Environ Toxicol Chem, 2004 Dec, 23(12), 2816 - 22 Enhancement of phenanthrene solubilization and biodegradation by trehalose lipid biosurfactants; Chang JS et al.; Effects of trehalose lipid biosurfactants produced by Rhodococcus erythropolis on the solubilization and biodegradation of phenanthrene (PHE) were investigated . Based on surface tension measurements, the average critical micelle concentration (CMC) of trehalose lipids was determined to be approximately 16 mg total organic carbon (TOC)/L . In solubilization assays, the addition of biosurfactants at 20-fold the CMC increased the apparent solubility of PHE by more than 30-fold . Using a known PHE degrader (isolate P5-2), batch PHE biodegradation experiments were conducted, with and without trehalose lipids, in three systems: Water (devoid of soil solids), soil (Kenansville loamy sand having 0.72% organic matter), and soil-water slurry . Addition of trehalose lipids at 10-fold the CMC enhanced both the rate and the extent of PHE mineralization by isolate P5-2 in the liquid culture . The addition of biosurfactant (32.2 mg TOC/kg soil) to the soil system also increased both the initial rate (by more than twofold) and the extent of PHE mineralization . Biosurfactants increased the rate, but not the extent, of PHE mineralization in the soil-water slurry . The results obtained in the present study indicate that the trehalose lipid biosurfactants produced by R . erythropolis have good solubilization capacity for hydrophobic organic compounds and great potential for applications in bioremediation of sites contamination with polycyclic aromatic hydrocarbons. Res Microbiol, 2005 Jan-Feb, 156(1), 68 - 75 Low-temperature biodegradation of high amounts of phenol by Rhodococcus spp . and basidiomycetous yeasts; Margesin R et al.; Four cold-adapted microbial strains able to degrade high amounts of phenol were isolated from hydrocarbon-contaminated alpine soils . Two of the strains were bacteria identified as Rhodococcus spp., and two strains were basidiomycetous yeasts . One of the yeasts was identified as Trichosporon dulcitum, while the second yeast strain belonged to the Urediniomycetes and probably represents a novel species . This strain was not able to grow at temperatures above 20 degrees C, while the other three strains were cold-tolerant and could grow at temperatures ranging from 1-25 degrees C (T . dulcitum) or 1-30 degrees C (rhodococci) . The yeast strains were characterized by a substantially lower optimum temperature for growth and biodegradation compared to the bacteria . The urediniomycete strain degraded 5 mM phenol at 1 degrees C faster than the two bacteria at 10 degrees C . The optimum temperature for phenol degradation was 10 degrees C (novel yeast species), 20 degrees C (T . dulcitum), or 30 degrees C (rhodococci) . Using fed-batch cultivation in mineral medium with phenol as the sole carbon source, high amounts of phenol were degraded at 10 degrees C . Both rhodococci degraded up to 12.5 mM phenol, while the two yeast strains even utilized as much as 15 mM phenol. Chemosphere, 2005 Jan, 58(4), 529 - 533 Diversity of biphenyl degraders in a chlorobenzene polluted aquifer; Abraham WR et al.; Biphenyl degrading bacteria (40 strains) have been isolated along a gradient of chlorobenzene pollution from an aquifer which did not contain any PCB to answer the question of how metabolic/catabolic abilities exist in ecosystems that have not been stressed with the relevant substrates is important for intrinsic bioremediations . Only few of the isolates were characterized by 16S rRNA gene sequence analyses as Pseudomonas species while the majority were Gram-positive, belonging to the order Actinomycetales and representing the genera Rhodococcus and Arthrobacter . The strains could grow on a variety of chlorobenzoates but no pattern of substrate usage and phylogeny or pollution gradient could be found . Strains which were able to grow on 2,5-dichlorobenzoate were often also able to use 3,4- and 3,5-dichloro- and 2,3,5-trichlorobenzoate or those using 2-chlorobenzoate could usually use 2,6-dichlorobenzoate as well . From that results, it is concluded that a highly diverse, basic metabolic activity for PCB degradation existed at this site despite the absence of PCB. J Appl Microbiol, 2005, 98(1), 96 - 105 Characterization of micro-organisms isolated from dairy industry after cleaning and fogging disinfection with alkyl amine and peracetic acid; Bore E et al.; Abstract e . bore and s . langsrud . 2004.Aims: To characterize micro-organisms isolated from Norwegian dairy production plants after cleaning and fogging disinfection with alkyl amine/peracetic acid and to indicate reasons for survival . Methods and Results: Microbial samples were collected from five dairy plants after cleaning and fogging disinfection . Isolates from two of these production plants, which used fogging with alkylamino acetate (plant A), and peracetic acid (plant B), were chosen for further characterization . The sequence of the 16S ribosomal DNA, fatty acid analysis and biochemical characteristics were used to identify isolates . Three isolates identified as Rhodococcus erythropolis, Methylobacterium rhodesianum and Rhodotorula mucilaginosa were isolated from plant A and one Sphingomonas sp . and two M . extorquens from plant B . Different patterns of resistance to seven disinfectants in a bactericidal suspension test and variable degree of attachment to stainless steel were found . The strains with higher disinfectant resistance showed lower degree of attachment than susceptible strains . Conclusions: The study identifies and characterizes micro-organisms present after cleaning and fogging disinfection . Both surface attachment and resistance were shown as possible reasons for the presence of the isolates after cleaning and disinfection . Significance and Impact of the Study: These results contribute to the awareness of disinfectant resistance as well as attachment as mechanisms of survival in dairy industry . It also strengthens the argument of frequent alternation of disinfectants in the food processing industry to avoid the establishment of resistant house strains. Biochem Biophys Res Commun, 2005 Jan 28, 326(4), 880 - 6 Functional characterization and molecular modeling of methylcatechol 2,3-dioxygenase from o-xylene-degrading Rhodococcus sp . strain DK17; Kim D et al.; Rhodococcus sp . strain DK17 is known to metabolize o-xylene and toluene through the intermediates 3,4-dimethylcatechol and 3- and 4-methylcatechol, respectively, which are further cleaved by a common catechol 2,3-dioxygenase . A putative gene encoding this enzyme (akbC) was amplified by PCR, cloned, and expressed in Escherichia coli . Assessment of the enzyme activity expressed in E . coli combined with sequence analysis of a mutant gene demonstrated that the akbC gene encodes the bona fide catechol 2,3-dioxygenase (AkbC) for metabolism of o-xylene and alkylbenzenes such as toluene and ethylbenzene . Analysis of the deduced amino acid sequence indicates that AkbC consists of a new catechol 2,3-dioxygenase class specific for methyl-substituted catechols . A computer-aided molecular modeling studies suggest that amino acid residues (particularly Phe177) in the beta10-beta11 loop play an essential role in characterizing the substrate specificity of AkbC. J Biotechnol, 2005 Jan 26, 115(2), 157 - 66 A chemoenzymatic route to mannosamine derivatives bearing different N-acyl groups; Kristova V et al.; The chemoenzymatic route to 2-deoxy-2-propionamido-d-mannose (1b), 2-butyramido-2-deoxy-d-mannose (2b) and 2-deoxy-2-phenylacetamido-d-mannose (3b) involved N-acylation of 2-amino-2-deoxy-d-glucose followed by alkaline C-2 epimerization and selective microbial removal of the epimers with gluco-configuration . The latter step employed whole cells of Rhodococcus equi A4 able to degrade 2-deoxy-2-propionamido-d-glucose (1a), 2-butyramido-2-deoxy-d-glucose (2a) and 2-deoxy-2-phenylacetamido-d-glucose (3a) but inactive towards the corresponding manno-isomers . The metabolism of the gluco-isomers probably involved phosphorylation and subsequent deacylation . 2-Acetamido-2-deoxy-6-O-phospho-d-glucose amidohydrolase {EC 3.5.1.25} but not 2-acetamido-2-deoxy-d-glucose amidohydrolase was detected in the cell extract, the former enzyme being partially purified (15.8-fold with an overall yield of 18.1% and a specific activity of 0.95units mg-1 protein) . According to SDS-PAGE electrophoresis, gel filtration and mass spectrometry, the enzyme was a monomer with an apparent molecular mass of approximately 42kDa . The optimum temperature and pH of the enzyme were 60 degrees C and 8.0-9.0, respectively . 2-Acetamido-2-deoxy-6-O-phospho-d-glucose and 2-acetamido-2-deoxy-6-O-sulfo-d-glucose but not 2-acetamido-2-deoxy-1-O-phospho-d-glucose or 2-acetamido-2-deoxy-d-glucose were substrates of the enzyme . Its activity was slightly inhibited by the addition of 1mM Al(3+), Ca(2+), Co(2+), Cu(2+), Mn(2+) or Zn(2+) and activated by 1mM Mg(2+) . The concentrated enzyme is highly stable at 4 degrees C in the presence of 0.1M ammonium sulfate. J Biotechnol, 2005 Jan 26, 115(2), 129 - 36 Epub 2004 Nov 24. Isolation and characterization of Rhodococcus sp . strains TMP2 and T12 that degrade 2,6,10,14-tetramethylpentadecane (pristane) at moderately low temperatures; Kunihiro N et al.; Branched alkanes including 2,6,10,14-tetramethylpentadecane (pristane) are more resistant to biological degradation than straight-chain alkanes especially under low-temperature conditions, such as 10 degrees C . Two bacterial strains, TMP2 and T12, that are capable of degrading pristane at 10 degrees C were isolated and characterized . Both strains grew optimally at 30 degrees C and were identified as Rhodococcus sp . based on the 16S rRNA gene sequences . Strain T12 degraded comparable amounts of pristane in a range of temperatures from 10 to 30 degrees C and strain TMP2 degraded pristane similarly at 10 and 20 degrees C but did not degrade it at 30 degrees C . These data suggest that the strains have adapted their pristane degradation system to moderately low-temperature conditions. Biotechnol Lett, 2004 Nov, 26(21), 1675 - 80 Enzymatic hydrolysis of cyanohydrins with recombinant nitrile hydratase and amidase from hodococcus erythropolis; Reisinger Ch et al.; Nitrile hydratase and amidase from Rhodococcus erythropolis CIMB11540 were both cloned and expressed in Escherichia coli .Crude cell free extracts were used for the hydrolysis of different aromatic cyanohydrins . Nitrile hydratase expression was increased up to 5-fold by redesign of the expression cassette . The recombinant enzymes were successfully used for the conversion of several cyanohydrins to the corresponding alpha-hydroxy amides and acids while retaining enantiopurity. Biotechnol Lett, 2004 Sep, 26(17), 1379 - 84 Rhodococcus pyridinovorans MW3, a bacterium producing a nitrile hydratase; Precigou S et al.; Rhodococcus pyridinovorans MW3 was isolated from an arable land of manioc from the Congo for its ability to transform acrylonitrile to acrylamide . This strain contains a cobalt nitrile hydratase (NHase) showing high sequence homology with NHases so far described . The specific NHase activity was 97 U mg(-1) dry wt . NHase production by R . pyridinovorans MW3 was urea and Co-dependent . The NHase was active for acrylamide up to 60% (w/v) indicating its potential for acrylamide production. Biotechnol Bioeng, 2005 Jan 5, 89(1), 18 - 23 Enhanced biotransformations and product recovery in a membrane bioreactor through application of a direct electric current; Mustacchi R et al.; The simultaneous enhancement of biotransformation coupled to product recovery, purification and concentration is presented . The nitrilase of Rhodococcus rhodochrous LL100-21 catalyses the single-step hydrolytic biotransformation of benzonitrile to benzoic acid and ammonia . When a direct electric current is applied across a bioreactor containing the bacterium and benzonitrile, the charged product (benzoic acid) can be removed in situ across an anion exchange membrane and recovered in a separate compartment . Over the course of a 24-hour biotransformation, benzonitrile was converted to benzoic acid which was completely removed from the bioreactor chamber and concentrated 3-fold in a separate chamber . The rate of production of benzoic acid increased by 42% when the current was applied (0.044 mmol/min/g dry cell weight in the presence of current as compared to 0.03 mmol/min/g dry cell weight in its absence) . The enhanced reaction rate was achieved irrespective of product separation and therefore appears to be a direct effect upon the bacterial cells . This process has potential for enhanced productivity from biotransformations through a simultaneous increase in metabolic activity and in situ product recovery . (c) 2004 Wiley Periodicals, Inc. Appl Environ Microbiol, 2004 Dec, 70(12), 7378 - 87 Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations; Tiago I et al.; Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4 . One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods . To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis . Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates . Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates) . Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus . Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the alpha-Proteobacteria lineage . Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11. Appl Environ Microbiol, 2004 Dec, 70(12), 7086 - 92 Identification of a novel dioxygenase involved in metabolism of o-xylene, toluene, and ethylbenzene by Rhodococcus sp . strain DK17; Kim D et al.; Rhodococcus sp . strain DK17 is able to grow on o-xylene, benzene, toluene, and ethylbenzene . DK17 harbors at least two megaplasmids, and the genes encoding the initial steps in alkylbenzene metabolism are present on the 330-kb pDK2 . The genes encoding alkylbenzene degradation were cloned in a cosmid clone and sequenced completely to reveal 35 open reading frames (ORFs) . Among the ORFs, we identified two nearly exact copies (one base difference) of genes encoding large and small subunits of an iron sulfur protein terminal oxygenase that are 6 kb apart from each other . Immediately downstream of one copy of the dioxygenase genes (akbA1a and akbA2a) is a gene encoding a dioxygenase ferredoxin component (akbA3), and downstream of the other copy (akbA1b and akbA2b) are genes putatively encoding a meta-cleavage pathway . RT-PCR experiments show that the two copies of the dioxygenase genes are operonic with the downstream putative catabolic genes and that both operons are induced by o-xylene . When expressed in Escherichia coli, AkbA1a-AkbA2a-AkbA3 transformed o-xylene into 2,3- and 3,4-dimethylphenol . These were apparently derived from an unstable o-xylene cis-3,4-dihydrodiol, which readily dehydrates . This indicates a single point of attack of the dioxygenase on the aromatic ring . In contrast, attack of AkbA1a-AkbA2a-AkbA3 on ethylbenzene resulted in the formation of two different cis-dihydrodiols resulting from an oxidation at the 2,3 and the 3,4 positions on the aromatic ring, respectively. Comp Immunol Microbiol Infect Dis, 2005 Jan, 28(1), 53 - 61 Molecular epidemiology of virulent Rhodococcus equi from foals in Brazil: virulence plasmids of 85-kb type I, 87-kb type I, and a new variant, 87-kb type III; Ribeiro MG et al.; We investigated the prevalence of virulent Rhodococcus equi in clinical isolates from 41 foals (19 sporadic and seven endemic cases) in Brazil between 1991 and 2003 . Of the 41 virulent isolates, six contained an 85-kb type I plasmid, 33 contained an 87-kb type I plasmid, both of which have been found in isolates from the Americas, and the remaining two contained a new variant, which did not display the EcoRI, EcoT22I and BamHI digestion patterns of the 11 representative plasmids already reported (85-kb types I-IV; 87-kb types I and II; 90-kb types I-V) . We tentatively designated the new variant as the '87-kb type III' plasmid, because its BamHI digestion pattern is similar to that of the 87-kb type I plasmid . This is the first report of the molecular epidemiology surveillance of virulent R . equi in clinical isolates from Brazilian foals. Infect Immun, 2004 Dec, 72(12), 7073 - 83 Rhodococcus equi-infected macrophages are recognized and killed by CD8+ T lymphocytes in a major histocompatibility complex class I-unrestricted fashion; Patton KM et al.; The goal of this research was to examine the role of cytotoxic T lymphocytes (CTL) in the control of Rhodococcus equi and specifically to determine if R . equi-specific CD8+ CTL occurred in the blood of immune horses . Equine peripheral blood mononuclear cells stimulated with antigen-presenting cells either infected with R . equi or exposed to soluble R . equi antigen lysed R . equi-infected target cells . Lysis was decreased to background by depletion of either CD2+ or CD3+ cells, indicating that the effector cell had a T-lymphocyte, but not NK cell, phenotype . Stimulation induced an increased percentage of CD8+ T cells in the effector population, and depletion of CD8+ T cells resulted in significantly decreased lysis of infected targets . Killing of R . equi-infected macrophages by effector cells was equally effective against autologous and equine leukocyte antigen A (classical major histocompatibility complex {MHC} class I) mismatched targets . To evaluate potential target antigens, target cells were infected with either virulent (80.6-kb plasmid-containing) or avirulent (plasmid-cured) R . equi . The degree of lysis was not altered by the presence of the plasmid, providing evidence that the virulence plasmid, which is required for survival within macrophages, was not necessary for recognition and killing of R . equi-infected cells . These data indicate that immunocompetent adult horses develop R . equi-specific CD8+ CTL, which may play a role in immunity to R . equi . The apparent lack of restriction via classical MHC class I molecules suggests a novel or nonclassical method of antigen processing and presentation, such as presentation by CD1 or other nonclassical MHC molecules. Zh Mikrobiol Epidemiol Immunobiol, 2004 Sep-Oct, (5), 103 - 5 {Characterization of bacteria of the genera Mycobacterium, Rhodococcus and Nocardia isolated from environmental objects in the Republic of Daghestan} {Lysozyme of the mollusk Unio pictorum and the sensitivity of alkanotrophic rhodococci to its effect} {No authors listed} A preparation of lysozyme from a freshwater bivalve, Unio pictorum, has been isolated by sorption to chitin, and its physicochemical properties have been studied . An assessment of the sensitivity of 48 strains of rhodococci, belonging to the species Rhodococcus rubber, R . luteus, and R . erythropolis (Specialized Collection of Alkanotrophic Microorganisms of the Institute of Ecology and Genetics of Microorganisms, Ural Division of the Russian Academy of Sciences), which were isolated from diverse natural waters, to lysozyme of the mollusk Unio pictorum demonstrated that the three species differ in their sensitivity to its effects . The high resistance of rhodococci to lysozyme is indicative of their considerable permanence in hydrobiocenoses (and, therefore, ability to maintain self-purification of microbiocenoses from hydrocarbons). Prikl Biokhim Mikrobiol, 2004 Sep-Oct, 40(5), 544 - 50 {Production of surfactants by Rhodococcus erythropolis strain EK-1, grown on hydrophilic and hydrophobic substrates}; Novel beta-carotene ketolases from non-photosynthetic bacteria for canthaxanthin synthesis; Biological and Chemical Sciences and Engineering, Central Research and Development, Experimental Station, E328/B48, E . I . DuPont de Nemours Inc., DE 19880-0328, Wilmington, USAWe reported previously that the Rhodococcus erythropolis strain AN12 synthesizes the monocyclic carotenoids 4-keto gamma-carotene and gamma-carotene . We also identified a novel lycopene beta-monocyclase in this strain . Here we report the identification of the rest of the carotenoid synthesis genes in AN12 . Two of these showed apparent homology to putative phytoene dehydrogenases . Analysis of Rhodococcus knockout mutants suggested that one of them ( crtI) encodes a phytoene dehydrogenase, whereas the other ( crtO) encodes a beta-carotene ketolase . Expression of the beta-carotene ketolase gene in an Escherichia coli strain which accumulates beta-carotene resulted in the production of canthaxanthin . In vitro assays using a crude extract of the E . coli strain expressing the crtO gene confirmed its ketolase activity . A crtO homologue (DR0093) from Deinococcus radiodurans R1 was also shown to encode a beta-carotene ketolase, despite its sequence homology to phytoene dehydrogenases . The Rhodococcus and Deinococcus CrtO ketolases both catalyze the symmetric addition of two keto groups to beta-carotene to produce canthaxanthin . Even though this activity is similar to the CrtW-type of ketolase activity, the CrtO ketolases show no significant sequence homology to CrtW-type ketolases . The presence of six conserved regions may be a signature for the CrtO-type of beta-carotene ketolases. Vet Microbiol, 2004 Nov 30, 104(1-2), 73 - 81 Foal IgG and opsonizing anti-Rhodococcus equi antibodies after immunization of pregnant mares with a protective VapA candidate vaccine; Cauchard J et al.; The aim of this study was to evaluate serum IgG antibody levels and opsonizing activity in foals from pregnant mares immunized with either proteins from an R . equi strain containing virulence-associated protein A (VapA), an immunodominant surface-expressed lipoprotein encoded by a virulence plasmid crucial for virulence in foals, or a whole killed virulent R . equi preparation . Forty-eight pregnant mares were distributed into three groups, i.e . 24 immunized with R . equi VapA protein antigen associated with a water-based nanoparticle adjuvant (Montanide IMS 3012), 8 immunized with whole killed R . equi, and 16 non-immunized as control . Serum IgG and opsonizing capacity were evaluated during pregnancy in mares, and up to day 45 post-delivery in foals in which R . equi infections were recorded in the first 6 months of life . Pregnant mares immunized with virulent R . equi proteins developed higher serum IgG and opsonic activity which were transferred to the foals than either in the whole R . equi immunized or the control group . Four foals developed pneumonia in the control group while none in immunized groups . Results support further evaluation of VapA protein antigen associated with a water-based nanoparticle adjuvant as a candidate vaccine for immunization of pregnant mares resulting in passive antibody-mediated protection of foals. Mikrobiologiia, 2004 Jul-Aug, 73(4), 465 - 71 {Utilization of H2O2 as the oxygen source by bacteria of the genera Pseudomonas and Rhodococcus}; Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp . strain RHA1; Genome Sciences Centre, Vancouver, CanadaRhodococcus sp . strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb . As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3 . The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene . The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function . Most of these are organized into three clusters . One of the catabolic clusters was predicted to include limonene degradation genes . Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source . The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes . Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase . Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs . One of the genomic islands appears to encode resistance to heavy metals . The plasmid does not appear to contain any housekeeping genes . However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism. Clin Transplant, 2004 Dec, 18(6), 748 - 52 Rhodococcus equi pneumonia in a renal transplant patient: a case report and review of literature; Arya B et al.; Immunocompromised patients are susceptible to many pathogens, including those that are predominantly problems in veterinary medicine . We report a case of a 42-yr-old white male who presented 19 months post-cadaveric renal transplant (for IgA nephropathy) with a 5 d history of nausea, vomiting, abdominal cramping and diarrhea . Admission chest X-ray revealed a suspicious mass lesion in the left lower lobe . Computed tomography (CT) guided biopsy of the lesion showed a large zone of CD68 +ve histiocytes in a non-caseating granuloma . Gram stain revealed multiple gram-positive rods within the histiocytes, which were eventually identified as R . equi . After 4 months of therapy with fluoroquinolones (Avelox) and Azithromycin a repeat CT showed complete resolution of the lesion . We reviewed the literature with special focus on the clinical features, challenges in diagnosis, and treatment of this rare infection (especially in the transplant patients who are also on immunosuppressive therapy). Vet Microbiol, 2004 Nov 15, 103(3-4), 219 - 30 The effect of mutation on Rhodococcus equi virulence plasmid gene expression and mouse virulence; Ren J et al.; An 81 kb virulence plasmid containing a pathogenicity island (PI) plays a crucial role in the pathogenesis of Rhodococcus equi pneumonia in foals but its specific function in virulence and regulation of plasmid-encoded virulence genes is unclear . Using a LacZ selection marker developed for R . equi in this study, in combination with an apramycin resistance gene, an efficient two-stage homologous recombination targeted gene mutation procedure was used to mutate three virulence plasmid genes, a LysR regulatory gene homologue (ORF4), a ResD-like two-component response regulator homologue (ORF8), and a gene (ORF10) of unknown function that is highly expressed by R . equi inside macrophages, as well as the chromosomal gene operon, phoPR . Virulence testing by liver clearance after intravenous injection in mice showed that the ORF4 and ORF8 mutants were fully attenuated, that the phoPR mutant was hypervirulent, and that virulence of the ORF10 mutant remained unchanged . A virulence plasmid DNA microarray was used to compare the plasmid gene expression profile of each of the four gene-targeted mutants against the parental R . equi strain . Changes were limited to PI genes and gene induction was observed for all mutants, suggesting that expression of virulence plasmid genes is dominated by a negative regulatory network . The finding of attenuation of ORF4 and ORF8 mutants despite enhanced transcription of vapA suggests that factors other than VapA are important for full expression of virulence . ORF1, a putative Lsr antigen gene, was strongly and similarly induced in all mutants, implying a common regulatory pathway affecting this gene for all four mutated genes . ORF8 is apparently the centre of this common pathway . Two distinct highly correlated gene induction patterns were observed, that of the ORF4 and ORF8 mutants, and that of the ORF10 and phoPR mutants . The gene induction pattern distinguishing these two groups paralleled their virulence in mice. Appl Microbiol Biotechnol . 2004 Oct 13; {Epub ahead of print} Adaptation of Rhodococcus erythropolis DCL14 to growth on n-alkanes, alcohols and terpenes; de Carvalho CC et al.; Rhodococcus erythropolis DCL14 has the ability to convert the terpene (-)-carveol to the valuable flavour compound (-)-carvone when growing on a wide range of carbon sources . To study the effect of carbon and energy sources such as alkanes, alkanols and terpenes on the biotechnological process, the cellular adaptation at the level of fatty acid composition of the membrane phospholipids and the (-)-carvone production were examined . All tested carbon sources caused a dose-dependent increase in the degree of saturation of the fatty acids . The exception was observed with short-chain alcohols such as methanol and ethanol, to which the cells adapted with a concentration-dependent decrease in the saturation degree of the membrane phospholipids . This influence of the different carbon sources on the rigidity of the cell membrane also had an impact on the (-)-carvone productivity of the strain. Rev Argent Microbiol, 2004 Apr-Jun, 36(2), 57 - 62 {Variation in the composition of Rhodococcus rodochrous GNP-OHP-38r cell membrane fatty acids in response to temperature and salinity}; Pucci GN et al.; The members of the genus Rhodococcus are frequent and abundant inhabitants of polluted areas with hydrocarbons and they resist the salinity present in the central Patagonia . This genus has good capacity to eliminate pollution produced by hydrocarbons that constitutes the biggest pollutant agent in the region . The present work studies the answer in the composition of its fatty acids under the combined action of the temperature and saline concentration of an isolated stump of a landfarming system . The strategy of Rhodococcus rodochrous strain GNP-OHP-38r in front of the thermal-osmotic stress is the increase of the percentage of the total saturated fatty acids (n:0); fatty acids branched in the terminal carbon with hidroxyl group in position 2 (n:0 iso 2 OH) and saturated with group methyl in carbon 10 (n:0 10 metil) when the temperature is increased . These acids increase while the percentage of n:1 cis decrease. Appl Environ Microbiol, 2004 Oct, 70(10), 6315 - 9 Metabolism of 2-mercaptobenzothiazole by Rhodococcus rhodochrous; Haroune N et al.; 2-Mercaptobenzothiazole, which is mainly used in the rubber industry as a vulcanization accelerator, is very toxic and is considered to be recalcitrant . We show here for the first time that it can be biotransformed and partially mineralized by a pure-culture bacterial strain of Rhodococcus rhodochrous . Three metabolites, among four detected, were identified. J Microbiol, 2004 Sep, 42(3), 188 - 93 Genetic organization of the dhlA gene encoding 1,2-dichloroethane dechlorinase from Xanthobacter flavus UE15; Song JS et al.; Xanthobacter flavus strain UE15 was isolated in wastewater obtained from the Ulsan industrial complex, Korea . This strain functions as a 1,2-dichloroethane (1,2-DCA) degrader, via a mechanism of hydrolytic dechlorination, under aerobic conditions . The UE15 strain was also capable of dechlorinating other chloroaliphatics, such as 2-chloroacetic acid and 2-chloropropionic acid . The dhlA gene encoding 1,2-DCA dechlorinase was cloned from the genomic DNA of the UE15 strain, and its nucleotide sequence was determined to consist of 933 base pairs . The deduced amino acid sequence of the DhlA dechlorinase exhibited 100% homology with the corresponding enzyme from X . autotrophicus GJ10, but only 27 to 29% homology with the corresponding enzymes from Rhodococcus rhodochrous, Pseudomonas pavonaceae, and Mycobacterium sp . strain GP1, which all dechlorinate haloalkane compounds . The UE15 strain has an ORF1 (1,356 bp) downstream from the dhlA gene . The OFR1 shows 99% amino acid sequence homology with the transposase reported from X . autotrophicus GJ10 . The transposase gene was not found in the vicinity of the dhlA in the GJ10 strain, but rather beside the dhlB gene coding for haloacid dechlorinase . The dhlA and dhlB genes were confirmed to be located at separate chromosomal loci in the Xanthobacter flavus UE15 strain as well as in X . autotrophicus GJ10 . The dhlA and transposase genes of the UE15 strain were found to be parenthesized by a pair of insertion sequences, IS1247, which were also found on both sides of the transposase gene in the GJ10 strain . This unique structure of the dhlA gene organization in X . flavus strain UE15 suggested that the dechlorinase gene, dhlA, is transferred with the help of the transposase gene . FEMS Microbiol Rev, 2004 Jun, 28(3), 377 - 403 Can whole genome analysis refine the taxonomy of the genus Rhodococcus? Gurtler V, Mayall BC, Seviour R. The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data . This has resulted in the reclassification and description of many new species . Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form . This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions . In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons . Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians . Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp . that may distinguish the genus Rhodococcus into two further genera . The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics. Bioprocess Biosyst Eng, 2004 Dec, 26(6), 361 - 75 Epub 2004 Sep 17. Solvent toxicity in organic-aqueous systems analysed by multivariate analysis; de Carvalho CC et al.; The effect of several solvents present in a biphasic reaction system on cells of Rhodococcus erythropolis DCL14, Xanthobacter Py2, Arthrobacter simplex and Mycobacterium sp . NRRL B-3805 was evaluated . These four strains have been widely exploited, from bioremediation to the production of fine chemicals, in two-phase reaction media . The solvents tested were ethyl butyrate, n-hexane, cyclohexane, iso-octane, n-dodecane, DMSO, bis(2-ethylhexyl) phthalate and fluorinert FC-70 . The cell population was monitored by fluorescence microscopy and analysis of the images captured provided single-cell-level information on cell viability, morphological factors of both viable and non-viable cells, and on the number of viable cells in clusters . These data, and those concerning the initial carveol concentration, the carbon source used during growth, the adaptation time to the solvent prior to substrate addition, and the properties of the organic solvent, were interpreted using principal components analysis (PCA) . For R . erythropolis, X . Py2, and A . simplex, between 70.1 and 80.4% of the variability of the data could be explained by six principal components, while 86.7% of the variance in the results obtained with Mycobacterium sp . could be represented by seven principal components . In all cases, solvent toxicity could explain over a third of the variability in the data . R . erythropolis cells were able to maintain their viability under harsh conditions . A period of contact between cells and solvent, prior to the addition of substrate, was prejudicial for R . erythropolis and A . simplex cells, at least for the most toxic solvents, but was beneficial for X . Py2 cells . The number of Mycobacterium sp . cells in clusters was lower after an adaptation period compared to the number of cells in aggregates when the substrate was added at time zero . The substrates transformed by R . erythropolis and A . simplex cells increased the toxicity of the system by decreasing the log P of the reaction mixture . Hydrocortisone was responsible for a reduction in the ability of A . simplex to respond to stress conditions . Mycobacterium sp . cells were apparently unaffected by beta-sitosterol . The results obtained are useful for the design of more efficient two-phase reaction systems where solvent toxicity may be overcome in order to increase cell productivity. Proc Natl Acad Sci U S A, 2004 Sep 28, 101(39), 14031 - 5 Epub 2004 Sep 17. Hyper-inducible expression system for streptomycetes; Herai S et al.; Streptomycetes produce useful enzymes and a wide variety of secondary metabolites with potent biological activities (e.g., antibiotics, immunosuppressors, pesticides, etc.) . Despite their importance in the pharmaceutical and agrochemical fields, there have been no reports for practical expression systems in streptomycetes . Here, we developed a "P(nitA)-NitR" system for regulatory gene expression in streptomycetes based on the expression mechanism of Rhodococcus rhodochrous J1 nitrilase, which is highly induced by an inexpensive and safe inducer, epsilon-caprolactam . Heterologous protein expression experiments demonstrated that the system allowed suppressed basal expression and hyper-inducible expression, yielding target protein levels of as high as approximately 40% of all soluble protein . Furthermore, the system functioned in important streptomycete strains . Thus, the P(nitA)-NitR system should be a powerful tool for improving the productivity of various useful products in streptomycetes. J Ind Microbiol Biotechnol, 2004 Oct, 31(9), 415 - 20 Epub 2004 Oct. Biodegradation of seven polychlorinated biphenyls by a newly isolated aerobic bacterium (Rhodococcus sp . R04); Yang X et al.; An aerobic bacterial strain, designated R04, belonging to the genus Rhodococcus has been isolated and characerized by 16S rDNA analysis . The capability of this strain to degrade seven different polychlorinated biphenyls (CBs), 500 ppm 3-CB, 3,4-CB, 4,4'-CB, 2,4,6-CB, 2,4',5-CB, 2,3,4,5-CB and 3,4,3',4'-CB in liquid medium, was evaluated . After 5 days of incubation, the concentration of chloride increased to 0.35 mM in cultures containing 3-CB and R04, whereas in cultures with 3,4-CB, 2,3,4,5-CB or 3,4,3',4'-CB plus R04 the chloride content increased to 0.1 mM . However, non-stoichiometric amounts of chloride were produced in cultures with R04 and 4,4'-CB, 2,4,6-CB and 2,4',5-CB . The spectrum of supernatants from R04 grown on seven PCBs had a UV-visible (UV-VIS) absorption at 200-500 nm, characteristic of biphenyl-derived cleavage products . Gas-chromatographic (GC) analysis showed that R04 was able to transform 100% of 3-CB and 3,4-CB after 1 day of incubation, and 95% of 4,4'-CB, 2,4,6-CB, 2,4',5-CB, 2,3,4,5-CB and 3,4,3',4'-CB after 5 days of incubation . The position of the chlorine substituents on the rings strongly influenced the degradation of polychlorinated biphenyls (PCBs) and their intermediate metabolites by Rhodococcus sp . R04 . The degradation of PCBs was further evaluated by monitoring intermediate metabolites of PCBs. Bioresour Technol, 2005 Jan, 96(1), 41 - 6 Removal of volatile fatty acids with immobilized Rhodococcus sp . B261; Yun SI et al.; The removal of aqueous volatile fatty acids (VFA) in wastewater and spoiled waste-foods by immobilized Rhodococcus sp . B261 was investigated . The n-valeric acid (0.5%) was completely removed within 25 h under the following conditions; solution pH, 8.0; air flow rate, 0.2 l/min; superficial velocity, 0.96 h(-1); temperature, 37 degrees C . Under the optimized conditions, the acetic (8525 ppm), propionic (7310 ppm) and n-butyric (4360 ppm) except n-valeric (2572 ppm) acids from the wastewater were completely removed by immobilized Rhodococcus sp . B261 in 24 h . The acetic (7810 ppm), propionic (8942 ppm) and butyric (5730 ppm) acids from the solution of spoiled waste-foods were effectively removed by immobilized Rhodococcus sp . B261 from 48 h within 60 h but n-valeric acid (3625 ppm) took 72 h. J Microbiol, 2004 Jun, 42(2), 160 - 2 Molecular cloning and identification of a novel oxygenase gene specifically induced during the growth of Rhodococcus sp . strain T104 on limonene; Choi KY et al.; Rhodococcus sp . strain T104 is able to utilize both limonene and biphenyl as growth substrates . Furthermore, T104 possesses separate pathways