Structured Review

Eurofins amplicons
Rarefaction analysis of the <t>amplicons</t> obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.
Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 94/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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amplicons - by Bioz Stars, 2020-09
94/100 stars

Images

1) Product Images from "Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river"

Article Title: Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river

Journal: MicrobiologyOpen

doi: 10.1002/mbo3.80

Rarefaction analysis of the amplicons obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.
Figure Legend Snippet: Rarefaction analysis of the amplicons obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.

Techniques Used:

2) Product Images from "Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics"

Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics

Journal: Virology Journal

doi: 10.1186/s12985-016-0504-8

Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide
Figure Legend Snippet: Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

Techniques Used: Recombinase Polymerase Amplification, Generated, Infection, Polymerase Chain Reaction, Purification, Amplification, Staining

3) Product Images from "A genetic switch for worker nutrition-mediated traits in honeybees"

Article Title: A genetic switch for worker nutrition-mediated traits in honeybees

Journal: PLoS Biology

doi: 10.1371/journal.pbio.3000171

Size polyphenism of gonads in genetic females at larval stage 5 that were double mutants for the fem gene. (a) Model of the known components of the sex-determining pathway in honeybees with nutritional differences in females. (b) Gonad development at larval stage 5. (Right) A pair of large gonads (male type) from fem sgRNA2 -treated genetic females reared on worker nutrition. The gonads display densely packed layers of folded testioles, similar to those observed in haploid males (WT males). (Left) Pairs of small gonads (female type) from WT workers and genetic female bees reared on worker nutrition. A WT large queen ovary from a queen reared in a colony on queen nutrition. A large WT testis of a haploid male manually reared on worker nutrition. (c) Male dsx ( dsx M ) and female dsx ( dsx F ) transcripts in mutated genetic females with male phenotypes ( fem-sgRNA1 or fem-sgRNA2 ). Male and female transcripts were separately amplified by RT-PCR [ 64 ], and the male and female fragments of each single bee were resolved via agarose gel electrophoresis. Numbers indicate different control and mutated bees. (d) Deduced amino acid sequences from sequenced amplicons of the fem gene at the designated CRISPR/Cas9 cleavage sites for the four worker nutrition-reared genetic female larvae with large gonads of the male type. Stars indicate premature translation stop codons. Numbers indicate different mutated bees. Scale bars, 1 mm. CRISPR/Cas9, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9; dsx F , female dsx ; dsx M , male dsx ; RT-PCR, reverse transcription PCR; sgRNA, single guide RNA; WT, wild type.
Figure Legend Snippet: Size polyphenism of gonads in genetic females at larval stage 5 that were double mutants for the fem gene. (a) Model of the known components of the sex-determining pathway in honeybees with nutritional differences in females. (b) Gonad development at larval stage 5. (Right) A pair of large gonads (male type) from fem sgRNA2 -treated genetic females reared on worker nutrition. The gonads display densely packed layers of folded testioles, similar to those observed in haploid males (WT males). (Left) Pairs of small gonads (female type) from WT workers and genetic female bees reared on worker nutrition. A WT large queen ovary from a queen reared in a colony on queen nutrition. A large WT testis of a haploid male manually reared on worker nutrition. (c) Male dsx ( dsx M ) and female dsx ( dsx F ) transcripts in mutated genetic females with male phenotypes ( fem-sgRNA1 or fem-sgRNA2 ). Male and female transcripts were separately amplified by RT-PCR [ 64 ], and the male and female fragments of each single bee were resolved via agarose gel electrophoresis. Numbers indicate different control and mutated bees. (d) Deduced amino acid sequences from sequenced amplicons of the fem gene at the designated CRISPR/Cas9 cleavage sites for the four worker nutrition-reared genetic female larvae with large gonads of the male type. Stars indicate premature translation stop codons. Numbers indicate different mutated bees. Scale bars, 1 mm. CRISPR/Cas9, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9; dsx F , female dsx ; dsx M , male dsx ; RT-PCR, reverse transcription PCR; sgRNA, single guide RNA; WT, wild type.

