16s rrna Search Results


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  • 99
    ATCC 16s rrna
    ( a ) Apparatus schematic. A micropipette drawn to a 2 µm diameter bridges two chambers filled with electrolyte. Negatively charged 3 µm diameter beads placed in the micropipette are electrophoretically drawn to the narrow end of the micropipette by an electric field applied by electrodes in each of the chambers; ( b ) When a bead reaches the narrow end of the micropipette, it blocks the current, which is measured by the electrodes; ( c ) Schematic of target <t>16S</t> <t>rRNA</t> (10 pM, red) hybridized to PNA-bead conjugates in the drawn micropipette under applied electric field in the presence of nonspecifically bound, background RNA (blue): (i) open pore state as bead with bound RNA approaches the micropipette tip (“pore”); and (ii) blockade of the pore by the PNA-bead conjugate with bound RNA (blocked pore state). Nonspecifically bound RNA (blue) detaches from the bead in the strong electric field at the micropipette tip, while the specifically bound RNA remains, leading to a persistent blocked pore state; ( d ) Measured ionic current through the pore: (i) open pore current; and (ii) current blockade by PNA-bead conjugates with bound RNA.
    16s Rrna, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 286 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Millipore 16s rrna
    ( a ) Apparatus schematic. A micropipette drawn to a 2 µm diameter bridges two chambers filled with electrolyte. Negatively charged 3 µm diameter beads placed in the micropipette are electrophoretically drawn to the narrow end of the micropipette by an electric field applied by electrodes in each of the chambers; ( b ) When a bead reaches the narrow end of the micropipette, it blocks the current, which is measured by the electrodes; ( c ) Schematic of target <t>16S</t> <t>rRNA</t> (10 pM, red) hybridized to PNA-bead conjugates in the drawn micropipette under applied electric field in the presence of nonspecifically bound, background RNA (blue): (i) open pore state as bead with bound RNA approaches the micropipette tip (“pore”); and (ii) blockade of the pore by the PNA-bead conjugate with bound RNA (blocked pore state). Nonspecifically bound RNA (blue) detaches from the bead in the strong electric field at the micropipette tip, while the specifically bound RNA remains, leading to a persistent blocked pore state; ( d ) Measured ionic current through the pore: (i) open pore current; and (ii) current blockade by PNA-bead conjugates with bound RNA.
    16s Rrna, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 239 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    PerkinElmer 16s rrna
    Amounts of selected RNA species in cultures of M. tuberculosis H37Rv in the slowly stirred 0.5 HSR model. (A) RNA expressed as number of molecules per genome. (B) mRNA expressed as number of molecules (×10,000) per molecule of <t>16S</t> <t>rRNA</t> (mRNA/rRNA). The ×10,000 factor was used to reflect the approximate numbers of transcripts per cell equivalent.
    16s Rrna, supplied by PerkinElmer, used in various techniques. Bioz Stars score: 92/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher 16s rrna
    Amounts of selected RNA species in cultures of M. tuberculosis H37Rv in the slowly stirred 0.5 HSR model. (A) RNA expressed as number of molecules per genome. (B) mRNA expressed as number of molecules (×10,000) per molecule of <t>16S</t> <t>rRNA</t> (mRNA/rRNA). The ×10,000 factor was used to reflect the approximate numbers of transcripts per cell equivalent.
    16s Rrna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 1777 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc 16s rrna
    Gene copy numbers of <t>16S</t> <t>rRNA</t> of different treatments at 0–20 cm soil depth on the sampling dates in 2013. Different letters indicate significant differences ( P
    16s Rrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 1235 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Otsuka Holdings 16s rrna
    Gene copy numbers of <t>16S</t> <t>rRNA</t> of different treatments at 0–20 cm soil depth on the sampling dates in 2013. Different letters indicate significant differences ( P
    16s Rrna, supplied by Otsuka Holdings, used in various techniques. Bioz Stars score: 92/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Sangon Biotech 16s rrna
    Phylogenetic tree of strain L-2 on <t>16S</t> <t>rRNA</t> gene sequences.
    16s Rrna, supplied by Sangon Biotech, used in various techniques. Bioz Stars score: 92/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Roche 16s rrna
    Phylogenetic tree of bacterial diversity, based on the <t>16S</t> <t>rRNA</t> gene sequences obtained by 16S gene-based PCR-DGGE, in relation to cultured- and the closest uncultured relatives. Parentheses indicate the number of individual sequences within the OTU. Bootstrap values, calculated from 1,000 repetitions, are shown at branch points with > 50% support. The scale bar indicates 0.08 nucleic acid substitutions. The tree is rooted by Aquifex aeolicus.
    16s Rrna, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 254 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Eurofins 16s rrna
    Rate of wound healing at week 4 in Buruli patients with a negative or positive M . ulcerans <t>16S</t> <t>rRNA.</t> Rate of healing was highest in patients where M . ulcerans 16S rRNA was negative at baseline or 4 weeks after starting antibiotic treatment. The rate of healing at week 4 (ROH) was computed in millimeters per week by subtracting the mean diameter of the lesion at week 4 from that at week 0 and dividing this result by 4.
    16s Rrna, supplied by Eurofins, used in various techniques. Bioz Stars score: 91/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 16s ribosomal rna rrna
    Gut microbial composition depicting phyla ( A ) and class ( B ) of saline-treated control animals. Antibiotic treatment resulted in no amplification of the <t>16S</t> <t>rRNA</t> gene and thus we were unable to assess fecal microbiota composition. Taxonomic structure of
    16s Ribosomal Rna Rrna, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Second Genome Inc 16s rrna phylochip
    Gut microbial composition depicting phyla ( A ) and class ( B ) of saline-treated control animals. Antibiotic treatment resulted in no amplification of the <t>16S</t> <t>rRNA</t> gene and thus we were unable to assess fecal microbiota composition. Taxonomic structure of
    16s Rrna Phylochip, supplied by Second Genome Inc, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc 16s ribosomal rna rrna
    Gut microbial composition depicting phyla ( A ) and class ( B ) of saline-treated control animals. Antibiotic treatment resulted in no amplification of the <t>16S</t> <t>rRNA</t> gene and thus we were unable to assess fecal microbiota composition. Taxonomic structure of
    16s Ribosomal Rna Rrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Red Sea 16s rrna sequences
    Maximum likelihood tree of <t>16S</t> mitochondrial <t>rRNA</t> gene sequences from Cytaeis , Podocorynoides , and their closest relatives (BLAST similarity > 90%). P . minima from Mediterranean and New Zealand clusters within other representatives of the family Rathkeidae ( Rathkea and Lizzia ). The Red Sea Cytaeis sp clusters with the sequence of Cytaeis sp. (EU883541) from Japan and Cytaeis capitata from Indonesia. Schematic images of the polyps of Cytaeis sp. from Japan and the Red Sea indicate location of the fluorescence.
    16s Rrna Sequences, supplied by Red Sea, used in various techniques. Bioz Stars score: 90/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Gen-Probe 16s ribosomal rna rrna
    Maximum likelihood tree of <t>16S</t> mitochondrial <t>rRNA</t> gene sequences from Cytaeis , Podocorynoides , and their closest relatives (BLAST similarity > 90%). P . minima from Mediterranean and New Zealand clusters within other representatives of the family Rathkeidae ( Rathkea and Lizzia ). The Red Sea Cytaeis sp clusters with the sequence of Cytaeis sp. (EU883541) from Japan and Cytaeis capitata from Indonesia. Schematic images of the polyps of Cytaeis sp. from Japan and the Red Sea indicate location of the fluorescence.
    16s Ribosomal Rna Rrna, supplied by Gen-Probe, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    GE Healthcare 16s ribosomal rna rrna
    Maximum likelihood tree of <t>16S</t> mitochondrial <t>rRNA</t> gene sequences from Cytaeis , Podocorynoides , and their closest relatives (BLAST similarity > 90%). P . minima from Mediterranean and New Zealand clusters within other representatives of the family Rathkeidae ( Rathkea and Lizzia ). The Red Sea Cytaeis sp clusters with the sequence of Cytaeis sp. (EU883541) from Japan and Cytaeis capitata from Indonesia. Schematic images of the polyps of Cytaeis sp. from Japan and the Red Sea indicate location of the fluorescence.
    16s Ribosomal Rna Rrna, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    TaKaRa 16s ribosomal rna rrna
    Transcriptional analyses of Ag43 under green light induction. Relative units of ag43 transcription were normalized to <t>16S</t> <t>rRNA</t> amounts. Relative units in cells grown under green light are shown with white circles , and relative units in cells grown under red light are shown with black circles . There is no significant difference in the cell density under red light at each incubation time from at 0 min incubation. The asterisks indicate statistical difference from the cells exposed to red light (*P
    16s Ribosomal Rna Rrna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Kaneka Corp 16s rrna probes
    CLSM image of the FISH-stained 24 h four species biofilm on titanium specimen. Individual images with a z-step size of 2 μm of the 24 h four-species biofilm stained with species-specific <t>16S</t> <t>rRNA</t> FISH probes for S . oralis (MIT-588-Alexa-405; blue), A . naeslundii (ANA-103-Alexa-488; green), V . dispar (VEI-217-Alexa-568; yellow) and P . gingivalis (POGI-Alexa-647; red) were overlaid to one image. (a)–(d) shows the individual color channels for the four individual species, (e) shows the overlay of the four color channels. Scale bars: 30μm.
    16s Rrna Probes, supplied by Kaneka Corp, used in various techniques. Bioz Stars score: 92/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Gen-Probe 16s rrna probes
    CLSM image of the FISH-stained 24 h four species biofilm on titanium specimen. Individual images with a z-step size of 2 μm of the 24 h four-species biofilm stained with species-specific <t>16S</t> <t>rRNA</t> FISH probes for S . oralis (MIT-588-Alexa-405; blue), A . naeslundii (ANA-103-Alexa-488; green), V . dispar (VEI-217-Alexa-568; yellow) and P . gingivalis (POGI-Alexa-647; red) were overlaid to one image. (a)–(d) shows the individual color channels for the four individual species, (e) shows the overlay of the four color channels. Scale bars: 30μm.
    16s Rrna Probes, supplied by Gen-Probe, used in various techniques. Bioz Stars score: 88/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher 16s rrna phylochip
    Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the <t>16S</t> <t>rRNA</t>
    16s Rrna Phylochip, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc miseq 16s ribosomal rna rrna
    Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the <t>16S</t> <t>rRNA</t>
    Miseq 16s Ribosomal Rna Rrna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/miseq 16s ribosomal rna rrna/product/Illumina Inc
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    88
    Thermo Fisher 16s rrna specific primers
    Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the <t>16S</t> <t>rRNA</t>
    16s Rrna Specific Primers, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Second Genome Inc 16s rrna sequencing
    Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the <t>16S</t> <t>rRNA</t>
    16s Rrna Sequencing, supplied by Second Genome Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Eurofins 16s rrna sequencing
    Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the <t>16S</t> <t>rRNA</t>
    16s Rrna Sequencing, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    ( a ) Apparatus schematic. A micropipette drawn to a 2 µm diameter bridges two chambers filled with electrolyte. Negatively charged 3 µm diameter beads placed in the micropipette are electrophoretically drawn to the narrow end of the micropipette by an electric field applied by electrodes in each of the chambers; ( b ) When a bead reaches the narrow end of the micropipette, it blocks the current, which is measured by the electrodes; ( c ) Schematic of target 16S rRNA (10 pM, red) hybridized to PNA-bead conjugates in the drawn micropipette under applied electric field in the presence of nonspecifically bound, background RNA (blue): (i) open pore state as bead with bound RNA approaches the micropipette tip (“pore”); and (ii) blockade of the pore by the PNA-bead conjugate with bound RNA (blocked pore state). Nonspecifically bound RNA (blue) detaches from the bead in the strong electric field at the micropipette tip, while the specifically bound RNA remains, leading to a persistent blocked pore state; ( d ) Measured ionic current through the pore: (i) open pore current; and (ii) current blockade by PNA-bead conjugates with bound RNA.

    Journal: Biosensors

    Article Title: PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

    doi: 10.3390/bios6030037

    Figure Lengend Snippet: ( a ) Apparatus schematic. A micropipette drawn to a 2 µm diameter bridges two chambers filled with electrolyte. Negatively charged 3 µm diameter beads placed in the micropipette are electrophoretically drawn to the narrow end of the micropipette by an electric field applied by electrodes in each of the chambers; ( b ) When a bead reaches the narrow end of the micropipette, it blocks the current, which is measured by the electrodes; ( c ) Schematic of target 16S rRNA (10 pM, red) hybridized to PNA-bead conjugates in the drawn micropipette under applied electric field in the presence of nonspecifically bound, background RNA (blue): (i) open pore state as bead with bound RNA approaches the micropipette tip (“pore”); and (ii) blockade of the pore by the PNA-bead conjugate with bound RNA (blocked pore state). Nonspecifically bound RNA (blue) detaches from the bead in the strong electric field at the micropipette tip, while the specifically bound RNA remains, leading to a persistent blocked pore state; ( d ) Measured ionic current through the pore: (i) open pore current; and (ii) current blockade by PNA-bead conjugates with bound RNA.

    Article Snippet: Conclusions Our previously described, PCR-free, optics-free detector for nucleic acids of specific sequence was used successfully to detect E. coli (ATCC 25922) 16S rRNA at 10 fM, which corresponds to ~100–1000 CFU/mL.

    Techniques:

    ( a ) Schematic of control (noncomplementary) Pseudomonas putida rRNA (blue, 10 pM) nonspecifically bound to bead-PNA probe conjugates under applied electric field in the drawn micropipette tip: (i) open pore state as bead with bound RNA approaches the micropipette tip (“pore”); (ii) transient blockade of the pore by the PNA-bead conjugate with nonspecifically bound noncomplementary RNA (blocked pore state); and (iii) relief of the pore blockade after the noncomplementary RNA of control bacteria was detached from the bead in the strong electric field at the micropipette tip and the bead is carried away from the pore by the opposing electroosmotic flow (red arrows) (open pore state). ( b ) Measured ionic current through the pore: (i) open pore current; (ii) current blockade by PNA-bead conjugates with bound RNA; and (iii) relief of the current blockade after the nonspecifically bound RNA was detached from the bead and the lack of tightly bound, complementary 16S rRNA resulted in the bead conjugate being swept from the pore by the opposing electroosmotic flow.

