bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial confinement effect on the atomic structure of solid argon
Authors: Nishio Kengo , Shinoda Wataru , Morishita Tetsuya , Mikami Masuhiro
Published: March 2005

Molecules confined in nanopores show unusual behavior not seen in bulk systems. The present paper reports on molecular dynamics simulations of unusual freezing behavior in confined Ar. Similar to bulk Ar, liquid Ar confined in pores with a diameter D>15σ (5.1nm), where σ is the diameter of the Ar atom, crystallizes when the cooling rate is lower than a critical value (Qc). We also find that the spatial confinement does not have significant influence on Qc when D>15σ (5.1nm). In the pore of 10σ (3.4nm) in diameter, on the other hand, the behavior is dramatically changed. Crystalline Ar does not appear inside the pore even when the system is cooled at a rate lower than the Qc in the bulk system by over two orders of magnitude. Instead, amorphous Ar characterized by local icosahedral configurations is formed in the pore. We further find that, even when crystalline Ar is formed outside the pore, it does not grow deeply into the pore. This supports that the amorphous Ar is actually the most stable phase in the pore. It is well known that Ar is a poor glass former. Our finding that even such an amorphous Ar is the most stable in the pore suggests that, in any system, it is possible to prepare amorphous structure selectively by using nano-molds.
Reduction of dust acoustic soliton amplitude due to dust charge variation
Authors: Moolla S. , Bharuthram R. , Baboolal S.
Published: March 2005

The effect of dust charge variation on dust acoustic solitons is investigated using the full charging equation, with exact expressions for the electron and ion currents. Reduction in the amplitude of the soliton profile in the presence of charge variation is found to be more significant for larger dust grains.
Modal analysis of microcantilever sensors with environmental damping
Authors: Dareing Don W. , Thundat Thomas , Jeon Sangmin , Nicholson Matthew
Published: March 2005

The vibration response of microcantilevers to simple harmonic base motion is formulated in terms of base motion plus modal responses relative to the moving base frame. Environmental damping is evaluated. The analysis gives the frequency responses of the first four modes and shows that the phase angle of each mode relative to the moving base frame is constant but that the phase angle of the absolute motion varies along the length of cantilevers. This finding is verified with experimental data. Phase changes along cantilevers depend on frequency ratios and the magnitude of environmental damping. Experimental data are used to establish damping factors, and phase angles are measured experimentally and compared with theoretical predictions.
Electronic control of nonresonant random lasing from a dye-doped smectic A* liquid crystal scattering device
Authors: Morris S. M. , Ford A. D. , Pivnenko M. N. , Coles H. J.
Published: March 2005

The electronic control of the excitation threshold for random lasing in a dye-doped smectic A* liquid crystal is demonstrated. Random lasing is the term given to the nonlinear amplification of light which is the result of feedback due to multiple scattering. With the application of an electric field the smectic A* phase forms a highly scattering texture for which the nonlinear amplification of light occurs at an excitation threshold of 10μJ∕pulse. In comparison, nonlinear amplification is not observed in the field induced homeotropic texture. As a result, a device has been conceived and demonstrated whereby random lasing is switched “on” or “off” with an applied electric field.
Measurement of single electron spin with submicron Hall magnetometer
Authors: Jin Jinshuang , Li Xin-Qi
Published: March 2005

Submicron Hall magnetometry has been demonstrated as an efficient technique to probe extremely weak magnetic fields. In this letter, we analyze the possibility of employing it to detect single electron spin. Signal strength and readout time are estimated and discussed with respect to a number of practical issues.
Is the lotus leaf superhydrophobic?
Authors: Cheng Yang-Tse , Rodak Daniel E.
Published: March 2005

Superhydrophobic surfaces have important technical applications ranging from self-cleaning window glasses, paints, and fabrics to low-friction surfaces. The archetype superhydrophobic surface is that of the lotus leaf. When rain falls on lotus leaves, water beads up with a contact angle in the superhydrophobic range of about 160°. The water drops promptly roll off the leaves collecting dirt along the way. This lotus effect has, in recent years, stimulated much research effort worldwide in the fabrication of surfaces with superhydrophobicity. But, is the lotus surface truly superhydrophobic? This work shows that the lotus leaves can be either hydrophobic or hydrophilic, depending on how the water gets on to their surfaces. This finding has significant ramifications on how to make and use superhydrophobic surfaces.
Activation volume for phosphorus diffusion in silicon and Si0.93Ge0.07
Authors: Zhao Yuechao , Aziz Michael J. , Zangenberg Nikolaj R. , Larsen Arne Nylandsted
Published: March 2005

The hydrostatic pressure dependence of the diffusivity of P in compressively strained Si0.93Ge0.07 and unalloyed Si has been measured. In both cases the diffusivity is almost independent of pressure, characterized by an activation volume V* of (+0.09±0.11) times the atomic volume Ω for the unalloyed Si, and (+0.01±0.06) Ω for Si0.93Ge0.07. The results are used in conjunction with the reported effect of biaxial strain on diffusion normal to the surface to test the prediction for an interstitialcy-based mechanism of Aziz’s phenomenological thermodynamic treatment of diffusion under uniform nonhydrostatic stress states. The prediction agrees well with measured behavior, lending additional credence to the interstitial-based mechanism and supporting the nonhydrostatic thermodynamic treatment.
Epitaxial DySi2 nanowire formation on stepped Si(111)
Authors: He Zhian , Smith David J. , Bennett P. A.
Published: March 2005

We report the growth of epitaxial DySi2 nanowires (NW) with a single orientation on miscut Si(111). Using high-resolution electron microscopy, we determine that the islands are hexagonal DySi2 with orientation DySi2(0001)‖Si(111), corresponding to a near-perfect lattice match. The NW islands develop extended defects that correlate perfectly with individual step bunches at the buried interface, produced during growth. By contrast, islands grown on step-free substrates develop a broad, two-dimensional shape with no defects. We suggest that the NW shape results from the energy cost of extended defects, which inhibits growth across step edges.
Diffusion and dissociation mechanisms of vacancy-oxygen complex in silicon
Authors: Furuhashi Masayuki , Taniguchi Kenji
Published: March 2005

We are examining diffusion mechanisms of the vacancy-oxygen complex (VO) in bulk Si using ab initio calculations based on a 64-atom supercell. We found two atomic mechanisms involved in the VO diffusion; one is caused by migration of an interstitial oxygen atom, another by migration of a vacancy. The energy barrier of the mechanism due to an oxygen migration is 2.02eV, and that caused by a vacancy migration is 1.98eV. These energy barriers are close to the experimental activation energy of 2.0eV required for the dissociation and diffusion of VO. The derived activation energies of the two mechanisms suggest that these mechanisms plausibly occur simultaneously. In addition, we clarify that the dissociation energy of VO, 1.85eV, is lower than the diffusion energy of VO.
Electronic and atomic structures of quasi-one-dimensional K0.3MoO3
Authors: Huang C. H. , Jan J. C. , Chiou J. W. , Tsai H. M. , Pao C. W. , Du C. H. , Pong W. F. , Tsai M.-H. , Tang M. T. , Lee J. J. , Lee J. F.
Published: March 2005

The electronic and atomic structures of quasi-one-dimensional blue bronze K0.3MoO3 were investigated by polarization-dependent O K-edge x-ray absorption near-edge structure (XANES) and Mo K-edge extended x-ray absorption fine structure (EXAFS) measurements at various temperature and applied voltages. The O K-edge XANES spectra suggest that the number of unoccupied O 2p–Mo 4d hybridized states increases and decreases with temperature, respectively, below and above a critical temperature of 180K. The along b-axis electric current measurements show a threshold applied voltage, beyond which the current increases rapidly. The Mo K-edge EXAFS measurements show that the Mo–O bond lengths are insensitive to the temperature even beyond 180K.
Dense arrays of Co nanocrystals epitaxially grown on ion-patterned Cu(110) substrates
Authors: Molle Alessandro , de Mongeot F. Buatier , Boragno C. , Moroni R. , Granone F. , Sekiba D. , Buzio R. , Valbusa U. , Felici R. , Quirós C.
Published: March 2005

We report on the growth of {111}-faceted Co nanocrystals endowed with fcc structure during multilayer epitaxial deposition on a flat Cu(110) substrate. Lateral ordering of the Co nanocrystals into a periodic array is achieved if the Co deposition is performed on a Cu(110) substrate, prepatterned by ion sculpting. While for low coverages the Co film growth is conformal, reproducing the underlying arrangement of the Cu substrate pattern, for film thicknesses above 16 monolayers, size-selected {111}-faceted Co nanocrystals nucleate in registry with the underlying pattern periodicity.
Transmission properties of terahertz pulses through an ultrathin subwavelength silicon hole array
Authors: Azad Abul K. , Zhao Y. , Zhang W.
Published: March 2005

We demonstrate extraordinary THz transmission of an array of subwavelength apertures patterned on ultrathin highly doped silicon by reactive ion etching. The zero-order transmission spectra exhibit well-defined maxima and minima which are attributed to the excitation of surface-plasmon polaritons and Wood’s anomaly. The transmission anisotropy is investigated with respect to the orientation of the elliptical hole array in the frequency range from 0.2to3.5THz, and we notice that the transmission increases significantly when the major axis of the elliptical hole is perpendicular to the polarization of THz beam. In addition, redshift and reduction in transmission amplitude are observed when the surrounding dielectric permittivity is increased.
Role of interface traps on breakdown process of a magnetic tunnel junction
Authors: Kim Kwang-Seok , Cho B. K.
Published: March 2005

Time dependent dielectric breakdown (TDDB) measurements were carried out for magnetic tunneling junctions (MTJs) with different electron trap densities at the interface between a bottom electrode and an insulating barrier. The TDDB shows a strong bias-polarity dependence, which becomes bigger with increasing trap density. In addition, the current creep before total dielectric breakdown consistently shows bias-polarity dependence. The polarity dependence of the breakdown in MTJs with an ultrathin tunneling barrier (15–20Å) is believed to be caused by precursor effect of the traps at the bottom interface, which enhances the trap generation rate in a tunneling barrier, resulting in acceleration of the breakdown process.
Long-wavelength light emission and lasing from InAs∕GaAs quantum dots covered by a GaAsSb strain-reducing layer
Authors: Liu H. Y. , Steer M. J. , Badcock T. J. , Mowbray D. J. , Skolnick M. S. , Navaretti P. , Groom K. M. , Hopkinson M. , Hogg R. A.
Published: March 2005

The effects of a thin GaAsSb strain-reducing layer on the optical properties of InAs∕GaAs quantum dots (QDs) are investigated. With increasing Sb composition, the room-temperature emission wavelength of the InAs QDs increases to ∼1.43μm. For Sb compositions above 14%, the system becomes Type II, with a decrease of the photoluminescence (PL) efficiency. At a composition of 14%, the room-temperature PL efficiency is maximized, and is also significantly enhanced when compared to that of conventional InGaAs-capped InAs QDs grown under the same conditions. Room-temperature ground-state lasing at 1.292μm is demonstrated for an InAs∕GaAsSb∕GaAs structure.
Design, fabrication, and characterization of a two-dimensional photonic-crystal symmetric Mach-Zehnder interferometer for optical integrated circuits
Authors: Tanaka Yu , Sugimoto Yoshimasa , Ikeda Naoki , Nakamura Hitoshi , Kanamoto Kyozo , Asakawa Kiyoshi , Inoue Kuon
Published: March 2005

We report on the design, fabrication, and optical characterization of a GaAs two-dimensional photonic-crystal-based symmetric Mach-Zehnder interferometer (PC-SMZ) aimed at all-optical switches in planar photonic integrated systems. The directional couplers that constitute the PC-SMZ interferometer prevent the occurrence of ring resonance which degrades the interference, and allow control pulses for the switching operation to be received. We show 50%- and 100%-power couplings from the transmission characteristics of the directional couplers, thus demonstrating their operation as 3-dB dividers in the PC-SMZ. We also show experimentally wavelength selectivity between signal and control pulses with a separation of ∼7nm. These results indicate that the structure is promising as an all-optical switch when a nonlinear material such as a quantum dot is introduced into both arms of the interferometer.
Dual ring laser emission of conducting polymers in microcapillary structures
Authors: Yoshida Y. , Nishimura T. , Fujii A. , Ozaki M. , Yoshino K.
Published: March 2005

We have demonstrated photopumped multimode laser emission from cylindrical microcavities of conducting polymer thin films, which were formed by deposition on the inside surface of the glass microcapillary with capillary action. The laser emission was characterized by narrow emission lines and a well-defined excitation threshold. We also fabricated dual ring cavities on inner and outer surfaces of microcapillaries, and laser emission from both sides of capillaries was observed by photopumping with one excitation source. Fabricating two cylindrical microcavities on inner and outer surfaces of the microcapillary by utilizing a different sort of conducting polymers, dual laser emissions, blue and red in color, were obtained concurrently.
Gate current leakage and breakdown mechanism in unpassivated AlGaN∕GaN high electron mobility transistors by post-gate annealing
Authors: Kim Hyeongnam , Lee Jaesun , Liu Dongmin , Lu Wu
Published: March 2005

Gate leakage/breakdown mechanism in unpassivated AlGaN∕GaN high electron mobility transistors (HEMTs) is investigated by performing temperature-dependent pulsed current–voltage (I–V) and current transient measurements of AlGaN∕GaN HEMTs without and with annealing after Schottky gate formation. After post-gate annealing, the devices exhibited significantly smaller gate leakage current and higher breakdown voltage even without any gate dielectrics or passivation layer. The temperature-dependent current transient measurements show that the current dispersion in the unannealed HEMTs is attributed to traps with an emission time constant (tE) of ∼0.5μs at 295 K and an activation energy of ∼38meV. On the contrary, the 20-min annealed devices have traps with tE of 21.6μs at 295 K and an activation energy of ∼0.31eV. The results suggest that the post-gate annealing removes shallow traps, and creates or activates deeper traps. We propose that the breakdown and gate leakage current is mainly due to the emission current from shallow traps in unpassivated AlGaN∕GaN HEMTs. The breakdown voltage improvement after the post-gate annealing is due to the removal of shallow traps near the Schottky gate metal∕AlGaN interface.
Generic concepts within hornworts: historical review, contemporary insights and future directions
Authors: Cargill D. Christine , Renzaglia Karen S. , Villarreal Juan Carlos , Duff R. Joel
Published: March 2005

Although the hornworts (anthocerotes) are a relatively small assemblage of approximately 150 species, generic boundaries and relationships within the group are controversial. The four prevailing classification schemes are based mainly on morphology and show little congruency. Here we set the foundation for contemporary phylogenetic and taxonomic studies by presenting an historical overview of generic concepts within the anthocerotes. An overview of recent morphological and molecular studies that concentrate on hornworts points to intuitive, novel relationships and a degree of diversity hitherto unknown in the group. Phylogenetically informative characters at the morphological level are identified, with emphasis on newly acquired ultrastructural data. A recent molecular analysis based on rbcL sequences is presented and the levels of suitability of several molecular markers to answer phylogenetic questions within the group are explored. On-going intensive studies that sample a wider range of species and utilise multiple genes and comprehensive morphological data are likely to revolutionise interpretations of the taxonomic relationships and character evolution within hornworts.
Majority rules, when systematists disagree
Authors: Entwisle Timothy J. , Weston Peter H.
Published: March 2005

The creation of Australia’s Virtual Herbarium forced the Australian plant systematics community to find a mechanism for deciding between alternative taxonomies. Following a workshop on the Orchidaceae and the publication of some simple draft guidelines, a set of ‘rules of thumb’ are presented here that we believe represent the view of most practising systematists. Not everyone will agree, and we have provided alternative views where possible. We include the need for monophyletic taxa, minimising taxonomic change, understanding that some taxa have strong ‘interest groups’, making it clear that ‘preferred name’ does not necessarily imply ‘best name’ on all criteria, avoiding epithets used in possible congeners, and the concept of ‘majority rules’ when states and territories have differing views.
Generic concepts in Australian mosses
Authors: Klazenga Niels
Published: March 2005

The impact of changes in generic concepts as a result of changes in philosophy and methodology associated with phylogenetic systematics on the taxonomy of Australian mosses is discussed. It is concluded that, while phylogenetic systematics has already had a significant impact on the taxonomy of Australian mosses, many taxonomic changes that have occurred in recent years are the result of an enormous taxonomic backlog that is being gradually eliminated. The relative impact of phylogenetic systematics is expected to increase in coming years.
Generic delimitation and phylogenetic uncertainty: an example from a group that has undergone an explosive radiation
Authors: Orthia L. A. , Cook L. G. , Crisp M. D.
Published: March 2005

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience.
What to do with Hibiscus? A proposed nomenclatural resolution for a large and well known genus of Malvaceae and comments on paraphyly
Authors: Pfeil B. E. , Crisp M. D.
Published: March 2005

The generic classification of Hibisceae has long been unstable. A new understanding of the phylogeny of Hibisceae has found that genera from three tribes (Decaschistieae, Hibisceae and Malvavisceae) are nested within Hibiscus. We discuss issues that impinge upon the classification of Hibiscus in a general sense, including the genus concept, monophyletic and paraphyletic taxa, the use of characters and phylogenies to define taxa, and the current ranked system (based on the International Code of Botanical Nomenclature) v. a rank free alternative (the PhyloCode). We conclude that genera are subjective constructs that are only real in the sense of their phylogenetic origins (i.e. the taxa they denote may be real discoverable monophyletic groups), that paraphyletic taxa are not necessary in classification, that overemphasis of ‘distinctive’ characters in preference to phylogenies leads to recognition of paraphyletic taxa, and that there is no objective fixed and discoverable rank for any taxon. While the PhyloCode avoids some of these problems, it fails to adequately provide an alternative to the mnemonically powerful and information rich Linnean binomial and its advantages do not, in our opinion, outweigh the utility of the ICBN system when the latter employs only monophyletic taxa. With these conclusions in mind, we offer a brief set of guidelines for higher level classification and apply this to Hibiscus. The severe paraphyly in Hibiscus means that no classification using the ICBN system with exclusively monophyletic taxa will be free of major nomenclatural changes. We argue that including over 200 species from several genera within a broadly defined Hibiscus causes fewer nomenclatural changes overall than do alternative schemes, while promoting stability and attempting to minimise change to well known species. A hybrid formal ranked and informal rank free system is discussed and proposed for this group. A series of rank free names that are nested within Hibiscus s.l. are proposed to convey information about membership of distinctive clades within Hibiscus s.l. in lieu of a complete ranked subgeneric classification that awaits more investigation.
An overview of Chara L. in Australia (Characeae, Charophyta)
Authors: Casanova Michelle T.
Published: March 2005

Charophytes (family Characeae) are a cohesive group within the green algae. The genus Chara is abundant and diverse in a variety of Australian habitats. Approximately 37 taxa of Chara have been described on the basis of Australian collections. The current status of charophyte taxonomy is confused. RD Wood revised Australian charophytes in 1972 on the basis of an erroneous species concept, and charophytes are rarely identified lower than genus by ecologists and water managers. Many species were described by overseas experts in the mid-1800s, and this trend continues to the present day. Typically, species descriptions have been based on examination of few specimens, and sometimes not even fertile representatives of each species. In this study Wood’s (1972) taxonomic treatment of Australian members of the genus Chara is examined and analysed in relation to historical species concepts and more recent experimental taxonomy and oospore morphology. Thorough studies based on determination of reliable indicators of genetic incompatibility through culture studies, including oospore morphology and genetic analysis and objective analysis of fertile specimens, are now required.
Phylogenetic analysis of the Australian Salicornioideae (Chenopodiaceae) based on morphology and nuclear DNA
Authors: Shepherd K. A. , Macfarlane T. D. , Waycott M.
Published: March 2005

The Salicornioideae Kostel. are distinctive among the Chenopodiaceae Venet.. However, their phylogenetic relationships are poorly understood. Analyses of morphological and molecular characters were undertaken to evaluate relationships within the subfamily and to test the monophyly of the endemic Australian genera Halosarcia Paul G. Wilson, Pachycornia Hook.f., Sclerostegia Paul G. Wilson, Tecticornia Hook.f. and Tegicornia Paul G. Wilson. Kalidium Moq. and Halopeplis Bunge ex Ung.-Sternb. of the tribe Halopeplideae were used as outgroup representatives in the morphological analysis and resolved sister to the tribe Salicornieae. Allenrolfea Kuntze; Halocnemum Bieb. and Heterostachys Meyer formed an early branching group sister to a moderately supported clade comprised of the remaining Salicornieae. Only terminal groups of closely related species received significant bootstrap support in this analysis. In contrast, the current tribal classification of the Salicornioideae was not supported in the molecular analysis as Allenrolfea occidentalis Kuntz (tribe Salicornieae) positioned sister to Kalidium foliatum Moq. (tribe Halopeplideae) and the remaining Salicornieae. Three major clades received strong bootstrap support: Microcnemum+Arthrocnemum, Sarcocornia+Salicornia, and the endemic Australian genera. None of the endemic Australian genera was individually supported as monophyletic in either the morphological or the molecular analyses. Subspecies complexes, polyploids and hybrids may contribute to the lack of resolution and apparently high levels of homoplasy in the morphological analysis. A greater understanding of population level processes is required to begin to resolve the phylogeny of this complex group.
Patterns of evolution in Australian Mimulus and related genera (Phrymaceae~Scrophulariaceae): a molecular phylogeny using chloroplast and nuclear sequence data
Authors: Beardsley Paul M. , Barker William R.
Published: March 2005

The aim of this work was to develop rigorous phylogenetic hypotheses for the mostly Australian species of Mimulus, Glossostigma, Peplidium, Microcarpaea and Elacholoma (Phrymaceae sensu Beardsley and Olmstead 2002), and to use the phylogeny to explore morphological patterns of evolution. Chloroplast trnL/F and nuclear ribosomal internal and external transcribed spacer sequence data were used to analyse phylogenetic relationships. The results of these analyses confirmed the following conclusions proposed in previous morphological analyses: (1) Glossostigma and Peplidium are supported as monophyletic groups, although support is weak for Peplidium; (2) Australian endemic Elacholoma, in the past of uncertain family placement, is embedded within the same clade as the former two genera despite its unique pair of terete stigmatic lobes; (3) a relatively recent dispersal event from Australia to Iraq and the Middle East for P. maritimum is inferred; (4) a reduction in stamen number from four to two has evolved independently several times in Glossostigma, Peplidium, Microcarpaea and Elacholoma; (5) a switch to an obligately autogamous breeding system has evolved several times independently in the group. New findings include the following: (1) Glossostigma, Peplidium, Microcarpaea and Elacholoma are derived from within Mimulus; (2) Mimulus prostratus is part of a clade that contains Elacholoma and Glossostigma, and this clade is not a part of the same clades as other Mimulus species in Australia; (3) there is some support for Microcarpaea being sister to a clade including Elacholoma, Mimulus prostratus, Glossostigma and Peplidium. The discovery that four mostly Australian genera are derived from within the mostly western North American genus Mimulus has important implications for generic assignments. Phylogenetic interpretations of additional morphological character transformations are discussed.
Intracellular
Helicobacter pylori
in gastric epithelial progenitors
Authors: Oh Jung D. , Karam Sherif M. , Gordon Jeffrey I.
Published: March 2005

Helicobacter pylori
is generally viewed as an extracellular pathogen. We have analyzed the tropism of
H. pylori
clinical isolates in a gnotobiotic transgenic mouse model of human chronic atrophic gastritis, a preneoplastic condition. These mice lack acid-producing parietal cells and have an amplified population of dividing gastric epithelial progenitors (GEPs) that express NeuAcα2,3Galβ1,4-glycans recognized by
H. pylori
adhesins. Scanning confocal and transmission electron microscopic studies of stomachs that had been colonized for 1 month or 1 year revealed intracellular bacterial collections (IBCs) in a small subset of multi- and oligopotential epithelial progenitors. Transmission electron microscopic and multilabel immunohistochemical analyses disclosed bacteria with several morphotypes, including spiral-shaped, in the cytoplasm and endosomes. Several stages in IBC evolution were documented, from a few solitary bacteria to consolidated populations in dividing and nondividing GEPs, to microorganisms traversing breaches in the GEP plasma cell membrane. IBC formation was not a unique feature of
H. pylori
strains isolated from patients with chronic atrophic gastritis. The notion that adult mammalian epithelial progenitors can function as a repository for
H. pylori
broadens the view of host habitats available to this and perhaps other pathogens.
Xenopus
as a model system to study transcriptional regulatory networks
Authors: Koide Tetsuya , Hayata Tadayoshi , Cho Ken W. Y.
Published: March 2005

Development is controlled by a complex series of events requiring sequential gene activation. Understanding the logic of gene networks during development is necessary for a complete understanding of how genes contribute to phenotype. Pioneering work initiated in the sea urchin and
Drosophila
has demonstrated that reasonable transcriptional regulatory network diagrams representing early development in multicellular animals can be generated through use of appropriate genomic, genetic, and biochemical tools. Establishment of similar regulatory network diagrams for vertebrate development is a necessary step. The amphibian
Xenopus
has long been used as a model for vertebrate early development and has contributed greatly to the elucidation of gene regulation. Because the best and most extensively studied transcriptional regulatory network in
Xenopus
is that underlying the formation and function of Spemann's organizer, we describe the current status of our understanding of this gene regulatory network and its relationship to mesodermal patterning. Seventy-four transcription factors currently known to be expressed in the mesoendoderm of
Xenopus
gastrula were characterized according to their modes of action, DNA binding consensus sequences, and target genes. Among them, nineteen transcription factors were characterized sufficiently in detail, allowing us to generate a gene regulatory network diagram. Additionally, we discuss recent amphibian work using a combined DNA microarray and bioinformatics approach that promises to accelerate regulatory network studies.
Discovery of the ergothioneine transporter
Authors: Gründemann Dirk , Harlfinger Stephanie , Golz Stefan , Geerts Andreas , Lazar Andreas , Berkels Reinhard , Jung Norma , Rubbert Andrea , Schömig Edgar
Published: March 2005

Variants of the
SLC22A4
gene are associated with susceptibility to rheumatoid arthritis and Crohn's disease.
SLC22A4
codes for an integral membrane protein, OCTN1, that has been presumed to carry organic cations like tetraethylammonium across the plasma membrane. Here, we show that the key substrate of this transporter is in fact ergothioneine (ET). Human OCTN1 was expressed in 293 cells. A substrate lead, stachydrine (alias proline betaine), was identified by liquid chromatography MS difference shading, a new substrate search strategy. Analysis of transport efficiency of stachydrine-related solutes, affinity, and Na
+
dependence indicates that the physiological substrate is ET. Efficiency of transport of ET was as high as 195 μl per min per mg of protein. By contrast, the carnitine transporter OCTN2 from rat did not transport ET at all. Because ET is transported >100 times more efficiently than tetraethylammonium and carnitine, we propose the functional name ETT (ET transporter) instead of OCTN1. ET, all of which is absorbed from food, is an intracellular antioxidant with metal ion affinity. Its particular purpose is unresolved. Cells with expression of ETT accumulate ET to high levels and avidly retain it. By contrast, cells lacking ETT do not accumulate ET, because their plasma membrane is virtually impermeable for this compound. The real-time PCR expression profile of human ETT, with strong expression in CD71
+
cells, is consistent with a pivotal function of ET in erythrocytes. Moreover, prominent expression of ETT in monocytes and
SLC22A4
polymorphism associations suggest a protective role of ET in chronic inflammatory disorders.
Cytolysin-dependent evasion of lysosomal killing
Authors: Håkansson Anders , Bentley Colette Cywes , Shakhnovic Elizabeth A. , Wessels Michael R.
Published: March 2005

Local host defenses limit proliferation and systemic spread of pathogenic bacteria from sites of mucosal colonization. For pathogens such as streptococci that fail to grow intracellularly, internalization and killing by epithelial cells contribute to the control of bacterial growth and dissemination. Here, we show that group A
Streptococcus
(GAS), the agent of streptococcal sore throat and invasive soft tissue infections, evades internalization and intracellular killing by pharyngeal epithelial cells. Production of the cholesterol-binding cytotoxin streptolysin O (SLO) prevented internalization of GAS into lysosomes. In striking contrast, GAS rendered defective in production of SLO were internalized directly or rapidly transported into lysosomes, where they were killed by a pH-dependent mechanism. Because SLO is the prototype of cholesterol-dependent cytolysins produced by many Gram-positive bacteria, cytolysin-mediated evasion of lysosomal killing may be a general mechanism to protect such pathogens from clearance by host epithelial cells.
Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the
Drosophila
embryo
Authors: Papatsenko Dmitri , Levine Michael
Published: March 2005

Dorsal is a sequence-specific transcription factor that is distributed in a broad nuclear gradient across the dorsal–ventral (DV) axis of the early Drosophila embryo. It initiates gastrulation by regulating at least 30–50 target genes in a concentration-dependent fashion. Previous studies identified 18 enhancers that are directly regulated by different concentrations of Dorsal. Here, we employ computational methods to determine the basis for these distinct transcriptional outputs. Orthologous enhancers were identified in a variety of divergent
Drosophila
species, and their comparison revealed several conserved sequence features responsible for DV patterning. In particular, the quality of Dorsal and Twist recognition sequences correlates with the DV coordinates of gene expression relative to the Dorsal gradient. These findings are entirely consistent with a gradient threshold model for DV patterning, whereby the quality of individual Dorsal binding sites determines
in vivo
occupancy of target enhancers by the Dorsal gradient. Linked Dorsal and Twist binding sites constitute a conserved composite element in certain “type 2” Dorsal target enhancers, which direct gene expression in ventral regions of the neurogenic ectoderm in response to intermediate levels of the Dorsal gradient. Similar motif arrangements were identified in orthologous loci in the distant mosquito genome,
Anopheles gambiae
. We discuss how Dorsal and Twist work either additively or synergistically to activate different target enhancers.
Perceptual learning in clear displays optimizes perceptual expertise: Learning the limiting process
Authors: Dosher Barbara Anne , Lu Zhong-Lin
Published: March 2005

Human operators develop expertise in perceptual tasks by practice or perceptual learning. For noisy displays, practice improves performance by learned external-noise filtering. For clear displays, practice improves performance by improved amplification or enhancement of the stimulus. Can these two mechanisms of perceptual improvement be trained separately? In an orientation task, we found that training with clear displays generalized to performance in noisy displays, but we did not find the reverse to be true. In noisy displays, the noise in the stimulus limits performance. In clear displays, performance is limited by noisiness of internal representations and processes. Our results suggest that training in one display condition optimizes the limiting factor(s) in performance in that condition and that noise filtering is also improved by exposure to the stimulus in clear displays. The asymmetric pattern of transfer implies the existence of two independent mechanisms of perceptual learning, which may reflect channel reweighting in adult visual system. These results also suggest that training operators with clear stimuli may suffice to improve performance in a range of clear and noisy environments by simultaneous learning by two mechanisms.
Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis
Authors: McElheny Dan , Schnell Jason R. , Lansing Jonathan C. , Dyson H. Jane , Wright Peter E.
Published: March 2005

Dynamic processes are implicit in the catalytic function of all enzymes. To obtain insights into the relationship between the dynamics and thermodynamics of protein fluctuations and catalysis, we have measured millisecond time scale motions in the enzyme dihydrofolate reductase using NMR relaxation methods. Studies of a ternary complex formed from the substrate analog folate and oxidized NADP+cofactor revealed conformational exchange between a ground state, in which the active site loops adopt a closed conformation, and a weakly populated (4.2% at 30°C) excited state with the loops in the occluded conformation. Fluctuations between these states, which involve motions of the nicotinamide ring of the cofactor into and out of the active site, occur on a time scale that is directly relevant to the structural transitions involved in progression through the catalytic cycle.
High-resolution functional proteomics by active-site peptide profiling
Authors: Okerberg Eric S. , Wu Jiangyue , Zhang Baohong , Samii Babak , Blackford Kelly , Winn David T. , Shreder Kevin R. , Burbaum Jonathan J. , Patricelli Matthew P.
Published: March 2005

Characterization and functional annotation of the large number of proteins predicted from genome sequencing projects poses a major scientific challenge. Whereas several proteomics techniques have been developed to quantify the abundance of proteins, these methods provide little information regarding protein function. Here, we present a gel-free platform that permits ultrasensitive, quantitative, and high-resolution analyses of protein activities in proteomes, including highly problematic samples such as undiluted plasma. We demonstrate the value of this platform for the discovery of both disease-related enzyme activities and specific inhibitors that target these proteins.
Visual working memory in decision making by honey bees
Authors: Zhang Shaowu , Bock Fiola , Si Aung , Tautz Juergen , Srinivasan Mandyam V.
Published: March 2005

The robustness and plasticity of working memory were investigated in honey bees by using a delayed matching-to-sample (DMTS) paradigm. The findings are summarized as follows: first, performance in the DMTS task decreases as the duration between the presentation of the sample stimulus and the presentation of the comparison stimuli is increased. This decrease is well approximated by an exponential decay function. Performance is significantly better than random-choice level even at delays as long as 5 sec and is reduced to random-choice levels at an average delay time of 8.68 ± 0.06 sec. Second, when the DMTS task involves two samples (one relevant, the other irrelevant), bees can be trained to learn to use the relevant sample to perform the task if (
i
) the relevant sample is always at a fixed position, or (
ii
) the relevant sample always has the same place in the sequence of presentation (always first or always second). Bees that have learned to use the relevant sample and to ignore the irrelevant sample can generalize this learning, and apply it to novel sets of sample and comparison stimuli that they have never previously encountered. The findings point to a remarkably robust, and yet plastic, working memory in the honey bee.
Functional diffusion map: A noninvasive MRI biomarker for early stratification of clinical brain tumor response
Authors: Moffat Bradford A. , Chenevert Thomas L. , Lawrence Theodore S. , Meyer Charles R. , Johnson Timothy D. , Dong Qian , Tsien Christina , Mukherji Suresh , Quint Douglas J. , Gebarski Stephen S. , Robertson Patricia L. , Junck Larry R. , Rehemtulla Alnawaz , Ross Brian D.
Published: April 2005

Assessment of radiation and chemotherapy efficacy for brain cancer patients is traditionally accomplished by measuring changes in tumor size several months after therapy has been administered. The ability to use noninvasive imaging during the early stages of fractionated therapy to determine whether a particular treatment will be effective would provide an opportunity to optimize individual patient management and avoid unnecessary systemic toxicity, expense, and treatment delays. We investigated whether changes in the Brownian motion of water within tumor tissue as quantified by using diffusion MRI could be used as a biomarker for early prediction of treatment response in brain cancer patients. Twenty brain tumor patients were examined by standard and diffusion MRI before initiation of treatment. Additional images were acquired 3 weeks after initiation of chemo- and/or radiotherapy. Images were coregistered to pretreatment scans, and changes in tumor water diffusion values were calculated and displayed as a functional diffusion map (fDM) for correlation with clinical response. Of the 20 patients imaged during the course of therapy, 6 were classified as having a partial response, 6 as stable disease, and 8 as progressive disease. The fDMs were found to predict patient response at 3 weeks from the start of treatment, revealing that early changes in tumor diffusion values could be used as a prognostic indicator of subsequent volumetric tumor response. Overall, fDM analysis provided an early biomarker for predicting treatment response in brain tumor patients.
A unique loop in T7 DNA polymerase mediates the binding of helicase-primase, DNA binding protein, and processivity factor
Authors: Hamdan Samir M. , Marintcheva Boriana , Cook Timothy , Lee Seung-Joo , Tabor Stanley , Richardson Charles C.
Published: March 2005

Bacteriophage T7 DNA polymerase (gene 5 protein, gp5) interacts with its processivity factor,
Escherichia coli
thioredoxin, via a unique loop at the tip of the thumb subdomain. We find that this thioredoxin-binding domain is also the site of interaction of the phage-encoded helicase/primase (gp4) and ssDNA binding protein (gp2.5). Thioredoxin itself interacts only weakly with gp4 and gp2.5 but drastically enhances their binding to gp5. The acidic C termini of gp4 and gp2.5 are critical for this interaction in the absence of DNA. However, the C-terminal tail of gp4 is not required for binding to gp5 when the latter is bound to a primer/template. We propose that the thioredoxin-binding domain is a molecular switch that regulates the interaction of T7 DNA polymerase with other proteins of the replisome.
Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter
Authors: Wan Yisong Y. , Flavell Richard A.
Published: March 2005

Regulatory T cells are critical for maintaining self-tolerance and to negatively regulate immune responses. Foxp3 is a regulatory T cell-specific transcription factor that functions as the master regulator of the development and function of regulatory T cells. Here, we report the generation of a mouse model, in which a bicistronic reporter expressing a red fluorescent protein has been knocked into the endogenous Foxp3 locus. Using this mouse model, we assessed Foxp3 expression in various lymphocyte compartments and identified previously unreported Foxp3-expressing cells. In addition, we showed thatde novoFoxp3 expression along with suppressive function were induced by TGF-β in activated CD4 T cellsin vitro. Finally, we demonstrated that non-Foxp3-expressing CD4 T cells could not be converted into Foxp3-expressing cells upon adoptive transfer into immunodeficient hosts. This Foxp3 bicistronic reporter knockin mouse model should greatly enhance the study of regulation and function of Foxp3-expressing regulatory T cells.
Repeated stimulation of CD4 effector T cells can limit their protective function
Authors: Jelley-Gibbs Dawn M. , Dibble John P. , Filipson Svetlana , Haynes Laura , Kemp Roslyn A. , Swain Susan L.
Published: March 2005

Chronic infections often result in CD8 T-cell deletion or functional nonresponsiveness. However, to date no definitive studies have attempted to determine the impact of repeated T cell receptor stimulation on CD4 effector T cell generation. We have determined that when antigen presentation is limited to 2 d, optimum in vitro CD4 effector generation is achieved. Alternatively, repeated stimulation results in decreased CD4 effector expansion, decreased cytokine production, and altered migration. Similarly, functionally impaired effectors develop in vivo when antigen-pulsed antigen-presenting cells are replenished every 24 h during a primary immune response. CD4 effectors that are generated with repeated stimulation provide no protection during influenza infection, and have an impaired ability to provide cognate help to B cells. These results suggest that duration of antigen presentation dictates CD4 effector function, and repeated T cell receptor stimulation in vitro and in vivo that exceeds an optimal threshold results in effectors with impaired function.
Mutation of the phospholipase C-γ1–binding site of LAT affects both positive and negative thymocyte selection
Authors: Sommers Connie L. , Lee Jan , Steiner Kevin L. , Gurson Jordan M. , DePersis Corinne L. , El-Khoury Dalal , Fuller Claudette L. , Shores Elizabeth W. , Love Paul E. , Samelson Lawrence E.
Published: March 2005

Linker for activation of T cells (LAT) is a scaffolding adaptor protein that is critical for T cell development and function. A mutation of LAT (Y136F) that disrupts phospholipase C-γ1 activation and subsequent calcium influx causes a partial block in T cell development and leads to a severe lymphoproliferative disease in homozygous knock-in mice. One possible contribution to the fatal disease of LAT Y136F knock-in mice could be from autoreactive T cells generated in these mice because of altered thymocyte selection. To examine the impact of the LAT Y136F mutation on thymocyte positive and negative selection, we bred this mutation onto the HY T cell receptor (TCR) transgenic, recombination activating gene-2 knockout background. Female mice with this genotype showed a severe defect in positive selection, whereas male mice exhibited a phenotype resembling positive selection (i.e., development and survival of CD8hi HY TCR-specific T cells) instead of negative selection. These results support the hypothesis that in non-TCR transgenic, LAT Y136F knock-in mice, altered thymocyte selection leads to the survival and proliferation of autoreactive T cells that would otherwise be negatively selected in the thymus.