Assessment of allelic diversity in intron-containing Mal d 1 genes and their association to apple allergenicity

Abstract Mutations in KIT encoding the mast/stem cell growth factor receptor (MGF) are responsible for coat color variation in domestic pigs. The dominant white phenotype is caused by two mutations, a gene duplication and a splice mutation in one of the copies leading to skipping of exon 17. Here we applied minisequencing and pyrosequencing for quantitative analysis of the number of copies with the splice form. An unexpectedly high genetic diversity was revealed in white pigs. We found four different KIT alleles in a small sample of eight Large White females used as founder animals in a wild boar intercross. A similar number of KIT alleles was found in commercial populations of white Landrace and Large White pigs. We provide evidence for at least two new KIT alleles in pigs, both with a triplication of the gene. The results imply that KIT alleles with the duplication are genetically unstable and new alleles are most likely generated by unequal crossing over. This study provides an improved method for genotyping the complicated Dominant white/KIT locus in pigs. The results also suggest that some alleles may be associated with negative pleiotropic effects on other traits.

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Relationship between Phenolic Compounds, Antioxidant Properties, and the Allergenic Protein Mal d 1 in Different Selenium-Biofortified Apple Cultivars (Malus domestica)

Molecules ◽

10.3390/molecules26092647 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2647

Author(s):

Sabrina Groth ◽

Christoph Budke ◽

Timo Weber ◽

Susanne Neugart ◽

Sven Brockmann ◽

...

Keyword(s):

Phenolic Compounds ◽

Antioxidant Properties ◽

Total Phenolic ◽

Allergenic Protein ◽

Antibody Recognition ◽

Allergenic Potential ◽

Allergenic Proteins ◽

Other Substances ◽

Mal D 1 ◽

Apple Cultivars

Notable parts of the population in Europe suffer from allergies towards apples. To address this health problem, the analysis of the interactions of relevant allergens with other substances such as phenolic compounds is of particular importance. The aim of this study was to evaluate the correlations between the total phenolic content (TPC), polyphenol oxidase (PPO) activity, antioxidant activity (AOA), and the phenolic compound profile and the content of the allergenic protein Mal d 1 in six apple cultivars. It was found that the PPO activity and the content of individual phenolic compounds had an influence on the Mal d 1 content. With regard to the important constituents, flavan-3-ols and phenolic acids, it was found that apples with a higher content of chlorogenic acid and a low content of procyanidin trimers and/or epicatechin had a lower allergenic potential. This is probably based on the reaction of phenolic compounds (when oxidized by the endogenous PPO) with proteins, thus being able to change the conformation of the (allergenic) proteins, which further corresponds to a loss of antibody recognition. When apples were additionally biofortified with selenium, the composition of the apples, with regard to TPC, phenolic profile, AOA, and PPO, was significantly affected. Consequently, this innovative agronomic practice seems to be promising for reducing the allergenic potential of apples.

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A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic

Animals ◽

10.3390/ani11061701 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1701

Author(s):

Lenka Štohlová Putnová ◽

Radek Štohl ◽

Martin Ernst ◽

Kateřina Svobodová

Keyword(s):

Red Deer ◽

Sika Deer ◽

Molecular Genetic ◽

Allelic Diversity ◽

Molecular Genetic Analysis ◽

Genetic Introgression ◽

Statistical Framework ◽

Western Bohemia ◽

The Mean ◽

Species Hybrids

Although inter-species hybrids between the red and sika deer can be phenotypically determined only exceptionally, there is the eventuality of identification via molecular genetic analysis. We used bi-parentally inherited microsatellite markers and a Bayesian statistical framework to re-examine the proportion of hybrids in the Czech red and sika deer populations. In total, 123 samples were collected, and the nuclear dataset consisted of 2668 allelic values. The number of alleles per locus ranged from 10 (BM1818) to 22 (BM888 and T193), yielding the mean of 16 alleles per locus across the deer. The mean allelic diversity of the red deer markedly exceeded that of the Japanese sika deer. Interspecific hybrids were detected, enabling us to confirm the genetic introgression of the sika deer into the red deer populations and vice versa in western Bohemia. The mean hybrid score equaled 10.6%, with 14.3% of the hybrids being among red deer–like individuals and 6.7% among sika-like ones. At two western Bohemian locations, namely, Doupovské hory and Slavkovský les, the total percentages of hybrid animals equaled 18.8 and 8.9, respectively. No red deer alleles were detected in the sika populations of the subregions of Kladská, Žlutice, and Lány. The NeighborNet network clearly separated the seven red and sika deer sampling populations according to the geography. The knowledge gained from the evaluated data is applicable in hunting management to reduce hybridization with the European deer.

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Allelic diversity of merozoite surface protein genes (msp1 and msp2) and clinical manifestations of Plasmodium falciparum malaria cases in Aceh, Indonesia

Malaria Journal ◽

10.1186/s12936-021-03719-w ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Kurnia Fitri Jamil ◽

Nandha Rizki Pratama ◽

Sylvia Sance Marantina ◽

Harapan Harapan ◽

Muhammad Riza Kurniawan ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Liver Function ◽

Severe Malaria ◽

Clinical Manifestation ◽

Allelic Diversity ◽

Surface Protein ◽

Merozoite Surface Protein ◽

Malaria Control Programme ◽

Co Morbidity ◽

Aceh Province

Abstract Background The malaria control programme in Indonesia has successfully brought down malaria incidence in many parts in Indonesia, including Aceh Province. Clinical manifestation of reported malaria cases in Aceh varied widely from asymptomatic, mild uncomplicated to severe and fatal complications. The present study aims to explore the allelic diversity of merozoite surface protein 1 gene (msp1) and msp2 among the Plasmodium falciparum isolates in Aceh Province and to determine their potential correlation with the severity of malaria clinical manifestation. Methods Screening of over 500 malaria cases admitted to the hospitals in 11 districts hospital within Aceh Province during 2013–2015, identified 90 cases of P. falciparum mono-infection without any co-morbidity. The subjects were clinically phenotyped and parasite DNA was extracted and polymerase chain reaction (PCR) amplified for the msp1 and msp2 allelic subfamilies. Results Analysis of clinical manifestation revealed that fever-chill is the most frequent symptom. Based on WHO criteria showed 19 cases were classified as severe and 71 as mild malaria. Analysis of msp1 gene revealed the presence of K1 allele subfamily in 34 subjects, MAD20 in 42 subjects, RO33 in 1 subject, and mixed allelic of K1 + MAD20 in 5 subjects, K1 + RO33 in 4 subjects, and MAD20 + RO33 in 4 subjects. Analysis of msp2 gene revealed 34 subjects carried the FC27 allelic subfamily, 37 subjects carried the 3D7 and 19 subjects carried the mixed FC27 + 3D7. Analysis of multiplicity of infection revealed that msp1 alleles is slightly higher than msp2 with the mean of MOI were 2.69 and 2.27, respectively. Statistical analysis to determine the association between each clinical manifestation and msp1 and msp2 alleles revealed that liver function abnormal value was associated with the msp2 mixed alleles (odds ratio (OR):0.13; 95%CI: 0.03–0.53). Mixed msp1 of K1 + RO33 was associated with severe malaria (OR: 28.50; 95%CI: 1.59–1532.30). Conclusion This study found a strong association between severe malaria in Aceh with subjects carrying the msp1 mixed alleles of K1 and RO33. The liver function abnormal value associated with the msp2 mixed allelic subfamilies. Further study in different geographic areas is recommended.

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THE GEOGRAPHICAL DISTRIBUTION OF ALLELIC DIVERSITY, A PRACTICAL MEANS OF PRESERVING AND USING MINOR ROOT CROP GENETIC RESOURCES

Experimental Agriculture ◽

10.1017/s0014479705002875 ◽

2005 ◽

Vol 41 (4) ◽

pp. 475-489 ◽

Cited By ~ 21

Author(s):

VINCENT LEBOT ◽

ANTON IVANCIC ◽

KUTTOLAMADATHIL ABRAHAM

Keyword(s):

Genetic Resources ◽

Geographical Distribution ◽

Allelic Diversity ◽

Core Sample ◽

Ex Situ ◽

Breeding Strategies ◽

Current Conservation ◽

Crop Genetic Resources ◽

Root Crop

This paper addresses the preservation and use of minor root crop genetic resources, mostly aroids and yams. Conservation is fraught with difficulty: ex situ collections are expensive to maintain and methods for on-farm conservation have not been studied. Conventional breeding strategies present serious limitations when applied to these species. Furthermore, the evaluation and distribution of improved material are as problematical as its conservation. The similarities shared by these species regarding their domestication, breeding constraints and improvement strategies as well as farmers' needs, are briefly reviewed. Based on these biological constraints, we propose a practical alternative to current conservation and breeding strategies. This approach focuses on the geographical distribution of allelic diversity rather than localized ex situ and/or in situ preservation of genotypes. The practical steps are described and discussed. First, a core sample representing the useful diversity of the species is assembled from accessions selected for their diverse and distant geographic origins, wide genetic distances, quality, agronomic performances and functional sexuality. Second, the geographical distribution of this core sample, in vitro via a transit centre, allows the direct use of selected genotypes by farmers or for breeding purposes. Third, the distribution of genes is realized in the form of clones resulting from segregating progenies and, fourth, farmers select clones with local adaptation.

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MHC class II DR allelic diversity in bighorn sheep

Gene ◽

10.1016/j.gene.2012.06.048 ◽

2012 ◽

Vol 506 (1) ◽

pp. 217-222 ◽

Cited By ~ 2

Author(s):

Renuka Subramaniam ◽

Stephen N. White ◽

Lynn M. Herrmann-Hoesing ◽

Subramaniam Srikumaran

Keyword(s):

Mhc Class Ii ◽

Allelic Diversity ◽

Bighorn Sheep ◽

Class Ii

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The evolution of allelic diversity at the primate major histocompatibility complex class II loci

Human Immunology ◽

10.1016/0198-8859(91)90079-o ◽

1991 ◽

Vol 30 (2) ◽

pp. 110-118 ◽

Cited By ~ 10

Author(s):

Henry A. Erlich ◽

Ulf B. Gyllensten

Keyword(s):

Major Histocompatibility Complex ◽

Major Histocompatibility Complex Class ◽

Allelic Diversity ◽

Class Ii ◽

Complex Class ◽

Major Histocompatibility ◽

Histocompatibility Complex ◽

Primate Major Histocompatibility Complex

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Diversity of Listeria Species in Urban and Natural Environments

Applied and Environmental Microbiology ◽

10.1128/aem.00282-12 ◽

2012 ◽

Vol 78 (12) ◽

pp. 4420-4433 ◽

Cited By ~ 95

Author(s):

Brian D. Sauders ◽

Jon Overdevest ◽

Esther Fortes ◽

Katy Windham ◽

Ynte Schukken ◽

...

Keyword(s):

Urban Areas ◽

Environmental Samples ◽

Nearest Neighbor ◽

Allelic Diversity ◽

Urban Environments ◽

Source Tracking ◽

Natural Environments ◽

Content Type ◽

Molecular Source ◽

Listeria Seeligeri

ABSTRACTA total of 442Listeriaisolates, including 234Listeria seeligeri, 80L. monocytogenes, 74L. welshimeri, 50L. innocua, and 4L. marthiiisolates, were obtained from 1,805 soil, water, and other environmental samples collected over 2 years from four urban areas and four areas representing natural environments.Listeriaspp. showed similar prevalences in samples from natural (23.4%) and urban (22.3%) environments. WhileL. seeligeriandL. welshimeriwere significantly associated with natural environments (P≤ 0.0001),L. innocuaandL. monocytogeneswere significantly associated with urban environments (P≤ 0.0001). Sequencing ofsigBfor all isolates revealed 67 allelic types with a higher level of allelic diversity among isolates from urban environments. SomeListeriaspp. andsigBallelic types showed significant associations with specific urban and natural areas. Nearest-neighbor analyses also showed that certainListeriaspp. andsigBallelic types were spatially clustered within both natural and urban environments, and there was evidence that these species and allelic types persisted over time in specific areas. Our data show that members of the genusListerianot only are common in urban and natural environments but also show species- and subtype-specific associations with different environments and areas. This indicates thatListeriaspecies and subtypes within these species may show distinct ecological preferences, which suggests (i) that molecular source-tracking approaches can be developed forListeriaand (ii) that detection of someListeriaspecies may not be a good indicator forL. monocytogenes.

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Occurrence, distribution and possible functional roles of simple sequence repeats in phytoplasma genomes

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000273 ◽

2015 ◽

Vol 65 (Pt_8) ◽

pp. 2748-2760 ◽

Cited By ~ 4

Author(s):

Wei Wei ◽

Robert E. Davis ◽

Xiaobing Suo ◽

Yan Zhao

Keyword(s):

Simple Sequence Repeats ◽

Computational Analysis ◽

Allelic Diversity ◽

Regulation Of Transcription ◽

Phase Variable ◽

Functional Roles ◽

Rapid Responses ◽

Computational Analyses ◽

Simple Sequence ◽

Diverse Plant

Phytoplasmas are unculturable, cell-wall-less bacteria that parasitize plants and insects. This transkingdom life cycle requires rapid responses to vastly different environments, including transitions from plant phloem sieve elements to various insect tissues and alternations among diverse plant hosts. Features that enable such flexibility in other microbes include simple sequence repeats (SSRs) — mutation-prone, phase-variable short DNA tracts that function as ‘evolutionary rheostats’ and enhance rapid adaptations. To gain insights into the occurrence, distribution and potentially functional roles of SSRs in phytoplasmas, we performed computational analysis on the genomes of five completely sequenced phytoplasma strains, ‘Candidatus Phytoplasma asteris’-related strains OYM and AYWB, ‘Candidatus Phytoplasma australiense’-related strains CBWB and SLY and ‘Candidatus Phytoplasma mali’-related strain AP-AT. The overall density of SSRs in phytoplasma genomes was higher than in representative strains of other prokaryotes. While mono- and trinucleotide SSRs were significantly overrepresented in the phytoplasma genomes, dinucleotide SSRs and other higher-order SSRs were underrepresented. The occurrence and distribution of long SSRs in the prophage islands and phytoplasma-unique genetic loci indicated that SSRs played a role in compounding the complexity of sequence mosaics in individual genomes and in increasing allelic diversity among genomes. Findings from computational analyses were further complemented by an examination of SSRs in varied additional phytoplasma strains, with a focus on potential contingency genes. Some SSRs were located in regions that could profoundly alter the regulation of transcription and translation of affected genes and/or the composition of protein products.

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