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  1. AU="Rahman, Thahira J"
  2. AU="Williams, Olivia O F"
  3. AU="Glickman, Scott"
  4. AU="Pokrovsky, Daniil"
  5. AU="Kotansky, Brian"
  6. AU="Kumaravel, Arthi"
  7. AU="Lordkipanize, David"
  8. AU="Kurzawinski, Tom R"
  9. AU="Wu, Xinwu"
  10. AU="Grijalva, Marcelo"
  11. AU="van Zuylen, Wendy J"
  12. AU="Asarnow, L D"
  13. AU="So, Ronald"
  14. AU="deSouza, Ashwin L"
  15. AU="Härtlova, Anetta"
  16. AU="Ghanem, Ahmed I"
  17. AU="Yue Lu"
  18. AU="Pincus, Laura B"
  19. AU="Ibrahim, Nashwan"
  20. AU=Bray Molly S AU=Bray Molly S
  21. AU="Bregy, Amadé"
  22. AU=Kaper J B
  23. AU="León-Ramón, Susana"
  24. AU="Simpson, Andrew"
  25. AU="Peters, Wibke"
  26. AU="Malik, Sajid Ali"
  27. AU="V, Gomathi"

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  1. Artikel: In silico engineering of

    Occhipinti, Annalisa / Eyassu, Filmon / Rahman, Thahira J / Rahman, Pattanathu K S M / Angione, Claudio

    PeerJ

    2018  Band 6, Seite(n) e6046

    Abstract: Background: Rhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including : Methods: We investigate in silico the metabolic ... ...

    Abstract Background: Rhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including
    Methods: We investigate in silico the metabolic capabilities of
    Results: We identify a substantial increase in synthesis of rhamnolipids by the engineered model compared to the control model. We apply statistical and machine learning techniques on the metabolic reaction rates to identify distinct features on the structure of the variables and individual components driving the variation of growth and rhamnolipids production. We finally provide a computational framework for integrating multi-omics data and identifying latent pathways and genes for the production of rhamnolipids in
    Conclusions: We anticipate that our results will provide a versatile methodology for integrating multi-omics data for topological and functional analysis of
    Sprache Englisch
    Erscheinungsdatum 2018-12-17
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.6046
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Effects of Rhamnolipids from Pseudomonas aeruginosa DS10-129 on Luminescent Bacteria: Toxicity and Modulation of Cadmium Bioavailability

    Bondarenko, Olesja / Rahman, Pattanathu K. S. M / Rahman, Thahira J / Kahru, Anne / Ivask, Angela

    Microbial ecology. 2010 Apr., v. 59, no. 3

    2010  

    Abstract: In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri ...

    Abstract In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri and recombinant bioluminescent Pseudomonas fluorescens, P. aeruginosa, Escherichia coli, and Gram-positive Bacillus subtilis were used as model organisms. Rhamnolipids reduced the bioluminescence of these bacteria in less than a second of exposure even in relatively low concentrations (30-min EC₅₀ 45-167 mg l⁻¹). Toxicity of Cd to Gram-negative bacteria (30-min EC₅₀ values 0.16 mg l⁻¹ for E. coli, 0.96 mg l⁻¹ for P. fluorescens, and 4.4 mg l⁻¹ for V. fischeri) was remarkably (up to 10-fold) reduced in the presence of 50 mg l⁻¹ rhamnolipids. Interestingly, the toxicity of Cd to Gram-positive B. subtilis (30-min EC₅₀ value 0.49 mg l⁻¹) was not affected by rhamnolipids. Rhamnolipids had an effect on desorption of Cd from soil: 40 mg l⁻¹ rhamnolipids increased the water-extracted fraction of Cd twice compared with untreated control. However, this additionally desorbed fraction of Cd remained bound with rhamnolipids and was not available to bacteria. Hence, in carefully chosen concentrations (still effectively complexing heavy metals but not yet toxic to soil bacteria), rhamnolipids could be applied in remediation of polluted areas.
    Schlagwörter Bacillus subtilis ; Escherichia coli ; Gram-negative bacteria ; Gram-positive bacteria ; Pseudomonas aeruginosa ; Pseudomonas fluorescens ; Vibrio fischeri ; bioavailability ; bioluminescence ; cadmium ; heavy metals ; soil bacteria ; soil toxicity ; toxicity
    Sprache Englisch
    Erscheinungsverlauf 2010-04
    Umfang p. 588-600.
    Verlag Springer-Verlag
    Erscheinungsort New York
    Dokumenttyp Artikel
    ZDB-ID 1462065-0
    ISSN 1432-184X ; 0095-3628
    ISSN (online) 1432-184X
    ISSN 0095-3628
    DOI 10.1007/s00248-009-9626-5
    Datenquelle NAL Katalog (AGRICOLA)

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  3. Artikel ; Online: Common variation in the CD36 (fatty acid translocase) gene is associated with left-ventricular mass.

