bluuebunny/crossref_metadata_2025 huggingface dataset:
Polycrystalline tetrabenzoporphyrin organic field-effect transistors with nanostructured channels
Authors: Shea Patrick B. , Chen Charlene , Kanicki Jerzy , Pattison Lisa R. , Petroff Pierre , Yamada Hiroko , Ono Noboru
Published: June 2007

Solution-processed organic thin-film field-effect transistors (OFETs) were fabricated using a precursor form of the organic semiconductor tetrabenzoporphyrin (TBP) deposited on a thermal silicon oxide gate insulator patterned with nanometer-scale trenches. Thermal conversion of the precursor film to TBP was enhanced by ordered TBP aggregation in the prepatterned trenches, demonstrating precise control and placement of long- and short-range ordering of the organic semiconductor. OFETs with channels parallel to trench direction growth were found to have field-effect mobility approaching one order of magnitude greater than transistors fabricated with the channel oriented perpendicular to dendrimer growth.
Filtered cathodic arc deposition with ion-species-selective bias
Authors: Anders André , Pasaja Nitisak , Sansongsiri Sakon
Published: June 2007

A dual-cathode arc plasma source was combined with a computer-controlled bias amplifier to synchronize substrate bias with the pulsed production of plasma. In this way, bias can be applied in a material-selective way. The principle has been applied to the synthesis of metal-doped diamondlike carbon films, where the bias was applied and adjusted when the carbon plasma was condensing and the substrate was at ground when the metal was incorporated. In doing so, excessive sputtering by energetic metal ions can be avoided while the sp3∕sp2 ratio can be adjusted. It is shown that the resistivity of the film can be tuned by this species-selective bias; Raman spectroscopy was used to confirm expected changes of the amorphous ta-C:Mo films. The species-selective bias principle could be extended to multiple material plasma sources and complex materials.
Photoactivated and patternable charge transport materials and their use in organic light-emitting devices
Authors: Liu Jie , Lewis Larry N. , Duggal Anil R.
Published: June 2007

Organic light-emitting devices (OLEDs) usually employ at least one organic semiconductor layer that acts as a hole-injection material. The prototypical example is a conjugated polymer such as poly(3,4-ethylenedioxythiophene) heavily p doped with polystyrene sulfonic acid. Here, the authors describe a chemical doping strategy for hole injection material formulation that enables spatial patterning of the material conductivity through optical activation. The strategy utilizes an organic photoacid generator (PAG) dispersed in a polymeric organic semiconductor host. Upon UV irradiation, the PAG decomposes and generates a strong protonic acid that subsequently p dopes the host. The authors demonstrate an OLED made with such a light-activated hole-injection material and show that arbitrary emission patterning can be accomplished. This approach may provide a simple, low cost path toward specialty lighting and signage applications for OLED technology.
In situ assembled diffraction grating for biomolecular detection
Authors: Chang Chun-Li , Acharya Ghanashyam , Savran Cagri A.
Published: June 2007

The authors report experiments with a diffraction-based biosensor based on self-assembly of target-containing nanobeads that form optical diffraction gratings. They demonstrate that the diffraction signal is a function of the bead size, and that noise is minimized by normalizing the intensities of the diffraction modes. They characterize the dependence of the diffraction signal on equivalent bead size and demonstrate the potential of the scheme in detecting biologically significant molecules.
Layer rotation mechanism in the chiral smectic C phase
Authors: Jang J. N. , Davey A. B. , Crossland W. A.
Published: June 2007

The authors propose a model for the layer rotation of the chiral smectic C (SmC*) phase, which is intended to give answers to some basic questions about smectic layer rotation. They have proposed that layer rotation is related to the electroclinic effect, by which an induced asymmetric population density of the director for each asymmetric ac cycle is induced. In our modeling, the driving force for the layer rotation is the deformation of the molecular coupling configuration and a volume change by the tilt cone rotation.
High power and high efficiency blue light emitting diode on freestanding semipolar (101¯1¯) bulk GaN substrate
Authors: Zhong Hong , Tyagi Anurag , Fellows Natalie N. , Wu Feng , Chung Roy B. , Saito Makoto , Fujito Kenji , Speck James S. , DenBaars Steven P. , Nakamura Shuji
Published: June 2007

Blue InGaN∕GaN multiple-quantum-well light emitting diodes with a peak emission wavelength of 444nm were grown on low extended defect density semipolar (101¯1¯) bulk GaN substrates by conventional metal-organic chemical vapor deposition. The calculated external quantum efficiency and output power at a drive current of 20mA under pulsed operations (10% duty cycle) were 29% and 16.21mW, respectively. The device exhibited virtually no peak electroluminescence wavelength shift with increasing drive currents, indicating a significant reduction of polarization-related internal electric fields.
Conversion of circularly polarized light into linearly polarized light in anisotropic phase gratings using photo-cross-linkable polymer liquid crystals
Authors: Ono Hiroshi , Nakamura Manabu , Kawatsuki Nobuhiro
Published: June 2007

The polarization state of the diffraction light from the polarization holographic grating on varying the polarization conditions of the writing beams has been investigated on the basis of Jones theory. The authors found that the polarization holographic grating, which was fabricated by irradiating the two writing beams with around 0.2 of polarization ellipticity, could convert circularly polarized light into linearly polarized light, and the anisotropic phase grating under above-mentioned condition was really fabricated using the photo-cross-linkable polymer liquid crystal. This function, not observed in the conventional polarization gratings, should be widely applied as highly functionalized optical devices.
Very high quantum efficiency in type-II InAs∕GaSb superlattice photodiode with cutoff of 12μm
Authors: Nguyen Binh-Minh , Hoffman Darin , Wei Yajun , Delaunay Pierre-Yves , Hood Andrew , Razeghi Manijeh
Published: June 2007

