bluuebunny/crossref_metadata_2025 huggingface dataset:
Suppression of Schottky leakage current in island-in amorphous silicon thin film transistors with the Cu∕CuMg as source/drain metal
Authors: Wang M. C. , Chang T. C. , Liu Po-Tsun , Xiao R. W. , Lin L. F. , Li Y. Y. , Huang F. S. , Chen J. R.
Published: August 2007

The feasibility of using Cu∕CuMg as a source/drain metal for the island-in amorphous silicon thin film transistors (a-Si:H TFTs) has been investigated. The issue of adhesion between the Cu film and n+–a-Si layer has been overcome by introducing the Cu∕CuMg alloy. Furthermore, the suppression of Schottky leakage current in metal/a-Si:H structure was also observed in the island-in a-Si:H TFT. The island-in a-Si:H TFT exhibited the mobility of 0.52cm2∕Vs, the subthreshold slope of 0.78V∕decade, and the Vth of 3.02V. The experimental result also showed superior performance of the a-Si:H TFT with minimal loss of critical dimension and good thermal stability.
Comparative dynamics of magnetically, acoustically, and Brownian motion driven microcantilevers in liquids
Authors: Xu Xin , Raman Arvind
Published: August 2007

Magnetic, acoustic, and thermal (Brownian motion induced) excitations are commonly used for dynamic atomic force microscopy (AFM) in liquids, yet the fundamental differences in microcantilever vibration response for these different excitations remain poorly understood. In this work we discuss theoretically and experimentally several major differences between the amplitude and phase response of magnetically, acoustically, and thermally excited cantilevers in liquids and propose a way to estimate quantitatively the unsteady structure-borne and fluid-borne excitation forces acting on the acoustically excited AFM cantilever. The results have significant implications both for amplitude and frequency modulated AFM operation in liquids.
Crystal and electronic structures of the complex hydride Li4BN3H10
Authors: Yang J. B. , Wang X. J. , Cai Q. , Yelon W. B. , James W. J.
Published: August 2007

The crystal structure of Li4BN3H10 was investigated using powder neutron diffraction with high sensitivity. The compound crystallizes in the cubic space group I213 with lattice parameters a=10.64519(52)Å with an ordered arrangement of [NH2]−1 and [BH4]−1 anions in a molar ratio of 3:1. The bond lengths between the nearest nitrogen and hydrogen atoms are 1.04(4) and 1.14(4)Å. The bond angle between H(1)–N–H(2) is about 126(6)°, while those between H(3)–B–H(3) and H(3)–B–H(4) are about 109(6)°–110(7)°. There are three different Li sites surrounded by [NH2]−1 and [BH4]−1 anions in distorted tetrahedral configurations. The Li(3)–B and Li(3)–N bond distances are about 1.72(3) and 2.32(2)Å, respectively, while the Li(1)–N and Li(2)–N distances are both around 2.09Å. The strong bonding of Li(3) to the [BH4]−1 and the weaker Li(3)–[NH2]−1 bond are evidenced by the presence of the LiBH4 moiety in a projection of the crystal structure onto the a-b plane. First-principle calculations have been performed based on the structural data. Analyses of the density of states and charge density indicate that H(1) and H(2) strongly interact with N, and H(3) and H(4) interact with B to form [NH2]−1 and [BH4]−1, respectively. It is confirmed that Li(1) and Li(2) are strongly bonded to N and Li(3) is strongly bonded to B. These results are significantly different from some of the previous studies.
Multistability of nematic liquid crystals realized on microscopic orientation patterns
Authors: Lee Eun-Kyu , Kim Jong-Hyun
Published: August 2007

We construct quasi four-fold symmetric orientation patterns by irradiating laser light on a photoactive alignment layer. Double irradiations of spatially modulating interference light in orthogonal directions form symmetric patterns consisted of two stably and dominantly aligning liquid crystal (LC) domains. The LC texture continuously changes accompanying the switching, each state is definitely memorized, with changing electric field strength. A large number of quasistable but effectively stable states exist between two equivalently stable states. This will be suitable for next generation displays that will express full gray scale with multistability.
Nondestructive thickness measurement of biological layers at the nanoscale by simultaneous topography and capacitance imaging
Authors: Casuso Ignacio , Fumagalli Laura , Gomila Gabriel , Padrós Esteve
Published: August 2007

Nanoscale capacitance images of purple membrane layers are obtained simultaneously to topography in a nondestructive manner by operating alternating current sensing atomic force microscopy in jumping mode. Capacitance images show excellent agreement with theoretical modeling and prove to be a noninvasive method for measuring the thickness of purple membrane layers beyond the single monolayer limit with nanoscale lateral spatial resolution. With the ability of spatially resolving the capacitance while preserving the sample from damaging, this technique can be applied for nanoscale thickness measurement of other biological layers and soft materials in general.
Friction of partially embedded vertically aligned carbon nanofibers inside elastomers
Authors: Aksak Burak , Sitti Metin , Cassell Alan , Li Jun , Meyyappan Meyya , Callen Phillip
Published: August 2007

Vertically aligned carbon nanofibers partially embedded inside polyurethane (eVACNFs) are proposed as a robust high friction fibrillar material with a compliant backing. Carbon nanofibers with 50–150nm in diameter and 20–30μm in length are vertically grown on silicon and transferred completely inside an elastomer by vacuum molding. By using time controlled and selective oxygen plasma etching, fibers are partially released up to 5μm length. Macroscale friction experiments show that eVACNFs exhibit reproducible effective friction coefficients up to 1. Besides high friction, the proposed fabrication method improves fiber-substrate bond strength, and enables uniform height nanofibers with a compliant backing.
Rectifying characteristics and transport behavior of SrTiO3−δ(110)∕p-Si (100) heterojunctions
Authors: Luo Z. , Hao J. H. , Gao J.
Published: August 2007

