bluuebunny/crossref_metadata_2025 huggingface dataset:
Polycomb complexes act redundantly to repress genomic repeats and genes
Authors: Leeb Martin , Pasini Diego , Novatchkova Maria , Jaritz Markus , Helin Kristian , Wutz Anton
Published: February 2010

Polycomb complexes establish chromatin modifications for maintaining gene repression and are essential for embryonic development in mice. Here we use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb-repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas simultaneous loss of PRC1 and PRC2 abrogates differentiation. On the molecular level, the differentiation defect is caused by the derepression of a set of genes that is redundantly repressed by PRC1 and PRC2 in ES cells. Furthermore, we find that genomic repeats are Polycomb targets and show that, in the absence of Polycomb complexes, endogenous murine leukemia virus elements can mobilize. This indicates a contribution of the Polycomb group system to the defense against parasitic DNA, and a potential role of genomic repeats in Polycomb-mediated gene regulation.
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation
Authors: Soler Eric , Andrieu-Soler Charlotte , de Boer Ernie , Bryne Jan Christian , Thongjuea Supat , Stadhouders Ralph , Palstra Robert-Jan , Stevens Mary , Kockx Christel , van IJcken Wilfred , Hou Jun , Steinhoff Christine , Rijkers Erikjan , Lenhard Boris , Grosveld Frank
Published: February 2010

One of the complexes formed by the hematopoietic transcription factor Gata1 is a complex with the Ldb1 (LIM domain-binding protein 1) and Tal1 proteins. It is known to be important for the development and differentiation of the erythroid cell lineage and is thought to be implicated in long-range interactions. Here, the dynamics of the composition of the complex—in particular, the binding of the negative regulators Eto2 and Mtgr1—are studied, in the context of their genome-wide targets. This shows that the complex acts almost exclusively as an activator, binding a very specific combination of sequences, with a positioning relative to transcription start site, depending on the type of the core promoter. The activation is accompanied by a net decrease in the relative binding of Eto2 and Mtgr1. A Chromosome Conformation Capture sequencing (3C-seq) assay also shows that the binding of the Ldb1 complex marks genomic interaction sites in vivo. This establishes the Ldb1 complex as a positive regulator of the final steps of erythroid differentiation that acts through the shedding of negative regulators and the active interaction between regulatory sequences.
A new strategy for genome assembly using short sequence reads and reduced representation libraries
Authors: Young Andrew L. , Abaan Hatice Ozel , Zerbino Daniel , Mullikin James C. , Birney Ewan , Margulies Elliott H.
Published: February 2010

We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality.
Calculating Linear Flow Velocity from Volumetric Flow Rate
Authors: Hedlund Helena
Published: February 2010

INTRODUCTION

In chromatography, flow rates should be standardized for columns of different dimensions by expressing the flow rate as linear flow velocity (cm/h). This is defined as the volumetric flow rate (cm3/h) per unit cross-sectional area (cm2) of a given column. However, flow rates are usually measured as volumetric flow rates (mL/min). It is therefore necessary to be able to convert between the units, which can be done using the equation described here.
DEAE-Dextran Transfection of Lymphocyte Cell Lines
Authors: Smale Stephen T.
Published: February 2010

INTRODUCTION

In this procedure, negatively charged DNA binds to the positively charged diethylaminoethanol (DEAE) moieties of a DEAE-dextran polymer. The soluble complex is added to the cells, which take it up by nonspecific endocytosis. The method described here uses an initial incubation with a DNA/DEAE-dextran mixture, followed by a second incubation in growth medium supplemented with chloroquine. Chloroquine is thought to enhance transfection efficiencies by neutralizing lysosomal hydrolases, which can degrade the DNA. This protocol describes transfection of lymphocyte cell lines, but it can be used for transient transfection of both adherent and nonadherent cells. However, it rarely is used for stable transfection experiments because toxicity prevents long-term maintenance of the transfected cells. One notable advantage of the DEAE-dextran method is that a relatively small amount of DNA is needed for each experiment.
BiFC Imaging Assay for Plant Protein-Protein Interactions
Authors: Fang Yuda , Spector David L.
Published: February 2010

INTRODUCTION

Live cell imaging is an essential approach for studying the structure, dynamics, and functions of cells in a living plant under normal or stressed growth conditions. The tiny flowering plant, Arabidopsis thaliana, provides an ideal system to apply various live microscopy techniques. Its small size allows fluorescent light to penetrate the tissues, and its plantlets contain different cell types with different ploidy levels and differentiation stages. Its 2C nucleus contains only five pairs of chromosomes in which heterochromatin domains are organized as chromocenters, and these domains are easily resolved under the microscope. In addition, the availability of powerful genetic tools facilitates the investigation of the molecular mechanisms underlying various cellular phenomena. In designing live imaging experiments, one must keep in mind that plants sense light, temperature, osmolarity, humidity, gravity, and nutrition. In addition, plants also have strong circadian rhythms of physiological behavior and gene expression. Moreover, plant tissues are normally thick (having multiple cell layers), and can have strong autofluorescence, especially in green leaves. Therefore, optimized culturing and imaging conditions are essential for successful live cell studies in plants. This protocol describes a bimolecular fluorescence complementation (BiFC) imaging assay for protein-protein interactions via their transient coexpression in tobacco. The example used here examines interactions among the plant primary microRNA processing proteins Dicer-like 1, Hyponastic Leaves 1, and SERRATE, but the procedure can be modified easily to accommodate other proteins or structures of interest.
Genome-Wide Analysis of DNA Synthesis by BrdU Immunoprecipitation on Tiling Microarrays (BrdU-IP-chip) in Saccharomyces cerevisiae
Authors: Viggiani Christopher J. , Knott Simon R.V. , Aparicio Oscar M.
Published: February 2010

