bluuebunny/crossref_metadata_2025 huggingface dataset:
Culturing and environmental DNA sequencing uncover hidden kinetoplastid biodiversity and a major marine clade within ancestrally freshwater Neobodo designis
Authors: von der Heyden Sophie , Cavalier-Smith Thomas
Published: November 2005

Bodonid flagellates (class Kinetoplastea) are abundant, free-living protozoa in freshwater, soil and marine habitats, with undersampled global biodiversity. To investigate overall bodonid diversity, kinetoplastid-specific PCR primers were used to amplify and sequence 18S rRNA genes from DNA extracted from 16 diverse environmental samples; of 39 different kinetoplastid sequences, 35 belong to the subclass Metakinetoplastina, where most group with the genus Neobodo or the species Bodo saltans, whilst four group with the subclass Prokinetoplastina (Ichthyobodo). To study divergence between freshwater and marine members of the genus Neobodo, 26 new Neobodo designis strains were cultured and their 18S rRNA genes were sequenced. It is shown that the morphospecies N. designis is a remarkably ancient species complex with a major marine clade nested among older freshwater clades, suggesting that these lineages were constrained physiologically from moving between these environments for most of their long history. Other major bodonid clades show less-deep separation between marine and freshwater strains, but have extensive genetic diversity within all lineages and an apparently biogeographically distinct distribution of B. saltans subclades. Clade-specific 18S rRNA gene primers were used for two N. designis subclades to test their global distribution and genetic diversity. The non-overlap between environmental DNA sequences and those from cultures suggests that there are hundreds, possibly thousands, of different rRNA gene sequences of free-living bodonids globally.
Telonema antarcticum sp. nov., a common marine phagotrophic flagellate
Authors: Klaveness Dag , Shalchian-Tabrizi Kamran , Thomsen Helge Abildhauge , Eikrem Wenche , Jakobsen Kjetill S.
Published: November 2005

Telonema is a widely distributed group of phagotrophic flagellates with two known members. In this study, the structural identity and molecular phylogeny of Telonema antarcticum was investigated and a valid description is proposed. Molecular phylogeny was studied using small-subunit rRNA (SSU rRNA) gene sequences. The pear-shaped cell had two subequal flagella that emerged laterally on the truncated antapical tail. One flagellum had tripartite hairs. The cell was naked, but had subsurface vesicles containing angular paracrystalline bodies of an unknown nature. A unique complex cytoskeletal structure, the subcortical lamina, was found to be an important functional and taxonomic feature of the genus. Telonema has an antero-ventral depression where food particles are ingested and then transferred to a conspicuous anterior food vacuole. The molecular phylogeny inferred from the SSU rRNA gene sequence suggested that Telonema represents an isolated and deep branch among the tubulocristate protists.
Vibrio gigantis sp. nov., isolated from the haemolymph of cultured oysters (Crassostrea gigas)
Authors: Roux F. Le , Goubet A. , Thompson F. L. , Faury N. , Gay M. , Swings J. , Saulnier D.
Published: November 2005

Polyphasic analysis of four new Vibrio isolates originating from the haemolymph of diseased cultured oysters is described. The new isolates were closely related to Vibrio splendidus, having 98 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on DNA gyrase subunit B (gyrB), RNA polymerase σ
70 factor (rpoD), replication origin-binding protein (rctB) and transmembrane regulatory protein (toxR) genes, fluorescent amplified fragment length polymorphism and DNA–DNA hybridization experiments clearly showed that the new isolates form a tight genomic group that is different from the currently known Vibrio species. It is proposed that these new isolates should be accommodated in a novel species, Vibrio gigantis sp. nov. Phenotypic features that differentiate V. gigantis from other known Vibrio species include arginine dihydrolase, gelatinase and β-galactosidase activities, NO2 production, growth at 35 °C, and utilization of sucrose, melibiose, amygdalin, glycerol, galactose, starch and glycogen. The type strain is LGP 13T (=LMG 22741T=CIP 108656T).
Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor
Authors: Quan Zhe-Xue , Bae Hee-Sung , Baek Jong-Hwan , Chen Wen-Feng , Im Wan-Taek , Lee Sung-Taik
Published: November 2005

A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61Tand L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genusRhizobiumcomprising the type strains ofRhizobium giardinii,Rhizobium radiobacter,Rhizobium rubi,Rhizobium larrymoorei,Rhizobium vitis,Rhizobium undicola,Rhizobium loessense,Rhizobium galegaeandRhizobium huautlense. Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0·6–0·7×1·1–1·3 μm), with peritrichous flagella. The DNA G+C content is 60·1–60·9 mol%. Cellular fatty acids are C16 : 0(2·2–3·3 %), C18 : 0(2·1–3·2 %), C19 : 0cycloω8c(9·9–16·8 %), C20 : 3ω6,9,12c(2·7–3·3 %), summed feature 3 (7·2–7·7 %) and summed feature 7 (67·8–73·7 %). The strains formed nodules on a legume plant,Medicago sativa. AnifHgene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61Tby PCR amplification by using anifH-specific primer system. Strains L61Tand L22 were distinguished from the type strains of recognizedRhizobiumspecies in the same sublineage based on low DNA–DNA hybridization values (2–4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61Tand L22 fromRhizobiumspecies in the same sublineage. Based on the results obtained in this study, L61Tand L22 are considered to be representatives of a novel species ofRhizobium, for which the nameRhizobium daejeonensesp. nov. is proposed. The type strain is L61T(=KCTC 12121T=IAM 15042T=CCBAU 10050T).
Suttonella ornithocola sp. nov., from birds of the tit families, and emended description of the genus Suttonella
Authors: Foster Geoffrey , Malnick Henry , Lawson Paul A. , Kirkwood James , MacGregor Shaheed K. , Collins Matthew D.
Published: November 2005

Phenotypic and phylogenetic studies were performed on three strains of Gram-negative, rod-shaped organisms recovered from dead birds of the tit families (blue tit, coal tit and long-tailed tit). Morphological, cultural and biochemical studies indicated that the organisms were related to the family Cardiobacteriaceae in the gamma-subclass of the Proteobacteria. Comparative 16S rRNA gene sequencing studies confirmed these findings and demonstrated that the bacterium represents a hitherto unknown subline within this family. The closest phylogenetic relative of the strains isolated from the birds was found to be Suttonella indologenes, although a sequence divergence of approximately 5 % demonstrated that the unknown bacterium represented a novel species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacteria recovered from the diseased birds represent a novel species, Suttonella ornithocola sp. nov., with strain B6/99/2T (=CCUG 49457T=NCTC 13337T) as the type strain.
Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert
Authors: de Groot Arjan , Chapon Virginie , Servant Pascale , Christen Richard , Saux Marion Fischer-Le , Sommer Suzanne , Heulin Thierry
Published: November 2005

Two gamma- and UV-radiation-tolerant, Gram-negative, rod-shaped bacterial strains, VCD115T and VCD117, were isolated from a mixture of sand samples collected in the Sahara Desert in Morocco and Tunisia, after exposure of the sand to 15 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences and DNA–DNA hybridizations showed that VCD115T and VCD117 are members of a novel species belonging to the genus Deinococcus, with Deinococcus grandis as its closest relative. The DNA G+C contents of VCD115T and VCD117 are 59·8 and 60·6 mol%, respectively. The major fatty acids (straight-chain 15 : 1, 16 : 1, 17 : 1 and 16 : 0), polar lipids (dominated by phosphoglycolipids and glycolipids) and quinone type (MK-8) support the affiliation to the genus Deinococcus. The strains did not grow on rich medium such as trypticase soy broth (TSB), but did grow as whitish colonies on tenfold-diluted TSB. The genotypic and phenotypic properties allowed differentiation of VCD115T and VCD117 from recognized Deinococcus species. Strains VCD115T and VCD117 are therefore identified as representing a novel species, for which the name Deinococcus deserti sp. nov. is proposed, with the type strain VCD115T (=DSM 17065T=LMG 22923T).
Actinoalloteichus spitiensis sp. nov., a novel actinobacterium isolated from a cold desert of the Indian Himalayas
Authors: Singla A. K. , Mayilraj S. , Kudo Takuji , Krishnamurthi S. , Prasad G. S. , Vohra R. M.
Published: November 2005

An actinobacterial strain, RMV-1378T, isolated from a cold desert of the Indian Himalayas, was subjected to polyphasic taxonomic characterization. The strain formed branching, non-fragmenting vegetative hyphae and did not produce diffusible pigments. Neither aerial mycelium nor spore formation was observed. The G+C content of the DNA was 72·0 mol%. The strain had chemotaxonomic characteristics typical of the genus Actinoalloteichus and was closely related (99·3 % 16S rRNA gene sequence similarity) to Actinoalloteichus cyanogriseus, currently the only Actinoalloteichus species with a validly published name. However, the results of DNA–DNA hybridization experiments showed 51·9 % relatedness with the type strain of A. cyanogriseus. On the basis of the above data and the physiological and biochemical distinctiveness of RMV-1378T (=MTCC 6194T=JCM 12472T=DSM 44848T), this strain should be classified as the type strain of a novel species of Actinoalloteichus, for which the name Actinoalloteichus spitiensis sp. nov. is proposed.
Leadbetterella byssophila gen. nov., sp. nov., isolated from cotton-waste composts for the cultivation of oyster mushroom
Authors: Weon Hang-Yeon , Kim Byung-Yong , Kwon Soon-Wo , Park In-Cheol , Cha In-Bae , Tindall Brian J. , Stackebrandt Erko , Trüper Hans G. , Go Seung-Joo
Published: November 2005

A bacterial strain, designated 4M15T, was isolated from cotton-waste composts used as mushroom cultivation in South Korea. Properties of this isolate were studied on the basis of physiological and biochemical characteristics, fatty acid profile, isoprenoid quinone, DNA G+C content and phylogenetic position based on 16S rRNA gene sequence analysis. The strain was found to form a distinct phylogenetic lineage related to the family ‘Flexibacteraceae’ within the phylum ‘Bacteroidetes’. No recognized species showed >85 % 16S rRNA gene sequence similarity to strain 4M15T. The fatty acid profile of strain 4M15T included C16 : 1
ω7c/iso-C15 : 0 2-OH (30·5 %), iso-C15 : 0 (24·2 %), iso-C15 : 0 2-OH/C16 : 1
ω7c (15·9), iso-C17 : 0 3-OH (10·5 %) and C16 : 0 (5·6 %). The major isoprenoid quinone was menaquinone MK-7. The DNA G+C content was 33·0 mol%. Cells were Gram-negative, strictly aerobic, rod-shaped, non-motile, catalase-positive, oxidase-positive and flexirubin-positive. The strain hydrolysed aesculin, gelatin, starch and tyrosine. Several phenotypic tests could be used to differentiate strain 4M15T from other members of the family ‘Flexibacteraceae’. On the basis of the data presented, strain 4M15T should be assigned to the phylum ‘Bacteroidetes’ as a novel genus and species, for which the name Leadbetterella byssophila gen. nov., sp. nov. is proposed. The type strain is 4M15T (=KACC 11308T=DSM 17132T).
Haloterrigena saccharevitans sp. nov., an extremely halophilic archaeon from Xin-Jiang, China
Authors: Xu Xue-Wei , Liu Shuang-Jiang , Tohty Dilbar , Oren Aharon , Wu Min , Zhou Pei-Jin
Published: November 2005

A novel extremely halophilic strain, isolated from Aibi salt lake, Xin-Jiang, China, was subjected to polyphasic taxonomic characterization. This strain, designated AB14T, is neutrophilic, motile and requires at least 10 % (w/v) NaCl for growth. Strain AB14T grows at 24–58 °C, with optimal growth at 42–45 °C. Mg2+ is not required, but growth is observed in MgCl2 concentrations as high as 1·0 M. Strain AB14T possesses the diphytanyl (C20C20) and phytanyl-sesterterpanyl diether (C20C25) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6 disulfate 1→2 glucose-glycerol diether. The genomic DNA G+C content is 66·6 mol%. The 16S rRNA gene sequence similarity values of strain AB14T with its nearest phylogenetic neighbours (Haloterrigena thermotolerans and Haloterrigena turkmenica) are 98·6 and 96·0 %, respectively. DNA–DNA hybridization revealed 54 % relatedness between strain AB14T and Haloterrigena thermotolerans JCM 11050T and 21 % between strain AB14T and Haloterrigena turkmenica JCM 9101T. It is therefore proposed that strain AB14T represents a novel species, for which the name Haloterrigena saccharevitans sp. nov. is proposed. The type strain is AB14T (=AS 1.3730T=JCM 12889T).
Alteromonas hispanica sp. nov., a polyunsaturated-fatty-acid-producing, halophilic bacterium isolated from Fuente de Piedra, southern Spain
Authors: Martínez-Checa Fernando , Béjar Victoria , Llamas Inmaculada , del Moral Ana , Quesada Emilia
Published: November 2005

Strain F-32T, which produces exopolysaccharides and contains polyunsaturated fatty acids, was isolated from a hypersaline water sample collected from Fuente de Piedra (southern Spain). Phylogenetic analyses indicated conclusively that the strain in question belonged to the genus Alteromonas. Phenotypic tests showed that it could be assigned to the genus Alteromonas although it had a number of distinctive characteristics: it is moderately halophilic, growing best with 7·5–10 % w/v NaCl; it grows at 4 °C and produces H2S; it does not grow with d-cellobiose, d-fructose, d-galactose, d-glucose or lactose as sole sources of carbon and energy; and its fatty-acid profile is typical of Alteromonas but it also contains a large amount of an unusual acid with three double bonds [18 : 3ω6c (6, 9, 12); 5·01 %, w/v]. The major isoprenoid quinone is Q8. The DNA G+C content is 46·3 mol%. The phylogenetic, phenotypic and genetic properties of strain F-32T place it within a novel species, for which the name Alteromonas hispanica sp. nov. is proposed. The type strain is F-32T (=CECT 7067T=LMG 22958T).
Bacillus ruris sp. nov., from dairy farms
Authors: Heyndrickx Marc , Scheldeman Patsy , Forsyth Gillian , Lebbe Liesbeth , Rodríguez-Díaz Marina , Logan Niall A. , De Vos Paul
Published: November 2005

Four novel ellipsoidal spore-forming Bacillus isolates with swollen sporangia, isolated from raw milk and feed concentrate, showed a high level of similarity in SDS-PAGE, fatty acid methyl esters and routine phenotypic tests. However, 16S rRNA gene sequence comparisons showed that this taxon was different from other related Bacillus species, and only a low level of DNA relatedness was found with the closest phylogenetic and phenotypic relative, Bacillus galactosidilyticus. This taxon could be differentiated from B. galactosidilyticus on the basis of morphological differences, stronger acid reactions with a wide range of substrates after 48 h incubation, and qualitative and quantitative differences in fatty acid content. On the basis of these data, a novel species, Bacillus ruris sp. nov., is proposed, with LMG 22866T (=DSM 17057T) as the type strain.
Marinomonas dokdonensis sp. nov., isolated from sea water
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Tae-Kwang
Published: November 2005

Two Gram-negative, motile, non-spore-forming, slightly halophilic bacteria (strains DSW10-10T and DSW10-19) were isolated from sea water and subjected to a polyphasic taxonomic study. They grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW10-10T and DSW10-19 were characterized chemotaxonomically as containing Q-8 as the predominant ubiquinone and C18 : 1
ω7c, C16 : 0 and C16 : 1
ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. Their DNA G+C contents were 45·3–45·7 mol%. Strains DSW10-10T and DSW10-19 exhibited a 16S rRNA gene sequence similarity value of 100 % and possessed a mean DNA–DNA relatedness level of 85 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW10-10T and DSW10-19 fell within the radiation of the cluster encompassed by the genus Marinomonas. Strains DSW10-10T and DSW10-19 had 16S rRNA gene sequence similarity levels of 95·7–97·7 % with respect to the type strains of Marinomonas species with validly published names. Levels of DNA–DNA relatedness were low enough to indicate that the two strains constitute a distinct Marinomonas species. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains DSW10-10T (=KCTC 12394T=DSM 17202T) and DSW10-19 were placed in the genus Marinomonas as members of a novel species, Marinomonas dokdonensis sp. nov.
Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’
Authors: Yang Hee-Chan , Im Wan-Taek , An Dong-Shan , Park Woo-shin , Kim In S. , Lee Sung-Taik
Published: November 2005

A taxonomic study was carried out on a bacterial strain, designated KM-45T, isolated from forest soil collected near Daejeon, South Korea. Comparative 16S rRNA gene sequence analysis indicated a clear affiliation of this bacterium to the ‘Betaproteobacteria’ and that it was related most closely to Chitinibacter tainanensis BCRC 17254T, Formivibrio citricus DSM 6150T and Iodobacter fluviatilis ATCC 33051T (92·4, 91·2 and 88·9 % 16S rRNA gene sequence similarity, respectively). Cells were Gram-negative, facultatively anaerobic, motile and rod-shaped. The strain grew well on R2A medium and utilized a broad spectrum of carbon sources. The G+C content of the genomic DNA was 58 mol% and the predominant ubiquinone was Q-8. Major fatty acids were C16 : 0, C16 : 1
ω7c/iso-C15 : 0 2-OH, C18 : 1
ω7c/ω9t/ω12t and C17 : 0 cyclo. On the basis of the evidence presented, it is proposed that strain KM-45T should be placed in a novel genus and species, for which the name Silvimonas terrae gen. nov., sp. nov. is proposed. The type strain is KM-45T (=KCTC 12358T=NBRC 100961T).
Alcaligenes aquatilis sp. nov., a novel bacterium from sediments of the Weser Estuary, Germany, and a salt marsh on Shem Creek in Charleston Harbor, USA
Authors: Van Trappen Stefanie , Tan Tjhing-Lok , Samyn Emly , Vandamme Peter
Published: November 2005

Four nitrite-dissimilating strains, isolated from Weser Estuary sediments, were investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the ‘Betaproteobacteria’ and are related to the genus Alcaligenes. The highest level of sequence similarity (100 %) was found with strain M3A (=ATCC 700596), a dimethyl sulfide-producing marine isolate that was included in this study. DNA–DNA hybridizations between the five strains and related Alcaligenes faecalis strains confirmed that the former belong to a single and novel species within the genus Alcaligenes. The isolates are Gram-negative, motile, rod-shaped cells with a DNA G+C content of about 56 mol%. The whole-cell fatty acid profiles of the isolates were very similar and included C16 : 0, C17 : 0 cyclo, C18 : 1
ω7c, summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid of equivalent chain length 10·928, C16 : 1 iso I and C14 : 0 3-OH) and summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1
ω7c) as the major fatty acid components. On the basis of their phylogenetic, genomic and phenotypic properties, the five novel strains can be assigned to the genus Alcaligenes as a novel species, for which the name Alcaligenes aquatilis sp. nov. is proposed. The type strain is LMG 22996T (=CCUG 50924T).
Enterococcus devriesei sp. nov., associated with animal sources
Authors: Švec Pavel , Vancanneyt Marc , Koort Joanna , Naser Sabri M. , Hoste Bart , Vihavainen Elina , Vandamme Peter , Swings Jean , Björkroth Johanna
Published: November 2005

The taxonomic position of two bovine strains, LMG 13603 and LMG 14595, assigned to the species Enterococcus raffinosus on the basis of biochemical features, was reinvestigated. Both reference strains and two other isolates, 6/1 (=LMG 22829) originating from a charcoal-broiled river lamprey and IE38.4 (=LMG 22830) from the air of a poultry slaughter by-product processing plant, occupied a clearly separate position, on the basis of sequence analysis of the housekeeping gene pheS (encoding the phenylalanyl-tRNA synthase α-subunit), relative to the type strain of E. raffinosus and all other enterococcal species with validly published names. 16S rRNA gene sequencing of strains LMG 13603, LMG 14595, 6/1 and IE38.4 confirmed their phylogenetic position in the Enterococcus avium species group, there being more than 99 % 16S rRNA gene sequence similarity to most members of the group, including E. raffinosus, and revealed Enterococcus pseudoavium as the closest phylogenetic relative (99·8–99·9 %). Further phenotypic and genotypic analyses using whole-cell-protein electrophoresis, (GTG)5-PCR fingerprinting, ribotyping and DNA–DNA hybridization experiments demonstrated that all four strains represent a novel enterococcal species, for which the name Enterococcus devriesei sp. nov. is proposed. The type strain is LMG 14595T (=CCM 7299T).
Palleronia marisminoris gen. nov., sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium belonging to the ‘Alphaproteobacteria’, isolated from a saline soil
Authors: Martínez-Checa Fernando , Quesada Emilia , Martínez-Cánovas M. José , Llamas Inmaculada , Béjar Victoria
Published: November 2005

Strain B33T is a moderately halophilic, exopolysaccharide-producing, Gram-negative, non-motile rod isolated from a hypersaline soil bordering a saline saltern on the Mediterranean seaboard in Murcia (Spain). The bacterium is chemoheterotrophic and strictly aerobic. It contains a pink pigment but does not synthesize bacteriochlorophyll a. It requires 0·66 M Na+, 0·1 M Mg2+ and 0·1 M K+ for optimum growth. It does not produce acid from carbohydrates. It cannot grow with carbohydrates, organic acids, sugars, alcohols or amino acids as sole sources of carbon and energy. Its major fatty-acids are 18 : 1ω7c (68·9 %) and 19 : 0 cyclo ω8c (12·8 %). The sole respiratory lipoquinone found in strain B33T is ubiquinone-10. The DNA G+C content is 64·2 mol%. 16S rRNA gene sequence comparisons show that the isolate is a member of the Roseobacter clade within the class ‘Alphaproteobacteria’. The similarity values with Roseivivax halodurans and Roseivivax halotolerans are 88·2 and 88·0 % respectively and 92·2 % with Salipiger mucosus. DNA–DNA hybridization values with these species are <30 %. In the light of the polyphasic evidence gathered in this study it is proposed that the isolate be classified as a novel genus and species with the name Palleronia marisminoris gen. nov., sp. nov. The proposed type strain is strain B33T (=CECT 7066T=LMG 22959T).
The preparation of the Approved Lists of Bacterial Names
Authors: Sneath P. H. A.
Published: November 2005

To celebrate the 25th anniversary of the publication of the Approved Lists of Bacterial Names in 1980, the surviving editor Peter Sneath reflects on the conception, preparation and publication of this seminal document in the nomenclature of not just prokaryotes but all organisms.
Distinct and Cooperative Functions of Phytochromes A, B, and C in the Control of Deetiolation and Flowering in Rice
Authors: Takano Makoto , Inagaki Noritoshi , Xie Xianzhi , Yuzurihara Natsu , Hihara Fukiko , Ishizuka Toru , Yano Masahiro , Nishimura Minoru , Miyao Akio , Hirochika Hirohiko , Shinomura Tomoko
Published: November 2005

We have isolated phytochrome B (phyB) and phyC mutants from rice (Oryza sativa) and have produced all combinations of double mutants. Seedlings of phyB and phyB phyC mutants exhibited a partial loss of sensitivity to continuous red light (Rc) but still showed significant deetiolation responses. The responses to Rc were completely canceled in phyA phyB double mutants. These results indicate that phyA and phyB act in a highly redundant manner to control deetiolation under Rc. Under continuous far-red light (FRc), phyA mutants showed partially impaired deetiolation, and phyA phyC double mutants showed no significant residual phytochrome responses, indicating that not only phyA but also phyC is involved in the photoperception of FRc in rice. Interestingly, the phyB phyC double mutant displayed clear R/FR reversibility in the pulse irradiation experiments, indicating that both phyA and phyB can mediate the low-fluence response for gene expression. Rice is a short-day plant, and we found that mutation in either phyB or phyC caused moderate early flowering under the long-day photoperiod, while monogenic phyA mutation had little effect on the flowering time. The phyA mutation, however, in combination with phyB or phyC mutation caused dramatic early flowering.
Caesarean section delivery and the risk of allergic disorders in childhood
Authors: Renz‐Polster H. , David M. R. , Buist A. S. , Vollmer W. M. , O'Connor E. A. , Frazier E. A. , Wall M. A.
Published: November 2005

Background
The composition of the intestinal flora in young children, if unfavourable, may increase the susceptibility to allergic disorders. Beneficial intestinal microbes originate from the maternal vaginal tract and thus are more likely to be transferred during vaginal births than during Caesarean sections (C‐sections).

Objective
To determine whether children born by C‐section have a different risk of allergic disorders compared with those delivered vaginally. We also tested the hypothesis that the risk of allergic disorders is highest for children born after ‘repeat C‐sections’.

Methods
A retrospective cohort study of 8953 children aged 3–10 years. Children diagnosed with allergic rhinoconjunctivitis (AR), asthma, atopic dermatitis (AD), or food allergies were identified from the Kaiser Permanente Northwest Region electronic records. The children's sex, birth weight, birth order, postnatal exposure to antibiotics as well as the mothers' age, ethnicity, education, marital status, smoking status during pregnancy, and use of asthma or hayfever medications were identified through the mothers' medical records or through the Oregon Birth Registry.

Results
The risk of being diagnosed with AR was significantly higher in the children born by C‐section than in those delivered vaginally: adjusted odds ratio (OR)=1.37%, 95% confidence interval (CI)=1.14–1.63. Delivery by C‐section was also associated with the subsequent diagnosis of asthma (OR=1.24%, 95% CI=1.01–1.53); this association was gender specific, with a positive association restricted to girls (OR for asthma in girls: OR=1.53%, 95% CI=1.11–2.10; in boys: OR=1.08%, 95% CI=0.81–1.43). There was no significant association between mode of delivery and AD.

If children born in a ‘repeat C‐section’ were considered separately the risk of being diagnosed with AR increased further (OR=1.78%, 95% CI=1.34–2.37). The same increase was noted for asthma in girls (OR=1.83%, 95% CI=1.13–2.97) but not in boys.

Conclusion
Caesarean sections may be associated with an increased risk of developing AR in childhood.
A case–control study of bronchial asthma associated with ulcerative colitis: role of airway microvascular permeability
Authors: Kanazawa H. , Yoshikawa J.
Published: November 2005

Background
Recent attention has been devoted to the respiratory manifestations that may be associated with diseases of distant organs. The most prevalent and distinctive pattern of respiratory involvement in ulcerative colitis (UC) is airway inflammation.

Objective
This study was designed to examine the contribution of airway microvascular permeability to the pathophysiological association of asthma with UC.

Methods
Sputum induction and methacholine provocation test were performed in 27 asthmatic patients (15 without UC and 12 with UC), nine patients with UC and 15 normal controls. Inflammatory indexes, vascular endothelial growth factor (VEGF) levels in induced sputum, airway vascular permeability index and exhaled nitric oxide (NO) levels were examined in all subjects.

Results
The percentage of eosinophils and concentration of eosinophil cationic protein in induced sputum were similar in all four groups. Though exhaled NO levels were significantly higher in asthmatics with or without UC than in normal controls or UC patients, these levels were comparable in asthmatics with and without UC. VEGF levels in induced sputum and airway vascular permeability index were significantly higher in asthmatics without UC (VEGF: 1920 (990) pg/mL; airway vascular permeability index: 0.018 (0.008)) and asthmatics with UC (6570 (1000) pg/mL; 0.040 (0.006)) than in normal controls (950 (700) pg/mL; 0.009 (0.003)), whose levels were comparable to those of UC patients (900 (600) pg/mL; 0.011 (0.003)). In particular, these parameters were markedly increased in asthmatics with UC than in asthmatics without UC. VEGF level was significantly correlated with airway vascular permeability index in asthmatics with UC. Moreover, VEGF level and airway vascular permeability index was inversely correlated with degree of airway obstruction and airway hyper‐reactivity to methacholine in these asthmatics.

Conclusion
Airway microvascular hyper‐permeability induced by VEGF may have a profound effect on airway function and can explain the heightened airway hyper‐responsiveness characteristic of asthma associated with UC.
Vascular endothelial growth factor up‐regulation and bronchial wall remodelling in asthma
Authors: Chetta A. , Zanini A. , Foresi A. , D'Ippolito R. , Tipa A. , Castagnaro A. , Baraldo S. , Neri M. , Saetta M. , Olivieri D.
Published: November 2005

Background
There is increasing in vitro evidence to support a role for vascular endothelial growth factor (VEGF), a major regulator of angiogenesis, as a mediator of fibrosis associated with neovascularization.

Objective
We tested the hypothesis that VEGF is involved both in increased airway mucosal vascularity and in the subepithelial fibrosis of asthmatic patients.

Methods
Bronchial biopsies were performed in 24 asthmatic patients and eight healthy controls. Immunostaining, using computerized image analysis, was performed using monoclonal antibodies against VEGF+ cells, type IV collagen, to outline the basement membrane thickness, and tryptase and EG2, to identify mast cells and eosinophils, respectively.

Results
The counts of VEGF+ cells (P<0.05), mast cells and EG2+ cells (both P<0.01) were higher in asthmatics than in controls. The number of vessels, the vascular area in the lamina propria, and the basement membrane thickness were significantly higher in asthmatics than in healthy volunteers (P<0.01). Moreover, in asthmatic patients, the number of VEGF+ cells was significantly related to the number of vessels (P<0.01), to mast cells (P<0.01) and to basement membrane thickness (P<0.01). A colocalization study also revealed that mast cells were a relevant cellular source of VEGF. High doses of inhaled fluticasone propionate significantly reduced VEGF+ cells (P<0.05), vessel number (P<0.05), vascular area (P<0.05) and basement membrane thickness (P<0.05) in a subgroup of asthmatic patients.

Conclusions
This study shows that VEGF, in addition to being involved in the vascular component of airway remodelling, may play a role in the thickening of the basement membrane in asthma.
Molecular cloning and immunoglobulin E reactivity of a natural rubber latex lecithinase homologue, the major allergenic component of Hev b 4
Authors: Sunderasan E. , Bahari A. , Arif S. A. M. , Zainal Z. , Hamilton R. G. , Yeang H. Y.
Published: November 2005

Background
Hev b 4 is an allergenic natural rubber latex (NRL) protein complex that is reactive in skin prick tests and in vitro immunoassays. On SDS‐polyacrylamide gel electrophoresis (SDS‐PAGE), Hev b 4 is discerned predominantly at 53–55 kDa together with a 57 kDa minor component previously identified as a cyanogenic glucosidase. Of the 13 NRL allergens recognized by the International Union of Immunological Societies, the 53–55 kDa Hev b 4 major protein is the only candidate that lacks complete cDNA and protein sequence information.

Objective
We sought to clone the transcript encoding the Hev b 4 major protein, and characterize the native protein and its recombinant form in relation to IgE binding.

Methods
The 5′/3′ rapid amplification of cDNA ends method was employed to obtain the complete cDNA of the Hev b 4 major protein. A recombinant form of the protein was over‐expressed in Escherichia coli. The native Hev b 4 major protein was deglycosylated by trifluoromethane sulphonic acid. Western immunoblots of the native, deglycosylated and recombinant proteins were performed using both polyclonal antibodies and sera from latex‐allergic patients.

Results
The cDNA encoding the Hev b 4 major protein was cloned. Its open reading frame matched lecithinases in the conserved domain database and contained 10 predicted glycosylation sites. Detection of glycans on the Hev b 4 lecithinase homologue confirmed it to be a glycoprotein. The deglycosylated lecithinase homologue was discerned at 40 kDa on SDS‐PAGE, this being comparable to the 38.53 kDa mass predicted by its cDNA. Deglycosylation of the lecithinase homologue resulted in the loss of IgE recognition, although reactivity to polyclonal rabbit anti‐Hev b 4 was retained. IgE from latex‐allergic patients also failed to recognize the non‐glycosylated E. coli recombinant lecithinase homologue.

Conclusion
The IgE epitopes of the Hev b 4 lecithinase homologue reside mainly in its carbohydrate moiety, which also account for the discrepancy between the observed molecular weight of the protein and the value calculated from its cDNA.
Long‐term seasonal variation in the biological traits of benthic‐macroinvertebrates in two Mediterranean‐climate streams in California, U.S.A.
Authors: BÊCHE LEAH A. , MCELRAVY ERIC P. , RESH VINCENT H.
Published: November 2005

1. We investigated the seasonal variation of biological traits and the influence of interannual rainfall variability on this pattern. Using long‐term survey data (6–19 years) from an intermittent and a perennial stream in the Mediterranean‐climate region of northern California, we examined 16 fuzzy‐coded biological traits (e.g. maximum size, life cycle duration, and mode of respiration).

2. Seasonal habitat variability is higher in the intermittent stream than in the perennial stream. During the winter and spring wet‐season both streams flood; however, during the summer dry‐season, the intermittent stream forms isolated pools in (occasionally drying completely).

3. Seasonal habitat variability influenced both taxonomic and biological trait composition. Distinct taxonomic communities were present in each season, particularly in the intermittent stream. The intermittent stream also exhibited more seasonal variation in biological traits than the perennial stream.

4. Despite statistically significant seasonal variation, trait composition was relatively stable among seasons in comparison with taxonomic composition and abundance. Taxonomic composition varied considerably between seasons, because of high seasonal and interannual replacement of taxa resulting from seasonal habitat changes.

5. The seasonality of taxonomic composition and abundance was sensitive to interannual rainfall variability. In dry years, the taxonomic composition of communities was more similar between seasons than in wet years, while trait composition was relatively insensitive to rainfall variability.

6. Despite high seasonal variation in abundance and taxonomic composition, biological traits of aquatic macroinvertebrates varied less and exhibited seasonal stability, which may be a result of the unpredictability and harshness of stream environments.
Effect of landscape factors on fish distribution in arctic Alaskan lakes
Authors: HERSHEY A. E. , BEATY S. , FORTINO K. , KEYSE M. , MOU P. P. , O'BRIEN W. J. , ULSETH A. J. , GETTEL G. A. , LIENESCH P. W. , LUECKE C. , MCDONALD M. E. , MAYER C. H. , MILLER M. C. , RICHARDS C. , SCHULDT J. A. , WHALEN S. C.
Published: November 2005

1. The distribution of species is affected by many factors operating at a variety of temporal and spatial scales in a heterogeneous landscape. In lakes, fish communities are dynamic, influenced by landscape‐level factors that control colonisation and extinction.

2. We used classification and regression tree (CART) analyses to quantify the importance of landscape‐level factors in determining the distribution of fish species in 168 arctic Alaskan lakes. Factors including lake size, depth, outflow gradient, distance to other lakes, lake order, altitude, river drainage and age of glacial surface were analysed. These factors could affect either access of fish to a lake (colonisation variables), or their survival in a lake that already had been colonised (extinction variables).

3. The presence of a species was predicted accurately in 78.4% ± 10.5% (mean ± SD) of cases, and absence in 75.0% ± 6.1% of cases. The relative importance of extinction versus colonisation variables varied with species. Extinction variables were most important for lake trout (Salvelinus namaycush) and slimy sculpin (Cottus cognatus), a mixture of extinction and colonisation variables was important for arctic char (Salvelinus alpinus), and colonisation variables were most important for arctic grayling (Thymallus arcticus) and round whitefish (Prosopium cylindraceum).

4. Ecological differences among species account for much of the difference in relative importance of colonisation versus extinction variables. In addition, stream piracy events have occurred over geologic time scales, which have resulted in lakes that are currently inaccessible but support relict fish populations.

5. Climate warming, currently occurring in the arctic, is likely to alter further the stream network, which could have dramatic effects on fish distributions by affecting access to isolated lakes or isolating lakes that are currently accessible.
Are behavioural traits in prey sensitive to the risk imposed by predatory fish?
Authors: WOHLFAHRT BIANCA , MIKOLAJEWSKI DIRK JOHANNES , JOOP GERRIT , SUHLING FRANK
Published: November 2005

1. Behavioural differences among prey species may result from evolutionary adaptations that facilitate coexistence with different predators and influence vulnerability to predators. It has been hypothesised that prey species modify their behaviour in relation to the risk posed by particular predators.

2. We examined the relationship between anti‐predator behaviour and predation risk in five species of larval odonates in combination with three predatory fish species (perch, gudgeon and rudd) that differ in foraging behaviour. The odonates,Platycnemis pennipes,Coenagrion puella,Lestes sponsa,Sympetrum striolatumandLibellula depressa, differ with regard to their life cycle and habitat, including water depth, occurrence in temporary ponds and co‐existence with fish.

3. The odonate species differed in their response to fish: (i) Two species showed a flexible response. LarvalC. puellareduced activity in the presence of fish, regardless of species, whereasL. depressaaltered their activity only in the presence of gudgeon. (ii) Independent of fish species, all odonates exceptL. depressaexhibited spatial avoidance of fish. This was interpreted as a more general anti‐predator response. (iii) In some cases the odonates showed no response to predators and their behaviour was thus independent of predation risk.

4. Our results confirm that all odonates responded to the presence of at least some predatory fish, and that some odonate species discriminated between fish species. However, we found no significant correlation between behavioural modifications and predation risk, indicating that anti‐predator responses and predation risk depend on the particular predator and the species being preyed on.
Trade‐offs between the shade‐avoidance response and plant resistance to herbivores? Tests with mutant Cucumis sativus
Authors: McGUIRE R. , AGRAWAL A. A.
Published: November 2005

Plants exhibit adaptations to many stresses, including light competition and herbivory. The expression of these traits may interact negatively, potentially instigating a trade‐off.

We employed a combination of genetically altered Cucumis sativus varieties and phenotypic manipulations to test for trade‐offs in field experiments. The different genetic lines of C. sativus were altered in their phytochrome‐mediated shade responses and the production of terpenoid defence compounds.

Cucumber plants constitutively expressing the shade‐avoidance response had 93% more herbivory by specialist beetles compared with wild types. The long‐hypocotyl mutants also produced leaves with fewer trichomes, greater toughness and a higher carbon to nitrogen ratio (C : N) than wild types. Plants lacking defensive cucurbitacins had 23% longer internodes than the cucurbitacin‐producing line.

We then manipulated the plant phenotype by artificially imposing neighbours’ shade on plants with and without cucurbitacins. As expected, plants responded to shade by growing longer hypocotyls and first internodes, but few trade‐offs were found between plant line and shade treatment and, although herbivory levels were very low, there was a trend towards reduced damage on shaded plants.

The use of genetically altered plant lines provided strong evidence for the trade‐off hypothesis, while phenotypic manipulations did not support the hypothesis.
A distinct seasonal pattern of the ratio of soil respiration to total ecosystem respiration in a spruce‐dominated forest
Authors: Davidson E. A. , Richardson A. D. , Savage K. E. , Hollinger D. Y.
Published: November 2005

Annual budgets and fitted temperature response curves for soil respiration and ecosystem respiration provide useful information for partitioning annual carbon budgets of ecosystems, but they may not adequately reveal seasonal variation in the ratios of these two fluxes. Soil respiration (Rs) typically contributes 30–80% of annual total ecosystem respiration (Reco) in forests, but the temporal variation of these ratios across seasons has not been investigated. The objective of this study was to investigate seasonal variation in the Rs/Reco ratio in a mature forest dominated by conifers at Howland, ME, USA. We used chamber measurements of Rs and tower‐based eddy covariance measurements of Reco. The Rs/Reco ratio reached a minimum of about 0.45 in the early spring, gradually increased through the late spring and early summer, leveled off at about 0.65 for the summer, and then increased again to about 0.8 in the autumn. A spring pulse of aboveground respiration presumably causes the springtime minimum in this ratio. Soil respiration ‘catches up’ as the soils warm and as root growth presumably accelerates in the late spring, causing the Rs/Reco ratios to increase. The summertime plateau of Rs/Reco ratios is consistent with summer drought suppressing Rs that would otherwise be increasing, based on increasing soil temperature alone, thus causing the Rs/Reco ratios to not increase as soils continue to warm. Declining air temperatures and litter fall apparently contribute to increased Rs/Reco ratios in the autumn. Differences in phenology of growth of aboveground and belowground plant tissues, mobilization and use of stored substrates within woody plants, seasonal variation in photosynthate and litter substrates, and lags between temperature changes of air and soil contribute to a distinct seasonal pattern of Rs/Reco ratios.
An unusual distribution of the kdr gene among populations of Anopheles gambiae on the island of Bioko, Equatorial Guinea
Authors: Reimer L. J. , Tripet F. , Slotman M. , Spielman A. , Fondjo E. , Lanzaro G. C.
Published: November 2005

In West Africa, Anopheles gambiae exists in discrete subpopulations known as the M and S molecular forms. Although these forms occur in sympatry, pyrethroid knock‐down resistance (kdr) is strongly associated with the S molecular form. On the island of Bioko, Equatorial Guinea we found high frequencies of the kdr mutation in M form individuals (55.8%) and a complete absence of kdr in the S form. We also report the absence of the kdr allele in M and S specimens from the harbour town of Tiko in Cameroon, representing the nearest continental population to Bioko. The kdr allele had previously been reported as absent in populations of An. gambiae on Bioko. Contrary to earlier reports, sequencing of intron‐1 of this sodium channel gene revealed no fixed differences between M form resistant and susceptible individuals. The mutation may have recently arisen independently in the M form on Bioko due to recent and intensive pyrethroid application.
Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels
Authors: Arvestad L. , Visa N. , Lundeberg J. , Wieslander L. , Savolainen P.
Published: November 2005

Expressed sequence tags (ESTs) were generated from two Chironomus tentans cDNA libraries, constructed from an embryo epithelial cell line and from larva midgut tissue. 8584 5′‐end ESTs were generated and assembled into 3110 tentative unique transcripts, providing the largest contribution of C. tentans sequences to public databases to date. Annotation using Blast gave 1975 (63.5%) transcripts with a significant match in the major gene/protein databases, 1170 with a best match to Anopheles gambiae and 480 to Drosophila melanogaster. 1091 transcripts (35.1%) had no match to any database. Studies of open reading frames suggest that at least 323 of these contain a coding sequence, indicating that a large proportion of the genes in C. tentans belong to previously unknown gene families.
Characterization of a blood activated chitinolytic system in the midgut of the sand fly vectors Lutzomyia longipalpis and Phlebotomus papatasi
Authors: Ramalho‐Ortigão J. M. , Kamhawi S. , Joshi M. B. , Reynoso D. , Lawyer P. G. , Dwyer D. M. , Sacks D. L. , Valenzuela J. G.
Published: November 2005

We characterized a cDNA from Phlebotomus papatasi, PpChit1, which encodes a midgut specific chitinase and show the presence of a functional, blood‐induced chitinolytic system in sand flies. PpChit1 is detected only in the midgut and is regulated by blood feeding. A recombinant protein (rPpChit1) produced in HEK 293‐F cells exhibited a similar activity profile to that found in the native protein against several specific substrates, including an oligomeric glycol chitin and synthetic 4‐methyl‐umbelliferone labelled substrates. Western blotting showed that the native protein is recognized by mouse polyclonal antibodies against rPpChit1. Additionally, the rPpChit1 and the native chitinase displayed similar retention times in a HPLC size fractionation column. When added to rPpChit1 or to midgut lysates, PpChit1 sera reduced chitinolytic activity by 65–70%.