The authors report the dependence of the quantum efficiency on device thickness of type-II InAs∕GaSb superlattice photodetectors with a cutoff wavelength around 12μm. The quantum efficiency and responsivity show a clear delineation in comparison to the device thickness. An external single-pass quantum efficiency of 54% is obtained for a 12μm cutoff wavelength photodiodes with a π-region thickness of 6.0μm. The R0A value is kept stable for the range of structure thicknesses allowing for a specific detectivity (2.2×1011cmHz∕W).
In
As
Sb
∕
Ga
Sb
heterostructure based mid-wavelength-infrared detector for high temperature operation
Authors: Sharabani Y. , Paltiel Y. , Sher A. , Raizman A. , Zussman A.
Published: June 2007

The properties of a midinfrared photodetector, based on a lattice matched n-N InAs0.91Sb0.09∕GaSb type-II heterostructure, were investigated. The relatively simple two layer structure shows very promising characteristics for sensitive and dual color infrared detection. I-V characteristics and spectral response were measured at the temperature range of 10–300K. High zero-bias resistance area product R0A of 2.5Ωcm2 was obtained at room temperature. The measured background limited infrared photodetection temperature was 180K corresponding to 4.1μm cutoff. Shot and Johnson noise limited detectivities corresponding to InAsSb absorption were measured to be 1.3×1010 and 4.9×109cmHz1∕2W−1 at 180 and 300K, respectively. An enhanced optical response with gain larger than unity was observed below 120K. Bias tunable dual color detection was demonstrated at all measured temperatures.
Huntingtin facilitates dynein/dynactin-mediated vesicle transport
Authors: Caviston Juliane P. , Ross Jennifer L. , Antony Sheila M. , Tokito Mariko , Holzbaur Erika L. F.
Published: June 2007

Cytoplasmic dynein is a multisubunit microtubule motor complex that, together with its activator, dynactin, drives vesicular cargo toward the minus ends of microtubules. Huntingtin (Htt) is a vesicle-associated protein found in both neuronal and nonneuronal cells that is thought to be involved in vesicular transport. In this study, we demonstrate through yeast two-hybrid and affinity chromatography assays that Htt and dynein intermediate chain interact directly; endogenous Htt and dynein coimmunoprecipitate from mouse brain cytosol. Htt RNAi in HeLa cells results in Golgi disruption, similar to the effects of compromising dynein/dynactin function.
In vitro
studies reveal that Htt and dynein are both present on vesicles purified from mouse brain. Antibodies to Htt inhibited vesicular transport along microtubules, suggesting that Htt facilitates dynein-mediated vesicle motility.
In vivo
inhibition of dynein function results in a significant redistribution of Htt to the cell periphery, suggesting that dynein transports Htt-associated vesicles toward the cell center. Together these findings indicate that Htt binds to dynein and acts in a complex along with dynactin and Htt-associated protein-1 to facilitate vesicular transport.
Structure of a receptor-binding fragment of reelin and mutational analysis reveal a recognition mechanism similar to endocytic receptors
Authors: Yasui Norihisa , Nogi Terukazu , Kitao Tomoe , Nakano Yoshimi , Hattori Mitsuharu , Takagi Junichi
Published: June 2007

Reelin, a large secreted protein implicated in the cortical development of the mammalian brain, is composed of eight tandem concatenations of “reelin repeats” and binds to neuronal receptors belonging to the low-density lipoprotein receptor gene family. We found that both receptor-binding and subsequent Dab1 phosphorylation occur solely in the segment spanning the fifth and sixth reelin repeats (R5–6). Monomeric fragment exhibited a suboptimal level of signaling activity and artificial oligomerization resulted in a 10-fold increase in activity, indicating the critical importance of higher-order multimerization in physiological reelin. A 2.0-Å crystal structure from the R5–6 fragment revealed not only a unique domain arrangement wherein two repeats were aligned side by side with the same orientation, but also the unexpected presence of bound Zn ions. Structure-guided alanine mutagenesis of R5–6 revealed that two Lys residues (Lys-2360 and Lys-2467) constitute a central binding site for the low-density lipoprotein receptor class A module in the receptor, indicating a strong similarity to the ligand recognition mode shared among the endocytic lipoprotein receptors.
Load-dependent mechanism of nonmuscle myosin 2
Authors: Kovács Mihály , Thirumurugan Kavitha , Knight Peter J. , Sellers James R.
Published: June 2007

Loads on molecular motors regulate and coordinate their function. In a study that directly measures properties of internally strained myosin 2 heads bound to actin, we find that human nonmuscle myosins 2A and 2B show marked load-dependent changes in kinetics of ADP release but not in nucleotide binding. We show that the ADP release rate constant is increased 4-fold by the assisting load on one head and decreased 5-fold (for 2A) or 12-fold (for 2B) by the resisting load on the other. Thus these myosins, especially 2B, have marked mechanosensitivity of product release. By regulating the actin attachment of myosin heads, this provides a basis for energy-efficient tension maintenance without obstructing cellular contractility driven by other motors such as smooth muscle myosin. Whereas forward load accelerates the cycle of interaction with actin, resistive load increases duty ratio to favor tension maintenance by two-headed attachment.
Dissection of the components for PIP
2
activation and thermosensation in TRP channels
Authors: Brauchi Sebastian , Orta Gerardo , Mascayano Carolina , Salazar Marcelo , Raddatz Natalia , Urbina Hector , Rosenmann Eduardo , Gonzalez-Nilo Fernando , Latorre Ramon
Published: June 2007