INTRODUCTION

The incorporation of thymidine analogs, such as 5-bromo-2′-deoxyuridine (BrdU), into newly synthesized DNA is a powerful tool for analysis of DNA replication, repair, and other aspects of DNA metabolism. In Saccharomyces cerevisiae, several assays have been developed to identify chromosomal DNA that has incorporated BrdU. Here we describe an approach that couples BrdU immunoprecipitation with DNA microarrays (BrdU-IP-chip) supplied by Roche NimbleGen to enable the genome-wide identification of BrdU-labeled chromosomal DNA. In this procedure, yeast cells that have been engineered to assimilate BrdU from the growth medium and incorporate it into replicating DNA are grown in the presence of BrdU under experimental conditions. These cells are harvested, the genomic DNA is isolated and randomly sheared, and the BrdU-labeled DNA is then immunoprecipitated. This immunoprecipitated DNA is polymerase chain reaction (PCR)-amplified, labeled with a fluorophore, and cohybridized along with a reference sample (typically total genomic DNA not subject to immunoprecipitation, but amplified and labeled with a different fluorophore) onto DNA microarrays. The data are then normalized, and chromosomal regions of BrdU incorporation (BrdU peaks) are identified. BrdU peak heights can be quantified and compared with BrdU peak heights at different genomic locations or under different experimental conditions (e.g., different mutants or time points). BrdU-IP-chip has many potential applications and has already been used to identify replication origins, make quantitative comparisons of origin firing between strains, and examine replication fork progression.
Analysis of Nonsense-Mediated mRNA Decay by Monitoring mRNA Half-Lives in Mammalian Cells
Authors: Yamashita Akio , Ohno Shigeo
Published: February 2010

INTRODUCTION

This protocol uses a tetracycline-response-element-regulated (Tet-Off) promoter system and Northern blotting to analyze the half-lives of premature termination codon (PTC)-containing mRNAs following the activation or suppression of the nonsense-mediated mRNA decay (NMD) pathway in mammalian cells. Reporter plasmids are cotransfected with or without effector plasmid(s) and/or small interfering RNA(s) (siRNA[s]) targeted to genes suspected of involvement in NMD. After transfection, cells are harvested and reseeded to five or six plates. Thirty-six to 72 h after transfection, the cells are treated with doxycycline (or tetracycline) to terminate reporter mRNA transcription from the Tet-Off promoter. Cells are then harvested at specific time points, and RNAs are purified for Northern blot analysis. Although various alternative methods (e.g., RNase protection assay, reverse transcriptase polymerase chain reaction [RT-PCR], and quantitative-RT-PCR [qRT-PCR]) are available, the use of Northern blotting to analyze mRNA half-lives to confirm correct mRNA processing is highly recommended. Using this protocol to analyze mRNA half-lives provides an assay that is dependent on the activities of NMD transacting factor(s) in mammalian cells.
CrkL is a novel target of Sprouty2 in fibroblast growth factor signaling
Authors: Satoh Takayuki , Torii Satoru , Nakayama Kei , Nishida Eisuke
Published: February 2010

Sprouty, an inhibitor of receptor tyrosine kinase signaling, plays an important role in the regulation of a wide variety of biological processes. Although it is established that the Sprouty inhibitory activity is induced by tyrosine phosphorylation in response to stimuli, its action mechanisms have not been fully elucidated. Here, we report identification of a novel target of Sprouty. We find that Sprouty1 and Sprouty2 bind to the adaptor protein CrkL in a stimulus‐dependent manner. Biochemical analyses show that the binding requires tyrosine phosphorylation of Sprouty and that both the SH2 domain and the N‐terminal SH3 domain of CrkL are necessary for the binding. In fibroblast growth factor‐stimulated NIH3T3 cells, CrkL binding to Sprouty2 occurs concomitantly with tyrosine phosphorylation of Sprouty2, which occurs slowly but is sustained. Importantly, our results show that tyrosine‐phosphorylated Sprouty2 suppresses Rap1 activation. These results taken together indicate that Sprouty2 acts as an inhibitor of CrkL‐Rap1 signaling.
Measurement and correlates of ano‐genital distance in healthy, newborn infants
Authors: Sathyanarayana S. , Beard L. , Zhou C. , Grady R.
Published: February 2010

