bluuebunny/crossref_metadata_2025 huggingface dataset:
Levels of superoxide dismutase and malondialdehyde in primary spontaneous pneumothorax
Authors: Tabakoglu Erhan , Ciftci Senturk , Hatipoglu Osman Nuri , Altıay Gündeniz , Caglar Tuncay
Published: August 2004

THE aim of the present study is to determine whether patients with primary spontaneous pneumothorax (PSP) are subject to oxidative stress. For this purpose, we measured the activities of red blood cell superoxide dismutase, which is an antioxidant enzyme, and the level of plasma malondialdehyde, which is one of the lipid peroxidation markers, in a group of patients with PSP. The study was carried out with 16 patients with PSP and 24 healthy individuals. The two groups were similar to each other in terms of sex, age and smoking attitudes. Erythrocyte superoxide dismutase activity was found to be significantly lower in patients with PSP than in the control group (p < 0.01). The plasma malondialdehyde levels were significantly high in patients with PSP (p < 0.01). Our results suggest that oxidative stress may contribute to the pathogenesis of PSP.
Clinical significance of circulating dendritic cells in patients with systemic lupus erythematosus
Authors: Robak E. , Smolewski P. , Woźniacka A. , Sysa-Jędrzejowska A. , Robak T.
Published: August 2004

DENDRITIC cells are a complex group of mainly bone‐marrow‐derived leukocytes that play a role in autoimmune diseases. The total number of circulating dendritic cells (tDC), and their plasmacytoid dendritic cell (pDC) and myeloid dendritic cell (mDC1 and mDC2) subpopulations were assessed using flow cytometry. The number of tDC and their subsets were significantly lower in systemic lupus erythematosus patients than in the control group. The count of tDC and their subsets correlated with the number of T cells. The number of tDC and pDC subpopulation were lower in the patients with lymphopenia and leucopoenia than in the patients without these symptoms. Our data suggest that fluctuations in blood dendritic cell count in systemic lupus erythematosus patients are much more significant in pDC than in mDC, what may be caused by their migration to the sites of inflammation including skin lesions. Positive correlation between dendritic cell number and TCD4+, TCD8+ and CD19+ B cells, testify of their interactions and influence on SLE pathogenesis. The association between dendritic cell number and clinical features seems to be less clear.
Tumour necrosis factor α, lipid peroxidation and NOº are increased and associated with decreased free‐radical scavenging enzymes in patients with Weill‐Marchesani syndrome
Authors: Evereklioglu Cem , Turkoz Yusuf , Calis Mustafa , Duygulu Fuat , Karabulut Aysun B.
Published: August 2004

AIM: Weill‐Marchesani syndrome (WMS) is a rare systemic disorder with both autosomal recessive and dominant inheritances. Accumulation of reactive oxygen species such as , H2O2 and OH• causes lipid peroxidation (LPO), whereas antioxidant enzymes (superoxide dismutase (SOD), glutathione peroxidase (GSHPx)) mediate defence against oxidative stress. Excess tumour necrosis factor (TNF)‐α and NO• react with and cause further antioxidant depletion with an increase in mutation frequency by H2O2. This study investigated the levels of SOD, GSHPx, catalase (CAT), TNF‐α, NO• and LPO in patients with WMS.

Methods: A group of 10 WMS patients (four males, six females; age, 26.5±19.0 years) and 10 age‐matched and sex‐matched controls (five males, five females; age, 27.3±18.2 years) were included. Serum TNF‐α levels were determined by a spectrophotometer technique using immulite chemiluminescent immunometric assay. Malondialdehyde (MDA) was determined in plasma; CAT in red blood cells (RBCs), and SOD and GSHPx in both plasma and RBCs. Total serum NO• levels were evaluated by Griess reaction.

Results: Mean levels of TNF‐α (8.3±0.6 pg/ml) in WMS patients were significantly (p < 0.001) higher than controls (4.3±0.2 pg/ml). Plasma MDA levels in patients and controls were 5.4±0.8 and 1.8±0.6 μmol/l, respectively, and the difference was significant (p = 0.0002). SOD and GSHPx activities were significantly lower in both RBCs and plasma of WMS than in controls (RBC‐SOD, 3981.9±626.6 versus 5261.6±523.0 U/g haemoglobin (Hb), p = 0.0005; plasma‐SOD, 529.4±49.3 versus 713.4±55.7 U/g protein, p = 0.0002; RBC‐GSHPx, 682.7±42.0 versus 756.5±47.6 U/g Hb, p = 0.0011; plasma‐GSHPx, 107.3±15.0 versus 131.4±19.7 U/g protein, p = 0.0113). In addition, serum NO• () levels were also significantly (p = 0.0002) increased in WMS patients (54.4±5.7 versus 26.9±6.7 μmol/l). RBC‐CAT levels were similar between groups (125.6±21.3 versus 131.0±21.5 k/g Hb, p = 0.8798).

