bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling shellfish growth with dynamic energy budget models: an application for cockles and mussels in the Oosterschelde (southwest Netherlands)
Authors: Troost T. A. , Wijsman J. W. M. , Saraiva S. , Freitas V.
Published: September 2010

Dynamic energy budget models for growth of individual cockles (
Cerastoderma edule
) and mussels (
Mytilus edulis
) are adjusted and calibrated to the Oosterschelde by formulating and parametrizing their functional responses using an extensive set of field observations. The resulting model predictions fit the observations satisfactorily. Results indicate that food quality and the importance of detritus as a food source are site-specific as well as species-specific. Despite these differences in their calibrated parameter values, both species show a very similar functional response. Compared with other systems, however, the functional responses of mussels in the present study are clearly higher than those of mussels in other systems. This may be explained by the absence of intra-specific competition in the measurement set-up that was used, and therefore supports the idea that the generally small functional response of
M. edulis
is caused by intra-specific competition.
The impact of metabolism on stable isotope dynamics: a theoretical framework
Authors: Pecquerie Laure , Nisbet Roger M. , Fablet Ronan , Lorrain Anne , Kooijman Sebastiaan A. L. M.
Published: September 2010

Stable isotope analysis is a powerful tool used for reconstructing individual life histories, identifying food-web structures and tracking flow of elemental matter through ecosystems. The mechanisms determining isotopic incorporation rates and discrimination factors are, however, poorly understood which hinders a reliable interpretation of field data when no experimental data are available. Here, we extend dynamic energy budget (DEB) theory with a limited set of new assumptions and rules in order to study the impact of metabolism on stable isotope dynamics in a mechanistic way. We calculate fluxes of stable isotopes within an organism by following fluxes of molecules involved in a limited number of macrochemical reactions: assimilation, growth but also structure turnover that is here explicitly treated. Two mechanisms are involved in the discrimination of isotopes: (i) selection of
molecules
occurs at the partitioning of assimilation, growth and turnover into anabolic and catabolic sub-fluxes and (ii) reshuffling of
atoms
occurs during transformations. Such a framework allows for isotopic routing which is known as a key, but poorly studied, mechanism. As DEB theory specifies the impact of environmental conditions and individual state on molecule fluxes, we discuss how scenario analysis within this framework could help reveal common mechanisms across taxa.
Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories
Authors: Vinga S. , Neves A. R. , Santos H. , Brandt B. W. , Kooijman S. A. L. M.
Published: September 2010

The dynamic modelling of metabolic networks aims to describe the temporal evolution of metabolite concentrations in cells. This area has attracted increasing attention in recent years owing to the availability of high-throughput data and the general development of systems biology as a promising approach to study living organisms. Biochemical Systems Theory (BST) provides an accurate formalism to describe biological dynamic phenomena. However, knowledge about the molecular organization level, used in these models, is not enough to explain phenomena such as the driving forces of these metabolic networks. Dynamic Energy Budget (DEB) theory captures the quantitative aspects of the organization of metabolism at the organism level in a way that is non-species-specific. This imposes constraints on the sub-organismal organization that are not present in the bottom-up approach of systems biology. We usein vivodata of lactic acid bacteria under various conditions to compare some aspects of BST and DEB approaches. Due to the large number of parameters to be estimated in the BST model, we applied powerful parameter identification techniques. Both models fitted equally well, but the BST model employs more parameters. The DEB model uses similarities of processes under growth and no-growth conditions and under aerobic and anaerobic conditions, which reduce the number of parameters. This paper discusses some future directions for the integration of knowledge from these two rich and promising areas, working top-down and bottom-up simultaneously. This middle-out approach is expected to bring new ideas and insights to both areas in terms of describing how living organisms operate.
Dynamic energy budget theory restores coherence in biology
Authors: Sousa Tânia , Domingos Tiago , Poggiale J.-C. , Kooijman S. A. L. M.
Published: September 2010

We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
Authors: Murat Florent , Xu Jian-Hong , Tannier Eric , Abrouk Michael , Guilhot Nicolas , Pont Caroline , Messing Joachim , Salse Jérôme
Published: September 2010

The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms leading to mosaic synteny blocks have been lacking due to relevant examples of evolutionary zooms from genomic sequences. Such studies require genomes of species that belong to the same family but are diverged to fall into different subfamilies. Our most important crops belong to the family of the grasses, where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5–12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes, representing three different subfamilies and different polyploidization events. By focusing on these sequence intervals, we could show that the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events. It appeared that the centromeric/telomeric illegitimate recombination between nonhomologous chromosomes led to nested chromosome fusions (NCFs) and synteny break points (SBPs). When intervals comprising NCFs were compared in their structure, we concluded that SBPs (1) were meiotic recombination hotspots, (2) corresponded to high sequence turnover loci through repeat invasion, and (3) might be considered as hotspots of evolutionary novelty that could act as a reservoir for producing adaptive phenotypes.
Algorithms for the calculation of X-ray diffraction patterns from finite element data
Authors: Wintersberger E. , Kriegner D. , Hrauda N. , Stangl J. , Bauer G.
Published: September 2010