for the degradation of limonene and biphenyl . Previously, we found that a gene(s) involved in limonene degradation was also related to indigo-producing ability . To further corroborate this observation, we have cloned and sequenced a 8,842-bp genomic DNA region with four open reading frames, including one for indole oxygenase, which converts indole to indigo (a blue pigment), The reverse transcription PCR data demonstrated that the identified indole oxygenase gene is specifically induced by limonene, thereby implicating this gene in the degradation of limonene by T104. Microbiology, 2004 Sep, 150(Pt 9), 3075 - 87 A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP; Konig C et al.; The Gram-positive actinobacterium Rhodococcus opacus 1CP is able to utilize several (chloro)aromatic compounds as sole carbon sources, and gene clusters for various catabolic enzymes and pathways have previously been identified . Pulsed-field gel electrophoresis indicates the occurrence of a 740 kb megaplasmid, designated p1CP . Linear topology and the presence of covalently bound proteins were shown by the unchanged electrophoretic mobility after S1 nuclease treatment and by the immobility of the native plasmid during non-denaturing agarose gel electrophoresis, respectively . Sequence comparisons of both termini revealed a perfect 13 bp terminal inverted repeat (TIR) as part of an imperfect 583/587 bp TIR, as well as two copies of the highly conserved centre (GCTXCGC) of a palindromic motif . An initial restriction analysis of p1CP was performed . By means of PCR and hybridization techniques, p1CP was screened for several genes encoding enzymes of (chloro)aromatic degradation . A single maleylacetate reductase gene macA, the clc gene cluster for 4-chloro-/3,5-dichlorocatechol degradation, and the clc2 gene cluster for 3-chlorocatechol degradation were found on p1CP whereas the cat and pca gene clusters for the catechol and the protocatechuate pathways, respectively, were not . Prolonged cultivation of the wild-type strain 1CP under non-selective conditions led to the isolation of the clc- and clc2-deficient mutants 1CP.01 and 1CP.02 harbouring the shortened plasmid variants p1CP.01 (500 kb) and p1CP.02 (400 kb). DNA Seq, 2004 Apr, 15(2), 96 - 103 Nucleotide sequence of a portion of the camphor-degrading gene cluster from Rhodococcus sp . NCIMB 9784; Roberts GA et al.; Rhodococcus sp . NCIMB 9784 is a camphor-degrading Gram-positive organism originally isolated from activated sewage sludge . A 5.4kbp portion of a proposed camphor degradation gene cluster from this organism was cloned and its nucleotide sequence determined . Four open reading frames (ORFs) were identified encoding proteins possibly involved in camphor metabolism; sequence alignment of the translation products suggested that the ORFs encode for a ferredoxin reductase, acyl-CoA ligase, epimerase and an acyl-CoA dehydrogenase . The last three activities are thought to be involved in the poorly understood late stage of camphor degradation . Our findings are entirely consistent with the proposed formation of a branched 9-carbon acid intermediate (3,4,4-trimethyl-5-oxo-trans-2-hexenoic acid) which has been isolated from the fermentation broth of camphor-grown cells. Appl Environ Microbiol, 2004 Sep, 70(9), 5557 - 68 Isolation and characterization of a rolling-circle-type plasmid from Rhodococcus erythropolis and application of the plasmid to multiple-recombinant-protein expression; Nakashima N et al.; We isolated, sequenced, and characterized the cryptic plasmid pRE8424 from Rhodococcus erythropolis DSM8424 . Plasmid pRE8424 is a 5,987-bp circular plasmid; it carries six open reading frames and also contains cis-acting elements, specifically a single-stranded origin and a double-stranded origin, which are characteristic of rolling-circle-replication plasmids . Experiments with pRE8424 derivatives carrying a mutated single-stranded origin sequence showed that single-stranded DNA intermediates accumulated in the cells because of inefficient conversion from single-stranded DNA to double-stranded DNA . This result indicates that pRE8424 belongs to the pIJ101/pJV1 family of rolling-circle-replication plasmids . Expression vectors that are functional in several Rhodococcus species were constructed by use of the replication origin from pRE8424 . We previously reported a cryptic plasmid, pRE2895, from R . erythropolis, which may replicate by a theta-type mechanism, like ColE2 plasmids . The new expression vectors originating from pRE8424 were compatible with those derived from pRE2895 . Coexpression experiments with these compatible expression vectors indicated that the plasmids are suitable for the simultaneous expression of multiple recombinant proteins. J Mol Biol, 2004 Sep 17, 342(3), 1041 - 52 Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp . strain RHA1; Furusawa Y et al.; Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring . This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants . We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp . RHA1 in substrate-free and complex forms . These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket . Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket . The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme. Equine Vet J, 1997 Jul, 29(4), 274 - 8 Clinical evaluation of the serodiagnostic value of enzyme-linked immunosorbent assay for Rhodococcus equi infection in foals; Higuchi T et al.; An enzyme-linked immunosorbent assay (ELISA) for detection of serum IgG antibodies against Tween 20-extracted antigen of strain ATCC 6939 was applied in Hidaka, Japan to a total of 752 sick foals showing a variety of signs of infectious disease . An optical density (OD) value of more than 0.3 was tentatively fixed to be positive on the basis of readings made of healthy horse sera in previous studies . During a 2 year study, 138 of the 752 sick foals showed an OD value of 0.3 or higher and were designated as 'suspected of R . equi infection' . Age distribution during the initial medical examination of the 138 seropositive foals was significant in that most (64%) foals were age 31-60 days, with a sharp decrease in subjects beyond that age . Of the 138 foals suspected of having R . equi infection, 34 foals (25%) showed OD values of over 0.9 at the initial medical examination, in addition to high blood leucocyte counts and serum fibrinogen and alpha-globulin values . The infectious foals had been treated with antibiotics just before and after serodiagnosis and 126 foals (91%) recovered from the disease . However, no clinical improvement was observed in 12 foals (9%) . At necropsy, these foals revealed suppurative pneumonia and lymphadenitis of gut associated lymph nodes accompanied by abdominal abscesses . All isolates from the pulmonary and abdominal abscesses revealed R . equi . These results suggest that OD readings in the high range are associated with severe disseminated infection with R . equi. Acta Crystallogr D Biol Crystallogr, 2004 Sep, 60(Pt 9), 1636 - 8 Epub 2004 Aug 26. Crystallization and preliminary X-ray analyses of desulfurization enzyme DszB and its C27S mutant complexed with biphenyl-2-sulfinic acid; Lee WC et al.; DszB is a hydrolase involved in the biodegradation of dibenzothiophene in the soil bacterium Rhodococcus sp . IGTS8 . DszB catalyzes the hydrolysis of 2'-hydroxybiphenyl-2-sulfinic acid to sulfite and biphenyl-2-ol . DszB and DszB C27S mutant complexed with biphenyl-2-sulfinic acid were crystallized and preliminary X-ray crystallographic analyses were conducted . The crystals of DszB were found to belong to the orthorhombic P2(1)2(1)2(1) space group, with unit-cell parameters a = 36.7, b = 82.6, c = 139.6 A, and to contain one molecule of DszB in the asymmetric unit . Crystals of DszB C27S complexed with biphenyl-2-sulfinic acid belong to space group C2, with unit-cell parameters a = 153.4, b = 45.9, c = 112.9 A, beta = 115.93 degrees . The calculated Matthews coefficient V(M) for the C2 crystals is approximately 2.3 A(3) Da(-1) if two molecules of DszB are present in the asymmetric unit. J Vet Med B Infect Dis Vet Public Health, 2004 Jun, 51(5), 249 - 50 Haemolytic Rhodococcus equi Isolated from a Swine Lymph Node with Granulomatous Lesions; Pate M et al.; Rhodococcus equi is generally thought to be non-haemolytic although some earlier investigations reported minor haemolytic activity . A case of a haemolytic R . equi isolate from a swine lymph node with granulomatous lesions is described . This is a new contribution to knowledge of the cultural properties of R . equi. Phytomedicine, 2004 Jul, 11(5), 416 - 23 Antioxidant activity of medicinal herb Rhodococcum vitis-idaea on galactosamine-induced liver injury in rats; Myagmar BE et al.; Aim of the study was to evaluate in vivo antioxidant action of medicinal herb Rhodococcum vitis-idaea (Rh.v) on galactosamine (GalN)-induced rat liver toxicity . The results showed that the hepatotoxicity and oxidative stress induced by GalN (700 mg/kg, s.c.) after 24 h evidenced by an increase in serum alanine aminotransferase and glutathione (GSH) S-transferase activities, and lipid peroxidation in liver homogenate were significantly inhibited, when 10 times diluted Rh.v . extract (5 ml/kg, i.p.) was given to rats 12 and 1 h before GalN treatment demonstrating that the extract of Rh.v is a potent antioxidant and protective against GalN-induced hepatotoxicity . The main antioxidant compound of the herb water extract used in the experiment was determined as arbutin, which possess 8% of dry weight of the herb . The electron spin resonance (ESR) spectrometer analysis revealed that the arbutin isolated from Rh.v exhibited strong superoxide and hydroxyl radical scavenging ability. J Vet Intern Med, 2004 Jul-Aug, 18(4), 568 - 73 Retrospective comparison of azithromycin, clarithromycin, and erythromycin for the treatment of foals with Rhodococcus equi pneumonia; Giguere S et al.; The objective of this retrospective study was to compare the efficacy of azithromycin-rifampin, clarithromycin-rifampin, and erythromycin-rifampin for the treatment of pneumonia caused by Rhodococcus equi in foals . Eighty-one foals with naturally acquired pneumonia caused by R . equi were included in the study . Information on age, sex, breed, physical examination findings, laboratory testing, and thoracic radiography was abstracted from each medical record . Foals were divided in 3 groups based on the antimicrobial agent selected for therapy . Short-term (discharge from the hospital) and long-term (apparently healthy as a yearling) success rates, days of hospitalization, days with fever, days with tachypnea, and percentage of radiographic improvement were compared among groups . Foals treated with clarithromycin-rifampin had significantly (P = .02) higher odds of overall short-term (odds ratio {OR} = 12.2) and long-term (OR = 20.6) treatment success and significantly fewer days with fever than foals treated with erythromycin-rifampin . Foals treated with clarithromycin-rifampin had a significantly (P = .03) higher percentage of radiographic improvement and a tendency (P = .06) toward higher odds of overall short-term (OR = 8.1) and long-term (OR = 11.8) treatment success compared to foals treated with azithromycin-rifampin . Among foals with severe radiographic lesions, the success rates of foals treated with clarithromycin-rifampin both short-term (88%) and long-term (83%) were significantly (P = .02) higher than that of foals treated with azithromycin-rifampin (0%) . For each treatment group, the only reported adverse effect was diarrhea that was mild and self-limiting in most cases . The combination clarithromycin-rifampin is superior to azithromycin-rifampin or erythromycin-rifampin for the treatment of pneumonia caused by R . equi in foals in a referral population. J Bacteriol, 2004 Sep, 186(17), 5576 - 84 The LysR-type transcriptional regulator VirR is required for expression of the virulence gene vapA of Rhodococcus equi ATCC 33701; Russell DA et al.; The virulence of the intracellular pathogen Rhodococcus equi in foals is dependent on the presence of an 81-kb virulence plasmid encoding the virulence protein VapA . Expression of this protein is induced by exposure to oxidative stress, high temperatures, and low pHs, which reflect the conditions encountered by R . equi when it enters the host environment . The aim of this study was to determine whether the LysR-type transcriptional regulator VirR, which is encoded by the virulence plasmid, is required for the expression of vapA . It was shown that the virR gene is cotranscribed with four downstream genes, one of which encodes a two-component response regulator . The expression of VapA, as monitored by Western blotting, was completely dependent on the presence of virR . Maximal expression was observed when vapA was present together with the complete virR operon, suggesting that at least one of the virR operon genes, in addition to virR, is