that geographically isolated hot springs are readily able to exchange viruses. The importance of virus movement is supported by the detection of virus particles in air samples collected over YNP hot springs and by their detection in metacommunity sequencing projects conducted in the Sargasso Sea. Rapid rates of virus movement are not expected to be unique to these archaeal viruses but rather a common feature among virus metacommunities. The finding that virus immigration rather than mutation can dominate community structure has significant implications for understanding virus circulation and the role that viruses play in ecology and evolution by providing a reservoir of mobile genetic material.
The Rise and Fall of ‘Mediterranean Atlanticism’ in Italian Foreign Policy: the Case of the Near East
Authors: Graziano Manlio
Published: November 2007

The article aims at studying the reasons for the new way of looking at the Palestinian-Israeli conflict by the Italian political world: the mutual recognition of Israel and the Vatican, the visit to Jerusalem by the leader of the formerly fascist party, Mr. Gianfranco Fini, and the beginnings of a movement of interest towards the Jewish State also within the political left. From a historical viewpoint, anti-Semitism in Italy found its origins in the Church's attitude toward the ‘deicide people’. Beginning with WWI, to this position was added the worry that the Holy Places might fall under Jewish control. From those times dates the Holy See's evermore manifest liking for the Arab populations of Palestine. Nowadays the line of conduct of the Church has as its basic objective the defense of Christian minorities in the Middle East, and for this reason it maintains dialogues with all actors in the region. The weight of the Church influenced also the attitude of the Italian State, even though from its inception the latter had to make adjustments because of other international requirements. This multiple subordination caused the different republican governments to always keep an official equidistant stance among the conflicting parties in the Near East. Behind this apparent neutrality, however, the feelings of benevolence for the Arab countries and the Palestinians have gradually intensified. Italian leaders have been trying to conduct a Mediterranean policy on the borders of the Western alliance, and their feelings have been oriented in consequence. During the 1970s, the governments went as far as to conclude a secret pact with Palestinian terrorists, to avoid terror acts on the Peninsula in exchange for some freedom of action. And in the mid-eighties the Craxi government did not hesitate to challenge the US in order to guarantee the continuity of that line of conduct. On that occasion Craxi, speaking in Parliament, compared Arafat to Mazzini. The end of the Yalta-established order has modified the traditional data of Italian foreign policy. However, the increased attention paid to Israel has also other causes: the changed attitude of the Church after the civil war and the Syrian occupation in Lebanon, events which both caused difficulties for the consistent Christian minorities; the hope that the Oslo process could reward the Italian ‘clear-sightedness’; last, but not least, the quarrelsome internal politics that make the Palestine conflict a mirror of the Roman conflicts. Lastly, the article connects the recent goodwill for Israel with the threats of Islamic terrorism in Italy. A political opinion trend would revisit the Middle Eastern conflict as the upturned perspective of a ‘clash of civilizations’ already existent nowadays. And a possible act of terrorism in Italy might give to this opinion a mass basis.
Addressing ‘the People’: A Comparative Study of the Lega Nord's and Lega dei Ticinesi's Political Rhetoric and Styles of Propaganda
Authors: Albertazzi Daniele
Published: November 2007

In recent years two populist regionalist parties have emerged in the alpine region, the Lega dei Ticinesi (LDT) in Switzerland and the Lega Nord (LN) in Italy. However, while typical populist themes such as the constant attacks against professional politicians and appeals to the ‘people’ resonate in the rhetoric of both movements, what differentiates them is the style of their propaganda, as the LDT's paper, Il Mattino della Domenica, constantly strives to shock its readers in ways that are alien to the Italian leghisti. Following a discussion of the strength, organisation and rhetoric of the two parties, this articles addresses the reasons why they have adopted different strategies of communication by considering the parties’ constituencies, the nature of their media and the personalities of their leaders.
Red Brigades (1969–1974): An Italian Phenomenon and a Product of the Cold War
Authors: Bartali Roberto
Published: November 2007