Techniques Used: Amplification, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, CRISPR, Polymerase Chain Reaction

4) Product Images from "Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae"

Article Title: Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

Journal: Plant Methods

doi: 10.1186/s13007-020-00662-w

PCR amplicons flanking a 4.8 kb insertion in the chloroplast genome of H. ammodendron (2–6) and H. persicum (8–12). Agarose gel electrophoresis of PCR products ( a ); diagram representing location and length of each amplicon ( b ). Expected amplicon sizes are 6607 (2 and 8), 7172 (3 and 9), 8132 (4 and 6), 3810 (5 and 11), and 4458 nt (6 and 12). Primers for PCRs 2–4 and 8–10 flank the ycf1 and ndhF genes. Primers for PCRs 5 and 11 flank flank the middle section of the 4.8 kb insertion and the ndhF gene. Primers for PCRs 6 and 12 flank the ycf1 gene and the middle section of the 4.8 kb insertion. 1 and 7: exACTGene DNA Ladders 1 kb DNA Ladder
Figure Legend Snippet: PCR amplicons flanking a 4.8 kb insertion in the chloroplast genome of H. ammodendron (2–6) and H. persicum (8–12). Agarose gel electrophoresis of PCR products ( a ); diagram representing location and length of each amplicon ( b ). Expected amplicon sizes are 6607 (2 and 8), 7172 (3 and 9), 8132 (4 and 6), 3810 (5 and 11), and 4458 nt (6 and 12). Primers for PCRs 2–4 and 8–10 flank the ycf1 and ndhF genes. Primers for PCRs 5 and 11 flank flank the middle section of the 4.8 kb insertion and the ndhF gene. Primers for PCRs 6 and 12 flank the ycf1 gene and the middle section of the 4.8 kb insertion. 1 and 7: exACTGene DNA Ladders 1 kb DNA Ladder

Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification

5) Product Images from "Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast"

Article Title: Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast

Journal: bioRxiv

doi: 10.1101/476804

CASTLING for tagging 215 nuclear proteins with a green fluorescent protein. ( a ) Three oligonucleotide pools of the same design (1,577 sequences, Supplementary Table 1 ) were used to create four tag libraries by CASTLING in duplicate sampling the indicated amount of starting material for PCR. ( b ) Detected oligonucleotide sequences of the design after PCR amplification (blue), self-integrating cassette (SIC) assembly (green) and in the final library (orange); oligonucleotides with copy number estimates (unique UMI counts) in the lowest quartile (lower 25%) are shown in light shade. ( c ) Same as (b), but evaluated in terms of open reading frames (ORFs) represented by the oligonucleotides or SICs. ( d ) Copy number of PCR amplicons recovered (red) or lost (blue) after recombineering; black horizontal lines indicate median UMI counts. ( e ) Pearson’s pairwise correlation of oligonucleotide or SIC copy number between replicates after PCR or rolling-circle amplification (RCA) respectively; n.s., not significant (p > 0.05). ( f ) Kernel density estimates of copy number in replicate 1a as normalized to the median copy number observed in the oligonucleotide pool (before recombineering) and after recombineering into the SIC pool (left panel); the distribution of fold-changes (right panel) highlights two frequency ranges: [0.1–0.9], i.e. 80% of SICs, and [0.25–0.75], i.e. 50% of SICs. ( g ) Representative fluorescence microscopy images of cells displaying nuclear, diffuse non-nuclear (asterisks), or no mNeonGreen fluorescence (arrows); scale bar 5 µm. ( h ) Quantification of fluorescence localization in > 1,000 cells in each replicate. ( i ) Recurrence of off-target events as revealed by Anchor-Seq across all library replicates and all genomic loci (left panel); the fraction of cells with SICs integrated at off-target sites (blue) within each clone population (red) is shown (right panel, axis trimmed). Panels b–i: Source data are provided as a Source Data file.
Figure Legend Snippet: CASTLING for tagging 215 nuclear proteins with a green fluorescent protein. ( a ) Three oligonucleotide pools of the same design (1,577 sequences, Supplementary Table 1 ) were used to create four tag libraries by CASTLING in duplicate sampling the indicated amount of starting material for PCR. ( b ) Detected oligonucleotide sequences of the design after PCR amplification (blue), self-integrating cassette (SIC) assembly (green) and in the final library (orange); oligonucleotides with copy number estimates (unique UMI counts) in the lowest quartile (lower 25%) are shown in light shade. ( c ) Same as (b), but evaluated in terms of open reading frames (ORFs) represented by the oligonucleotides or SICs. ( d ) Copy number of PCR amplicons recovered (red) or lost (blue) after recombineering; black horizontal lines indicate median UMI counts. ( e ) Pearson’s pairwise correlation of oligonucleotide or SIC copy number between replicates after PCR or rolling-circle amplification (RCA) respectively; n.s., not significant (p > 0.05). ( f ) Kernel density estimates of copy number in replicate 1a as normalized to the median copy number observed in the oligonucleotide pool (before recombineering) and after recombineering into the SIC pool (left panel); the distribution of fold-changes (right panel) highlights two frequency ranges: [0.1–0.9], i.e. 80% of SICs, and [0.25–0.75], i.e. 50% of SICs. ( g ) Representative fluorescence microscopy images of cells displaying nuclear, diffuse non-nuclear (asterisks), or no mNeonGreen fluorescence (arrows); scale bar 5 µm. ( h ) Quantification of fluorescence localization in > 1,000 cells in each replicate. ( i ) Recurrence of off-target events as revealed by Anchor-Seq across all library replicates and all genomic loci (left panel); the fraction of cells with SICs integrated at off-target sites (blue) within each clone population (red) is shown (right panel, axis trimmed). Panels b–i: Source data are provided as a Source Data file.

Techniques Used: Sampling, Polymerase Chain Reaction, Amplification, Fluorescence, Microscopy

6) Product Images from "Attenuated Virulence and Genomic Reductive Evolution in the Entomopathogenic Bacterial Symbiont Species, Xenorhabdus poinarii"

Article Title: Attenuated Virulence and Genomic Reductive Evolution in the Entomopathogenic Bacterial Symbiont Species, Xenorhabdus poinarii

Journal: Genome Biology and Evolution

doi: 10.1093/gbe/evu119

The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent amplicons are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).
Figure Legend Snippet: The xaxAB locus, its genomic context and its shuffling point exbD / rdgC in the X. doucetiae FRM16 ( Xd ), X. nematophila ATCC19061 ( Xn ), X. bovienii SS-2004 ( Xb ), X. poinarii G6 ( Xp_G6 ), AZ26 ( Xp_AZ26 ), NC33 ( Xp_NC33 ), SK72 ( Xp_SK72 ), and CU01 ( Xp_CU01 ) genomes. The large arrows represent individual ORFs, and the names of the genes are indicated above the arrows. Genes encoding proteins of unknown function are marked with an asterisk. Orthologous genes are indicated by arrows in the same color. Black and chequered arrows represent core-genome genes and transposase genes, respectively. The thin arrows indicate the binding sites of the primers used for PCR amplification. The vertical parallel lines indicate the end of the sequenced area and the dotted lines represent an unsequenced genomic region. The cladogram was obtained by the maximum-likelihood phylogenetic analysis of five concatenated protein-coding sequences ( recA , gyrB , dnaN , gltX , and infB ), as already described in figure 1 . The accession numbers of the sequences of the subsequent amplicons are HG934736 (strain AZ26), HG934737 (strain NC33), HG934738 (strain SK72), HG934739 and HG934740 (strain CU01).

Techniques Used: Binding Assay, Polymerase Chain Reaction, Amplification

7) Product Images from "Molecular Pap smear: HPV genotype and DNA methylation of ADCY8, CDH8, and ZNF582 as an integrated biomarker for high-grade cervical cytology"

Article Title: Molecular Pap smear: HPV genotype and DNA methylation of ADCY8, CDH8, and ZNF582 as an integrated biomarker for high-grade cervical cytology

