bluuebunny/crossref_metadata_2025 huggingface dataset:
Complexation and release isotherm of arsenic in arsenic-humic/fulvic equilibrium study
Authors: Mukhopadhyay D. , Sanyal S. K.
Published: November 2004

Soil organic fractions were extracted from 2 surface soils of West Bengal, one of which was arsenic-contaminated, and were fractionated into fulvic and humic acid fractions following standard procedures. These, and one humic acid sample synthesised in the laboratory, were characterised by pH-potentiometric titrations, viscometric measurements, visible spectrophotometry, and surface tension determinations. The results have been correlated with coiling–decoiling behaviour, as well as aliphatic/aromatic balance of these acids. The stability constant (logK) of the complexes formed by these natural humic/fulvic and synthetic humic acids with arsenic in aqueous phase was evaluated by the ion-exchange method. These logK values tend to suggest that the organo-arsenic complexes were quite stable. Further, the logK values displayed an approximately inverse relationship with the viscosity-average molecular weight, excess time needed to attain a stable higher pH during the pH-potentiometric titration, and also the surface excess (in water) of the given humic/fulvic acid samples. These trends were explained in terms of the relative hydrophobic character of the acids, and their resultant tendencies to complex arsenic in the aqueous phase.
The release potential of arsenic from the arsenic–humic/fulvic complexes by soluble phophate and nitrate salts was also examined in terms of the appropriate exchange isotherms. In general, phosphate demonstrated a greater degree of exchangeability with arsenic than did nitrate, at both the lower and higher concentrations.
Biological and chemical assays to estimate nitrogen supplying power of soils with contrasting management histories
Authors: Curtin D. , McCallum F. M.
Published: November 2004

Nitrogen (N) mineralised from soil organic matter can be an important source of N for crop uptake, particularly following cultivation of pastures. Difficulty in predicting the contribution of mineralisation continues to be a serious obstacle to implementating best management practices for fertiliser N. We evaluated biological tests (i.e. net N mineralised in a 28-day aerobic incubation and anaerobically mineralisable N, AMN) and chemical tests (ammonium-N hydrolysis in hot 2 m KCl) as predictors of N supply to a glasshouse-grown oat (Avena sativa L.) crop. The oat plants were grown to maturity without added N on 30 soils representing a range of management histories, including soils collected from long-term pastures and intensive arable cropping sites. The majority (average 83%) of the N accumulated in grain and straw was mineralised N. Plant N derived from mineralisation (PNDM), estimated by subtracting soil mineral N at sowing from N uptake, was generally higher for long-term pasture soils (mean 82 mg/kg, n = 9) than for long-term arable soils (mean 48 mg/kg, n = 9). The 2 measures of N mineralisation were not closely related [R2 = 0.11 (0.37*** when one outlying observation was omitted)], indicating that aerobic and anaerobic assays can give quite different N fertility rankings. Aerobically mineralisable N was the best predictor of PNDM (R2 = 0.79***). The ratio of CO2-C evolved to net N mineralised in the aerobic incubation was highly variable (e.g. mean of 13.6 for pasture soils v. 7.5 for long-term arable soils), likely due to differences in N immobilisation. The correlations of AMN (R2 = 0.32**) and hot KCl N (R2 = 0.24**) with PNDM were not much better than that between total soil N and PNDM (R2 = 0.16*), suggesting that these tests would not provide reliable estimates of N mineralisation potential in soils with diverse management histories.
Damage to soil physical properties caused by soil sampler devices as assessed by gamma ray computed tomography
Authors: Pires Luiz F. , Bacchi Osny O. S. , Reichardt Klaus
Published: November 2004

Soil sample physical properties can be greatly affected during soil sampling procedures. Improper procedures can impose modifications on soil sample structure and consequently lead to wrong measurements of soil properties. The objective of this work was to evaluate the damage caused by soil samplers to soil structure through the analysis of computed tomography (CT) images. A first generation tomograph was used, having a 241Am source and a 7.62 × 7.62 cm NaI(Tl) scintillation crystal detector coupled to a photomultiplier tube. Results confirm the effect of soil sampler devices on the structure of soil samples, and that the compaction caused during sampling causes significant alterations to soil bulk density. Through the use of CT it was possible to determine the level of compaction and to make a detailed analysis of the soil bulk density distribution within the soil sample.
Participatory soil quality assessment: The case of smallholder farmers in Ethiopian highlands
Authors: Erkossa Teklu , Stahr Karl , Gaiser Thomas
Published: November 2004

The study was conducted at Caffee Doonsa (08°88′N, 39°08′E; 2400 m asl), a small watershed in the central highlands of Ethiopia, in order to identify farmers’ goals of soil management and the indicators they use in selecting soils for a certain function, and to categorise the soils in different quality groups with respect to the major functions. Thirty-six male farmers of different age and wealth groups participated in a Participatory Rural Appraisal technique. They listed and prioritised 12 soil functions in the area and itemised the soil quality indicators (characteristics). Based on the indicators, the soils in the watershed were classified into 3 soil quality (SQ) groups (Abolse, Kooticha, and Carii). The SQ groups have been evaluated and ranked for the major soil functions. For crop production, Abolse was graded best, followed by Kooticha and Carii, respectively. The grain and straw yield data of wheat (Triticum aestivum L.) taken from the SQ groups confirmed the farmers claim, in that Abolse gave the highest grain yield (4573 kg/ha), followed by 4411 and 3657 kg/ha for Kooticha and Carii, respectively. Local insights should be included in systematic soil quality assessment, and in planning and implementation of various soil management interventions.
Delivery of nutrition services in health systems in sub-Saharan Africa: opportunities in Burkina Faso, Mozambique and Niger
Authors: Hampshire Rachel D , Aguayo Victor M , Harouna Hamani , Roley Julie A , Tarini Ann , Baker Shawn K
Published: November 2004