    Hall, Darroch / Mayosi, Bongani M / Rahman, Thahira J / Avery, Peter J / Watkins, Hugh C / Keavney, Bernard

    Journal of hypertension

    2011  Band 29, Heft 4, Seite(n) 690–695

    Abstract: Aims: Genetic variation in the fatty acid translocase (CD36) gene has been shown in animal models to affect several risk factors for the development of left-ventricular hypertrophy, but this phenotype has not, thus far, been investigated in humans. We ... ...

    Abstract Aims: Genetic variation in the fatty acid translocase (CD36) gene has been shown in animal models to affect several risk factors for the development of left-ventricular hypertrophy, but this phenotype has not, thus far, been investigated in humans. We examined the relationship between common genetic polymorphisms in the CD36 gene and left-ventricular mass.
    Methods and results: We studied a cohort of 255 families comprising 1425 individuals ascertained via a hypertensive proband. Seven single-nucleotide polymorphisms which together tagged common genetic variation in the CD36 gene were genotyped using a SEQUENOM MALDI-TOF instrument. There was evidence of association between the rs1761663 polymorphism in intron 1 of the CD36 gene and left-ventricular mass determined either by echocardiography (P=0.003, N=780) or electrocardiography (P=0.001, N=814). There was also association between rs1761663 genotype and body mass index (P<0.001, N=1354). Genotype was associated with between 2 and 8% differences in these phenotypes per allele. After adjustment for the effect of body mass index, there remained significant associations between genotype and left ventricular mass measured either by echo (P=0.017) or ECG (P=0.007).
    Conclusions: Genotype at the rs1761663 polymorphism has independent effects both on body mass index and left-ventricular mass. Genes with such pleiotropic effects may be particularly attractive therapeutic targets for interventions to modify multiple risk factors for cardiovascular events.
    Mesh-Begriff(e) CD36 Antigens/genetics ; Cohort Studies ; Electrocardiography ; Heart Ventricles/pathology ; Humans ; Introns ; Organ Size/genetics ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide
    Chemische Substanzen CD36 Antigens
    Sprache Englisch
    Erscheinungsdatum 2011-02-23
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 605532-1
    ISSN 1473-5598 ; 0263-6352 ; 0952-1178
    ISSN (online) 1473-5598
    ISSN 0263-6352 ; 0952-1178
    DOI 10.1097/HJH.0b013e3283440115
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Using population data for assessing next-generation sequencing performance.

    Houniet, Darren T / Rahman, Thahira J / Al Turki, Saeed / Hurles, Matthew E / Xu, Yaobo / Goodship, Judith / Keavney, Bernard / Santibanez Koref, Mauro

    Bioinformatics (Oxford, England)

    2014  Band 31, Heft 1, Seite(n) 56–61

    Abstract: Motivation: During the past 4 years, whole-exome sequencing has become a standard tool for finding rare variants causing Mendelian disorders. In that time, there has also been a proliferation of both sequencing platforms and approaches to analyse their ... ...

    Abstract Motivation: During the past 4 years, whole-exome sequencing has become a standard tool for finding rare variants causing Mendelian disorders. In that time, there has also been a proliferation of both sequencing platforms and approaches to analyse their output. This requires approaches to assess the performance of different methods. Traditionally, criteria such as comparison with microarray data or a number of known polymorphic sites have been used. Here we expand such approaches, developing a maximum likelihood framework and using it to estimate the sensitivity and specificity of whole-exome sequencing data.
    Results: Using whole-exome sequencing data for a panel of 19 individuals, we show that estimated sensitivity and specificity are similar to those calculated using microarray data as a reference. We explore the effect of frequency misspecification arising from using an inappropriately selected population and find that, although the estimates are affected, the rankings across procedures remain the same.
    Availability and implementation: An implementation using Perl and R can be found at busso.ncl.ac.uk (Username: igm101; Password: Z1z1nts).
    Mesh-Begriff(e) Algorithms ; Computational Biology/methods ; Exome/genetics ; Genetic Variation/genetics ; Genetics, Population ; Genome, Human ; Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sample Size
    Sprache Englisch
    Erscheinungsdatum 2014-09-17
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btu606
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel: Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov.

