bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigations on the impact of a drop onto a small spherical target
Authors: Bakshi Shamit , Roisman Ilia V. , Tropea Cam
Published: March 2007

This paper reports on experimental and theoretical investigations of the impact of a droplet onto a spherical target. Spatial and temporal variation of film thickness on the target surface is measured. Three distinct temporal phases of the film dynamics are clearly visible from the experimental results, namely the initial drop deformation phase, the inertia dominated phase, and the viscosity dominated phase. Experiments are also conducted to study the effect of droplet Reynolds number and target-to-drop size ratio on the dynamics of the film flow on the surface of the target. It is observed that for a given target-to-drop size ratio, the nondimensional temporal variation of film thickness collapses onto a single curve in the first and second phases. The transition to the viscosity dominated regime occurs earlier for the low Reynolds number cases and residual thickness is also larger. A simplified quasi-one-dimensional approach has been used to model the flow on the spherical target. The theory accounts for the inertial and viscous effects. Gravity and the curvature of the target are also taken into account. An analytical expression for the time-dependent film profile on the sphere is obtained for the inviscid, inertia dominated phase of spreading. Then, the evolution equation for the film thickness near the north pole in the viscosity dominated phase is obtained and solved. Good agreement is observed between the theoretical predictions and the measurements when the values of the drop and target diameters are comparable. No adjustable parameters have been used in the model.
Auger recombination and intraband absorption of two-photon-excited carriers in colloidal CdSe quantum dots
Authors: Qu Yingli , Ji Wei , Zheng Yuangang , Ying Jackie Y.
Published: March 2007

Auger recombination, quantized Auger rate, and intraband absorption of two-photon-excited carriers in colloidal CdSe quantum dots have been investigated systematically with femtosecond Z scans and transient absorption measurements. The Auger constant is revealed to be on the order of 10−30cm6s−1, while the intraband absorption cross sections are found to be in the range of 10−18–10−17cm2. The authors’ experimental evidence demonstrates that the Auger recombination or the intraband absorption takes place under the condition that the average electron-hole pair per quantum dot is in excess of the unity.
Hydrogen equilibration in polycrystalline silicon
Authors: von Maydell K. , Nickel N. H.
Published: March 2007

Hydrogen equilibration in polycrystalline silicon was investigated as a function of annealing time and temperature using electron spin resonance and hydrogen effusion measurements. During a vacuum anneal at least 1.5×1021cm−3 H atoms are mobile in the lattice, however, only about 3.7×1018cm−3 H atoms passivate Si dangling bonds. The results show that the annealing treatment can cause the vast majority of H atoms to accumulate in H stabilized platelets. Since defect passivation preferentially occurs at grain boundaries and platelet nucleation and growth are confined to the interior of single-crystal grains, H equilibration is governed by two spatially separated processes. Moreover, the data demonstrate that the hydrogen density-of-states distribution is dynamic and changes in response to experimental parameters.
Single-shot characterization of independent femtosecond extreme ultraviolet free electron and infrared laser pulses
Authors: Radcliffe P. , Düsterer S. , Azima A. , Redlin H. , Feldhaus J. , Dardis J. , Kavanagh K. , Luna H. , Gutierrez J. Pedregosa , Yeates P. , Kennedy E. T. , Costello J. T. , Delserieys A. , Lewis C. L. S. , Taïeb R. , Maquet A. , Cubaynes D. , Meyer M.
Published: March 2007

Two-color above threshold ionization of helium and xenon has been used to analyze the synchronization between individual pulses of the femtosecond extreme ultraviolet (XUV) free electron laser in Hamburg and an independent intense 120fs mode-locked Ti:sapphire laser. Characteristic sidebands appear in the photoelectron spectra when the two pulses overlap spatially and temporally. The cross-correlation curve points to a 250fs rms jitter between the two sources at the experiment. A more precise determination of the temporal fluctuation between the XUV and infrared pulses is obtained through the analysis of the single-shot sideband intensities.
Magnetic-fluid optical-fiber modulators via magnetic modulation
Authors: Chieh J. J. , Yang S. Y. , Horng H. E. , Hong Chin-Yih , Yang H. C.
Published: March 2007

The authors develop an optical-fiber modulator using magnetic fluid as a cladding layer in this work. By applying magnetic fields, the authors reduced the optical-fiber modulator transmission. Experimental results show that the magnetically induced transmission loss of an optical-fiber modulator under external magnetic fields is dominated by the number of magnetic clusters in the cladding magnetic fluid. Furthermore, it was observed that the formation of magnetic clusters depends on the length of the fiber modulator. In this work, the authors also develop a theoretical model to clarify the transmission characterization of magnetic-fluid optical-fiber modulators.
Improved surface and structural properties of InAs∕GaSb superlattices on (001) GaSb substrate by introducing an InAsSb layer at interfaces
Authors: Zhang X. B. , Ryou J. H. , Dupuis R. D. , Xu C. , Mou S. , Petschke A. , Hsieh K. C. , Chuang S. L.
Published: March 2007

In As ∕ Ga Sb type-II superlattices (SLs) were grown on (001) GaSb substrates by metal organic chemical vapor deposition. Besides the expected tensile stress introduced by the InAs layers in the SLs, additional tensile stress is found in the InAs∕GaSb SLs from the simulation of x-ray diffraction (XRD) curves of the SLs. High-resolution transmission electron microscopy and XRD of the SLs grown with different interface gas switching procedures suggest that the additional tensile stress is mainly located at the GaSb→InAs interface. To compensate for the tensile stress in the SL structures, we show that introducing ∼2-ML-thick InAs0.8Sb0.2 layer at the interfaces of the SL improves the morphology and the structural properties of the SLs significantly.
Regrowth-related defect formation and evolution in 1MeV amorphized (001) Ge
Authors: Hickey D. P. , Bryan Z. L. , Jones K. S. , Elliman R. G. , Haller E. E.
Published: March 2007

Ge implanted with 1MeV Si+ at a dose of 1×1015cm−2 creates a buried amorphous layer that, upon regrowth, exhibits several forms of defects–end-of-range (EOR), regrowth-related, and clamshell defects. Unlike Si, no planar {311} defects are observed. The minimal EOR defects are small dotlike defects and are very unstable, dissolving between 450 and 550°C. This is in contrast to Si, where the EOR defects are very stable. The amorphous layer results in both regrowth-related defects and clamshell defects, which were more stable than the EOR damage.
Air stable, high performance pentacene thin-film transistor fabricated on SiO2 gate insulator treated with β-phenethyltrichlorosilane
Authors: Kumaki Daisuke , Yahiro Masayuki , Inoue Youji , Tokito Shizuo
Published: March 2007

A pentacene thin-film transistor (TFT) was fabricated on a SiO2 gate insulator treated with β-phenethyltrichlorosilane (β-PTS). Employing β-PTS for the surface treatment of SiO2, large grains were present in the initial stage of pentacene crystal growth. The field effect mobility was as high as 1.5cm2∕Vs and the on/off ratio was over 106. The surface treatment dramatically improved the stability in air of the pentacene-TFT’s electrical characteristics. A field effect mobility of over 1cm2∕Vs and on/off ratio of over 105 were maintained after scanning the gate voltage 2000 times in air. This result indicates that the surface treatment with β-PTS not only improved TFT performance but also significantly suppressed the device’s degradation.
Thickness effects on the electrical characteristics of Ba0.7Sr0.3TiO3 capacitors with nano-Cr interlayer
Authors: Ho Chia-Cheng , Chiou Bi-Shiou , Chang Li-Chun
Published: March 2007

A multilayer Ba0.7Sr0.3TiO3∕Cr∕Ba0.7Sr0.3TiO3 (BST/Cr/BST) structure was sputtered sequentially onto Pt∕Ti∕SiO2∕Si substrate. With the insertion of a 2nm Cr interlayer, the temperature coefficient of capacitance of the BST/Cr/BST dielectric is about 69% lower than that of BST monolayer dielectric. The dielectric constant and dissipation factor as the function of Cr thickness are studied. X-ray diffraction patterns, the analysis results of energy dispersive spectroscopy, and the survey scan profiles of Auger electron spectroscopy reveal the formation of a TiO2 secondary phase after the multilayer is annealed at 800°C in O2 atmosphere. The insertion of nano-Cr interlayer improves the electrical properties of BST capacitors.
Spin transfer switching in dual MgO magnetic tunnel junctions
Authors: Diao Zhitao , Panchula Alex , Ding Yunfei , Pakala Mahendra , Wang Shengyuan , Li Zhanjie , Apalkov Dmytro , Nagai Hideyasu , Driskill-Smith Alexander , Wang Lien-Chang , Chen Eugene , Huai Yiming
Published: March 2007

Dual magnetic tunnel junction (MTJ) structures consisting of two MgO insulating barriers of different resistances, two pinned reference layers aligned antiparallel to one another, and a free layer embedded between the two insulating barriers have been developed. The electron transport and spin dependent resistances in the dual MTJ structures are accounted for by sequential tunneling with some spin-flip relaxation in the central electrode (the free layer). With a tunneling magnetoresistance ratio of 70%, a switching current density Jc (at 30ms) of 0.52MA∕cm2 is obtained, corresponding to an intrinsic value of Jc0 (at 1ns) of 1.0MA∕cm2. This value of Jc0 is 2–3 times smaller than that of a single MgO insulating barrier MTJ structure and results from improvements in the spin-transfer torque efficiency. The asymmetry between JcAP→P and JcP→AP is significantly improved, which widens the read-write margin for memory device design. In addition, the experimental results show that the switching current density can be further reduced when an external field is applied along the hard axis of the free layer.
Magnetic properties of Ni-doped MgO diluted magnetic insulators
Authors: Ramachandran S. , Narayan J. , Prater J. T.
Published: March 2007

Magnesium oxide doped with Ni has been studied in two different forms: one in which the Ni ions are incorporated into the substitutional sites and the other in which Ni is present both in substitutional sites and in the form of metallic Ni precipitates embedded in the MgO matrix. Magnetic properties of these materials have been studied and correlated with the microstructural properties. There is a significant difference in the magnetic properties between the two forms. From these studies the authors envisage that a diluted magnetic insulator will be paramagnetic in the absence of intrinsic defects such as vacancies and interstitials. MgO is a good system to perform the present studies as it can be synthesized as a high quality crystal devoid of defects to a high degree. Moreover, the magnetic properties of the Ni precipitates can be used to compare the results when a diluted magnetic semiconductor material is not fully devoid of nanoclusters/precipitates and secondary phases.
Finite Larmor radius magnetohydrodynamic analysis of the Rayleigh-Taylor instability in Z pinches with sheared axial flow
Authors: Qiu X. M. , Huang L. , Jian G. D.
Published: March 2007

The Rayleigh-Taylor (RT) instability in Z pinches with sheared axial flow (SAF) is analyzed using finite Larmor radius (FLR) magnetohydrodynamic theory, in whose momentum equation the FLR effect (also referred to as the effect of gyroviscosity) is introduced through an anisotropic ion (FLR) stress tensor. A dispersion relation is derived for the linear RT instability. Both analytical and numerical solutions of the dispersion equation are given. The results indicate that the short-wavelength modes of the RT instability can be stabilized by a sufficient FLR, whereas the long-wavelength modes can be stabilized by a sufficient SAF. In the small-wavenumber region, for normalized wavenumber K<2.4, the hybrid RT/KH (Kelvin-Helmholtz) instability is shown to be the most difficult to stabilize. However the synergistic effect of the SAF and gyroviscosity can mitigate both the RT instability in the large-wavenumber region (K>2.4) and the hybrid RT/KH instability in the small-wavenumber region. In addition, this synergistic effect can compress the RT instability to a narrow wavenumber region. Even the thorough stabilization of the RT instability in the large-wavenumber region is possible with a sufficient SAF and a sufficient gyroviscosity.
Lubrication in a flat cone: The transition from a cone to a plane wall
Authors: Lecoq N. , Feuillebois F.
Published: March 2007

A lubrication formula is derived for the drag on a sphere settling in a viscous fluid on the axis of a flat cone vessel. This formula provides the link between the classical ε−1 result for the plane wall and our earlier ε−5∕2 result for the cone [Masmoudi et al., Phys. Fluids 10, 1231 (1998)], where ε is the gap between the sphere and wall. An excellent agreement is obtained with experimental results based on the measurement of the displacement of a sphere with laser interferometry. Moreover, this formula practically applies for a large range of values of cone angles; it then proves better than the earlier formula [Masmoudi et al. (1998)] in describing experimental results.
Encapsulation of segmented Pd–Co nanocomposites into vertically aligned carbon nanotubes by plasma-hydrogen-induced demixing
Authors: Fujita Takeshi , Hayashi Yasuhiko , Tokunaga Tomoharu , Butler T. , Rupesinghe N. L. , Teo K. B. K. , Amaratunga G. A. J.
Published: March 2007

Vertically aligned carbon nanotubes (VA-CNTs) filled with Pd–Co nanocomposites on an Si substrate have been synthesized by microwave plasma-enhanced chemical vapor deposition. It was confirmed that adjacent Pd–Co nanocomposites in the VA-CNTs were compositionally separated. Most CNTs contained Co pillars on top; however, Pd pillars were rarely present. The strong magnetic induction from an individual Co pillar was revealed by electron holography. The simultaneous phenomenon of the demixing by plasma hydrogen irradiation and the preferential encapsulation into CNTs realized the unique Pd–Co nanocomposites.
Structural and magnetic properties of epitaxially grown Ge1−xFex thin films: Fe concentration dependence
Authors: Shuto Yusuke , Tanaka Masaaki , Sugahara Satoshi
Published: March 2007

Ge 1 − x Fe x films (x=2.0%–24.0%) grown by low-temperature molecular beam epitaxy were shown to have a diamond-type crystal structure without any other crystallographic phase of precipitates, although they contain slightly nonuniform Fe distribution and tiny stacking fault defects. The lattice constant decreases linearly with increasing the Fe content x from 0% to 13.0%, and is saturated for x>13.0%. The Curie temperature (TC) increases in proportion to x (⩽13.0%) and is saturated for x>13.0%. The maximum TC value was ∼170K at x>13.0%. The structural and magnetic properties indicate that Ge1−xFex is an “intrinsic” ferromagnetic semiconductor.
Engineering carrier transport across organic heterojunctions by interface doping
Authors: Tsang S. W. , Lu Z. H. , Tao Y.
Published: March 2007

Two common hole transporting materials, 4,4′,4″-tris(N-3-methylphenyl-N-phenyl-amino) triphenylamine (MTDATA) and N,N′-diphenyl-N,N′-bis(1-naphthyl) (1,1′-biphenyl)-4,4′diamine (NPB), and a p-type dopant tetrafluorotetracyanoquinodimethane (F4-TCNQ) were used to build various hole-only heterojunction devices. Both experimental results and theoretical modeling show that the current flow in such devices is limited by the heterojunction potential barrier or band offset at the MTDATA/NPB interface. It was found that the device current flow can be modulated to increase or decrease dramatically by introducing a 2nm p-doped NPB:F4-TCNQ or MTDATA:F4-TCNQ interlayer, respectively. The observed phenomena were discussed using quasi-Fermi energy level realignment at the doped/undoped organic-organic interface.
High-resolution species trees without concatenation
Authors: Edwards Scott V. , Liu Liang , Pearl Dennis K.
Published: March 2007

The vast majority of phylogenetic models focus on resolution of gene trees, despite the fact that phylogenies of species in which gene trees are embedded are of primary interest. We analyze a Bayesian model for estimating species trees that accounts for the stochastic variation expected for gene trees from multiple unlinked loci sampled from a single species history after a coalescent process. Application of the model to a 106-gene data set from yeast shows that the set of gene trees recovered by statistically acknowledging the shared but unknown species tree from which gene trees are sampled is much reduced compared with treating the history of each locus independently of an overarching species tree. The analysis also yields a concentrated posterior distribution of the yeast species tree whose mode is congruent with the concatenated gene tree but can do so with less than half the loci required by the concatenation method. Using simulations, we show that, with large numbers of loci, highly resolved species trees can be estimated under conditions in which concatenation of sequence data will positively mislead phylogeny, and when the proportion of gene trees matching the species tree is <10%. However, when gene tree/species tree congruence is high, species trees can be resolved with just two or three loci. These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories.
Rapid induction of virus-neutralizing antibodies and viral clearance in a single-source outbreak of hepatitis C
Authors: Pestka Jan M. , Zeisel Mirjam B. , Bläser Edith , Schürmann Peter , Bartosch Birke , Cosset Francois-Loïc , Patel Arvind H. , Meisel Helga , Baumert Jens , Viazov Sergei , Rispeter Kay , Blum Hubert E. , Roggendorf Michael , Baumert Thomas F.
Published: March 2007

In contrast to a detailed understanding of antiviral cellular immune responses, the impact of neutralizing antibodies for the resolution of acute hepatitis C is poorly defined. The analysis of neutralizing responses has been hampered by the fact that patient cohorts as well as hepatitis C virus (HCV) strains are usually heterogeneous, and that clinical data from acute-phase and long-term follow-up after infection are not readily available. Using an infectious retroviral HCV pseudoparticle model system, we studied a cohort of women accidentally exposed to the same HCV strain of known sequence. In this single-source outbreak of hepatitis C, viral clearance was associated with a rapid induction of neutralizing antibodies in the early phase of infection. Neutralizing antibodies decreased or disappeared after recovery from HCV infection. In contrast, chronic HCV infection was characterized by absent or low-titer neutralizing antibodies in the early phase of infection and the persistence of infection despite the induction of cross-neutralizing antibodies in the late phase of infection. These data suggest that rapid induction of neutralizing antibodies during the early phase of infection may contribute to control of HCV infection. This finding may have important implications for understanding the pathogenesis of HCV infection and for the development of novel preventive and therapeutic antiviral strategies.
Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes
Authors: Robinson Nicholas P. , Bell Stephen D.
Published: March 2007

In all three domains of life, DNA replication begins at specialized loci termed replication origins. In bacteria, replication initiates from a single, clearly defined site. In contrast, eukaryotic organisms exploit a multitude of replication origins, dividing their genomes into an array of short contiguous units. Recently, the multiple replication origin paradigm has also been demonstrated within the archaeal domain of life, with the discovery that the hyperthermophilic archaeon
Sulfolobus
has three replication origins. However, the evolutionary mechanism driving the progression from single to multiple origin usage remains unclear. Here, we demonstrate that
Aeropyrum pernix
, a distant relative of
Sulfolobus
, has two origins. Comparison with the
Sulfolobus
origins provides evidence for evolution of replicon complexity by capture of extrachromosomal genetic elements. We additionally identify a previously unrecognized candidate archaeal initiator protein that is distantly related to eukaryotic Cdt1. Our data thus provide evidence that horizontal gene transfer, in addition to its well-established role in contributing to the information content of chromosomes, may fundamentally alter the manner in which the host chromosome is replicated.
Regulation of
Caenorhabditis elegans
lifespan by a proteasomal E3 ligase complex
Authors: Ghazi Arjumand , Henis-Korenblit Sivan , Kenyon Cynthia
Published: March 2007

The proteasome maintains cellular homeostasis by degrading oxidized and damaged proteins, a function known to be impaired during aging. The proteasome also acts in a regulatory capacity through E3 ligases to mediate the spatially and temporally controlled breakdown of specific proteins that impact biological processes. We have identified components of a Skp1-Cul1-F-Box E3 ligase complex that are required for the extended lifespan of
Caenorhabditis elegans
insulin/insulin-like growth factor-1-signaling (IIS) mutants. The CUL-1 complex functions in postmitotic, adult somatic tissues of IIS mutants to enhance longevity. Reducing IIS function leads to the nuclear accumulation of the DAF-16/FOXO transcription factor, which extends lifespan by regulating downstream longevity genes. These CUL-1 complex genes act, at least in part, by promoting the transcriptional activity of DAF-16/FOXO. Together, our findings describe a role for an important cellular pathway, the proteasomal pathway, in the genetic determination of lifespan.
A validation of the diagnosis of obstetric sphincter tears in two Norwegian databases, the Medical Birth Registry and the Patient Administration System
Authors: BAGHESTAN ELHAM , Børdahl Per E. , RASMUSSEN SVEIN A. , SANDE ANNE K. , LYSLO INGVILL , SOLVANG ISABEL
Published: March 2007

Background. The purpose of the present study was to validate the registration of obstetric sphincter tears in 2 registers, the Medical Birth Registry of Norway [MBRN] and Patient Administration System [PAS]. Methods. A retrospective cohort study of all obstetric sphincter tears that occurred in our department in 1990–1992 and 2000–2002 was performed. The case records of all patients registered either in MBRN, PAS or the birth logs were compared with the information in the medical records, which constituted the ‘golden standard’. Results. The incidence of obstetric sphincter tears in 1990–1992 was 5.8% (774/13381), 5.6% (745/13381) had a perineal tear of third degree and 0.2% (29/13381) of fourth degree. In 2000–2002, the total incidence was 6.6% (813/12380), 5.9% (731/12380) was a third degree perineal tear and 0.7% (82/12380) fourth degree, respectively. The sensitivity and specificity of the MBRN database to detect obstetric sphincter tears was 85.3 and 99.5% in 1990–1992, and 91.8 and 99.7% in 2000–2002, respectively. The positive and negative predictive values of a MBRN‐registered diagnosis of obstetric sphincter tears in 1990–1992 were 91.4 and 99.1%, while the corresponding percentages in 2000–2002 were 95.4 and 99.4%, respectively. The sensitivity and specificity of the PAS database was correspondingly 52.1 and 99.0% in 1990–1992, and 84.6 and 98.5% in 2000–2002. The positive and negative predictive values of a PAS‐diagnosis of obstetric sphincter tears were 75.8 and 97.1% in 1990–1992. In 2000–2002, they were 92.7 and 98.9%, respectively. Conclusion. The validity of a diagnosis of obstetric sphincter tears, based on the MBRN, is sufficiently high to justify future large‐scale epidemiologic studies based on this database, while the validity of a PAS diagnosis is lower, but improves.
Sediment impacts in Africa's transboundary lake/river basins: Case study of the East African Great Lakes
Authors: Olago Daniel O. , Odada Eric O.
Published: March 2007

The current population pressure, inappropriate cultivation practices, forest removal and high grazing intensities on forests, wetlands, rangelands and marginal agricultural lands leads to unwanted sediment and stream flow changes that mainly impacts the downstream human and natural communities. Forests and bush are cleared, and wetlands are encroached to create space for human settlement, roads construction and to satisfy wood fuel energy demands. Similarly, pastoral areas are subjected to growing human and livestock populations, leading to land degradation, soil erosion and to an increase in the load of non-point pollutants. Landscape disturbance over many decades, and the resulting increase in soil erosion and sedimentation is the dominant cause of the ongoing eutrophication in many of the lakes in eastern Africa. Increased sedimentation in the rivers and lakes has many impacts. For example, it has altered some aquatic habitats and communities, contributed to increasing eutrophication, abetted the proliferation of algal blooms and water hyacinth reduced the amount of dissolved oxygen, etc. This paper outlines some of the problems created by increased sedimentation within the East African Great Lakes basin, and provides some possible solutions to the mitigation of sediment flux through integrated sediment management approaches.
The Response Regulator RRG-1 Functions Upstream of a Mitogen-activated Protein Kinase Pathway Impacting Asexual Development, Female Fertility, Osmotic Stress, and Fungicide Resistance inNeurospora crassa
Authors: Jones Carol A. , Greer-Phillips Suzanne E. , Borkovich Katherine A.
Published: March 2007

Two-component systems, consisting of proteins with histidine kinase and/or response regulator domains, regulate environmental responses in bacteria, Archaea, fungi, slime molds, and plants. Here, we characterize RRG-1, a response regulator protein from the filamentous fungus Neurospora crassa. The cell lysis phenotype of Δrrg-1 mutants is reminiscent of osmotic-sensitive (os) mutants, including nik-1/os-1 (a histidine kinase) and strains defective in components of a mitogen-activated protein kinase (MAPK) pathway: os-4 (MAPK kinase kinase), os-5 (MAPK kinase), and os-2 (MAPK). Similar to os mutants, Δrrg-1 strains are sensitive to hyperosmotic conditions, and they are resistant to the fungicides fludioxonil and iprodione. Like os-5, os-4, and os-2 mutants, but in contrast to nik-1/os-1 strains, Δrrg-1 mutants do not produce female reproductive structures (protoperithecia) when nitrogen starved. OS-2-phosphate levels are elevated in wild-type cells exposed to NaCl or fludioxonil, but they are nearly undetectable in Δrrg-1 strains. OS-2-phosphate levels are also low in Δrrg-1, os-2, and os-4 mutants under nitrogen starvation. Analysis of the rrg-1D921Nallele, mutated in the predicted phosphorylation site, provides support for phosphorylation-dependent and -independent functions for RRG-1. The data indicate that RRG-1 controls vegetative cell integrity, hyperosmotic sensitivity, fungicide resistance, and protoperithecial development through regulation of the OS-4/OS-5/OS-2 MAPK pathway.
Gangliosides GM1 and GM3 in the Living Cell Membrane Form Clusters Susceptible to Cholesterol Depletion and Chilling
Authors: Fujita Akikazu , Cheng Jinglei , Hirakawa Minako , Furukawa Koichi , Kusunoki Susumu , Fujimoto Toyoshi
Published: March 2007

Presence of microdomains has been postulated in the cell membrane, but two-dimensional distribution of lipid molecules has been difficult to determine in the submicrometer scale. In the present paper, we examined the distribution of gangliosides GM1 and GM3, putative raft molecules in the cell membrane, by immunoelectron microscopy using quick-frozen and freeze-fractured specimens. This method physically immobilized molecules in situ and thus minimized the possibility of artifactual perturbation. By point pattern analysis of immunogold labeling, GM1 was shown to make clusters of <100 nm in diameter in normal mouse fibroblasts. GM1-null fibroblasts were not labeled, but developed a similar clustered pattern when GM1 was administered. On cholesterol depletion or chilling, the clustering of both endogenous and exogenously-loaded GM1 decreased significantly, but the distribution showed marked regional heterogeneity in the cells. GM3 also showed cholesterol-dependent clustering, and although clusters of GM1 and GM3 were found to occasionally coincide, these aggregates were separated in most cases, suggesting the presence of heterogeneous microdomains. The present method enabled to capture the molecular distribution of lipids in the cell membrane, and demonstrated that GM1 and GM3 form clusters that are susceptible to cholesterol depletion and chilling.
RNAi Knockdown of Nopp140 InducesMinute-like Phenotypes inDrosophila
Authors: Cui Zhengfang , DiMario Patrick J.
Published: March 2007

Nopp140 associates with small nucleolar RNPs to chaperone pre-rRNA processing and ribosome assembly. Alternative splicing yields two isoforms in Drosophila: Nopp140-True is homologous to vertebrate Nopp140 particularly in its carboxy terminus, whereas Nopp140-RGG contains a glycine and arginine-rich (RGG) carboxy terminus typically found in vertebrate nucleolin. Loss of ribosome function or production at critical points in development leads to Minute phenotypes in Drosophila or the Treacher Collins syndrome (TCS) in humans. To ascertain the functional significance of Nopp140 in Drosophila development, we expressed interfering RNA using the GAL4/UAS system. Reverse transcription-PCR showed variable losses of Nopp140 mRNA in larvae from separate RNAi-expressing transgenic lines, whereas immunofluorescence microscopy with isoform-specific antibodies showed losses of Nopp140 in imaginal and polyploid tissues. Phenotypic expression correlated with the percent loss of Nopp140 transcripts: a ≥50% loss correlated with larval and pupal lethality, disrupted nuclear structures, and in some cases melanotic tumors, whereas a 30% loss correlated with adult wing, leg, and tergite deformities. We consider these adult phenotypes to be Minute-like and reminiscent of human craniofacial malformations associated with TCS. Similarly, overexpression of either isoform caused embryonic and larval lethality, thus indicating proper expression of Nopp140 is critical for normal development.
Nucleotide Exchange Factors for Hsp70s Are Required for [URE3] Prion Propagation inSaccharomyces cerevisiae
Authors: Kryndushkin Dmitry , Wickner Reed B.
Published: March 2007

The [URE3] and [PSI+] prions are infectious amyloid forms of Ure2p and Sup35p. Several chaperones influence prion propagation: Hsp104p overproduction destabilizes [PSI+], whereas [URE3] is sensitive to excess of Ssa1p or Ydj1p. Here, we show that overproduction of the chaperone, Sse1p, can efficiently cure [URE3]. Sse1p and Fes1p are nucleotide exchange factors for Ssa1p. Interestingly, deletion of either SSE1 or FES1 completely blocked [URE3] propagation. In addition, deletion of SSE1 also interfered with [PSI+] propagation.
DPTF: a database of poplar transcription factors
Authors: Zhu Qi-Hui , Guo An-Yuan , Gao Ge , Zhong Ying-Fu , Xu Meng , Huang Minren , Luo Jinchu
Published: March 2007

Summary: The database of poplar transcription factors (DPTF) is a plant transcription factor (TF) database containing 2576 putative poplar TFs distributed in 64 families. These TFs were identified from both computational prediction and manual curation. We have provided extensive annotations including sequence features, functional domains, GO assignment and expression evidence for all TFs. In addition, DPTF contains cross-links to the Arabidopsis and rice transcription factor databases making it a unique resource for genome-scale comparative studies of transcriptional regulation in model plants.

Availiability: DPTF is available at http://dptf.cbi.pku.edu.cn

Contact:  dptf@mail.cbi.pku.edu.cn
Classification based upon gene expression data: bias and precision of error rates
Authors: Wood Ian A. , Visscher Peter M. , Mengersen Kerrie L.
Published: March 2007

Motivation: Gene expression data offer a large number of potentially useful predictors for the classification of tissue samples into classes, such as diseased and non-diseased. The predictive error rate of classifiers can be estimated using methods such as cross-validation. We have investigated issues of interpretation and potential bias in the reporting of error rate estimates. The issues considered here are optimization and selection biases, sampling effects, measures of misclassification rate, baseline error rates, two-level external cross-validation and a novel proposal for detection of bias using the permutation mean.

Results: Reporting an optimal estimated error rate incurs an optimization bias. Downward bias of 3–5% was found in an existing study of classification based on gene expression data and may be endemic in similar studies. Using a simulated non-informative dataset and two example datasets from existing studies, we show how bias can be detected through the use of label permutations and avoided using two-level external cross-validation. Some studies avoid optimization bias by using single-level cross-validation and a test set, but error rates can be more accurately estimated via two-level cross-validation. In addition to estimating the simple overall error rate, we recommend reporting class error rates plus where possible the conditional risk incorporating prior class probabilities and a misclassification cost matrix. We also describe baseline error rates derived from three trivial classifiers which ignore the predictors.

Availability: R code which implements two-level external cross-validation with the PAMR package, experiment code, dataset details and additional figures are freely available for non-commercial use from http://www.maths.qut.edu.au/profiles/wood/permr.jsp

Contact: i.wood@qut.edu.au

Supplementary information: Supplementary data are available at Bioinformatics online.
Lesions attributed to vaccination of sheep with Gudair™ for the control of ovine paratuberculosis: post farm economic impacts at slaughter
Authors: Eppleston J , Windsor PA
Published: March 2007

Objective   To determine i) the prevalence of lesions at the site of vaccination with Gudair™, and ii) the incidence of discounting of slaughtered sheep carcasses due to the presence of these lesions.

Design   A survey of the prevalence of injection lesions and actual discounts applied to 20 consignments of vaccinates slaughtered in abattoirs in New South Wales.

Procedure   Consignments of sheep previously vaccinated against ovine Johne's disease (OJD) were assessed on the slaughter chain for the prevalence of vaccination site lesions and any costs associated with carcass trimming were estimated. In addition a telephone survey was conducted to determine the experiences and risk attitudes of 8 abattoirs in south east New South Wales likely to have previously processed vaccinates.

Results   The prevalence of lesions observed was 18% for adult (mutton) and 65% for lamb carcasses. The value of the trim removed was insignificant, the labour cost of its removal was nil and no carcass was downgraded to a lower value grade.

Conclusion   Under the market conditions existing at the time the study was conducted, in sheep vaccinated at the recommended site high on the neck, it is unlikely that OJD vaccination site lesions will be a significant cost to producers or the processing industry and will represent only a very small proportion of the total cost of OJD control by vaccination.
The tightly regulated promoter of the xanA gene of Aspergillus nidulans is included in a helitron
Authors: Cultrone Antonietta , Domínguez Yazmid Reyes , Drevet Christine , Scazzocchio Claudio , Fernández‐Martín Rafael
Published: March 2007

In Aspergillus nidulans the xanA gene codes for a xanthine α‐ketoglutarate‐dependent dioxygenase, an enzyme only present in the fungal kingdom. The 5′ region of this gene, including its putative promoter and the first 54 codons of the open reading frame, together with the first intron is duplicated in the genome. This duplication corresponds to a helitron, a eukaryotic element proposed to transpose replicatively by the rolling circle mechanism. We show that the regulation of xanA conforms to that of other genes of the purine degradation pathway, necessitating the specific UaY transcription factor and the AreA GATA factor. The promoter of the duplicated region is active ectopically and the difficulty in detecting an mRNA from the duplicated region is at least partially due to nonsense‐mediated decay. Comparative genomic data are only consistent with the hypothesis that the 5′ region of xanA pre‐existed the helitron insertion, and that a ‘secondary helitron’ was generated from an insertion 5′ to it and a pre‐existing 3′ consensus sequence within the open reading frame. It is possible to propose a role of helitrons in promoter shuffling and thus in recruiting new genes into specific regulatory circuits.
Chromosomal toxin–antitoxin loci can diminish large‐scale genome reductions in the absence of selection
Authors: Szekeres Silvia , Dauti Mira , Wilde Caroline , Mazel Didier , Rowe‐Magnus Dean A.
Published: March 2007

Superintegrons (SIs) are chromosomal genetic elements containing assemblies of genes, each flanked by a recombination sequence (attC site) targeted by the integron integrase. SIs may contain hundreds of attC sites and intrinsic instability is anticipated; yet SIs are remarkably stable. This implies that either selective pressure maintains the genes or mechanisms exist which favour their persistence in the absence of selection. Toxin/antitoxin (TA) systems encode a stable toxin and a specific, unstable antitoxin. Once activated, the continued synthesis of the unstable antitoxin is necessary for cell survival. A bioinformatic search of accessible microbial genomes for SIs and TA systems revealed that large SIs harboured TA gene cassettes while smaller SIs did not. We demonstrated the function of TA loci in different genomic contexts where large‐scale deletions can occur; in SIs and in a 165 kb dispensable region of the Escherichia coli genome. When devoid of TA loci, large‐scale genome loss was evident in both environments. The inclusion of two TA loci, relBE1 and parDE1, which we identified in the Vibrio vulnificus SI rendered these environments refractory to gene loss. Thus, chromosomal TA loci can stabilize massive SI arrays and limit the extensive gene loss that is a hallmark of reductive evolution.
Control of IS911 target selection: how OrfA may ensure IS dispersion
Authors: Rousseau Philippe , Loot Céline , Guynet Catherine , Ah‐Seng Yoan , Ton‐Hoang Bao , Chandler Mick
Published: March 2007

IS911 transposition involves a closed circular insertion sequence intermediate (IS‐circle) and two IS‐encoded proteins: the transposase OrfAB and OrfA which regulates IS911 insertion. OrfAB alone promotes insertion preferentially next to DNA sequences resembling IS911 ends while the addition of OrfA strongly stimulates insertion principally into DNA targets devoid of the IS911 end sequences. OrfAB shares its N‐terminal region with OrfA. This includes a helix–turn–helix (HTH) motif and the first three of four heptads of a leucine zipper (LZ). OrfAB binds specifically to IS911 ends via its HTH whereas OrfA does not. We show here: that OrfA binds DNA non‐specifically and that this requires the HTH; that OrfA LZ is required for its multimerization; and that both motifs are essential for OrfA activity. We propose that these OrfA properties are required to assemble a nucleoprotein complex committed to random IS911 insertion. This control of IS911 insertion activity by OrfA in this way would assure its dispersion.
The telomere system of the Streptomyces linear plasmid SCP1 represents a novel class
Authors: Huang Chih‐Hung , Tsai Hsiu‐Hui , Tsay Yeou‐Guang , Chien Yu‐Nien , Wang Shan‐Li , Cheng Ming‐Yuan , Ke Chia‐Hui , Chen Carton W.
Published: March 2007

Linear plasmids and chromosomes of Streptomyces carry terminal proteins (TPs) covalently attached to the 5′ ends of the DNA. Most known telomeres are conserved in primary sequence and in the potential secondary structures formed during replication. The TP that caps these telomeres is also highly conserved and its coding gene, tpg, is present in all Streptomyces chromosomes and some linear plasmids. Linear plasmid SCP1 contains atypical telomere sequences and no tpg homologue, and can replicate in the absence of tpg, suggesting that it carries a novel TP gene. To isolate the TP on the SCP1 telomeres, we constructed a multicopy mini‐SCP1 plasmid. The TP capping the plasmid was isolated and subjected to tryptic digestion and mass spectrometric analysis, and the results indicated that the TP was encoded by an open reading frame (ORF), SCP1.127 (tpc), on SCP1. Of the two ORFs upstream of tpc, SCP1.125 (tac) but not SCP1.126 was essential for replication of mini‐SCP1. The Tac–Tpc system of SCP1 represents a convergently evolved novel telomere‐capping system of Streptomyces linear replicons.
Cell cycle‐regulated vesicular trafficking of Toxoplasma APT1, a protein localized to multiple apicoplast membranes
Authors: Karnataki Anuradha , DeRocher Amy , Coppens Isabelle , Nash Coral , Feagin Jean E. , Parsons Marilyn
Published: March 2007

The apicoplast is a relict plastid essential for viability of the apicomplexan parasites Toxoplasma and Plasmodium. It is surrounded by multiple membranes that proteins, substrates and metabolites must traverse. Little is known about apicoplast membrane proteins, much less their sorting mechanisms. We have identified two sets of apicomplexan proteins that are homologous to plastid membrane proteins that transport phosphosugars or their derivatives. Members of the first set bear N‐terminal extensions similar to those that target proteins to the apicoplast lumen. While Toxoplasma gondii lacks this type of translocator, the N‐terminal extension from the Plasmodium falciparum sequence was shown to be functional in T. gondii. The second set of translocators lacks an N‐terminal targeting sequence. This translocator, TgAPT1, when tagged with HA, localized to multiple apicoplast membranes in T. gondii. Contrasting with the constitutive targeting of luminal proteins, the localization of the translocator varied during the cell cycle. Early‐stage parasites showed circumplastid distribution, but as the plastid elongated in preparation for division, vesicles bearing TgAPT1 appeared adjacent to the plastid. After plastid division, the protein resumes a circumplastid colocalization. These studies demonstrate for the first time that vesicular trafficking likely plays a role in the apicoplast biogenesis.
The type III secretion system needle tip complex mediates host cell sensing and translocon insertion
Authors: Veenendaal Andreas K. J. , Hodgkinson Julie L. , Schwarzer Lynn , Stabat David , Zenk Sebastian F. , Blocker Ariel J.
Published: March 2007

Type III secretion systems (T3SSs) are essential virulence determinants of many Gram‐negative bacterial pathogens. The Shigella T3SS consists of a cytoplasmic bulb, a transmembrane region and a hollow ‘needle’ protruding from the bacterial surface. Physical contact with host cells initiates secretion and leads to assembly of a pore, formed by IpaB and IpaC, in the host cell membrane, through which proteins that facilitate host cell invasion are translocated. As the needle is implicated in host cell sensing and secretion regulation, its tip should contain components that initiate host cell contact. Through biochemical and immunological studies of wild‐type and mutant Shigella T3SS needles, we reveal tip complexes of differing compositions and functional states, which appear to represent the molecular events surrounding host cell sensing and pore formation. Our studies indicate that the interaction between IpaB and IpaD at needle tips is key to host cell sensing, orchestration of IpaC secretion and its subsequent assembly at needle tips. This allows insertion into the host cell membrane of a translocation pore that is continuous with the needle.
Transposition and target specificity of the typical IS30 family element IS1655 from Neisseria meningitidis
Authors: Kiss János , Nagy Zita , Tóth Gábor , Kiss György Botond , Jakab Júlia , Chandler Michael , Olasz Ferenc
Published: March 2007

We have analysed the transposition and target selection strategy of IS1655, a typical IS30 family member resident in Neisseria meningitidis. We have redefined IS1655 as a 1080 bp long element with 25 bp imperfect inverted repeats (IRs), which generates a 3 bp target duplication and have shown that it transposes using an intermediate with abutted IRs separated by 2 bp. IS1655 exhibits bipartite target specificity inserting preferentially either next to sequences similar to its IRs or into an unrelated but well defined sequence. IR‐targeting leads to the formation of a new junction in which the targeted IR and one of the donor IRs are separated by 2 bp. The non‐IR targets were characterized as an imperfect 19 bp palindrome in which the central five positions show slight GC excess and the distal region is AT‐rich. Artificial targets designed according to the consensus were recognized by the element as hot spots for insertion. The organization of IS1655 is similar to that of other IS30 family members. Moreover, it shows striking similarity to IS30 in transposition strategy even though their transposases differ in their N‐terminal regions, which, for IS30, appears to determine target specificity. Comparative analysis of the transposases and the evolutionary aspects of sequence variants are also briefly discussed.
Enteropathogenic Escherichia coli Tir is an SH2/3 ligand that recruits and activates tyrosine kinases required for pedestal formation
Authors: Bommarius Bettina , Maxwell David , Swimm Alyson , Leung Sara , Corbett Anita , Bornmann William , Kalman Daniel
Published: March 2007

Enteropathogenic Escherichia coli (EPEC) cause intestinal inflammation, severe diarrhoea and mortality, particularly among children in developing nations. Upon attachment to intestinal epithelial cells, EPEC induces actin‐filled membrane protrusions called ‘pedestals’ and disrupts microvilli to form attaching and effacing (A/E) lesions. EPEC also disrupts epithelial barrier function and causes colitis. Here we have investigated how virulence factors which orchestrate formation of actin pedestals interface with host tyrosine kinases. We show that Tec‐family tyrosine kinases localize beneath EPEC and, with Abl‐family kinases, comprise a set of redundant host kinases utilized by EPEC to form actin pedestals. We also show that Tir, a virulence factor required for pathogenesis, contains a polyproline region (PPR) that interacts with SH3 domains of redundant kinases, and a phosphorylation site (Y474) that interacts with kinase SH2 domains. These interactions are essential for pedestal formation, and mimic activation of kinases by cellular ligands. Our results suggest that a positive feedback loop exists in which initial phosphorylation of Tir on Y474 by tyrosine kinases causes recruitment of additional redundant kinases via PPR–SH3 interactions and PO3–Y474–SH2 interactions, which in turn phosphorylate other Tir molecules as well as proteins that catalyse formation of actin pedestals.