scholarly journals Phylostratigraphic analysis of gene networks of human diseases

2021 ◽  
Vol 25 (1) ◽  
pp. 46-56
Author(s):  
Z. S. Mustafin ◽  
S. A. Lashin ◽  
Yu. G. Matushkin
Keyword(s):  
Genetic Variability ◽  
Gene Networks ◽  
Gene Evolution ◽  
Chemical Compounds ◽  
Human Diseases ◽  
Orthologous Group ◽  
Stabilizing Selection ◽  
Gene Origin ◽  
Reliable Correlation ◽  
Time Of Origin

Phylostratigraphic analysis is an approach to the study of gene evolution that makes it possible to determine the time of the origin of genes by analyzing their orthologous groups. The age of a gene belonging to an orthologous group is def ined as the age of the most recent ancestor of all species represented in that group. Such an analysis can reveal important stages in the evolution of both the organism as a whole and groups of functionally related genes, in particular gene networks. In addition to investigating the time of origin of a gene, the level of its genetic variability and what type of selection the gene is subject to in relation to the most closely related organisms is studied. Using the Orthoscape application, gene networks from the KEGG Pathway, Human Diseases database describing various human diseases were analyzed. It was shown that the majority of genes described in gene networks are under stabilizing selection and a high reliable correlation was found between the time of gene origin and the level of genetic variability: the younger the gene, the higher the level of its variability is. It was also shown that among the gene networks analyzed, the highest proportion of evolutionarily young genes was found in the networks associated with diseases of the immune system (65 %), and the highest proportion of evolutionarily ancient genes was found in the networks responsible for the formation of human dependence on substances that cause addiction to chemical compounds (88 %); gene networks responsible for the development of infectious diseases caused by parasites are signif icantly enriched for evolutionarily young genes, and gene networks responsible for the development of specif ic types of cancer are signif icantly enriched for evolutionarily ancient genes.

Genetic, geographical and temporal variation of porcine reproductive and respiratory syndrome virus in Illinois

Microbiology ◽  
2000 ◽  
Vol 81 (1) ◽  
pp. 171-179 ◽  
Author(s):  
Tony L. Goldberg ◽  
Edwin C. Hahn ◽  
Ronald M. Weigel ◽  
Gail Scherba
Keyword(s):  
Genetic Variability ◽  
Genetic Similarity ◽  
Pseudorabies Virus ◽  
Amino Acid Level ◽  
Effective Vaccine ◽  
Respiratory Syndrome Virus ◽  
Stabilizing Selection ◽  
Gene Sequences ◽  
Long Distance ◽  
Geographical Regions

Porcine reproductive and respiratory syndrome virus (PRRSV) ORF5 gene sequences were generated by RT–PCR from 55 field isolates collected in Illinois and eastern Iowa. Spatial and temporal patterns of genetic variation in the virus were examined on a local geographical scale in order to test the hypothesis that the genetic similarity of PRRSV isolates (measured as their percentage pairwise ORF5 nucleotide similarity) was positively correlated with their geographical proximity. Levels of genetic variability in the Illinois/eastern Iowa PRRSV sample were similar to levels of variability seen across broader geographical regions within North America. The genetic similarity of isolates did not correlate with their geographical distance. These results imply that the movement of PRRSV onto farms does not generally occur via distance-limited processes such as wind or wildlife vectors, but more typically occurs via the long-distance transport of animals or semen. Genetic distances between PRRSV isolates collected from the same farms at different times increased as the time separating the collection events increased. This result implies rapid movement of new genetic types of PRRSV into and out of farms. PRRSV ORF5 displayed a pattern of third-codon-position diversity bias that was not evident in a geographically comparable sample of pseudorabies virus (a swine alphaherpesvirus) gC gene sequences. This result provides evidence that PRRSV ORF5 is experiencing stabilizing selection against structural novelty. Despite high genetic variability at all geographical levels, PRRSV ORF5 nevertheless contained potentially antigenic regions that were invariant at the amino acid level. These regions should make effective vaccine targets if they prove to be immunogenic.

Maintenance of genetic variability by mutation–selection balance: a child's guide through the jungle

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 761-767 ◽  
Author(s):  
M. G. Bulmer
Keyword(s):  
Genetic Variability ◽  
Theoretical Work ◽  
Complex Problem ◽  
Recurrent Mutation ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
House Of Cards ◽  
Model Account ◽  
Optimal Value ◽  
Selection For

Metric characters closely connected with fitness have little additive genetic variability, presumably because it is quickly exhausted under continuous directional selection on fitness. Other metric characters have substantial additive genetic variability with a typical heritability of about 0.5. A popular model is that the second class of characters is subject to weak stabilizing selection for an optimal value, which depletes genetic variability, while recurrent mutation tends to restore it. Can this model account for the variability observed, given the evidence available about the strength of selection and mutation rates? Much theoretical work has been done on this complex problem. This work is reviewed, with the intention of simplifying it as much as possible.Key words: mutation–selection balance, genetic variability, continuum-of-alleles model, house-of-cards approximation.