Background:

In sub-Saharan Africa, underweight and micronutrient deficiencies account for an estimated 25% of the burden of disease. As the coverage of national health systems expands, increased opportunities exist to address the needs of children and women, the most vulnerable to these deficiencies, through high-quality nutrition services.

Objectives:

To assess health providers' knowledge and practice with regard to essential nutrition services for women and children in Burkina Faso, Mozambique and Niger, in order to assist the development of a standard guide and tools to assess and monitor the quality of the nutrition services delivered through national health systems.

Findings:

The three surveys reveal the extent of missed opportunities to deliver nutrition services during routine prenatal, postnatal and child-care consultations for the prevention and treatment of highly prevalent nutritional deficiencies.

Conclusion:

A commitment to improving the quality of facility-based nutrition services is necessary to impact on the health outcomes of women and children ‘covered’ by national health systems. Rigorous assessment and monitoring of the quality of nutrition services should inform health programme and policy development. Building on the lessons learned in these three assessments, Helen Keller International has developed a standard Guide and Tools to assess the quality of the nutrition services delivered through national health systems. These tools can be adapted to assess ongoing nutrition services in health facilities, provide a framework for nutrition programming, inform the development of pre-service as well as in-service nutrition training curricula for providers, and evaluate the impact of nutrition training on providers' practices.
Food store access and household fruit and vegetable use among participants in the US Food Stamp Program
Authors: Rose Donald , Richards Rickelle
Published: November 2004

Objective:

Recent research on access to food among low-income populations in industrialised countries has begun to focus on neighbourhood food availability as a key determinant of dietary behaviour. This study examined the relationship between various measures of food store access and household fruit and vegetable use among participants in the Food Stamp Program, America's largest domestic food assistance programme.

Design:

A secondary data analysis was conducted using the 1996–97 National Food Stamp Program Survey. The survey employed a 1-week food inventory method, including two at-home interviews, to determine household food use. Separate linear regression models were developed to analyse fruit and vegetable use. Independent variables included distance to store, travel time to store, ownership of a car and difficulty of supermarket access. All models controlled for a full set of socio-economic variables.

Subjects:

A nationally representative sample of participants (n = 963) in the Food Stamp Program.

Results:

After controlling for confounding variables, easy access to supermarket shopping was associated with increased household use of fruits (84 grams per adult equivalent per day; 95% confidence interval 5, 162). Distance from home to food store was inversely associated with fruit use by households. Similar patterns were seen with vegetable use, though associations were not significant.

Conclusions:

Environmental factors are importantly related to dietary choice in a nationally representative sample of low-income households, reinforcing the importance of including such factors in interventions that seek to effect dietary improvements.
Diffusion property following functional hemispherectomy in hemimegalencephaly
Authors: Mori H. , Aoki S. , Abe O. , Hayashi N. , Masutani Y. , Ohtomo K. , Oya S. , Morita A.
Published: November 2004

Diffusion-tensor imaging (DTI), a unique magnetic resonance technique for analysis of diffusion-anisotropy of the brain, can identify subtle white matter changes in vivo. To investigate changes of truncated neurofibers, DTI was conducted prior to and following functional hemispherectomy in a female infant for refractory epilepsy associated with hemimegalencephaly. Anisotropy of the amputated pyramidal tract decreased relative to the unaffected side after surgery, which reflects secondary degeneration in neurofibers. In DTI applied to infants, differentiation between developmental changes and changes associated with the current phenomenon must be evaluated cautiously. Standardization of diffusion-tensor analysis of developmental change is desirable.
Magnetic resonance evaluation of the presence of an extensive intraductal component in breast cancer
Authors: Ikeda O. , Nishimura R. , Miyayama H. , Yasunaga T. , Ozaki Y. , Tsuji A. , Yamashita Y.
Published: November 2004

Purpose: To determine whether the presence of extensive intraductal components (EIC) in breast carcinomas can be accurately evaluated on magnetic resonance (MR) images.

Material and Methods: Ninety-three women with breast cancer, aged between 32 and 79 years (mean 54 years), underwent three-dimensional dynamic MR imaging (dyMRI) with fat suppression and magnetization transfer contrast before breast-conserving surgery. The tumors were classified on dyMRI as circumscribed, microlobulated, and/or speculated, and their size was measured. Spotty or linear continuous enhancement (SLE) from the main tumor to the nipple and segmental enhancement surrounding the main tumor (SE) were considered indicative of intraductal tumor spread. The correlation between preoperative MRI and macroscopic and microscopic findings was examined.

