bluuebunny/crossref_metadata_2025 huggingface dataset:
Between Reasoning
Authors: Hörnig Robin , Oberauer Klaus , Weidenfeld Andrea
Published: January 2006

In two experiments we investigated three-term reasoning with spatial relational assertions using the preposition between as compared to projective prepositions (such as to the left of). For each kind of assertion we distinguish the referent expression (i.e., the grammatical subject) from the relatum expression (i.e., the internal argument of the preposition; e.g., [ The hedgehog]referent_expression is to the left of [ the frog]relatum_expression; [ the snake]referent_expression is between [ the donkey and the deer]relatum_expression). Previous research has shown that integrating premises with projective prepositions is easier (a) when the relatum expression of the second premise denotes an element already given by the first premise (relatum = given), and (b) when the term denoting a given element precedes the term denoting a new element (given–new). Experiment 1 extended this finding to second premises with the preposition between. In Experiment 2, between figured in the first premise. In this case, participants built an initial preferred model already from the first premise, although such a premise is indeterminate with respect to the array that it describes. Since there is no need left for integrating the second premise, this premise is instead used to verify the initial model and to modify it when necessary. A further investigation of conclusion evaluation times showed that conclusions were evaluated faster when they first mentioned the element that was included most recently into the mental model of the premises. The use of premises with between permitted the separation of recency of model inclusion from recency of appearance of an element in a premise.
Orthogonal Stimulus–Response Compatibility Effects Emerge Even when the Stimulus Position is Task Irrelevant
Authors: Nishimura Akio , Yokosawa Kazuhiko
Published: January 2006

The above-right/below-left mapping advantage with vertical stimuli and horizontal responses is known as the orthogonal stimulus–response compatibility (SRC) effect. We investigated whether the orthogonal SRC effect emerges with irrelevant stimulus dimensions. In Experiment 1, participants responded with a right or left key press to the colour of the stimulus presented above or below the fixation. We observed an above-right/below-left advantage (orthogonal Simon effect). In Experiment 2, we manipulated the polarity in the response dimension by varying the horizontal location of the response set. The orthogonal Simon effect decreased and even reversed as the left response code became more positive. This result provides evidence for the automatic activation of the positive and negative response codes by the corresponding positive and negative stimulus codes. These findings extended the orthogonal SRC effect based on coding asymmetry to an irrelevant stimulus dimension.
A Context-Specific Latent Inhibition Effect in a Human Conditioned Suppression Task
Authors: Byron Nelson James , Del Carmen Sanjuan Maria
Published: January 2006

Three studies used a computer video game preparation to demonstrate latent inhibition in adult humans. In all studies participants fired torpedoes at a target spaceship by clicking the mouse. Conditioned stimuli (CSs) were presented in the form of coloured “sensors” at the bottom of the screen. Conditioning was conducted by pairing a sensor with an attack from the target spaceship. Participants learned to suppress their rate of mouse clicking in preparation for an attack. In Experiment 1 a total of 10 preexposures to the sensor CS, prior to conditioning, retarded acquisition of suppression. In Experiment 2 the effect of preexposure was shown to be context specific. Experiment 3 showed little generalization of the preexposure effect from one sensor CS to another. Experiment 3 also showed that preexposure did not make the sensor CS inhibitory. Comparisons with conditioned suppression procedures with animals and negative-priming procedures are briefly discussed.
The role of response selection in sequence learning
Authors: Deroost Natacha , Soetens Eric
Published: January 2006

We investigated the role of response selection in sequence learning in the serial reaction time (SRT) task, by manipulating stimulus–response compatibility. Under conditions in which other types of learning, like perceptual, response-based, and response-effect learning, were unaffected, sequence learning was better with an incompatible than with a compatible stimulus–response mapping. Stimulus discriminability, on the other hand, had no influence on the amount of sequence learning. This indicates that the compatibility effects cannot be accounted for by a different level of task difficulty. Relating our results to the dimensional overlap model (Kornblum, Hasbroucq, & Osman, 1990), which assumes that incompatible stimulus–response mappings require more controlled response selection than do compatible stimulus–response mapping, we suggest that sequence learning in the SRT task is particularly effective when response selection occurs in a controlled way.
Adaptation and increased susceptibility to infection associated with constitutive expression of misfolded SP-C
Authors: Bridges James P. , Xu Yan , Na Cheng-Lun , Wong Hector R. , Weaver Timothy E.
Published: January 2006

Mutations in the gene encoding SP-C (surfactant protein C; SFTPC) have been linked to interstitial lung disease (ILD) in children and adults. Expression of the index mutation, SP-CΔexon4, in transiently transfected cells and type II cells of transgenic mice resulted in misfolding of the proprotein, activation of endoplasmic reticulum (ER) stress pathways, and cytotoxicity. In this study, we show that stably transfected cells adapted to chronic ER stress imposed by the constitutive expression of SP-CΔexon4 via an NF-κB–dependent pathway. However, the infection of cells expressing SP-CΔexon4 with respiratory syncytial virus resulted in significantly enhanced cytotoxicity associated with accumulation of the mutant proprotein, pronounced activation of the unfolded protein response, and cell death. Adaptation to chronic ER stress imposed by misfolded SP-C was associated with increased susceptibility to viral-induced cell death. The wide variability in the age of onset of ILD in patients with SFTPC mutations may be related to environmental insults that ultimately overwhelm the homeostatic cytoprotective response.
AP-2α: a regulator of EGF receptor signaling and proliferation in skin epidermis
Authors: Wang Xuan , Bolotin Diana , Chu David H. , Polak Lisa , Williams Trevor , Fuchs Elaine
Published: January 2006

AP-2 transcription factors have been implicated in epidermal biology, but their functional significance has remained elusive. Using conditional knockout technology, we show that AP-2α is essential for governing the balance between growth and differentiation in epidermis. In vivo, epidermis lacking AP-2α exhibits elevated expression of the epidermal growth factor receptor (EGFR) in the differentiating layers, resulting in hyperproliferation when the receptors are activated. Chromatin immunoprecipitation and promoter activity assays identify EGFR as a direct target gene for AP-2α repression, and, in the absence of AP-2α, this is manifested primarily in excessive EGF-dependent phosphoinositol-3 kinase/Akt activity. Together, our findings unveil a hitherto unrecognized repressive role for AP-2α in governing EGFR gene transcription as cells exit the basal layer and withdraw from the cell cycle. These results provide insights into why elevated AP-2α levels are often associated with terminal differentiation and why tumor cells often display reduced AP-2α and elevated EGFR proteins.
A checkpoint for autoreactivity in human IgM+ memory B cell development
Authors: Tsuiji Makoto , Yurasov Sergey , Velinzon Klara , Thomas Saskia , Nussenzweig Michel C. , Wardemann Hedda
Published: January 2006

Autoantibodies are removed from the repertoire at two checkpoints during B cell development in the bone marrow and the periphery. Despite these checkpoints, up to 20% of the antibodies expressed by mature naive B cells in healthy humans show low levels of self-reactivity. To determine whether self-reactive antibodies are also part of the antigen-experienced memory B cell compartment, we analyzed recombinant antibodies cloned from single circulating human IgM+ memory B cells. Cells expressing antibodies specific for individual bacterial polysaccharides were expanded in the IgM+ memory compartment. In contrast, B cells expressing self-reactive and broadly bacterially reactive antibodies were removed from the repertoire in the transition from naive to IgM+ memory B cell. Selection against self-reactive antibodies was implemented before the onset of somatic hypermutation. We conclude that a third checkpoint selects against self-reactivity during IgM+ memory B cell development in humans.
Different Transport Mechanisms in Plant and Human AMT/Rh-type Ammonium Transporters
Authors: Mayer Maria , Schaaf Gabriel , Mouro Isabelle , Lopez Claude , Colin Yves , Neumann Petra , Cartron Jean-Pierre , Ludewig Uwe
Published: January 2006

The conserved family of AMT/Rh proteins facilitates ammonium transport across animal, plant, and microbial membranes. A bacterial homologue, AmtB, forms a channel-like structure and appears to function as an NH3 gas channel. To evaluate the function of eukaryotic homologues, the human RhCG glycoprotein and the tomato plant ammonium transporter LeAMT1;2 were expressed and compared in Xenopus oocytes and yeast. RhCG mediated the electroneutral transport of methylammonium (MeA), which saturated with Km = 3.8 mM at pHo 7.5. Uptake was strongly favored by increasing the pHo and was inhibited by ammonium. Ammonium induced rapid cytosolic alkalinization in RhCG-expressing oocytes. Additionally, RhCG expression was associated with an alkali-cation conductance, which was not significantly permeable to NH4+ and was apparently uncoupled from the ammonium transport. In contrast, expression of the homologous LeAMT1;2 induced pHo-independent MeA+ uptake and specific NH4+ and MeA+ currents that were distinct from endogenous currents. The different mechanisms of transport, including the RhCG-associated alkali-cation conductance, were verified by heterologous expression in appropriate yeast strains. Thus, homologous AMT/Rh-type proteins function in a distinct manner; while LeAMT1;2 carries specifically NH4+, or cotransports NH3/H+, RhCG mediates electroneutral NH3 transport.
Distinct Populations of HCN Pacemaker Channels Produce Voltage-dependent and Voltage-independent Currents
Authors: Proenza Catherine , Yellen Gary
Published: January 2006

Hyperpolarization-activated HCN pacemaker channels are critical for the generation of spontaneous activity and the regulation of excitability in the heart and in many types of neurons. These channels produce both a voltage-dependent current (Ih) and a voltage-independent current (Iinst or VIC). In this study, we explored the molecular basis of the voltage-independent current. We found that for the spHCN isoform, VIC averaged ∼4% of the maximum HCN conductance that could be activated by hyperpolarization. Cyclic AMP increased the voltage-independent current in spHCN to ∼8% of maximum. In HCN2, VIC was ∼2% of the maximal current, and was little affected by cAMP. VIC in both spHCN and HCN2 was blocked rapidly both by ZD7288 (an HCN channel blocker that is thought to bind in the conduction pore) and by application of Cd2+ to channels containing an introduced cysteine in the pore (spHCN-464C or HCN2-436C). These results suggest that VIC flows through the main conduction pathway, down the central axis of the protein. We suspected that VIC simply represented a nonzero limiting open probability for HCN channels at positive voltages. Surprisingly, we found instead that the spHCN channels carrying VIC were not in rapid equilibrium with the channels carrying the voltage-dependent current, because they could be blocked independently; a single application of blocker at a depolarized potential essentially eliminated VIC with little change in Ih. Thus, VIC appears to be produced by a distinct population of HCN channels. This voltage-independent current could contribute significantly to the role of HCN channels in neurons and myocytes; VIC flowing through the channels at physiological potentials would tend to promote excitability by accelerating both depolarization and repolarization.
Characterization of high-quality MgB2(0001) epitaxial films on Mg(0001)
Authors: Petaccia Luca , Cepek Cinzia , Lizzit Silvano , Larciprete Rosanna , Macovez Roberto , Sancrotti Massimo , Goldoni Andrea
Published: January 2006

High-grade MgB2(0001) films were grown on Mg(0001) by means of ultra-high-vacuum molecular beam epitaxy. Low-energy electron diffraction and x-ray diffraction data indicate that thick films are formed by epitaxially oriented grains with MgB2bulk structure. The quality of the films allowed angle-resolved photoemission and polarization dependent x-ray absorption measurements. For the first time, we report the band mapping along the Γ-A direction and the estimation of the electron–phonon coupling constant λ = 0.55 ± 0.06 for the surface state electrons.
Floer theory and low dimensional topology
Authors: McDuff Dusa
Published: January 2006

The new

3
3

- and

4
4

-manifold invariants recently constructed by Ozsváth and Szabó are based on a Floer theory associated with Heegaard diagrams. The following notes try to give an accessible introduction to their work. In the first part we begin by outlining traditional Morse theory, using the Heegaard diagram of a

3
3

-manifold as an example. We then describe Witten’s approach to Morse theory and how this led to Floer theory. Finally, we discuss Lagrangian Floer homology. In the second part, we define the Heegaard Floer complexes, explaining how they arise as a special case of Lagrangian Floer theory. We then briefly describe some applications, in particular the new

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-manifold invariant, which is conjecturally just the Seiberg–Witten invariant.
The Green-Tao Theorem on arithmetic progressions in the primes: an ergodic point of view
Authors: Kra Bryna
Published: January 2006

A long-standing and almost folkloric conjecture is that the primes contain arbitrarily long arithmetic progressions. Until recently, the only prog- ress on this conjecture was due to van der Corput, who showed in 1939 that there are infinitely many triples of primes in arithmetic progression. In an amazing fusion of methods from analytic number theory and ergodic theory, Ben Green and Terence Tao showed that for any positive integer

k
k

, there exist infinitely many arithmetic progressions of length

k
k

consisting only of prime numbers. This is an introduction to some of the ideas in the proof, concentrating on the connections to ergodic theory.
Role of Toll‐like Receptors in Adjuvant‐Augmented Immune Therapies
Authors: Seya Tsukasa , Akazawa Takashi , Tsujita Tadayuki , Matsumoto Misako
Published: January 2006

Effective therapeutic vaccines contain two primary constituents, antigen and adjuvant. Adjuvants consisting of microbial pattern molecules play a central role in vaccination. Successful vaccine requires efficient induction of antibody (Ab), type I interferons (IFN), cytokines/chemokines, cytotoxic T lymphocytes (CTL) and/or NK cells. Toll‐like receptors (TLRs) in myeloid dendritic cells (mDC) essentially act as adjuvant receptors and sustain the molecular basis of adjuvant activity. Current consensus is that TLRs and their adapters introduce signals to preferentially induce IFN‐α/β, chemokines and proinflammatory cytokines, and mature mDC to augment antigen presentation. Although most of these data were obtained with mice, the results are presumed to be adaptable to humans. Whenever TLR pathway is activated in mDC, NK and/or CTL activation is promoted. For induction of antigen‐specific CTL toward phagocytosed material, cross‐priming must be induced in mDC, which is also sustained by TLR signaling in mDC. Since the TLR responses vary with different adjuvants, mDC functions are skewed depending on adjuvant‐specific direction of mDC maturation. It appears that the directed maturation of mDC largely relies on selection of appropriate sets of TLRs and their adapter signaling pathways. Synthetic chimera molecules consisting of TLR agonists and target antigens are found to be effective in induction of CTL to eliminate target cells in vivo. Here, we review the role of human TLRs and adapters in a variety of host immune responses. We will also describe the relevance of adjuvants in the manipulation of receptors and adapters in vaccine therapy.
Analytical solution and shape optimization for groundwater flow through a leaky porous trough subjacent to an aquifer
Authors: Kacimov A.R
Published: January 2006

Steady two-dimensional groundwater flow in a porous low-permeable trough is studied by the method of boundary-value problems for holomorphic functions. In the overlying highly permeable aquifer the hydraulic head varies linearly, i.e. flow is unidirectional. The exchange of groundwater between aquifer and trough does not affect the flow in the aquifer. It is assumed that through a horizontal aquifer–trough interface the head is transmitted into the trough, where the bounding effect of the bed causes circulatory seepage. Triangular troughs are studied and an isosceles form with a base angle of 38° is proved to have the highest circulation rate at a given cross-sectional area. In the class of arbitrary forms, solution to this optimal shape design problem is obtained by tackling the Schwartz and Signorini singular integrals and a unique and global maximum of the rate is found. The extreme curve coincides with an optimal soil channel of minimal seepage losses having depth to width ratio of 0.371. The global maximum differs from that one for the triangular class in 3% only that corroborates stability and robustness of the optimization criterion and makes possible isoperimetric estimates of the seepage intensity through arbitrary troughs.
Femtosecond electron diffraction: ‘making the molecular movie’
Authors: Dwyer Jason R , Hebeisen Christoph T , Ernstorfer Ralph , Harb Maher , Deyirmenjian Vatche B , Jordan Robert E , Dwayne Miller R.J
Published: January 2006

Femtosecond electron diffraction (FED) has the potential to directly observe transition state processes. The relevant motions for this barrier-crossing event occur on the hundred femtosecond time-scale. Recent advances in the development of high-flux electron pulse sources with the required time resolution and sensitivity to capture barrier-crossing processes are described in the context of attaining atomic level details of such structural dynamics—seeing chemical events as they occur. Initial work focused on the ordered-to-disordered phase transition of Al under strong driving conditions for which melting takes on nm or molecular scale dimensions. This work has been extended to Au, which clearly shows a separation in time-scales for lattice heating and melting. It also demonstrates that superheated face-centred cubic (FCC) metals melt through thermal mechanisms involving homogeneous nucleation to propagate the disordering process. A new concept exploiting electron–electron correlation is introduced for pulse characterization and determination oft=0 to within 100 fs as well as for spatial manipulation of the electron beam. Laser-based methods are shown to provide further improvements in time resolution with respect to pulse characterization, absolutet=0 determination, and the potential for electron acceleration to energies optimal for time-resolved diffraction.
Roseibacterium elongatum gen. nov., sp. nov., an aerobic, bacteriochlorophyll-containing bacterium isolated from the west coast of Australia
Authors: Suzuki Tomonori , Mori Youichirou , Nishimura Yukimasa
Published: January 2006

A novel aerobic, chemoheterotrophic, bacteriochlorophyll-containing bacterium, strain OCh 323T, was isolated from sand at Monkey Mia, Shark Bay, located on the west coast of Australia. The cells were Gram-negative, non-motile rods of variable length; one or both cell poles was narrower. Bacteriochlorophyll a was synthesized under aerobic conditions. Catalase, oxidase and urease were produced. The ONPG reaction was positive. The major component of the cellular fatty acid was octadecenoic acid (18 : 1). The DNA G+C content was 68·1 mol%. The results of 16S rRNA gene sequence comparisons revealed that strain OCh 323T formed a novel, separate line of descent within the α-3 group of the Alphaproteobacteria. The similarity value for the 16S rRNA gene sequence of strain OCh 323T and that of the most closely related species, Rhodovulum sulfidophilum, was 91·4 %. It is concluded that strain OCh 323T (=JCM 11220T=CIP 107377T) should be placed in a novel genus, Roseibacterium gen. nov., as the type strain of a novel species Roseibacterium elongatum sp. nov.
Tepidimicrobium ferriphilum gen. nov., sp. nov., a novel moderately thermophilic, Fe(III)-reducing bacterium of the order Clostridiales
Authors: Slobodkin A. I. , Tourova T. P. , Kostrikina N. A. , Lysenko A. M. , German K. E. , Bonch-Osmolovskaya E. A. , Birkeland N.-K.
Published: January 2006

A moderately thermophilic, anaerobic bacterium (strain SB91T) was isolated from a freshwater hot spring at Barguzin Valley, Buryatiya, Russia. Cells of strain SB91Twere straight to slightly curved rods, 0·5–0·6 μm in diameter and 3·0–7·0 μm in length. Formation of endospores was not observed. The temperature range for growth was 26–62 °C, with an optimum at 50 °C. The pH range for growth was 5·5–9·5, with an optimum at pH 7·5–8·0. The substrates utilized by strain SB91Tin the presence of 9,10-anthraquinone 2,6-disulfonate included peptone, tryptone, Casamino acids, yeast extract, beef extract, casein hydrolysate, alanine plus glycine, alanine plus proline,l-valine and n-propanol. Carbohydrates were not utilized. Strain SB91Treduced amorphous Fe(III) oxide, Fe(III) citrate, Fe(III) EDTA or Fe(III) nitrilotriacetate with peptone,l-valine or n-propanol as an electron donor. Strain SB91Treduced 9,10-anthraquinone 2,6-disulfonate, thiosulfate, elemental sulfur, fumarate and selenite. Strain SB91Tsurvived after exposure to gamma-radiation at a dose of 5·4 kGy. The G+C content of the DNA of strain SB91Twas 33 mol%. Analysis of the 16S rRNA gene sequence revealed that the isolated organism belonged to cluster XII of the clostridia. On the basis of its physiological properties and the results of phylogenetic analyses, it is proposed that strain SB91Trepresents the sole species of a novel genus,Tepidimicrobium; the nameTepidimicrobium ferriphilumgen. nov., sp. nov. is proposed, with strain SB91T(=DSM 16624T=VKM B-2348T) as the type strain.
Kribbella lupini sp. nov., isolated from the roots of Lupinus angustifolius
Authors: Trujillo Martha E. , Kroppenstedt Reiner M. , Schumann Peter , Martínez-Molina Eustoquio
Published: January 2006

Strain LU14T, isolated from the roots of Lupinus angustifolius, was characterized using a polyphasic approach. 16S rRNA gene sequence studies showed a similarity of 98·7 % to the corresponding sequence of Kribbella sandramycini DSM 15626T. Chemotaxonomic data gathered for fatty acids, phospholipids, cell-wall peptidoglycan and menaquinones strongly supported the classification of this strain in the genus Kribbella and DNA–DNA hybridization studies suggested that it may represent a novel species. Many physiological features were found that clearly distinguished isolate LU14T from other Kribbella species. Based on the above data, a novel species of the genus Kribbella, Kribbella lupini sp. nov., is proposed with the type strain LU14T (=DSM 16683T=LMG 22957T).
Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.
Authors: Takahashi Yōko , Matsumoto Atsuko , Morisaki Kurimi , Ōmura Satoshi
Published: January 2006

A novel Gram-positive bacterial strain, designated KV-614T, was isolated from a soil sample using an agar medium supplemented with superoxide dismutase. Based on 16S rRNA gene sequence analysis, it was found that the strain represented a novel deep-rooting lineage within the classActinobacteriaand clustered with yet-uncultivated bacteria from terrestrial environments and some unidentified strains isolated by unique methods. The most closely related established genus wasConexibacter(92·4 % sequence similarity toConexibacter woeseiDSM 14684T). Cells of strain KV-614Twere rod-shaped and motile with long flagella. The strain was catalase-positive, oxidase-negative and grew under aerobic conditions. The cell-wall peptidoglycan containedmeso-diaminopimelic acid as the diagnostic diamino acid and alanine and glutamic acid. The peptidoglycan acyl type was acetyl. The only detected isoprenoid quinone was demethylmenaquinone with seven isoprene units (DMK-7). Mycolic acids were not detected. The predominant cellular fatty acid wasω9c-octadecenoic acid (C18 : 1ω9c). Minor components were 12-methyl tetradecanoic acid (anteiso-C15 : 0) and 14-methyl hexadecanoic acid (anteiso-C17 : 0). The DNA G+C content was 72 mol%. On the basis of phenotypic and genotypic characteristics, it is proposed that strain KV-614Trepresents a new genus and a novel species,Patulibacter minatonensisgen. nov., sp. nov., in the classActinobacteria. The type strain is KV-614T(=NRRL B-24346T=JCM 12834T=NBRC 100761T). The creation of the familyPatulibacteraceaefam. nov. is proposed to encompass the genusPatulibactergen. nov.
Thalassomonas loyana sp. nov., a causative agent of the white plague-like disease of corals on the Eilat coral reef
Authors: Thompson F. L. , Barash Y. , Sawabe T. , Sharon G. , Swings J. , Rosenberg E.
Published: January 2006

The taxonomic position of the coral pathogen strain CBMAI 722T was determined on the basis of molecular and phenotypic data. We clearly show that the novel isolate CBMAI 722T is a member of the family Colwelliaceae, with Thalassomonas ganghwensis as the nearest neighbour (95 % 16S rRNA gene sequence similarity). CBMAI 722T can be differentiated from its nearest neighbour on the basis of phenotypic and chemotaxonomic features, including the utilization of cellobiose and l-arginine, the production of alginase and amylase, but not oxidase, and the presence of the fatty acids 12 : 0 3-OH and 14 : 0, but not 10 : 0 or 15 : 0. The DNA G+C content of CBMAI 722T is 39·3 mol%. We conclude that this strain represents a novel species for which we propose the name Thalassomonas loyana sp. nov., with the type strain CBMAI 722T (=LMG 22536T). This is the first report of the involvement of a member of the family Colwelliaceae in coral white plague-like disease.
Streptomyces cheonanensis sp. nov., a novel streptomycete with antifungal activity
Authors: Kim Hyo Jin , Lee Sung Chul , Hwang Byung Kook
Published: January 2006

Actinomycete strain VC-A46T, which exhibits antifungal activity, was isolated from a soil sample collected from Cheonan, Korea. The strain was determined to belong to the genus Streptomyces, based on its morphological and chemotaxonomic characteristics. The cell wall of this strain contained ll-diaminopimelic acid. The predominant fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1
cis 9. The DNA G+C content of strain VC-A46T was 75·5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence of this strain revealed that it differed from those of the described streptomycetes available in public databases. Analyses of DNA–DNA relatedness data, together with data regarding the strain's morphological, physiological and biochemical characteristics, also confirmed that this strain constitutes a novel Streptomyces taxon, which is distinguishable from closely related reference strains. Therefore, it is proposed that strain VC-A46T (=KCCM 42119T=NBRC 100940T) represents the type strain of a novel species, named Streptomyces cheonanensis sp. nov.
Krokinobacter gen. nov., with three novel species, in the family Flavobacteriaceae
Authors: Khan Shams Tabrez , Nakagawa Yasuyoshi , Harayama Shigeaki
Published: January 2006

Five strains belonging to the family Flavobacteriaceae were isolated from marine-sediment samples collected in Sagami and Tokyo bays on the Pacific coastline of Japan. The five isolates formed a coherent and novel genus-level lineage within the family Flavobacteriaceae. The most closely related species with a validly published name was Cellulophaga lytica. The five isolates were rod-shaped, Gram-negative, aerobic, catalase- and oxidase-positive, flexirubin-negative and yellow-pigmented. The dominant fatty acids were branched or hydroxy acids, i.e. i-C15 : 0, i-C15 : 1 and i-C17 : 0 3-OH. These strains degraded gelatin, casein, DNA and Tween 80. The G+C content of their DNAs ranged between 33 and 39 mol%. Although analysis of the 16S rRNA gene sequence similarity divided these strains into two subgroups with a 2·3 % sequence difference, the results of DNA–DNA hybridization indicated the grouping of these strains into three distinct species. On the basis of phenotypic and genotypic analyses, the novel genus Krokinobacter is proposed, with Krokinobacter genikus sp. nov., containing three of the strains, as the type species. The type strain is Cos-13T (=NBRC 100811T=CIP 108744T). The names Krokinobacter eikastus sp. nov. (type strain PMA-26T=NBRC 100814T=CIP 108743T) and Krokinobacter diaphorus sp. nov. (type strain MSKK-32T=NBRC 100817T=CIP 108745T) are proposed for the other two isolates.
Catellicoccus marimammalium gen. nov., sp. nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium from porpoise and grey seal
Authors: Lawson Paul A. , Collins Matthew D. , Falsen Enevold , Foster Geoffrey
Published: January 2006

Two strains of an unknown Gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped bacterium, originating from a porpoise and a grey seal, were characterized using phenotypic, biochemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on l-lysine (type l-lys–gly–d-Asp) and a DNA G+C content of 38 mol%. Comparative 16S rRNA gene sequencing showed that this unidentified coccus-shaped organism formed a hitherto unknown subline closely related to, albeit distinct from, a number of other catalase-negative genera which included Enterococcus, Melissococcus, Tetragenococcus and Vagococcus. Other known Gram-positive, catalase-negative taxa were more distantly related. Tree-branching considerations and sequence divergence values of >6 % with recognized taxa were indicative of this novel bacterium representing a separate genus. Based on phenotypic and phylogenetic evidence, it is proposed that this unknown bacterium, recovered from a porpoise and a grey seal, be classified as a novel genus and species, Catellicoccus marimammalium gen. nov., sp. nov. The type strain is M35/04/3T (=CCUG 49459T=CIP 108575T).
Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004
Authors: Naser Sabri M. , Vancanneyt Marc , Hoste Bart , Snauwaert Cindy , Vandemeulebroecke Katrien , Swings Jean
Published: January 2006

The taxonomic relatedness between the speciesEnterococcus casseliflavusandEnterococcus flavescensand betweenEnterococcus italicusandEnterococcus saccharominimuswas investigated. Literature data had already indicated the synonymy betweenE. casseliflavusandE. flavescens, but this observation had not been formally published. Additional evidence that the two taxa represent a single species was provided by comparison of the partial sequences for three housekeeping genes, phenylalanyl-tRNA synthase alpha subunit (pheS), RNA polymerase alpha subunit (rpoA) and the alpha subunit of ATP synthase (atpA). Additional genomic data derived from DNA–DNA hybridization demonstrated that the two species are synonymous. ForE. italicusandE. saccharominimus, two recently described taxa, a high 16S rRNA gene sequence similarity of >99 % and analogous phenotypic features indicated a close taxonomic relatedness. The same multilocus sequence analysis scheme for the three housekeeping genes was also applied forE. italicusandE. saccharominimusand indicated possible conspecificity, an observation that was also confirmed by a high DNA–DNA hybridization value (⩾78 %). Data from the present study led to the proposal thatE. flavescensshould be reclassified as a later synonym ofE. casseliflavusand thatE. saccharominimusshould be reclassified as a later synonym ofE. italicus.
Acaricomes phytoseiuli gen. nov., sp. nov., isolated from the predatory mite Phytoseiulus persimilis
Authors: Pukall Rüdiger , Schumann Peter , Schütte Conny , Gols Rieta , Dicke Marcel
Published: January 2006

A Gram-positive, rod-shaped, non-spore-forming bacterium, strain CSCT, was isolated from diseased, surface-sterilized specimens of the predatory mite Phytoseiulus persimilis Athias-Henriot and subjected to polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain was a new member of the family Micrococcaceae. Nearest phylogenetic neighbours were determined as Renibacterium salmoninarum (94·0 %), Arthrobacter globiformis (94·8 %) and Arthrobacter russicus (94·6 %). Although the predominant fatty acids (anteiso C15 : 0), cell-wall sugars (galactose, glucose) and polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol) are in accordance with those of members of the genus Arthrobacter, strain CSCT can be distinguished from members of the genus Arthrobacter by biochemical tests, the absence of a rod–coccus life cycle and the occurrence of the partially saturated menaquinone MK-10(H2) as the predominant menaquinone. The DNA G+C content is 57·7 mol%. On the basis of morphological, chemotaxonomic and phylogenetic differences from other species of the Micrococcaceae, a novel genus and species are proposed, Acaricomes phytoseiuli gen. nov., sp. nov. The type strain is CSCT (=DSM 14247T=CCUG 49701T).
Shinella granuli gen. nov., sp. nov., and proposal of the reclassification of Zoogloea ramigera ATCC 19623 as Shinella zoogloeoides sp. nov.
Authors: An Dong-Shan , Im Wan-Taek , Yang Hee-Chan , Lee Sung-Taik
Published: January 2006

The taxonomic position of a novel bacterial strain, Ch06T, isolated from an upflow anaerobic sludge blanket reactor was determined. Strain Ch06Twas Gram-negative, aerobic, motile and oxidase- and catalase-positive. A comparative 16S rRNA gene sequence analysis showed a clear affiliation of strain Ch06Tto theAlphaproteobacteriaand it was most closely related toZoogloea ramigeraATCC 19623 andMycoplana dimorphaIAM 13154T(97·9 and 96·3 % sequence similarity, respectively). The major respiratory quinone was Q-10 and the predominant fatty acids were C16 : 0, 3-OH C16 : 0, C18 : 0, C19 : 0cycloω8c and summed feature 7 (C18 : 1ω7c/ω9t/ω12t, C18 : 1ω7c/ω9c/ω12t). On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, the novel isolate was assigned to a new genus,Shinellagen. nov., asShinella granuligen. nov., sp. nov. (type strain Ch06T=KCTC 12237T=JCM 13254T). It is proposed thatZoogloea ramigeraATCC 19623 is reclassified into the novel genusShinellaasShinella zoogloeoidessp. nov. (type strain ATCC 19623T=IAM 12669T=I-16-MT).
The status of the genus name Halovibrio Fendrich 1989 and the identity of the strains Pseudomonas halophila DSM 3050 and Halomonas variabilis DSM 3051. Request for an Opinion
Authors: Sorokin D. Yu. , Tindall B. J.
Published: January 2006

During the course of studies on halophilic, Gram-negative bacteria, a comparison of two strains of halophilic bacteria, Pseudomonas halophila DSM 3050 and Halomonas variabilis DSM 3051 (formerly Halovibrio variabilis) demonstrated that the characteristics of strain DSM 3050 corresponded to the original description of Halovibrio variabilis and those of DSM 3051 to P. halophila, both of which had been isolated from the Great Salt Lake in Utah [Fendrich, C. (1988). Syst Appl Microbiol
11, 36–43]. It was concluded that these two strains did not correspond with their original descriptions, e.g. the original description of Halovibrio variabilis matched that of Pseudomonas halophila DSM 3050 and the original description of Pseudomonas halophila matched that of Halovibrio variabilis DSM 3051, which was subsequently transferred to the genus Halomonas as Halomonas variabilis DSM 3051. These findings raise the question of whether the genus name Halovibrio, with the type species Halovibrio variabilis, should be associated with type strain DSM 3050 and recognition of strain DSM 3051 as the type strain of Pseudomonas halophila.
Methylobacterium adhaesivum sp. nov., a methylotrophic bacterium isolated from drinking water
Authors: Gallego Virginia , García Maria Teresa , Ventosa Antonio
Published: January 2006

A pink-pigmented, facultatively methylotrophic strain, AR27T, isolated from the drinking water distribution system of Seville, Spain, was characterized taxonomically. Cells were Gram-negative rods, motile, non-spore-forming and strictly aerobic. Growth in liquid media was flocculant whereas on solid media growth produced colonies that usually adhered to the agar surface. On the basis of its phenotypic characteristics, 16S rRNA gene sequence data and DNA G+C content (63·6 mol%), strain AR27T(=CECT 7069T=CCM 7305T) is proposed as the type strain of a novel species of the genusMethylobacterium,Methylobacterium adhaesivumsp. nov.
Lactobacillus rennini sp. nov., isolated from rennin and associated with cheese spoilage
Authors: Chenoll Empar , Macián M. Carmen , Aznar Rosa
Published: January 2006

Two bacterial strains, DSM 20253Tand DSM 20254, isolated from rennin and regarded as causing cheese spoilage, were deposited in the DSMZ asLactobacillussp. by J. Stadhouders. The strains show 99·9 % 16S rRNA gene sequence similarity and have less than 94·3 % similarity with any other species of the genus.Lactobacillus coryniformisis their closest phylogenetic neighbour. DNA–DNA hybridization experiments confirmed that the two strains are members of the same species with separate status within the genusLactobacillus. The strains are homofermentative lactic acid bacteria and can be phenotypically and genotypically distinguished from their closest relatives. 16S rRNA gene-targeted specific primers were designed to enable PCR detection of the novel species. The nameLactobacillus renninisp. nov. is proposed for the novel isolates, with strain CECT 5922T(=DSM 20253T) as the type strain.
Proposal that Agrobacterium radiobacter has priority over Agrobacterium tumefaciens. Request for an Opinion
Authors: Young J. M. , Pennycook S. R. , Watson D. R. W.
Published: January 2006

It is proposed that Agrobacterium radiobacter has priority as the earlier heterotypic (subjective) synonym when it is united with Agrobacterium tumefaciens. The nomenclatural status of A. tumefaciens as a later heterotypic synonym of the united species is not lost and it remains the type species of the genus. Request for an Opinion.
Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China
Authors: Zhang Yu-Qin , Li Wen-Jun , Zhang Ke-Yun , Tian Xin-Peng , Jiang Yi , Xu Li-Hua , Jiang Cheng-Lin , Lai Ren
Published: January 2006

Four Gram-negative, motile, rod-shaped bacterial strains were isolated from soil samples collected from south-east China. A taxonomic study including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics was performed. DNA G+C contents of the four strains were 63–66 mol%. Their predominant ubiquinone was Q-8. The fatty acid profiles contained C16 : 1
ω7c (36·9–54·7 %) and C16 : 0 (22·8–25·5 %) as the major components. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and DNA–DNA hybridization results, the four isolates are considered to represent four novel species of the genus Massilia, for which the names Massilia dura sp. nov. (type strain 16T=CCTCC AB 204070T=KCTC 12342T), Massilia albidiflava sp. nov. (type strain 45T=CCTCC AB 204071T=KCTC 12343T), Massilia plicata sp. nov. (type strain 76T=CCTCC AB 204072T=KCTC 12344T) and Massilia lutea sp. nov. (type strain 101T=CCTCC AB 204073T=KCTC 12345T) are proposed.
T‐cell development: an extrathymic perspective
Authors: Blais Marie‐Ève , Louis Isabelle , Perreault Claude
Published: January 2006

Summary:  The lymph nodes (LNs) harbor a cryptic T‐lymphopoietic pathway that is dramatically amplified by oncostatin M (OM). OM‐transgenic mice generate massive amounts of T lymphocytes in the absence of Lin–c‐KithiIL‐7Rα– lymphoid progenitors and of reticular epithelial cells. Extrathymic T cells that develop along the OM‐dependent LN pathway originate from Lin–c‐KitloIL‐7Rα+ lymphoid progenitors and are different from classic T cells in terms of turnover kinetics and function. Positive selection does not obey the same rules in the thymus and the LNs, where positive selection of developing T cells is supported primarily by epithelial and hematopoietic cells, respectively. Extrathymic T cells undergo enhanced homeostatic proliferation and thereby acquire some properties of memory T cells. Following antigen encounter, extrathymic T‐cells initiate proliferation and cytokine secretion more readily than classic T cells, but their accumulation is limited by an exquisite susceptibility to apoptosis. Studies on in vitro and in vivo extrathymic T‐cell development have yielded novel insights into the essence of a primary T‐lymphoid organ. Furthermore, comparison of the thymic and OM‐dependent extrathymic pathways shows how the division of labor between primary and secondary lymphoid organs influences the repertoire and homeostasis of T lymphocytes.
Regulation of T‐cell progenitor survival and cell‐cycle entry by the pre‐T‐cell receptor
Authors: Aifantis Iannis , Mandal Malay , Sawai Katie , Ferrando Adolfo , Vilimas Tomas
Published: January 2006

Summary:  Pre‐T‐cell receptor (pre‐TCR) functions and the study of early thymocyte development continue to fascinate immunologists more than 10 years after the first description and cloning of the receptor. Although multiple reports have addressed several aspects of pre‐TCR signaling and function, its ability to regulate diverse functions, including proliferation, survival, and allelic exclusion of the TCR‐β locus, remains an open question. What fascinates us is its central role in the fine balance between physiological differentiation and thymocyte transformation that leads to T‐cell leukemia and lymphomas. In this review, we integrate pre‐TCR signaling pathways and study their effects on the regulation of T‐cell progenitor cell‐cycle entry and cell survival. We also connect aberrant pre‐TCR signaling to deregulated proliferation and apoptotic balances and thymocyte transformation.
Role of the transcription factor Th‐POK in CD4:CD8 lineage commitment
Authors: Kappes Dietmar J. , He Xi , He Xiao
Published: January 2006

Summary:  The molecular basis of CD4:CD8 lineage commitment, in particular the mechanism by which the precise correlation between lineage choice and T‐cell receptor (TCR) specificity toward class I or II major histocompatibility complex is achieved, remains controversial. Both stochastic/selective and instructive models in various forms have been proposed to explain this correlation. The two main experimental approaches previously employed to elucidate this process have focused on the beginning and end of the process, i.e. the influence of TCR signaling and the alternate transcriptional control of the CD4 and CD8 loci during commitment. The recent finding that the transcription factor Th‐POK is necessary and sufficient for CD4 commitment has now provided a direct entry point for studying the intracellular pathways that govern lineage commitment. Here, we review data leading to the identification and characterization of this factor and discuss the implications of these studies in the context of current models of lineage commitment.
Commitment issues: linking positive selection signals and lineage diversification in the thymus
Authors: Aliahmad Parinaz , Kaye Jonathan
Published: January 2006

Summary:  The thymus is responsible for the production of CD4+ helper and CD8+ cytotoxic T cells, which constitute the cellular arm of the immune system. These cell types derive from common precursors that interact with thymic stroma in a T‐cell receptor (TCR)‐specific fashion, generating intracellular signals that are translated into function‐specific changes in gene expression. This overall process is termed positive selection, but it encompasses a number of temporally distinct and possibly mechanistically distinct cellular changes, including rescue from apoptosis, initiation of cell differentiation, and commitment to the CD4+ or CD8+ T‐cell lineage. One of the puzzling features of positive selection is how specificity of the TCR controls lineage commitment, as both helper and cytolytic T cells utilize the same antigen‐receptor components, with the exception of the CD4 or CD8 coreceptors themselves. In this review, we focus on the signals required for positive selection, particularly as they relate to lineage commitment. Identification of genes encoding transcriptional regulators that play a role in T‐cell development has led to significant recent advances in the field. We also provide an overview of nuclear factors in this context and, where known, how their regulation is linked to the same TCR signals that have been implicated in initiating and regulating positive selection.
Establishment and functioning of intrathymic microenvironments
Authors: Anderson Graham , Jenkinson William E. , Jones Terry , Parnell Sonia M. , Kinsella Francesca A. M. , White Andrea J. , Pongrac'z Judit E. , Rossi Simona W. , Jenkinson Eric J.
Published: January 2006

Summary:  The thymus supports the production of self‐tolerant T cells from immature precursors. Studying the mechanisms regulating the establishment and maintenance of stromal microenvironments within the thymus therefore is essential to our understanding of T‐cell production and ultimately immune system functioning. Despite our ability to phenotypically define stromal cell compartments of the thymus, the mechanisms regulating their development and the ways by which they influence T‐cell precursors are still unclear. Here, we review recent findings and highlight unresolved issues relating to the development and functioning of thymic stromal cells.
Central tolerance: good but imperfect
Authors: Gallegos Alena M. , Bevan Michael J.
Published: January 2006

Summary:  T‐cell development is a highly coordinated process that depends on interactions between thymocytes, thymic epithelium, and bone marrow (BM)‐derived dendritic cells (DCs). Before entering the peripheral T‐cell pool, thymocytes are subject to negative selection, a process that eliminates (or deletes) T cells with high affinity toward self‐antigens and therefore promotes self‐tolerance. These self‐antigens include those that are broadly expressed ubiquitous antigens and those whose expression is restricted to a few tissues, tissue‐specific antigens (TSAs). Expression of TSAs in the thymus is mostly a property of medullary thymic epithelial cells (mTECs), and because these cells may be less capable than BM‐derived DCs at mediating negative selection to ubiquitous antigens, we investigated the roles of both of these cell types in tolerance to TSAs. Here, we review our studies in which we found that mTECs were competent mediators of negative selection to a subset of TSA‐reactive T cells, while thymic DCs extend the range of TSA‐reactive T cells that undergo negative selection by capturing TSAs from mTECs. In addition, we recently investigated the efficiency of central tolerance to TSA during ontogeny, and we report that this process was less efficient in neonates than adult animals.