Introducing oxygen vacancy causes the dielectric insulator SrTiO3 to evolve to a n-type semiconductor. The authors have fabricated n-SrTiO3−δ(110)∕p-Si (100) heterojunctions, showing clear rectifying characteristics at different temperatures from 100to292K. A forward-to-reverse bias ratio of about 1200 was found at V=±2V for the p-n junction operated at T=292K. The current-voltage characteristic follows I∝exp(eV∕ηkT) for the p-n junction at relatively low forward-bias voltage, while the relation of I∼V1.9 describes the transport behavior of p-n junction at relatively high forward-bias voltage. The measured results have been discussed in Anderson model and space charge limited model.
Higher permittivity rare earth doped HfO2 for sub-45-nm metal-insulator-semiconductor devices
Authors: Govindarajan S. , Böscke T. S. , Sivasubramani P. , Kirsch P. D. , Lee B. H. , Tseng H.-H. , Jammy R. , Schröder U. , Ramanathan S. , Gnade B. E.
Published: August 2007

Rare earth (RE) doping (Gd, Er, Dy) of HfO2 reduces leakage current by three orders of magnitude compared with pure HfO2. The key to reducing HfO2 leakage current and equivalent oxide thickness (EOT) is stabilization of the higher permittivity tetragonal phase. RE doping of 10–20at.% stabilizes tetragonal HfO2 and increases permittivity. The maximum permittivity achieved for HfREOx is 28. The maximum permittivity for ZrREO is 32. HfGdO metal-insulator-semiconductor capacitors with EOT=1.93nm and leakage current <1×10−8A∕cm2 after 1070°C have been demonstrated.
Magnetocaloric effect in MnSi
Authors: Arora Parul , Chattopadhyay M. K. , Roy S. B.
Published: August 2007

The temperature dependence of heat capacity of MnSi has been measured in the presence of different values of magnetic field. When the magnetic field is applied, an appreciable adiabatic temperature change is observed in the compound. The entropy change due to isothermal change of magnetic field is found to be significant well above the ordering temperature of the compound. This produces a large refrigerant capacity in MnSi, making it important for applications in refrigeration cycles.
Effect of metal-polymer interface on the breakdown electric field of poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene) terpolymer
Authors: Chen Qin , Chu Baojin , Zhou Xin , Zhang Q. M.
Published: August 2007

The authors investigate the effect of electrode material and charge injection on the breakdown electric field of poly(vinylidene fluoride-trifluoroethylene-chlorofluoroethylene) terpolymer. The results indicate that the breakdown is mainly initiated at electrode-polymer interfaces, the properties of which are controlled by metal materials and deposition conditions. Interfaces with lower leakage currents display higher breakdown fields. Terpolymer films with Al and Cr electrodes have lower leakage current and higher breakdown field compared to those with Au and Ag electrodes. The difference in charge injection and breakdown field is attributed to both the existence of interfacial blocking layers and the difference in Schottky barrier height.
Tuned permeability in terahertz split-ring resonators for devices and sensors
Authors: Driscoll T. , Andreev G. O. , Basov D. N. , Palit S. , Cho S. Y. , Jokerst N. M. , Smith D. R.
Published: August 2007

A process is demonstrated for tuning the magnetic resonance frequency of a fixed split-ring resonator array, by way of adding material near the split-ring elements. Applying drops of a silicon-nanospheres/ethanol solution to the surface of the sample decreases the magnetic resonance frequency of the split-ring array in incremental steps of 0.03THz. This fine tuning is done post fabrication and is demonstrated to be reversible. The exhibited sensitivity of the split-ring resonance frequency to the presence of silicon nanospheres also suggests further application possibilities as a sensor device.
Effect of ferromagnetic nanoparticles on the transport properties of a GaMnAs microbridge
Authors: Sapozhnikov M. V. , Fraerman A. A. , Vdovichev S. N. , Gribkov B. A. , Gusev S. A. , Klimov A. Yu. , Rogov V. V. , Chang Joonyeon , Kim Hyungjun , Koo Hyun Cheol , Han Suk-Hee , Chun S. H.
Published: August 2007

A chain of Co nanoparticles was formed along a GaMnAs microbridge by electron beam lithography. The magnetic state of the particles was manipulated by a magnetic force microscope probe. It was found that resistance of the microbridge depended on the state of the particles and was different for the particles in the single-domain and vortex states. The resistance exhibited steplike behavior in an external magnetic field. This behavior was the result of the effect of the inhomogeneous stray fields of the particles on the microbridge resistance. The observed phenomenon can be used as an alternative way to control GaMnAs transport properties.
Hybrid approach for free energy calculations with high-level methods: Application to the SN2 reaction of CHCl3 and OH− in water
Authors: Valiev Marat , Garrett Bruce C. , Tsai Ming-Kang , Kowalski Karol , Kathmann Shawn M. , Schenter Gregory K. , Dupuis Michel
Published: August 2007