Results: On MR images, the tumor sizes ranged from 0.8 to 3.4 cm. These measurements coincided with histologic measurements in circumscribed tumors. However, in tumors with microlobulated or spiculated borders, tumor size tended to be underestimated on MR images. Of 93 patients, 59 (63.4%) had histologically confirmed EIC; 42 of the 59 cancers (71.2%) manifested SLE or SE on MR images. The sensitivity, specificity, and accuracy of MR imaging in detecting EIC were 71%, 85%, and 76%, respectively.

Conclusion: MR imaging facilitates the detection of EIC in breast masses. This information is valuable for the planning of breast-conserving surgery.
Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response
Authors: Jones Nicola A. , Wei Xiping , Flower Darren R. , Wong MaiLee , Michor Franziska , Saag Michael S. , Hahn Beatrice H. , Nowak Martin A. , Shaw George M. , Borrow Persephone
Published: November 2004

CD8+ cytotoxic T lymphocytes (CTLs) play an important role in containment of virus replication in primary human immunodeficiency virus (HIV) infection. HIV's ability to mutate to escape from CTL pressure is increasingly recognized; but comprehensive studies of escape from the CD8 T cell response in primary HIV infection are currently lacking. Here, we have fully characterized the primary CTL response to autologous virus Env, Gag, and Tat proteins in three patients, and investigated the extent, kinetics, and mechanisms of viral escape from epitope-specific components of the response. In all three individuals, we observed variation beginning within weeks of infection at epitope-containing sites in the viral quasispecies, which conferred escape by mechanisms including altered peptide presentation/recognition and altered antigen processing. The number of epitope-containing regions exhibiting evidence of early CTL escape ranged from 1 out of 21 in a subject who controlled viral replication effectively to 5 out of 7 in a subject who did not. Evaluation of the extent and kinetics of HIV-1 escape from >40 different epitope-specific CD8 T cell responses enabled analysis of factors determining escape and suggested that escape is restricted by costs to intrinsic viral fitness and by broad, codominant distribution of CTL-mediated pressure on viral replication.
Absence of Caspase 8 and High Expression of PED Protect Primitive Neural Cells from Cell Death
Authors: Ricci-Vitiani Lucia , Pedini Francesca , Mollinari Cristiana , Condorelli Gerolama , Bonci Désirée , Bez Alessandra , Colombo Augusto , Parati Eugenio , Peschle Cesare , De Maria Ruggero
Published: November 2004

The mechanisms that control neural stem and progenitor cell survival are unknown. In several pathological conditions, death receptor (DR) ligands and inflammatory cytokines exert a deleterious effect on neurons, whereas primitive neural cells migrate and survive in the site of lesion. Here, we show that even in the presence of inflammatory cytokines, DRs are unable to generate death signals in primitive neural cells. Neural stem and progenitor cells did not express caspase 8, the presence of which is required for initiating the caspase cascade. However, exogenous or cytokine-mediated expression of caspase 8 was not sufficient to restore their DR sensitivity. Searching for molecules potentially able to block DR death-inducing signaling complex (DISC), we found that primitive neural cells expressed high levels of the death effector domain-containing protein PED (also known as PEA-15). PED localized in the DISC and prevented caspase 8 recruitment and activation. Moreover, lentiviral-mediated delivery of PED antisense DNA resulted in dramatic down-regulation of the endogenous gene expression and sensitization of primitive neural cells to apoptosis mediated by inflammatory cytokines and DRs. Thus, absence of caspase 8 and high expression of PED constitute two levels of protection from apoptosis induced by DRs and inflammatory cytokines in neural stem and progenitor cells.
DC-SIGN–mediated Infectious Synapse Formation Enhances X4 HIV-1 Transmission from Dendritic Cells to T Cells
Authors: Arrighi Jean-François , Pion Marjorie , Garcia Eduardo , Escola Jean-Michel , van Kooyk Yvette , Geijtenbeek Teunis B. , Piguet Vincent
Published: November 2004

Dendritic cells (DCs) are essential for the early events of human immunodeficiency virus (HIV) infection. Model systems of HIV sexual transmission have shown that DCs expressing the DC-specific C-type lectin DC-SIGN capture and internalize HIV at mucosal surfaces and efficiently transfer HIV to CD4+ T cells in lymph nodes, where viral replication occurs. Upon DC–T cell clustering, internalized HIV accumulates on the DC side at the contact zone (infectious synapse), between DCs and T cells, whereas HIV receptors and coreceptors are enriched on the T cell side. Viral concentration at the infectious synapse may explain, at least in part, why DC transmission of HIV to T cells is so efficient.

Here, we have investigated the role of DC-SIGN on primary DCs in X4 HIV-1 capture and transmission using small interfering RNA–expressing lentiviral vectors to specifically knockdown DC-SIGN. We demonstrate that DC-SIGN− DCs internalize X4 HIV-1 as well as DC-SIGN+ DCs, although binding of virions is reduced. Strikingly, DC-SIGN knockdown in DCs selectively impairs infectious synapse formation between DCs and resting CD4+ T cells, but does not prevent the formation of DC–T cells conjugates.

