bluuebunny/crossref_metadata_2025 huggingface dataset:
Normal motor learning during pharmacological prevention of Purkinje cell long-term depression
Authors: Welsh John P. , Yamaguchi Hidetoshi , Zeng Xiao-Hui , Kojo Masanobu , Nakada Yasushi , Takagi Akiko , Sugimori Mutsuyuki , Llinás Rodolfo R.
Published: November 2005

Systemic delivery of (1R-1-benzo thiophen-5-yl-2[2-diethylamino)-ethoxy] ethanol hydrochloride (T-588) prevented long-term depression (LTD) of the parallel fiber (PF)-Purkinje cell (PC) synapse induced by conjunctive climbing fiber and PF stimulationin vivo. However, similar concentrations of T-588 in the brains of behaving mice and rats affected neither motor learning in the rotorod test nor the learning of motor timing during classical conditioning of the eyeblink reflex. Rats given doses of T-588 that prevented PF-PC LTD were as proficient as controls in learning to adapt the timing of their conditioned eyeblink response to a 150- or 350-ms change in the timing of the paradigm. The experiment indicates that PF-PC LTD under control of the climbing fibers is not required for general motor adaptation or the learning of response timing in two common models of motor learning for which the cerebellum has been implicated. Alternative mechanisms for motor timing and possible functions for LTD in protection from excitotoxicity are discussed.
Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
Authors: Li Huai , Zhan Ming
Published: November 2005

Motivation: A major challenge in post-genomic research has been to understand how physiological and pathological phenotypes arise from the networks of expressed genes. Here, we addressed this issue by developing an algorithm to mimic the behavior of regulatory networks in silico and to identify the dynamic response to disease and changing cellular conditions.

Results: With regulatory pathway and gene expression data as input, the algorithm provides quantitative assessments of a wide range of responses, including susceptibility to disease, potential usefulness of a given drug, or consequences to such external stimuli as pharmacological interventions or caloric restriction. The algorithm is particularly amenable to the analysis of systems that are difficult to recapitulate in vitro, yet they may have important clinical value. The hypotheses derived from the algorithm were biologically relevant and were successfully validated via independent experiments, as illustrated here in the analysis of the leukemia-associated BCR–ABL pathway and the insulin/IGF pathway related to longevity. The algorithm correctly identified the leukemia drug target and genes important for longevity, and also provided new insights into our understanding of these two processes.

Availability: The software package is available upon request to the authors.

Contact:  

Supplementary information: Supplementary data are available at Bioinformatics online.
Post‐Traumatic Stress Disorder: Evidence‐Based Research for the Third Millennium
Authors: Iribarren Javier , Prolo Paolo , Neagos Negoita , Chiappelli Francesco
Published: November 2005

The stress that results from traumatic events precipitates a spectrum of psycho‐emotional and physiopathological outcomes. Post‐traumatic stress disorder (PTSD) is a psychiatric disorder that results from the experience or witnessing of traumatic or life‐threatening events. PTSD has profound psychobiological correlates, which can impair the person′s daily life and be life threatening. In light of current events (e.g. extended combat, terrorism, exposure to certain environmental toxins), a sharp rise in patients with PTSD diagnosis is expected in the next decade. PTSD is a serious public health concern, which compels the search for novel paradigms and theoretical models to deepen the understanding of the condition and to develop new and improved modes of treatment intervention. We review the current knowledge of PTSD and introduce the role of allostasis as a new perspective in fundamental PTSD research. We discuss the domain of evidence‐based research in medicine, particularly in the context of complementary medical intervention for patients with PTSD. We present arguments in support of the notion that the future of clinical and translational research in PTSD lies in the systematic evaluation of the research evidence in treatment intervention in order to insure the most effective and efficacious treatment for the benefit of the patient.
Simplification and its consequences in biological modelling: conclusions from a study of calcium oscillations in hepatocytes
Authors: Hetherington James P.J , Warner Anne , Seymour Robert M
Published: November 2005

Systems Biology requires that biological modelling is scaled up from small components to system level. This can produce exceedingly complex models, which obscure understanding rather than facilitate it. The successful use of highly simplified models would resolve many of the current problems faced in Systems Biology. This paper questions whether the conclusions of simple mathematical models of biological systems are trustworthy. The simplification of a specific model of calcium oscillations in hepatocytes is examined in detail, and the conclusions drawn from this scrutiny generalized. We formalize our choice of simplification approach through the use of functional ‘building blocks’. A collection of models is constructed, each a progressively more simplified version of a well-understood model. The limiting model is a piecewise linear model that can be solved analytically.

We find that, as expected, in many cases the simpler models produce incorrect results. However, when we make a sensitivity analysis, examining which aspects of the behaviour of the system are controlled by which parameters, the conclusions of the simple model often agree with those of the richer model. The hypothesis that the simplified model retains no information about the real sensitivities of the unsimplified model can be very strongly ruled out by treating the simplification process as a pseudo-random perturbation on the true sensitivity data. We conclude that sensitivity analysis is, therefore, of great importance to the analysis of simple mathematical models in biology. Our comparisons reveal which results of the sensitivity analysis regarding calcium oscillations in hepatocytes are robust to the simplifications necessarily involved in mathematical modelling. For example, we find that if a treatment is observed to strongly decrease the period of the oscillations while increasing the proportion of the cycle during which cellular calcium concentrations are rising, without affecting the inter-spike or maximum calcium concentrations, then it is likely that the treatment is acting on the plasma membrane calcium pump.
On the indentation of a polymeric membrane
Authors: Selvadurai A.P.S , Yu Q
Published: November 2005

The paper examines the problem of the transverse indentation of a polymeric membrane that is fixed at its circular boundary. Axisymmetric and asymmetric deformations are induced by axial and off-axis indentation by a rigid indentor with a spherical profile. The mechanical behaviour of the polymeric material is modelled by a constitutive relationship that takes into consideration large strains and viscoplastic strain-rate effects. The results of experimental investigations are compared with predictions of computational modelling of the membrane indentation problem that utilizes a documented finite element code with facilities for user-prescribed constitutive models. It is shown that the computational procedure can accurately model the experimental indentation responses particularly during the loading stage. During unloading stages the trends of the model predictions show a satisfactory correlation.
Strong association between a single gene and fertilization efficiency of males and fecundity of their mates in the bulb mite
Authors: Konior Magdalena , Radwan Jacek , Kołodziejczyk Maria , Keller Laurent
Published: November 2005

Although variation in male fertilization efficiency has been shown to have a genetic basis in several species, the genes responsible for the effect are generally unknown. Here, we show a strong association between the fertilization success of males and their phosphogluconate dehydrogenase (Pgdh) genotype in the bulb miteRhizoglyphus robini. Males homozygous for the slow (S) allele fathered a significantly greater proportion of offspring when competing with males homozygous for the fast (F) allele. There was no evidence that female fecundity was influenced by theirPgdhgenotype. The fecundity of FF females did not differ significantly from the fecundity of SS females but female fecundity was significantly influenced by the genotype of their mate. Females paired with SS males laid significantly fewer eggs than females paired with FF males. Altogether these data show a trade-off, with the male SS genotype associated with their higher fertilization efficiency but at the cost of a negative impact on the fecundity of females mating with them.
Evolution of host resistance: looking for coevolutionary hotspots at small spatial scales
Authors: Laine Anna-Liisa
Published: November 2005

Natural plant populations are often found to be extremely diverse in their resistance to pathogens. While the potential of pathogens in driving the evolution of resistance in hosts has been widely recognized, empirical evidence linking disease dynamics to host population genetic structure has remained scarce. Here I show that current coevolutionary selection for resistance can be divergent even on a very fine spatial scale. In a natural plant–pathogen metapopulation, disease occurrence patterns were highly aggregated over space and time within host populations. A laboratory inoculation experiment showed higher resistance within areas of the host populations where encounter rates with the pathogen have been high. Higher resistance to sympatric than to allopatric strains of the pathogen suggests that this change has taken place as a response to local selection. These results constitute evidence of adaptive microevolution of resistance resulting from disease epidemics in natural plant–pathogen associations, and highlight the importance of finding the relevant scale at which to address questions of current coevolutionary selection.
Rapid adjustments of sperm characteristics in relation to social status
Authors: Rudolfsen Geir , Figenschou Lars , Folstad Ivar , Tveiten Helge , Figenschou Marie
Published: November 2005

Sperm competition models predict that males typically mating in disfavoured roles should be selected to compensate for their disadvantage by investing more into sperm. We studied the effect of rapid changes in social status on ejaculate investments during experimental trials with an externally fertilizing teleost—the Arctic charr (Salvelinus alpinus). We document that males becoming dominant produce less sperm with lower velocity, but have higher sex steroid concentrations than subordinate males. These differences in sperm characteristics seem mainly to result from a decreased investment in sperm among fish that become dominant compared to pre-trial levels. Moreover, these adjustments of sperm production and sperm velocity seem not to be traded against sperm longevity. Our results support theoretical models of sperm competition, as males forced to mate in disfavoured roles seem to invest more into ejaculate quality than males in favoured roles. Additionally, we are the first to report that males, in a species with status-dependent shifts in reproductive tactics, have evolved rapid tactic specific adjustments of sperm production and sperm velocity corresponding to what could be predicted from their reproductive roles.
Inadvertent social information in breeding site selection of natal dispersing birds
Authors: Nocera Joseph J , Forbes Graham J , Giraldeau Luc-Alain
Published: November 2005

Several species use the number of young produced as public information (PI) to assess breeding site quality. PI is inaccessible for synchronously breeding birds because nests are empty by the time the young can collect this information. We investigate if location cues are the next best source of inadvertent social information (ISI) used by young prospectors during breeding site choice. We experimentally deployed ISI as decoys and song playbacks of breeding males in suitable and sub-optimal habitats during pre- and post-breeding periods, and monitored territory establishment during the subsequent breeding season for a social, bobolink (Dolichonyx oryzivorus), and a more solitary species, Nelson's sharp-tailed sparrow (Ammodramus nelsoni). The sparrows did not respond to treatments, but bobolinks responded strongly to post-breeding location cues, irrespective of habitat quality. The following year, 17/20 sub-optimal plots to which bobolink males were recruited were defended for at least two weeks, indicating that song heard the previous year could exert a ‘carry-over attraction’ effect on conspecifics the following year. Sixteen recruited males were natal dispersers, as expected when animals have little opportunity to directly sample their natal habitat quality. We suggest that differences in breeding synchronicity may induce an equivalent clinal distribution of ISI use.
Phenotypic differentiation and pre-mating isolation between allopatric populations of
Girardinichthys multiradiatus
Authors: González Zuarth Cesar , Macías Garcia Constantino
Published: November 2005

Sexual selection may lead to reproductive isolation between populations through divergence in female mate choice, and population differentiation driven by female mate choice is expected to produce pre- but not post-mating isolation. We tested these hypotheses by looking at whether allopatric populations of the Amarillo (
Girardinichthys multiradiatus
), a sexually dimorphic viviparous fish with effective female choice, (i) have undergone phenotypical differentiation that may be attributed to divergence in female mate choice, and (ii) are already separated by pre- and/or post-mating reproductive barriers. We found substantial divergence in morphological traits which are the target of female mate choice, and in male courtship behaviour. Strong female preferences for homogametic males indicate substantial and symmetric pre-copulatory isolation, but the few successful heterogametic crosses produced in confinement yielded litters of the same size as those produced in homogametic matings, suggesting that post-copulatory isolation between populations is non-existent or weak. It appears that the studied populations have undergone incipient speciation with a pattern that is consistent with speciation driven by sexual selection, yet further work should assess whether divergence in female preferences has promoted male phenotypic differentiation or whether variation in male attributes has driven divergence in female preferences.
Dispersal is not female biased in a resource-defence mating ungulate, the European roe deer
Authors: Coulon A , Cosson J.-F , Morellet N , Angibault J.-M , Cargnelutti B , Galan M , Aulagnier S , Hewison A.J.M
Published: November 2005

Dispersal is frequently more prevalent in one sex compared to the other. Greenwood proposed that patterns of sex-biased dispersal among birds and mammals are linked to their mating strategies. For species where males defend resources rather than females, he predicted female-biased dispersal, because males should remain at their birth site where they are familiar with the distribution of the resources that they must defend. Greenwood's hypothesis has been extensively supported among birds, where most species exhibit a resource-defence mating strategy. However, almost no equivalent information is available for mammals as males generally defend mates in this group. An exception is the European roe deer, a resource-defence mating ungulate. We thus tested Greenwood's hypothesis on this atypical mammalian model, looking for female-biased dispersal using sex-specific inter-individual genetic distances. We conclusively show that gene flow is not higher among females compared to males in the studied roe deer population, and hence that dispersal is not female-biased, suggesting that male mating strategy is not the primary selective force driving the evolution of dispersal in roe deer. We discuss the role of female mate choice and intra-sexual competition as possible alternative selective pressures involved.
Sexual reproduction reshapes the genetic architecture of digital organisms
Authors: Misevic Dusan , Ofria Charles , Lenski Richard E
Published: November 2005

Modularity and epistasis, as well as other aspects of genetic architecture, have emerged as central themes in evolutionary biology. Theory suggests that modularity promotes evolvability, and that aggravating (synergistic) epistasis among deleterious mutations facilitates the evolution of sex. Here, by contrast, we investigate the evolution of different genetic architectures using digital organisms, which are computer programs that self-replicate, mutate, compete and evolve. Specifically, we investigate how genetic architecture is shaped by reproductive mode. We allowed 200 populations of digital organisms to evolve for over 10 000 generations while reproducing either asexually or sexually. For 10 randomly chosen organisms from each population, we constructed and analysed all possible single mutants as well as one million mutants at each mutational distance from 2 to 10. The genomes of sexual organisms were more modular than asexual ones; sites encoding different functional traits had less overlap and sites encoding a particular trait were more tightly clustered. Net directional epistasis was alleviating (antagonistic) in both groups, although the overall strength of this epistasis was weaker in sexual than in asexual organisms. Our results show that sexual reproduction profoundly influences the evolution of the genetic architecture.
Compound mimicry and trading predators by the males of sexually dimorphic Batesian mimics
Authors: Nelson Ximena J , Jackson Robert R
Published: November 2005

Sexual dimorphism is pronounced inMyrmarachne, a large genus of ant-like jumping spiders (Salticidae) and one of the major animal groups in which Batesian mimicry of ants has evolved. Although adult females and juveniles of both sexes are distinctly ant-like in appearance,Myrmarachnemales have elongated chelicerae that might appear to detract from their resemblance to ants. Experimental findings suggest that theMyrmarachnemale's solution is to adopt compound mimicry (i.e. the male's model seems to be not simply an ant worker but a combination of an ant and something carried in the ant's mandibles: an ‘encumbered ant’). By becoming a mimic of a particular subset of worker ants,Myrmarachnemales may have retained their Batesian-mimicry defence against ant-averse predators, but at the price of receiving the unwanted attention of predators for which encumbered ants are preferred prey. Two salticid species were used as predators in the experiments.Portia fimbriatais known to choose other salticids as preferred prey and to avoid unencumbered ants and their mimics (Myrmarachnefemales). In experiments reported here,P. fimbriataavoided encumbered ants andMyrmarachnemales. Ants are the preferred prey ofChalcotropis gulosus. In our experiments,C. gulosuschose safer encumbered ants in preference to more dangerous unencumbered ants, choseMyrmarachnemales more often thanMyrmarachnefemales and showed no evidence of distinguishing betweenMyrmarachnemales and encumbered ants. The cost of reconciling sexual dimorphism with Batesian mimicry appears to be thatMyrmarachnemales attract the unwanted attention of specialist predators of their compound model.
Cross talk between Ca2+and redox signalling cascades in muscle and neurons through the combined activation of ryanodine receptors/Ca2+release channels
Authors: Hidalgo Cecilia
Published: November 2005

Calcium release mediated by the ryanodine receptors (RyR) Ca2+release channels is required for muscle contraction and contributes to neuronal plasticity. In particular, Ca2+activation of RyR-mediated Ca2+release can amplify and propagate Ca2+signals initially generated by Ca2+entry into cells. Redox modulation of RyR function by a variety of non-physiological or endogenous redox molecules has been reported. The effects of RyR redox modification on Ca2+release in skeletal muscle as well as the activation of signalling cascades and transcription factors in neurons will be reviewed here. Specifically, the different effects ofS-nitrosylation orS-glutathionylation of RyR cysteines by endogenous redox-active agents on the properties of skeletal muscle RyRs will be discussed. Results will be presented indicating that these cysteine modifications change the activity of skeletal muscle RyRs, modify their behaviour towards both activators and inhibitors and affect their interactions with FKBP12 and calmodulin. In the hippocampus, sequential activation of ERK1/2 and CREB is a requisite for Ca2+-dependent gene expression associated with long-lasting synaptic plasticity. The effects of reactive oxygen/nitrogen species on RyR channels from neurons and RyR-mediated sequential activation of neuronal ERK1/2 and CREB produced by hydrogen peroxide and other stimuli will be discussed as well.
Mycoplasma amphoriforme sp. nov., isolated from a patient with chronic bronchopneumonia
Authors: Pitcher D. G. , Windsor D. , Windsor H. , Bradbury J. M. , Yavari C. , Jensen J. S. , Ling C. , Webster D.
Published: November 2005

A mycoplasma was isolated from the sputum of an immunodeficient patient with recurrent bronchitis. The isolate designated strain A39T was very fastidious and atypical for a mycoplasma in its colonial appearance. Classical biochemical tests for mycoplasma speciation could not differentiate the isolate from the pathogens Mycoplasma pneumoniae and Mycoplasma genitalium and serological identification as a recognized Mycoplasma species was lacking. Specific PCR detection for these two species was negative. Subsequently, other strains were isolated from human patients that appeared to be similar to strain A39T in their physiological and genetic characteristics. Analysis of the 16S rRNA gene placed strain A39T and other isolates in the pneumoniae group of mycoplasmas, with the highest sequence similarity to Mycoplasma testudinis (96·8 %), but with only 93·0 % similarity to M. pneumoniae and M. genitalium. Examination of the 16S–23S rRNA internally transcribed spacer sequence, protein electrophoresis profile, genome size and serological reactions indicated that this organism represents a novel species, for which the name Mycoplasma amphoriforme sp. nov. is proposed, with strain A39T (=NCTC 11740T=ATCC BAA-992T) as the type strain.
Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake
Authors: Dimitriu Pedro A. , Shukla Sanjay K. , Conradt Jennifer , Márquez M. Carmen , Ventosa Antonio , Maglia Anne , Peyton Brent M. , Pinkart Holly C. , Mormile Melanie R.
Published: November 2005

A novel alkaliphilic bacterium, strain 4CAT, was isolated from decomposing wood taken from the shore of Soap Lake, a saline, alkaline lake in Grant County, WA, USA. Cells of the isolate were Gram-negative, asporogenous, short, motile rods that utilized only a limited range of organic acids as sole carbon and energy sources. In addition to oxygen, the strain possessed the ability to reducein the presence of acetate. Strain 4CATwas oxidase- and catalase-positive; it degraded Tween 60, but not DNA, urea, gelatin or starch. It grew at pH values from 7·5 to 11·0, with optimum growth occurring at pH 9·0, and growth was observed in NaCl concentrations of 0·2–1·3 M, with optimum growth at 0·8 M NaCl. The optimum temperature for growth was 37 °C. Strain 4CATwas resistant to erythromycin, bacitracin, novobiocin, polymyxin B, neomycin, gentamicin, streptomycin, carbenicillin, rifampicin and tetracycline, and was susceptible to nalidixic acid, chloramphenicol, ampicillin and penicillin. The isolate's 16S rRNA gene sequence indicated that it belonged to theγ-Proteobacteria, showing 90–94 % similarity to its closest relatives. Maximum-likelihood phylogenetic inferences placed strain 4CATwithin a novel lineage related to the marine bacterial generaNeptunomonasandMarinobacterium. The DNA G+C content of the isolate was 47·4 mol%. On the basis of genotypic and phenotypic characterization, it was concluded that strain 4CATshould be placed in a separate taxon as a novel genus and species, with the proposed nameNitrincola lacisaponensisgen. nov., sp. nov. The type strain is 4CAT(=ATCC BAA-920T=DSM 16316T).
Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species
Authors: Nogi Yuichi , Takami Hideto , Horikoshi Koki
Published: November 2005

Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA–DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA–DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genusBacillus:Bacillus wakoensissp. nov. (type strain N-1T=JCM 9140T=DSM 2521T),Bacillus hemicellulosilyticussp. nov. (type strain C-11T=JCM 9152T=DSM 16731T),Bacillus cellulosilyticussp. nov. (type strain N-4T=JCM 9156T=DSM 2522T),Bacillus akibaisp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) andBacillus mannanilyticussp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T).
Sphingomonas yunnanensis sp. nov., a novel Gram-negative bacterium from a contaminated plate
Authors: Zhang Yu-Qin , Chen Yi-Guang , Li Wen-Jun , Tian Xin-Peng , Xu Li-Hua , Jiang Cheng-Lin
Published: November 2005

A Gram-negative bacterium, YIM 003T, which was isolated from a contaminated plate in the laboratory, was subjected to a polyphasic taxonomic study. The organism had short-rod-shaped, motile cells, formed yellow-pigmented colonies on ISP2 medium and its optimum growth pH was 7·0–7·5. The major respiratory lipoquinone was ubiquinone Q-10. The phosphate-containing lipids detected in strain YIM 003Twere diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and one unidentified phospholipid. The major fatty acids were C18 : 1ω7c(59·8 %), C16 : 0(9·9 %), ai-C17 : 0(5·3 %), i-C17 : 0(4·4 %) and C14 : 02-OH (15·8 %). The G+C content of the genomic DNA was 67·5 mol%. Strain YIM 003Texhibited levels of 16S rRNA gene sequence similarity of 98·2 % toSphingomonas phyllosphaeraeFA2Tand 98·0 % toSphingomonas adhaesivaDSM 7418Tbut showed less than 97·0 % similarity with respect to other species with validly published names. The DNA–DNA relatedness values of the isolate withS. phyllosphaeraeFA2TandS. adhaesivaDSM 7418Twere 59 and 26 %, respectively. The phenotypic characteristics and genotypic data indicate that strain YIM 003Tshould be distinguished fromS. phyllosphaeraeFA2TandS. adhaesivaDSM 7418T. Therefore, on the basis of the polyphasic taxonomic data presented, a novel species of the genusSphingomonas,Sphingomonas yunnanensissp. nov., is proposed, with the type strain YIM 003T(=CCTCC AB 204064T=KCTC 12346T).
Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic, sulfur-oxidizing bacterium from Yellowstone National Park, and emended descriptions of the genus Sulfurihydrogenibium, Sulfurihydrogenibium subterraneum and Sulfurihydrogenibium azorense
Authors: Nakagawa S. , Shtaih Z. , Banta A. , Beveridge T. J. , Sako Y. , Reysenbach A.-L.
Published: November 2005

A novel thermophilic, sulfur-oxidizing Gram-negative bacterium, designated strain SS-5T, was isolated from the Calcite Hot Springs in Yellowstone National Park, USA. The cells were motile rods (1·2–2·8 μm long and 0·6–0·8 μm wide). The new isolate was a facultative heterotroph capable of using elemental sulfur or thiosulfate as an electron donor and O2(1–18 %; optimum 6 %, v/v) as an electron acceptor. Hydrogen did not support growth. The isolate grew autotrophically with CO2. In addition, strain SS-5Tutilized various organic carbon sources such as yeast extract, tryptone, sugars, amino acids and organic acids. Growth was observed between 55 and 78 °C (optimum 70 °C; 3·5 h doubling time), pH 6·0 and 8·0 (optimum pH 7·5), and 0 and 0·6 % (w/v) NaCl (optimum 0 %). The G+C content of the genomic DNA was 32 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate was a member of the genusSulfurihydrogenibium. On the basis of the physiological and molecular characteristics of the new isolate, we propose the nameSulfurihydrogenibium yellowstonensesp. nov. with SS-5T(=JCM 12773T=OCM 840T) as the type strain. In addition, emended descriptions of the genusSulfurihydrogenibium,Sulfurihydrogenibium subterraneumandSulfurihydrogenibium azorenseare proposed.
Cellular identity of an 18S rRNA gene sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framvarensis sp. nov.
Authors: Stoeck Thorsten , Schwarz M. V. Julian , Boenigk Jens , Schweikert Michael , von der Heyden Sophie , Behnke Anke
Published: November 2005

Environmental molecular surveys of microbial diversity have uncovered a vast number of novel taxonomic units in the eukaryotic tree of life that are exclusively known by their small-subunit (SSU) rRNA gene signatures. In this study, we reveal the cellular and taxonomic identity of a novel eukaryote SSU rRNA gene sequence clade within the Kinetoplastea. Kinetoplastea are ubiquitously distributed flagellated protists of high ecological and medical importance. We isolated an organism from the oxic–anoxic interface of the anoxic Framvaren Fjord (Norway), which branches within an unidentified kinetoplastean sequence clade. Ultrastructural studies revealed a typical cellular organization that characterized the flagellated isolate as a member of the order Neobodonida Vickerman 2004, which contains five genera. The isolate differed in several distinctive characters fromDimastigella,Cruzella,RhynchobodoandRhynchomonas. The arrangement of the microtubular rod that supports the apical cytostome and the cytopharynx differed from the diagnosis of the fifth described genus (NeobodoVickerman 2004) within the order Neobodonida. On the basis of both molecular and microscopical data, a novel genus within the order Neobodonida,Actuariolagen. nov., is proposed. Here, we characterize its type species,Actuariola framvarensissp. nov., and provide anin situtool to access the organism in nature and study its ecology.
Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Yeo Soo-Hwan , Oh Tae-Kwang
Published: November 2005

A Gram-positive, rod-shaped, motile and endospore-forming bacterial strain, KSL-134T, was isolated from an alkaline soil in Korea, and its taxonomic position was investigated by a polyphasic study. Strain KSL-134Tgrew optimally at pH 7·5 and 30 °C. Its cell wall peptidoglycan containedmeso-diaminopimelic acid. Strain KSL-134Twas characterized as having MK-7 as the predominant menaquinone and anteiso-C15 : 0as the major fatty acid. The DNA G+C content was 49·4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KSL-134Tformed a distinct lineage within the evolutionary radiation encompassed by the genusPaenibacillus. Similarity levels between the 16S rRNA gene sequence of strain KSL-134Tand those of the type strains of recognizedPaenibacillusspecies ranged from 90·4 to 96·5 %. DNA–DNA relatedness levels and some differential phenotypic properties were enough to distinguish strain KSL-134Tfrom several phylogenetically relatedPaenibacillusspecies. On the basis of phenotypic and phylogenetic data, strain KSL-134T(=KCTC 3956T=DSM 17040T) was classified in the genusPaenibacillusas a member of a novel species, for which the namePaenibacillus alkaliterraesp. nov. is proposed.
Cyclobacterium amurskyense sp. nov., a novel marine bacterium isolated from sea water
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Lee Myung Sook , Park Myung Soo , Lee Kang Hyun , Lysenko Anatoly M. , Oh Hyun Woo , Mikhailov Valery V. , Bae Kyung Sook
Published: November 2005

The taxonomic position of a novel marine, heterotrophic, aerobic, pigmented, non-motile bacterium isolated from sea water was determined. 16S rRNA gene sequence analysis revealed that strain KMM 6143T is a member of the genus Cyclobacterium. The results of DNA–DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolate represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium amurskyense sp. nov. is proposed. The type strain is KMM 6143T (=KCTC 12363T=LMG 23026T).
Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria
Authors: Gao Beile , Gupta Radhey S.
Published: November 2005

Gram-positive bacteria with a high G+C content are currently recognized as a distinct phylum,Actinobacteria, on the basis of their branching in 16S rRNA trees. Except for an insert in the 23S rRNA, there are no unique biochemical or molecular characteristics known at present that can distinguish this group from all other bacteria. In this work, three conserved indels (i.e. inserts or deletions) are described in three widely distributed proteins that are distinctive characteristics of theActinobacteriaand are not found in any other groups of bacteria. The identified signatures are a 2 aa deletion in cytochrome-coxidase subunit 1 (Cox1), a 4 aa insert in CTP synthetase and a 5 aa insert in glutamyl-tRNA synthetase (GluRS). Additionally, the actinobacterial specificity of the large insert in the 23S rRNA was also tested. Using primers designed for conserved regions flanking these signatures, fragments of most of these genes were amplified from 23 actinobacterial species, covering many different families and orders, for which no sequence information was previously available. All the 61 sequenced fragments, except two in GluRS, were found to contain the indicated signatures. The presence of these signatures in various species from 20 families within this phylum provides evidence that they are likely distinctive characteristics of the entire phylum, which were introduced in a common ancestor of this group. The absence of all four of these signatures inSymbiobacterium thermophilumsuggests that this species, which is distantly related to other actinobacteria in 16S rRNA and CTP synthetase trees, may not be a part of the phylumActinobacteria. The identified signatures provide novel molecular means for defining and circumscribing the phylumActinobacteria. Functional studies on them should prove helpful in understanding novel biochemical and physiological characteristics of this group of bacteria.
Halobacillus yeomjeoni sp. nov., isolated from a marine solar saltern in Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Lee Choong-Hwan , Oh Hyun Woo , Oh Tae-Kwang
Published: November 2005

A Gram-positive or Gram-variable, motile, endospore-forming, halophilic bacterial strain, MSS-402T, was isolated from a marine solar saltern in Korea, and subjected to a polyphasic taxonomic study. Some cells of strain MSS-402Twere long filamentous rods. The isolate grew optimally at 37 °C and in the presence of 3–5 % (w/v) NaCl. Strain MSS-402Thad cell-wall peptidoglycan based onl-orn–d-Asp, MK-7 as the predominant menaquinone and anteiso-C15 : 0, anteiso-C17 : 0and iso-C16 : 0as major fatty acids. The DNA G+C content was 42·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MSS-402Tfalls within the evolutionary radiation of species of the genusHalobacillus. Levels of 16S rRNA gene sequence similarity between strain MSS-402Tand the type strains of recognizedHalobacillusspecies ranged from 98·0 % (withHalobacillus halophilus) to 99·2 % (withHalobacillus litoralisandHalobacillus trueperi). Levels of DNA–DNA binding indicated that strain MSS-402Trepresents a genomic species that is distinct from recognizedHalobacillusspecies. Strain MSS-402Twas differentiated fromHalobacillusspecies by means of several phenotypic characteristics. On the basis of its phenotypic properties and phylogenetic and genetic distinctiveness, strain MSS-402T(=KCTC 3957T=DSM 17110T) should be classified as the type strain of a novelHalobacillusspecies, for which the nameHalobacillus yeomjeonisp. nov. is proposed.
Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater
Authors: Chen Shuangya , Dong Xiuzhu
Published: November 2005

Two proteolytic, strictly anaerobic bacterial strains (TB107Tand TB6-6) were isolated from the granule sludge of an upflow anaerobic sludge blanket reactor treating brewery wastewater. The strains were Gram-negative, non-spore-forming and motile. Cells were rod-shaped (0·6–0·9×1·9–2·2 μm). Growth of the strains was observed at 20–45 °C and pH 6·0–9·7. The strains were proteolytic. Yeast extract, peptone, pyruvate, glycine andl-arginine could be used as carbon and energy sources. Weak growth was also observed with tryptone,l-serine,l-threonine andl-alanine as carbon and energy sources. Both strains did not use any of the tested carbohydrates, alcohols and fatty acids except pyruvate. Acetic acid and NH3were produced from yeast extract, peptone andl-arginine, and propionic acid was also produced from yeast extract. Pyruvate was converted to acetic acid and CO2. Gelatin was not hydrolysed. Indole and H2S were not produced. The two strains did not grow in medium containing 20 % bile. Addition of strain TB107Tto a syntrophic propionate-degrading co-culture accelerated the propionate-degradation rate. The predominant cellular fatty acid was the branched-chain fatty acid anteiso-C15 : 0(46·21 %). The genomic DNA G+C contents of strains TB107Tand TB6-6 were 46·6 and 48·9 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represent a new phyletic sublineage within theCytophaga–Flavobacterium–Bacteroides(CFB) group, with <91 % 16S rRNA gene sequence similarity to the closest species with validly published names. On the basis of polyphasic evidence from this study, a new genus and species,Proteiniphilum acetatigenesgen. nov., sp. nov., is proposed, with strain TB107T(=JCM 12891T=AS 1.5024T) as the type strain.
Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol
Authors: Jiang B. , Parshina S. N. , van Doesburg W. , Lomans B. P. , Stams A. J. M.
Published: November 2005

A novel thermophilic, obligately methylotrophic, methanogenic archaeon, strain L2FAWT, was isolated from a thermophilic laboratory-scale upflow anaerobic sludge blanket reactor fed with methanol as the carbon and energy source. Cells of strain L2FAWT were non-motile, irregular cocci, 0·7–1·5 μm in diameter and usually occurred singly (sometimes forming clusters of two or four cells). The cells stained Gram-negative and lysed immediately in 0·1 % (w/v) SDS. Growth was inhibited by chloramphenicol and tetracycline, but not by penicillin, bacitracin, spectinomycin, vancomycin or kanamycin. Methanol and mono-, di- and trimethylamine were used as substrates, but H2/CO2, formate, acetate, propanol, dimethyl sulfide and methanethiol were not. The temperature range for growth was 42–58 °C, with an optimum at 50 °C. The fastest growth was observed at a salinity below 100 mM NaCl; no growth occurred above 300 mM NaCl. The optimal pH for growth was 6·5; growth was observed from pH 5 to pH 7·5. The G+C content of the genomic DNA was 37·6 mol%. Analysis of the 16S rRNA gene sequence and the partial methyl-CoM reductase gene sequence revealed that the organism was phylogenetically closely related to Methanomethylovorans hollandica DMS1T (98 % similarity for the 16S rRNA gene sequence and 91 % similarity for the methyl-CoM reductase gene sequence). The DNA–DNA relatedness between L2FAWT and Methanomethylovorans hollandica DMS1T was 46 %. On the basis of these results, strain L2FAWT (=DSM 17232T=ATCC BAA-1173T) represents the type strain of a novel species, for which the name Methanomethylovorans thermophila sp. nov. is proposed.
Gramella portivictoriae sp. nov., a novel member of the family Flavobacteriaceae isolated from marine sediment
Authors: Lau Stanley C. K. , Tsoi Mandy M. Y. , Li Xiancui , Plakhotnikova Ioulia , Dobretsov Sergey , Wong Po-Keung , Qian Pei-Yuan
Published: November 2005

A yellow-pigmented, Gram-negative, slowly gliding, rod-shaped, strictly aerobic bacterium (UST040801-001T) was isolated from marine sediment. The DNA G+C content was 39·9 mol%. The predominant fatty acids were a15 : 0, i15 : 0, i15 : 0 3-OH, i17 : 1ω9c, i17 : 0 3-OH and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c (altogether representing 76·2 % of the total). MK-6 was the only respiratory quinone. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Gramella echinicola KMM 6050T (the only species in the genus) was the closest relative of UST040801-001T, sharing 98·0 % sequence similarity. The DNA–DNA relatedness between UST040801-001T and Gramella echinicola KMM 6050T was 13 %. Strain UST040801-001T can be distinguished from G. echinicola by means of 11 phenotypic traits. The results of molecular and phenotypic analyses suggested that UST040801-001T represents a novel species of Gramella. The name Gramella portivictoriae sp. nov. is proposed for this bacterium, with UST040801-001T (=NRRL 41137T=JCM 13192T) as the type strain.
Bacteroides coprosuis sp. nov., isolated from swine-manure storage pits
Authors: Whitehead Terence R. , Cotta Michael A. , Collins Matthew D. , Falsen Enevold , Lawson Paul A.
Published: November 2005

Two Gram-negative, anaerobic, non-spore-forming, rod-shaped organisms were isolated from a swine-manure storage pit. Based on morphological and biochemical criteria, the strains were tentatively identified as belonging to the genus Bacteroides but they did not appear to correspond to any recognized species of the genus. Comparative 16S rRNA gene sequencing studies showed that the strains were related closely to each other and confirmed their placement in the genus Bacteroides, but sequence divergence values of >10 % from reference Bacteroides species demonstrated that the organisms from manure represent a novel species. Based on biochemical criteria and molecular genetic evidence, it is proposed that the unknown isolates from manure be assigned to a novel species of the genus Bacteroides, as Bacteroides coprosuis sp. nov. The type strain is PC139T (=CCUG 50528T=NRRL B-41113T).
Lactobacillus arizonensis is a later heterotypic synonym of Lactobacillus plantarum
Authors: Kostinek Melanie , Pukall Rüdiger , Rooney Alejandro P. , Schillinger Ulrich , Hertel Christian , Holzapfel Wilhelm H. , Franz Charles M. A. P.
Published: November 2005

The ‘Lactobacillus plantarum group’ encompasses the taxa Lactobacillus plantarum subsp. plantarum, Lactobacillus plantarum subsp. argentoratensis, Lactobacillus paraplantarum, Lactobacillus pentosus and Lactobacillus arizonensis. In this study, the phylogenetic position of L. arizonensis was examined using 16S rRNA gene-specific methodologies (16S rRNA sequencing and ribotyping) and genomic DNA-based investigations [repetitive extragenic palindromic DNA (rep)-PCR and DNA–DNA hybridization]. Our results show that the L. arizonensis type strain could not be distinguished from the type strain of L. plantarum or from various L. plantarum reference strains. Therefore, it is proposed that the species L. arizonensis should be reclassified as a heterotypic synonym of L. plantarum.
Interactions between the Cell Cycle and Embryonic Patterning inArabidopsisUncovered by a Mutation in DNA Polymerase ε
Authors: Jenik Pablo D. , Jurkuta Rebecca E.J. , Barton M. Kathryn
Published: November 2005

Pattern formation and morphogenesis require coordination of cell division rates and orientations with developmental signals that specify cell fate. A viable mutation in the TILTED1 locus, which encodes the catalytic subunit of DNA polymerase ε of Arabidopsis thaliana, causes a lengthening of the cell cycle by ∼35% throughout embryo development and alters cell type patterning of the hypophyseal lineage in the root, leading to a displacement of the root pole from its normal position on top of the suspensor. Treatment of preglobular and early globular stages, but not later stage, embryos with the DNA polymerase inhibitor aphidicolin leads to a similar phenotype. The results uncover an interaction between the cell cycle and the processes that determine cell fate during plant embryogenesis.
Eosinophil infiltration of the oesophageal mucosa in patients with pollen allergy during the season
Authors: Onbasi K. , Sin A. Z. , Doganavsargil B. , Onder G. F. , Bor S. , Sebik F.
Published: November 2005

Background
The oesophagus is normally devoid of eosinophils. There are some disorders accompanying with eosinophil infiltration. Food allergy has been reported as a common reason, especially in children but some other studies have also indicated that aeroallergens might have a role in oesophageal eosinophil accumulation.

Objective
In this study we investigated whether there is any eosinophil recruitment in the oesophagus of pollen‐allergic patients who had respiratory symptoms during the season.

Methods
Thirty‐eight symptomatic patients (allergic rhinitis (AR) with or without asthma) who had sensitization to grass pollen were included in the study during the pollen season. Controls were composed of 25 healthy non‐atopics and 24 patients diagnosed as having gastro‐oesophageal reflux disease. Reflux was excluded in allergic and non‐atopic groups, whereas the presence of allergy was eliminated in control groups. Gastrointestinal endoscopy was performed in all participants, and biopsy specimens were taken from both the proximal and the distal oesophagus to evaluate eosinophil accumulation. At the same time, blood eosinophil numbers were counted.

Results
Oesophageal eosinophil accumulation was found in 10 allergic patients (26%) and in five patients (21%) with gastro‐oesophageal reflux disease but none of the healthy controls had eosinophils (0%) (P<0.05). Blood eosinophils were higher in these 10 patients than the rest of the 28 patients without infiltration. In this group, blood eosinophils were also correlated with the number of accumulated eosinophils in the oesophagus (P<0.001). There was more intense eosinophil infiltration at the distal part of the oesophagus in the reflux group when compared with the allergic group (mean 7.6±5.6 vs. 3.2±3.7). Nevertheless, eosinophils were found to be concentrated (mean 5.5±7.3) in the proximal oesophagus of allergic patients, although it was 1.7±1.5 in reflux patients (P>0.05).

Conclusion
Our results showed that eosinophil infiltration might be observed in oesophageal tissue of patients with respiratory tract allergy during the symptomatic period. This finding may possibly reflect the systemic and common mucosal aspects of allergic inflammation.