Phosphatidylinositol 4,5-bisphosphate (PIP
2
) plays a central role in the activation of several transient receptor potential (TRP) channels. The role of PIP
2
on temperature gating of thermoTRP channels has not been explored in detail, and the process of temperature activation is largely unexplained. In this work, we have exchanged different segments of the C-terminal region between cold-sensitive (TRPM8) and heat-sensitive (TRPV1) channels, trying to understand the role of the segment in PIP
2
and temperature activation. A chimera in which the proximal part of the C-terminal of TRPV1 replaces an equivalent section of TRPM8 C-terminal is activated by PIP
2
and confers the phenotype of heat activation. PIP
2
, but not temperature sensitivity, disappears when positively charged residues contained in the exchanged region are neutralized. Shortening the exchanged segment to a length of 11 aa produces voltage-dependent and temperature-insensitive channels. Our findings suggest the existence of different activation domains for temperature, PIP
2
, and voltage. We provide an interpretation for channel–PIP
2
interaction using a full-atom molecular model of TRPV1 and PIP
2
docking analysis.
Proteolysis of the barley receptor-like protein kinase RPG1 by a proteasome pathway is correlated with
Rpg1
-mediated stem rust resistance
Authors: Nirmala Jayaveeramuthu , Dahl Stephanie , Steffenson Brian J. , Kannangara C. Gamini , von Wettstein Diter , Chen Xianming , Kleinhofs Andris
Published: June 2007

In plants, disease resistance mediated by the gene-for-gene mechanism involves the recognition of specific effector molecules produced by the pathogen either directly or indirectly by the resistance-gene products. This recognition triggers a series of signals, thereby serving as a molecular switch in regulating defense mechanisms by the plants. To understand the mechanism of action of the barley stem rust resistance gene
Rpg1
, we investigated the fate of the RPG1 protein in response to infection with the stem rust fungus,
Puccinia graminis
f. sp.
tritici
. The investigations revealed that RPG1 disappears to undetectable limits only in the infected tissues in response to avirulent, but not virulent pathotypes. The RPG1 protein disappearance is rapid and appears to be due to specific protein degradation via the proteasome-mediated pathway as indicated by inhibition with the proteasomal inhibitor MG132, but not by other protease inhibitors.
82,000-year-old shell beads from North Africa and implications for the origins of modern human behavior
Authors: Bouzouggar Abdeljalil , Barton Nick , Vanhaeren Marian , d'Errico Francesco , Collcutt Simon , Higham Tom , Hodge Edward , Parfitt Simon , Rhodes Edward , Schwenninger Jean-Luc , Stringer Chris , Turner Elaine , Ward Steven , Moutmir Abdelkrim , Stambouli Abdelhamid
Published: June 2007

The first appearance of explicitly symbolic objects in the archaeological record marks a fundamental stage in the emergence of modern social behavior in
Homo
. Ornaments such as shell beads represent some of the earliest objects of this kind. We report on examples of perforated
Nassarius gibbosulus
shell beads from Grotte des Pigeons (Taforalt, Morocco), North Africa. These marine shells come from archaeological levels dated by luminescence and uranium-series techniques to ≈82,000 years ago. They confirm evidence of similar ornaments from other less well dated sites in North Africa and adjacent areas of southwest Asia. The shells are of the same genus as shell beads from slightly younger levels at Blombos Cave in South Africa. Wear patterns on the shells imply that some of them were suspended, and, as at Blombos, they were covered in red ochre. These findings imply an early distribution of bead-making in Africa and southwest Asia at least 40 millennia before the appearance of similar cultural manifestations in Europe.
Deubiquitinating enzyme CYLD negatively regulates the ubiquitin-dependent kinase Tak1 and prevents abnormal T cell responses
Authors: Reiley William W. , Jin Wei , Lee Andrew Joon , Wright Ato , Wu Xuefeng , Tewalt Eric F. , Leonard Timothy O. , Norbury Christopher C. , Fitzpatrick Leo , Zhang Minying , Sun Shao-Cong
Published: June 2007

The deubiquitinating enzyme CYLD has recently been implicated in the regulation of signal transduction, but its physiological function and mechanism of action are still elusive. In this study, we show that CYLD plays a pivotal role in regulating T cell activation and homeostasis. T cells derived from Cyld knockout mice display a hyperresponsive phenotype and mediate the spontaneous development of intestinal inflammation. Interestingly, CYLD targets a ubiquitin-dependent kinase, transforming growth factor–β-activated kinase 1 (Tak1), and inhibits its ubiquitination and autoactivation. Cyld-deficient T cells exhibit constitutively active Tak1 and its downstream kinases c-Jun N-terminal kinase and IκB kinase β. These results emphasize a critical role for CYLD in preventing spontaneous activation of the Tak1 axis of T cell signaling and, thereby, maintaining normal T cell function.
Altering the distribution of Foxp3+ regulatory T cells results in tissue-specific inflammatory disease
Authors: Sather Blythe D. , Treuting Piper , Perdue Nikole , Miazgowicz Mike , Fontenot Jason D. , Rudensky Alexander Y. , Campbell Daniel J.
Published: June 2007

CD4+Foxp3+ regulatory T cells (T reg) are essential for maintaining self-tolerance, but their functional mechanisms and sites of action in vivo are poorly defined. We examined the homing receptor expression and tissue distribution of T reg cells in the steady state and determined whether altering their distribution by removal of a single chemokine receptor impairs their ability to maintain tissue-specific peripheral tolerance. We found that T reg cells are distributed throughout all nonlymphoid tissues tested, and are particularly prevalent in the skin, where they express a unique CCR4+CD103hi phenotype. T reg cell expression of CCR4 and CD103 is induced by antigen-driven activation within subcutaneous lymph nodes, and accumulation of T reg cells in the skin and lung airways is impaired in the absence of CCR4 expression. Mice with a complete loss of CCR4 in the T reg cell compartment develop lymphocytic infiltration and severe inflammatory disease in the skin and lungs, accompanied by peripheral lymphadenopathy and increased differentiation of skin-tropic CD4+Foxp3+ T cells. Thus, selectively altering T reg cell distribution in vivo leads to the development of tissue-specific inflammatory disease.
A novel inhibitor of the alternative pathway of complement reverses inflammation and bone destruction in experimental arthritis
Authors: Katschke Kenneth J. , Helmy Karim Y. , Steffek Micah , Xi Hongkang , Yin JianPing , Lee Wyne P. , Gribling Peter , Barck Kai H. , Carano Richard A.D. , Taylor Robin E. , Rangell Linda , Diehl Lauri , Hass Philip E. , Wiesmann Christian , van Lookeren Campagne Menno
Published: June 2007

Complement is an important component of the innate and adaptive immune response, yet complement split products generated through activation of each of the three complement pathways (classical, alternative, and lectin) can cause inflammation and tissue destruction. Previous studies have shown that complement activation through the alternative, but not classical, pathway is required to initiate antibody-induced arthritis in mice, but it is unclear if the alternative pathway (AP) plays a role in established disease. Previously, we have shown that human complement receptor of the immunoglobulin superfamily (CRIg) is a selective inhibitor of the AP of complement. Here, we present the crystal structure of murine CRIg and, using mutants, provide evidence that the structural requirements for inhibition of the AP are conserved in human and mouse. A soluble form of CRIg reversed inflammation and bone loss in two experimental models of arthritis by inhibiting the AP of complement in the joint. Our data indicate that the AP of complement is not only required for disease induction, but also disease progression. The extracellular domain of CRIg thus provides a novel tool to study the effects of inhibiting the AP of complement in established disease and constitutes a promising therapeutic with selectivity for a single complement pathway.
Do carotenoids buffer testosterone-induced immunosuppression? An experimental test in a colourful songbird
Authors: McGraw Kevin J , Ardia Daniel R
Published: June 2007

Testosterone (T) is hypothesized to be an important honesty reinforcer of animal sexual signals. Owing to its immunosuppressive effects, only those individuals that can immunologically withstand high T levels can develop the most exaggerated traits. To date, few studies have isolated phenotypic or genotypic buffers that provide ‘high-quality’ animals with such an advantage. Dietary carotenoid pigments may in fact confer such a benefit because when in high supply carotenoids boost immunocompetence and coloration in animals like birds and fishes. We examined the experimental effect of T elevation on carotenoid and immune status in male and female zebra finches (Taeniopygia guttata) and found that T was immunostimulatory in a generalized cell-mediated challenge. We also detected a significant interaction between T treatment and the change in plasma carotenoids that occurred during the immune challenge; the relationship between blood carotenoid change and immunity was positive in controls and negative in T-implanted birds. This suggests that, while correlationally birds with high carotenoid stores were inherently better at mounting strong immune responses, experimentally administered T induced birds to deplete carotenoids for maximizing their health. Our findings highlight a nutrient-specific mechanism by which animals escape high immune costs of T elevation and thus can still elevate ornamentation.
Low host–pathogen specificity in the leaf-cutting ant–microbe symbiosis
Authors: Taerum Stephen J , Cafaro Matías J , Little Ainslie E.F , Schultz Ted R , Currie Cameron R
Published: June 2007

Host–parasite associations are shaped by coevolutionary dynamics. One example is the complex fungus-growing ant–microbe symbiosis, which includes ancient host–parasite coevolution. Fungus-growing ants and the fungi they cultivate for food have an antagonistic symbiosis with
Escovopsis
, a specialized microfungus that infects the ants' fungus gardens. The evolutionary histories of the ant, cultivar and
Escovopsis
are highly congruent at the deepest phylogenetic levels, with specific parasite lineages exclusively associating with corresponding groups of ants and cultivar. Here, we examine host–parasite specificity at finer phylogenetic levels, within the most derived clade of fungus-growing ants, the leaf-cutters (
Atta
spp. and
Acromyrmex
spp.). Our molecular phylogeny of
Escovopsis
isolates from the leaf-cutter ant–microbe symbiosis confirms specificity at the broad phylogenetic level, but reveals frequent host-switching events between species and genera of leaf-cutter ants.
Escovopsis
strains isolated from
Acromyrmex
and
Atta
gardens occur together in the same clades, and very closely related strains can even infect the gardens of both ant genera. Experimental evidence supports low host–parasite specificity, with phylogenetically diverse strains of
Escovopsis
being capable of overgrowing all leaf-cutter cultivars examined. Thus, our findings indicate that this host–pathogen association is shaped by the farming ants having to protect their cultivated fungus from phylogenetically diverse
Escovopsis
garden pathogens.
The key mimetic features of hoverflies through avian eyes
Authors: Bain Roderick S , Rashed Arash , Cowper Verity J , Gilbert Francis S , Sherratt Thomas N
Published: June 2007

Batesian mimicry occurs when a palatable species (the mimic) gains protection from predators by resembling an unpalatable or otherwise protected species (the model). While some mimetic species resemble their models closely, other species (‘imperfect mimics’) are thought to bear only a crude likeness. In an earlier study, pigeons (
Columba livia
) were trained to recognize wasp images in one experiment and non-mimetic (NM) fly images in another by rewarding the pigeons for pecking on the respective image types. These pigeons were subsequently presented with different images, including seemingly wasp-like hoverfly species, and the recorded peck rates on these images were used as a measure of the pigeons' perception of the hoverflies' mimetic similarity. To identify a candidate set of morphological features that the pigeons used when assessing this mimetic similarity, we first extracted a range of biometrical measurements from images originally presented to the pigeons. We then repeatedly optimized an empirical model in an attempt to match the recorded pigeon peck rates while using as few biometrical features as input as possible. Our models were able to fit the pigeon peck rates with considerable accuracy even while excluding many input features. Antennal length, a feature commonly used to discriminate between flies and wasps, was regularly retained as an input variable, but overall a different set of biometrical features was important for predicting the peck rates of pigeons rewarded for identifying wasps compared to those rewarded for identifying NM flies. In highlighting the importance of specific biometrical features in promoting mimicry and the irrelevance of others, our optimized models provide an explanation as to why certain species that appear to be poor mimics to humans are judged to be good mimics by birds.
Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost
Authors: Kang Myung-Suk , Im Wan-Taek , Jung Hae-Min , Kim Myung Kyum , Goodfellow Michael , Kim Kwang Kyu , Yang Hee-Chan , An Dong-Shan , Lee Sung-Taik
Published: June 2007

A bacterial strain, TR7-06T, which has cellulase and β-glucosidase activities, was isolated from compost at a cattle farm near Daejeon, Republic of Korea. It was a Gram-positive, aerobic or facultatively anaerobic, non-motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas, with highest sequence similarity to Cellulomonas uda DSM 20107T (98.5 %). Cell wall analysis revealed the presence of type A4β, l-orn–d-Glu peptidoglycan. The cell-wall sugars detected were mannose and glucose. The predominant menaquinone was MK-9(H4); MK-8(H4) was detected in smaller quantities. The major fatty acids were anteiso-C15 : 0, C16 : 0, C14 : 0 and C18 : 0. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that TR7-06T represents a novel species. The combined genotypic and phenotypic data show that strain TR7-06T (=KCTC 19030T=NBRC 100758T) merits description as the type strain of a novel Cellulomonas species, Cellulomonas composti sp. nov.
Reclassification of Pseudomonas aurantiaca as a synonym of Pseudomonas chlororaphis and proposal of three subspecies, P. chlororaphis subsp. chlororaphis subsp. nov., P. chlororaphis subsp. aureofaciens subsp. nov., comb. nov. and P. chlororaphis subsp. aurantiaca subsp. nov., comb. nov.
Authors: Peix Alvaro , Valverde Angel , Rivas Raúl , Igual José M. , Ramírez-Bahena Martha-Helena , Mateos Pedro F. , Santa-Regina Ignacio , Rodríguez-Barrueco Claudino , Martínez-Molina Eustoquio , Velázquez Encarna
Published: June 2007

Pseudomonas chlororaphis, Pseudomonas aureofaciens and Pseudomonas aurantiaca were considered as separate species until 1989, when P. aureofaciens was proposed as a later heterotypic synonym of P. chlororaphis with P. aurantiaca remaining as a separate species. Nevertheless, analysis of the almost complete 16S rRNA gene sequences revealed that the type strain of P. aurantiaca, NCIMB 10068T, shows gene sequence similarities close to 99.5 % with respect to P. chlororaphis DSM 50083T and P. aureofaciens DSM 6698T. DNA–DNA hybridization experiments among strains of P. aurantiaca, P. chlororaphis and P. aureofaciens showed values higher than 70 %, confirming that they represent members of the same species. The results of fatty acid analysis and phenotypic traits showed that these strains are closely related, although there are some differences among the strains belonging to P. aurantiaca, those from P. chlororaphis and those from P. aureofaciens. All these results confirm the previous reclassification of P. aureofaciens into P. chlororaphis and support the reclassification of P. aurantiaca as a synonym of P. chlororaphis. Phenotypic and molecular data permit the description of three novel subspecies within this last species, for which the following names are proposed: P. chlororaphis subsp. chlororaphis subsp. nov. [with the type strain DSM 50083T (=ATCC 9446T=NCIMB 9392T)], P. chlororaphis subsp. aureofaciens subsp. nov., comb. nov. [with the type strain DSM 6698T (=ATCC 13985T=NCIMB 9030T)] and P. chlororaphis subsp. aurantiaca subsp. nov., comb. nov. [with the type strain NCIMB 10068T (=ATCC 33663T=CIP 106718T)].
Planococcus columbae sp. nov., isolated from pigeon faeces
Authors: Suresh K. , Mayilraj S. , Bhattacharya A. , Chakrabarti T.
Published: June 2007

An orange-pigmented, Gram-positive bacterial strain, designated PgEx11T, was isolated from pigeon faeces. Analysis of the 16S rRNA gene sequence of the isolate indicated that it had 94.2–98.2 % sequence identity with respect to those of seven recognized species of the genusPlanococcus. The strain PgEx11Tcontained anteiso-C15 : 0as a major cellular fatty acid and MK-7 and MK-8 as the major menaquinones. The DNA G+C content of strain PgEx11Twas 50.5 mol%. Furthermore, analysis of the 16S rRNA gene sequence indicated high levels of similarity withPlanococcus rifietoensis(98.2 %),Planococcus maitriensis(97.6 %),Planococcus citreus(97.5 %) andPlanococcus maritimus(97.1 %). However, the mean value for DNA–DNA relatedness between PgEx11Tand these four closely related species was in the range 45.4–16.8 %, respectively. Moreover, strain PgEx11Talso differs from its close relatives with regard to biochemical and chemotaxonomic characteristics. On the basis of phenotypic, chemotaxonomic and genotypic differences, strain PgEx11Trepresents a novel species of the genusPlanococcus, for which the namePlanococcus columbaesp. nov. is proposed. The type strain is PgEx11T(=MTCC 7251T=DSM 17517T).
Alteromonas tagae sp. nov. and Alteromonas simiduii sp. nov., mercury-resistant bacteria isolated from a Taiwanese estuary
Authors: Chiu Hsiu-Hui , Shieh Wung Yang , Lin Silk Yu , Tseng Chun-Mao , Chiang Pei-Wen , Wagner-Döbler Irene
Published: June 2007

Two mercury-resistant strains of heterotrophic, aerobic, marine bacteria, designated AT1T and AS1T, were isolated from water samples collected from the Er-Jen River estuary, Tainan, Taiwan. Cells were Gram-negative rods that were motile by means of a single polar flagellum. Buds and prosthecae were produced. The two isolates required NaCl for growth and grew optimally at about 30 °C, 2–4 % NaCl and pH 7–8. They grew aerobically and were incapable of anaerobic growth by fermenting glucose or other carbohydrates. They grew and expressed Hg2+-reducing activity in liquid media containing HgCl2. Strain AS1T reduced nitrate to nitrite. The predominant isoprenoid quinone was Q8 (91.3–99.9 %). The polar lipids of strain AT1T consisted of phosphatidylethanolamine (46.6 %), phosphatidylglycerol (28.9 %) and sulfolipid (24.5 %), whereas those of AS1T comprised phosphatidylethanolamine (48.2 %) and phosphatidylglycerol (51.8 %). The two isolates contained C16 : 1
ω7c and/or iso-C15 : 0 2-OH (22.4–33.7 %), C16 : 0 (19.0–22.7 %) and C18 : 1
ω7c (11.3–11.7 %) as the major fatty acids. Strains AT1T and AS1T had DNA G+C contents of 43.1 and 45.3 mol%, respectively. Phylogeny based on 16S rRNA gene sequences, together with data from morphological, physiological and chemotaxonomic characterization, indicated that the two isolates could be classified as representatives of two novel species in the genus Alteromonas, for which the names Alteromonas tagae sp. nov. (type strain AT1T=BCRC 17571T=JCM 13895T) and Alteromonas simiduii sp. nov. (type strain AS1T=BCRC 17572T=JCM 13896T) are proposed.
Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan
Authors: Lee Fwu-Ling , Kuo Hsiao-Ping , Tai Chun-Ju , Yokota Akira , Lo Chi-Chu
Published: June 2007

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3T, was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA–DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genusPaenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C15 : 0(40.5 %), iso-C15 : 0(13.1 %), iso-C16 : 0(10.8 %) and anteiso-C17 : 0(7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3Twere the type strains ofPaenibacillus assamensis,Paenibacillus alveiandPaenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA–DNA hybridization experiments showed levels of relatedness of 2.8–9.0 % of strain G-soil-2-3Twith these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3Twas clearly distinguishable fromP. assamensis,P. alveiandP. apiariusand thus represents a novel species of the genusPaenibacillus, for which the namePaenibacillus taiwanensissp. nov. is proposed. The type strain is G-soil-2-3T(=BCRC 17411T=IAM 15414T=LMG 23799T=DSM 18679T).
Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep
Authors: Hua Ngoc-Phuc , Kanekiyo Atsuko , Fujikura Katsunori , Yasuda Hisato , Naganuma Takeshi
Published: June 2007

Two Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4T and IS-Hb7T, were spore-forming and non-motile. They were able to grow at temperatures as low as 9 °C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7T to Halobacillus halophilus NCIMB 9251T) to 99.4 % (strain IS-Hb4T to Halobacillus dabanensis D-8T), the strains were shown to belong to this genus. DNA–DNA relatedness values of 49.5 % and 1.0–33.0 %, respectively, were determined between strains IS-Hb4T and IS-Hb7T and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and l-orn–d-Asp cell-wall peptidoglycan type. Straight-chain C16 : 0, unsaturated C16 : 1
ω7c alcohol and C18 : 1
ω7c and cyclopropane C19 : 0 cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4T and IS-Hb7T were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA–DNA hybridization results allowed us to place strains IS-Hb4T (=JCM 14154T=DSM 18394T) and IS-Hb7T (=JCM 14155T=DSM 18393T) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.
‘Candidatus Magnetoglobus multicellularis’, a multicellular, magnetotactic prokaryote from a hypersaline environment
Authors: Abreu Fernanda , Martins Juliana Lopes , Silveira Thaís Souza , Keim Carolina Neumann , de Barros Henrique G. P. Lins , Filho Frederico J. Gueiros , Lins Ulysses
Published: June 2007

Phylogenetic analysis and phenotypic characterization were used to assign a multicellular magnetotactic prokaryote the name ‘Candidatus Magnetoglobus multicellularis’. ‘Candidatus Magnetoglobus multicellularis' lives in a large hypersaline coastal lagoon from Brazil and has properties that are unique among prokaryotes. It consists of a compact assembly or aggregate of flagellated bacterial cells, highly organized in a sphere, that swim in either helical or straight trajectories. The life cycle of ‘Candidatus Magnetoglobus multicellularis' is completely multicellular, in which one aggregate grows by enlarging the size of its cells and approximately doubling the volume of the whole organism. Cells then divide synchronously, maintaining the spherical arrangement; finally the cells separate into two identical aggregates. Phylogenetic 16S rRNA gene sequence analysis showed that ‘Candidatus Magnetoglobus multicellularis' is related to the dissimilatory sulfate-reducing bacteria within the Deltaproteobacteria and to other previously described, but not yet well characterized, multicellular magnetotactic prokaryotes.
Paenibacillus fonticola sp. nov., isolated from a warm spring
Authors: Chou Jui-Hsing , Chou Yi-Ju , Lin Kuan-Yin , Sheu Shih-Yi , Sheu Der-Shyan , Arun A. B. , Young Chiu-Chung , Chen Wen-Ming
Published: June 2007

A novel bacterial strain, designated ZLT, isolated from a warm spring in Jhonglun, Taiwan, was characterized by using a polyphasic taxonomic approach. The novel strain had chemotaxonomic and morphological properties consistent with its classification in the genus Paenibacillus. Cells were Gram-variable, aerobic, sporulating, motile rods. 16S rRNA gene sequence analysis demonstrated that this novel isolate was unique, showing 94.3 % sequence similarity to Paenibacillus assamensis GPTSA 11T and lower levels to Paenibacillus timonensis 2301032T (94.0 %), Paenibacillus macerans ATCC 8244T (93.3 %), Paenibacillus barengoltzii SAFN-016T (93.3 %) and Paenibacillus sanguinis 2301083T (93.2 %). The novel isolate could be distinguished from the type strains of all of these species based on a range of phenotypic data. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one unknown phosphoglycolipid. The predominant isoprenologue was an unsaturated menaquinone with seven isoprene units (MK-7). The major fatty acids of strain ZLT were C16 : 0 (33.5 %), anteiso-C15 : 0 (32.5 %) and iso-C16 : 0 (9.3 %). The G+C content of the genomic DNA was 49.2 mol%. It is evident from the genotypic and phenotypic data that strain ZLT should be classified as representing a novel species of the genus Paenibacillus, for which the name Paenibacillus fonticola sp. nov. is proposed. The type strain is ZLT (=BCRC 17579T=LMG 23577T).
Caenispirillum bisanense gen. nov., sp. nov., isolated from sludge of a dye works
Authors: Yoon Jung-Hoon , Kang So-Jung , Park Sooyeon , Oh Tae-Kwang
Published: June 2007

Two Gram-negative, non-spore-forming, motile and helical-shaped bacterial strains, K92T and K93, were isolated from sludge from a dye works in Korea, and their taxonomic positions were investigated by means of a polyphasic approach. Strains K92T and K93 grew optimally at 37 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. They contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified amino-group-containing lipids that were ninhydrin-positive. Their DNA G+C contents were 70.0 mol%. The 16S rRNA gene sequences of K92T and K93 showed no differences, and the two strains had a mean DNA–DNA relatedness of 93 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains K92T and K93 formed a distinct evolutionary lineage within the Alphaproteobacteria. The 16S rRNA gene sequences of strains K92T and K93 exhibited similarity values of less than 91.5 % with respect to the 16S rRNA gene sequences of other members of the Alphaproteobacteria. The two strains were distinguishable from phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strains K92T and K93 represent a novel genus and species, for which the name Caenispirillum bisanense gen. nov., sp. nov. is proposed. The type strain of Caenispirillum bisanense is K92T (=KCTC 12839T=JCM 14346T).
Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: June 2007

A Gram-negative, rod-shaped bacterial strain, K105T, was isolated from wastewater of a textile dye works in Korea and subjected to a polyphasic taxonomic study. Strain K105T grew optimally at pH 6.5–7.5 and 30–37 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 1
ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content was 36.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K105T belonged to the genus Chryseobacterium. Strain K105T exhibited 16S rRNA gene sequence similarity values of less than 96.9 % to the type strains of recognized Chryseobacterium species. Strain K105T differed from phylogenetically related Chryseobacterium species in several phenotypic properties. On the basis of phenotypic and phylogenetic data, strain K105T (=KCTC 12841T=JCM 14362T) is placed in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium daeguense sp. nov. is proposed.
Sphingomonas pseudosanguinis sp. nov., isolated from the water reservoir of an air humidifier
Authors: Kämpfer Peter , Meurer Uwe , Esser Michael , Hirsch Thomas , Busse Hans-Jürgen
Published: June 2007

A yellow-pigmented bacterial isolate, strain G1-2T, obtained from the surface of an air humidifier, was characterized taxonomically. 16S rRNA gene sequence analysis, physiological characterization and estimation of the ubiquinone and polar lipid patterns and fatty acid composition revealed that strain G1-2T was similar to Sphingomonas yabuuchiae and Sphingomonas sanguinis, but also showed pronounced differences. On the basis of these results, a novel species of the genus Sphingomonas is described, for which the name Sphingomonas pseudosanguinis sp. nov. is proposed. The type strain is G1-2T (=CCUG 54232T=CIP 109431T).
Chromohalobacter salarius sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almería, southern Spain
Authors: Aguilera Margarita , Cabrera Antonio , Incerti Claudia , Fuentes Susana , Russell Nick J. , Ramos-Cormenzana Alberto , Monteoliva-Sánchez Mercedes
Published: June 2007

A moderately halophilic, Gram-negative bacterium (strain CG4.1T), which was isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile rod that produced colonies with a yellow pigment. Strain CG4.1T grew at salinities of 3–25 % (w/v), at 15–45 °C and at pH 5–9. The organism reduced nitrate, hydrolysed starch and had phenylalanine deaminase activity. The major fatty acids were C18 : 1
ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 63.6 mol%. On the basis of phenotypic and phylogenetic data, strain CG4.1T appears to be a member of the genus Chromohalobacter and clustered closely with Chromohalobacter species, with 95–96 % similarity between their 16S rRNA gene sequences. However, DNA–DNA relatedness between the isolate and the type strains of Chromohalobacter species was low. Therefore, it is proposed that strain CG4.1T represents a novel species, Chromohalobacter salarius sp. nov. The type strain is strain CG4.1T (=CECT 5903T=LMG 23626T).
Bacteroides coprophilus sp. nov., isolated from human faeces
Authors: Hayashi Hidenori , Shibata Kensaku , Bakir Mohammad Abdul , Sakamoto Mitsuo , Tomita Shinichi , Benno Yoshimi
Published: June 2007

Three Gram-negative, anaerobic, rod-shaped bacteria (strains CB40, CB41 and CB42T) were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included in the genusBacteroides, and 16S rRNA gene sequence analysis indicated that these strains represented a novel species. The strains were most closely related to the type strains ofBacteroides barnesiaeandBacteroides salanitronis, with sequence similarities of 93.4 and 89.8 %, respectively. The G+C content of strain CB42Tis 44.7 mol%. Major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C17 : 03-OH and C18 : 1ω9c. On the basis of the data presented, a novelBacteroidesspecies,Bacteroides coprophilussp. nov., is proposed, with CB42T(=JCM 13818T=DSM 18228T) as the type strain.
Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia
Authors: Yoon Jung-Hoon , Kang So-Jung , Park Sooyeon , Oh Tae-Kwang
Published: June 2007

A Gram-negative, motile, aerobic and oval- or rod-shaped bacterial strain, DS-56T, which is phylogenetically closely related to the genus Devosia, was isolated from soil from Dokdo, Korea. Strain DS-56T grew optimally at pH 6.5–7.5 and 25 °C in the presence of 0.5 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DS-56T joins the cluster comprising Devosia species, at a bootstrap resampling value of 100 %. The levels of 16S rRNA gene sequence similarity between strain DS-56T and the type strains of recognized Devosia species ranged from 95.4 to 96.4 %. Strain DS-56T contained Q-11 as the predominant ubiquinone, unlike Devosia species, which contain Q-10 as the predominant ubiquinone. The novel strain also contained some fatty acids, including branched and hydroxy fatty acids, that are not detected in Devosia species. The DNA G+C content of strain DS-56T was 66.2 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-56T represents a novel species of the genus Devosia, for which the name Devosia insulae sp. nov. is proposed. The type strain is DS-56T (=KCTC 12821T=DSM 17955T).
En-1 and En-2, two mouse genes with sequence homology to the Drosophila engrailed gene: expression during embryogenesis.
Authors: Joyner A L , Martin G R
Published: June 2007

Two mouse genes, En-1 and En-2, have sequence homology to the engrailed (en) and invected (inv) genes of Drosophila (Joyner et al. 1985). Partial nucleotide sequence analyses of genomic and cDNA clones show that the homologous sequences can encode a stretch of 107 amino acids, including a centrally located, 60-amino-acid homeo box. Within the homologous regions of the mouse and Drosophila genes, 78 (73%) of the amino acids are identical. Such extensive conservation of sequence outside the homeo box between vertebrate and Drosophila homeo box-containing genes is thus far unique. En-1 and En-2 are expressed during mouse embryogenesis. Transcripts from both genes were detected in RNA samples from teratocarcinoma cells, which serve as in vitro models for the early embryo, and from embryos at 9.5 through 17.5 days of development. For each gene we observed a unique pattern of changes in the number and relative intensities of transcripts detectable during embryonic development. Transcripts from both genes are represented abundantly in RNA extracted from the posterior portion of the fetal brain, and are much less abundant in RNA from other fetal tissues, including the anterior portion of the brain and the spinal cord. The chromosome map positions of En-1 and En-2 were determined by recombinant inbred strain analyses. Unlike their Drosophila counterparts, they are unlinked: En-1 is in the central portion of the mouse chromosome 1 and En-2 is in the proximal portion of mouse chromosome 5. Both genes map in the vicinity of mutations that are known to cause abnormalities during development.