Synergistic effects of injection of bone marrow cells into both portal vein and bone marrow on tolerance induction in transplantation of allogeneic pancreatic islets

We have established a new method for allogeneic pancreatic islet (PI) transplantation: relatively low doses of irradiation followed by simultaneous transplantation of PIs and bone marrow cells (BMCs) via the portal vein (PV). In the present study, we have compared this method with intra-bone marrow (IBM)-bone marrow transplantation (BMT), and with a combination of both methods. Streptozotocin (STZ)-induced diabetic-recipient rats, Fischer 344 (F344, RT1A(l), RT1B(l)), were irradiated 1 day before transplantation. PIs of Brown Norway rats (BN, RT1A(n), RT1B(n)) were transplanted into the liver of the diabetic F344 rats via the PV. BMCs from BN rats were injected into the recipients' bone marrow (IBM), PV or intravenously (IV) or by a simultaneous combination of PV plus IBM (PV+IBM). We compared graft survival among the groups of '9 Gy+IBM'(10/10 accepted), '9 Gy+PV'(7/10 accepted), '9 Gy+IV'(0/7 accepted), '9 Gy+PV+IBM'(8/8 accepted), '8.5 Gy+IBM'(4/9 accepted), '8.5 Gy+PV'(0/7 accepted), '8.5 Gy+IV'(0/7 accepted), '8.5 Gy+PV+IBM'(9/12 accepted), '8 Gy+IBM'(2/10 accepted) and '8 Gy+PV+IBM'(2/8 accepted). As we reported previously, PV-BMT is more effective in inducing the acceptance of allogeneic PIs than IV-BMT. However, IBM-BMT requires less pretreatment than PV-BMT. (PV+IBM)-BMT was found to be the most effective in inducing the acceptance of allogeneic PIs. These results suggest that allogeneic PI-transplantation in conjunction with (PV+IBM)-BMT could become a viable strategy.

Microbial indices of soil fertility

AIMS

To find the new microbial parameters explaining the soil fertility from the microbial community viewpoint.

METHODS AND RESULTS

Fatty acid methyl ester (FAME) analysis and terminal-restriction fragment length polymorphism (T-RFLP) analysis were carried out using 16 differently treated plots from the same field that had been kept under different fertilizer management systems since 1984. It was found that organic fertilizer application had small impact, whereas chemical fertilizer application, especially ammonium-nitrogen fertilizer, had strong impact on microbial community structures. Principal component analysis was conducted based on soil chemical and physical parameters, crop yields, FAMEs and terminal-restriction fragments (T-RFs) to provide 10 FAMEs and 10 T-RFs showing strong relation with soil fertility.

CONCLUSION

We defined these 10 FAMEs and 10 T-RFs as 'keystone' biological parameters explaining soil fertility in the soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report on the FAMEs and T-RFs related to soil fertility. Both analyses are rapid, inexpensive and reproducible means. As field assessment needs precise and rapid analysis, FAME and T-RFLP analyses and these new parameters are very useful to analyse soil fertility at biological viewpoint.

Involvement of dendritic cells in sarcoidosis

BACKGROUND

Sarcoidosis is a systemic granulomatous disease of unknown aetiology. It has been suggested that T helper type 1 (Th1) polarisation is associated with the pathophysiology of sarcoidosis, but the mechanism of skewing towards Th1 has not been elucidated. Dendritic cells (DCs) are known to regulate immune responses. This study was performed to determine whether DCs are involved in the aetiology of sarcoidosis.

METHODS

The numbers of peripheral blood DCs in 24 patients with sarcoidosis were analysed and biopsy specimens from four patients were stained immunohistochemically using monoclonal antibodies.

RESULTS

The numbers of both myeloid and lymphoid DC subsets were significantly decreased in the blood and mature DCs were found in the granulomas of patients with sarcoidosis. A number of interferon-gamma (IFN-gamma) producing T cells were also detected in the sarcoid granuloma, as well as many interleukin (IL)-4 producing T cells. Double staining of the biopsy specimen using anti-fascin and anti-CD3 antibodies showed an anatomical interaction between DCs and T cells.

CONCLUSIONS

These findings suggest that the blood DC subsets may migrate into the affected tissues, contributing to the formation of the granulomas in sarcoidosis. It is hypothesised that the migrating DCs may regulate the T cell response in sarcoidosis, at least in the granulomatous lesions.

Degradation of polycyclic aromatic hydrocarbons by a newly isolated dibenzofuran-utilizing Janibacter sp. strain YY-1

The dibenzofuran (DF)-utilizing bacterium strain YY-1 was newly isolated from soil. The isolate was identified as Janibacter sp. with respect to its 16S rDNA sequence and fatty acid profiles, as well as various physiological characteristics. In addition to DF, strain YY-1 could grow on fluorene and dibenzothiophene as sole sources of carbon and energy. It was also able to cometabolize a variety of polycyclic aromatic hydrocarbons including dibenzo- p-dioxin, phenanthrene, and anthracene. The major metabolites formed from DF, biphenyl, dibenzothiophene, and naphthalene were identified by using gas chromatography-mass spectrometry as 2,3,2'-trihydroxybiphenyl, biphenyl-dihydrodiol, dibenzothiophene 5-oxide, and coumarin, respectively. These results indicate that strain YY-1 can catalyze angular dioxygenation, lateral dioxygenation, and sulfoxidation.

Relationships between bacterial tolerance levels and forms of copper and zinc in soils

The effects of various fractions of copper (Cu) and zinc (Zn) on soil bacteria were evaluated by the heavy metal tolerance level of the bacterial community (IC50) in soil samples collected near a mine. The IC50 values had no relationship with the total concentrations of Zn and Cu in the soils, but were weakly correlated with the 0.05 M CaCl2-extractable form of each metal in the soils (Cu: R2 = 0.670, p < 0.01; Zn: R2 = 0.453, p < 0.05). It was found that the IC50 correlated strongly with the total concentration of each metal in the extracts from water-saturated soil samples, described below as "soil solution" (Cu: R2 = 0.789, p < 0.01; Zn: R2 = 0.617, p < 0.01). The speciation of these metals in the soil solutions was estimated using an equilibrium thermodynamic computer model, SOILCHEM. Simulated free Cu ion ranged from 18 to 98% of total Cu, and organic complexes of Cu ranged from < 1 to 56%. In all samples, Zn existing as the free ion was estimated to be more than 80% of total Zn in the soil solutions. The IC50 values were also correlated with the estimated free metal ion activities, but with slightly lower correlation coefficients than found for total concentration in the soil solutions (Cu: R2 = 0.735, p < 0.01; Zn: R2 = 0.610, p < 0.01). The results suggest that not only high metal ion activities, but also total dissolved metal concentrations in soil solutions may affect the bacterial community.

