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    Name:
    NED Matrix Standard
    Description:
    The NED Matrix Standard can be used to analyze 6 FAM VIC NED and ROX labeled DNA fragments in fragment analysis applications The standard can be used on the Applied Biosystems 310 Genetic Analyzers The Data Collection Software for these instruments uses the multicomponent matrix to automatically analyze the four different colored fluorescent dye labeled samples in a single capillary For Research Use Only Not for use in diagnostics procedures
    Catalog Number:
    402996
    Price:
    None
    Applications:
    Genotyping & Genomic Profiling|Kits & Reagents for Sanger Sequencing|Sanger Sequencing|Sanger Sequencing Technology & Accessories|Gene Expression Analysis & Genotyping|Sequencing|Genotyping Instruments, Software & Calibration
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    Structured Review

    Thermo Fisher ned
    The NED Matrix Standard can be used to analyze 6 FAM VIC NED and ROX labeled DNA fragments in fragment analysis applications The standard can be used on the Applied Biosystems 310 Genetic Analyzers The Data Collection Software for these instruments uses the multicomponent matrix to automatically analyze the four different colored fluorescent dye labeled samples in a single capillary For Research Use Only Not for use in diagnostics procedures
    https://www.bioz.com/result/ned/product/Thermo Fisher
    Average 99 stars, based on 167 article reviews
    Price from $9.99 to $1999.99
    ned - by Bioz Stars, 2020-01
    99/100 stars

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    Related Articles

    Multiplexing:

    Article Title: In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)
    Article Snippet: Genotyping at polymorphic SSR marker loci For tri-nucleotide repeat SSR loci showing polymorphism on agarose gels, fluorescent forward primers labeled with 6FAM or HEX were ordered from Integrated DNA Technologies (Coralville, IA) and fluorescent forward primers labeled with NED were ordered from Applied Biosystems (Foster City, CA). .. The use of fluorescent primers and PCR products of different size ranges allowed efficient post-PCR multiplexing of 5–7 primer pairs in a single well.

    Marker:

    Article Title: Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird, et al. Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
    Article Snippet: Given the absence of evident sexual dimorphism in rayaditos (Moreno et al., ), sex was determined using one chromosome‐linked marker (P2/P8; Griffiths, Double, Orr, & Dawson, ). .. The forward primer of each pair was fluorescently labeled with 6‐FAM™ , VIC® , PET® , or NED™ (Dye Set G5; Thermo Fisher Scientific).

    Article Title: In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)
    Article Snippet: .. Genotyping at polymorphic SSR marker loci For tri-nucleotide repeat SSR loci showing polymorphism on agarose gels, fluorescent forward primers labeled with 6FAM or HEX were ordered from Integrated DNA Technologies (Coralville, IA) and fluorescent forward primers labeled with NED were ordered from Applied Biosystems (Foster City, CA). .. DNA from 48 diverse accessions and the two parents was amplified with the fluorescent forward and non-fluorescent reverse primers.

    Article Title: Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia ▿
    Article Snippet: The forward primer of each microsatellite marker was labeled with an M13 (−21) tail (5′-TGTAAAACGACGGCCAGT-3′). .. The reverse primers were retained in their original forms, and a third universal M13 (−21) reporter primer that was fluorescently labeled with either VIC, FAM (6-carboxyfluorescein), or NED (Invitrogen) was added ( ).

    Multiplex Assay:

    Article Title: Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird, et al. Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
    Article Snippet: Microsatellite amplifications were performed in multiplex PCRs using the Type‐it® Microsatellite PCR Kit (QIAGEN® #206246) and primer mixes containing four to five primer pairs (mix 1, 2, and 3; see Table ). .. The forward primer of each pair was fluorescently labeled with 6‐FAM™ , VIC® , PET® , or NED™ (Dye Set G5; Thermo Fisher Scientific).

    Article Title: Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia ▿
    Article Snippet: The reverse primers were retained in their original forms, and a third universal M13 (−21) reporter primer that was fluorescently labeled with either VIC, FAM (6-carboxyfluorescein), or NED (Invitrogen) was added ( ). .. The primers used ( ) were Abmic-5 and Abmic-8 in a multiplex reaction with a Ta of 60°C, whereas Abmic-1, -3, -7, -9, -10, and -12 were amplified at a Ta of 55°C and Abmic-2, -6, and -11 at a Ta of 60°C.

    Article Title: A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers
    Article Snippet: PCR reactions were performed with the Qiagen Multiplex PCR kit (Qiagen, Hilden, Germany), containing 2·5 µL Master Mix (Taq DNA polymerase, PCR buffer and dNTPs), 0·5 µL Q solution and 0·4–0·7 µL of ultra-pure water (depending on the number of primers amplified in the same PCR), 0·1 µL of each primer (10 µ m ) and 1 µL genomic DNA (2·5 ng μL−1 ), in a final volume of 5 µL. .. The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems).

    Article Title: Genetic Variability of Wild Cherry (Prunus avium L.) Seed Stands in Slovenia as Revealed by Nuclear Microsatellite Loci
    Article Snippet: The multiplex reactions were carried out using the following combinations of primers: Multiplex–A: EMPaS10, EMPaS12, and EMPaS14; Multiplex–B: EMPa4, EMPa5, EMPaS2, EMPaS6. .. The forward primers were labelled with fluorescent dyes FAM, HEX, or NED (Applied Biosystems).

    Article Title: Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa
    Article Snippet: The PCR mix contained a final volume of 10 μl with 5 μl of 2X Qiagen Multiplex PCR Master Mix, 1 μl of Primer mix (0.2 μM of each forward and reverse primers), 1 μl of Q-Solution, 1 μl of RNase free water and 2 μl of template DNA (10 ng/μl). .. PCR products were amplified using 6-FAM-, VIC-, NED-, and PET-labelled primers (Applied Biosystems, Foster City, California, USA).

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA). .. To amplify the fragments from multiple primer pairs in a PCR reaction, a QIAGEN Multiplex PCR Kit (QIAGEN) was used.

    Amplification:

    Article Title: Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing 1
    Article Snippet: These loci were screened for positive PCR amplification using agarose gel electrophoresis following . .. From the 33 loci tested, 19 were chosen for screening using fluorescently labeled (6FAM, VIC, PET, NED; Applied Biosystems, Foster City, California, USA) forward primers as described by .

    Article Title: Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird, et al. Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
    Article Snippet: The forward primer of each pair was fluorescently labeled with 6‐FAM™ , VIC® , PET® , or NED™ (Dye Set G5; Thermo Fisher Scientific). .. Primer concentrations in these mixes were adapted due to differences in amplification efficiency and dye strength (see Table ).

    Article Title: Two closely related species differ in their regional genetic differentiation despite admixing
    Article Snippet: .. DNA from each sample was amplified with the common tag containing one of four fluorescent dyes, 6-FAM, PET, VIC or NED (Applied Biosystems). .. PCRs were carried out as follows: preliminary denaturation at 95 °C for 5 min, 35 cycles at 95 °C for 1 min, annealing temperature 53.6–60 °C for 1 min, 72 °C for 1 min and a final extension step at 72 °C for 30 min, using a Techne TC-5000 thermocycler (Bibby Scientific).

    Article Title: In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)
    Article Snippet: Genotyping at polymorphic SSR marker loci For tri-nucleotide repeat SSR loci showing polymorphism on agarose gels, fluorescent forward primers labeled with 6FAM or HEX were ordered from Integrated DNA Technologies (Coralville, IA) and fluorescent forward primers labeled with NED were ordered from Applied Biosystems (Foster City, CA). .. DNA from 48 diverse accessions and the two parents was amplified with the fluorescent forward and non-fluorescent reverse primers.

    Article Title: Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia ▿
    Article Snippet: The reverse primers were retained in their original forms, and a third universal M13 (−21) reporter primer that was fluorescently labeled with either VIC, FAM (6-carboxyfluorescein), or NED (Invitrogen) was added ( ). .. The primers used ( ) were Abmic-5 and Abmic-8 in a multiplex reaction with a Ta of 60°C, whereas Abmic-1, -3, -7, -9, -10, and -12 were amplified at a Ta of 55°C and Abmic-2, -6, and -11 at a Ta of 60°C.

    Article Title: Markers for Mapping by Admixture Linkage Disequilibrium in African American and Hispanic Populations
    Article Snippet: Loci were amplified with Ampli Taq DNA polymerase under the following conditions: 2 min at 95°C; 10 cycles of 30 s at 94°C, 15 s at 55°C, and 15 s at 72°C; 20 cycles with a lowered (89°C) denaturation temperature, followed by a 72°C final extension for 10 min. .. Fluorescently labeled PCR products (FAM, HEX, TET, and NED) were separated on Applied Biosystems 373 and 377 sequencers.

    Article Title: Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content
    Article Snippet: PCR was carried out with a Techne FlexigeneDNA thermal cycler (AFAB Lab Resources, Frederick, USA) that was programmed as follows: 5 min at 94 °C, followed by 35 cycles of 1 min at 94 °C, 40 s at 65 °C and 40 s at 63 °C (depending on the primers) and 72 °C for 5 min. First, unlabeled primers were used for the amplification of the expected polymorphic regions for the four genotypes (cv. .. The 5‘end of the forward primer of INT_F1 was labeled by 6-FAM, INT_F2 with HEX and INT_F3 with NED (Applied Biosystems, Foster City, USA).

    Article Title: A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers
    Article Snippet: Paragraph title: PCR amplification of SSR loci ... The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems).

    Article Title: Diversity of Mycoplasma hominis clinical isolates from Bordeaux, France, as assessed by multiple-locus variable-number tandem repeat analysis
    Article Snippet: .. The forward primers were fluorescently labelled at the 5’ end using 4,4,7,2’,4’,5’,7’-hexachloro-6-carboxy-fluorescein (HEX), 6-carboxyfluorescein (FAM; Eurogentec, Angers, France) or NED (2’-chloro-5’-fluoro-7’,8’-fused phenyl-1,4-dichloro-6-carboxyfluorescein; Applied Biosystems, Life Technologies, Carlsbad, CA, USA), depending on the locus to be amplified (Additional file : Table S2). .. Prior to GeneScan analysis, 0.3 μl of GeneScan ROX 500 size standard (Applied Biosystems) was added to 1 μl of each PCR product.

    Article Title: Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa
    Article Snippet: .. PCR products were amplified using 6-FAM-, VIC-, NED-, and PET-labelled primers (Applied Biosystems, Foster City, California, USA). .. The touchdown cycling program was used on a Mastercycler 2050 model thermal cycler (Thermo Fisher Scientific, Waltham, Massachusetts, USA).

    Article Title: Sperm competitiveness in frogs: slow and steady wins the race
    Article Snippet: These were multiplexed into one polymerase chain reaction (PCR) containing 1× PCR buffer (10 mM Tris–HCl pH 8.3, 50 mM KCl) (Invitrogen), 3 mM MgCl2 (Invitrogen), 200 µM of each dNTP (Invitrogen), 250 nM of each forward primer, Cg2Ca24 labelled with NED (Applied Biosystems), Cg3Ca8 labelled with VIC (Applied Biosystems), Cg1Ca9 labelled with 6-FAM (Geneworks) (each labelled primer was diluted with unlabelled primer 1:10, except Cg1Ca9 which was diluted 1:1), 250 nM of each reverse primer, 0.5 U of Platinum Taq polymerase (Invitrogen) and 1–10 ng DNA. .. PCR amplification was performed with the following cycling conditions: 94°C for 3 min, then 30 cycles of 94°C for 30 s, 57°C for 30 s and 72°C for 1 min and finally 72°C for 30 min.

    Agarose Gel Electrophoresis:

    Article Title: Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing 1
    Article Snippet: These loci were screened for positive PCR amplification using agarose gel electrophoresis following . .. From the 33 loci tested, 19 were chosen for screening using fluorescently labeled (6FAM, VIC, PET, NED; Applied Biosystems, Foster City, California, USA) forward primers as described by .

    Article Title: A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers
    Article Snippet: The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems). .. The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems).

    Polymerase Chain Reaction:

    Article Title: Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing 1
    Article Snippet: These loci were screened for positive PCR amplification using agarose gel electrophoresis following . .. From the 33 loci tested, 19 were chosen for screening using fluorescently labeled (6FAM, VIC, PET, NED; Applied Biosystems, Foster City, California, USA) forward primers as described by .

    Article Title: Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird, et al. Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
    Article Snippet: Microsatellite amplifications were performed in multiplex PCRs using the Type‐it® Microsatellite PCR Kit (QIAGEN® #206246) and primer mixes containing four to five primer pairs (mix 1, 2, and 3; see Table ). .. The forward primer of each pair was fluorescently labeled with 6‐FAM™ , VIC® , PET® , or NED™ (Dye Set G5; Thermo Fisher Scientific).

    Article Title: Two closely related species differ in their regional genetic differentiation despite admixing
    Article Snippet: The extracted DNA was dissolved in 100 µL of TE buffer and diluted to 1:10 for further PCR analyses. .. DNA from each sample was amplified with the common tag containing one of four fluorescent dyes, 6-FAM, PET, VIC or NED (Applied Biosystems).

    Article Title: In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)
    Article Snippet: Genotyping at polymorphic SSR marker loci For tri-nucleotide repeat SSR loci showing polymorphism on agarose gels, fluorescent forward primers labeled with 6FAM or HEX were ordered from Integrated DNA Technologies (Coralville, IA) and fluorescent forward primers labeled with NED were ordered from Applied Biosystems (Foster City, CA). .. The use of fluorescent primers and PCR products of different size ranges allowed efficient post-PCR multiplexing of 5–7 primer pairs in a single well.

    Article Title: Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia ▿
    Article Snippet: The reverse primers were retained in their original forms, and a third universal M13 (−21) reporter primer that was fluorescently labeled with either VIC, FAM (6-carboxyfluorescein), or NED (Invitrogen) was added ( ). .. The following PCR conditions were used for each locus: each 20-μl PCR mixture contained 5 to 20 ng of DNA template, 1× PCR buffer, 0.25 mM dNTPs, 2.0 mM MgCl2 , 0.5 units of Taq polymerase, 0.1 μM −21M13-labeled forward primer, 0.25 μM reverse primer, and 0.2 μM fluorescently labeled (VIC, FAM, or NED) −21M13 universal primer.

    Article Title: Markers for Mapping by Admixture Linkage Disequilibrium in African American and Hispanic Populations
    Article Snippet: .. Fluorescently labeled PCR products (FAM, HEX, TET, and NED) were separated on Applied Biosystems 373 and 377 sequencers. .. Gels were analyzed with Genescan collection and analysis software, and genotypes were called using Genotyper software (Applied Biosystems).

    Article Title: Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content
    Article Snippet: PCR was carried out with a Techne FlexigeneDNA thermal cycler (AFAB Lab Resources, Frederick, USA) that was programmed as follows: 5 min at 94 °C, followed by 35 cycles of 1 min at 94 °C, 40 s at 65 °C and 40 s at 63 °C (depending on the primers) and 72 °C for 5 min. First, unlabeled primers were used for the amplification of the expected polymorphic regions for the four genotypes (cv. .. The 5‘end of the forward primer of INT_F1 was labeled by 6-FAM, INT_F2 with HEX and INT_F3 with NED (Applied Biosystems, Foster City, USA).

    Article Title: Linkage Mapping of 1454 New Maize Candidate Gene Loci
    Article Snippet: .. The second-round PCR used M13 forward primer (5′-CACGACGTTGTAAAACGAC-3′) 5′-end labeled with NED (PE Applied Biosystems) and M13 reverse primer (5′-CAGGAAACAGCTATGACC-3′) 5′-end labeled with 6-FAM (5-carboxyfluorescein). .. The cycling program was 94° for 2 min; 25 cycles of 94° for 1 min, 58° for 50 sec, and 72° for 1 min 30 sec; and 72° for 10 min. Four microliters of the second-round PCR product diluted 1:10 was then added for capillary electrophoresis to a 13.25-μl loading solution containing 64% Hi-Di formamide, 0.01 n NaOH, and 1.9% MegaBACE ET900-R size standard.

    Article Title: A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers
    Article Snippet: Paragraph title: PCR amplification of SSR loci ... The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems).

    Article Title: Diversity of Mycoplasma hominis clinical isolates from Bordeaux, France, as assessed by multiple-locus variable-number tandem repeat analysis
    Article Snippet: The reaction mixtures contained 1X Qiagen PCR buffer with 1.5 mM MgCl2 , 0.2 mM deoxynucleotide triphosphate, 3 mM MgCl2, 0.625 U of Hot Start Taq DNA polymerase (Qiagen, Hilden, Germany), 0.125 μM of each primer and 1 μl of template DNA from clinical isolates. .. The forward primers were fluorescently labelled at the 5’ end using 4,4,7,2’,4’,5’,7’-hexachloro-6-carboxy-fluorescein (HEX), 6-carboxyfluorescein (FAM; Eurogentec, Angers, France) or NED (2’-chloro-5’-fluoro-7’,8’-fused phenyl-1,4-dichloro-6-carboxyfluorescein; Applied Biosystems, Life Technologies, Carlsbad, CA, USA), depending on the locus to be amplified (Additional file : Table S2).

    Article Title: Genetic Variability of Wild Cherry (Prunus avium L.) Seed Stands in Slovenia as Revealed by Nuclear Microsatellite Loci
    Article Snippet: Two multiplex polymerase chain reactions (PCR) were carried out as well as three simplex PCRs (EMPa15, UDP98-412 and PceGA34). .. The forward primers were labelled with fluorescent dyes FAM, HEX, or NED (Applied Biosystems).

    Article Title: Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa
    Article Snippet: .. PCR products were amplified using 6-FAM-, VIC-, NED-, and PET-labelled primers (Applied Biosystems, Foster City, California, USA). .. The touchdown cycling program was used on a Mastercycler 2050 model thermal cycler (Thermo Fisher Scientific, Waltham, Massachusetts, USA).

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA). .. To amplify the fragments from multiple primer pairs in a PCR reaction, a QIAGEN Multiplex PCR Kit (QIAGEN) was used.

    Article Title: Sperm competitiveness in frogs: slow and steady wins the race
    Article Snippet: .. These were multiplexed into one polymerase chain reaction (PCR) containing 1× PCR buffer (10 mM Tris–HCl pH 8.3, 50 mM KCl) (Invitrogen), 3 mM MgCl2 (Invitrogen), 200 µM of each dNTP (Invitrogen), 250 nM of each forward primer, Cg2Ca24 labelled with NED (Applied Biosystems), Cg3Ca8 labelled with VIC (Applied Biosystems), Cg1Ca9 labelled with 6-FAM (Geneworks) (each labelled primer was diluted with unlabelled primer 1:10, except Cg1Ca9 which was diluted 1:1), 250 nM of each reverse primer, 0.5 U of Platinum Taq polymerase (Invitrogen) and 1–10 ng DNA. .. PCR amplification was performed with the following cycling conditions: 94°C for 3 min, then 30 cycles of 94°C for 30 s, 57°C for 30 s and 72°C for 1 min and finally 72°C for 30 min.

    Isolation:

    Article Title: Two closely related species differ in their regional genetic differentiation despite admixing
    Article Snippet: Total genomic DNA was isolated from silica-dried leaves using the CTAB method ( ). .. DNA from each sample was amplified with the common tag containing one of four fluorescent dyes, 6-FAM, PET, VIC or NED (Applied Biosystems).

    Genomic Sequencing:

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: By using the read2Marker program , we designed another 156 cowpea SSR primer pairs from cowpea genomic sequences in the Cowpea Genomics Knowledge Base (CGKB) database ( ; http://cowpeagenomics.med.virginia.edu/CGKB/ ) and screened them for polymorphism between the mapping parents. .. The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA).

    Size-exclusion Chromatography:

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA). .. PCR amplifications were performed by the modified ‘Touchdown PCR’ program described by Sato et al. using the following reaction conditions: 15 min at 95°C for initial denaturation, 3 cycles of 30 sec at 94°C and 3 min at 59°C, followed by 3 rounds of the same program in which the annealing temperatures were decreased by 3°C every 3 cycles, then 2 rounds of a 3-step program of 3 cycles of 30 sec at 94°C, 3 min at 48°C, 1 min at 72°C, followed by 40 cycles of 30 sec at 94°C, 3 min at 45°C, 1 min at 72°C, with a final extension for 10 min at 72°C.

    Labeling:

    Article Title: Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing 1
    Article Snippet: .. From the 33 loci tested, 19 were chosen for screening using fluorescently labeled (6FAM, VIC, PET, NED; Applied Biosystems, Foster City, California, USA) forward primers as described by . .. Fragment analysis was conducted using the GeneScan 500 LIZ Size Standard (Applied Biosystems) on an ABI 3730 DNA Analyzer (Applied Biosystems) by the Biotechnology Resource Center (BRC) at Cornell University.

    Article Title: Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird, et al. Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
    Article Snippet: .. The forward primer of each pair was fluorescently labeled with 6‐FAM™ , VIC® , PET® , or NED™ (Dye Set G5; Thermo Fisher Scientific). .. Primer concentrations in these mixes were adapted due to differences in amplification efficiency and dye strength (see Table ).

    Article Title: In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)
    Article Snippet: .. Genotyping at polymorphic SSR marker loci For tri-nucleotide repeat SSR loci showing polymorphism on agarose gels, fluorescent forward primers labeled with 6FAM or HEX were ordered from Integrated DNA Technologies (Coralville, IA) and fluorescent forward primers labeled with NED were ordered from Applied Biosystems (Foster City, CA). .. DNA from 48 diverse accessions and the two parents was amplified with the fluorescent forward and non-fluorescent reverse primers.

    Article Title: Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia ▿
    Article Snippet: .. The reverse primers were retained in their original forms, and a third universal M13 (−21) reporter primer that was fluorescently labeled with either VIC, FAM (6-carboxyfluorescein), or NED (Invitrogen) was added ( ). .. The following PCR conditions were used for each locus: each 20-μl PCR mixture contained 5 to 20 ng of DNA template, 1× PCR buffer, 0.25 mM dNTPs, 2.0 mM MgCl2 , 0.5 units of Taq polymerase, 0.1 μM −21M13-labeled forward primer, 0.25 μM reverse primer, and 0.2 μM fluorescently labeled (VIC, FAM, or NED) −21M13 universal primer.

    Article Title: Markers for Mapping by Admixture Linkage Disequilibrium in African American and Hispanic Populations
    Article Snippet: .. Fluorescently labeled PCR products (FAM, HEX, TET, and NED) were separated on Applied Biosystems 373 and 377 sequencers. .. Gels were analyzed with Genescan collection and analysis software, and genotypes were called using Genotyper software (Applied Biosystems).

    Article Title: Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content
    Article Snippet: .. The 5‘end of the forward primer of INT_F1 was labeled by 6-FAM, INT_F2 with HEX and INT_F3 with NED (Applied Biosystems, Foster City, USA). .. A total of 0.4 μl of PCR product that was diluted ten-fold with water was mixed with 10 μl of Hi-Di formamide containing 1 μl of GeneScan 500 LIZ- internal size standard (Applied Biosystems, Foster City, USA).

    Article Title: Linkage Mapping of 1454 New Maize Candidate Gene Loci
    Article Snippet: .. The second-round PCR used M13 forward primer (5′-CACGACGTTGTAAAACGAC-3′) 5′-end labeled with NED (PE Applied Biosystems) and M13 reverse primer (5′-CAGGAAACAGCTATGACC-3′) 5′-end labeled with 6-FAM (5-carboxyfluorescein). .. The cycling program was 94° for 2 min; 25 cycles of 94° for 1 min, 58° for 50 sec, and 72° for 1 min 30 sec; and 72° for 10 min. Four microliters of the second-round PCR product diluted 1:10 was then added for capillary electrophoresis to a 13.25-μl loading solution containing 64% Hi-Di formamide, 0.01 n NaOH, and 1.9% MegaBACE ET900-R size standard.

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: .. The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA). .. To amplify the fragments from multiple primer pairs in a PCR reaction, a QIAGEN Multiplex PCR Kit (QIAGEN) was used.

    Electrophoresis:

    Article Title: A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers
    Article Snippet: The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems). .. The PCR products were denatured and size fractioned using capillary electrophoresis on an ABI 3700 automated DNA sequencer (Applied Biosystems).

    Sequencing:

    Article Title: Markers for Mapping by Admixture Linkage Disequilibrium in African American and Hispanic Populations
    Article Snippet: In addition, a Taq gold (PE Biosystems) touchdown protocol was also used later in the project; this protocol consisted of 10 min at 95°C; 10 cycles of 30 s at 94°C, 30 s at 65°C, and 30 s at 72°C; 20 cycles of the same conditions but dropping the annealing temperature by 0.5°C, to 55°C; 15 cycles of annealing at 55°C; and a 72°C final extension for 10 min. Loci that yielded banding patterns characteristic of +A addition were tried again, using a 90-min final extension, no final extension, and/or by redesigning the unlabeled reverse primer to add a guanine or to finish with the sequence of GTTT (G/A/C) at the 5′ end (Brownstein et al. ; Magnuson et al. ). .. Fluorescently labeled PCR products (FAM, HEX, TET, and NED) were separated on Applied Biosystems 373 and 377 sequencers.

    Article Title: Linkage Mapping of 1454 New Maize Candidate Gene Loci
    Article Snippet: The first-round PCR used specific primers extended at their 5′-end with a modified M13 universal sequence. .. The second-round PCR used M13 forward primer (5′-CACGACGTTGTAAAACGAC-3′) 5′-end labeled with NED (PE Applied Biosystems) and M13 reverse primer (5′-CAGGAAACAGCTATGACC-3′) 5′-end labeled with 6-FAM (5-carboxyfluorescein).

    Positron Emission Tomography:

    Article Title: Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing 1
    Article Snippet: .. From the 33 loci tested, 19 were chosen for screening using fluorescently labeled (6FAM, VIC, PET, NED; Applied Biosystems, Foster City, California, USA) forward primers as described by . .. Fragment analysis was conducted using the GeneScan 500 LIZ Size Standard (Applied Biosystems) on an ABI 3730 DNA Analyzer (Applied Biosystems) by the Biotechnology Resource Center (BRC) at Cornell University.

    Article Title: Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird, et al. Variation in fine‐scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
    Article Snippet: .. The forward primer of each pair was fluorescently labeled with 6‐FAM™ , VIC® , PET® , or NED™ (Dye Set G5; Thermo Fisher Scientific). .. Primer concentrations in these mixes were adapted due to differences in amplification efficiency and dye strength (see Table ).

    Article Title: Two closely related species differ in their regional genetic differentiation despite admixing
    Article Snippet: .. DNA from each sample was amplified with the common tag containing one of four fluorescent dyes, 6-FAM, PET, VIC or NED (Applied Biosystems). .. PCRs were carried out as follows: preliminary denaturation at 95 °C for 5 min, 35 cycles at 95 °C for 1 min, annealing temperature 53.6–60 °C for 1 min, 72 °C for 1 min and a final extension step at 72 °C for 30 min, using a Techne TC-5000 thermocycler (Bibby Scientific).

    Article Title: Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa
    Article Snippet: .. PCR products were amplified using 6-FAM-, VIC-, NED-, and PET-labelled primers (Applied Biosystems, Foster City, California, USA). .. The touchdown cycling program was used on a Mastercycler 2050 model thermal cycler (Thermo Fisher Scientific, Waltham, Massachusetts, USA).

    Spectrophotometry:

    Article Title: A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers
    Article Snippet: The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems). .. The forward primer was labelled with one of three fluorescent dyes, HEX, 6-FAM or NED (Applied Biosystems).

    Touchdown PCR:

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA). .. PCR amplifications were performed by the modified ‘Touchdown PCR’ program described by Sato et al. using the following reaction conditions: 15 min at 95°C for initial denaturation, 3 cycles of 30 sec at 94°C and 3 min at 59°C, followed by 3 rounds of the same program in which the annealing temperatures were decreased by 3°C every 3 cycles, then 2 rounds of a 3-step program of 3 cycles of 30 sec at 94°C, 3 min at 48°C, 1 min at 72°C, followed by 40 cycles of 30 sec at 94°C, 3 min at 45°C, 1 min at 72°C, with a final extension for 10 min at 72°C.

    Modification:

    Article Title: Linkage Mapping of 1454 New Maize Candidate Gene Loci
    Article Snippet: The first-round PCR used specific primers extended at their 5′-end with a modified M13 universal sequence. .. The second-round PCR used M13 forward primer (5′-CACGACGTTGTAAAACGAC-3′) 5′-end labeled with NED (PE Applied Biosystems) and M13 reverse primer (5′-CAGGAAACAGCTATGACC-3′) 5′-end labeled with 6-FAM (5-carboxyfluorescein).

    Article Title: Construction of a Genetic Linkage Map and Genetic Analysis of Domestication Related Traits in Mungbean (Vigna radiata)
    Article Snippet: The 5′-end of each forward primer was labeled with one of three fluorescent dyes: FAM, HEX or NED (Applied Biosystems, Foster City, CA, USA). .. PCR amplifications were performed by the modified ‘Touchdown PCR’ program described by Sato et al. using the following reaction conditions: 15 min at 95°C for initial denaturation, 3 cycles of 30 sec at 94°C and 3 min at 59°C, followed by 3 rounds of the same program in which the annealing temperatures were decreased by 3°C every 3 cycles, then 2 rounds of a 3-step program of 3 cycles of 30 sec at 94°C, 3 min at 48°C, 1 min at 72°C, followed by 40 cycles of 30 sec at 94°C, 3 min at 45°C, 1 min at 72°C, with a final extension for 10 min at 72°C.

    IA:

    Article Title: In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.)
    Article Snippet: .. Genotyping at polymorphic SSR marker loci For tri-nucleotide repeat SSR loci showing polymorphism on agarose gels, fluorescent forward primers labeled with 6FAM or HEX were ordered from Integrated DNA Technologies (Coralville, IA) and fluorescent forward primers labeled with NED were ordered from Applied Biosystems (Foster City, CA). .. DNA from 48 diverse accessions and the two parents was amplified with the fluorescent forward and non-fluorescent reverse primers.

    Software:

    Article Title: Markers for Mapping by Admixture Linkage Disequilibrium in African American and Hispanic Populations
    Article Snippet: Fluorescently labeled PCR products (FAM, HEX, TET, and NED) were separated on Applied Biosystems 373 and 377 sequencers. .. Gels were analyzed with Genescan collection and analysis software, and genotypes were called using Genotyper software (Applied Biosystems).

    Article Title: Diversity of Mycoplasma hominis clinical isolates from Bordeaux, France, as assessed by multiple-locus variable-number tandem repeat analysis
    Article Snippet: The forward primers were fluorescently labelled at the 5’ end using 4,4,7,2’,4’,5’,7’-hexachloro-6-carboxy-fluorescein (HEX), 6-carboxyfluorescein (FAM; Eurogentec, Angers, France) or NED (2’-chloro-5’-fluoro-7’,8’-fused phenyl-1,4-dichloro-6-carboxyfluorescein; Applied Biosystems, Life Technologies, Carlsbad, CA, USA), depending on the locus to be amplified (Additional file : Table S2). .. The GeneScan data were subsequently analysed using GeneMapper software (version 3.7; Applied Biosystems) to perform sizing and to calculate the number of repeats in the PCR fragments.

    Article Title: Genetic Variability of Wild Cherry (Prunus avium L.) Seed Stands in Slovenia as Revealed by Nuclear Microsatellite Loci
    Article Snippet: The forward primers were labelled with fluorescent dyes FAM, HEX, or NED (Applied Biosystems). .. The conditions for the remaining two simplex PCRs were: 94°C for 2 min. followed by 35 cycles of 94°C for 30 s, Ta°C for 45 s, and 72°C for 60 s with an elongation step of 72°C for 5 min. PCR products were genotyped with a capillary sequencer (SpectruMedix model SCE 960) and scored using GenoSpectrum software.

    Article Title: Sperm competitiveness in frogs: slow and steady wins the race
    Article Snippet: These were multiplexed into one polymerase chain reaction (PCR) containing 1× PCR buffer (10 mM Tris–HCl pH 8.3, 50 mM KCl) (Invitrogen), 3 mM MgCl2 (Invitrogen), 200 µM of each dNTP (Invitrogen), 250 nM of each forward primer, Cg2Ca24 labelled with NED (Applied Biosystems), Cg3Ca8 labelled with VIC (Applied Biosystems), Cg1Ca9 labelled with 6-FAM (Geneworks) (each labelled primer was diluted with unlabelled primer 1:10, except Cg1Ca9 which was diluted 1:1), 250 nM of each reverse primer, 0.5 U of Platinum Taq polymerase (Invitrogen) and 1–10 ng DNA. .. The PCR product (1.5 µl) was then analysed on an ABI3730 Sequencer, sized using Genescan-500 LIZ internal size standard and genotyped using G enemapper software (v. 3.7).

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    Thermo Fisher ned
    Ned, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 167 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ned/product/Thermo Fisher
    Average 99 stars, based on 167 article reviews
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    79
    Thermo Fisher ned 19
    <t>Ned-19</t> activity on different stages of the P. falciparum asexual cycle. Synchronized ring stage parasites (initial parasitaemia 1.4%) were used to yield subcultures, numbered 1–8, which were incubated with DMSO control ( blue line ) or exposed to 100 μM Ned-19 ( red line ) at different times of the parasite asexual cycle. a Stages of the parasite asexual cycle. Black arrows indicate times at which the cultures were sampled. b Histograms showing parasitaemia and distribution of the different parasite stages for the cultures in each time-point. ER early rings, LR late rings, ET early trophozoites, LT late trophozoites, ES early schizonts, LS late schizonts. A representative sample of these forms is shown in Additional file 2 : Figure S2
    Ned 19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ned 19 - by Bioz Stars, 2020-01
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    80
    Thermo Fisher ned yellow fluorescent dyes
    <t>Ned-19</t> activity on different stages of the P. falciparum asexual cycle. Synchronized ring stage parasites (initial parasitaemia 1.4%) were used to yield subcultures, numbered 1–8, which were incubated with DMSO control ( blue line ) or exposed to 100 μM Ned-19 ( red line ) at different times of the parasite asexual cycle. a Stages of the parasite asexual cycle. Black arrows indicate times at which the cultures were sampled. b Histograms showing parasitaemia and distribution of the different parasite stages for the cultures in each time-point. ER early rings, LR late rings, ET early trophozoites, LT late trophozoites, ES early schizonts, LS late schizonts. A representative sample of these forms is shown in Additional file 2 : Figure S2
    Ned Yellow Fluorescent Dyes, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ned yellow fluorescent dyes/product/Thermo Fisher
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    Ned-19 activity on different stages of the P. falciparum asexual cycle. Synchronized ring stage parasites (initial parasitaemia 1.4%) were used to yield subcultures, numbered 1–8, which were incubated with DMSO control ( blue line ) or exposed to 100 μM Ned-19 ( red line ) at different times of the parasite asexual cycle. a Stages of the parasite asexual cycle. Black arrows indicate times at which the cultures were sampled. b Histograms showing parasitaemia and distribution of the different parasite stages for the cultures in each time-point. ER early rings, LR late rings, ET early trophozoites, LT late trophozoites, ES early schizonts, LS late schizonts. A representative sample of these forms is shown in Additional file 2 : Figure S2

    Journal: Malaria Journal

    Article Title: Ned-19 inhibition of parasite growth and multiplication suggests a role for NAADP mediated signalling in the asexual development of Plasmodium falciparum

    doi: 10.1186/s12936-017-2013-7

    Figure Lengend Snippet: Ned-19 activity on different stages of the P. falciparum asexual cycle. Synchronized ring stage parasites (initial parasitaemia 1.4%) were used to yield subcultures, numbered 1–8, which were incubated with DMSO control ( blue line ) or exposed to 100 μM Ned-19 ( red line ) at different times of the parasite asexual cycle. a Stages of the parasite asexual cycle. Black arrows indicate times at which the cultures were sampled. b Histograms showing parasitaemia and distribution of the different parasite stages for the cultures in each time-point. ER early rings, LR late rings, ET early trophozoites, LT late trophozoites, ES early schizonts, LS late schizonts. A representative sample of these forms is shown in Additional file 2 : Figure S2

    Article Snippet: Microscopy Parasite cultures were incubated with 200 μM Ned-19 and 1 μM Lysotracker Green DND-26 (ThermoFisher Scientific) for 30 min at 37 °C in agitation and observed with a fluorescence microscope.

    Techniques: Activity Assay, Incubation

    Ned-19 colocalizes with Lysotracker in asexual and sexual parasites. a Parasites stained with 200 μM Ned-19. b Parasites stained with 1 μM Lysotracker. c Parasites stained with 200 μM Ned-19 and 1 μM Lysotracker. BF bright field. Scale bar 5 μm

    Journal: Malaria Journal

    Article Title: Ned-19 inhibition of parasite growth and multiplication suggests a role for NAADP mediated signalling in the asexual development of Plasmodium falciparum

    doi: 10.1186/s12936-017-2013-7

    Figure Lengend Snippet: Ned-19 colocalizes with Lysotracker in asexual and sexual parasites. a Parasites stained with 200 μM Ned-19. b Parasites stained with 1 μM Lysotracker. c Parasites stained with 200 μM Ned-19 and 1 μM Lysotracker. BF bright field. Scale bar 5 μm

    Article Snippet: Microscopy Parasite cultures were incubated with 200 μM Ned-19 and 1 μM Lysotracker Green DND-26 (ThermoFisher Scientific) for 30 min at 37 °C in agitation and observed with a fluorescence microscope.

    Techniques: Staining

    Ned-19 activity on the late phase of the asexual cycle of P. falciparum . Left asexual P. falciparum cultures were synchronized (initial parasitaemia 1.2%) and trophozoites at 32 h post invasion were incubated with DMSO ( blue line ) or 100 μM Ned-19 ( red line ) at the indicated time-points. Right parasitaemia and asexual stages of the cultures 2 h after merozoite egress (determined in the DMSO treated culture). N = 2. *p

    Journal: Malaria Journal

    Article Title: Ned-19 inhibition of parasite growth and multiplication suggests a role for NAADP mediated signalling in the asexual development of Plasmodium falciparum

    doi: 10.1186/s12936-017-2013-7

    Figure Lengend Snippet: Ned-19 activity on the late phase of the asexual cycle of P. falciparum . Left asexual P. falciparum cultures were synchronized (initial parasitaemia 1.2%) and trophozoites at 32 h post invasion were incubated with DMSO ( blue line ) or 100 μM Ned-19 ( red line ) at the indicated time-points. Right parasitaemia and asexual stages of the cultures 2 h after merozoite egress (determined in the DMSO treated culture). N = 2. *p

    Article Snippet: Microscopy Parasite cultures were incubated with 200 μM Ned-19 and 1 μM Lysotracker Green DND-26 (ThermoFisher Scientific) for 30 min at 37 °C in agitation and observed with a fluorescence microscope.

    Techniques: Activity Assay, Incubation

    Ned-19 specific blockage of P. falciparum asexual growth. a Structure of Ned-19 and of its inactive analogue Ned-20, adapted from Rosen et al. b Synchronous early ring stage parasites (initial parasitaemia 0.16%) were cultured for 48 h in the presence of 100 μM concentration of the indicated compounds. At the end of the incubation, parasitaemias were measured through Giemsa-stained preparations. Parasitaemia of the DMSO treated culture (1.08%) was set as 1. N = 3. ***p

    Journal: Malaria Journal

    Article Title: Ned-19 inhibition of parasite growth and multiplication suggests a role for NAADP mediated signalling in the asexual development of Plasmodium falciparum

    doi: 10.1186/s12936-017-2013-7

    Figure Lengend Snippet: Ned-19 specific blockage of P. falciparum asexual growth. a Structure of Ned-19 and of its inactive analogue Ned-20, adapted from Rosen et al. b Synchronous early ring stage parasites (initial parasitaemia 0.16%) were cultured for 48 h in the presence of 100 μM concentration of the indicated compounds. At the end of the incubation, parasitaemias were measured through Giemsa-stained preparations. Parasitaemia of the DMSO treated culture (1.08%) was set as 1. N = 3. ***p

    Article Snippet: Microscopy Parasite cultures were incubated with 200 μM Ned-19 and 1 μM Lysotracker Green DND-26 (ThermoFisher Scientific) for 30 min at 37 °C in agitation and observed with a fluorescence microscope.

    Techniques: Cell Culture, Concentration Assay, Incubation, Staining

    Ned-19 inhibits spontaneous calcium oscillations in P. falciparum early rings and early trophozoites. a Representative traces of spontaneous calcium oscillations in early rings (ER) and early trophozoites (ET) in the presence of Ned-19 or vehicle DMSO. b Bar charts showing the average peak height of the spontaneous calcium oscillations in Ned-19 treated early rings (ER) or early trophozoites (ET) compared to controls. **p

    Journal: Malaria Journal

    Article Title: Ned-19 inhibition of parasite growth and multiplication suggests a role for NAADP mediated signalling in the asexual development of Plasmodium falciparum

    doi: 10.1186/s12936-017-2013-7

    Figure Lengend Snippet: Ned-19 inhibits spontaneous calcium oscillations in P. falciparum early rings and early trophozoites. a Representative traces of spontaneous calcium oscillations in early rings (ER) and early trophozoites (ET) in the presence of Ned-19 or vehicle DMSO. b Bar charts showing the average peak height of the spontaneous calcium oscillations in Ned-19 treated early rings (ER) or early trophozoites (ET) compared to controls. **p

    Article Snippet: Microscopy Parasite cultures were incubated with 200 μM Ned-19 and 1 μM Lysotracker Green DND-26 (ThermoFisher Scientific) for 30 min at 37 °C in agitation and observed with a fluorescence microscope.

    Techniques: