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haloferax volcanii strain ds2  (ATCC)


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    ATCC haloferax volcanii strain ds2
    Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. <t>volcanii</t> growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.
    Haloferax Volcanii Strain Ds2, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 71 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/haloferax+volcanii+strain+ds2/Haloferax+volcanii/bio_rxiv__2024__11__20__624553-172-8-20
    Average 93 stars, based on 71 article reviews
    haloferax volcanii strain ds2 - by Bioz Stars, 2026-09
    93/100 stars

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    1) Product Images from "Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions"

    Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

    Journal: bioRxiv

    doi: 10.1101/2024.11.20.624553

    Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. volcanii growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.
    Figure Legend Snippet: Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. volcanii growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.

    Techniques Used: Titration

    hv RosR activates arlA1 and arlA2 , encoding structural components of the archaellum in Hfx. volcanii . (A) Top, genomic region encoding the archaellum and related motility functions; middle, ChIP-seq data for the region highlighted in teal (read depth y-axis is shown at right); bottom, chromosomal coordinates for genes in the zoomed region, with genes on the forward strand depicted on top of the line and reverse strand below the line. (B) Scatterplot of normalized counts from RNA-seq data, with parental control strain counts on the X-axis and hv Δ rosR counts on the y-axis. Genes passing the significance threshold of p < 0.05 and log2 fold change >= |1| are shown in blue, those significant genes also bound in ChIP-seq data in pink (see legend). (C) ChIP-qPCR validation of ChIP-seq data. Bar height represents the mean enrichment of hv RosR binding each site relative to a control region. Error bars represent the standard deviation from the mean of triplicate samples. hv RosR-HA enrichment is shown in salmon and PyrE2-HA parent strain control in grey. Amplicons tested are shown in orange below the bar graph (“peak 1, peak 2, peak 3”) and are set relative to chromosomal position of the corresponding genes. Asterisks indicate the statistical significance of enrichment for each peak (salmon bars) relative to the parent control (grey bars) by two-sided unpaired Student’s t-test, * p < 1.02 x 10 -3 , ** p < 4.71 x 10 -4 , *** p < 6.31 x 10 -5 . (D) Logo of the consensus binding motif detected computationally from hv RosR ChIP-seq binding site sequences. Motif position in nucleotides is given on the x-axis and bit score of per-base representation in the position weight matrix is given on the y-axis. See also Supplementary Table S4 for detailed RNA-seq, ChIP-seq, and motif data.
    Figure Legend Snippet: hv RosR activates arlA1 and arlA2 , encoding structural components of the archaellum in Hfx. volcanii . (A) Top, genomic region encoding the archaellum and related motility functions; middle, ChIP-seq data for the region highlighted in teal (read depth y-axis is shown at right); bottom, chromosomal coordinates for genes in the zoomed region, with genes on the forward strand depicted on top of the line and reverse strand below the line. (B) Scatterplot of normalized counts from RNA-seq data, with parental control strain counts on the X-axis and hv Δ rosR counts on the y-axis. Genes passing the significance threshold of p < 0.05 and log2 fold change >= |1| are shown in blue, those significant genes also bound in ChIP-seq data in pink (see legend). (C) ChIP-qPCR validation of ChIP-seq data. Bar height represents the mean enrichment of hv RosR binding each site relative to a control region. Error bars represent the standard deviation from the mean of triplicate samples. hv RosR-HA enrichment is shown in salmon and PyrE2-HA parent strain control in grey. Amplicons tested are shown in orange below the bar graph (“peak 1, peak 2, peak 3”) and are set relative to chromosomal position of the corresponding genes. Asterisks indicate the statistical significance of enrichment for each peak (salmon bars) relative to the parent control (grey bars) by two-sided unpaired Student’s t-test, * p < 1.02 x 10 -3 , ** p < 4.71 x 10 -4 , *** p < 6.31 x 10 -5 . (D) Logo of the consensus binding motif detected computationally from hv RosR ChIP-seq binding site sequences. Motif position in nucleotides is given on the x-axis and bit score of per-base representation in the position weight matrix is given on the y-axis. See also Supplementary Table S4 for detailed RNA-seq, ChIP-seq, and motif data.

