bluuebunny/crossref_metadata_2025 huggingface dataset:
Pedobacter insulae sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Oh Hyun Woo , Oh Tae-Kwang
Published: September 2007

A Gram-negative, non-motile, rod-shaped bacterium, DS-139T, was isolated from a soil sample collected from Dokdo, Korea, and subjected to a polyphasic taxonomic analysis. Strain DS-139T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–0.5 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1
ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-39T belongs to the genus Pedobacter in the family Sphingobacteriaceae. The similarity values between the 16S rRNA gene sequence of strain DS-139T and those of the type strains of recognized Pedobacter species, except Pedobacter saltans, were in the range 93.9–96.7 %. The differential phenotypic properties, together with the phylogenetic distinctiveness, were sufficient to assign strain DS-139T to a species that is separate from recognized Pedobacter species. On the basis of the phenotypic and phylogenetic data, therefore, strain DS-139T represents a novel species of the genus Pedobacter, for which the name Pedobacter insulae sp. nov. is proposed. The type strain is DS-139T (=KCTC 12820T =DSM 18684T).
Bacillus acidiceler sp. nov., isolated from a forensic specimen, containing Bacillus anthracis pX02 genes
Authors: Peak K. Kealy , Duncan Kathleen E. , Veguilla William , Luna Vicki A. , King Debra S. , Heller Loreé , Heberlein-Larson Lea , Reeves Frank , Cannons Andrew C. , Amuso Philip , Cattani Jacqueline
Published: September 2007

Research at the Center for Biological Defense identified plasmid-borne forms of Bacillus anthracis pXO2 genes in a Gram-positive, endospore-forming rod, isolated from a forensic specimen considered a credible threat of harbouring anthrax. Conventional, commercial and molecular-based methods indicated that the isolate (CBD 119T) was not B. anthracis and considered not to be a member of the Bacillus cereus group. Based on the 16S rRNA gene sequence similarities, strain CBD 119T was most closely related to Bacillus luciferensis LMG 18422T (99.3 %). Phenotyping and fatty acid methyl ester analysis of the isolate were conducted alongside B. luciferensis JCM 12212T. The major cellular fatty acids (anteiso-C15 : 0, iso-C15 : 0, and >7 iso or anteiso forms) supported inclusion of the isolate in the genus Bacillus. Strain CBD 119T was inconsistent with B. luciferensis JCM 12212T for 18 of 96 traits evaluated including motility, degree of endospore-driven swelling and pH optimum; the two were linked by fatty acid methyl ester analysis as separate but closely related species. DNA–DNA relatedness between strain CBD 119T and B. luciferensis JCM 12212T resulted in less than 20 % hybridization. The results of biochemical and physiological characterization, chemotaxonomic analysis and DNA–DNA hybridization differentiated strain CBD 119T both phenotypically and genotypically from the only species with validly published name with greater than 97 % 16S rRNA gene sequence similarity. The isolate has an accelerated doubling time when grown in aerated broth at pH 5.9 relative to that at pH 7.1. Therefore, it is proposed that strain CBD 119T represents a novel species, Bacillus acidiceler sp. nov. The type strain is strain CBD 119T (=NRRL B-41736T=DSM 18954T).
Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas
Authors: Martini M. , Lee I.-M. , Bottner K. D. , Zhao Y. , Botti S. , Bertaccini A. , Harrison N. A. , Carraro L. , Marcone C. , Khan A. J. , Osler R.
Published: September 2007

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes,rplV(rpl22) andrpsC(rps3), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered withAcholeplasmaspecies and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.
Jannaschia donghaensis sp. nov., isolated from seawater of the East Sea, Korea
Authors: Yoon Jung-Hoon , Kang So-Jung , Park Sooyeon , Oh Tae-Kwang
Published: September 2007

A Gram-negative, non-motile and rod-, oval- or coccoid-shaped strain, DSW-17T, was isolated from seawater of the East Sea, Korea, and subjected to a polyphasic taxonomic study. Strain DSW-17T grew optimally at pH 7.0–8.0 and 25 °C. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c as the major fatty acid. Major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The DNA G+C content was 65.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DSW-17T was phylogenetically most closely affiliated to the genus Jannaschia. Strain DSW-17T exhibited 16S rRNA gene sequence similarity values of 96.5 % with the type strains of three recognized species of the genus Jannaschia. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DSW-17T is distinguishable from the recognized species of the genus Jannaschia. On the basis of phenotypic, phylogenetic and genetic data, strain DSW-17T was classified in the genus Jannaschia as a member of a novel species, for which the name Jannaschia donghaensis sp. nov. is proposed. The type strain is DSW-17T (=KCTC 12862T=JCM 14563T).
Halochromatium roseum sp. nov., a non-motile phototrophic gammaproteobacterium with gas vesicles, and emended description of the genus Halochromatium
Authors: Anil Kumar P. , Srinivas T. N. R. , Sasikala Ch. , Ramana Ch. V.
Published: September 2007

A rod-shaped, marine, phototrophic, purple sulfur bacterium containing gas vesicles was isolated from a marine solar saltern at Kakinada, India. Cells of strain JA134T are Gram-negative, non-motile rods, with vesicular intracytoplasmic membranes, and the strain has an absolute requirement for NaCl for growth. Bacteriochlorophyll a and the carotenoid okenone are present as photosynthetic pigments. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA134T clusters with members of the genus Halochromatium, but is distinctly separated from the species reported so far. The morphological and physiological differences of strain JA134T from other Halochromatium species support the description of strain JA134T (=ATCC BAA-1363T =DSM 18859T =JCM 14151T) as the type strain of a novel species, Halochromatium roseum sp. nov.
Streptomyces synnematoformans sp. nov., a novel actinomycete isolated from a sand dune soil in Egypt
Authors: Hozzein Wael N. , Goodfellow Michael
Published: September 2007

A polyphasic taxonomic study was undertaken to establish the status of a novel actinomycete, strain S155T, isolated from a sand dune soil in Egypt. The organism formed characteristic synnemata-like structures and exhibited chemical and morphological features consistent with its classification in the genusStreptomyces. An almost-complete 16S rRNA gene sequence of the isolate was compared with corresponding sequences of representative streptomycetes. The 16S rRNA gene sequence data supported the assignment of the strain to the genusStreptomycesand showed that it formed a distinct phyletic line; the organism was most similar to the type strains ofStreptomyces ruber(97.0 %),Streptomyces rubiginosus(97.0 %),Streptomyces roseiscleroticus(96.9 %) andStreptomyces thermoalcalitolerans(97.1 %). It was readily distinguished from the type strains of these species using a combination of phenotypic properties. On the basis of these results, strain S155T(=CGMCC 4.2055T=DSM 41902T) is proposed as the type strain of the novel speciesStreptomyces synnematoformanssp. nov.
Stenotrophomonas terrae sp. nov. and Stenotrophomonas humi sp. nov., two nitrate-reducing bacteria isolated from soil
Authors: Heylen Kim , Vanparys Bram , Peirsegaele Filip , Lebbe Liesbeth , De Vos Paul
Published: September 2007

Three Gram-negative, rod-shaped, non-spore-forming, nitrate-reducing isolates (R-32746, R-32768Tand R-32729T) were obtained from soil. Analysis of repetitive sequence-based PCR showed that the three isolates represented two different strains. 16S rRNA gene sequence analysis and DNA–DNA hybridization placed them within the genusStenotrophomonasand revealed that they were genotypically different from each other and from all recognizedStenotrophomonasspecies. Analysis of the fatty acid composition and physiological and biochemical tests allowed differentiation from their closest phylogenetic neighbours. They are therefore considered to represent two novel species, for which the namesStenotrophomonas terraesp. nov. andStenotrophomonas humisp. nov. are proposed, with strains R-32768T(=LMG 23958T=DSM 18941T) and R-32729T(=LMG 23959T=DSM 18929T), respectively, as the type strains.
Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine
Authors: Carlsohn Marc René , Groth Ingrid , Spröer Cathrin , Schütze Barbara , Saluz Hans-Peter , Munder Thomas , Stackebrandt Erko
Published: September 2007

Three actinomycetes (strains HKI 0478T, HKI 0479 and HKI 0480) isolated from the surfaces of rocks in the Feengrotten medieval alum slate mine (Thuringia, Germany) were examined in a polyphasic taxonomic study. The following morphological and chemotaxonomic features supported their classification as members of the genus Kribbella: the presence of ll-diaminopimelic acid in the cell-wall peptidoglycan; glucose together with minor amounts of mannose and ribose as the whole-cell sugars; polar lipids comprising phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unknown phospho- and glycolipids; fatty acid profiles characterized by the predominance of anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 9-methyl; and the presence of MK-9(H4) as the main menaquinone. The isolates had almost identical 16S rRNA gene sequences (99.9–100 %) and were most closely related to the type strains of Kribbella jejuensis (98.9 % sequence similarity), Kribbella swartbergensis and Kribbella solani (both 98.8 %). A wide range of genotypic and phenotypic markers as well as the low levels of DNA–DNA relatedness between strain HKI 0478T and the type strains of K. jejuensis (41.3 %), K. swartbergensis (18.6 %) and K. solani (14.2 %) distinguished the novel strains from their closest phylogenetic neighbours. On the basis of these results, strain HKI 0478T represents a novel member of the genus Kribbella, for which the name Kribbella aluminosa sp. nov. is proposed. The type strain is HKI 0478T (=DSM 18824T =JCM 14599T).
Glycomyces sambucus sp. nov., an endophytic actinomycete isolated from the stem of Sambucus adnata Wall
Authors: Gu Qiang , Zheng Wen , Huang Ying
Published: September 2007

An actinomycete, designated strain E71T, was isolated from the stem of Sambucus adnata Wall, a Chinese medicinal plant, and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence showed that the organism was a member of the genus Glycomyces, and formed a distinct phyletic line distantly related to recognized species of the genus Glycomyces. Morphological and chemotaxonomic data supported the affiliation of strain E71T to the genus Glycomyces. A number of physiological properties and a unique menaquinone profile allowed differentiation of the strain from related Glycomyces species. It is therefore proposed that strain E71T represents a novel species of the genus Glycomyces, for which the name Glycomyces sambucus sp. nov. is proposed. The type strain is E71T (=CGMCC 4.3147T=DSM 45047T).
Humihabitans oryzae gen. nov., sp. nov.
Authors: Kageyama Akiko , Takahashi Yoko , Ōmura Satoshi
Published: September 2007

Strain KV-657T was isolated from a paddy field soil sample collected in Japan using GPM agar plates supplemented with catalase. The strain was a Gram-positive, aerobic organism that formed branching hyphae with ll-diaminopimelic acid as the diagnostic peptidoglycan diamino acid. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 70 mol%. 16S rRNA gene sequence analysis revealed that this strain is closely related to Intrasporangium calvum DSM 43043T, with a similarity of 97.6 %. Based on the morphological, biochemical and chemotaxonomic properties of this strain and phylogenetic analysis, it was concluded that this isolate represents a new genus and species in the family Intrasporangiaceae, for which the name Humihabitans oryzae gen. nov., sp. nov. is proposed. The type strain of Humihabitans oryzae is KV-657T (=NRRL B-24470T =NBRC 101802T).
Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Kwon Kae Kyoung , Shin Dong Sung , Luo Xuseong , Kim Sang-Jin , Mikhailov Valery V.
Published: September 2007

A taxonomic study of a novel marine, heterotrophic, non-gliding, halotolerant and light-pink-pigmented bacterium was carried out using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain KMM 6241T is a member of the phylum Bacteroidetes. Strain KMM 6241T formed a cluster with the genera Algoriphagus, Chimaereicella and Hongiella with sequence similarities of 94.0–98.2 %. Hongiella ornithinivorans was the closest relative of the novel isolate. Comparative analysis of phenotypic, chemotaxonomic and genotypic characteristics of strain KMM 6241T and representatives of the genera Algoriphagus, Chimaereicella and Hongiella revealed many similar features. Consequently, phylogenetic evidence supported by phenotypic and genotypic similarities support the transfer of members of the genera Chimaereicella and Hongiella to the genus Algoriphagus and the establishment of a novel species, Algoriphagus vanfongensis sp. nov., with strain KMM 6241T (=DSM 17529T=KCTC 12716T) as the type strain.
Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter
Authors: Srinivas T. N. R. , Anil Kumar P. , Sasikala Ch. , Ramana Ch. V. , Imhoff J. F.
Published: September 2007

A rod-shaped, phototrophic, purple non-sulfur bacterium was isolated in pure culture from seawater collected from the seashore of Visakhapatnam, on the east coast of India, in a medium that contained 2 % NaCl (w/v). Strain JA123T was Gram-negative and non-motile and had a requirement for NaCl. Photo-organoheterotrophic and chemo-organoheterotrophic growth occurred with organic compounds as carbon sources and electron donors. Photolithoautotrophic, chemolithoautotrophic and fermentative growth could not be demonstrated. Strain JA123T contained vesicular intracellular photosynthetic membrane structures. Bacteriochlorophyll a and probably carotenoids of the spheroidene series were present as photosynthetic pigments. Biotin was required for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA123T clustered with species of the genus Rhodobacter. Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA123T is sufficiently different from other Rhodobacter species to propose a novel species, Rhodobacter vinaykumarii sp. nov., to accommodate this strain; the type strain is JA123T (=DSM 18714T =JCM 14544T =CCUG 54311T).
Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996
Authors: Ntougias Spyridon , Zervakis Georgios I. , Fasseas Constantinos
Published: September 2007

A novel Gram-negative, motile, nonsporulating, rod-shaped bacterium isolated from alkaline sludge-like wastes (‘alpeorujo’ or ‘alperujo’) of two-phase olive oil extraction is described. The strain, designated AW-7T, is an obligate aerobe that is halotolerant (tolerating up to 15 % w/v NaCl), sugar-tolerant (tolerating up to 45 % and 60 % w/v (+)-d-glucose and maltose respectively; these are the highest concentrations tolerated by any known members of the Bacteria domain) and alkalitolerant (growing at a broad pH range of 5–11). Strain AW-7T is chemo-organotrophic. Ubiquinone-9 was detected in the respiratory chain of strain AW-7T. The major fatty acids present are C18 : 1
ω7c, C16 : 0, C19 : 0 cyclo ω8c, C12 : 0 3-OH and C16 : 1
ω7c/iso-C15 : 0 2-OH. Based on 16S rRNA gene sequence analysis, strain AW-7T showed almost equal phylogenetic distances from Zymobacter palmae (95.6 % similarity) and Carnimonas nigrificans (95.4 % similarity). In addition, low DNA–DNA relatedness values were found for strain AW-7T against Carnimonas nigrificans CECT 4437T (22.5–25.4 %) and Z. palmae DSM 10491T (11.9–14.4 %). The DNA G+C content of strain AW-7T is 64.4 mol%. Physiological and chemotaxonomic data further confirmed the differentiation of strain AW-7T from the genera Zymobacter and Carnimonas. Thus, strain AW-7T represents a novel bacterial genus within the family Halomonadaceae, for which the name Halotalea gen. nov. is proposed. Halotalea alkalilenta sp. nov. (type strain AW-7T=DSM 17697T=CECT 7134T) is proposed as the type species of the genus Halotalea gen. nov. A reassignment of the descriptive 16S rRNA signature characteristics of the family Halomonadaceae permitted the placement of the novel genus Halotalea into the family; in contrast, the genus Halovibrio possessed only 12 out of the 18 signature characteristics proposed, and hence it was excluded from the family Halomonadaceae.
Cerasicoccus arenae gen. nov., sp. nov., a carotenoid-producing marine representative of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’, isolated from marine sand
Authors: Yoon Jaewoo , Matsuo Yoshihide , Matsuda Satoru , Adachi Kyoko , Kasai Hiroaki , Yokota Akira
Published: September 2007

A polyphasic taxonomic study was performed on strain YM26-026T, which was isolated from acid-treated sediment in Kamaishi, Japan. The bacterial cells were pale-pink-pigmented, Gram-negative, obligately aerobic, non-spore-forming, spherical and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate was a member of the phylum ‘Verrucomicrobia’ and shared approximately 84–87 % sequence similarity with strains of the class Opitutae that have been cultivated to date. Strain YM26-026T produced pale-pink pigments of carotenoid. β-Lactam antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolate did not contain muramic acid or diaminopimelic acid in the cell wall, suggesting that the strain lacks peptidoglycan. The G+C content of the DNA of strain YM26-026T was 54.0 mol%. Menaquinone-7 was the major quinone and C14 : 0 and C18 : 1
ω9c were the major fatty acids. On the basis of polyphasic taxonomic studies, it was concluded that strain YM26-026T represents a new genus of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia’, for which the name Cerasicoccus arenae gen. nov., sp. nov. is proposed. The type strain is YM26-026T (=MBIC08280T=KCTC 12870T).
Enterococcus camelliae sp. nov., isolated from fermented tea leaves in Thailand
Authors: Sukontasing Sirapan , Tanasupawat Somboon , Moonmangmee Somporn , Lee Jung-Sook , Suzuki Ken-ichiro
Published: September 2007

A Gram-positive and catalase-negative coccus that formed chains, strain FP15-1T, isolated from fermented tea leaves (‘miang’), was studied systematically. The strain was facultatively anaerobic and producedl-lactic acid from glucose. Demethylmenaquinone (DMK-7) was the major menaquinone. Straight-chain unsaturated fatty acids C16 : 1and C18 : 1were the dominant components. The DNA G+C content was 37.8 mol%. On the basis of 16S rRNA and RNA polymeraseαsubunit (rpoA) gene sequence analysis, strain FP15-1Twas closely related toEnterococcus italicusKCTC 5373T, with 99.2 and 93.8 % similarity, respectively. The strain could be clearly distinguished fromE. italicusATCC 5373Tby low DNA–DNA relatedness (≤33.8 %) and phenotypic characteristics. Therefore, this strain represent a novel species of the genusEnterococcus, for which the nameEnterococcus camelliaesp. nov. is proposed. The type strain is FP15-1T(=KCTC 13133T=NBRC 101868T=NRIC 0105T=TISTR 932T=PCU 277T).
Rhodotorula psychrophila sp. nov., Rhodotorula psychrophenolica sp. nov. and Rhodotorula glacialis sp. nov., novel psychrophilic basidiomycetous yeast species isolated from alpine environments
Authors: Margesin Rosa , Fonteyne Pierre-Alain , Schinner Franz , Sampaio José Paulo
Published: September 2007

Three novel psychrophilic species of the genus Rhodotorula are described. Rhodotorula psychrophila sp. nov. (type strain PB19T=CBS 10440T=DSM 18768T), Rhodotorula psychrophenolica sp. nov. (type strain AG21T=CBS 10438T=DSM 18767T) and Rhodotorula glacialis sp. nov. (type strain A19T=CBS 10436T=DSM 18766T) were isolated from soil collected from an alpine railway area, from mud in the thawing zone of a glacier foot and from glacier cryoconite, respectively. All three species have been assigned to the genus Rhodotorula on the basis of molecular sequence data and physiological and morphological properties. Rhodotorula psychrophila is not able to grow at temperatures above 15 °C. Rhodotorula psychrophenolica and Rhodotorula glacialis degrade high concentrations of phenol (up to 12.5 and 5 mM, respectively) as the sole carbon source at 10 °C. Sequence analyses of the 26S rDNA D1/D2 regions indicated that the novel species are phylogenetically related and belong to a clade that includes other psychrophilic yeasts.
Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea
Authors: Ryu Seung Hyun , Park Minjeong , Jeon Yeji , Lee Jung Ro , Park Woojun , Jeon Che Ok
Published: September 2007

A Gram-negative bacterium, designated strain EMB34T, was isolated from a wastewater treatment plant in Korea. Growth was observed between 10 and 40 °C (optimum, 25–35 °C) and between pH 6.0 and 9.5 (optimum, pH 7.5–8.0). The cells were non-motile rods, linked with extracellular fibrils. The predominant fatty acids of strain EMB34T were iso-C15 : 0, C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH and the strain contained phosphatidylethanolamine and phosphatidylinositol as the polar lipids. The G+C content of the genomic DNA was 34.2 mol% and the major quinone was menaquinone-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB34T formed a distinct phyletic line within the genus Flavobacterium. The levels of 16S rRNA gene sequence similarity with other Flavobacterium species were less than 94.5 %. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB34T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium filum sp. nov. is proposed. The type strain is EMB34T (=KCTC 12610T=DSM 17961T).
Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium
Authors: Kim Hee Gon , Doronina Nina V. , Trotsenko Yuri A. , Kim Si Wouk
Published: September 2007

A novel restricted facultatively methylotrophic marine strain, MPT, possessing the ribulose monophosphate pathway of C1-carbon compound assimilation was isolated from a seawater sample obtained from Mokpo, South Korea. The novel isolate is aerobic, Gram-negative, asporogenous and a non-motile short rod. It grows well on methanol, methylated amines, dimethylsulfide and DMSO. Optimal growth occurs with 3 % NaCl at 30 °C and pH 7.0. Fructose is utilized as a multicarbon source. Growth factors are not required and vitamin B12 does not stimulate growth. The cellular fatty acid profile of the novel strain consists primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content is 44.9 mol% (T
m). Based on 16S rRNA gene sequence analysis and DNA–DNA relatedness (25–41 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, it is suggested that isolate MPT represents a novel species, Methylophaga aminisulfidivorans sp. nov. (type strain MPT=KCTC 12909T=VKM B-2441T=JCM 14647T).
Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil
Authors: Yoon Jung-Hoon , Kang So-Jung , Park Sooyeon , Oh Tae-Kwang
Published: September 2007

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).
Algibacter mikhailovii sp. nov., a novel marine bacterium of the family Flavobacteriaceae, and emended description of the genus Algibacter
Authors: Nedashkovskaya Olga I. , Vancanneyt Marc , Kim Seung Bum , Hoste Bart , Bae Kyung Sook
Published: September 2007

A novel marine bacterium, designated strain KMM 6171T, was subjected to taxonomic analysis by using a polyphasic approach. Colonies were yellow-pigmented and cells were Gram-negative, heterotrophic rods displaying slow gliding motility. 16S rRNA gene sequence analysis indicated that strain KMM 6171T was closely related to the genus Algibacter, a member of the family Flavobacteriaceae, with sequence similarity of 96.7–96.8 %. The predominant cellular fatty acids were iso-C15 : 1, iso-C15 : 0, anteiso-C15 : 0, C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3, comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content was 35.1 mol%. On the basis of the phenotypic, genotypic, chemotaxonomic and phylogenetic data, strain KMM 6171T represents a novel species of the genus Algibacter, for which the name Algibacter mikhailovii sp. nov. is proposed. The type strain is KMM 6171T (=KCTC 12710T=LMG 23988T). An emended description of the genus Algibacter based on the new data is also given.
Methylibium aquaticum sp. nov., a betaproteobacterium isolated from a eutrophic freshwater pond
Authors: Song Jaeho , Cho Jang-Cheon
Published: September 2007

A freshwater bacterium, designated IMCC1728T, was isolated from a eutrophic pond. The strain was Gram-negative, chemoheterotrophic and facultatively aerobic, forming non-motile rods that contained poly-β-hydroxybutyrate granules. Based on 16S rRNA gene sequence comparisons, the most closely related species to strain IMCC1728T was Methylibium petroleiphilum (97.0 % similarity). Phylogenetic trees generated using 16S rRNA gene sequences showed that this isolate formed an independent phyletic line of the genus Methylibium clade of the class Betaproteobacteria. The DNA G+C content of the strain was 66.2±0.4 mol%. The predominant cellular fatty acid constituents were C16 : 1
ω7c and/or iso-C15 : 0 2-OH (43.1 %), C16 : 0 (20.3 %), C12 : 0 (13.4 %) and C10 : 0 3-OH (7.3 %). The strain contained Q-8 as the predominant ubiquinone. Several phenotypic characteristics, including flagellation, temperature range for growth and carbon source utilization patterns, differentiated strain IMCC1728T from species of the genus Methylibium. Therefore, it is proposed that strain IMCC1728T represents a novel species, Methylibium aquaticum sp. nov. The type strain is IMCC1728T (=KCCM 42364T=NBRC 102349T).
Pedobacter koreensis sp. nov., isolated from fresh water
Authors: Baik Keun Sik , Park Yoon-Dong , Kim Mi Sun , Park Seong Chan , Moon Eun Young , Rhee Moon Soo , Choi Ji Hyeok , Seong Chi Nam
Published: September 2007

A motile, rod-shaped bacterium, designated strain WPCB189T, was isolated from fresh water collected from the Woopo wetland (Republic of Korea). The cells were found to be Gram-negative, aerobic and catalase- and oxidase-positive. A phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate forms a lineage within the genus Pedobacter, showing sequence similarities of 89.7–96.4 % with respect to recognized species of the genus, and represents a novel member of this genus. The major fatty acids were iso-C15 : 0 2-OH and/or C16 : 1
ω7c (summed feature 3, 29.7 %), iso-C15 : 0 (26.4 %) and iso-C17 : 1 3-OH (10.1 %). The DNA G+C content was 38.0 mol%. On the basis of data obtained from this polyphasic taxonomic study, strain WPCB189T represents a novel species of the genus Pedobacter, for which the name Pedobacter koreensis sp. nov. is proposed. The type strain is WPCB189T (=KCTC 12536T=NBRC 101153T).
Marinobacter salicampi sp. nov., isolated from a marine solar saltern in Korea
Authors: Yoon Jung-Hoon , Lee Mi-Hwa , Kang So-Jung , Oh Tae-Kwang
Published: September 2007

A Gram-negative, motile, rod-shaped, Marinobacter-like bacterial strain, ISL-40T, was isolated from a marine solar saltern of the Yellow Sea in Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. Strain ISL-40T grew optimally at pH 7.0–8.0 and at 30 °C. It contained Q-9 as the predominant ubiquinone. The major fatty acids were C16 : 0, C16 : 1
ω7c and/or iso-C15 : 0 2-OH and 10-methyl C16 : 0. The DNA G+C content was 58.1 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-40T belongs to the genus Marinobacter. Strain ISL-40T exhibited 16S rRNA gene sequence similarity values of 93.5–96.4 % to the type strains of recognized Marinobacter species. The differential phenotypic properties and phylogenetic distinctiveness of strain ISL-40T revealed that it is separate from recognized Marinobacter species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain ISL-40T represents a novel species of the genus Marinobacter, for which the name Marinobacter salicampi sp. nov. is proposed. The type strain is ISL-40T (=KCTC 12972T=CCUG 54357T).
Structural Manipulation of Eicosanoid Receptors and Cellular Signaling
Authors: Brink Charles
Published: September 2007

Eicosanoids are lipid mediators derived from the metabolism of arachidonic acid. These agents are locally released and activate different cell membrane receptors, and the latter are part of the G-protein coupled receptor family. While activation of eicosanoid receptors is associated with a wide variety of actions, there is limited information concerning the structural components of the eicosanoid receptors. To date, our understanding of the eicosanoid ligand-receptor binding interaction has been based on the rhodopsin template model. While receptors in the same family do share a common architecture, there are amino acid residues in the membrane binding pocket that play a key role in ligand recognition as well as the diversity observed in the cellular signaling. In order to understand the eicosanoid receptor binding interaction, attention must be focused on both the nature of the endogenous ligands as well as the template G-protein model that has been proposed. The data derived from chemical alterations in the endogenous ligands, together with the mutagenesis studies involving the structural modifications of the eicosanoid receptors, have suggested a working model of the eicosanoid receptors. However, the data also document various nuances in the receptor structure associated with ligand binding as well as a number of differences that will require further investigation.
Activation and Regulation of Cellular Eicosanoid Biosynthesis
Authors: Brock Thomas G. , Peters-Golden Marc
Published: September 2007

There is a growing appreciation for the wide variety of physiological responses that are regulated by lipid messengers. One particular group of lipid messengers, the eicosanoids, plays a central role in regulating immune and inflammatory responses in a receptor-mediated fashion. These mediators are related in that they are all derived from one polyunsaturated fatty acid, arachidonic acid. However, the various eicosanoids are synthesized by a wide variety of cell types by distinct enzymatic pathways, and have diverse roles in immunity and inflammation. In this review, the major pathways involved in the synthesis of eicosanoids, as well as key points of regulation, are presented.
Regulation of Immune Cells by Eicosanoid Receptors
Authors: Kim Nancy D. , Luster Andrew D.
Published: September 2007

Eicosanoids are potent, bioactive, lipid mediators that regulate important components of the immune response, including defense against infection, ischemia, and injury, as well as instigating and perpetuating autoimmune and inflammatory conditions. Although these lipids have numerous effects on diverse cell types and organs, a greater understanding of their specific effects on key players of the immune system has been gained in recent years through the characterization of individual eicosanoid receptors, the identification and development of specific receptor agonists and inhibitors, and the generation of mice genetically deficient in various eicosanoid receptors. In this review, we will focus on the receptors for prostaglandin D2, DP1and DP2/CRTH2; the receptors for leukotriene B4, BLT1and BLT2; and the receptors for the cysteinyl leukotrienes, CysLT1and CysLT2, by examining their specific effects on leukocyte subpopulations, and how they may act in concert towards the development of immune and inflammatory responses.
Prostaglandin Receptor Signaling in Disease
Authors: Matsuoka Toshiyuki , Narumiya Shuh
Published: September 2007

Prostanoids, consisting of the prostaglandins (PGs) and the thromboxanes (TXs), are a group of lipid mediators formed in response to various stimuli. They include PGD2, PGE2, PGF2α, PGI2, and TXA2. They are released outside of the cells immediately after synthesis, and exert their actions by binding to a G-protein coupled rhodopsin-type receptor on the surface of target cells. There are eight types of the prostanoid receptors conserved in mammals from mouse to human. They are the PGD receptor (DP), four subtypes of the PGE receptor (EP1, EP2, EP3, and EP4), the PGF receptor (FP), PGI receptor (IP), and TXA receptor (TP). Recently, mice deficient in each of these prostanoid receptors were generated and subjected to various experimental models of disease. These studies have revealed the roles of PG receptor signaling in various pathological conditions, and suggest that selective manipulation of the prostanoid receptors may be beneficial in treatment of the pathological conditions. Here we review these recent findings of roles of prostanoid receptor signaling and their therapeutic implications.
Cytokine-Leukotriene Receptor Interactions
Authors: Rola-Pleszczynski Marek , Stankova Jana
Published: September 2007

Biochemical and pharmacological studies have identified the structure of leukotrienes, the pathways that lead to their synthesis, and the signaling events they trigger when they interact with their cognate receptors. A privileged interaction exists between these lipid mediators and another group of molecules essential for inflammation and immune modulation, namely, cytokines. Whereas leukotrienes can trigger the synthesis and release of selected cytokines in distinct cell populations, many cytokines can affect cellular responsiveness to leukotrienes by modulating leukotriene receptor expression. As we progressively begin to unravel these complex interactions, new areas of cell-cell communication and eventual therapeutic interventions will emerge.
Prostanoid Receptors in the Human Vascular Wall
Authors: Norel Xavier
Published: September 2007

The mechanisms involved in vascular homeostasis and disease are mostly dependent on the interactions between blood, vascular smooth muscle, and endothelial cells. There is an accumulation of evidence for the involvement of prostanoids, the arachidonic acid metabolites derived from the cyclooxygenase enzymatic pathway, in physiological and/or pathophysiological conditions. In humans, the prostanoids activate different receptors. The classical prostanoid receptors (DP, EP1–4, FP, IP, and TP) are localized at the cell plasma or nuclear membrane. In addition, CRTH2 and the nuclear PPAR receptors are two other targets for prostanoids, namely, prostacyclin (PGI2) or the natural derivatives of prostaglandin D2. While there is little information on the role of CRTH2, there are many reports on PPAR activation and the consecutive expression of genes involved in the human vascular system. The role of the classical prostanoid receptors stimulated by PGI2and thromboxane in the control of the vascular tone has been largely documented, whereas the other receptor subtypes have been overlooked. There is now increasing evidence that suggests a role of PGE2and the EP receptor subtypes in the control of the human vascular tone and remodeling of the vascular wall. These receptors are also present on leukocytes and platelets, and they are implicated in most of the inflammatory processes within the vascular wall. Consequently, the EP receptor subtypes or isoforms would provide a novel and specific cardiovascular therapeutic approach in the near future.
Lipoxin Receptors
Authors: Romano Mario , Recchia Irene , Recchiuti Antonio
Published: September 2007

Lipoxins (LXs) represent a class of arachidonic acid (AA) metabolites that carry potent immunoregulatory and anti-inflammatory properties, LXA4and LXB4being the main components of this series. LXs are generated by cooperation between 5-lipoxygenase (LO) and 12- or 15-LO during cell-cell interactions or by single cell types. LX epimers at carbon 15, the 15-epi-LXs, are formed by aspirin-acetylated cyclooxygenase-2 (COX-2) in cooperation with 5-LO. 15-epi-LXA4is also termed aspirin-triggered LX (ATL).In vivostudies with stable LX and ATL analogs have established that these eicosanoids possess potent anti-inflammatory activities. A LXA4receptor has been cloned. It belongs to the family of chemotactic receptors and clusters with formyl peptide receptors on chromosome 19. Therefore, it was initially denominated formyl peptide receptor like 1 (FPRL1). This receptor binds with high affinity and stereoselectivity LXA4and ATL. It also recognizes a variety of peptides, synthetic, endogenously generated, or disease associated, but with lower affinity compared to LXA4. For this reason, this receptor has been renamed ALX. This review summarizes the current knowledge on ALX expression, signaling, and potential pathophysiological role. The involvement of additional recognition sites in LX bioactions is also discussed.
Sexual Health in Adult Men with Spina Bifida
Authors: Bong Gary W. , Rovner Eric S.
Published: September 2007

Medical and surgical advances in the treatment of spina bifida (SB) have resulted in increasing numbers of patients reaching adulthood. As such, issues related to sexual maturity are being investigated to offer optimal healthcare to men with spina bifida. This report constitutes a review of the current literature relating to adults with spina bifida and issues of sexuality, erectile dysfunction and fertility. In general, adult males with spina bifida have normal sexual desires and an interest in addressing these issues with healthcare providers. Sexual education and access to intimacy are delayed compared to the general population. 75% of men achieve erections, but maintaining erections is a problem and some may be merely reflexive in nature. The many of these men show marked improvement with sildenafil. In SB erectile dysfunction and infertility are related to the level of neurological lesion with the best performance status in those with sacral lesions and intact reflexes. Men with lesions higher than T10 are at risk for azoospermia. There is an increased risk of neural tube defects in the children of men with spina bifida, but the current incidence with modern folic acid therapy is unknown. As the number of males with spina bifida reaching sexual maturity increases, further investigation into sexuality, sex education, intimacy, and treatments for erectile dysfunction and infertility will be needed.
The Role of Leukotriene Receptor Signaling in Inflammation and Cancer
Authors: Massoumi Ramin , Sjölander Anita
Published: September 2007

Leukotrienes (LTs) and prostaglandins (PGs) are metabolites of arachidonic acid that play major roles in various inflammatory conditions. The release of these mediators, by cells recruited to or present at the site of inflammation, modulate/influence the magnitude of the inflammatory response. A better understanding of eicosanoids and how their receptors trigger intracellular signaling during inflammatory conditions is helping to elucidate the well-known connection between chronic inflammatory disease and neoplastic transformation. In the current review, we summarize the role of LTs and PGs in chronic inflammation and, in particular, we focus on recent insights into the role of CysLT1receptor signaling pathway. In addition, we delineate how continuous CysLT1receptor activation and signaling can increase cell survival and proliferation as important early steps toward oncogenicity.
PDZ and LIM Domain-Encoding Genes: Molecular Interactions and their Role in Development
Authors: te Velthuis Aartjan J. W. , Bagowski Christoph P.
Published: September 2007

PDZ/LIM genes encode a group of proteins that play very important, but diverse, biological roles. They have been implicated in numerous vital processes, e.g., cytoskeleton organization, neuronal signaling, cell lineage specification, organ development, and oncogenesis.

In mammals, there are ten genes that encode for both a PDZ domain, and one or several LIM domains: four genes of the ALP subfamily (ALP, Elfin, Mystique, and RIL), three of the Enigma subfamily (Enigma, Enigma Homolog, and ZASP), the two LIM kinases (LIMK1 and LIMK2), and the LIM only protein 7 (LMO7). Functionally, all PDZ and LIM domain proteins share an important trait, i.e., they can associate with and/or influence the actin cytoskeleton.

We review here the PDZ and LIM domain—encoding genes and their different gene structures, their binding partners, and their role in development and disease. Emphasis is laid on the important questions: why the combination of a PDZ domain with one or more LIM domains is found in such a diverse group of proteins, and what role the PDZ/LIM module could have in signaling complex assembly and localization.

Furthermore, the current knowledge on splice form specific expression and the function of these alternative transcripts during vertebrate development will be discussed, since another source of complexity for the PDZ and LIM domain—encoding proteins is introduced by alternative splicing, which often creates different domain combinations.
Nonadditive Expression and Parent-of-Origin Effects Identified by Microarray and Allele-Specific Expression Profiling of Maize Endosperm
Authors: Stupar Robert M. , Hermanson Peter J. , Springer Nathan M.
Published: September 2007

Plant endosperm cells have a nuclear ratio of two maternal genomes to one paternal genome. This 2 to 1 dosage relationship provides a unique system for studying the additivity of gene expression levels in reciprocal hybrids. A combination of microarray profiling and allele-specific expression analysis was performed using RNA isolated from endosperm tissues of maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal hybrids at two developmental stages, 13 and 19 d after pollination. The majority of genes exhibited additive expression in reciprocal hybrids based on microarray analyses. However, a substantial number of genes exhibited nonadditive expression patterns, including maternal like, paternal like, high parent like, low parent like, and expression patterns outside the range of the parental inbreds. The frequency of hybrid expression patterns outside of the parental range in maize endosperm tissue is much higher than that observed for vegetative tissues. For a set of 90 genes, allele-specific expression assays were employed to monitor allelic bias and regulatory variation. Eight of these genes exhibited evidence for maternally or paternally biased expression at multiple stages of endosperm development and are potential examples of differential imprinting. Our data indicate that parental effects on gene expression are much stronger in endosperm than in vegetative tissues.