required for the expression of vapA to wild-type levels . The transcriptional start site of vapA was determined to be a cytidine located 226 bp upstream from the vapA initiation codon . His-tagged VirR protein was expressed in Escherichia coli and purified by nickel affinity chromatography . DNA binding studies showed that purified VirR binds to a DNA fragment containing the vapA promoter . We therefore conclude that VirR is required for the activation of vapA transcription. Commun Agric Appl Biol Sci, 2003, 68(2 Pt A), 155 - 8 Comparison of yeast (Candida maltosa) and bacterial (Rhodococcus erythropolis) phenol hydroxylase activity and its properties in the phenolic compounds biodegradation; Fialova A et al.; Aromatic contaminants of the environment, to which belongs phenol and its derivatives, are toxic and in most of the cases hard to degrade . Removal of these pollutants by biological, gentle and effective way, depends on specific environmental conditions in the locality and on the biodegradation potential of the used microbial population . Closer characterization of the biodegradation and enzyme mechanisms is therefore an essential assumption of the successful implementation of microbes . This paper is focused on comparison of the biodegradation activity between the soil yeast Candida maltosa and bacteria Rhodococcus erythropolis towards various aromatics connected with determination of the first enzyme of the phenol biodegradation pathway: phenol hydroxylase (PH) . The effect of substrate type, substrate concentration, growth phase of the microorganisms and presence of humic acids in the cultivation medium, on phenol biodegradation and PH activity are discussed. Prikl Biokhim Mikrobiol, 2004 May-Jun, 40(3), 317 - 22 {Intensification of microbial degradation of crude oil and oil products in the presence of perfluorodecalin}; Bakulin MK et al.; The possibility of using perfluorinated organic compounds for growing microorganisms and degrading xenobiotics has been demonstrated for the first time with perfluorodecalin (PFD), a gas-transporting component of the blood substitute Perftoran . In particular, this is promising for intensifying microbial degradation of oil and oil products and production of biodegrader biomass in synthetic mineral media . Addition of PFD to a mineral medium with crude oil and masut increased 4.5-10.2 times maximum concentrations and growth rates of all bacterial strains under study (Pseudomonas, Rhodococcus, and Bacillus genera) . The degree of oil product consumption was increased 8.7-12.7 times. Prikl Biokhim Mikrobiol, 2004 May-Jun, 40(3), 312 - 6 {Low-temperature microbial degradation of crude oil products differing in the extent of condensation}; Belousova NI et al.; Out of the 30 strains capable of oil degradation at 4-6 degrees C, four were selected by the ability to degrade 40% of the oil substrate present in the growth medium: Rhodococcus spp . DS-07 and DS-21 and Pseudomonas spp . DS-09 and DS-22 . We studied the activity of these strains as degraders of oil products of various condensation degrees (crude oil, masut, petroleum oils, benzene resins and ethanol-benzene resins) at 4-6 degrees C . The maximum degrees of degradation of masut and ethanol-benzene resins were observed in Pseudomonas spp . DS-22 (17.2% and 5.2%, respectively) . The maximum degradation of petroleum oils and benzene resins was observed in Rhodococcus spp . DS-07 (40% and 16.6%, respectively) . The strains provide a basis for developing biodegrader preparations applicable to bioremediation of oil-polluted sites under the conditions of cold climate. Prikl Biokhim Mikrobiol, 2004 May-Jun, 40(3), 307 - 11 {Degradation of 2,4-dinitrophenol by free and immobilized cells of Rhodococcus erythropolis HL PM-1}; Kitova AE et al.; Degradation of 2,4-dinitrophenol (2,4-DNP) by the cells of Rhodococcus erythropolis HL PM-1 was studied . The enzymes involved in 2,4-DNP degradation were inducible, and their resynthesis took place during the process . Cell immobilization by embedding into agar gels decreased the degrader activity . Maximum rates of 2,4-DNP degradation by free and immobilized cells were 10.0 and 5.4 nmol/min per mg cells, respectively . The concentration dependence of 2,4-DNP degradation was typical of substrate inhibition kinetics . The immobilized cells were used in a model reactor designed for 2,4-DNP biodegradation . Its maximum capacity was 0.45 nmol/min per mg cells at a volumetric flow rate of 20 h-1 . The reactor operated for 14 days without losing capacity; its half-lifetime equaled 16 days. J Biochem (Tokyo), 2004 Jul, 136(1), 115 - 21 Thermal equilibrium of two conformations in photosensitive nitrile hydratase probed by the FTIR band of nitric oxide bound to the non-heme iron center; Suzuki H et al.; Nitrile hydratase (NHase) from Rhodococcus N-771 is a novel enzyme that is inactive in the dark due to an enodogenous nitric oxide (NO) molecule bound to the non-heme iron center, and is activated by its photodissociation . FTIR spectra in the NO stretching region of the dark-inactive NHase were recorded in the temperature range of 270-80 K . Two NO peaks were observed at 1854 and 1846 cm-1 at 270 K, and both frequencies upshifted as the temperature was lowered, retaining the peak separation of 8-9 cm-1 . The relative intensity of the lower-frequency peak increased with decreasing temperature up to ~120 K, whereas it was mostly unchanged below this temperature . This observation indicates that two distinct conformations with slightly different NO structures are thermally equilibrated in the dark-inactive NHase above ~120 K, and the interconversion is frozen-in at lower temperatures . The intensity ratio of the NO bands changed gradually upon increasing the pH from 5.5 to 11.0, but no specific pKa value was found . This result, together with the comparison of the light-induced FTIR difference spectra measured at pH 6.5 and 9.0, suggests that the protonation/deprotonation of a specific amino acid group in the active site of NHase is not a direct cause of the occurrence of the two conformations, although several protonatable groups in the protein may influence the energetics of the two conformers . From the previous observation that the isolated alpha subunit of NHase exhibited a single broad NO peak, it is suggested that interaction of the beta subunit forming the reactive cavity is essential for the double-minimum potential of the active-site structure . The frequencies and widths of the two NO bands changed upon addition of propionamide, 1,4-dioxane, and cyclohexyl isocyanide, indicating that these compounds are bound to the active pocket and change the interactions of the iron center or the dielectric environments around the NO molecule . Thus, the NO bands of NHase can also be a useful probe to monitor the binding of substrates and their analogues to the active pocket. FEMS Microbiol Lett, 2004 Aug 1, 237(1), 35 - 40 Isolation and characterization of the Rhodococcus opacus thiostrepton-inducible genes tipAL and tipAS: application for recombinant protein expression in Rhodococcus; Dong L et al.; We cloned the Rhodococcus opacus (strain DSM 44193) tipA gene, which encodes two translation products, TipAL and TipAS . The gene products are homologous to the Streptomyces spp . TipAL and TipAS proteins, respectively . The tipA promoter is highly active and TipAS protein is predominantly accumulated in R . opacus cells when the inducer of transcription, thiostrepton, was presented in culture medium . We found that thiostrepton is also induced the expression of an endogenous TipA-family protein in Rhodococcus erythropolis (strain JCM3201) . The minimal tipA promoter region was defined (57 bp) and the conserved nucleotide sequence of the putative TipAL protein binding site (TipA-box) was identified in that region . The tipA gene is presumed to be transcribed into a leaderless mRNA . We applied the tipA promoter successfully for recombinant protein expression in R . erythropolis cells. J Immunol, 2004 Aug 1, 173(3), 1914 - 24 Innate immune responses to Rhodococcus equi; Darrah PA et al.; We examined innate immune responses to the intracellular bacterium Rhodococcus equi and show that infection of macrophages with intact bacteria induced the rapid translocation of NF-kappa B and the production of a variety of proinflammatory mediators, including TNF, IL-12, and NO . Macrophages from mice deficient in MyD88 failed to translocate NF-kappa B and produced virtually no cytokines in response to R . equi infection, implicating a TLR pathway . TLR4 was not involved in this response, because C3H/HeJ macrophages were fully capable of responding to R . equi infection, and because RAW-264 cells transfected with a dominant negative form of TLR4 responded normally to infection by R . equi . A central role for TLR2 was identified . A TLR2 reporter cell was activated by R . equi, and RAW-264 cells transfected with a dominant negative TLR2 exhibited markedly reduced cytokine responses to R . equi . Moreover, macrophages from TLR2(-/-) mice exhibited diminished cytokine responses to R . equi . The role of the surface-localized R . equi lipoprotein VapA (virulence-associated protein A), in TLR2 activation was examined . Purified rVapA activated a TLR2-specific reporter cell, and it induced the maturation of dendritic cells and the production of cytokines from macrophages . Importantly, TLR2(-/-)-deficient but not TLR4(-/-)-deficient mice were found to be compromised in their ability to clear a challenge with virulent R . equi . We conclude that the efficient activation of innate immunity by R . equi may account for the relative lack of virulence of this organism in immunocompetent adults. Vet Immunol Immunopathol, 2004 Sep, 101(1-2), 1 - 17 Construction and application of a bovine immune-endocrine cDNA microarray; Tao W et al.; A variety of commercial DNA arrays specific for humans and rodents are widely available; however, microarrays containing well-characterized genes to study pathway-specific gene expression are not as accessible for domestic animals, such as cattle, sheep and pigs . Therefore, a small-scale application-targeted bovine immune-endocrine cDNA array was developed to evaluate genetic pathways involved in the immune-endocrine axis of cattle during periods of altered homeostasis provoked by physiological or environmental stressors, such as infection, vaccination or disease . For this purpose, 167 cDNA sequences corresponding to immune, endocrine and inflammatory response genes were collected and categorized . Positive controls included 5 housekeeping genes (glyceraldehydes-3-phosphate dehydrogenase, hypoxanthine phosphoribosyltransferase, ribosomal protein L19, beta-actin, beta2-microglobulin) and bovine genomic DNA . Negative controls were a bacterial gene (Rhodococcus equi 17-kDa virulence-associated protein) and a partial sequence of the plasmid pACYC177 . In addition, RNA extracted from un-stimulated, as well as superantigen (Staphylococcus aureus enterotoxin-A, S . aureus Cowan Pansorbin Cells) and mitogen-stimulated (LPS, ConA) bovine blood leukocytes was mixed, reverse transcribed and PCR amplified using gene-specific primers . The endocrine-associated genes were amplified from cDNA derived from un-stimulated bovine hypothalamus, pituitary, adrenal and thyroid gland tissues . The array was constructed in 4 repeating grids of 180 duplicated spots by coupling the PCR amplified 213-630 bp gene fragments onto poly-l-lysine coated glass slides . The bovine immune-endocrine arrays were standardized and preliminary gene expression profiles generated using Cy3 and Cy5 labelled cDNA from un-stimulated and ConA (5 microg/ml) stimulated PBMC of 4 healthy Holstein cows (2-4 replicate arrays/cow) in a time course study . Mononuclear cell-derived cytokine and chemokine (IL-2, IL-1alpha, TNFalpha, IFN-gamma, TGFbeta-1, MCP-1, MCP-2 and MIP-3alpha) mRNA exhibited a repeatable and consistently low expression in un-stimulated cells and at least a two-fold increased expression following 6 and 24 h ConA stimulation as compared to 0 h un-stimulated controls . In contrast, expression of antigen presenting molecules, MHC-DR, MHC-DQ and MHC-DY, were consistently at least two-fold lower following 6 and 24 h ConA stimulation . The only endocrine gene with differential expression following ConA stimulation was prolactin . Additionally, due to the high level of genetic homology between ovine, swine and bovine genes, RNA similarly acquired from sheep and pigs was evaluated and similar gene expression patterns were noted . These data demonstrate that this application-targeted array containing a set of well characterized genes can be used to determine the relative gene expression corresponding to immune-endocrine responses of cattle and related species, sheep and pigs. Chemistry, 2004 Jul 19, 10(14), 3467 - 78 Biocatalytic asymmetric rearrangement of a methylene-interrupted bis-epoxide: simultaneous control of four asymmetric centers through a biomimetic reaction cascade; Glueck SM et al.; Asymmetric enzyme-catalyzed hydrolysis of methylene-interrupted bis-epoxides 1 a and 1 b catalyzed by bacterial epoxide hydrolases furnished tetrahydrofuran derivatives 2 a and 2 b through a hydrolysis-rearrangement cascade . Whereas racemic bis-oxiranes 1 b-d underwent kinetic resolution with moderate stereoselectivities to yield products with up to 92 % ee and 66 % de: meso-bis-oxirane cis,cis-1 a was transformed into (6R,7R,9S,10S)-2 a in 94 % ee and 89 % de at high conversion (85 %) by Rhodococcus sp . CBS 717.73 as the major product . The reaction sequence resembles a biomimetic reaction cascade and provides an efficient entry into the structural core of annonaceous acetogenins with simultaneous control of four stereocenters. Appl Environ Microbiol, 2004 Jul, 70(7), 4398 - 401 Degradation of alkyl ethers, aralkyl ethers, and dibenzyl ether by Rhodococcus sp . strain DEE5151, isolated from diethyl ether-containing enrichment cultures; Kim YH et al.; Twenty strains isolated from sewage sludge were found to degrade various ethers, including alkyl ethers, aralkyl ethers, and dibenzyl ether . In Rhodococcus strain DEE5151, induction of ether degradation needed substrates exhibiting at least one unsubstituted Calpha-methylene moiety as the main structural prerequisite . The cleavage reaction observed with anisole, phenetole, and dibenzyl ether indicates that the initial oxidation occurs at such respective Calpha positions . Diethyl ether-induced strain DEE5151 degraded dibenzyl ether via intermediately accumulated benzoic acid . Phenetole seems to be subject also to another ether-cleaving enzyme . Other strains of this group showed different enzymatic activities towards the substrate classes investigated. Appl Environ Microbiol, 2004 Jul, 70(7), 4230 - 41 Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the hanford site, washington state; Fredrickson JK et al.; Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface . The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), (137)Cs, and (99)Tc . Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation . The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to approximately 10(4) CFU g(-1), but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 microCi of (137)Cs/g) . The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria . Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia . Two isolates from the second-most radioactive sample (>20 microCi of (137)Cs g(-1)) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy . Many of the gram-positive isolates were resistant to lower levels of gamma radiation . These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste. Vet Res, 2004 Jul-Aug, 35(4), 383 - 96 Rhodococcus equi; Meijer WG et al.; Rhodococcus equi is an important cause of subacute or chronic abscessating bronchopneumonia of foals up to 3-5 months of age . It shares the lipid-rich cell wall envelope characteristic of the mycolata, including Mycobacterium tuberculosis, as well as the ability of pathogenic members of this group to survive within macrophages . The possession of a large virulence plasmid in isolates recovered from pneumonic foals is crucial for virulence . The plasmid contains an 27 kb pathogenicity island (PI) that encodes seven related virulence-associated proteins (Vaps), including the immunodominant surface-expressed protein, VapA . Only PI genes are differentially expressed when the organism is grown in macrophages in vitro . Ten of the PI genes, including six Vap genes, have signal sequences, suggesting that they are exported from the cell to interact with the macrophage . Different PI genes are regulated by temperature, pH, iron, oxidative stress and probably also by magnesium, all environmental changes encountered after environmental R . equi are inhaled in dust and are ingested into macrophages in the lung . The basis of pathogenicity of R . equi is its ability to multiply in and eventually to destroy alveolar macrophages . Infectivity is largely or exclusively limited to cells of the monocyte-macrophage lineage . Current evidence suggests that infection of foals with virulent R . equi results in some foals in subversion of cell-mediated immunity and development of an ineffective and sometimes lethal Th2-based immune response . Significant progress has been made recently in the development of R . equi-E . coli shuttle vectors, transformation and random and site specific mutagenesis procedures, all of which will be important in molecular dissection of the mechanisms by which R . equi subverts normal macrophage killing mechanisms and cell-mediated immunity. Carbohydr Res, 2004 Jul 12, 339(10), 1761 - 71 Facile synthesis of arabinomannose penta- and decasaccharide fragments of the lipoarabinomannan of the equine pathogen, Rhodococcus equi; Ma Z et al.; Pentasaccharide repeating unit 20 of the lipoarabinomannan from the equine pathogen, Rhodococcus equi, and its dimer 31, were synthesized . The pentasaccharide was obtained by assembling a benzoylated 2,6-branched mannosyl trisaccharide acceptor 13 with a free hydroxyl group at C-2' of the mannose residue attached to the core mannose residue by (1 --> 6)-linkage, followed by coupling with 2,3,5-tri-O-benzoyl-alpha-D-arabinofuranosyl-(1 --> 2)-3,4,6-tri-O-benzoyl-alpha-D-mannopyranosyl trichloroacetimidate (18), and by deacylation . Meanwhile, the decamer 31 was obtained by firstly preparing a benzoylated mannose (1 --> 6)-linked tetrasaccharide backbone 26 with 2-, 2"-O-ClAc, and 2'-, 2'''-O-Ac groups, respectively, then by dechloroacetylation and subsequent condensation with perbenzoylated trichloroacetimidate, and then by deacetylation and subsequent coupling with 18, and finally, by deacylation. Biosci Biotechnol Biochem, 2004 Jun, 68(6), 1249 - 58 Biphenyl-inducible promoters in a polychlorinated biphenyl-degrading bacterium, Rhodococcus sp . RHA1; Takeda H et al.; Five transcriptional promoters of biphenyl-degradation genes in Rhodococcus sp . RHA1 were characterized . We newly identified the etbA4 promoter region, which was located adjacent upstream from a ferredoxin reductase gene, etbA4 and a dihydrodiol dehydrogenase gene, bphB2 . The etbA4 promoter activity was determined in RHA1 using a promoter probe vector with a luxAB luciferase reporter gene, and was induced by a variety of aromatic compounds as well as the bphA1, ebdA1, etbA1, and etbD1 promoters . All these promoters were induced by aromatic compounds in a closely related heterologous host, R . erythropolis IAM1399 in the presence of RHA1 bphST genes, suggesting that these five promoters are under the control of bphST-coding two-component regulatory system . Sequence comparison of the bphA1 promoter with the ebdA1 and etbA1 promoters, whose transcription starts were determined by primer extension analysis, revealed a consensus sequence centering 42-bp upstream from the transcription start . This consensus was also conserved in the etbA4 and etbD1 promoters, and deletions of the bphA1 promoter affecting the consensus impaired inducible promoter activity . These results suggest that this consensus plays a role in transcription induction and/or the promotion of biphenyl degradation genes in RHA1. Curr Opin Microbiol, 2004 Jun, 7(3), 255 - 61 Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications; van der Geize R et al.; The field of Rhodococcus cell engineering is rapidly advancing because of the availability of improved genetic tools and increased insights in their broad catabolic and biochemical diversity . Rhodococci harbor large linear plasmids that may contribute to their catabolic diversity . In addition, multiple pathways and gene homologs are often present, thus further increasing Rhodococcus catabolic versatility and efficiency . The recent development of effective genetic tools for Rhodococcus, such as unmarked gene deletion, transposon-based mutagenesis, and gene expression systems, now allows the construction of biocatalysts with desirable properties for industrial purposes . This is exemplified here by a description of cell engineering of biocatalysts for improved desulphurization and steroid biotransformation. J Infect, 2004 Jul, 49(1), 17 - 9 Cavitary pneumonia secondary to Tsukamurella in an AIDS patient . First case and a review of the literature; Alcaide ML et al.; Tsukamurella is a Gram-positive, variable rod-shaped, weakly acid-alcohol-fast, non motile, aerobic bacterium that belongs to the genus Rhodococcus . Tsukamurella has been reported as a cause of infections in humans with immunosuppression and indwelling foreign bodies . It has also been isolated in one patient with AIDS (Acquired Immunodeficiency Syndrome) as a saprophytic organism . Optimal management of infections secondary to this micro-organism is still uncertain due to the paucity of cases . The combination of a beta-lactam and an aminoglycoside, along with removal of medical devices, appear to be the treatment of choice . We report the case of an AIDS patient who presented with multiple lung cavitary lesions secondary to Tsukamurella . This is the first case reported of Tsukamurella as a pathogenic agent in an AIDS patient . We also propose a successful oral antibiotic regimen with fluoroquinolone and rifampin to treat infections secondary to this uncommon micro-organism. Microbiology, 2004 Jun, 150(Pt 6), 1859 - 67 Rhodococcus opacus expresses the xsc gene to utilize taurine as a carbon source or as a nitrogen source but not as a sulfur source; Denger K et al.; The Gram-positive bacteria Rhodococcus opacus ISO-5 and Rhodococcus sp . RHA1 utilized taurine (2-aminoethanesulfonate) as the sole source of carbon or of nitrogen or of sulfur for growth . Different gene clusters and enzymes were active under these different metabolic situations . Under carbon- or nitrogen-limited conditions three enzymes were induced, though to different levels: taurine-pyruvate aminotransferase (Tpa), alanine dehydrogenase (Ald) and sulfoacetaldehyde acetyltransferase (Xsc) . The specific activities of these enzymes in R . opacus ISO-5 were sufficient to explain the growth rates under the different conditions . These three enzymes were purified and characterized, and the nature of each reaction was confirmed . Analyses of the genome of Rhodococcus sp . RHA1 revealed a gene cluster, tauR-ald-tpa, putatively encoding regulation and oxidation of taurine, located 20 kbp from the xsc gene and separate from two candidate phosphotransacetylase (pta) genes, as well as many candidate ABC transporters (tauBC) . PCR primers allowed the amplification and sequencing of the tauR-ald-tpa gene cluster and the xsc gene in R . opacus ISO-5 . The N-terminal sequences of the three tested proteins matched the derived amino acid sequences of the corresponding genes . The sequences of the four genes found in each Rhodococcus strain shared high degrees of identity (>95 % identical positions) . RT-PCR studies proved transcription of the xsc gene when taurine was the source of carbon or of nitrogen . Under sulfur-limited conditions no xsc mRNA was generated and no Xsc was detected . Taurine dioxygenase (TauD), the enzyme catalysing the anticipated desulfonative reaction when taurine sulfur is assimilated, was presumed to be present because oxygen-dependent taurine disappearance was demonstrated with taurine-grown cells only . A putative tauD gene (with three other candidates) was detected in strain ISO-5 . Regulation of the different forms of metabolism of taurine remains to be elucidated. Vet Immunol Immunopathol, 2004 Jul, 100(1-2), 33 - 48 Hematologic and immunophenotypic factors associated with development of Rhodococcus equi pneumonia of foals at equine breeding farms with endemic infection; Chaffin MK et al.; Rhodococcus equi causes severe pyogranulomatous pneumonia in foals and in immunocompromised people . In mice, both CD4+ and CD8+ T lymphocytes contribute to host defense against R . equi, but CD4+ T lymphocytes are required for pulmonary clearance of the bacteria . In this prospective study of 208 foals at two equine breeding farms with endemic R . equi infections, we collected peripheral blood samples at 2 and 4 weeks of age and at the time of diagnosis of R . equi pneumonia . Samples were analyzed for concentrations of total and differential leukocytes, EqCD4+ and EqCD8+ T lymphocytes, and B lymphocytes . Thirty (14.4%) foals developed R . equi pneumonia . At the 2nd week of life, affected foals had significantly lower concentrations of white blood cells (WBC) and segmented neutrophils, significantly lower proportions of EqCD4+ T lymphocytes, and significantly higher proportions of EqCD8+ T lymphocytes . The EqCD4:EqCD8 ratio was significantly lower for affected foals . At the 4th week of life, affected foals had significantly lower concentrations of segmented neutrophils and EqCD4+ T lymphocytes than did unaffected foals . The ratio of EqCD4:EqCD8 was significantly lower for affected foals . Two- and 4-week-old foals