    Techniques Used: ChIP-sequencing, RNA Sequencing, Control, ChIP-qPCR, Biomarker Discovery, Binding Assay, Standard Deviation

    Related Articles

    Transformation Assay:

    Article Title: Microbial enhanced oil recovery methods utilizing a microorganism that is deficient in its ability to degrade short chain hydrocarbons
    Article Snippet: The DNA construct was linearized by restriction digestion and ligated into pNG168, an archaeal/E. coli shuttle vector containing an archaeal origin of replication and a mevinolin resistance gene for selection in archaea (S. DasSarma, 1995). .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the pNG168-smRS-GFP plasmid, or pNG168, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the three LadA expression plasmids, or with the original pNG168 plasmid, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods utilizing a microorganism that is deficient in its ability to degrade short chain hydrocarbons
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the three LadA expression plasmids, or with the original pNG168 plasmid, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the pNG168-smRS-GFP plasmid, or pNG168, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Plasmid Preparation:

    Article Title: Microbial enhanced oil recovery methods utilizing a microorganism that is deficient in its ability to degrade short chain hydrocarbons
    Article Snippet: The DNA construct was linearized by restriction digestion and ligated into pNG168, an archaeal/E. coli shuttle vector containing an archaeal origin of replication and a mevinolin resistance gene for selection in archaea (S. DasSarma, 1995). .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the pNG168-smRS-GFP plasmid, or pNG168, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the three LadA expression plasmids, or with the original pNG168 plasmid, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods utilizing a microorganism that is deficient in its ability to degrade short chain hydrocarbons
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the three LadA expression plasmids, or with the original pNG168 plasmid, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the pNG168-smRS-GFP plasmid, or pNG168, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Expressing:

    Article Title: Microbial enhanced oil recovery methods
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the three LadA expression plasmids, or with the original pNG168 plasmid, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..

    Article Title: Microbial enhanced oil recovery methods utilizing a microorganism that is deficient in its ability to degrade short chain hydrocarbons
    Article Snippet: .. Haloferax volcanii strain DS2 (ATCC 29605) was transformed with the three LadA expression plasmids, or with the original pNG168 plasmid, using established PEG-based transformation methods (Dyall-Smith, The Halohandbook: Protocols for Haloarchaeal Genetics, 2009), and transformants were selected on rich medium plates containing 2 μg/ml lovastatin (Tocris). ..



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    haloferax volcanii strain ds2  (ATCC)
    93
    ATCC haloferax volcanii strain ds2
    Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. <t>volcanii</t> growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.
    Haloferax Volcanii Strain Ds2, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/haloferax+volcanii+strain+ds2/Haloferax+volcanii/bio_rxiv__2024__11__20__624553-172-8-20
    Average 93 stars, based on 1 article reviews
    haloferax volcanii strain ds2 - by Bioz Stars, 2026-09
    93/100 stars
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    volcanii strain ds2  (ATCC)
    93
    ATCC volcanii strain ds2
    Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. <t>volcanii</t> growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.
    Volcanii Strain Ds2, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 1 article reviews
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    Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. volcanii growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.

    Journal: bioRxiv

    Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

    doi: 10.1101/2024.11.20.624553

    Figure Lengend Snippet: Haloarchaeal species exhibit differential susceptibility to oxidative stress conditions. Growth is plotted as the log10 optical density at 600 nm (OD600) over time (hours). Each curve represents the generalized additive model (GAM) fit to the raw data from at least 3 biological replicate experiments (seeded from starter cultures inoculated with separate colonies), each with 3 technical replicates (aliquots from the same starter culture). Shaded grey ribbons indicate the standard error. Error is low where ribbons are not visible. Concentrations are written above the corresponding growth curve in each panel. Concentrations surrounded by a box is that condition chosen for testing Δ rosR growth in subsequent experiments. (A) Hfx. volcanii growth under a titration of peroxide (H 2 O 2 ) concentrations. (B) Hfx. mediterranei growth under H 2 O 2 . (C) Hfx. volcanii growth under varying paraquat (PQ) concentrations. (D) Hfx. mediterranei growth under PQ.

