bluuebunny/crossref_metadata_2025 huggingface dataset:
The Retinoblastoma family member p107 regulates the rate of progenitor commitment to a neuronal fate
Authors: Vanderluit Jacqueline L. , Wylie Crystal A. , McClellan Kelly A. , Ghanem Noel , Fortin Andre , Callaghan Steve , MacLaurin Jason G. , Park David S. , Slack Ruth S.
Published: June 2007

The Retinoblastoma protein p107 regulates the neural precursor pool in both the developing and adult brain. As p107-deficient mice exhibit enhanced levels of Hes1, we questioned whether p107 regulates neural precursor self-renewal through the repression of Hes1. p107 represses transcription at the Hes1 promoter. Despite an expanded neural precursor population, p107-null mice exhibit a striking reduction in the number of cortical neurons. Hes1 deficiency rescues neurosphere numbers in p107-null embryos. We find that the loss of a single Hes1 allele in vivo restores the number of neural precursor cells at the ventricular zone. Neuronal birthdating analysis reveals a dramatic reduction in the rate of neurogenesis, demonstrating impairment in p107−/− progenitors to commit to a neuronal fate. The loss of a single Hes1 allele restores the number of newly generated neurons in p107-deficient brains. Together, we identify a novel function for p107 in promoting neural progenitor commitment to a neuronal fate.
Notch–RBP-J signaling controls the homeostasis of CD8− dendritic cells in the spleen
Authors: Caton Michele L. , Smith-Raska Matthew R. , Reizis Boris
Published: June 2007

Signaling through Notch receptors and their transcriptional effector RBP-J is essential for lymphocyte development and function, whereas its role in other immune cell types is unclear. We tested the function of the canonical Notch–RBP-J pathway in dendritic cell (DC) development and maintenance in vivo. Genetic inactivation of RBP-J in the bone marrow did not preclude DC lineage commitment but caused the reduction of splenic DC fraction. The inactivation of RBP-J in DCs using a novel DC-specific deleter strain caused selective loss of the splenic CD8− DC subset and reduced the frequency of cytokine-secreting CD8− DCs after challenge with Toll-like receptor ligands. In contrast, other splenic DC subsets and DCs in the lymph nodes and tissues were unaffected. The RBP-J–deficient splenic CD8− DCs were depleted at the postprogenitor stage, exhibited increased apoptosis, and lost the expression of the Notch target gene Deltex1. In the spleen, CD8− DCs were found adjacent to cells expressing the Notch ligand Delta-like 1 in the marginal zone (MZ). Thus, canonical Notch–RBP-J signaling controls the maintenance of CD8− DCs in the splenic MZ, revealing an unexpected role of the Notch pathway in the innate immune system.
CREB/ATF-dependent T cell receptor–induced FoxP3 gene expression: a role for DNA methylation
Authors: Kim Hyoung-Pyo , Leonard Warren J.
Published: June 2007

Regulatory T cells (T reg cells) are a population of CD4+ T cells that limit immune responses. FoxP3 is a master control transcription factor for development and function of these cells, but its regulation is poorly understood. We have identified a T cell receptor–responsive enhancer in the FoxP3 first intron that is dependent on a cyclic-AMP response element binding protein (CREB)/activating transcription factor (ATF) site overlapping a CpG island. Methylation of this island inversely correlates with CREB binding and FoxP3 expression. Interestingly, transforming growth factor-β, which induces T reg cell formation, decreases methylation of the CpG island and increases FoxP3 expression. Similarly, inhibiting methylation with 5-azacytidine or knocking down the DNA methyltransferase Dnmt1 also induces FoxP3 expression. Conversely, methylation of the CpG island, which decreases CREB binding or expression of dominant-negative CREB, decreases FoxP3 gene expression. Thus, T cell receptor–induced FoxP3 expression in T reg cells is controlled both by sequence-specific binding of CREB/ATF and by DNA methylation of a CpG island.
Web-based GeneChip analysis system for large-scale collaborative projects
Authors: Dai Manhong , Wang Pinglang , Jakupovic Elvis , Watson Stanley J. , Meng Fan
Published: June 2007

Summary: The Web-Based GeneChip Analysis System (WGAS) is developed to overcome limitations in analysis setup efficiency, data and procedure sharing, as well as security issues in existing commercial and public domain solutions. It also incorporates unique functions and resources for more accurate and flexible GeneChip analysis.

Availability: WGAS is freely available at: http://arrayanalysis.mbni.med.umich.edu/arrayanalysis.html

Contact:  mengf@umich.edu
TASSEL: software for association mapping of complex traits in diverse samples
Authors: Bradbury Peter J. , Zhang Zhiwu , Kroon Dallas E. , Casstevens Terry M. , Ramdoss Yogesh , Buckler Edward S.
Published: June 2007

Summary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.

Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www.maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel.

Contact:  pjb39@cornell.edu
beadarray: R classes and methods for Illumina bead-based data
Authors: Dunning Mark J. , Smith Mike L. , Ritchie Matthew E. , Tavaré Simon
Published: June 2007

Summary: The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes. Users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software. The package also allows quality assessment to be carried out on the raw data. The data can then be summarized and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner.

Availability: The beadarray package is available from the Bioconductor web page at www.bioconductor.org. A user's; guide and example data sets are provided with the package.

Contact:  md392@cam.ac.uk
HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies
Authors: Laramie Jason M. , Wilk Jemma B. , DeStefano Anita L. , Myers Richard H.
Published: June 2007

Summary: We have created a program that searches densely genotyped regions for associated non-contiguous haplotypes using a standard family based haplotype association test. This program was designed to expand upon the ‘sliding window’ methodologies commonly used for haplotype construction by allowing the association of subsets of single nucleotide polymorphisms (SNPs) to drive the construction of the haplotype. This strategy permits HaploBuild to construct more biologically relevant haplotypes that are not constrained by arbitrary length and contiguous orientation.

Availability:  http://snp.bumc.bu.edu

Contact:  laramiej@bu.edu
BiVisu: software tool for bicluster detection and visualization
Authors: Cheng K.O. , Law N.F. , Siu W.C. , Lau T.H.
Published: June 2007

Summary: BiVisu is an open-source software tool for detecting and visualizing biclusters embedded in a gene expression matrix. Through the use of appropriate coherence relations, BiVisu can detect constant, constant-row, constant-column, additive-related as well as multiplicative-related biclusters. The biclustering results are then visualized under a 2D setting for easy inspection. In particular, parallel coordinate (PC) plots for each bicluster are displayed, from which objective and subjective cluster quality evaluation can be performed.

Availability: BiVisu has been developed in Matlab and is available at http://www.eie.polyu.edu.hk/~nflaw/Biclustering/

Contact:  k.o.cheng@polyu.edu.hk
The effect of diet on Paraoxonase 1/Arylesterase activities in patients with disorders of galactose metabolism
Authors: Schulpis Kleopatra H. , Karikas George A. , Bartzeliotou Anastasia , Papakonstantinou Evangelos D. , Kalogerakou Maria , Tsakiris Stylianos
Published: June 2007

Objective  To investigate the effects of diet on the antiatherogenic enzyme Paraoxonase 1/Arylesterase (PON1/Aryl) activities in patients with disorders of galactose metabolism.

Patients and methods  Eleven poorly dietary controlled children with classical galactosaemia (GALT deficiency), 7 with epimerase deficiency and 12 with duarte 1 variant ‘off diet’ underwent clinical and laboratory investigations before and after 10 days on galactose restricted diet whereas controls (N = 20) were examined once. Serum lipids, lipoproteins and apolipoprotein A1 (ApoA1) were measured with routine methods, PON1/Aryl activities and total antioxidant status (TAS) spectrophotometrically, and galactose‐1‐phosphate (Gal‐1‐P) enzymatically.

Results  Lipids, lipoproteins, ApoA1, PON1/Aryl, TAS remained unaltered in all groups, except in those with classical galactosaemia pre‐ versus postdiet. In patients with classical galactosaemia, TAS, PON1, Aryl (0·98 ± 0·2 mmol/l, 60 ± 12 U/min/ml, 56 ± 16 KU/min/ml, respectively) were significantly reduced prediet as compared with those postdiet (1·63 ± 0·2 mmol/l, 136 ± 15 U/min/ml, 112 ± 18 KU/min/ml, respectively; P < 0·001) and controls. The enzyme activities positively correlated with TAS (r = 0·56, P < 0·001) in all groups and negatively with Gal‐1‐P (r = –0·54, P < 0·001) in group with GALT deficiency.

Conclusions  Low TAS and high Gal‐1‐P levels may reduce PON1/Aryl activities. Patients with classical galactosaemia, when on strict diet, may benefit with a generous antiatherogenic capacity.
Soil organic matter chemistry in allophanic soils: a pyrolysis‐GC/MS study of a Costa Rican Andosol catena
Authors: Buurman P. , Peterse F. , Almendros Martin G.
Published: June 2007

Soil organic matter (SOM) in allophanic soils is supposed to accumulate due to protection caused by binding to allophane, aluminium and iron. We investigated a catena of allophanic and non‐allophanic soils in Costa Rica to determine the effect of such binding mechanisms on SOM chemistry. These soils contain no contribution of black carbon. Molecular characterization of litter, extractable and dispersed organic matter was done by Curie‐point pyrolysis‐GC/MS. The molecular chemistry of the organic fractions indicates a strong decomposition of plant‐derived organic matter and a strong contribution of microbial sugars and N‐compounds to SOM. Both the decomposition of plant‐derived SOM – including that of relatively recalcitrant compounds – and the relative contribution of microbial SOM were greater in allophanic samples than in non‐allophanic ones. This suggests that chemical protection does not act on primary OM, although it may influence the accumulation of secondary OM in these soils. The effect of allophane on SOM contents in such perhumid soils is probably through incorporation of decomposition products and microbial SOM in very fine aggregates that – in a perhumid environment – remain saturated with water during much of the year. Greater concentrations of aliphatics are found in allophanic residues, but there is no evidence of any specific mineral‐organic binding. The results do not support the existing theory of chemical protection of plant‐derived components through binding to allophane, iron and aluminium.
Sulphate adsorption at the Fe (hydr)oxide–H2O interface: comparison of cluster and periodic slab DFT predictions
Authors: Paul K. W. , Kubicki J. D. , Sparks D. L.
Published: June 2007

The transport and bioavailability of sulphate in soils are significantly affected by adsorption reactions at the mineral–H2O interface. Therefore, an understanding of the mechanisms and kinetics of sulphate adsorption is of fundamental importance in soil chemistry. In this investigation, the binding geometries of bidentate bridging and monodentate sulphate complexes at the Fe (hydr)oxide–H2O interface were predicted with static cluster and periodic slab density functional theory (DFT) calculations. The cluster calculations were performed with edge‐sharing dioctahedral Fe3+ models, using the unrestricted PBE0 exchange‐correlation functional and a combination of effective core potential (LanL2DZ – Fe atoms) and all‐electron (6–311+G(d,p) or 6–311+G(3df,p) – S, O, and H atoms) basis sets. The periodic slab calculations were performed with a (3 × 2) slab of the (100) α‐FeOOH surface, by means of the projector‐augmented wave method and a plane‐wave basis set. For the periodic slab DFT calculations, the spin‐polarized (SP) PBE exchange‐correlation functional, with and without explicit consideration of an on‐site Coulomb interaction parameter (i.e. SP‐PBE and SP‐PBE+U methods), was used. Despite the lack of long‐range order, cluster model predictions of the interatomic distances and angles of bidentate bridging and monodentate sulphate were in good agreement with the periodic slab model predictions. Quantitative analysis of the cluster and periodic slab DFT predictions is expected to result from theoretical fitting of extended X‐ray absorption fine structure measurements. The application of computational chemistry methods to soil chemistry research is anticipated to provide novel insight into the mechanisms and kinetics of ion sorption.
Long‐term use of Swedish moist snuff and the risk of myocardial infarction amongst men
Authors: Hergens M.‐P. , Alfredsson L. , Bolinder G. , Lambe M. , Pershagen G. , Ye W.
Published: June 2007

Background.  The scientific evidence on cardiovascular risks associated with long‐term use of snuff is limited and inconclusive. The use of this smokeless tobacco has increased in recent decades, and adverse health effects associated with snuff use could be of great public health concern.

Objective.  We aimed to study whether long‐term use of snuff affects the risk of myocardial infarction.

Design.  Between 1978 and 1993 all construction workers in Sweden were offered repeated health check‐ups by the Swedish Construction Industry's Organization for Working Environment Safety and Health. A cohort was created with information on tobacco use and other risk factors, collected through questionnaires.

Setting.  In total, 118 395 nonsmoking men without a history of myocardial infarction were followed through 2004. Information on myocardial infarction morbidity and mortality was obtained from national registers. Relative risk estimates were derived from Cox proportional hazards regression model, with adjustment for age, body mass index and region of residence.

Results.  Almost 30% of the men had used snuff. In total, 118 395 nonsmoking men without a history of myocardial infarction were followed through 2004. The multivariable‐adjusted relative risks for ever snuff users were 0.91 (95% confidence interval, 0.81–1.02) for nonfatal cases and 1.28 (95% confidence interval, 1.06–1.55) for fatal cases. Heavy users (≥50 g day−1) had a relative risk of fatal myocardial infarction of 1.96 (95% confidence interval, 1.08–3.58). Snuff use increased the probability of mortality from cardiovascular disease amongst nonfatal myocardial infarction patients.

Conclusion.  Our results indicate that snuff use is associated with an increased risk of fatal myocardial infarction.
Impaired cortisol response to acute stressors in patients with coronary disease. Implications for inflammatory activity
Authors: Nijm J. , Kristenson M. , Olsson A. G. , Jonasson L.
Published: June 2007

Objectives. Inflammation is assumed to play a major role in the progress of atherosclerotic disease. We hypothesized that an altered hypothalamic‐pituitary adrenal (HPA) axis activity was linked to a disinhibited inflammatory activity in patients with coronary artery disease (CAD).

Methods. Thirty CAD patients were assessed 12–14 weeks after a first‐time acute coronary syndrome. Serum samples were assayed for C‐reactive protein (CRP) and interleukin‐6. Free cortisol was measured in a 24‐h urine sample and in repeated saliva samples 30 min after awakening and at bedtime. The levels of inflammatory markers and cortisol were also determined before and after standardized physical and psychological stress tests.

Results. The CAD patients had a higher 24‐h cortisol secretion and a flattened diurnal slope, resulting from significantly higher cortisol levels at bedtime, compared to clinically healthy controls. The levels of evening cortisol were strongly related to inflammatory markers in serum. When exposed to acute physical and psychological stressors, the CAD patients showed a significantly blunted cortisol response compared to controls. In addition, a stress‐induced increase in CRP was only observed in the patient group.

Conclusions. Patients with CAD exhibited a cortisol pattern that markedly differed from controls. The data indicate that a dysfunctional HPA axis response involves a failure to contain inflammatory activity in CAD patients, thus providing a possible link between stress and inflammation in disease.
Matrix metalloproteinase‐1 and its inhibitor, TIMP‐1, in systolic heart failure: relation to functional data and prognosis
Authors: Jordán A. , Roldán V. , García M. , Monmeneu J. , De Burgos F. G. , Lip G. Y. H. , Marín F.
Published: June 2007

Background.  Structural remodelling of left ventricle is a common feature in the progression of congestive heart failure (CHF). Matrix metalloproteinases (MMPs) have been directly implicated as they degrade extracellular proteins. To test the hypothesis that MMP‐and its inhibitor, tissue type inhibitor of matrix metalloproteinases (TIMP‐1), could be related to functional status and prognosis in CHF, we examined the relationship of MMP‐1 and TIMP‐1 to peak oxygen consumption (VO2) and peak minute ventilation/carbon dioxide production relationship (VE/VCO2), and assessed their prognostic value.

Methods.  We studied 50 patients with CHF, who were compared with 53 controls echocardiogram and ergoespirometry were performed, and serum levels of MMP‐1 and TIMP‐1 were assayed by ELISA. Patients were followed up for 17.5 ± 8.9 months, and total mortality, readmissions for heart failure and cardiac transplantation were recorded.

Results.  Patients with CHF had lower levels of MMP‐1 (P = 0.027), and higher levels of TIMP‐1 and TIMP‐1/MMP‐1 ratio (both P < 0.01) than controls. TIMP‐1 levels and the TIMP‐1/MMP‐1 ratio correlated negatively with peak VO2 (Spearman, r:−0.51; P = 0.001 and r: −0.42; P = 0.030, respectively). During the follow‐up period, 23 patients (47.9%) suffered endpoints – these patients had higher baseline peak VE/VCO2 (P = 0.001), TIMP‐1 (P = 0.004), and TIMP‐1/MMP‐1 ratio values (P = 0.002), whereas MMP‐1 levels were lower (P = 0.027). On multivariate analysis, VE/VCO2, MMP‐1 levels and age were the only variables independently related to prognosis (all P < 0.05).

Conclusion.  Poor functional capacity in CHF can be related to abnormal extracellular matrix turnover. Patients who suffered endpoints had more abnormal indices of matrix turnover, where MMP‐1 levels showed independent prognostic value.
Strong population structure despite evidence of recent migration in a selfing hermaphroditic vertebrate, the mangrove killifish (Kryptolebias marmoratus)
Authors: TATARENKOV ANDREY , GAO HONG , MACKIEWICZ MARK , TAYLOR D. SCOTT , TURNER BRUCE J. , AVISE JOHN C.
Published: June 2007

We employ a battery of 33 polymorphic microsatellite loci to describe geographical population structure of the mangrove killifish (Kryptolebias marmoratus), the only vertebrate species known to have a mixed‐mating system of selfing and outcrossing. Significant population genetic structure was detected at spatial scales ranging from tens to hundreds of kilometres in Florida, Belize, and the Bahamas. The wealth of genotypic information, coupled with the highly inbred nature of most killifish lineages due to predominant selfing, also permitted treatments of individual fish as units of analysis. Genetic clustering algorithms, neighbour‐joining trees, factorial correspondence, and related methods all earmarked particular killifish specimens as products of recent outcross events that could often be provisionally linked to specific migration events. Although mutation is the ultimate source of genetic diversity in K. marmoratus, our data indicate that interlocality dispersal and outcross‐mediated genetic recombination (and probably genetic drift also) play key proximate roles in the local ‘clonal’ dynamics of this species.
A sharper view of the outer Galaxy at 1420 and 408 MHz from the Canadian Galactic Plane Survey II: the catalogue of extended radio sources
Authors: Kerton C. R. , Murphy J. , Patterson J.
Published: June 2007

A new catalogue of extended radio sources has been prepared based on arcminute-resolution 1420-MHz images from the Canadian Galactic Plane Survey (CGPS). The new catalogue provides both 1420- and 408-MHz flux density measurements on sources found near the Galactic plane in the second quadrant of our Galaxy. In addition cross-identifications are made with other major radio catalogues and information is provided to facilitate the recovery of CGPS image data associated with each catalogued source. Numerous new radio sources are identified and the catalogue provides a comprehensive summary of both newly discovered and previously known H ii regions and supernova remnants in the outer Galaxy. The catalogue should be of use both for synoptic studies of Galactic structure and for placing higher resolution observations, at radio and other wavelengths, in context.
phyB‐1 sorghum maintains responsiveness to simulated shade, irradiance and red light : far‐red light
Authors: FINLAYSON SCOTT A. , HAYS DIRK B. , MORGAN PAGE W.
Published: June 2007

The sorghum [Sorghum bicolor (L.) Moench]phyB‐1 mutant exhibits a constitutive shade‐avoidance phenotype including excessive shoot elongation. It was previously shown that this mutant also overproduces ethylene. Although phytochrome B (phyB) is assumed to be the pigment most important in sensing and transducing shade signals, the sorghum phyB‐1 mutant still responds to light signals characteristic of shade. Specifically, it was determined that the leaf blade : leaf sheath elongation of phyB‐1 is responsive to red : far red (R : FR), but this response is opposite that of wild type (WT). Reducing the photosynthetic photon flux density (PPFD) strongly reduced the leaf blade : leaf sheath of WT but did not affect phyB‐1, demonstrating a role for phyB in sensing PPFD. Using light‐emitting diode (LED) lighting, it was found that WT ethylene production was increased with low R : FR while PPFD had no effect. Conversely, phyB‐1 ethylene production increased only with high PPFD, high R : FR which was the treatment resulting in the least ethylene production by WT. Elevated ethylene production inhibits shoot elongation, but may contribute to shade avoidance by reducing leaf blade : leaf sheath elongation. Ethylene responses to light treatments designed to promote or reduce phytochrome A (phyA) activity, and the analysis of PHYA levels in the two cultivars suggests that phyA could be involved in transducing shade signals in light‐grown sorghum. Responses potentially tranduced by phyA are elevated in phyB‐1 which also over‐expresses PHYA.
17p11.2p12 triplication and del(17)q11.2q12 in a severely affected child with dup(17)p11.2p12 syndrome
Authors: Girirajan S , Williams SR , Garbern JY , Nowak N , Hatchwell E , Elsea SH
Published: June 2007

Multiple congenital anomalies/mental retardation syndromes due to genomic rearrangements involving chromosome 17p11.2 include deletion resulting in Smith–Magenis syndrome and a reciprocal duplication of the same region resulting in the 17p11.2 duplication syndrome. We present the clinical and molecular analysis of an 8‐year‐old male with a dup(17p11.2p12) who was evaluated for unusual severity of the phenotype. Fluorescent in situ hybridization (FISH) analysis not only confirmed the 17p duplication but also identified an ∼25% mosaicism for tetrasomy 17p11.2p12. Whole‐genome array comparative genomic hybridization (aCGH) was performed to identify other genomic rearrangements possibly contributing to the severe phenotype and the unusual features in the patient. The 17p duplication was determined by FISH and aCGH to encompass ∼7.5 Mb, from COX10 to KCNJ12. An ∼830 Kb deletion of 17q11.2q12, including exon 1 of an amiloride‐sensitive cation channel neuronal gene, ACCN1, was also identified by aCGH; breakpoints of the deletion were confirmed by FISH. Sequencing the non‐deleted allele of ACCN1 did not show any mutations. Western analysis of human tissue‐specific proteins revealed that ACCN1 is expressed not only in the brain as previously reported but also in all tissues examined, including heart, liver, kidneys, and spleen. The large‐sized 17p11.2p12 duplication, partial triplication of the same region, and the 17q11.2q12 deletion create a complex chromosome 17 rearrangement that has not been previously identified. This is the first case of triplication reported for this chromosome. Our study emphasizes the utility of whole‐genome analysis for known cases with deletion/duplication syndromes with unusual or severe phenotypes.
An annual cycle of dimethylsulfoniopropionate‐sulfur and leucine assimilating bacterioplankton in the coastal NW Mediterranean
Authors: Vila‐Costa Maria , Pinhassi Jarone , Alonso Cecilia , Pernthaler Jakob , Simó Rafel
Published: June 2007

The contribution of major phylogenetic groups to heterotrophic bacteria assimilating sulfur from dissolved dimethylsulfoniopropionate (DMSP) and assimilating leucine was analysed in surface seawaters from Blanes Bay (NW Mediterranean) over an annual study between March 2003 and April 2004. The percentage of bacteria assimilating DMSP‐S showed a strong seasonal pattern, with a steady increase from winter (8 ± 5%) to summer (23 ± 3%). The same seasonal pattern was observed for the rate of DMSP‐S assimilation. The annual average percentage of DMSP‐S‐assimilating bacteria (16 ± 8%) was lower than the corresponding percentage of leucine‐assimilating cells (35 ± 16%), suggesting that not all bacteria synthesizing protein incorporated DMSP‐S. Smaller differences between both percentages were recorded in summer. Members of the Alphaproteobacteria (Roseobacter and SAR11) and Gammaproteobacteria groups accounted for most of bacterial DMSP‐S‐assimilating cells over the year. All major bacterial groups showed an increase of the percentage of cells assimilating DMSP‐S during summer, and contributed to the increase of the DMSP‐S assimilation rate in this period. In these primarily P‐limited waters, enrichment with P + DMSP resulted in a stimulation of bacterial heterotrophic production comparable to, or higher than, that with P + glucose in summer, while during the rest of the year P + glucose induced a stronger response. This suggested that DMSP was more important a S and C source for bacteria in the warm stratified season. Overall, our results suggest that DMSP‐S assimilation is controlled by the contribution of DMSP to S (and C) sources rather than by the phylogenetic composition of the bacterioplankton.
Candidatus Symbiothrix dinenymphae: bristle‐like Bacteroidales ectosymbionts of termite gut protists
Authors: Hongoh Yuichi , Sato Tomoyuki , Noda Satoko , Ui Sadaharu , Kudo Toshiaki , Ohkuma Moriya
Published: June 2007

Many reports have stated that flagellated protists in termite guts harbour ectosymbiotic spirochetes on their cell surface. In this study, we describe another bristle‐like ectosymbiont affiliated with the order Bacteroidales. The 16S rRNA phylotype Rs‐N74 predominates among Bacteroidales clones obtained from the gut of the termite Reticulitermes speratus. An Rs‐N74 phylotype‐specific probe was designed in this study and used for detection of the corresponding bacteria in the gut by fluorescence in situ hybridization (FISH) analysis. Surprisingly, the signals were detected specifically from the bristle‐like ‘appendages’ of various flagellate species belonging to the genus Dinenympha; these ‘appendages’ had been believed to be spirochetal ectosymbionts or structures of the protists. The Rs‐N74 bacteria attached to the cell surface of the protists by a tip and coexisted with the spirochetal ectosymbionts. An electron micrograph revealed their morphology to be similar to a typical Bacteroidales bacterium. This bacterium is proposed to represent a novel genus and species, ‘Candidatus Symbiothrix dinenymphae’, phylogenetically affiliated with a cluster consisting exclusively of uncultured strains from termite guts. A Bacteroidales‐specific probe for FISH further revealed that this type of symbiosis exists also in various other protists, including parabasalids and oxymonads, and is widespread in termite guts.
Environmental significance of O‐demethylation of chloroanisoles by soil bacterial isolates as a mechanism that improves the overall biodegradation of chlorophenols
Authors: Goswami Mandira , Recio Eliseo , Campoy Sonia , Martín Juan Francisco , Coque Juan‐José R.
Published: June 2007

The biodegradation rate of chlorophenols in the environment seems to be limited by a competitive mechanism of O‐methylation which produces chloroanisoles with a high potential of being bioconcentrated in living organisms. In this work we report for the first time the isolation of three soil bacterial strains able to efficiently degrade 2,4,6‐trichloroanisole (2,4,6‐TCA). These strains were identified as Xanthomonas retroflexus INBB4, Pseudomonas putida INBP1 and Acinetobacter radioresistens INBS1. In these isolates 2,4,6‐TCA was efficiently metabolized in a minimal medium containing methanol and 2,4,6‐TCA as the only carbon sources, with a concomitant release of 3 mol of chloride ion from 1 mol of 2,4,6‐TCA, indicating complete dehalogenation of 2,4,6‐TCA. 2,4,6‐trichlorophenol (2,4,6‐TCP) was identified as a degradative intermediate, indicating that 2,4,6‐TCA underwent O‐demethylation as the first step in the biodegradation process. 2,4,6‐TCP was further transformed into 2,6‐dichloro‐para‐hydroquinone (2,6‐DCHQ) and subsequently mineralized. The degradation of chloroanisoles could improve the overall biodegradation of chlorophenols in the environment, because those chlorophenols previously biomethylated might also be later biodegraded. Xanthomonas retroflexus INBB4 has two O‐demethylation systems: one is an oxygenase‐type demethylase, and the other is a tetrahydrofolate (THF)‐dependent O‐demethylase. On the contrary O‐demethylation of 2,4,6‐TCA in P. putida INBP1 is just catalysed by an oxygenase‐type NADH/NADPH‐dependent O‐demethylase, whereas in A. radioresistens INBS1 a THF‐dependent O‐demethylase activity was detected.
PPAR‐alpha: therapeutic role in diabetes‐related cardiovascular disease
Authors: Cheng Alice Y. Y. , Leiter Lawrence A.
Published: June 2007

Among individuals with diabetes mellitus, cardiovascular disease remains the leading cause of death, despite the many treatment modalities that have been developed over time. The PPAR family, including PPAR‐alpha, play important roles in glucose and lipid metabolism and atherosclerosis and thus are potential therapeutic targets. Fibrates act upon PPAR‐alpha and appear to target the typical dyslipidaemia of diabetes. Several large prospective clinical trials have shown both primary prevention and secondary prevention benefit with fibrates, although they only had small subgroups of patients with diabetes. The first large outcome study to exclusively study those with diabetes was the FIELD study, which showed no reduction in the primary cardiovascular end‐point and only some benefit in the secondary end‐point. There are many potential explanations for these results; however, it would appear that at present, there is no role for fibrates as monotherapy for the reduction of cardiovascular risk among those with diabetes. However, their potential role in combination with statin therapy remains to be further elucidated with ongoing studies.
Growing Pains: Commentary on the Field of Posttraumatic Growth and Hobfoll and Colleagues’ Recent Contributions to it
Authors: Butler Lisa D.
Published: June 2007

The field of research on benefit‐finding and growth following traumatic experience lacks consensus with respect to some central conceptual questions, and a number of these issues are apparent in the research reported by Stevan Hobfoll and his colleagues. In this commentary I briefly discuss, and at times dispute, some of the assertions and assumptions in this target article that I believe reflect these broader issues, including that: psychosocial gains (or benefits) and psychological growth are equivalent, reporting gains (or benefits) represents maladaptive efforts at coping, posttraumatic growth (PTG) is necessarily linked with positive psychological adjustment, and trauma symptoms represent poor adjustment following traumatic event exposure. I also discuss the intriguing proposal of this research: that action is essential to true growth.

Les recherches sur la maturation et les avantages que l’on peut tirer d’une expérience traumatisante sont en désaccord sur des aspects théoriques majeurs, et certains de ces problèmes apparaissent dans l’étude présentée par Stevan Hobfoll et ses collègues. Dans ce commentaire, je discute brièvement et parfois conteste certaines des affirmations et hypothèses de cet article de référence qui, je pense, renvoie à des questions plus vastes telles que: les gains (ou bénéfices) psychosociaux et le développement psychologique sont équivalents; signaler des gains (ou des bénéfices) représente un effort inapproprié pour faire face à la situation; le développement post‐traumatique est nécessairement en relation avec une adaptation psychologique positive; les symptômes traumatiques traduisent une adaptation faible suite à l’exposition à l’évènement pénible. Je discute aussi cette idée curieuse selon laquelle l’action est essentielle au vrai développement.
Posttraumatic Growth as a Cognitive Process with Behavioral Components: A Commentary on Hobfoll et al. (2007)
Authors: Wagner Birgit , Forstmeier Simon , Maercker Andreas
Published: June 2007

The commentary highlights some of the key points to emerge from the paper by Hobfoll, Hall, Canetti‐Nisim, Galea, Johnson, and Palmieri (2007, in this issue) about the relationship between posttraumatic growth and action, psychological functioning, and cognitive processing. In our commentary, we question the sequence of steps that Hobfoll et al. took to critique current theoretical cognitive models of posttraumatic growth. On the basis of the Janus‐face model (Maercker & Zöllner, 2004) of posttraumatic growth, we argue that, in addition to a cognitive core, posttraumatic growth may, but does not necessarily, involve an action component.

Ce commentaire souligne quelques‐unes des idées maîtresses de l’article de Hobfoll & al. concernant la relation existant entre le développement post‐traumatique et l’action, le fonctionnement psychologique et les processus cognitifs. Nous nous interrogeons sur les étapes que les auteurs retiennent pour critiquer les modèles cognitifs théoriques actuels du développement post‐traumatique. A partir du modèle bifacial de Maercker & Zöllner, nous défendons l’idée qu’en plus d’un noyau cognitif le développement post‐traumatique peut s’accompagner d’une composante action, mais que ce n’est pas nécessaire.
Posttraumatic Growth: Action and Reaction
Authors: Johnson Robert J. , Hobfoll Stevan E. , Hall Brian J. , Canetti‐Nisim Daphna , Galea Sandro , Palmieri Patrick A.
Published: June 2007

We respond to the commentators who raise several key issues. Points of agreement include the need to incorporate several new concepts within the broader umbrella of posttraumatic growth (PTG), a need to understand more of the context under which PTG might have positive, negative, or limited influence, and a need to understand aspects of persons and populations who might use PTG in different ways. A major point of disagreement remains with the original formulation of PTG which poses PTG as a universally positive contribution to well‐being, or even that it is beneficial in its own right. Illusion may have positive aspects, but we remain interested in the idea that it is most beneficial when translated into action. Some of these actions may be cognitive, but they should in such instances have lasting meaning for individuals’ lives. Too often, PTG represents the belief that one has grown in some deep way, without validation of that depth of experience.

Il nous faut répondre aux commentateurs qui soulèvent plusieurs questions importantes. Les points d’accord concernent la nécessité d’introduire de nouveaux concepts sous la notion générale de développement post‐traumatique (PTG), de mieux cerner les contextes où le PTG peut avoir une influence positive, négative ou limitée et d’évaluer les dimensions des personnes et des populations susceptibles d’exploiter le PTG de différentes façons. Le désaccord majeur porte sur la définition originelle du PTG qui implique que celui‐ci contribue au bien‐être de façon universellement positive, ou même qu’il est en lui‐même source de bénéfices. L’illusion peut avoir des retombées positives, mais nous restons convaincus qu’elle est plus efficace quand elle s’investit dans l’action. Certaines de ces actions peuvent être d’ordre cognitif, mais elles doivent en ce cas revêtir une signification durable pour l’existence de l’individu. Trop souvent le PTG se résume à la conviction que l’on a mûri en profondeur sans qu’il y ait la moindre preuve de cette évolution profonde.
Posttraumatic Growth and Resilience to Trauma: Different Sides of the Same Coin or Different Coins?
Authors: Westphal Maren , Bonanno George A.
Published: June 2007

Posttraumatic growth (PTG) is an appealing but poorly understood construct. Hobfoll, Hall, Canetti‐Nisim, Galea, Johnson, and Palmieri's (2007) insightful paper highlights important weaknesses in existing theory and data. Although we commend Hobfoll et al. for offering a provocative new way to conceptualise PTG in terms of action‐focused growth, we also find a number of limitations in their approach. In this article, we attempt to place PTG within a broader framework of individual differences in response to potential trauma. As in most of the literature on PTG, Hobfoll et al. implicitly equate growth with resilience or view it as superior to resilient outcomes. We argue, however, that many if not most people are resilient in the face of trauma and that resilient outcomes typically provide little need or opportunity for PTG. We close by exploring the literature on resilience for possible mechanisms underlying a link between PTG and adaptation. For example, Hobfoll et al. dismiss some forms of reported growth as illusory. In contrast, we review evidence for the adaptive value of self‐enhancing illusions in coping with adversity.

Le développement post‐traumatique (PTG) est un concept attrayant mais insuffisamment approfondi. L’article stimulant de Hobfoll & al. met en relief des carences significatives dans les données et théories existantes. Bien que nous approuvions Hobfoll & al. quand ils présentent une conception aussi nouvelle que provocante du PTG en terme de développement centré sur l’action, nous estimons aussi que cette approche a ses limites. On essaie, dans cet article, de replacer le PTG dans le cadre plus vaste des différences individuelles en réponse au traumatisme potentiel. Comme souvent dans la littérature sur le PTG, Hobfoll & al. assimilent le développement à la résilience ou le considèrent comme supérieur aux conséquences de la résilience. Nous défendons au contraire l’idée que beaucoup de gens, voire la plupart, sont résilients face au traumatisme et que les apports de la résilience peuvent se passer ou n’offrent habituellement que peu d’opportunités au PTG. On termine en examinant la littérature sur la résilience à la recherche d’éventuels processus sous‐tendant un lien entre PTG et adaptation. Par exemple, Hobfoll & al. rejettent certains témoignages de développement comme relevant de l’illusion; nous avons par contre relevé des preuves que des illusions valorisant le moi contribuent à l’adaptation dans la lutte contre l’adversité.
Multilevel models for repeated measures research designs in psychophysiology: An introduction to growth curve modeling
Authors: Kristjansson Sean D. , Kircher John C. , Webb Andrea K
Published: June 2007

Psychophysiologists often use repeated measures analysis of variance (RMANOVA) and multivariate analysis of variance (MANOVA) to analyze data collected in repeated measures research designs. ANOVA and MANOVA are nomothetic approaches that focus on group means. Newer multilevel modeling techniques are more informative than ANOVA because they characterize both group‐level (nomothetic) and individual‐level (idiographic) effects, yielding a more complete understanding of the phenomena under study. This article was written as an introduction to growth curve modeling for applied researchers. A growth model is defined that can be used in place of RMANOVAs and MANOVAs for single‐group and mixed repeated measures designs. The model is expanded to test and control for the effects of baseline levels of physiological activity on stimulus‐specific responses. Practical, conceptual, and statistical advantages of growth curve modeling are discussed.
Neuroticism is associated with larger and more prolonged electrodermal responses to emotionally evocative pictures
Authors: Norris Catherine J. , Larsen Jeff T. , Cacioppo John T.
Published: June 2007

Elevated neuroticism is associated with increased psychological reactivity to stressors. Research on individual differences and physiological reactivity (e.g., electrodermal activity), however, has focused on clinical samples and measures of basal activity (e.g., nonspecific skin conductance responses) or responses to nonaffective stimuli. Surprisingly, there is a dearth of work on physiological reactivity to emotional stimuli as a function of neuroticism. Thus, the authors sought to examine the relationship between neuroticism and skin conductance reactivity to emotionally evocative pictures in a nonclinical sample. Individuals higher in neuroticism exhibited both greater skin conductance reactivity to emotional (and particularly aversive) pictures as well as more extended reactivity than did emotionally stable individuals. Implications for health are discussed.
msatcommander: detection of microsatellite repeat arrays and automated, locus‐specific primer design
Authors: FAIRCLOTH BRANT C.
Published: June 2007

msatcommander is a platform‐independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single‐sequence or concatenated, fasta‐formatted files. Search data and locus‐specific primers are written to comma‐separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8.
 msatcommander is available from http://code.google.com/p/msatcommander/.
Image Processing to Estimate the Heat Sources Related to Phase Transformations during Tensile Tests of NiTi Tubes
Authors: Schlosser P. , Louche H. , Favier D. , Orgéas L.
Published: June 2007

Abstract:  Temperature and strain fields have been observed during superelastic tensile tests on NiTi tubes. They show strong localisations that take the shape of helical bands with characteristics that depend on global tensile strain and strain rate. To obtain quantitative energy information, allowing a better recognition of the deformation mechanisms involved inside and outside the helical bands, an estimation of the local heat sources based on image processing of the temperature fields is proposed in the present paper. This processing method is first calibrated and validated on numerically simulated temperature fields calculated using theoretical heat sources close to those associated with martensitic phase transformation. It is then applied to experimentally observed temperature fields during a typical superelastic tensile test of an NiTi tube.
Microcalorimetry: a novel method for detection of microbial contamination in platelet products
Authors: Trampuz Andrej , Salzmann Simone , Antheaume Jeanne , Daniels Alma U.
Published: June 2007

BACKGROUND: Measuring heat from replicating microorganisms in culture may be a rapid, accurate, and simple screening method for platelets (PLTs). Microcalorimetry for detection of microorganisms in in vitro contaminated PLT products was evaluated.

STUDY DESIGN AND METHODS: Staphylococcus epidermidis, Staphylococcus aureus, Streptococcus sanguinis, Escherichia coli, Propionibacterium acnes, and Candida albicans were inoculated in single‐donor apheresis PLTs to achieve target concentrations of 105, 103, 10, or 1 colony‐forming units (CFU) per mL of PLTs. Contaminated PLTs in growth medium were incubated at 37°C for 5 days in a calorimeter. Positivity was defined as heat flow of at least 10 µW above the lowest value of the power–time curve.

RESULTS: With microcalorimetry, inocula of 10 CFUs per mL PLTs could be detected with the following detection times: S. epidermidis (31.65 hr), S. aureus (24.24 hr), S. sanguinis (7.82 hr), E. coli (7.53 hr), P. acnes (73.57 hr), and C. albicans (43.77 hr). The detection time was less than 4 hr at 105 CFUs per mL PLTs for S. aureus, S. sanguinis, and E. coli. Noncontaminated PLTs remained negative. The total heat ranged from 2.8 (S. sanguinis) to 8.3 J (E. coli).The shape of the power–time curve was species‐specific and independent from the initial concentration of microorganisms.

CONCLUSION: The detection limit of microcalorimetry was 1 to 10 CFUs per mL PLTs. Microcalorimetry is a promising novel method for detection of contaminated PLTs. Applying this method to all PLT products could reduce the frequency of transfusion‐related sepsis and prolong the shelf life of PLTs.