Conclusions: The elevated LPO, TNF‐α and NO• with decreased antioxidant enzyme activities indicated impaired antioxidative defence mechanisms with an oxidative injury and cell toxicity in WMS patients. The use of multiple antioxidants and free radical scavengers might be helpful in this genetic disorder.
Single dose of inducible nitric oxide synthase inhibitor induces prolonged inflammatory cell accumulation and fibrosis around injured tendon and synovium
Authors: Darmani Homa , Crossan James C. , Curtis Adam
Published: August 2004

THE aim of the current study was to investigate the effect of inhibition of nitric oxide (NO) production after injury on inflammatory cell accumulation and fibrosis around digital flexor tendon and synovium. A standard crush injury was applied to the flexor tendons of the middle digit of the hindpaw and the overlying muscle and synovium of female Wistar rats. Thirty animals received an intraperitoneal injection of either isotonic saline or N(G)‐nitro‐l‐arginine methyl ester (L‐NAME; 5 mg/kg) immediately following the crush injury, and five animals were then sacrificed at various intervals and the paws processed for histology. Another group of five animals was sacrificed after 3 days for nitrite determinations. The results showed that nitrite production and hence NO synthase activity is doubled at the acute phase of tendon wound healing, and we can prevent this by administering a single dose of L‐NAME immediately after injury. The incidence and severity of fibrocellular adhesions between tendon and synovium was much more marked in animals treated with L‐NAME. Treatment with L‐NAME elicited a chronic inflammatory response characterised by a persistent and extraordinarily severe accumulation of large numbers of inflammatory cells in the subcutaneous tissues, in muscle and in tendon. These findings indicate that in the case of injured tendon and synovium, NO could act to protect the healing tissue from an uncontrolled inflammatory response.
Granulocyte colony‐stimulating factor and leukemogenesis
Authors: de Figueiredo Lorena Lobo , e Lima Rodrigo Siqueira de Abreu , Rego Eduardo Magalhães
Published: August 2004

THE granulocyte colony‐stimulating factor (G‐CSF) plays an important role in normal granulopoiesis. Its functions are mediated by specific receptors on the surface of responsive cells and, upon ligand binding, several cytoplasmic tyrosine kinases are activated. The cytoplasmic region proximal to the membrane of the G‐CSF receptor (G‐CSF‐R) transduces proliferative and survival signals, whereas the distal carboxy‐terminal region transduces maturation signals and suppresses the receptor′s proliferative signals. Mutations in the G‐CSF‐R gene resulting in truncation of the carboxy‐terminal region have been detected in a subset of patients with severe congenital neutropenia who developed acute myelogenous leukemia (AML). In addition, the AML1‐ETO fusion protein, expressed in leukemic cells harboring the t(8;21), disrupt the physiological function of transcription factors such as C/EBPα and C/EBPε, which in turn deregulate G‐CSF‐R expression. The resulting high levels of G‐CSF‐R and G‐CSF‐dependent cell proliferation may be associated with pathogenesis of AML with t(8;21). Moreover, in vitro and in vivo studies demonstrated that G‐CSF may act as a co‐stimulus augmenting the response of PML‐RARα acute promyelocytic leukemia cells to all‐trans‐retinoic acid treatment. Finally, in the PLZF-RARα acute promyelocytic leukemia transgenic model, G‐CSF deficiency suppressed leukemia development. Altogether, these data suggest that the G‐CSF signaling pathway may play a role in leukemogenesis.
A stochastic model simulating the capture of pathogenic micro-organisms by superparamagnetic particles in an isodynamic magnetic field
Authors: O Rotariu  , N J C Strachan  , V Badescu
Published: August 2004

The method of immunomagnetic separation (IMS) has become an established technique to concentrate and separate animal cells, biologically active compounds and pathogenic micro-organisms from clinical, food and environmental matrices. One drawback of this technique is that the analysis is only possible for small sample volumes. We have developed a stochastic model that involves numerical simulations to optimize the process of concentration of pathogenic micro-organisms onto superparamagnetic carrier particles (SCPs) in a gradient magnetic field. Within the range of the system parameters varied in the simulations, optimal conditions favour larger particles with higher magnetite concentrations. The dependence on magnetic field intensity and gradient together with concentration of particles and micro-organisms was found to be less important for larger SCPs but these parameters can influence the values of the collision time for small particles. These results will be useful in aiding the design of apparatus for immunomagnetic separation from large volume samples.
Predicting GPCR–G-protein coupling using hidden Markov models
Authors: Sreekumar Kodangattil R. , Huang Youping , Pausch Mark H. , Gulukota Kamalakar
Published: August 2004

Motivation: Determining the coupling specificity of G-protein coupled receptors (GPCRs) is important for understanding the biology of this class of pharmacologically important proteins. Currently available in silico methods for predicting GPCR–G-protein coupling specificity have high error rate.

Method: We introduce a new approach for creating hidden Markov models (HMMs) based on a first guess about the importance of various residues. We call these knowledge restricted HMMs to emphasize the fact that the state space of the HMM is restricted by the application of a priori knowledge. Specifically, we use only those amino acid residues of GPCRs which are likely to interact with G-proteins, namely those that are predicted to be in the intra-cellular loops. Furthermore, we concatenate these predicted loops into one sequence rather than considering them as four disparate units. This reduces the HMM state space by drastically decreasing the sequence length.

