bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimating EAF indicators from scientific trawl surveys: theoretical and practical concerns
Authors: Jouffre Didier , Borges Maria de Fatima , Bundy Alida , Coll Marta , Diallo Ibrahima , Fulton Elizabeth A. , Guitton Jérôme , Labrosse Pierre , Abdellahi Khairdine ould Mohamed , Masumbuko Bora , Thiao Djiga
Published: December 2009

Jouffre, D., Borges, M. F., Bundy, A., Coll, M., Diallo, I., Fulton, E. A., Guitton, J., Labrosse, P., Mohamed Abdellahi, K. o., Masumbuko, B., and Thiao, D. 2010. Estimating EAF indicators from scientific trawl surveys: theoretical and practical concerns. – ICES Journal of Marine Science, 67: 796–806. Under the context of an ecosystem approach to fisheries (EAF), there is keen interest in providing insights into the evolution of exploited ecosystems using simple ecosystem indicators. Many nations have long-term scientific research surveys, originally driven by conventional approaches in fisheries assessment and management. The aim of this study is to address the practical concerns linked to current objectives of monitoring simple EAF indicators, using data from surveys that were not historically designed for the purpose. Based on the results of an expert survey designed to collect expert knowledge on research surveys from scientists working on different ecosystems worldwide, a list of challenges faced during indicator estimation is highlighted, along with associated concerns and constraints. The work provides additional information useful in the interpretation of the results obtained on the state and trends of ecosystems using EAF indicators by the IndiSeas WG. Further, the related discussion provides potential pathways that could be useful for future research and development aiming to improve the ecosystem indicator approach in the operational context of EAF. The question of the utility for EAF of using historical dataseries of scientific trawl series is also discussed. Such long-term series are concluded to be useful, that they are even inescapable (since the past cannot be resamplied), and that EAF therefore brings a supplementary reason for continuing such monitoring and to incorporate new insights in how research surveys may be conducted.
Fixed negative charge and the Donnan effect: a description of the driving forces associated with brain tissue swelling and oedema
Authors: Elkin Benjamin S. , Shaik Mohammed A. , Morrison Barclay
Published: January 2010

Cerebral oedema or brain tissue swelling is a significant complication following traumatic brain injury or stroke that can increase the intracranial pressure (ICP) and impair blood flow. Here, we have identified a potential driver of oedema: the negatively charged molecules fixed within cells. This fixed charge density (FCD), once exposed, could increase ICP through the Donnan effect. We have shown that metabolic processes and membrane integrity are required for concealing this FCD as slices of rat cortex swelled immediately (within 30 min) following dissection if treated with 2 deoxyglucose + cyanide (2DG+CN) or Triton X-100. Slices given ample oxygen and glucose, however, did not swell significantly. We also found that dead brain tissue swells and shrinks in response to changes in ionic strength of the bathing medium, which suggests that the Donnan effect is capable of pressurizing and swelling brain tissue. As predicted, a non-ionic osmolyte, 1,2 propanediol, elicited no volume change at 2000×10
−3
 osmoles l
−1
(Osm). Swelling data were well described by triphasic mixture theory with the calculated reference state FCD similar to that measured with a 1,9 dimethylmethylene blue assay. Taken together, these data suggest that intracellular fixed charges may contribute to the driving forces responsible for brain swelling.
A multi-scale view of skin thermal pain: from nociception to pain sensation
Authors: Zhu Y. J. , Lu T. J.
Published: January 2010

All biological bodies live in a thermal environment, including the human body, where skin is the interface with a protecting function. When the temperature is out of the normal physiological range, skin fails to protect, and the pain sensation is evoked. Furthermore, in medicine, with advances in laser, microwave and similar technologies, various thermal therapeutic methods have been widely used to cure disease/injury involving skin tissue. However, the corresponding problem of pain relief has limited further application and development of these thermal treatments. Skin thermal pain is induced through both direct (i.e. an increase/decrease in temperature) and indirect (e.g. thermomechanical and thermochemical) ways, and is governed by complicated thermomechanical–chemical–neurophysiological responses. However, a complete understanding of the underlying mechanisms is still far from clear. In this article, starting from an engineering perspective, we aim to recast the biological behaviour of skin in engineering system parlance. Then, by coupling the concepts of engineering with established methods in neuroscience, we attempt to establish multi-scale modelling of skin thermal pain through ion channel to pain sensation. The model takes into account skin morphological plausibility, the thermomechanical response of skin tissue and the biophysical and neurological mechanisms of pain sensation.
Regulation of the p53 transcriptional response by structurally diverse core promoters
Authors: Morachis José M. , Murawsky Christopher M. , Emerson Beverly M.
Published: December 2009

p53 target promoters are structurally diverse and display pronounced differences in RNA polymerase II (RNAP II) occupancy even in unstressed cells, with higher levels observed on cell cycle arrest genes (p21) compared with apoptotic genes (Fas/APO1). This occupancy correlates well with their ability to undergo rapid or delayed stress induction. To understand the basis for such distinct temporal assembly of transcription complexes, we examined the role of core promoter structures in this process. We find that thep21core promoter directs rapid, TATA box-dependent assembly of RNAP II preinitiation complexes (PICs), but permits few rounds of RNAP II reinitiation. In contrast, PIC formation at theFas/APO1core promoter is very inefficient but supports multiple rounds of transcription. We define a downstream element within theFas/APO1core promoter that is essential for its activation, and identify nuclear transcription factor Y (NF-Y) as its binding partner. NF-Y acts as a bifunctional transcription factor that regulates basal expression ofFas/APO1in vivo. Thus, two critical parameters of the stress-induced p53 transcriptional response are the kinetics of gene induction and duration of expression through frequent reinitiation. These features are intrinsic, DNA-encoded properties of diverse core promoters that may be fundamental to anticipatory programming of p53 response genes upon stress.
A histone chaperone, DEK, transcriptionally coactivates a nuclear receptor
Authors: Sawatsubashi Shun , Murata Takuya , Lim Jinseon , Fujiki Ryoji , Ito Saya , Suzuki Eriko , Tanabe Masahiko , Zhao Yue , Kimura Shuhei , Fujiyama Sally , Ueda Takashi , Umetsu Daiki , Ito Takashi , Takeyama Ken-ichi , Kato Shigeaki
Published: December 2009

Chromatin reorganization is essential for transcriptional control by sequence-specific transcription factors. However, the molecular link between transcriptional control and chromatin reconfiguration remains unclear. By colocalization of the nuclear ecdysone receptor (EcR) on the ecdysone-induced puff in the salivary gland, Drosophila DEK (dDEK) was genetically identified as a coactivator of EcR in both insect cells and intact flies. Biochemical purification and characterization of the complexes containing fly and human DEKs revealed that DEKs serve as histone chaperones via phosphorylation by forming complexes with casein kinase 2. Consistent with the preferential association of the DEK complex with histones enriched in active epigenetic marks, dDEK facilitated H3.3 assembly during puff formation. In some human myeloid leukemia patients, DEK was fused to CAN by chromosomal translocation. This mutation significantly reduced formation of the DEK complex, which is required for histone chaperone activity. Thus, the present study suggests that at least one histone chaperone can be categorized as a type of transcriptional coactivator for nuclear receptors.
Mounting, Embedding, and Sectioning of Early Rabbit Embryos
Authors: Püschel Bernd , Bitzer Eva , Blum Martin , Viebahn Christoph
Published: January 2010

INTRODUCTION

This protocol describes various methods for visualizing cellular labeling in early rabbit embryos at high resolution using stereomicroscopy, compound light microscopy, or electron microscopy. Embedding media are chosen according to the level of resolution needed: For low-magnification stereomicroscopy, optimal spreading of large, flat, thin embryonic discs is achieved by mounting embryos in Mowiol on regular microscope slides. Gelatin/BSA embedding is useful for quickly cutting a complete series of thick (e.g., 30-μm) sections in defined planes from large (e.g., somite stage) paraformaldehyde-fixed embryos prelabeled by immunofluorescence or in situ hybridization. Higher cellular and subcellular resolution of such specimens usually requires embedding in Technovit, a hydrophilic methacrylate-based resin suited for light microscopic analysis of 5-μm serial sections. Araldite is a translucent, hydrophobic epoxy-based resin used for serial semi-thin (1-μm) and ultrathin (80-nm) sections amenable to consecutive (and correlative) light and electron microscopic analysis. Specimens to be embedded in Araldite must be much harder than those embedded in hydrophilic resins, requiring at least 1% glutaraldehyde in the primary fixative. Unfortunately, strong cross-linking by glutaraldehyde prevents the use of antibodies/nucleotide probes post-fixation; glutaraldehyde autofluorescence also thwarts the use fluorescent stains. Finally, semi-thin cryosections can be cut from unfixed or paraformaldehyde-fixed specimens embedded in “tissue freezing medium,” offering the opportunity for highly sensitive light microscopic analysis of antigen distribution. Here, subcellular structures can be identified up to the level of individual mitochondria; greater resolution can be obtained by correlating such samples with similar specimens analyzed using other techniques.
Embryo Transfer in Rabbits: Figure 1.
Authors: Daniel Nathalie , Renard Jean-Paul
Published: January 2010

INTRODUCTION

Because there is a particularly narrow time window for implantation in rabbits, embryo transfer in this species requires a high degree of synchrony between the physiological status of the recipient doe and the developmental stage of the embryo at the time of transfer. In some cases, however, especially after in vitro culture of reconstructed embryos or after an extended culture period (e.g. overnight), the pregnancy rate obtained after embryo transfer into asynchronous recipients can be increased relative to synchronous transfers. In addition to the surgical methods required, this protocol describes two scenarios for the preparation of recipient does: an asynchronous scenario for embryos produced by intracytoplasmic sperm injection (ICSI) and a synchronous scenario for the transfer of thawed morulae.
Mass Culture of Paramecium tetraurelia: Figure 1.
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda
Published: January 2010

INTRODUCTION

Clonal cell lines of Paramecium tetraurelia can be established easily by single cell isolation. Given a constant supply of food, P. tetraurelia cells will remain in the vegetative phase of their life cycle and, at 27°C, will divide by binary fission every 6 h. P. tetraurelia is suitable for a range of biochemical and molecular studies such as mitochondrial genetics, post-translational tubulin modifications, variant genetic codes, programmed genome rearrangements (and their epigenetic regulation by noncoding RNAs), and RNA interference. This protocol describes the methods required to grow high-density mass cultures of P. tetraurelia in quantities sufficient to provide the material required for biochemical and molecular biological studies.
Silencing Specific Paramecium tetraurelia Genes by Feeding Double-Stranded RNA
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda
Published: January 2010

INTRODUCTION

This protocol describes an easy and efficient method to knock down gene expression in a homology-dependent manner by feeding Paramecium with bacteria-producing double-stranded (ds) RNA corresponding to a portion of the target gene. The target sequence is cloned in a plasmid between two convergent T7 promoters (the L4440 plasmid) and used to transform an E. coli strain devoid of RNase III activity and expressing the T7 polymerase gene under the control of an inducible Plac promoter (strain HT115-DE3). Inserts corresponding to ~400 bp of the coding sequence to be silenced are recommended; very short inserts (<100 bp) have variable silencing efficiencies. As a rule, pairs of paralogs resulting from the most recent whole-genome duplication are so similar in sequence that dsRNA from one paralog will cosilence both. Although the level of sequence identity required has not been explored fully, more divergent paralogs can occasionally be co-silenced too. When Paramecium tetraurelia cells feed on these bacteria, dsRNA reaches the cytoplasm through unknown mechanisms and triggers a potent RNA interference (RNAi) response, resulting in the degradation of the targeted mRNA. The protocol generally gives a visible phenotype in 24-48 h, depending on the targeted gene, a delay which might correspond to the time necessary for the pre-existing protein stock to be diluted by cell growth. Silencing induced in this manner is only post-transcriptional; when cells are transferred back to normal medium bacterized with Klebsiella pneumoniae, the phenotype usually reverts to wild type within a few cell divisions.
DNA Microinjection into the Macronucleus of Paramecium
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda
Published: January 2010

INTRODUCTION

This protocol describes a highly efficient procedure for transforming the vegetative macronucleus of Paramecium tetraurelia by DNA microinjection. Any microinjected DNA will be replicated without the need for specific origins and can be stably maintained at a wide range of copy numbers throughout vegetative growth as minichromosomes that are formed in vivo by the addition of telomeric sequences to the ends of linear monomers and multimers. A variable fraction of the injected DNA also integrates into endogenous macronuclear chromosomes by nonhomologous recombination. Endogenous transcription signals are recognized, allowing appropriate regulation of gene expression. This technique is used for complementation cloning of genes altered in mutants and for expression of modified genes, e.g., green fluorescent protein (GFP) fusions. Microinjection of nonexpressible constructs at high copy numbers can also be used to specifically silence homologous endogenous genes by transgene-induced RNA interference. Note that transformed clones are somatic transformants, and therefore can be maintained only during the vegetative phase of the life cycle (<200 cell divisions), i.e., only as long as they do not enter sexual reproduction or senescence. Cells must be kept in continuous exponential growth by providing a constant supply of food; starving cells with a clonal age ≥20 divisions, since the last sexual event will inevitably trigger meiosis, resulting in the loss of the transformed macronucleus and its replacement by a new macronucleus that develops from the germline micronuclei.
Auxin Response inArabidopsisunder Cold Stress: Underlying Molecular Mechanisms
Authors: Shibasaki Kyohei , Uemura Matsuo , Tsurumi Seiji , Rahman Abidur
Published: December 2009

To understand the mechanistic basis of cold temperature stress and the role of the auxin response, we characterized root growth and gravity response of Arabidopsis thaliana after cold stress, finding that 8 to 12 h at 4°C inhibited root growth and gravity response by ∼50%. The auxin-signaling mutants axr1 and tir1, which show a reduced gravity response, responded to cold treatment like the wild type, suggesting that cold stress affects auxin transport rather than auxin signaling. Consistently, expression analyses of an auxin-responsive marker, IAA2-GUS, and a direct transport assay confirmed that cold inhibits root basipetal (shootward) auxin transport. Microscopy of living cells revealed that trafficking of the auxin efflux carrier PIN2, which acts in basipetal auxin transport, was dramatically reduced by cold. The lateral relocalization of PIN3, which has been suggested to mediate the early phase of root gravity response, was also inhibited by cold stress. Additionally, cold differentially affected various protein trafficking pathways. Furthermore, the inhibition of protein trafficking by cold is independent of cellular actin organization and membrane fluidity. Taken together, these results suggest that the effect of cold stress on auxin is linked to the inhibition of intracellular trafficking of auxin efflux carriers.
PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants
Authors: Proost Sebastian , Van Bel Michiel , Sterck Lieven , Billiau Kenny , Van Parys Thomas , Van de Peer Yves , Vandepoele Klaas
Published: December 2009

The number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.
DGAT1andPDAT1Acyltransferases Have Overlapping Functions inArabidopsisTriacylglycerol Biosynthesis and Are Essential for Normal Pollen and Seed Development
Authors: Zhang Meng , Fan Jilian , Taylor David C. , Ohlrogge John B.
Published: December 2009

Triacylglycerol (TAG) biosynthesis is a principal metabolic pathway in most organisms, and TAG is the major form of carbon storage in many plant seeds. Acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) is the only acyltransferase enzyme that has been confirmed to contribute to TAG biosynthesis in Arabidopsis thaliana seeds. However, dgat1 null mutants display only a 20 to 40% decrease in seed oil content. To determine whether other enzymes contribute to TAG synthesis, candidate genes were expressed in TAG-deficient yeast, candidate mutants were crossed with the dgat1-1 mutant, and target genes were suppressed by RNA interference (RNAi). An in vivo role for phospholipid:diacylglycerol acyltransferase 1 (PDAT1; At5g13640) in TAG synthesis was revealed in this study. After failing to obtain double homozygous plants from crossing dgat1-1 and pdat1-2, further investigation showed that the dgat1-1 pdat1-2 double mutation resulted in sterile pollen that lacked visible oil bodies. RNAi silencing of PDAT1 in a dgat1-1 background or DGAT1 in pdat1-1 background resulted in 70 to 80% decreases in oil content per seed and in disruptions of embryo development. These results establish in vivo involvement of PDAT1 in TAG biosynthesis, rule out major contributions by other candidate enzymes, and indicate that PDAT1 and DGAT1 have overlapping functions that are essential for normal pollen and seed development of Arabidopsis.
Diet composition ofXenopus borealisin Taita Hills: effects of habitat and predator size
Authors: Bwong Beryl A. , John Measey G.
Published: January 2010

Frogs in the genusXenopusare ubiquitous in sub‐Saharan Africa, yet very little is recorded on their ecology. They are commonly found in anthropogenically disturbed habitats, but how do these compare to conspecifics from natural habitats? The diet ofXenopus borealisfrom three different sites in Taita Hills, Kenya was established based on a sample of 77 (54 females and 23 males) specimens from two disturbed and one pristine sites.Xenopus borealisfrom all the sites was found to be a dietary generalist, feeding predominantly on invertebrates. A total of twelve invertebrate orders both terrestrial and aquatic were recorded in addition to amphibian eggs, tadpoles and fish. Frogs from the pristine forest were smaller and had ingested more terrestrial prey items than frogs in the disturbed open habitat ponds. The stomach content (both by mass and quantity) was independent of body size. The results suggest thatX. borealisis an opportunistic generalist predator which may be constrained by food availability in its natural habitat. However, disturbed habitats provide abundant food items which are enough to significantly increase the mean size of the population.
Review article: omega‐3 fatty acids – a promising novel therapy for non‐alcoholic fatty liver disease
Authors: MASTERTON G. S. , PLEVRIS J. N. , HAYES P. C.
Published: December 2009

Aliment Pharmacol Ther 31, 679–692

Background  Non‐alcoholic fatty liver disease affects 10–35% of the adult population worldwide; there is no consensus on its treatment. Omega‐3 fatty acids have proven benefits for hyperlipidaemia and cardiovascular disease, and have recently been suggested as a treatment for non‐alcoholic fatty liver disease.

Aims  To review the evidence base for omega‐3 fatty acids in non‐alcoholic fatty liver disease and critically appraise the literature relating to human trials.

Methods  A Medline and PubMed search was performed to identify relevant literature using search terms ‘omega‐3’, ‘N‐3 PUFA’, ‘eicosapentaenoic acid’, ‘docosahexaenoic acid’, ‘non‐alcoholic fatty liver disease’ and ‘NAFLD’.

Results  Omega‐3 fatty acids are important regulators of hepatic gene transcription. Animal studies demonstrate that they reduce hepatic steatosis, improve insulin sensitivity and reduce markers of inflammation. Clinical trials in human subjects generally confirm these findings, but have significant design inadequacies.

Conclusions  Omega‐3 fatty acids are a promising treatment for non‐alcoholic fatty liver disease which require to be tested in randomized placebo‐controlled trials.
Differences in defensive behaviour between host‐adapted races of the pea aphid
Authors: KUNERT GRIT , BELZ ELODIE , SIMON JEAN‐CHRISTOPHE , WEISSER WOLFGANG W. , OUTREMAN YANNICK
Published: January 2010

1. Host races, i.e. host‐adapted populations in partial reproductive isolation, have been reported in a growing number of insect herbivores including aphids. The pea aphid Acyrthosiphon pisum encompasses distinct races highly specialised on various Fabaceae plants. Races have been well documented at both the ecological and genetic level. However, little is known about possible behavioural differences between host races other than those involved in plant choice.

2. The aim of this study was to determine whether pea aphid host races differ in the behavioural response to the aphid alarm pheromone that was used to simulate immediate predation risk. The behaviour of aphids towards a synthetic alarm pheromone applied in their vicinity was measured in several pea aphid clones originating from various legumes including Medicago sativa, Pisum sativum, Trifolium pratense, and Vicia faba. To control for the influence of plant traits, experiments were conducted on the preferred host plant and on the universal host plant Vicia faba.

3. Host races differed in their defensive responses, with stronger behavioural responses in host races originating from M. sativa and T. pratense compared with those coming from P. sativum and V. faba. These differences in behaviour are inherent to the pea aphid host race but not dependent on the test plant.

4. Our work shows that host‐plant specialisation may involve behavioural traits in addition to host choice. Possible mechanisms of how different defensive behaviours might have evolved are discussed.
Matrix metalloproteinase (MMP)‐2 and MMP‐9 activity and localization during ventral prostate atrophy and regrowth
Authors: Justulin Jr L. A. , Della‐Coleta H. H. M. , Taboga S. R. , Felisbino S. L.
Published: January 2010

Matrix metalloproteinses (MMPs) are enzymes involved in prostatic development, growth, disease‐induced tissue remodelling and secretory fluid. Although the prostate function depends upon androgen regulation, the relationship between MMPs and androgen has not been well established. Here, we evaluated MMP‐2 and MMP‐9 gelatinolytic activity in association with tissue localization during ventral prostate atrophy and regrowth induced by testosterone replacement (TR). Adult male Wistar rats were divided into three experimental groups: control, castrated (CS) and TR 21 days after castration. Ventral prostate (VP) was excised at 3, 5, 7 and 21 days after castration in CS group, and at 3, 5, 7 and 10 days after TR (4 mg/kg/day) in TR group. The VP was dissected, weighed and processed for histology, immunohistochemistry, ultrastructure and zymography analyses. Castration elicited the typical parenchymal atrophy and stromal condensation. TR induced intense epithelial growth towards the stromal space to restore the prostate histoarchitecture. MMP‐2 and MMP‐9 immunostaining presented intense reaction in CS and TR groups, mainly in the epithelial and endothelial cells. After TR, a strong immunoreaction for MMP‐2 was observed in the activated stromal fibroblasts. Zymography showed that MMP‐2 and MMP‐9 activity, mainly the active form, increased after castration. In contrast, TR induced an additional increase in MMP‐2 activity, but not in MMP‐9. In conclusion, the overall behaviour of MMP‐2 and MMP‐9 within the prostate under androgen handling is highly complex, as each glandular compartment and cell type is affected differently by the androgenic status. Prostate regrowth appears to involve a more effective participation of MMP‐2 in both epithelial and stromal compartments, while MMP‐9 plays a major role in the late prostate atrophy and early regrowth.
Endocrine disruptors targeting ERβ function
Authors: Swedenborg E. , Pongratz I. , Gustafsson J.‐Å.
Published: December 2009

Endocrine disruptive chemicals (EDCs) circulating in the environment constitute a risk to ecosystems, wildlife and human health. Oestrogen receptor (ER) alpha and beta are targeted by various kinds of EDCs but the molecular mechanisms and long‐term consequences of exposure are largely unknown. Some biological effects of EDCs are mediated by the aryl hydrocarbon receptor (AhR), which is a key player in the cellular defence against xenobiotic substances. Adding complexity to the picture, there is also accumulating evidence that AhR‐ER pathways have an intricate interplay at multiple levels. In this review, we discuss some EDCs that affect the oestrogen pathway by targeting ERβ. Furthermore, we describe some effects of AhR activities on the oestrogen system. Mechanisms as well as potential adverse effects on human health are discussed.
Relating juvenile spatial distribution to breeding patterns in anadromous salmonid populations
Authors: Foldvik Anders , Finstad Anders Gravbrøt , Einum Sigurd
Published: December 2009

1. Spatial within‐population heterogeneity in density probably affects competition intensity and may have a fundamental role in shaping population dynamics and carrying capacity. This may be particularly relevant for organisms where limitations on juvenile mobility cause maternal choice of breeding locations to influence the spatial distribution of younger life stages.

2. In this study, we mapped redd locations and the resulting densities of juveniles the following year along the entire reach (9·2 km) of a river holding natural populations of anadromous salmonids (Atlantic salmon and brown trout). These data were used to quantify the spatial scale over which breeding influences juvenile densities, and hence becomes important for density‐dependent processes.

3. Although the observed cumulative distributions indicated a relatively uniform distribution of breeding along the river, autocorrelation analyses identified spatial patchiness of both breeding and resulting juveniles on a local scale. Furthermore, cross‐correlations suggested a close spatial relationship between distribution of redds and juveniles.

4. Using spatially explicit hockey‐stick stock–recruitment functions, we found juvenile salmonid density to be mostly influenced by the amount of breeding upstream of a given location. This influence decreased rapidly within the first 75–150 m. Thus, female choice with regard to breeding location gave rise to a heterogeneous distribution of offspring on a spatial scale of almost two orders of magnitude finer than that of the whole population (9·2 km).

5. The results are consistent with smaller scale experimental studies of salmonids, and emphasize the role for maternal choice of breeding locations in causing substantial spatial heterogeneity in juvenile densities within natural populations. Due to effects of density heterogeneity on overall levels of competition, this adds another layer of complexity to the dynamics of salmonid populations even in populations where breeding appears to be relatively uniformly distributed through space, and potentially also for a range of other organisms where juvenile dispersal is constrained.
Recovery of anuran community diversity following habitat replacement
Authors: Lesbarrères David , Fowler Mike S. , Pagano Alain , Lodé Thierry
Published: December 2009

1. Recently habitat degradation, road construction and traffic have all increased with human populations, to the detriment of aquatic habitats and species. While numerous restoration programmes have been carried out, there is an urgent need to follow their success to better understand and compensate for the decline of amphibian populations. To this end, we followed the colonization success of an anuran community across multiple replacement ponds created to mitigate large‐scale habitat disturbance.

2. Following construction of a highway in western France, a restoration project was initiated in 1999 and the success of restoration efforts was monitored. The amphibian communities of eight ponds were surveyed before they were destroyed. Replacement ponds were created according to precise edaphic criteria, consistent with the old pond characteristics and taking into account the amphibian species present in each. The presence of amphibian species was recorded every year during the breeding period for 4 years following pond creation.

3. Species richness initially declined following construction of the replacement ponds but generally returned to pre‐construction levels. Species diversity followed the same pattern but took longer to reach the level of diversity recorded before construction. Pond surface area, depth and sun exposure were the most significant habitat characteristics explaining both amphibian species richness and diversity. Similarly, an increase in the number of vegetation strata was positively related to anuran species richness, indicating the need to maintain a heterogeneous landscape containing relatively large open wetland areas.

4. Synthesis and applications. We highlight the species‐specific dynamics of the colonization process, including an increase in the number of replacement ponds inhabited over time by some species and, in some cases, an increase in population size. Our work suggests that successful replacement ponds can be designed around simple habitat features, providing clear benefits for a range of amphibian species, which will have positive cascading effects on local biodiversity. However, consideration must also be given to the terrestrial buffer zone when management strategies are being planned. Finally, our study offers insight into the successful establishment of anuran communities over a relatively short time in restored or replacement aquatic environments.
Barriers to tree seedling emergence on human‐induced grasslands in Sri Lanka
Authors: Gunaratne A. M. T. A. , Gunatilleke C. V. S. , Gunatilleke I. A. U. N. , Madawala Weerasinghe H. M. S. P. , Burslem D. F. R. P.
Published: December 2009

1. Colonization by woody plants is often very slow or absent on grasslands occupying degraded land in the tropics. Seed dispersal limitation is widely reported, but the constraints to forest succession imposed by barriers to seedling establishment are poorly understood. We tested the hypotheses that seedling emergence of woody plants is limited by interactions of anthropogenic fire, vertebrate herbivory and competition with the dominant grass sward in human‐induced montane grasslands in Sri Lanka.

2. Seedling emergence was determined fortnightly for 18 months in response to experimental manipulation of fire regimes, access by vertebrate herbivores and competition from the dominant grass canopy at the forest/grassland edge and at 10, 20 and 40 m from the edge into four blocks of grassland. Seedling emergence was also monitored in the absence of any experimental manipulation at 10, 20 and 40 m into adjacent blocks of lower montane rainforest.

3. Emergence of seedlings of woody plants was much lower in the grassland (mean <0·1 seedlings m−2 year−1) than in natural forest patches (mean 6·0 seedlings m−2 year−1), but was maximal at the forest/grassland edge (mean 9·5 m−2 year−1). In the grassland, fire reduced seedling emergence by 36% in fenced vertebrate exclosures but increased seedling emergence by 68% in unfenced plots. Exclusion of vertebrate herbivores had no impact on seedling emergence at the forest/grassland edge. Removal of the grass canopy by clipping or tilling increased seedling emergence at the edge, but had no effect in the grassland. Seedlings of the woody pioneer speciesMacaranga indicadominated the community of emergents in the grassland and at the edge.

4. Synthesis and applications. Although dispersal limitation represents the primary constraint to forest succession on degraded montane grasslands in Sri Lanka, management of fire regimes, vertebrate herbivory and competition from the dominant grasses would influence the abundance and composition of tree seedling emergents. Tilling in narrow strips, 2–5 m wide and within 10 m of the forest edge, would facilitate the emergence and establishment of early successional trees in the grassland, but the strips would require protection from fire for at least 2 years. Within the interior of grassland patches, a combination of controlled burning and short‐term access to vertebrate dispersers would promote tree seedling emergence, but the burned patches would then require long‐term protection from fire and grazing subsequently to allow the emergents to establish and catalyse forest succession.
Genetic diversity and antimicrobial resistance of Flavobacterium psychrophilum isolated from cultured rainbow trout, Onchorynchus mykiss (Walbaum), in Spain
Authors: Del Cerro A , Márquez I , Prieto J M
Published: January 2010

Flavobacterium psychrophilum is the causative agent of bacterial cold‐water disease (CWD) and rainbow trout fry syndrome (RTFS) in salmonids. These diseases are a major problem in the aquaculture industry in Spain, and a better understanding of the epidemiology of F. psychrophilum isolates is necessary to improve management strategies. In this study, to investigate genetic variability of this bacterium, pulsed‐field gel electrophoresis after DNA digestion with endonuclease StuI, plasmid profiling analysis and antimicrobial susceptibility testing were undertaken with 25 isolates of F. psychrophilum from Spain. These isolates were classified into 17 patterns by PFGE analysis, which were grouped into four clusters and seven independent branches. Twenty isolates (80%) possessed plasmids of 3.5 kb (n = 13) or 5.5 kb (n = 7). No plasmids were associated with antibiotic resistance to oxytetracycline (OTC) or florfenicol (FLO). Twenty isolates (80%) had minimum inhibitory concentrations (MICs) to OTC of between 2.4 and 9.7 μg mL−1, and all isolates were susceptible to FLO. A relationship between the origin of the isolates and PFGE genotypes was found. Plasmid profile typing correlated with PFGE profile typing, whereas no correlation was found between antimicrobial susceptibility testing and PFGE profiles. These results suggest that the population of F. psychrophilum with pathogenic potential in northern Spain is quite heterogeneous.
Exploratory factor analysis of the Brazilian OHIP for edentulous subjects
Authors: SOUZA R. F. , LELES C. R. , GUYATT G. H. , PONTES C. B. , DELLA VECCHIA M. P. , NEVES F. D.
Published: December 2009

Summary  The use of seven domains for the Oral Health Impact Profile (OHIP)‐EDENT was not supported for its Brazilian version, making data interpretation in clinical settings difficult. Thus, the aim of this study was to assess patients’ responses for the translated OHIP‐EDENT in a group of edentulous subjects and to develop factor scales for application in future studies. Data from 103 conventional and implant‐retained complete denture wearers (36 men, mean age of 69·1 ± 10·3 years) were assessed using the Brazilian version of the OHIP‐EDENT. Oral health‐related quality of life domains were identified by factor analysis using principal component analysis as the extraction method, followed by varimax rotation. Factor analysis identified four factors that accounted for 63% of the 19 items total variance, named masticatory discomfort and disability (four items), psychological discomfort and disability (five items), social disability (five items) and oral pain and discomfort (five items). Four factors/domains of the Brazilian OHIP‐EDENT version represent patient‐important aspects of oral health‐related quality of life.
Neonatal sepsis, antibiotic therapy and later risk of asthma and allergy
Authors: Sobko Tanja , Schiött Jessica , Ehlin Anna , Lundberg Jon , Montgomery Scott , Norman Mikael
Published: December 2009

Sobko T, Schiött J, Ehlin A, Lundberg J, Montgomery S, Norman M. Neonatal sepsis, antibiotic therapy and later risk of asthma and allergy. Paediatric and Perinatal Epidemiology 2010; 24: 88–92.

Neonatal sepsis and early antibiotic therapy affect bacterial colonisation and immune activation after birth. This could have implications for later risk of allergy and asthma. Using a validated questionnaire (International Study of Asthma and Allergies in Children, ISAAC), we screened for asthma and allergy in three cohorts (total n = 834; median age 12, range 7–23 years) with different perinatal exposures as regards infection and antibiotics.

Asthma, but not hay fever, was more prevalent after neonatal sepsis with adjusted odds ratio (OR) 1.63 [95% confidence interval (CI) 1.04, 2.56] and early antibiotic therapy (OR 1.48 [0.93, 2.35]) as compared with a control group. There was a trend towards increased atopic eczema after neonatal sepsis (OR = 1.39 [CI = 0.98, 1.98]). We conclude that neonatal sepsis is associated with an increased risk for later development of asthma. Early antibiotic exposure may contribute to this association.
Accuracy of reporting bleeding during pregnancy
Authors: Hasan Reem , Jonsson Funk Michele L. , Herring Amy H. , Olshan Andrew F. , Hartmann Katherine E. , Baird Donna D.
Published: December 2009

Hasan R, Jonsson Funk ML, Herring AH, Olshan AF, Hartmann KE, Baird DD. Accuracy of reporting bleeding during pregnancy. Paediatric and Perinatal Epidemiology 2010; 24: 31–34.

Vaginal bleeding during pregnancy has been considered a marker of an at‐risk pregnancy, but the accuracy of reported bleeding has not been assessed. We sought to evaluate the agreement in vaginal bleeding reports based on prospective daily diary and retrospective recall at first‐trimester interview and to investigate predictors of reporting accuracy. Participants recruited prior to pregnancy for a community‐based pregnancy cohort (n = 153) completed web‐based daily diaries beginning before pregnancy until the end of the first trimester. A comprehensive first‐trimester interview was conducted, and the bleeding data from diary and interview were compared. Kappa statistics were used to quantify agreement. Log‐linear models were used to investigate maternal age, prior miscarriage, and current pregnancy outcome as potential predictors of agreement.

We found that bleeding characteristics (number of bleeding episodes, bleeding heaviness, duration and gestational timing) from the diary and interview were reported with high levels of agreement. Kappas ranged from 0.77 to 0.84. Retrospective report of any bleeding had a sensitivity of 0.80 and specificity of 1.0; however, sensitivity was lower when examined within smaller time intervals. Important predictors of agreement were not identified in this analysis, but the sample was small. Overall, the presence of vaginal bleeding, a common and potentially alarming symptom of early pregnancy, may be assessed by interview later in pregnancy with reasonable accuracy.
Modelling hydration and photosystem II activation in relation to in situ rain and humidity patterns: a tool to compare performance of rare and generalist epiphytic lichens
Authors: JONSSON ČABRAJIĆ ANNA V. , LIDÉN MARLENE , LUNDMARK TOMAS , OTTOSSON‐LÖFVENIUS MIKAELL , PALMQVIST KRISTIN
Published: December 2009

A dynamic water and activity model was developed to assess how efficiently lichens can exploit in situ rain and humid air. The capacity to rehydrate and activate photosynthesis [i.e. photosystem II (PSII)] by these water sources was compared among four hydrophilic and one generalist epiphytic lichen. Hydration status, potential (instant activation) and realized (delayed activation) day‐light activity were simulated using a model based on species‐specific hydration, PSII activation characteristics and in situ water content for Platismatia norvegica in three microclimatic scenarios. The results showed that delayed PSII activation could have profound effects on lichens' ability to exploit environmental water sources. During rain, realized activity was reduced by 19, 34 and 56% compared to simulations assuming instant activation for three hydrophilic lichens in the driest microclimate. During humid air, the reduction was 81% for the most extreme species and scenario, because of slow hydration and low equilibrium water content. Many and brief hydration events may thus hamper species with slow activation and fast desiccation kinetics. No evidence of compensation by a ‘water‐holding’ morphology was observed among studied species. The developed model may provide a tool for identifying suitable habitats for long‐term persistence of lichens with physiological constraints.
The effect of the heterologous expression of Phragmites australis γ‐glutamylcysteine synthetase on the Cd2+ accumulation of Agrostis palustris
Authors: ZHAO CUIZHU , QIAO MENG , YU YANCHONG , XIA GUANGMIN , XIANG FENGNING
Published: December 2009

Heavy metal pollution has become one of the most serious environmental problems today. To develop a more efficient plant to clean up heavy metal contaminated soils, a γ‐glutamylcysteine synthetase (GCS) cDNA, named PaGCS, was isolated by PCR from Phragmites australis. The PaGCS sequence was transformed via agroinfection into the heavy metal intolerant grass Agrostis palustris. Five confirmed transgenic A. palustris plants expressing PaGCS were compared with the wild‐type line for growth and Cd2+ accumulation, as well as for the expression of a number of phytochelatin synthesis and stress‐responsive enzymes when challenged with Cd2+ stress. GCS and phytochelatin synthase (PCS) were up‐regulated in the transgenic lines. All the transgenic lines accumulated more Cd2+ and phytochelatins (PCs) than the wild‐type line, and three of the five lines grew more effectively than the wild‐type after either five or 21 d of Cd2+ stress. Variation among the transgenics was observed for the distribution of Cd2+ in the root, shoot and leaf. The malondialdehyde content of all the transgenic lines was lower than that of the wild type under Cd2+ treatment, while the activity of both superoxide dismutase and peroxidase present in the transgenic lines increased markedly 24 h after Cd2+ stress, and then rapidly declined.
Baltic amber Ibaliidae (Hymenoptera: Cynipoidea): a new genus with implications for the phylogeny and historical biogeography of the family
Authors: LIU ZHIWEI , ENGEL MICHAEL S.
Published: January 2010

Abstract. The first definitive ibaliid wasp (Cynipoidea: Ibaliidae) is described and illustrated from a female preserved in middle Eocene (Lutetian) Baltic amber. Archaeibalia succinica Liu & Engel gen. et sp.n. is distinct from all other members of the family, cladistically placed as sister to all other Ibaliidae, and classified in its own subfamily, Archaeibaliinae Liu & Engel subfam.n. The genus was putatively a parasitoid of wood‐boring insects in hardwood trees. Given that the species is exceptionally rare in Baltic amber (a single individual) despite a habitat that would have placed it in immediate proximity with resin flows, the host of A. succinica was probably not living in the ‘Baltic amber tree’. The historical biogeography and evolution of ibaliids is reconsidered based on the present paleontological evidence.
How to read a report of a randomized controlled trial
Authors: JUN MIN , ZOUNGAS SOPHIA , PERKOVIC VLADO , WEBSTER ANGELA C
Published: January 2010

Proper evaluation of up‐to‐date clinical evidence is essential for the provision of optimal patient care. Randomized controlled trials (RCTs) are the ideal study type to investigate the benefit or harm of an intervention, such as a drug therapy. RCTs aims to avoid biased assessment of clinical interventions through the even distribution of both known and unknown factors that may influence outcomes. However, not all RCTs are well designed, conducted or reported. As such, the clinician needs to critically appraise RCTs in order to determine their strengths and weaknesses. This paper aims to explain how to approach critical appraisal, by highlighting and illustrating important questions that help determine the reliability of results from randomized trials.