Journal: Clinical Epigenetics

doi: 10.1186/s13148-016-0263-9

PCR amplification of HPV DNA by three consensus primer sets and HPV genotyping by amplicon sequencing. a Representative gel image of PCR amplicon detection by high-resolution capillary gel electrophoresis. Representative samples #285 (LSIL) and #179 (HSIL) reveal MY09/11, FAP59/64, and GP-E6/E7 F/B amplicons with expected yield of ~450-, 480- (or 260-bp fragment), and 660-bp fragments, respectively. b Parallel PCR testing for HPV by three primer sets. Venn diagrams show intersecting and complementary sets of cytological samples ( N ) detected of HPV DNA by MY-, FAP-, and E6/E7 primer sets according to cytological diagnoses, i.e., NILM, LSIL, and HSIL. The net positivity of simultaneous testing for HPV ( union of the circles ) in NILM, LSIL, and HSIL are 31/100 (31 %), 95/100 (95 %), and 71/77 (92 %), respectively. c HPV genotype distribution of 191 cytology samples with PCR-detected HPV DNA according to cytological diagnoses: NILM, LSIL, and HSIL. The increase in carcinogenic HPV genotypes was coincident with cytological grade (Spearman’s ρ = 0.658, p
Figure Legend Snippet: PCR amplification of HPV DNA by three consensus primer sets and HPV genotyping by amplicon sequencing. a Representative gel image of PCR amplicon detection by high-resolution capillary gel electrophoresis. Representative samples #285 (LSIL) and #179 (HSIL) reveal MY09/11, FAP59/64, and GP-E6/E7 F/B amplicons with expected yield of ~450-, 480- (or 260-bp fragment), and 660-bp fragments, respectively. b Parallel PCR testing for HPV by three primer sets. Venn diagrams show intersecting and complementary sets of cytological samples ( N ) detected of HPV DNA by MY-, FAP-, and E6/E7 primer sets according to cytological diagnoses, i.e., NILM, LSIL, and HSIL. The net positivity of simultaneous testing for HPV ( union of the circles ) in NILM, LSIL, and HSIL are 31/100 (31 %), 95/100 (95 %), and 71/77 (92 %), respectively. c HPV genotype distribution of 191 cytology samples with PCR-detected HPV DNA according to cytological diagnoses: NILM, LSIL, and HSIL. The increase in carcinogenic HPV genotypes was coincident with cytological grade (Spearman’s ρ = 0.658, p

Techniques Used: Polymerase Chain Reaction, Amplification, Sequencing, Nucleic Acid Electrophoresis

8) Product Images from "Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix"

Article Title: Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix

Journal: BMC Genomics

doi: 10.1186/s12864-017-3612-y

HPV DNA detection by PCR amplification, capillary electrophoresis and dideoxy (Sanger) sequencing. a Gel image and electropherogram of amplicon detection by high-resolution capillary electrophoresis. Representative samples #311, 312, 319, and 330 (HSIL) reveal 1 or 2 amplicons after using consensus primers (GP-E6/E7 F/B) to amplify an E6/E7 segment with an expected fragment size of ~660 bp (range, 619-819 bp). Amplicon size variability reflects sequence differences between HPV genotypes. In general, deep sequencing resolved a greater number of HPV genotypes than capillary electrophoresis per sample. Sample #330 illustrates this with detection of 2 amplicons on electrophoresis, but 8 genotypes by deep sequencing. b Representative sample (#311) with a single HPV infection revealing 1 amplicon (699 bp peak on electropherogram) and clean sequencing chromatogram. Representative sample (#319) with multiple HPV infections revealing 2 amplicons (619 and 656 bp peaks on electropherogram) and “noisy” overlapping peaks on the chromatogram. AM, alignment marker; B, buffer; bp, base pair; M, molecular-weight marker
Figure Legend Snippet: HPV DNA detection by PCR amplification, capillary electrophoresis and dideoxy (Sanger) sequencing. a Gel image and electropherogram of amplicon detection by high-resolution capillary electrophoresis. Representative samples #311, 312, 319, and 330 (HSIL) reveal 1 or 2 amplicons after using consensus primers (GP-E6/E7 F/B) to amplify an E6/E7 segment with an expected fragment size of ~660 bp (range, 619-819 bp). Amplicon size variability reflects sequence differences between HPV genotypes. In general, deep sequencing resolved a greater number of HPV genotypes than capillary electrophoresis per sample. Sample #330 illustrates this with detection of 2 amplicons on electrophoresis, but 8 genotypes by deep sequencing. b Representative sample (#311) with a single HPV infection revealing 1 amplicon (699 bp peak on electropherogram) and clean sequencing chromatogram. Representative sample (#319) with multiple HPV infections revealing 2 amplicons (619 and 656 bp peaks on electropherogram) and “noisy” overlapping peaks on the chromatogram. AM, alignment marker; B, buffer; bp, base pair; M, molecular-weight marker

Techniques Used: Polymerase Chain Reaction, Amplification, Electrophoresis, Sequencing, Infection, Marker, Molecular Weight

