bluuebunny/crossref_metadata_2025 huggingface dataset:
Widespread metabolic potential for nitrite and nitrate assimilation among
Prochlorococcus
ecotypes
Authors: Martiny Adam C. , Kathuria Satish , Berube Paul M.
Published: June 2009

The marine cyanobacterium
Prochlorococcus
is the most abundant photosynthetic organism in oligotrophic regions of the oceans. The inability to assimilate nitrate is considered an important factor underlying the distribution of
Prochlorococcus
, and thought to explain, in part, low abundance of
Prochlorococcus
in coastal, temperate, and upwelling zones. Here, we describe the widespread occurrence of a genomic island containing nitrite and nitrate assimilation genes in uncultured
Prochlorococcus
cells from marine surface waters. These genes are characterized by low GC content, form a separate phylogenetic clade most closely related to marine
Synechococcus
, and are located in a different genomic region compared with an orthologous cluster found in marine
Synechococcus
strains. This sequence distinction suggests that these genes were not transferred recently from
Synechococcus
. We demonstrate that the nitrogen assimilation genes encode functional proteins and are expressed in the ocean. Also, we find that their relative occurrence is higher in the Caribbean Sea and Indian Ocean compared with the Sargasso Sea and Eastern Pacific Ocean, which may be related to the nitrogen availability in each region. Our data suggest that the ability to assimilate nitrite and nitrate is associated with microdiverse lineages within high- and low-light (LL) adapted
Prochlorococcus
ecotypes. It challenges 2 long-held assumptions that (
i
)
Prochlorococcus
cannot assimilate nitrate, and (
ii
) only LL adapted ecotypes can use nitrite. The potential for previously unrecognized productivity by
Prochlorococcus
in the presence of oxidized nitrogen species has implications for understanding the biogeography of
Prochlorococcus
and its role in the oceanic carbon and nitrogen cycles.
The neural bases of empathic accuracy
Authors: Zaki Jamil , Weber Jochen , Bolger Niall , Ochsner Kevin
Published: June 2009

Theories of empathy suggest that an accurate understanding of another's emotions should depend on affective, motor, and/or higher cognitive brain regions, but until recently no experimental method has been available to directly test these possibilities. Here, we present a functional imaging paradigm that allowed us to address this issue. We found that empathically accurate, as compared with inaccurate, judgments depended on (
i
) structures within the human mirror neuron system thought to be involved in shared sensorimotor representations, and (
ii
) regions implicated in mental state attribution, the superior temporal sulcus and medial prefrontal cortex. These data demostrate that activity in these 2 sets of brain regions tracks with the accuracy of attributions made about another's internal emotional state. Taken together, these results provide both an experimental approach and theoretical insights for studying empathy and its dysfunction.
Stoichiometric and temporal requirements of Oct4, Sox2, Klf4, and c-Myc expression for efficient human iPSC induction and differentiation
Authors: Papapetrou Eirini P. , Tomishima Mark J. , Chambers Stuart M. , Mica Yvonne , Reed Evan , Menon Jayanthi , Tabar Viviane , Mo Qianxing , Studer Lorenz , Sadelain Michel
Published: June 2009

Human-induced pluripotent stem cells (hiPSCs) are generated from somatic cells by ectopic expression of the 4 reprogramming factors (RFs) Oct-4, Sox2, Klf4, and c-Myc. To better define the stoichiometric requirements and dynamic expression patterns required for successful hiPSC induction, we generated 4 bicistronic lentiviral vectors encoding the 4 RFs co-expressed with discernable fluorescent proteins. Using this system, we define the optimal stoichiometry of RF expression to be highly sensitive to Oct4 dosage, and we demonstrate the impact that variations in the relative ratios of RF expression exert on the efficiency of hiPSC induction. Monitoring of expression of each individual RF in single cells during the course of reprogramming revealed that vector silencing follows acquisition of pluripotent cell markers. Pronounced lentiviral vector silencing was a characteristic of successfully reprogrammed hiPSC clones, but lack of complete silencing did not hinder hiPSC induction, maintenance, or directed differentiation. The vector system described here presents a powerful tool for mechanistic studies of reprogramming and the optimization of hiPSC generation.
Increased InsP
3
Rs in the junctional sarcoplasmic reticulum augment Ca
2+
transients and arrhythmias associated with cardiac hypertrophy
Authors: Harzheim Dagmar , Movassagh Mehregan , Foo Roger S.-Y. , Ritter Oliver , Tashfeen Aslam , Conway Stuart J. , Bootman Martin D. , Roderick H. Llewelyn
Published: June 2009

Cardiac hypertrophy is a growth response of the heart to increased hemodynamic demand or damage. Accompanying this heart enlargement is a remodeling of Ca
2+
signaling. Due to its fundamental role in controlling cardiomyocyte contraction during every heartbeat, modifications in Ca
2+
fluxes significantly impact on cardiac output and facilitate the development of arrhythmias. Using cardiomyocytes from spontaneously hypertensive rats (SHRs), we demonstrate that an increase in Ca
2+
release through inositol 1,4,5-trisphosphate receptors (InsP
3
Rs) contributes to the larger excitation contraction coupling (ECC)-mediated Ca
2+
transients characteristic of hypertrophic myocytes and underlies the more potent enhancement of ECC-mediated Ca
2+
transients and contraction elicited by InsP
3
or endothelin-1 (ET-1). Responsible for this is an increase in InsP
3
R expression in the junctional sarcoplasmic reticulum. Due to their close proximity to ryanodine receptors (RyRs) in this region, enhanced Ca
2+
release through InsP
3
Rs served to sensitize RyRs, thereby increasing diastolic Ca
2+
levels, the incidence of extra-systolic Ca
2+
transients, and the induction of ECC-mediated Ca
2+
elevations. Unlike the increase in InsP
3
R expression and Ca
2+
transient amplitude in the cytosol, InsP
3
R expression and ECC-mediated Ca
2+
transients in the nucleus were not altered during hypertrophy. Elevated InsP
3
R2 expression was also detected in hearts from human patients with heart failure after ischemic dilated cardiomyopathy, as well as in aortic-banded hypertrophic mouse hearts. Our data establish that increased InsP
3
R expression is a general mechanism that underlies remodeling of Ca
2+
signaling during heart disease, and in particular, in triggering ventricular arrhythmia during hypertrophy.
Interaction of CDK5RAP2 with EB1 to Track Growing Microtubule Tips and to Regulate Microtubule Dynamics
Authors: Fong Ka-Wing , Hau Shiu-Yeung , Kho Yik-Shing , Jia Yue , He Lisheng , Qi Robert Z.
Published: June 2009

Mutations in cdk5rap2 are linked to autosomal recessive primary microcephaly, and attention has been paid to its function at centrosomes. In this report, we demonstrate that CDK5RAP2 localizes to microtubules and concentrates at the distal tips in addition to centrosomal localization. CDK5RAP2 interacts directly with EB1, a prototypic member of microtubule plus-end tracking proteins, and contains the basic and Ser-rich motif responsible for EB1 binding. The EB1-binding motif is conserved in the CDK5RAP2 sequences of chimpanzee, bovine, and dog but not in those of rat and mouse, suggesting a function gained during the evolution of mammals. The mutation of the Ile/Leu-Pro dipeptide within the motif abolishes EB1 interaction and plus-end attachment. In agreement with the mutational analysis, suppression of EB1 expression inhibits microtubule tip-tracking of CDK5RAP2. We have also found that the CDK5RAP2–EB1 complex regulates microtubule dynamics and stability. CDK5RAP2 depletion by RNA interference impacts the dynamic behaviors of microtubules. The CDK5RAP2–EB1 complex induces microtubule bundling and acetylation when expressed in cell cultures and stimulates microtubule assembly and bundle formation in vitro. Collectively, these results show that CDK5RAP2 targets growing microtubule tips in association with EB1 to regulate microtubule dynamics.
Swift: primary data analysis for the Illumina Solexa sequencing platform
Authors: Whiteford Nava , Skelly Tom , Curtis Christina , Ritchie Matt E. , Löhr Andrea , Zaranek Alexander Wait , Abnizova Irina , Brown Clive
Published: June 2009

Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. Openly documented analysis tools enable the user to understand the primary data, this is important for the optimization and validity of their scientific work.

Results: In this article, we describe Swift, a new tool for performing primary data analysis on the Illumina Solexa Sequencing Platform. Swift is the first tool, outside of the vendors own software, which completes the full analysis process, from raw images through to base calls. As such it provides an alternative to, and independent validation of, the vendor supplied tool. Our results show that Swift is able to increase yield by 13.8%, at comparable error rate.

Availability and Implementation: Swift is implemented in C++and supported under Linux. It is supplied under an open source license (LGPL3), allowing researchers to build upon the platform. Swift is available from http://swiftng.sourceforge.net.

Contact:  new@sgenomics.org; nava.whiteford@nanoporetech.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
SOLpro: accurate sequence-based prediction of protein solubility
Authors: Magnan Christophe N. , Randall Arlo , Baldi Pierre
Published: June 2009

Motivation: Protein insolubility is a major obstacle for many experimental studies. A sequence-based prediction method able to accurately predict the propensity of a protein to be soluble on overexpression could be used, for instance, to prioritize targets in large-scale proteomics projects and to identify mutations likely to increase the solubility of insoluble proteins.

Results: Here, we first curate a large, non-redundant and balanced training set of more than 17 000 proteins. Next, we extract and study 23 groups of features computed directly or predicted (e.g. secondary structure) from the primary sequence. The data and the features are used to train a two-stage support vector machine (SVM) architecture. The resulting predictor, SOLpro, is compared directly with existing methods and shows significant improvement according to standard evaluation metrics, with an overall accuracy of over 74% estimated using multiple runs of 10-fold cross-validation.

Availability: SOLpro is integrated in the SCRATCH suite of predictors and is available for download as a standalone application and as a web server at: http://scratch.proteomics.ics.uci.edu.

Contact:  pfbaldi@ics.uci.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Heart failure in left‐sided native valve infective endocarditis: characteristics, prognosis, and results of surgical treatment
Authors: Nadji Georges , Rusinaru Dan , Rémadi Jean‐Paul , Jeu Antoine , Sorel Claire , Tribouilloy Christophe
Published: June 2009

Aims

Although congestive heart failure (CHF) represents the most common cause of death in native valve infective endocarditis (IE), recent data on the outcome of IE complicated by CHF are lacking. We aimed to analyse the characteristics and prognosis of patients with left‐sided native valve IE complicated by CHF and to evaluate the impact of early surgery on 1 year outcome.

Methods and results

Two hundred and fifty‐nine consecutive patients with definite left‐sided native valve IE according to the Duke criteria were included in this analysis. When compared with patients without CHF (n = 151), new heart murmur, high comorbidity index, aortic valve IE, and severe valve regurgitation were more frequently observed in CHF patients (n = 108, 41.6%). Mitral valve IE, embolic events and neurological events were less frequent in CHF patients. Congestive heart failure was independently predictive of in‐hospital [OR 3.8 (1.7–9.0); P = 0.0013] and 1 year mortality [HR 1.8 (1.1–3.0); P = 0.007]. Early surgery was performed in 46% of CHF patients with a peri‐operative mortality of 10%. In the CHF group, comorbidity index, Staphylococcus aureus IE, uncontrolled infection, and major neurological events were univariate predictors of 1 year mortality. Early surgery was independently associated with improved 1 year survival [HR 0.45 (0.22–0.93); P = 0.03].

Conclusion

Left‐sided native valve IE complicated by CHF is more frequent in aortic IE and is associated with severe regurgitation. Congestive heart failure is an independent predictor of in‐hospital and 1 year mortality. In CHF patients, early surgery is independently associated with reduced mortality and should be widely considered to improve outcome.
A meta‐analysis of the prognostic significance of atrial fibrillation in chronic heart failure
Authors: Mamas Mamas A. , Caldwell Jane C. , Chacko Sanoj , Garratt Clifford J. , Fath‐Ordoubadi Farzin , Neyses Ludwig
Published: June 2009

Aims

Atrial fibrillation (AF) is one of the commonest sustained arrhythmias in chronic heart failure (CHF), although the prognostic implications of the presence of AF in CHF remain controversial. We have therefore performed this meta‐analysis to study the effects of the presence of AF on mortality in CHF patients.

Methods and results

A systematic MEDLINE search for all randomized trials and observational studies in which the influence of AF on CHF mortality was investigated and meta‐analysis of the mortality data was performed. A total of 16 studies were identified of which 7 were randomized trials and 9 were observational studies including 30 248 and 23 721 patients, respectively. An adjusted meta‐analysis of the data revealed that the presence of AF is associated with an adverse effect on total mortality with an odds ratio (OR) of 1.40 [95% confidence interval (CI) 1.32–1.48, P < 0.0001] in randomized trials and an OR of 1.14 (95% CI 1.03–1.26, P < 0.05) in observational studies. This increase in mortality associated with the presence of AF was observed in subgroups of CHF patients with both preserved and impaired left ventricular (LV) systolic function.

Conclusion

In conclusion, meta‐analysis of 16 studies involving 53 969 patients suggests that the presence of AF is associated with an adverse prognosis in CHF irrespective of LV systolic function.
A critical comparison of echocardiographic measurements used for optimizing cardiac resynchronization therapy: stroke distance is best
Authors: Thomas Dewi E. , Yousef Zaheer R. , Fraser Alan G.
Published: June 2009

Aims

Dyssynchrony assessment in cardiac resynchronization therapy (CRT) is controversial, and there are no standard protocols for optimizing treatment. We studied the feasibility and reproducibility of several echocardiographic measures to optimize CRT pacemaker settings. We also assessed the utility of ‘stroke distance’ [left ventricular outflow tract velocity–time integral (LVOT VTI)] in performing this function.

Methods and results

Thirty patients underwent the following functional assessments; 6 min walk test distance, peak VO2 consumption on cardiopulmonary exercise testing (VO2 peak), quality‐of‐life scoring, and echocardiography; before and at 3 and 6 months after implantation of the CRT device. At 3 months, patients received LVOT VTI‐guided optimization of interventricular (VV) and atrioventricular (AV) delays. The feasibility and reproducibility of each optimization measurement was statistically analysed, and the functional benefits of optimization examined. Left ventricular outflow tract VTI, interventricular mechanical delay (IVMD), and tissue Doppler lateral‐septal delay showed good feasibility (>90%), whereas LVOT VTI, IVMD, and the 12‐segment tissue Doppler dyssynchrony index showed good reproducibility (coefficient of variation <20%). The most feasible and reproducible measure was LVOT VTI. Our optimization protocol necessitated alteration of AV and/or VV delays in 60% of patients at 3 months and was associated with a 50% improvement in functional responder status between 3 and 6 months.

Conclusion

Left ventricular outflow tract VTI provides us with a single, direct measure of global LV function which is robust, and easily applicable in routine clinical practice, and which is effective at improving response to CRT.
Les Démêlés de Merleau-Ponty avec Freud: des pulsions à une psychanalyse de la Nature
Authors: Beaulieu Alain
Published: June 2009

Avec la phénoménologie, la psychanalyse constitue l'autre point d'entrée dans l'œuvre de Maurice Merleau-Ponty qui demeure sans doute le seul philosophe français d'importance à avoir entretenu un dialogue ininterrompu avec la pensée freudienne. Merleau-Ponty n'adopte pas la perspective clinicienne et son point de vue sur la psychanalyse n'est pas toujours orthodoxe. C'est une lecture tantôt critique, tantôt intempestive, de la démarche freudienne à laquelle il nous convie. Le nouveau défi consiste à soutenir que la phénoménologie husserlienne et la psychanalyse freudienne n'entretiennent qu'un minimum de contradictions, et à la limite qu'elles abordent les mêmes domaines d'étude à travers une problématisation incessante de la conscience. Nous verrons comment le lexique merleau-pontien se développe au contact de la psychanalyse (pulsion, ambiguïté, chiasma, investissement, culture–nature, etc.) et comment aussi la psychanalyse permet à Merleau-Ponty de faire avancer ses thèses phénoménologiques (monde, autrui, corps propre, perception, chair, etc.). Pour ce faire, nous analyserons la percée des années 1940 (distinction entre pulsions et instincts), ainsi que les recherches des années d'enseignement à la Sorbonne (psychologie de l'enfant) et au Collège de France (psychanalyse de la nature).
How to Begin a Novel: Proust's
A la recherche du temps perdu
and the Author–Reader Relation
Authors: Dow Suzanne
Published: June 2009

This article offers a reconsideration, from a Lacanian psychoanalytic perspective, of the opening to Proust's
A la recherche du temps perdu
. The discussion reopens the debate on the founding status of the madeleine scene for the novel as a whole with reference to the narrator's own promotion thereof and critical accounts offered by Beckett, Genette, Landy and Doubrovsky. While these critics have tended to identify a single founding cause to the narrative that is discovered in this scene, this article finds in Proust's circuitous path to the start of his
Recherche
an inscription of the Lacanian account of subject-formation given in the eleventh seminar via the twin processes of alienation and separation. This account of the coming to desire, furthermore, is identified as consonant with Roland Barthes's presentation of the author–reader relation in
Le Plaisir du texte
as a ‘dialectique du désir’. What Proust thus discovers in the madeleine scene, it is argued here, is desiring subjectivity itself as condition of possibility of narrative, furnishing simultaneously a narrating subject of the unconscious susceptible to involuntary memory, the economic means for that narration to proceed (metonymy) and, at the metatextual level, the mode of appeal identified by Barthes as proper to the author–reader relation itself.
How community ecology links natural mortality, growth, and production of fish populations
Authors: Andersen K. H. , Farnsworth K. D. , Pedersen M. , Gislason H. , Beyer J. E.
Published: June 2009

Andersen, K. H., Farnsworth, K. D., Pedersen, M., Gislason, H., and Beyer, J. E. 2009. How community ecology links natural mortality, growth, and production of fish populations. – ICES Journal of Marine Science, 66: 1978–1984. Size-spectrum theory is used to show that (i) predation mortality is a decreasing function of individual size and proportional to the consumption rate of predators; (ii) adult natural mortality M is proportional to the von Bertalanffy growth constant K; and (iii) productivity rate P/B is proportional to the asymptotic weight W∞−1/3. The constants of proportionality are specified using individual level parameters related to physiology or prey encounter. The derivations demonstrate how traditional fisheries theory can be connected to community ecology. Implications for the use of models for ecosystem-based fisheries management are discussed.
Seabed mapping for selecting cold-water coral protection areas on Hatton Bank, Northeast Atlantic
Authors: Durán Muñoz P. , Sayago-Gil M. , Cristobo J. , Parra S. , Serrano A. , Díaz del Rio V. , Patrocinio T. , Sacau M. , Murillo F. J. , Palomino D. , Fernández-Salas L. M.
Published: June 2009

Durán Muñoz, P., Sayago-Gil, M., Cristobo, J., Parra, S., Serrano, A., Díaz del Rio, V., Patrocinio, T., Sacau, M., Murillo, F. J., Palomino, D., and Fernández-Salas, L. M. 2009. Seabed mapping for selecting cold-water coral protection areas on Hatton Bank, Northeast Atlantic. – ICES Journal of Marine Science, 66: 2013–2025. Research into vulnerable marine ecosystems (VMEs) on the high seas and the impacts of bottom fishing and ad hoc management measures are high priority today thanks to UN General Assembly Resolution 61/105. An interdisciplinary methodology (specifically designed for selecting cold-water coral protection areas) and a case study focused on the Hatton Bank (NE Atlantic) are presented. This interdisciplinary approach, developed under the ECOVUL/ARPA project, was based on conventional fisheries science, geomorphology, benthic ecology, and sedimentology. It contributes to defining practical criteria for identifying VMEs, to improving knowledge of their distribution off Europe's continental shelf, and to providing advice on negative fishing impacts and habitat protection. The approach was used to identify the bottom-trawl deep-sea fishery footprint on the western slope of Hatton Bank, to map the main fishing grounds and related deep-sea habitats (1000–1500 m deep), and to study the interactions between fisheries and cold-water corals. The results lead to a proposal to close the outcrop area (4645 km2) located on the western slope of Hatton Bank as a conservation measure for cold-water corals.
A critical review of Pacific salmon marine research relating to climate
Authors: Chittenden Cedar M. , Beamish Richard J. , McKinley R. Scott
Published: June 2009

Chittenden, C. M., Beamish, R. J., and McKinley, R. S. 2009. A critical review of Pacific salmon marine research relating to climate. – ICES Journal of Marine Science, 66: 2195–2204. Several studies in the North Pacific Ocean have documented the consequences of rising sea surface temperatures and the advancement of the spring freshet on ocean productivity. The altering of ocean productivity has also been correlated with changes in the marine survival and geographic occurrence of some Pacific salmon populations. Knowledge of the marine survival and position of salmon in the Pacific Ocean are derived typically from mark-recapture studies. As a result, the migratory behaviour and associated survival estimates of salmon in real time are not known. Major information gaps also exist in terms of stock-specific marine behaviour and survival—especially as they relate to recent changes in climate. Acoustic telemetry and other modern tools enable researchers to answer specific questions about environmental, physiological, and genetic effects on individual salmon survival and behaviour, which had not been possible previously. As climate trends increasingly exceed those found in historical records, there is an urgent need for information that will improve fishery management and conservation decisions. International, multidisciplinary research teams using modern technologies could accomplish this.
Biased stock assessment when using multiple, hardly overlapping, tuning series if fishing trends vary spatially
Authors: Kraak Sarah B. M. , Daan Niels , Pastoors Martin A.
Published: June 2009

Kraak, S. B. M., Daan, N., and Pastoors, M. A. 2009. Biased stock assessment when using multiple, hardly overlapping, tuning series if fishing trends vary spatially. – ICES Journal of Marine Science, 66: 2272–2277. Fishing-effort distributions are subject to change, for autonomous reasons and in response to management regulations. Ignoring such changes in a stock-assessment procedure may lead to a biased perception. We simulated a stock distributed over two regions with inter-regional migration and different trends in exploitation and tested the performance of extended survivors analysis (XSA) and a statistical catch-at-age model in terms of bias, when spatially restricted tuning series were applied. If we used a single tuning index that covered only the more heavily fished region, estimates of fishing mortality and spawning-stock biomass were seriously biased. If two tuning series each exclusively covering one region were used (without overlap but together covering the whole area), estimates were also biased. Surprisingly, a moderate degree of overlap of spatial coverage of the two tuning indices was sufficient to reduce bias of the XSA assessment substantially. However, performance was best when one tuning series covered the entire stock area.
Lutein Accumulation in the Absence of Zeaxanthin Restores Nonphotochemical Quenching in the Arabidopsis thaliana npq1 Mutant
Authors: Li Zhirong , Ahn Tae Kyu , Avenson Thomas J. , Ballottari Matteo , Cruz Jeffrey A. , Kramer David M. , Bassi Roberto , Fleming Graham R. , Keasling Jay D. , Niyogi Krishna K.
Published: June 2009

Plants protect themselves from excess absorbed light energy through thermal dissipation, which is measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). The major component of NPQ, qE, is induced by high transthylakoid ΔpH in excess light and depends on the xanthophyll cycle, in which violaxanthin and antheraxanthin are deepoxidized to form zeaxanthin. To investigate the xanthophyll dependence of qE, we identified suppressor of zeaxanthin-less1 (szl1) as a suppressor of the Arabidopsis thaliana  npq1 mutant, which lacks zeaxanthin. szl1 npq1 plants have a partially restored qE but lack zeaxanthin and have low levels of violaxanthin, antheraxanthin, and neoxanthin. However, they accumulate more lutein and α-carotene than the wild type. szl1 contains a point mutation in the lycopene β-cyclase (LCYB) gene. Based on the pigment analysis, LCYB appears to be the major lycopene β-cyclase and is not involved in neoxanthin synthesis. The Lhcb4 (CP29) and Lhcb5 (CP26) protein levels are reduced by 50% in szl1 npq1 relative to the wild type, whereas other Lhcb proteins are present at wild-type levels. Analysis of carotenoid radical cation formation and leaf absorbance changes strongly suggest that the higher amount of lutein substitutes for zeaxanthin in qE, implying a direct role in qE, as well as a mechanism that is weakly sensitive to carotenoid structural properties.
Tumor suppressor function of BCSC‐1 in nasopharyngeal carcinoma
Authors: Zhou Y. Q. , Chen S. L. , Ju J. Y. , Shen L. , Liu Y. , Zhen S. , Lv N. , He Z. G. , Zhu L. P.
Published: June 2009

BCSC‐1 is dramatically upregulated in CNE‐2L2 human nasopharyngeal carcinoma cells with reduced malignancy (AS cells) and is proposed to be a candidate tumor suppressor gene. We therefore examined the effect of BCSC‐1 expression on malignant behaviors of CNE‐2L2 cells. Growth in vitro and tumorigenesis in nude mice of wild‐type CNE‐2L2 cells (W cells) were inhibited by ectopic BCSC‐1, and those of AS cells were promoted by BCSC‐1 suppression. The tumor suppressor function of BCSC‐1 was further confirmed by a study showing that intratumor BCSC‐1 injection caused growth suppression of the tumor from W cells inoculated in nude mice. Immunohistochemistry exhibited marked reduction of BCSC‐1 expression in 11 of 39 human nasopharyngeal carcinoma specimens. Because BCSC‐1 expression was as rich as that in normal cells in the rest of the carcinoma specimens and was poor in CNE‐2L2 cells, HNE‐1 human nasopharyngeal carcinoma cells with rich BCSC‐1 expression were used as a control in the study. No effect of BCSC‐1 transfection on growth of the cells was observed. The data suggest that BCSC‐1 suppression might play roles in tumorigenesis of some nasopharyngeal carcinomas and that BCSC‐1 might be a potential gene therapy target in nasopharyngeal carcinomas with poor BCSC‐1 expression. Enhanced aggregation of cells together with increased E‐cadherin and α‐catenin expression and reduced Wnt signaling might be involved in the mechanisms of tumor suppressor function of BCSC‐1. (Cancer Sci 2009; 100: 1817–1822)
In vivo effects of mesalazine or E. coli Nissle 1917 on microsatellite instability in ulcerative colitis
Authors: GOEL A. , MITTAL A. , EVSTATIEV R. , NEMETH M. , KRUIS W. , STOLTE M. , BOLAND C. R. , GASCHE C.
Published: June 2009

Background  Microsatellite instability (MSI) occurs in chronically inflamed colorectal tissue and may evolve to colitis‐associated cancer. In vitro data suggest that mesalazine (5‐ASA) improves MSI.

Aim  To analyse the changes in MSI in 156 distal colonic biopsies of 39 patients with ulcerative colitis that had been treated within a randomized, double‐blind trial comparing 5‐ASA with E. coli Nissle (EcN).

Methods  Two biopsies had been collected before and after 1 year of treatment. MSI testing was performed using a panel of eight markers, including 3 dinucleotide and 5 mononucleotide repeats.

Results  No MSI was observed with any of the mono‐repeats, and among dinucleotide repeats, only D5S346 (maps to APC) and D17S250 (p53) were consistently informative. Overall, 31/156 (20%) biopsies displayed MSI. After 1 year, 3/11 patients displayed MSI improvement [change to microsatellite stability (MSS); 1 on 5‐ASA, 2 on EcN] at D5S346 and 4/11 showed MSI worsening (change from MSS to MSI; all 5‐ASA). For D17S250, the corresponding data were for 3/9 patients (2 on 5‐ASA, 1 on EcN) and 2/9 (both on 5‐ASA), respectively.

Conclusions  In the set of biopsies taken from patients treated with 1.5 g 5‐ASA for 1 year, there was no improvement in the prevalence of MSI in the distal colon.
Population‐based studies of antithyroid drugs and sudden cardiac death
Authors: Van Noord Charlotte , Sturkenboom Miriam C. J. M. , Straus Sabine M. J. M. , Hofman Albert , Witteman Jacqueline C. M. , Stricker Bruno H. Ch.
Published: June 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Thyroid hormone free T4 is associated with QTc‐interval prolongation, which is a risk factor for sudden cardiac death.

• The association between hyperthyroidism and ventricular arrhythmias or sudden cardiac death has been reported in several case reports.

WHAT THIS STUDY ADDS

• We investigated in a prospective population‐based cohort study and in a case–control study whether use of antithyroid drugs (as a direct cause or as an indicator of poorly controlled hyperthyroidism) is associated with an increased risk of sudden cardiac death.

• Use of antithyroid drugs was associated with a threefold increased risk of sudden cardiac death.

• Although this might be due to antithyroid drug use, it could be more readily explained by underlying hyperthyroidism.

AIM

Thyroid free T4 is associated with QTc‐interval prolongation, which is a risk factor for sudden cardiac death (SCD). Hyperthyroidism has been associated with SCD in case reports, but there are no population‐based studies confirming this. The aim was to investigate whether use of antithyroid drugs (as a direct cause or as an indicator of poorly controlled hyperthyroidism) is associated with an increased risk of SCD.

METHODS

We studied the occurrence of SCD in a two‐step procedure in two different Dutch populations. First, the prospective population‐based Rotterdam Study including 7898 participants (≥55 years old). Second, we used the Integrated Primary Care Information (IPCI) database, which is a longitudinal general practice research database to see whether we could replicate results from the first study. Drug use at the index date was assessed with prescription information from automated pharmacies (Rotterdam Study) or drug prescriptions from general practices (IPCI). We used a Cox proportional hazards model in a cohort analysis, adjusted for age, gender and use of QTc prolonging drugs (Rotterdam Study) and conditional logistic regression analysis in a case–control analysis, matched for age, gender, practice and calendar time and adjusted for arrhythmia and cerebrovascular ischaemia (IPCI).

RESULTS

In the Rotterdam Study, 375 participants developed SCD during follow‐up. Current use of antithyroid drugs was associated with SCD [adjusted hazard ratio 3.9; 95% confidence interval (CI) 1.7, 8.7]. IPCI included 1424 cases with SCD and 14 443 controls. Also in IPCI, current use of antithyroid drugs was associated with SCD (adjusted odds ratio 2.9; 95% CI 1.1, 7.4).

CONCLUSIONS

Use of antithyroid drugs was associated with a threefold increased risk of SCD. Although this might be directly caused by antithyroid drug use, it might be more readily explained by underlying poorly controlled hyperthyroidism, since treated patients who developed SCD still had low thyroid‐stimulating hormone levels shortly before death.
Systemic chemerin is related to inflammation rather than obesity in type 2 diabetes
Authors: Weigert Johanna , Neumeier Markus , Wanninger Josef , Filarsky Michael , Bauer Sabrina , Wiest Reiner , Farkas Stefan , Scherer Marcus N. , Schäffler Andreas , Aslanidis Charalampos , Schölmerich Jürgen , Buechler Christa
Published: June 2009

Background  The adipokine chemerin modulates the function of innate immune cells and may link obesity and inflammation, and therefore, a possible relation of chemerin to inflammatory proteins in obesity and type 2 diabetes (T2D) was analysed. As visceral fat contributes to systemic inflammation, chemerin was measured in portal venous (PVS), hepatic venous (HVS) and systemic venous (SVS) blood of patients with liver cirrhosis.

Patients and methods  Systemic chemerin was determined by ELISA in the serum of normal‐weight, overweight and T2D males, in the serum of T2D patients of both sexes, and in PVS, HVS and SVS of patients with liver cirrhosis.

Results  Circulating chemerin was similar in T2D and obese individuals but was significantly elevated in both cohorts compared to normal‐weight individuals. Chemerin positively correlated with leptin, resistin and C‐reactive protein (CRP). In T2D, chemerin was similar in male and female patients and increased in patients with elevated CRP. Chemerin was similar in PVS and SVS, indicating that visceral fat is not a major site of chemerin synthesis. Higher levels of chemerin in HVS demonstrate that chemerin is also released by the liver.

Conclusions  Visceral fat is not a major site of chemerin release, and elevated systemic levels of chemerin in obesity and T2D seem to be associated with inflammation rather than body mass index.
The inhibitory effect of resveratrol on leptin secretion from rat adipocytes
Authors: Szkudelska K. , Nogowski L. , Szkudelski T.
Published: June 2009

Background  Resveratrol was found to alleviate consequences of some metabolic disturbances which may be due to inappropriate dietary habits. It decreases mortality, increases insulin sensitivity and improves motor functions; these effects are accompanied by reduced plasma leptin and insulin. Leptin plays a significant role in the regulation of food intake and energy expenditure – elevated level in blood is one of the reasons of leptin‐resistance and obesity. In this study, the direct effect of resveratrol on leptin secretion from isolated adipocytes was investigated.

Material and methods  Isolated rat adipocytes were incubated with resveratrol (62·5, 125 or 250 μM) and its effects on leptin secretion were studied. Cells were incubated with resveratrol in the presence of glucose (5 and 20 mM) and insulin (10 nM); glucose and nicotinic acid (1 mM); glucose and insulin in the presence of an inhibitor of protein kinase A (H‐89, 50 μM) or alanine (10 mM) and insulin. The glucose uptake, glycerol release to the incubation medium, lactate and ATP produced by the cells were also measured.

Results  Resveratrol inhibited leptin secretion in all experimental designs in a dose‐dependent manner. The effect was not accompanied by changes in glycerol release and glucose uptake. Adipocyte exposure to resveratrol enhanced the lactate formation. It was found that resveratrol dramatically reduced ATP in adipocytes.

Conclusion  The obtained results revealed the direct ability of resveratrol to reduce leptin secretion from isolated rat adipocytes. Resveratrol is therefore a compound affecting the endocrine function of adipocytes.
Phosphorus speciation in temperate basaltic grassland soils by solution31P NMR spectroscopy
Authors: Murphy P. N. C. , Bell A. , Turner B. L.
Published: June 2009

Phosphorus (P) speciation in 21 basaltic and four non‐basaltic Irish grassland soils was determined by NaOH–EDTA extraction and31P NMR spectroscopy. Organic P in basaltic soils ranged between 30 and 697 mg P kg−1 and consisted of phosphate monoesters (84–100%), DNA (0–16%) and phosphonates (0–5%). Inorganic P was mainly phosphate (83–100%) with small concentrations of pyrophosphate (0–17%). Phosphate monoesters were more important as a proportion of extracted P in basaltic soils, probably because of their greater oxalate‐extractable Fe and Al contents. Phosphate monoesters appeared to be strongly associated with non‐crystalline Al and increased with total soil P concentration, indicating that they do accumulate in grassland soils. In non‐basaltic soilsmyo‐inositol hexakisphosphate constituted between 20 and 52% of organic P, whilescyllo‐inositol hexakisphosphate constituted between 12 and 17%. These compounds were not quantified separately in basaltic soils because of poor NMR resolution in the phosphate monoester region, but appeared to represent a considerable proportion of the organic P in most samples. DNA concentrations were greater in basaltic soils compared with non‐basaltic soils and were associated with acidic pH and large total C contents. The inability of the Olsen P test to assess effectively the P status of basaltic soils may result from strong phosphate sorption to Fe and Al oxides, inducing plant utilization of soil organic P. Phosphorus nutrient management should account for this to avoid over‐application of P and associated financial and environmental costs.
Influence of drying conditions on wettability and DRIFT spectroscopic C–H band of soil samples
Authors: Diehl D. , Ellerbrock R. H. , Schaumann G. E.
Published: June 2009

This study assesses the effect of various drying procedures on water repellency measured by water drop penetration time (WDPT) and spectroscopic parameters gauged by Diffuse Reflectance Infrared Fourier Transform spectroscopy (DRIFT) of two anthropogenically‐influenced soils at sites in Berlin. Wettable and water‐repellent samples were dried at various temperatures and at prescribed relative humidity. WDPT and DRIFT spectroscopic characteristics were obtained from both dried and field‐moist subsamples. Normalization of DRIFT spectral C–H band intensity (‘surface hydrophobicity’) against the integral absorption intensity over the wave number range 4000–400 cm−1 resulted in an apparent resolution between the effects of water content and changes in C‐H absorption at the surface. To our current knowledge, the latter could be best explained with changes in the three‐dimensional rearrangement of organic molecules or moieties on inner and outer soil organic matter (SOM) surfaces, whereas the former could be a direct consequence of the fraction of inner and outer soil surfaces covered with water and of the mean thickness of the respective water films. Further evidence for this model is required from other investigations focusing on the surfaces in soil, before drawing final conclusions. The results show that the method of drying affects WDPT to a greater extent than soil water content after drying. DRIFT spectra suggest that exposure to high temperature results in some reorganization of SOM in the outer layer. It is further suggested that short exposure may result in a heterogeneous distribution of water leading to localized variation and inconsistency in WDPTs. Drying for 4 weeks under controlled relative humidity at 20°C is suggested as a reference preparation method combining the benefits of an almost unchanged SOM surface compared with field‐moist samples with homogeneous moisture distribution.
Microbial leaf degraders in boreal streams: bringing together stochastic and deterministic regulators of community composition
Authors: FISCHER HELMUT , BERGFUR JENNY , GOEDKOOP WILLEM , TRANVIK LARS
Published: June 2009

1. Leaves that fall into the water represent a new habitat for microorganisms to colonise in streams, providing an opportunity to study colonisation and the subsequent regulation of community structure. We explored community composition of bacteria and fungi on decomposing alder leaves in nine streams in central Sweden, and describe their relationship with environmental variables. Succession of the microbial community was studied in one of the streams for 118 days. Microbial community composition was examined by denaturing gradient gel electrophoresis on replicate samples of leaves from each stream.

2. During succession in one stream, maximum taxon richness was reached after 34 days for bacteria and 20 days for fungi respectively. Replicate samples within this stream differed between each other earlier in colonisation, while subsequently such variation among replicate communities was low and remained stable for several weeks. Replicate samples taken from all the nine streams after 34 days of succession showed striking similarities in microbial communities within‐streams, although communities differed more strongly between streams.

3. Canonical analysis of microbial communities and environmental variables revealed that water chemistry had a significant influence on community composition. This influence was superimposed on a statistical relationship between the properties of stream catchments and microbial community composition.

4. The catchment regulates microbial communities in two different ways. It harbours the species pool from which the in‐stream microbial community is drawn and it governs stream chemistry and the composition of organic substrates that further shape the communities. We suggest that there is a random element to colonisation early in succession, whereas other factors such as species interactions, stream chemistry and organic substrate properties, result in a more deterministic regulation of communities during later stages.
Phylogeography of the cactophilic species Drosophila gouveai: demographic events and divergence timing in dry vegetation enclaves in eastern Brazil
Authors: Moraes Evandro M. , Yotoko Karla S. C. , Manfrin Maura H. , Solferini Vera N. , Sene Fábio M.
Published: June 2009

Aim  The aim of this study was to assess the causal mechanisms underlying populational subdivision in Drosophila gouveai, a cactophilic species associated with xeric vegetation enclaves in eastern Brazil. A secondary aim was to investigate the genetic effects of Pleistocene climatic fluctuations on these environments.

Location  Dry vegetation enclaves within the limits of the Cerrado domain in eastern Brazil.

Methods  We determined the mitochondrial DNA haplotypes of 55 individuals (representing 12 populations) based on sequence data of a 483‐bp fragment from the cytochrome c oxidase subunit II (COII) gene. Phylogenetic and coalescent analyses were used to test for the occurrence of demographic events and to infer the time of divergence amongst genetically independent groups.

Results  Our analyses revealed the existence of two divergent subclades (G1 and G2) plus an introgressed clade restricted to the southernmost range of D. gouveai. Subclades G1 and G2 displayed genetic footprints of range expansion and segregated geographical distributions in south‐eastern and some central highland regions, east and west of the Paraná River valley. Molecular dating indicated that the main demographic and diversification events occurred in the late to middle Pleistocene.

Main conclusions  The phylogeographical and genetic patterns observed for D. gouveai in this study are consistent with changes in the distribution of dry vegetation in eastern Brazil. All of the estimates obtained by molecular dating indicate that range expansion and isolation pre‐dated the Last Glacial Maximum, occurring during the late to middle Pleistocene, and were probably triggered by climatic changes during the Pleistocene. The current patchy geographical distribution and population subdivision in D. gouveai is apparently closely linked to these past events.
The relationship between marine fronts and fish diversity in the Patagonian Shelf Large Marine Ecosystem
Authors: Alemany D. , Acha E. M. , Iribarne O.
Published: June 2009

Aim  To evaluate the relationship between marine fronts and (1) fish diversity patterns, (2) fish biomass distribution, and (3) fish assemblage structure.

Location  Patagonian Shelf, Southwestern Atlantic Ocean.

Methods  Three main frontal systems and eight nearby zones (frontal vs. non‐frontal areas) were compared. An extensive fishery database, obtained during an a priori sampling scheme (spatial resolution 1 × 1) from 1978 to 1979, was employed. Analyses of 248 trawling stations were performed using a combination of diversity measures (species richness, Shannon diversity and evenness), biomass analyses and multivariate analyses [nonparametric analysis of similarity (ANOSIM), non‐metric multidimensional scaling ordination (NMDS) and similarity percentages (SIMPER)] to evaluate the effect of fronts on fish communities.

Results  In total, 46 fish taxa were identified. Demersal fish diversity increased at the tidal front of Península Valdés but decreased in the frontal zones of the Southern Shelf‐Break and Magellan frontal systems. The richness and biomass of pelagic fish were higher at the Península Valdés Tidal Front, while the biomass of demersal fish was higher at its non‐frontal counterpart. Fish diversity did not differ consistently along the Northern Shelf‐Break Front. However, a higher fish biomass was registered at the non‐frontal zone. Demersal and pelagic fish assemblages differed between frontal and non‐frontal zones.

Main conclusions  The Patagonian Shelf Large Marine Ecosystem has diverse frontal types that appear to have different effects on fish diversity and assemblage structure. Seasonal (tidal) or permanent fronts have different effects on the parameters analysed, which could be due to productivity–diversity relationships. The Península Valdés Tidal Front, a relatively short temporal scale system, demonstrates a stronger influence on fish diversity, biomass and assemblage structure than the other frontal areas studied. The seasonality of nutrient input owing to frontogenesis, which begins during the austral spring, may play an important role in determining local diversity. At permanent frontal features, diversity decreases when the nutrient availability is high. This is potentially because, when food resources increase, a few species become dominant.