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    • dsm 25411  (DSMZ)
    86
    DSMZ dsm 25411
    Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, <t>LL02,</t> and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.
    Dsm 25411, supplied by DSMZ, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 86 stars, based on 1 article reviews
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    dsm 25411 - by Bioz Stars, 2024-10
    86/100 stars
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    naproxen pfizer chronic low back pain 3 nct027 25411  (Pfizer Inc)
    86
    Pfizer Inc naproxen pfizer chronic low back pain 3 nct027 25411
    Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, <t>LL02,</t> and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.
    Naproxen Pfizer Chronic Low Back Pain 3 Nct027 25411, supplied by Pfizer Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/naproxen pfizer chronic low back pain 3 nct027 25411/product/Pfizer Inc
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    naproxen pfizer chronic low back pain 3 nct027 25411 - by Bioz Stars, 2024-10
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    pegfpm dad m1041a plasmid 25411  (Addgene inc)
    N/A
    Standard format Plasmid sent in bacteria as agar stab
    		   Buy from Supplier

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    Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, LL02, and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: Degradation assays for HCH isomers. Degradation of α-HCH, β-HCH, γ-HCH, and δ-HCH (left-hand axis) by UT26, LL01, LL02, and LL03 and relative quantification of metabolites by peak area (right-hand axis). Time postinoculation is shown on the bottom axis and the timescale for the γ-HCH assay has been adjusted to observe both the very fast (less than 1 hr) and very slow (96 hr) degradation of γ-HCH by different strains. Values are the mean of three biological replicates, with standard deviations. Identity of metabolites was confirmed by comparison to authentic standards or to metabolites produced with purified UT26 LinA or LinB enzymes. HCH, hexachlorocyclohexane; PCCH, pentachlorocyclohexene; PCHL, pentachlorocyclohexanol; TCB, trichlorobenzene.

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques: Produced, Purification

    Assembly summary: summary of the final genome assemblies produced for this study

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: Assembly summary: summary of the final genome assemblies produced for this study

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques: Produced, Plasmid Preparation

    IS 6100 elements in the studied genomes

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: IS 6100 elements in the studied genomes

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques:

    Whole-genome alignments of sequenced strains. Whole-genome alignments of the other 12 genomes (see the Materials and Methods section for names and accession numbers) to each of the UT26, LL01, LL02, and LL03 genomes. The color gradient of the inner rings indicates homology to the reference genome sequence. On display starting from the innermost ring are three non−HCH-degrading strains, then 10 HCH-degrading strains, with the reference genome the outermost ring. Reference chromosomes or scaffolds predicted to be from chromosomes are colored blue, plasmids are colored red, and small scaffolds that cannot be unambiguously determined to be from either chromosomal or plasmid origin are colored yellow. The positions of IS 6100 elements (purple) and lin genes (black) in the reference genome are indicated. Predicted genomic islands are highlighted in green. HCH, hexachlorocyclohexane.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: Whole-genome alignments of sequenced strains. Whole-genome alignments of the other 12 genomes (see the Materials and Methods section for names and accession numbers) to each of the UT26, LL01, LL02, and LL03 genomes. The color gradient of the inner rings indicates homology to the reference genome sequence. On display starting from the innermost ring are three non−HCH-degrading strains, then 10 HCH-degrading strains, with the reference genome the outermost ring. Reference chromosomes or scaffolds predicted to be from chromosomes are colored blue, plasmids are colored red, and small scaffolds that cannot be unambiguously determined to be from either chromosomal or plasmid origin are colored yellow. The positions of IS 6100 elements (purple) and lin genes (black) in the reference genome are indicated. Predicted genomic islands are highlighted in green. HCH, hexachlorocyclohexane.

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques: Sequencing, Plasmid Preparation

    lin pathway composition of studied strains. Presence of lin genes in the 10 HCH-degrading strains studied, along with the percent identity of each encoded protein to the equivalent in UT26. Genes grouped in operons are indicated with braces to the left of the gene names. Multiple values indicate duplicate copies of the gene in a strain. The neighbor-joining phylogeny above the strain names was produced from a clustalw alignment of the 16S rDNA sequences (UT26: AF039168, B90A: AY519129, IP26: EF190507, HDIP04: EF424393, LL01: JN646865, P25: EU781657, LL03: JN695620, RL-3: EF207155, MM-1: CP004036;G432_r19183, LL02: JN695619) of each strain with E. coli (ECK3843) as an outgroup (not shown). HCH, hexachlorocyclohexane.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: lin pathway composition of studied strains. Presence of lin genes in the 10 HCH-degrading strains studied, along with the percent identity of each encoded protein to the equivalent in UT26. Genes grouped in operons are indicated with braces to the left of the gene names. Multiple values indicate duplicate copies of the gene in a strain. The neighbor-joining phylogeny above the strain names was produced from a clustalw alignment of the 16S rDNA sequences (UT26: AF039168, B90A: AY519129, IP26: EF190507, HDIP04: EF424393, LL01: JN646865, P25: EU781657, LL03: JN695620, RL-3: EF207155, MM-1: CP004036;G432_r19183, LL02: JN695619) of each strain with E. coli (ECK3843) as an outgroup (not shown). HCH, hexachlorocyclohexane.

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques: Produced

    Genomic organization of downstream lin genes. Alignments detailing conservation and rearrangements in the genomic regions of the downstream lin genes. Alignments of the regions surrounding (A) linDER and (B) linFEb and linGHIJ , were performed with MEGABLAST and ordered to give maximal pairwise alignment lengths. Conserved regions are indicated by red shading where the matches are in the same orientation and by blue shading where the matches are in reverse orientation. Note that association of IS 6100 elements with linGHIJ is unique to strains LL01, LL02 and LL03.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: Genomic organization of downstream lin genes. Alignments detailing conservation and rearrangements in the genomic regions of the downstream lin genes. Alignments of the regions surrounding (A) linDER and (B) linFEb and linGHIJ , were performed with MEGABLAST and ordered to give maximal pairwise alignment lengths. Conserved regions are indicated by red shading where the matches are in the same orientation and by blue shading where the matches are in reverse orientation. Note that association of IS 6100 elements with linGHIJ is unique to strains LL01, LL02 and LL03.

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques:

    Comparison of LinA sequence variants. (A) Amino acid differences between major LinA variants and the uncharacterized LinA of LL02. (B) Proposed mechanism for the IS6100-mediated 21-bp deletion in LL02. The initial insertion site of the IS 6100 cointegrates (yellow) in a LinA UT26 -like sequence is marked with a black triangle. The insertion induces the duplication of 8bp at the insertion site (DR1 and DR1´ in blue). IS 6100 elements are capable of reversion through homologous recombination between the induced direct repeats (DR1×DR1´). A near-identical sequence (DR2) is slightly further downstream of the insertion, however, and recombination between DR1 and DR2 gives rise to the sequence observed in LL02, with the deletion of one DR and the intervening sequence (colored red). Also shown is the sequence of LinA1 in B90A, containing the IS 6100 insertion and a different downstream sequence. This has likely arisen through homologous recombination between IS 6100 elements, deleting the intervening region containing the original C-terminus of LinA.

    Journal: G3: Genes|Genomes|Genetics

    Article Title: Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains

    doi: 10.1534/g3.114.015933

    Figure Lengend Snippet: Comparison of LinA sequence variants. (A) Amino acid differences between major LinA variants and the uncharacterized LinA of LL02. (B) Proposed mechanism for the IS6100-mediated 21-bp deletion in LL02. The initial insertion site of the IS 6100 cointegrates (yellow) in a LinA UT26 -like sequence is marked with a black triangle. The insertion induces the duplication of 8bp at the insertion site (DR1 and DR1´ in blue). IS 6100 elements are capable of reversion through homologous recombination between the induced direct repeats (DR1×DR1´). A near-identical sequence (DR2) is slightly further downstream of the insertion, however, and recombination between DR1 and DR2 gives rise to the sequence observed in LL02, with the deletion of one DR and the intervening sequence (colored red). Also shown is the sequence of LinA1 in B90A, containing the IS 6100 insertion and a different downstream sequence. This has likely arisen through homologous recombination between IS 6100 elements, deleting the intervening region containing the original C-terminus of LinA.

    Article Snippet: Bacterial strains used in this study were obtained from the DSMZ ( www.dsmz.de ) under the accession numbers DSM-16413 ( S. japonicum UT26), DSM-25410 ( S. czechense LL01), DSM-25411 ( N. barchaimii LL02), and DSM-25433 ( S. baderi LL03).

    Techniques: Sequencing, Homologous Recombination