Oligonucleotide probe for detecting Enterobacteriaceae by in situ hybridization

AIMS

To develop oligonucleotide probes for visualizing bacteria belonging to Enterobacteriaceae.

METHODS AND RESULTS

24-mer oligonucleotide probe (probe D) was designed by comparison of 16S rDNA sequences of 35 species of Enterobacteriaceae, eight species of Vibrionaceae and six species of Pasteurellaceae. The sequence of the probe corresponding to the complementary sequence of a position 1251-1274 of Escherichia coli 16S rRNA was found to be a highly conserved region of 16S rDNA sequence in Enterobacteriaceae different from that of Vibrionaceae and Pasteurellaceae. The fluorescent dye-labelled probe was tested for the specificity by in situ hybridization and epifluorescence microscopy. Seventy-six out of 78 strains belonging to Enterobacteriaceae were visualized in an optimal hybridization condition. No bacterial strains belonging to Vibrionaceae (31 strains) and Gram-positive bacteria (three strains) were visualized.

CONCLUSIONS

In situ hybridization using probe D allows the detection of bacterial cells belonging to Enterobacteriaceae without false positive reaction.

SIGNIFICANCE AND IMPACT OF THE STUDY

In situ hybridization techniques using the probe D are potential tools for detecting Enterobacteriaceae in food and water samples.

Protection of T cells from radiation-induced apoptosis by Cepharanthin

Cepharanthin (CE) is a medicine that contains several biscoclaurine alkaloids. We examined the effects of CE on radiation-induced T cell apoptosis. Radiation induced apoptosis on T cells in a dose-dependent manner, while CE inhibited radiation-induced apoptosis. CE also attenuated the cytotoxic effects of radiation on the proliferative response of T cells. CE inhibited not only the loss of mitochondrial transmembrane potential but also the activation of caspase 3 in irradiated T cells. Radiation plus CE induced the up-regulation of Bax and the down-regulation of Bcl-2 in T cells in comparison with radiation alone. These results suggest that CE inhibits the signal transduction pathway of apoptosis induced by radiation, regardless of the expression of Bcl-2 or Bax.

The response of the phosphate uptake system and the organic acid exudation system to phosphate starvation in Sesbania rostrata

It is well known that the P(i) uptake system via the high-affinity P(i) transporter and the organic acid exudation system via PEPC are enhanced in the roots of P(i)-starved plants. In this paper, we compared the expression of these two systems in Sesbania rostrata, a leguminous plant, on whose roots and stems it forms nodules. When S. rostrata plants were transferred to a 0 microM P(i) nutrient solution, the expression of both the high-affinity P(i) transporter and PEPC was enhanced within 2 d. The enhancement of the expression of the high-affinity P(i) transporter genes and the PEPC gene coordinated with the increases in the P(i) uptake rate and the PEPC activity, respectively. This suggests that the expression of the high-affinity P(i) transporters and PEPC is regulated in part at the transcript level. Furthermore, we examined which of the environmental or the endogenous P(i) level regulates the expression of these two systems. The P(i) content in the 6-day-old plants decreased to a lower level than that in the 15-day-old plants when grown in a 30 microM P(i) solution. At that time, the expression of the high-affinity P(i) transporters and PEPC was enhanced only in the 6-day-old plants. Moreover, the P(i) content in plants forming many nodules on their stems decreased. The expression of the high-affinity P(i) transporters and PEPC was then enhanced in the nodulated plants. These facts suggest that the expression of these two systems may be regulated by the P(i) content in the plants, not by the P(i) concentration in the soil.

Gram-positive bacteria: possible photosynthetic ancestry

A 16S ribosomal RNA gene has been sequenced from Heliobacterium chlorum, the recently discovered photosynthetic bacterium that contains a novel form of chlorophyll. Comparisons with other 16S ribosomal RNA sequences show that the organism belongs to the Gram-positive bacteria (one of ten eubacterial "phyla")--more precisely to the so-called low G + C (G, guanine; C, cytosine) subdivision thereof. This brings to five the number of such phyla that contain photosynthetic species, the other four being the purple bacteria and relatives, the green sulfur bacteria, the green nonsulfur bacteria, and the cyanobacteria. The finding suggests that Gram-positive bacteria may be of photosynthetic ancestry, and it strengthens the case for a common photosynthetic ancestry for all eubacteria.

The green non-sulfur bacteria: a deep branching in the eubacterial line of descent

Ribosomal RNA sequence comparisons define a phylogenetic grouping, the green non-sulfur bacteria and relatives (GNS), known to contain the genera Chloroflexus, Herpetosiphon and Thermomicrobium--organisms that have little phenotypic similarity. The unit is phylogenetically deep, but entirely distinct from any other eubacterial division (phylum). It is also relatively ancient--branching from the common eubacterial stem earlier than any other group of eubacteria reported thus far. The group phenotype is predominantly thermophilic, and its thermophilic members, especially Thermomicrobium, are more slowly evolving than Herpetosiphon, a mesophile. The GNS unit appears significantly older than either the green sulfur bacteria or the cyanobacteria--making it likely that organisms such as Chloroflexus, not the cyanobacteria, generated the oldest stromatolites, which formed over three billion years ago.

Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA-DNA hybridization among Methanoculleus species

A strictly anaerobic, irregularly coccoid, methanogenic archaeon, strain MG62T (= JCM 10825T = DSM 13459T), was isolated from paddy field soil in Chikugo, Fukuoka, Japan. The cells stained gram-negative, were 1.0-2.0 microm in diameter, were lysed by SDS and hypotonic solutions and were flagellated. Motility was not observed. The strain was able to use H2/CO2, 2-propanol/CO2, formate, 2-butanol/CO2 and cyclopentanol/CO2 as substrates for methanogenesis, but did not utilize acetate, ethanol, methanol or methylamines. The optimum temperature and pH were 25-30 degrees C and 6.7-7.2. Analysis of lipid component parts (core lipids, phospholipid polar head groups and glycolipid sugar moieties) showed the characteristic pattern of members of the family Methanomicrobiaceae except for the absence of glucose as a glycolipid sugar moiety. The G+C content of the DNA was 62.2 mol %. Sequence analysis of the 16S rDNA revealed that the strain belonged to the genus Methanoculleus. The strain had DNA-DNA hybridization values of less than 50% with type strains of Methanoculleus species. On the basis of phenotypic, genotypic and phylogenetic characteristics, the name Methanoculleus chikugoensis sp. nov. is proposed for strain MG62T (= JCM 10825T = DSM 13459T). The DNA hybridization study also revealed the close relationships of three species, Methanoculleus olentangyi, Methanoculleus bourgensis and Methanoculleus oldenburgensis, among Methanoculleus species.