A set of algorithms is presented for the calculation of X-ray diffraction patterns from strained nanostructures. Their development was triggered by novel developments in the recording of scattered intensity distributions as well as in simulation practice. The increasing use of two-dimensional CCD detectors in X-ray diffraction experiments, with which three-dimensional reciprocal-space maps can be recorded in a reasonably short time, requires efficient simulation programs to compute one-, two- and three-dimensional intensity distributions. From the simulation point of view, the finite element method (FEM) has become the standard tool for calculation of the strain and displacement fields in nanostructures. Therefore, X-ray diffraction simulation programs must be able to handle FEM data properly. The algorithms presented here make use of the deformation fields calculated on a mesh, which are directly imported into the calculation of diffraction patterns. To demonstrate the application of the developed algorithms, they were applied to several examples such as diffraction data from a dislocated quantum dot, from a periodic array of dislocations in a PbSe epilayer grown on a PbTe pseudosubstrate, and from ripple structures at the surface of SiGe layers deposited on miscut Si substrates.
Interesting growth features in potassium dihydrogen phosphate: unravelling the origin and dynamics of point defects in single crystals
Authors: Bhagavannarayana G. , Rajesh P. , Ramasamy P.
Published: September 2010

In a potassium dihydrogen phosphate single crystal grown by the temperature-lowering technique, some interesting growth features revealing the origin of point defects, their agglomeration and dynamics were observed. High-resolution X-ray diffractometry was employed for in-depth studies of the observed defects. Since the crucial properties of crystal-based devices are very much influenced by such defects, this is an important experimental finding with respect to improving growth techniques or conditions to avoid such defects.
Determination of twinning relationships between diopside dendrites
Authors: Zhao Shan-Rong , Xu Hai-Jun , Liu Hong-Wei , Mason Roger , Liu Hui-Fang
Published: September 2010

Electron backscattered diffraction, used to determine the orientations of dendritic crystals of synthetic diopside, revealed novel twinning relationships between three dendrite crystals. The three crystals, considered pairwise, are related by two twinning laws: for two pairs, twin plane {\overline 251} and twin axis 〈\overline 142〉 perpendicular to the twin plane; and for the third pair, twin plane {\overline 221} and twin axis 〈\overline 356〉 perpendicular to the twin plane. The twin axes and twin planes between the latter pair of crystals closely match the twofold axis and symmetry plane inside the third crystal. The distribution of the three dendrite crystals in the twin structure shows overall 2/msymmetry, so the point group of diopside controls the whole combination of three crystals. The twin laws have been analysed using the theories of Mallard and Friedel, and twin indices and twin obliquity calculated. The complex twin laws yield a good lattice coincidence, and lattice relationship analysis based on the {201} plane confirms the twin laws.
Analysis of the Beaucage model
Authors: Hammouda Boualem
Published: September 2010

The Beaucage model is used to analyze small-angle scattering (SAS) data from fractal and particulate systems. It models the Guinier and Porod regions with a smooth transition between them and yields a radius of gyration and a Porod exponent. This model is an approximate form of an earlier polymer fractal model that has been generalized to cover a wider scope. The practice of allowing both the Guinier and the Porod scale factors to vary independently during nonlinear least-squares fits introduces undesired artefacts in the fitting of SAS data to this model. Such artefacts as well as an error in the original formulation of the model are discussed. This model is compared with other published models.
DART: a robust algorithm for fast reconstruction of three-dimensional grain maps
Authors: Batenburg K. J. , Sijbers J. , Poulsen H. F. , Knudsen E.
Published: September 2010

A novel algorithm is introduced for fast and nondestructive reconstruction of grain maps from X-ray diffraction data. The discrete algebraic reconstruction technique (DART) takes advantage of the intrinsic discrete nature of grain maps, while being based on iterative algebraic methods known from classical tomography. To test the properties of the algorithm, three-dimensional X-ray diffraction microscopy data are simulated and reconstructed with DART as well as by a conventional iterative technique, namely SIRT (simultaneous iterative reconstruction technique). For 100 × 100 pixel reconstructions and moderate noise levels, DART is shown to generate essentially perfect two-dimensional grain maps for as few as three projections per grain with running times on a PC in the range of less than a second. This is seen as opening up the possibility for fast reconstructions in connection within situstudies.
Scanning small-angle X-ray scattering analysis of the size and organization of the mineral nanoparticles in fluorotic bone using a stack of cards model
Authors: Gourrier Aurélien , Li Chenghao , Siegel Stefan , Paris Oskar , Roschger Paul , Klaushofer Klaus , Fratzl Peter
Published: September 2010

A model describing the size and arrangement of mineral particles in bone tissues is used to analyse the results of a scanning small-angle X-ray scattering (SAXS) experiment on a pathological bone biopsy. The overall description assumes that the nanometre-sized mineral platelets are arranged in a parallel fashion with possible fluctuations in their relative position, orientation and thickness. This method is tested on a thin sample section obtained from the biopsy of an osteoporotic patient treated with a high cumulative dose of NaF. The mineralization pattern of fluorotic bone is known to exhibit significant differences as compared to healthy bone in terms of density, particle size and organization. This is the first attempt to provide quantitative indicators of the degree of regularity in the packing of the mineral platelets in human pathological bone. Using scanning SAXS with a synchrotron microbeam of 15 µm allows discrimination between pathological and healthy bone at the tissue level. Additionally, the benefits of this method are discussed with respect to the accuracy of particle size determination using SAXS.
Hawk: the image reconstruction package for coherent X-ray diffractive imaging
Authors: Maia Filipe R. N. C. , Ekeberg Tomas , van der Spoel David , Hajdu Janos
Published: September 2010

The past few years have seen a tremendous growth in the field of coherent X-ray diffractive imaging, in large part due to X-ray free-electron lasers which provide a peak brilliance billions of times higher than that of synchrotrons. However, this rapid development in terms of hardware has not been matched on the software side. The release ofHawkis intended to close this gap. To the authors' knowledgeHawkis the first publicly available and fully open source software program for reconstructing images from continuous diffraction patterns. The software handles all steps leading from a raw diffraction pattern to a reconstructed two-dimensional image including geometry determination, background correction, masking and phasing. It also includes preliminary three-dimensional support and support for graphics processing units using the Compute Unified Device Architecture, which speeds up processing by orders of magnitude compared to a single central processing unit.Hawkimplements numerous algorithms and is easily extended. This, in combination with its open-source licence, provides a platform for other groups to test, develop and distribute their own algorithms.Hawkis available under the GNU General Public License from http://xray.bmc.uu.se/hawk.
There is an association between selective serotonin reuptake inhibitor use and uncomplicated peptic ulcers: a population‐based case–control study
Authors: Dall M. , Schaffalitzky de Muckadell O. B. , Lassen A. T. , Hallas J.
Published: September 2010

Aliment Pharmacol Ther 2010; 32: 1383–1391

Background  Persons who use serotonin reuptake inhibitors (SSRIs) seem to be at increased risk of having serious upper gastrointestinal bleeding. In vitro studies have shown that SSRIs inhibit platelet aggregation. It remains unknown if SSRIs have a direct ulcerogenic effect.

Aim  To investigate if there is a possible association between use of SSRIs and uncomplicated peptic ulcers.

Methods  A population‐based case–control study was conducted in the county of Funen, Denmark, using local prescription database and patient register. The 4862 cases all had a first diagnosis of uncomplicated peptic ulcers from 1995 to 2009. Controls (n = 19 448), matched for age and gender, were selected by risk‐set sampling.

Results  The adjusted odds ratios (OR) of uncomplicated peptic ulcers among current, recent and past users of SSRIs were 1.50 (95% CI 1.18–1.90), 1.56 (95% CI 0.98–2.49) and 1.32 (95% CI 1.08–1.61). There was no association with tricyclic antidepressants [OR 0.94 (95% CI 0.65‐1.35)]. The adjusted OR for the SSRI‐uncomplicated peptic ulcers association was 0.76 (95% CI 0.46–1.25) among users of proton pump inhibitors.

Conclusions  Use of SSRI is associated with uncomplicated peptic ulcers, possibly by some effect on the healing process. We cannot exclude some effects of residual confounding or bias by frequent physician contact.
The impact of a child protection investigation: a personal reflective account
Authors: Davies Pamela
Published: September 2010

Researchers who undertake parental perception studies agree that the views of the parents can offer valuable insights in relation to child protection work. Respondents to such studies and others who have shared their experiences of child protection investigations are usually mothers. Taken together, this body of work sheds light on some very private, emotive and often painful experiences of child protection intervention and its impact. This article lends my voice to this literature and gives further insight into the ways a mother can experience a child protection investigation. Drawing upon one incident – a swelling on a baby's head – this article draws attention to my feelings and emotions as the baby's mother. Despite a co‐operative social worker–client relationship and case closure, my analysis draws attention to issues concerning power imbalances and the concept of ‘secondary victimization’ to explain the awfulness of my experience and my convoluted emotional disquiet. The article proposes that more attention is directed to the negative feelings and emotions experienced during the investigative process through further research.
Relative down‐regulation of apoptosis and autophagy genes in colorectal cancer
Authors: Chang Ying‐Tse , Tseng Hsien‐Chun , Huang Chi‐Chou , Chen Ya‐Pei , Chiang Huei‐Ching , Chou Fen‐Pi
Published: September 2010

Eur J Clin Invest 2010; 41 (1): 84–92

Background  Cancer is often caused by disturbance in the regulation and/or execution of programmed cell death (PCD, including apoptosis and autophagy). Our aim was to investigate these two pathways simultaneously in the same samples to understand further the pathological roles of PCDs in colorectal cancer.

Materials and methods  Real time quantitative PCR (RT‐qPCR) array was used to analyse the mRNA levels of 22 apoptosis and autophagy‐related genes involved in pro‐ and anti‐action of the pathways in 15 paired (tumour and non‐cancerous part) colorectal samples using Glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) as the reference gene.

Results  GAPDH mRNA content was significantly higher (approximately 4·01 fold) in tumour tissue than that of paired non‐cancerous part. The absolute mRNA levels for most of the 22 genes were higher in the tumour tissue also. However, after normalization with GAPDH Ct, the expressions of all the analysed genes were decreased in the tumour tissues, except for damage‐regulated autophagy modulator (DRAM). The expression of most of the genes involved in the same pathway was closely correlated to each other in both tumour and non‐cancerous tissues, and the correlation of tumour necrosis factor receptor (TNFR) and Akt to other genes in the same pathway was increased in tumour tissues.

Conclusions  The high level expression of GAPDH might reflect the metabolic state of cancer cells, and PCDs were down‐regulated in the tumour tissues when metabolic state was taken into consideration. This relative suppression of PCDs in tumour tissue is supposed to be in favour of cancer cell survival.
Ecological genetics and genomics of plant defences: evidence and approaches
Authors: Anderson Jill T. , Mitchell‐Olds Thomas
Published: September 2010

1. Herbivores exert significant selection on plants, and plants have evolved a variety of constitutive and inducible defences to resist and tolerate herbivory. Assessing the genetic mechanisms that influence defences against herbivores will deepen our understanding of the evolution of essential phenotypic traits.

2. Ecogenomics is a powerful interdisciplinary approach that can address fundamental questions about the ecology and evolutionary biology of species, such as: which evolutionary forces maintain variation within a population? and What is the genetic architecture of adaptation? This field seeks to identify gene regions that influence ecologically important traits, assess the fitness consequences under natural conditions of alleles at key quantitative trait loci (QTLs), and test how the abiotic and biotic environment affects gene expression.

3. Here, we review ecogenomics techniques and emphasize how this framework can address long‐standing and emerging questions relating to anti‐herbivore defences in plants. For example, ecogenomics tools can be used to investigate: inducible vs. constitutive defences; tradeoffs between resistance and tolerance; adaptation to the local herbivore community; selection on alleles that confer resistance and tolerance in natural populations; and whether different genes are activated in response to specialist vs. generalist herbivores and to different types of damage.

4. Ecogenomic studies can be conducted with model species, such as Arabidopsis, or their relatives, in which case myriad molecular tools are already available. Burgeoning sequence data will also facilitate ecogenomic studies of non‐model species. Throughout this paper, we highlight approaches that are particularly suitable for ecological studies of non‐model organisms, discuss the benefits and disadvantages of specific techniques and review bioinformatic tools for analysing data.

5. We focus on established and promising techniques, such as QTL mapping with pedigreed populations, genome wide association studies, transcription profiling strategies, population genomics and transgenic methodologies. Many of these techniques are complementary and can be used jointly to investigate the genetic architecture of defence traits and selection on alleles in nature.
Abrupt spatial and numerical responses of overabundant foxes to a reduction in anthropogenic resources
Authors: Bino Gilad , Dolev Amit , Yosha Dotan , Guter Amichay , King Roni , Saltz David , Kark Salit
Published: September 2010

1. Carnivore overabundance that results from exploitation of human derived resources can have numerous detrimental effects on local human populations and ecological communities. Experimental studies on the responses of overabundant carnivores to reductions of such resources are necessary to understand the effectiveness and impacts of resource reduction.

2. We conducted controlled experiments in two villages in which we drastically reduced the availability of anthropogenic food sources in half of each village. Spatial and numerical responses of radio‐collared red foxes Vulpes vulpes were recorded and contrasted with those of radio‐collared foxes in three similar untreated villages and pristine areas in the region. In total, we looked at survival rates of 134 foxes.

3. Prior to the resource manipulation, home range sizes (0·47 and 0·56 km2) and population densities (30 and 36 foxes km−2) in the two villages were comparable to documented low and high‐end values, respectively.

4. Fast and distinct spatial responses were observed in response to the resource manipulation, and were manifested in either increased home range size or home range shifts. In one village, foxes exposed to reduced resource availability more than doubled their home range size.

5. Survival rates of individuals in the treated areas were drastically reduced. Actual fox mortality in the two treated areas reached 100% and 64% within 12 months of the onset of resource manipulation. Estimated monthly survival in the two treated areas declined from 0·96–0·98 and 0·98–0·99 (∼0·69 and 0·78 derived annual survival) before treatment to 0·80–0·83 and 0·92–0·94 (∼<0·01 and 0·42 derived annual survival) after treatment, respectively. By contrast, average monthly survivorship in pristine areas was nearly 0·97 (∼0·69 annual survival) and in the untreated areas and other non‐treated villages was 0·95–0·99 (∼0·54–0·89 annual survival).

