bluuebunny/crossref_metadata_2025 huggingface dataset:
PP2A Regulates HDAC4 Nuclear Import
Authors: Paroni Gabriela , Cernotta Nadia , Dello Russo Claudio , Gallinari Paola , Pallaoro Michele , Foti Carmela , Talamo Fabio , Orsatti Laura , Steinkühler Christian , Brancolini Claudio
Published: November 2007

Different signal-regulated serine/threonine kinases phosphorylate class II histone deacetylases (HDACs) to promote nuclear export, cytosolic accumulation, and activation of gene transcription. However, little is known about mechanisms operating in the opposite direction, which, possibly through phosphatases, should promote class II HDACs nuclear entry and subsequent gene repression. Here we show that HDAC4 forms a complex with the PP2A holoenzyme Cα, Aα, B/PR55α. In vitro and in vivo binding studies demonstrate that the N-terminus of HDAC4 interacts with the catalytic subunit of PP2A. HDAC4 is dephosphorylated by PP2A and experiments using okadaic acid or RNA interference have revealed that PP2A controls HDAC4 nuclear import. Moreover, we identified serine 298 as a putative phosphorylation site important for HDAC4 nuclear import. The HDAC4 mutant mimicking phosphorylation of serine 298 is defective in nuclear import. Mutation of serine 298 to alanine partially rescues the defect in HDAC4 nuclear import observed in cells with down-regulated PP2A. These observations suggest that PP2A, via the dephosphorylation of multiple serines including the 14-3-3 binding sites and serine 298, controls HDAC4 nuclear import.
Myosin Transducer Mutations Differentially Affect Motor Function, Myofibril Structure, and the Performance of Skeletal and Cardiac Muscles
Authors: Cammarato Anthony , Dambacher Corey M. , Knowles Aileen F. , Kronert William A. , Bodmer Rolf , Ocorr Karen , Bernstein Sanford I.
Published: November 2007

Striated muscle myosin is a multidomain ATP-dependent molecular motor. Alterations to various domains affect the chemomechanical properties of the motor, and they are associated with skeletal and cardiac myopathies. The myosin transducer domain is located near the nucleotide-binding site. Here, we helped define the role of the transducer by using an integrative approach to study how Drosophila melanogaster transducer mutations D45 and Mhc5affect myosin function and skeletal and cardiac muscle structure and performance. We found D45 (A261T) myosin has depressed ATPase activity and in vitro actin motility, whereas Mhc5(G200D) myosin has these properties enhanced. Depressed D45 myosin activity protects against age-associated dysfunction in metabolically demanding skeletal muscles. In contrast, enhanced Mhc5myosin function allows normal skeletal myofibril assembly, but it induces degradation of the myofibrillar apparatus, probably as a result of contractile disinhibition. Analysis of beating hearts demonstrates depressed motor function evokes a dilatory response, similar to that seen with vertebrate dilated cardiomyopathy myosin mutations, and it disrupts contractile rhythmicity. Enhanced myosin performance generates a phenotype apparently analogous to that of human restrictive cardiomyopathy, possibly indicating myosin-based origins for the disease. The D45 and Mhc5mutations illustrate the transducer's role in influencing the chemomechanical properties of myosin and produce unique pathologies in distinct muscles. Our data suggest Drosophila is a valuable system for identifying and modeling mutations analogous to those associated with specific human muscle disorders.
Modeling the adaptive immune system: predictions and simulations
Authors: Lundegaard Claus , Lund Ole , Keşmir Can , Brunak Søren , Nielsen Morten
Published: November 2007

Motivation: Immunological bioinformatics methods are applicable to a broad range of scientific areas. The specifics of how and where they might be implemented have recently been reviewed in the literature. However, the background and concerns for selecting between the different available methods have so far not been adequately covered.

Summary: Before using predictions systems, it is necessary to not only understand how the methods are constructed but also their strength and limitations. The prediction systems in humoral epitope discovery are still in their infancy, but have reached a reasonable level of predictive strength. In cellular immunology, MHC class I binding predictions are now very strong and cover most of the known HLA specificities. These systems work well for epitope discovery, and predictions of the MHC class I pathway have been further improved by integration with state-of-the-art prediction tools for proteasomal cleavage and TAP binding. By comparison, class II MHC binding predictions have not developed to a comparable accuracy level, but new tools have emerged that deliver significantly improved predictions not only in terms of accuracy, but also in MHC specificity coverage. Simulation systems and mathematical modeling are also now beginning to reach a level where these methods will be able to answer more complex immunological questions.

Contact:  lunde@cbs.dtu.dk

Supplementary information: Supplementary data are available at Bioinformatics online.
‘Per mia particolare devotione’: Orlando di Lasso'sLagrime di San Pietroand Catholic Spirituality in Counter-Reformation Munich
Authors: Fisher Alexander J.
Published: November 2007

In his magisterialLagrime di San Pietro(1595) Orlando di Lasso composed a cycle of 20 madrigals on texts by Luigi Tansillo on the theme of St Peter's denial of Christ and his subsequent remorse, capped by a Latin motet (‘Vide homo‘) representing the rebuke of the crucified Christ. TheLagrimemay be seen as a penitential gesture on Lasso's part, but a textual and musical analysis also suggests numerous parallels with contemporary Catholic spiritual exercises, particularly those of Ignatius of Loyola and Luis of Granada. The cycle thus takes its place in a broader Counter-Reformation discourse of meditation and penance.
‘So to the wood went I’: Politicizing the Greenwood in Two Songs by John Dowland
Authors: Gibson Kirsten
Published: November 2007

Figurations of woods as sites of solitude, political exile and authenticity are drawn upon in a number of John Dowland's songs. ‘Can she excuse’ quotes from the ballad tuneWoods so wild, while ‘O sweet woods’ makes reference to Wanstead woods, associated with both Philip Sidney and Robert Devereux during their lifetimes. This article examines how courtly experiences of political withdrawal and exile are articulated through musical and literary references to woods in these songs.
Cohnella laeviribosi sp. nov., isolated from a volcanic pond
Authors: Cho Eun-Ah , Lee Jung-Sook , Lee Keun Chul , Jung Heung-Chae , Pan Jae-Gu , Pyun Yu-Ryang
Published: November 2007

A novel thermophilic and endospore-forming Gram-positive bacterium capable of assimilating and isomerizingl-ribose was isolated from a volcanic area in Likupang, Indonesia. The isolate, RI-39T, was able to grow at high temperatures (37–60 °C); optimum growth was observed at pH 6.5 and 45 °C. The strain contained MK-7 (87 %) as the main respiratory quinone and had a DNA G+C content of 51 mol%. The major cellular fatty acids of the isolate were iso-C16 : 0and anteiso-C15 : 0and the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents an evolutionary lineage that is distinct from those of otherCohnellaspecies. Based on morphological, physiological and chemotaxonomic characteristics and 16S rRNA gene sequence comparisons, it is proposed that strain RI-39Trepresents a novel species,Cohnella laeviribosisp. nov. The type strain is RI-39T(=KCTC 3987T=KCCM 10653PT=CCUG 52217T).
Lapillicoccus jejuensis gen. nov., sp. nov., a novel actinobacterium of the family Intrasporangiaceae, isolated from stone
Authors: Lee Soon Dong , Lee Dong Wan
Published: November 2007

A novel, yellow-pigmented actinobacterium was isolated from a small stone collected in Jeju, Republic of Korea. The cells of the organism, designated strain R-Ac013T, were Gram-positive, aerobic, non-motile cocci that occurred singly or in pairs. The strain showed growth at 10–37 °C and pH 4.1–11.1, and tolerated 2 % NaCl. On the basis of the 16S rRNA gene sequence, the organism was phylogenetically related to members of the generaTetrasphaera(94.6–97.1 % sequence similarity),Terrabacter(96.5 %),Knoellia(96.4 %),Terracoccus(96.4 %),Oryzihumus(96.4 %),Janibacter(96.1–96.4 %) andIntrasporangium(96.2 %). The chemotaxonomic results for the organism were as follows:ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan, acetyl-type murein, MK-8(H4) as the major menaquinone, a DNA G+C content of 74.1 mol%, and a polar lipid profile that comprised diphosphatidylglycerol and phosphatidylinositol. The fatty acid profile consisted of iso- and anteiso-methyl-branched, straight-chain saturated and monounsaturated types, the major components being iso-C16 : 0, C17 : 1ω8cand iso-C15 : 0. The combination of the phenotypic and phylogenetic data revealed that this strain represents a novel genus and species of the familyIntrasporangiaceae, for which the nameLapillicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain is strain R-Ac013T(=KCTC 19200T=DSM 18607T).
Methylohalomonas lacus gen. nov., sp. nov. and Methylonatrum kenyense gen. nov., sp. nov., methylotrophic gammaproteobacteria from hypersaline lakes
Authors: Sorokin Dimitry Yu. , Trotsenko Yuri A. , Doronina Nina V. , Tourova Tatjana P. , Galinski Erwin A. , Kolganova Tatjana V. , Muyzer Gerard
Published: November 2007

Aerobic enrichment at 4 M NaCl, pH 7.5, with methanol as carbon and energy source from sediments of hypersaline chloride–sulfate lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of a moderately halophilic and obligately methylotrophic bacterium, strain HMT 1T. The bacterium grew with methanol and methylamine within a pH range of 6.8–8.2 with an optimum at pH 7.5 and at NaCl concentrations of 0.5–4 M with an optimum at 2 M. In addition to methanol and methylamine, it can oxidize ethanol, formate, formaldehyde and dimethylamine. Carbon is assimilated via the serine pathway. The main compatible solute is glycine betaine. 16S rRNA gene sequence analysis placed the isolate as a new lineage in the familyEctothiorhodospiraceae(Gammaproteobacteria). It is proposed, therefore, to accommodate this bacterium within a novel genus and species,Methylohalomonas lacusgen. nov., sp. nov., with HMT 1T(=DSM 15733T=NCCB 100208T=UNIQEM U237T) as the type strain. Two strains were obtained in pure culture from sediments of soda lake Magadi in Kenya and the Kulunda Steppe (Russia) on a mineral medium at pH 10 containing 0.6 M total Na+using methanol as a substrate. Strain AMT 1Twas enriched with methanol, while strain AMT 3 originated from an enrichment culture with CO. The isolates are restricted facultative methylotrophs, capable of growth with methanol, formate and acetate as carbon and energy sources. With methanol, the strains grew within a broad salinity range from 0.3 to 3.5–4 M total Na+, with an optimum at 0.5–1 M. The pH range for growth was between 8.3 and 10.5, with an optimum at pH 9.5, which characterized the soda lake isolates as obligate haloalkaliphiles. Carbon is assimilated autotrophically via the Calvin–Benson cycle. Sequence analysis of the gene coding for the key enzyme RuBisCO demonstrated that strain AMT 1Tpossessed a singlecbbLgene of the ‘green’ form I, clustering with members of the familyEctothiorhodospiraceae. Analysis of the 16S rRNA gene sequence showed that strains AMT 1Tand AMT 3 belong to a single species that forms a separate lineage within the familyEctothiorhodospiraceae. On the basis of phenotypic and genetic data, the novel haloalkaliphilic methylotrophs are described as representing a novel genus and species,Methylonatrum kenyensegen. nov., sp. nov. (type strain AMT 1T=DSM 15732T=NCCB 100209T=UNIQEM U238T).
Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas
Authors: Young J. M. , Park D.-C.
Published: November 2007

The relationships of the genus Azotobacter, Azomonas macrocytogenes and the genus Pseudomonas were revealed by comparative analysis of partial 16S rRNA and atpD, carA and recA gene sequences and as concatenated nucleotide and peptide sequences. Sequence similarities of Azotobacter species and Azomonas macrocytogenes indicated that these may be considered to be synonyms at the molecular level. In addition, these species show an intimate relationship with species of Pseudomonas, especially P. aeruginosa (the type species of the genus). In terms of the current circumscription of the genus Pseudomonas, Azotobacter and Azomonas macrocytogenes should be considered for amalgamation with Pseudomonas. Azotobacter and Azomonas comprise nitrogen-fixing strains with large pleomorphic cells that form cysts, and peritrichous flagella insertion; characteristics not included in the current circumscription of Pseudomonas. The data are discussed in the light of whether lateral transfer of genes could be involved in the determination of significant morphological characteristics, thus leading to a problem that may be encountered more frequently: how to resolve classification of taxa based on conserved sequences with those based on their phenotype. More fundamentally, the results illuminate problems that will increasingly be encountered: by what criteria can taxa be delineated, what are the most appropriate methods for classification, and what are the proper assumptions of bacterial classification?
Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.
Authors: Labeda D. P. , Kroppenstedt R. M.
Published: November 2007

In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2T was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H4) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2T (=NRRL B-24463T =DSM 44720T =FERM P-16053T =JCM 10302T =NBRC 16184T).
Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium
Authors: Xu Jing-Liang , He Jian , Wang Zhi-Chun , Wang Kun , Li Wen-Jun , Tang Shu-Kun , Li Shun-Peng
Published: November 2007

A Gram-positive, aerobic, non-motile, mesophilic strain, djl-6T, able to degrade carbendazim, was isolated from a carbendazim-contaminated soil sample from Jiangsu province, China. The taxonomic position of this isolate was analysed by using a polyphasic approach. Chemotaxonomic analysis including peptidoglycan type, diagnostic sugar composition, fatty acid profile, menaquinones, polar lipids and mycolic acids showed that the characteristics of strain djl-6Twere in good agreement with those of the genusRhodococcus. DNA–DNA hybridization showed that it had low genomic relatedness withRhodococcus baikonurensisDSM 44587T(31.8 %),Rhodococcus erythropolisDSM 43066T(23.8 %) andRhodococcus globerulusDSM 43954T(17.7 %), the three type strains to which strain djl-6Twas most closely related based on 16S rRNA gene sequence analysis (99.78, 99.25 and 98.91 % similarity, respectively). Based on the phenotypic properties and DNA–DNA hybridization data, strain djl-6T(=CGMCC 1.6580T=KCTC 19205T) is proposed as the type strain of a novelRhodococcusspecies,Rhodococcus qingshengiisp. nov.
Veillonella denticariosi sp. nov., isolated from human carious dentine
Authors: Byun Roy , Carlier Jean-Philippe , Jacques Nicholas A. , Marchandin Helene , Hunter Neil
Published: November 2007

Selective culture of human carious dentine for Veillonella strains resulted in the isolation of two strains of a Gram-negative, coccus-shaped bacterium that has not been described previously. Comparative 16S rRNA and dnaK gene sequence analysis indicated that the two strains were homogeneous and comprised a distinct lineage within the genus Veillonella, phylogenetically most closely related to Veillonella rodentium. This was supported by DNA–DNA hybridization, which showed clearly that the two strains were similar and distinct from other Veillonella species, and the production of major cellular fatty acids (C13 : 0 and C17 : 1
ω8), which is consistent with other members of the genus Veillonella. Based on these observations, strains RBV81 and RBV106T represent a novel species, for which the name Veillonella denticariosi sp. nov. is proposed, with the type strain RBV106T (=CIP 109448T =CCUG 54362T =DSM 19009T).
Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbreds
Authors: Morita Hidetoshi , Shiratori Chiharu , Murakami Masaru , Takami Hideto , Kato Yukio , Endo Akihito , Nakajima Fumihiko , Takagi Misako , Akita Hiroaki , Okada Sanae , Masaoka Toshio
Published: November 2007

Two strains, KBL13T and GBL13, were isolated as one of intestinal lactobacilli from the faecal specimens from different thoroughbreds of the same farm where they were born in Hokkaido, Japan. They were Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming and non-motile rods. KBL13T and GBL13 homofermentatively metabolize glucose, and produce lactate as the sole final product from glucose. The 16S rRNA gene sequence, DNA–DNA hybridization, DNA G+C content and biochemical characterization indicated that these two strains, KBL13T and GBL13, belong to the same species. In the representative strain, KBL13T, the DNA G+C content was 34.3 mol%. Lactobacillus salivarius JCM 1231T (=ATCC 11741T; AF089108) is the type strain most closely related to the strain KBL13T as shown in the phylogenetic tree, and the 16S rRNA gene sequence identity showed 96.0 % (1425/1484 bp). Comparative 16S rRNA gene sequence analysis of this strain indicated that the two isolated strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives, L. salivarius, Lactobacillus aviarius, Lactobacillus saerimneri and Lactobacillus acidipiscis. DNA–DNA reassociation experiments with L. salivarius and L. aviarius confirmed that KBL13T represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13T (=JCM 14209T=DSM 18933T).
Tetrasphaera remsis sp. nov., isolated from the Regenerative Enclosed Life Support Module Simulator (REMS) air system
Authors: Osman Shariff , Moissl Christine , Hosoya Naofumi , Briegel Ariane , Mayilraj Shanmugam , Satomi Masataka , Venkateswaran Kasthuri
Published: November 2007

Two Gram-positive, coccoid, non-spore-forming bacteria (strains 3-M5-R-4Tand 3-M5-R-7), cells of which formed diploid, tetrad and cluster arrangements, were isolated from air of the Regenerative Enclosed Life Support Module Simulator system. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the familyIntrasporangiaceaeand were related to members of the genusTetrasphaera, with similarities to the seven known species of the genusTetrasphaeraof 96.71–97.76 %. The fatty acid profile supported affiliation of these novel isolates to the genusTetrasphaera, although larger amounts of octadecanoic acid (C18 : 0) andcis-9-octadecenoic acid (C18 : 1) were observed in the isolates, thus enabling them to be differentiated from otherTetrasphaeraspecies. In addition, DNA–DNA hybridization studies indicated that these strains belonged to a novel species that could be readily distinguished from its nearest neighbour,Tetrasphaera japonicaDSM 13192T, which had less than 20 % DNA–DNA relatedness. Physiological and biochemical tests showed few phenotypic differences, but genotypic analysis enabled these gelatin-liquefying strains to be differentiated from the sevenTetrasphaeraspecies. The strains described in this study therefore represent a novel species, for which the nameTetrasphaera remsissp. nov. is proposed; the type strain is 3-M5-R-4T(=ATCC BAA-1496T=CIP 109413T).
Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6
Authors: Borchert Martin S. , Nielsen Preben , Graeber Ingeborg , Kaesler Ines , Szewzyk Ulrich , Pape Thomas , Antranikian Garabed , Schäfer Thomas
Published: November 2007

The Gram-positive, alkali- and salt-tolerant marine bacterium strain P203Tis described together with its closest phylogenetic neighbour, terrestrial isolate LMG 21005T. Strain P203Twas isolated from material from the spongePlakortis simplexthat was obtained from the Sula-Ridge, Norwegian Sea. Strain LMG 21005Twas an undescribed strain that was isolated from a church wall mural in Germany. Strains P203Tand LMG 21005Twere identified as novel alkalitolerant members of theBacillusrRNA group 6 with a 16S rRNA gene sequence similarity of 99.5 %. The closest described neighbour,Bacillus gibsoniiDSM 8722T, showed 99.0 % gene sequence similarity with P203Tand 98.8 % similarity with strain LMG 21005T. Despite the high 16S rRNA gene sequence similarity, DNA–DNA cross-hybridization revealed only 25.8–34.1 % similarity amongst the three strains. The DNA G+C contents were 41.1 mol% for strain P203Tand 39.6 mol% for strain LMG 21005T. Both strains grew well between pH 7 and pH 11. Strain P203Tshowed growth at moderate temperatures (from 4 to 30 °C) and in the presence of up to 12 % (w/v) NaCl at pH 9.7, whereas strain LMG 21005Twas not salt tolerant (up to 4 % NaCl) and no growth was observed at 4 °C. The major fatty acids of strains P203T, LMG 21005Tand the type strain ofB. gibsoniiwere the saturated terminally methyl-branched compounds iso-C15 : 0(19.8, 15.6 and 28.0 %, respectively) and anteiso-C15 : 0(57.1, 48.6 and 45.2 %, respectively). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains P203Tand LMG 21005Tfrom the six relatedBacillusspecies with validly published names and supported the proposal of two novel species,Bacillus plakortidis[type strain P203T(=DSM 19153T=NCIMB 14288T)] andBacillus murimartini[type strain LMG 21005T(=NCIMB 14102T)].
Phylogenetic analysis of Xanthomonas species by comparison of partial gyrase B gene sequences
Authors: Parkinson Neil , Aritua Valentine , Heeney John , Cowie Claire , Bew Janice , Stead David
Published: November 2007

The genus Xanthomonas currently comprises 27 species with validly published names that are important crop and horticultural pathogens. We have constructed a phylogram from alignment of gyrase B (gyrB) sequences for all xanthomonad species, both to indicate inter-species relatedness and as an aid for rapid and accurate species-level identification. The phylogeny indicated a monophyletic group, with X. albilineans and X. sacchari as the most ancestral species. Three species, X. hyacinthi, X. translucens and X. theicola, formed an early-branching group. Three clades were supported by high bootstrap values: group 1 comprised X. cucurbitae, X. cassavae and X. codiaei; group 2 comprised X. arboricola, X. campestris, X. populi, X. hortorum, X. gardneri and X. cynarae; group 3 contained the remaining species, within which two further clades, supported by a 100% bootstrap value, were identified. Group 3A comprised X. axonopodis, X. euvesicatoria, X. perforans and X. melonis, together with X. alfalfae, X. citri and X. fuscans, whose names were recently validly published. Group 3B contained the monocot pathogens X. vasicola and X. oryzae. Two recently identified species, X. cynarae and X. gardneri, were poorly discriminated and were related closely to X. hortorum. Three species, X. perforans, X. euvesicatoria and X.
alfalfae, had identical gyrB sequences. Partial sequencing of a further five genes from these species found only minor sequence differences that confirmed their close relatedness. Although branch lengths between species varied, indicating different degrees of genetic distinctiveness, the majority (n=21) were well-differentiated, indicating the utility of the method as an identification tool, and we now use this method for routine diagnosis of xanthomonad species.
Candida flosculorum sp. nov. and Candida floris sp. nov., two yeast species associated with tropical flowers
Authors: Rosa Carlos A. , Pagnocca Fernando C. , Lachance Marc-André , Ruivo Carla C. C. , Medeiros Adriana O. , Pimentel Mariana R. C. , Fontenelle Julio C. R. , Martins Rogério P.
Published: November 2007

Two ascomycetous yeast species, Candida flosculorum sp. nov. and Candida floris sp. nov., were isolated from tropical flowers and their associated insects. C. flosculorum was isolated from flower bracts of Heliconia velloziana and Heliconia episcopalis (Heliconiaceae) collected from two Atlantic rain forest sites in Brazil. C. floris was isolated from flowers of Ipomoea sp. (Convolvulaceae) growing on the banks of the river Paraguai in the pantanal ecosystem in Brazil and from an adult of the stingless bee Trigona sp. and a flower of Merremia quinquefolia (Convolvulaceae) in Costa Rica. C. flosculorum belongs to the Metschnikowiaceae clade and C. floris belongs to the Starmerella clade. The type strain of C. flosculorum is UFMG-JL13T (=CBS 10566T=NRRL Y-48258T) and the type strain of C. floris is UWO(PS) 00-226.2T (=CBS 10593T=NRRL Y-48255T).
Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts
Authors: Weon Hang-Yeon , Lee Seon-Young , Kim Byung-Yong , Noh Hyung-Jun , Schumann Peter , Kim Jong-Shik , Kwon Soon-Wo
Published: November 2007

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145Tand HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145Tand HC148Tand comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genusUreibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existingUreibacillusspecies were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains ofUreibacillusspecies ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type wasl-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145Tand HC148Twere 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145Tand HC148Trepresent members of the genusUreibacillus, for which the namesUreibacillus compostisp. nov. andUreibacillus thermophilussp. nov., respectively, are proposed. The type strain ofU. compostiis HC145T(=KACC 11361T=DSM 17951T) and the type strain ofU. thermophilusis HC148T(=KACC 11362T=DSM 17952T).
Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov.
Authors: Albert Richard A. , Archambault Julieta , Lempa Melissa , Hurst Beth , Richardson Christine , Gruenloh Stephanie , Duran Metin , Worliczek Hanna Lucia , Huber Birgit E. , Rosselló-Mora Ramon , Schumann Peter , Busse Hans-Jürgen
Published: November 2007

A polyphasic study was undertaken to clarify the taxonomic position of endospore-forming strains 433-D9, 433-E17 and 121-X1. BOX-PCR-generated fingerprints indicated that they may be members of a single species. 16S rRNA gene sequence similarity demonstrated that a representative of this group, 433-D9, is affiliated closely with Bacillus arvi DSM 16317T (100 %), Bacillus arenosi DSM 16319T (99.8 %) and Bacillus neidei NRRL BD-87T (97.1 %). Sequence similarities revealed Bacillus pycnus NRRL NRS-1691T and several Kurthia species as the next nearest relatives. DNA–DNA hybridization results showed that strain 433-D9 is a member of B. arvi. Detection of l-Lys–d-Asp-based peptidoglycan in strain 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T was in agreement with their close relationship, but differentiated these strains from B. neidei NRRL BD-87T and B. pycnus NRRL NRS-1691T, for which l-Lys–d-Glu was reported. A similar quinone system was detected in strains 433-D9, 433-E17, 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T. This system, unusual for bacilli, consisted of the major compound menaquinone MK-8 (69–80 %) and moderate amounts of MK-7 (19–30 %). This observation was in contrast to the predominance of MK-7 of the closest relative B. pycnus NRRL NRS-1691T, as also reported for representatives of the closely related non-endospore-forming genus Kurthia. Strains 433-D9, B. arvi DSM 16317T and B. arenosi DSM 16319T exhibited homogeneous and discriminative polar lipid profiles and fatty acid profiles consisting of major acids i-C15 : 0 and ai-C15 : 0 and moderate amounts of i-C17 : 1
ω10c and i-C17 : 1 I/ai-C17 : 1 B that discriminated them from closely related strains such as B. neidei NRRL BD-87T. On the basis of clear-cut discriminative chemotaxonomic markers, we propose strains 433-D9, 433-E17 and 121-X1, B. arvi DSM 16317T, B. arenosi DSM 16319T and B. neidei NRRL BD-87T to be reclassified within a separate genus. For this new taxon, we propose the name Viridibacillus gen. nov., and we propose the reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov. (the type species of Viridibacillus, with the type strain DSM 16317T =LMG 22165T), Viridibacillus arenosi comb. nov. (type strain DSM 16319T =LMG 22166T) and Viridibacillus neidei comb. nov. (type strain NRRL BD-87T =DSM 15031T =JCM 11077T).
Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species
Authors: De Bruyne Katrien , Schillinger Ulrich , Caroline Lily , Boehringer Benjamin , Cleenwerck Ilse , Vancanneyt Marc , De Vuyst Luc , Franz Charles M. A. P. , Vandamme Peter
Published: November 2007

A Gram-positive, ovoid lactic acid bacterium, strain LMG 23990T, was isolated from Ethiopian coffee fermentation. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc citreum and Leuconostoc lactis as the closest neighbours (99.6 and 99.0 % 16S rRNA gene sequence similarity, respectively). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism, whole-cell protein electrophoresis, DNA–DNA hybridizations, comparative sequence analysis of pheS, rpoA, atpA, and physiological and biochemical tests allowed us to differentiate strain LMG 23990T from all established Leuconostoc species. Strain LMG 23990T (=CCUG 54536T) therefore represents a novel species, for which the name Leuconostoc holzapfelii sp. nov. is proposed.
On the restriction of representations of GL2(F) to a Borel subgroup
Authors: Paskunas Vytautas
Published: November 2007

Let F be a non-Archimedean local field and let p be the residual characteristic of F. Let G=GL2(F) and let P be a Borel subgroup of G. In this paper we study the restriction of irreducible smooth representations of G on $\overline {\mathbf {F}}_{p}$-vector spaces to P. We show that in a certain sense P controls the representation theory of G. We then extend our results to smooth $\mathcal {O}[G]$-modules of finite length and unitary K-Banach space representations of G, where $\mathcal {O}$ is the ring of integers of a complete discretely valued field K with residue field $\overline {\mathbf {F}}_{p}$.
Maximal symplectic packings in
Authors: Opshtein Emmanuel
Published: November 2007

In this paper we describe the intersections between the balls of maximal symplectic packings of $\mathbb {P}^2$. This analysis shows the existence of singular points for maximal packings of $\mathbb {P}^2$ by more than three equal balls. It also yields a construction of a class of very regular examples of maximal packings by five balls.
Integrality of quantum 3-manifold invariants and a rational surgery formula
Authors: Beliakova Anna , Lê Thang T. Q.
Published: November 2007

We prove that the Witten–Reshetikhin–Turaev (WRT) SO(3) invariant of an arbitrary 3-manifold M is always an algebraic integer. Moreover, we give a rational surgery formula for the unified invariant dominating WRT SO(3) invariants of rational homology 3-spheres at roots of unity of order co-prime with the torsion. As an application, we compute the unified invariant for Seifert fibered spaces and for Dehn surgeries on twist knots. We show that this invariant separates Seifert fibered integral homology spaces and can be used to detect the unknot.
Using Q-Learning and Genetic Algorithms to Improve the Efficiency of Weight Adjustments for Optimal Control and Design Problems
Authors: Kamali Kaivan , Jiang L. J. , Yen John , Wang K. W.
Published: November 2007

In traditional optimal control and design problems, the control gains and design parameters are usually derived to minimize a cost function reflecting the system performance and control effort. One major challenge of such approaches is the selection of weighting matrices in the cost function, which are usually determined via trial-and-error and human intuition. While various techniques have been proposed to automate the weight selection process, they either can not address complex design problems or suffer from slow convergence rate and high computational costs. We propose a layered approach based on Q-learning, a reinforcement learning technique, on top of genetic algorithms (GA) to determine the best weightings for optimal control and design problems. The layered approach allows for reuse of knowledge. Knowledge obtained via Q-learning in a design problem can be used to speed up the convergence rate of a similar design problem. Moreover, the layered approach allows for solving optimizations that cannot be solved by GA alone. To test the proposed method, we perform numerical experiments on a sample active-passive hybrid vibration control problem, namely adaptive structures with active-passive hybrid piezoelectric networks. These numerical experiments show that the proposed Q-learning scheme is a promising approach for automation of weight selection for complex design problems.
Constraint Wrench Formulation for Closed-Loop Systems Using Two-Level Recursions
Authors: Chaudhary Himanshu , Saha Subir Kumar
Published: November 2007

In order to compute the constraint moments and forces, together referred here as wrenches, in closed-loop mechanical systems, it is necessary to formulate a dynamics problem in a suitable manner so that the wrenches can be computed efficiently. A new constraint wrench formulation for closed-loop systems is presented in this paper using two-level recursions, namely, subsystem level and body level. A subsystem is referred here as the serial- or tree-type branches of a spanning tree obtained by cutting the appropriate joints of the closed loops of the system at hand. For each subsystem, unconstrained Newton–Euler equations of motion are systematically reduced to a minimal set in terms of the Lagrange multipliers representing the constraint wrenches at the cut joints and the driving torques/forces provided by the actuators. The set of unknown Lagrange multipliers and the driving torques/forces associated to all subsystems are solved in a recursive fashion using the concepts of a determinate subsystem. Next, the constraint forces and moments at the uncut joints of each subsystem are calculated recursively from one body to another. Effectiveness of the proposed algorithm is illustrated using a multiloop planar carpet scraping machine and the spatial RSSR (where R and S stand for revolute and spherical, respectively) mechanism.
Design of Dissipative and Stable Assist Robots
Authors: Agrawal Sunil K. , Ryu Ji-Chul
Published: November 2007

This paper presents a methodology for design of dissipative assist robots with proven stability during set-point control. A dissipative assist robot is defined as one where the actuators continuously dissipate energy from the robot until the robot reaches the desired set point. We have discussed in this paper that, under well known control laws, it is hard to characterize dissipativity of a general assist robot. However, by appropriately designing the robot through inertia redistribution, the dynamic equations can be modified so that the control laws can now be proven to be both dissipative and stable under set-point control. The proposed method is demonstrated through simulation of a three-link planar manipulator used as an assist robot to modify human functional movements in a vertical plane.
Degeneracy Study of the Forward Kinematics of Planar 3-RP̱R Parallel Manipulators
Authors: Wenger P. , Chablat D. , Zein M.
Published: November 2007

This paper investigates two situations in which the forward kinematics of planar 3-RP̱R parallel manipulators degenerates. These situations have not been addressed before. The first degeneracy arises when the three input joint variables ρ1, ρ2, and ρ3 satisfy a certain relationship. This degeneracy yields a double root of the characteristic polynomial in t=tan(φ∕2), which could be erroneously interpreted as two coalesce assembly modes. However, unlike what arises in nondegenerate cases, this double root yields two sets of solutions for the position coordinates (x,y) of the platform. In the second situation, we show that the forward kinematics degenerates over the whole joint space if the base and platform triangles are congruent and the platform triangle is rotated by 180deg about one of its sides. For these “degenerate” manipulators, which are defined here for the first time, the forward kinematics is reduced to the solution of a third-degree polynomial and a quadratic in sequence. Such manipulators constitute, in turn, a new family of analytic planar manipulators that would be more suitable for industrial applications.
A Parallelogram-Based Parallel Manipulator for Schönflies Motion
Authors: Salgado Oscar , Altuzarra Oscar , Amezua Enrique , Hernández Alfonso
Published: November 2007

A parallelogram-based 4 degrees-of-freedom parallel manipulator is presented in this paper. The manipulator can generate the so-called Schönflies motion that allows the end effector to translate in all directions and rotate around an axis parallel to a fixed direction. The theory of group of displacements is applied in the synthesis of this manipulator, which employs parallelograms in every limb. The planar parallelogram kinematic chain provides a high rotational capability and an improved stiffness to the manipulator. This paper shows the kinematic analysis of the manipulator, including the closed-form resolution of the forward and inverse position problems, the velocity, and the singularity analysis. Finally, a prototype of the manipulator, adding some considerations about its singularity-free design, and some technical applications in which the manipulator can be used are presented.
Applying Multiobjective Cost and Weight Optimization to the Initial Design of Turbine Disks
Authors: Rao A. R. , Scanlan J. P. , Keane A. J.
Published: November 2007

Aerospace design optimization typically explores the effects of structural performance and aerodynamics on the geometry of a component. This paper presents a methodology to incorporate manufacturing cost and fatigue life models within an integrated system to simultaneously trade off the conflicting objectives of minimum weight and manufacturing cost while satisfying constraints placed by structural performance and fatigue. A case study involving the design of a high pressure turbine disk from an aircraft engine is presented. Manufacturing cost and fatigue life models are developed in DECISIONPRO™, a generic modeling tool, whereas finite element analysis is carried out in the Rolls-Royce PLC proprietary solver SC03. A multiobjective optimization approach based on the nondominated sorting genetic algorithm (NSGA) is used to evaluate the Pareto front for minimum cost and volume designs. A sequential workflow of the different models embedded within a scripting environment developed in MATLAB™ is used for automating the entire process.
Computer-Aided Modeling and Manufacturing of Spherical Mechanisms via a Novel Web Tool
Authors: Schuler J. , Ketchel J. , Larochelle P.
Published: November 2007

In this paper, we present a novel web-based computer-aided modeling and manufacturing software tool for spherical mechanisms. Our purpose is to facilitate the analysis, dynamic simulation, and manufacture of one degree of freedom spherical four-bar mechanisms. First, a brief review of some of the current computer-aided design software for spherical four-bar mechanisms is presented. These software packages provide the three-dimensional visualization and computational capabilities necessary to synthesize and analyze spherical four-bar mechanisms. However, to date, no readily available and effective tools exist to aid in the modeling and manufacture of spherical mechanisms. Next, the kinematics of spherical four-bar mechanisms are reviewed as they pertain to their geometric modeling and manufacture. Finally, we present our web-based implementation of a computer-aided modeling, simulation, and manufacturing methodology for spherical four-bar mechanisms called SFBDESIGNER (for spherical four-bar designer). SFBDESIGNER facilitates the design, dynamic simulation, prototyping, and manufacture of spherical four-bar mechanisms.
Using Tolerance-Maps to Generate Frequency Distributions of Clearance and Allocate Tolerances for Pin-Hole Assemblies
Authors: Ameta Gaurav , Davidson Joseph K. , Shah Jami J.
Published: November 2007

A new mathematical model for representing the geometric variations of lines is extended to include probabilistic representations of one-dimensional (1D) clearance, which arise from positional variations of the axis of a hole, the size of the hole, and a pin-hole assembly. The model is compatible with the ASME/ ANSI/ISO Standards for geometric tolerances. Central to the new model is a Tolerance-Map (T-Map) (Patent No. 69638242), a hypothetical volume of points that models the 3D variations in location and orientation for a segment of a line (the axis), which can arise from tolerances on size, position, orientation, and form. Here, it is extended to model the increases in yield that occur when maximum material condition (MMC) is specified and when tolerances are assigned statistically rather than on a worst-case basis; the statistical method includes the specification of both size and position tolerances on a feature. The frequency distribution of 1D clearance is decomposed into manufacturing bias, i.e., toward certain regions of a Tolerance-Map, and into a geometric bias that can be computed from the geometry of multidimensional T-Maps. Although the probabilistic representation in this paper is built from geometric bias, and it is presumed that manufacturing bias is uniform, the method is robust enough to include manufacturing bias in the future. Geometric bias alone shows a greater likelihood of small clearances than large clearances between an assembled pin and hole. A comparison is made between the effects of choosing the optional material condition MMC and not choosing it with the tolerances that determine the allowable variations in position.
Search-Guided Sampling to Reduce Uncertainty of Minimum Deviation Zone Estimation
Authors: Barari Ahmad , ElMaraghy Hoda A. , Knopf George K.
Published: November 2007

Integrating computational tasks in coordinate metrology and its effect on the inspection’s uncertainty is studied. It is shown that implementation of an integrated inspection system is crucial to reduce the uncertainty in minimum deviation zone (MDZ) estimation. An integrated inspection system based on the iterative search procedure and online MDZ estimation is presented. The search procedure uses the Parzen Windows technique to estimate the probability density function of the geometric deviations between the actual and substitute surfaces. The computed probability density function is used to recognize the critical points in the MDZ estimation and to identify portions of the surface that require further iterative measurements until the desired level of convergence is achieved. Reduction of the uncertainty in the MDZ estimation using the developed search method compared to the MDZ estimations using the traditional sampling methods is demonstrated by presenting experiments including both actual and virtual inspection data. The proposed search method can be used for assessing any geometric deviations when no prior assumptions about the fundamental form and distribution of the underlying manufacturing errors are required. The search method can be used to inspect and evaluate both primitive geometric features and complicated sculptured surfaces. Implementation of this method reduces inspection cost as well as the cost of rejecting good parts or accepting bad parts.
Model and Algorithms for Point Cloud Construction Using Digital Projection Patterns
Authors: Peng Tao , Gupta Satyandra K.
Published: November 2007

This paper describes a computational framework for constructing point clouds using digital projection patterns. The basic principle behind the approach is to project known patterns on the object using a digital projector. A digital camera is then used to take images of the object with the known projection patterns imposed on it. Due to the presence of 3D faces of the object, the projection patterns appear distorted in the images. The images are analyzed to construct the 3D point cloud that is capable of introducing the observed distortions in the images. The approach described in this paper presents three advances over the previously developed approaches. First, it is capable of working with the projection patterns that have variable fringe widths and curved fringes and hence can provide improved accuracy. Second, our algorithm minimizes the number of images needed for creating the 3D point cloud. Finally, we use a hybrid approach that uses a combination of reference plane images and estimated system parameters to construct the point cloud. This approach provides good run-time computational performance and simplifies the system calibration.
Blurring the Boundary: The Nuclear Envelope Extends Its Reach
Authors: Stewart Colin L. , Roux Kyle J. , Burke Brian
Published: November 2007

The past decade has seen a complete rethinking of the traditional view of the nuclear envelope as simply a passive enclosure for the chromosomes. The convergence of several lines of clinical and basic research has revealed additional roles in both signaling and mitotic progression. It is becoming apparent that the nuclear envelope defines not only nuclear organization but also that of the cytoskeleton and, in this way, integrates both nuclear and cytoplasmic architecture.