bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface NH3 anneal on strained Si0.5Ge0.5 for metal-oxide-semiconductor applications with HfO2 as gate dielectric
Authors: Huang Jidong , Wu Nan , Zhang Qingchun , Zhu Chunxiang , Li M. F. , Tay Andrew A. O. , Cheng Zhi-Yuan , Leitz Chris W. , Lochtefeld Anthony
Published: April 2006

In this Letter, metal-oxide-semiconductor capacitors were fabricated and characterized on compressively strained Si50Ge50 on Si0.8Ge0.2 virtual substrates by using metal-organic chemical vapor deposition HfO2 as gate dielectric and TaN as metal gate electrode. It is demonstrated that surface nitridation treatment using NH3 annealing prior to HfO2 deposition effectively prevents the growth of GeOx at the interfacial layer which exists on SiGe surface with direct deposition of HfO2. X-ray photoelectron spectroscopic analysis suggests that the nitridation process tends to occur to Si atoms rather than to Ge atoms and results in the formation of an interfacial layer of SiNxOy on the SiGe surface. Capacitors with the surface nitridation treatment show good capacitance-voltage characteristics with negligible hysteresis, much smaller interface trap charge density, and significantly improved gate leakage current in comparison with those of capacitors made without nitridation treatment. The surface nitridation seems to be a promising method for the formation of high quality high-κ gate stack on strained SiGe substrate.
Defects in silicon nanowires
Authors: Wang R. P.
Published: April 2006

Defects in silicon nanowires have been investigated using the electron spin resonance (ESR) method. The ESR signals consist of three features: a strong resonance at g=2.00249, a weak line at g=2.00048, and a broad feature at g=2.00541. From the saturation behavior and oxidation-related and temperature dependence analysis, we ascribe that the strong resonance corresponds to the EX center and the weak line to the well-assigned E′ center. We argue that the assignment of the broad feature to Pb centers [A. Baumer et al., Appl. Phys. Lett. 85, 943 (2004)] is oversimplified, and its physical origins may include dangling bonds in amorphous silicon.
Multiferroic BiFeO3 thin films prepared via a simple sol-gel method
Authors: Wang Yao , Jiang Qing-hui , He Hong-cai , Nan Ce-Wen
Published: April 2006

Single-phase multiferroic BiFeO3 thin films were grown on (111) Pt∕Ti∕SiO2∕Si substrates via a simple sol-gel spin-coating technique, as evidenced by x-ray diffraction. The thickness of the films can be controlled by the number of layers spin coated. Scanning electron microscope confirmed good surface and cross-section morphology of the films. Obvious multiferroic behavior with small saturation polarization but high saturation magnetization was observed in the films. X-ray photoelectron spectroscopy was used to examine the combination state of Fe 2p electron in the BiFeO3 films.
Magnetoelectric effect in laminate composite of magnets/0.7Pb(Mg1∕3Nb2∕3)O3–0.3PbTiO3 single crystal
Authors: Jia Yanmin , Zhao Xiangyong , Luo Haosu , Or Siu Wing , Chan Helen Lai Wa
Published: April 2006

A magnetoelectric (ME) laminate composite was fabricated by sandwiching one 0.7Pb(Mg1∕3Nb2∕3)O3–0.3PbTiO3 (PMN-PT) piezoelectric single crystal layer between two NdFeB magnet layers along the thickness direction. The high ME effect was obtained by the product of the magnetic attractive-repellent effect in the magnet layers and the piezoelectric effect in the piezoelectric layer. The magnetoelectric voltage coefficient of the composite was measured to be ∼12.5mV∕cmOe with a flat frequency response in the range of 0.1–20kHz. The induced ME voltage showed an excellent linear relationship to the applied ac magnetic field with field amplitude varying from 10−3to10Oe. Other advantages included low heat generation, no bias magnetic field required, and high scale-down capability. These made the composite to be a promising ME material for realizing high-performance, small-size, and low-cost magnetic sensors.
Nanoscale characterization of strained silicon by tip-enhanced Raman spectroscope in reflection mode
Authors: Saito Y. , Motohashi M. , Hayazawa N. , Iyoki M. , Kawata S.
Published: April 2006

We observe localized strains in strained silicon by tip-enhanced near-field Raman spectroscope in reflection mode. The tip-enhanced Raman spectra show that the Raman frequency and intensity of strained silicon were different within a crosshatch pattern induced by lattice mismatch. Micro-Raman measurements, however, show only uniform features because of averaging effect due to the diffraction limit of light. Nanoscale characterization of strained silicon is essential for developing reliable next generation integrated circuits. This technique can be applicable not only to strained silicon but also to any other crystals.
Pulsed laser ignition of reactive multilayer films
Authors: Picard Yoosuf N. , Adams David P. , Palmer Jeremy A. , Yalisove Steven M.
Published: April 2006

Nanostructured Al∕Pt multilayer films were ignited by single pulse irradiation from a Ti:sapphire femtosecond laser system. Critical ignition fluences (0.9–22J∕cm2) required to initiate a self-propagating reaction were quantified for different multilayer designs. Multilayers with smaller bilayer thickness required relatively lower fluence for ignition. Ignition threshold fluence was also found to be 1.4–3.6 times higher for Al-capped multilayers than for Pt-capped multilayers. Ablation threshold fluences were measured for Al (860±70mJ∕cm2) and Pt (540±50mJ∕cm2) and related to the observed difference in ignition fluences for Al- and Pt-capped multilayers.
Control of the nonlinear carrier response time of AlGaAs photonic crystal waveguides by sample design
Authors: Murzyn P. , Garcia-Deniz A. Z. , Kundys D. O. , Fox A. M. , Wells J.-P. R. , Whittaker D. M. , Skolnick M. S. , Krauss T. F. , Roberts J. S.
Published: April 2006