Copper and zinc fractions affecting microorganisms in long-term sludge-amended soils

The influences of Zn and Cu on soil enzyme activities (acid phosphatase, alkaline phosphatase, arylsulfatase, cellulase, dehydrogenase, protease (z-FLase), urease, beta-D-glucosidase and beta-D-fructofuranosidase (invertase)) and microbial biomass carbon were investigated in agricultural soils amended with municipal sewage sludge or compost since 1978. The trace metals in the soils were fractionated using a sequential extraction method. Long-term application of the sewage sludge and composts caused accumulations of Cu and Zn in the soils, ranging from 140 to 144 and from 216 to 292 mg kg(-1), respectively. The percentage of Cu was highest in the NaOH- and HNO3-extractable fractions (44-51% and 38-46%, respectively), while the percentage of Zn was highest in the HNO3- and EDTA-extractable fractions (65-83% and 11-32%, respectively). Although the percentage of the bioavailable fractions (sum of KNO3 + H2O-, NaOH-, and EDTA-extractable amounts) of Cu (53-64%) was higher than that of Zn (15-37%), the percentage of the most labile fractions (KNO3 + H2O) of Zn (2.1-5.9%) was larger than that of Cu (1.1-2.4%). The size of the microbial biomass carbon increased with the application of sewage sludge or compost. For some enzymes, however, the ratio of the enzyme activity to microbial biomass was lower in the soils amended with sewage sludge or compost than that in the control soil. The soil enzyme activities were more adversely affected by Zn than by Cu. From a multiple regression analysis, it was found that dehydrogenase, urease, and beta-D-glucosidase activities were reduced by the KNO3 + H2O-extractable fraction of Zn in the soils. These microbial activities seem to be sensitive to Zn stress, indicating the possibility that they might be useful bioindicators for evaluation of the toxic effects of Zn on microorganisms in the soils.

Proteasome inhibitor 1 enhances paclitaxel-induced apoptosis in human lung adenocarcinoma cell line

Paclitaxel is a chemotherapeutic drug that induces apoptosis in tumor cells by stabilizing microtubules, prevents normal mitosis, and blocks the cell cycle at the G2/M phase. We have previously reported that the activation of caspase-3 and caspase-8 plays a crucial role in paclitaxel-induced apoptosis. Anti-tumor reagents including paclitaxel, irradiation, and other stimuli activate the transcription factor NF-kappaB, which has the ability to suppress the apoptotic potential of those stimuli. Using a human lung adenocarcinoma cell line (LC-2-AD), we therefore examined whether the inhibition of NF-kappaB activity by proteasome inhibitor 1 (PS1) could become a new adjuvant therapy for cancer. A synergistic effect on apoptosis induction was observed with the combination of more than 0.1 microg/ml paclitaxel and 0.5 microM PS1. An increase in the cell number of apoptotic cells is correlated with the loss of Deltaphim and the activation of caspase-3 and caspase-8. Furthermore, augmented apoptosis is related to NF-kappaB activation. Based on these findings, we propose that the combination of paclitaxel with PS1 could be a new strategy for cancer treatment.

A proposal for the unification of five species of the cyanobacterial genus Microcystis Kützing ex Lemmermann 1907 under the rules of the Bacteriological Code

Genomic DNA homologies were examined from six Microcystis (cyanobacteria) strains, including five different species, Microcystis aeruginosa, Microcystis ichthyoblabe, Microcystis novacekii, Microcystis viridis and Microcystis wesenbergii. All DNA-DNA reassociation values between two strains of M. aeruginosa and the other four species exceeded 70%, which is considered high enough for them to be classified within the same bacterial species. It is proposed to unify these five species into M. aeruginosa under the Rules of the Bacteriological Code and NIES843T (= IAM M-247T) is proposed as the type strain. Two other species, Microcystis flos-aquae and Microcystis pseudofilamentosa, should be regarded as morphological variations of this unified M. aeruginosa. The current taxonomy of cyanobacteria depends too much upon morphological characteristics and must be reviewed by means of bacteriological methods as well as traditional botanical methods.

A new method for bone marrow cell harvesting

To minimize contamination of bone marrow cells (BMCs) with T cells from the peripheral blood, a new "perfusion method" for collecting BMCs is proposed using cynomolgus monkeys. Two BM puncture needles are inserted into a long bone such as the humerus, femur, or tibia. One needle is connected to an extension tube and the end of the tube is inserted into a culture flask to collect the BM fluid. The other needle is connected to a syringe containing 30 ml of phosphate-buffered saline. The solution is pushed gently from the syringe into the medullary cavity, and the medium containing the BM fluid is collected into the culture flask. There is significantly less contamination with peripheral blood, determined from the frequencies of CD4(+) and CD8(+) T cells, when using this method (<6%) than when using the conventional method (>20%) consisting of multiple BM aspirations from the iliac crest. Furthermore, the number and progenitor activities of the cells harvested using this "perfusion method" are greater than those harvested using the conventional aspiration method. This perfusion method was carried out 42 times using 15 cynomolgus monkeys, and no complications such as pulmonary infarction or paralysis were observed. These findings suggest that the "perfusion method" is safe and simple and would be of great advantage in obtaining pure BMCs, resulting in a less frequent occurrence of acute graft-versus-host-disease in allogeneic BM transplantation.

An autopsy case of giant cell myocarditis probably due to a non-steroidal anti-inflammatory drug

An autopsy case of giant cell myocarditis (GCM) in a 74-year-old woman is presented. She suffered from hepatic dysfunction, skin eruption and disseminated intravascular coagulation due to the side-effects of a non-steroidal anti-inflammatory drug. After admission, heart failure progressed rapidly, and the patient died suddenly. At autopsy, her heart was slightly enlarged and the heart muscle was thickened with many small whitish nodules. She was diagnosed with GCM because of the infiltration of multinuclear giant cells, histiocytes, eosinophils and lymphocytes into the heart. We did not find any similar lesions in any other organs. Giant cell myocarditis, the etiology of which is not defined, is a rare disease with unfavorable prognosis. This case suggests the possibility of drug-induced GCM.