With the removal of Khrushchev in 1964 the Soviet Union adopted—at the level of the secret service—a more aggressive policy towards western countries, with a more intensive recourse to so-called ‘covert operations’. These operations regarded even western communist parties, such as the Italian Communist Party (PCI), which were close to being viewed as ‘orthodox’ by the Soviet leadership. The so-called ‘active measures’ which resulted were realised through the infiltration of agents, the training of (usually young) extremists, and (through them) the sending of warnings to the PCI leadership about its divergence from the Soviet line. This context helps us to understand better than before three key events of the years 1968–1973: the emergence of the first terrorist groups in Italy (the Partisans Action Groups and the Red Brigades); the bombing of the electric mains line where Giangiacomo Feltrinelli lost his life; and the car crash in which Enrico Berlinguer was involved in 1973 during an official visit to Bulgaria. An analysis of the Cold War context in which Italian terrorism (and specifically the Red Brigades) developed reveals origins and patterns that are different to those usually identified in the literature.
A viral CTL escape mutation leading to immunoglobulin-like transcript 4–mediated functional inhibition of myelomonocytic cells
Authors: Lichterfeld Mathias , Kavanagh Daniel G. , Williams Katie L. , Moza Beenu , Mui Stanley K. , Miura ToshiYuki , Sivamurthy Rohini , Allgaier Rachel , Pereyra Florencia , Trocha Alicja , Feeney Margaret , Gandhi Rajesh T. , Rosenberg Eric S. , Altfeld Marcus , Allen Todd M. , Allen Rachel , Walker Bruce D. , Sundberg Eric J. , Yu Xu G.
Published: November 2007

Viral mutational escape can reduce or abrogate recognition by the T cell receptor (TCR) of virus-specific CD8+ T cells. However, very little is known about the impact of cytotoxic T lymphocyte (CTL) epitope mutations on interactions between peptide–major histocompatibility complex (MHC) class I complexes and MHC class I receptors expressed on other cell types. Here, we analyzed a variant of the immunodominant human leukocyte antigen (HLA)-B2705–restricted HIV-1 Gag KK10 epitope (KRWIILGLNK) with an L to M amino acid substitution at position 6 (L6M), which arises as a CTL escape variant after primary infection but is sufficiently immunogenic to elicit a secondary, de novo HIV-1–specific CD8+ T cell response with an alternative TCR repertoire in chronic infection. In addition to altering recognition by HIV-1–specific CD8+ T cells, the HLA-B2705–KK10 L6M complex also exhibits substantially increased binding to the immunoglobulin-like transcript (ILT) receptor 4, an inhibitory MHC class I–specific receptor expressed on myelomonocytic cells. Binding of the B2705–KK10 L6M complex to ILT4 leads to a tolerogenic phenotype of myelomonocytic cells with lower surface expression of dendritic cell (DC) maturation markers and co-stimulatory molecules. These data suggest a link between CTL-driven mutational escape, altered recognition by innate MHC class I receptors on myelomonocytic cells, and functional impairment of DCs, and thus provide important new insight into biological consequences of viral sequence diversification.
Clustering of change patterns using Fourier coefficients
Authors: Kim Jaehee , Kim Haseong
Published: November 2007

Motivation: To understand the behavior of genes, it is important to explore how the patterns of gene expression change over a time period because biologically related gene groups can share the same change patterns. Many clustering algorithms have been proposed to group observation data. However, because of the complexity of the underlying functions there have not been many studies on grouping data based on change patterns. In this study, the problem of finding similar change patterns is induced to clustering with the derivative Fourier coefficients. The sample Fourier coefficients not only provide information about the underlying functions, but also reduce the dimension. In addition, as their limiting distribution is a multivariate normal, a model-based clustering method incorporating statistical properties would be appropriate.