    Article Snippet: Wild-type strains Halobacterium salinarum NRC-1 ( Hs) , Haloferax volcanii strain DS2 ( Hv) , and Haloferax mediterranei ( Hm) ATCC 33500 were used in this study.

    Techniques: Titration

    hv RosR activates arlA1 and arlA2 , encoding structural components of the archaellum in Hfx. volcanii . (A) Top, genomic region encoding the archaellum and related motility functions; middle, ChIP-seq data for the region highlighted in teal (read depth y-axis is shown at right); bottom, chromosomal coordinates for genes in the zoomed region, with genes on the forward strand depicted on top of the line and reverse strand below the line. (B) Scatterplot of normalized counts from RNA-seq data, with parental control strain counts on the X-axis and hv Δ rosR counts on the y-axis. Genes passing the significance threshold of p < 0.05 and log2 fold change >= |1| are shown in blue, those significant genes also bound in ChIP-seq data in pink (see legend). (C) ChIP-qPCR validation of ChIP-seq data. Bar height represents the mean enrichment of hv RosR binding each site relative to a control region. Error bars represent the standard deviation from the mean of triplicate samples. hv RosR-HA enrichment is shown in salmon and PyrE2-HA parent strain control in grey. Amplicons tested are shown in orange below the bar graph (“peak 1, peak 2, peak 3”) and are set relative to chromosomal position of the corresponding genes. Asterisks indicate the statistical significance of enrichment for each peak (salmon bars) relative to the parent control (grey bars) by two-sided unpaired Student’s t-test, * p < 1.02 x 10 -3 , ** p < 4.71 x 10 -4 , *** p < 6.31 x 10 -5 . (D) Logo of the consensus binding motif detected computationally from hv RosR ChIP-seq binding site sequences. Motif position in nucleotides is given on the x-axis and bit score of per-base representation in the position weight matrix is given on the y-axis. See also Supplementary Table S4 for detailed RNA-seq, ChIP-seq, and motif data.

    Journal: bioRxiv

    Article Title: Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions

    doi: 10.1101/2024.11.20.624553

    Figure Lengend Snippet: hv RosR activates arlA1 and arlA2 , encoding structural components of the archaellum in Hfx. volcanii . (A) Top, genomic region encoding the archaellum and related motility functions; middle, ChIP-seq data for the region highlighted in teal (read depth y-axis is shown at right); bottom, chromosomal coordinates for genes in the zoomed region, with genes on the forward strand depicted on top of the line and reverse strand below the line. (B) Scatterplot of normalized counts from RNA-seq data, with parental control strain counts on the X-axis and hv Δ rosR counts on the y-axis. Genes passing the significance threshold of p < 0.05 and log2 fold change >= |1| are shown in blue, those significant genes also bound in ChIP-seq data in pink (see legend). (C) ChIP-qPCR validation of ChIP-seq data. Bar height represents the mean enrichment of hv RosR binding each site relative to a control region. Error bars represent the standard deviation from the mean of triplicate samples. hv RosR-HA enrichment is shown in salmon and PyrE2-HA parent strain control in grey. Amplicons tested are shown in orange below the bar graph (“peak 1, peak 2, peak 3”) and are set relative to chromosomal position of the corresponding genes. Asterisks indicate the statistical significance of enrichment for each peak (salmon bars) relative to the parent control (grey bars) by two-sided unpaired Student’s t-test, * p < 1.02 x 10 -3 , ** p < 4.71 x 10 -4 , *** p < 6.31 x 10 -5 . (D) Logo of the consensus binding motif detected computationally from hv RosR ChIP-seq binding site sequences. Motif position in nucleotides is given on the x-axis and bit score of per-base representation in the position weight matrix is given on the y-axis. See also Supplementary Table S4 for detailed RNA-seq, ChIP-seq, and motif data.

    Article Snippet: Wild-type strains Halobacterium salinarum NRC-1 ( Hs) , Haloferax volcanii strain DS2 ( Hv) , and Haloferax mediterranei ( Hm) ATCC 33500 were used in this study.

    Techniques: ChIP-sequencing, RNA Sequencing, Control, ChIP-qPCR, Biomarker Discovery, Binding Assay, Standard Deviation