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Biomedical subjects

J L Garcia

Publications and source records attributed to J L Garcia.

At least 19 recordsLinked to original sources
PubMed2004

Comprehensive conventional and molecular cytogenetic characterization of B-CPAP, a human papillary thyroid carcinoma-derived cell line.

Cell lines derived from different thyroid tumor histotypes are useful for the in vitro study of both the phenotypic and genetic features of these cancers. Although karyotypic changes are known to be associated with thyroid lesions, the chromosome patterns of only a few cell lines have been published. Herein, we report an extensive conventional and molecular cytogenetic investigation of the human papillary thyroid carcinoma derived cell line B-CPAP. Morphological studies and expression of tumor markers in this cell line have been reported previously, but no detailed characterization on the origin of the chromosome markers is available. B-CPAP cells have a rather stable hypertriploid karyotype, with chromosome polysomies and structural chromosome abnormalities featuring whole chromosome arm imbalances. Chromosome banding revealed a main clone with nine chromosome markers, and fluorescence in situ hybridization (FISH) with whole chromosome paint (wcp), partial chromosome paint (pcp), and centromeric probes clarified their origin. The use of centromeric probes provided accurate refinement of the rearrangements classified as whole-arm translocations by banding and FISH with wcp probes. Both chromosomal and array-based comparative genomic hybridization experiments confirmed the cytogenetic characterization of this cell line. Moreover, the use of fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms (FICTION) technique, which simultaneously shows nuclear ploidy and cytoplasmic immunofluorescence, detailed the oncocytic feature of the cells. Intriguingly, despite their origin, they lack most of the features expressed in papillary thyroid tumor cells and have a chromosomal pattern reminiscent of that of a subgroup of oncocytic malignant thyroid tumors.

Carcinoma, Papillary↗
PubMed2003

Calcitonin for metastatic bone pain.

BACKGROUND: Pain is the most frequent symptom experienced by cancer patients, its intensity dependent on the site of the tumour. Tumours that compromise bone or nervous structures due to the bone destruction process are the most painful. There are several treatments to deal with pain (and other symptoms) caused by bone metastasis. The hormone, calcitonin, has the potential to relieve pain, and also retain bone density, thus reducing the risk of fractures. OBJECTIVES: To assess the effectiveness of calcitonin in controlling metastatic bone pain and reducing bone complications (hypercalcemia, fractures and nervous compression) in patients with bone metastases. SEARCH STRATEGY: Electronic searches were performed in MEDLINE (1966-2001), EMBASE (1974-2001), the Cochrane Central Register of Controlled Trials (Issue 2, 2001), specialised registers of the Cochrane Cancer Network and of the Cochrane Pain, Palliative and Supportive Care Group. Registers of clinical trials in progress were also searched. SELECTION CRITERIA: Studies were included if they were randomised, double-blind clinical trials of patients with metastatic bone pain, treated with calcitonin, where the major outcome measure was pain, assessed at four weeks or longer. DATA COLLECTION AND ANALYSIS: Study selection and data extraction were performed by two independent reviewers. Only two studies (90 patients) were eligible for inclusion in the review and therefore meta-analysis of the data was not possible. Intention-to-treat analysis was performed by imputing all missing values as adverse outcomes. MAIN RESULTS: Of the two small studies included in the review, one study showed a non-significant effect of calcitonin in the number of patients with total pain reduction (RR 2.50; CI 95%, 0.55 to 11.41). The second study provided no evidence that calcitonin reduced analgesia consumption (RR 1.05; CI 95%, 0.90 to 1.21) in patients with painful bone metastases. There was no evidence that calcitonin was effective in controlling complications due to bone metastases; for improving quality of life; or patients' survival. Although not statistically significant, a greater number of adverse effects were observed in the groups given calcitonin in the two included studies (RR 3.35, CI 95%, 0.72 to 15.66). REVIEWER'S CONCLUSIONS: The limited evidence currently available for systematic review does not support the use of calcitonin to control pain from bone metastases. Until new studies provide additional information on this treatment, other therapeutic approaches should be considered.

Bone Neoplasms↗
PubMed2003

Radioisotopes for metastatic bone pain.