    Banat, Ibrahim M / Marchant, Roger / Rahman, Thahira J

    International journal of systematic and evolutionary microbiology

    2004  Band 54, Heft Pt 6, Seite(n) 2197–2201

    Abstract: Several aerobic, motile, rod-shaped, thermophilic, spore-forming Geobacillus bacteria predominantly giving a Gram-positive staining reaction were isolated from a cool soil environment in Northern Ireland and taxonomically investigated. Two isolates, F10 ... ...

    Abstract Several aerobic, motile, rod-shaped, thermophilic, spore-forming Geobacillus bacteria predominantly giving a Gram-positive staining reaction were isolated from a cool soil environment in Northern Ireland and taxonomically investigated. Two isolates, F10 and Tf(T), showed low 16S rRNA gene sequence similarity to recognized members of the genus Geobacillus. Phylogenetic tree investigation using neighbour-joining, maximum-likelihood and parsimony methods indicated that strains F10 and Tf(T) represent a single novel species, for which the name Geobacillus debilis sp. nov. is proposed, with type strain Tf(T) (=DSM 16016(T)=NCIMB 13995(T)) and which belongs to a subgroup of the genus Geobacillus comprising Geobacillus toebii and Geobacillus caldoxylosilyticus. However, G. debilis showed closest affinities to Bacillus pallidus, which we propose should become Geobacillus pallidus comb. nov.
    Mesh-Begriff(e) Aerobiosis ; Bacillaceae/classification ; Bacillaceae/cytology ; Bacillaceae/isolation & purification ; Bacillaceae/physiology ; Bacterial Typing Techniques ; DNA, Bacterial/chemistry ; DNA, Bacterial/isolation & purification ; DNA, Ribosomal/chemistry ; DNA, Ribosomal/isolation & purification ; Genes, rRNA ; Gentian Violet ; Hot Temperature ; Molecular Sequence Data ; Movement ; Northern Ireland ; Phenazines ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; Spores, Bacterial/cytology ; Temperature
    Chemische Substanzen DNA, Bacterial ; DNA, Ribosomal ; Gram's stain ; Phenazines ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Gentian Violet (J4Z741D6O5)
    Sprache Englisch
    Erscheinungsdatum 2004-10-18
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2002336-4
    ISSN 1466-5034 ; 1466-5026
    ISSN (online) 1466-5034
    ISSN 1466-5026
    DOI 10.1099/ijs.0.63231-0
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Effects of rhamnolipids from Pseudomonas aeruginosa DS10-129 on luminescent bacteria: toxicity and modulation of cadmium bioavailability.

    Bondarenko, Olesja / Rahman, Pattanathu K S M / Rahman, Thahira J / Kahru, Anne / Ivask, Angela

    Microbial ecology

    2010  Band 59, Heft 3, Seite(n) 588–600

    Abstract: In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri ...

    Abstract In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri and recombinant bioluminescent Pseudomonas fluorescens, P. aeruginosa, Escherichia coli, and Gram-positive Bacillus subtilis were used as model organisms. Rhamnolipids reduced the bioluminescence of these bacteria in less than a second of exposure even in relatively low concentrations (30-min EC(50) 45-167 mg l(-1)). Toxicity of Cd to Gram-negative bacteria (30-min EC(50) values 0.16 mg l(-1) for E. coli, 0.96 mg l(-1) for P. fluorescens, and 4.4 mg l(-1) for V. fischeri) was remarkably (up to 10-fold) reduced in the presence of 50 mg l(-1) rhamnolipids. Interestingly, the toxicity of Cd to Gram-positive B. subtilis (30-min EC(50) value 0.49 mg l(-1)) was not affected by rhamnolipids. Rhamnolipids had an effect on desorption of Cd from soil: 40 mg l(-1) rhamnolipids increased the water-extracted fraction of Cd twice compared with untreated control. However, this additionally desorbed fraction of Cd remained bound with rhamnolipids and was not available to bacteria. Hence, in carefully chosen concentrations (still effectively complexing heavy metals but not yet toxic to soil bacteria), rhamnolipids could be applied in remediation of polluted areas.
    Mesh-Begriff(e) Absorption ; Bacteria/drug effects ; Biodegradation, Environmental ; Biological Availability ; Cadmium/metabolism ; Cell Membrane Permeability ; DNA, Bacterial/genetics ; Glycolipids/toxicity ; Luminescence ; Phylogeny ; Pseudomonas aeruginosa/chemistry ; Pseudomonas aeruginosa/genetics ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Toxicity Tests
    Chemische Substanzen DNA, Bacterial ; Glycolipids ; RNA, Ribosomal, 16S ; rhamnolipid ; Cadmium (00BH33GNGH)
    Sprache Englisch
    Erscheinungsdatum 2010-01-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1462065-0
    ISSN 1432-184X ; 0095-3628
    ISSN (online) 1432-184X
    ISSN 0095-3628
    DOI 10.1007/s00248-009-9626-5
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Common variation at the 11-β hydroxysteroid dehydrogenase type 1 gene is associated with left ventricular mass.

    Rahman, Thahira J / Mayosi, Bongani M / Hall, Darroch / Avery, Peter J / Stewart, Paul M / Connell, John M C / Watkins, Hugh / Keavney, Bernard

    Circulation. Cardiovascular genetics

    2011  Band 4, Heft 2, Seite(n) 156–162

    Abstract: Background: Polymorphisms in 11-β hydroxysteroid dehydrogenase type 1 (11β-HSD1, encoded by HSD11B1) have been reported to be associated with obesity-related cardiovascular risk factors, such as type II diabetes and hypertension. Left ventricular ... ...

    Abstract Background: Polymorphisms in 11-β hydroxysteroid dehydrogenase type 1 (11β-HSD1, encoded by HSD11B1) have been reported to be associated with obesity-related cardiovascular risk factors, such as type II diabetes and hypertension. Left ventricular hypertrophy (LVH) is an independent risk factor for cardiovascular death associated with these factors but has significant additional heritability, the cause of which is undetermined. The 11β-HSD1 is believed to maintain tonic inhibition of the mineralocorticoid receptor in cardiomyocytes, and mineralocorticoid receptor activation is involved in the pathophysiology of LVH. We assessed the association between polymorphisms in the HSD11B1 gene and left ventricular mass (LVM) in 248 families ascertained through a proband with hypertension.
    Methods and results: LVM was measured by electrocardiography and echocardiography in 868 and 829 participants, respectively. Single-nucleotide polymorphisms (SNPs) tagging common variation in the HSD11B1 gene were genotyped by mass spectrometry. The rs846910 SNP, which lies in the flanking region 5' to exon 1B of HSD11B1, was associated with LVM both by electrocardiography (≈5% lower LVM per copy of the rare allele, P=0.02) and by echocardiography (≈10% lower LVM per copy of the rare allele, P=0.003). Genotype explained 1% to 2% of the population variability in LVM, or approximately 5% of the heritable fraction. There were no significant associations between any HSD11B1 SNP and blood pressure or body mass index that could have confounded the association with LVM.
    Conclusions: Genotype at HSD11B1 has a small, but significant effect on LVM, apparently independently of any effect on obesity-related traits. These findings suggest a novel action of 11β-HSD1 in the human cardiomyocyte, which may be of therapeutic importance.
    Mesh-Begriff(e) 11-beta-Hydroxysteroid Dehydrogenase Type 1/genetics ; 11-beta-Hydroxysteroid Dehydrogenase Type 1/metabolism ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Blood Pressure/physiology ; Body Mass Index ; Electrocardiography ; Female ; Genotype ; Humans ; Hypertension/complications ; Hypertrophy, Left Ventricular/complications ; Hypertrophy, Left Ventricular/genetics ; Hypertrophy, Left Ventricular/physiopathology ; Male ; Mass Spectrometry ; Middle Aged ; Polymorphism, Single Nucleotide ; Receptors, Mineralocorticoid/chemistry ; Receptors, Mineralocorticoid/metabolism ; Risk Factors
    Chemische Substanzen Receptors, Mineralocorticoid ; 11-beta-Hydroxysteroid Dehydrogenase Type 1 (EC 1.1.1.146) ; HSD11B1 protein, human (EC 1.1.1.146)
    Sprache Englisch
    Erscheinungsdatum 2011-03-14
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2477394-3
    ISSN 1942-3268 ; 1942-325X
    ISSN (online) 1942-3268
    ISSN 1942-325X
    DOI 10.1161/CIRCGENETICS.110.958496
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Functionally significant, rare transcription factor variants in tetralogy of Fallot.

    Töpf, Ana / Griffin, Helen R / Glen, Elise / Soemedi, Rachel / Brown, Danielle L / Hall, Darroch / Rahman, Thahira J / Eloranta, Jyrki J / Jüngst, Christoph / Stuart, A Graham / O'Sullivan, John / Keavney, Bernard D / Goodship, Judith A

    PloS one

    2014  Band 9, Heft 8, Seite(n) e95453

    Abstract: Objective: Rare variants in certain transcription factors involved in cardiac development cause Mendelian forms of congenital heart disease. The purpose of this study was to systematically assess the frequency of rare transcription factor variants in ... ...

    Abstract Objective: Rare variants in certain transcription factors involved in cardiac development cause Mendelian forms of congenital heart disease. The purpose of this study was to systematically assess the frequency of rare transcription factor variants in sporadic patients with the cardiac outflow tract malformation tetralogy of Fallot (TOF).
    Methods and results: We sequenced the coding, 5'UTR, and 3'UTR regions of twelve transcription factor genes implicated in cardiac outflow tract development (NKX2.5, GATA4, ISL1, TBX20, MEF2C, BOP/SMYD1, HAND2, FOXC1, FOXC2, FOXH, FOXA2 and TBX1) in 93 non-syndromic, non-Mendelian TOF cases. We also analysed Illumina Human 660W-Quad SNP Array data for copy number variants in these genes; none were detected. Four of the rare variants detected have previously been shown to affect transactivation in in vitro reporter assays: FOXC1 p.P297S, FOXC2 p.Q444R, FOXH1 p.S113T and TBX1 p.P43_G61del PPPPRYDPCAAAAPGAPGP. Two further rare variants, HAND2 p.A25_A26insAA and FOXC1 p.G378_G380delGGG, A488_491delAAAA, affected transactivation in in vitro reporter assays. Each of these six functionally significant variants was present in a single patient in the heterozygous state; each of the four for which parental samples were available were maternally inherited. Thus in the 93 TOF cases we identified six functionally significant mutations in the secondary heart field transcriptional network.
    Significance: This study indicates that rare genetic variants in the secondary heart field transcriptional network with functional effects on protein function occur in 3-13% of patients with TOF. This is the first report of a functionally significant HAND2 mutation in a patient with congenital heart disease.
    Mesh-Begriff(e) Gene Dosage ; Gene Regulatory Networks ; Genetic Predisposition to Disease ; Heart/physiopathology ; Humans ; Mutation/genetics ; RNA Splicing/genetics ; Sequence Analysis, DNA ; Tetralogy of Fallot/genetics ; Transcription Factors/genetics ; Transcription, Genetic
    Chemische Substanzen Transcription Factors
    Sprache Englisch
    Erscheinungsdatum 2014-08-05
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0095453
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel: The degradation of n-hexadecane in soil by thermophilic geobacilli.

    Marchant, Roger / Sharkey, Freddie H / Banat, Ibrahim M / Rahman, Thahira J / Perfumo, Amedea

    FEMS microbiology ecology

    2006  Band 56, Heft 1, Seite(n) 44–54

    Abstract: Soil microcosms have been used to demonstrate the ability of indigenous soil thermophiles to degrade effectively a representative alkane (n-hexadecane). A fragment of the alkane mono-oxygenase gene (alkB) was amplified from thermophilic Geobacillus ... ...

