PCR: Identification of Genetic Polymorphisms

Harbison, Amanda M.; Nguyen, Joanne

doi:10.1007/978-1-4939-6990-6_13

Cited by 4 publications

(5 citation statements)

References 38 publications

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“…PCR optimization requires the right DNA polymerase. Harbison & Nguyen (2017) stated that the annealing temperature ranged from 55-72 o C. Besides that, the optimal temperature of annealing was influenced by the concentration of MgCl 2 (Viljoen et al, 2005). Incorrect annealing temperature can cause no primary attachment.…”

Section: Discussionmentioning

confidence: 99%

“…This result can be used as an indication of the degree of endogamy (inbreeding) as a result of an intensive selection process (Machado et al, 2003;Ryan & Ray, 2014). A large difference between the values of Ho and He can be used as an indicator of the presence of genotype imbalances in the population analyzed (Tambasco et al, 2003;Harbison & Nguyen, 2017).…”

Section: Discussionmentioning

confidence: 99%

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Polymorphisms and Associations of the NRAMP-1 and iNOS Genes on Newcastle Disease and Salmonella enteritidis Resistances in SenSi-1 Agrinak Chickens

Ardiyana

Gunawan

Murtini

et al. 2020

Trop. Anim. Sci. J.

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NRAMP-1 and iNOS genes were reported to be associated with a defense mechanism against bacteria and virus infections. This study aimed to identify NRAMP-1 and iNOS genes polymorphisms and their associations with the defense mechanisms against Salmonella enteritidis and Newcastle Disease (ND) in SenSi-1 Agrinak chicken. The present study used a total number of 172 SenSi-1 Agrinak chicken. Identifications of NRAMP-1 and iNOS genes polymorphisms were performed by PCR-RFLP method. NRAMP-1 and iNOS genotypes were associated with immunoglobulin Y (IgY) concentration, specific antibodies against S. enteritidis and ND using General Linear Model (GLM). Immunity characteristics were further grouped into high, medium, and low categories. NRAMP-1|SacI exon 11 and iNOS|AluI intron 24 in SenSi-1 Agrinak chickens were polymorphic. TC genotype has a higher immune response to infectious agents compared to TT and CC genotypes. The frequency of C allele was higher than the T allele in the concentration of immunoglobulin Y (IgY), antibodies titers against S enteritidis and ND. The TC genotype of NRAMP-1 gene was significantly associated with ND antibody titers, and the TT genotype of iNOS was significantly associated with S. enteritidis specific antibody. NRAMP-1 and iNOS genes can be used as potential candidate genes for immune traits in SenSi-1 Agrinak chickens.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Polymorphisms and Associations of the NRAMP-1 and iNOS Genes on Newcastle Disease and Salmonella enteritidis Resistances in SenSi-1 Agrinak Chickens

Ardiyana

Gunawan

Murtini

et al. 2020

Trop. Anim. Sci. J.

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“…Some bacteria transition into a non-culturable state [66], and therefore, these would not have been detected by the microbiological methods used in this study. To visualise the full scope of bacteria present, other microbiological methods could be useful, e.g., ultrafiltration of a larger amount of water that flows through the drinking equipment and analysing the sediments with PCR [67][68][69]. To visualise the actual biofilm, an electron microscopic scan could be used [70].…”

Section: Biofilm Formationmentioning

confidence: 99%

Drinking Pipes and Nipple Drinkers in Pig Abattoir Lairage Pens—A Source of Zoonotic Pathogens as a Hazard to Meat Safety

Buder,

Meemken,

Fürstenberg

et al. 2023

Microorganisms

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The water distribution system in the lairage pens of abattoirs could act as a route of contamination for produced meat. In this study, biofilm formation and the occurrence of specific pathogens in drinking equipment was investigated in different lairage pens in a German commercial pig abattoir. Samples of the water and the drinkers in different locations were microbiologically cultivated and examined. After new drinking equipment had been installed for one month, three months and five years, biofilm formation was detectable, and retrograde growth from the nipple drinkers was seen up to the connection with the main water distribution system. In particular, Enterobacteriaceae and Pseudomonas spp. were found in all samplings of the nipple drinkers. Zoonotic pathogens, Salmonella, pathogenic Yersinia enterocolitica and methicillin-resistant Staphylococcus aureus, were also isolated from the nipple drinkers, while Listeria monocytogenes was not detected via microbial cultivation methods in any of the samples. Since the pigs take the contaminated nipple drinkers into their mouths to drink, or drink contaminated water containing the pathogens, transmission and even infection of the pigs in the lairage can be assumed. This could consequently lead to contamination or cross-contamination of the meat during slaughter and processing and to a public health risk.

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“…The annealing temperature difference was caused by the different conditions of the PCR machine and the PCR reagent mixture. According to [19] the annealing temperature ranges from 55-72 ˚C, but the optimal annealing temperature is also influenced by the concentration of the PCR reagent mixture [20].…”

Section: Hsp70 Gene Amplificationmentioning

confidence: 99%

SNP g.1117G>A HSP70 Gene Polymorphism in Domestic Beef Cattle using PCR-RFLP Method

Haddar

Jakaria

Noor

2022

IOP Conf. Ser.: Earth Environ. Sci.

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Temperature increases have detrimental impacts on livestock, such as decreased metabolism, reproduction, and performance. The response of livestock to heat stress can be shown by the expression of HSP70 gene. This study aims to identify the SNP g.1117G>A HSP70 gene polymorphism (HSP70|BanI) using the PCR-RFLP method. This study used 118 DNA samples of 5 breeds of cattle consisting of 20 heads of PO cattle, 20 heads of Madura cattle, 12 heads of Kuantan cattle, 53 heads of Bali cattle, and 13 heads of Pesisir cattle. The PCR-RFLP approach was used to analyze the diversity of the HSP70 gene. The enzyme used for cutting was BanI with forwarding primer 5‘-GAA AGG AAA AAA GAG ACA GA-3’ and reverse primers 5‘-AAT ACG CAG GAG TAG GTG GT-3’. The variation of the HSP gene was analyzed using allele frequency, genotype frequency, and level of heterozygosity. The Hardy-Weinberg equilibrium was evaluated using the Chi-Square test on PopGen 32. HSP70 gene amplification resulted in 539 bp fragments and 2 alleles (A and G). The HSP70 gene consisted of three genotypes i.e., AA (475 bp), AG (475 bp, 369 bp, and 106 bp), and GG (369 bp and 106 bp). The highest allele frequency of the A allele was found in PO and G allele in Bali cattle. Based on the results, it can be concluded that the HSP70 gene in 5’ UTR (untranslated region) in local beef cattle was polymorphic.

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PCR: Identification of Genetic Polymorphisms

Cited by 4 publications

References 38 publications

Polymorphisms and Associations of the NRAMP-1 and iNOS Genes on Newcastle Disease and Salmonella enteritidis Resistances in SenSi-1 Agrinak Chickens

Polymorphisms and Associations of the NRAMP-1 and iNOS Genes on Newcastle Disease and Salmonella enteritidis Resistances in SenSi-1 Agrinak Chickens

Drinking Pipes and Nipple Drinkers in Pig Abattoir Lairage Pens—A Source of Zoonotic Pathogens as a Hazard to Meat Safety

SNP g.1117G>A HSP70 Gene Polymorphism in Domestic Beef Cattle using PCR-RFLP Method

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