ccm  (ATCC)


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    ATCC ccm
    Q-PCR expression data for relevant validated genes
    Ccm, supplied by ATCC, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans"

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-394

    Q-PCR expression data for relevant validated genes
    Figure Legend Snippet: Q-PCR expression data for relevant validated genes

    Techniques Used: Expressing, Transduction

    Microarray expression data for iron induced genes
    Figure Legend Snippet: Microarray expression data for iron induced genes

    Techniques Used: Microarray, Expressing, Transduction

    acidithiobacillus ferridurans atcc 33020  (ATCC)


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    ATCC acidithiobacillus ferridurans atcc 33020
    Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.
    Acidithiobacillus Ferridurans Atcc 33020, supplied by ATCC, 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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    1) Product Images from "Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level"

    Article Title: Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2024.1357152

    Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.
    Figure Legend Snippet: Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.

    Techniques Used: Bacteria, Titration

    a ferridurans atcc 33020  (ATCC)


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    ATCC a ferridurans atcc 33020
    Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.
    A Ferridurans Atcc 33020, supplied by ATCC, 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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    1) Product Images from "Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level"

    Article Title: Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2024.1357152

    Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.
    Figure Legend Snippet: Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.

    Techniques Used: Bacteria, Titration

    Summary of determined redox potentials of the c 4 cytochromes CytC-18, CytC-78, and homologous proteins.
    Figure Legend Snippet: Summary of determined redox potentials of the c 4 cytochromes CytC-18, CytC-78, and homologous proteins.

    Techniques Used: Titration

    afd atcc 33020  (ATCC)


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    ATCC afd atcc 33020
    Afd Atcc 33020, supplied by ATCC, 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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    a ferridurans atcc 33020 t  (ATCC)


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    ATCC a ferridurans atcc 33020 t
    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans <t>ATCC</t> <t>33020</t> <t>T</t> plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    A Ferridurans Atcc 33020 T, supplied by ATCC, 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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    1) Product Images from "Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains"

    Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

    Journal: Scientific Reports

    doi: 10.1038/s41598-023-37341-4

    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    Figure Legend Snippet: Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Techniques Used: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Genomic Sequencing

    a ferridurans atcc 33020 t plasmid ptf5  (ATCC)


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    ATCC a ferridurans atcc 33020 t plasmid ptf5
    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans <t>ATCC</t> <t>33020</t> <t>T</t> plasmid <t>pTF5</t> (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    A Ferridurans Atcc 33020 T Plasmid Ptf5, supplied by ATCC, 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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    1) Product Images from "Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains"

    Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

    Journal: Scientific Reports

    doi: 10.1038/s41598-023-37341-4

    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    Figure Legend Snippet: Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Techniques Used: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Genomic Sequencing

    afd atcc 33020  (ATCC)


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    ATCC afd atcc 33020
    Genomic relatedness and synteny coverage of A. ferrooxidans clade 2 strains. ( A ) Average nucleotide identity (ANIb) calculated as in Pritchard et al. vs. in silico digital DNA–DNA hybridization index (dDDH) assessed using the Genome-to-Genome Distance Calculator with recommended formula 2 and species cut-off limits defined by Meier-Kolthoff et al. showing a clear-cut distinction between A. ferrooxidans clade 2A and 2B strains (excepting strain F221 with comparisons crossing this threshold). ( B ) Basic statistics for intra- and interclade genomic relatedness indexes distributions. Thresholds used for species delimitation are the following: digital DNA:DNA hybridization dDDH > 70% (same genomic species , ); Average Nucleotide Identity ANI > 96% (same genomic species , ). ( C ) Synteny coverage fraction (using 9 anchors, 2 to 10 calculated as in Drillon et al. ) between A. ferrooxidans strains sublineage 2A and 2B showing high levels of synteny between strains of the same sublineage (in blue; 2A vs. 2A or 2B vs. 2B strains) with respect to inter sublineage comparisons (in green; 2A vs. 2B and 2B vs. 2A strains). Strain ATCC 23270 T (circles) is a reference strain for the 2A sublineage and strain PQ505 (triangles) for the clade 2B sublineage. Interspecies comparisons in brown are included as a control ( A. ferrianus DSM 107098 , A. ferridurans <t>ATCC</t> <t>33020</t> , A. ferriphilus DSM 100412, and `A. ferruginosus´ CF3).
    Afd Atcc 33020, supplied by ATCC, 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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    1) Product Images from "Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains"

    Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

    Journal: Scientific Reports

    doi: 10.1038/s41598-023-37341-4

    Genomic relatedness and synteny coverage of A. ferrooxidans clade 2 strains. ( A ) Average nucleotide identity (ANIb) calculated as in Pritchard et al. vs. in silico digital DNA–DNA hybridization index (dDDH) assessed using the Genome-to-Genome Distance Calculator with recommended formula 2 and species cut-off limits defined by Meier-Kolthoff et al. showing a clear-cut distinction between A. ferrooxidans clade 2A and 2B strains (excepting strain F221 with comparisons crossing this threshold). ( B ) Basic statistics for intra- and interclade genomic relatedness indexes distributions. Thresholds used for species delimitation are the following: digital DNA:DNA hybridization dDDH > 70% (same genomic species , ); Average Nucleotide Identity ANI > 96% (same genomic species , ). ( C ) Synteny coverage fraction (using 9 anchors, 2 to 10 calculated as in Drillon et al. ) between A. ferrooxidans strains sublineage 2A and 2B showing high levels of synteny between strains of the same sublineage (in blue; 2A vs. 2A or 2B vs. 2B strains) with respect to inter sublineage comparisons (in green; 2A vs. 2B and 2B vs. 2A strains). Strain ATCC 23270 T (circles) is a reference strain for the 2A sublineage and strain PQ505 (triangles) for the clade 2B sublineage. Interspecies comparisons in brown are included as a control ( A. ferrianus DSM 107098 , A. ferridurans ATCC 33020 , A. ferriphilus DSM 100412, and `A. ferruginosus´ CF3).
    Figure Legend Snippet: Genomic relatedness and synteny coverage of A. ferrooxidans clade 2 strains. ( A ) Average nucleotide identity (ANIb) calculated as in Pritchard et al. vs. in silico digital DNA–DNA hybridization index (dDDH) assessed using the Genome-to-Genome Distance Calculator with recommended formula 2 and species cut-off limits defined by Meier-Kolthoff et al. showing a clear-cut distinction between A. ferrooxidans clade 2A and 2B strains (excepting strain F221 with comparisons crossing this threshold). ( B ) Basic statistics for intra- and interclade genomic relatedness indexes distributions. Thresholds used for species delimitation are the following: digital DNA:DNA hybridization dDDH > 70% (same genomic species , ); Average Nucleotide Identity ANI > 96% (same genomic species , ). ( C ) Synteny coverage fraction (using 9 anchors, 2 to 10 calculated as in Drillon et al. ) between A. ferrooxidans strains sublineage 2A and 2B showing high levels of synteny between strains of the same sublineage (in blue; 2A vs. 2A or 2B vs. 2B strains) with respect to inter sublineage comparisons (in green; 2A vs. 2B and 2B vs. 2A strains). Strain ATCC 23270 T (circles) is a reference strain for the 2A sublineage and strain PQ505 (triangles) for the clade 2B sublineage. Interspecies comparisons in brown are included as a control ( A. ferrianus DSM 107098 , A. ferridurans ATCC 33020 , A. ferriphilus DSM 100412, and `A. ferruginosus´ CF3).

    Techniques Used: In Silico, DNA-DNA Hybridization

    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    Figure Legend Snippet: Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Techniques Used: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Genomic Sequencing

    a ferridurans atcc 33020 t plasmid ptf5  (ATCC)


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    ATCC a ferridurans atcc 33020 t plasmid ptf5
    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans <t>ATCC</t> <t>33020</t> <t>T</t> plasmid <t>pTF5</t> (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    A Ferridurans Atcc 33020 T Plasmid Ptf5, supplied by ATCC, 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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    1) Product Images from "Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains"

    Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

    Journal: Scientific Reports

    doi: 10.1038/s41598-023-37341-4

    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
    Figure Legend Snippet: Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Techniques Used: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Genomic Sequencing

    ccm  (ATCC)


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    ATCC ccm
    Q-PCR expression data for relevant validated genes
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    1) Product Images from "Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans"

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-394

    Q-PCR expression data for relevant validated genes
    Figure Legend Snippet: Q-PCR expression data for relevant validated genes

    Techniques Used: Expressing, Transduction

    Microarray expression data for iron induced genes
    Figure Legend Snippet: Microarray expression data for iron induced genes

    Techniques Used: Microarray, Expressing, Transduction

    ccm  (ATCC)


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    ATCC ccm
    Q-PCR expression data for relevant validated genes
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    1) Product Images from "Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans"

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-394

    Q-PCR expression data for relevant validated genes
    Figure Legend Snippet: Q-PCR expression data for relevant validated genes

    Techniques Used: Expressing, Transduction

    Microarray expression data for iron induced genes
    Figure Legend Snippet: Microarray expression data for iron induced genes

    Techniques Used: Microarray, Expressing, Transduction

    33020 cells  (ATCC)


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    ATCC 33020 cells
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    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-394

    Q-PCR expression data for relevant validated genes
    Figure Legend Snippet: Q-PCR expression data for relevant validated genes

    Techniques Used: Expressing, Transduction

    Microarray expression data for iron induced genes
    Figure Legend Snippet: Microarray expression data for iron induced genes

    Techniques Used: Microarray, Expressing, Transduction

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    ATCC acidithiobacillus ferridurans atcc 33020
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    ATCC a ferridurans atcc 33020
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    ATCC a ferridurans atcc 33020 t
    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans <t>ATCC</t> <t>33020</t> <t>T</t> plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
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    ATCC a ferridurans atcc 33020 t plasmid ptf5
    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans <t>ATCC</t> <t>33020</t> <t>T</t> plasmid <t>pTF5</t> (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .
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    Q-PCR expression data for relevant validated genes

    Journal: BMC Genomics

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    doi: 10.1186/1471-2164-10-394

    Figure Lengend Snippet: Q-PCR expression data for relevant validated genes

    Article Snippet: AFE_3146 , rus , rusticyanin , 2,1 , 0,00* , ATCC 33020/[ ] CCM 4253/[ ] ATCC 19859/[ ] .

    Techniques: Expressing, Transduction

    Microarray expression data for iron induced genes

    Journal: BMC Genomics

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    doi: 10.1186/1471-2164-10-394

    Figure Lengend Snippet: Microarray expression data for iron induced genes

    Article Snippet: AFE_3146 , rus , rusticyanin , 2,1 , 0,00* , ATCC 33020/[ ] CCM 4253/[ ] ATCC 19859/[ ] .

    Techniques: Microarray, Expressing, Transduction

    Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.

    Journal: Frontiers in Microbiology

    Article Title: Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

    doi: 10.3389/fmicb.2024.1357152

    Figure Lengend Snippet: Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.

    Article Snippet: Acidithiobacillia , Acidithiobacillus ferridurans ATCC 33020 , Hip , E m , 7 = 510 mV (± 5 mV) , Cyclic voltammetry, square wave voltammetry (protein film) , .

    Techniques: Bacteria, Titration

    Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.

    Journal: Frontiers in Microbiology

    Article Title: Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

    doi: 10.3389/fmicb.2024.1357152

    Figure Lengend Snippet: Overview of redox potentials of HiPIP-41 and homologous proteins in other bacteria.

    Article Snippet: Acidithiobacillia , A. ferridurans ATCC 33020 , Cyc1 , E m , 3 = 385 mV (± 20 mV) E m , 3 = 480 mV (± 20 mV) , Optical redox titration , .

    Techniques: Bacteria, Titration

    Summary of determined redox potentials of the c 4 cytochromes CytC-18, CytC-78, and homologous proteins.

    Journal: Frontiers in Microbiology

    Article Title: Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

    doi: 10.3389/fmicb.2024.1357152

    Figure Lengend Snippet: Summary of determined redox potentials of the c 4 cytochromes CytC-18, CytC-78, and homologous proteins.

    Article Snippet: Acidithiobacillia , A. ferridurans ATCC 33020 , Cyc1 , E m , 3 = 385 mV (± 20 mV) E m , 3 = 480 mV (± 20 mV) , Optical redox titration , .

    Techniques: Titration

    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Journal: Scientific Reports

    Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

    doi: 10.1038/s41598-023-37341-4

    Figure Lengend Snippet: Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Article Snippet: Additional comparisons against related iron-oxidizing species were performed as indicated ( A. ferrianus DSM 107098 T , A. ferridurans ATCC 33020 T , A. ferrooxidans ATCC 23270 T , A. ferriphilus DSM100412 T , A. ferrivorans DSM 22755 T , and 'A. ferruginosus CF3 T ').

    Techniques: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Genomic Sequencing

    Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Journal: Scientific Reports

    Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

    doi: 10.1038/s41598-023-37341-4

    Figure Lengend Snippet: Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp). The localization and orientation of predicted genes and the position of the putative origin of replication are indicated. ( D ) Bam HI restriction analysis of pTF5-like plasmid of strain CCM 4253. Lane M represents a 1-kb DNA ladder; lane 1 represents uncut plasmid DNA; lane 2 represents plasmid DNA digested with a BamHI-HF® restriction endonuclease (New England Biolabs) for 1 h at 37 °C. The plasmid and restriction products were analyzed by electrophoresis in a 0.7% agarose gel. The gel image has been cropped for display. The original gel image is shown in Supplementary Table B. Accession numbers for the A. ferrooxidans genomic sequences in section B are listed in Supplementary Table B, and additional sequences in the alignment are the following: YNTRS-40 p1 (NZ_CP040512.1); ATCC 19377 (AFOH01000025); ATCC 8085 (JABBDT010000069), RW2 (JAAOMP010000076); GG1-14 (JABBOU010000150); AFERRIp (NZ_LT841306.1); pTF91 (U14129); AFE GGI-221 (AEFB01001388); AFE CCM 4253 (QKQP01000015); AFE COP1 (JABBDN000000171); AFE IST3091 (U32113.1); AFE HEL18 (LQRJ01000060); AFE DSM 16786 (JABFOH000000031); AFE YQH-1 (LJBT01000038); AFE TNTRS-40, plasmid p1 (CP040512.1); ATH ATCC 19377 (AFOH01000025); ATH ATCC 8085 (JABBDT010000069); ‘ASU’ RW2 (JAAOMP010000076); ‘AMO’ GG1-14 (JABBOU010000150); AFV PRJEB5721, AFERRIp (LT841306.1); AFD ATCC 33020 (NC_005023). Abbreviations of species names are the following: AFE, A. ferrooxidans ; AFD, A. ferridurans ; ATH, A. thiooxidans ; ASU, ‘ A. sulfurivorans ’; AMO, ‘ A. monserratiensis ’; AFV, A. ferrivorans .

    Article Snippet: Figure 4 Analysis of candidate eMGEs in the genomes of A. ferrooxidans strains. ( A ) Stand-alone contigs and contig fragments aligned against A. ferridurans ATCC 33020 T plasmid pTF5 (NC_005023) showing modular organization and variations among sublineage 2A strains. ( B ) The alignment of the oriV region identified in the replication module of pTF5-like plasmids of A. ferrooxidans sublineage 2A strains and matching sequenced recovered from NCBI. ( C ) A schematic map of the pTF5-like plasmid of strain CCM 4253 showing contig circularization (17,826 bp).

    Techniques: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Genomic Sequencing

    Q-PCR expression data for relevant validated genes

    Journal: BMC Genomics

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    doi: 10.1186/1471-2164-10-394

    Figure Lengend Snippet: Q-PCR expression data for relevant validated genes

    Article Snippet: In agreement with these data, highest expression of ORF1 was detected in iron-compared to sulfur-grown ATCC 33020 cells [ ].

    Techniques: Expressing, Transduction

    Microarray expression data for iron induced genes

    Journal: BMC Genomics

    Article Title: Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

    doi: 10.1186/1471-2164-10-394

    Figure Lengend Snippet: Microarray expression data for iron induced genes

    Article Snippet: In agreement with these data, highest expression of ORF1 was detected in iron-compared to sulfur-grown ATCC 33020 cells [ ].

    Techniques: Microarray, Expressing, Transduction