    Abstract Soil microcosms have been used to demonstrate the ability of indigenous soil thermophiles to degrade effectively a representative alkane (n-hexadecane). A fragment of the alkane mono-oxygenase gene (alkB) was amplified from thermophilic Geobacillus thermoleovorans strain T70 by PCR using degenerate primers. The amplicon demonstrated 96% sequence similarity with the alkB gene from Rhodococcus erythropolis. Critical controls ensured that the positive PCR signal detected was not a result of mesophilic soil organisms. A reverse transcription PCR (RT-PCR) assay was developed to determine if expression of the gene was inducible in the presence of an alkane or constitutively expressed in soil. In the presence of n-hexadecane, expression of the alkane mono-oxygenase gene was induced in pure cultures and soil samples and was dependent on temperature. No positive RT-PCR signal was detected at mesophilic growth temperatures either in pure cultures or in soil microcosms, whereas at 55 degrees C positive RT-PCR signals were obtained for both pure cultures of T70 and soil samples. Many different amplicons of the alkB gene fragment were obtained from the soil used in the microcosms. Thirty cloned fragments yielded 27 different sequences showing 85-96% sequence similarity with the alkB sequence of T70. To establish that the amplified alkB gene sequences from soil were derived from thermophilic geobacilli, additional strains were isolated on a selective medium containing n-hexadecane as sole carbon source. The 16S rRNA gene sequences were determined to identify the 50 isolates obtained (G. thermoleovorans, 27; G. caldoxylosilyticus, 17; G. pallidus, 2; G. toebiii, 1; Geobacillus sp., 3) representing 18 different strains and alkB gene sequences determined and deposited with the European Bioinformatics Institute.
    Mesh-Begriff(e) Alkanes/metabolism ; Bacillus/enzymology ; Bacillus/genetics ; Bacillus/metabolism ; Biodegradation, Environmental ; Cytochrome P-450 CYP4A/genetics ; Cytochrome P-450 CYP4A/metabolism ; Phylogeny ; RNA, Bacterial/chemistry ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/chemistry ; RNA, Ribosomal, 16S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soil Microbiology ; Temperature
    Chemische Substanzen Alkanes ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Cytochrome P-450 CYP4A (EC 1.14.15.3) ; n-hexadecane (F8Z00SHP6Q)
    Sprache Englisch
    Erscheinungsdatum 2006-04
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 283722-5
    ISSN 1574-6941 ; 0168-6496
    ISSN (online) 1574-6941
    ISSN 0168-6496
    DOI 10.1111/j.1574-6941.2006.00061.x
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel: The frequency and characteristics of highly thermophilic bacteria in cool soil environments.

    Marchant, Roger / Banat, Ibrahim M / Rahman, Thahira J / Berzano, Marco

    Environmental microbiology

    2002  Band 4, Heft 10, Seite(n) 595–602

    Abstract: Following enrichment at 70 degrees C and 80 degrees C, five highly thermophilic aerobic eubacteria have been isolated from cool soil environments. These organisms show a temperature range for growth of 40-80 degrees C and have optimal and very high ... ...

    Abstract Following enrichment at 70 degrees C and 80 degrees C, five highly thermophilic aerobic eubacteria have been isolated from cool soil environments. These organisms show a temperature range for growth of 40-80 degrees C and have optimal and very high growth rates around 70 degrees C with generation times less than 30 min. All isolates are narrow rods, which stain Gram-negative, but have a Gram-positive cell wall structure and only one of five isolates is a spore former. All cultures contain a small proportion of previously unreported extremely long flexuous rods, which can be seen to divide eventually. Biochemical testing of five strains reveals a significant ability to utilize alkanes and some aromatic hydrocarbons. Using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of 16S rDNA the five strains were differentiated into three categories, which paralleled the biochemical results. 16S rDNA sequences showed high similarity with thermophilic Bacillus species now reclassified as Geobacillus. These bacteria are present in high numbers in apparently all soils and the question is raised of how these organisms, which are apparently unable to grow at the temperatures experienced in these cool soils, are so prominent.
    Mesh-Begriff(e) Bacillus/genetics ; Bacillus/growth & development ; Bacillus/isolation & purification ; DNA, Bacterial/analysis ; DNA, Bacterial/chemistry ; DNA, Ribosomal/analysis ; DNA, Ribosomal/chemistry ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Soil Microbiology ; Temperature
    Chemische Substanzen DNA, Bacterial ; DNA, Ribosomal
    Sprache Englisch
    Erscheinungsdatum 2002-10-03
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1046/j.1462-2920.2002.00344.x
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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