Ano‐genital distance (AGD) is a sexually dimorphic trait that is a well established reproductive toxicity endpoint in animals. In male animals, a shortened AGD is associated with a variety of genital abnormalities including hypospadias and cryptorchidism. Consensus on the anatomical definition of AGD in humans remains to be established and few data exist on the determinants and normal variance in the general population. We implemented a standardized anthropometric protocol to measure AGD, ano‐scrotal distance (ASD), and ano‐fourchette distance (AFD) in 169 (82 male, 87 female) infants in the University of Washington newborn nursery in 2008. We collected data on the following characteristics: weight, length, and occipital head circumference, race and relevant gestational complications. Using linear regression modelling, we examined AGD/ASD/AFD for sexual dimorphism, normal population variance and predictors of the measurement in infants. The mean male and female AGD measurements were 52.0 mm (SD ± 5.5) and 37.2 mm (SD ± 3.7). The mean ASD and AFD were 23.0 mm (SD ± 3.8) and 15.1 mm (SD ± 2.9). Weight, length, occipital head circumference and gestational age were associated with AGD (p < 0.05). Weight and length were the most important correlates to AGD. We confirmed previous findings that AGD is a sexually dimorphic measurement that is most strongly predicted by infant weight. The application of this measurement to clinically relevant outcomes remains to be explored in further depth.
The effect of environmental diversification on species diversification in New Caledonian caddisflies (Insecta: Trichoptera: Hydropsychidae)
Authors: Espeland Marianne , Johanson Kjell A.
Published: February 2010

Aim To test whether environmental diversification played a role in the diversification of the New Caledonian Hydropsychinae caddisflies.

Location New Caledonia, south‐west Pacific.

Methods The phylogeny of the New Caledonian Hydropsychinae caddisflies was hypothesized using parsimony and Bayesian methods on molecular characters. The Bayesian analysis was the basis for a comparative analysis of the correlation between phylogeny and three environmental factors: geological substrate (ultrabasic, non‐ultrabasic), elevation and precipitation. Phylogenetic divergence times were estimated using a relaxed clock method, and environmental factors were mapped onto a lineage‐through‐time plot to investigate the timing of environmental diversification in relation to species radiation. The correlation between rainfall and elevation was tested using independent contrasts, and the gamma statistic was calculated to infer the diversification pattern of the group.

Results The diversification of extantOrthopsyche–Caledopsychespecies began in the Middle–Late Oligocene, when much of the island of New Caledonia was covered by ultrabasic substrate and mountain forming was prevalent. Most lineages originated in the Middle–Late Miocene, a period associated with long‐term climate oscillation. Optimization of environmental factors on the phylogeny demonstrated that the New Caledonian Hydropsychinae group adapted to ultrabasic substrate early in its evolutionary history. The clade living mostly on ultrabasic substrate was far more species‐rich than the clade living mostly on non‐ultrabasic substrate. Elevation and rainfall were significantly correlated with each other. The lineage‐through‐time plot revealed that the main environmental diversification preceded species diversification. A constant speciation through time was rejected, and the negative gamma indicates that most of the diversification occurred early in the history of the clade. According to the inferred phylogeny, the genusOrthopsycheMcFarlane is a synonym underCaledopsycheKimmins, andAbacaria caledonaOláh & Barnard should also be included inCaledopsyche.

Main conclusions The age of the radiation does not support a vicariance origin of New Caledonian Hydropsychinae caddisflies. Environmental diversification pre‐dates lineage diversification, and thus environmental heterogeneity potentially played a role in the diversification of the group, by providing a variety of fragmented habitats to disperse into, promoting speciation. The negative gamma indicates that the speciation rate slowed as niches started to fill.
Phosphatidylserine synthase and phosphatidylserine decarboxylase are essential for cell wall integrity and virulence in Candida albicans
Authors: Chen Ying‐Lien , Montedonico Anthony E. , Kauffman Sarah , Dunlap John R. , Menn Fu‐Min , Reynolds Todd B.
Published: February 2010

Phospholipid biosynthetic pathways play crucial roles in the virulence of several pathogens; however, little is known about how phospholipid synthesis affects pathogenesis in fungi such as Candida albicans. A C. albicans phosphatidylserine (PS) synthase mutant, cho1Δ/Δ, lacks PS, has decreased phosphatidylethanolamine (PE), and is avirulent in a mouse model of systemic candidiasis. The cho1Δ/Δ mutant exhibits defects in cell wall integrity, mitochondrial function, filamentous growth, and is auxotrophic for ethanolamine. PS is a precursor for de novo PE biosynthesis. A psd1Δ/Δ psd2Δ/Δ double mutant, which lacks the PS decarboxylase enzymes that convert PS to PE in the de novo pathway, has diminished PE levels like those of the cho1Δ/Δ mutant. The psd1Δ/Δ psd2Δ/Δ mutant exhibits phenotypes similar to those of the cho1Δ/Δ mutant; however, it is slightly more virulent and has less of a cell wall defect. The virulence losses exhibited by the cho1Δ/Δ and psd1Δ/Δ psd2Δ/Δ mutants appear to be related to their cell wall defects which are due to loss of de novo PE biosynthesis, but are exacerbated by loss of PS itself. Cho1p is conserved in fungi, but not mammals, so fungal PS synthase is a potential novel antifungal drug target.
The role of the FliK molecular ruler in hook‐length control in Salmonella enterica
Authors: Erhardt Marc , Hirano Takanori , Su Yichu , Paul Koushik , Wee Daniel H. , Mizuno Shino , Aizawa Shin‐Ichi , Hughes Kelly T.
Published: February 2010

A molecular ruler, FliK, controls the length of the flagellar hook. FliK measures hook length and catalyses the secretion‐substrate specificity switch from rod‐hook substrate specificity to late substrate secretion, which includes the filament subunits. Here, we show normal hook‐length control and filament assembly in the complete absence of the C‐ring thus refuting the previous ‘cup’ model for hook‐length control. Mutants of C‐ring components, which are reported to produce short hooks, show a reduced rate of hook–basal body assembly thereby allowing for a premature secretion‐substrate specificity switch. Unlike fliK null mutants, hook‐length control in an autocleavage‐defective mutant of flhB, the protein responsible for the switch to late substrate secretion, is completely abolished. FliK deletion variants that retain the ability to measure hook length are secreted thus demonstrating that FliK directly measures rod‐hook length during the secretion process. Finally, we present a unifying model accounting for all published data on hook‐length control in which FliK acts as a molecular ruler that takes measurements of rod‐hook length while being intermittently secreted during the assembly process of the hook–basal body complex.
Mitochondrial DNA polymerase POLIB is essential for minicircle DNA replication in African trypanosomes
Authors: Bruhn David F. , Mozeleski Brian , Falkin Laurie , Klingbeil Michele M.
Published: February 2010

The unique mitochondrial DNA of trypanosomes is a catenated network of minicircles and maxicircles called kinetoplast DNA (kDNA). The network is essential for survival, and requires an elaborate topoisomerase‐mediated release and reattachment mechanism for minicircle theta structure replication. At least seven DNA polymerases (pols) are involved in kDNA transactions, including three essential proteins related to bacterial DNA pol I (POLIB, POLIC and POLID). How Trypanosoma brucei utilizes multiple DNA pols to complete the topologically complex task of kDNA replication is unknown. To fill this gap in knowledge we investigated the cellular role of POLIB using RNA interference (RNAi). POLIB silencing resulted in growth inhibition and progressive loss of kDNA networks. Additionally, unreplicated covalently closed precursors become the most abundant minicircle replication intermediate as minicircle copy number declines. Leading and lagging strand minicircle progeny similarly declined during POLIB silencing, indicating POLIB had no apparent strand preference. Interestingly, POLIB RNAi led to the accumulation of a novel population of free minicircles that is composed mainly of covalently closed minicircle dimers. Based on these data, we propose that POLIB performs an essential role at the core of the minicircle replication machinery.
Epigenetic mechanisms regulate stage differentiation in the minimized protozoan Giardia lamblia
Authors: Sonda Sabrina , Morf Laura , Bottova Iveta , Baetschmann Hansruedi , Rehrauer Hubert , Caflisch Amedeo , Hakimi Mohamed‐Ali , Hehl Adrian B.
Published: February 2010

Histone modification is an important mechanism regulating both gene expression and the establishment and maintenance of cellular phenotypes during development. Regulation of histone acetylation via histone acetylases and deacetylases (HDACs) appears to be particularly crucial in determining gene expression patterns. In this study we explored the effect of HDAC inhibition on the life cycle of the human pathogen Giardia lamblia, a highly reduced parasitic protozoan characterized by minimized cellular processes. We found that the HDAC inhibitor FR235222 increased the level of histone acetylation and induced transcriptional regulation of ∼2% of genes in proliferating and encysting parasites. In addition, our analyses showed that the levels of histone acetylation decreased during differentiation into cysts, the infective stage of the parasite. Importantly, FR235222 treatment during encystation reversed this histone hypo‐acetylation and potently blocked the formation of cysts. These results provide the first direct evidence for epigenetic regulation of gene expression in this simple eukaryote. This suggests that regulation of histone acetylation is involved in the control of Giardia stage differentiation, and identifies epigenetic mechanisms as a promising target to prevent Giardia transmission.
AcrA suppressor alterations reverse the drug hypersensitivity phenotype of a TolC mutant by inducing TolC aperture opening
Authors: Weeks Jon W. , Celaya‐Kolb Teresa , Pecora Sara , Misra Rajeev
Published: February 2010

In Escherichia coli, the TolC–AcrAB complex forms a major antibiotic efflux system with broad substrate specificity. During the complex assembly, the periplasmic helices and bottom turns of TolC are thought to interact with a hairpin helix of AcrA and hairpin loops of AcrB respectively. In the present study we show that a four‐residue substitution in TolC's turn 1, which connects outer helices 3 and 4 proximal to TolC's periplasmic aperture, confers antibiotic hypersensitivity, without affecting TolC‐mediated phage or colicin infection. However, despite the null‐like drug sensitivity phenotype, chemical cross‐linking analysis revealed no apparent defects in the ability of the mutant TolC protein to physically interact with AcrA and AcrB. A role for TolC turn 1 residues in the functional assembly of the tripartite efflux pump complex was uncovered through isolating suppressor mutations of the mutant TolC protein that mapped within acrA and by utilizing a labile AcrA protein. The data showed that AcrA‐mediated suppression of antibiotic sensitivity was achieved by dilating the TolC aperture/channel in an AcrB‐dependent manner. The results underscore the importance of the periplasmic turn 1 of TolC in the functional assembly of the tripartite efflux complex and AcrA in transitioning TolC from its closed to open state.
Assessment of the clinical transfusion practice at a regional referral hospital in Uganda
Authors: Natukunda B. , Schonewille H. , Smit Sibinga C. Th.
Published: February 2010

The aim of this study was to determine the indications for transfusion, blood ordering practices and post‐transfusion complications, and to assess the clinical transfusion practice at Mbarara Regional Referral Hospital (MRRH) in Mbarara, Uganda. There are no guidelines on the appropriate use of blood at MRRH. Therefore, there was a need to assess the local clinical transfusion practice. Patients' hospital files were studied for evidence of blood transfusions in 2008. All five wards were reviewed and details on the transfusion process were recorded. A total of 1730 patients (median age, 19·0 years; range, 1 day to 88 years; female‐to‐male ratio, 1·4), for whom blood was cross‐matched, were studied. Of these, 1674 (96·8%) patients actually received transfusions, which were as whole blood in 58·4% of recipients. The mean number of units per recipient was 1·7 and the cross‐match‐to‐transfusion ratio was 1·3. The three most frequent indications for transfusion were malaria (38·8%), bleeding (27·1%) and other infections (16·1%). There were no records for pre‐transfusion haemoglobin, compatibility testing, transfusion start‐times and vital signs in 30·2, 51·8, 21·5 and 97·6% of the recipients, respectively. Transfusion reactions were recorded for 10 (0·6%) patients. Although there was no evidence of blood wastage, inadequacies were noted in the documentation of the transfusion process. There is a need to train staff in blood transfusion and to design a ‘blood transfusion form’ for easy monitoring and evaluation. A hospital transfusion committee and guidelines on the appropriate use of blood should be put in place at MRRH.
Health‐related quality of life of food allergic patients measured with generic and disease‐specific questionnaires
Authors: Flokstra‐de Blok B. M. J. , Van Der Velde J. L. , Vlieg‐Boerstra B. J. , Oude Elberink J. N. G. , DunnGalvin A. , Hourihane J. O’B. , Duiverman E. J. , Dubois A. E. J.
Published: February 2010

To cite this article: Flokstra‐de Blok BMJ, van der Velde JL, Vlieg‐Boerstra BJ, Oude Elberink JNG, DunnGalvin A, Hourihane JO’B, Duiverman EJ, Dubois AEJ. Health‐related quality of life of food allergic patients measured with generic and disease‐specific questionnaires. Allergy 2010; 65: 1031–1038.

Background:  Health‐related quality of life (HRQL) has never been measured with both generic and disease‐specific questionnaires in the same group of food allergic patients. The aim of this study was to compare HRQL of food allergic patients as measured with generic and disease‐specific questionnaires.

Methods:  Generic questionnaires (CHQ‐CF87 and RAND‐36) and disease‐specific HRQL questionnaires (FAQLQ‐CF, ‐TF and ‐AF) were completed by 79 children, 74 adolescents and 72 adults with food allergy. Floor and ceiling effects, percentage of agreement and multivariate stepwise regression analysis were used to compare the generic and disease‐specific measurements.

Results:  The Food Allergy Quality of Life Questionnaires (FAQLQs) showed minimal floor or ceiling effects. The CHQ‐CF87 and RAND‐36 showed minimal floor effects, but remarkable ceiling effects (>73%) were found for the scales role functioning‐emotional (RE), role functioning‐behaviour (RB), role functioning‐physical (RP) in children and adolescents and the scale RE (>79%) in adults. Additionally, we found low percentages of agreement between the generic and disease‐specific questionnaires to identify the same food allergic patients with the best or worst HRQL. Only patients with the best disease‐specific HRQL also tended to have the best generic HRQL. Finally, the explained variance in HRQL by patient characteristics was higher in the disease‐specific questionnaires (30.7–62.8%) than in the generic scales (6.7–31.7%).

Conclusion:  Disease‐specific HRQL questionnaires may be more suitable to measure clinically important impairments in HRQL or HRQL differences over time in food allergic patients. However, generic HRQL questionnaires are indispensable for the comparison between different diseases and are thus complementary.
CD8+ T cells mediate skin allergy to amoxicillin in a mouse model
Authors: Rozieres A. , Vocanson M. , Rodet K. , Benetiere J. , Bienvenu J. , Berard F. , Hennino A. , Nicolas J.‐F.
Published: February 2010

To cite this article: Rozieres A, Vocanson M, Rodet K, Benetiere J, Bienvenu J, Berard F, Hennino A, Nicolas J‐F. CD8+ T cells mediate skin allergy to amoxicillin in a mouse model. Allergy 2010; 65: 996–1003.

Background:  Delayed allergic skin reactions to drugs are common iatrogenic diseases mediated by activation of specific T cells in the skin.

Methods:  To better understand the role of T cells in these diseases, we developed a mouse model of drug allergy induced by skin sensitization to amoxicillin (amox), a penicillin antibiotic frequently involved in delayed drug allergy.

Results:  Whereas wild‐type mice could not be sensitized to amox, CD4+ T‐cell‐deficient mice developed an amox‐specific allergic skin response, mediated by IFN‐γ‐producing CD8+ T cells. Amox‐specific CD8+ T cells, induced in lymphoid organs at a high frequency during sensitization, were recruited in the skin upon challenge. CD8+ T cells were effectors of the allergic skin reaction to amox as in vivo treatment with depleting anti‐CD8 mAbs abrogated the skin inflammatory reaction and as purified CD8+ T cells could adoptively transfer the allergic response to naive recipients.

Conclusion:  CD8+ T cells mediate penicillin skin allergy.
Primary cutaneous carcinosarcoma: Dermoscopic and immunohistochemical features
Authors: Upjohn Edward , Braue Anna , Ryan Andrew
Published: February 2010

A 73‐year‐old man presented a 9‐month history of an enlarging nodule on his right temple. Dermoscopy revealed a non‐pigmented lesion with ulceration, fibrosis and pale globules. An excisional biopsy was carried out and histology showed a biphasic tumour with a basal cell carcinoma like epithelial component and a dermal undifferentiated sarcoma, with pleomorphic spindle cells and numerous osteoclast‐like giant cells. Based on immunohistochemistry findings, a diagnosis of primary cutaneous carcinosarcoma was made and the patient underwent wide local excision.
Clinical improvement in Darier's disease with photodynamic therapy
Authors: Avery Helen L , Hughes Bronwyn R , Coley Carol , Cooper Hywel L
Published: February 2010

We report a patient with Darier's disease successfully treated with photodynamic therapy. She had previously been recalcitrant to treatment with emollients, topical corticosteroids and retinoids. Photodynamic therapy was trialled with significant clinical improvement in her cutaneous symptoms and signs that was maintained for over 27 months.
Annular erythema as a sign of recurrent breast cancer
Authors: Tan Eugene , Kuper‐Hommel Marion , Rademaker Marius
Published: February 2010

Three women with known breast cancer presented with very similar annular erythemas of their chest walls. All women were in remission from their breast cancer for at least 6 months. Their breast cancers had initially responded well to multi‐modality treatment with no clinical or radiologic evidence of recurrence, until the development of the annular erythema. In the first case, the annular erythema was treated unsuccessfully as a dermatitis and then as tinea corporis. In the second case, subacute cutaneous lupus was considered but lupus antibodies were negative. In the third case, the annular erythema was promptly recognized and biopsied. Histology in all three cases revealed identical findings of invasive ductal carcinoma involving the lymphatics of the skin. Immunohistochemical staining of the carcinoma was positive for human epidermal growth factor receptor 2 but negative for oestrogen and progesterone receptors. Annular erythema can pose a wide differential but rarely has it been described as a sign of locally recurrent cancer. These cases highlight the importance of recognizing this entity in the oncologic patient, where prompt skin biopsies can confirm the diagnosis and allow early initiation of therapy.
Relationship of alexithymia and temperament and character dimensions with lifetime post‐traumatic stress disorder in male alcohol‐dependent inpatients
Authors: Evren Cuneyt , Dalbudak Ercan , Cetin Rabia , Durkaya Mine , Evren Bilge
Published: February 2010

Aims:  The purpose of the present study was to evaluate the prevalence of lifetime post‐traumatic stress disorder (PTSD) in male alcohol‐dependent inpatients and to investigate the relationship of PTSD with alexithymia and temperament and character dimensions.

Methods:  Participants were 156 consecutively admitted male alcohol‐dependent subjects. Patients were investigated using the Clinician‐Administered PTSD Scale (CAPS), the Toronto Alexithymia Scale (TAS‐20) and the Temperament and Character Inventory (TCI).

Results:  Among alcohol‐dependent inpatients 32.1% were considered as having lifetime PTSD. Mean scores of alexithymia, novelty seeking (NS), harm avoidance (HA) and self‐transcendence (ST) were higher in the PTSD group, whereas age and self‐directedness (S) were lower. Among age and other factors of TAS‐20, ‘difficulty in identifying feelings (DIF)’ predicted PTSD in a logistic regression model. When age and personality dimensions of TCI were taken as independent variables, S predicted PTSD in the logistic regression model. Finally, among subscales of TCI, ‘impulsiveness versus reflection’ (NS2) and ‘congruent second nature versus bad habits’ (S5) predicted PTSD.

Conclusions:  Alexithymia and personality traits, particularly high DIF and S scores are related with lifetime PTSD diagnosis, even when controlling for age among alcohol‐dependent inpatients. Causal relationships between alexithymia, personality dimensions and PTSD, and their implications on treatment are not clear and should be evaluated in longitudinal studies.
Randomized, single‐blind, trial of sertraline and buspirone for treatment of elderly patients with generalized anxiety disorder
Authors: Mokhber Naghmeh , Azarpazhooh Mahmoud Reza , Khajehdaluee Mohammad , Velayati Arash , Hopwood Malcolm
Published: February 2010

Aim:  Generalized anxiety disorder (GAD) in elderly people is common, but few systematic studies regarding the best treatments have been performed. The aim of the present study was to evaluate the efficacy and safety of sertraline and buspirone in the treatment of elderly patients with GAD.

Methods:  Based on selection criteria, 46 patients were recruited who met DSM‐IV criteria for GAD. Patients were randomly assigned to sertraline (50–100 mg/day) or buspirone (10–15 mg/day) for 8 weeks in a single‐blind trial. The primary outcome measure used in the present study was the Hamilton Rating Scale for Anxiety (HRSA).

Results:  Both sertraline and buspirone had significant anxiolytic efficacy. A steady decrease in the total HRSA scores for both groups was observed throughout the study period. After 2 and 4 weeks, buspirone was found to be significantly superior to sertraline (P < 0.001), but at the end of study period this difference did not reach statistical significance (P = 0.16). The mean HRSA score after 8 weeks significantly decreased in subjects treated with sertraline (P < 0.001), and buspirone (P < 0.001). No clinically adverse events or changes in laboratory test results were observed during the study period.

Conclusion:  Both sertraline and buspirone appear to be efficacious and well tolerated in the treatment of GAD in elderly patients. Further studies with larger sample size, evaluating the effect of medical illness, cognitive impairment, depression, and combined therapy with support and psychotherapy are needed.
Regional cerebral blood flow changes in female to male gender identity disorder
Authors: Nawata Hideyuki , Ogomori Koji , Tanaka Mariko , Nishimura Ryoji , Urashima Hajime , Yano Rika , Takano Koichi , Kuwabara Yasuo
Published: February 2010

Aims:  Despite a range of research on gender identity disorder (GID), at present there is no scientific consensus on whether the etiology of GID is mental or physical. In particular recent advances in the technology of neuroimaging research have led to an increased understanding of the biological basis of various mental disorders. GID also should be evaluated from this perspective. The aim of the present study was therefore to do the first trial to examine the regional cerebral blood flow (rCBF) in GID.

Methods:  Persons considered biologically male fulfilling the GID criteria are termed male to female (MTF) and, conversely, persons considered biological female are termed female to male (FTM). We compared 11 FTM subjects and nine age‐ and handedness‐matched female control subjects. None of the subjects was regularly taking medication and none had any kind of physical or psychiatric comorbidity. To evaluate rCBF in GID subjects and control subjects, statistical parametric mapping analysis of 99mTc‐ethyl‐cysteinate dimer single‐photon emission computed tomography was used.

Results:  GID subjects had a significant decrease in rCBF in the left anterior cingulate cortex (ACC) and a significant increase in the right insula compared to control subjects.

Conclusions:  The ACC and insula are regions that have been noted as being related to human sexual behavior and consciousness. From these findings, useful insights into the biological basis of GID were suggested.
Factors associated with postpartum depression and abusive behavior in mothers with infants
Authors: Choi Hyungin , Yamashita Tatsuhisa , Wada Yoshihisa , Narumoto Jin , Nanri Hiromi , Fujimori Akihito , Yamamoto Haruka , Nishizawa Susumu , Masaki Daiki , Fukui Kenji
Published: February 2010

Aims: This study was conducted to examine factors associated with postpartum depression and abusive behavior in mothers with infants.

Methods: Data were collected from baby check‐ups in Japan and 413 participants were included in an analysis using: (i) an Original Questionnaire; (ii) the Zung Self‐rating Depression Scale (ZSDS); (iii) the Parental Bonding Instrument; and (iv) the Childcare Anxiety Scale (CAS). Covariance structural analyses were performed to examine interconnections among the Parental Bonding Instrument subscales, CAS subscales (‘worry about parenting’, ‘burden of nursing time’, ‘difficulty of bonding’), ZSDS, ‘fear of being abusive’, and ‘abusive behavior’.

Results: Of the 413 mothers, 14.5% showed higher than moderate levels of depression (ZSDS ≥ 50). In covariance structural analyses, ‘depression’ was strongly influenced by ‘worry about parenting’ in all variances, but was not associated with ‘abusive behavior’. ‘Worry about parenting’ also had a strong influence on ‘fear of being abusive’, but did not affect ‘abusive behavior’. Low ‘maternal care’ had most influence on ‘difficulty of bonding’, and ‘difficulty of bonding’ only affected ‘abusive behavior’.

Conclusions: The outcome of this study suggests that excessive worrying related to postpartum depression, ‘fear of being abusive’, and bonding difficulty are primary predictors of child abuse. Postpartum depression was not a predictor for abusive behavior after exclusion of the impact of bonding difficulties on abusive behavior. Therefore, the correlation between postpartum depression and abusive behavior identified in previous reports may have been influenced by bonding difficulties.
Extensive evolutionary rate variation in floral color determining genes in the genus Ipomoea
Authors: TOLENO DONNA M. , DURBIN MARY L. , LUNDY KAREN E. , CLEGG MICHAEL T.
Published: February 2010

Flower color is an important adaptive trait in many plant species because it determines reproductive success through differential attractiveness to insect pollinators. The genus Ipomoea is a pan tropically distributed plant genus characterized by showy flowers that often differ in color among closely related species. Flower color is determined primarily by products of the anthocyanin biosynthesis pathway. To determine whether flower color evolution among members of the genus is driven by adaptive molecular evolution of the anthocyanin pathway genes, we analyzed data from 10 genes sequenced from 19 species of Ipomoea. Six protein‐coding genes from the anthocyanin pathway were drawn for evolutionary analysis in addition to three genes from the unrelated leucine biosynthesis pathway and one MADS box regulatory gene for comparison. The analyses provided: (i) no convincing evidence for positive selection on anthocyanin pathway structural genes, or on the other sampled genes, despite shifts in flower color among species included in the sample; (ii) pathway position correlated weakly with estimates of the intensity of evolutionary constraint on the anthocyanin pathway enzyme coding genes; and (iii) there was substantial gene‐specific heterogeneity in the rates of synonymous site evolution. Synonymous rate heterogeneity does not appear to be accounted for by codon bias or local contextual or compositional sequence differences, leading us to implicate heterogeneous rates of mutation among genes as the most probable cause of synonymous rate heterogeneity.
Relationship between height and blood pressure in Japanese schoolchildren
Authors: Fujita Yuki , Kouda Katsuyasu , Nakamura Harunobu , Nishio Nobuhiro , Takeuchi Hiroichi , Iki Masayuki
Published: February 2010

Background:  Blood pressure examinations for health education use have been conducted at several schools in Japan. It has been reported that blood pressure is closely associated with bodyweight and height in US children. The aim of the present paper was to evaluate the association between height and blood pressure in Japanese schoolchildren.

Methods:  In Iwata city in Japan, blood pressure screening was conducted by the school administration. A total of 98.9% (10 152/10 270 children) of all fifth (10‐year‐olds) and ninth graders (14‐year‐olds) residing in the Old Iwata area from 2002 to 2007 were analyzed.

Results:  In 10‐year‐old and 14‐year‐old boys, regression analysis indicated that a positive correlation between weight and blood pressure was the strongest among the three body size indices (height, weight, and body mass index), but the association between height and blood pressure was also significant. For girls from both the 10 and 14 year age groups, the correlation of weight and blood pressure was stronger than those for the other body size indices, but there were also significant associations between height and blood pressure, except for height and diastolic blood pressure in the 14‐year‐olds.

Conclusions:  There is a significant positive relationship between height and blood pressure. Further study is necessary to provide a blood pressure reference based on height in the Japanese program to prevent children from developing lifestyle‐related risk factors.
Multilevel analysis of effects of individual characteristics and household factors on self‐rated health among older adults in rural Vietnam
Authors: Van Minh Hoang , Byass Peter , Wall Stig
Published: February 2010

Aim:  This paper aims to describe self‐rated health (SRH) status among older adults in a rural community of Vietnam, and examine individual and household‐level factors associated with good health rating among the study populations.

Methods:  The study was carried out in the Bavi district, a rural community located 60 km west of Hanoi, the capital, within the Epidemiological Field Laboratory of Bavi (FilaBavi) in Vietnam in 2006. All people aged 50 years and over who lived within the district were surveyed. Face‐to‐face household interviews were conducted by trained surveyors using standard World Health Organization/INDEPTH network questionnaire–summary version. A logistic multilevel modeling approach was applied to analyze the association between SRH and both individual and household‐level factors.

Results:  The proportion of people aged 50 years and older in FilaBavi reported having good/very good health and poor/very poor health was 15.1% and 24.8%, respectively. SRH status was reported to be better among: (i) men; (ii) younger people; (iii) people with higher education; (iv) people who were currently in marital a partnership; (v) those from wealthier households; and (vi) those who were living in riverside/island or highland areas compared to those of other categories of the same variable.

Conclusion:  The findings reveal that there exist problems of inequality in health among older adults in the study setting by sex, age, education, wealth status and place of residence. We also found a considerable contribution of the household‐level factors to SRH of the study populations..
Homologues of nitrite reductases in ammonia‐oxidizing archaea: diversity and genomic context
Authors: Bartossek Rita , Nicol Graeme W. , Lanzen Anders , Klenk Hans‐Peter , Schleper Christa
Published: February 2010

Ammonia‐oxidizing archaea are frequent and ubiquitous inhabitants of terrestrial and marine environments. As they have only recently been detected, most aspects of their metabolism are yet unknown. Here we report on the occurrence of genes encoding potential homologues of copper‐dependent nitrite reductases (NirK) in ammonia‐oxidizing archaea of soils and other environments using metagenomic approaches and PCR amplification. Two pairs of highly overlapping 40 kb genome fragments, each containing nirK genes of archaea, were isolated from a metagenomic soil library. Between 68% and 85% of the open reading frames on these genome fragments had homologues in the genomes of the marine archaeal ammonia oxidizers Nitrosopumilus maritimus and Cenarchaeum symbiosum. Extensions of NirK homologues with C‐terminal fused amicyanin domains were deduced from two of the four fosmids indicating structural variation of these multicopper proteins in archaea. Phylogenetic analyses including all major groups of currently known NirK homologues revealed that the deduced protein sequences of marine and soil archaea were separated into two highly divergent lineages that did not contain bacterial homologues. In contrast, another separated lineage contained potential multicopper oxidases of both domains, archaea and bacteria. More nirK gene variants directly amplified by PCR from several environments indicated further diversity of the gene and a widespread occurrence in archaea. Transcription of the potential archaeal nirK in soil was demonstrated at different water contents, but no significant increase in transcript copy number was observed with increased denitrifying activity.
A KOREAN PERSPECTIVE ON DEVELOPING A GLOBAL POLICY FOR ADVANCE DIRECTIVES
Authors: KIM SOYOON , HAHM KI‐HYUN , PARK HYOUNG WOOK , KANG HYUN HEE , SOHN MYONGSEI
Published: February 2010

Despite the wide and daunting array of cross‐cultural obstacles that the formulation of a global policy on advance directives will clearly pose, the need is equally evident. Specifically, the expansion of medical services driven by medical tourism, just to name one important example, makes this issue urgently relevant. While ensuring consistency across national borders, a global policy will have the additional and perhaps even more important effect of increasing the use of advance directives in clinical settings and enhancing their effectiveness within each country, regardless of where that country's state of the law currently stands. One cross‐cultural issue that may represent a major obstacle in formulating, let alone applying, a global policy is whether patient autonomy as the underlying principle for the use of advance directives is a universal norm or a construct of western traditions that must be reconciled with alternative value systems that may place lesser significance on individual choice. A global policy, at a minimum, must emphasize respect for patient autonomy, provision of medical information, limits to the obligations for physicians, and portability. And though the development of a global policy will be no easy task, active engagement in close collaboration with the World Health Organization can make it possible.