MHC class II expression in skin biopsies from the franciscana dolphin Pontoporia blainvillei and the southern right whale Eubalaena australis

2009 ◽  
Vol 89 (5) ◽  
pp. 1009-1013 ◽  
Author(s):  
Larissa Heinzelmann ◽  
Maurício Tavares ◽  
Paulo H. Ott ◽  
Ignacio M.B. Moreno ◽  
José Artur B. Chies
Keyword(s):  
Mhc Class Ii ◽  
Balancing Selection ◽  
Rna Extraction ◽  
Exon 2 ◽  
Right Whale ◽  
Eubalaena Australis ◽  
Skin Biopsies ◽  
Pontoporia Blainvillei ◽  
First Time ◽  
Franciscana Dolphin

Presently, there is no information about the functionality of the immune system in the franciscana dolphin (Pontoporia blainvillei), a small dolphin from southern Brazil. As in the case of the franciscana, the population of southern right whale (Eubalaena australis) which inhabits Brazilian waters has not yet been surveyed in what concerns MHC expression. For the first time it was possible to observe the DQB gene expression in skin of these two species of cetacean using RT-PCR. Skin pieces of the animals were collected to RNA extraction. The fragment corresponding to DQB exon 2 was amplified, cloned and sequenced. A total of five alleles were found, one to franciscana and four to southern right whale. The observed dN/dS ratio of 2.77 (P = 0.03) suggests that this gene is under balancing selection pressure (positive Darwinian selection). The sequences indicate that, in both species analysed, the DQB gene is functional.

scholarly journals Patterns of evolution of MHC Class II genes of crows (Corvus) suggest trans-species polymorphism

2015 ◽  
Author(s):  
John A Eimes ◽  
Andrea K Townsend ◽  
Irem Sepil ◽  
Isao Nishiumi ◽  
Yoko Satta
Keyword(s):  
Mhc Class Ii ◽  
Convergent Evolution ◽  
Phylogenetic Trees ◽  
Balancing Selection ◽  
Bird Species ◽  
Evolutionary Divergence ◽  
Exon 2 ◽  
Synonymous Substitutions ◽  
American Crows ◽  
Mhc Iib

A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, a pattern consistent with convergence, the overall phylogenetic patterns we observed suggest that TSP, rather than convergence, explains the interspecific allelic similarity of MHC IIB genes in these species of crows.

scholarly journals Have whales returned to a historical hotspot of industrial whaling? The pattern of southern right whale Eubalaena australis recovery at South Georgia

2020 ◽  
Vol 43 ◽  
pp. 323-339
Author(s):  
JA Jackson ◽  
A Kennedy ◽  
M Moore ◽  
A Andriolo ◽  
CCG Bamford ◽  
...  
Keyword(s):  
Visual Observation ◽  
Humpback Whales ◽  
Lower Latitude ◽  
The South ◽  
South Georgia ◽  
Right Whale ◽  
Eubalaena Australis ◽  
Antarctic Waters ◽  
Skin Biopsies ◽  
Strong Contrast

Around 176500 whales were killed in the sub-Antarctic waters off South Georgia (South Atlantic) between 1904 and 1965. In recent decades, whales have once again become summer visitors, with the southern right whale (SRW) the most commonly reported species until 2011. Here, we assess the distribution, temporal pattern, health status and likely prey of SRWs in these waters, combining observations from a summertime vessel-based expedition to South Georgia, stable isotope data collected from SRWs and putative prey and sightings reports collated by the South Georgia Museum. The expedition used directional acoustics and visual surveys to localise whales and collected skin biopsies and photo-IDs. During 76 h of visual observation effort over 19 expedition days, SRWs were encountered 15 times (~31 individuals). Photo-IDs, combined with publicly contributed images from commercial vessels, were reconciled and quality-controlled to form a catalogue of 6 fully (i.e. both sides) identified SRWs and 26 SRWs identified by either left or right sides. No photo-ID matches were found with lower-latitude calving grounds, but 3 whales had gull lesions supporting a direct link with Península Valdés, Argentina. The isotopic position of SRWs in the South Georgia food web suggests feeding on a combination of copepod and krill species. Opportunistic reports of SRW sightings and associated group sizes remain steady over time, while humpback whales provide a strong contrast, with increased sighting rates and group sizes seen since 2013. These data suggest a plateau in SRWs and an increasing humpback whale presence in South Georgia waters following the cessation of whaling.

scholarly journals Patterns of evolution of MHC Class II genes of crows (Corvus) suggest trans-species polymorphism

2015 ◽  
Author(s):  
John A Eimes ◽  
Andrea K Townsend ◽  
Irem Sepil ◽  
Isao Nishiumi ◽  
Yoko Satta
Keyword(s):  
Mhc Class Ii ◽  
Convergent Evolution ◽  
Phylogenetic Trees ◽  
Balancing Selection ◽  
Bird Species ◽  
Evolutionary Divergence ◽  
Exon 2 ◽  
Synonymous Substitutions ◽  
American Crows ◽  
Mhc Iib

A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, a pattern consistent with convergence, the overall phylogenetic patterns we observed suggest that TSP, rather than convergence, explains the interspecific allelic similarity of MHC IIB genes in these species of crows.

scholarly journals 5′ Region Large Genomic Rearrangements in the BRCA1 Gene in French Families: Identification of a Tandem Triplication and Nine Distinct Deletions with Five Recurrent Breakpoints

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3171
Author(s):  
Sandrine M. Caputo ◽  
Dominique Telly ◽  
Adrien Briaux ◽  
Julie Sesen ◽  
Maurizio Ceppi ◽  
...  
Keyword(s):  
Brca1 Gene ◽  
Genomic Rearrangements ◽  
Comparative Genomic ◽  
Homologous Region ◽  
Exon 2 ◽  
Large Genomic Rearrangements ◽  
Causality Score ◽  
Frequent Site ◽  
First Time ◽  
Intron 2

Background: Large genomic rearrangements (LGR) in BRCA1 consisting of deletions/duplications of one or several exons have been found throughout the gene with a large proportion occurring in the 5′ region from the promoter to exon 2. The aim of this study was to better characterize those LGR in French high-risk breast/ovarian cancer families. Methods: DNA from 20 families with one apparent duplication and nine deletions was analyzed with a dedicated comparative genomic hybridization (CGH) array, high-resolution BRCA1 Genomic Morse Codes analysis and Sanger sequencing. Results: The apparent duplication was in fact a tandem triplication of exons 1 and 2 and part of intron 2 of BRCA1, fully characterized here for the first time. We calculated a causality score with the multifactorial model from data obtained from six families, classifying this variant as benign. Among the nine deletions detected in this region, eight have never been identified. The breakpoints fell in six recurrent regions and could confirm some specific conformation of the chromatin. Conclusions: Taken together, our results firmly establish that the BRCA1 5′ region is a frequent site of different LGRs and highlight the importance of the segmental duplication and Alu sequences, particularly the very high homologous region, in the mechanism of a recombination event. This also confirmed that those events are not systematically deleterious.

Microsatellite markers for the endangered franciscana dolphin (Pontoporia blainvillei)

2021 ◽  
Author(s):  
Haydée A. Cunha ◽  
Teresa E. C. dos Santos ◽  
Luísa C. Alvarenga ◽  
Nathalia P. Cavaleiro ◽  
Marta J. Cremer ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Pontoporia Blainvillei ◽  
Franciscana Dolphin

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 Molecular characterization of cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) gene and frequency of blood types in stray cats of İzmir, Turkey

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hüseyin Can ◽  
Sedef Erkunt Alak ◽  
Ahmet Efe Köseoğlu ◽  
Umut Şahar ◽  
Berna Bostanbaş ◽  
...  
Keyword(s):  
Type A ◽  
Type B ◽  
Exon 2 ◽  
Blood Types ◽  
Acetylneuraminic Acid ◽  
Stray Cats ◽  
High Prevalence ◽  
Heterozygous Form ◽  
Type Ab ◽  
First Time

Abstract Background Cytidine monophospho-n-acetylneuraminic acid hydroxylase (CMAH) gene associated with blood groups in cats encodes CMAH enzyme that converts Neu5Ac to Neu5Gc. Although variations in CMAH gene of pedigree cats have been revealed, the presence/lack of them in non-pedigree stray cats is unknown. Therefore, the present study aimed to investigate the variations in CMAH gene and the quantity of Neu5Ac and Neu5Gc on erythrocytes of non-pedigree stray cats (n:12) living in İzmir, Turkey. Also, the frequency of blood types was determined in 76 stray cats including 12 cats that were used for CMAH and Neu5A/Neu5Gc analysis. Results In total, 14 SNPs were detected in 5’UTR as well as in exon 2, 4, 9, 10, 11 and 12 of CMAH gene. Among these SNPs, -495 C > T in 5’UTR was detected for the first time as heterozygous in type A and AB cats, and homozygous and heterozygous in type B cats. The remaining 13 that have been detected in previous studies were also found as homozygous or heterozygous. Both Neu5Gc and Neu5Ac were detected in type A and AB cats. In type B cats, only Neu5Ac was detected. Among two type AB cats, the level of Neu5Ac was found higher in cat carrying heterozygous form (T/C) of 1392T > C. The prevalence of type B cats (67.1 %) was higher than others. Conclusions The presence of a new SNP as well as previous SNPs indicates that more variations can be found in stray cats with a more comprehensive study in the future. Also, the high prevalence of type B cats demonstrates the possible risk of neonatal isoerythrolysis among stray cats living in İzmir, Turkey.

scholarly journals Prediction of IL4 Inducing Peptides

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Sandeep Kumar Dhanda ◽  
Sudheer Gupta ◽  
Pooja Vir ◽  
G. P. S. Raghava
Keyword(s):  
Mhc Class Ii ◽  
Critical Role ◽  
Interleukin 4 ◽  
Th2 Response ◽  
Data Set ◽  
T Helper 2 ◽  
Cell Responses ◽  
Antibody Class ◽  
First Time ◽  
Motif Information

The secretion of Interleukin-4 (IL4) is the characteristic of T-helper 2 responses. IL4 is a cytokine produced by CD4+ T cells in response to helminthes and other extracellular parasites. It has a critical role in guiding antibody class switching, hematopoiesis and inflammation, and the development of appropriate effector T-cell responses. In this study, it is the first time an attempt has been made to understand whether it is possible to predict IL4 inducing peptides. The data set used in this study comprises 904 experimentally validated IL4 inducing and 742 noninducing MHC class II binders. Our analysis revealed that certain types of residues are preferred at certain positions in IL4 inducing peptides. It was also observed that IL4 inducing and noninducing epitopes differ in compositional and motif pattern. Based on our analysis we developed classification models where the hybrid method of amino acid pairs and motif information performed the best with maximum accuracy of 75.76% and MCC of 0.51. These results indicate that it is possible to predict IL4 inducing peptides with reasonable precession. These models would be useful in designing the peptides that may induce desired Th2 response.

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