    Journal: Biosensors

    Article Title: PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

    doi: 10.3390/bios6030037

    Figure Lengend Snippet: ( a ) Schematic of control (noncomplementary) Pseudomonas putida rRNA (blue, 10 pM) nonspecifically bound to bead-PNA probe conjugates under applied electric field in the drawn micropipette tip: (i) open pore state as bead with bound RNA approaches the micropipette tip (“pore”); (ii) transient blockade of the pore by the PNA-bead conjugate with nonspecifically bound noncomplementary RNA (blocked pore state); and (iii) relief of the pore blockade after the noncomplementary RNA of control bacteria was detached from the bead in the strong electric field at the micropipette tip and the bead is carried away from the pore by the opposing electroosmotic flow (red arrows) (open pore state). ( b ) Measured ionic current through the pore: (i) open pore current; (ii) current blockade by PNA-bead conjugates with bound RNA; and (iii) relief of the current blockade after the nonspecifically bound RNA was detached from the bead and the lack of tightly bound, complementary 16S rRNA resulted in the bead conjugate being swept from the pore by the opposing electroosmotic flow.

    Article Snippet: Conclusions Our previously described, PCR-free, optics-free detector for nucleic acids of specific sequence was used successfully to detect E. coli (ATCC 25922) 16S rRNA at 10 fM, which corresponds to ~100–1000 CFU/mL.

    Techniques: Flow Cytometry

    Amounts of selected RNA species in cultures of M. tuberculosis H37Rv in the slowly stirred 0.5 HSR model. (A) RNA expressed as number of molecules per genome. (B) mRNA expressed as number of molecules (×10,000) per molecule of 16S rRNA (mRNA/rRNA). The ×10,000 factor was used to reflect the approximate numbers of transcripts per cell equivalent.

    Journal: Journal of Bacteriology

    Article Title: Microaerophilic Induction of the Alpha-Crystallin Chaperone Protein Homologue (hspX) mRNA of Mycobacterium tuberculosis

    doi: 10.1128/JB.183.18.5311-5316.2001

    Figure Lengend Snippet: Amounts of selected RNA species in cultures of M. tuberculosis H37Rv in the slowly stirred 0.5 HSR model. (A) RNA expressed as number of molecules per genome. (B) mRNA expressed as number of molecules (×10,000) per molecule of 16S rRNA (mRNA/rRNA). The ×10,000 factor was used to reflect the approximate numbers of transcripts per cell equivalent.

    Article Snippet: The 50-μl reaction mixture consisted of 1× PCR Buffer II (Perkin-Elmer), 3 mM MgCl2 , 200 μM concentrations of each deoxynucleoside triphosphate (dATP, dCTP, and dGTP), 400 μM dUTP, 0.5 U of uracil DNA glycosylase, 1 U of Taq polymerase (ISC Bioexpress, Kaysville, Utah) or AmpliTaq Gold polymerase for 16S rRNA (Perkin-Elmer), 0.2 μM concentrations of each primer, and a 0.1 μM concentration of the TaqMan probe.

    Techniques:

    Gene copy numbers of 16S rRNA of different treatments at 0–20 cm soil depth on the sampling dates in 2013. Different letters indicate significant differences ( P

    Journal: Scientific Reports

    Article Title: Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil

    doi: 10.1038/srep43283

    Figure Lengend Snippet: Gene copy numbers of 16S rRNA of different treatments at 0–20 cm soil depth on the sampling dates in 2013. Different letters indicate significant differences ( P

    Article Snippet: The remainder of each sample was stored at −80 °C for subsequent DNA extraction and downstream analysis, including the quantitative real-time PCR (Q-PCR) of the 16 S rRNA gene, functional genes of amoA gene of bacterial, nitrate reductase gene (narG ), nitrite reductase genes (nirS and nirK ), and N2 O reductase gene (nosZ ), by high-throughput sequencing of 16S rRNA based on an Illumina platform analysis (Illumina Inc., San Diego, CA).

    Techniques: Sampling

    Neighbor‐joining phylogenetic tree of Deltaproteobacteria affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. These OTU s were represented by more than 1% of the reads from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), and ( C3 , D2 , E2 , and F3 ), respectively. Methanococcus maripaludis (U38941) was used as the out‐group.

    Journal: MicrobiologyOpen

    Article Title: Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

    doi: 10.1002/mbo3.330

    Figure Lengend Snippet: Neighbor‐joining phylogenetic tree of Deltaproteobacteria affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. These OTU s were represented by more than 1% of the reads from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), and ( C3 , D2 , E2 , and F3 ), respectively. Methanococcus maripaludis (U38941) was used as the out‐group.