BACKGROUND: Bone metastases manifest through pain, which can arise even before the injury is radiologically detected. Pain occurs as a result of bone destruction and, as more destruction ensues, more pain can be experienced. Radiculopathies, plexopathies and shrinkage of spinal nerves due to tumour growth and fractures are very frequent in these patients. Relief of pain from bone metastasis can be achieved by treating the cancer itself; radiotherapy; conventional analgesics; and specific drugs that work on the bone tumour-induced alteration: biphosphonates, calcitonin or radioactive agents. OBJECTIVES: To determine the efficacy of radioisotopes to control metastatic pain in patients with bone metastases and complications due to bone metastases (hypercalcaemia, bone fracture and spinal cord compression) as well as its efficacy in terms of patient survival and adverse effects. SEARCH STRATEGY: Randomised and controlled clinical trials related to this review were retrieved electronically using MEDLINE (1966-2003), EMBASE (1974-2003) and Cochrane Central Register of Controlled Trials (CENTRAL) (Issue 1 2003). general strategies to identify RCTs were combined with specific commands to identify trials of radioisotopes and metastatic bone pain. SELECTION CRITERIA: The inclusion criteria were: randomised trials of patients with metastatic bone pain that compared treatment with radioisotopes and placebo, and where the major outcome was either pain or complications of bone metastases (eg, hypercalcaemia, bone fracture, spinal cord compression) assessed at least four weeks after treatment. DATA COLLECTION AND ANALYSIS: The quality of included studies was assessed using the Jadad scale and the Oxford Pain Validity Score. Two independent reviewers extracted the data and completed a standard form designed for that purpose. An intention-to-treat analysis was performed, and global estimates of effect were calculated using a random effects model. MAIN RESULTS: Four trials (325 patients) provided data that suggest a small effect of radioisotopes on pain control both at short and medium term (one to six months). No evidence was available to assess long-term effects (12 months). Only one study provided data on analgesia use and concluded that patients given either radioisotopes or placebo showed similar levels of analgesic use when compared to baseline use. Leukocytopenia and thrombocytopenia are secondary effects associated with the administration of radioisotopes. The incidence of leukocytopenia is significantly greater in patients treated with radioisotopes (RR=4.56, 95% CI (1.22,17.08)). There were also a greater number of thrombocytopenia events in the treatment group, without reaching statistical significance. REVIEWER'S CONCLUSIONS: The efficacy of radioisotopes has been assessed in clinical trials with small sample sizes and short-term evaluations of the outcomes. There is some evidence indicating that radioisotopes may give complete reduction in pain over one to six months with no increase in analgesic use, but adverse effects, specifically leukocytopenia and thrombocytopenia, have also been experienced.

Bone Neoplasms↗
PubMed2001

Affinity chromatography of polyhistidine tagged enzymes. New dextran-coated immobilized metal ion affinity chromatography matrices for prevention of undesired multipoint adsorptions.

New immobilized metal ion affinity chromatography (IMAC) matrices containing a high concentration of metal-chelate moieties and completely coated with inert flexible and hydrophilic dextrans are here proposed to improve the purification of polyhistidine (poly-His) tagged proteins. The purification of an interesting recombinant multimeric enzyme (a thermoresistant beta-galactosidase from Thermus sp. strain T2) has been used to check the performance of these new chromatographic media. IMAC supports with a high concentration (and surface density) of metal chelate groups promote a rapid adsorption of poly-His tagged proteins during IMAC. However, these supports also favor the promotion of undesirable multi-punctual adsorptions and problems may arise for the simple and effective purification of poly-His tagged proteins: (a) more than 30% of the natural proteins contained in crude extracts from E. coli become adsorbed, in addition to our target recombinant protein, on these IMAC supports via multipoint weak adsorptions; (b) the multimeric poly-His tagged enzyme may become adsorbed via several poly-His tags belonging to different subunits. In this way, desorption of the pure enzyme from the support may become quite difficult (e.g., it is not fully desorbed from the support even using 200 mM of imidazole). The coating of these IMAC supports with dextrans greatly reduces these undesired multi-point adsorptions: (i) less than 2% of natural proteins contained in crude extracts are now adsorbed on these novel supports; and (ii) the target multimeric enzyme may be fully desorbed from the support using 60 mM imidazole. In spite of this dramatic reduction of multi-point interactions, this dextran coating hardly affects the rate of the one-point adsorption of poly-His tagged proteins (80% of the rate of adsorption compared to uncoated supports). Therefore, this dextran coating of chromatographic matrices seems to allow the formation of strong one-point adsorptions that involve small areas of the protein and support surface. However, the dextran coating seems to have dramatic effects for the prevention of weak or strong multipoint interactions that should involve a high geometrical congruence between the enzyme and the support surface.

