bluuebunny/crossref_metadata_2025 huggingface dataset:
X-ray diffraction evidence for myosin-troponin connections and tropomyosin movement during stretch activation of insect flight muscle
Authors: Perz-Edwards Robert J. , Irving Thomas C. , Baumann Bruce A. J. , Gore David , Hutchinson Daniel C. , Kržič Uroš , Porter Rebecca L. , Ward Andrew B. , Reedy Michael K.
Published: December 2010

Stretch activation is important in the mechanical properties of vertebrate cardiac muscle and essential to the flight muscles of most insects. Despite decades of investigation, the underlying molecular mechanism of stretch activation is unknown. We investigated the role of recently observed connections between myosin and troponin, called “troponin bridges,” by analyzing real-time X-ray diffraction “movies” from sinusoidally stretch-activated
Lethocerus
muscles. Observed changes in X-ray reflections arising from myosin heads, actin filaments, troponin, and tropomyosin were consistent with the hypothesis that troponin bridges are the key agent of mechanical signal transduction. The time-resolved sequence of molecular changes suggests a mechanism for stretch activation, in which troponin bridges mechanically tug tropomyosin aside to relieve tropomyosin’s steric blocking of myosin–actin binding. This enables subsequent force production, with cross-bridge targeting further enhanced by stretch-induced lattice compression and thick-filament twisting. Similar linkages may operate in other muscle systems, such as mammalian cardiac muscle, where stretch activation is thought to aid in cardiac ejection.
Attribution in high-and low-graded persuasive essays by tertiary students
Authors: Lee Sook Hee
Published: December 2010

This paper explores cross-cultural and grade-based differences in the use of intertextual resources in persuasive essays written by tertiary students. Expressions of explicit intertextuality are analysed using the model of Attribution, an element of the engagement system formulated within the interpersonal metafunction of Systemic Functional Linguistics. The text analysis, supported by interview results, reveals that while there are some differences in the overall use of Attribution between native English speaking and ESL students, the most significant grade-based differences were found in expressions of Attribution and in the Attribution patterns adopted in the presentation of intersubjective claims supported by evidence. The differences identified are interpreted in terms of dialogic literacy perspectives. Pedagogical implications are discussed in terms of the contribution of the differences to the success of the essays, and the need to support academic literacy.
Cause and subjectivity, a comparative study of French and Italian
Authors: Fagard Benjamin , Degand Liesbeth
Published: December 2010

In this paper, we propose a contrastive corpus study of French car and parce que and Italian ché and perché, meaning “because”. Our goal is to assess the importance of subjectivity in grammaticalization in general, and in the renewal of causal conjunctions in particular. The evolution of these two pairs of conjunctions is quite similar: on the one hand, the most grammaticalized items of each pair, car and ché, are also the most intersubjective; they tend not to change meaning and to fall into disuse. On the other, the less grammaticalized items, parce que and perché, are also the less intersubjective, but gradually change meaning, possibly acquiring (more) intersubjective uses, and seem to have become the default causal conjunctions in Modern French and Italian — more clearly so in the spoken than in the formal, written varieties. There thus seems to be a link between the degree of grammaticalization and that of (inter)subjectification.
A contrastive analysis of absolute constructions in French, German and Norwegian
Authors: Hobæk Haff Marianne
Published: December 2010

This paper is an exploration of similarities and differences concerning absolute constructions in French, German and Norwegian. In the first part, I have examined a more general question raised by these constructions: the connections between these types of absolute constructions and the matrix subject. I have shown that the means by which the absolute constructions are related to the subject can be morphosyntactic, semantic and pragmatic. The second part contains a purely contrastive analysis. Two issues have been examined: on the one hand, the absolute constructions and their congruent and non-congruent correspondences, on the other, the use of determiners. Essentially, French is different from the two Germanic languages, but similarities also exist between French and German, which are the center of a European Sprachbund.
Les systèmes prépositionnels en français et en néerlandais
Authors: Magnus Ilse , Peeters Isabelle
Published: December 2010

The French spatial preposition sur (‘on’) has recently developed new spatial usages. It has evolved from expressing a spatial configuration of superposition to also expressing extent and even a location which is merely relational. The aim of our study is to provide evidence for the hypothesis of the grammaticalization of sur. This task is carried out by comparing these new spatial usages of sur with their Dutch translations. Eighteen attestated cases of sur were selected from a unilingual French corpus, which were then translated by ten native speakers of Dutch. The analysis of these translations showed, first of all, that the new uses of sur are rendered by a wide range of Dutch prepositions. Second, when expressing a location which is merely relational, i.e. when sur is used as a synonym for à (‘to’), the only translation proposed by the native speakers of Dutch is in (‘in’). It comes as no surprise that this preposition is also the most frequent translation of à, which is the French desemantized preposition par excellence.
Inalienable possession in French and in Bulgarian
Authors: Mostrov Vassil
Published: December 2010

In this paper I try to find the ways of expression of Inalienable possession (IA) in Bulgarian, in comparison with French. I discuss the morphology and the interpretation of the determiners of these two languages, likely to function as A-bound morphemes according to Guéron’s (1985, 2005) binding hypothesis concerning the IA construal, based on the presence of phi-features on the determiners. I use an additional condition for a determiner to be A-bound (which comes from Vergnaud & Zubizarreta 1992), namely the possibility for a determiner to have expletive uses. I claim that only the French definite article and the Bulgarian null determiner are subject to binding, the Bulgarian definite article being excluded due to its strong referential power.
Nutrition challenges for the twenty-first century
Authors: Dangour Alan D. , Uauy Ricardo
Published: December 2010

Although progress has been made towards international goals for the eradication of hunger and malnutrition, considerable work is still required to achieve them and to respond to emerging public health nutrition challenges. The present paper outlines sixteen major inter-linked nutrition challenges recently identified by the UN Standing Committee on Nutrition. While many of the challenges relate to the nutritional needs of children and mothers, an increased emphasis on nutrition-related chronic diseases that affect later life is also evident. Promoting healthy ageing and the maintenance of physical and mental function in older age are undoubtedly major challenges for the future, and the present paper also informs on the role of nutrition, specifically n-3 essential fatty acids, in the prevention of cognitive decline. The importance of determining the cost-effectiveness of nutrition interventions is advocated, in order that the nutrition community can respond appropriately to global nutrition challenges.
The Spanish strategy for nutrition, physical activity and the prevention of obesity
Authors: Neira Maria , de Onis Mercedes
Published: December 2010

The prevalence and increasing trends of obesity in Spain are a matter of concern. In adults, the prevalence of obesity and overweight is 14·5 and 38·5 %, respectively, whereas in children and adolescents it is 13·9 and 26·3 %. This situation prompted the Spanish Ministry of Health and Consumer Affairs to draw up the Strategy for Nutrition, Physical Activity and the Prevention of Obesity (NAOS), which aims to improve the diet and encourage the regular practice of physical activity by all citizens, with special emphasis on children. Coordinated by the Spanish Food Safety Agency and the General Directorate of Public Health, a wide range of stakeholders participated in drafting the Strategy through a broad consultative process. Anchored on the core goal of adopting a lifelong perspective in the prevention and control of obesity, NAOS encompasses recommendations for action in four fields: family and community, schools, private sector, and the health system. Launched on 10 February 2005, the Strategy will undergo careful monitoring and evaluation. A newly created Obesity Observatory will carry out epidemiological surveillance, define indicators to measure impact of interventions, facilitate the exchange of experiences among different initiatives, identify research priorities, monitor adherence and application of the self-regulation agreements, and conduct rigorous evaluation of initiatives to identify those that are successful and should be prioritized. To our knowledge, NAOS is the first strategy of its kind in Europe and we recommend it as an example to be followed by countries that, like Spain, face the challenge of combating the pervasive epidemic of obesity.
General characteristics of food in developing regions–a situational diagnostic assessment
Authors: Avila-Curiel Abelardo
Published: December 2010

Since the founding of the Food and Agriculture Organization of the United Nations in 1946, it has reported on the serious problem of hunger in the world and has undertaken various initiatives for eradicating this problem; however, they have ended in failure. The number of people suffering from hunger has increased from 500 to 800 million in a period of six decades, despite constant growth in world food production, which has been more than sufficient to cover the needs of all of humanity since the 1970s. This paper analyses FAO initiatives in the framework of the evolution of the nutritional situation in developing countries and identifies national and regional contexts in which technical solutions may be successful, as well as those requiring the implementation of economic, political and social measures.
Community nutrition programmes, globalization and sustainable development
Authors: Suárez-Herrera José Carlos
Published: December 2010

On an international scale, the last seventy-five years have been a period of deep social, economic and political transformation for the developing countries. They have been especially influenced by the international phenomenon of globalization, the benefits of which have been unequally distributed among countries. In this context, the strategies used to improve the general nutritional health of the population of developing countries include broad approaches integrating nutritional interventions in a context of sustainable community development, while valuing the existing relations between fields as diverse as agriculture, education, sociology, economy, health, environment, hygiene and nutrition. The community nutrition programmes are emblematic of these initiatives. Nevertheless, in spite of the increasing evidence of the potential possibilities offered by these programmes to improve the nutritional status and contribute to the development and the self-sufficiency of the community, their success is relatively limited, due to the inappropriate planning, implementation and evaluation of the programmes. In the present article, I attempt to emphasie the importance of community participation of the population of developing countries in the community nutrition programmes within the context of globalization. This process is not only an ethical imperative, but a pragmatic one. It is a crucial step in the process of liberation, democratization and equality that will lead to true sustainable development.
Improvement of cholesterol levels and reduction of cardiovascular risk via the consumption of phytosterols
Authors: Ortega Rosa M. , Palencia Ana , López-Sobaler Ana M
Published: December 2010

Hypercholesterolaemia is one of the main factors contributing to the appearance and progression of CVD, which is the main cause of death in the adult population of industrialized societies. By 2020, projections suggest that it will continue to hold first place, by then causing 37 % of all deaths. Therapeutic life-style changes to reduce cardiovascular risk include dietary modifications, such as the inclusion of phytosterols or plant sterols (known since the 1950s to reduce cholesterol levels). These help prevent the absorption of cholesterol and thus condition a reduction in total cholesterol and LDL-cholesterol levels, and ultimately in cardiovascular mortality. The fat-soluble nature of these sterols rendered margarine one of the best vehicles by which to supply them in the diet. Indeed, margarine was the first food to contain cholesterol-reducing phytosterols to be approved by the EU (in agreement with its regulations on new foods and food ingredients, 258/97/CE). Presently, phytosterols can be emulsified with lecithin and thus delivered in non-fat or low-fat foods and beverages. Margarine and dairy products (yoghurt and milk) enriched in phytosterols have proved better at lowering total cholesterol and LDL-cholesterol levels than have enriched cereals and their derivatives, although all can be of help, depending on the characteristics of each subject. The reduction in carotenoid bioavailability caused by sterols is minimized by increasing fruit and vegetable consumption. Individuals who habitually consume phytosterols should also follow traditional advice such as eating less dietary fat and increasing their physical activity. Phytosterols have been shown to be safe and effective in lowering cholesterol levels in many rigorous studies. In few areas of nutrition is there such consensus. Diet professionals should feel comfortable in prescribing phytosterols/stanols for the treatment of hypercholesterolaemia. They are safe whether taken alone or in combination with cholesterol-reducing drugs, such as statins and fibrates. Reinforcement counselling is essential, as therapy is effective only if compliance is good.
X-RAY EMISSION FROM OPTICALLY SELECTED RADIO-INTERMEDIATE AND RADIO-LOUD QUASARS
Authors: Miller B. P. , Brandt W. N. , Schneider D. P. , Gibson R. R. , Steffen A. T. , Wu Jianfeng
Published: December 2010

We present the results of an investigation into the X-ray properties of radio-intermediate and radio-loud quasars (RIQs and RLQs, respectively). We combine large, modern optical (e.g., SDSS) and radio (e.g., FIRST) surveys with archival X-ray data from Chandra, XMM-Newton, and ROSAT to generate an optically selected sample that includes 188 RIQs and 603 RLQs. This sample is constructed independently of X-ray properties but has a high X-ray detection rate (85%); it provides broad and dense coverage of the ℓ–z plane, including at high redshifts (22% of objects have z = 2–5), and it extends to high radio-loudness values (33% of objects have R* = 3–5, using logarithmic units). We measure the “excess” X-ray luminosity of RIQs and RLQs relative to radio-quiet quasars (RQQs) as a function of radio loudness and luminosity, and parameterize the X-ray luminosity of RIQs and RLQs both as a function of optical/UV luminosity and also as a joint function of optical/UV and radio luminosity. RIQs are only modestly X-ray bright relative to RQQs; it is only at high values of radio loudness (R* ≳ 3.5) and radio luminosity that RLQs become strongly X-ray bright. We find no evidence for evolution in the X-ray properties of RIQs and RLQs with redshift (implying jet-linked IC/CMB emission does not contribute substantially to the nuclear X-ray continuum). Finally, we consider a model in which the nuclear X-ray emission contains both disk/corona-linked and jet-linked components and demonstrate that the X-ray jet-linked emission is likely beamed but to a lesser degree than applies to the radio jet. This model is used to investigate the increasing dominance of jet-linked X-ray emission at low inclinations.
Coercivity enhancement in exchange biased CoO/Co3Pt bilayers
Authors: Kosub T , Schubert C , Schletter H , Daniel M , Hietschold M , Neu V , Maret M , Makarov D , Albrecht M
Published: December 2010

A study on the exchange bias (EB) effect in an hcp (0 0 0 2)-textured Co3Pt alloy film biased by a thin CoO film is presented. The Co3Pt film reveals an out-of-plane easy axis of magnetization although it was grown on an amorphous silica substrate at room temperature. Similar EB fields measured in in-plane and out-of-plane directions of the CoO/Co3Pt bilayer system were observed for maximum cooling field. Whereas a pronounced cooling field dependence of the EB field is observed in the in-plane geometry, it remains constant in the out-of-plane direction. The temperature evolution of the coercivity and the shift of the hysteresis loop caused by the EB effect are discussed in terms of thermal activation accounting for the temperature dependent competition between the interfacial exchange energy and the anisotropy energy of antiferromagnetic grains.
Electrical properties of grain boundaries in polycrystalline materials under intrinsic or low doping
Authors: Chowdhury M H , Kabir M Z
Published: December 2010

An analytical model is developed to study the electrical properties (electric field and potential distributions, potential energy barrier height and polarization phenomenon) of polycrystalline materials at intrinsic or low doping for detector and solar cell applications by considering an arbitrary amount of grain boundary charge and a finite width of grain boundary region. The general grain boundary model is also applicable to highly doped polycrystalline materials. The electric field and potential distributions are obtained by solving Poisson's equation in both depleted grains and grain boundary regions. The electric field and potential distributions across the detector are analysed under various doping, trapping and applied biases. The electric field collapses, i.e. a nearly zero-average electric field region exists in some part of the biased detector at high trapped charge densities at the grain boundaries. The model explains the conditions of existence of a zero-average field region, i.e. the polarization mechanisms in polycrystalline materials. The potential energy barrier at the grain boundary exists if the electric field changes its sign at the opposite side of the grain boundary. The energy barrier does not exist in all grain boundaries in the low-doped polycrystalline detector and it never exists in intrinsic polycrystalline detectors under applied bias condition provided that there is no charge trapping in the grain.
Operation of a permanent-magnets- expanding plasma source connected to a large-volume diffusion chamber
Authors: Takahashi Kazunori , Itoh Yuki , Fujiwara Tamiya
Published: December 2010

A 6.6 cm-inner-diameter permanent-magnets-expanding plasma source is connected to a large-volume diffusion chamber of about 76 cm diameter and 100 cm length, and is operated over a range of 20–300 mPa argon gas pressures. An rf power of 13.56 MHz for plasma production is maintained at 200 W and an expanding magnetic field of about 200 G in the source is provided by permanent magnet arrays. A potential drop of a few tens of volts is observed; a supersonic ion beam with energy corresponding to the potential drop is detected in the diffusion chamber. Radial investigation of the ion beam in the diffusion chamber indicates a detachment of the ion beam from the expanding magnetic field lines provided by the permanent magnets, at about several centimetres downstream of the source exit.
N incorporation and optical properties of GaAsN epilayers on (3 1 1)A/B GaAs substrates
Authors: Han Xiuxun , Suzuki Hidetoshi , Lee Jong-Han , Kojima Nobuaki , Ohshita Yoshio , Yamaguchi Masafumi
Published: December 2010

We compared the N incorporation and optical emission in GaAsN epilayers grown on (3 1 1)A/B and (1 0 0) GaAs substrates using a chemical beam expitaxy system. Over the growth-temperature range 420 –460 °C, N composition was enhanced 2–3 times for the epitaxial growth following [3 1 1]B orientation, but reduced in the [3 1 1]A direction. Both (3 1 1) A and B substrates are effective to weaken the photoluminescence emission from the deep levels as compared with the (1 0 0) plane. The deep-level emission can be further suppressed for all substrates by increasing the growth temperature and/or performing postgrowth annealing. However, in contrast to the continuous increase in total emission intensities of (3 1 1)B sample, a decreasing tendency was recorded for (3 1 1)A with the rise in growth temperature. The optimum growth temperature and annealing conditions for better crystal quality were found to depend on the growth orientation and surface polarity. These results present a potential approach to improving the N incorporation efficiency in Ga(In)AsN materials through adopting high-index substrates such as (3 1 1)B.
Synthesis and transfer of Si nanowire arrays embedded in photo-sensitive polymer films for non-planar electronics
Authors: Son Kwangsoo , Lee Dong Hyun , Yi Jaeseok , Lee Won Woo , Park Won Il
Published: December 2010

In this study, hybrid composite films (HCFs) consisting of aligned Si nanowires (SiNWs) and a photoresist polymer were prepared and their applicability to nanomaterial assembly and pattern transfer onto various substrates, including curved surfaces, was demonstrated. The synthesis and transfer of the HCFs can be scaled up to large areas. Transfer of the HCFs, when performed immediately after a UV-exposure step, enabled direct patterning of fine features on curved surfaces. The unique feature of this approach was further exploited to fabricate a new type of SiNW electronic device that can conform to non-planar surfaces without strain.
CDase is a pan-ceramidase inDrosophila
Authors: Yuan Changqing , Rao Raghavendra Pralhada , Jesmin Nahid , Bamba Takeshi , Nagashima Kunio , Pascual Alberto , Preat Thomas , Fukusaki Eiichiro , Acharya Usha , Acharya Jairaj K.
Published: December 2010

Ceramidases catalyze the conversion of ceramide to sphingosine. They are acylaminohydrolases that catalyze the deacylation of the amide-linked saturated fatty acid from ceramide to generate sphingosine. They also catalyze the reverse reaction of ceramide biosynthesis using sphingosine and fatty acid. In mammals, different proteins catalyze these reactions while individually exhibiting optimal activity over a narrow pH range and have been accordingly called acid, neutral, and alkaline ceramidases. Several genes encode for variants of alkaline ceramidase in mammals. Brainwashing (Bwa) is the only putative alkaline ceramidase homologue present in Drosophila. In this study we have demonstrated that BWA does not exhibit ceramidase activity and that bwa null mutants display no loss of ceramidase activity. Instead, the neutral ceramidase gene CDase encodes the protein that is responsible for all measurable ceramidase activity in Drosophila. Our studies show strong genetic interaction of Bwa with CDase and the Drosophila ceramide kinase gene (DCERK). We show that, although BWA is unlikely to be a ceramidase, it is a regulator of sphingolipid flux in Drosophila. Bwa exhibits strong genetic interaction with other genes coding for ceramide-metabolizing enzymes. This interaction might partly explain its original identification as a ceramidase.
Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeonThermococcus kodakarensis
Authors: Maruyama Hugo , Shin Minsang , Oda Toshiyuki , Matsumi Rie , Ohniwa Ryosuke L. , Itoh Takehiko , Shirahige Katsuhiko , Imanaka Tadayuki , Atomi Haruyuki , Yoshimura Shige H. , Takeyasu Kunio
Published: December 2010

Being distinct from bacteria and eukaryotes, Archaea constitute a third domain of living things. The DNA replication, transcription, and translation machineries of Archaea are more similar to those of eukaryotes, whereas the genes involved in metabolic processes show more similarity to their bacterial counterparts. We report here that TK0471/TrmB-like 2 (TrmBL2), in addition to histone, is a novel type of abundant chromosomal protein in the model euryarchaeon Thermococcus kodakarensis. The chromosome of T. kodakarensis can be separated into regions enriched either with histone, in which the genetic material takes on a “beads-on-a-string” appearance, or with TK0471/TrmBL2, in which it assumes a thick fibrous structure. TK0471/TrmBL2 binds to both coding and intergenic regions and represses transcription when bound to the promoter region. These results show that the archaeal chromosome is organized into heterogeneous structures and that TK0471/TrmBL2 acts as a general chromosomal protein as well as a global transcriptional repressor.
Actin cables and the exocyst form two independent morphogenesis pathways in the fission yeast
Authors: Bendezú Felipe O. , Martin Sophie G.
Published: December 2010

Cell morphogenesis depends on polarized exocytosis. One widely held model posits that long-range transport and exocyst-dependent tethering of exocytic vesicles at the plasma membrane sequentially drive this process. Here, we describe that disruption of either actin-based long-range transport and microtubules or the exocyst did not abolish polarized growth in rod-shaped fission yeast cells. However, disruption of both actin cables and exocyst led to isotropic growth. Exocytic vesicles localized to cell tips in single mutants but were dispersed in double mutants. In contrast, a marker for active Cdc42, a major polarity landmark, localized to discreet cortical sites even in double mutants. Localization and photobleaching studies show that the exocyst subunits Sec6 and Sec8 localize to cell tips largely independently of the actin cytoskeleton, but in a cdc42 and phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2)–dependent manner. Thus in fission yeast long-range cytoskeletal transport and PIP2-dependent exocyst represent parallel morphogenetic modules downstream of Cdc42, raising the possibility of similar mechanisms in other cell types.
Three sorting nexins drive the degradation of apoptotic cells in response to PtdIns(3)P signaling
Authors: Lu Nan , Shen Qian , Mahoney Timothy R. , Liu Xianghua , Zhou Zheng
Published: December 2010

Apoptotic cells are swiftly engulfed by phagocytes and degraded inside phagosomes. Phagosome maturation requires phosphatidylinositol 3-phosphate [PtdIns(3)P], yet how PtdIns(3)P triggers phagosome maturation remains largely unknown. Through a genome-wide PtdIns(3)P effector screen in the nematode Caenorhabditis elegans, we identified LST-4/SNX9, SNX-1, and SNX-6, three BAR domain-containing sorting nexins, that act in two parallel pathways to drive PtdIns(3)P-mediated degradation of apoptotic cells. We found that these proteins were enriched on phagosomal surfaces through association with PtdIns(3)P and through specific protein–protein interaction, and they promoted the fusion of early endosomes and lysosomes to phagosomes, events essential for phagosome maturation. Specifically, LST-4 interacts with DYN-1 (dynamin), an essential phagosome maturation initiator, to strengthen DYN-1’s association to phagosomal surfaces, and facilitates the maintenance of the RAB-7 GTPase on phagosomal surfaces. Furthermore, both LST-4 and SNX-1 promote the extension of phagosomal tubules to facilitate the docking and fusion of intracellular vesicles. Our findings identify the critical and differential functions of two groups of sorting nexins in phagosome maturation and reveal a signaling cascade initiated by phagocytic receptor CED-1, mediated by PtdIns(3)P, and executed through these sorting nexins to degrade apoptotic cells.
The ERM proteins interact with the HOPS complex to regulate the maturation of endosomes
Authors: Chirivino Dafne , Del Maestro Laurence , Formstecher Etienne , Hupé Philippe , Raposo Graça , Louvard Daniel , Arpin Monique
Published: December 2010

In the degradative pathway, the progression of cargos through endosomal compartments involves a series of fusion and maturation events. The HOPS (homotypic fusion and protein sorting) complex is part of the machinery that promotes the progression from early to late endosomes and lysosomes by regulating the exchange of small GTPases. We report that an interaction between subunits of the HOPS complex and the ERM (ezrin, radixin, moesin) proteins is required for the delivery of EGF receptor (EGFR) to lysosomes. Inhibiting either ERM proteins or the HOPS complex leads to the accumulation of the EGFR into early endosomes, delaying its degradation. This impairment in EGFR trafficking observed in cells depleted of ERM proteins is due to a delay in the recruitment of Rab7 on endosomes. As a consequence, the maturation of endosomes is perturbed as reflected by an accumulation of hybrid compartments positive for both early and late endosomal markers. Thus, ERM proteins represent novel regulators of the HOPS complex in the early to late endosomal maturation.
A Bayesian approach for estimating vertical chlorophyll profiles from satellite remote sensing: proof-of-concept
Authors: Williamson Robert , Field John G. , Shillington Frank A. , Jarre Astrid , Potgieter Anet
Published: December 2010

Williamson, R., Field, J. G., Shillington, F. A., Jarre, A., and Potgieter, A. 2011. A Bayesian approach for estimating vertical chlorophyll profiles from satellite remote sensing: proof-of-concept. – ICES Journal of Marine Science, 68: 792–799. A proof-of-concept demonstration is presented using a novel method for estimating vertical distributions of chlorophyll a (Chl a) from archives of data from ships, combined with remotely sensed data of sea surface temperature, surface Chl a, and wind (U and V vectors) from satellites. Our study area has contrasting hydrographic regimes that include the dynamic southern Benguela upwelling system and the stratified waters of the Agulhas Bank. Cluster analysis is used to identify “typical” Chl a profiles from an archive of profiles recorded in 2002–2008. Bayesian networks were then used to relate characteristic profiles to remotely sensed surface features, subregions, seasons, and depths. The proposed method could be used to predict daily Chl a profiles for each pixel of a satellite image to estimate biomass and subsurface light fields, and these combined with a light algorithm to model primary production for the Benguela large marine ecosystem.
Contrasting Genetic Structure Between Magnaporthe grisea Populations Associated with the Golf Course Turfgrasses Lolium perenne (Perennial Ryegrass) and Pennisetum clandestinum (Kikuyugrass)
Authors: Douhan Greg W. , de la Cerda Karla A. , Huryn Karyn L. , Greer Christopher A. , Wong Francis P.
Published: December 2010

Gray leaf spot (GLS) disease of perennial ryegrass (Lolium perenne) and kikuyugrass (Pennisetum clandestinum) in golf courses in California was first noted in 2001 and 2003, respectively, and within 5 years had become well established. The causal agent of the disease is the fungus Magnaporthe grisea, which is known to consist primarily of clonal lineages that are highly host specific. Therefore, our objective was to investigate host specificity and population dynamics among isolates associated primarily from perennial ryegrass and kikuyugrass since the disease emerged at similar times in California. We also obtained isolates from additional hosts (tall fescue, St. Augustinegrass, weeping lovegrass, and rice) and from the eastern United States for comparative purposes. A total of 38 polymorphic amplified fragment length polymorphism makers were scored from 450 isolates which clustered by host with high bootstrap support (71 to 100%). Genetic structure between kikuyugrass and perennial ryegrass isolates differed significantly. Isolates from kikuyugrass were genotypically diverse (n = 34), possessed both mating types, and some tests for random mating could not be rejected, whereas isolates from perennial ryegrass were less genotypically diverse (n = 10) and only consisted of a single mating type. Low genotypic diversity was also found among the other host specific isolates which also only consisted of a single mating type. This is the first study to document evidence for the potential of sexual reproduction to occur in M. grisea isolates not associated with rice (Oryza sativa). Moreover, given the significant host specificity and contrasting genetic structures between turfgrass-associated isolates, the recent emergence of GLS on various grass hosts in California suggests that potential cultural practices or environmental changes have become conducive for the disease and that the primary inoculum may have already been present in the state, despite the fact that two genotypes associated with perennial ryegrass and St. Augustinegrass in California were the same as isolates collected from the eastern United States.
Somatic Complaints in Childhood Functional Abdominal Pain Are Associated With Functional Gastrointestinal Disorders in Adolescence and Adulthood
Authors: Dengler‐Crish Christine M , Horst Sara N , Walker Lynn S
Published: December 2010

Objectives:

Nongastrointestinal (non‐GI) somatic complaints are common in children and adults with functional gastrointestinal disorders (FGIDs). The aim of the present study was to determine whether non‐GI somatic complaints in children with functional abdominal pain (FAP) were associated with FGIDs in adolescence and young adulthood.

Patients and Methods:

In a prospective clinic‐based study, children and adolescents (ages 8–16 years) with FAP (n = 188) and well controls (n = 61) completed a validated measure of somatic symptoms. Participants were assessed 4 to 15 years later (as older adolescents and young adults) for presence of current FGIDs as defined by the Rome III criteria.

Results:

Of the 188 youths with pediatric FAP, 35.6% met criteria for FGIDs at follow‐up. Initial levels of non‐GI somatic symptoms were significantly higher in pediatric FAP participants who subsequently met criteria for FGIDs at follow‐up compared with controls and pediatric FAP participants who did not meet criteria for FGIDs at follow‐up.

Conclusions:

The association of non‐GI somatic symptoms with FAP in children may identify a group that is at risk for FGIDs later in life.
clpB, a class III heat-shock gene regulated by CtsR, is involved in thermotolerance and virulence of Enterococcus faecalis
Authors: de Oliveira Naira Elane Moreira , Abranches Jaqueline , Gaca Anthony O. , Laport Marinella Silva , Damaso Clarissa R. , Bastos Maria do Carmo de Freire , Lemos José A. , Giambiagi-deMarval Marcia
Published: December 2010

Here, we transcriptionally and phenotypically characterized theclpBgene fromEnterococcus faecalis. Northern blot analysis identified a monocistronic mRNA strongly induced at 48 and 50 °C.In silicoanalysis identified that theclpBgene encodes a protein of 868 aa with a predicted molecular mass of approximately 98 kDa, presenting two conserved ATP-binding domains. Sequence analysis also identified a CtsR-binding box upstream of the putative −10 sequence, and inactivation of thectsRgene resulted in an approximately 2-log increase inclpBmRNA expression, confirming ClpB as a member of the CtsR regulon. While expression ofclpBwas induced by heat stress, a ΔclpBstrain grew relatively well under many different stressful conditions, including elevated temperatures. However, expression of ClpB appears to play a major role in induced thermotolerance and in pathogenesis, as assessed by using theGalleria mellonellavirulence model.
Yeast response and tolerance to polyamine toxicity involving the drug : H+ antiporter Qdr3 and the transcription factors Yap1 and Gcn4
Authors: Teixeira Miguel C. , Cabrito Tânia R. , Hanif Zaitunnissa M. , Vargas Rita C. , Tenreiro Sandra , Sá-Correia Isabel
Published: December 2010

The yeast QDR3 gene encodes a plasma membrane drug : H+ antiporter of the DHA1 family that was described as conferring resistance against the drugs quinidine, cisplatin and bleomycin and the herbicide barban, similar to its close homologue QDR2. In this work, a new physiological role for Qdr3 in polyamine homeostasis is proposed. QDR3 is shown to confer resistance to the polyamines spermine and spermidine, but, unlike Qdr2, also a determinant of resistance to polyamines, Qdr3 has no apparent role in K+ homeostasis. QDR3 transcription is upregulated in yeast cells exposed to spermine or spermidine dependent on the transcription factors Gcn4, which controls amino acid homeostasis, and Yap1, the main regulator of oxidative stress response. Yap1 was found to be a major determinant of polyamine stress resistance in yeast and is accumulated in the nucleus of yeast cells exposed to spermidine-induced stress. QDR3 transcript levels were also found to increase under nitrogen or amino acid limitation; this regulation is also dependent on Gcn4. Consistent with the concept that Qdr3 plays a role in polyamine homeostasis, QDR3 expression was found to decrease the intracellular accumulation of [3H]spermidine, playing a role in the maintenance of the plasma membrane potential in spermidine-stressed cells.
Regulation of the AcrAB multidrug efflux pump in Salmonella enterica serovar Typhimurium in response to indole and paraquat
Authors: Nikaido Eiji , Shirosaka Ikue , Yamaguchi Akihito , Nishino Kunihiko
Published: December 2010

Salmonella entericaserovar Typhimurium has at least nine multidrug efflux pumps. Among these, AcrAB is constitutively expressed and is the most efficient, playing a role in both drug resistance and virulence. TheacrABlocus is induced by indole,Escherichia coli-conditioned medium, and bile salts. This induction is dependent on RamA through the binding sequence in the upstream region ofacrAthat binds RamA. In the present study, we made a detailed investigation of theramAandacrABinduction mechanisms inSalmonellain response to indole, a biological oxidant for bacteria. We found thatacrABandramAinduction in response to indole is dependent on RamR. However, the cysteine residues of RamR do not play a role in the induction oframAin response to indole, and the oxidative effect of indole is therefore not related toramAinduction via RamR. Furthermore, we showed that paraquat, a superoxide generator, inducesacrABbut notramA. We further discovered that the mechanism ofacrABinduction in response to paraquat is dependent on SoxS. The data indicate that there are at least two independent induction pathways foracrABin response to extracellular signals such as indole and paraquat. We propose thatSalmonellautilizes these regulators foracrABinduction in response to extracellular signals in order to adapt itself to environmental conditions.
VirtualLeaf: An Open-Source Framework for Cell-Based Modeling of Plant Tissue Growth and Development
Authors: Merks Roeland M.H. , Guravage Michael , Inzé Dirk , Beemster Gerrit T.S.
Published: December 2010

Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects (“cells”, “regulation networks”) required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf for plant tissue morphogenesis. The current version defines a set of biologically intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.
Understanding what controls the spatial distribution of fish populations using a multi‐model approach
Authors: PLANQUE BENJAMIN , LOOTS CHRISTOPHE , PETITGAS PIERRE , LINDSTRøM ULF , VAZ SANDRINE
Published: December 2010

Understanding and predicting the distribution of organisms in heterogeneous environments lies at the heart of ecology. The spatial distribution of fish populations observed in the wild results from the complex interactions of multiple controls both external or internal to the fish populations. Whilst species distribution models (SDMs) have been mostly concerned with static description of species distribution as a function of environmental constraints, models of animal movements (MAMs) have focussed on the dynamic nature of spatial distribution of groups of individuals under a number of constraints external and internal to the population. Besides SDMs and MAMs, modelling the spatial distribution of fish populations can be achieved by models that are fundamentally static (like SDMs) but can also incorporate many hypotheses on the control of fish spatial distribution (like MAMs). The hypotheses underlying these models need to make sense at the population level ‐ rather than at the individual or species level –we term these ‘population distribution models’ (PDMs). PDMs are statistical models that rely on several hypotheses, which include: (i) control through geographical attachment, (ii) environmental conditions, (iii) density‐dependent habitat selection, (iv) spatial dependency, (v) population demographic structure, (vi) species interactions and (vii) population memory. We review the basis behind each of these conceptual models and we examine corresponding numerical applications. We argue that the conceptual models are complementary rather than competing, that existing numerical applications are still rarely compared and combined, and that PDMs can offer a statistical framework to achieve this. We recommend that the numerical models associated with different hypotheses be constructed within such a common general framework. This will permit evaluation, comparison and combination of the multiple hypotheses on fish spatial distribution. It will ultimately lead to a more comprehensive understanding of the factors controlling the spatial distribution of fish populations and to more accurate predictions in which model uncertainty is accounted for.
Understanding what controls the spawning distribution of North Sea whiting (Merlangius merlangus) using a multi‐model approach
Authors: LOOTS CHRISTOPHE , VAZ SANDRINE , PLANQUE BENJAMIN , KOUBBI PHILIPPE
Published: December 2010

The processes that control the spatial distribution of North Sea whiting (Merlangius merlangus) spawning adults are investigated using a statistical multi‐model approach. Models of external and internal controls on the population, such as environmental conditions, spatial constraints, present or past spatial distribution, and demographic state of the population, are evaluated, compared and ranked to select those that are the best able to predict the observed distribution of spawning adults. Model selection is greatly influenced by the selection method, either based on data fitting or prediction, as well as by the threshold value used to stop the selection. Model selection based on prediction tends to select simpler models than selection based on data fitting. The hypotheses underlying the selected models are inferred to play a significant role in controlling North Sea whiting spatial distribution. The multi‐model inference approach developed in this study enables comparison of several theoretical concepts and hypotheses and the results provide important clues on the processes involved in the control of the spatial distribution of whiting. We conclude that whiting has a high spatial fidelity to spawning site which can be linked to either geographical attachment or year‐to‐year persistence of the spatial distribution of the population. Environmental factors – temperature and salinity – appear to influence the geographical extent of spawning whiting distribution, whereas local abundance levels are primarily controlled by internal factors, i.e., population size and spatial segregation between ages.
A matter of timing: the role of ocean conditions in the initiation of spawning migration by late‐run Fraser River sockeye salmon (Oncorhynchus nerka)
Authors: THOMSON RICHARD E. , HOURSTON ROY A. S.
Published: December 2010

Year 1995 marked the start of a major shift to earlier river entry of late‐run Fraser River sockeye salmon (Oncorhynchus nerka) en route to the spawning grounds. Earlier entry has typically been accompanied by considerably greater in‐river mortality. We examine this behavioral change using correlation analyses between the entry timing of the Adams River and Weaver Creek stocks and the surface marine conditions encountered by the stocks during their homing migration from the northeast Pacific several months earlier. For Adams stocks, maximum correlation is between entry timing and offshore winds, such that the weaker the wind stress in the direction of the prevailing surface currents in early July, the earlier the river entry in late summer. For Weaver stocks, maximum correlation is with salinity, such that the lower the surface salinity along the coast in August, the earlier the river entry. We hypothesize that oceanic changes lead to changes in late‐run sockeye physiology which then leads to changes in behavior. Physiological changes are postulated to arise from two types of preconditioning: Type‐1 occurs in the offshore region, whereby the weaker the prevailing currents that normally hinder eastward migration, the more endogenous energy available for maturation and the earlier the river entry. Type‐2 occurs in coastal regions, whereby the lower the salinity, the more rapid the osmoregulatory adaptation to freshwater (and possible susceptibility to water‐borne pathogens) and the earlier the entry. Results suggest that the earlier entry that began in the mid‐1990s is linked to weaker ocean currents and lower coastal salinities.