    Article Snippet: A number of bacterial diversity indices for the 16S rRNA Illumina reads are shown in Table .

    Techniques: Environmental Sampling, Sequencing

    Neighbor‐joining phylogenetic tree of Gammaproteobacteria affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. These OTU s were represented by more than 1% of the reads from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), ( C3 , D2 , E2 , and F3 ). Roseobacter sp. N05I (AJ968647) was used as the out‐group.

    Journal: MicrobiologyOpen

    Article Title: Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

    doi: 10.1002/mbo3.330

    Figure Lengend Snippet: Neighbor‐joining phylogenetic tree of Gammaproteobacteria affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. These OTU s were represented by more than 1% of the reads from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), ( C3 , D2 , E2 , and F3 ). Roseobacter sp. N05I (AJ968647) was used as the out‐group.

    Article Snippet: A number of bacterial diversity indices for the 16S rRNA Illumina reads are shown in Table .

    Techniques: Environmental Sampling, Sequencing

    Neighbor‐joining phylogenetic tree of Bacteroidetes affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. These OTU s were represented by more than 1% of the reads from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), and ( C3 , D2 , E2 , and F3 ). Methanococcus maripaludis (U38941) was used as the out‐group.

    Journal: MicrobiologyOpen

    Article Title: Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

    doi: 10.1002/mbo3.330

    Figure Lengend Snippet: Neighbor‐joining phylogenetic tree of Bacteroidetes affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. These OTU s were represented by more than 1% of the reads from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), and ( C3 , D2 , E2 , and F3 ). Methanococcus maripaludis (U38941) was used as the out‐group.

    Article Snippet: A number of bacterial diversity indices for the 16S rRNA Illumina reads are shown in Table .

    Techniques: Environmental Sampling, Sequencing

    Neighbor‐joining phylogenetic tree of Planctomycetes affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. OTU s contained more than 50 sequences within Planctomycetacia or Phycisphaerae and 20 sequences within OM190 from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), and ( C3 , D2 , E2 , and F3 ). Chlamydophila psittaci 6BC (AB01778) and Verrucomicrobium spinosum DSM4136 (X90515) were used as out‐groups.

    Journal: MicrobiologyOpen

    Article Title: Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

    doi: 10.1002/mbo3.330

    Figure Lengend Snippet: Neighbor‐joining phylogenetic tree of Planctomycetes affiliated 16S rRNA sequences of the representative operational taxonomic units ( OTU s) and their closest environmental sample entries in the NCBI GenBank. OTU s contained more than 50 sequences within Planctomycetacia or Phycisphaerae and 20 sequences within OM190 from a single sample and/or from multiple samples. The OTU s obtained in this study are shown in bold type. The scale bar represents the estimated number of nucleotide changes per sequence position. The symbols at the nodes show the bootstrap values (only those > 50% are indicated) obtained after 1000 resamplings. The numbers in parentheses indicate the number of reads in each station in the following order (Group O, Group J, Group T, and Group S) and color ( A2 , A3 , A5 , B2 , and M2 ), ( A8 ), ( M7 and N6 ), and ( C3 , D2 , E2 , and F3 ). Chlamydophila psittaci 6BC (AB01778) and Verrucomicrobium spinosum DSM4136 (X90515) were used as out‐groups.

    Article Snippet: A number of bacterial diversity indices for the 16S rRNA Illumina reads are shown in Table .

    Techniques: Environmental Sampling, Sequencing

    Phylogenetic tree of strain L-2 on 16S rRNA gene sequences.

    Journal: Preventive Nutrition and Food Science

    Article Title: Purification and Characterization of a Protease Produced by a Planomicrobium sp. L-2 from Gut of Octopus vulgaris

    doi: 10.3746/pnf.2013.18.4.273

    Figure Lengend Snippet: Phylogenetic tree of strain L-2 on 16S rRNA gene sequences.

    Article Snippet: The amplified 16S rRNA was cloned into strain E. coli 110 (Sangon Biotech Co. Ltd., Shanghai, China) and sequenced by Sangon Biotech Company.

    Techniques:

    Phylogenetic tree of bacterial diversity, based on the 16S rRNA gene sequences obtained by 16S gene-based PCR-DGGE, in relation to cultured- and the closest uncultured relatives. Parentheses indicate the number of individual sequences within the OTU. Bootstrap values, calculated from 1,000 repetitions, are shown at branch points with > 50% support. The scale bar indicates 0.08 nucleic acid substitutions. The tree is rooted by Aquifex aeolicus.