Our results demonstrate that DC-SIGN is required downstream from viral capture for the formation of the infectious synapse between DCs and T cells. These findings provide a novel explanation for the role of DC-SIGN in the transfer and enhancement of HIV infection from DCs to T cells, a crucial step for HIV transmission and pathogenesis.
NKG2D Recognition and Perforin Effector Function Mediate Effective Cytokine Immunotherapy of Cancer
Authors: Smyth Mark J. , Swann Jeremy , Kelly Janice M. , Cretney Erika , Yokoyama Wayne M. , Diefenbach Andreas , Sayers Thomas J. , Hayakawa Yoshihiro
Published: November 2004

Single and combination cytokines offer promise in some patients with advanced cancer. Many spontaneous and experimental cancers naturally express ligands for the lectin-like type-2 transmembrane stimulatory NKG2D immunoreceptor; however, the role this tumor recognition pathway plays in immunotherapy has not been explored to date. Here, we show that natural expression of NKG2D ligands on tumors provides an effective target for some cytokine-stimulated NK cells to recognize and suppress tumor metastases. In particular, interleukin (IL)-2 or IL-12 suppressed tumor metastases largely via NKG2D ligand recognition and perforin-mediated cytotoxicity. By contrast, IL-18 required tumor sensitivity to Fas ligand (FasL) and surprisingly did not depend on the NKG2D–NKG2D ligand pathway. A combination of IL-2 and IL-18 stimulated both perforin and FasL effector mechanisms with very potent effects. Cytokines that stimulated perforin-mediated cytotoxicity appeared relatively more effective against tumor metastases expressing NKG2D ligands. These findings indicate that a rational choice of cytokines can be made given the known sensitivity of tumor cells to perforin, FasL, and tumor necrosis factor–related apoptosis-inducing ligand and the NKG2D ligand status of tumor metastases.
Paenibacillus elgii sp. nov., with broad antimicrobial activity
Authors: Kim Dal-Soo , Bae Cheol-Yong , Jeon Jae-Jin , Chun Sam-Jae , Oh Hyun Woo , Hong Soon Gyu , Baek Keun-Sik , Moon Eun Young , Bae Kyung Sook
Published: November 2004

Two novel spore-forming bacteria with broad antimicrobial activity were isolated from roots of Perilla frutescens. The isolates, SD17T and SD18, were facultatively anaerobic and showed variable Gram reaction. Growth was observed between 20 and 45 °C. DNA G+C content of SD17T was 51·7 mol%, and the major fatty acid was anteiso-C15 : 0 (54·1 %). 16S rRNA gene sequence similarity of SD17T ranged from 98·6 to 91·3 % with other Paenibacillus species. The phylogenetic tree showed that isolate SD17T formed a significant monophyletic clade with Paenibacillus koreensis KCTC 2393T and Paenibacillus ehimensis IFO 15659T. DNA–DNA relatedness values for strain SD17T with Paenibacillus koreensis KCTC 2393T and Paenibacillus ehimensis IFO 15659T were 17·4 and 19·8 %, respectively. These isolates thus merit species status within Paenibacillus, for which the name Paenibacillus elgii sp. nov. is proposed. The type strain is SD17T (=KCTC 10016BPT=NBRC 100335T).
Streptomyces ferralitis sp. nov., a novel streptomycete isolated from a New-Caledonian ultramafic soil
Authors: Saintpierre-Bonaccio Danielle , Amir Hamid , Pineau René , Lemriss Sanaa , Goodfellow Michael
Published: November 2004

The taxonomic position of an actinomycete isolated from an ultramafic soil in New Caledonia was determined using a polyphasic approach. The isolate, which was designated SFOp68T, was shown to have chemical and morphological properties typical of streptomycetes. An almost complete 16S rRNA gene sequence of the isolate was generated and compared with sequences of representative streptomycetes. The 16S rRNA data not only supported the classification of the strain in the genusStreptomyces, but also showed that it formed a distinct phyletic line that was most closely related to one composed of the type strain ofStreptomyces rimosus. The two organisms can be readily separated using a diverse range of phenotypic properties. It is proposed that strain SFOp68T(=DSM 41836T=NCIMB 13954T) be classified in the genusStreptomycesasStreptomyces ferralitissp. nov.
Reclassification of Mesoplasma pleciae as Acholeplasma pleciae comb. nov. on the basis of 16S rRNA and gyrB gene sequence data
Authors: Knight Thomas F.
Published: November 2004

Genomic DNA sequence data for the 16S rRNA gene and the gyrB gene of Mesoplasma pleciae PS-1T (=ATCC 49582T=NBRC 100476T) demonstrate a much closer relationship to Acholeplasma laidlawii and Acholeplasma oculi than to other species in the order Entomoplasmatales. In addition, the preferred use of UGG rather than UGA as the codon for tryptophan in the gyrB sequence probably places the organism outside the order Entomoplasmatales. It is proposed that M. pleciae be reclassified in the genus Acholeplasma, as Acholeplasma pleciae comb. nov.
Saccharibacter floricola gen. nov., sp. nov., a novel osmophilic acetic acid bacterium isolated from pollen
Authors: Jojima Yasuko , Mihara Yasuhiro , Suzuki Sonoko , Yokozeki Kenzo , Yamanaka Shigeru , Fudou Ryosuke
Published: November 2004

Three Gram-negative, aerobic, rod-shaped bacterial strains were isolated, from the pollen of Japanese flowers, as producers of xylitol; these strains were subjected to a polyphasic taxonomic study. Phylogenetic analyses of the 16S rRNA gene sequences demonstrated that these three isolates formed a new cluster within a group of acetic acid bacteria in theα-Proteobacteria. The characteristics of the three isolates were as follows: (i) their predominant quinone was Q-10; (ii) their cellular fatty acid profile contained major amounts of 2-hydroxy acids and an unsaturated straight-chain acid (C18 : 1ω7c); and (iii) their DNA G+C contents were in the range 51·9–52·3 mol%, which is around the lower limit of the reported range for the genera of acetic acid bacteria. The negligible or very weak productivity of acetic acid from ethanol and the osmophilic growth properties distinguished these strains from other acetic acid bacteria. The unique phylogenetic and phenotypic characteristics suggest that the three isolates should be classified within a novel genus and species with the proposed nameSaccharibacter floricolagen. nov., sp. nov. The type strain is strain S-877T(=AJ 13480T=JCM 12116T=DSM 15669T).
Geobacillus lituanicus sp. nov.
Authors: Kuisiene Nomeda , Raugalas Juozas , Chitavichius Donaldas
Published: November 2004

Obligately thermophilic, aerobic, proteolytic, endospore-forming strain N-3Twas isolated from a high-temperature oilfield in Lithuania. 16S rRNA gene sequence analysis placed this strain in genetic group 5 of the endospore formers.Geobacillus thermoleovoransappeared to be the closest phylogenetic neighbour (99·4 % sequence similarity). The G+C content of strain N-3Twas 52·5 mol% and matched the range established for the genusGeobacillus. Studies of DNA–DNA relatedness and morphological and physiological analyses enabled strain N-3Tto be described as a member of the genusGeobacillus, but could not assign this strain to any other known species of this genus. Results of this polyphasic study allowed characterization of strain N-3Tas a novel species in the genusGeobacillus – Geobacillus lituanicussp. nov. This species can be distinguished fromG. thermoleovoransandGeobacillus stearothermophiluson the basis of 16S rRNA gene PCR-RFLP assays with the restriction endonucleasesAluI,HaeIII andTaqI. The type strain of the novel species is N-3T(=DSM 15325T=VKM B-2294T).
Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora
Authors: Tamura Tomohiko , Sakane Takeshi
Published: November 2004

An actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).
Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species
Authors: Derz Kerstin , Klinner Ulrich , Schuphan Ingolf , Stackebrandt Erko , Kroppenstedt Reiner M.
Published: November 2004

The taxonomic position of a polycyclic-aromatic-hydrocarbon-degrading bacterium, strain 17A3T, isolated from contaminated soil was determined using a combination of phenotypic and genotypic properties. The isolate showed phenotypic properties that were diagnostic for species of the genusMycobacterium. Comparative 16S rRNA gene sequence analysis assigned 17A3Tto the 16S rRNA gene subgroup that containsMycobacterium aurum,Mycobacterium austroafricanum,Mycobacterium vaccaeandMycobacterium vanbaalenii, but it could clearly be distinguished from these species using a combination of physiological, chemotaxonomic markers and internal rRNA gene spacer analyses. The data showed that strain 17A3T(=DSM 44605T=NRRL B-24244T) merits recognition as the type strain of a novel species of the genusMycobacterium. The nameMycobacterium pyrenivoranssp. nov. is proposed for the species because of its ability to use pyrene as a sole source of carbon and energy.
Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent
Authors: Urios Laurent , Cueff-Gauchard Valérie , Pignet Patricia , Postec Anne , Fardeau Marie-Laure , Ollivier Bernard , Barbier Georges
Published: November 2004

A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1·8 μm long and 0·4 μm wide, surrounded by an outer sheath-like structure (toga). They grew at 45–80 °C (optimum 65 °C), pH 5·0–9·0 (optimum pH 6·0) and at sea salt concentrations of 20–60 g l−1(optimum 30 g l−1). Strain DV1140Twas able to ferment yeast extract, peptone, brain heart infusion, gelatin, starch, galactose, arabinose, glucose, trehalose and cellobiose. The fermentation products identified on glucose in the presence of yeast extract and peptone were acetate, isovalerate and hydrogen. The G+C content of the genomic DNA was 33 mol%. Phylogenetic analysis of the 16S rRNA gene sequence (GenBank accession number AJ577471) located the strain within the genusThermosiphoin the bacterial domain. On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species, for which the nameThermosipho atlanticussp. nov. is proposed. The type strain is DV1140T(=CIP 108053T=DSM 15807T).
Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification
Authors: Shieh Wung Yang , Lin Yu-Te , Jean Wen Dar
Published: November 2004

Two denitrifying strains of heterotrophic, facultatively anaerobic, marine bacteria, designated DN34Tand DN33, were isolated from sea-water samples collected in Nanwan Bay, Kenting National Park, Taiwan. They were Gram-negative. Cells in late exponential to early stationary phase of growth were predominantly straight or curved rods, but Y- or V-shaped forms were also observed. They were motile by means of one to several lateral or subpolar flagella. Both strains required NaCl for growth and exhibited optimal growth at about 30 °C, pH 8 and 3 % NaCl. They were capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors or, alternatively, by fermenting glucose, mannose, sucrose or trehalose as substrates. Anaerobic fermentative growth on glucose resulted in formation of various organic acids, including formate, lactate, acetate, pyruvate and fumarate. The major cellular fatty acids were 2-OH-14 : 0, 3-OH-14 : 0 and 16 : 0. DN34Tand DN33 had DNA G+C contents of 51·7 and 51·6 mol%, respectively. Physiological characterization, together with phylogenetic analysis based on 16S rRNA gene sequence analysis, revealed that the two denitrifying strains could be accommodated in a novel genus, for which the namePseudovibriogen. nov. is proposed.Pseudovibrio denitrificanssp. nov. is the type species, with DN34T(=BCRC 17323T=JCM 12308T) as the type strain.
Arthrobacter gangotriensis sp. nov. and Arthrobacter kerguelensis sp. nov. from Antarctica
Authors: Gupta P. , Reddy G. S. N. , Delille D. , Shivaji S.
Published: November 2004

