bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in diet and trophic position of a top predator 10 years after a mass mortality of a key prey
Authors: Chiaradia André , Forero Manuela G. , Hobson Keith A. , Cullen J. Mike
Published: June 2010

Chiaradia, A., Forero, M. G., Hobson, K. A., and Cullen, J. M. 2010. Changes in diet and trophic position of a top predator 10 years after a mass mortality of a key prey. – ICES Journal of Marine Science, 67: 1710–1720. After the disappearance of primary prey, seabirds exhibit gradually decreased breeding performance, and eventually the population size drops. Results are presented of an investigation into the diet of little penguins (Eudyptula minor) at Phillip Island, Australia, during a period when their key prey, pilchard (Sardinops sagax), declined dramatically. Data from stomach flushing (1982–2006) were used, supported by stable isotope (δ15N, δ13C) analyses of blood samples (2003, 2004, and 2006). The effect of the pilchard mortality on penguin diet was immediate, the birds shifting to a diet almost devoid of pilchard, and this was followed by 2 years of low breeding success, with considerably fewer penguins coming ashore. During periods when pilchard was not part of the diet, penguins consumed prey of a higher trophic level, e.g. higher values of δ15N. Variability in penguin blood δ15N coincided with years of low prey diversity. The disappearance of pilchard resulted in a decrease in prey diversity and led penguins to “fish up” the foodweb, possibly because of the simplified trophic structure. After 1998, however, breeding success re-attained average levels and the numbers of penguins coming ashore increased, probably because of increased abundance of prey other than pilchard after a 3-year period of food scarcity. Although little penguins apparently compensated over time, a less-flexible diet could make them ultimately vulnerable to further changes in their foodweb.
Bowel Habits in the First 24 Months of Life: Preterm‐ Versus Term‐born Infants
Authors: Bekkali N , Moesker FM , Van Toledo L , Reitsma JB , Hamers SL , Valerio PG , Benninga MA
Published: July 2010

Background and Aim:

New prospective studies concerning feeding and bowel habits of term and preterm infants from birth to 24 months of life are needed. The aim of the present study was to describe and compare feeding and bowel habits between term‐ and preterm‐born infants starting from birth up to the age of 24 months.

Patients and Methods:

Between August and November 2006 all of the infants admitted to an academic and nonacademic neonatal care unit with gestational age 25 to 42 weeks participated in the study. Bowel diaries were recorded 1 and 2 weeks, and 3, 6, 12, and 24 months after birth. Infants with gastrointestinal surgery, neurological diseases, metabolic diseases, or congenital abnormalities were excluded.

Results:

A total of 199 (126 preterm) infants were eligible; 153 gave consent for participation. Although feeding frequency was higher in the first 3 months in the preterm born, overall feeding frequency decreased between the first 3 follow‐up periods (P < 0.001) in both groups. In the first and second week, breast‐fed infants had 2.41 more episodes of defecation per week compared with the formula‐fed infants (P = 0.017 and P = 0.021, respectively). Higher median (10th percentile–90th percentile) defecation frequency was only found in week 1 in the term compared with the preterm group (24 [9.4–31.6] versus 16 [6.5–31]; P = 0.002). The overall median defecation frequency was 16 (7–30) per week from birth up to the age of 24 months over the total group of participating infants.

Conclusions:

Term and preterm infants have a comparable defecation frequency from the second week of life up to the age of 24 months.
Complications of Congenital Portosystemic Shunts in Children: Therapeutic Options and Outcomes
Authors: Franchi‐Abella Stéphanie , Branchereau Sophie , Lambert Virginie , Fabre Monique , Steimberg Clarisa , Losay Jean , Riou Jean‐Yves , Pariente Danièle , Gauthier Frédéric , Jacquemin Emmanuel , Bernard Olivier
Published: July 2010

Background and Objective:

Congenital portosystemic shunts are rare vascular malformations that lead to severe complications. Their management is controversial. The aim of this study was to propose a clear definition of the risks and management of congenital portosystemic shunts in children according to our experience and a review of the literature.

Patients and Methods:

Twenty‐two children with a complicated congenital portosystemic shunt were studied in our institution. When necessary, management included portal pressure measurement and portal vein angiography during an occlusion test and closure of the shunt by surgical and/or endovascular methods.

Results:

Five neonates with intrahepatic shunts presented with cholestasis that resolved spontaneously, and 17 older children presented with liver tumors (13) and/or hepatopulmonary syndrome (2), pulmonary artery hypertension (3), portosystemic encephalopathy (3), heart failure (1), and glomerulonephritis (1). The portosystemic shunt was extrahepatic (11) or intrahepatic (6). Portosystemic shunts were closed by endovascular methods in 5 children and surgically in 10, 4 of whom had portal pressure during occlusion above 35 mmHg and extremely hypoplastic or undetectable portal veins requiring banding of the fistula before closure. Shunt closure resulted in restoration of intrahepatic portal flow in all, with complete or partial regression of benign liver masses, and regression or stabilization of pulmonary, cardiac, neurological, and renal complications.

Conclusions:

Congenital portosystemic shunt carries risks of severe complications in children. Closure of a shunt persisting after age 2 years should be considered preventively. Intrahepatic portal flux restoration can be expected, even when intrahepatic portal veins are extremely hypoplastic or undetectable.
The May threshold and life-history allometry
Authors: Ginzburg Lev R. , Burger Oskar , Damuth John
Published: July 2010

One of Robert May's classic results was finding that population dynamics become chaotic when the average lifetime rate of reproduction exceeds a certain value. Populations whose reproductive rates exceed thisMay thresholdprobably become extinct. The May threshold in each case depends upon the shape of the density-dependence curve, which differs among models of population growth. However, species of different sizes and generation times that share a roughly similar density-dependence curve will also share a similar May threshold. Here, we argue that this fact predicts a striking allometric regularity among animal taxa: lifetime reproductive rate should be roughly independent of body size. Such independence has been observed in diverse taxa, but has usually been ascribed to a fortuitous combination of physiologically based life-history allometries. We suggest, instead, that theecological eliminationof unstable populations within groups that share a value of the May threshold is a likely cause of this allometry.
Titanium oral implants: surface characteristics, interface biology and clinical outcome
Authors: Palmquist Anders , Omar Omar M. , Esposito Marco , Lausmaa Jukka , Thomsen Peter
Published: July 2010

Bone-anchored titanium implants have revolutionized oral healthcare. Surface properties of oral titanium implants play decisive roles for molecular interactions, cellular response and bone regeneration. Nevertheless, the role of specific surface properties, such as chemical and phase composition and nanoscale features, for the biologicalin vivoperformance remains to be established. Partly, this is due to limited transfer of state-of-the-art preparation techniques to complex three-dimensional geometries, analytical tools and access to minute, intact interfacial layers. As judged by the available results of a few randomized clinical trials, there is no evidence that any particular type of oral implant has superior long-term success. Important insights into the recruitment of mesenchymal stem cells, cell–cell communication at the interface and high-resolution imaging of the interface between the surface oxide and the biological host are prerequisites for the understanding of the mechanisms of osseointegration. Strategies for development of the next generation of material surface modifications for compromised tissue are likely to include time and functionally programmed properties, pharmacological modulation and incorporation of cellular components.
Luminescence from hydrodynamic cavitation
Authors: Farhat M. , Chakravarty A. , Field J. E.
Published: July 2010

The majority of the research on cavitation luminescence has focused on the sonoluminescence or chemiluminescence generated by cavitation induced through ultrasound, with a lesser body of work on the luminescence induced by laser- or spark-induced cavitation. In such circumstances, the cavitation is generated in liquids where, on the broad scale, there is usually assumed to be no net liquid flow (although of course there are small-scale flows as a result of the cavitation itself, through radiation forces, streaming, microstreaming and turbulence). Little attention has been paid to the luminescence that accompanies (undesirable) cavitation in pumps and turbines or in marine propellers. In the present study, the sonoluminescence specific to air/water vapour bubbles, collapsing within a cavitation tunnel, is addressed. The particular case of leading edge cavitation over a two-dimensional hydrofoil is considered in detail. Hence, strong instabilities develop, causing the attached cavity to shed large clouds of micro bubbles. The spatial and temporal properties of the emitted luminescence were studied using an intensified charge coupled device video camera and a photomultiplier (PM). The light emission was found to extend downstream from the region of cavity closure, to the region where the travelling vortices collapse. Examination of the PM signal on short time scales showed that the emitted luminescence consisted of relatively intense flashes of short duration (as with other forms of luminescence). Individual flashes were often found to be clustered in time. Over longer time scales, clear evidence of periodicity was found in the PM signals. Further analysis showed that bursts of light were being emitted at the Strouhal frequency (for the shedding of transcient cavities).
Effects of personality on territory defence in communication networks: a playback experiment with radio-tagged great tits
Authors: Amy Mathieu , Sprau Philipp , de Goede Piet , Naguib Marc
Published: July 2010

Individuals often differ consistently in behaviour across time and contexts, and such consistent behavioural differences are commonly described as personality. Personality can play a central role in social behaviour both in dyadic interactions and in social networks. We investigated whether explorative behaviour, as proxy of personality of territorial male great tits (
Parus major
), predicts their own and their neighbours' territorial responses towards simulated intruders. Several weeks prior to playback, subjects were taken from the wild to test their exploratory behaviour in a standard context in the laboratory. Exploratory behaviour provides a proxy of personality along a slow–fast explorer continuum. Upon release, males were radio-tracked and subsequently exposed to interactive playback simulating a more or a less aggressive territorial intruder (by either overlapping or alternating broadcast songs with the subjects' songs). At the same time, we radio-tracked a neighbour of the playback subject. Male vocal responses during playback and spatial movements after playback varied according to male explorative behaviour and playback treatment. Males with lower exploration scores approached the loudspeaker less, and sang more songs, shorter songs and songs with slower element rates than did males with higher exploration scores. Moreover, neighbour responses were related to the explorative behaviour of the subject receiving the playback but not to their own explorative behaviour. Our overall findings reveal for the first time how personality traits affect resource defence within a communication network providing new insights on the cause of variation in resource defence behaviour.
Limited CD4+ T cell proliferation leads to preservation of CD4+ T cell counts in SIV-infected sooty mangabeys
Authors: Chan Ming Liang , Petravic Janka , Ortiz Alexandra M. , Engram Jessica , Paiardini Mirko , Cromer Deborah , Silvestri Guido , Davenport Miles P.
Published: July 2010

Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) infections result in chronic virus replication and progressive depletion of CD4+ T cells, leading to immunodeficiency and death. In contrast, ‘natural hosts’ of SIV experience persistent infection with high virus replication but no severe CD4+ T cell depletion, and remain AIDS-free. One important difference between pathogenic and non-pathogenic infections is the level of activation and proliferation of CD4+ T cells. We analysed the relationship between CD4+ T cell number and proliferation in HIV, pathogenic SIV in macaques, and non-pathogenic SIV in sooty mangabeys (SMs) and mandrills. We found that CD4+ T cell proliferation was negatively correlated with CD4+ T cell number, suggesting that animals respond to the loss of CD4+ T cells by increasing the proliferation of remaining cells. However, the level of proliferation seen in pathogenic infections (SIV in rhesus macaques and HIV) was much greater than in non-pathogenic infections (SMs and mandrills). We then used a modelling approach to understand how the host proliferative response to CD4+ T cell depletion may impact the outcome of infection. This modelling demonstrates that the rapid proliferation of CD4+ T cells in humans and macaques associated with low CD4+ T cell levels can act to ‘fuel the fire’ of infection by providing more proliferating cells for infection. Natural host species, on the other hand, have limited proliferation of CD4+ T cells at low CD4+ T cell levels, which allows them to restrict the number of proliferating cells susceptible to infection.
Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature
Authors: Bradbury Ian R. , Hubert Sophie , Higgins Brent , Borza Tudor , Bowman Sharen , Paterson Ian G. , Snelgrove Paul V. R. , Morris Corey J. , Gregory Robert S. , Hardie David C. , Hutchings Jeffrey A. , Ruzzante Daniel E. , Taggart Chris T. , Bentzen Paul
Published: July 2010

Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n= 40) for which allele frequencies show parallel temperature-associated clines (p< 0.001,r2= 0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted ‘neutral’ loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.
Chryseobacterium xinjiangense sp. nov., isolated from alpine permafrost
Authors: Zhao Qi , Bai Yu , Zhang Gaosen , Zhu Shan , Sheng Hongmei , Sun Yaxuan , An Lizhe
Published: June 2010

Strain TSBY 67T was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China. On the basis of 16S rRNA gene sequence analysis, strain TSBY 67T was closely related to members of the genus Chryseobacterium and exhibited 96.8 % 16S rRNA gene sequence similarity to Chryseobacterium aquaticum 10-46T and Chryseobacterium soldanellicola PSD 1-4T. Strain TSBY 67T grew aerobically, at 4–37 °C, with 0–2 % NaCl and at pH 6–8. Cells were Gram-staining negative, non-motile and non-spore-forming rods. The dominant cellular fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.1 %) and iso-C17 : 1ω9c (15.4 %). The G+C content of the DNA was 33.5 mol%. Strain TSBY 67T was distinguishable from its closest phylogenetic neighbours by a combination of phenotypic characteristics. Therefore, strain TSBY 67T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium xinjiangense sp. nov. is proposed. The type strain is TSBY 67T ( = NRRL B-51308T = CCTCC AB 207183T).
The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin
Authors: Müller Philipp , Park Sookhee , Shor Erika , Huebert Dana J. , Warren Christopher L. , Ansari Aseem Z. , Weinreich Michael , Eaton Matthew L. , MacAlpine David M. , Fox Catherine A.
Published: July 2010

The origin recognition complex (ORC) binds to the specific positions on chromosomes that serve as DNA replication origins. Although ORC is conserved from yeast to humans, the DNA sequence elements that specify ORC binding are not. In particular, metazoan ORC shows no obvious DNA sequence specificity, whereas yeast ORC binds to a specific DNA sequence within all yeast origins. Thus, whereas chromatin must play an important role in metazoan ORC's ability to recognize origins, it is unclear whether chromatin plays a role in yeast ORC's recognition of origins. This study focused on the role of the conserved N-terminal bromo-adjacent homology domain of yeast Orc1 (Orc1BAH). Recent studies indicate that BAH domains are chromatin-binding modules. We show that the Orc1BAH domain was necessary for ORC's stable association with yeast chromosomes, and was physiologically relevant to DNA replication in vivo. This replication role was separable from the Orc1BAH domain's previously defined role in transcriptional silencing. Genome-wide analyses of ORC binding in ORC1 and orc1bahΔ cells revealed that the Orc1BAH domain contributed to ORC's association with most yeast origins, including a class of origins highly dependent on the Orc1BAH domain for ORC association (orc1bahΔ-sensitive origins). Orc1bahΔ-sensitive origins required the Orc1BAH domain for normal activity on chromosomes and plasmids, and were associated with a distinct local nucleosome structure. These data provide molecular insights into how the Orc1BAH domain contributes to ORC's selection of replication origins, as well as new tools for examining conserved mechanisms governing ORC's selection of origins within eukaryotic chromosomes.
New chaps in the histone chaperone arena
Authors: Campos Eric I. , Reinberg Danny
Published: July 2010