Results: Our knowledge restricted HMM based method to predict GPCR–G-protein coupling specificity has an error rate of <1%, when applied to a test set of GPCRs with known G-protein coupling specificity.

Availability: Academic users can get the data set mentioned herein and HMMs from the authors.
Training HMM structure with genetic algorithm for biological sequence analysis
Authors: Won Kyoung-Jae , Prügel-Bennett Adam , Krogh Anders
Published: August 2004

Summary: Hidden Markov models (HMMs) are widely used for biological sequence analysis because of their ability to incorporate biological information in their structure. An automatic means of optimizing the structure of HMMs would be highly desirable. However, this raises two important issues; first, the new HMMs should be biologically interpretable, and second, we need to control the complexity of the HMM so that it has good generalization performance on unseen sequences. In this paper, we explore the possibility of using a genetic algorithm (GA) for optimizing the HMM structure. GAs are sufficiently flexible to allow incorporation of other techniques such as Baum–Welch training within their evolutionary cycle. Furthermore, operators that alter the structure of HMMs can be designed to favour interpretable and simple structures.

In this paper, a training strategy using GAs is proposed, and it is tested on finding HMM structures for the promoter and coding region of the bacterium Campylobacter jejuni. The proposed GA for hidden Markov models (GA-HMM) allows, HMMs with different numbers of states to evolve. To prevent over-fitting, a separate dataset is used for comparing the performance of the HMMs to that used for the Baum–Welch training. The GA-HMM was capable of finding an HMM comparable to a hand-coded HMM designed for the same task, which has been published previously.
Network structures and algorithms in Bioconductor
Authors: Carey Vincent J. , Gentry Jeff , Whalen Elizabeth , Gentleman Robert
Published: August 2004

Summary: In this paper, we review the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T Graphviz) and network algorithms (Boost) have been developed to support analysis of graphical structures in genomics and computational biology.

Availability: Packages graph, Rgraphviz, RBGL of Bioconductor (www.bioconductor.org).

Contact:  stvjc@channing.harvard.edu
PIML: the Pathogen Information Markup Language
Authors: He Yongqun , Vines Richard R. , Wattam Alice R. , Abramochkin Georgiy V. , Dickerman Allan W. , Eckart J. Dana , Sobral Bruno W. S.
Published: August 2004

Motivation: A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data.

Results: The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents.

Availability: All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/

Contact:  pathinfo@vbi.vt.edu
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
Authors: Chou Kuo-Chen
Published: August 2004

Motivation: With protein sequences entering into databanks at an explosive pace, the early determination of the family or subfamily class for a newly found enzyme molecule becomes important because this is directly related to the detailed information about which specific target it acts on, as well as to its catalytic process and biological function. Unfortunately, it is both time-consuming and costly to do so by experiments alone. In a previous study, the covariant-discriminant algorithm was introduced to identify the 16 subfamily classes of oxidoreductases. Although the results were quite encouraging, the entire prediction process was based on the amino acid composition alone without including any sequence-order information. Therefore, it is worthy of further investigation.

Results: To incorporate the sequence-order effects into the predictor, the ‘amphiphilic pseudo amino acid composition’ is introduced to represent the statistical sample of a protein. The novel representation contains 20 + 2λ discrete numbers: the first 20 numbers are the components of the conventional amino acid composition; the next 2λ numbers are a set of correlation factors that reflect different hydrophobicity and hydrophilicity distribution patterns along a protein chain. Based on such a concept and formulation scheme, a new predictor is developed. It is shown by the self-consistency test, jackknife test and independent dataset tests that the success rates obtained by the new predictor are all significantly higher than those by the previous predictors. The significant enhancement in success rates also implies that the distribution of hydrophobicity and hydrophilicity of the amino acid residues along a protein chain plays a very important role to its structure and function.

Contact:  kchou@san.rr.com
Construction of robust prognostic predictors by using projective adaptive resonance theory as a gene filtering method
Authors: Takahashi Hiro , Kobayashi Takeshi , Honda Hiroyuki
Published: August 2004

Motivation: For establishing prognostic predictors of various diseases using DNA microarray analysis technology, it is desired to find selectively significant genes for constructing the prognostic model and it is also necessary to eliminate non-specific genes or genes with error before constructing the model.

Results: We applied projective adaptive resonance theory (PART) to gene screening for DNA microarray data. Genes selected by PART were subjected to our FNN-SWEEP modeling method for the construction of a cancer class prediction model. The model performance was evaluated through comparison with a conventional screening signal-to-noise (S2N) method or nearest shrunken centroids (NSC) method. The FNN-SWEEP predictor with PART screening could discriminate classes of acute leukemia in blinded data with 97.1% accuracy and classes of lung cancer with 90.0% accuracy, while the predictor with S2N was only 85.3 and 70.0% or the predictor with NSC was 88.2 and 90.0%, respectively. The results have proven that PART was superior for gene screening.

Availability: The software is available upon request from the authors.