HPV genotype composition found in LSIL and HSIL samples. Deep sequencing of HPV E6/E7 amplicons derived from each LSIL or HSIL sample identified 1 to 8 HPV genotypes and quantitated their composition (%) based on number of mapped reads to total mapped reads. The top three dominant (highest proportion) genotypes found in LSIL were HPV-39, -16, and -35 [ red , solid/hashed]. The carcinogenicity of LSIL dominant genotypes were: carcinogenic 29/43 (67%, red ); possibly carcinogenic 6/43 (14%, blue ); and not classifiable/probably not carcinogenic 8/43 (19%, green ). For HSIL, the dominant genotype was primarily HPV-16 (21/29, 72%); and the dominant genotypes were all carcinogenic 29/29 (100%, red ). The HPV carcinogenicity is based on IARC’s classification of human carcinogens [ 8 ]. HSIL, high-grade squamous intraepithelial lesion; IARC, International Agency for Research on Cancer; LSIL, low-grade squamous intraepithelial lesion; ID, identification
Figure Legend Snippet: HPV genotype composition found in LSIL and HSIL samples. Deep sequencing of HPV E6/E7 amplicons derived from each LSIL or HSIL sample identified 1 to 8 HPV genotypes and quantitated their composition (%) based on number of mapped reads to total mapped reads. The top three dominant (highest proportion) genotypes found in LSIL were HPV-39, -16, and -35 [ red , solid/hashed]. The carcinogenicity of LSIL dominant genotypes were: carcinogenic 29/43 (67%, red ); possibly carcinogenic 6/43 (14%, blue ); and not classifiable/probably not carcinogenic 8/43 (19%, green ). For HSIL, the dominant genotype was primarily HPV-16 (21/29, 72%); and the dominant genotypes were all carcinogenic 29/29 (100%, red ). The HPV carcinogenicity is based on IARC’s classification of human carcinogens [ 8 ]. HSIL, high-grade squamous intraepithelial lesion; IARC, International Agency for Research on Cancer; LSIL, low-grade squamous intraepithelial lesion; ID, identification

Techniques Used: Sequencing, Derivative Assay

9) Product Images from "Paenibacillus larvae Chitin-Degrading Protein PlCBP49 Is a Key Virulence Factor in American Foulbrood of Honey Bees"

Article Title: Paenibacillus larvae Chitin-Degrading Protein PlCBP49 Is a Key Virulence Factor in American Foulbrood of Honey Bees

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1004284

Disruption of the gene coding for Pl CBP49 in P. larvae ATCC9545 (ERIC I) and in P. larvae DSM25430 (ERIC II). (A) Migration properties of amplicons from the wild-type (ATCC9545 wt, DSM25430 wt) and mutant bacteria (ATCC9545 Δ cbp , DSM25430 Δ cbp ) confirmed the successful insertion of the targetron into the gene cbp 49. (B) Growth curves of the knockout strain ATCC9545 Δ cbp (open circle) in comparison to the parent wild-type strain ATCC9545 (closed circle). (C) Growth curves of the knockout strain DSM25430 Δ cbp (open triangle) in comparison to the parent wild-type strain DSM25430 (closed triangle). Both results showed that disrupting Pl CBP49 expression did not influence bacterial growth.
Figure Legend Snippet: Disruption of the gene coding for Pl CBP49 in P. larvae ATCC9545 (ERIC I) and in P. larvae DSM25430 (ERIC II). (A) Migration properties of amplicons from the wild-type (ATCC9545 wt, DSM25430 wt) and mutant bacteria (ATCC9545 Δ cbp , DSM25430 Δ cbp ) confirmed the successful insertion of the targetron into the gene cbp 49. (B) Growth curves of the knockout strain ATCC9545 Δ cbp (open circle) in comparison to the parent wild-type strain ATCC9545 (closed circle). (C) Growth curves of the knockout strain DSM25430 Δ cbp (open triangle) in comparison to the parent wild-type strain DSM25430 (closed triangle). Both results showed that disrupting Pl CBP49 expression did not influence bacterial growth.

Techniques Used: Migration, Mutagenesis, Knock-Out, Expressing

Related Articles

Sequencing:

Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics
Article Snippet: .. Direct sequencing was attempted from amplicons cleaned using QIAquick columns or incubation at 65 °C for 15 min followed by centrifugation at 3800 rcf for 20 s. Amplicons were sent to Eurofins Genomics (Huntsville, AL) for sequencing using primer pair TYL828F/TYL834R. .. Clinical trial The UF Plant Diagnostic Center received 13 field samples from suspected TYLCV-infected tomato plants from two locations.

Article Title: Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix
Article Snippet: .. Dideoxy sequencing of the amplicons (~200 ng DNA/sample) was performed using primer GP-E6-3 F at Eurofins Operon (USA). .. Sequence quality was assessed using Sequence Scanner 2.0 (appliedbiosystems.com) where a “high quality” Trace Score (TS) was defined as ≥20 and a QV20+ value (total number of bases in the sequence with TS ≥20) as ≥100.

Article Title: Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae
Article Snippet: .. Amplicons, ranging in size from 0.2 to 0.5 kb, were Sanger sequenced to ensure sequence fidelity of the DNA assembly output (Eurofins Genomics, KY). .. A primer walking and Sanger sequencing method was utilized to identify non-overlapping regions in the LSC + IRa and IRb + LSC junctions of T. indica and the IRa + SSC and SSC + IRb junctions of S. eltonica.

Article Title: Molecular Pap smear: HPV genotype and DNA methylation of ADCY8, CDH8, and ZNF582 as an integrated biomarker for high-grade cervical cytology
Article Snippet: .. Sanger sequencing of the amplicons (~200 ng DNA/sample) was performed by using sequencing primers MY11, FAP59, and GP-E6-3F (Eurofins Operon). .. Sequence quality was assessed using the Sequence Scanner 2.0 (appliedbiosystems.com), where a “high-quality” trace score (TS) (average base call quality value) was defined as ≥20 and a QV20+ value (total number of bases in the sequence with TS ≥ 20) as ≥100.

Article Title: A genetic switch for worker nutrition-mediated traits in honeybees
Article Snippet: .. Amplicons were either cloned and sequenced (Sanger sequencing [Eurofins]) or sequenced via NGS. .. NGS index PCR was performed using the Nextera XT Index Kit (Illumina, San Diego, CA), and purification of the Index PCR products was performed using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

Clone Assay:

Article Title: A genetic switch for worker nutrition-mediated traits in honeybees
Article Snippet: .. Amplicons were either cloned and sequenced (Sanger sequencing [Eurofins]) or sequenced via NGS. .. NGS index PCR was performed using the Nextera XT Index Kit (Illumina, San Diego, CA), and purification of the Index PCR products was performed using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

Incubation:

Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics
Article Snippet: .. Direct sequencing was attempted from amplicons cleaned using QIAquick columns or incubation at 65 °C for 15 min followed by centrifugation at 3800 rcf for 20 s. Amplicons were sent to Eurofins Genomics (Huntsville, AL) for sequencing using primer pair TYL828F/TYL834R. .. Clinical trial The UF Plant Diagnostic Center received 13 field samples from suspected TYLCV-infected tomato plants from two locations.

Centrifugation:

Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics
Article Snippet: .. Direct sequencing was attempted from amplicons cleaned using QIAquick columns or incubation at 65 °C for 15 min followed by centrifugation at 3800 rcf for 20 s. Amplicons were sent to Eurofins Genomics (Huntsville, AL) for sequencing using primer pair TYL828F/TYL834R. .. Clinical trial The UF Plant Diagnostic Center received 13 field samples from suspected TYLCV-infected tomato plants from two locations.

Next-Generation Sequencing:

Article Title: A genetic switch for worker nutrition-mediated traits in honeybees
Article Snippet: .. Amplicons were either cloned and sequenced (Sanger sequencing [Eurofins]) or sequenced via NGS. .. NGS index PCR was performed using the Nextera XT Index Kit (Illumina, San Diego, CA), and purification of the Index PCR products was performed using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

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    Eurofins gel purified amplicon
    Infectious bursal disease virus (IBDV) VP 2 gene <t>amplicon</t> 627 bp (Lane 2: Marker, Lane 4: VP 2 (IBDV, PS, Nagpur, India), Lane 5: IBDV-Positive control, Lane 6: Negative control).
    Gel Purified Amplicon, supplied by Eurofins, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Eurofins amplicons
    Rarefaction analysis of the <t>amplicons</t> obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.
    Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 94/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplicons/product/Eurofins
    Average 94 stars, based on 87 article reviews
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    Eurofins β tubulin amplicons
    Consensus tree inferred from a Bayesian analysis of ITS and nLSU rDNA and <t>β-tubulin</t> gene sequences. Bayesian posterior probabilities are given as % values at the nodes. The tree was rooted with Verruculina enalia (CBS 304.66).
    β Tubulin Amplicons, supplied by Eurofins, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Infectious bursal disease virus (IBDV) VP 2 gene amplicon 627 bp (Lane 2: Marker, Lane 4: VP 2 (IBDV, PS, Nagpur, India), Lane 5: IBDV-Positive control, Lane 6: Negative control).

    Journal: Veterinary World

    Article Title: Identification and characterization of a novel infectious bursal disease virus from outbreaks in Maharashtra Province of India

    doi: 10.14202/vetworld.2018.1516-1525

    Figure Lengend Snippet: Infectious bursal disease virus (IBDV) VP 2 gene amplicon 627 bp (Lane 2: Marker, Lane 4: VP 2 (IBDV, PS, Nagpur, India), Lane 5: IBDV-Positive control, Lane 6: Negative control).

    Article Snippet: The gel purified amplicon was subjected for commercial sequencing from Eurofins (I) Ltd., Bengaluru.

    Techniques: Amplification, Marker, Positive Control, Negative Control

    Rarefaction analysis of the amplicons obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.

    Journal: MicrobiologyOpen

    Article Title: Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river

    doi: 10.1002/mbo3.80

    Figure Lengend Snippet: Rarefaction analysis of the amplicons obtained with the different pairs of primers at a level of 97% 16S rRNA similarity.

    Article Snippet: Amplicons were then subjected to pyrosequencing using a Genome Sequencer 454 Titanium GS FLX (Eurofins, MWG/Operon, Germany).

    Techniques:

    Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

    Journal: Virology Journal

    Article Title: Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics

    doi: 10.1186/s12985-016-0504-8

    Figure Lengend Snippet: Comparison of selected treatments on the visualization of RPA-generated amplicons. a Results using primer pair TYL828F/TYL834R from crude extracts prepared in 0.5 N NaOH from Tomato yellow leaf curl virus (TYLCV)-infected tomato leaves and cleaned by heating to 65 °C for 15 min. Lane M: 50 bp ladder MW standard, size is indicated in kilobases (kb); Lane 1 fresh tissue; Lane 2 tissue kept frozen at −20 °C for 5 months; Lane 3 tissue kept frozen at −80 °C for 3 months; Lane 4 desiccated tissue maintained at room temperature for 15 years; Lane 5 non-inoculated tissue kept frozen at −80 °C for 3 months. b Detection of TYLCV from crude extracts prepared in 0.5 N NaOH and cleaned as follows: Lane 1 untreated; Lane 2 QIAquick PCR purification column; Lane 3 heated at 65 °C for 10 min; Lane 4 heated at 95 °C for 10 min; Lane 5 amplicon loading buffer contained 5 % SDS; Lane 6 amplicon loading buffer contained 10 % SDS; Lane 7 amplicon loading buffer contained 5 % formamide; Lane 8 amplicon loading buffer contained 15 % formamide. Ten μl of amplified product were loaded into each lane of the 1.5 % agarose gels and stained with ethidium bromide

    Article Snippet: Direct sequencing was attempted from amplicons cleaned using QIAquick columns or incubation at 65 °C for 15 min followed by centrifugation at 3800 rcf for 20 s. Amplicons were sent to Eurofins Genomics (Huntsville, AL) for sequencing using primer pair TYL828F/TYL834R.

    Techniques: Recombinase Polymerase Amplification, Generated, Infection, Polymerase Chain Reaction, Purification, Amplification, Staining

    Consensus tree inferred from a Bayesian analysis of ITS and nLSU rDNA and β-tubulin gene sequences. Bayesian posterior probabilities are given as % values at the nodes. The tree was rooted with Verruculina enalia (CBS 304.66).

    Journal: IMA Fungus

    Article Title: Westerdykella reniformis sp. nov., producing the antibiotic metabolites melinacidin IV and chetracin B

    doi: 10.5598/imafungus.2012.03.02.11

    Figure Lengend Snippet: Consensus tree inferred from a Bayesian analysis of ITS and nLSU rDNA and β-tubulin gene sequences. Bayesian posterior probabilities are given as % values at the nodes. The tree was rooted with Verruculina enalia (CBS 304.66).

    Article Snippet: DNA sequencing and sequence alignment The ITS, nLSU, and β-tubulin amplicons were sent to a commercial sequencing facility (Eurofins MWG Biotech) and sequenced on a 3730xl DNA Analyzer coupled with BigDye Terminator v. 3.1 Cycle Sequencing reagents, Applied Biosystems (ABI).

    Techniques: