scholarly journals House sparrows do not exhibit a preference for the scent of potential partners with different MHC-I allele numbers and genetic distances

2022 ◽  
Author(s):  
Luisa Amo ◽  
Guillermo Amo de Paz ◽  
Johanna Kabbert ◽  
Annie Machordom
Keyword(s):  
Amino Acid ◽  
House Sparrow ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Immune Recognition ◽  
House Sparrows ◽  
Mhc I ◽  
Mhc Genes ◽  
Functional Variants ◽  
Amino Acid Variants

MHC genes play a fundamental role in immune recognition of pathogens and parasites. Therefore, females may increase offspring heterozygosity and genetic diversity by selecting MHC genetically compatible or heterozygous males. In birds, several studies suggest that MHC genes play a role in mate choice, and recent evidence suggest that olfaction may play a role in such discrimination. Previous studies indicated that house sparrow females with low allelic diversity prefer males with higher diversity in MHC-I alleles. Here, we directly explored whether both house sparrow females and males could estimate by scent the number in MHC amino acid and functional variants as well as the level of MHC-I similarity or dissimilarity of potential partners. Our results show that neither females nor males exhibit a preference related to the number of MHC-I amino acid variants or functional variants or in relation to MHC amino acid or functional similarity of potential partners, suggesting that MHC-I is not detected through olfaction. Further studies are needed to understand the mechanisms responsible for MHC-I based mate discrimination in birds.

scholarly journals Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

2012 ◽  
Vol 367 (1590) ◽  
pp. 820-829 ◽  
Author(s):  
Marcelo A. Fernandez Vina ◽  
Jill A. Hollenbach ◽  
Kirsten E. Lyke ◽  
Marcelo B. Sztein ◽  
Martin Maiers ◽  
...  
Keyword(s):  
Allelic Diversity ◽  
Genetic Distances ◽  
Distance Measurements ◽  
Allele Distribution ◽  
Hla Alleles ◽  
Hla System ◽  
Functional Variants ◽  
Balanced Distribution ◽  
Almost All ◽  
And Function

The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans.

scholarly journals Multiplex Assessment of Protein Variant Abundance by Massively Parallel Sequencing

2018 ◽  
Author(s):  
Kenneth A. Matreyek ◽  
Lea M. Starita ◽  
Jason J. Stephany ◽  
Beth Martin ◽  
Melissa A. Chiasson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Massively Parallel Sequencing ◽  
Dominant Negative ◽  
Massively Parallel ◽  
Single Amino Acid ◽  
Protein Variant ◽  
Parallel Sequencing ◽  
Missense Variants ◽  
Functional Variants ◽  
Amino Acid Variants

ABSTRACTDetermining the pathogenicity of human genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes will likely require generalizable, scalable assays. Here we describe Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance in a single experiment. We apply VAMP-seq to quantify the abundance of 7,595 single amino acid variants of two proteins, PTEN and TPMT, in which functional variants are clinically actionable. We identify 1,079 PTEN and 805 TPMT single amino acid variants that result in low protein abundance, and may be pathogenic or alter drug metabolism, respectively. We observe selection for low-abundance PTEN variants in cancer, and our abundance data suggest that a PTEN variant accounting for ~10% of PTEN missense variants in melanomas functions via a dominant negative mechanism. Finally, we demonstrate that VAMP-seq can be applied to other genes, highlighting its potential as a generalizable assay for characterizing missense variants.

scholarly journals The Role of Arg13 in Protein Phosphatase M tPphA from Thermosynechococcus elongatus

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Jiyong Su ◽  
Karl Forchhammer
Keyword(s):  
Amino Acid ◽  
Protein Phosphatase ◽  
Arginine Residue ◽  
Side Chain ◽  
Wild Type ◽  
Catalytic Center ◽  
Nitrophenyl Phosphate ◽  
Reduced Activity ◽  
Amino Acid Variants

A highly conserved arginine residue is close to the catalytic center of PPM/PP2C-type protein phosphatases. Different crystal structures of PPM/PP2C homologues revealed that the guanidinium side chain of this arginine residue can adopt variable conformations and may bind ligands, suggesting an important role of this residue during catalysis. In this paper, we randomly mutated Arginine 13 of tPphA, a PPM/PP2C-type phosphatase from Thermosynechococcus elongatus, and obtained 18 different amino acid variants. The generated variants were tested towards p-nitrophenyl phosphate and various phosphopeptides. Towards p-nitrophenyl phosphate as substrate, twelve variants showed 3–7 times higher Km values than wild-type tPphA and four variants (R13D, R13F, R13L, and R13W) completely lost activity. Strikingly, these variants were still able to dephosphorylate phosphopeptides, although with strongly reduced activity. The specific inability of some Arg-13 variants to hydrolyze p-nitrophenyl phosphate highlights the importance of additional substrate interactions apart from the substrate phosphate for catalysis. The properties of the R13 variants indicate that this residue assists in substrate binding.

scholarly journals The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Bargavi Thyagarajan ◽  
Jesse D Bloom
Keyword(s):  
Amino Acid ◽  
H1n1 Influenza ◽  
Influenza Hemagglutinin ◽  
Functional Variants ◽  
Viral Hemagglutinin ◽  
Before And After ◽  
Amino Acid Mutations ◽  
And Function ◽  
Phylogenetic Models ◽  
Better Than

Influenza is notable for its evolutionary capacity to escape immunity targeting the viral hemagglutinin. We used deep mutational scanning to examine the extent to which a high inherent mutational tolerance contributes to this antigenic evolvability. We created mutant viruses that incorporate most of the ≈104 amino-acid mutations to hemagglutinin from A/WSN/1933 (H1N1) influenza. After passaging these viruses in tissue culture to select for functional variants, we used deep sequencing to quantify mutation frequencies before and after selection. These data enable us to infer the preference for each amino acid at each site in hemagglutinin. These inferences are consistent with existing knowledge about the protein's structure and function, and can be used to create a model that describes hemagglutinin's evolution far better than existing phylogenetic models. We show that hemagglutinin has a high inherent tolerance for mutations at antigenic sites, suggesting that this is one factor contributing to influenza's antigenic evolution.

scholarly journals Variations in MHC class I antigen presentation and immunopeptidome selection pathways

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1177
Author(s):  
Anita J. Zaitouna ◽  
Amanpreet Kaur ◽  
Malini Raghavan
Keyword(s):  
Cell Surface ◽  
Antigen Presentation ◽  
Surface Expression ◽  
Structural Features ◽  
Class I ◽  
Cell Surface Expression ◽  
Immune Recognition ◽  
Antigen Receptors ◽  
Class I Mhc ◽  
Mhc I

Major histocompatibility class I (MHC-I) proteins mediate immunosurveillance against pathogens and cancers by presenting antigenic or mutated peptides to antigen receptors of CD8+ T cells and by engaging receptors of natural killer (NK) cells. In humans, MHC-I molecules are highly polymorphic. MHC-I variations permit the display of thousands of distinct peptides at the cell surface. Recent mass spectrometric studies have revealed unique and shared characteristics of the peptidomes of individual MHC-I variants. The cell surface expression of MHC-I–peptide complexes requires the functions of many intracellular assembly factors, including the transporter associated with antigen presentation (TAP), tapasin, calreticulin, ERp57, TAP-binding protein related (TAPBPR), endoplasmic reticulum aminopeptidases (ERAPs), and the proteasomes. Recent studies provide important insights into the structural features of these factors that govern MHC-I assembly as well as the mechanisms underlying peptide exchange. Conformational sensing of MHC-I molecules mediates the quality control of intracellular MHC-I assembly and contributes to immune recognition by CD8 at the cell surface. Recent studies also show that several MHC-I variants can follow unconventional assembly routes to the cell surface, conferring selective immune advantages that can be exploited for immunotherapy.

scholarly journals High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Amali Malshani Samaraweera ◽  
Ranga Liyanage ◽  
Mohamed Nawaz Ibrahim ◽  
Ally Mwai Okeyo ◽  
Jianlin Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Microsatellite Markers ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Population Substructure ◽  
High Genetic Diversity ◽  
Naked Neck ◽  
Local Chicken ◽  
Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

scholarly journals Electromagnetic Pollution as a Possible Explanation for the Decline of House Sparrows in Interaction with Other Factors

Birds ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 329-337
Author(s):  
Alfonso Balmori
Keyword(s):  
Electromagnetic Radiation ◽  
Thermal Effects ◽  
House Sparrow ◽  
Bird Species ◽  
Passer Domesticus ◽  
The Other ◽  
Rapid Decline ◽  
House Sparrows ◽  
Electromagnetic Pollution ◽  
The Impact

In recent decades, there has been a decline of the House Sparrow (Passer domesticus), mainly in European cities, and several hypotheses have been proposed that attempt to determine the causes of this rapid decline. Previous studies indicated that house sparrows were significantly negatively associated with increasing electromagnetic radiation and sparrows disappeared from areas most polluted. In addition, there are many studies on the impact of radiation on other bird and non-bird species, as well as numerous laboratory studies that demonstrated detrimental effects at electric field strength levels that can be found in cities today. Electromagnetic radiation is the most plausible factor for multiple reasons, including that this is the only one that affects the other hypotheses proposed so far. It is a type of pollution that affects productivity, fertility, decreases insects (chicken feed), causes loss of habitat, decreases immunity and can promote disease. Additionally, the recent sparrow decline matches the deployment of mobile telephony networks. Further, there are known mechanisms of action for non-thermal effects of electromagnetic radiation that may affect sparrows causing their decline. Thus, electromagnetic radiation must be seriously considered as a factor for house sparrows’ decline, probably in synergy with the other factors previously proposed.

scholarly journals Multiple Advantageous Amino Acid Variants in the NAT2 Gene in Human Populations

PLoS ONE ◽  
2008 ◽  
Vol 3 (9) ◽  
pp. e3136 ◽  
Author(s):  
Francesca Luca ◽  
Giuseppina Bubba ◽  
Massimo Basile ◽  
Radim Brdicka ◽  
Emmanuel Michalodimitrakis ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Populations ◽  
Nat2 Gene ◽  
Amino Acid Variants

scholarly journals MaveRegistry: a collaboration platform for multiplexed assays of variant effect

2020 ◽  
Author(s):  
Da Kuang ◽  
Jochen Weile ◽  
Nishka Kishore ◽  
Alan F. Rubin ◽  
Stanley Fields ◽  
...  
Keyword(s):  
Amino Acid ◽  
International Community ◽  
Human Variation ◽  
Single Nucleotide ◽  
Clinical Interpretation ◽  
Link Type ◽  
Variant Effect ◽  
Genomic Regions ◽  
Amino Acid Variants

AbstractSummaryMultiplexed assays of variant effect (MAVEs) are capable of experimentally testing all possible single nucleotide or amino acid variants in selected genomic regions, generating ‘variant effect maps’, which provide biochemical insight and functional evidence to enable more rapid and accurate clinical interpretation of human variation. Because the international community applying MAVE approaches is growing rapidly, we developed the online MaveRegistry platform to catalyze collaboration, reduce redundant efforts, allow stakeholders to nominate targets, and enable tracking and sharing of progress on ongoing MAVE projects.Availability and implementationhttps://[email protected]

Glucose and amino acid absorption in house sparrow intestine and its dietary modulation

1996 ◽  
Vol 271 (3) ◽  
pp. R561-R568 ◽  
Author(s):  
E. Caviedes-Vidal ◽  
W. H. Karasov
Keyword(s):  
Glucose Uptake ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Glucose Absorption ◽  
Uptake Capacity ◽  
House Sparrows ◽  
High Lipid ◽  
In Vivo Absorption ◽  
High Starch

We acclimated house sparrows (Passer domesticus; 26 g) to high-starch (HS), high-protein (HP), and high-lipid (HL) diets and tested the predictions that uptake of D-glucose and amino acids will be increased with increased levels of dietary carbohydrate and protein, respectively. HS birds had lower mediated D-glucose uptake rate than HP birds. Total uptake of L-leucine at low concentration (0.01 mM), but not of L-proline at 50mM, was increased by dietary protein. Measures of D-glucose maximal mediated uptake (1.2 +/- 0.2 nmol.min-1.mg-1) and intestinal mass (1 g) indicated that the intestine's mediated uptake capacity was only approximately 10% of the D-glucose absorbed at the whole animal level. This implied that nonmediated glucose absorption predominated. We applied a pharmacokinetic technique to measure in vivo absorption of L-glucose, the stereoisomer that does not interact with the Na(+)-glucose cotransporter. At least 75% of L-glucose that was ingested was apparently absorbed. This adds to the increasing evidence that substantial passive glucose absorption occurs in birds and may explain why mediated D-glucose uptake does not increase on high-carbohydrate diets.

Sign in / Sign up

Export Citation Format

Share Document