with ratios of EqCD4:EqCD8<3 were significantly more likely to develop R . equi pneumonia . There was a significant farm effect which diluted our statistical power to detect differences; however; after adjusting for the farm effect, 2-week-old foals with ratios of EqCD4:EqCD8<3 remained significantly more likely to develop R . equi pneumonia . There were no significant differences in immunophenotypic variables between affected foals (at the time of diagnosis) and age-matched control foals . These data suggest that there are hematologic and immunophenotypic differences between affected and unaffected foals during the first 2-4 weeks of life, prior to onset of clinical signs of R . equi pneumonia . These differences may represent important immunologic mechanisms associated with increased susceptibility of individual foals to infection with R . equi . Because there was considerable overlap between values for affected and unaffected foals, we cannot yet recommend immunophenotyping of foals at endemically-infected farms as a clinically useful screening tool to identify foals at increased risk of developing R . equi pneumonia. Acta Vet Hung, 2004, 52(2), 143 - 50 Isolation and characterisation of Mycobacterium avium and Rhodococcus equi from granulomatous lesions of swine lymph nodes in Slovenia; Pate M et al.; Granulomatous lesions in bovine and especially swine lymph nodes are still frequently observed during routine veterinary meat inspections even though Mycobacterium bovis infections are no longer detected in domestic animals in Slovenia . Different lymph nodes of pigs (n = 260) were investigated using classical bacteriological and molecular methods . Mycobacterium avium alone was isolated in 47.3% of pigs and in mixed infection with Rhodococcus equi in 3.9% of pigs . R . equi alone was isolated in 27.3% and in mixed infection with mycobacteria other than M . avium in 1.5% of pigs . A total of 133 M . avium isolates were typed using the IS1245, IS901 and FR300 PCR . Almost two thirds (60.9%) of isolates belonged to M . avium hominissuis (IS901-, IS1245+ genotype), 33.8% of isolates belonged to M . avium avium (IS901+, IS1245+ genotype) and 5.3% of isolates remained non-typed . Fifty out of 85 R . equi isolates were tested for the virulence-associated antigens (VapA and VapB) . Nearly two thirds (60.0%) were positive for VapB while all the other isolates were VapA- and VapB-negative. Biotechnol Appl Biochem, 2004 Jun, 39(Pt 3), 303 - 6 Biotransformation of geraniol by Rhodococcus sp . strain GR3; Chatterjee T; Microbial degradation of geraniol, a natural monoterpene alcohol, was studied using a Rhodococcus sp . strain GR3 isolated from soil . The bioconversion product was identified as geranic acid {(2 E )-3,7-dimethylocta-2,6-dienoic acid} and its structure was established by (1)H-NMR, Fourier-transform IR spectrometry and GC-MS . The optimum temperature for this bioconversion was found to be 30 degrees C, and the reaction proceeds to a saturation with a time constant of 12.5 h . No appreciable degradation of product was observed using this bacterium. Int J Syst Evol Microbiol, 2004 May, 54(Pt 3), 827 - 35 Rothia aeria sp . nov., Rhodococcus baikonurensis sp . nov . and Arthrobacter russicus sp . nov., isolated from air in the Russian space laboratory Mir; Li Y et al.; Four Gram-positive bacteria, strains A1-17B(T), A1-22(T), A1-3(T) and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study . Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17B(T)), Rhodococcus (A1-22(T)) and Arthrobacter (A1-3(T) and A1-8) . Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus . 16S rDNA similarity values between strain A1-17B(T) and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa, Rothia mucilaginosa and Rothia nasimurium, were respectively 99.8, 98.0, 96.4 and 95.4 % . Polyphasic taxonomic evidence indicated that strain A1-17B(T) should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus ROTHIA: Strain A1-22(T) formed a coherent cluster with Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA-DNA relatedness values were only 45.5, 35.3, 18.9 and 21.9 % . Strains A1-3(T) and A1-8 shared 99.9 % 16S rDNA sequence similarity, and strain A1-3(T) showed the highest level of 16S rDNA similarity, 96.6 %, to Arthrobacter polychromogenes . Contrasting biochemical characteristics were also identified . Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp . nov . (A1-17B(T)=GTC 867(T)=JCM 11412(T)=DSM 14556(T)), Rhodococcus baikonurensis sp . nov . (A1-22(T)=GTC 1041(T)=JCM 11411(T)=DSM 44587(T)) and Arthrobacter russicus sp . nov . (A1-3(T)=GTC 863(T)=JCM 11414(T)=DSM 14555(T)). Vet Microbiol, 2004 May 20, 100(1-2), 121 - 7 Identification and differentiation of avirulent and virulent Rhodococcus equi using selective media and colony blotting DNA hybridization to determine their concentrations in the environment; Muscatello G et al.; Selective agar media have been used for many years to facilitate the isolation of Rhodococcus equi from environmental and clinical samples . However, characterisation of R . equi still requires the use of immunochemical or polymerase chain reaction (PCR) analysis to differentiate between virulent and avirulent isolates . Here, we describe a novel method to detect and differentiate between R . equi isolates using colony blotting and DNA hybridization . Radiolabelled PCR product derived from the R . equi rrnA gene and specific hybridization conditions enabled differentiation of colonies of R . equi from environmental species, whilst radiolabelled PCR product derived from the R . equi vapA gene, under specific hybridization conditions, allowed differentiation between avirulent and virulent R . equi . This technique has the potential to be used for quantitative screening of large environmental and clinical samples for both avirulent and virulent R . equi . Its use in ecological and epidemiological studies of R . equi has the potential to improve understanding of the relationship between the environment, the foal and the disease. Appl Microbiol Biotechnol, 2004 Sep, 65(4), 440 - 5 Epub 2004 May 07. Relation between bacterial strain resistance to solvents and biodesulfurization activity in organic medium; Bouchez-Naitali M et al.; Microorganisms used in biodesulfurization of petroleum products have to withstand high concentrations of hydrocarbons . The capacities of seven desulfurizing strains of Rhodococcus to be active in the presence of solvents were evaluated . Octanol and toluene (log P=2.9) were selected as toxic solvents . The effect of the solvents was determined by measuring either inhibition of growth or the decrease in respiratory activity of the cells . Differences among strains in their resistance to solvent responses were observed, but these variations were dependent on the test used . Resistance to solvents was then compared to the capacity of the different strains to retain biodesulfurization activity in the presence of hexadecane . Inhibition of desulfurization by high concentrations of hexadecane was found to be well correlated to the sensitivity of the strains to respiration inhibition by toluene, but not to growth inhibition . This result also showed that the respirometric test was a rapid and reliable test to select solvent-resistant strains for use as resting cells in biocatalysis processes, such as biodesulfurization, in organic media. Appl Environ Microbiol, 2004 May, 70(5), 2854 - 60 Nitrite elimination and hydrolytic ring cleavage in 2,4,6-trinitrophenol (picric acid) degradation; Hofmann KW et al.; Two hydrogenation reactions in the initial steps of degradation of 2,4,6-trinitrophenol produce the dihydride Meisenheimer complex of 2,4,6-trinitrophenol . The npdH gene (contained in the npd gene cluster of the 2,4,6-trinitrophenol-degrading strain Rhodococcus opacus HL PM-1) was shown here to encode a tautomerase, catalyzing a proton shift between the aci-nitro and the nitro forms of the dihydride Meisenheimer complex of 2,4,6-trinitrophenol . An enzyme (which eliminated nitrite from the aci-nitro form but not the nitro form of the dihydride complex of 2,4,6-trinitrophenol) was purified from the 2,4,6-trinitrophenol-degrading strain Nocardioides simplex FJ2-1A . The product of nitrite release was the hydride Meisenheimer complex of 2,4-dinitrophenol, which was hydrogenated to the dihydride Meisenheimer complex of 2,4-dinitrophenol by the hydride transferase I and the NADPH-dependent F(420) reductase from strain HL PM-1 . At pH 7.5, the dihydride complex of 2,4-dinitrophenol is protonated to 2,4-dinitrocyclohexanone . A hydrolase was purified from strain FJ2-1A and shown to cleave 2,4-dinitrocyclohexanone hydrolytically to 4,6-dinitrohexanoate. Appl Environ Microbiol, 2004 May, 70(5), 2667 - 77 Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense; Idris R et al.; Thlaspi goesingense is able to hyperaccumulate extremely high concentrations of Ni when grown in ultramafic soils . Recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet . In this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing T . goesingense were characterized in detail by using both cultivation and cultivation-independent techniques . Bacteria were identified by 16S rRNA sequence analysis, and isolates were further characterized regarding characteristics that may be relevant for a beneficial plant-microbe interaction-Ni tolerance, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and siderophore production . In the rhizosphere a high percentage of bacteria belonging to the Holophaga/Acidobacterium division and alpha-Proteobacteria were found . In addition, high-G+C gram-positive bacteria, Verrucomicrobia, and microbes of the Cytophaga/Flexibacter/Bacteroides division colonized the rhizosphere . The community structure of shoot-associated bacteria was highly different . The majority of clones affiliated with the Proteobacteria, but also bacteria belonging to the Cytophaga/Flexibacter/Bacteroides division, the Holophaga/Acidobacterium division, and the low-G+C gram-positive bacteria, were frequently found . A high number of highly related Sphingomonas 16S rRNA gene sequences were detected, which were also obtained by the cultivation of endophytes . Rhizosphere isolates belonged mainly to the genera Methylobacterium, Rhodococcus, and Okibacterium, whereas the majority of endophytes showed high levels of similarity to Methylobacterium mesophilicum . Additionally, Sphingomonas spp . were abundant . Isolates were resistant to Ni concentrations between 5 and 12 mM; however, endophytes generally tolerated higher Ni levels than rhizosphere bacteria . Almost all bacteria were able to produce siderophores . Various strains, particularly endophytes, were able to grow on ACC as the sole nitrogen source. Vet Immunol Immunopathol, 2004 Mar, 98(1-2), 91 - 100 The immunogenicity of Rhodococcus equi GroEL2-based vaccines in a murine model; Vanniasinkam T et al.; Rhodococcus equi is a significant intracellular bacterial pathogen in foals . However, at present there is no commercially available vaccine for the prevention of R . equi-induced disease in these animals . Studies have shown that GroEL based vaccines can afford protection against some intracellular pathogens . In this study, the R . equi gene encoding the heat shock protein GroEL2 was cloned and sequenced, with a view to using it as a vaccine candidate . The promoter region of the gene contained two copies of controlling inverted repeat of chaperone expression (CIRCE) motifs, which are well-recognised transcriptional regulators of bacterial heat shock proteins . The R . equi GroEL2 was expressed in E . coli BL21 DE3 with a C-terminal His-tag and sequenced to confirm its identity . The R . equi purified His-tagged GroEL2 protein and a groEL2-based DNA vaccine were used in separate experiments to immunise BALB/c mice . The recombinant protein-based vaccine elicited a mixed Th1/Th2 response whereas the DNA vaccine was found to elicit a predominantly Th1 biased immune response . However, when vaccinated mice were challenged intravenously with 1.5 x 10(7) R . equi neither vaccine elicited enhanced bacterial clearance from the spleen or liver in this model . The reasons for this apparent lack of success are discussed. Appl Microbiol Biotechnol, 2004 Nov, 66(1), 92 - 9 Epub 2004 Nov. Degradation pathways of cyclic alkanes in Rhodococcus sp . NDKK48; Koma D et al.; The degradation pathways for cyclic alkanes (c-alkanes) in Rhodococcus sp . NDKK48 were investigated . Strain NDKK48 used dodecylcyclohexane as a sole carbon and energy source, and five metabolites in the dodecylcyclohexane degradation pathway were detected by gas-chromatography/mass spectra . The metabolites were identified as cyclohexanecarboxylic acid, cyclohexylacetic acid, 1-cyclohexene-1-acetic acid, 4-dodecylcyclohexanol, and 4-dodecylcyclohexanone . The strain degrades dodecylcyclohexane via a ring oxidation pathway and an alkyl side chain oxidation pathway . Cyclohexanecarboxylic acid was further oxidized to muconic acid via 1-cyclohexene-1-carboxylic acid and benzoic acid, and the muconic acid was finally used by strain NDKK48 for growth . Methylcyclohexane and cyclohexane were co-oxidized with hexadecane by strain NDKK48 . Methylcyclohexane was degraded via a ring oxidation pathway, and the degradation pathway contained part of the Baeyer-Villiger oxidation for ring cleavage . Cyclohexane was also degraded by the same pathway as methylcyclohexane . Thus, strain NDKK48 has two pathways for the complete degradation of c-alkanes. Biosci Biotechnol Biochem, 2004 Apr, 68(4), 787 - 95 Multiplicity of 2,3-dihydroxybiphenyl dioxygenase genes in the Gram-positive polychlorinated biphenyl degrading bacterium Rhodococcus rhodochrous K37; Taguchi K et al.; Rhodococcus rhodochrous K37, a Gram-positive bacterium grown under alkaline conditions, was isolated for its ability to metabolize PCBs . Analysis revealed that it has eight genes encoding extradiol dioxygenase, which has 2,3-dihydroxybiphenyl 1,2-dioxygenase activity, and these genes were designated bphC1 to bphC8 . According to the classification of extradiol dioxygenases {Eltis, L . D., and Bolin, J . T., J . Bacteriol., 178, 5930-5937 (1996)}, BphC3 and BphC6 belong to the type II enzyme group . The other six BphCs were classified as members of the type I extradiol dioxygenase group . BphC4 and BphC8 were classified into a new subfamily of type I, family 3 . Two linear plasmids, 200 kb and 270 kb in size, were found in K37, and the bphC6 and bphC8 genes were located in the 200 kb linear plasmid . Northern hybridization analysis revealed that the bphC1, bphC2, and bphC7 genes were induced in the presence of testosterone, the bphC6 gene was induced by fluorene, and the bphC8 gene was induced by biphenyl . All eight BphC products exhibited much higher substrate activity for 2,3-dihydroxybiphenyl than for catechol, 3-methylcatechol, or 4-methylcatechol. BMC Microbiol . 2004 Apr 14;4(1):15. pB264, a small, mobilizable, temperature sensitive plasmid from Rhodococcus; Lessard PA et al.; BACKGROUND: Gram-positive bacteria of the genus Rhodococcus have shown an extraordinary capacity for metabolizing recalcitrant organic compounds . One hindrance to the full exploitation of Rhodococcus is the dearth of genetic tools available for strain manipulation . To address this issue, we sought to develop a plasmid-based system for genetic manipulation of a variety of Rhodococcus strains . RESULTS: We isolated and sequenced pB264, a 4,970 bp cryptic plasmid from Rhodococcus sp . B264-1 with features of a theta-type replication mechanism . pB264 was nearly identical to pKA22, a previously sequenced but uncharacterized cryptic plasmid . Derivatives of pB264 replicate in a diverse range of Rhodococcus species, showing that this plasmid does not bear the same host range restrictions that have been exhibited by other theta replicating plasmids . Replication or maintenance of pB264 is inhibited at 37 degrees C, making pB264 useful as a suicide vector for genetic manipulation of Rhodococcus . A series of deletions revealed that ca . 1.3 kb from pB264 was sufficient to support replication and stable inheritance of the plasmid . This region includes two open reading frames that encode functions (RepAB) that can support replication of pB264 derivatives in trans . Rhodococcus sp . B264-1 will mobilize pB264 into other Rhodococcus species via conjugation, making it possible to genetically modify bacterial strains that are otherwise difficult to transform . The cis-acting element (oriT) required for conjugal transfer of pB264 resides within a ca . 0.7 kb region that is distinct from the regions responsible for replication . CONCLUSION: Shuttle vectors derived from pB264 will be useful for genetic studies and strain improvement in Rhodococcus, and will also be useful for studying the processes of theta replication and conjugal transfer among actinomycetes. Vet Radiol Ultrasound, 2004 Mar-Apr, 45(2), 172 - 6 Diagnostic contribution of thoracic ultrasonography in 17 foals with Rhodococcus equi pneumonia; Ramirez S et al.; The aim of this retrospective study was to determine the clinical usefulness of thoracic ultrasonography compared to thoracic radiography in evaluation of Rhodococcus equi pneumonia . Criteria for patient inclusion in this study were: (1) isolation of R . equi from transtracheal aspirate, (2) radiographic evaluation of the pulmonary parenchyma, and (3) sonographic evaluation of the pulmonary parenchyma . Seventeen foals met this criteria and their medical records were reviewed . Pyogranulomatous pneumonia was identified radiographically in 13 foals . Severe consolidative pneumonia with no detectable abscessation was identified radiographically in three others . Both consolidation and abscessation were identified radiographically in one . In this foal only consolidation was ultrasonographically identified . Ultrasonographically, pulmonary abscessation was identified in 12 foals and pulmonary consolidation with no detectable abscessation was identified in three others . Sonographic examination allowed detection of only pleural irregularities in one foal, which was subsequently found to have pyogranulomatous pneumonia radiographically . Results indicate that ultrasonography may be an accurate alternative imaging modality for detection of pulmonary pathology attributed to R . equi pneumonia in foals when thoracic radiography is not available. Appl Microbiol Biotechnol, 2004 Aug, 65(2), 168 - 76 Epub 2004 Apr 07. Indene bioconversion by a toluene inducible dioxygenase of Rhodococcus sp . I24; Priefert H et al.; Rhodococcus sp . I24 can oxygenate indene via at least three independent enzyme activities: (i) a naphthalene inducible monooxygenase (ii) a naphthalene inducible dioxygenase, and (iii) a toluene inducible dioxygenase (TID) . Pulsed field gel analysis revealed that the I24 strain harbors two megaplasmids of approximately 340 and approximately 50 kb . Rhodococcus sp . KY1, a derivative of the I24 strain, lacks the approximately 340 kb element as well as the TID activity . Southern blotting and sequence analysis of an indigogenic, I24-derived cosmid suggested that an operon encoding a TID resides on the approximately 340 kb element . Expression of the tid operon was induced by toluene but not by naphthalene . In contrast, naphthalene did induce expression of the nid operon, encoding the naphthalene dioxygenase in I24 . Cell free protein extracts of Escherichia coli cells expressing tidABCD were used in HPLC-based enzyme assays to characterize the indene bioconversion of TID in vitro . In addition to 1-indenol, indene was transformed to cis-indandiol with an enantiomeric excess of 45.2% of cis-(1S,2R)-indandiol over cis-(1R,2S)-indandiol, as revealed by chiral HPLC analysis . The Km of TID for indene was 380 microM . The enzyme also dioxygenated naphthalene to cis-dihydronaphthalenediol with an activity of 78% compared to the formation of cis-indandiol from indene . The Km of TID for naphthalene was 28 microM . TID converted only trace amounts of toluene to 1,2-dihydro-3-methylcatechol after prolonged incubation time . The results indicate the role of the tid operon in the bioconversion of indene to 1-indenol and cis-(1S,2R)-indandiol by Rhodococcus sp . I24. Syst Appl Microbiol, 2004 Feb, 27(1), 61 - 5 Rhodococcus aetherivorans sp . nov., a new species that contains methyl t-butyl ether-degrading actinomycetes; Goodfellow M et al.; The taxonomic positions of two actinomycetes, strains Bc663 and 10bc312T, provisionally assigned to the genus Rhodococcus were determined using a combination of genotypic and phenotypic properties . The organisms have phenotypic properties typical of members of the genus Rhodococcus and were assigned to the 16S rRNA subgroup which contains Rhodococcus rhodochrous and closely related species . The two strains, which have many phenotypic features in common, belong to the same genomic species albeit one readily separated from Rhodococcus ruber with which they form a distinct phyletic line . The organisms were also distinguished from all of the species classified in the R . rhodochrous subgroup, including R . ruber, using a combination of phenotypic properties . The genotypic and phenotypic data show that strains Bc663 and 10bc312T merit recognition as a new species of Rhodococcus . The name proposed for the new species is Rhodococcus aetherivorans (10bc312T = DSM 44752T = NCIMB 13964T). Biotechnol Bioeng, 2004 Apr 20, 86(2), 136 - 48 A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35 degrees C; Nakashima N et al.; Escherichia coli cells are the most commonly used host cells for large-scale production of recombinant proteins, but some proteins are difficult to express in E . coli . Therefore, we tested the nocardioform actinomycete Rhodococcus erythropolis, which grows at temperatures ranging from 4 to 35 degrees C, as an expression host cell . We constructed inducible expression vectors, where the expression of the target genes could be controlled with the antibiotic thiostrepton . Using these expression vectors, several milligrams of reporter proteins could be isolated from 1 liter of culture of R . erythropolis cells grown at a temperature range from 4 to 35 degrees C . Moreover, we successfully purified serum amyloid A1, NADH dehydorogenase 1 alpha subcomplex 4, cytochrome b5-like protein, apolipoprotein A-V, cathepsin D, pancreatic Rnase, and HMG-1 that are all difficult to express in E . coli . In the case of kallikrein 6, mouse deoxyribonuclease I and Kid1, which are also difficult to express in E . coli, the expression level of each protein increased when proteins were expressed at low temperature (4 degrees C) . Based on these results, we conclude that a recombinant protein expression system using R . erythropolis as the host cell is superior to respective E . coli systems . Environ Sci Technol, 2004 Mar 1, 38(5), 1265 - 74 Hydrocarbon spills on Antarctic soils: effects and management; Aislabie JM et al.; Antarctic exploration and research have led to some significant although localized impacts on the environment . Human impacts occur around current or past scientific research stations, typically located on ice-free areas that are predominantly soils . Fuel spills, the most common occurrence, have the potential to cause the greatest environmental impact in the Antarctic through accumulation of aliphatic and aromatic compounds . Effective management of hydrocarbon spills is dependent on understanding how they impact soil properties such as moisture, hydrophobicity, soil temperature, and microbial activity . Numbers of hydrocarbon-degrading bacteria, typically Rhodococcus, Sphingomonas, and Pseudomonas species for example, may become elevated in contaminated soils, but overall microbial diversity declines . Alternative management practices to the current approach of "dig it up and ship it out" are required but must be based on sound information . This review summarizes current understanding of the extent and effects of hydrocarbon spillage on Antarctic soils; the observed physical, chemical, and biological responses of such soils; and current gaps in knowledge. Immunogenetics, 2004 Apr, 56(1), 65 - 7 Epub 2004 Mar 26. Nramp1 deletion does not confer susceptibility to Rhodococcus equi infection in mice; Cohen ND et al.; Rhodococcus equi is an intracellular bacterium that causes pneumonia in immunocompromised people and foals . The Nramp1 gene influences susceptibility to a variety of intracellular bacteria (including mycobacterial species), but not to Mycobacterium tuberculosis . In this study, we demonstrate that mice functionally deleted of the Nramp1 gene were not more susceptible to infection with virulent R . equi (ATCC 33701) than wild-type mice . Susceptibility of mice to infection with the intracellular bacterium R . equi is more similar to that of M . tuberculosis than to other intracellular bacteria, including other mycobacteria. J Struct Biol, 2004 Apr-May, 146(1-2), 155 - 65 The N-terminal coiled coil of the Rhodococcus erythropolis ARC AAA ATPase is neither necessary for oligomerization nor nucleotide hydrolysis; Zhang X et al.; Deletion mutants of the Rhodococcus erythropolis ARC AAA ATPase were generated and characterized by biochemical analysis and electron microscopy . Based on sequence comparisons the ARC protein was divided into three consecutive regions, the N-terminal coiled coil, the central ARC-specific inter domain and the C-terminal AAA domain . When the ARC AAA domain was expressed separately it formed aggregates of undefined structure . However, when the AAA domain was expressed in conjunction with the preceeding inter domain, but without the N-terminal coiled coil, high-molecular weight-complexes were formed (ARC-DeltaCC) which showed an {Formula: see text} -ethylmaleimide-sensitive ATPase activity . In 2D crystallization experiments the ARC-DeltaCC particles yielded crystals nearly identical to those formed by the wild-typ