bluuebunny/crossref_metadata_2025 huggingface dataset:
Simplistic approach for in situ generation of ZnS quantum dots in polyphenylene sulphide matrix via chalcogen enriched solid–solid reaction technique
Authors: Rumale Narendra , Arbuj Sudhir , Umarji Govind , Shinde Manish , Mulik Uttam , Pokle Anuj , Amalnerkar Dinesh
Published: November 2012

Herein, we report in situ synthesis of zinc sulphide (ZnS) quantum dots in polyphenylene sulphide (PPS) matrix employing facile solid–solid reaction. The resultant product reveals formation of cubic nanocrystalline zinc sulphide structure. The HRTEM confirms the formation of zinc sulphide quantum dots (size ∼ 3–4 nm) embedded in the polymer matrix.

magnified image

Scheme: ZnS QDs by enriched solid–solid reaction in polymer matrix.
Genotoxic and Antigenotoxic Activity of Acerola (Malpighia glabra L.) Extract in Relation to the Geographic Origin
Authors: Da Silva Nunes Roberta , Silva Kahl Vivian Francília , Da Silva Sarmento Merielen , Richter Marc François , Abin‐Carriquiry Juan Andres , Martinez Marcela María , De Barros Falcão Ferraz Alexandre , Da Silva Juliana
Published: November 2012

Malpighia glabra L, popularly known as acerola, is considered a functional fruit and therefore is taken to prevent disease or as adjuvant to treatment strategies, since the fruit is an undeniable source of vitamin C, carotenoids, and flavonoids. Acerola is a natural source of vitamin C, flavonoids, and carotenoids. Its chemical composition is affected by genetic uniformity of the orchards and environmental factors. Considering the extensive growth of the culture of acerola in Brazil as well as its widespread use, this study evaluates the genotoxic and antigenotoxic activity of acerola in relation to geographical origin using the comet assay in mice blood cells in vitro. No acerola samples showed potential to induce DNA damage, independently of origin. Also, for antigenotoxicity activity, only the acerola sample from São Paulo reduced DNA damage induced by hydrogen peroxide (by about 56%). The sample from Ceará showed good antioxidant activity by the 2,2‐diphenyl‐1‐picrylhydrazyl assay, in agreement with its higher rutin, quercetin, and vitamin C levels. Additional studies with other treatment regimens are necessary to better understand the impact of the complex mixture of acerola on genomic stability. Copyright © 2012 John Wiley & Sons, Ltd.
Efficient identity‐based strong designated verifier signature schemes
Authors: Duan Meijiao , Xu Jing , Feng Dengguo
Published: November 2012

Strong designated verifier signature (SDVS) makes it possible for a signer to convince a designated verifier that he or she has signed a message in such a way that the designated verifier cannot transfer the signature to any third party and no third party can even verify the validity of the signature. Recently, Kang et al. proposed an identity‐based SDVS (IBSDVS) scheme that is claimed to be unforgeable and strong. However, in this paper, we show that their scheme is actually forgeable, delegatable, and not strong. We then propose an improved efficient IBSDVS scheme with short signature size and provide formal security proofs based on the computational Diffie–Hellman assumption in the random oracle model. We also show that the performance of our scheme outperforms all the existing IBSDVS schemes known in the literature. Furthermore, we propose an extension of our scheme achieving the stronger notion of nondelegatability and provide formal security proofs. The extended scheme is also showed to achieve high efficiency and short signature size. Copyright © 2012 John Wiley & Sons, Ltd.
A Luminescent Cage‐Like Complex Constructed by Bidentate Pyridine‐Containing Ligand and Silver Nitrate
Authors: Liu Ying , Yu Ying‐Hui , Liu Yi‐Fu , Hou Guang‐Feng , Wang Xiao‐Dan , Wen Bo , Gao Jin‐Sheng
Published: November 2012

The cage‐like complex, Ag4L4(NO3)4 (1) [L = 1, 4‐bis(pyridine‐2‐ylmethoxy)benzene] was synthesized by the reaction of the flexible bidentate ligand and silver nitrate. It was characterized by elemental analysis, IR spectroscopy, TG, and single‐crystal X‐ray analysis. Complex 1 is reported as the first cage‐like cluster constructed by four nitrate anions bridging two [2+2] macrocycles. A blue luminescent emission and luminescent enhancement effect are observed in complex 1.
Repressing anarchy in neutrino mass textures
Authors: Altarelli Guido , Feruglio Ferruccio , Masina Isabella , Merlo Luca
Published: November 2012

Abstract

The recent results that θ
13 is relatively large, of the order of the previous upper bound, and the indications of a sizable deviation of θ
23 from the maximal value are in agreement with the predictions of Anarchy in the lepton sector. The quark and charged lepton hierarchies can then be reproduced in a SU(5) GUT context by attributing non-vanishing U(1)FN charges, different for each family, only to the SU(5) tenplet states. The fact that the observed mass hierarchies are stronger for up quarks than for down quarks and charged leptons supports this idea. As discussed in the past, in the flexible context of SU(5) ⊗ U(1)FN, different patterns of charges can be adopted going from Anarchy to various types of hierarchy. We revisit this approach by also considering new models and we compare all versions to the present data. As a result we confirm that, by relaxing the ansatz of equal U(1)FN charges for all SU(5) pentaplets and singlets, better agreement with the data than for Anarchy is obtained without increasing the model complexity. We also present the distributions obtained in the different models for the Dirac CP-violating phase. Finally we discuss the relative merits of these simple models.
Effect of Additives on the Cloud Point of the Octylphenol Ethoxylate (30EO) Nonionic Surfactant
Authors: Rocha Sarah A. N. , Costa Cibele R. , Celino Joil J. , Teixeira Leonardo S. G.
Published: November 2012

The effect of different additives on the cloud point (CP) of an octylphenol ethoxylate (OPEO30) aqueous solution was investigated. The CP of OPEO30 is higher than 100 °C due to its approximately 30 oxyethylene units per molecule, which limits its use in cloud point extraction (CPE) procedures at room temperature. However, the presence of additives can promote a decrease in CP, allowing its use in CPE. Halide presence decreased the CP of OPEO30 in the following order F− > Cl− > Br−. It was also observed that the addition of divalent anions resulted in a more pronounced salting‐out effect than monovalent anions. Blends of OPEO30 and its counterpart with 7.5 units of ethylene oxide (OPEO7.5) were also investigated, and it was verified that the CP of OPEO30 decreased linearly with increasing OPEO7.5 concentration, showing that mixing surfactants is a strategy to be explored. In the presence of small amounts of alcohols that are partially soluble in aqueous solution, such as isobutanol and pentanol, cloudiness was observed at temperatures below the CP of pure OPEO30 solution.
Political Parties: Communities Built Around Values or Communities Built around Programmes
Authors: Debié Franck René
Published: November 2012

A comparison between France and the US shows that political parties tend to behave as social communities comparable to trade unions or churches. Those communities are built around common habits, values, interests and programmes. But when it comes to successful coalition building, programmes and lead candidates remain decisive.
Identity and Power in Ukraine
Authors: Korostelina Karina V.
Published: November 2012

This paper analyzes the coercive and legitimate forms of power in Ukraine. It describes the crisis of legitimacy in Ukraine as a contradiction between a blatantly cruel system of capitalism dominated by a few oligarchs, and the lingering remnants of a Soviet mentality. Two strategies are used by the Government to stoke the crisis. First, increased identification with ethnic or regional groups are instrumentally used by the Government to take attention from economic and class issues. Second, the incorporation of a Soviet meaning of power into the new national identity and presentation of it as core norms, believes, and values of the people of Ukraine competes with alternative Ukrainian identity concepts. The paper analyzes five main features of the Soviet meanings of power – political, social, and economic paternalism, perception of power as source of profit and violence, and the dual reality of power with the gap between official narratives of power and a real life. The process of incorporation of the Soviet concept of power into national identity is facilitated by the process of national identity formation that helped to preserve the Soviet perception of power, because of the absence of a new ideology, a lack of critical assessment of the Soviet past, an absence of the vision of outcome, an embryonic culture of democracy, and contributions of all the presidents to the preservation of the Soviet meaning of power. People justify the system as legitimate and fair for many reasons: out of historic habit and deemed moral obligations, self-interests and/or a fear of sanctions, identification with the ruler, zones of indifference, an absence of will and self-confidence, desire to support a strong leader based on ambiguity intolerance, hierarchy – enhancing ideologies, and a general tolerance of injustice. The obedience of subjects is connected with the strength of will of the subjects and the social structures of the society. In Ukraine, the society is not united, not organized, has no identity of “us”, no civic accountability, nor even any real interest in such matters. Civil society levels are very low, as reflected by limited opportunities for civic responsibility and participation and few demands from the society.
Androgen receptor gene polymorphism and polycystic ovary syndrome
Authors: Lin Lawrence H. , Baracat Maria C.P. , Maciel Gustavo A.R. , Soares José M. , Baracat Edmund C.
Published: November 2012

Background

Polycystic ovary syndrome (PCOS) is characterized by ovulatory dysfunction and hyperandrogenism. Its etiopathology is not well understood but genetic factors seem to have a role. Polymorphism of the androgen receptor (AR) gene has been associated with different androgen pattern diseases.

Objective

To review the association between AR gene polymorphism and PCOS.

Search strategy

A systematic review was performed via PUBMED, EMBASE, and LILACS (up to May 31, 2011).

Selection criteria

Studies assessing the presence of the (CAG)n polymorphism of the AR gene in at least 2 comparison groups (PCOS and control). Studies that did not contain adequate information were excluded.

Data collection and analysis

Study characteristics and results were analyzed. Meta‐analysis could not be performed because only 2 articles provided odds ratios.

Main results

Ten studies met the inclusion criteria. Three studies reported a correlation between the polymorphism and PCOS; 2 studies linked the disorder to shorter repeats, whereas the other associated it with longer repeats.

Conclusion

Polymorphism of the AR gene seems to be a promising biomarker for PCOS because shorter repeats may be linked to the disorder. However, further studies are needed to understand the association fully.
Sex trafficking, physical and sexual violence, and HIV risk among young female sex workers in Andhra Pradesh, India
Authors: George Annie , Sabarwal Shagun
Published: November 2012

Objective

To estimate the prevalence of sex trafficking as a mode of entry into sex work and to examine associations between sex trafficking and HIV vulnerability, recent violence experience, and symptoms of sexual ill health among young female sex workers (FSWs).

Methods

A cross‐sectional survey of 1137 FSWS aged 18–25 years residing in Andhra Pradesh, India, was conducted.

Results

In total, 574 (50.5%) FSWs entered sex work via trafficking. Trafficked FSWs had an increased risk of experiencing sexual violence (adjusted odds ratio [AOR] 2.09; 95% confidence interval [CI], 1.42–3.06) and physical/sexual violence (AOR 1.93; 95% CI, 1.24–3.01), and reporting more clients (AOR 2.25; 95% CI, 1.56–3.22) and more work days per week (AOR 1.48; 95% CI, 1.09–2.02). Symptoms of sexual ill health were not associated with mode of entry into sex work.

Conclusion

There is a high prevalence of entry into sex work via trafficking among young FSWs. A history of sex trafficking is associated with greater risk of recent physical and sexual violence and of HIV. Public health interventions must focus attention on young FSWs.
Phase shifts of magneto-acoustic solitons in spin-1/2 fermionic quantum plasma during head-on collision
Authors: CHATTERJEE PRASANTA , ROYCHOUDHURY RAJKUMAR , GHORUI MALAY KUMAR
Published: November 2012

The head-on collision between two magneto-acoustic solitons in spin-1/2 fermionic quantum plasma is studied in the framework of the model proposed by Marklund et al. (Marklund, M., Eliasson, B. and Shukla, P. K. 2007 Phys. Rev. E. 76, 067401). The extended Poincare–Lighthill–Kuo method is used to obtain the phase shifts and the trajectories during the head-on collision of two solitons. The effect of the Zeeman energy for different speeds of the waves, the effect of the total mass density of the charged plasma particles for different strengths of magnetic field, the effect of the speed of the wave for different values of the Zeeman energy, and that of the ratio of the sound speed to Alfven speed for different values of Zeeman energ on the phase shift are studied. It is observed that the phase shifts are significantly affected in all the cases. The most interesting observation of this paper is that the phase shifts increase as well as decrease, and also they may be positive as well as negative depending upon the domain of the chosen parameters.
Dark energy and dark matter as due to zero point energy
Authors: LEHNERT BO
Published: November 2012

An attempt is made to explain dark energy and dark matter of the expanding universe in terms of the zero point vacuum energy. This analysis is mainly limited to later stages of an observable nearly flat universe. It is based on a revised formulation of the spectral distribution of the zero point energy, for an ensemble in a defined statistical equilibrium having finite total energy density. The steady and dynamic states are studied for a spherical cloud of zero point energy photons. The ‘antigravitational’ force due to its pressure gradient then represents dark energy, and its gravitational force due to the energy density represents dark matter. Four fundamental results come out of the theory. First, the lack of emitted radiation becomes reconcilable with the concepts of dark energy and dark matter. Second, the crucial coincidence problem of equal orders of magnitude of mass density and vacuum energy density cannot be explained by the cosmological constant, but is resolved by the present variable concepts, which originate from the same photon gas balance. Third, the present approach becomes reconcilable with cosmical dimensions and with the radius of the observable universe. Fourth, the deduced acceleration of the expansion agrees with the observed one. In addition, mass polarity of a generalized gravitation law for matter and antimatter is proposed as a source of dark flow.
Odd deposits and average practice. A critical history of the concept of structured deposition
Authors: Garrow Duncan
Published: November 2012

This paper presents a critical history of the concept of ‘structured deposition’. It examines the long-term development of this idea in archaeology, from its origins in the early 1980s through to the present day, looking at how it has been moulded and transformed. On the basis of this historical account, a number of problems are identified with the way that ‘structured deposition’ has generally been conceptualized and applied. It is suggested that the range of deposits described under a single banner as being ‘structured’ is unhelpfully broad, and that archaeologists have been too willing to view material culture patterning as intentionally produced – the result of symbolic or ritual action. It is also argued that the material signatures of ‘everyday’ practice have been undertheorized and all too often ignored. Ultimately, it is suggested that if we are ever to understand fully the archaeological signatures of past practice, it is vital to consider the ‘everyday’ as well as the ‘ritual’ processes which lie behind the patterns we uncover in the ground.
Some deposits are more structured than others
Authors: Thomas Julian
Published: November 2012

I congratulate Duncan Garrow on his very engaging history of the concept of structured deposition, although I find it slightly terrifying that this history now extends over nearly 30 years. I find much to agree with in his account, notably the distressing point that what was originally intended as a heuristic has sometimes become an end in itself: the identification of a class of deposits that are ‘structured’. Thus, for instance, Bishop, Church and Rowley-Conwy argue (2009, 82) that pits in Neolithic Scotland may have represented ‘places of structured deposition rather than domestic settlements’, and that therefore the plant remains contained within them should be regarded as unrepresentative. Here, structured deposits take on the abject character that used to be afforded to ‘ritual’ phenomena in archaeology: having been identified as irrational and abnormal, their interpretation is considered beyond archaeological competence, and they are not subjected to further analysis.
Curation as research. A case study in orphaned and underreported archaeological collections
Authors: Voss Barbara L.
Published: November 2012

As archaeologists grapple with the international curation crisis, new attention is being given to the problem of ‘orphaned’ archaeological collections and collections that are underanalysed and underreported. The common rationale for curating such collections is to restore research potential, but such efforts are met with frustration because of the difficulties of re-establishing provenance and quantitative control for artefacts long separated from their original archaeological context. Moreover, most archaeologists view curation as a process that manages, rather than investigates, archaeological collections. To the contrary, this article argues that accessioning, inventory, cataloguing, rehousing and conservation are not simply precursors to research, but rather meaningful generative encounters between scholars and objects. Examples from the curation of the Market Street Chinatown archaeological collection illustrate how the process of curation can generate innovative research undertakings. Because archaeological research on this collection cannot proceed in a typical way, the research developed through the curation process departs from archaeological conventions to bring new perspectives on the social history of the Overseas Chinese diaspora.
The uncreated man. A story of archaeology and imagination
Authors: Shepherd Nick
Published: November 2012

What is the place of imagination in archaeology? This paper works with a set of materials from the deep archive of the South African archaeologist John Goodwin (1900–59) to explore the relationship between archaeology and imagination. The first half of the paper focuses on a short story written by Goodwin, describing the accidental creation and subsequent ‘uncreation’ of an indigenous person of the Cape (described in the story as a ‘Hottentot’) by the gods on Olympus. The second half of the paper describes two encounters in life between Goodwin and indigenous people of the Cape (the first with the so-called ‘Tweerivieren Bushmen’, exhibited in life at the Empire Exhibition of 1936; the second with the human remains from Oakhurst Cave). Encounters in life, in death and in imagination, the terms of these three episodes double and repeat one another in the different forms of writing to which they give rise (the imagined world of the short story, and the ‘bare description’ of Goodwin's archaeological texts). At the centre of each is the haunted figure of the ‘Bushman’/‘Hottentot’, a being whose status is figured as a kind of ‘death-in-life’. In my telling, forms of actual and epistemic violence are never far from these events. Looking, showing and telling are described as activities which range across a set of characteristic sites: the body, the archive and the grave. In so doing, they summon their counterparts, the categories of the unspeakable and the untellable.
GREEK LOVE, ORIENTALISM AND RACE: INTERSECTIONS IN CLASSICAL RECEPTION
Authors: Orrells Daniel
Published: November 2012

Classics has been characterised as both a radical and a conservative discipline. Classical reception studies has enjoyed exploring this paradox: antiquity has provided an erotic example for modern homosexual counter-culture as well as a model for running exploitative empires. This article brings these aspects of reception studies together, to examine how the Victorian homosexual reception of the ancient Greeks was framed and worked out in a particular imperial context at the end of the nineteenth century.
PLATO AND THE DICE: A REASSESSMENT OFTHEAETETUS154A–155D
Authors: Piazza Mario
Published: November 2012

This paper focuses on the pair of philosophical puzzles, in the first section of Plato'sTheaetetus, concerning the comparison between cardinalities and sizes. My initial task is to analyse some difficulties and distractions which affect our understanding of the argumentation that Socrates puts forward on Protagoras' behalf. I then offer a revised interpretation that integrates the puzzles with the rest of the Protagorean/Heraclitean theory. The emerging discussion, far from being a bridging passage or detour, is a unit with its own specific identity. Its goal is to stretch the Protagorean/Heraclitean metaphysics of events to a new limit: thedematerialisationof change. Change may also be the simple effect of quantitative comparisons as such. At the same time, important traces of Plato's indirect move against Protagoras are detected: theconceivabilityitself of this Protagorean view descends from acommonapplication of mathematics.
THE ‘PHOENICIAN LETTERS’ OF DICTYS OF CRETE AND DIONYSIUS SCYTOBRACHION
Authors: Ní Mheallaigh Karen
Published: November 2012

Dictys of Crete'sJournal of the Trojan Warseems to invite the reader to imagine two different versions of the imaginary ancient Ur-text: one that was written in Phoenician language and script, and another that was written using ‘Phoenician letters’ but whose language was Greek. What is the meaning of the text's different fantasies of its own origins? And how is the reader to understand the puzzlingly implausible Punico-Greek text that is envisaged in Septimius' prefatory letter? This article examines first why theJournal's fantasy Ur-text changed as the Dictys-text itself evolved, and what the text's fiction of its own origins can tell us, not only about its readers' contemporary context, but also about their fantasies about their own literary past – and future as well. Secondly, comparison with the work of Dionysius Skytobrachion, himself the author of a pseudo-documentary Troy-history, offers a new interpretation of what, precisely, Septimius' ‘Punic letters’ may have represented in ancient readers' minds, and opens up a new (imaginary) literary hinterland in the heroic past for the fictional author Dictys and his text.
The Beijing Twin Study (BeTwiSt): A Longitudinal Study of Child and Adolescent Development
Authors: Chen Jie , Li Xinying , Zhang Jianxin , Natsuaki Misaki N. , Leve Leslie D. , Harold Gordon T. , Chen Zhiyan , Yang Xiaodong , Guo Fei , Zhang Jie , Ge Xiaojia
Published: November 2012

Rates of emotional and behavioral problems among children and adolescents in China are increasing and represent a major public health concern. To investigate the etiology of such problems, including the effects and interplay of genes and environment, the Beijing Twin Study (BeTwiSt) was established. A representative sample of adolescent twins in Beijing (N= 1,387 pairs of adolescent twins, mostly between the ages of 10 and 18 years) was recruited and assessed longitudinally. Data collection included the following: emotional and behavioral problems (e.g., depressive symptoms, anxiety, delinquency, drinking, and smoking); family, peer, and school environments; stress; social and academic competence; cognitive traits (e.g., emotion suppression, rumination, and effortful control); and saliva samples for DNA genotyping and sequencing. The combination of quantitative and molecular genetic approaches and the timeliness of the project, with the sample residing in a region with a rapidly changing economic and cultural climate, are particular strengths of this study. Findings from this study are expected to help understanding of the etiological mechanisms underlying child and adolescent normal and abnormal development in regions undergoing substantial social, cultural, and economic changes.
The Vietnam Era Twin Registry: A Quarter Century of Progress
Authors: Tsai Melyssa , Mori Alaina M. , Forsberg Christopher W. , Waiss Nicole , Sporleder Jennifer L. , Smith Nicholas L. , Goldberg Jack
Published: November 2012

Now celebrating its 26th year of existence, the Vietnam Era Twin Registry continues to be one of the largest national samples of adult twins in the United States. The Registry twin member population is composed of 7,369 US male–male twin pair Veterans (14,738 total individuals) who served on active duty in the military during the Vietnam conflict (1964–1975). The Registry also maintains a register, data repository, and a biospecimen repository. Details on the operations of the Registry are described, as well as an overview of specific studies. Registry maintenance activities are also described, including the updating of contact information and vital status. Future plans include expanding the biospecimen repository and obtaining input from twins about study methods and diseases and conditions they would like to see investigated.
Expanded stream gauging includes groundwater data and trends
Authors: Constantz J. , Barlow J. , Eddy‐Miller C. , Caldwell R. , Wheeler J.
Published: November 2012

Population growth has increased water scarcity to the point that documenting current amounts of worldwide water resources is now as critical as any data collection in the Earth sciences. As a key element of this data collection, stream gauges yield continuous hydrologic information and document long‐term trends, recording high‐frequency hydrologic information over decadal to centennial time frames.
Dealing with contaminated groundwater sites
Authors: Showstack Randy
Published: November 2012

Dealing with contaminated groundwater sites Restoration of about 12,000 “problematic” contaminated groundwater sites across the United States is unlikely to be achieved in the next 50–100 years, according to an 8 November report by a committee of the U.S. National Research Council.
Advancing the Gemini Observatory
Authors: Hammel Heidi B. , Levenson Nancy A.
Published: November 2012

Gemini Science and User Meeting; San Francisco, California, 17–20 July 2012 More than 100 astronomers gathered in San Francisco to discuss results from the Gemini Observatory and to plan for its future. The Gemini Observatory consists of twin 8.1 meter diameter optical/infrared telescopes located on mountaintops in Hawai'i and Chile. Gemini was built and is operated by an international partnership that currently includes the United States, the United Kingdom, Canada, Chile, Australia, Brazil, and Argentina.
Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean
Authors: Dixon Joanna L , Sargeant Stephanie , Nightingale Philip D , Colin Murrell J
Published: November 2012

Methanol biogeochemistry and its importance as a carbon source in seawater is relatively unexplored. We report the first microbial methanol carbon assimilation rates (k) in productive coastal upwelling waters of up to 0.117±0.002 d−1 (∼10 nmol l−1d−1). On average, coastal upwelling waters were 11 times greater than open ocean northern temperate (NT) waters, eight times greater than gyre waters and four times greater than equatorial upwelling (EU) waters; suggesting that all upwelling waters upon reaching the surface (⩽20 m), contain a microbial population that uses a relatively high amount of carbon (0.3–10 nmol l−1d−1), derived from methanol, to support their growth. In open ocean Atlantic regions, microbial uptake of methanol into biomass was significantly lower, ranging between 0.04–0.68 nmol l−1d−1. Microbes in the Mauritanian coastal upwelling used up to 57% of the total methanol for assimilation of the carbon into cells, compared with an average of 12% in the EU, and 1% in NT and gyre waters. Several methylotrophic bacterial species were identified from open ocean Atlantic waters using PCR amplification of mxaF encoding methanol dehydrogenase, the key enzyme in bacterial methanol oxidation. These included Methylophaga sp., Burkholderiales sp., Methylococcaceae sp., Ancylobacter aquaticus, Paracoccus denitrificans, Methylophilus methylotrophus, Methylobacterium oryzae, Hyphomicrobium sp. and Methylosulfonomonas methylovora. Statistically significant correlations for upwelling waters between methanol uptake into cells and both chlorophyll a concentrations and methanol oxidation rates suggest that remotely sensed chlorophyll a images, in these productive areas, could be used to derive total methanol biological loss rates, a useful tool for atmospheric and marine climatically active gas modellers, and air–sea exchange scientists.
Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm
Authors: Probst Alexander J , Holman Hoi-Ying N , DeSantis Todd Z , Andersen Gary L , Birarda Giovanni , Bechtel Hans A , Piceno Yvette M , Sonnleitner Maria , Venkateswaran Kasthuri , Moissl-Eichinger Christine
Published: November 2012

Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth’s energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.
Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages
Authors: Flores Cesar O , Valverde Sergi , Weitz Joshua S
Published: November 2012

Bacteriophages are the most abundant biological life forms on Earth. However, relatively little is known regarding which bacteriophages infect and exploit which bacteria. A recent meta-analysis showed that empirically measured phage-bacteria infection networks are often significantly nested, on average, and not modular. A perfectly nested network is one in which phages can be ordered from specialist to generalist such that the host range of a given phage is a subset of the host range of the subsequent phage in the ordering. The same meta-analysis hypothesized that modularity, in which groups of phages specialize on distinct groups of hosts, should emerge at larger geographic and/or taxonomic scales. In this paper, we evaluate the largest known phage-bacteria interaction data set, representing the interaction of 215 phage types with 286 host types sampled from geographically separated sites in the Atlantic Ocean. We find that this interaction network is highly modular. In addition, some of the modules identified in this data set are nested or contain submodules, indicating the presence of multi-scale structure, as hypothesized in the earlier meta-analysis. We examine the role of geography in driving these patterns and find evidence that the host range of phages and the phage permissibility of bacteria is driven, in part, by geographic separation. We conclude by discussing approaches to disentangle the roles of ecology and evolution in driving complex patterns of interaction between phages and bacteria.
A metabolic model for members of the genus Tetrasphaera involved in enhanced biological phosphorus removal
Authors: Kristiansen Rikke , Nguyen Hien Thi Thu , Saunders Aaron Marc , Nielsen Jeppe Lund , Wimmer Reinhard , Le Vang Quy , McIlroy Simon Jon , Petrovski Steve , Seviour Robert J , Calteau Alexandra , Nielsen Kåre Lehmann , Nielsen Per Halkjær
Published: November 2012

Members of the genus Tetrasphaera are considered to be putative polyphosphate accumulating organisms (PAOs) in enhanced biological phosphorus removal (EBPR) from wastewater. Although abundant in Danish full-scale wastewater EBPR plants, how similar their ecophysiology is to ‘Candidatus Accumulibacter phosphatis’ is unclear, although they may occupy different ecological niches in EBPR communities. The genomes of four Tetrasphaera isolates (T. australiensis, T. japonica, T. elongata and T. jenkinsii) were sequenced and annotated, and the data used to construct metabolic models. These models incorporate central aspects of carbon and phosphorus metabolism critical to understanding their behavior under the alternating anaerobic/aerobic conditions encountered in EBPR systems. Key features of these metabolic pathways were investigated in pure cultures, although poor growth limited their analyses to T. japonica and T. elongata. Based on the models, we propose that under anaerobic conditions the Tetrasphaera-related PAOs take up glucose and ferment this to succinate and other components. They also synthesize glycogen as a storage polymer, using energy generated from the degradation of stored polyphosphate and substrate fermentation. During the aerobic phase, the stored glycogen is catabolized to provide energy for growth and to replenish the intracellular polyphosphate reserves needed for subsequent anaerobic metabolism. They are also able to denitrify. This physiology is markedly different to that displayed by ‘Candidatus Accumulibacter phosphatis’, and reveals Tetrasphaera populations to be unusual and physiologically versatile PAOs carrying out denitrification, fermentation and polyphosphate accumulation.
Gut bacteria–host metabolic interplay during conventionalisation of the mouse germfree colon
Authors: El Aidy Sahar , Derrien Muriel , Merrifield Claire A , Levenez Florence , Doré Joël , Boekschoten Mark V , Dekker Jan , Holmes Elaine , Zoetendal Erwin G , van Baarlen Peter , Claus Sandrine P , Kleerebezem Michiel
Published: November 2012

The interplay between dietary nutrients, gut microbiota and mammalian host tissues of the gastrointestinal tract is recognised as highly relevant for host health. Combined transcriptome, metabonome and microbial profiling tools were employed to analyse the dynamic responses of germfree mouse colonic mucosa to colonisation by normal mouse microbiota (conventionalisation) at different time-points during 16 days. The colonising microbiota showed a shift from early (days 1 and 2) to later colonisers (days 8 and 16). The dynamic changes in the microbial community were rapidly reflected by the urine metabolic profiles (day 1) and at later stages (day 4 onward) by the colon mucosa transcriptome and metabolic profiles. Correlations of host transcriptomes, metabolite patterns and microbiota composition revealed associations between Bacilli and Proteobacteria, and differential expression of host genes involved in energy and anabolic metabolism. Differential gene expression correlated with scyllo- and myo-inositol, glutamine, glycine and alanine levels in colonic tissues during the time span of conventionalisation. Our combined time-resolved analyses may help to expand the understanding of host–microbe molecular interactions during the microbial establishment.
Experimental validation of in silico target predictions on synergistic protein targets
Authors: Cortes-Ciriano Isidro , Koutsoukas Alexios , Abian Olga , Glen Robert C. , Velazquez-Campoy Adrian , Bender Andreas
Published: November 2012

Two relatively recent trends have become apparent in current early stage drug discovery settings: firstly, a revival of phenotypic screening strategies and secondly, the increasing acceptance that some drugs work by modulating multiple targets in parallel (‘multi-target drugs’).
Diel and seasonal variation in the use of a nearshore sandflat by a ray community in a near pristine system
Authors: Vaudo Jeremy J. , Heithaus Michael R.
Published: November 2012

Knowledge of movements and habitat use is necessary to assess a species’ ecological role and is especially important for mesopredators because they provide the link between upper and lower trophic levels. Using acoustic telemetry, we examined coarse-scale diel and seasonal movements of elasmobranch mesopredators on a shallow sandflat in Shark Bay, Western Australia. Giant shovelnose rays (Glaucostegus typus) and reticulate whiprays (Himantura uarnak) were most often detected in nearshore microhabitats and were regularly detected throughout the day and year, although reticulate whiprays tended to frequent the monitored array over longer periods. Pink whiprays (H. fai) and cowtail stingrays (Pastinachus atrus) were also detected throughout the day, but were far less frequently detected. Overall, there was no apparent spatial or temporal partitioning of the sandflats, but residency to the area varied between species. In addition, ray presence throughout the year suggests that previously observed differences in seasonal abundance are likely because of seasonal changes in habitat use rather than large-scale migrations. Continuous use of the sandflats and limited movements within this ray community suggests that rays have the potential to be a structuring force on this system and that focusing on nearshore habitats is important for managing subtropical ray populations.
Hydrogen sulfide intrusion in seagrasses from Shark Bay, Western Australia
Authors: Cambridge Marion L. , Fraser Matthew W. , Holmer Marianne , Kuo John , Kendrick Gary A.
Published: November 2012

Sulfides in sediments and hydrogen sulfide (H2S) intrusion in plant tissues were investigated for six species of seagrass in Shark Bay, Western Australia, at two sites with elevated salinities of 42 and 45 psu. H2S intrusion ranged from <20% to 100% in roots and rhizomes, indicating a high degree of sulfide intrusion in some cases, although this did not vary consistently between larger, long-lived species and smaller, less persistent species. There were significant differences in accumulation of total sulfur (TS) among species. Anatomy of rhizomes and roots showed species-specific differences in aerenchyma, the air channels that allow oxygen to diffuse down to the roots and sediments, and tissues with thickened cell walls that could present a barrier to diffusion of H2S, suggesting that morphology may influence sulfide intrusion and sulfur accumulation. Sulfide concentrations in seagrass sediments were far lower in Shark Bay than in Florida Bay, a subtropical embayment where sulfide toxicity has been implicated in seagrass dieback. Despite significant H2S intrusion into tissues of some Shark Bay seagrasses, there was no evidence of any deleterious effects in the current conditions.
The ecological importance of intact top-predator populations: a synthesis of 15 years of research in a seagrass ecosystem
Authors: Heithaus Michael. R. , Wirsing A. J. , Dill L. M.
Published: November 2012

The worldwide decline of large-bodied marine taxa has made it difficult to draw conclusions about the relative importance of top-down control, and the mechanisms through which it might operate, in coastal marine ecosystems. Since 1997, the Shark Bay Ecosystem Research Project has used the relatively pristine seagrass community of Shark Bay, Australia, to investigate the potential for tiger sharks, the apex predator in the ecosystem, to have an impact on their large-bodied prey through non-consumptive (‘risk’) effects. Here, we synthesise nearly 15 years of data to demonstrate that tiger sharks have widespread risk effects on both large-bodied herbivores and mesopredators in Shark Bay and explore the possibility that these impacts may cascade to lower trophic levels. Although much work remains to be done, our studies suggest that losses of top predators in subtropical estuaries may have greater consequences than generally appreciated and that efforts to conserve and restore their populations should be a priority. Furthermore, future management strategies and studies must explicitly consider the potential for predators to influence behaviour of even large-bodied marine taxa.
Characterising the sources and fate of dissolved organic matter in Shark Bay, Australia: a preliminary study using optical properties and stable carbon isotopes
Authors: Cawley Kaelin M. , Ding Yan , Fourqurean James , Jaffé Rudolf
Published: November 2012

Low latitude, seagrass-dominated coastal bays, such as Shark Bay, Australia, are potential sources of chromophoric dissolved organic matter (CDOM) to coastal regions. Dissolved organic matter (DOM) is known to influence aquatic nutrient dynamics, microbial community structure, and depth of light penetration in estuarine systems. Shark Bay is a sub-tropical ecosystem with limited freshwater inputs and restricted tidal flushing. As such, much of the DOM is expected to be seagrass-derived. However, combining excitation/emission fluorescence spectroscopy and parallel factor analysis (EEM-PARFAC) with 13C stable isotope analysis of DOM, we found evidence for DOM inputs from terrestrial (riverine and possibly groundwater), autochthonous plankton, macroalgae, and seagrass sources. Isotopic analysis of 13C in DOM supports the idea that seagrass inputs contribute substantially to the DOM pool in Shark Bay, whereas, EEM-PARAFAC data suggests that much of this input is derived from decomposing seagrass detritus and to a lesser extent due to exudation during primary production. We also report increases in DOM concentrations and changes in DOM characteristics with increasing salinity in surface water samples, indicating that evaporation is an important control on DOM concentration and photo-degradation may play a critical role in transforming DOM within the system.
Feeding preferences of herbivores in a relatively pristine subtropical seagrass ecosystem
Authors: Burkholder Derek A. , Heithaus Michael R. , Fourqurean James W.
Published: November 2012

Understanding forage choice of herbivores is important for predicting the potential impacts of changes in their abundance. Such studies, however, are rare in ecosystems with intact populations of both megagrazers (sirenians, sea turtles) and fish grazers. We used feeding assays and nutrient analyses of seagrasses to determine whether forage choice of grazers in Shark Bay, Australia, are influenced by the quality of seagrasses. We found significant interspecific variation in removal rates of seagrasses across three habitats (shallow seagrass bank interior, shallow seagrass bank edge, deep), but we did not detect variation in gazing intensity among habitats. In general, grazers were more likely to consume fast-growing species with lower carbon : nitrogen (C : N) and carbon : phosphorus (C : P) ratios, than the slower-growing species that are dominant in the bay. Grazer choices were not, however, correlated with nutrient content within the tropical seagrasses. Slow-growing temperate seagrasses that experienced lower herbivory provide greater habitat value as a refuge for fishes and may facilitate fish grazing on tropical species. Further studies are needed, however, to more fully resolve the factors influencing grazer foraging preferences and the possibility that grazers mediate indirect interactions among seagrass species.
A comparative assessment of approaches and outcomes for seagrass revegetation in Shark Bay and Florida Bay
Authors: Statton John , Dixon Kingsley W. , Hovey Renae K. , Kendrick Gary A.
Published: November 2012

Here, we review the literature to evaluate seagrass revegetation projects focussed on Posidonia australis and Amphibolis antarctica, the main affected species in Shark Bay in the World Heritage Area in Western Australia, together with projects from Florida Bay, an analogous system with a long history of seagrass revegetation. We assessed the effectiveness of anchoring planting units, plant-unit density and size on planting-unit survival. We found no positive trends in our assessment, suggesting that there is no discrete technique, approach or technology that could be used with confidence to deliver cost-effective, scalable revegetation. Of concern was that revegetation success was evaluated over comparatively short time frames (1–3 years), driven by the strict time frames or deadlines of governing grant funding and commercial activities, leading to concerns that long-term revegetation outcomes may be difficult to assess with confidence. Several factors influenced revegetation outcomes which were grouped into three ‘filter’ categories; abiotic, biotic and socioeconomic. We recommend that future revegetation programs involving seagrass have greater emphasis on understanding how these filters act independently or collectively to drive successful revegetation as well as developing cost-effective, proven and scalable technology supported by longer-term monitoring to ensure revegetation programs do achieve the desired ecological outcomes.
Tagging studies reveal restricted movement of snapper (Pagrus auratus) within Shark Bay, supporting fine-scale fisheries management
Authors: Norriss Jeffrey V. , Moran Michael , Jackson Gary
Published: November 2012

The snapper (Pagrus auratus) fisheries of Shark Bay’s complex inner gulfs are managed on a fine spatial scale (tens of kilometres). Following the splitting of the Western Gulf into two management zones, results from an earlier 1980s tagging study were revisited to assess the suitability of management arrangements. Recaptures up to 15 years at liberty showed highly restricted movement, with 300 of 491 occurring within 5 nautical miles of the tagging site and only 3.3% crossing the new zone boundary. A simple stock-trajectory model simulating the two Western Gulf populations demonstrated a negligible impact from a 1% per annum level of mixing. The 1980s study was repeated between 1998 and 2003 by tagging 2558 snapper, mainly in areas previously under-represented. Recaptures up to 2 years at liberty again showed highly restricted movement, with 181 of 197 recaptures occurring at the tagging site. Juveniles were more sedentary than adults, the latter showing limited evidence of inter-annual spawning-site fidelity. Together, both studies support the use of three small management zones. Community acceptance of these complex arrangements was aided by collaborating with volunteers on research programs, which improved their understanding of the population structure.