Two coryneform bacteria were isolated from a penguin rookery soil sample collected in Antarctica, near the Indian station Dakshin Gangotri (strain Lz1yT), and from sea water from Kerguelen island, Antarctica (strain KGN15T). They have morphological and chemotaxonomic properties (peptidoglycan A4αtype; major menaquinones MK-8, MK-9 and MK-10; predominant fatty acids anteiso-C15 : 0and anteiso-C17 : 0) that are characteristic of members of the genusArthrobacter. The isolates shared 97·8 % 16S rRNA gene sequence similarity to each other and were most closely related toArthrobacter sulfureus(about 98·5 % sequence similarity). DNA–DNA hybridization experiments revealed 50 % relatedness between the isolates, while the levels of DNA–DNA relatedness between strains Lz1yTand KGN15Tand their phylogenetic relative,A. sulfureus, were respectively 54 and 12 %. Based on the above data and distinct phenotypic differences between the isolates andA. sulfureus, two novel species are proposed,Arthrobacter gangotriensissp. nov. (type strain Lz1yT=DSM 15796T=JCM 12166T) andArthrobacter kerguelensissp. nov. (type strain KGN15T=DSM 15797T=JCM 12165T).
Description of ‘Candidatus Helicobacter heilmannii’ based on DNA sequence analysis of 16S rRNA and urease genes
Authors: O'Rourke Jani L. , Solnick Jay V. , Neilan Brett A. , Seidel Karin , Hayter Robert , Hansen Lori M. , Lee Adrian
Published: November 2004

While Helicobacter pylori is accepted as the major bacterial agent of gastric disease in humans, some patients and many animals are infected with a larger, tightly helical-shaped bacterium previously referred to as ‘Helicobacter heilmannii’ or ‘Gastrospirillum hominis’. Taxonomic classification of these bacteria has been hampered by the inability to cultivate them in vitro and by the inadequate discriminatory power of 16S rRNA gene sequence analysis. This study describes the detection and phylogenetic analysis of 26 different gastrospirillum isolates from humans and animals, which incorporates sequence data based on the 16S rRNA and urease genes. Fifteen gastrospirilla detected in humans, primates and pigs clustered with ‘Candidatus Helicobacter suis’, thus expanding the host range for this organism. By comparison, based on 16S rRNA data, the remaining 11 gastrospirilla could not be differentiated from Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis. However, urease gene sequence analysis allowed for the discrimination of this latter group into four discrete clusters, three of which contained the above recognized species. The fourth cluster contained isolates from human and feline hosts, and should provisionally be considered a unique bacterial species, for which the name ‘Candidatus Helicobacter heilmannii’ is proposed.
Mycobacterium nebraskense sp. nov., a novel slowly growing scotochromogenic species
Authors: Mohamed Amr M. , Iwen Peter C. , Tarantolo Stefano , Hinrichs Steven H.
Published: November 2004

The characterization of a novel slowly growing, scotochromogenic Mycobacterium species is reported. This previously undescribed mycobacterial species was isolated from five different patients with symptomatic pulmonary infections. All isolates were acid-fast-positive and the mycolic acid profiles were unique and supported placement into the genus Mycobacterium. Phenotypic characteristics of each strain included optimal growth after 3 weeks at a temperature range of 30–35 °C, yellow pigmentation after incubation in the dark and production of a heat-stable catalase. The 16S rRNA gene and internal transcribed spacer 1 sequences were identical for all five strains, but distinct from all known mycobacterial species. Phylogenetic analysis based on the 16S rRNA gene sequence placed the novel species within the slowly growing mycobacteria group in close proximity to Mycobacterium malmoense, Mycobacterium avium, Mycobacterium kansasii and Mycobacterium scrofulaceum. These data support the conclusion that the related five described organisms represent a novel Mycobacterium species, for which the name Mycobacterium nebraskense sp. nov. is proposed, with the type strain UNMC-MY1349T (=ATCC BAA-837T=DSM 44803T).
Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium
Authors: Kanso Sungwan , Patel Bharat K. C.
Published: November 2004