Adsorption↗
PubMed2001

One-step purification, covalent immobilization, and additional stabilization of poly-His-tagged proteins using novel heterofunctional chelate-epoxy supports.

Epoxy supports covalently immobilize proteins following a two-step mechanism; that is, the protein is physically adsorbed and then the covalent reaction takes place. This mechanism has been exploited to combine the selectivity of metal chelate affinity chromatography with the covalent immobilization capacity of epoxy supports. In this way, it has been possible to accomplish, in a simple manner, the purification, immobilization, and stabilization of a poly-His-tagged protein. To fulfill this objective we developed a new kind of multifunctional epoxy support (chelate epoxy support [CES]), which was tested using a poly-His-tagged glutaryl acylase as a model protein (an alphabeta-heterodimeric enzyme of significant industrial interest). The selectivity of the immobilization in CES toward poly-His-tagged proteins was dependent to a large extent on the density and nature of the chelated metal. The highest selectivity was achieved by using low-density chelate groups (e.g., 5 micromol/g) and metals with a low affinity (e.g., Co). However, the rate of covalent immobilization of the protein by its reaction with the epoxy groups on the support significantly increased at alkaline pH values. The multipoint attachment to the CES also depended on the reaction time. The immobilization of both glutaryl acylase subunits was achieved by incubation of the enzyme derivative at pH 10 for 24 h, with the best enzyme derivative 100-fold more stable than the soluble enzyme. By taking advantage of the selectivity properties of the novel support, we were able to immobilize up to 30 mg of protein per gram of modified Eupergit 250 using either pure enzyme or a very crude enzyme extract.

Amidohydrolases↗
PubMed2001

Methanobacterium congolense sp. nov., from a methanogenic fermentation of cassava peel.

Strain CT, a non-motile, mesophilic, hydrogenotrophic, methanogenic bacterium, was isolated from an anaerobic digester used for the treatment of raw cassava-peel waste in Congo. The cells were rods, 0.4-0.5 x 2-10 microm in size, and stained Gram-positive. Hydrogen and carbon dioxide were the only substrates that supported growth and methane production. Methane production, but not growth, occurred with CO2 in the presence of either 2-propanol, 2-butanol or cyclopentanol as hydrogen donors. The temperature range for growth was 25-50 degrees C, the optimum being between 37 and 42 degrees C. The optimum pH for growth was 7.2; consistent growth and methane production were not observed below pH 5.9 or above pH 8.2. The doubling time under optimal growth conditions was 7.5 h. The DNA base composition was 39.5 mol% G+C. On the basis of 16S rRNA gene sequence analysis and phenotypic characteristics, the isolate is proposed as a new species of the genus Methanobacterium, namely Methanobacterium congolense sp. nov. The type strain is strain CT (= DSM 7095T = OCM 779T).

Bioreactors↗
PubMed2001

Transfer of thermobacteroides leptospartum and Clostridium thermolacticum as Clostridium stercorarium subsp. leptospartum subsp. thermolacticum subsp. nov., comb. nov. and C. stercorarium subsp. thermolacticum subsp. nov., comb. nov.

16S rRNA sequencing and sequence analysis of the sole member of the genus Thermobacteroides, Thermobacteroides leptospartum, revealed that it was related to members of cluster III (according to the scheme of Collins et al. 1994) represented exclusively by cellulolytic Clostridium species. Phenotypic studies indicated that Thermobacteroides leptospartum was also able to grow on cellulose, providing further evidence of its affiliation to members of cluster III. Its closest phylogenetic relatives, Clostridium thermolacticum and Clostridium stercorarium, were almost equidistantly placed with a similarity value of 99%. DNA hybridization studies also indicated that Thermobacteroides leptospartum, C. thermolacticum and C. stercorarium were closely related to each other (values of over 95% homology). Similarities based on the comparison of the 16S rRNA gene sequences and DNA homology are sufficiently high to regard all three strains as subspecies of a single species. It is therefore proposed that Thermobacteroides leptospartum and C. thermolacticum be transferred to cluster III as C. stercorarium subsp. leptospartum subsp. nov., comb. nov. and C. stercorarium subsp. thermolacticum subsp. nov., comb. nov., respectively, thus automatically creating C. stercorarium subsp. stercorarium subsp. nov., comb. nov. The transfer of the sole member of Thermobacteroides invalidates the taxonomic status of the genus.

Clostridium↗
PubMed2001

Propionibacterium microaerophilum sp. nov., a microaerophilic bacterium isolated from olive mill wastewater.

A new gram-positive, facultative anaerobic, microaerophilic bacterium, designated strain M5T, was isolated from a decantation reservoir of olive mill wastewater. The cells were rod-shaped, non-motile, non-spore-forming and catalase-negative. Growth occurred at pH ranging from 4.5 to 9.5, with optimum growth at 7.0. The optimum temperature for growth was around 30 degrees C. Although growth occurred under anaerobic and aerobic conditions, the optimum O2 concentration for growth was determined as 5% in the gas phase of the culture. During anaerobic growth, glucose or lactate were mainly fermented to propionate, acetate and CO2. In the presence of O2 (more than 2%), glucose was oxidized completely to CO2. The G+C content of the DNA was 67.7+/-0.6 mol% and 16S rRNA gene analysis revealed that the new isolate belonged to the cluster of 'dairy' propionibacteria, Propionibacterium acidipropionici being its closest phylogenic relative (97.5% similarity). However, the level of DNA relatedness between strain M5T and P. acidipropionici was 56.2%. Consequently, both the phenotypic (range of substrates used) and genotypic characteristics of strain M5T allow it to be assigned as a new species of the genus Propionibacterium, Propionibacterium microaerophilum sp. nov. The type strain is strain M5T (= CNCM I-2360T = DSM 13435T).

Aerobiosis↗
PubMed2001

Isolation of a cinnamic acid-metabolizing Clostridium glycolicum strain from oil mill wastewaters and emendation of the species description.

A strictly anaerobic, gram-positive, motile, sporulated bacterium, designated strain CIN5, was isolated from olive mill wastewaters after enrichment on cinnamic acid. The rod-shaped cells were slightly curved (0.4-1.1 x 2.0-15 microm) and occurred singly or in pairs. Strain CIN5 utilized a limited number of carbohydrates (glucose, fructose, maltose, sorbitol), grew optimally at 37 degrees C and at pH 7.3-7.5 and had a DNA G+C content of 29.1+/-0.3 mol%. Strain CIN5 was very closely related to Clostridium glycolicum DSM 1288T. Both strain CIN5 and the type strain of C. glycolicum transformed cinnamic acid to hydrocinnamic acid and a wide range of other cinnamic acid derivatives, including o-, m- and p-coumaric, o-, m- and p-methoxycinnamic, p-methylcinnamic, caffeic, ferulic and isoferulic acids, to their corresponding 3-phenylpropionic acids by reducing the double bond of the side chain. Glucose supplementation increased the rate of conversion markedly. The emendation of the description of C. glycolicum is proposed to include these new characteristics.

Biodegradation, Environmental↗
PubMed2001

Metabolism of cinnamic acids by some Clostridiales and emendation of the descriptions of Clostridium aerotolerans, Clostridium celerecrescens and Clostridium xylanolyticum.