    Journal: Frontiers in Microbiology

    Article Title: Microbially induced corrosion of carbon steel in deep groundwater environment

    doi: 10.3389/fmicb.2015.00647

    Figure Lengend Snippet: Phylogenetic tree of bacterial diversity, based on the 16S rRNA gene sequences obtained by 16S gene-based PCR-DGGE, in relation to cultured- and the closest uncultured relatives. Parentheses indicate the number of individual sequences within the OTU. Bootstrap values, calculated from 1,000 repetitions, are shown at branch points with > 50% support. The scale bar indicates 0.08 nucleic acid substitutions. The tree is rooted by Aquifex aeolicus.

    Article Snippet: Quantitative PCR Quantitative PCR (qPCR) was used to determine the abundance of bacteria and sulfate reducers based on the amount of 16S rRNA and dsr B gene copies in the groundwater and in the biofilm. qPCR was performed in 10 μL reaction volumes using LightCycler 480 qPCR instrument and LightCycler 480 Software 1.5.0 (Roche Applied Science, Germany).

    Techniques: Polymerase Chain Reaction, Denaturing Gradient Gel Electrophoresis, Cell Culture

    Denaturing gradient gel electrophoresis (DGGE), (A) 16S rRNA (B) dsr B gene .

    Journal: Frontiers in Microbiology

    Article Title: Microbially induced corrosion of carbon steel in deep groundwater environment

    doi: 10.3389/fmicb.2015.00647

    Figure Lengend Snippet: Denaturing gradient gel electrophoresis (DGGE), (A) 16S rRNA (B) dsr B gene .

    Article Snippet: Quantitative PCR Quantitative PCR (qPCR) was used to determine the abundance of bacteria and sulfate reducers based on the amount of 16S rRNA and dsr B gene copies in the groundwater and in the biofilm. qPCR was performed in 10 μL reaction volumes using LightCycler 480 qPCR instrument and LightCycler 480 Software 1.5.0 (Roche Applied Science, Germany).

    Techniques: Denaturing Gradient Gel Electrophoresis

    (A) 16S rRNA gene copies ml -1 groundwater or carbon steel (cm 2 ) -1 . The error bars present SE of mean ( n = 3). (B) dsr B gene copies ml -1 groundwater or carbon steel (cm 2 ) -1 . The error bars present SE of mean ( n = 3).

    Journal: Frontiers in Microbiology

    Article Title: Microbially induced corrosion of carbon steel in deep groundwater environment

    doi: 10.3389/fmicb.2015.00647

    Figure Lengend Snippet: (A) 16S rRNA gene copies ml -1 groundwater or carbon steel (cm 2 ) -1 . The error bars present SE of mean ( n = 3). (B) dsr B gene copies ml -1 groundwater or carbon steel (cm 2 ) -1 . The error bars present SE of mean ( n = 3).

    Article Snippet: Quantitative PCR Quantitative PCR (qPCR) was used to determine the abundance of bacteria and sulfate reducers based on the amount of 16S rRNA and dsr B gene copies in the groundwater and in the biofilm. qPCR was performed in 10 μL reaction volumes using LightCycler 480 qPCR instrument and LightCycler 480 Software 1.5.0 (Roche Applied Science, Germany).

    Techniques:

    Rate of wound healing at week 4 in Buruli patients with a negative or positive M . ulcerans 16S rRNA. Rate of healing was highest in patients where M . ulcerans 16S rRNA was negative at baseline or 4 weeks after starting antibiotic treatment. The rate of healing at week 4 (ROH) was computed in millimeters per week by subtracting the mean diameter of the lesion at week 4 from that at week 0 and dividing this result by 4.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Clearance of viable Mycobacterium ulcerans from Buruli ulcer lesions during antibiotic treatment as determined by combined 16S rRNA reverse transcriptase /IS 2404 qPCR assay

    doi: 10.1371/journal.pntd.0005695

    Figure Lengend Snippet: Rate of wound healing at week 4 in Buruli patients with a negative or positive M . ulcerans 16S rRNA. Rate of healing was highest in patients where M . ulcerans 16S rRNA was negative at baseline or 4 weeks after starting antibiotic treatment. The rate of healing at week 4 (ROH) was computed in millimeters per week by subtracting the mean diameter of the lesion at week 4 from that at week 0 and dividing this result by 4.

    Article Snippet: This was not attributable to lesion size at baseline because there was no significant difference in initial size of patient lesions with or without detectable 16S rRNA at week 4 (p = 0.0798, Mann Whitney). shows that the rate of wound healing (ROH) determined at week 4 was higher for patients with undetectable 16S rRNA at week 4 [2.4 (0.8 to 6.2) mm/week; median (interquartile range)] compared to those with positive 16S rRNA at week 4 [0.3 (-2.0 to 3.3) mm/week] (p = 0.0003, Mann Whitney).

    Techniques:

    Kaplan-Meier analysis of M . ulcerans 16S rRNA in Buruli patients on antibiotic treatment. Blue line: Median time (weeks) for detection of M . ulcerans 16S rRNA. Red line: Proportion of patients with positive M . ulcerans 16S rRNA at week 4.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Clearance of viable Mycobacterium ulcerans from Buruli ulcer lesions during antibiotic treatment as determined by combined 16S rRNA reverse transcriptase /IS 2404 qPCR assay

    doi: 10.1371/journal.pntd.0005695

    Figure Lengend Snippet: Kaplan-Meier analysis of M . ulcerans 16S rRNA in Buruli patients on antibiotic treatment. Blue line: Median time (weeks) for detection of M . ulcerans 16S rRNA. Red line: Proportion of patients with positive M . ulcerans 16S rRNA at week 4.

    Article Snippet: This was not attributable to lesion size at baseline because there was no significant difference in initial size of patient lesions with or without detectable 16S rRNA at week 4 (p = 0.0798, Mann Whitney). shows that the rate of wound healing (ROH) determined at week 4 was higher for patients with undetectable 16S rRNA at week 4 [2.4 (0.8 to 6.2) mm/week; median (interquartile range)] compared to those with positive 16S rRNA at week 4 [0.3 (-2.0 to 3.3) mm/week] (p = 0.0003, Mann Whitney).

    Techniques:

    Survival curve for time to healing in Buruli patients with a negative or positive M . ulcerans 16S rRNA at week 4. Purple lines: Median time to healing.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Clearance of viable Mycobacterium ulcerans from Buruli ulcer lesions during antibiotic treatment as determined by combined 16S rRNA reverse transcriptase /IS 2404 qPCR assay

    doi: 10.1371/journal.pntd.0005695

    Figure Lengend Snippet: Survival curve for time to healing in Buruli patients with a negative or positive M . ulcerans 16S rRNA at week 4. Purple lines: Median time to healing.

    Article Snippet: This was not attributable to lesion size at baseline because there was no significant difference in initial size of patient lesions with or without detectable 16S rRNA at week 4 (p = 0.0798, Mann Whitney). shows that the rate of wound healing (ROH) determined at week 4 was higher for patients with undetectable 16S rRNA at week 4 [2.4 (0.8 to 6.2) mm/week; median (interquartile range)] compared to those with positive 16S rRNA at week 4 [0.3 (-2.0 to 3.3) mm/week] (p = 0.0003, Mann Whitney).

    Techniques:

    Comparison of baseline M . ulcerans IS 2404 in Buruli ulcer patients with a positive or negative 16S rRNA result at week 4.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Clearance of viable Mycobacterium ulcerans from Buruli ulcer lesions during antibiotic treatment as determined by combined 16S rRNA reverse transcriptase /IS 2404 qPCR assay

    doi: 10.1371/journal.pntd.0005695

    Figure Lengend Snippet: Comparison of baseline M . ulcerans IS 2404 in Buruli ulcer patients with a positive or negative 16S rRNA result at week 4.

    Article Snippet: This was not attributable to lesion size at baseline because there was no significant difference in initial size of patient lesions with or without detectable 16S rRNA at week 4 (p = 0.0798, Mann Whitney). shows that the rate of wound healing (ROH) determined at week 4 was higher for patients with undetectable 16S rRNA at week 4 [2.4 (0.8 to 6.2) mm/week; median (interquartile range)] compared to those with positive 16S rRNA at week 4 [0.3 (-2.0 to 3.3) mm/week] (p = 0.0003, Mann Whitney).

    Techniques:

    Gut microbial composition depicting phyla ( A ) and class ( B ) of saline-treated control animals. Antibiotic treatment resulted in no amplification of the 16S rRNA gene and thus we were unable to assess fecal microbiota composition. Taxonomic structure of

    Journal: Gastroenterology

    Article Title: Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats

    doi: 10.1053/j.gastro.2016.07.009

    Figure Lengend Snippet: Gut microbial composition depicting phyla ( A ) and class ( B ) of saline-treated control animals. Antibiotic treatment resulted in no amplification of the 16S rRNA gene and thus we were unable to assess fecal microbiota composition. Taxonomic structure of

    Article Snippet: Real-time quantitative polymerase chain reaction amplification of 16S ribosomal RNA (rRNA) was performed with a Roche 480 II Light Cycler (Roche, Indianapolis, IN).

    Techniques: Amplification

    Maximum likelihood tree of 16S mitochondrial rRNA gene sequences from Cytaeis , Podocorynoides , and their closest relatives (BLAST similarity > 90%). P . minima from Mediterranean and New Zealand clusters within other representatives of the family Rathkeidae ( Rathkea and Lizzia ). The Red Sea Cytaeis sp clusters with the sequence of Cytaeis sp. (EU883541) from Japan and Cytaeis capitata from Indonesia. Schematic images of the polyps of Cytaeis sp. from Japan and the Red Sea indicate location of the fluorescence.

    Journal: PLoS ONE

    Article Title: Green Fluorescence of Cytaeis Hydroids Living in Association with Nassarius Gastropods in the Red Sea

    doi: 10.1371/journal.pone.0146861

    Figure Lengend Snippet: Maximum likelihood tree of 16S mitochondrial rRNA gene sequences from Cytaeis , Podocorynoides , and their closest relatives (BLAST similarity > 90%). P . minima from Mediterranean and New Zealand clusters within other representatives of the family Rathkeidae ( Rathkea and Lizzia ). The Red Sea Cytaeis sp clusters with the sequence of Cytaeis sp. (EU883541) from Japan and Cytaeis capitata from Indonesia. Schematic images of the polyps of Cytaeis sp. from Japan and the Red Sea indicate location of the fluorescence.

    Article Snippet: However, three 16S mitochondrial rDNA sequences of P . minima and one of Cytaeis capitata are present in GenBank, and the novel 16S rRNA sequences from the Red Sea specimens were 92% similar to a sequence of P . minima from Japan ( EU883541) and 91% similar to a sequence of Cytaeis capitata from Indonesia (KP776769), but only 77% similar to two other 16S rDNA sequences identified as P . minima from New Zealand and the Mediterranean (AM183125, AM411420, respectively).

    Techniques: Sequencing, Fluorescence

    Transcriptional analyses of Ag43 under green light induction. Relative units of ag43 transcription were normalized to 16S rRNA amounts. Relative units in cells grown under green light are shown with white circles , and relative units in cells grown under red light are shown with black circles . There is no significant difference in the cell density under red light at each incubation time from at 0 min incubation. The asterisks indicate statistical difference from the cells exposed to red light (*P

    Journal: Microbial Cell Factories

    Article Title: Development of a light-regulated cell-recovery system for non-photosynthetic bacteria

    doi: 10.1186/s12934-016-0426-6

    Figure Lengend Snippet: Transcriptional analyses of Ag43 under green light induction. Relative units of ag43 transcription were normalized to 16S rRNA amounts. Relative units in cells grown under green light are shown with white circles , and relative units in cells grown under red light are shown with black circles . There is no significant difference in the cell density under red light at each incubation time from at 0 min incubation. The asterisks indicate statistical difference from the cells exposed to red light (*P

    Article Snippet: Quantitative PCR was performed to measure the transcriptional level of ag43 and 16S ribosomal RNA (rRNA) (housekeeping genes) with SYBR® Premix Ex TaqTM II (Tli RNaseH Plus) (Takara Bio Inc.).

    Techniques: Incubation

    CLSM image of the FISH-stained 24 h four species biofilm on titanium specimen. Individual images with a z-step size of 2 μm of the 24 h four-species biofilm stained with species-specific 16S rRNA FISH probes for S . oralis (MIT-588-Alexa-405; blue), A . naeslundii (ANA-103-Alexa-488; green), V . dispar (VEI-217-Alexa-568; yellow) and P . gingivalis (POGI-Alexa-647; red) were overlaid to one image. (a)–(d) shows the individual color channels for the four individual species, (e) shows the overlay of the four color channels. Scale bars: 30μm.

    Journal: PLoS ONE

    Article Title: Development and characterization of an oral multispecies biofilm implant flow chamber model

    doi: 10.1371/journal.pone.0196967

    Figure Lengend Snippet: CLSM image of the FISH-stained 24 h four species biofilm on titanium specimen. Individual images with a z-step size of 2 μm of the 24 h four-species biofilm stained with species-specific 16S rRNA FISH probes for S . oralis (MIT-588-Alexa-405; blue), A . naeslundii (ANA-103-Alexa-488; green), V . dispar (VEI-217-Alexa-568; yellow) and P . gingivalis (POGI-Alexa-647; red) were overlaid to one image. (a)–(d) shows the individual color channels for the four individual species, (e) shows the overlay of the four color channels. Scale bars: 30μm.

    Article Snippet: The applied 16S rRNA probes (Eurogentec, Cologne, Germany) are listed in in the supporting information.

    Techniques: Confocal Laser Scanning Microscopy, Fluorescence In Situ Hybridization, Staining

    Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the 16S rRNA

    Journal: Annals of the American Thoracic Society

    Article Title: Significance of the Microbiome in Chronic Obstructive Pulmonary Disease

    doi: 10.1513/AnnalsATS.201306-204AW

    Figure Lengend Snippet: Principal component analysis (PCoA) of four respiratory tract sample types (n= 6 for each sample type) and samples from the oral cavity of healthyindividuals (n = 16) according to the microbial composition, as inferred bypyrosequencing of the 16S rRNA

    Article Snippet: An alternateapproach, which is particularly useful for identification of less abundant bacterialcommunity members, is the 16S rRNA PhyloChip (designed at Lawrence Berkeley NationalLaboratory, manufactured by Affymetrix Corporation, Santa Clara, CA) ( , ).

    Techniques: