scholarly journals High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice

2020 ◽  
Author(s):  
Martin Stervander ◽  
Elisa G. Dierickx ◽  
Jack Thorley ◽  
M. de L. Brooke ◽  
Helena Westerdahl
Keyword(s):  
Mate Choice ◽  
Gene Diversity ◽  
Gene Copy Number ◽  
Small Population ◽  
Critically Endangered ◽  
Gene Copy ◽  
Immune Gene ◽  
Class I Mhc ◽  
Mhc I ◽  
Island Endemic

AbstractSmall population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso lark Alauda razae, a species restricted to the 7 km2 islet of Raso (Cape Verde) since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by co-segregation of multiple haplotypes comprising 2–8 linked MHC-I loci. Within-locus homozygosity is high, contributing to comparably low population-wide diversity. Conversely, each individual had comparably many alleles, 6–16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species’ adaptive potential.

scholarly journals High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single‐island endemic bird, but no evidence of MHC‐based mate choice

2020 ◽  
Vol 29 (19) ◽  
pp. 3578-3592 ◽  
Author(s):  
Martin Stervander ◽  
Elisa G. Dierickx ◽  
Jack Thorley ◽  
M. de L. Brooke ◽  
Helena Westerdahl
Keyword(s):  
Mate Choice ◽  
Copy Number ◽  
Gene Copy Number ◽  
Critically Endangered ◽  
Gene Copy ◽  
Island Endemic

scholarly journals Wetter climates select for higher immune gene diversity in resident, but not migratory, songbirds

2020 ◽  
Vol 287 (1919) ◽  
pp. 20192675 ◽  
Author(s):  
Emily A. O'Connor ◽  
Dennis Hasselquist ◽  
Jan-Åke Nilsson ◽  
Helena Westerdahl ◽  
Charlie K. Cornwallis
Keyword(s):  
Immune System ◽  
Gene Diversity ◽  
Immune Gene ◽  
Class I Mhc ◽  
Mhc I ◽  
Tropical Regions ◽  
Immune Genes ◽  
Histocompatibility Complex ◽  
Geographical Regions ◽  
Migratory Songbirds

Pathogen communities can vary substantially between geographical regions due to different environmental conditions. However, little is known about how host immune systems respond to environmental variation across macro-ecological and evolutionary scales. Here, we select 37 species of songbird that inhabit diverse environments, including African and Palaearctic residents and Afro-Palaearctic migrants, to address how climate and habitat have influenced the evolution of key immune genes, the major histocompatibility complex class I (MHC-I). Resident species living in wetter regions, especially in Africa, had higher MHC-I diversity than species living in drier regions, irrespective of the habitats they occupy. By contrast, no relationship was found between MHC-I diversity and precipitation in migrants. Our results suggest that the immune system of birds has evolved greater pathogen recognition in wetter tropical regions. Furthermore, evolving transcontinental migration appears to have enabled species to escape wet, pathogen-rich areas at key periods of the year, relaxing selection for diversity in immune genes and potentially reducing immune system costs.

The potential of soil microorganisms to mineralize atrazine as predicted by MCH-PCR followed by nested PCR

2000 ◽  
Vol 46 (5) ◽  
pp. 425-432 ◽  
Author(s):  
Nir Shapir ◽  
Sebastien Goux ◽  
Raphi T Mandelbaum ◽  
Luc Pussemier
Keyword(s):  
Nested Pcr ◽  
Copy Number ◽  
Soil Microorganisms ◽  
Target Genes ◽  
Gene Copy Number ◽  
Small Population ◽  
Gene Copy ◽  
Mineralization Rate ◽  
Magnetic Capture ◽  
High Concentrations

The potential of soil microorganisms to mineralize atrazine was studied in soil samples collected from fields with various histories of atrazine application. In contrast to many previous studies, which showed no atrazine mineralization activity, all the tested soils mineralized atrazine regardless of their atrazine application history. However, the delay before mineralization and the variation in the subsequent mineralization rate were in agreement with the initial copy number of the atrazine dechlorinaze gene, and the proliferation rate of the degraders. Soils from corn fields, which had up to 100 copies of the atzA gene per gram of soil, had a lag period of 4-5 days before atrazine mineralization started, and final mineralization percentages ranged from 40% to 54%. However, soils from fields that were never amended with atrazine had much longer lag periods (more than 17 days), which decreased after enrichment of the degrader population with high concentrations of atrazine for 15 days. Generally the mineralization rate and the atzA gene copy number increased after the enrichment period. The atrazine mineralization potential was measured by PCR of genes from the atrazine mineralization pathway. Magnetic capture hybridization was the most efficient of the two tested methods for purifying target DNA of PCR inhibitors, without reducing the copy number of the required fragment. Nested PCR proved to be the most effective method for predicting the exact potential of the soil to mineralize the pollutant even without enrichment of a small population with the target genes. This method can complement microcosm studies and eliminate futile efforts when the potential to mineralize the pollutant does not exist in the soil.Key words: MCH-PCR, mineralization, atrazine.

Low innate immune-gene diversity in the critically endangered orange-bellied parrot (Neophema chrysogaster)

2019 ◽  
Vol 120 (1) ◽  
pp. 56-64 ◽  
Author(s):  
Caitlin E. Morrison ◽  
Carolyn J. Hogg ◽  
Rosemary Gales ◽  
Rebecca N. Johnson ◽  
Catherine E. Grueber
Keyword(s):  
Gene Diversity ◽  
Innate Immune ◽  
Critically Endangered ◽  
Immune Gene ◽  
Innate Immune Gene

Major histocompatibility I gene diversity in the critically endangered Laysan duck (Anas laysanensis).

2014 ◽  
Vol 20 (1) ◽  
pp. 86 ◽  
Author(s):  
Philip Lavretsky ◽  
Andrew Engilis Jr ◽  
Jefferey L Peters
Keyword(s):  
Captive Breeding ◽  
Gene Diversity ◽  
Cost Effective ◽  
Major Histocompatibility ◽  
Mhc I ◽  
Island Endemic ◽  
Low Genetic Diversity ◽  
Cost Effective Method ◽  
Founder Populations ◽  
Breeding Programmes

Quantifying the genetic composition of founder populations is important to the success of reintroduction programmes, especially for bottlenecked and/or specialized species, such as island endemics. By implementing admixture schemes based on genetic variability, captive breeding programmes can minimize the detrimental effects of bottlenecking, inbreeding depression, outbreeding depression, etc. Particular attention has been given to genes within the major histocompatibility complex (MHC) due to their direct correlation to an individual’s immunity. However, isolating and amplifying MHC haplotypes remains difficult owing to the high diversity and paralogous nature. We describe a method of MHC I haplotype isolation based on an iterative process of primer design for the endangered island endemic, the Laysan duck (Anas laysanensis). Ultimately, haplotype-specific primers allow for direct genotyping after gel electrophoresis based on the presence/absence of their respective amplicons. Using the developed techniques, a total of eight unique haplotypes were isolated and assayed across 21 Laysan duck individuals from Laysan Island (N = 10) and Midway Atoll (N = 11). The presence/absence of seven haplotypes were variable across individuals with three haplotypes present in 95% of individuals, three in 38% of individuals, and one in 90% of individuals. The protocols described herein provide a simple, cost-effective method for isolating haplotypes and monitoring existing MHC variation in Laysan ducks, and the general approach can be applied to other molecular markers and species with low genetic diversity.

Ligand Design for Specific MHC Class I Molecules on the Cell Surface

2020 ◽  
Author(s):  
Xizheng Sun ◽  
Reika Tokunaga ◽  
Yoko Nagai ◽  
Ryo Miyahara ◽  
Akihiro Kishimura ◽  
...  
Keyword(s):  
Cell Surface ◽  
Mhc Class I ◽  
Targeted Delivery ◽  
Peptide Ligands ◽  
Class I ◽  
Class I Mhc ◽  
Mhc I ◽  
Histocompatibility Complex ◽  
High Binding Affinity ◽  
Mhc Class I Molecules

<p><a></a><a></a><a>We have validated that ligand peptides designed from antigen peptides could be used for targeting specific major histocompatibility complex class I (MHC-I)</a> molecules on cell surface. To design the ligand peptides, we used reported antigen peptides for each MHC-I molecule with high binding affinity. From the crystal structure of the peptide/MHC-I complexes, we determined a modifiable residue in the antigen peptides and replaced this residue with a lysine with an ε-amine group modified with functional molecules. The designed ligand peptides successfully bound to cells expressing the corresponding MHC-I molecules via exchange of peptides bound to the MHC-I. We demonstrated that the peptide ligands could be used to transport a protein or a liposome to cells expressing the corresponding MHC-I. The present strategy may be useful for targeted delivery to cells overexpressing MHC-I, which have been observed autoimmune diseases.</p>

scholarly journals Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 283
Author(s):  
Eyal Seroussi
Keyword(s):  
Copy Number ◽  
Sanger Sequencing ◽  
Cytosine Methylation ◽  
Direct Sequencing ◽  
Information Source ◽  
Gene Copy Number ◽  
Cost Effective ◽  
Gene Copy ◽  
Base Editing ◽  
Recent Developments

Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.

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