We have used reflection geometry pump-probe spectroscopy to investigate the free carrier response time of AlGaAs high refractive index contrast one-dimensional photonic crystal waveguides. We have observed pump-induced shifts of photonic resonances in the near infrared spectral region, and have studied the dependence of the decay time on the sample parameters. We find that the response time can be varied from 8to33ps by changing the structure period and etch depth. This, combined with the large changes observed in the reflectivity, demonstrates excellent potential for application as ultrafast photonic switches with a controllable recovery time.
Optimization of laser parameters for the maximum efficiency in the generation of water-window radiation using a liquid nitrogen jet
Authors: Kim B. , Ahn B. , Lee D. , Kim J. , Kim D.
Published: April 2006

A laser-produced plasma is a suitable compact x-ray source that can be of broad band or quasimonochromatic with a proper choice of material and filter. To address the maximum conversion efficiency for an efficient, quasimonochromatic source at 2.88 nm (NVI1s2-1s2p transition) using liquid nitrogen jet for soft x-ray microscopy, the radiation characteristics such as absolute intensity, spectra, and angular distribution have been investigated for different laser pulse durations (picosecond and femtosecond pulses) and laser energies The comparison of conversion efficiencies between picosecond [120 ps full width at half maximum (FWHM)] and femtosecond (40–500fs FWHM) lasers indicates that the picosecond laser would provide better conversion efficiency, which is 1.6% at 2×1013W∕cm2. The investigation shows that the laser intensity for the maximum conversion efficiency scales as Im∝1∕τα, where α=0.9±0.15. This empirical formula is useful to choose the laser parameters properly for a given pulse width.
Coating thickness and elastic modulus measurement using ultrasonic bulk wave resonance
Authors: Dixon S. , Lanyon B. , Rowlands G.
Published: April 2006

Measurement of the resonant through thickness ultrasonic modes of a homogeneous plate using a fast Fourier transform of the temporal data can be used to calculate plate thickness very accurately. We describe an extension of this principle to two-layer systems, examining a thin coating on a substrate of known properties. The resonant behavior of these systems is predicted and we explain how this approach is used to measure coating thickness and elastic modulus. Noncontact electromagnetic acoustic transducers are used for ultrasonic measurement, as they do not significantly affect the resonant response of the system, unlike alternative contact transducers.
Crossover in thermal transport mechanism in nanocrystalline silicon
Authors: Bodapati Arun , Keblinski Pawel , Schelling Patrick K. , Phillpot Simon R.
Published: April 2006

Using vibrational mode analysis, we demonstrate that lattice vibrations in small grain (≲3nm) structurally inhomogeneous nanocrystalline silicon are almost identical to those in homogeneous amorphous structures with the majority of the vibrations delocalized and unpolarized. As a consequence the principal thermal conductivity mechanism in such a nanocrystalline material is the same as in the amorphous material. With increasing grain size the ability of vibrations to homogenize over the nanocrystalline structure is gradually lost and the phonon spectrum becomes progressively more like that of a crystalline material; this is reflected in a crossover in the mechanism of thermal transport.
Monte Carlo simulation of grain growth in two-phase nanocrystalline materials
Authors: Zheng Y. G. , Lu C. , Mai Y.-W. , Gu Y. X. , Zhang H. W. , Chen Z.
Published: April 2006

The normal grain growth in volume-conserved two-phase nanocrystalline materials is studied using a modified Potts model, in which the grain boundary migration is driven by the interfacial energy between two phases and the grain boundary energy inside each phase. Monte Carlo simulation results show that the grain growth of one phase is constrained by the presence of the other phase. The power-law grain growth kinetics with an almost temperature-independent exponent of 0.16±0.01 (0.5 in a pure single-phase system) is predicted for two immiscible phases, which is in agreement with experimental observations.
Comparative study for colloidal quantum dot conduction band state calculations
Authors: Luo Jun-Wei , Li Shu-Shen , Xia Jian-Bai , Wang Lin-Wang
Published: April 2006

By comparing the results of some well-controlled calculation methods, we analyze the relative importance of bulk band structure, multi-bulk-band coupling, and boundary conditions in determining colloidal quantum dot conduction band eigenenergies. We find that while the bulk band structure and correct boundary conditions are important, the effects of multi-bulk-band coupling are small.
Effect of hafnium germanate formation on the interface of HfO2/germanium metal oxide semiconductor devices
Authors: Van Elshocht S. , Caymax M. , Conard T. , De Gendt S. , Hoflijk I. , Houssa M. , De Jaeger B. , Van Steenbergen J. , Heyns M. , Meuris M.
Published: April 2006

We have studied the thermal stability of HfO2 thin layers on germanium and the substrate interface development. HfO2 was deposited on Ge substrates and annealed in O2 or N2 at 500°C (substrate temperature). After O2 anneal, we observed the formation of hafnium germanate, which is stable at 500°C in N2 as opposed to GeO2 that desorbs as GeO. We believe that this hafnium germanate is an oxygen barrier and as such is at the origin of the much thinner interface between HfO2 and germanium as compared to silicon. In addition, results suggest that the HfGeOx is related to the high interface state density frequently reported for germanium metal oxide semiconductor devices.
Ferromagnetism in 200-MeV Ag+15-ion-irradiated Co-implanted ZnO thin films
Authors: Angadi Basavaraj , Jung Y. S. , Choi Won-Kook , Kumar Ravi , Jeong K. , Shin S. W. , Lee J. H. , Song J. H. , Wasi Khan M. , Srivastava J. P.
Published: April 2006

Structural, electrical resistivity, and magnetization properties of 200-MeV Ag+15-ion-irradiated Co-implanted ZnO thin films are presented. The structural studies show the presence of Co clusters whose size is found to increase with increase of Co implantation. The implanted films were irradiated with 200-MeV Ag+15 ions to fluence of 1×1012ions∕cm2. The Co clusters on irradiation dissolve in the ZnO matrix. The electrical resistivity of the irradiated samples is lowered to half. The magnetization hysteresis measurements show ferromagnetic behavior at 300K, and the coercive field increases with the Co implantation. The ferromagnetism at room temperature is confirmed by magnetic force microscopy measurements. The results are explained on the basis of the close interplay between the electrical and the magnetic properties.
Determination of electron-phonon interaction parameters from time-domain terahertz spectroscopy
Authors: Gilmore M. A. , Kamal Saeid , Broun D. M. , Dodge J. S.
Published: April 2006

We present an analytical framework for determining metallic electron-phonon interaction parameters from time-domain terahertz spectroscopy measurements. We apply this analysis to the case of lead, where we obtain values that are consistent with existing estimates. We discuss the statistical and systematic errors that limit the uncertainty in the parameter estimates.
Highly strain-relaxed ultrathin SiGe-on-insulator structure by Ge condensation process combined with H+ irradiation and postannealing
Authors: Miyao Masanobu , Tanaka Masanori , Tsunoda Isao , Sadoh Taizoh , Enokida Toyotsugu , Hagino Hiroyasu , Ninomiya Masaharu , Nakamae Masahiko
Published: April 2006

Strain-relaxation process of SiGe-on-insulator (SGOI) structures in the oxidation induced Ge condensation method has been investigated as a function of the SiGe thickness. Complete relaxation was obtained for thick SGOI layers (>100nm). However, the relaxation rates abruptly decreased with decreasing SiGe thickness below 50nm, i.e., the relaxation rate of 30% at 30nm SiGe thickness. In order to improve this phenomenon, a method combined with H+ irradiation with a medium dose (5×1015cm−2) and postannealing (1200°C) has been developed. This successfully achieved the high relaxation rate (70%) in the ultrathin SGOI (30nm).
Silver nanocrystal superlattices: Self-assembly and optical emission
Authors: Qiu T. , Wu X. L. , Cheng Y. C. , Siu G. G. , Chu Paul K.
Published: April 2006

Unique passivated silver nanocrystal superlattices were fabricated via a conventional hydrothermal method. The method is based on a general phase transfer and separation mechanism occurring at the interfaces of the liquid, solid, and solution phases present during the synthesis. A photoluminescence (PL) band centered at 390nm was recorded from the obtained superlattice samples. Spectral analyses suggest that the PL arises from the radiative recombination of sp-band electrons with d-band holes in the silver nanocrystals and its intensity enhancement is due to the surface plasmon and an electrostatic enhancement mechanism analogous to that in surface enhanced Raman scattering.
Optimisation of tobacco rattle virus-induced gene silencing in Arabidopsis
Authors: Wang Changchun , Cai Xinzhong , Wang Xuemin , Zheng Zhong
Published: April 2006

Arabidopsis thaliana (L.) Heynh. is a model plant species in which to study plant gene functions. Recently developed virus-induced gene silencing (VIGS) offers a rapid and high-throughput technique platform for gene function analysis. In this paper we report optimisation of tobacco rattle virus (TRV)-induced gene silencing in Arabidopsis. The parameters potentially affecting the efficiency of VIGS in Arabidopsis were investigated. These included the concentration and pre-incubation of Agrobacterium inocula (agro-inocula), the concentration of acetosyringone included in agro-inocula, the Agrobacterium inoculation (agro-inoculation) method, the ecotypes and the growth stages of Arabidopsis plants for agro-inoculation, and the growth temperature of agro-inoculated plants. The optimised VIGS procedure involves preparing the agro-inocula with OD600 of 2.0, pre-incubating for 2 h in infiltration buffer containing 200 μm acetosyringone, agro-inoculating by vacuum infiltration, and growth of agro-inoculated plants at 22 −24°C. Following this procedure consistent and highly efficient VIGS was achieved for the genes encoding phytoene desaturase (PDS) and actin in Arabidopsis. The silencing phenotype lasts for at least 6 weeks, and is applicable in at least seven ecotypes, including Col-0, Cvi-0, Sd, Nd-1, Ws-0, Bay-0 and Ler. TRV-induced VIGS was expressed not only in leaves, but also in stems, inflorescences and siliques. However, VIGS was not transmissible through seed to the subsequent generation. The optimised procedure of the TRV-induced gene silencing should facilitate high-throughput functional analysis of genes in Arabidopsis.
Seawater stress applied at germination affects mitochondrial function in durum wheat (Triticum durum) early seedlings
Authors: Flagella Zina , Trono Daniela , Pompa Marianna , Di Fonzo Natale , Pastore Donato
Published: April 2006