The ability of Clostridium aerotolerans DSM 5434T, Clostridium celerecrescens DSM 5628T, Clostridium methoxybenzovorans DSM 12182T, Clostridium stercorarium ATCC 35414T, Clostridium subterminale DSM 2636, Clostridium termitidis DSM 5398T, Clostridium thermolacticum DSM 2910T, Clostridium thermopalmarium DSM 5974T and Clostridium xylanolyticum DSM 6555T to metabolize cinnamic acid and various derivatives, with or without glucose supplementation, was examined. Only C aerotolerans DSM 5434T and C. xylanolyticum DSM 6555T, closely related species, transformed cinnamic acid to 3-phenylpropionic acid. Both species also reduced a wide range of cinnamic acid derivatives, including o-, m- and p-coumaric, o-, m- and p-methoxycinnamic, p-methylcinnamic, caffeic, ferulic, isoferulic and 3,4,5-trimethoxycinnamic acids to their corresponding 3-phenylpropionic acid derivatives. C. aerotolerans DSM 5434T, however, also decarboxylated p-coumaric acid into 4-vinylphenol, which was then reduced to 4-ethylphenol. C. celerecrescens was grouped with C. aerotolerans and C. xylanolyticum in subcluster XIVa of the Clostridiales. C. celerecrescens DSM 5628T only metabolized m- and p-methoxycinnamic and p-methylcinnamic acids to their corresponding 3-phenylpropionic acid derivatives, reducing the double bond in the C3 aliphatic side chain. Addition of glucose markedly increased the yield of the biotransformations by these three species. An emendation of the descriptions of C. aerotolerans, C. celerecrescens and C. xylanolyticum is proposed, based on these observations.

Bacterial Typing Techniques↗
PubMed2001

Splenic marginal zone B-cell lymphomas: two cytogenetic subtypes, one with gain of 3q and the other with loss of 7q.

BACKGROUND AND OBJECTIVES: Splenic marginal zone B-cell lymphoma (SMZBCL) has clinical, immunophenotypic and histologic features distinct from other B-cell malignancies, but few chromosome studies have been previously reported. In the present study we performed conventional cytogenetics and in situ hybridization studies in 47 patients with SMZBCL. DESIGN AND METHODS: We studied 47 cases of splenic marginal zone B-cell lymphoma combining conventional cytogenetics and in situ hybridization (ISH) techniques using centromeric probes (chromosomes 3 and 12), locus specific probes (7q31 and 17p13) and cross-species color banding fluorescent ISH probes (RxFISH). The diagnosis of SMZBCL was ascertained in all cases after studying, morphologically and immunologically, peripheral blood and splenectomy specimens. RESULTS: A clonal chromosome abnormality detected by conventional cytogenetics and/or FISH was found in 33/47 patients (70%) being identified in 18 (18/33, 55%) as a complex abnormality. The most frequently recurrent abnormalities were: gain of 3q (10 cases), del(7q) (12 cases), and involvement of chromosomes 1, 8 and 14. No patient showed translocation t(11;14) (q13;q32) or t(14;18) (q21;q32). Trisomy 3 was detected in eight cases (8/47, 17%). Two novel cytogenetic abnormalities involving 14q32, t(6;14)(p12;q32) and t(10;14) (q24;q32) were reported. Deletion of 17p13 (P53) was observed by FISH in one case. Only one patient showed a gain of 3q or trisomy 3 and deletion 7q in the same karyotype. INTERPRETATION AND CONCLUSIONS: Our findings support the interpretation that two forms of SMZBCL could be considered, one with gain of 3q and the other with deletions at 7q.

Chromosome Aberrations↗
PubMed2000

Do sequence repeats play an equivalent role in the choline-binding module of pneumococcal LytA amidase?

LytA amidase breaks down the N-acetylmuramoyl-l-alanine bonds in the peptidoglycan backbone of Streptococcus pneumoniae. Its polypeptide chain has two modules: the NH(2)-terminal module, responsible for the catalytic activity, and the COOH-terminal module, constructed by six tandem repeats of 20 or 21 amino acids (p1-p6) and a short COOH-terminal tail. The polypeptide chain must contain at least four repeats to efficiently anchor the autolysin to the choline residues of the cell wall. Nevertheless, the catalytic efficiency decreases by 90% upon deletion of the final tail. The structural implications of deleting step by step the two last (p5 and p6) repeats and the final COOH-tail and their effects on choline-amidase interactions have been examined by comparing four truncated mutants with LytA amidase by means of different techniques. Removal of this region has minor effects on secondary structure content but significantly affects the stability of native conformations. The last 11 amino acids and the p5 repeat stabilize the COOH-terminal module; each increases the module transition temperature by about 6 degrees C. Moreover, the p5 motif also seems to participate, in a choline-dependent way, in the stabilization of the NH(2)-terminal module. The effects of choline binding on the thermal stability profile of the mutant lacking the p5 repeat might reflect a cooperative pathway providing molecular communication between the choline-binding module and the NH(2)-terminal region. The three sequence motives favor the choline-amidase interaction, but the tail is an essential factor in the monomer <--> dimer self-association equilibrium of LytA and its regulation by choline. The final tail is required for preferential interaction of choline with LytA dimers and for the existence of different sets of choline-binding sites. The p6 repeat scarcely affects the amidase stability but could provide the proper three-dimensional orientation of the final tail.

Choline↗
PubMed2000

Aminobacterium mobile sp. nov., a new anaerobic amino-acid-degrading bacterium.

A novel, curved (0.3 x 4.0-5.0 microm), Gram-negative, non-sporulating, mesophilic bacterium, designated strain ILE-3T (T = type strain), was isolated from an anaerobic lagoon in a dairy wastewater treatment plant. Optimal growth occurred at 37 degrees C and pH 7.4 on a medium containing serine as an energy source and yeast extract. The strain was motile by means of one or two lateral flagella. It required yeast extract for growth on serine, glycine, threonine and pyruvate. Poor growth was obtained on cysteine, Casamino acids, biotrypcase, peptone and 2-oxoglutarate. In the presence of Methanobacterium formicicum, strain ILE-3T oxidized alanine, glutamate, leucine, isoleucine, valine and aspartate to a minor extent. The G+C content of the DNA was 44 mol%. Phylogenetic analysis of the 16S rRNA gene of strain ILE-3T indicated that it was related to Aminobacterium colombiense (95% similarity value). On the basis of the phenotypic and phylogenetic characteristics, strain ILE-3T is designated as a new species of the genus Aminobacterium, namely Aminobacterium mobile sp. nov. (= DSM 12262T).

Amino Acids↗
PubMed2000

Methanobacterium oryzae sp. nov., a novel methanogenic rod isolated from a Philippines ricefield.

A rod (0.3-0.4 micron x 3-10 microns) to filamentous (up to 40 microns) non-motile methanogenic bacterium, designated strain FPiT (T = type strain), was isolated from ricefield soil in the Philippines. The strain uses H2 + CO2 or formate for growth and produces CH4. Optimum growth temperature is 40 degrees C; no growth is observed at 15 degrees C or 45 degrees C. Optimum pH for growth is 7; no growth is observed at pH 5.5 or 9.0. Strain FPiT is halotolerant and grows at NaCl concentrations of 0-25 g l-1. The G + C content of its DNA is 31 mol%. Based on 16S rRNA gene sequence analysis, the isolate was identified as a new species of the genus Methanobacterium: Methanobacterium oryzae sp. nov. The type strain is FPiT (= DSM 11106T).

Agriculture↗
PubMed2000

Thermohalobacter berrensis gen. nov., sp. nov., a thermophilic, strictly halophilic bacterium from a solar saltern.

A new thermophilic, strictly halophilic, anaerobic, non-sporulating rod-shaped bacterium, measuring 0.5 x 3.0-8.0 microns and designated strain CTT3T, was isolated from a solar saltern. Strain CTT3T stained Gram-negative, was motile by means of laterally inserted flagella, had a genome G + C content of 33 mol% and grew optimally at 65 degrees C and pH 7.0 with 5% NaCl. The strain also grew readily at 70 degrees C in the presence of 15% NaCl. Strain CTT3T fermented cellobiose, fructose, glucose, maltose, mannitol, mannose, sucrose, glycerol, N-acetylglucosamine, starch, pyruvate and bio-Trypticase. It produced acetate, ethanol, H2 and presumably CO2 from glucose. 16S rRNA gene sequence analysis indicated that it is a member of cluster XII of the Clostridiales and related genera of the subphylum of the Gram-positive bacteria containing genomes of low G + C content. Its phenotypic and phylogenetic characteristics clearly differentiated it from all other members of this cluster. Based on the findings it is proposed that strain CTT3T be designated as a new species of a new genus, Thermohalobacter berrensis gen. nov., sp. nov. The type strain is CTT3T (= CNCM 105955T).

Base Composition↗
PubMed2000

Salinivibrio costicola subsp. vallismortis subsp. nov., a halotolerant facultative anaerobe from Death Valley, and emended description of Salinivibrio costicola.

Strain DVT, a halotolerant, Gram-negative, facultatively anaerobic bacterium, was isolated from a hypersaline pond located in Death Valley, California. The cells were non-spore-forming, motile, curved rods (1.0-1.8 x 0.5-0.6 microns) and occurred singly, in pairs or rarely in chains. Strain DVT was oxidase-, catalase-, Voges-Proskauer-, amylase-, gelatinase- and lipase-positive and indole-negative. Nitrate, sulfate and fumarate were not used as electron acceptors. Carbohydrates served as energy sources both aerobically and anaerobically. Strain DVT grew optimally at 37 degrees C (temperature range 20-50 degrees C) with 2.5% NaCl (NaCl range 0-12.5%) and pH 7.3 (pH range of 5.5-8.5) in a glucose/yeast extract medium with a doubling time of 20 min (aerobically) or 41 min (anaerobically). The end products of glucose fermentation were ethanol, isobutyrate, propionate, lactate, formate and CO2. Strain DVT was resistant to penicillin, D-cycloserine, streptomycin and tetracycline (200 micrograms ml-1). The G + C content was 50 mol%. 16S rRNA gene sequence analysis indicated that it was closely related to Salinivibrio costicola (97.7%) and this was confirmed by DNA-DNA hybridization (93% relatedness). However, phenotypic characteristics such as halotolerance, gas production, growth at 50 degrees C, antibiotic resistance, sugar-utilization spectrum and phylogenetic signatures are sufficiently different from Salinivibrio costicola to warrant designating strain DVT as a new subspecies of Salinivibrio costicola, Salinivibrio costicola subsp. vallismortis subsp. nov. (= DSM 8285T).

California↗
PubMed2000

Papillibacter cinnamivorans gen. nov., sp. nov., a cinnamate-transforming bacterium from a shea cake digester.

A new, strictly anaerobic, Gram-positive, non-sporulating, mesophilic bacterium, designated strain CIN1T (T=type strain) was isolated from an anaerobic digester fed with shea cake rich in tannins and aromatic compounds. Cells of strain CIN1T were rod-shaped, had characteristically pointed ends (1.3-3.0 x 0.5-0.6 microm) and occurred singly, in pairs and sometimes in chains of up to six. The pH range for growth was 6.9-8.5 and the temperature growth range was 15-40 degrees C. Optimum growth occurred with yeast extract and cinnamate at 37 degrees C and a pH of 7.5. The isolate transformed cinnamate by degrading the aliphatic side chain to produce acetate and benzoate rather than by aromatic ring cleavage or demethoxylation. The position of the methoxyl group appears to be important in the degradation of the aliphatic side chain of cinnamate; consequently, 3-methoxycinnamate and 4-methoxycinnamate, but not 2-methoxycinnamate, are transformed to produce acetate and methoxybenzoates, namely 3-methoxybenzoate and 4-methoxybenzoate, respectively. Crotonate is degraded to acetate and butyrate. The G+C content of the DNA is 56 mol%. Phylogenetic analysis of the 16S rRNA gene of strain CIN1T indicated that it was a member of the low-G+C-containing Gram-positive branch with a specific relationship to Sporobacter termitidis (sequence identity of 88%). The phylogenetic results concur with the phenotypic data which reveals that the isolate is a novel bacterium and, based on these findings, strain CIN1T (= DSM 12816T = ATCC 700879T) has been designated Papillibacter cinnamivorans gen. nov., sp. nov.

Anaerobiosis↗