Results: This work is aimed at discovering gene groups with similar change patterns that share similar biological properties. We developed a statistical model using derivative Fourier coefficients to identify similar change patterns of gene expression. We used a model-based method to cluster the Fourier series estimation of derivatives. The model-based method is advantageous over other methods in our proposed model because the sample Fourier coefficients asymptotically follow the multivariate normal distribution. Change patterns are automatically estimated with the Fourier representation in our model. Our model was tested in simulations and on real gene data sets. The simulation results showed that the model-based clustering method with the sample Fourier coefficients has a lower clustering error rate than K-means clustering. Even when the number of repeated time points was small, the same results were obtained. We also applied our model to cluster change patterns of yeast cell cycle microarray expression data with alpha-factor synchronization. It showed that, as the method clusters with the probability-neighboring data, the model-based clustering with our proposed model yielded biologically interpretable results. We expect that our proposed Fourier analysis with suitably chosen smoothing parameters could serve as a useful tool in classifying genes and interpreting possible biological change patterns.

Availability: The R program is available upon the request.

Contact:  jaehee@duksung.ac.kr

Supplementary information: Supplementary data are available at Bioinformatics online.
Straightening Caenorhabditis elegans images
Authors: Peng Hanchuan , Long Fuhui , Liu Xiao , Kim Stuart K. , Myers Eugene W.
Published: November 2007

Motivation:  Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must ‘straighten’ the worms if they are to be compared under a canonical coordinate system.

Results: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a ‘backbone’ that models the anterior–posterior axis of the worm. We formulate the backbone as a parametric cubic spline defined by a series of control points. We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images.

Contact:  pengh@janelia.hhmi.org

Supplementary information: The example data sets and programs are available upon request.
The consumption of zooplankton by early life stages of fish in the North Sea
Authors: Heath Michael R.
Published: November 2007

Heath, M. R. 2007. The consumption of zooplankton by early life stages of fish in the North Sea. – ICES Journal of Marine Science, 64: 1650–1663. Previous work has shown that during the 1970s, fish and carnivorous macrozooplankton together consumed ∼22 gC m−2 year−1 of mesozooplankton, principally copepods. Consumption declined to ∼17 gC m−2 year−1 during the 1990s, mainly because of a reduction in fish production. The zooplankton production required to meet this demand seems to be approximately accounted for by estimates of new primary production, but there are additional sinks for zooplankton production attributable to predation by, for example, gelatinous species. Additionally, the consumption of zooplankton by early life stages of fish is difficult to assess and could be larger than implied by the earlier analysis. Here, the role of fish early life stages in zooplankton consumption is re-assessed, and found to be approximately double that previously estimated. Some 28% of the zooplankton consumption by fish is now estimated to be attributable to early life stages, resulting in an estimate of zooplankton consumption by the fish community as a whole 14% higher. Taken overall, the consumption of zooplankton production by fish and other planktivorous predators is now estimated to be 19–25 gC m−2 year−1.
Cyclotron resonance of electrons and holes in graphene monolayers
Authors: Chuang Kai-Chieh , Deacon Russell S , Nicholas Robin J , Novoselov Kostya S , Geim Andre K
Published: November 2007

We report studies of cyclotron resonance in monolayer graphene. Cyclotron resonances are detected by observing changes in the photoconductive response of the sample. An electron velocity at the Dirac point of 1.093×10
6
 m s
−1
is obtained, which is the fastest velocity recorded for all known carbon materials. In addition, a significant asymmetry exists between band structure for electrons and holes, which gives rise to a 5% difference between the velocities at energies of 125 meV away from the Dirac point.
Genomics, transcriptomics, and peptidomics of neuropeptides and protein hormones in the red flour beetle Tribolium castaneum
Authors: Li Bin , Predel Reinhard , Neupert Susanne , Hauser Frank , Tanaka Yoshiaki , Cazzamali Giuseppe , Williamson Michael , Arakane Yasuyuki , Verleyen Peter , Schoofs Liliane , Schachtner Joachim , Grimmelikhuijzen Cornelis J.P. , Park Yoonseong
Published: November 2007

Neuropeptides and protein hormones are ancient molecules that mediate cell-to-cell communication. The whole genome sequence from the red flour beetle Tribolium castaneum, along with those from other insect species, provides an opportunity to study the evolution of the genes encoding neuropeptide and protein hormones. We identified 41 of these genes in the Tribolium genome by using a combination of bioinformatic and peptidomic approaches. These genes encode >80 mature neuropeptides and protein hormones, 49 peptides of which were experimentally identified by peptidomics of the central nervous system and other neuroendocrine organs. Twenty-three genes have orthologs in Drosophila melanogaster: Sixteen genes in five different groups are likely the result of recent gene expansions during beetle evolution. These five groups contain peptides related to antidiuretic factor-b (ADF-b), CRF-like diuretic hormone (DH37 and DH47 of Tribolium), adipokinetic hormone (AKH), eclosion hormone, and insulin-like peptide. In addition, we found a gene encoding an arginine-vasopressin-like (AVPL) peptide and one for its receptor. Both genes occur only in Tribolium and not in other holometabolous insects with a sequenced genome. The presence of many additional osmoregulatory peptides in Tribolium agrees well with its ability to live in very dry surroundings. In contrast to these extra genes, there are at least nine neuropeptide genes missing in Tribolium, including the genes encoding the prepropeptides for corazonin, kinin, and allatostatin-A. The cognate receptor genes for these three peptides also appear to be absent in the Tribolium genome. Our analysis of Tribolium indicates that, during insect evolution, genes for neuropeptides and protein hormones are often duplicated or lost.
Genomic architecture and inheritance of human ribosomal RNA gene clusters
Authors: Stults Dawn M. , Killen Michael W. , Pierce Heather H. , Pierce Andrew J.
Published: November 2007

The finishing of the Human Genome Project largely completed the detailing of human euchromatic sequences; however, the most highly repetitive regions of the genome still could not be assembled. The 12 gene clusters producing the structural RNA components of the ribosome are critically important for cellular viability, yet fall into this unassembled region of the Human Genome Project. To determine the extent of human variation in ribosomal RNA gene content (rDNA) and patterns of rDNA cluster inheritance, we have determined the physical lengths of the rDNA clusters in peripheral blood white cells of healthy human volunteers. The cluster lengths exhibit striking variability between and within human individuals, ranging from 50 kb to >6 Mb, manifest essentially complete heterozygosity, and provide each person with their own unique rDNA electrophoretic karyotype. Analysis of these rDNA fingerprints in multigenerational human families demonstrates that the rDNA clusters are subject to meiotic rearrangement at a frequency >10% per cluster, per meiosis. With this high intrinsic recombinational instability, the rDNA clusters may serve as a unique paradigm of potential human genomic plasticity.
Solution structure of the region 51–160 of human KIN17 reveals an atypical winged helix domain
Authors: Carlier Ludovic , Couprie Joël , le Maire Albane , Guilhaudis Laure , Milazzo‐Segalas Isabelle , Courçon Marie , Moutiez Mireille , Gondry Muriel , Davoust Daniel , Gilquin Bernard , Zinn‐Justin Sophie
Published: November 2007

