bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical complexity in the Horsehead photodissociation region
Authors: Guzmán Viviana V. , Pety Jérôme , Gratier Pierre , Goicoechea Javier R. , Gerin Maryvonne , Roueff Evelyne , Le Petit Franck , Le Bourlot Jacques
Published: January 2014

The interstellar medium is known to be chemically complex. Organic molecules with up to 11 atoms have been detected in the interstellar medium, and are believed to be formed on the ices around dust grains. The ices can be released into the gas-phase either through thermal desorption, when a newly formed star heats the medium around it and completely evaporates the ices; or through non-thermal desorption mechanisms, such as photodesorption, when a single far-UV photon releases only a few molecules from the ices. The first mechanism dominates in hot cores, hot corinos and strongly UV-illuminated PDRs, while the second dominates in colder regions, such as low UV-field PDRs. This is the case of the Horsehead were dust temperatures are ≃20–30 K, and therefore offers a clean environment to investigate the role of photodesorption. We have carried out an unbiased spectral line survey at 3, 2 and 1mm with the IRAM-30m telescope in the Horsehead nebula, with an unprecedented combination of bandwidth, high spectral resolution and sensitivity. Two positions were observed: the warm PDR and a cold condensation shielded from the UV field (dense core), located just behind the PDR edge. We summarize our recently published results from this survey and present the first detection of the complex organic molecules HCOOH, CH2CO, CH3CHO and CH3CCH in a PDR. These species together with CH3CN present enhanced abundances in the PDR compared to the dense core. This suggests that photodesorption is an efficient mechanism to release complex molecules into the gas-phase in far-UV illuminated regions.
Synthesis of highly dispersed metal sulfide catalysts via low temperature sulfidation in dielectric barrier discharge plasma
Authors: Zhao Lu , Wang Yao , Sun Zhili , Wang Anjie , Li Xiang , Song Chunshan , Hu Yongkang
Published: January 2014

Highly dispersed metal sulfide catalysts were synthesized by low temperature sulfidation in a non-thermal plasma directly from the metal salts.
Systematic study of exciton diffusion length in organic semiconductors by six experimental methods
Authors: Lin Jason D. A. , Mikhnenko Oleksandr V. , Chen Jingrun , Masri Zarifi , Ruseckas Arvydas , Mikhailovsky Alexander , Raab Reilly P. , Liu Jianhua , Blom Paul W. M. , Loi Maria Antonietta , García-Cervera Carlos J. , Samuel Ifor D. W. , Nguyen Thuc-Quyen
Published: January 2014

Six techniques are used to measure the exciton diffusion length as a function of systematic chemical modifications.
A sub 6 nanometer plasmonic gold nanoparticle for pH-responsive near-infrared photothermal cancer therapy
Authors: Hwang Sekyu , Nam Jutaek , Song Jaejung , Jung Sungwook , Hur Jaehyun , Im Kyuhyun , Park Nokyoung , Kim Sungjee
Published: January 2014

A small (sub 6 nm hydrodynamic diameter) and pH-responsive gold nanoparticle photothermal agent is reported.
Cβ conformer formation in poly(9,9-dioctylfluorene) single chains facilitated by endcapping with an electron deficient moiety
Authors: Chen Pei-Yin , Rassamesard Areefen , Hung Ming-Chin , Chen Hsin-Lung , Chen Show-An
Published: January 2014

Using single molecule spectroscopy, we reveal that endcapping poly(9,9-dioctylfluorene) (PFO) with an electron deficient moiety (EDM) can promote the population of Cβ conformers at the intra-chain level.
Electron induced chemistry of disilane
Authors: Gupta Dhanoj , Naghma Rahla , Goswami Biplab , Antony Bobby
Published: January 2014

Theoretical study of electron impact scattering by disilane molecule is reported in this article.
Electrically programmable digital memory behaviors based on novel functional aromatic polyimide/TiO2hybrids with a high ON/OFF ratio
Authors: Chen Chih-Jung , Tsai Chia-Liang , Liou Guey-Sheng
Published: January 2014

A novel sulfur-containing polyimide3SOH-6FPIand the3SOH-6FPI/TiO2hybrids were synthesized and used for memory applications. The resulted hybrid films with different TiO2concentrations exhibited tunable memory properties. The crystalline phase of titania exhibited higher trapping ability to increase the retention time in the ON state.
Elucidating the regulation of complex signalling systems in plant cells
Authors: Liu Junli , Lindsey Keith , Hussey Patrick J.
Published: January 2014

The pollen tube represents a model system for the study of tip growth, and the root provides a valuable system to study gene and signalling networks in plants. In the present article, using the two systems as examples, we discuss how to elucidate the regulation of complex signalling systems in plant cells. First, we discuss how hormones and related genes in plant root development form a complex interacting network, and their activities are interdependent. Therefore their roles in root development must be analysed as an integrated system, and elucidation of the regulation of each component requires the adaptation of a novel modelling methodology: regulation analysis. Secondly, hydrodynamics, cell wall and ion dynamics are all important properties that regulate plant cell growth. We discuss how regulation analysis can be applied to study the regulation of hydrodynamics, cell wall and ion dynamics, using pollen tube growth as a model system. Finally, we discuss future prospects for elucidating the regulation of complex signalling systems in plant cells.
Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA
Authors: Gorgoni Barbara , Marshall Elizabeth , McFarland Matthew R. , Romano M. Carmen , Stansfield Ian
Published: January 2014

Gene expression can be regulated by a wide variety of mechanisms. One example concerns the growing body of evidence that the protein-production rate can be regulated at the level of translation elongation by controlling ribosome flux across the mRNA. Variations in the abundance of tRNA molecules cause different rates of translation of their counterpart codons. This, in turn, produces a variable landscape of translational rate across each and every mRNA, with the dynamic formation and deformation of ribosomal queues being regulated by both tRNA availability and the rates of translation initiation and termination. In the present article, a range of examples of tRNA control of gene expression are reviewed, and the use of mathematical modelling to develop a predictive understanding of the consequences of that regulation is discussed and explained. These findings encourage a view that predicting the protein-synthesis rate of each mRNA requires a holistic understanding of how each stage of translation, including elongation, contributes to the overall protein-production rate.
Pleiotropic molecular effects of theMycobacterium ulceransvirulence factor mycolactone underlying the cell death and immunosuppression seen in Buruli ulcer
Authors: Hall Belinda , Simmonds Rachel
Published: January 2014

Mycolactone is a polyketide macrolide lipid-like secondary metabolite synthesized by Mycobacterium ulcerans, the causative agent of BU (Buruli ulcer), and is the only virulence factor for this pathogen identified to date. Prolonged exposure to high concentrations of mycolactone is cytotoxic to diverse mammalian cells (albeit with varying efficiency), whereas at lower doses it has a spectrum of immunosuppressive activities. Combined, these pleiotropic properties have a powerful influence on local and systemic cellular function that should explain the pathophysiology of BU disease. The last decade has seen significant advances in our understanding of the molecular mechanisms underlying these effects in a range of different cell types. The present review focuses on the current state of our knowledge of mycolactone function, and its molecular and cellular targets, and seeks to identify commonalities between the different functional and cellular systems. Since mycolactone influences fundamental cellular processes (cell division, cell death and inflammation), getting to the root of how mycolactone achieves this could have a profound impact on our understanding of eukaryotic cell biology.
Cdc42 regulates polarized growth and cell integrity in fission yeast
Authors: Rincón Sergio A. , Estravís Miguel , Pérez Pilar
Published: January 2014

Polarized cell growth requires a well-orchestrated number of events, namely selection of growth site, organization of cytoskeleton elements and delivery of new material to the growth region. The small Rho GTPase Cdc42 has emerged as a major organizer of polarized growth through its participation in many of these events. In the present short review, we focus on the regulation of Cdc42 activity and localization as well as how it controls downstream events necessary for polarized cell growth in Schizosaccharomyces pombe. Owing to the high level of similarity of the polarity pathways, analogies between fission yeast and other model systems can be useful to decipher how cells can actively define their shape by polarized growth.
The diverse roles of the eIF4A family: you are the company you keep
Authors: Lu Wei-Ting , Wilczynska Anna , Smith Ewan , Bushell Martin
Published: January 2014

The eIF4A (eukaryotic initiation factor 4A) proteins belong to the extensive DEAD-box RNA helicase family, the members of which are involved in many aspects of RNA metabolism by virtue of their RNA-binding capacity and ATPase activity. Three eIF4A proteins have been characterized in vertebrates: eIF4A1 and eIF4A2 are cytoplasmic, whereas eIF4A3 is nuclear-localized. Although highly similar, they have been shown to possess rather diverse roles in the mRNA lifecycle. Their specific and diverse functions are often regulated and dictated by interacting partner proteins. The key differences between eIF4A family members are discussed in the present review.
Functional implications of assigned, assumed and assembled PKC structures
Authors: Linch Mark , Riou Philippe , Claus Jeroen , Cameron Angus J. , de Naurois Julien , Larijani Banafshe , Ng Tony , McDonald Neil Q. , Parker Peter J.
Published: January 2014

The empirical derivation of PKC (protein kinase C) domain structures and those modelled by homology or imputed from protein behaviour have been extraordinarily valuable both in the elucidation of PKC pathway mechanisms and in the general lessons that extrapolate to other signalling pathways. For PKC family members, there are many domain/subdomain structures and models, covering all of the known domains, variably present in this family of protein serine/threonine kinases (C1, C2, PB1, HR1, kinase domains). In addition to these structures, there are a limited number of complexes defined, including the structure of the PKCε V3–14-3-3 complex. In the context of structure-driven insights into PKC pathways, there are several broadly applicable principles and mechanisms relevant to the operation of and intervention in signalling pathways. These principles have an impact in unexpected ways, from the regulation of membrane targeting, through strategies for pharmacological intervention, to biomarkers.
Structure–function relationships and supramolecular organization of the EGFR (epidermal growth factor receptor) on the cell surface
Authors: Needham Sarah R. , Zanetti-Domingues Laura C. , Hirsch Michael , Rolfe Daniel J. , Tynan Christopher J. , Roberts Selene K. , Martin-Fernandez Marisa L. , Clarke David T.
Published: January 2014

Dimerization and higher-order oligomerization are believed to play an important role in the activation of the EGFR (epidermal growth factor receptor). Understanding of the process has been limited by the lack of availability of suitable methods for the measurement in cells of distances in the range 10–100 nm, too short for imaging methods and too long for spectroscopic methods such as FRET. In the present article, we review the current state of our knowledge of EGFR oligomerization, and describe results from a new single-molecule localization method that has allowed the quantitative characterization of the distribution of EGFR–EGFR distances in cells. Recent data suggest the involvement of cortical actin in regulating the formation of EGFR complexes.
Discontinuous leading-strand synthesis: a stop–start story
Authors: Yeeles Joseph T.P.
Published: January 2014

Reconstitution experiments using replication proteins from a number of different model organisms have firmly established that, in vitro, DNA replication is semi-discontinuous: continuous on the leading strand and discontinuous on the lagging strand. The mechanism by which DNA is replicated in vivo is less clear. In fact, there have been many observations of discontinuous replication in the absence of exogenous DNA-damaging agents. It has also been proposed that replication is discontinuous on the leading strand at least in part because of DNA lesion bypass. Several recent studies have revealed mechanistic details of pathways where replication of the leading strand introduces discontinuities. These mechanisms and their potential contributions to observations of discontinuous replication in vivo will be discussed.
Regulation of IL-6-type cytokine responses by MAPKs
Authors: Costa-Pereira Ana P.
Published: January 2014

IL-6 (interleukin 6)-type cytokines are pleiotropic molecules, critical for cellular homoeostasis and with well-recognized roles in several human diseases. They all activate JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling and, depending on the particular cytokine, cell type and cellular environment, they can also trigger the activation of MAPK (mitogen-activated protein kinase) and PI3K (phosphoinositide 3-kinase) cascades. Although it is clear that JAK/STAT and MAPK reciprocally regulate each other, how these signalling pathways are fully integrated remains to be fully understood. Not only do cells have to be able to integrate and conciliate what are often contradictory signalling cues, but they are also subject to complex regulatory mechanisms involving these pathways. More specifically, we have shown recently that ERK2 (extracellular-signal-regulated kinase 2) is required for the transcriptional regulation of gp130 (glycoprotein 130), a key receptor complex component for most IL-6-type cytokines. ERK2 not only binds to the gp130 promoter and is required for full expression of the protein, but it also regulates the stability of gp130 mRNA. This function of ERK2 is not shared by ERK1 and it probably represents an entirely novel function for this prominent kinase.
First-principles studies on vacancy-modified interstitial diffusion mechanism of oxygen in nickel, associated with large-scale atomic simulation techniques
Authors: Fang H. Z. , Shang S. L. , Wang Y. , Liu Z. K. , Alfonso D. , Alman D. E. , Shin Y. K. , Zou C. Y. , van Duin A. C. T. , Lei Y. K. , Wang G. F.
Published: January 2014

This paper is concerned with the prediction of oxygen diffusivities in fcc nickel from first-principles calculations and large-scale atomic simulations. Considering only the interstitial octahedral to tetrahedral to octahedral minimum energy pathway for oxygen diffusion in fcc lattice, greatly underestimates the migration barrier and overestimates the diffusivities by several orders of magnitude. The results indicate that vacancies in the Ni-lattice significantly impact the migration barrier of oxygen in nickel. Incorporation of the effect of vacancies results in predicted diffusivities consistent with available experimental data. First-principles calculations show that at high temperatures the vacancy concentration is comparable to the oxygen solubility, and there is a strong binding energy and a redistribution of charge density between the oxygen atom and vacancy. Consequently, there is a strong attraction between the oxygen and vacancy in the Ni lattice, which impacts diffusion.
Evolution of phase and microstructure in anisotropic nanocrystalline SmCo6.1Si0.9 magnets
Authors: An Shizhong , Zhang Tianli , Jiang Chengbao
Published: January 2014

The evolution of phase and microstructure has been investigated for the spark plasma sintered anisotropic nanocrystalline SmCo6.1Si0.9 magnets. With the increasing of sintering temperature from room temperature to 680 °C, the phase evolves from 1:7H (TbCu7-type) single phase to 1:7H dominant phase plus 2:17 R (Th2Zn17-type) minor phase, and then to 2:17 R dominant phase with phase-transformation twins structure plus minor 1:5 H (CaCu5-type) precipitated phase with particulate morphology. The evolution of phase and microstructure in anisotropic nanocrystalline SmCo6.1Si0.9 alloys, as well as its effect on the coercivity is discussed and compared with that in nanostructured 2:17 type SmCo alloys.
Anisotropic magnetoresistance of epitaxial Pr0.5Sr0.5MnO3 film
Authors: Chen X. G. , Yang J. B. , Yang Y. B. , Wang C. S. , Liu S. Q. , Zhang Y. , Han J. Z. , Yang Y. C.
Published: January 2014

The magnetic field and temperature dependent anisotropic magnetoresistance (AMR) of the epitaxial grown Pr0.5Sr0.5MnO3 thin films was investigated. It was found that the magnetoresistance exhibited the characteristics of magnetic polaron hopping. A two-fold symmetric AMR occurred in the ferromagnetic region (∼220 K < T < ∼150 K), while a four-fold symmetric AMR appeared under a high magnetic field in the antiferromagnetic orbital ordered region (T < ∼150 K). The angular dependence of the resistance showed a hysteresis effect under magnetic field at low temperature. It is believed that these phenomena are attributed to the spin canting effect, which originates from the melting of orbital ordering under the external magnetic field in the antiferromagnetic region.
“Any Advice is Welcome Isn't it?”: Neoliberal Parenting Education, Local Mothering Cultures, and Social Class
Authors: Holloway Sarah L , Pimlott-Wilson Helena
Published: January 2014

Geographers have shown considerable interest in neoliberal educational restructuring as states across the Global North have sought to respond to the challenges of economic change through the development of a skilled population. Existing research provides a wide-ranging analysis of the ways neoliberal states seek to shape individual citizens through their own learning. Greater attention now needs to be paid to new and developing ways in which they seek to influence the context in which future citizen-workers are raised. This paper focuses on parenting education which is growing across OECD countries. Social science critiques suggest that parenting classes are part of a professionalisation of parenting which has sought to impose middle-class mores on working-class parents, at the same time as parenting has been unwarrantedly cast as a context-free skill. This paper uses quantitative and qualitative data to explore the attitudes of parents of different social class positions to parenting education, tracing the ways these emerge in and through particular sociospatial contexts. The paper reveals the importance of local class-based cultures of mothering in influencing both the attitudes of individual mothers to parenting classes, and the success of neoliberal policy implementation in diverse socioeconomic neighbourhoods. In conclusion the paper emphasises: The importance of geographical research into newly emerging forms of education; the value of engaging with the subjects of neoliberal education policy because their attitudes influence its implementation in practice; and the need to set educational provision in its wider geographical context, as this can shape the success of policies delivered in and through educational institutions.
What's in a Name? Place Branding and Toponymic Commodification
Authors: Medway Dominic , Warnaby Gary
Published: January 2014

If places are increasingly regarded as brands in both the practice of place marketing and its associated theory, then the study of place names (toponymy) arguably overlaps with theories and concepts involving brand naming within the marketing literature. This paper synthesises the diverse literature streams surrounding critical toponymy and brand naming through an exploration of place branding activities. The paper develops the concept of place name commodification, beyond the limited attention it has received within existing critical toponymy research, before examining the issues of endogenous and exogenous contestation that surround it. The paper concludes by discussing how the commodifying effects of places as brand names, with their associated brand values and imagery, can potentially suppress the alternative place perceptions of users, and in doing so stifle the natural potential for cocreation of the place ‘product’ and its related value.
Imagineering Mobility: Constructing Utopias for Future Urban Transport
Authors: Timms Paul , Tight Miles , Watling David
Published: January 2014

Over the past fifty years a growing body of work has sought to address the problem of planning for transportation in the long-term future through scenario building. Such thinking has generally been restricted to issues concerned with environmental sustainability and the ‘images’ of future transport so created are usually weak in terms of their social sustainability content, either treating social issues superficially, or ignoring them entirely, or even creating images that are socially undesirable. At the same time, there has generally been a marked decrease over the past twenty years in socially oriented Utopian thinking. As a direct result of these two factors, hardly any consideration has been given recently to imagining socially sustainable views of transport in a future utopia. The key underlying aim of this paper is to provide some background thinking about how this lack might be addressed. To do so, it examines concepts about utopia in terms of their form, content, and function, and considers possible reasons for the recent decline in Utopian thinking and their ‘replacement’ by a type of futures-thinking that is referred to as dystopian avoidance. It then examines transport characteristics of Utopian thinking in urban planning in the 20th century and considers various ‘antinomies of transport’ with respect to future Utopias. Based upon the insights gained, the paper comments on two existing ‘practical’ sets of transport-related scenarios in terms of their Utopian and dystopian characteristics. One particular result is that the Utopian aspects of these scenario sets in terms of their social content are relatively weak, in line with the hypothesised recent general decline in (social) Utopian thinking. Various conclusions are made which emphasise the usefulness of Utopian thinking in transport planning, particularly in participatory approaches. It is suggested that three elements of the transport system should be separately ‘utopianised’: The mobility of people and goods; physical aspects that facilitate or inhibit such mobility; and the system of governance with respect to formulating and implementing transport policy.
Probing large conformational rearrangements in wild-type and mutant spectrin using structural mass spectrometry
Authors: Sriswasdi Sira , Harper Sandra L. , Tang Hsin-Yao , Gallagher Patrick G. , Speicher David W.
Published: January 2014

Significance

Chemical cross-linking coupled with mass spectrometry has recently emerged as a powerful method for providing medium-resolution spatial information for proteins that are too large or too flexible for crystallography or NMR. To date, crystal structures of only small segments of the highly flexible, conformationally dynamic spectrin family of proteins have been obtained. In this study we combined cross-link–derived spatial constraints with homology modeling to produce the first experimentally verified medium-resolution structures of wild-type spectrin closed dimers and tetramers. These structures coupled with the closed dimer structure of a very common spectrin mutation associated with hereditary hemolytic anemia provide mechanistic insights into how some mutations located large distances from the spectrin tetramerization site can destabilize red cell membranes.
Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival
Authors: Sun Shengyi , Shi Guojun , Han Xuemei , Francisco Adam B. , Ji Yewei , Mendonça Nuno , Liu Xiaojing , Locasale Jason W. , Simpson Kenneth W. , Duhamel Gerald E. , Kersten Sander , Yates John R. , Long Qiaoming , Qi Ling
Published: January 2014

Significance

This study provides insights into the physiological role of Sel1L, an adaptor protein for the ubiquitin ligase Hrd1 in endoplasmic reticulum-associated degradation (ERAD). Using both animal and cell models, this study provides unequivocal evidence for an indispensable role of Sel1L in Hrd1 stabilization, mammalian ERAD, endoplasmic reticulum homeostasis, protein translation, and cellular and organismal survival. Moreover, generation of inducible knockout mouse and cell models deficient in both Sel1L and Hrd1 provides an unprecedented opportunity to elucidate the functional importance of this key branch of ERAD in vivo and to identify its physiological substrates.
Provision of Interventions in Adolescent Forensic Units – A European Perspective
Authors: Berg Johanna , Öberg David , Haack Marie-Jeanne , Välimäki Maritta , Kaltiala-Heino Riittakerttu
Published: January 2014

This study aimed to describe treatment settings and interventions provided by adolescent forensic inpatient units in four Northern European countries. Data were collected with the Monitoring Area and Phase System (MAPS). Data were analyzed using descriptive statistics and qualitative methods. Results showed that there were differences in intake criteria and in theoretical orientation between the units studied. In addition, there were differences in treatment focus. The results can be used in service planning and provision of care in adolescent forensic setting. Exchange of information cross-nationally facilitates the advancement of knowledge and sets parameters for education in the clinical forensic setting.
Comparing Ultrasonography and Endoscopy for Early Gender Identification of Juvenile Siberian Sturgeon
Authors: Munhofen Jennifer L , Jiménez David A , Peterson Doug L , Camus Alvin C , Divers Stephen J
Published: January 2014

Early gender identification is economically advantageous in sturgeon aquaculture to facilitate the targeting of food and spatial resources to females for caviar production. In addition, many species of free-ranging sturgeon are threatened or critically endangered, and the ability to identify gender and evaluate gonads can reveal pertinent biological information that can lead to better management and recovery plans. We compared the speed and accuracy of ultrasonography and endoscopy in identifying gender in 143 juvenile Siberian Sturgeon Acipenser baeri using gonadal histology as the gold standard. The age-3 and age-4 sturgeon were anesthetized with buffered tricaine methanesulfonate and evaluated using ultrasonography and endoscopy; endoscopic gonadal biopsy was then done for histologic confirmation. All fish recovered normally, and there was no postprocedural morbidity or mortality. Histology confirmed the gender for 128 of the 140 (91.4%) fish. Histology and endoscopy agreed on the gender of 124 of the 128 (96.9%) fish, while histology and ultrasonography agreed on 113 of the 128 (88.3%) fish. Ultrasonography (mean time, 11.2 s) was significantly faster than endoscopy (22.3 s), while endoscopy was more accurate but more invasive. Diagnostic accuracy, speed, and invasiveness are factors to consider when selecting a method of gender identification for commercial and free-ranging populations.
Relation between Nucleic Acid Indices and Growth Rate in Fed and Fasting Juvenile Scup
Authors: Mercaldo-Allen Renee , Kuropat Catherine A , Perry Dean M , Redman Dylan H
Published: January 2014

The relationship between nucleic acid indices and daily instantaneous growth rate was determined for juvenile Scup Stenotomus chrysops in the laboratory. Weight-based growth of Scup was measured for three 1-week intervals during a 6-week feeding experiment and showed a significant positive correlation with both RNA concentration (RNA; μg/mg tissue wet weight) and DNA concentration (DNA; μg/mg tissue wet weight), while the RNA: DNA ratio was not significantly correlated with the weight- or length-based growth rate. The concentration of DNA showed a significant negative correlation with length-based growth rate. Mean fish weight increased from 1.022 to 10.404 g, and mean TL increased from 43.219 to 85.377 mm. Changes in nucleic acid indices were measured in fish that were deprived of food over a 9-d period. The RNA and RNA: DNA ratio values declined significantly within 5 d after fasting began, while DNA remained relatively stable. This study provides baseline nucleic acid values for fed and starved juvenile Scup over a range of fish sizes.
Hatchery Steelhead Smolt Release Size Effects on Adult Production and Straying
Authors: Clarke Lance R , Flesher Michael W , Carmichael Richard W
Published: January 2014

Studies have demonstrated higher postrelease survival for larger hatchery steelhead Oncorhynchus mykiss smolts than for smaller ones. However, the ideal release size should also maximize adult returns and minimize interactions of hatchery fish with wild fish. We conducted a study over five release years with paired groups of anadromous hatchery steelhead smolts reared to target sizes of either 90 g (small size) or 113 g (large size). After stream release, we monitored out-migration travel times and survival to a downstream dam using freeze-brand marks in a subsample of each release group. Steelhead smolts that out-migrate quickly may interact less with wild fish. Across all release groups, travel time was about 3 d slower for small-sized smolts than for large ones, but this difference was not statistically significant, and there was no significant difference in the percentage of brands detected at the dam between the two smolt sizes. Coded wire tag recovery was used to compare smolt-to-adult survival (SAS), the number of adults produced per 100 kg of smolts released, and the percentage of adults that strayed. Across all years, large-sized smolts had an average SAS of 1.31% compared with 0.92% for small-sized smolts, a statistically significant difference of 42.0%. The average number of adult steelhead produced per 100 kg of smolts released also was higher for the large-sized group (11.4 adults/100 kg of smolts) over the small-sized group (10.1 adults/100 kg of smolts), though the 12.8% difference was not statistically significant. Adults originating from large-sized smolt releases strayed at a rate of 13.1% compared with a 7.9% rate for the small-sized smolt groups, a difference that was statistically significant. In this study, larger hatchery steelhead smolts had a higher survival after release; however, we found tradeoffs between management objectives associated with maximizing adult production and those aimed at minimizing ecological risks.
Effect of Altering Dietary Protein: Energy Ratios on Juvenile Pallid Sturgeon Growth Performance
Authors: Kittel Elliott C. , Small Brian C.
Published: January 2014

Pallid SturgeonScaphirhynchus albusare endemic to the large, freshwater, river systems of North America and have long been prized for caviar production. Declining wild populations and fishing prohibitions have created interest in the culture of these fish. Protein and energy are often the first nutrients examined when attempting to identify diets appropriate for a novel culture species. Therefore, the present study evaluated the effects of different dietary protein: energy ratios on Pallid Sturgeon growth and body composition. Twelve semipurified diets composed of four crude protein (CP) levels (32, 39, 46, and 53%) and three gross energy (GE) levels (3,600, 4,200, and 4,800 kcal/kg) were fed to 180 juvenile Pallid Sturgeon for 18 weeks. Diets were offered to triplicate groups of five fish each in separate tanks. Fish were fed 2% body weight daily and sampled every 3 weeks. Mean weight gain and body composition were significantly affected by GE content of the dietary treatment (P≤ 0.05), but not by dietary CP or protein and energy interactions (P> 0.05). The most energetically dense diets yielded significantly larger fish than the least energetically dense diets and the intermediate diets were not significantly different from either extreme. These results suggest that Pallid Sturgeon are able to perform similarly across a wide range of protein: energy ratios (79–147 mg protein/kcal), as long as adequate dietary energy (≥3,800 kcal GE/kg) is provided and essential amino acids are not limiting. This research is the first to evaluate dietary protein: energy ratios forScaphirhynchussturgeon culture.
Development of a Methodology for Intensive Larviculture of Atlantic Croakers
Authors: Lemus Jason T , Sarkisian Brie L , Lee Michael S , Bardon-Albaret Agnes , Saillant Eric A
Published: January 2014

The Atlantic Croaker Micropogonias undulatus (Sciaenidae) is a candidate species for marine baitfish aquaculture in the southeastern United States because of its high value and common use as live bait by recreational fishers. However, an efficient larviculture procedure has not been reported to date; development of such a procedure was the impetus for this study. Embryos were obtained from captive broodstock that were induced to spawn volitionally by using a single injection of a luteinizing hormone releasing hormone agonist. Larvae were cultured at low density (initial density = 6.4 larvae/L) via intensive culture methods, including the use of recirculating filtration systems and of rotifers, brine shrimp Artemia spp., and micropellets as larval foods. The trial was performed in six 1,100-L tanks at a salinity of 14–29‰, with average rearing temperatures of 23.6°C and 24.6°C. At the completion of the study (39 d posthatch), mean SLs were 24.7 mm (SE = 0.738) for larvae cultured at 24.6°C and 23.0 mm (SE = 0.624) for larvae cultured at 23.6°C. Mean survival at 39 d posthatch was 25.9% and did not differ significantly between temperature groups. This work demonstrated a successful methodology for intensive larviculture of Atlantic Croakers and can serve as a platform for the experimentation that will be necessary to develop economically viable procedures for intensive production of this species.
Transcriptional repression of hypoxia-inducible factor-1 (HIF-1) by the protein arginine methyltransferase PRMT1
Authors: Lafleur Véronique N. , Richard Stéphane , Richard Darren E.
Published: January 2014

Hypoxia-inducible factors (HIF-1 and HIF-2) are essential mediators for the adaptive transcriptional response of cells and tissues to low-oxygen conditions. Under hypoxia or when cells are treated with various nonhypoxic stimuli, the active HIF-α subunits are mainly regulated through increased protein stabilization. For HIF-1α, it is clear that further transcriptional, translational, and posttranslational regulations are important for complete HIF-1 activity. Novel evidence links hypoxia and HIF-1 to arginine methylation, an important protein modification. These studies suggest that arginine methyltransferases may be important for hypoxic responses. Protein arginine methyltransferase 1 (PRMT1), the predominant arginine methyltransferase, can act as a transcriptional activator or repressor by modifying a diverse set of substrates. In this work, we show that PRMT1 is a repressor of both HIF-1 and HIF-2. The cellular depletion of PRMT1 by small interference RNA targeting leads to increased HIF transcriptional activity. This activation is the result of enhanced HIF-α subunit transcription, which allows increased HIF-α subunit availability. We provide evidence that PRMT1-dependent HIF-1α regulation is mediated through the activities of both specificity protein 1 (Sp1) and Sp3, two transcription factors known to control HIF-1α expression. This study therefore identifies PRMT1 as a novel regulator of HIF-1– and HIF-2–mediated responses.
NAADP and the two-pore channel protein 1 participate in the acrosome reaction in mammalian spermatozoa
Authors: Arndt Lilli , Castonguay Jan , Arlt Elisabeth , Meyer Dorke , Hassan Sami , Borth Heike , Zierler Susanna , Wennemuth Gunther , Breit Andreas , Biel Martin , Wahl-Schott Christian , Gudermann Thomas , Klugbauer Norbert , Boekhoff Ingrid
Published: January 2014

The functional relationship between the formation of hundreds of fusion pores during the acrosome reaction in spermatozoa and the mobilization of calcium from the acrosome has been determined only partially. Hence, the second messenger NAADP, promoting efflux of calcium from lysosome-like compartments and one of its potential molecular targets, the two-pore channel 1 (TPC1), were analyzed for its involvement in triggering the acrosome reaction using a TPCN1 gene–deficient mouse strain. The present study documents that TPC1 and NAADP-binding sites showed a colocalization at the acrosomal region and that treatment of spermatozoa with NAADP resulted in a loss of the acrosomal vesicle that showed typical properties described for TPCs: Registered responses were not detectable for its chemical analogue NADP and were blocked by the NAADP antagonist trans-Ned-19. In addition, two narrow bell-shaped dose-response curves were identified with maxima in either the nanomolar or low micromolar NAADP concentration range, where TPC1 was found to be responsible for activating the low affinity pathway. Our finding that two convergent NAADP-dependent pathways are operative in driving acrosomal exocytosis supports the concept that both NAADP-gated cascades match local NAADP concentrations with the efflux of acrosomal calcium, thereby ensuring complete fusion of the large acrosomal vesicle.
MEMBPLUGIN: studying membrane complexity in VMD
Authors: Guixà-González Ramon , Rodriguez-Espigares Ismael , Ramírez-Anguita Juan Manuel , Carrió-Gaspar Pau , Martinez-Seara Hector , Giorgino Toni , Selent Jana
Published: January 2014

Summary: Computer simulations are giving way to more complex and accurate studies of biological membranes by molecular dynamics (MD) simulations. The analysis of MD trajectories comprises the biophysical characterization of membrane properties or the study of protein–lipid interactions and dynamics. However, there is a lack of automated tools to analyse MD simulations of complex membrane or membrane-protein systems. Here we present MEMBPLUGIN, a plugin for the Visual Molecular Dynamics package that provides algorithms to measure a host of essential biophysical properties in simulated membranes. MEMBPLUGIN features are accessible both through a user-friendly graphical interface and as command-line procedures to be invoked in analysis scripts.

Availability and implementation: MEMBPLUGIN is a VMD extension written in Tcl. Multi-platform source code, documentation and tutorials are freely available at http://membplugin.sourceforge.net.

Contact:  toni.giorgino@isib.cnr.it or jana.selent@upf.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape
Authors: Pupov Danil , Kuzin Ivan , Bass Irina , Kulbachinskiy Andrey
Published: January 2014

The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 that directly contacts promoter DNA immediately upstream of the RNAP active centre and occupies the RNA exit path. Analysis of the transcription effects of substitutions and deletions in this region in Escherichia coli σ70 subunit, performed in this work, suggests that (i) individual residues in the σ3.2 finger collectively contribute to RNA priming by RNAP, likely by the positioning of the template DNA strand in the active centre, but are not critical to promoter escape; (ii) the physical presence of σ3.2 in the RNA exit channel is important for promoter escape; (iii) σ3.2 promotes σ dissociation during initiation and suppresses σ-dependent promoter-proximal pausing; (iv) σ3.2 contributes to allosteric inhibition of the initiating NTP binding by rifamycins. Thus, region σ3.2 performs distinct functions in transcription initiation and its inhibition by antibiotics. The B-reader element of eukaryotic factor TFIIB likely plays similar roles in RNAPII transcription, revealing common principles in transcription initiation in various domains of life.
Transcriptome-wide investigation of genomic imprinting in chicken
Authors: Frésard Laure , Leroux Sophie , Servin Bertrand , Gourichon David , Dehais Patrice , Cristobal Magali San , Marsaud Nathalie , Vignoles Florence , Bed'hom Bertrand , Coville Jean-Luc , Hormozdiari Farhad , Beaumont Catherine , Zerjal Tatiana , Vignal Alain , Morisson Mireille , Lagarrigue Sandrine , Pitel Frédérique
Published: January 2014

Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
Adjacent single-stranded regions mediate processing of tRNA precursors by RNase E direct entry
Authors: Kime Louise , Clarke Justin E. , Romero A. David , Grasby Jane A. , McDowall Kenneth J.
Published: January 2014

The RNase E family is renowned for being central to the processing and decay of all types of RNA in many species of bacteria, as well as providing the first examples of endonucleases that can recognize 5′-monophosphorylated ends thereby increasing the efficiency of cleavage. However, there is increasing evidence that some transcripts can be cleaved efficiently by Escherichia coli RNase E via direct entry, i.e. in the absence of the recognition of a 5′-monophosphorylated end. Here, we provide biochemical evidence that direct entry is central to the processing of transfer RNA (tRNA) in E. coli, one of the core functions of RNase E, and show that it is mediated by specific unpaired regions that are adjacent, but not contiguous to segments cleaved by RNase E. In addition, we find that direct entry at a site on the 5′ side of a tRNA precursor triggers a series of 5′-monophosphate-dependent cleavages. Consistent with a major role for direct entry in tRNA processing, we provide additional evidence that a 5′-monophosphate is not required to activate the catalysis step in cleavage. Other examples of tRNA precursors processed via direct entry are also provided. Thus, it appears increasingly that direct entry by RNase E has a major role in bacterial RNA metabolism.
Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry
Authors: Vranken Charlotte , Deen Jochem , Dirix Lieve , Stakenborg Tim , Dehaen Wim , Leen Volker , Hofkens Johan , Neely Robert K.
Published: January 2014

We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).
Genetic and physical interaction of Ssp1 CaMKK and Rad24 14-3-3 during low pH and osmotic stress in fission yeast
Authors: Freitag Silja I. , Wong Jimson , Young Paul G.
Published: January 2014

The Ssp1 calmodulin kinase kinase (CaMKK) is necessary for stress-induced re-organization of the actin cytoskeleton and initiation of growth at the new cell end following division inSchizosaccharomyces pombe. In addition, it regulates AMP-activated kinase and functions in low glucose tolerance.ssp1−cells undergo mitotic delay at elevated temperatures and G2arrest in the presence of additional stressors. Following hyperosmotic stress, Ssp1-GFP forms transient foci which accumulate at the cell membrane and form a band around the cell circumference, but not co-localizing with actin patches. Hyperosmolarity-induced localization to the cell membrane occurs concomitantly with a reduction of its interaction with the 14-3-3 protein Rad24, but not Rad25 which remains bound to Ssp1. The loss ofrad24inssp1−cells reduces the severity of hyperosmotic stress response and relieves mitotic delay. Conversely, overexpression ofrad24exacerbates stress response and concomitant cell elongation.rad24−does not impair stress-induced localization of Ssp1 to the cell membrane, however this response is almost completely absent in cells overexpressingrad24.
Identification of genes essential for anaerobic growth of Listeria monocytogenes
Authors: Müller-Herbst Stefanie , Wüstner Stefanie , Mühlig Anna , Eder Daniela , M. Fuchs Thilo , Held Claudia , Ehrenreich Armin , Scherer Siegfried
Published: January 2014

The facultative anaerobic bacteriumListeria monocytogenesencounters microaerophilic or anaerobic conditions in various environments, e.g. in soil, in decaying plant material, in food products and in the host gut. To elucidate the adaptation ofListeria monocytogenesto variations in oxygen tension, global transcription analyses using DNA microarrays were performed. In total, 139 genes were found to be transcribed differently during aerobic and anaerobic growth; 111 genes were downregulated and 28 genes were upregulated anaerobically. The oxygen-dependent transcription of central metabolic genes is in agreement with results from earlier physiological studies. Of those genes more strongly expressed under lower oxygen tension, 20 were knocked out individually. Growth analysis of these knock out mutants did not indicate an essential function for the respective genes during anaerobiosis. However, even if not essential, transcriptional induction of several genes might optimize the bacterial fitness ofListeria monocytogenesin anaerobic niches, e.g. during colonization of the gut. For example, expression of the anaerobically upregulated genelmo0355, encoding a fumarate reductase α chain, supported growth on 10 mM fumarate under anaerobic but not under aerobic growth conditions. Genes essential for anaerobic growth were identified by screening a mutant library. Eleven out of 1360 investigated mutants were sensitive to anaerobiosis. All 11 mutants were interrupted in theatplocus. These results were further confirmed by phenotypic analysis of respective in-frame deletion and complementation mutants, suggesting that the generation of a proton motive force via F1F0-ATPase is essential for anaerobic proliferation ofListeria monocytogenes.