Understanding exactly how chromatin is assembled is paramount to addressing how select histone modifications may be transmitted, a putative epigenetic process. In the June 15, 2010, issue of Genes & Development, Drané and colleagues (pp. 1253–1265) identified DAXX as a novel H3.3-specific chaperone. This finding, in the context of others published by Goldberg and colleauges in Cell and Sawatsubashi and colleagues (pp. 159–170) in the January 15, 2010, issue of Genes & Development, provides the impetus for uncovering the mechanistic and functional properties of alternative histone deposition pathways.
Novel role for a bacterial nucleoid protein in translation of mRNAs with suboptimal ribosome-binding sites
Authors: Park Hyun-Sook , Östberg Yngve , Johansson Jörgen , Wagner E. Gerhart H. , Uhlin Bernt Eric
Published: July 2010

In Escherichia coli, the major nucleoid protein H-NS limits transcription by acting as a repressor or transcriptional silencer, presumably by its ability to close the looped chromosome domains in the nucleoid through DNA–protein–DNA bridging. Here, we demonstrate the direct involvement of H-NS as a positive factor stimulating translation of the malT mRNA. In vitro studies showed that H-NS facilitates a repositioning of the 30S preinitiation complex on the malT mRNA. H-NS stimulation of translation depended on the AU-rich −35 to −40 region of the mRNA. Several additional examples were found demonstrating a novel function for H-NS in translation of genes with suboptimal ribosome-binding sequences.
Preparation of Pseudotyped Lentiviral Vectors Resistant to Inactivation by Serum Complement
Authors: Guibinga Ghiabe H. , Friedmann Theodore
Published: July 2010

INTRODUCTION

A major obstacle to in vivo delivery of lentivirus or other retroviral vectors is their lability in the presence of serum. In vivo, these viral particles are rapidly destroyed by nonspecific complement-mediated degradation mechanisms. The eventual effective use of retroviral vectors for in vivo gene delivery would be greatly facilitated by the development of methods to protect the viral particles from such degradation. This protocol describes methods for the production of complement-stabilized lentiviral vectors either by pseudotyping the viral particles with a fusion envelope protein containing the complement-regulatory protein CD55 (decay accelerating factor, DAF) or by coassembly with the native DAF protein. An in vitro serum inactivation assay is also described.
Purification of Epitope-Tagged Transcription Factor IID
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: July 2010

INTRODUCTION

Transcription factor IID (TFIID) is one of the most critical factors in transcription complex assembly because it recognizes a core promoter and interacts with chromatin and activator proteins. This protocol uses immunoaffinity chromatography in a simple two-step procedure to purify modified TFIID to homogeneity with limited loss of activity. In brief, a short peptide containing the influenza virus hemagglutinin (HA) tag is fused onto the amino terminus of TATA-binding protein (TBP), and a retroviral transfer system is used to generate a HeLa cell line stably expressing the HA-tagged TBP. Extracts from this cell line contain TFIID, which stably incorporates the epitope-tagged TBP. The TFIID is partially purified from these extracts using phosphocellulose chromatography and then immunopurified using a resin containing protein A-Sepharose beads cross-linked to a monoclonal antibody against the influenza epitope. The TFIID is then eluted from the immunoaffinity resin in pure form using an HA peptide. The resulting TFIID contains a complete complement of TBP-associated factors (TAFs) and can be used in transcription, electrophoretic mobility shift assays (EMSA), and footprinting assays; its purity is well suited for many other studies.
Homogenization of Mammalian Tissue
Authors: Simpson Richard J.
Published: July 2010

INTRODUCTION

To purify or characterize an intracellular protein, it is important to choose an efficient method for disrupting the cell or tissue that rapidly releases the protein from its intracellular compartment into a buffer that is not harmful to the biological activity of the protein of interest. One of the most widely used methods for disrupting soft tissues is homogenization. This protocol describes three processes for homogenization of animal tissues using mechanical shear: a Potter-Elvehjem glass-Teflon homogenizer, a Dounce hand homogenizer, or a handheld Waring Blendor. These methods are rapid and pose little risk to proteins other than the release of proteases from other cellular compartments. Proteolytic degradation can be minimized by the inclusion of protease inhibitors in the homogenization buffers. An optional procedure to remove mucin from tissue homogenates is also presented.
Transfection of Cells with DNA Encoding a Visible Fluorescent Protein-Tagged Lipid-Binding Domain
Authors: Schultz Carsten , Neef Anne B. , Gadella Theodorus W. , Goedhart Joachim
Published: July 2010

INTRODUCTION

Visualization of a certain lipid species can be achieved by producing a fusion protein between a lipid-binding domain and a visible fluorescent protein (VFP). After a DNA construct for a VFP-tagged lipid-binding domain has been prepared, the desired cell line is transfected with the DNA and visualized using fluorescence microscopy, as described here. The DNA encoding a VFP-tagged lipid-binding domain is isolated from Escherichia coli, and the cells to be transfected are grown on glass-bottom dishes or on coverslips. We routinely perform transfection with commercially available reagents, although, depending on the cell line, the calcium phosphate precipitation method may provide an economic alternative.
Labeling Lipids for Imaging in Fixed Cells: Figure 1.
Authors: Schultz Carsten , Neef Anne B. , Gadella Theodorus W. , Goedhart Joachim
Published: July 2010

INTRODUCTION

Fluorescently tagged lipid-binding domains have become a popular tool to image lipids that are involved in intracellular signaling processes. The readout usually involves the translocation of the lipid-binding domain from the cytosol or nucleosol to the membrane of interest, or vice versa. Unfortunately, this method seems to work predominantly for lipids in the plasma membrane, whereas lipids such as phosphatidylinositol 4,5-bisphosphate (PIP2) are not recognized in the membranes of the endoplasmic reticulum or the Golgi. Very recently, we developed an alternative way of localizing a lipid of interest by fluorescent labeling of minimally modified lipid derivatives using a single specific chemical reaction. This protocol describes how to directly label lipids in fixed cells for lipid location analyses.
Imaging Lipids in Living Cells
Authors: Schultz Carsten , Neef Anne B. , Gadella Theodorus W. , Goedhart Joachim
Published: July 2010

INTRODUCTION

The investigation of lipids in living cells is one of the underdeveloped areas in cell biology. Although it is possible to analyze the global lipid composition of a cell type, fractionation of the various types of membranes from cells is extraordinarily difficult, mainly because most membranes appear to be in contact with each other. Therefore, we know the lipid components, but we have a difficult time finding out their exact position, how dynamically they change location, and how rapidly they are metabolized. Imaging lipids in cells seems to be the obvious solution to the problem. The most common way to image molecules is by the artificial addition of a fluorescent tag. The use of fluorescent proteins has become the mainstay of protein imaging, but this method is, of course, not suitable for small molecules such as lipids. Unfortunately, the fluorescent tag is usually as large as the lipid and is therefore likely to have a severe influence on lipid location and metabolism. To circumvent this problem, two solutions have been developed--namely, the use of fluorescently labeled proteins that specifically recognize lipids and a chemical method to introduce the fluorescent tag inside the cell. This article describes procedures necessary to image lipids by fluorescently tagged lipid-binding domains and by labeling lipid derivatives in fixed and living cells.
Ethylene Signaling Regulates Accumulation of the FLS2 Receptor and Is Required for the Oxidative Burst Contributing to Plant Immunity
Authors: Mersmann Sophia , Bourdais Gildas , Rietz Steffen , Robatzek Silke
Published: July 2010

Reactive oxygen species (ROS) are potent signal molecules rapidly generated in response to stress. Detection of pathogen-associated molecular patterns induces a transient apoplastic ROS through the function of the NADPH respiratory burst oxidase homologs D (RbohD). However, little is known about the regulation of pathogen-associated molecular pattern-elicited ROS or its role in plant immunity. We investigated ROS production triggered by bacterial flagellin (flg22) in Arabidopsis (Arabidopsis thaliana). The oxidative burst was diminished in ethylene-insensitive mutants. Flagellin Sensitive2 (FLS2) accumulation was reduced in etr1 and ein2, indicating a requirement of ethylene signaling for FLS2 expression. Multiplication of virulent bacteria was enhanced in Arabidopsis lines displaying altered ROS production at early but not late stages of infection, suggesting an impairment of preinvasive immunity. Stomatal closure, a mechanism used to reduce bacterial entry into plant tissues, was abolished in etr1, ein2, and rbohD mutants. These results point to the importance of flg22-triggered ROS at an early stage of the plant immune response.
Diet overlap among three sympatric African annual killifish species Nothobranchius spp. from Mozambique
Authors: Polačik M. , Reichard M.
Published: June 2010

The diet patterns of three Nothobranchius species (N. furzeri, N. orthonotus and N. rachovii), small, short‐lived annual killifish from temporary pools in African savannah were investigated. Four sites with contrasting fish density and water surface area were sampled in 2008 and 2009 in southern Mozambique. Stomach content analysis showed that all the species examined were generalists, with diets largely based on aquatic invertebrates. The same invertebrate prey categories were consumed by all three species, but their relative proportions varied across species. The largest species, N. orthonotus, showed the most distinct diet and consumed vertebrates (juvenile lungfish Protopterus annectens and larval Amphibia) and a relatively high proportion of Odonata, Coleoptera and Ephemeroptera larvae. The diet of the other two species (N. furzeri and N. rachovii) showed a stronger overlap, did not include vertebrates, but was rich in small crustaceans (Cladocera, Copepoda, Ostracoda and Conchostraca). Mosquito (Diptera) larvae formed only a negligible part of the diet of all the three species.
Cytodiagnosis through use of a z‐axis video by volunteer observers: a promising tool for external quality assessment
Authors: Yamashiro K. , Tagami M. , Azuma K. , Nakamura A. , Kato O. , Taira K. , Azuma M. , Takeda H. , Suzuki H.
Published: June 2010

K. Yamashiro, M. Tagami, K. Azuma, A. Nakamura, O. Kato, K. Taira, M. Azuma, H. Takeda and H. Suzuki

Cytodiagnosis through use of a z‐axis video by volunteer observers: a promising tool for external quality assessment

Objective:  This study examined whether cytological diagnosis through the use of a video, which shows the changing depth of focus in the microscopic field, described as a z‐axis video, is useful compared with a still image.

Methods:  From 17 cytology preparations of fine needle aspiration of the breast, we made six z‐axis videos per case. A frame exhibiting the characteristic features was then extracted from each video and saved as a representative still image. One hundred and twenty‐eight volunteer cytotechnologists were randomly divided into two groups of video observers and still image observers. The participants were asked to make a diagnosis of benign, indeterminate, suspicious or malignant without having any clinical information other than the age of the patient. Diagnoses were categorized as ‘recommended’ or ‘unacceptable’ according to degree of correlation with histology.

Results:  The number of definitive diagnoses of ‘benign’ or ‘malignant’ were increased in video observers, and indeterminate or suspicious categories were decreased (P = 0.013). The distribution of diagnostic categories in three of the 17 cases was significantly different; the distribution in the remaining cases was similar between the two groups. The z‐axis video observers may have selected the definite diagnoses with confidence because they observed valuable microscopic findings by ‘focusing through observation’. The average number of ‘recommended’ diagnoses by individual observers was significantly higher in the video observer group than in the still image observer group (P = 0.016). In contrast, the average number of ‘unacceptable’ diagnoses was significantly lower (P = 0.019).

Conclusions:  A z‐axis video is easy to obtain and is therefore expected to become a powerful diagnostic modality for the external quality assessment of clinical cytology and even in the field of primary cytodiagnosis.
Biases in the analysis of stable isotope discrimination in food webs
Authors: Auerswald Karl , Wittmer Maximilian H. O. M. , Zazzo Antoine , Schäufele Rudi , Schnyder Hans
Published: June 2010

1. Recently, Caut, Angulo & Courchamp (2009, Journal of Applied Ecology) published a review on diet‐tissue isotopic shifts in animals. They concluded that diet‐tissue shifts are influenced by the isotopic composition of the diet for both 13C and 15N in a wide range of animal taxa.

2. We suggest that the conclusion of Caut, Angulo & Courchamp is in error, and provide a discussion of sources of error in the assessment of diet‐tissue discrimination.

3. Errors in the derivation of diet‐tissue shifts include imprecise definitions, mathematical artefacts and invalid statistical analysis. It is likely that the work also suffers from experimental bias. The mathematical artefacts and statistical invalidity result from using the same variable (diet isotopic composition) in the independent and dependent variable for regression analysis and failure to correct for the resulting bias. Experimental bias can result from the incomplete turnover of body pools after diet switches or during natural fluctuations in diet isotope composition. Unfortunately, the main sources of error work in the same direction, strengthening the biased relationship between the diet‐tissue shift and diet isotope composition. Therefore, the analysis of Caut et al. (2009) does not provide proof of a relationship between diet‐tissue shift and diet isotope composition.

4.
Synthesis and application. Future work on diet‐tissue discrimination factors should (i) follow the mathematical rules resulting from how isotope data are presented, (ii) be based on appropriate statistics analysis that avoids or corrects for spurious self‐correlations, and (iii) consider possible complications associated with the presence of slowly turning‐over stores and non‐equilibrating ‘dead’ body pools.
Trophic experiments to estimate isotope discrimination factors
Authors: Caut Stephane , Angulo Elena , Courchamp Franck , Figuerola Jordi
Published: June 2010

1. In Caut, Angulo & Courchamp (2008a) rats were fed with experimental diets of distinct isotopic values (δ13C and δ15N) in order to infer the discrimination factors. We showed negative relationships between discrimination factors and diet isotopic values. In Caut, Angulo & Courchamp (2009), our aim was to generalize these relationships to other taxonomic groups with a view to providing ecologists with a general and flexible method to obtain discrimination factors for diet reconstruction studies when difficult to obtain otherwise.

2.
Perga & Grey (2010) claims that there is an artefact of experimental design (due to protein contents) and partly reanalyzes our data, taking into account the type of diet (mixed or not; carnivorous, omnivorous or herbivorous). However, (i) the role of protein content through isotopic routing is not clear; (ii) a reanalysis of our data shows that the relationships between discrimination factors and diet isotopic values remain significant even when following Perga’s suggestions.

3.
Auerswald et al. (2010) criticized the imprecise definitions, mathematical artefacts and invalid statistical analysis of Caut, Angulo & Courchamp (2009). However, (i) their arguments are not new; they challenge the use of stable isotope in ecological trophic studies in general, and lack both alternative suggestions and ecological perspective; (ii) none of their statistical and mathematical objections has a significant effect on the results.

4.
Synthesis and applications. Neither reply reflects the current context of debate. The complementarity between experimental studies and their application in field studies is indispensable for the use of stable isotopes in ecology. Protocols should be very well assessed in order to represent field conditions with accuracy. Further analyses are necessary to remove some of the flaws in the use of stable isotopes (carrying out an in‐depth analysis of isotopic routing, turnover, and dynamic during trophic experiments to ensure accurate attainment of equilibrium), but none of the issues raised by Perga & Grey (2010) and Auerswald et al. (2010) alter our main conclusions.
Biological roles of translesion synthesis DNA polymerases in eubacteria
Authors: Andersson Dan I. , Koskiniemi Sanna , Hughes Diarmaid
Published: June 2010

Biological systems are strongly selected to maintain the integrity of their genomes by prevention and repair of external and internal DNA damages. However, some types of DNA lesions persist and might block the replication apparatus. The universal existence of specialized translesion synthesis DNA polymerases (TLS polymerases) that can bypass such lesions in DNA implies that replication blockage is a general biological problem. We suggest that the primary function for which translesion synthesis polymerases are selected is to rescue cells from replication arrest at lesions in DNA, a situation that, if not amended, is likely to cause an immediate and severe reduction in cell fitness and survival. We will argue that the mutagenesis observed during translesion synthesis is an unavoidable secondary consequence of this primary function and not, as has been suggested, an evolved mechanism to increase mutation rates in response to various stresses. Finally, we will discuss recent data on additional roles for translesion synthesis polymerases in the formation of spontaneous deletions and in transcription‐coupled TLS, where the coupling of transcription to TLS is proposed to allow the rescue of the transcription machinery arrested at DNA lesions.
Spatiotemporal expression pattern of an encephalopsin orthologue of the sea urchin Hemicentrotus pulcherrimus during early development, and its potential role in larval vertical migration
Authors: Ooka Shioh , Katow Tomoko , Yaguchi Shunsuke , Yaguchi Junko , Katow Hideki
Published: July 2010

We have cloned and studied Hp‐ECPN, an encephalopsin orthologue of the sea urchin Hemicentrotus pulcherrimus. Hp‐ecpn cDNA was produced and found to contain a 1461‐bp open reading frame that encodes 486 amino acids. Accumulation of Hp‐ecpn mRNA and protein expression occurred at the 14 h postfertilization (hpf) swimming blastula stage and thereafter. The Hp‐ECPN protein was N‐glycosylated, and the amino acid sequence was similar to that of vertebrate encephalopsins. Whole‐mount immunohistochemistry revealed the presence of Hp‐ECPN in cells (ECPN cells) that appeared initially around the tip of the archenteron in 20 hpf early gastrulae. By the 54 hpf pluteus stage, ECPN cells had spread through the aboral ectoderm, and, by the eight‐arm pluteus stage, were restricted to the tips of the larval arms and the posterior end of the body. The number of ECPN cells increased under conditions of continuous light, but decreased under continuous dark. Knockdown of Hp‐ecpn mRNA using morpholino antisense oligonucleotides decreased the number of ECPN cells considerably, and inhibited the vertical swimming of the larvae. This suggested that Hp‐ECPN plays a role in photosensitive larval swimming vertical migration. In adult tissues, the ECPN cells were detected exclusively in tube feet.
Laterality of nephrocalcinosis in kidney stone formers with severe hypocitraturia
Authors: Le Jesse D. , Eisner Brian H. , Tseng Timothy Y. , Chi Thomas , Stoller Marshall L.
Published: June 2010

Study Type – Aetiology (case series) Level of Evidence 4

What’s known on the subject? and What does the study add?

Systemic urinary stone‐forming conditions such as hypocitraturia or cystinuria should theoretically lead to symmetric and diffuse stone formation. Small studies have shown that some patients with such conditions produce stones primarily on one side. No studies, however, have attempted to quantify the frequency at which such patients form stones asymmetrically.

This study demonstrates that despite having a severe systemic condition such as hypocitraturia, patients frequently have asymmetric and focal nephrocalcinosis. This suggests that additional intrinsic local factors such as renal perfusion or vascular injury must also play a role in stone formation.

OBJECTIVE To examine the hypothesis that the distribution of nephrocalcinosis in patients with severe hypocitraturia should be symmetric.

PATIENTS AND METHODS Patients with profound hypocitraturia defined as a 24‐h urine citrate <50 mg at the time of initial presentation were identified from the metabolic stone clinic database at our academic medical center. Two independent blinded reviewers evaluated all of the abdominal radiographs for the segmental distribution of macroscopic nephrocalcinosis.

RESULTS A total of 44 patients met study criteria, with an equal distribution of males and females and a mean age of 55.4 ± 13.7 years. Mean urinary citrate was 28 ± 11 mg/day. Nephrocalcinosis was present in at least one renal segment in 22 patients (50%). Of the 22 patients with nephrocalcinosis, 9 patients (41%) had unilateral nephrocalcinosis and 13 patients (59%) had bilateral nephrocalcinosis. Of the 35 kidneys with nephrocalcinosis, 14 kidneys (40%) had nephrocalcinosis in only one renal segment, 13 kidneys (37%) had nephrocalcinosis in two segments and eight kidneys (23%) had nephrocalcinosis involving all three segments.

CONCLUSIONS Despite the systemic nature of severe hypocitraturia, nephrocalcinosis is frequently asymmetric and focal in nature. This suggests that local factors intrinsic to the renal medullary interstitium, such as vascular injury, must play a role in the formation of nephrocalcinosis. Further study to elucidate these intrinsic local factors may further improve the treatment and prevention of urinary stone disease.
Detection of urinary leakage after radical retropubic prostatectomy by contrast enhanced ultrasound – do we still need conventional retrograde cystography?
Authors: Schoeppler Gita M. , Buchner Alexander , Zaak Dirk , Khoder Wael , Staehler Michael , Stief Christian G. , Reiser Maximilian F. , Clevert Dirk‐Andre
Published: June 2010

Study Type – Diagnostic (exploratory cohort) Level of Evidence 2b

INTRODUCTION To prospectively evaluate the accuracy of transvesical contrast‐enhanced ultrasound (CEUS) as an alternative method for the detection of anastomotic leakage after radical retropubic prostatectomy (RRP) in comparison with the current standard method of conventional retrograde cystography (CG).

PATIENTS AND METHODS Forty‐three patients underwent RRP for histologically proven localized prostate cancer. The vesico‐urethral anastomosis was evaluated 8 days after RRP by CG and CEUS. Any peri‐anastomotic leakage was assessed and determined in CG and CEUS as follows: no extravasation (EV), small leakage (≤0.5 cm), moderate leakage (>0.5 cm to ≤2 cm), large leakage (>2 cm diameter of EV seen).

RESULTS In total, 21 (49%) patients showed a watertight anastomosis. Ten (23%), two (4.7%) and ten (23%) patients showed a small, intermediate and large EV, respectively. In 31 cases (72%) there was 100% agreement of CG and CEUS for detection of no, moderate and large EV, respectively. In nine cases a small and in two cases a moderate EV was categorized as watertight anastomosis by CEUS. Only in one case did CG detect a small EV where a large EV was detected in CEUS. The agreement between both methods was 95% for detecting absence or large leakages.

CONCLUSION CEUS is a promising imaging modality that seems to be equivalent to CG for detecting the presence of a large anastomotic leakage that is clinically relevant for postoperative persistence of the indwelling catheter. CEUS could be a cheap and time‐saving alternative to the CG without exposure of the patient to radiation.
A Spatial Analysis System for Integrating Data, Methods and Models on Environmental Risks and Health Outcomes
Authors: Tiwari Chetan , Rushton Gerard
Published: June 2010

Integrating data on health outcomes with methods of disease mapping and spatially explicit models of environmental contaminants are important aspects of environmental health surveillance. In this article, we describe a modular, web‐based spatial analysis system that uses GIS, spatial analysis methods and software services delivered over computer networks to achieve this end. The Environmental Health Surveillance System (EHSS) is a prototype system that is designed to serve three purposes: a secure environment for producing maps of disease outcomes from individual‐level data while preserving privacy; an automated process of linking environmental data, environmental models, and GIS tasks like geocoding for the purposes of estimating individual exposures to environmental contaminants; and mechanisms to visualize the spatial patterns of disease outcomes via Web‐based mapping interfaces and interactive tools like Google Earth.
Fiscal Policy Shocks in the Euro Area and the US: An Empirical Assessment*
Authors: Burriel Pablo , De Castro Francisco , Garrote Daniel , Gordo Esther , Paredes Joan , Pérez Javier J.
Published: June 2010

We analyse the impact of fiscal policy shocks in the euro area as a whole, using a newly‐available quarterly data set of fiscal variables for the period 1981–2007. To allow for comparability with previous results on euro‐area countries and the US, we use a standard structural vector autoregressive (VAR) framework, and study the impact of aggregated and disaggregated government spending and net‐tax shocks. In addition, to frame euro‐area results, we apply the same methodology for the same sample period to US data. We also explore the sensitivity of the results to the inclusion of variables aiming to control for underlying financial and fiscal conditions. The main new findings are that: expansionary fiscal shocks have a short‐term positive impact on GDP and private consumption, with government spending shocks entailing, in general, higher effects on economic activity than (net) tax reductions; output multipliers to government expenditure shocks are of similar size in the euro area and in the US; the persistence of a fiscal spending shock is higher in the US than in the euro area, which appears to be related to military spending in the US; and fiscal multipliers have increased over the recent past in both geographical areas.
The autism‐epilepsy connection
Authors: Levisohn Paul M.
Published: June 2010

Summary  The high prevalence of epilepsy in children with autism supports a neurobiologic etiology for autism. It remains unclear whether seizures and epileptiform activity on the EEG are causative or comorbid. It is also uncertain if focal epileptiform EEG abnormalities may be associated with stable cognitive impairment. Even less clear is whether these EEG abnormalities can result in the combination of language and social dysfunction seen in autistic spectrum disorders.