The source of SYBR green master mix determines outcome of nucleic acid amplification reactions

Yang, Jianxin; Kemps-Mols, B.M.; Spruyt-Gerritse, Marijke; Anholts, J.; Claas, Frans H.J.; Eikmans, Michael

doi:10.1186/s13104-016-2093-4

Cited by 15 publications

(15 citation statements)

References 23 publications

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“…The present study successfully utilized qRT-PCR / HRMA-based assay for polymorphism study of HSP-70 gene in four Nigerian Zebu breeds of cattle. The findings of this study showed that 12 genetic variants of HSP-70 gene were detected in four Nigerian zebu cattle studied and agrees with other variant detection studies [20-22].…”

Section: Resultssupporting

confidence: 91%

“…Possible genetic variants of HSP-70 gene were evaluated via qReal-Time PCR followed by HRMA-based assay in four Zebu breeds of Nigerian cattle [20-22]. Subsequently, qRT-PCR / HRM data generated from across the breeds of Nigerian Bos indicus for HSP 70 gene were analysed using Roche High Resolution Melting Software version 1.1.0.1320.…”

Section: Dna Extractionmentioning

confidence: 99%

“…Subsequently, qRT-PCR / HRM data generated from across the breeds of Nigerian Bos indicus for HSP 70 gene were analysed using Roche High Resolution Melting Software version 1.1.0.1320. Individual samples of HSP-70 gene were differentiated into distinct genetic variants via high resolution melting curve profiles (derivative HRM curve / dissociation curve, differential plot and normalised melt curves) as depicted with distinct SYBR green (dye) fluorescence; Purple (PRP), Red (RED), Orange (ORG), Green (GRN), Lemon (LMN), Brown (BRN), Chocolate (CHO), Yellow (YLO), Magenta (MGT), Blue (BLU), Army green (AGN) and Navy blue (NBL) where individual fluorescence depicted distinct genetic variants [21, 22].…”

Section: Dna Extractionmentioning

confidence: 99%

“…It is a simple and fast technique based on PCR melting (dissociation) curve techniques, enabled through improved double-stranded DNA (dsDNA)– binding dyes along with next-generation real-time PCR instrumentation and analysis software [19]. The combine usage of High Resolution Melting analysis (HRMA) with quantitative real time polymerase chain reaction (qRT-PCR) permits efficient and rapid genotyping and detection of polymorphism in double stranded DNA (Bester et al, 2012; Gori et al, 2012; Yang et al, 2016) [20-22]. This technique generates DNA melt curve profiles that are very specific and sensitive enough to distinguish sequence variation enabling mutation scan, methylation and genotyping analysis.…”

Section: Introductionmentioning

confidence: 99%

“…The evolution of qRT-PCR/HRMA based assay involving the use of fluorescent intercalating dye (SYBR Green) with a new generation of light cyclers is a high throughput technology with an established average temperature range of 66 °C to 96 °C for mutation analyses, genetic variants analyses, polymorphism study and SNP genotyping of large population which has become emerging cutting edge technology with high efficiency and cost-effectiveness [26, 27]. This technology is gradually becoming a technique of choice for rapid genotyping and study of polymorphism [20-22].…”

Section: Introductionmentioning

confidence: 99%

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qRT-PCR/High Resolution Melting Analyses detected polymorphisms of HSP-70 gene in Zebu cattle

Onasanya

Okpeku

Thiruvekander

et al. 2018

Preprint

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28Concerns over environmental heat stress have increased in recent years with the 29 realization of global warming effects on environment and subsequently on animal production. 30 Heat stress indicators help to monitor adaptability and survivability of livestock to thermal 31 assault; a consequent effect of global warming. Heat shock proteins (HSPs) are highly 32 conserved and are classified into six groups. Heat shock protein (HSP) 70 gene is a member of 33 molecular chaperone, known to be highly expressed under stressful environmental and 34 physiological conditions. In this study, we used a one-step qReal-Time PCR, followed by 35 high-resolution melting analyses (HRMA) for detection and identification of polymorphism of 2 36 HSP-70 gene in four extant cattle breeds of (White Fulani, Sokoto Gudali, Red Bororo and 37 Ambala). qRT-PCR/HRMA-based assay detected twelve (12) genetic variant groups of HSP-38 70 gene. Ambala breed of Nigerian Zebu cattle had the highest number (7) of genetic variants 39 of HSP-70 gene followed by Red Bororo breed (6 genetic variants), Sokoto Gudali breed had 40 5 genetic variants while White Fulani breed had the least (4 genetic variants) number of 41 genetic variants in the population of Nigerian Zebu cattle breeds examined. We therefore 42 hypothesize that the detected variant groups can be interrogated for their possible effects on 43 thermo-tolerance performance of zebu cattle bred under thermal assaults of tropical 44 conditions. 45 46 Introduction 47 Cattle industry is a very important sector of livestock husbandry in many developing 48 countries all over the world. Cattle serve as valuable source of animal proteins and hide, and 49 contribute in no small measure to national economy. Heat stress is a significant issue in the 50 livestock industry. 51 The impact of heat stress on livestock, particularly on cattle can be overwhelming [1], 52 resulting in reduced feed intake, reduced fertility, increased respiratory and heart rates, 53 increased peripheral blood flow and profuse sweating, reduced milk production and lower 54 milk quality [2]. These impacts according [2], can result in significant loss of income and 55 increase in management costs. Losses to the cattle industry due to heat stress was estimated at 56 about $900 million per annum [3]. The issue is more exacerbated with increased global 57 warming, as such, the impact of heat stress needs to be addressed and ameliorated to maintain 58 animal health status, adaptability, survivability and performance.59 Heat shock proteins (HSPs), are a group of proteins conserved in both prokaryotic and 60 eukaryotic organisms. The expression of HSP genes are related to thermal stress, they play 61 vital roles in cell response to environmental stress [4, 5]. Studies have shown that the 62 expression of HSP genes affects follicular development, embryonic survival and pregnancy 63 maintenance [6-8]. For this reason, the functional characterization of this gene family is 3 64 important. The HSP-70 protein, also referred to as HSP-70 ge...

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Section: Resultssupporting

confidence: 91%

Section: Dna Extractionmentioning

confidence: 99%

Section: Dna Extractionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

qRT-PCR/High Resolution Melting Analyses detected polymorphisms of HSP-70 gene in Zebu cattle

Onasanya

Okpeku

Thiruvekander

et al. 2018

Preprint

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Identification of a melatonin receptor type 1A gene (AccMTNR1A) in Apis cerana cerana and its possible involvement in the response to low temperature stress

Zhang

et al. 2018

Sci Nat

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It is known that melatonin plays an indispensable role in the defense against some environment-induced stresses. The melatonin receptor (MTNR) is also closely linked to the environmental stress response in mammals. However, little is known about the function of the MTNR in insects, including honeybees. In this study, we identified a MTNR from Apis cerana cerana named AccMTNR1A, which contained a typical seven-transmembrane domain common to this family of receptors. A subcellular localization analysis showed that AccMTNR1A was localized in the cytomembrane. Additionally, we found that cold stress apparently boosted AccMTNR1A transcription, indicating that AccMTNR1A possibly connects to the cold stress response. The knockdown of AccMTNR1A attenuated the expression level of some genes associated with the cold stress response, suggesting that AccMTNR1A likely plays an analogous role with these genes during low temperature stress response. Moreover, silencing of AccMTNR1A also suppressed the transcription of some antioxidant genes, prompting the possibility that the response of AccMTNR1A to cold stress response may be related to antioxidant signaling pathways. Collectively, the findings presented here provide evidence that AccMTNR1A may play essential roles in protecting Apis cerana cerana from cold stress.

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Directional X Chromosome Skewing of White Blood Cells from Subjects with Heterozygous Mosaicism for the Variant IRAK1 Haplotype

et al. 2019

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The source of SYBR green master mix determines outcome of nucleic acid amplification reactions

Cited by 15 publications

References 23 publications

qRT-PCR/High Resolution Melting Analyses detected polymorphisms of HSP-70 gene in Zebu cattle

qRT-PCR/High Resolution Melting Analyses detected polymorphisms of HSP-70 gene in Zebu cattle

Identification of a melatonin receptor type 1A gene (AccMTNR1A) in Apis cerana cerana and its possible involvement in the response to low temperature stress

Directional X Chromosome Skewing of White Blood Cells from Subjects with Heterozygous Mosaicism for the Variant IRAK1 Haplotype

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