Human KIN17 is a 45‐kDa eukaryotic DNA‐ and RNA‐binding protein that plays an important role in nuclear metabolism and in particular in the general response to genotoxics. Its amino acids sequence contains a zinc finger motif (residues 28–50) within a 30‐kDa N‐terminal region conserved from yeast to human, and a 15‐kDa C‐terminal tandem of SH3‐like subdomains (residues 268–393) only found in higher eukaryotes. Here we report the solution structure of the region 51–160 of human KIN17. We show that this fragment folds into a three‐α‐helix bundle packed against a three‐stranded β‐sheet. It belongs to the winged helix (WH) family. Structural comparison with analogous WH domains reveals that KIN17 WH module presents an additional and highly conserved 310‐helix. Moreover, KIN17 WH helix H3 is not positively charged as in classical DNA‐binding WH domains. Thus, human KIN17 region 51–160 might rather be involved in protein–protein interaction through its conserved surface centered on the 310‐helix.
Characterization of substrate binding and catalysis in the potential antibacterial target N‐acetylglucosamine‐1‐phosphate uridyltransferase (GlmU)
Authors: Mochalkin Igor , Lightle Sandra , Zhu Yaqi , Ohren Jeffrey F. , Spessard Cindy , Chirgadze Nickolay Y. , Banotai Craig , Melnick Michael , McDowell Laura
Published: November 2007

N‐Acetylglucosamine‐1‐phosphate uridyltransferase (GlmU) catalyzes the first step in peptidoglycan biosynthesis in both Gram‐positive and Gram‐negative bacteria. The products of the GlmU reaction are essential for bacterial survival, making this enzyme an attractive target for antibiotic drug discovery. A series of Haemophilus influenzae GlmU (hiGlmU) structures were determined by X‐ray crystallography in order to provide structural and functional insights into GlmU activity and inhibition. The information derived from these structures was combined with biochemical characterization of the K25A, Q76A, D105A, Y103A, V223A, and E224A hiGlmU mutants in order to map these active‐site residues to catalytic activity of the enzyme and refine the mechanistic model of the GlmU uridyltransferase reaction. These studies suggest that GlmU activity follows a sequential substrate‐binding order that begins with UTP binding noncovalently to the GlmU enzyme. The uridyltransferase active site then remains in an open apo‐like conformation until N‐acetylglucosamine‐1‐phosphate (GlcNAc‐1‐P) binds and induces a conformational change at the GlcNAc‐binding subsite. Following the binding of GlcNAc‐1‐P to the UTP‐charged uridyltransferase active site, the non‐esterified oxygen of GlcNAc‐1‐P performs a nucleophilic attack on the α‐phosphate group of UTP. The new data strongly suggest that the mechanism of phosphotransfer in the uridyltransferase reaction in GlmU is primarily through an associative mechanism with a pentavalent phosphate intermediate and an inversion of stereochemistry. Finally, the structural and biochemical characterization of the uridyltransferase active site and catalytic mechanism described herein provides a basis for the structure‐guided design of novel antibacterial agents targeting GlmU activity.
Therapeutic alliance, patient behaviour and dropout in a drug rehabilitation programme: the moderating effect of clinical subpopulations
Authors: Cournoyer Louis‐Georges , Brochu Serge , Landry Michel , Bergeron Jacques
Published: November 2007

Aim Treatment dropout is an important concern for professionals working in mental health. While this problem is common, the highest attrition rates have been observed in drug rehabilitation programmes. The present study focuses on the therapeutic alliance, a process variable that has been associated repeatedly with positive treatment outcome in the scientific literature. Respondent behaviour indicative of commitment or resistance to treatment was examined in combination with therapist prognoses.

Design A total of 248 subjects, classified into three subpopulations (justice,n = 50; mental health,n = 53; comparison group,n = 145), participated in the study. Analyses aimed at predicting dropout were conducted using Cox proportional‐hazards regressions. The moderating effect of sub‐population was tested.

Measurements Respondents completed a multi‐dimensional measure of alliance [California Psychotherapeutic Alliance Scale (CALPAS‐P)]. Therapists rated the behaviour of respondents in treatment and made prognoses about perseverance and improvement.

Findings An increased risk of dropout was predicted when patients viewed themselves as less committed and perceived the therapist as less understanding and less involved. Therapist prognosis of perseverance was also predictive of dropout. The relationship between patient/therapist evaluations and dropout is affected differently across subpopulations by means of a moderation effect.

Conclusion This paper demonstrates the capacity to predict dropout by measuring therapeutic alliance, therapist prognoses and therapist appraisal of patient behaviour. Moreover, the moderation effect of clinical subpopulation on treatment process variables and dropout is supported in the context of drug rehabilitation programmes.
Papain‐like cysteine proteases: key players at molecular battlefields employed by both plants and their invaders
Authors: SHINDO TAKAYUKI , VAN DER HOORN RENIER A. L.
Published: November 2007

Papain‐like cysteine proteases (PLCPs) play crucial roles in plant–pathogen/pest interactions. During these parasitic interactions, PLCPs act on non‐self substrates, provoking the selection of counteracting inhibitors and other means to evade proteolysis. We review examples of PLCPs acting on molecular battlefields in the extracellular space, plant cytoplasm and herbivore gut. Examples are maize Mir1 (Maize inbred resistance 1), tomato Rcr3 (Required for Cladosporium resistance‐3), Pseudomonas AvrRpt2 and AurPphB, insect DvCAL1 (Diabrotica virgifera cathepsin L‐like protease‐1) and nematode MiCpl1 (Meloidogyne incognita cathepsin L‐like protease 1). The data suggest that PLCPs cleave specific proteins and that their translocation, activation and inhibition of PLCPs are tightly regulated.
Investigation of X‐ and Y‐specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle
Authors: Anderung C. , Hellborg L. , Seddon J. , Hanotte O. , Götherström A.
Published: November 2007

Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X‐chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y‐chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X‐chromosome individuals, recombinant X‐chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.
Association of a single‐nucleotide substitution in TYRP1 with roux in Japanese quail (Coturnix japonica)
Authors: Nadeau N. J. , Mundy N. I. , Gourichon D. , Minvielle F.
Published: November 2007

We investigated TYRP1 as a candidate locus for the recessive, sex‐linked roux (brr) phenotype in Japanese quail. A screen of the entire coding sequence of TYRP1 in roux and wild‐type quail revealed a non‐synonymous T‐to‐C substitution in exon 3, leading to a Phe282Ser mutation. This was perfectly associated with plumage phenotype: all roux birds were homozygous for Ser282. Co‐segregation of the Phe282Ser mutation with the roux phenotype was confirmed in three brr/BR+ × brr/– backcrosses. We found no significant difference in TYRP1 expression between roux and wild‐type birds, suggesting that this association is not due to linkage disequilibrium with an unknown regulatory mutation. In addition, the Phe282 amino acid appears to be of functional significance, as it is highly conserved across the vertebrates. This is the first demonstration that TYRP1 has a role in pigmentation in birds.
Bone marrow microvessel density in chronic myeloproliferative disorders: a study of 115 patients with clinicopathological and molecular correlations
Authors: Boveri Emanuela , Passamonti Francesco , Rumi Elisa , Pietra Daniela , Elena Chiara , Arcaini Luca , Pascutto Cristiana , Castello Alessandro , Cazzola Mario , Magrini Umberto , Lazzarino Mario
Published: November 2007

Philadelphia‐negative chronic myeloproliferative disorders (CMD) include polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF). Angiogenesis is critical in the pathogenesis of PMF. We studied angiogenesis in 115 patients with CMD (23 PV, 24 ET, 46 PMF, 12 post‐PV and 10 post‐ET myelofibrosis) by assessment of microvessel density (MVD) in bone marrow (BM). Kruskall–Wallis analysis of variance showed that patients with PMF had significantly higher values of MVD than those with PV (P < 0·001), ET (P < 0·001) and controls (P < 0·001). Mann–Whitney U‐test demonstrated that patients with PMF at the prefibrotic stage had significantly higher MVD values than those with ET (P = 0·02). Patients with post‐PV myelofibrosis showed significantly higher MVD values than those with PV (P < 0·001), as did patients with post‐ET myelofibrosis compared with ET (P < 0·001). In patients with CMD, the multivariate generalized linear regression model showed that the JAK2 (V617F) mutational burden (P = 0·01), serum lactate dehydrogenase level (P = 0·003), and anaemia (P < 0·001) independently correlated with MVD. In summary, this study indicates that assessment of BM angiogenesis, as measured by MVD, may be a useful additional tool in the histopathological definition of CMD.
Serum lactate dehydrogenase activity as a biomarker in children with sickle cell disease
Authors: O’Driscoll Sandra , Height Susan E. , Dick Moira C. , Rees David C.
Published: November 2007

