hhai  (Thermo Fisher)


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    Structured Review

    Thermo Fisher hhai
    Fecal microbiota composition of the donor and recipient measured by T-RFLP (A, T-RF area ratio digested by <t>HhaI</t> ; B, T-RF area ratio digested by <t>MspI</t> ). The patient underwent probiotic therapy with Clostridium butyricum throughout the treatment until colectomy. The graphs demonstrate that the patient did not show a coherent microbiota composition compared to the healthy donor before treatment. After fecal microbiota transplantation (FMT), the patient's fecal microbiota composition was quite different from that of the donor. Thus, the transferred donor fecal microbiota was not retained in the patient's gut. T-RF: terminal restriction fragments, T-RFLP: T-RF length polymorphism.
    Hhai, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hhai/product/Thermo Fisher
    Average 86 stars, based on 40 article reviews
    Price from $9.99 to $1999.99
    hhai - by Bioz Stars, 2022-09
    86/100 stars

    Images

    1) Product Images from "Failure of Fecal Microbiota Transplantation in a Three-Year-Old Child with Severe Refractory Ulcerative Colitis"

    Article Title: Failure of Fecal Microbiota Transplantation in a Three-Year-Old Child with Severe Refractory Ulcerative Colitis

    Journal: Pediatric Gastroenterology, Hepatology & Nutrition

    doi: 10.5223/pghn.2016.19.3.214

    Fecal microbiota composition of the donor and recipient measured by T-RFLP (A, T-RF area ratio digested by HhaI ; B, T-RF area ratio digested by MspI ). The patient underwent probiotic therapy with Clostridium butyricum throughout the treatment until colectomy. The graphs demonstrate that the patient did not show a coherent microbiota composition compared to the healthy donor before treatment. After fecal microbiota transplantation (FMT), the patient's fecal microbiota composition was quite different from that of the donor. Thus, the transferred donor fecal microbiota was not retained in the patient's gut. T-RF: terminal restriction fragments, T-RFLP: T-RF length polymorphism.
    Figure Legend Snippet: Fecal microbiota composition of the donor and recipient measured by T-RFLP (A, T-RF area ratio digested by HhaI ; B, T-RF area ratio digested by MspI ). The patient underwent probiotic therapy with Clostridium butyricum throughout the treatment until colectomy. The graphs demonstrate that the patient did not show a coherent microbiota composition compared to the healthy donor before treatment. After fecal microbiota transplantation (FMT), the patient's fecal microbiota composition was quite different from that of the donor. Thus, the transferred donor fecal microbiota was not retained in the patient's gut. T-RF: terminal restriction fragments, T-RFLP: T-RF length polymorphism.

    Techniques Used: Transplantation Assay

    2) Product Images from "Binary control of enzymatic cleavage of DNA origami by structural antideterminants"

    Article Title: Binary control of enzymatic cleavage of DNA origami by structural antideterminants

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1204

    Empirical modelling of sharp triangle REase reactivity. (A ) Double-helical models for four HhaI sites (reactive sites 7 and 16, and unreactive sites 20 and 17) in the sharp triangle. For each site, ΔXO min is defined as the minimum distance (in bp) between the REase recognition sequence and nearest crossover junction. ( B ) Site-specific diagrams relative to the adjacent double-helical models, with structural states defined as (a|site|b), and with ‘a’ and ‘b’ as ‘mechanical’ indexes. A ‘tight’ spring has a mechanical index = 0, while a ‘relaxed’ (or absent) spring has a mechanical index = 1. ( C ) For each mechanical state, ΔXO min is plotted in ascending order as a function of HhaI site index (see Supplementary Figure S8 ). ‘on’ (red), ‘ int’ (pink), and ‘off’ (grey) labels are defined by the legend in Figure 3D . Dotted columns are for those sites whose REase activity is significantly influenced by the presence of a structural defect in the sharp triangle (Figure 4 ). The configuration (0|site|0) is found to correspond to unreactive sites only, except for site 8, while the configurations (1|site|1) and (1|site|0)/(0|site|1) include nearly all HhaI reactive sites. ( D ) (Left) number of recognition sites in the sharp triangle for seven REases (the E1 and E2 isoschizomers are not shown) with 4-bp specificities. (Centre) percentage of unreactive sites in the unmodified sharp triangle estimated experimentally (pale grey) and predicted (grey) by assuming that, for any REase, the reactive sites are either (1|site|1) or (1|site|0)/(0|site|1) configuration, and have ΔXO ≥ 5 bp. Experimental estimates are obtained by counting the number of M13 fragments produced by each REase (Figure 1B , Supplementary Table S3 ). On the left in the histogram, average percentages are calculated from the values on the right as means ± S.D. (Right) Site-specific analysis of model accuracy for Hin1II and HhaI. T ON , ‘true ON rate’, fraction of reactive sites predicted ‘on’ (red); F OFF , ‘False OFF rate’, fraction of reactive sites prediction ‘off’ (pale red); T OFF , ‘True OFF rate’, fraction of unreactive sites predicted ‘off’ (grey); F ON , ‘False ON rate’, fraction of unreactive sites predicted ‘on’ (pale grey). Model accuracy is calculated as (T ON + T OFF ) / (T ON + T OFF + F ON + F OFF ) (blue line) (see Supplementary Figure S23 ).
    Figure Legend Snippet: Empirical modelling of sharp triangle REase reactivity. (A ) Double-helical models for four HhaI sites (reactive sites 7 and 16, and unreactive sites 20 and 17) in the sharp triangle. For each site, ΔXO min is defined as the minimum distance (in bp) between the REase recognition sequence and nearest crossover junction. ( B ) Site-specific diagrams relative to the adjacent double-helical models, with structural states defined as (a|site|b), and with ‘a’ and ‘b’ as ‘mechanical’ indexes. A ‘tight’ spring has a mechanical index = 0, while a ‘relaxed’ (or absent) spring has a mechanical index = 1. ( C ) For each mechanical state, ΔXO min is plotted in ascending order as a function of HhaI site index (see Supplementary Figure S8 ). ‘on’ (red), ‘ int’ (pink), and ‘off’ (grey) labels are defined by the legend in Figure 3D . Dotted columns are for those sites whose REase activity is significantly influenced by the presence of a structural defect in the sharp triangle (Figure 4 ). The configuration (0|site|0) is found to correspond to unreactive sites only, except for site 8, while the configurations (1|site|1) and (1|site|0)/(0|site|1) include nearly all HhaI reactive sites. ( D ) (Left) number of recognition sites in the sharp triangle for seven REases (the E1 and E2 isoschizomers are not shown) with 4-bp specificities. (Centre) percentage of unreactive sites in the unmodified sharp triangle estimated experimentally (pale grey) and predicted (grey) by assuming that, for any REase, the reactive sites are either (1|site|1) or (1|site|0)/(0|site|1) configuration, and have ΔXO ≥ 5 bp. Experimental estimates are obtained by counting the number of M13 fragments produced by each REase (Figure 1B , Supplementary Table S3 ). On the left in the histogram, average percentages are calculated from the values on the right as means ± S.D. (Right) Site-specific analysis of model accuracy for Hin1II and HhaI. T ON , ‘true ON rate’, fraction of reactive sites predicted ‘on’ (red); F OFF , ‘False OFF rate’, fraction of reactive sites prediction ‘off’ (pale red); T OFF , ‘True OFF rate’, fraction of unreactive sites predicted ‘off’ (grey); F ON , ‘False ON rate’, fraction of unreactive sites predicted ‘on’ (pale grey). Model accuracy is calculated as (T ON + T OFF ) / (T ON + T OFF + F ON + F OFF ) (blue line) (see Supplementary Figure S23 ).

    Techniques Used: Sequencing, Activity Assay, Produced

    3) Product Images from "Survivin repression by p53, Rb, and E2F2 in normal human melanocytes"

    Article Title: Survivin repression by p53, Rb, and E2F2 in normal human melanocytes

    Journal:

    doi: 10.1093/carcin/bgm219

    Methylation-independent regulation of Survivin. ( a ) Schematic depicting survivin promoter and proximal exonic sequence, and location of HpaII (open circles) and HhaI (filled circles) sites, and binding sites for p53 (open box) and E2F factors (shaded
    Figure Legend Snippet: Methylation-independent regulation of Survivin. ( a ) Schematic depicting survivin promoter and proximal exonic sequence, and location of HpaII (open circles) and HhaI (filled circles) sites, and binding sites for p53 (open box) and E2F factors (shaded

    Techniques Used: Methylation, Sequencing, Binding Assay

    4) Product Images from "Anatoxin-a Synthetase Gene Cluster of the Cyanobacterium Anabaena sp. Strain 37 and Molecular Methods To Detect Potential Producers ▿ sp. Strain 37 and Molecular Methods To Detect Potential Producers ▿ †"

    Article Title: Anatoxin-a Synthetase Gene Cluster of the Cyanobacterium Anabaena sp. Strain 37 and Molecular Methods To Detect Potential Producers ▿ sp. Strain 37 and Molecular Methods To Detect Potential Producers ▿ †

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.06022-11

    RFLP analysis of anaC amplicons (366 bp) of cyanobacterial strains and environmental samples with the HhaI and HinfI restriction enzymes. The amplicons are indicated above the lanes according to the strain/sample used for amplification: Anabaena sp. 37
    Figure Legend Snippet: RFLP analysis of anaC amplicons (366 bp) of cyanobacterial strains and environmental samples with the HhaI and HinfI restriction enzymes. The amplicons are indicated above the lanes according to the strain/sample used for amplification: Anabaena sp. 37

    Techniques Used: Environmental Sampling, Amplification

    5) Product Images from "Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA"

    Article Title: Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-Deoxy-7-amido-7-deazaguanosine-Modified DNA

    Journal: International Journal of Molecular Sciences

    doi: 10.3390/ijms22147333

    Restriction patterns of phage MED16 genomic DNA by Type II REases. REases are indicated on top of each lane as well as the number of guanine bases (G) in the recognition sequence. The exact number of dADG bases in a particular restriction site is unknown. M—GeneRuler™ DNA Ladder Mix (Thermo Fisher Scientific, Vilnius, Lithuania); gDNA—undigested genomic DNA of MED16. Methylation sensitivity of REases: MboI (Dam methylation-sensitive); EcoRII (Dcm methylation-sensitive); HhaI (CpG methylation-sensitive); Bsu15I (CpG methylation-sensitive, Dam methylation-sensitive); BamHI, Csp6I, DpnI, DraI, EcoRI, EcoRV, HaeIII, NdeI (not Dam methylation-sensitive, not Dcm methylation-sensitive, not CpG methylation-sensitive). Below the gel is the representation of the expected restriction pattern.
    Figure Legend Snippet: Restriction patterns of phage MED16 genomic DNA by Type II REases. REases are indicated on top of each lane as well as the number of guanine bases (G) in the recognition sequence. The exact number of dADG bases in a particular restriction site is unknown. M—GeneRuler™ DNA Ladder Mix (Thermo Fisher Scientific, Vilnius, Lithuania); gDNA—undigested genomic DNA of MED16. Methylation sensitivity of REases: MboI (Dam methylation-sensitive); EcoRII (Dcm methylation-sensitive); HhaI (CpG methylation-sensitive); Bsu15I (CpG methylation-sensitive, Dam methylation-sensitive); BamHI, Csp6I, DpnI, DraI, EcoRI, EcoRV, HaeIII, NdeI (not Dam methylation-sensitive, not Dcm methylation-sensitive, not CpG methylation-sensitive). Below the gel is the representation of the expected restriction pattern.

    Techniques Used: Sequencing, Methylation, CpG Methylation Assay

    6) Product Images from "Salivary Microbiota Is Significantly Less Diverse in Patients with Chronic Spontaneous Urticaria Compared to Healthy Controls: Preliminary Results"

    Article Title: Salivary Microbiota Is Significantly Less Diverse in Patients with Chronic Spontaneous Urticaria Compared to Healthy Controls: Preliminary Results

    Journal: Life

    doi: 10.3390/life11121329

    Boxplot was used to display the differences in alpha diversity visually. The Shannon index was significantly lower in Chronic Spontaneous Urticaria (CSU) group compared to the HC group. ( a ) HhaI -digestion. ( b ) MspI -digestion.
    Figure Legend Snippet: Boxplot was used to display the differences in alpha diversity visually. The Shannon index was significantly lower in Chronic Spontaneous Urticaria (CSU) group compared to the HC group. ( a ) HhaI -digestion. ( b ) MspI -digestion.

    Techniques Used:

    Dendogram of the salivary microbiota profiles of Chronic Spontaneous Urticaria (CSU) patients and HC. ( a ) HhaI -digestion. ( b ) MspI -digestion.
    Figure Legend Snippet: Dendogram of the salivary microbiota profiles of Chronic Spontaneous Urticaria (CSU) patients and HC. ( a ) HhaI -digestion. ( b ) MspI -digestion.

    Techniques Used:

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    Thermo Fisher hha i
    Microbial community composition reflected by T-RFLP profiles of 16S rRNA genes digested with <t>Hha</t> I, in bulk coal tar-contaminated sediment ( A ) and CsCl gradient-ultracentrifuged preparations from the sediment 12 C-DNA ( B ) and 13 C-DNA ( C ) fractions.
    Hha I, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hha i/product/Thermo Fisher
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hha i - by Bioz Stars, 2022-09
    96/100 stars
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    Microbial community composition reflected by T-RFLP profiles of 16S rRNA genes digested with Hha I, in bulk coal tar-contaminated sediment ( A ) and CsCl gradient-ultracentrifuged preparations from the sediment 12 C-DNA ( B ) and 13 C-DNA ( C ) fractions.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment

    doi: 10.1073/pnas.1735529100

    Figure Lengend Snippet: Microbial community composition reflected by T-RFLP profiles of 16S rRNA genes digested with Hha I, in bulk coal tar-contaminated sediment ( A ) and CsCl gradient-ultracentrifuged preparations from the sediment 12 C-DNA ( B ) and 13 C-DNA ( C ) fractions.

    Article Snippet: Fluorescently labeled PCR products were digested for 6 h with Hha I and electrophoretically separated in an Applied Biosystems 3730 DNA analyzer (Applied Biosystems), and the data were analyzed by using genemapper software (Applied Biosystems).

    Techniques:

    (A and B). A is Agarose gel electrophoresis of c-myc PCR products. Lane M: 1.5 Kb DNA ladder, lane 1: negative sample, lanes 2-6: c-myc PCR products (681 bp). B is Agarose gel electrophoresis of digested c-myc PCR with HhaI restriction endonuclease. Lane M: 1 kb DNA ladder, lane 2: CC genotype (681 bp), lane 3: CG genotype (681, 480 and 201 bp) and lanes 1, 4 and 5: GG genotype (480 and 201 bp)

    Journal: Asian Pacific Journal of Cancer Prevention : APJCP

    Article Title: Association of C-myc and p53 Gene Expression and Polymorphisms with Hepatitis C (HCV) Chronic Infection, Cirrhosis and Hepatocellular Carcinoma (HCC) Stages in Egypt

    doi: 10.22034/APJCP.2017.18.8.2049

    Figure Lengend Snippet: (A and B). A is Agarose gel electrophoresis of c-myc PCR products. Lane M: 1.5 Kb DNA ladder, lane 1: negative sample, lanes 2-6: c-myc PCR products (681 bp). B is Agarose gel electrophoresis of digested c-myc PCR with HhaI restriction endonuclease. Lane M: 1 kb DNA ladder, lane 2: CC genotype (681 bp), lane 3: CG genotype (681, 480 and 201 bp) and lanes 1, 4 and 5: GG genotype (480 and 201 bp)

    Article Snippet: The digestion reaction included 10 μl amplified PCR product, 1 μl HhaI restriction, 2 μl 10X restriction enzyme digestion buffer (Fermentas Life Science, Germany) and 7 μl sterile ddH2O was spun at 500 rpm for 3 sec and incubated at 37ºC overnight.

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction

    TSG methylation predictive for classification of acute leukemia cell lines . Methylation was assessed by MS-MLPA (see also Additional file 1 ) or by DNA digestion with methylation-sensitive Hha I plus promoter-specific quantitative real-time PCR (for analysis of BEX2 ). Green: methylation level ≥ 10%; yellow: methylation level

    Journal: Molecular Cancer

    Article Title: Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in Acute Myeloid Leukemia

    doi: 10.1186/1476-4598-8-86

    Figure Lengend Snippet: TSG methylation predictive for classification of acute leukemia cell lines . Methylation was assessed by MS-MLPA (see also Additional file 1 ) or by DNA digestion with methylation-sensitive Hha I plus promoter-specific quantitative real-time PCR (for analysis of BEX2 ). Green: methylation level ≥ 10%; yellow: methylation level

    Article Snippet: This semi-quantitative technique is based on digestion of DNA with the methylation-sensitive restriction enzyme Hha I (Fermentas, St. Leon-Rot, Germany) and a subsequent multiplex PCR followed by fragment analysis via capillary electrophoresis [ ].

    Techniques: Methylation, Mass Spectrometry, Multiplex Ligation-dependent Probe Amplification, Real-time Polymerase Chain Reaction

    Relative abundances of T-RF of amplified nirS genes (A) and 16S rDNAs of Bacteria (B) and Archaea (C) within sediment samples from Puget Sound (C/1 to C/3) and the Washington margin (301/1 to 301/6; 306/1 to 306/5; 304/1 to 304/3). Diagrams show results after cleavage with Hha I ( nirS ), Hae III ( Bacteria ), and Hha I ( Archaea ). Numbers on top of the columns indicate the numbers of detectable T-RFs for individual samples. Numbers in the keys indicate the lengths of the T-RFs in base pairs for fragments with a relative abundance of more than 2%.

    Journal: Applied and Environmental Microbiology

    Article Title: Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

    doi: 10.1128/AEM.67.4.1893-1901.2001

    Figure Lengend Snippet: Relative abundances of T-RF of amplified nirS genes (A) and 16S rDNAs of Bacteria (B) and Archaea (C) within sediment samples from Puget Sound (C/1 to C/3) and the Washington margin (301/1 to 301/6; 306/1 to 306/5; 304/1 to 304/3). Diagrams show results after cleavage with Hha I ( nirS ), Hae III ( Bacteria ), and Hha I ( Archaea ). Numbers on top of the columns indicate the numbers of detectable T-RFs for individual samples. Numbers in the keys indicate the lengths of the T-RFs in base pairs for fragments with a relative abundance of more than 2%.

    Article Snippet: Hydrolysis was performed with three different restriction endonucleases in digestions with a single tetrameric enzyme each (for bacterial 16S rDNAs, Hae III [GG′CC] [where the prime shows the site of cleavage], Hha I [GCG′C], and Msp I [C′CGG]; for archaeal 16S rDNAs, Hae III, Hha I, and Rsa I [GT′CA]; and for nirS genes, Hha I, Msp I, and Taq I [T′GCA]; Gibco BRL).

    Techniques: Amplification