bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular dynamics simulation of effective thermal conductivity and study of enhanced thermal transport mechanism in nanofluids
Authors: Sarkar Suranjan , Selvam R. Panneer
Published: October 2007

Nanofluids have been proposed as a route for surpassing the performance of currently available heat transfer liquids in the near future. In this study an equilibrium molecular dynamics simulation was used to model a nanofluid system. The thermal conductivity of the base fluid and nanofluid was computed using the Green-Kubo method for various volume fractions of nanoparticle loadings. This study showed the ability of molecular dynamics to predict the enhanced thermal conductivity of nanofluids. Through molecular dynamics calculation of mean square displacements for liquid phase in base fluid and for liquid and solid phases in nanofluid, this study tried to investigate the mechanisms involved in thermal transport of nanofluids at the atomic level. The result showed that the thermal transport enhancement of nanofluids was mostly due to the increased movement of liquid atoms in the presence of nanoparticle. Diffusion coefficients were also calculated for base fluid and nanofluids. Similarity of enhancement in thermal conductivity and diffusion coefficient for nanofluids indicates similar transport process for mass and heat.
Characterization of hot wall grown silver phthalocyanine films
Authors: Gupta Himani , Bedi R. K. , Mahajan Aman
Published: October 2007

Silver phthalocyanine (AgPc) has attracted considerable interest because of its outstanding chemical stability, optical and electrical properties, and wide variety of potential applications in modern optical recording and optoelectronic devices. To improve the performance of devices based on AgPc, hot wall technique has been used to grow thin layers of AgPc onto the glass substrates kept at different temperatures in a vacuum of 10−5Torr. The films so obtained are annealed and studied for structural, electrical, and optical characterization. The x-ray diffraction and scanning electron microscopy pattern of these films show a crystalline behavior of films. The films deposited at higher substrate temperature suggest the formation of more ordered and crystalline films. An analysis of optical absorption measurements on the films indicates that the interband transition energies lie in the range 4.1–4.13eV.
Dependence of the dielectric permittivity of single-crystal quartz on thermal deformation at cryogenic temperatures
Authors: Hartnett John G. , Tobar Michael E. , Krupka Jerzy
Published: October 2007

The whispering gallery mode technique applied to single-crystal quartz has been used as a precise method to determine the dependence of the dielectric permittivity of pure single-crystal quartz on temperature-induced dimensional changes at cryogenic temperatures. The anisotropic temperature coefficients of permittivity (TCP) perpendicular and parallel to the crystal axis have been determined between 4.7 and 280 K. The difference between TCPs perpendicular and parallel to the crystal axis, near 17 GHz, between 160 and 300 K is approximately half the thermal expansion coefficient perpendicular to the crystal axis. Over this temperature range, the fractional change in the relative permittivity values perpendicular and parallel to the crystal axis, as a result of thermal expansion of the perpendicular dimension of the crystal, only differs by a small constant value.
Band offsets and growth mode of molecular beam epitaxy grown MgO (111) on GaN (0002) by x-ray photoelectron spectroscopy
Authors: Craft H. S. , Collazo R. , Losego M. D. , Mita S. , Sitar Z. , Maria J.-P.
Published: October 2007

MgO is a proposed dielectric for use as a tunneling barrier in devices integrating GaN and ferroelectric oxides. In this study, we present data regarding the growth mode and band offsets of MgO grown epitaxially on GaN (0002) surfaces using molecular beam epitaxy. Using in situ x-ray photoelectron spectroscopy (XPS) and molecular beam epitaxy, we determine, from sequential growth experiments, that the growth of MgO proceeds via the Volmer-Weber (three-dimensional) mode, and full coalescence of the film does not occur until approximately 12nm of MgO has been deposited. The observation of a three-dimensional growth mode is in agreement with previously published data. For the valence band offset, we find a value of 1.2±0.2eV, which corresponds to a 3.2eV conduction band offset. XPS measurements suggest a chemically abrupt interface and no effect on band lineup due to the slow coalescence behavior.
Auger recombination in InGaN measured by photoluminescence
Authors: Shen Y. C. , Mueller G. O. , Watanabe S. , Gardner N. F. , Munkholm A. , Krames M. R.
Published: October 2007

The Auger recombination coefficient in quasi-bulk InxGa1−xN (x∼9%–15%) layers grown on GaN (0001) is measured by a photoluminescence technique. The samples vary in InN composition, thickness, and threading dislocation density. Throughout this sample set, the measured Auger coefficient ranges from 1.4×10−30to2.0×10−30cm6s−1. The authors argue that an Auger coefficient of this magnitude, combined with the high carrier densities reached in blue and green InGaN∕GaN (0001) quantum well light-emitting diodes (LEDs), is the reason why the maximum external quantum efficiency in these devices is observed at very low current densities. Thus, Auger recombination is the primary nonradiative path for carriers at typical LED operating currents and is the reason behind the drop in efficiency with increasing current even under room-temperature (short-pulsed, low-duty-factor) injection conditions.
Review of zincblende ZnO: Stability of metastable ZnO phases
Authors: Ashrafi A. , Jagadish C.
Published: October 2007

Common II-VI compound semiconducting materials are stable thermodynamically with zincblende phase, while the II-O materials such as zinc oxide (ZnO) and beryllium oxide (BeO) are stable with wurtzite phase, and cadmium oxide (CdO) and magnesium oxide (MgO) are stable in rocksalt phase. This phase disharmony in the same material family laid a challenge for the basic physics and in practical applications in optoelectronic devices, where ternary and quaternary compounds are employed. Thermodynamically the zincblende ZnO is a metastable phase which is free from the giant internal electric fields in the [001] directions and has an easy cleavage facet in the ⟨110⟩ directions for laser cavity fabrication that combined with evidence for the higher optical gain. The zincblende materials also have lower ionicity that leads to the lower carrier scattering and higher doping efficiencies. Even with these outstanding features in the zincblende materials, the growth of zincblende ZnO and its fundamental properties are still limited. In this paper, recent progress in growth and fundamental properties of zincblende ZnO material has been reviewed.
Atomic-scale observation of the grain-boundary structure of Yb-doped and heat-treated silicon nitride ceramics
Authors: Ziegler A. , Cinibulk M. K. , Kisielowski C. , Ritchie R. O.
Published: October 2007

The effect of secondary sintering additives and/or a post-sintering heat treatment on the semicrystalline atomic structure of the intergranular phase in silicon nitride ceramics is investigated. Three different Yb-doped Si3N4 ceramic compositions are examined using a scanning transmission electron microscope, whereby the intergranular atomic structure is directly imaged with Ångstrom resolution. The resulting high-resolution images show that the atomic arrangement of the Yb takes very periodic positions along the interface between the intergranular phase and the matrix grains, and that a postsintering 1250°C heat treatment, as well as a change of the secondary sintering additives (Al2O3 vs SiO2), does not alter the atomic positions of Yb. This result has implications for the understanding of how the mechanical properties of ceramics are influenced by the presence of the nanoscale intergranular phase, and for associated computational modeling of its precise role and atomic structure.
Temperature-dependent photoemission spectroscopy study of RExC60 (RE=Yb and Sm) films
Authors: He Shaolong , Nakatake Masashi , Arita Masashi , Cui Xiaoyu , Qiao Shan , Namatame Hirofumi , Taniguchi Masaki , Li Haiyang , Li Hongnian
Published: October 2007

Temperature-dependent electronic structures of RExC60 (where RE denotes Yb and Sm) films have been studied by high-resolution photoemission spectroscopy (PES). Our results indicate that Yb5C60 is the only metallic phase among all the phases in Yb doped C60 films. For the Sm fullerides, PES results show that there is no Sm valence transition during the negative thermal expansion in Sm2.75C60 below 32K. The Sm valence state in Sm2.75C60 films is nearly +2 at room temperature and remains stable in the films down to 16K. In addition, the negative thermal expansion effect does not result any distinct change in valence-band electronic structures of Sm2.75C60.
Patterning-controlled morphology of spatially and dimensionally constrained oxide nanostructures
Authors: Pan Zixiao , Li Shuyou , Wang Zhaoyu , Yu Min-Feng , Dravid Vinayak P.
Published: October 2007

This letter reports a facile approach for morphologic control of complex oxide nanostructures patterned by “soft” electron beam lithography (soft-eBL). The authors demonstrate fabrication of epitaxial nanofrustum and nanopyramidal morphologies of ferroelectric BaTiO3 and magnetic CoFe2O4 lines, with controlled zig-zag or smooth edges. The dimensional and shape control is achieved by simply tuning the patterning parameters such as resist thickness and patterning directions with respect to underlying substrate orientation. The crystal orientation, element distribution, and piezoelectric behavior of BaTiO3 nanofrustums are evaluated with analytical transmission electron microscopy and piezoresponse force microscopy. It is argued that soft-eBL allows for exquisite control over morphology, shape evolution, and orientation of zero- and one-dimensional nanostructures akin to what has been possible in the past with semiconductor heterostructures by thin film approaches.
Simple Penning ion source for laboratory research and development applications
Authors: Rovey Joshua L. , Ruzic Brandon P. , Houlahan Thomas J.
Published: October 2007

A simple Penning ion generator (PIG) that can be easily fabricated with simple machining skills and standard laboratory accessories is described. The PIG source uses an iron cathode body, samarium cobalt permanent magnet, stainless steel anode, and iron cathode faceplate to generate a plasma discharge that yields a continuous 1mA beam of positively charged hydrogen ions at 1mTorr of pressure. This operating condition requires 5.4kV and 32.4W of power. Operation with helium is similar to hydrogen. The ion source is being designed and investigated for use in a sealed-tube neutron generator; however, this ion source is thoroughly described so that it can be easily implemented by other researchers for other laboratory research and development applications.
Tuning the photoresponse of quantum dot infrared photodetectors across the 8–12μm atmospheric window via rapid thermal annealing
Authors: Aivaliotis P. , Zibik E. A. , Wilson L. R. , Cockburn J. W. , Hopkinson M. , Airey R. J.
Published: October 2007

We report on wide spectral tunability of narrow-band (Δλ∕λ∼12%) InAs∕In0.15Ga0.85As∕GaAs quantum dot-in-a-well infrared photodetectors using postgrowth rapid thermal annealing. The well resolved absorption and photocurrent peaks shift from 8to11.6μm by annealing the devices at 800°C for up to 4min. Upon annealing, the dot confinement potential becomes shallower and the tunneling probability increases, resulting not only in an increased responsivity but also in an increased dark current. The combined effect is to reduce detector detectivity from 1.1×1010cmHz1∕2W−1 at 8μmto3×109cmHz1∕2W−1 at 11μm (T=77K). Our results demonstrate that spectral tunability from 8to12μm can be achieved while maintaining good detector performance.
Characterization of metal-ferroelectric (BiFeO3)-insulator (ZrO2)-silicon capacitors for nonvolatile memory applications
Authors: Chiang Yu-Wei , Wu Jenn-Ming
Published: October 2007

The electric properties of ferroelectric BiFeO3 (BFO) thin films with ZrO2 insulating buffer on Si substrates fabricated by chemical solution deposition were investigated. ZrO2 demonstrates excellent insulating properties on Si substrates. The metal-ferroelectric-insulator-semiconductor (MFIS) structure exhibits clockwise capacitance-voltage hysteresis loops due to the ferroelectric polarization of BFO. The maximum memory windows are 0.66 and 0.78V, respectively, for BFO deposited on postannealed ZrO2 and on unannealed ZrO2 insulating layers. The small memory window of the BFO∕ZrO2 (postannealed) MFIS is caused by significant interface trap states on the BFO∕ZrO2 interface; this is supported by C-V measurements under varying frequency.
Two-layered metallic film induced surface plasmons for enhanced optical propulsion of microparticles
Authors: Tan Y. Y. , Yuan X.-C. , Ong B. H. , Bu J. , Lin Q. Y.
Published: October 2007

We demonstrate the use of surface plasmons (SPs) excited on a two-layered metallic film for enhanced particle propulsion. The extended SP field is predominantly attributed to propel particles with increased speed along metal-deposited regions. Various silver-gold combinations were used to quantify for the SP field enhancement. The underlying silver yields better SP evanescent field enhancement, while the overlying gold ensures that the stability of the sensing surface is not compromised. In comparison to the conventional single gold film SP resonance configuration for particle manipulation, the two-layered metallic structure enhances the propulsive force, as verified experimentally by ∼2.0 times increase in particle velocities.
Ferroelectric properties of lead zirconate titanate under radial load
Authors: Granzow T. , Leist Th. , Kounga A. B. , Aulbach E. , Rödel J.
Published: October 2007

Ferroelectric and ferroelastic properties are closely entwined in piezoelectric perovskites. Research on this topic has been mostly limited to collinear action of electric field and mechanical load. Here, the effect of a radial mechanical load and an axial electric field applied simultaneously to a cylindrical lead zirconate titanate sample is investigated. The dielectric constant after poling under load indicates that domain wall movement is facilitated, while the number of domain walls is reduced. Hysteresis measurements show that the remnant polarization and coercive field depend characteristically on the load, with a clear behavior change at the ferroelastic coercive stress.
Vacancy clusters in ultrafine grained Al by severe plastic deformation
Authors: Wu X. L. , Li B. , Ma E.
Published: October 2007

Bulk nanostructured metals are often formed via severe plastic deformation (SPD). The dislocations generated during SPD evolve into boundaries to decompose the grains. Vacancies are also produced in large numbers during SPD, but have received much less attention. Using transmission electron microscopy, here we demonstrate a high density of unusually large vacancy Frank loops in SPD-processed Al. They are shown to impede moving dislocations and should be a contributor to strength.
Enhanced Curie temperature and spin polarization in Mn4FeGe3
Authors: Chen T. Y. , Chien C. L. , Petrovic C.
Published: October 2007

Intermetallic ferromagnetic compound Mn5Ge3, with Curie temperature TC=296K, a spin polarization of P=42%, and a good lattice match to semiconductors, is a potential spin injector for spintronics. We report the enhanced magnetic properties and spin polarization of Mn4FeGe3. By replacing one Mn atom in Mn5Ge3 with Fe, the TC of Mn4FeGe3 has been enhanced to 319.50K, while still maintaining the same crystal structure, high electrical conductivity, and a high residual resistivity ratio of 5.33. More importantly, the spin polarization in excess of 60% of Mn4FeGe3, much higher than that of Mn5Ge3, has been realized.
Modeling and the signal-to-noise ratio research of magnetoelectric sensors at low frequency
Authors: Xing Zengping , Li Jiefang , Viehland Dwight
Published: October 2007

The authors have modeled magnetoelectric (ME) laminate sensor units by considering both the ME laminate and detection circuitry. Theory predicts and experiments confirm that the signal-to-noise ratio increases with increasing frequency in the low frequency range. Our findings provide useful insights into ME sensitivity estimation and “real-world” low frequency magnetic anomaly detection by ME sensors.
Optical properties of air-stable semiconducting copolymer based on polythiophene
Authors: Shimizu Yusuke , Kobayashi Takashi , Nagase Takashi , Naito Hiroyoshi
Published: October 2007

Optical properties of thiophene based copolymer poly(2,5-bis(3-dodecylthiophen-2-yl)thieno[2,3-b]thiophene) (pBTCT) thin films have been investigated by means of optical absorption, photoluminescene (PL), PL quantum efficiency, time-resolved PL, and electroluminescence measurements. It is found that pBTCT exhibits relatively higher PL quantum efficiency (ϕPL∼16%) in solid state than poly(3-hexylthiophene) (P3HT). Although the PL quantum efficiency is relatively higher, the transition dipole moment of the lowest excited state of pBTCT is not large, as found in P3HT. The electroluminescence from pBTCT light-emitting diodes is observed and its spectrum is essentially the same as the PL spectrum of pBTCT.
Ab initio study of the effects of thin CsI coatings on the work function of graphite cathodes
Authors: Vlahos Vasilios , Booske John H. , Morgan Dane
Published: October 2007

Cesium-iodide (CsI)-coated graphite cathodes are promising electron sources for high power microwave generators, but the mechanism driving the improved emission is not well understood. Therefore, an ab initio modeling investigation on the effects of thin CsI coatings on graphite has been carried out. It is demonstrated that the CsI coatings reduce the work function of the system significantly through a mechanism of induced dipoles. The results suggest that work function modification is a major contribution to the improved emission seen when CsI coatings are applied to C.
Territorial Justice and Neighbourhood Environmental Services: A Comparison of Provision to Deprived and Better-off Neighbourhoods in the UK
Authors: Hastings Annette
Published: October 2007

Do the poorest neighbourhoods receive the poorest environmental services? This paper explores whether local environmental service provision in the UK achieves ‘territorial justice’ with respect to deprived and nondeprived neighbourhoods within cities. Territorial justice is argued to pertain when the distribution of service provision to neighbourhoods reflects levels of need for the service. Focusing on the provision of street-level environmental services in four British local authorities, the paper shows that poor and better-off neighbourhoods have different levels of need for environmental services. It then examines whether the services provided are commensurate with variations in need, using observed cleanliness levels within the neighbourhoods to assess this. The author argues that—despite an increasing policy and practice focus on targeting public services towards deprived neighbourhoods in the UK—environmental service provision does not yet take full account of the complex needs of poor places, meaning that they tend to be dirtier than their more affluent counterparts.
EU Cohesion Policy and the Role of the Regions: Investigating the Influence of Structural Funds in the New Member States
Authors: Bachtler John , McMaster Irene
Published: October 2007

This paper undertakes a critical assessment of the influence of the EU Cohesion policy on regionalisation and the role of regional institutions in Central and Eastern Europe. It addresses questions that are central to ongoing theoretical debates about the role of the region in the new member states. Have the powers and resources of the regions been strengthened by their involvement in EU support programmes? Are regions increasingly involved in integrated ‘bottom-up’ responses to regional development challenges? The paper offers a fresh perspective on these issues, with a cross-national analysis of practical experience in the postenlargement period and a detailed assessment of the technical, variable, and complex reality of working with EU Structural Funds. A distinctive approach of the analysis is to disaggregate the stages of Structural Funds programme management and delivery, thereby highlighting the varied nature of regional involvement in Structural Funds. Ultimately, the paper questions the notion that Structural Funds build regional structures and competence, and lead to ‘stronger regions’. Instead, it is argued that there is no guarantee that the Structural Funds will necessarily promote regionalisation in Central and Eastern Europe, at least in the short to medium terms.
Community Participation: Using Social Network Analysis to Improve Developmental Benefits
Authors: Holman Nancy
Published: October 2007

Current British government policy leans heavily toward a participatory approach to urban development. The alleged benefits range from the growth of trust and social capital to better policy delivery and implementation involving a greater range of actors in the policy process. Yet, in many cases, poorly carried out partnership and participatory efforts can produce outcomes directly opposite to the benefits listed above. The author examines participation as a structural phenomenon and in doing so offers insights into how relationships could be strengthened in order to avoid these negative outcomes. Social network analysis is used to examine the structural relationships found within an urban redevelopment project in Portsmouth, England. Through the application of these measures, a number of relational patterns emerged which were not conducive to participation and left community groups feeling overwhelmed and underrepresented. The author concludes by noting how this technique could be used not only to highlight network imbalances, as seen in the case study, but also to offer community groups proactive advice in developing their network ties and communication structures, thus improving their overall position within the network and helping to deliver better levels of trust and social capital to the process.
Stimulus-dependent differential regulation in the
Escherichia coli
PhoQ–PhoP system
Authors: Miyashiro Tim , Goulian Mark
Published: October 2007

In
Escherichia coli
,
Salmonella
, and related bacteria, the PhoQ–PhoP system regulates the expression of a large collection of genes in response to conditions of low magnesium or to the presence of certain antimicrobial peptides. We measured transcription of four PhoP-regulated promoters in
E. coli
that have significantly different PhoP-binding sites. Surprisingly, three promoters show identical responses to magnesium concentrations that range over four orders of magnitude. By analyzing and testing a simple model of transcriptional regulation, we find an explanation for this puzzle and show that these promoters are indeed differentially regulated at sufficiently high levels of stimulus. We then use this analysis to infer an effective level of phosphorylated PhoP as a function of magnesium stimulus. Our results demonstrate that differential regulation generally depends on the strength of the stimulus and highlight how quantitative analysis of stimulus–response curves can be used to infer properties of cell regulatory circuits that cannot be easily obtained from
in vitro
measurements.
Category-specific attention for animals reflects ancestral priorities, not expertise
Authors: New Joshua , Cosmides Leda , Tooby John
Published: October 2007

Visual attention mechanisms are known to select information to process based on current goals, personal relevance, and lower-level features. Here we present evidence that human visual attention also includes a high-level category-specialized system that monitors animals in an ongoing manner. Exposed to alternations between complex natural scenes and duplicates with a single change (a change-detection paradigm), subjects are substantially faster and more accurate at detecting changes in animals relative to changes in all tested categories of inanimate objects, even vehicles, which they have been trained for years to monitor for sudden life-or-death changes in trajectory. This animate monitoring bias could not be accounted for by differences in lower-level visual characteristics, how interesting the target objects were, experience, or expertise, implicating mechanisms that evolved to direct attention differentially to objects by virtue of their membership in ancestrally important categories, regardless of their current utility.
Two electrical potential–dependent steps are required for transport by the Escherichia coli Tat machinery
Authors: Bageshwar Umesh K. , Musser Siegfried M.
Published: October 2007

The twin-arginine translocation (Tat) pathway in Escherichia coli transports fully folded and assembled proteins across the energy-transducing periplasmic membrane. In chloroplasts, Tat transport requires energy input only from the proton motive force. To elucidate the mechanism and energetics of bacterial Tat protein transport, we developed an efficient in vitro transport assay using TatABC-enriched inverted membrane vesicles and the physiological precursor pre-SufI. We report transport efficiencies of 60–80% for nanomolar pre-SufI concentrations. Dissipation of the pH gradient does not reduce pre-SufI transport efficiency. Instead, pre-SufI transport requires at least two electrical potential (Δψ)–dependent steps that differ in both the duration and minimum magnitude of the required Δψ. The data are consistent with a model in which a substantial Δψ of short duration is required for an early transport step, and in which a small Δψ of long duration is necessary to drive a later transport step.
JAK1–STAT1–STAT3, a key pathway promoting proliferation and preventing premature differentiation of myoblasts
Authors: Sun Luguo , Ma Kewei , Wang Haixia , Xiao Fang , Gao Yan , Zhang Wei , Wang Kepeng , Gao Xiang , Ip Nancy , Wu Zhenguo
Published: October 2007

Skeletal muscle stem cell–derived myoblasts are mainly responsible for postnatal muscle growth and injury-induced muscle regeneration. However, the cellular signaling pathways controlling the proliferation and differentiation of myoblasts are not fully understood. We demonstrate that Janus kinase 1 (JAK1) is required for myoblast proliferation and that it also functions as a checkpoint to prevent myoblasts from premature differentiation. Deliberate knockdown of JAK1 in both primary and immortalized myoblasts induces precocious myogenic differentiation with a concomitant reduction in cell proliferation. This is caused, in part, by an accelerated induction of MyoD, myocyte enhancer–binding factor 2 (MEF2), p21Cip1, and p27Kip1, a faster down-regulation of Id1, and an increase in MEF2-dependent gene transcription. Downstream of JAK1, of all the signal transducer and activator of transcriptions (STATs) present in myoblasts, we find that only STAT1 knockdown promotes myogenic differentiation in both primary and immortalized myoblasts. Leukemia inhibitory factor stimulates myoblast proliferation and represses differentiation via JAK1–STAT1–STAT3. Thus, JAK1–STAT1–STAT3 constitutes a signaling pathway that promotes myoblast proliferation and prevents premature myoblast differentiation.
p66Shc mediates anoikis through RhoA
Authors: Ma Zhenyi , Myers David P. , Wu Ru Feng , Nwariaku Fiemu E. , Terada Lance S.
Published: October 2007

Detachment of parenchymal cells from a solid matrix switches contextual cues from survival to death during anoikis. Marked shape changes accompany detachment and are thought to trigger cell death, although a working model to explain the coordination of attachment sensation, shape change, and cell fate is elusive. The constitutive form of the adapter Shc, p52Shc, confers survival properties, whereas the longer p66Shc signals death through association with cytochrome c. We find that cells that lack p66Shc display poorly formed focal adhesions and escape anoikis. However, reexpression of p66Shc restores anoikis through a mechanism requiring focal adhesion targeting and RhoA activation but not an intact cytochrome c–binding motif. This pathway stimulates the formation of focal adhesions and stress fibers in attached cells and tension-dependent cell death upon detachment. p66Shc may thus report attachment status to the cell by imposing a tension test across candidate anchorage points, with load failure indicating detachment.
Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies
Authors: Hoyle Nathaniel P. , Castelli Lydia M. , Campbell Susan G. , Holmes Leah E.A. , Ashe Mark P.
Published: October 2007

Cytoplasmic RNA granules serve key functions in the control of messenger RNA (mRNA) fate in eukaryotic cells. For instance, in yeast, severe stress induces mRNA relocalization to sites of degradation or storage called processing bodies (P-bodies). In this study, we show that the translation repression associated with glucose starvation causes the key translational mediators of mRNA recognition, eIF4E, eIF4G, and Pab1p, to resediment away from ribosomal fractions. These mediators then accumulate in P-bodies and in previously unrecognized cytoplasmic bodies, which we define as EGP-bodies. Our kinetic studies highlight the fundamental difference between EGP- and P-bodies and reflect the complex dynamics surrounding reconfiguration of the mRNA pool under stress conditions. An absence of key mRNA decay factors from EGP-bodies points toward an mRNA storage function for these bodies. Overall, this study highlights new potential control points in both the regulation of mRNA fate and the global control of translation initiation.
Opposing activities of two novel members of the IL-1 ligand family regulate skin inflammation
Authors: Blumberg Hal , Dinh Huyen , Trueblood Esther S. , Pretorius James , Kugler David , Weng Ning , Kanaly Suzanne T. , Towne Jennifer E. , Willis Cynthia R. , Kuechle Melanie K. , Sims John E. , Peschon Jacques J.
Published: October 2007

The interleukin (IL)-1 family members IL-1α, -1β, and -18 are potent inflammatory cytokines whose activities are dependent on heterodimeric receptors of the IL-1R superfamily, and which are regulated by soluble antagonists. Recently, several new IL-1 family members have been identified. To determine the role of one of these family members in the skin, transgenic mice expressing IL1F6 in basal keratinocytes were generated. IL1F6 transgenic mice exhibit skin abnormalities that are dependent on IL-1Rrp2 and IL-1RAcP, which are two members of the IL-1R family. The skin phenotype is characterized by acanthosis, hyperkeratosis, the presence of a mixed inflammatory cell infiltrate, and increased cytokine and chemokine expression. Strikingly, the combination of the IL-1F6 transgene with an IL1F5 deficiency results in exacerbation of the skin phenotype, demonstrating that IL-1F5 has antagonistic activity in vivo. Skin from IL1F6 transgenic, IL1F5−/− pups contains intracorneal and intraepithelial pustules, nucleated corneocytes, and dilated superficial dermal blood vessels. Additionally, expression of IL1RL2, -1F5, and -1F6 is increased in human psoriatic skin. In summary, dysregulated expression of novel agonistic and antagonistic IL-1 family member ligands can promote cutaneous inflammation, revealing potential novel targets for the treatment of inflammatory skin disorders.
Thymic emigration revisited
Authors: McCaughtry Tom M. , Wilken Matthew S. , Hogquist Kristin A.
Published: October 2007

Conventional αβ T cell precursors undergo positive selection in the thymic cortex. When this is successful, they migrate to the medulla and are exposed to tissue-specific antigens (TSA) for purposes of central tolerance, and they undergo maturation to become functionally responsive T cells. It is commonly understood that thymocytes spend up to 2 wk in the medulla undergoing these final maturation steps before emigrating to peripheral lymphoid tissues. In addition, emigration is thought to occur via a stochastic mechanism whereby some progenitors leave early and others leave late—a so-called “lucky dip” process. However, recent research has revealed that medullary thymocytes are a heterogeneous mix of naive αβ T cell precursors, memory T cells, natural killer T cells, and regulatory T cells. Given this, we revisited the question of how long it takes naive αβ T cell precursors to emigrate. We combined the following three approaches to study this question: BrdU labeling, intrathymic injection of a cellular tag, and RAG2p-GFP reporter mice. We established that, on average, naive αβ T cell precursors emigrate only 4–5 d after becoming single-positive (SP) thymocytes. Furthermore, emigration occurs via a strict “conveyor belt” mechanism, where the oldest thymocytes leave first.
Estimating and decomposing total uncertainty for survey-based abundance estimates of Norwegian spring-spawning herring
Authors: Løland Anders , Aldrin Magne , Ona Egil , Hjellvik Vidar , Holst Jens Christian
Published: October 2007

Løland, A., Aldrin, M., Ona, E., Hjellvik, V., and Holst, J. C. 2007. Estimating and decomposing total uncertainty for survey‐based abundance estimates of Norwegian spring‐spawning herring. – ICES Journal of Marine Science, 64: –. A method is developed to quantify the uncertainty of abundance and age-specific abundance estimates of Norwegian spring-spawning herring, accounting for the combined effect of several error sources. We present an abundance estimate adjusted for vessel avoidance, acoustic shadowing, and depth-dependent target strength, and highlight the potentially dramatic combined effect of these adjustments. Uncertainty in this estimate is affected by the precision of the adjustment formulae as well as by the sampling errors in acoustic and trawl measurements. This total uncertainty is decomposed into contributions from each source. Here, the method is applied to data from surveys on the overwintering stock in the Vestfjord system and off Vesteraalen in northern Norway in November/December of the years 2001–2004.
Modelling the growth, mortality, and predation interactions of cod juveniles and capelin larvae in the Barents Sea using a novel proto-moment population dynamics model
Authors: Hallfredsson Elvar H. , Pope John G.
Published: October 2007

Hallfredsson, E. H., and Pope, J. G. 2007. Modelling the growth, mortality, and predation interactions of cod juveniles and capelin larvae in the Barents Sea using a novel proto-moment population dynamics model. – ICES Journal of Marine Science, 64: 1313–1323. Proto-moments of a fish population, the sums of products of powers of length with numbers at length, relate both to the traditional statistical measures, the mean, the variance, the skewness, and the kurtosis of their size distribution, and to the biologically important measures of the abundance and the biomass of the population. Population models based on this approach are constructed as matrix delay-difference equations. They model moments of the length distributions rather than the age distributions, and express population dynamic problems in an analytically tractable form. Here, a modification of this approach is explored for a case involving a predator–prey relationship among young-of-the-year fish. The modelled species are juvenile cod (the predator) and capelin larvae (the prey) in the Barents Sea. Their population dynamics are modelled by the proto-moment method, but using two different approaches for the derivation of the predation mortality term. The first approach, a published matrix-based formulation, is formed purely in terms of the proto-moments. The second approach, developed here, converts the proto-moments back to consistent size distributions to calculate the rates of predation mortality on each proto-moment. The latter model produces a realistic development in time for the predator and prey length distributions, density in numbers, and biomass for their first summer. It also provides estimates of growth for both species along with estimates of the predation mortality that cod generate on capelin in this time period. The estimates permitted the accuracy of the matrix-based approach to be investigated, better understood, and improved.
Wheat Proteins Extracted from Flour and Batter with Aqueous Ethanol at Subambient Temperatures
Authors: Robertson George H. , Cao Trung K. , Orts William J.
Published: October 2007

Contact of wheat flour with aqueous ethanol may enrich protein by starch displacement or deplete protein by extraction depending on 1) extraction conditions and 2) the form of the substrate. Extraction at subambient temperatures has not been described for specific gliadins for either dry flour with the protein in native configurations or for wet, developed batter or dough. This limits the ability to interpret technologies such as the cold‐ethanol method. Here, we describe specific albumin and gliadin composition of flour extracts by capillary zone electrophoresis CZE in 0–100% (v/v) ethanol from –12 to 22°C. Extraction was reduced for albumin and gliadin protein as the temperature was reduced and the concentration range for extraction narrowed. Extraction dropped precipitously between 0 and –7°C for both albumins and gliadins. Electrophoretically defined gliadins extracted in constant proportion at 22°C and 30–80%(v/v) ethanol, but at lower temperature, the α‐gliadins were enriched and β‐gliadins depleted in the 30–55% (v/v) range. For extracts from wheat flour batter, depletion of α and β and enrichment of γ relative to the dry flour contact suggested that the electrophoretically slow migrating γ‐ and ω‐proteins are less well incorporated to the dough matrix than electrophoretically fast migrating α and β types.
Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum
Authors: Jung Seo-Youn , Lee Mi-Hwa , Oh Tae-Kwang , Yoon Jung-Hoon
Published: October 2007

Two Gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, UMS-37T and UMS-40, were isolated from rhizosphere soil of wild edible greens cultivated on Ulleung island, Korea, and their taxonomic positions were investigated by a polyphasic approach. They grew optimally at 25–30 °C and contained Q-8 as the predominant ubiquinone. The major cellular fatty acids (>10 % of total fatty acids) were C16 : 0, cyclo C17 : 0 and C16 : 1
ω7c and/oriso-C15 : 0 2-OH. The DNA G+C contents of the two isolates were 59.8 and 60.0 mol%. Isolates UMS-37T and UMS-40 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 94 %; they exhibited 16S rRNA gene sequence similarity levels of 96.8–98.2 % to the type strains of recognized Herbaspirillum species. Phylogenetic analyses based on 16S rRNA gene sequences showed that isolates UMS-37T and UMS-40 formed a distinct phylogenetic lineage within the genus Herbaspirillum. DNA–DNA relatedness levels between isolates UMS-37T and UMS-40 and the type strains of some phylogenetically related Herbaspirillum species were in the range 3–56 %. On the basis of differences in phenotypic properties and phylogenetic distinctiveness and genomic data, isolates UMS-37T and UMS-40 were classified in the genus Herbaspirillum within a novel species, for which the name Herbaspirillum rhizosphaerae sp. nov. is proposed, with the type strain UMS-37T (=KCTC 12558T =CIP 108917T).
Desulfothermus okinawensis sp. nov., a thermophilic and heterotrophic sulfate-reducing bacterium isolated from a deep-sea hydrothermal field
Authors: Nunoura Takuro , Oida Hanako , Miyazaki Masayuki , Suzuki Yohey , Takai Ken , Horikoshi Koki
Published: October 2007

A novel thermophilic and heterotrophic sulfate-reducing bacterium, strain TFISO9T, was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV in the Southern Okinawa Trough. The cells were motile rods 2.5–5.0 μm in length and 0.6–0.9 μm in width. Strain TFISO9Twas an obligate heterotroph and reduced sulfate. It grew between 35 and 60 °C (optimum 50 °C), at pH 5.4–7.9 (optimum pH 5.9–6.4) and with 1.5–4.5 % NaCl (optimum 2.5 %). The fatty acid composition was C16 : 0(61.5 %) and 12Me16 : 0(38.5 %). The DNA G+C content was 34.9 mol%. The 16S rRNA gene sequence analysis indicated that strain TFISO9Tbelonged to the genusDesulfothermus.Based on physiological and phylogenetic characteristics, strain TFISO9Trepresents a novel species for which the nameDesulfothermus okinawensissp. nov. is proposed. The type strain is TFISO9T(=JCM 13304T=DSM 17375T).
Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China
Authors: Chen Yi-Guang , Cui Xiao-Long , Pukall Rüdiger , Li Hui-Ming , Yang Ya-Ling , Xu Li-Hua , Wen Meng-Liang , Peng Qian , Jiang Cheng-Lin
Published: October 2007

A novel yellow-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, obligately aerobic, moderately halophilic, facultatively alkaliphilic Gram-positive coccus, strain YIM Y15T, was isolated from a brine sample from a salt mine in Yunnan, south-west China. Strain YIM Y15Tgrew in the presence of 0.5–25 % (w/v) NaCl and at pH 6.0–10.0, with optimum growth at 8–10 % (w/v) NaCl and pH 8.0. It grew at 4–45 °C, with optimum growth at 37.0 °C. The major cellular fatty acids were anteiso-C15 : 0and iso-C15 : 0. Menaquinone 6 (MK-6) was the major respiratory quinone. The cell wall contained Lys and Gly. The DNA G+C content was 46.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that strain YIM Y15Twas a member of the genusSalinicoccus, with low 16S rRNA gene sequence similarity to the type strains of the five described species of the genus,Salinicoccus alkaliphilusJCM 11311T(sequence similarity 96.0 %),Salinicoccus roseusDSM 5351T(94.9 %),Salinicoccus jeotgaliKCTC 13030T(94.8 %),Salinicoccus salsiraiaeLMG 22840T(94.8 %) andSalinicoccus hispanicusDSM 5352T(94.7 %). Together with the phenotypic differences, these results supported the proposal of a novel species of the genusSalinicoccus,Salinicoccus kunmingensissp. nov., with YIM Y15T(=DSM 17847T=CGMCC 1.6302T) as the type strain.
Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena
Authors: Chantangsi Chitchai , Lynn Denis H. , Brandl Maria T. , Cole Jeffrey C. , Hetrick Neil , Ikonomi Pranvera
Published: October 2007

The mitochondrial cytochrome-coxidase subunit 1 (cox1) gene has been proposed as a DNA barcode to identify animal species. To test the applicability of thecox1gene in identifying ciliates, 75 isolates of the genusTetrahymenaand three non-Tetrahymenaciliates that are close relatives ofTetrahymena,Colpidium campylum,Colpidium colpodaandGlaucoma chattoni, were selected. All tetrahymenines of unproblematic species could be identified to the species level using 689 bp of thecox1sequence, with about 11 % interspecific sequence divergence. Intraspecific isolates ofTetrahymena borealis,Tetrahymena lwoffi,Tetrahymena patulaandTetrahymena thermophilacould be identified by theircox1sequences, showing <0.65 % intraspecific sequence divergence. In addition, isolates of these species were clustered together on acox1neighbour-joining (NJ) tree. However, strains identified asTetrahymena pyriformisandTetrahymena tropicalisshowed high intraspecific sequence divergence values of 5.01 and 9.07 %, respectively, and did not cluster together on acox1NJ tree. This may indicate the presence of cryptic species. The mean interspecific sequence divergence ofTetrahymenawas about 11 times greater than the mean intraspecific sequence divergence, and this increased to 58 times when all isolates of species with high intraspecific sequence divergence were excluded. This result is similar to DNA barcoding studies on animals, indicating that congeneric sequence divergences are an order of magnitude greater than conspecific sequence divergences. Our analysis also demonstrated low sequence divergences of <1.0 % between some isolates ofT. pyriformisandTetrahymena setosaon the one hand and some isolates ofTetrahymena furgasoniandT. lwoffion the other, suggesting that the latter species in each pair is a junior synonym of the former. Overall, our study demonstrates the feasibility of using the mitochondrialcox1gene as a taxonomic marker for ‘barcoding’ and identifyingTetrahymenaspecies and some other ciliated protists.
Phylogeny of the Mycoplasma mycoides cluster based on analysis of five conserved protein-coding sequences and possible implications for the taxonomy of the group
Authors: Manso-Silván Lucía , Perrier Xavier , Thiaucourt François
Published: October 2007

A phylogenetic tree of theMycoplasma mycoidescluster was inferred from a set of concatenated sequences from five housekeeping genes (fusA,glpQ,gyrB,lepAandrpoB). The relevance of this phylogeny was reinforced by detailed analysis of the congruence of the phylogenies derived from each of the five individual gene sequences. Two subclusters were distinguished. TheM. mycoidessubcluster comprisedM. mycoidessubsp.mycoidesbiotypes Small Colony (SC) and Large Colony (LC) andM. mycoidessubsp.capri. The latter two groups could not be clearly separated, which supports previous proposals that they be united into a single taxonomic entity. TheMycoplasma capricolumsubcluster includedM. capricolumsubsp.capricolum,M. capricolumsubsp.capripneumoniaeandMycoplasmasp. bovine group 7 of Leach, a group of strains that remains unassigned. This group constituted a distinct branch within this cluster, supporting its classification as a subspecies ofM. capricolum.Mycoplasma cottewiiandMycoplasma yeatsiiclustered in a group that was distinct fromMycoplasma putrefaciensand they were all clearly separated from theM. mycoidescluster. In conclusion, this approach has allowed us to assign phylogenetic positions to all members of theM. mycoidescluster and related species and has proved the need to adjust the existing taxonomy. Furthermore, this method may be used as a reference technique to assign an unequivocal position to any particular strain related to this cluster and may lead to the development of new techniques for rapid species identification.
Reclassification of Marinococcus albus Hao et al. 1985 as Salimicrobium album gen. nov., comb. nov. and Bacillus halophilus Ventosa et al. 1990 as Salimicrobium halophilum comb. nov., and description of Salimicrobium luteum sp. nov.
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: October 2007

A Gram-positive, non-motile, coccoid-shaped, non-spore-forming halophilic bacterial strain, BY-5T, was isolated from a marine solar saltern in Korea and its taxonomic position was investigated by using a polyphasic approach. The novel strain grew optimally at 37 °C and in the presence of 10 % (w/v) NaCl. Strain BY-5T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C content was 47.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BY-5T formed a coherent cluster with Bacillus halophilus and Marinococcus albus. Strain BY-5T exhibited 16S rRNA gene sequence similarity values of 98.7 and 97.4 % to the type strains of B. halophilus and M. albus, respectively. Strain BY-5T was distinguished from B. halophilus and M. albus by several phenotypic properties and DNA–DNA relatedness data. On the basis of the combined chemotaxonomic and phylogenetic data, it is proposed that M. albus, B. halophilus and strain BY-5T should be placed in a new genus as three separate species. Marinococcus albus and Bacillus halophilus are reclassified in a new genus, Salimicrobium gen. nov., as Salimicrobium album comb. nov. and Salimicrobium halophilum comb. nov., respectively. The type species of the new genus is Salimicrobium album. Strain BY-5T (=KCTC 3989T=CIP 108918T) is placed in the genus Salimicrobium as a novel species Salimicrobium luteum sp. nov.