Seawater stress effects on mitochondrial ATP synthesis and membrane potential (ΔΨ) were investigated in germinating durum wheat seedlings under moderate (22% seawater osmolarity, –0.62 MPa) and severe (37% seawater osmolarity, –1.04 MPa) stress. To estimate the osmotic component of salt stress, mannitol solutions (0.25 and 0.42 m) iso-osmotic with the saline ones were used. Moderate stress intensity only delayed mean germination time (MGT), whereas higher seawater osmolarity reduced germination percentage as well. In contrast, Na+ and Cl– accumulation showed a sharp increase under moderate stress and only a small further increase under severe stress, which was more pronounced for Cl–. Only severe stress significantly damaged succinate-dependent oxidative phosphorylation, which may be related to the stress-induced alteration in inner mitochondrial membrane permeability, as indicated by changes in ΔΨ profiles. Proline-dependent oxidative phosphorylation, however, was inhibited under moderate stress. This suggests the occurrence of an adaptation mechanism leading to proline accumulation as an osmoprotectant. Moreover, both the osmotic and the toxic components of seawater stress were detrimental to oxidative phosphorylation. Damage to germination and MGT, in contrast, were mainly caused by osmotic stress. Therefore, mitochondrial function appears to be a more sensitive target of toxic stress than growth. In conclusion, the effects of seawater stress on mitochondrial ATP synthesis vary in relation to the substrate oxidised and stress level, inducing both adaptive responses and damage.
Research note: Avian gut passage reduces seed exit costs in Sorbus aucuparia (Rosaceae) as measured by a diametral compression test
Authors: Paulsen Torbjørn R. , Lindtjørn Ommund , Gjerdet Nils Roar , Högstedt Göran
Published: April 2006

Reduced seed exit costs have been suggested to explain advanced seedling emergence and increased seedling growth in Sorbus aucuparia L. (Rosaceae; rowan) following Turdus spp. (Turdidae; thrush) gut passage. In the present study, seed coat tension strength of Turdus merula L. (Turdidae; blackbird) gut-passed and non-ingested control seeds were tested with a diametral compression test. Both maximum load (N) and work (mJ) required for opening the seeds were reduced in gut-passed seeds, although scanning electron microscopy showed no visible differences in seed coat surface structure between treatments. In addition, gut passage increased dry seed weight by 0.64 mg (22%), weight of hydrated seeds by 0.62 mg (16%) and width of hydrated seeds by 0.1 mm (9%). Absorption causing the seed coat to yield more easily to the germinating seedling is proposed as an explanation for the reduction in seed exit costs. For the emerging seedling, the time and force needed to open the seed coat was reduced, thus lowering dispersal and germination costs of S. aucuparia.
Cloning and expression analysis of TSK1, a wheat SKP1 homologue, and functional comparison with Arabidopsis ASK1 in male meiosis and auxin signalling
Authors: Li Chijun , Liang Yu , Chen Changbin , Li Junhua , Xu Yunyuan , Xu Zhihong , Ma Hong , Chong Kang
Published: April 2006

Plants possess multiple homologues of the SKP1 gene encoding an essential subunit of the SCF ubiquitin ligases, but only ASK1 (Arabidopsis SKP1-like 1) and ASK2 have been characterised genetically. In addition, little is known about the function of SKP1 homologues in monocots. Here we report on a winter wheat homologue of SKP1 named TSK1 (Triticum aestivum SKP1-like 1). Expression analyses revealed that it was expressed predominantly in young roots and floral buds. RNA in situ hybridisation showed that it was expressed in the shoot apical meristem (SAM) and anthers, especially the tapetum and microsporocytes at the time of meiosis. It was also expressed in almost the entire meristematic and elongation zones of the root. These observations indicated that TSK1 might function in dividing cells. The Arabidopsis ask1-1 mutant with overexpressed TSK1 driven by the CaMV 35S promoter exhibited partial fertility, suggesting that TSK1 could partially restore function in meiosis to the ask1-1 mutant. In addition, overexpression of TSK1 in wild type Arabidopsis resulted in changes in auxin responses and auxin-related phenotypes, consistent with a role of ASK1 in Arabidopsis auxin response. These results suggest possible functional conservation between TSK1 and ASK1.
Ovine serum and pituitary isoforms of luteinising hormone during the luteal phase
Authors: Arrieta E. , Porras A. , González-Padilla E. , Murcia C. , Rojas S. , Perera-Marín G.
Published: April 2006

The relative abundance of the different isoforms of pituitary and circulating luteinising hormone (LH) in ewes, at different times after the administration of gonadotrophin-releasing hormone (GnRH), during the luteal phase of the oestrous cycle was investigated. Sixteen ewes on Day 9 of their cycle were divided into four groups (n = 4). The control group (T0) received saline solution; the remaining animals received 100 μg GnRH (i.m.) 30, 90 or 180 min (T30, T90 and T180, respectively) before serum and pituitary gland collection. Luteinising hormone polymorphism was analysed by chromatofocusing (pH 10.5–3.5). The LH eluted from each chromatofocusing was grouped on the basis of the following three criteria: (1) according to the pH of elution (pH ≥ 10–3.5); (2) as either a basic (pH ≥ 7.5), neutral (pH 7.4–6.5) and acidic (pH ≤ 6.4) elution of LH of serum and hypophyseal origin; and (3) on the basis of distinct isoforms, of which 10 (A–J) were identifiable in hypophyseal extracts and four (A–D) were found in the serum. In general, the most abundant forms of LH in both the pituitary and serum, at all times, were basic. However, that proportion was greater in hypophyseal extracts (84 ± 3%, 81 ± 4%, 82 ± 3% and 83 ± 2% at T0, T30, T90 and T180, respectively) than in serum (51 ± 5%, 48 ± 10% and 54 ± 6% at T30, T90 and T180, respectively). Neutral and acidic LH made up a larger proportion of the total LH in sera (neutral: 17 ± 4%, 20 ± 6% and 23 ± 3% at T30, T90 and T180, respectively; acidic: 32 ± 8%, 32 ± 11% and 23 ± 6% at T30, T90 and T180, respectively) than in the pituitary extracts (neutral: 4.0 ± 0.7%, 10 ± 4%, 7 ± 2% and 5.0 ± 0.5% at T0, T30, T90 and T180, respectively; acidic: 12 ± 3%, 11 ± 2%, 12 ± 2% and 12 ± 2% at T0, T30, T90 and T180, respectively) at all times. These data reveal that the relative composition of the LH present in the pituitary gland and the LH secreted into the circulation is different, with more neutral and acidic isoforms being secreted. The pattern of circulating LH isoforms changes between 30 and 180 min after GnRH peak induction, with a greater proportion of isoform C (eluting between pH 7.0 and 6.5) at T180 compared with T30 and T90.
Embryo development and embryo transfer in the European mink (Mustela lutreola), an endangered mustelid species
Authors: Amstislavsky S. , Kizilova E. , Ternovskaya Y. , Zudova G. , Lindeberg H. , Aalto J. , Valtonen M.
Published: April 2006

The European mink is an endangered Mustelidae species and thus requires effective conservation measures, although little is known about reproduction in this species. In particular, preimplantation development has not been studied and, therefore, embryonic development and the growth of embryos was documented in the present study for European mink using light and fluorescent microscopy. Embryos develop in the oviducts and then migrate into the uterus on Day 6 post coitum (p.c.) at the morula stage. Embryos expanded as blastocysts from Day 7 until implantation on Day 12 p.c. Based on these findings, the use of embryo transfer for a conservation programme for the European mink was evaluated. Embryos were flushed from European mink resource females and transferred into the uterine horns of recipient hybrid females (honoriks and nohoriks). These hybrids were obtained by mating European polecat males with European mink females and vice versa. A total of 40 embryos was transferred and 20 live kits were born. The rates of pre- and postnatal survival were 50% and 70%, respectively. Both male and female offspring were lighter at birth in the embryo transfer group compared with naturally born controls, but there was no difference at 3 months of age.
Spinal cord endoplasmic reticulum stress associated with a microsomal accumulation of mutant superoxide dismutase-1 in an ALS model
Authors: Kikuchi Hitoshi , Almer Gabriele , Yamashita Satoshi , Guégan Christelle , Nagai Makiko , Xu Zuoshang , Sosunov Alexander A. , McKhann Guy M. , Przedborski Serge
Published: April 2006

Mutation in superoxide dismutase-1 (SOD1), which is a cause of ALS, alters the folding patterns of this protein. Accumulation of misfolded mutant SOD1 might activate endoplasmic reticulum (ER) stress pathways. Here we show that transgenic mice expressing ALS-linked SOD1 mutants exhibit molecular alterations indicative of a recruitment of ER's signaling machinery. We demonstrate by biochemical and morphological methods that mutant SOD1 accumulates inside the ER, where it forms insoluble high molecular weight species and interacts with the ER chaperone immunoglobulin-binding protein. These alterations are age- and region-specific, because they develop over the course of the disease and occur in the affected spinal cord but not in the nonaffected cerebellum in transgenic mutant SOD1 mice. Our results suggest a toxic mechanism for mutant SOD1 by which this ubiquitously expressed pathogenic protein could affect motor neuron survival and contribute to the selective motor neuronal degeneration in ALS.
Coordinated binding of NF-κB family members in the response of human cells to lipopolysaccharide
Authors: Schreiber Joerg , Jenner Richard G. , Murray Heather L. , Gerber Georg K. , Gifford David K. , Young Richard A.
Published: April 2006

The NF-κB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-κB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale location analysis to identify targets of all five NF-κB proteins before and after stimulation of monocytic cells with bacterial lipopolysaccharide (LPS). In unstimulated cells, p50 and p52 bound to a large number of gene promoters that were also occupied by RNA polymerase II. After LPS stimulation, additional NF-κB subunits bound to these genes and to other genes. Genes that became bound by multiple NF-κB subunits were the most likely to show increases in RNA polymerase II occupancy and gene expression. This study identifies NF-κB target genes, reveals how the different NF-κB proteins coordinate their activity, and provides an initial map of the transcriptional regulatory network that underlies the host response to infection.
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans
Authors: Agrawal Ritesh , Stormo Gary D.
Published: April 2006

Motivation: Computational gene prediction methods are an important component of whole genome analyses. While ab initio gene finders have demonstrated major improvements in accuracy, the most reliable methods are evidence-based gene predictors. These algorithms can rely on several different sources of evidence including predictions from multiple ab initio gene finders, matches to known proteins, sequence conservation and partial cDNAs to predict the final product. Despite the success of these algorithms, prediction of complete gene structures, especially for alternatively spliced products, remains a difficult task.

Results: LOCUS (Length Optimized Characterization of Unknown Spliceforms) is a new evidence-based gene finding algorithm which integrates a length-constraint into a dynamic programming-based framework for prediction of gene products. On a Caenorhabditis elegans test set of alternatively spliced internal exons, its performance exceeds that of current ab initio gene finders and in most cases can accurately predict the correct form of all the alternative products. As the length information used by the algorithm can be obtained in a high-throughput fashion, we propose that integration of such information into a gene-prediction pipeline is feasible and doing so may improve our ability to fully characterize the complete set of mRNAs for a genome.

Availability: LOCUS is available from

Contact:  stormo@genetics.wustl.edu
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
Authors: Suzuki Ryota , Shimodaira Hidetoshi
Published: April 2006

Summary: Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option.

Availability: The program is freely distributed under GNU General Public License (GPL) and can directly be installed from CRAN (), the official R package archive. The instruction and program source code are available at

Contact:  ryota.suzuki@is.titech.ac.jp
Oceanobacillus oncorhynchi subsp. incaldanensis subsp. nov., an alkalitolerant halophile isolated from an algal mat collected from a sulfurous spring in Campania (Italy), and emended description of Oceanobacillus oncorhynchi
Authors: Romano Ida , Lama Licia , Nicolaus Barbara , Poli Annarita , Gambacorta Agata , Giordano Assunta
Published: April 2006

A halophilic, alkalitolerant bacterium, strain 20AGT, was isolated from an algal mat collected from a sulfurous spring located in Santa Maria Incaldana (Mondragone, Campania Region, southern Italy). The isolate is Gram-positive, ferments several carbohydrates and has motile, rod-shaped cells that do not sporulate. The isolate grows at pH 6·5–9·5 and in 5–20 % NaCl. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Oceanobacillus; strain 20AGT showed 96·6 % 16S rRNA gene sequence similarity to the type strain of Oceanobacillus iheyensis, DSM 14371T, and 99·5 % similarity to Oceanobacillus oncorhynchi NCIMB 14022T. Levels of DNA–DNA relatedness between strain 20AGT and O. iheyensis DSM 14371T and O. oncorhynchi NCIMB 14022T were respectively 29·4 and 59·0 %. The G+C content of the DNA of strain 20AGT was 40·1 mol%. The predominant respiratory quinone was MK-7, phosphatidylglycerol and phosphatidylcholine were the predominant polar lipids and minor phospholipids were also detected. ai-C14 : 0, ai-C15 : 0 and i-C15 : 0 were the major fatty acids. Strain 20AGT accumulated osmolytes and produced exopolysaccharide. On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, isolate 20AGT should be designated as the type strain of a subspecies of Oceanobacillus oncorhynchi, for which the name Oceanobacillus oncorhynchi subsp incaldanensis subsp. nov. is proposed. The type strain is 20AGT (=DSM 16557T=ATCC BAA-954T).
Pseudomonas otitidis sp. nov., isolated from patients with otic infections
Authors: Clark Linda L. , Dajcs Joseph J. , McLean Celeste H. , Bartell John G. , Stroman David W.
Published: April 2006

A novelPseudomonasspecies, for which the namePseudomonas otitidissp. nov. is proposed, was identified from clinical specimens of infected human ears. Forty-one pseudomonads (34 from patients with acute otitis externa, six from patients with acute otitis media with otorrhoea and one from a patient with chronic suppurative otitis media) were recovered that did not match any known species. On the basis of genetic analyses and biochemical characterization, these isolates were shown to belong to the genusPseudomonas. 16S rRNA gene sequence analysis and DNA–DNA hybridization studies indicated that this novel bacterium is closely related to, but different from,Pseudomonas aeruginosa. A description of this species is based on polyphasic studies of 11 clinical isolates. The type strain ofPseudomonas otitidisis MCC10330T(=ATCC BAA-1130T=DSM 17224T).
Clostridium ganghwense sp. nov., isolated from tidal flat sediment
Authors: Kim Seil , Jeong Hyunyoung , Kim Sanggoo , Chun Jongsik
Published: April 2006

A Gram-negative, strictly anaerobic, halophilic, motile, sporulating and rod-shaped bacterium, designated strain HY-42-06T, was isolated from tidal flat sediment from Ganghwa Island in South Korea. The isolate produced glycerol, ethanol and CO2as fermentation end-products from glucose. Strain HY-42-06Tgrew optimally at 35 °C, pH 7·5 and 3 % (w/v) artificial sea salts. No growth was observed in the absence of sea salts. In phylogenetic analyses based on 16S rRNA gene sequence, strain HY-42-06Tshowed a distinct phyletic line within the members of cluster I of the orderClostridiales. The closest phylogenetic neighbour to strain HY-42-06TwasClostridium novyiATCC 17861T(94·91 % 16S rRNA gene sequence similarity). Several phenotypic characters readily differentiate the tidal flat isolate from phylogenetically related clostridia. On the basis of polyphasic evidence, strain HY-42-06Tshould be classified as a representative of a novel species, for which the nameClostridium ganghwensesp. nov. is proposed. The type strain is HY-42-06T(=IMSNU 40127T=KCTC 5146T=JCM 13193T).
Clostridium schirmacherense sp. nov., an obligately anaerobic, proteolytic, psychrophilic bacterium isolated from lake sediment of Schirmacher Oasis, Antarctica
Authors: Alam Syed Imteyaz , Dixit Aparna , Reddy G. S. N. , Dube S. , Palit Meehir , Shivaji S. , Singh Lokendra
Published: April 2006

A novel obligately anaerobic, proteolytic bacterium, designated AP15T, was isolated from lake sediments of Schirmacher Oasis, Antarctica. The bacterium produced maximum cell mass between 5 and 10 °C in an anaerobic basal medium containing 0·5 % tryptone and peptone. The strain grew optimally at a pH around 8·0 and tolerated NaCl up to a concentration of 7·5 %. It contained diphosphatidylglycerol as the major phospholipid and C15 : 0, C16 : 0and C17 : 0as the major cellular fatty acids. Several amino acids, including arginine, leucine, isoleucine, cysteine, glutamate and serine, supported growth. Glutamate was degraded to acetate, propionate, CO2and H2. In addition, the strain degraded carbohydrates including glucose, raffinose, adonitol, ribose and rhamnose. The main fermentation products during growth on glucose were H2, CO2, formate, acetate, propionate and isovalerate. The DNA G+C content of the bacterium was 24 mol%. On the basis of a phylogenetic analysis, strain AP15Tis identified as a close relative ofClostridium subterminaleATCC 25774T, with which it shares 99·5 % similarity at the 16S rRNA gene sequence level; however, it exhibits a low DNA–DNA binding value (55 %) to this strain at the whole-genome level. In addition to showing other major differences with respect toC. subterminaleand other members of the genusClostridium, AP15Talso exhibits phenotypic differences. On the basis of these differences, strain AP15Tis identified as representing a novel species of the genusClostridium, for which the nameClostridium schirmacherensesp. nov. is proposed. The type strain is AP15T(=DSM 17394T=JCM 13289T).
Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water
Authors: Park Yoon-Dong , Baik Keun Sik , Seong Chi Nam , Bae Kyung Sook , Kim Sanggoo , Chun Jongsik
Published: April 2006

A marine bacterial strain, designated FR1311T, was isolated from a sea-water sample from Ganghwa Island, South Korea. Cells were Gram-negative, facultatively anaerobic, catalase- and oxidase-positive, motile, oval or rod-shaped and halophilic (optimum sea-salt concentration for growth of 5–6 %). Phylogenetic analysis of its 16S rRNA gene sequence revealed that it represented a distinct line of descent within the genusPhotobacterium. The major fatty acids were straight-chain saturated (C16 : 0) and monounsaturated fatty acids (C16 : 1ω7cand C18 : 1ω7c). The predominant respiratory lipoquinone was Q-8. The DNA G+C content was 44 mol%. The phenotypic features of strain FR1199Twere similar to those ofPhotobacterium damselaesubsp.damselaeandPhotobacterium damselaesubsp.piscicida, but several physiological and chemotaxonomic properties readily distinguish the new isolate from them. On the basis of the polyphasic results revealed in this study, FR1311Tis considered to be the type strain of a novel species, for which the namePhotobacterium ganghwensesp. nov. is proposed. The type strain is FR1311T(=IMSNU 60287T=KCTC 12328T=JCM 12487T).
Mycoplasma iguanae sp. nov., from a green iguana (Iguana iguana) with vertebral disease
Authors: Brown D. R. , Demcovitz D. L. , Plourdé D. R. , Potter S. M. , Hunt M. E. , Jones R. D. , Rotstein D. S.
Published: April 2006

Strain 2327T, first cultured from vertebral abscesses of green iguanas (Iguana iguana) collected in Florida, USA, was readily distinguished from all previously described mollicutes by 16S rRNA gene sequence comparisons. Strain 2327T lacks a cell wall, ferments glucose, does not hydrolyse arginine, aesculin or urea and is sensitive to digitonin. Western blots distinguished the novel isolate serologically from the most closely related members of the Mycoplasma neurolyticum cluster. On the basis of these data, the isolate represents a novel species for which the name Mycoplasma iguanae sp. nov. is proposed. The type strain is strain 2327T (=ATCC BAA-1050T=NCTC 11745T).
Millisia brevis gen. nov., sp. nov., an actinomycete isolated from activated sludge foam
Authors: Soddell Jacques A. , Stainsby Fiona M. , Eales Kathryn L. , Kroppenstedt Reiner M. , Seviour Robert J. , Goodfellow Michael
Published: April 2006

The taxonomic position of two mycolic-acid-producing actinomycetes, isolates J81Tand J82, which were recovered from activated sludge foam, was clarified. Comparative 16S rRNA gene sequence studies indicated that the organisms formed a distinct lineage within theCorynebacterineae16S rRNA gene tree. The taxonomic integrity of this group was underpinned by a wealth of phenotypic data, notably characteristic rudimentary right-angled branching. In addition, isolate J81Tcontained the following:meso-diaminopimelic acid, arabinose and galactose;N-glycolated muramic acid residues; a dihydrogenated menaquinone with eight isoprene units as the predominant isoprenologue; a fatty acid profile rich in oleic and palmitoleic acids and with relatively small proportions of myristic, stearic and tuberculostearic acids; mycolic acids with 44–52 carbons; and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides as major polar lipids. Strain J81Twas found to have a chemotaxonomic profile that serves to distinguish it from representatives of all of the other taxa classified as belonging to the suborderCorynebacterineae. In the light of these data, it is proposed that the two isolates be classified in a novel monospecific genus. The name proposed for this taxon isMillisia brevisgen. nov., sp. nov.; strain J81T(=DSM 44463T=NRRL B-24424T) is the type strain ofMillisia brevis.
Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt
Authors: Li Wen-Jun , Zhang Yu-Qin , Schumann Peter , Chen Hua-Hong , Hozzein Wael N. , Tian Xin-Peng , Xu Li-Hua , Jiang Cheng-Lin
Published: April 2006

