Protein profiling of Acanthamoeba species using MALDI-TOF MS for specific identification of Acanthamoeba genotype

Megha, Kirti; Sharma, Megha; Gupta, Amit; Sehgal, Rakesh; Khurana, Sumeeta

doi:10.1007/s00436-017-5743-0

Cited by 9 publications

(7 citation statements)

References 24 publications

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“…In addition, according to Cooper et al [26], the animal call rate was also related to genotyping accuracy, the individual call rate ranged from 96-99% in our study. All the above results demonstrated that the genotyping data got in the present study was validated, and the method of MALDI-TOF MS could be a stable platform for genotyping those SNPs [27,28].…”

Section: Resultssupporting

confidence: 63%

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Hu¹,

Liu²,

Chu³

et al. 2020

Preprint

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Combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel consisting of 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively. Knowledge of these results, we provided one low-cost and efficient method of SNP assays for running paternity testing in crossbred cattle population of Simmental and Holstein in China.

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Section: Resultssupporting

confidence: 63%

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Hu¹,

Liu²,

Chu³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, according to Cooper et al [21], the call rate of the animal was also related to genotyping accuracy, the individual call rate ranged from 96-99% in our study. All the above results revealed that the genotyping data got in the present study was validated, and the method of MALDI-TOF MS could be a stable platform for genotyping those SNPs [22,23].…”

Section: Discussionsupporting

confidence: 62%

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Liu

Chu

et al. 2020

Preprint

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Background: In China, the widespread crossbreeding between Simmental and Holstein is a universal way so as to better improve the comprehensive benefits, as well as decline the inbreeding coefficient. However, the wrong parentage appeared frequently in this population than others due to not only the reasons in pure breeds, but more importantly, the lack of enough attention, which caused the lower accuracy of genetic parameter estimation and genetic evaluation in breeding systems. Single nucleotide polymorphism (SNP) panel in a certain population as a powerful tool for parentage assignment has been reported in numerous studies, especially in cattle. Therefore, the aim of this study was to build an SNP panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein in China. Results: In the present study, combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel comprising 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively.Conclusion: Knowledge of these results, we provided one set of low-cost and efficient SNPs for running paternity testing in the crossbred cattle population of Simmental and Holstein in China. Keywords: Parentage analysis, Single nucleotide polymorphism (SNP), Chinese crossbred cattle

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“…A second recent alternative method for the rapid identification of isolates is MALDI-TOF MS, a mass spectrometry technology used for rapid, automated and, hopefully, accurate microbial phenotypic identification. This technology has been used in two small studies to correctly assign Acanthamoeba strains into appropriate sequence types [ 116 , 117 ]. Whether the use of MALDI-TOF MS expands in the analysis of Acanthamoeba remains to be seen.…”

Section: What Additional Approaches Are Available?mentioning

confidence: 99%

Species, Sequence Types and Alleles: Dissecting Genetic Variation in Acanthamoeba

Fuerst

Booton

2020

Pathogens

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Species designations within Acanthamoeba are problematic because of pleomorphic morphology. Molecular approaches, including DNA sequencing, hinted at a resolution that has yet to be fully achieved. Alternative approaches were required. In 1996, the Byers/Fuerst lab introduced the concept of sequence types. Differences between isolates of Acanthamoeba could be quantitatively assessed by comparing sequences of the nuclear 18S rRNA gene, ultimately producing 22 sequence types, designated T1 through T22. The concept of sequence types helps our understanding of Acanthamoeba evolution. Nevertheless, substantial variation in the 18S rRNA gene differentiates many isolates within each sequence type. Because the majority of isolates with sequences in the international DNA databases have been studied for only a small segment of the gene, designated ASA.S1, genetic variation within this hypervariable region of the 18S rRNA gene has been scrutinized. In 2002, we first categorized variation in this region in a sample of T3 and T4 isolates from Hong Kong, observing ten “alleles” within type T4 and five “alleles” within T3. Subsequently, confusion occurred when different labs applied redundant numerical labels to identify different alleles. A more unified approach was required. We have tabulated alleles occurring in the sequences submitted to the international DNA databases, and determined their frequencies. Over 150 alleles have occurred more than once within 3500+ isolates of sequence type T4. Results from smaller samples of other sequence types (T3, T5, T11 and T15, and supergroup T2/6) have also been obtained. Our results provide new insights into the evolutionary history of Acanthamoeba, further illuminating the degree of genetic separation between significant taxonomic units within the genus, perhaps eventually elucidating what constitutes a species of Acanthamoeba.

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Protein profiling of Acanthamoeba species using MALDI-TOF MS for specific identification of Acanthamoeba genotype

Cited by 9 publications

References 24 publications

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Species, Sequence Types and Alleles: Dissecting Genetic Variation in Acanthamoeba

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