[Rapid development of multiple meniscal signs complicating invasive pulmonary aspergillosis in a patient receiving chemotherapy for acute leukemia]

This report describes the rapid development of multiple meniscal signs complicating invasive pulmonary aspergillosis in a 53-year-old man receiving chemotherapy for acute leukemia. While undergoing first induction therapy for AML, he developed chest pain, and multiple bilateral infiltrations were seen in chest roentgenograms. Administration of antibiotics, antifungal agents, steroid pulse therapy and G-CSF was begun. Pulmonary cavities with meniscal signs developed. The next day, pneumothorax and hemothorax were noted. Although drainage and mechanical ventilation were performed, the patient died after massive hemoptysis. Invasive pulmonary aspergillosis was diagnosed at autopsy.

Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence

The broad and vague phenotypic definition allowed the genus Pseudomonas to become a dumping ground for incompletely characterized polarly flagellated, gram-negative, rod-shaped, aerobic bacteria, and a large number of species have been accommodated in the genus Pseudomonas. The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. These sequences were compared with the sequences of other species of the Proteobacteria. Fifty-seven valid or invalid species including Pseudomonas aeruginosa (type species of the genus Pseudomonas Migula 1894) belonged to the genus Pseudomonas (sensu stricto). Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA-DNA hybridization study by Palleroni (1984). The other species did not belong to the genus Pseudomonas (sensu stricto) and were related to other genera, which were placed in four subclasses of the Proteobacteria (alpha, beta, gamma and gamma-beta subclasses). Twenty-six examined species, which were not included in the cluster of the Pseudomonas (sensu stricto) and have not been transferred to other genera as yet, are listed alphabetically: 'Pseudomonas abikonensis', Pseudomonas antimicrobica, Pseudomonas beijerinckii, Pseudomonas beteli, Pseudomonas boreopolis, 'Pseudomonas butanovora', Pseudomonas carboxydohydrogena, Pseudomonas cissicola, Pseudomonas doudoroffii, Pseudomonas echinoides, Pseudomonas elongata, Pseudomonas flectens, Pseudomonas geniculata, Pseudomonas halophila, Pseudomonas hibiscicola, Pseudomonas huttiensis, Pseudomonas iners, Pseudomonas lanceolata, Pseudomonas lemoignei, Pseudomonas mephitica, Pseudomonas pictorum, Pseudomonas saccharophila, Pseudomonas spinosa, Pseudomonas stanier, Pseudomonas syzygii and Pseudomonas woodsii. The phylogenetic affiliations of these 26 pseudomonads species are shown.

[An autopsy case of thymic carcinoma producing various tumor markers and the examination of 222 autopsy cases of thymic malignant tumor in Japan]

The autopsy of a 76-year-old Japanese female patient, which revealed thymic carcinoma with various tumor markers such as NSE, CYFRA, and CA-125, is presented. The patient died from hepatic failure because the liver was overtaken by the tumors. At autopsy, the thymic carcinoma was found to have metastased only in the liver. From microscopical analyses and electron microscopical findings, we diagnosed poorly differenciated squamous cell carcinoma of thymic origin. In the histochemical analyses, the tumor cells were positively stained in CA 125, CA 19-9, EMA, NSE, AE 1, AE 3, CEA, S-100, glimerius and Bcl-2. These date suggest that the tumor cells produced various tumor markers. In 222 autopsy cases of thymic malignant tumor observed in Japan over a period of 4 years, the dominant pathohistological image was squamous cell carcinoma. It is interesting that the greatest number of combined malignant tumors with thymic malignancies were thyroid papillary carcinomas.

Comparison of gene arrangements of chloroplasts between two centric diatoms, Skeletonema costatum and Odontella sinensis

We have cloned and sequenced 3.4 kbp, 2.5 kbp, 1.9 kbp, 1.6 kbp and 0.5 kbp segments of a marine centric diatom, Skeletonema costatum, chloroplast DNA. These segments contain 28 genes. The genes which are not encoded on chloroplast genomes of chlorophyll a+b plants are found such as the psaD, ycf33, ycf35 and ycf47 genes. The gene sequences were compared with that of Odontella sinensis. At nucleic acid level, the ycf genes have lower homologies (69-87%) with O. sinensis than the other genes (78-100%), and some differences in the gene arrangement are found between two centric diatoms, O. sinensis and S. costatum.

Age-dependent abnormalities of hematopoietic stem cells in (NZW x BXSB)F1 mice

The (NZW x BXSB)F1 (W/BF1) mouse is known as an autoimmune-prone strain which develops lupus nephritis, thrombocytopenia due to platelet-specific autoantibodies, leukocytosis, and myocardial infarction. In this experiment, we investigated the age-dependent abnormalities of the hematopoietic stem cells (HSCs) and hematopoiesis in this mouse. White blood cell counts (especially Mac-1- or Gr-1-positive cells) in the peripheral blood of 12-week-old W/BF1 mice increased in comparison with those of four-week-old W/BF1 or normal mice. To investigate whether the abnormal hematopoiesis can be attributed to the HSCs of W/BF1 mice, colony-forming unit in spleen (CFU-S) and colony-forming unit in culture (CFU-C) assays were performed. Day 12 CFU-S counts of 12-week-old W/BF1 mice significantly increased in comparison with those of four-week-old W/BF1 mice or normal mice. In the CFU-C assay, CFU-GEMM and CFU-GM counts in 12-week-old W/BF1 mice increased in comparison with those of four-week-old W/BF1 or control mice. The bone marrow cells (BMCs) from 12-week-old W/BF1 mice showed a high level of G-CSF and a low level of GM-CSF in mRNA expression. To examine the effect of HSCs from 12-week-old W/BF1 mice on the onset of autoimmune diseases and the abnormal hematopoiesis, T- and B-cell-depleted BMCs of four-week-old or 12-week-old W/BF1 mice were transplanted to C3H mice. Recipient C3H mice that had received the BMCs from 12-week-old W/BF1 mice showed an earlier onset of autoimmune diseases and a shorter survival rate than those that had received the BMCs from four-week-old W/BF1 mice. These data suggest that the HSCs from 12-week-old W/BF1 mice showing the symptoms of autoimmune diseases have the capacity to induce autoimmune diseases earlier than the HSCs from four-week-old W/BF1 mice.

Apoptosis of colorectal adenocarcinoma induced by 5-FU and/or IFN-gamma through caspase 3 and caspase 8

The cytotoxic effect of 5-FU has been shown by the induction of apoptosis in cancer cells, and reported to be enhanced by IFN-gamma. We examined the role of caspases on the apoptosis induction of 5-FU and IFN-gamma using a colorectal adenocarcinoma cell line. The activities of caspase 3 and caspase 8 increased when apoptosis was induced by 5-FU and/or IFN-gamma. Moreover, all apoptotic cells showed high caspase 3 activity in these conditions. Although the inhibitors of caspase 3 and caspase 8 inhibit apoptosis, anti-Fas ligand antibody does not affect the apoptosis induced by 5-FU. Thus, caspase 3 and caspase 8 play crucial roles in apoptosis induced by 5-FU and/or IFN-gamma, regardless of the Fas-Fas ligand system.

Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers

In order to clarify the distribution of bifidobacterial species in the human intestinal tract, a 16S rRNA-gene-targeted species-specific PCR technique was developed and used with DNAs extracted from fecal samples obtained from 48 healthy adults and 27 breast-fed infants. To cover all of the bifidobacterial species that have been isolated from and identified in the human intestinal tract, species-specific primers for Bifidobacterium longum, B. infantis, B. dentium, and B. gallicum were developed and used with primers for B. adolescentis, B. angulatum, B. bifidum, B. breve, and the B. catenulatum group (B. catenulatum and B. pseudocatenulatum) that were developed in a previous study (T. Matsuki, K. Watanabe, R. Tanaka, and H. Oyaizu, FEMS Microbiol. Lett. 167:113-121, 1998). The specificity of the nine primers was confirmed by PCR, and the species-specific PCR method was found to be a useful means for identifying Bifidobacterium strains isolated from human feces. The results of an examination of bifidobacterial species distribution showed that the B. catenulatum group was the most commonly found taxon (detected in 44 of 48 samples [92%]), followed by B. longum and B. adolescentis, in the adult intestinal bifidobacterial flora and that B. breve, B. infantis, and B. longum were frequently found in the intestinal tracts of infants. The present study demonstrated that qualitative detection of the bifidobacterial species present in human feces can be accomplished rapidly and accurately.

Usefulness of the sensitivity-resistance index to estimate the toxicity of copper on bacteria in copper-contaminated soils

Examination was made of the fluctuations of numbers of the total bacteria and copper (Cu)-resistant bacteria with soluble/exchangeable Cu (Ex-Cu) fraction in three types of soils spiked with Cu at four concentrations. Drastic increase in Cu-resistant bacteria was observed in three soils spiked with 20 mmol Cu kg(-1) after 2 weeks of incubation, indicating the strong selection of individuals originally resistant to Cu. Adaptation and proliferation of bacteria were also observed in the soil environment under the long-term exposure to extremely high concentration of Cu (800 mg kg(-1) soil of Ex-Cu), deriving from the development of Cu resistance. These bacterial fluctuations and the toxic effects of Cu depended on soil types, due to the chemical forms in which Cu occurs. It was also found that the ratio of Cu-resistant bacterial number to total bacteria was significantly correlated with the amount of Ex-Cu in the soils. This sensitivity-resistance index seems to be useful for evaluating the toxic effects of Cu on the soil bacterial community. Whereas the toxicity of Cu depended on the soil properties, they also changed with time. This phenomenon can be explained by the decrease in the most labile Cu phase, Ex-Cu, with time in the soils.

Influences of copper forms on the toxicity to microorganisms in soils

Soil samples with wide ranges of pH (4.9 to 8.1), organic carbon (0.1 to 77%), and total Cu contents from 32 to 11700 mg kg(-1), collected near a copper mine, were used to investigate the relationships between microbial features and Cu speciation in order to clarify the form(s) of Cu adversely affecting microorganisms. The effects of Cu on soil microorganisms were evaluated by two indicators: the ratio of microbial biomass carbon to soil organic carbon (Cmic/Org-C) and Cu tolerance level of bacterial community (IC50). The sequential extraction scheme of McLaren and Crawford (1973) was used to quantify the different Cu forms (soluble and exchangeable, specifically adsorbed, and organically bound). These influences were investigated using simple correlation analysis, multiple regression analysis, and principal component analysis. The IC50 was positively correlated with the log concentration of soluble and exchangeable Cu (Ex-Cu) (r = 0.757, P<0.01). The IC50 value was also influenced by the amount of specifically adsorbed Cu. The Cmic/Org-C ratio was not significantly correlated with any Cu forms. Thus, other soil properties had more influence on the size of microbial biomass carbon in the soils used. The amount of Ex-Cu exerting high toxicity was affected by pH and the amount of total Cu.

A crucial role of caspase 3 and caspase 8 in paclitaxel-induced apoptosis

The anticancer drug paclitaxel is well known as an inhibitor of microtubule depolymerization, resulting in mitosis arrest. We investigated the mechanism underlying antitumor effects of paclitaxel on the lung adenocarcinoma cell line LC-2-AD. Less than 10 microg/ml paclitaxel induced mitosis arrest upon LC-2-AD, followed by apoptosis, but more than 30 microg/ml paclitaxel induced apoptosis without mitosis arrest. LC-2-AD with less than 1 microg/ml paclitaxel showed a loss of mitochondrial transmembrane potential (deltapsim), which correlated with antitumor effects. However, LC-2-AD with more than 10 microg/ml paclitaxel showed slight changes in the loss of deltapsim in spite of its ability to induce apoptosis significantly. The cleavage of caspase 3, caspase 8, and DFF45/ICAD was also observed in paclitaxel-induced apoptosis, and the inhibitor of caspase 3 and caspase 8 inhibited both antitumor effects and apoptosis induced by paclitaxel. These results suggest that activation of caspase 3 and caspase 8 plays a crucial role in paclitaxel-induced apoptosis under any concentrations of paclitaxel.

Phylogenetic relationships between toxic and non-toxic strains of the genus Microcystis based on 16S to 23S internal transcribed spacer sequence

16S to 23S ribosomal DNA internal transcribed spacer sequences of 47 strains of the genus Microcystis were determined. Derived maximum likelihood and DNA distance trees indicated that Microcystis can be divided into three clusters. The first cluster included toxic and non-toxic strains, the second only toxic ones, and the third only non-toxic ones. The tree topologies were not necessarily correlated with morphospecies distinction or phycobilin pigment composition, and one genotype may have more than one morphotype. Phylogenetic analysis based on intergenic spacer sequences was thought to be effective for understanding relationships among closely related species and strains.

Phylogenetic analysis of the genus Bifidobacterium and related genera based on 16S rDNA sequences

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifidobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridization. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.

Rapid identification of human intestinal bifidobacteria by 16S rRNA-targeted species- and group-specific primers

On the basis of 16S rRNA sequences, species- and group-specific primers for Bifidobacterium adolescentis, B. angulatum, B. bifidum, B. breve, the B. catenulatum group (B. catenulatum and B. pseudocatenulatum), and the B. longum group (B. longum and B. infantis), which are species commonly found in human intestinal tracts, were developed. The specificity of these primers was confirmed through the use of DNA extracted from 46 strains of 31 Bifidobacterium species, as well as 14 non-bifidobacterial species that are the predominant bacteria in the human intestinal tract. The present species-specific primers were applied to the identification of 43 isolated strains, consisting of six strains of B. adolescentis, eight of the B. catenulatum group, seven of B. bifidum, nine of B. breve, and 13 of the B. longum group.

[Hemophagocytic syndrome associated with tuberculosis and mycoplasma infection in two patients]

Patient 1: A 48-year-old man was admitted to Osaka Red Cross Hospital because of fever and dyspnea. Laboratory examination revealed pancytopenia, liver dysfunction and hematostatic abnormality. Chest radiographs obtained on admission revealed ground-glass opacity in both lung fields, and an analysis of arterial blood showed severe hypoxemia (PaO2:46.8 Torr). Pulse therapy with methylprednisolone was started. Although the hypoxemia subsided and radiographic findings rapidly improved, pancytopenia persisted. Examination of bone marrow aspirate revealed mature histiocytes with marked hemophagocytosis. Amplified Mycobacterium tuberculosis direct tests of bronchoalveolar lavage fluid, sputum, urine, and bone marrow were all positive, and Mycobacterium tuberculosis was cultured from sputum and urine. Although the patient was taking antituberculous agents, his pancytopenia persosted. Treatment with etoposide induced remssion. Patient 2: A 19-year-old woman was admitted to Osaka Red Cross Hospital because of prolonged cough and fever. Laboratory examination revealed leukocytosis, liver dysfunction, and hematostatic abnormality. Serologic tests provided conclusive evidence of Mycoplasma infection and a CRP test was strongly positive. Chest radiographs obtained on admission revealed infiltration shadows in the middle and lower lung fields on both sides, with left pleural effusion. An analysis of arterial blood showed hypoxemia (PaO2: 54.2 Torr). Examination of bone marrow and pleural effusion samples revealed mature histiocytes with marked hemophagocytosis. Although treatment with antibiotics and pulse therapy with methylprednisolone was started, the patients respiratory functions deteriorated. Endotracheal intubation was performed. Therapy with etoposide induced remission. Hemophagocytic syndrome associated with Mycoplasma infection and tuberculosis appears to be exceedingly rare. In these 2 cases, it was difficult to achieve remission with therapy for the underlying infections, but etoposide treatment was effective.

Laboratory-scale bioremediation of oil-contaminated soil of Kuwait with soil amendment materials

A huge amount of oil-contaminated soil remains unremediated in the Kuwait desert. The contaminated oil has the potentiality to cause pollution of underground water and to effect the health of people in the neighborhood. In this study, laboratory scale bioremediation experiments were carried out. Hyponex (Hyponex, Inc.) and bark manure were added as basic nutrients for microorganisms, and twelve kinds of materials (baked diatomite, microporous glass, coconut charcoal, an oil-decomposing bacterial mixture (Formula X from Oppenheimer, Inc.), and eight kinds of surfactants) were applied to accelerate the biodegradation of oil hydrocarbons. 15% to 33% of the contaminated oil was decomposed during 43 weeks' incubation. Among the materials tested, coconut charcoal enhanced the biodegradation. On the contrary, the addition of an oil-decomposing bacterial mixture impeded the biodegradation. The effects of the other materials were very slight. The toxicity of the biodegraded compounds was estimated by the Ames test and the tea pollen tube growth test. Both of the hydrophobic (dichloromethane extracts) and hydrophilic (methanol extracts) fractions showed a very slight toxicity in the Ames test. In the tea pollen tube growth test, the hydrophobic fraction was not toxic and enhanced the growth of pollen tubes.

Analysis of oil components and hydrocarbon-utilizing microorganisms during laboratory-scale bioremediation of oil-contaminated soil of Kuwait

A huge amount of oil-contaminated soil remains unremediated in the Kuwait desert. The contaminated oil has the potentiality to cause pollution of underground water and to effect the health of people in the neighborhood. We have been studying bioremediation of Kuwait oil-contaminated soil. Chemical analyses of biodegraded compounds and isolation of petroleum hydrocarbon-decomposing microorganisms were carried out. From the chemical analyses, it was revealed that the decomposed compounds were mainly saturated fractions from alumina column chromatography and that the aromatic fractions were not decomposed well. Isolation of bacteria was carried out for eight kinds of hydrocarbons which are components of crude petroleum (n-hexadecane, 2,6,10,14-tetramethylpentadecane, 1,4-diisopropylbenzene, naphthalene, 1-methylnaphthalene, phenanthrene, anthracene, and perylene). Many of the n-hexadecane- and 2,6,10,14-tetramethylpentadecane-decomposing bacteria were isolated, but aromatic compound-decomposing bacteria were not enriched. It was concluded that the slow decomposition of aromatic compounds was due to the low population of aromatic compound-decomposing bacteria in the Kuwait desert soil.

Peculiar archaea found in Japanese paddy soils

Archaeal 16S rDNA clones retrieved from paddy soil DNA were sequenced. Among 100 clones, 88 clones were assigned to methanogens and nine clones were assigned to crenarchaeota. However, three of the nine clones were phylogenetically far from the cultured crenarchaeota and closely related to marine planktonic archaea. The other three clones showed extremely novel 16S rDNA sequences and were phylogenetically far from both Crenarchaeola and Euryarchaeota. This paper reports the ubiquitous presence of crenarchaeotal and extremely novel clones in paddy soils.

The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera

The 16S rRNA sequences of Chryseomonas luteola, the type species of the genus Chryseomonas, and Flavimonas oryzihabitans, the type species of the genus Flavimonas, were determined. These sequences were compared with the sequences of 27 representative strains of the genus Pseudomonas. C. luteola and F. oryzihabitans were located in the cluster that contains Pseudomonas aeruginosa, the type species of genus Pseudomonas Migula 1894, and the levels of 16S rRNA sequence homology between P. aeruginosa and the other two species were more than 93.9%. All of the strains of the genus Pseudomonas sensu stricto whose sequences have been determined were included in the P. aeruginosa cluster. These results suggested that Chryseomonas, Flavimonas, and Pseudomonas are synonymous, and we concluded that Chryseomonas and Flavimonas are junior subjective synonyms of Pseudomonas.

Cloning and sequence analysis of czc genes in Alcaligenes sp. strain CT14

We have isolated 14 cadmium (Cd)-resistant, soil-borne bacteria. Among those, strain CT14, which was identified as an Alcaligenes sp., has a czc (cadmium, zinc, and cobalt divalent cation resistant determinant) system. Here we report the nucleotide sequence of 4 genes (czcCBAD) of the system. CzcCBA showed over 98% identity with those of A. eutrophus CH34, however, CzcD, the distal gene product, was 117 amino acids longer than that (199 amino acids) of A. eutrophus CH34, and had considerable similarity to the members of the CDF (cation diffusion facilitator) family proteins all over the region.

Morphological variation of new Thermoplasma acidophilum isolates from Japanese hot springs

We isolated 12 strains of Thermoplasma acidophilum from hot springs in Hakone, Japan. T. acidophilum strains showed morphological variation in the crystal-like structure in the cell and the fibrous structure on the cell surface. Two strains tested were sensitive to novobiocin. However, a novobiocin-resistant mutant was obtained by spontaneous mutation.

Nucleotide sequence of the SrRNA gene of Entamoeba gingivalis: applications for construction of a species-specific DNA probe and phylogenetic analysis

The small subunit ribosomal RNA (SrRNA) gene of Entamoeba gingivalis was amplified by PCR and the product of 1.9-kbp sequence was cloned into a plasmid vector pUC18. Four clones were isolated and sequenced. The insert DNAs were 1918- to 1921-bp long and A+T rich (65.5%). The four SrRNA sequences of E. gingivalis were found to be aligned with those of nine related protozoans while searching for E. gingivalis-specific sequences. A sequence of 28 oligonucleotides was chosen, chemically synthesized, and labeled with digoxigenin for use as a DNA probe. The probe thus constructed was shown to hybridize only with either the SrRNA-coding DNAs or the cells of the two E. gingivalis strains and not with those of other protozons or oral fungi tested. A representative SrRNA-sequence was analyzed and a phylogenetic tree was constructed by the neighbor-joining (NJ) method. Among the protists examined, E. gingivalis was placed next to Entamoeba histolytica as expected from the traditional taxonomy.

Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria

To clarify the taxonomic relationships of the genera Rhizomonas and Sphingomonas, the 16S rRNA sequence of Rhizomonas suberifaciens IFO 15211T (T = type strain) was determined. A phylogenetic analysis of aligned 16S rRNA gene sequences revealed that eight species of the genus Sphingomonas and R. suberifaciens are closely related to Erythrobacter longus and Porphyrobacter neustonensis and, therefore, belong in the alpha-4 subclass of the Proteobacteria. Within this subclass, Sphingomonas species and R. suberifaciens are phylogenetically interrelated and comprise several subgroups. Our findings show that the genus and species definitions of these organisms are in need of revision.

Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes

The 16S rRNA sequences of seven representative Agrobacterium strains, eight representative Rhizobium strains, and the type strains of Azorhizobium caulinodans and Bradyrhizobium japonicum were determined. These strains included the type strains of Agrobacterium tumefaciens, Agrobacterium rhizogenes, Agrobacterium radiobacter, Agrobacterium vitis, Agrobacterium rubi, Rhizobium fredii, Rhizobium galegae, Rhizobium huakuii, Rhizobium leguminosarum, Rhizobium loti, Rhizobium meliloti, and Rhizobium tropici. A phylogenetic analysis showed that the 15 strains of Agrobacterium and Rhizobium species formed a compact phylogenetic cluster clearly separated from the other members of the alpha subclass of the Proteobacteria. However, Agrobacterium species and Rhizobium species are phylogenetically entwined with one another, and the two genera cannot be separated. In the Agrobacterium species, the strains of biovar 1, biovar 2, Agrobacterium rubi, and Agrobacterium vitis were clearly separated. The two biovars exhibited homogeneity in their phenotypic, chemotaxonomic, and phylogenetic characteristics, and two species should be established for the two biovars. We considered the nomenclature of the two biovars, and revised descriptions of Agrobacterium radiobacter (for the biovar 1 strains) and Agrobacterium rhizogenes (for the biovar 2 strains) are proposed. The name Agrobacterium tumefaciens is rejected because the type strain of this species was assigned to Agrobacterium radiobacter, and consequently the description of the genus Agrobacterium is revised.

Phylogenetic diversity of phytopathogenic mycoplasmalike organisms

By using specific primers, the 16S rRNA genes of Japanese mycoplasmalike organisms (MLOs) were amplified by polymerase chain reactions from MLO-enriched fractions of plants infected with each of six different MLOs. Each of the polymerase chain reaction fragments (length, 1,370 nucleotides) was directly sequenced in both strands by using 17 oligonucleotide primers. A phylogenetic tree constructed by using the sequence data showed that these Japanese MLOs are phylogenetically diverse microorganisms that fall into three groups, group I (onion yellows, tomato yellows, mulberry dwarf, and paulownia witches' broom MLOs), group II (tsuwabuki witches' broom MLO), and group III (rice yellow dwarf MLO). A high level of sequence homology (99%) between the Oenothera hookeri MLO and the severe strain of the western aster yellows MLO on the one hand and group I MLOs on the other indicates that the O. hookeri MLO and the severe strain of the western aster yellows MLO belong to group I and suggests that these MLOs, isolated from two geographically separated locations, descended from a very similar ancestor. Although group I contains phylogenetically identical MLOs, the organisms are transmitted by diverse insect vectors. The three MLO groups are more closely related to Acholeplasma laidlawii than to Mycoplasma gallisepticum. Thus, although MLOs are phylogenetically diverse, they are evolutionarily distant from other mollicutes. These data, together with other information (including phylogenetic relationships, vector specificity, plant-pathogenic properties, and habitat in plant phloem sieve tubes), suggest that MLOs could be classified into at least three phylogenetic groups (groups I through III).