Serum lactate dehydrogenase (LDH) levels were studied in children with HbSS and HbSC in a single institution, and their relationship to cerebral vasculopathy as assessed by transcranial Doppler scanning (TCD). All children with HbSS (n = 97) and HbSC (n = 18) who underwent a TCD scan in 2006 were studied. LDH levels were higher in HbSS patients than HbSC (581 IU/l vs. 305 IU/l, P < 0·001). In children with HbSS, LDH correlated significantly with haemoglobin, reticulocytes, aspartate transaminase and creatinine. LDH also correlated positively and significantly with TCD measurements in the middle and anterior cerebral artery circulations in the children with HbSS.
Parenting and children's cardiovascular functioning
Authors: Bell B. G. , Belsky J.
Published: November 2007

Objectives  To test the hypothesis that more supportive/less negative parenting is associated with lower resting blood pressure and heart rates in children and to determine whether parent and/or child gender and developmental stage moderate the relations in question.

Design  Longitudinal data on 835 children/families who participated in the National Institute of Child Health and Human Development Study of Early Child Care and Youth Development were analysed. Children (one per family) were followed from age 1 month to 11 years.

Methods  Data were collected from children and their families via interviews, observations of parent–child interaction and physical health assessments.

Results  Correlations show that more supportive and less negative parenting prior to kindergarten entry (∼5 years) are associated with lower heart rates and blood pressure in children of primary school grades 4–6 (∼9 to 11 years), especially in the case of fathering, sons and parenting during the pre‐school years.

Conclusions  Such findings raise the prospect that interventions to enhance parenting, especially the early fathering of sons, may have beneficial effects on children's cardiovascular functioning. The inability to discount genetic mediation of parenting effects makes it clear that behaviour‐genetic and/or experimental research is needed to document cause and effect relations.
Administration of medicines to children using sports and leisure facilities: a survey of the South West of England
Authors: Bedwani S. , Baverstock A. , Finlay F.
Published: November 2007

Background  It is widely recognized that a healthy diet and regular exercise are important for general health. Sports and leisure centres are providing many opportunities for children to participate in various activities.

Methods  A pre‐piloted questionnaire was sent to the manager of sports and leisure centres throughout the South West of England to look at provision for the administration and storage of medication.

Results  Response rate is 66%. While 91% of centres have sessions for children without a parent present, only 57% had a policy for administration of medication.

Conclusion  Despite clear guidance on administration of medicine being available, relatively few sports and leisure facilities we surveyed are currently operating within this framework. At present, the current practice regarding administration of medicine in many leisure facilities seems to be suboptimal.
Interrelationship among selected measures of motor skills
Authors: Haga M. , Pedersen A. V. , Sigmundsson H.
Published: November 2007

Background This study set out to explore the interrelationship among selected measures of motor skills.

Methods Ninety‐one 4‐year‐old children from 10 nursery schools were tested using eight motor tasks from the Movement Assessment Battery for Children test.

Results The most striking finding was that there were very low correlations between the motor tasks.

Conclusions In relation to these findings, it is possible to argue that learning of particular motor skills is specific to that task. This is discussed in relation to the principle of task specificity of learning.
The immune system in healthy adults and patients with atopic dermatitis seems to be affected differently by a probiotic intervention
Authors: Roessler (nee Klein) A. , Friedrich U. , Vogelsang H. , Bauer A. , Kaatz M. , Hipler U. C. , Schmidt I. , Jahreis G.
Published: November 2007

Background
Probiotic bacteria are proposed to alleviate atopic dermatitis (AD) in infants. There are few indications about the effect of probiotics on AD in adults.