A facultative anaerobic bacterium, strain FaiI3T, was isolated from samples collected from the free-flowing waters of a bore well (Fairlea Bore, registration number 3768) which taps into the Australian Great Artesian Basin subsurface thermal aquifer. Strain FaiI3Tdeveloped yellow to pale-yellow colonies (0·5–1·5 mm) after 48 h. The non-spore forming rods (0·5×1–3 μm) were slightly curved, occurred singly and as pairs and were motile with a single polar flagellum. Cells tended to form clumps in liquid medium and rosettes were commonly observed. The cells stained Gram-negative and electron micrographs of thin sections revealed a multi-layered complex Gram-negative cell wall structure. Strain FaiI3Tgrew optimally at 40–41 °C, with growth observed at 45 °C but not at 50 °C. The pH growth range was between pH 6 and 9 and optimal growth occurred between pH 6 and 6·5. Strain FaiI3Tgrew best with yeast extract as the sole carbon and energy source. Peptone, yeast extract, acetate, xylose, sucrose, glucose, glycerol, succinate, butyrate, lactate, fumarate, citrate,l-phenylalanine, cellobiose and gelatin supported growth but maltose, fructose, glycine, ethanol, benzoate and oxalate did not. Tyrosine was produced froml-phenylalanine. Strain FaiI3Twas catalase-positive and oxidase-negative and did not hydrolyse starch. Growth was inhibited by neomycin, tetracycline, streptomycin, chloramphenicol, ampicillin, vancomycin and spectinomycin. The G+C content was determined to be 66·5±0·5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain FaiI3Twas assigned as a novel species of the genusPhenylobacterium,Phenylobacterium lituiformesp. nov. in the orderCaulobacterales, subclassα-Proteobacteria, classProteobacteria. The type strain is FaiI3T(=ATCC BAA-294T=DSM 14363T).
Chromohalobacter sarecensis sp. nov., a psychrotolerant moderate halophile isolated from the saline Andean region of Bolivia
Authors: Quillaguamán Jorge , Delgado Osvaldo , Mattiasson Bo , Hatti-Kaul Rajni
Published: November 2004

A moderately halophilic, aerobic, motile, Gram-negative, rod-shaped bacterium (strain LV4T) was isolated from saline soil around the lake Laguna Verde in the Bolivian Andes. The organism is a heterotroph, able to utilize various carbohydrates as a carbon source. It showed tryptophan deaminase, oxidase and catalase activity, but was unable to produce indole or H2S; nitrate was not reduced. The G+C content of the genomic DNA was 56·1 mol%. The pH range for growth was 5–10, temperature range was 0–45 °C and the range of NaCl concentrations was 0–25 % (w/v). On the basis of 16S rRNA gene sequence analysis, strain LV4T was found to be closely related to Chromohalobacter canadensis DSM 6769T and Pseudomonas beijerinckii DSM 7218T; however, its DNA–DNA relatedness with these type strains was low. Strain LV4T resembled other Chromohalobacter species with respect to various physiological, biochemical and nutritional characteristics but also exhibited differences. Thus, a novel species, Chromohalobacter sarecensis sp. nov., is proposed, with LV4T (=CCUG 47987T=ATCC BAA-761T) as the type strain.
Streptomyces glauciniger sp. nov., a novel mesophilic streptomycete isolated from soil in south China
Authors: Huang Ying , Li Wei , Wang Liming , Lanoot Benjamin , Vancanneyt Marc , Rodriguez Carlos , Liu Zhiheng , Swings Jean , Goodfellow Michael
Published: November 2004

A polyphasic study was undertaken to establish the taxonomic status of a soil isolate. The organism, strain FXJ14T, was found to have chemical and morphological properties characteristic of streptomycetes. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence of the strain and on the 120 nt variableγ-region of the 16S rRNA molecule showed that it formed a distinct phyletic line within the range of variation encompassed by the genusStreptomyces. The sharp separation of the organism from representatives of the genusStreptomyceswas strengthened by the fact that its BOX-PCR and RFLP of 16S rDNA-ITS fingerprints differed from those of over 450 recognizedStreptomycesspecies. The isolate also had a profile of phenotypic properties that readily distinguished it from the genotypically close type strains. It is evident from the combination of genotypic and phenotypic data that strain FXJ14T(=AS 4.1858T=JCM 12278T=LMG 22082T) should be classified as the type strain of a novel species of the genusStreptomyces, for which the nameStreptomyces glaucinigersp. nov. is proposed.
Enterococcus saccharominimus sp. nov., from dairy products
Authors: Vancanneyt M. , Zamfir M. , Devriese L. A. , Lefebvre K. , Engelbeen K. , Vandemeulebroecke K. , Amar M. , De Vuyst L. , Haesebrouck F. , Swings J.
Published: November 2004

Four isolates, which were obtained from Belgian, Moroccan and Romanian dairy products, constituted a homogeneous but unidentified taxon after screening with whole-cell protein fingerprinting. Complete 16S rRNA gene sequence analysis classified representative strains in the genus Enterococcus. Highest sequence similarities of 98·6 and 98·0 % were obtained with the species Enterococcus sulfureus and Enterococcus saccharolyticus, respectively. Growth characteristics, biochemical features, tRNA intergenic length polymorphism analysis, DNA–DNA hybridization and DNA G+C contents of selected strains demonstrated that they represent a single, novel Enterococcus species. It differs phenotypically from other enterococci in characteristics commonly considered as typical of this genus: no growth in 6·5 % NaCl or 0·4 % sodium azide, and no acid production from a wide range of carbohydrates. The name Enterococcus saccharominimus sp. nov. is proposed for this novel species; the type strain (LMG 21727T=CCM 7220T) was isolated from contaminated pasteurized cow's milk.
Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea
Authors: Lim Jee-Min , Yoon Jung-Hoon , Lee Jae-Chan , Jeon Che Ok , Park Dong-Jin , Sung Changkeun , Kim Chang-Jin
Published: November 2004

A moderately halophilic bacterium, strain SS20T, capable of growing at salinities of 1–20 % (w/v) NaCl was isolated from a solar saltern of the Dangjin area in Korea and was characterized taxonomically. Strain SS20Twas a Gram-negative bacterium comprising motile, short rods. Its major cellular fatty acids were C18 : 1ω7c, C19 : 0ω8ccyclo and C16 : 0. The DNA G+C content was 70 mol% and the predominant ubiquinone was Q-9. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SS20Tbelonged to the genusHalomonas. The levels of 16S rRNA gene sequence similarity to the type strains ofHalomonasspecies were in the range 93·0–97·5 %. The levels of DNA–DNA relatedness between strain SS20Tand the type strains of phylogenetically closely relatedHalomonasspecies were in the range 5·3–12·3 %. On the basis of physiological and molecular properties, strain SS20Trepresents a novel species of the genusHalomonas, for which the nameHalomonas koreensissp. nov. is proposed. The type strain is SS20T(=KCTC 12127T=JCM 12237T).
Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Yeo Soo-Hwan , Kim In-Gi , Oh Tae-Kwang
Published: November 2004

Two Gram-negative, motile, non-spore-forming, rod-shaped organisms, strains SW-117T and SW-120T, were isolated from sea water of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. Strains SW-117T and SW-120T simultaneously contained both menaquinones (MK) and ubiquinones (Q) as isoprenoid quinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acid detected in the two strains was iso-C15 : 0. The DNA G+C content of strains SW-117T and SW-120T was 51 and 54 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-117T and SW-120T fall within the radiation of the cluster comprising Shewanella species. Strains SW-117T and SW-120T showed a 16S rRNA gene sequence similarity of 97·4 % and a DNA–DNA relatedness level of 10·1 %. Strains SW-117T and SW-120T exhibited 16S rRNA gene sequence similarity levels of 93·8–98·5 % and 92·4–97·0 %, respectively, to Shewanella species. Strain SW-117T exhibited DNA–DNA relatedness levels of 8·3–20·3 % to the type strains of six phylogenetically related Shewanella species. On the basis of phenotypic, phylogenetic and genetic data, strains SW-117T and SW-120T were classified in the genus Shewanella as two distinct novel species, for which the names Shewanella marisflavi sp. nov. (type strain, SW-117T=KCCM 41822T=JCM 12192T) and Shewanella aquimarina sp. nov. (type strain, SW-120T=KCCM 41821T=JCM 12193T) are proposed, respectively.
Haloferax sulfurifontis sp. nov., a halophilic archaeon isolated from a sulfide- and sulfur-rich spring
Authors: Elshahed Mostafa S. , Savage Kristen N. , Oren Aharon , Gutierrez M. Carmen , Ventosa Antonio , Krumholz Lee R.
Published: November 2004

A pleomorphic, extremely halophilic archaeon (strain M6T) was isolated from a sulfide- and sulfur-rich spring in south-western Oklahoma (USA). It formed small (0·8–1·0 mm), salmon pink, elevated colonies on agar medium. The strain grew in a wide range of NaCl concentrations (6 % to saturation) and required at least 1 mM Mg2+ for growth. Strain M6T was able to reduce sulfur to sulfide anaerobically. 16S rRNA gene sequence analysis indicated that strain M6T belongs to the family Halobacteriaceae, genus Haloferax; it showed 96·7–98·0 % similarity to other members of the genus with validly published names and 89 % similarity to Halogeometricum borinquense, its closest relative outside the genus Haloferax. Polar lipid analysis and DNA G+C content further supported placement of strain M6T in the genus Haloferax. DNA–DNA hybridization values, as well as biochemical and physiological characterization, allowed strain M6T to be differentiated from other members of the genus Haloferax. A novel species, Haloferax sulfurifontis sp. nov., is therefore proposed to accommodate the strain. The type strain is M6T (=JCM 12327T=CCM 7217T=DSM 16227T=CIP 108334T).
Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa)
Authors: Bass David , Cavalier-Smith Thomas
Published: November 2004

This study presents the first 18S rRNA multi-library environmental PCR survey of a single protozoan phylum, Cercozoa Cavalier-Smith 1998, from a range of different habitats. Phylogenetic analysis reveals at least nine novel clades within the phylum, several possibly at the level of order or above. Further experiments are described to ascertain the true ecological and geographical distributions of some clades that might be inferred from the tree to be restricted in either or both ways. These results suggest that the diversity of cercozoan taxa may run into thousands of lineages, making it comparable in diversity to the largest better-characterized protozoan phyla, e.g. Ciliophora (ciliates and suctorians) and Foraminifera. New sequences of culturedSpongomonas,MetromonasandMetopionare also presented. In the light of these additions, and the increased taxon sampling from the environmental libraries, some revisions of cercozoan classification are made: the transfer of Spongomonadea from Reticulofilosa to Monadofilosa; the removal of Metopiida from Sarcomonadea; and the creation of the new order Metromonadida, currently containing the single genusMetromonas. AlthoughMetromonasgroups with weak to moderate support with Chlorarachnea, it is here placed in superclass Monadofilosa, to which it is morphologically more similar.