Phylogenetic relationships of marine bacteria, mainly members of the family Vibrionaceae, determined on the basis of 16S rRNA sequences

The phylogenetic relationships of 50 reference strains, mostly marine bacteria which require Na+ for growth, were determined on the basis of 600 16S rRNA nucleotides by using reverse transcriptase sequencing. Strains belonging to 10 genera were included (four genera of the family Vibrionaceae, the genus Aeromonas of the family Aeromonadaceae, and the genera Alteromonas, Marinomonas, Shewanella, Pseudomonas, and Deleya). The sequences were aligned, the similarity values and evolutionary distance values were determined, and a phylogenetic tree was constructed by using the neighbor-joining method. On the basis of our results, the family Vibrionaceae was separated into at least seven groups (genera and families). Vibrio marinus clearly was on a line of descent that was remote from other vibrios. As determined by the similarity and evolutionary distance values, V. marinus is more distantly related to the family Vibrionaceae than the members of the Aeromonadaceae are. Also, Vibrio cholerae strains formed a separate group with Vibrio mimicus at the genus level. Of 30 species of the Vibrionaceae, 17 formed a large phylogenetic cluster. The genus Listonella was found to be a heterogeneous group, and the species were distributed in various subgroups of the Vibrionaceae. The separation of the family Aeromonadaceae from the family Vibrionaceae and the separation of the genera Marinomonas and Shewanella from the genus Alteromonas were confirmed in this phylogenetic study. However, a marine Pseudomonas species, Pseudomonas nautica, was clearly separated from two terrestrial Pseudomonas species. Each group that was separated by the phylogenetic analysis had characteristic 16S rRNA sequence patterns that were common only to species in that group. Therefore, the characteristic sequences described in this paper may be useful for identification purposes.

Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov

Based on the 16S rRNA sequences, DNA-DNA homology values, cellular lipid and fatty acid composition, and phenotypic characteristics, a new genus Burkholderia is proposed for the RNA homology group II of genus Pseudomonas. Seven species in this group were transferred to the new genus. Thus seven new combinations, Burkholderia cepacia (Palleroni and Holmes 1981), Burkholderia mallei (Zopf 1885), Burkholderia pseudomallei (Whitmore 1913), Burkholderia caryophylli (Burkholder 1942), Burkholderia gladioli (Severini 1913), Burkholderia pickettii (Ralston et al 1973) and Burkholderia solanacearum (Smith 1896) were proposed.

Characterization of three thermophilic strains of Methanothrix ("Methanosaeta") thermophila sp. nov. and rejection of Methanothrix ("Methanosaeta") thermoacetophila

Three thermophilic Methanothrix ("Methanosaeta") strains, strains PTT (= DSM 6194T) (T = type strain), CALS-1 (= DSM 3870), and Z-517 (= DSM 4774), were characterized chemotaxonomically and compared with five mesophilic strains, Methanothrix soehngenii ("Methanosaeta concilii") GP6 (= DSM 3671), Opfikon (= DSM 2139), FE (= DSM 3013), UA, and PM. These methanogens were exclusively acetotrophic and had a characteristic sheathed structure. The DNA base compositions of the strains which we studied ranged from 50.3 to 54.3 mol% guanine plus cytosine. The thermophilic strains often had phase-refractive gas vesicles inside their cells. Denaturing electrophoresis of proteins showed that the mesophilic and thermophilic Methanothrix strains formed two distinct groups and that there were differences in protein patterns between the groups. The difference between the thermophiles and mesophiles was also verified by comparing partial 16S rRNA sequences (ca. 30 base differences in ca. 540 bases). On the basis of our results, we propose the name Methanothrix thermophila for the three thermophilic strains. The type strain of M. thermophila is strain PT (= DSM 6194). We also propose that the name Methanothrix thermoacetophila ("Methanosaeta thermoacetophila"), which was given to strain Z-517 (type strain), should be rejected because of its description, which was based on an enrichment culture, was inadequate.

Identification of Xenobiotic-Degrading Isolates from the Beta Subclass of the Proteobacteria by a Polyphasic Approach Including 16S rRNA Partial Sequencing

Nineteen gram-negative, aerobic, biodegradative isolates were identified by using a polyphasic taxonomic approach. The presence of the specific polyamine 2-hydroxyputrescine and the presence of a ubiquinone with eight isoprenoid units in the side chain (ubiquinone Q-8) allowed allocation of these organisms to the beta subclass of the Proteobacteria. On the basis of the results of additional characterization experiments (i.e., API 20NE tests, determinations of soluble protein patterns, and DNA-DNA hybridization experiments), we classified six isolates as either Comamonas testosteroni, Comamonas acidovorans, or Alcaligenes xylosoxidans subsp. denitrificans. By using the same criteria we allocated two additional isolates to the genus Alcaligenes. A comparison of a 16S rRNA fragment (positions 1220 to 1377; Escherichia coli nomenclature) indicated that the remaining isolates should be allocated as follows: one is a member of C. testosteroni and one is a member of Acidovorax facilis, as confirmed by the results of additional DNA-DNA hybridizations; two others probably belong to the family Alcaligenaceae; six are related to "Alcaligenes eutrophus"; and one, strain NRRL 12228, occupies an isolated position.

Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas

Based on the partial nucleotide sequence analysis of 16S ribosomal ribonucleic acid (rRNA), presence of unique sphingoglycolipids in cellular lipid, and the major type of ubiquinone (Q10), we propose Sphingomonas gen. nov. with the type species Sphingomonas paucimobilis (Holmes et al, 1977) comb. nov. From the homology values of deoxyribonucleic acid-deoxyribonucleic acid hybridization and the phenotypic characteristics, three new species, Sphingomonas parapaucimobilis, Sphingomonas yanoikuyae, Sphingomonas adhaesiva, and one new combination, Sphingomonas capsulata, are described. S. parapaucimobilis JCM 7510 (= GIFU 11387), S. yanoikuyae JCM 7371 (= GIFU 9882), and S. adhaesiva JCM 7370 (= GIFU 11458) are designated as the type strains of the three new species. Emended description of the type strain of S. capsulata is presented.

A phylogenetic analysis of the mycoplasmas: basis for their classification

Small-subunit rRNA sequences were determined for almost 50 species of mycoplasmas and their walled relatives, providing the basis for a phylogenetic systematic analysis of these organisms. Five groups of mycoplasmas per se were recognized (provisional names are given): the hominis group (which included species such as Mycoplasma hominis, Mycoplasma lipophilum, Mycoplasma pulmonis, and Mycoplasma neurolyticum), the pneumoniae group (which included species such as Mycoplasma pneumoniae and Mycoplasma muris), the spiroplasma group (which included species such as Mycoplasma mycoides, Spiroplasma citri, and Spiroplasma apis), the anaeroplasma group (which encompassed the anaeroplasmas and acholeplasmas), and a group known to contain only the isolated species Asteroleplasma anaerobium. In addition to these five mycoplasma groups, a sixth group of variously named gram-positive, walled organisms (which included lactobacilli, clostridia, and other organisms) was also included in the overall phylogenetic unit. In each of these six primary groups, subgroups were readily recognized and defined. Although the phylogenetic units identified by rRNA comparisons are difficult to recognize on the basis of mutually exclusive phenotypic characters alone, phenotypic justification can be given a posteriori for a number of them.