6.
Synthesis and applications. This study demonstrates that sound waste disposal measures are very effective in controlling populations of overabundant carnivores. Contrary to common notion, the response of foxes to reduced resources was fast, manifested more by reduced survival than by successful dispersal into adjacent pristine areas. The results offer support to the Resource Dispersion Hypothesis regarding both home range size and density (suggested by the sharp decrease in survival) as a function of the spatial and temporal dispersion of resource.
Biotic and abiotic controls on tree colonization in three early successional communities of Chiloé Island, Chile
Authors: Bustamante‐Sánchez Marcela A. , Armesto Juan J. , Halpern Charles B.
Published: September 2010

1. Most studies of tree regeneration are limited to particular environments and may not capture variation in the biotic or abiotic factors that regulate recruitment at larger spatial scales. Critical processes such as competition and facilitation can vary spatially, along gradients in resource availability and environmental stress, and temporally, with plant development.

2. We examined patterns of natural tree recruitment and experimentally followed germination and seedling survival of five tree species (pioneer to late seral) in three early successional communities of contrasting bio‐physical environments in a rural landscape on Chiloé Island, Chile.

3. We quantified natural recruitment of juveniles and saplings and assessed relationships between tree density and local environment. We used a removal experiment to test the influence of early successional vegetation on seed germination and early survival of tree species. In each community, seeds and seedlings were placed in paired experimental plots from which vegetation was removed or left intact (control). To identify potential correlates of germination and seedling survival, we measured light transmittance and soil properties in each plot.

4. In all communities, established vegetation had either a positive or neutral effect on germination and/or survival although responses varied among life stages and species. Germination and survival were correlated with the lower levels of light in controls, consistent with negative correlations between natural tree densities and light. Vegetation cover was not dense enough to facilitate survival of late successional species, but not too dense to inhibit survival of shade‐intolerant or mid‐tolerant species. Among communities, natural densities of juveniles were greatest under conditions where experimental germination rates were highest. Seedling height growth was lowest in the community characterized by waterlogged soils, consistent with the naturally low transition rate from juveniles to saplings and a negative correlation between density of shade‐intolerant trees and soil moisture.

5.
Synthesis. Our experiments indicate strong, mostly positive controls (facilitation) on tree recruitment in early seral shrublands with differing bio‐physical environments. Benefits of shading are manifested at different stages in the life history. However, community context is critical: variation in seasonal patterns of soil moisture may explain spatial variation in the density and size structure of natural tree recruitment.
Selective REM sleep deprivation in narcolepsy
Authors: VU MANH HOANG , HURNI CHRISTOPH , MATHIS JOHANNES , ROTH CORINNE , BASSETTI CLAUDIO L.
Published: September 2010

Narcolepsy is characterized by excessive daytime sleepiness and rapid eye movement (REM) sleep abnormalities, including cataplexy. The aim of this study was to assess REM sleep pressure and homeostasis in narcolepsy. Six patients with narcolepsy and six healthy controls underwent a REM sleep deprivation protocol, including one habituation, one baseline, two deprivation nights (D1, D2) and one recovery night. Multiple sleep latency tests (MSLTs) were performed during the day after baseline and after D2. During D1 and D2 REM sleep was prevented by awakening the subjects at the first polysomnographic signs of REM sleep for 2 min. Mean sleep latency and number of sleep‐onset REM periods (SOREMs) were determined on all MSLT. More interventions were required to prevent REM sleep in narcoleptics compared with control subjects during D1 (57 ± 16 versus 24 ± 10) and D2 (87 ± 22 versus 35 ± 8, P = 0.004). Interventions increased from D1 to D2 by 46% in controls and by 53% in narcoleptics (P < 0.03). Selective REM sleep deprivation was successful in both controls (mean reduction of REM to 6% of baseline) and narcoleptics (11%). Both groups had a reduction of total sleep time during the deprivation nights (P = 0.03). Neither group had REM sleep rebound in the recovery night. Narcoleptics had, however, an increase in the number of SOREMs on MSLT (P = 0.005). There was no increase in the number of cataplexies after selective REM sleep deprivation. We conclude that: (i) REM sleep pressure is higher in narcoleptics; (ii) REM sleep homeostasis is similar in narcoleptics and controls; (iii) in narcoleptics selective REM sleep deprivation may have an effect on sleep propensity but not on cataplexy.
Isolation by distance across the Hawaiian Archipelago in the reef‐building coralPorites lobata
Authors: POLATO NICHOLAS R. , CONCEPCION GREGORY T. , TOONEN ROBERT J. , BAUMS ILIANA B.
Published: September 2010

There is an ongoing debate on the scale of pelagic larval dispersal in promoting connectivity among populations of shallow, benthic marine organisms. The linearly arranged Hawaiian Islands are uniquely suited to study scales of population connectivity and have been used extensively as a natural laboratory in terrestrial systems. Here, we focus on Hawaiian populations of the lobe coralPorites lobata, an ecosystem engineer of shallow reefs throughout the Pacific. Patterns of recent gene flow and population structure inP. lobatasamples (n = 318) from two regions, the Hawaiian Islands (n = 10 sites) and from their nearest neighbour Johnston Atoll, were analysed with nine microsatellite loci. Despite its massive growth form, ∼6% of the samples from both regions were the product of asexual reproduction via fragmentation. Cluster analysis and measures of genetic differentiation indicated thatP. lobatafrom the Hawaiian Islands are strongly isolated from those on Johnston Atoll (FST = 0.311;P < 0.001), with the descendants of recent migrants (n = 6) being clearly identifiable. Within the Hawaiian Islands,P. lobataconforms to a pattern of isolation by distance. Here, over 37% (P = 0.001) of the variation in genetic distance was explained by geographical distance. This pattern indicates that while the majority of ongoing gene flow in HawaiianP. lobataoccurs among geographically proximate reefs, inter‐island distances are insufficient to generate strong population structure across the archipelago.
Carbon flux rerouting during Mycobacterium tuberculosis growth arrest
Authors: Shi Lanbo , Sohaskey Charles D. , Pfeiffer Carmen , Datta Pratik , Parks Michael , McFadden Johnjoe , North Robert J. , Gennaro Maria L.
Published: September 2010

A hallmark of the Mycobacterium tuberculosis life cycle is the pathogen's ability to switch between replicative and non‐replicative states in response to host immunity. Transcriptional profiling by qPCR of ∼ 50 M. tuberculosis genes involved in central and lipid metabolism revealed a re‐routing of carbon flow associated with bacterial growth arrest during mouse lung infection. Carbon rerouting was marked by a switch from metabolic pathways generating energy and biosynthetic precursors in growing bacilli to pathways for storage compound synthesis during growth arrest. Results of flux balance analysis using an in silico metabolic network were consistent with the transcript abundance data obtained in vivo. Similar transcriptional changes were seen in vitro when M. tuberculosis cultures were treated with bacteriostatic stressors under different nutritional conditions. Thus, altered expression of key metabolic genes reflects growth rate changes rather than changes in substrate availability. A model describing carbon flux rerouting was formulated that (i) provides a coherent interpretation of the adaptation of M. tuberculosis metabolism to immunity‐induced stress and (ii) identifies features common to mycobacterial dormancy and stress responses of other organisms.
Calcium ion‐mediated assembly and function of glycosylated flagellar sheath of marine magnetotactic bacterium
Authors: Lefèvre Christopher T. , Santini Claire‐Lise , Bernadac Alain , Zhang Wei‐Jia , Li Ying , Wu Long‐Fei
Published: September 2010

Flagella of some pathogens or marine microbes are sheathed by an apparent extension of the outer cell membrane. Although flagellar sheath has been reported for almost 60 years, little is known about its function and the mechanism of its assembly. Recently, we have observed a novel type of sheath that encloses a flagellar bundle, instead of a single flagellum, in a marine magnetotactic bacterium MO‐1. Here, we reported isolation and characterization of the sheath which can be described as a six‐start, right‐handed helical tubular structure with a diameter of about 100 nm, and a pitch of helix of about 260 nm. By proteomic, microscopic and immunolabelling analyses, we showed that the sheath of MO‐1 consists of glycoprotein with an apparent molecular mass > 350 kDa. This protein, named sheath‐associated protein (Sap), shows homology with bacterial adhesins and eukaryotic calcium‐dependent adherent proteins (cadherin). Most importantly, we showed that calcium ions mediate the assembly of the tubular‐shaped sheath and disintegration of the sheath was deleterious for smooth swimming of MO‐1 cells. The disintegrated sheath was efficiently reconstituted in vitro by adding calcium ions. Altogether, these results demonstrate a novel bacterial Ca2+‐dependent surface architecture, which is essential for bacterial swimming.
The dawning of a ‘Golden era’ in lantibiotic bioengineering
Authors: Field Des , Hill Colin , Cotter Paul D. , Ross R. Paul
Published: September 2010

There are many examples of highly modified antimicrobial peptides in nature, many of which are non‐ribosomally synthesized. However, the bacterial lantibiotics are produced as gene‐encoded pre‐peptides that are subsequently modified by dedicated enzyme systems to form extraordinarily potent inhibitors. Consequently, they are much more amenable to bioengineering which could lead to the generation of a new arsenal of potent antimicrobials. However, although bioengineering of these compounds has been underway for at least two decades, significant progress has only been reported in recent years. This review charts these recent developments which suggest that we are entering a ‘Golden era’ of lantibiotic bioengineering.
Evaluating delta asymmetry using three‐dimensional facies architecture and ichnological analysis, Ferron ‘Notom Delta’, Capital Reef, Utah, USA
Authors: LI WEIGUO , BHATTACHARYA JANOK P. , ZHU YIJIE , GARZA DANIEL , BLANKENSHIP ERIC
Published: September 2010

Delta asymmetry occurs where there is strong wave influence and net longshore transport. Differences in the morphology and facies architecture between updrift and downdrift sides of asymmetric deltas are potentially significant for exploration and exploitation of resources in this class of reservoirs. Although delta asymmetry has been recognized widely from modern wave‐influenced deltaic shorelines, there are few documented examples in the ancient record. Based on an integrated sedimentological and ichnological study, the along‐strike variability and delta asymmetry within a single parasequence (Ps 6) is documented in continuously exposed outcrops of the Cretaceous Ferron Sandstone Member of the Mancos Shale Formation near Hanksville in southern Utah. Two intra‐parasequence discontinuity surfaces are recognized which allow subdivision of the parasequence into three bedsets, marked as Ps 6‐1 to Ps 6‐3. Four facies successions are recognized: (i) wave/storm‐dominated shoreface; (ii) river‐dominated delta front; (iii) wave/storm‐reworked delta front; and (iv) distributary channel and mouth bar. Dips of cross‐strata within distributary‐mouth bars and shorefaces show a strong downdrift (southward) component. Ps 6‐3 predominantly consists of river‐dominated delta‐front deposits, whereas Ps 6‐1 and Ps 6‐2 show an along‐strike facies change with shoreface deposits in the north, passing into heterolithic, river‐dominated delta‐front successions south to south‐eastward, and wave/storm‐reworked delta‐front deposits further to the south‐east. Trace fossil suites correspondingly show distinct along‐strike changes from robust and diverse expressions of the archetypal Cruziana Ichnofacies and Skolithos Ichnofacies, into suites characterized by horizontal, morphologically simple, facies‐crossing ichnogenera, reflecting a more stressed, river‐dominated environment. Further south‐eastward, trace fossil abundance and diversity increase, reflecting a return to archetypal ichnofacies. The overall facies integrated with palaeocurrent data indicate delta asymmetry. The asymmetric delta consists of sandier shoreface deposits on the updrift side and mixed riverine and wave/storm‐reworked deposits on the downdrift side, similar to that observed in the modern examples. However, in contrast to the recent delta asymmetry models, significant paralic, lagoonal and bay‐fill facies are not documented in the downdrift regions of the asymmetric delta. This observation is attributed to a negative palaeoshoreline trajectory during delta progradation and subsequent transgressive erosion. The asymmetric delta was induced by net longshore transport from north to south. The forced regressive nature of the delta precludes significant preservation of topset mud.
Prevalence and genetic heterogeneity of SEN virus genotypes D and H in blood donors from Central and Western Europe and West Africa
Authors: Thom K. , Cleland A. , Salakova M. , Candotti D. , Petrik J.
Published: September 2010

Objectives: To establish prevalence and phylogenetic relationship of SEN virus (SENV) D and H in blood donors from Scotland, Czech Republic and Ghana.

Aim: To compare the data between three regions with differing prevalence of blood‐borne viruses.

Background: Anelloviruses are a ubiquitous group of viruses without a clear disease association. Although there is little evidence that they are pathogenic per se, they may have the ability to modify ongoing disease processes. They have a high degree of heterogeneity both within populations and across geographic regions.

Materials and Methods: Three sets of donor samples were analysed by nested polymerase chain reaction (PCR) and hybridisation. A proportion of amplified samples were sequenced and phylogenetic analysis was carried out.

Results: The prevalence figures (including mixed D + H infection) were established for SENV D: 1·0, 8·4 and 25·2% and H: 12·5, 34·8 and 61·0% in Scottish, Czech and Ghanaian blood donors, respectively. The compilation of prevalence figures indicates the changing ratio of SENV D/H in west‐east direction, most obvious between Western Europe (D/H < 1) and far East Asia (D/H > 1). Phylogenetic analysis grouped the samples mostly in accordance with geographic origin, despite the variability of short sequence analysed. The previously indicated link between SENV prevalence and age was statistically significant in this study, only for SENV H in Czech samples.

Conclusion: SENV D and H appear to reflect the incidence of other blood‐borne viruses in these locations. SENV H prevalence of 45·4% in Ghana represents the highest single‐SENV‐genotype prevalence described in blood donors to date.
Impact of climate and land use type on the distribution of Finnish casual arable weeds in Europe
Authors: HYVÖNEN T , GLEMNITZ M , RADICS L , HOFFMANN J
Published: September 2010

Hyvönen T, Glemnitz M, Radics L & Hoffmann J (2011). Impact of climate and land use type on the distribution of Finnish casual arable weeds in Europe. Weed Research51, 201–208.

The aim of the study was to explore the impact of climate and land use type on species richness and abundance of arable weeds found as casual aliens in Finland. We used an empirical data set collected along a European climate gradient, from which 163 plants were selected for the analyses. Using generalised linear modelling (GLMM) and redundancy analysis (RDA), we compared species richness and abundance of all species and three functional groups (dicotyledons and grasses, C3 and C4 species, alien and native species to Europe), as well as occurrence of the 13 most common individual species between three land use types (fallow, low‐input and conventionally cultivated) and six regions. In general, fallowing and low‐input cultivation, as well as warmer climate, supported greater weed species richness and abundance. Temperature was found to be a more important factor for weed abundance than land use. The only exception was C4 species richness, which did not respond to either factor. The impact of land use was independent of climate for all variables, except C4 species abundance. Non‐cultivated fallows had more weeds than cultivated fields, in most cases. No difference was found in the species richness and abundance of grasses or in the occurrence of individual species between low‐input and conventionally cultivated fields. It was evident that climate and land use affect the distribution of arable weed species currently found as casual aliens in Finland. This suggests that climate warming will increase the risk of the population establishment of new weed species in northern regions.
The role of latitude, ultraviolet radiation exposure and vitamin D in childhood asthma and hayfever: an Australian multicenter study
Authors: Hughes Ann Maree , Lucas Robyn Marjorie , Ponsonby Anne‐Louise , Chapman Caron , Coulthard Alan , Dear Keith , Dwyer Terry , Kilpatrick Trevor J. , McMichael Anthony J. , Pender Michael P. , Taylor Bruce V. , Valery Patricia , van der Mei Ingrid A. F. , Williams David
Published: September 2010

To cite this article: Hughes AM, Lucas RM, Ponsonby A‐L, Chapman C, Coulthard A, Dear K, Dwyer T, Kilpatrick TJ, McMichael AJ, Pender MP, Taylor BV, Valery P, van der Mei IAF, Williams D. The role of latitude, ultraviolet radiation exposure and vitamin D in childhood asthma and hayfever: an Australian multicenter study. Pediatr Allergy Immunol 2011; 22: 327–333.

Observations of increasing allergy prevalence with decreasing distance from the Equator and positive associations with ambient ultraviolet radiation have contributed to a growing interest in the possible role of vitamin D in the etiology of allergy. The aims of this study were to describe any latitudinal variation in the prevalence of childhood allergy in Australia and to evaluate, in parallel, the individual associations between ultraviolet radiation (UVR)‐ and vitamin D‐related measures and hayfever asthma and both conditions. Participants were population‐based controls who took part in a multicenter case–control study, aged 18–61 yr and resident in one of four study regions ranging in latitude from 27°S to 43°S. Data were derived from a self‐administered questionnaire, interview and examination by a research officer and biologic sampling. Latitude and longitude coordinates were geocoded from participants’ residential locations and climatic data were linked to postcodes of current residence. Stored serum was analyzed for 25‐hydroxyvitamin D concentrations and silicone rubber casts of the skin were used as an objective measure of cumulative actinic damage. There was an inverse latitude gradient for asthma (a 9% decrease per increasing degree of latitude); however, this pattern did not persist after adjusting for average daily temperature. There was no association between any of the UVR‐ or vitamin D‐related measures and childhood asthma, but greater time in the sun in winter between the ages 6–15 yr was associated with an increase in the odds of having hayfever [adjusted odds ratios (OR) 1.29; 95% CI 1.01–1.63]. Oral supplementation with cod liver oil in childhood increased the odds of a history of having both asthma and hayfever (2.87; 1.00–8.32). Further investigation of the possible role of early vitamin D supplementation in the development of allergy is warranted. Our results also suggest that solar exposure during childhood may be important in allergic sensitization. Plausible explanations, including biologic mechanisms, exist for both observations.
Platelet transfusion refractoriness attributable to HLA antibodies produced by donor‐derived cells after allogeneic bone marrow transplantation from one HLA‐antigen‐mismatched mother
Authors: Hatakeyama Naoki , Hori Tsukasa , Yamamoto Masaki , Inazawa Natsuko , Iesato Kotoe , Miyazaki Toru , Ikeda Hisami , Tsutsumi Hiroyuki , Suzuki Nobuhiro
Published: September 2010

Hatakeyama N, Hori T, Yamamoto M, Inazawa N, Iesato K, Miyazaki T, Ikeda H, Tsutsumi H, Suzuki N. Platelet transfusion refractoriness attributable to HLA antibodies produced by donor‐derived cells after allogeneic bone marrow transplantation from one HLA‐antigen‐mismatched mother.  Pediatr Transplantation 2011: 15: E177–E182. © 2010 John Wiley & Sons A/S.

Abstract:  PTR is a serious problem in patients being treated for hematologic disorders. Two patients with acute leukemia developed PTR after allogeneic BMT from one HLA‐antigen‐mismatched mother attributable to HLA antibodies, which could not be detected in their serum before BMT. HLA antibodies, whose specificity resembled that of each patient, were detected in each donor’s serum. Each donor had probably been immunized during pregnancy by their partner’s HLA antigens expressed by the fetus, consequently, transplanted donor‐derived cells provoked HLA antibodies in each recipient early after BMT, and those HLA antibodies induced PTR. If the mothers are selected as donors for their children, they should be tested for the presence of HLA antibodies.
Polyoma virus‐associated progressive multifocal leukoencephalopathy after renal transplantation: Regression following withdrawal of mycophenolate mofetil
Authors: Weber Sven C. , Uhlenberg Birgit , Raile Klemens , Querfeld Uwe , Müller Dominik
Published: September 2010

Weber SC, Uhlenberg B, Raile K, Querfeld U, Müller D. Polyoma virus‐associated progressive multifocal leukoencephalopathy after renal transplantation: Regression following withdrawal of mycophenolate mofetil. Pediatr Transplantation 2011: 15:E19–E24. © 2010 John Wiley & Sons A/S.

Abstract:  The 2008‐released FDA safety report described a potential association between use of MMF and progressive multifocal leukoencephalopathy. We here report the case of an 11‐yr‐old kidney transplanted boy suffering from PML who showed rapid improvement parallel to withdrawal of MMF. This case contributes to the increasing knowledge on side effects of MMF treatment in children.