scholarly journals Diversity of the BoLA-DRB3 Gene in Cattle Breeds From Tropical and Subtropical Regions of South America

2021 ◽  
Author(s):  
Magali Nicole Valenzano ◽  
María Eugenia Caffaro ◽  
Veronica Viviana Lía ◽  
Mario Poli ◽  
Silvina Elizabeth Wilkowsky
Keyword(s):  
Latin American ◽  
Nucleotide Diversity ◽  
Typing Method ◽  
Exon 2 ◽  
Peptide Recognition ◽  
Cattle Breeds ◽  
Leukocyte Antigens ◽  
Neutrality Tests ◽  
Gene Frequency Distribution

Abstract Background Bovine leukocyte antigens (BoLA) are widely used as markers of disease and immunological traits in cattle because of their primary function in the recognition of pathogens by the immune system. To date, however, the characterization of BoLA gene polymorphisms in Latin American Zebu and mixed zebuine breeds is scarce. By a sequence-based typing method, here we sequenced exon 2 of BoLA class II DRB3 gene of 264 animals from the five breeds (Creole, Brahman, Braford, Brangus and Nellore) most commonly used in northern Argentina. Results The taurine and zebuine breeds contained 61 previously reported alleles. Genetic diversity was high at allelic and molecular levels, particularly in the mixed breeds. Neutrality tests revealed that none of the breeds shows the even gene frequency distribution expected under a balanced selection scenario. The FST index shows significant differences across all populations (FST=0.052, P < 0.001), indicating a substantial differentiation between breeds. UPGMA trees and Metric multidimensional scaling (MDS) analysis show that, as expected, Creole is distantlyrelated to the other zebuinebreeds. Among them, Brahman, Braford and Brangus cluster closer together than with Nellore. These data are consistent with the historical and geographical origin of these breeds. A peptide binding region sequence analysis at the aminoacid level revealed that, despite the nucleotide diversity among the breeds, the key aminoacids involved in peptide recognition are greatly conserved. Conclusions This is the first report of BoLA-DRB3 diversity in pure and mixed zebuine cattle breeds from Argentina. Knowledge ofBoLA-DRB3 variability in breeds adapted to tropical and subtropical environments contributes not only to ongoing efforts to catalog bovine MHC allele frequencies by breed and location but also to the design of peptide-based vaccines.

Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds

Gene ◽  
2013 ◽  
Vol 519 (1) ◽  
pp. 150-158 ◽  
Author(s):  
Guillermo Giovambattista ◽  
Shin-nosuke Takeshima ◽  
Maria Veronica Ripoli ◽  
Yuki Matsumoto ◽  
Luz Angela Alvarez Franco ◽  
...  
Keyword(s):  
Latin American ◽  
Cattle Breeds ◽  
Creole Cattle

scholarly journals Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

2020 ◽  
Author(s):  
Guillermo Giovambattista ◽  
Kyaw Kyaw Moe ◽  
Meripet Polat ◽  
Liushiqi Borjigin ◽  
Si Thu Hein ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Immune Response ◽  
Latin American ◽  
Coat Color ◽  
Genetic Locus ◽  
The Philippines ◽  
Typing Method ◽  
Cattle Breeds ◽  
Holstein Friesian ◽  
Native Populations

Abstract Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). In addition, a database that included 2,428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software.Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations.Conclusion: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

scholarly journals Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

2020 ◽  
Author(s):  
Guillermo Giovambattista ◽  
Kyaw Kyaw Moe ◽  
Meripet Polat ◽  
Liushiqi Borjigin ◽  
Si Thu Hein ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Immune Response ◽  
Latin American ◽  
Coat Color ◽  
Genetic Locus ◽  
The Philippines ◽  
Typing Method ◽  
Cattle Breeds ◽  
Holstein Friesian ◽  
Native Populations

Abstract Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). In addition, a database that included 2,428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native form Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software. Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations form Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), while populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations. Conclusion: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

scholarly journals BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bashir Salim ◽  
Shin-nosuke Takeshima ◽  
Ryo Nakao ◽  
Mohamed A. M. Moustafa ◽  
Mohamed-Khair A. Ahmed ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Genetic Locus ◽  
Selection Index ◽  
Reproductive Capacity ◽  
High Survival ◽  
Typing Method ◽  
Indigenous Cattle ◽  
Exon 2 ◽  
Cattle Breeds ◽  
Nomadic Pastoralists

AbstractAutochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agro-ecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan's harsh environment.

scholarly journals Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

2020 ◽  
Author(s):  
Guillermo Giovambattista ◽  
Kyaw Kyaw Moe ◽  
Meripet Polat ◽  
Liushiqi Borjigin ◽  
Si Thu Hein ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Immune Response ◽  
Latin American ◽  
Coat Color ◽  
Genetic Locus ◽  
The Philippines ◽  
Typing Method ◽  
Cattle Breeds ◽  
Holstein Friesian ◽  
Native Populations

Abstract Background: Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly adapted to the harsh tropical climates of this region. Here, we analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus that has been linked to the immune response, in Myanmar cattle populations.Methods: Blood samples (n=294) were taken from two native breeds (Pyer Sein, n=163 and Shwe Ni, n=69) and a cattle crossbreed (Holstein-Friesian, n=62) distributed across six regions of Myanmar (Bago, n=38; Sagaing, n=77; Mandalay, n=46; Magway, n=46; Kayin, n=43; Yangon, n=44). In addition, a database that included 2,428 BoLA-DRB3 genotypes from European (Angus, Hereford, Holstein, Shorthorn, Overo Negro, Overo Colorado, and Jersey), Zebuine (Nellore, Brahman and Gir), Asian Native from Japan and Philippine and Latin-American Creole breeds was also included. Furthermore, the information from the IPD–MHC database was also used in the present analysis. DNA was genotyped using the sequence-based typing method. DNA electropherograms were analyzed using the Assign 400ATF software. Results: We detected 71 distinct alleles, including three new variants for the BoLA-DRB3 gene. Venn analysis showed that 11 of these alleles were only detected in Myanmar native breeds and 26 were only shared with Asian native and/or Zebu groups. The number of alleles ranged from 33 in Holstein-Friesians to 58 in Pyer Seins, and the observed versus unbiased expected heterozygosity were higher than 0.84 in all the three the populations analyzed. The FST analysis showed a low level of genetic differentiation between the two Myanmar native breeds (FST=0.003), and between these native breeds and the Holstein-Friesians (FST < 0.021). The average FST value for all the Myanmar Holstein-Friesian crossbred and Myanmar native populations was 0.0136 and 0.0121, respectively. Principal component analysis (PCA) and tree analysis showed that Myanmar native populations grouped in a narrow cluster that diverged clearly from the Holstein-Friesian populations. Furthermore, the BoLA-DRB3 allele frequencies suggested that while some Myanmar native populations from Bago, Mandalay and Yangon regions were more closely related to Zebu breeds (Gir and Brahman), populations from Kayin, Magway and Sagaing regions were more related to the Philippines native breeds. On the contrary, PCA showed that the Holstein-Friesian populations demonstrated a high degree of dispersion, which is likely the result of the different degrees of native admixture in these populations. Conclusion: This study is the first to report the genetic diversity of the BoLA-DRB3 gene in two native breeds and one exotic cattle crossbreed from Myanmar. The results obtained contribute to our understanding of the genetic diversity and distribution of BoLA-DRB3 gene alleles in Myanmar, and increases our knowledge of the worldwide variability of cattle BoLA-DRB3 genes, an important locus for immune response and protection against pathogens.

scholarly journals Genomic Organization and Characterization of the white Locus of the Mediterranean Fruitfly, Ceratitis capitata

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1245-1255 ◽  
Author(s):  
L M Gomulski ◽  
R J Pitts ◽  
S Costa ◽  
G Saccone ◽  
C Torti ◽  
...  
Keyword(s):  
Ceratitis Capitata ◽  
Dna Encoding ◽  
Cloning And Sequencing ◽  
Deletion Event ◽  
Exon 2 ◽  
Independent Events ◽  
White Locus ◽  
Primary Amino ◽  
Organizational Patterns

Abstract An ∼14-kb region of genomic DNA encoding the wild-type white eye (w+) color gene from the medfly, Ceratitis capitata has been cloned and characterized at the molecular level. Comparison of the intron-exon organization of this locus among several dipteran insects reveals distinct organizational patterns that are consistent with the phylogenetic relationships of these flies and the dendrogram of the predicted primary amino acid sequence of the white loci. An examination of w+ expression during medfly development has been carried out, displaying overall similarity to corresponding studies for white gene homologues in Drosophila melanogaster and other insects. Interestingly, we have detected two phenotypically neutral allelic forms of the locus that have arisen as the result of an apparently novel insertion or deletion event located in the large first intron of the medfly white locus. Cloning and sequencing of two mutant white alleles, w1 and w2, from the we,wp and M245 strains, respectively, indicate that the mutant conditions in these strains are the result of independent events—a frameshift mutation in exon 6 for w1 and a deletion including a large part of exon 2 in the case of w2.

scholarly journals Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 29
Author(s):  
Lilia González-Cerón ◽  
José Cebrián-Carmona ◽  
Concepción M. Mesa-Valle ◽  
Federico García-Maroto ◽  
Frida Santillán-Valenzuela ◽  
...  
Keyword(s):  
Amino Acid ◽  
B Cell ◽  
Plasmodium Vivax ◽  
Nucleotide Diversity ◽  
Protective Antigen ◽  
Balancing Selection ◽  
Southern Mexico ◽  
Exon 2 ◽  
Exon 1 ◽  
Tajima’S D

Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima’s D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima’s D, β-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.

scholarly journals Cloning and functional characterization of the human fractalkine receptor promoter regions

2002 ◽  
Vol 368 (3) ◽  
pp. 753-760 ◽  
Author(s):  
Alexandre GARIN ◽  
Philippe PELLET ◽  
Philippe DETERRE ◽  
Patrice DEBRÉ ◽  
Christophe COMBADIÈRE
Keyword(s):  
Functional Characterization ◽  
Cell Types ◽  
Promoter Regions ◽  
Exon 2 ◽  
Reading Frame ◽  
Fractalkine Receptor ◽  
A Cell ◽  
Exon 4 ◽  
Coronary Events

We have previously shown that reduced expression of the fractalkine receptor, CX3CR1, is correlated with rapid HIV disease progression and with reduced susceptibility to acute coronary events. In order to elucidate the mechanisms underlying transcriptional regulation of CX3CR1 expression, we structurally and functionally characterized the CX3CR1 gene. It consists of four exons and three introns spanning over 18kb. Three transcripts are produced by splicing the three untranslated exons with exon 4, which contains the complete open reading frame. The transcript predominantly found in leucocytes corresponds to the splicing of exon 2 with exon 4. Transcripts corresponding to splicing of exons 1 and 4 are less abundant in leucocytes and splicing of exons 3 and 4 are rare longer transcripts. A constitutive promoter activity was found in the regions extending upstream from untranslated exons 1 and 2. Interestingly, exons 1 and 2 enhanced the activity of their respective promoters in a cell-specific manner. These data show that the CX3CR1 gene is controlled by three distinct promoter regions, which are regulated by their respective untranslated exons and that lead to the transcription of three mature messengers. This highly complex regulation may allow versatile and precise expression of CX3CR1 in various cell types.

scholarly journals Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Silvia C Bobeica ◽  
Shi-Hui Dong ◽  
Liujie Huo ◽  
Nuria Mazo ◽  
Martin I McLaughlin ◽  
...  
Keyword(s):  
Structural Data ◽  
Leader Peptide ◽  
Gram Negative Bacteria ◽  
Protease Domain ◽  
Peptide Recognition ◽  
Gram Positive Bacteria ◽  
Dual Functional ◽  
Signaling Peptides

The secretion of peptides and proteins is essential for survival and ecological adaptation of bacteria. Dual-functional ATP-binding cassette transporters export antimicrobial or quorum signaling peptides in Gram-positive bacteria. Their substrates contain a leader sequence that is excised by an N-terminal peptidase C39 domain at a double Gly motif. We characterized the protease domain (LahT150) of a transporter from a lanthipeptide biosynthetic operon in Lachnospiraceae and demonstrate that this protease can remove the leader peptide from a diverse set of peptides. The 2.0 Å resolution crystal structure of the protease domain in complex with a covalently bound leader peptide demonstrates the basis for substrate recognition across the entire class of such transporters. The structural data also provide a model for understanding the role of leader peptide recognition in the translocation cycle, and the function of degenerate, non-functional C39-like domains (CLD) in substrate recruitment in toxin exporters in Gram-negative bacteria.

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