A coccoid, non-motile actinobacterium, designated strain YIM 70003T, was isolated from a saline, alkaline, desert-soil sample from Egypt. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a distinct phyletic line within the genusKocuriaand was most closely related toKocuria polarisDSM 14382T(98·6 % sequence similarity) andKocuria roseaDSM 20447T(98·2 %). Chemotaxonomic data, including the Lys–Ala3peptidoglycan type, the presence of phosphatidylglycerol and diphosphatidylglycerol as the predominant phospholipids, the presence of MK-8(H2) and MK-9(H2) as the major menaquinones, the predominance of fatty acids ai-C15 : 0and i-C15 : 0and the DNA G+C content, also supported the affiliation of the isolate to the genusKocuria. The low DNA–DNA relatedness withK. polarisDSM 14382T(56·6 %) andK. roseaDSM 20447T(15·5 %) in combination with phenotypic data show that strain YIM 70003Tshould be classified as a novel species of the genusKocuria. The nameKocuria aegyptiasp. nov. is proposed, with strain YIM 70003T(=CCTCC AA203006T=CIP 107966T=KCTC 19010T=DSM 17006T) as the type strain.
Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium
Authors: Brown June M. , Steigerwalt Arnold G. , Morey Roger E. , Daneshvar Maryam I. , Romero Leslie-Joy , McNeil Michael M.
Published: April 2006

Taxonomic studies were performed on 13 clinical isolates (ten of which were epidemiologically related) that had been previously identified asOerskovia turbata. Comparative phylogenetic analysis, based on 16S rRNA gene sequences, indicated that the isolates are closely related toCellulosimicrobium cellulanswith sequence similarity values ranging from 99·5 to 99·8 %. Chemotaxonomic results (fatty acid profiles and menaquinones) supported the inclusion of these isolates in the genusCellulosimicrobium. The DNA G+C content was 74·5 mol%. The results of DNA–DNA reassociation, whole-cell sugars (with galactose as the characteristic whole sugar) and phenotypic properties, including antimicrobial resistance, indicated that these isolates are representatives of a novel species of the genusCellulosimicrobium. The nameCellulosimicrobium funkeisp. nov. is proposed for the novel strains, with strain W6122T(=ATCC BAA-886T=DSM 16025T=CCUG 50705T) as the type strain. The definition of this novelCellulosimicrobiumspecies will assist in the understanding of the epidemiology and clinical significance of these micro-organisms.
Arcanobacterium bialowiezense sp. nov. and Arcanobacterium bonasi sp. nov., isolated from the prepuce of European bison bulls (Bison bonasus) suffering from balanoposthitis, and emended description of the genus Arcanobacterium Collins et al. 1983
Authors: Lehnen Alexandra , Busse Hans-Jürgen , Frölich Kai , Krasinska Malgorzata , Kämpfer Peter , Speck Stephanie
Published: April 2006

A taxonomic study was performed on 13 bacterial strains isolated from preputial swabs of European bison (Bison bonasus) bulls suffering from balanoposthitis. The isolates were Gram-positive, non-motile, facultatively anaerobic, diphtheroid-shaped cells. Based on biochemical profiles and BOX-PCR-generated genomic fingerprints, the isolates were grouped into two clusters represented by four and nine strains, respectively. Strains 1(W3/01)T and 2(W106/04)T, selected as representatives of the two clusters, shared 97·2 % 16S rRNA gene sequence similarity. The highest gene sequence similarities found (95·5–96·4 %) were to Arcanobacterium pyogenes DSM 20630T and Arcanobacterium bernardiae DSM 9152T, demonstrating that the novel strains are members of the genus Arcanobacterium, but are not members of a recognized species. The polar lipid profiles of the two novel strains displayed the major characteristics also found in A. pyogenes DSM 20630T and Arcanobacterium haemolyticum DSM 20595T. Detection of a quinone system with MK-10(H4) as the predominant compound confirmed phylogenetic relatedness of the novel strains to A. pyogenes and separated them from the type species of the genus, A. haemolyticum, which contains MK-9(H4) as the predominant quinone. Results from DNA–DNA hybridizations clearly demonstrated that strains 1(W3/01)T and 2(W106/04)T represent separate species. Based on these data, two novel species of the genus Arcanobacterium are described, for which the names Arcanobacterium bialowiezense sp. nov. [type strain 1(W3/01)T=DSM 17162T=NCTC 13354T] and Arcanobacterium bonasi sp. nov. [type strain 2(W106/04)T=DSM 17163T=NCTC 13355T] are proposed.
Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater
Authors: Xing Defeng , Ren Nanqi , Li Qiubo , Lin Ming , Wang Aijie , Zhao Lihua
Published: April 2006

Two strictly anaerobic bacterial strains (YUAN-3Tand X-29) were isolated from anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor. The strains were Gram-positive, non-spore-forming, mesophilic and motile. Cells were regular rods (0·4–0·8×1·5–8·0 μm) and occurred singly, in pairs and sometimes in chains of up to eight. Autoaggregative and autofluorescent growth of strain YUAN-3Tand non-aggregative growth of strain X-29 were observed at 20–44 °C and pH 3·5–9·0. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. Fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids iso-C16 : 0(44·18 %) and iso-C12 : 0(26·67 %). The DNA G+C contents of strains YUAN-3Tand X-29 were 47·8 and 49·0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a novel phyletic sublineage within theClostridium cellulosirRNA cluster, with <92 % 16S rRNA gene sequence similarity to currently known species. On the basis of polyphasic evidence from this study, it is proposed that the unknown bacterium should be classified in a new genus as a novel species,Ethanoligenens harbinensegen. nov., sp. nov. The type strain ofEthanoligenens harbinenseis YUAN-3T(=JCM 12961T=CGMCC 1.5033T).