Objective
The purpose of this study was to elucidate the influence of a probiotic drink containing a combination of the probiotics Lactobacillus paracasei Lpc‐37, Lactobacillus acidophilus 74‐2 and Bifidobacterium animalis subsp. lactis DGCC 420 (B. lactis 420) in healthy volunteers and in patients with AD on clinical and immunological parameters and their detection in feces.

Methods
A double‐blind, placebo‐controlled, randomized cross‐over study was conducted in 15 healthy adults and 15 patients with AD. The probiotic product or placebo was given over 8 weeks. A 2‐week washout period was interconnected before the intervention was crossed. At the end of each period, blood and stool samples were collected. In patients, the severity of AD was evaluated using the Scoring of Atopic Dermatitis (SCORAD).

Results
L. paracasei and B. lactis were recovered in high numbers in feces after supplementation, whereas L. acidophilus marginally increased. In patients, the SCORAD tended to decrease by 15.5% (P=0.081). Major lymphocyte subsets were not affected by the probiotic intervention. However, CD57+ increased significantly (P=0.034) in healthy subjects after probiotic intake and was not changed in patients, whereas CD4+CD54+ decreased significantly (P=0.031) in patients with AD and remained uninfluenced in healthy subjects. The expression of CD4+CD25+ T cells was similar in healthy subjects and AD patients. The phagocytic activity of monocytes and granulocytes was significantly increased in healthy subjects after probiotic intervention (P=0.014).

Conclusion
L. paracasei Lpc‐37 and B. lactis 420 are able to colonize the intestine transiently. This study reveals that the probiotics differently modulate peripheral immune parameters in healthy subjects and patients with AD.
Interaction of suplatast tosilate (IPD) with chloride channels in human blood eosinophils: a potential mechanism underlying its anti‐allergic and anti‐asthmatic effects
Authors: Agrawal D. K. , Cheng G. , Kim M.‐J. , Kiniwa M.
Published: November 2007

Introduction
Alterations in chloride ion channels have been implicated in the induction of changes in cell shape and volume. Because blood and tissue eosinophilia are hallmarks of bronchial asthma, in this study we examined the role of chloride channels in the underlying effects of suplatast tosilate (IPD), an anti‐allergic drug, in human blood eosinophils.

Methods
Eosinophils were isolated and purified from the blood of allergic asthmatic donors. Chloride ion currents were recorded using the whole‐cell patch‐clamp technique in freshly isolated eosinophils. The current–voltage relationship of whole‐cell currents in human blood eosinophils was calculated and recorded. The effect of chloride channel blockers was examined on superoxide release, eosinophil chemotaxis as measured by the Boyden chamber, and eosinophil adhesion to endothelial cells. Radioligand binding studies with [3H]IPD and competition curves with chloride channel blockers were performed.

Results
IPD increased both inward and outward chloride currents in human blood eosinophils. IPD in 1 ng/mL did not have significant effect on chloride current. However, at 5 ng/mL IPD activated both outward and inward currents in human blood eosinophils. Chloride channel blockers inhibited IPD‐induced respiratory burst in eosinophils, eosinophil chemotaxis, and eosinophil adhesion to endothelial cells. All these effects of IPD on chloride current and the resultant functional responses in human blood eosinophils were not due to its basic salt, p‐toluenesulphonic acid monohydrate. Human blood eosinophils contained specific binding sites for [3H]IPD with KD and Bmax values of 187.7±105.8 nm and 58.7±18.7 fmol/106 cells, respectively. Both NPPB and DIDS competed, in a dose‐dependent manner, for the specific binding of [3H]IPD in human blood eosinophils.

Conclusion
These data suggest that the anti‐allergic and anti‐asthmatic effects of IPD could be due to its interaction with chloride channels in human blood eosinophils.