We present an approach to calculate the free energy profile along a condensed-phase reaction path based on high-level electronic structure methods for the reactive region. The bulk of statistical averaging is shifted toward less expensive descriptions by using a hierarchy of representations that includes molecular mechanics, density functional theory, and coupled cluster theories. As an application of this approach we study the reaction of CHCl3 with OH− in aqueous solution.
Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals
Authors: Popadin Konstantin , Polishchuk Leonard V. , Mamirova Leila , Knorre Dmitry , Gunbin Konstantin
Published: August 2007

After the effective size of a population,Ne, declines, some slightly deleterious amino acid replacements which were initially suppressed by purifying selection become effectively neutral and can reach fixation. Here we investigate this phenomenon for a set of all 13 mitochondrial protein-coding genes from 110 mammalian species. By using body mass as a proxy forNe, we show that large mammals (i.e., those with lowNe) as compared with small ones (in our sample these are, on average, 369.5 kg and 275 g, respectively) have a 43% higher rate of accumulation of nonsynonymous nucleotide substitutions relative to synonymous substitutions, and an 8–40% higher rate of accumulation of radical amino acid substitutions relative to conservative substitutions, depending on the type of amino acid classification. These higher rates result in a 6% greater amino acid dissimilarity between modern species and their most recent reconstructed ancestors in large versus small mammals. Because nonsynonymous substitutions are likely to be more harmful than synonymous substitutions, and radical amino acid substitutions are likely to be more harmful than conservative ones, our results suggest that large mammals experience less efficient purifying selection than small mammals. Furthermore, because in the course of mammalian evolution body size tends to increase and, consequently,Netends to decline, evolution of mammals toward large body size may involve accumulation of slightly deleterious mutations in mitochondrial protein-coding genes, which may contribute to decline or extinction of large mammals.
β-Catenin regulates excitatory postsynaptic strength at hippocampal synapses
Authors: Okuda Takashi , Yu Lily M. Y. , Cingolani Lorenzo A. , Kemler Rolf , Goda Yukiko
Published: August 2007

The precise contribution of the cadherin–β-catenin synapse adhesion complex in the functional and structural changes associated with the pre- and postsynaptic terminals remains unclear. Here we report a requirement for endogenous β-catenin in regulating synaptic strength and dendritic spine morphology in cultured hippocampal pyramidal neurons. Ablating β-catenin after the initiation of synaptogenesis in the postsynaptic neuron reduces the amplitude of spontaneous excitatory synaptic responses without a concurrent change in their frequency and synapse density. The normal glutamatergic synaptic response is maintained by postsynaptic β-catenin in a cadherin-dependent manner and requires the C-terminal PDZ-binding motif of β-catenin but not the link to the actin cytoskeleton. In addition, ablating β-catenin in postsynaptic neurons accompanies a block of bidirectional quantal scaling of glutamatergic responses induced by chronic activity manipulation. In older cultures at a time when neurons have abundant dendritic spines, neurons ablated for β-catenin show thin, elongated spines and reduced proportion of mushroom spines without a change in spine density. Collectively, these findings suggest that the cadherin–β-catenin complex is an integral component of synaptic strength regulation and plays a basic role in coupling synapse function and spine morphology.
On the formation of gamma-coherent cell assemblies by oriens lacunosum-moleculare interneurons in the hippocampus
Authors: Tort Adriano B. L. , Rotstein Horacio G. , Dugladze Tamar , Gloveli Tengis , Kopell Nancy J.
Published: August 2007

Gamma frequency (30–80 Hz) network oscillations have been observed in the hippocampus during several behavioral paradigms in which they are often modulated by a theta frequency (4–12 Hz) oscillation. Interneurons of the hippocampus have been shown to be crucially involved in rhythms generation, and several subtypes with distinct anatomy and physiology have been described. In particular, the oriens lacunosum-moleculare (O-LM) interneurons were shown to synapse on distal apical dendrites of pyramidal cells and to spike preferentially at theta frequency, even in the presence of gamma-field oscillations. O-LM cells have also recently been shown to present higher axonal ramification in the longitudinal axis of the hippocampus. By using a hippocampal network model composed of pyramidal cells and two types of interneurons (O-LM and basket cells), we show here that the O-LM interneurons lead to gamma coherence between anatomically distinct cell modules. We thus propose that this could be a mechanism for coupling longitudinally distant cells excited by entorhinal cortex inputs into gamma-coherent assemblies.
Expression of dominant-negative Dmp53 in the adult fly brain inhibits insulin signaling
Authors: Bauer Johannes H. , Chang Chengyi , Morris Siti Nur Sarah , Hozier Suzanne , Andersen Sandra , Waitzman Joshua S. , Helfand Stephen L.
Published: August 2007

In
Drosophila melanogaster
, p53 (Dmp53) is an important mediator of longevity. Expression of dominant-negative (DN) forms of Dmp53 in adult neurons, but not in muscle or fat body cells, extends lifespan. The lifespan of calorie-restricted flies is not further extended by simultaneously expressing DN-Dmp53 in the nervous system, indicating that a decrease in Dmp53 activity may be a part of the CR lifespan-extending pathway in flies. In this report, we show that selective expression of DN-Dmp53 in only the 14 insulin-producing cells (IPCs) in the brain extends lifespan to the same extent as expression in all neurons and this lifespan extension is not additive with CR. DN-Dmp53-dependent lifespan extension is accompanied by reduction of
Drosophila
insulin-like peptide 2 (dILP2) mRNA levels and reduced insulin signaling (IIS) in the fat body, which suggests that Dmp53 may affect lifespan by modulating insulin signaling in the fly.
Management of Mental Health Patients Attending Victorian Emergency Departments
Authors: Knott Jonathan C. , Pleban Alex , Taylor David , Castle David
Published: August 2007

Objective: To evaluate the management of mental health presentations to Victorian emergency departments.

Method: An observational study in five Victorian emergency departments (four metropolitan and one regional). All patients with an ICD-10 discharge diagnosis for a predetermined mental health disorder were included. Data were collected on patient demographics, presentation, clinical management (emergency and mental health) and disposition.

Results: There were 3702 patients enrolled (96.0% of all mental health presentations). At presentation 39.1% were intoxicated and 39.9% arrived by ambulance, 17.6% with the police. There was a significant variation (p <0.001) between sites for: the median time to be seen by a clinician (14 vs 43 min), the time between referral to and review by mental health services (15 vs 50 min), the median time in the emergency department (208 min vs 380 min), the proportion who spent >24 h in the emergency department (0.0% vs 11.6%) and disposition (proportion discharged home from ED 49.8% vs 63.5%).

Conclusion: Important variations were identified in the management of patients with mental health presentations to Victorian emergency departments. This variation is most likely due to differing access to resources. All levels of administration must work with carers and patients to ensure that optimal patient care is provided at every site.
Right-hemisphere reading in a case of developmental deep dyslexia
Authors: Pitchford Nicola J. , Funnell Elaine , De Haan Bianca , Morgan Paul S.
Published: August 2007

The right-hemisphere hypothesis of deep dyslexia has received support from functional imaging studies of acquired deep dyslexia following damage to the left cerebral hemisphere, but no imaging studies of cases of developmental deep dyslexia, in which brain damage is not suspected, have been reported. In this paper, we report the first evidence of right hyperactivation in an adult case of developmental deep dyslexia. Hyperactivation was observed in the right inferior frontal cortex during functional magnetic resonance imaging (fMRI) of the oral reading of imageable content words and nonwords to which imageable lexical responses were frequently made. No evidence of right hyperactivation was observed in the oral reading of function words, nor during the naming of imageable words in response to pictured objects. The results reveal strategic and selective use of right-hemisphere functions for particular types of written stimuli. We propose that children with developmental deep dyslexia compensate for their lack of phonological skills by accessing right-hemisphere imageable associations that provide a mnemonic for linking written forms to spoken names.
An antigen-specific pathway for CD8 T cells across the blood-brain barrier
Authors: Galea Ian , Bernardes-Silva Martine , Forse Penny A. , van Rooijen Nico , Liblau Roland S. , Perry V. Hugh
Published: August 2007

CD8 T cells are nature's foremost defense in encephalitis and brain tumors. Antigen-specific CD8 T cells need to enter the brain to exert their beneficial effects. On the other hand, traffic of CD8 T cells specific for neural antigen may trigger autoimmune diseases like multiple sclerosis. T cell traffic into the central nervous system is thought to occur when activated T cells cross the blood-brain barrier (BBB) regardless of their antigen specificity, but studies have focused on CD4 T cells. Here, we show that selective traffic of antigen-specific CD8 T cells into the brain occurs in vivo and is dependent on luminal expression of major histocompatibility complex (MHC) class I by cerebral endothelium. After intracerebral antigen injection, using a minimally invasive technique, transgenic CD8 T cells only infiltrated the brain when and where their cognate antigen was present. This was independent of antigen presentation by perivascular macrophages. Marked reduction of antigen-specific CD8 T cell infiltration was observed after intravenous injection of blocking anti–MHC class I antibody. These results expose a hitherto unappreciated route by which CD8 T cells home onto their cognate antigen behind the BBB: luminal MHC class I antigen presentation by cerebral endothelium to circulating CD8 T cells. This has implications for a variety of diseases in which antigen-specific CD8 T cell traffic into the brain is a beneficial or deleterious feature.
Quantifying Loss Caused by Ray Blight Disease in Tasmanian Pyrethrum Fields
Authors: Pethybridge Sarah J. , Esker Paul , Dixon Phillip , Hay Frank , Groom Tim , Wilson Calum , Nutter Forrest W.
Published: August 2007

The efficacy of newly implemented fungicide recommendations on reducing the intensity of ray blight disease caused by Phoma ligulicola to achieve site-specific attainable yield potentials in Tasmanian pyrethrum fields was quantified over two seasons in 46 and 51 fields during the 2003 and 2004 growing seasons, respectively. Disease intensity and yield in two plots (10 × 24 m), one following the commercial fungicide protocol recommendations and the second receiving no fungicide, were assessed in each pyrethrum field. The commercial fungicide protocol consisted of one application of azoxystrobin at 150 g a.i./ha, followed by two applications of a tank mixture of difenoconazole at 125 g a.i./ha and chlorothalonil at 1,008 liters a.i./ha at 14- to 21-day intervals. This program resulted in significant decreases in defoliation severity and the incidence of stems and flowers with ray blight, and increases in the height of stems and number of flowers produced per stem in October and November. In plots receiving the commercial fungicide protocol, the dry weight of flowers was increased by 76 and 68% in 2003 and 2004, respectively. Moreover, pyrethrin yield increased by 81 and 78% when the commercial fungicide protocol was used compared with the nontreated plots. Tobit regression was used to examine the relationships and thresholds among disease intensity measures (defoliation severity, stem severity, and incidence of flowers with ray blight) assessed just prior to harvest. This regression utilized a left-censored regression model to define subminimal thresholds, as none of the disease intensity measures could be less than 0. Defoliation severity had a threshold of 35.3% before stem severity linearly increased and a threshold of 38.2% before the incidence of flowers with ray blight linearly increased. Finally, the threshold for stem severity was 13.7% before the incidence of flowers with ray blight linearly increased. These thresholds can be used to assist growers in making disease management decisions with the objective of minimizing loss of flowers by maintaining defoliation severity below the critical point at which the incidence of flowers with ray blight begins to linearly increase.
First Report of Uromyces transversalis, Causal Agent of Gladiolus Rust, in San Diego County, California
Authors: Blomquist C. L. , Thomas S. L. , McKemy J. M. , Nolan P. A. , Luque-Williams M.
Published: August 2007

In May 2006, signs and symptoms of a rust disease were observed on hybrid gladiolus plants in a home garden located in the city of San Diego, CA. Uredinial lesions were bright orange, variable in shape from globose to oval to transversely elongate, and measured 28 to 652 × 36 to 994 μm. Urediniospores measured 16 to 26 × 16 to 23 μm and had hyaline walls that were 2 μm thick and finely echinulate with recurved spines. Some uredinial lesions located primarily at the base of the leaves were surrounded by dark, irregular lesions (telia) by the epidermis. Telia contained nonseptate, light-to-chestnut brown teliospores that measured 20 to 30 × 13 to 20 μm with an apical thickening measuring 2 to 5 μm. Teliospore pedicels measured 3 to 33 × 2 to 5 μm. Groups of teliospores were separated into locules by upright, pale brown paraphyses. The rust was identified as Uromyces transversalis, the cause of gladiolus rust and a quarantine pest for the United States. An intensive 23 square mile survey was initiated and resulted in the detection of infected plants at one nearby residence 200 feet away, in a commercial nursery six miles east of the initial site of detection, and at a residence across the street from the infected nursery. Plants in the nursery were grown outdoors in three blocks, in which the disease incidences were 20, 80, and 100% with varying levels of severity. Telia were also found at this location. The nursery grows gladiolus flowers for sale at local farmer markets, sometimes supplemented by additional cut gladiolus from Mexico. U. transversalis is known to occur in Mexico (2). This rust is under eradication at all four sites. Gladiolus rust was reported in Florida in April 2006. To our knowledge, this is the first confirmed report of Gladiolus rust in California.

References: (1) J. R. Hernández. Invasive Fungi. Gladiolus Rust. Systemic Botany and Mycology Laboratory, Online publication. ARS, USDA, 2004. (2) G. Rodríguez-Alvarado et al. Plant Dis. 90:687, 2006.
Tropical soda apple mosaic virus Identified in Solanum capsicoides in Florida
Authors: Adkins S. , McAvoy G. , Rosskopf E. N.
Published: August 2007

Red soda apple (Solanum capsicoides All.), a member of the Solanaceae, is a weed originally from Brazil (3). It is a perennial in southern Florida and is characterized by abundant prickles on stems, petioles, and leaves. Prickles on stems are more dense than those on its larger, noxious weed relative, tropical soda apple (Solanum viarum Dunal), and the mature red soda apple fruits are bright red in contrast to the yellow fruits of tropical soda apple (2). Virus-like foliar symptoms of light and dark green mosaic were observed on the leaves of a red soda apple in a Lee County cow pasture during a tropical soda apple survey during the fall of 2004. The appearance of necrotic local lesions following inoculation of Nicotiana tabacum cv. Xanthi nc with sap from the symptomatic red soda apple leaves suggested the presence of a tobamovirus. Tropical soda apple mosaic virus (TSAMV), a recently described tobamovirus isolated from tropical soda apple in Florida, was specifically identified by a double-antibody sandwich-ELISA (1). An additional six similarly symptomatic red soda apple plants were later collected in the Devils Garden area of Hendry County. Inoculation of N. tabacum cv. Xanthi nc with sap from each of these symptomatic plants also resulted in necrotic local lesions. Sequence analysis of the TSAMV coat protein (CP) gene amplified from total RNA by reverse transcription (RT)-PCR with a mixture of upstream (SolA5′CPv = 5′-GAACTTWCAGAAGMAGTYGTTGATGAGTT-3′; SolB5′CPv = 5′-GAACTCACTGARRMRGTTGTTGAKGAGTT-3′) and downstream (SolA3′CPvc = 5′-CCCTTCGATTTAAGTGGAGGGAAAAAC-3′; SolB3′CPvc = 5′-CGTTTMKATTYAAGTGGASGRAHAAMCACT-3′) degenerate primers flanking the CP gene of Solanaceae-infecting tobamoviruses confirmed the presence of TSAMV in all plants from both locations. Nucleotide and deduced amino acid sequences of the 483-bp CP gene were both 98 to 99% identical to the original TSAMV CP gene sequences in GenBank (Accession No. AY956381). TSAMV was previously identified in tropical soda apple in these two locations in Lee and Hendry counties and three other areas in Florida (1). Sequence analysis of the RT-PCR products also revealed the presence of Tomato mosaic virus in the plant from Lee County. To our knowledge, this represents the first report of natural TSAMV infection of any host other than tropical soda apple and suggests that TSAMV may be more widely distributed in solanaceous weeds than initially reported.

References: (1) S. Adkins et al. Plant Dis. 91:287, 2007. (2) N. Coile. Fla. Dep. Agric. Consum. Serv. Div. Plant Ind. Bot. Circ. 27, 1993. (3) U.S. Dep. Agric., NRCS. The PLANTS Database. National Plant Data Center. Baton Rouge, LA. Published online, 2006.
Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil
Authors: Jeong Hyunyoung , Lim Young Woon , Yi Hana , Sekiguchi Yuji , Kamagata Yoichi , Chun Jongsik
Published: August 2007

A strictly anaerobic, Gram-positive, endospore-forming bacterium, strain HY-37-4T, was isolated from a forest-soil sample collected in Jeju, Republic of Korea. The cells were motile rods with peritrichous flagella. Strain HY-37-4T fermented various carbohydrates and the end products from glucose were formate, acetate and H2. The major cellular fatty acids were C16 : 0, C16 : 0 3-OH and iso-C17 : 1 I/anteiso B. The G+C content of the DNA was 41 mol%. A phylogenetic analysis based on 16S rRNA sequence data indicated that the forest isolate was most closely related to Clostridium herbivorans, Clostridium populeti, Clostridium polysaccharolyticum and Eubacterium xylanophilum, which belong to Clostridium cluster XIVa. However, the low levels of 16S rRNA gene sequence similarity (92.3–93.9 %) with respect to these taxa indicate that strain HY-37-4T represents a novel species. Several phenotypic characteristics readily allowed the isolate to be distinguished from other phylogenetically related taxa. On the basis of the polyphasic evidence, strain HY-37-4T represents a novel taxon, for which the name Anaerosporobacter mobilis gen. nov., sp. nov. is proposed. The type strain is HY-37-4T (=IMSNU 40011T=KCTC 5027T=DSM 15930T).
Bacillus niabensis sp. nov., isolated from cotton-waste composts for mushroom cultivation
Authors: Kwon Soon-Wo , Lee Seon-Young , Kim Byung-Yong , Weon Hang-Yeon , Kim Jung-Bong , Go Seung-Joo , Lee Gil-Bok
Published: August 2007

A group of five bacilli, designated strains 4T12, 4T19T, 5M45, 5M53 and 5T52, isolated from cotton-waste composts for mushroom cultivation, were examined. These strains were Gram-positive, aerobic, motile, spore-forming rods. 16S rRNA gene sequence analyses revealed that the isolates belonged to the genus Bacillus, showing the highest levels of similarity (approx. 96.6–96.9 %) with respect to Bacillus herbersteinensis DSM 16534T. The values for DNA–DNA hybridization (approx. 85–96 %) among these five strains revealed that they belong to the same species. The major menaquinone present was MK-7 and the predominant cellular fatty acids were anteiso-C15 : 0 (approx. 24.5–33.9 %) and C16 : 0 (approx. 15.1–34.1 %). The DNA G+C contents were 37.7–40.9 mol%. On the basis of physiological, biochemical, chemotaxonomic and comparative genomic analyses, the five isolates represent a novel species of the genus Bacillus, for which the name Bacillus niabensis sp. nov. is proposed. The type strain is 4T19T (=KACC 11279T =DSM 17723T).
Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer
Authors: Klouche Nihel , Fardeau Marie-Laure , Lascourrèges Jean-François , Cayol Jean-Luc , Hacene Hocine , Thomas Pierre , Magot Michel
Published: August 2007

A novel, strictly anaerobic, chemo-organotrophic bacterium, designated strain VNs68T, was isolated from a well that collected water from a deep aquifer at a depth of 800 m in the Paris Basin, France. Cells were thin, non-motile, Gram-positive rods forming terminal endospores (3.0–5.0×0.5 μm). Strain VNs68Tgrew at temperatures between 30 and 55 °C (optimum 42 °C) and at pH 5.6–8.4 (optimum pH 7.3). It did not require salt for growth but tolerated up to 40 g NaCl l−1. Strain VNs68Twas an obligate heterotroph fermenting carbohydrates such as glucose, xylose, fructose, ribose and cellobiose. Casamino acids and amino acids (arginine, serine, lysine, alanine, aspartate, asparagine, isoleucine, histidine) were also fermented. The main fermentation products from glucose were acetate with H2and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, nitrate and nitrite were not used as electron acceptors. The G+C content of the genomic DNA was 42.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs68Twas affiliated to cluster XI, orderClostridiales, domainBacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain VNs68Tis considered to represent a novel species of a new genus, for which the nameGeosporobacter subterraneusgen. nov., sp. nov. is proposed. The type strain ofGeosporobacter subterraneusis VNs68T(=DSM 17957T=JCM 14037T).
Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam
Authors: Iino Takao , Mori Koji , Tanaka Kenji , Suzuki Ken-ichiro , Harayama Shigeaki
Published: August 2007

A mesophilic, strictly anaerobic bacterium, strain Sjm18-20T, was isolated from the alimentary canal of a Japanese corbicula clam. Cells of strain Sjm18-20T were Gram-negative, non-sporulating, straight to slightly curved rods, 2.5–6.0 μm long, and were motile with oscillatory movements by means of peritrichous flagella. Cells elongated to 30 μm after prolonged cultivation. Optimum growth was observed at 30 °C and pH 6.0–6.5. Growth occurred below 4.0 % (w/v) NaCl. Strain Sjm18-20T produced acid from d-glucose and a few pentoses such as l-arabinose, d-ribose and d-xylose. n-Valeric acid was the major end product from glucose. The genomic DNA G+C content of strain Sjm18-20T was 52.9 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain Sjm18-20T could be accommodated in clostridial cluster IV of the low-G+C-content Gram-positive bacteria and that the closest neighbour of this organism (92.6–92.9 % similarity) was the cloned 16S rRNA gene sequence of a not-yet cultured bacterium, thought to represent Oscillospira guilliermondii. The nearest cultivated neighbours of strain Sjm18-20T were Clostridium orbiscindens DSM 6740T and Clostridium viride T2-7T, with sequence similarities of 91.3 and 89.1 %, respectively. On the basis of phenotypic features and phylogenetic position, it is proposed that this isolate represents a novel species in a new genus, Oscillibacter valericigenes gen. nov., sp. nov. The type strain of Oscillibacter valericigenes is Sjm18-20T (=NBRC 101213T =DSM 18026T).
Amycolatopsis echigonensis sp. nov. and Amycolatopsis niigatensis sp. nov., novel actinomycetes isolated from a filtration substrate
Authors: Ding Linxian , Hirose Taketo , Yokota Akira
Published: August 2007

The taxonomic position of two actinomycete strains, LC2T and LC11T, isolated from a filtration substrate made from Japanese volcanic soil, was determined using a polyphasic approach. The strains grew at temperatures from 5 to 45 °C, on media of pH between 6 and 11 and in the presence of 7 % NaCl. The major menaquinone was MK-9(H4). The major fatty acid was iso-C16 : 0. A phylogenetic tree based on 16S rRNA gene sequences showed that the two strains formed a distinct evolutionary lineage within the genus Amycolatopsis. On the basis of their morphological, physiological and genotypic characteristics, the isolates are proposed to represent two novel species of the genus Amycolatopsis, for which the names Amycolatopsis echigonensis sp. nov. (type strain LC2T =IAM 15387T =CCTCC AB206019T), and Amycolatopsis niigatensis sp. nov. (type strain LC11T =IAM 15388T =CCTCC AB206020T) are proposed.
Thalassococcus halodurans gen. nov., sp. nov., a novel halotolerant member of the Roseobacter clade isolated from the marine sponge Halichondria panicea at Friday Harbor, USA
Authors: Lee On On , Tsoi Mandy M. Y. , Li Xiancui , Wong Po-Keung , Qian Pei-Yuan
Published: August 2007

A Gram-negative, non-pigmented, ovoid-shaped, strictly aerobic, catalase- and oxidase-positive and highly halotolerant bacterial strain that was devoid of swimming and gliding motility, designated UST050418-052T, was isolated from the surface of the marine sponge Halichondria panicea at Friday Harbor, WA, USA. Strain UST050418-052T required NaCl for growth and could tolerate salt concentrations of up to 18 %. The primary respiratory quinone was ubiquinone-10 and the DNA G+C content was 57.8 mol%. The predominant fatty acids were the saturated fatty acids 16 : 0 and 18 : 0 and the monounsaturated fatty acids 18 : 1ω7c and 18 : 1ω9c, altogether representing 82.9 % of the total. Phylogenetic analysis based on the 16S rRNA gene sequence placed UST050418-052T in a distinct lineage within the Roseobacter clade in the family Rhodobacteraceae, with 95.0–95.8 % sequence similarity to members of the nearest genus Thalassobius. The DNA–DNA relatedness between UST050418-052T and Thalassobius gelatinovorus IAM 12617T was 9 %. Strain UST050418-052T could be differentiated from closely related members of the Roseobacter clade by a number of chemotaxonomic and phenotypic characteristics such as its distinct fatty acid profile, ability to reduce nitrate to nitrite and inability to utilize citrate, succinate, l-arginine and pyruvate. Based on the phylogenetic, chemotaxonomic and phenotypic evidence presented in this study, we suggest that strain UST050418-052T represents a novel genus in the family Rhodobacteraceae. The name Thalassococcus halodurans gen. nov., sp. nov., is thus proposed. The type strain of Thalassococcus halodurans is UST050418-052T (=JCM 13833T =NRRL B-41465T).
‘Candidatus Phytoplasma lycopersici’, a phytoplasma associated with ‘hoja de perejil’ disease in Bolivia
Authors: Arocha Yaima , Antesana Olivia , Montellano Ernesto , Franco Pablo , Plata G. , Jones Phil
Published: August 2007

New diseases known locally as ‘hoja de perejil’ of tomato (Lycopersicon esculentum Mill) and ‘brotes grandes’ of potato (Solanum tuberosum L.) were first recognized in surveys of production fields in Bolivia during 2000–2003. Alfalfa (Medicago sativa) witches' broom and little leaf diseases of native weeds Morrenia variegata and mora-mora (Serjania perulacea) were also identified near to production fields. Phytoplasma aetiology was attributed to each of these diseases following detection and initial identification of aster yellows group (16SrI) phytoplasmas in all five diseased plant species. While potato, alfalfa and mora-mora plants contained indistinguishable 16SrI-B strains, ‘hoja de perejil’ (THP) and morrenia little leaf (MVLL)-associated phytoplasma strains shared 97.5 % 16S rRNA gene sequence similarity with ‘Candidatus Phytoplasma asteris’ and related strains and <95 % similarity with all other ‘Candidatus Phytoplasma’ species. Phylogenetic analysis of 16S rRNA gene sequences indicated that the THP and MVLL phytoplasmas represent a novel lineage within the aster yellows (16SrI) group and, on the basis of unique 16S rRNA gene sequences, we propose that THP and MVLL phytoplasmas represent ‘Candidatus Phytoplasma lycopersici’, with THP as the reference strain.
Methylobacterium salsuginis sp. nov., isolated from seawater
Authors: Wang Xun , Sahr Foday , Xue Ting , Sun Baolin
Published: August 2007

Three pink-pigmented, facultatively methylotrophic strains, designated MP1, MP2 and MRT, were isolated from seawater from southern China and characterized. Analysis of their complete 16S rRNA gene sequences revealed that they constituted three separate phylogenetic groups, showing the highest levels of similarity with respect to some members of the genusMethylobacterium. PCR amplification also showed the gene coding for theα-subunit of methanol dehydrogenase (mxaF) to be present in all strains, indicating a methylotrophic metabolism. All three strains utilizedd-fructose, ethanol and nutrient agar as carbon sources, but did not utilize sucrose, citrate, acetate or formaldehyde. On the basis of the phenotypic, phylogenetic and genotypic analyses, strain MRTrepresents a novel species, for which the nameMethylobacterium salsuginissp. nov. is proposed, with MRT(=CGMCC 1.6474T=NCCB 100140T) as the type strain. Strains MP1 and MP2 respectively represent novel strains of the speciesMethylobacterium oryzaeandMethylobacterium lusitanum.
Prevotella pleuritidis sp. nov., isolated from pleural fluid
Authors: Sakamoto Mitsuo , Ohkusu Kiyofumi , Masaki Takayuki , Kako Hirofumi , Ezaki Takayuki , Benno Yoshimi
Published: August 2007

A strain isolated from pleural fluid of a patient with suppurative pleuritis (strain GTC 3021T) was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the isolate was a member of the genusPrevotella. The isolate was related toPrevotella enoecaATCC 51261Twith about 92 % 16S rRNA gene sequence similarity. The strain was an obligately anaerobic, non-pigmenting, non-spore-forming, non-motile, Gram-negative rod. Although the phenotypic and biochemical characteristics of the strain were similar to those ofP. enoecaJCM 12259T, the cellular fatty acid composition of the isolate was significantly different from that ofP. enoecaJCM 12259T(C18 : 1ω9cand anteiso-C15 : 0fatty acid content). Based on these data, we propose a novelPrevotellaspecies,Prevotella pleuritidissp. nov., with the type strain GTC 3021T(=JCM 14110T=CCUG 54350T). The G+C content of the type strain is 45.4 mol%.
Prevotella paludivivens sp. nov., a novel strictly anaerobic, Gram-negative, hemicellulose-decomposing bacterium isolated from plant residue and rice roots in irrigated rice-field soil
Authors: Ueki Atsuko , Akasaka Hiroshi , Satoh Atsuya , Suzuki Daisuke , Ueki Katsuji
Published: August 2007

Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).
Sporosarcina saromensis sp. nov., an aerobic endospore-forming bacterium
Authors: An Sun-Young , Haga Tomomi , Kasai Hiroaki , Goto Keiichi , Yokota Akira
Published: August 2007

Two Gram-positive, endospore-forming, rod-shaped bacterial strains, HG645T and HG711, were respectively isolated from surface water of a brackish lake and sediment of a fishery harbour in Japan and were subsequently characterized taxonomically using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HG645T and HG711 are affiliated phylogenetically to the genus Sporosarcina, and they exhibit sequence similarities of 95.7–97.3 % to the type strains of Sporosarcina species. DNA–DNA relatedness between strain HG645T and the type strain of the phylogenetically related species Sporosarcina aquimarina was less than 10 %. The DNA G+C content of strains HG645T and HG711 were respectively 46.0 and 45.2 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell-wall peptidoglycan type (Lys–Glu), major cellular fatty acids (iso-C15 : 0 and anteiso-C15 : 0) and quinone type (MK-7) of the isolates support their affiliation to the genus Sporosarcina. On the basis of phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent a novel species of the genus Sporosarcina, for which the name Sporosarcina saromensis sp. nov. is proposed. The type strain is strain HG645T (=MBIC08270T=IAM 15429T =KCTC 13119T).
Salinicoccus luteus sp. nov., isolated from a desert soil
Authors: Zhang Yu-Qin , Yu Li-Yan , Liu Hong-Yu , Zhang Yue-Qin , Xu Li-Hua , Li Wen-Jun
Published: August 2007

A moderately halophilic bacterium, strain YIM 70202T, was isolated from a desert soil sample collected from Egypt and was subjected to a taxonomic investigation. In a phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70202Twas affiliated to theSalinicoccusclade, showing 94.5–96.8 % 16S rRNA gene sequence similarity to the recognized species of the genusSalinicoccus, in whichSalinicoccus roseusCCM 3516Twas the nearest neighbour. The DNA–DNA relatedness value of the novel isolate withS. roseusCCM 3516Twas 12.7 %. The novel isolate grew at temperatures between 4 and 45 °C and at pH values ranging from 7.0 to 11.0, with an optimum of 30 °C and pH 8.0–9.0, respectively. Strain YIM 70202Tgrew optimally in the presence of 10 % NaCl (w/v) and growth was observed at NaCl concentrations in the range 1–25 % (w/v). Chemotaxonomic data revealed that strain YIM 70202Tcontained MK-6 as the predominant respiratory quinone, possessedl-Lys–Gly5as the cell-wall peptidoglycan, had phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid as the polar lipids and contained i-C15 : 0and ai-C15 : 0as the predominant fatty acids. The DNA G+C content was 49.7 mol%. The biochemical and chemotaxonomic properties demonstrate that strain YIM 70202Trepresents a novel species of the genusSalinicoccus. The nameSalinicoccus luteussp. nov. is proposed with strain YIM 70202T(=CGMCC 1.6511T=KCTC 3941T) as the type strain.