Contact:  honda@nubio.nagoya-u.ac.jp
Microarray data mining with visual programming
Authors: Curk Tomaz , Demsar Janez , Xu Qikai , Leban Gregor , Petrovic Uros , Bratko Ivan , Shaulsky Gad , Zupan Blaz
Published: August 2004

Summary: Visual programming offers an intuitive means of combining known analysis and visualization methods into powerful applications. The system presented here enables users who are not programmers to manage microarray and genomic data flow and to customize their analyses by combining common data analysis tools to fit their needs.

Availability:  http://www.ailab.si/supp/bi-visprog

Contact:  blaz.zupan@fri.uni-lj.si

Supplementary information:  http://www.ailab.si/supp/bi-visprog
Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan
Authors: Chern Lih-Ling , Stackebrandt Erko , Lee Shu-Fen , Lee Fwu-Ling , Chen Jeen-Kuan , Fu Huei-Mei
Published: August 2004

Five strains with strong chitinolytic activity were isolated from a soil sample collected from southern Taiwan. The strains shared more than 92 % DNA–DNA similarity, indicating membership of the same genospecies. This close relationship was supported by high similarities in fatty acid composition and biochemical characteristics. A 16S rRNA gene sequence analysis indicated that the isolates were members of the class ‘Betaproteobacteria’, in which they formed an individual subline of descent that was distantly related (<94 % similarity) to lineages defined by Formivibrio citricus DSM 6150T and Iodobacter fluviatilis DSM 3764T. On the basis of the phylogenetic and phenotypic distinctness of these novel chitin-degrading organisms, a new genus, Chitinibacter, is proposed, with Chitinibacter tainanensis (type strain, S1T=BCRC 17254T=DSM 15459T) as the type species.
‘Candidatus Phytoplasma spartii’, ‘Candidatus Phytoplasma rhamni’ and ‘Candidatus Phytoplasma allocasuarinae’, respectively associated with spartium witches'-broom, buckthorn witches'-broom and allocasuarina yellows diseases
Authors: Marcone C. , Gibb K. S. , Streten C. , Schneider B.
Published: August 2004

Spartium witches'-broom (SpaWB), buckthorn witches'-broom (BWB) and allocasuarina yellows (AlloY) are witches'-broom and yellows diseases of Spartium junceum (Spanish broom), Rhamnus catharticus (buckthorn) and Allocasuarina muelleriana (Slaty she-oak), respectively. These diseases are associated with distinct phytoplasmas. The SpaWB, BWB and AlloY phytoplasmas share <97·5 % 16S rDNA sequence similarity with each other and with other known phytoplasmas, including the closely related phytoplasmas of the apple proliferation group. Also, the SpaWB, BWB and AlloY phytoplasmas each have a different natural plant host. Based on their unique properties, it is proposed to designate the mentioned phytoplasmas as novel ‘Candidatus’ species under the names ‘Candidatus Phytoplasma spartii’, ‘Candidatus Phytoplasma rhamni’ and ‘Candidatus Phytoplasma allocasuarinae’, respectively.
Streptomyces drozdowiczii sp. nov., a novel cellulolytic streptomycete from soil in Brazil
Authors: Semêdo L. T. A. S. , Gomes R. C. , Linhares A. A. , Duarte G. F. , Nascimento R. P. , Rosado A. S. , Margis-Pinheiro M. , Margis R. , Silva K. R. A. , Alviano C. S. , Manfio G. P. , Soares R. M. A. , Linhares L. F. , Coelho R. R. R.
Published: August 2004

An actinomycete strain, isolated from a Mata Atlântica soil sample, showing cellulolytic activity was subjected to polyphasic taxonomic characterization to determine its identity. Strain M7aTpresented morphological and chemotaxonomic characteristics consistent with its assignment to the genusStreptomyces. Phylogenetic analysis of its 16S rDNA sequence revealed that the strain differed from described streptomycetes available in the public databases; the most closely related species wasStreptomyces laceyi, with 98·4 % nucleotide similarity. It also differed from other cellulolytic strains in its phenotypic characteristics. It is therefore proposed that strain M7aT, a cellulolytic strain with biotechnological potential, represents a novel species, namedStreptomyces drozdowicziisp. nov. The type strain is M7aT(=CBMAI 0498T=CIP 107837T=NRRL B-24297T).
Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites
Authors: Wagner-Döbler Irene , Rheims Holger , Felske Andreas , El-Ghezal Aymen , Flade-Schröder Dirk , Laatsch Hartmut , Lang Siegmund , Pukall Rüdiger , Tindall Brian J.
Published: August 2004

A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97·4 % sequence similarity to Sulfitobacter mediterraneus and 96·5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1–7 % sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25–30 °C. The DNA base composition (G+C content) is 60·1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1ω7c, 18 : 0, 16 : 1ω7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7 %) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1ω7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T).
Anoxybacillus voinovskiensis sp. nov., a moderately thermophilic bacterium from a hot spring in Kamchatka
Authors: Yumoto Isao , Hirota Kikue , Kawahara Tomoo , Nodasaka Yoshinobu , Okuyama Hidetoshi , Matsuyama Hidetoshi , Yokota Yuji , Nakajima Kenji , Hoshino Tamotsu
Published: August 2004

A novel moderately thermophilic bacterium, strain TH13T, was isolated from a hot spring in Kamchatka. It was found to be a Gram-positive, facultative aerobe; the straight, non-motile rods grew at 30–64 °C (optimum 54 °C). The isolate was positive for catalase and oxidase tests and reduced nitrate to nitrite, but was negative for H2S production and growth in more than 3 % NaCl (w/v). The isolate grew at pH 7–8, but not at pH values higher than 9. The DNA G+C content was 43·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain TH13Twas a member of the genusAnoxybacillus. DNA–DNA hybridization revealed a low relatedness (less than 30·2 %) between the isolate and its close phylogenetic neighboursAnoxybacillus pushchinoensisandAnoxybacillus flavithermus. On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA hybridization data, it was concluded that the isolate merited classification as a novel species, for which the nameAnoxybacillus voinovskiensissp. nov. is proposed. The type strain of this species is TH13T(=NCIMB 13956T=JCM 12111T).
Taxonomic characterization of nine strains isolated from clinical and environmental specimens, and proposal of Corynebacterium tuberculostearicum sp. nov.
Authors: Feurer Carole , Clermont Dominique , Bimet François , Candréa Adina , Jackson Mary , Glaser Philippe , Bizet Chantal , Dauga Catherine
Published: August 2004

Nine unidentified Gram-positive, lipophilic corynebacteria were isolated from clinical and food samples and subjected to a polyphasic taxonomic analysis. The bacteria were distinguished fromCorynebacteriumspecies with validly published names by biochemical tests, fatty acid content and whole-cell protein analysis. Comparative 16S rRNA gene sequence analysis demonstrated unambiguously that the nine strains were related phylogenetically to the species ‘Corynebacterium tuberculostearicum’ and represented a distinct subline within the genusCorynebacterium. On the basis of both phenotypic and phylogenetic evidence, the formal description ofCorynebacterium tuberculostearicumsp. nov. is proposed. The type strain ofC. tuberculostearicumis Medalle XT(=LDC-20T=CIP 107291T=CCUG 45418T=ATCC 35529T).
Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids
Authors: Abraham Wolf-Rainer , Strömpl Carsten , Vancanneyt Marc , Bennasar Antonio , Swings Jean , Lünsdorf Heinrich , Smit John , Moore Edward R. B.
Published: August 2004

Two cauliform bacteria (CM243Tand CM251) isolated by J. Poindexter from the Atlantic Ocean were characterized by 16S rRNA gene sequencing,TaqI restriction fragment length polymorphism and single-strand conformation polymorphism analyses of the internally transcribed 16S–23S rDNA spacer (ITS1) region, analysis of fatty acids from cellular lipids, mass spectrometry of polar lipids and physiological properties. The two strains showed very low diversity of polar lipids with diacyl-sulfoquinovosyl glycerols as the predominant lipids. The two bacterial strains were observed to have nearly identical 16S rRNA gene sequences and could not be differentiated by their ITS1 regions. The isolates differed from species of the genusMaricaulisby their 16S rRNA gene sequences, polar lipids and fatty acid patterns. On the basis of the genotypic analyses and estimations of phylogenetic similarities, physiological and chemotaxonomic characteristics, it is proposed that the isolates represent a new genus and species, for which the nameWoodsholea maritimagen. nov., sp. nov. (type strain CM243T=VKM B-1512T=LMG 21817T) is proposed.
Thiocapsa marina sp. nov., a novel, okenone-containing, purple sulfur bacterium isolated from brackish coastal and marine environments
Authors: Caumette Pierre , Guyoneaud Remy , Imhoff Johannes F. , Süling Jörg , Gorlenko Vladimir
Published: August 2004

Four marine, phototrophic, purple sulfur bacteria (strains 5811T, 5812, BM-3 and BS-1) were isolated in pure culture from different brackish to marine sediments in the Mediterranean Sea, the White Sea and the Black Sea. Single cells of these strains were coccus-shaped, non-motile and did not contain gas vesicles. The colour of cell suspensions that were grown in the light was purple–red. Bacteriochlorophyll a and carotenoids of the okenone series were present as photosynthetic pigments. Photosynthetic membrane systems were of the vesicular type. Hydrogen sulfide, thiosulfate, elemental sulfur and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions; carbon dioxide was utilized as the carbon source. During growth on sulfide, elemental sulfur globules were stored inside the cells. In the presence of hydrogen sulfide, several organic substances could be photoassimilated. Comparative 16S rDNA sequence analysis revealed an affiliation of these four strains to the genus Thiocapsa. Both phylogenetic analysis and the results of DNA–DNA hybridization studies revealed that these strains formed a separate cluster within the genus Thiocapsa. Thus, according to phenotypic characteristics and mainly the carotenoid composition, 16S rDNA sequence analysis and DNA–DNA hybridization data, it is proposed that these strains should be classified as a novel species, Thiocapsa marina sp. nov., with strain 5811T (=DSM 5653T=ATCC 43172T) as the type strain.
Salegentibacter holothuriorum sp. nov., isolated from the edible holothurian Apostichopus japonicus
Authors: Nedashkovskaya Olga I. , Suzuki Makoto , Vancanneyt Marc , Cleenwerck Ilse , Zhukova Natalia V. , Vysotskii Mikhail V. , Mikhailov Valery V. , Swings Jean
Published: August 2004

Strain KMM 3524Twas isolated from the holothurianApostichopus japonicusliving in the Sea of Japan. The bacterial strain was pigmented, non-motile, Gram-negative, strictly aerobic and oxidase-, catalase- andβ-galactosidase-positive. From the results of 16S rDNA sequence analysis, strain KMM 3524Twas found to be related closely toSalegentibacter salegens(98·1 %). DNA–DNA homology between strains KMM 3524TandS. salegensDSM 5424Twas 38 %; this showed clearly that the holothurian isolate KMM 3524Tbelongs to a novel species of the genusSalegentibacterfor which the nameSalegentibacter holothuriorumsp. nov. is proposed, with KMM 3524T(=NBRC 100249T=LMG 21968T) as the type strain.
Shewanella affinis sp. nov., isolated from marine invertebrates
Authors: Ivanova Elena P. , Nedashkovskaya Olga I. , Sawabe Tomoo , Zhukova Natalia V. , Frolova Galina M. , Nicolau Dan V. , Mikhailov Valery V. , Bowman John P.
Published: August 2004

Four marine bacterial strains, designated KMM 3587T, KMM 3586, KMM 3821 and KMM 3822, were isolated from the sipunculaPhascolosoma japonicum, a common inhabitant of Troitza Bay in the Gulf of Peter the Great (Sea of Japan region), and from an unidentified hydrocoral species collected in Makarov Bay (Iturup Islands), Kuril Islands, North-West Pacific Ocean. The strains were characterized to clarify their taxonomic position. 16S rRNA gene sequences of KMM 3587Tand KMM 3586 indicated 99 % similarity toShewanella colwelliana. Despite such a high level of 16S rRNA gene sequence similarity, DNA–DNA hybridization experiments demonstrated only 45–52 % binding with DNA ofS. colwellianaATCC 39565T. The DNA G+C contents of the novel strains were 45 mol% and the shared level of DNA hybridization was conspecific (81–97 %), indicating that they represent a single genospecies. The novel strains were mesophilic (able to grow at 10–34 °C), neutrophilic and haemolytic, and able to degrade gelatin, casein and Tween 20, 40 and 80, but not starch, agar, elastin, alginate or chitin. The major fatty acids were i13 : 0, i15 : 0, 16 : 0, 16 : 1ω7 and 17 : 1ω8 (68·9 % of total). The major isoprenoid quinones were Q7 (47–62 %) and Q8 (26–47 %). Eicosapentaenoic acid was produced in minor amounts. Based on these data, the strains are assigned to a novel species,Shewanella affinissp. nov. (type strain KMM 3587T=CIP 107703T=ATCC BAA-642T).
Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water
Authors: Ivanova Elena P. , Gorshkova Nataliya M. , Bowman John P. , Lysenko Anatoli M. , Zhukova Natalia V. , Sergeev Alexander F. , Mikhailov Valery V. , Nicolau Dan V.
Published: August 2004

Six marine bacterial strains, KMM 3597T, KMM 3775, KMM 3590, KMM 3772, KMM 3605 and KMM 3601, that produce polyunsaturated fatty acids were isolated from sea water samples collected from different locations and depths in Chazhma Bay (Sea of Japan, Pacific Ocean) and characterized to clarify their taxonomic position. The DNA G+C contents of these strains were 39·5–40·3 mol%. The level of DNA hybridization between these strains was conspecific (83–96 %), indicating that they represent a single genospecies. 16S rRNA gene sequence-based phylogenetic analysis of the novel strains revealed thatShewanella japonicaKMM 3299Twas the closest relative (99 % similarity). However, DNA–DNA hybridization experiments demonstrated only 45–50 % binding with DNA ofS. japonica. The novel organisms grew between 4 and 33 °C, were neutrophilic and haemolytic, and were able to degrade starch, gelatin, agar and Tween 80. The predominant fatty acids were (%±sd): i13 : 0 (9·3±1·1); i15 : 0 (33·9±1·5); 16 : 0 (8·9±1·6); and 16 : 1ω7 (14·8±1·1). The fatty acid 20 : 5ω3, formed at 28 °C, was present at up to 5·3 % total fatty acids. The major isoprenoid quinones were Q7 (21–41 %) and Q8 (50–59 %). The phylogenetic, genetic and physiological properties of the six strains placed them within a novel species,Shewanella pacificasp. nov., the type strain of which is R10SW1T(=KMM 3597T=CIP 107849T).
Comparative analysis of ribonuclease P RNA of the planctomycetes
Authors: Butler Margaret K. , Fuerst John A.
Published: August 2004

The planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses.
Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the γ-Proteobacteria active in alkane and aromatic hydrocarbon degradation
Authors: Palleroni Norberto J. , Port Ava M. , Chang Hung-Kuang , Zylstra Gerben J.
Published: August 2004

Novel alkane-degrading strains of bacteria were isolated from soil contaminated with fuel oil from a leaking underground tank in New Jersey, USA. Two phenotypically similar strains (designated AP102 and AP103T) possessed 16S rRNA sequences unique among the majority of known hydrocarbon-degrading bacteria. The 16S rRNA sequences showed a moderate but distant relationship to the genus Nevskia and a substantial similarity to strains that had previously been isolated for growth on phenol (in Japan) and on toluene (in Canada) by other researchers. The hydrocarbon-degrading strains from Japan, Canada and New Jersey showed no resemblance to the typical morphology of Nevskia but did share a striking similarity among themselves in cell morphology, in the unusual appearance of colonies on various solid media and in various physiological properties. A full taxonomic analysis was performed, including DNA–DNA hybridization and nutritional screening with 117 organic compounds as sole sources of carbon and energy. The strains are active in the degradation of important environmental pollutants, and their phenotypic, physiological, metabolic and genomic properties suggest that they are members of a novel taxon in the γ-Proteobacteria, for which the name Hydrocarboniphaga gen. nov. is proposed, with the single species Hydrocarboniphaga effusa sp. nov. The type strain is AP103T (=ATCC BAA-332T=DSM 16095T).
Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China
Authors: Fan Huapeng , Xue Yanfen , Ma Yanhe , Ventosa Antonio , Grant William D.
Published: August 2004

A novel haloalkaliphilic archaeon, strain 8W8T, was isolated from Lake Zabuye, on the Tibetan Plateau, China. On the basis of 16S rRNA gene sequence analysis, strain 8W8T was shown to belong to the genus Halorubrum and was related to Halorubrum vacuolatum (96·7 % sequence similarity), Halorubrum saccharovorum (96·0 %), Halorubrum lacusprofundi (95·4 %) and Halorubrum sodomense (95·3 %). The phylogenetic distance from any species within the other genera of Halobacteriales was lower than 90 %. The major polar lipids of strain 8W8T were C20C20 and C20C25 derivatives of phosphatidylglycerol phosphate and phosphatidylglycerol phosphate methyl ester. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 8W8T from the eight Halorubrum species with validly published names. Therefore, strain 8W8T represents a novel species, for which the name Halorubrum tibetense sp. nov. is proposed, with the type strain 8W8T (=AS 1.3239T=JCM 11889T).
Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India
Authors: Suresh K. , Prabagaran S. R. , Sengupta S. , Shivaji S.
Published: August 2004

Strain Sd/3T(=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23° 3′ N 88° 35′ E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genusBacillus, such as it had A4βmurein type (l-orn-d-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3Twas identified as a species of the genusBacillus. It exhibited maximum similarity (95 %) at the 16S rRNA gene level withBacillus cohnii; however, DNA–DNA similarity withB. cohniiwas 60·7 %. Strain Sd/3Talso exhibited a number of phenotypic differences fromB. cohnii(DSM 6307T). These data suggest that Sd/3Trepresents a novel species of the genusBacillus. The nameBacillus indicussp. nov. is proposed.
Candida asparagi sp. nov., Candida diospyri sp. nov. and Candida qinlingensis sp. nov., novel anamorphic, ascomycetous yeast species
Authors: Lu Hui-Zhong , Jia Jian-Hua , Wang Qi-Ming , Bai Feng-Yan
Published: August 2004

Among ascomycetous yeasts that were isolated from several nature reserve areas in China, three anamorphic strains isolated from soil (QL 5-5T) and fruit (QL 21-2T and SN 15-1T) were revealed, by conventional characterization and molecular phylogenetic analysis based on internal transcribed spacer and large subunit (26S) rRNA gene D1/D2 region sequencing, to represent three novel species in the genus Candida. Candida qinlingensis sp. nov. (type strain, QL 5-5T=AS 2.2524T=CBS 9768T) was related closely to a teleomorphic species, Williopsis pratensis. The close relatives of Candida diospyri sp. nov. (type strain, QL 21-2T=AS 2.2525T=CBS 9769T) are Candida friedrichii and Candida membranifaciens. Candida asparagi sp. nov. (type strain, SN 15-1T=AS 2.2526T=CBS 9770T) forms a clade with Candida fructus.
Lactobacillus saerimneri sp. nov., isolated from pig faeces
Authors: Pedersen Carsten , Roos Stefan
Published: August 2004

In studying the composition of the Lactobacillus flora of faeces from pigs fed different diets, isolates with notable differences in their 16S rRNA gene sequence compared to recognized species were found. Phenotypic characteristics together with 16S rRNA gene sequences revealed that the isolates represented a novel species belonging to the Lactobacillus mali subgroup of lactobacilli. The name Lactobacillus saerimneri sp. nov. is proposed (type strain GDA154T=LMG 22087T=DSM 16049T=CCUG 48462T).
Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov.
Authors: Stackebrandt Erko , Schumann Peter
Published: August 2004

The recently described facultatively anaerobicPromicromonospora pachnodaeis phylogenetically only moderately related to authentic members ofPromicromonospora.P. pachnodae is closely related toXylanibacterium ulmiand slightly less closely related toXylanimonas cellulosilyticaandIsoptericola variabilis(basonymCellulosimicrobium variabile). Members of the different genera ofPromicromonosporaceaehave similar chemotaxonomic properties; they share the same peptidoglycan type (A4α) and have similar profiles of polar lipids, menaquinones, fatty acids and whole cell sugars. However, they differ from each other in the detailed amino acid composition of peptidoglycan, a taxonomically significant character that has previously been used in the delineation of actinobacterial genera. RecognizedPromicromonosporaspecies andXylanibacterium ulmiexhibit thel-lys–l-ala–d-Glu type,Xylanimonas cellulosilyticaandI. variabilisshow thel-lys–d-Asp type, whereasP. pachnodaehas thel-lys–l-ser–d-Glu type. This property, together with the distinct phylogenetic position ofPromicromonospora pachnodae, suggests a novel genus for the xylanolytic organismXylanimicrobium pachnodae(Cazemieret al. 2004) gen. nov., comb. nov.
Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Yeo Soo-Hwan , Oh Tae-Kwang , Park Yong-Ha
Published: August 2004

A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1
ω7c and/or iso-C15 : 0 2-OH and C18 : 1
ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).
Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms
Authors: Scheldeman Patsy , Rodríguez-Díaz Marina , Goris Johan , Pil Annelies , De Clerck Elke , Herman Lieve , De Vos Paul , Logan Niall A. , Heyndrickx Marc
Published: August 2004

Forty-eight bacterial strains were isolated at dairy farms from raw milk, the milking apparatus, green fodder or feed concentrate after a heat treatment of 30 min at 100 °C. In this way, spore-forming bacteria with a very high intrinsic heat resistance were selected for. The aerobic spore-forming isolates were subjected to a polyphasic taxonomical study, including repetitive element sequence-based PCR typing, whole-cell protein profiling, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base composition, fatty acid analysis, and morphological and biochemical characteristics. A comparison of the REP- and (GTG)5-PCR and whole-cell protein SDS-PAGE profiles resulted in three clusters of similar strains. Analysis of the 16S rDNA sequences and DNA–DNA relatedness data showed that these clusters represented three novel species. The highest 16S rDNA similarity to a recognized species found for the three groups was around 94 % withBacillus lentusandBacillus sporothermodurans. Further phenotypic characterization supported the proposal of three novel species in the genusBacillus,Bacillus farraginis,Bacillus fortisandBacillus fordii. The respective type strains are R-6540T(=LMG 22081T=DSM 16013T), R-6514T(=LMG 22079T=DSM 16012T) and R-7190T(=LMG 22080T=DSM 16014T); their G+C DNA base contents are 43·7, 44·3 and 41·9 mol%, respectively. Although in variable amounts, a predominance of the branched fatty acids iso-C15 : 0and anteiso-C15 : 0was observed in all three novel species.
Haplotype Analysis in Multiple Crosses to Identify a QTL Gene
Authors: Wang Xiaosong , Korstanje Ron , Higgins David , Paigen Beverly
Published: August 2004

Identifying quantitative trait locus (QTL) genes is a challenging task. Herein, we report using a two-step process to identify Apoa2 as the gene underlying Hdlq5, a QTL for plasma high-density lipoprotein cholesterol (HDL) levels on mouse chromosome 1. First, we performed a sequence analysis of the Apoa2 coding region in 46 genetically diverse mouse strains and found five different APOA2 protein variants, which we named APOA2a to APOA2e. Second, we conducted a haplotype analysis of the strains in 21 crosses that have so far detected HDL QTLs; we found that Hdlq5 was detected only in the nine crosses where one parent had the APOA2b protein variant characterized by an Ala61-to-Val61 substitution. We then found that strains with the APOA2b variant had significantly higher (P ≤ 0.002) plasma HDL levels than those with either the APOA2a or the APOA2c variant. These findings support Apoa2 as the underlying Hdlq5 gene and suggest the Apoa2 polymorphisms responsible for the Hdlq5 phenotype. Therefore, haplotype analysis in multiple crosses can be used to support a candidate QTL gene.
Insertion of Telomeric Repeats at Intrachromosomal Break Sites During Primate Evolution
Authors: Nergadze Solomon G. , Rocchi Mariano , Azzalin Claus M. , Mondello Chiara , Giulotto Elena
Published: August 2004

Short blocks of telomeric-like DNA (Interstitial Telomeric Sequences, ITSs) are found far from chromosome ends. We addressed the question as to how such sequences arise by comparing the loci of 10 human ITSs with their genomic orthologs in 12 primate species. The ITSs did not derive from expansion of pre-existing TTAGGG units, as described for other microsatellites, but appeared suddenly during evolution. Nine insertion events were dated along the primate evolutionary tree, the dates ranging between 40 and 6 million years ago. Sequence comparisons suggest that in each case the block of (TTAGGG)n DNA arose as a result of double-strand break repair. In fact, ancestral sequences were either interrupted precisely by the tract of telomeric-like repeats or showed the typical modifications observed at double-strand break repair sites such as short deletions, addition of random sequences, or duplications. Similar conclusions were drawn from the analysis of a chimpanzee-specific ITS. We propose that telomeric sequences were inserted by the capture of a telomeric DNA fragment at the break site or by the telomerase enzyme. Our conclusions indicate that human ITSs are relics of ancient breakage rather than fragile sites themselves, as previously suggested.