scholarly journals Evaluation of genetic variability of the breed Norik of Muran according to pedigree information

2018 ◽  
Vol 63 (No. 5) ◽  
pp. 195-200 ◽  
Author(s):  
M. Halo ◽  
E. Mlyneková ◽  
M. Horná ◽  
M. Ivančíková ◽  
A. Hrdá
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Average Length ◽  
Pedigree Information ◽  
Common Ancestry ◽  
Generation Interval ◽  
The Core ◽  
Equivalent Number ◽  
The Common ◽  
Gene Origin

The Norik of Muran, a unique draught horse bred in Slovakia, belongs to country’s biodiversity treasures. The genetic diversity of this horse type was evaluated on the basis of indicators derived from the common ancestry and the probability of gene origin. The pedigree file of the analyzed horses involved 115 individuals (15 stallions and 100 mares). The number of complete generations was 4.49 on average. The maximum number of ancestor generations at the examined population of living horses was 5.38 and the equivalent number in the generation of ancestors was 5.14. The highest average length of the generation interval was 10.97 years in the father–son direction compared to father–daughter (9.74), mother–son (10.87), and mother–daughter (8.99 years – the lowest average length). The generation interval overall average length was 10.14 years. The total coefficient of relatedness was 1.72% on average. The efficient number of core ancestors evenly used in breeding in comparison with the core ancestors mildly decreased to 198. Therefore the Austrian Norik incorporation in the breeding program is the opportunity how to maintain genetic diversity.

Multiple lineages of FRUITFULL exhibit dynamic patterns of gene evolution after genome triplication in the Brassiceae tribe (Brassicaceae)

Botany ◽  
2019 ◽  
Vol 97 (5) ◽  
pp. 293-310 ◽  
Author(s):  
Kelsey C. Brock ◽  
Jocelyn C. Hall
Keyword(s):  
Gene Evolution ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Single Copy ◽  
Stabilizing Selection ◽  
Relaxed Selection ◽  
Major Species ◽  
Genome Triplication

Phylogenetic analyses of important development genes are necessary to identify trends in sequence divergence and gene retention/loss that underlie diversification after polyploidization. We investigated the evolution of FRUITFULL (FUL) in the tribe Brassiceae (Brassicaceae), where a recent genome triplication allows investigation into the fate of paralogs. Many Brassiceae members possess a unique fruit type exhibiting segmentation and variable dehiscence called heteroarthrocarpy, providing a case study to compare with FUL’s evolution, as a single copy is known to control fruit dehiscence in Arabidopsis. We constructed a phylogeny containing all major species lineages to investigate the number of retained FUL paralogs, trends in selective pressure and intron evolution, and their relationship to heteroarthrocarpy. We recovered four well-supported lineages that likely correspond to three FUL copies from hexaploidization. Rates of selection varied across lineages and comparatively relaxed selection was associated with fruit indehiscence. However, stabilizing selection predominated all lineages, indicating that paralogs retain functionality. Longer introns were correlated with relaxed selection on exons and, on average, heteroarthrocarpic taxa had longer introns and retained different FUL paralogs than nonheteroarthrocarpic taxa, although correlations were complex. The dynamic pattern of FUL evolution invites investigation into the role of upstream regulators in the dehiscence of heteroarthrocarpic fruits.

scholarly journals Pedigree Analysis of Mangalica Pig Breeds

2016 ◽  
Vol 16 (3) ◽  
pp. 701-709 ◽  
Author(s):  
János Posta ◽  
Péter Szabó ◽  
István Komlósi
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Gene Pool ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Small Populations ◽  
Gene Conservation ◽  
Generation Interval ◽  
Pig Breeds ◽  
Gene Origin

AbstractAn effective gene conservation programme requires the knowledge of genetic variability of the population. The genetic structure of Mangalica pig breeds (Blonde, Red and Swallow-bellied) was studied from pedigree records. Herdbook data available up to 2011 of registered Mangalica pig breeds (Blonde, Red and Swallow-bellied) were analysed. The number of complete generations was 6 for Blonde and 5 for Red and Swallow-bellied Mangalica whereas the average complete generation equivalent was between 3.51 and 6.01. The average level of inbreeding of the reference population was low (4.07–5.87%). The investigated breeds could be considered as small populations based on the probability of gene origin. The most important ancestor contributed between 9 and 16% of the gene pool of the reference populations. The longest generation interval was found for the sire-to-son pathways whereas the shortest for dam-to-daughter pathways for each breed.

scholarly journals Population epigenetics, ecotoxicology and human diseases

2012 ◽  
Vol 10 (4) ◽  
pp. 14-28
Author(s):  
Eugene L Patkin ◽  
Henry A Sofronov
Keyword(s):  
Environmental Factors ◽  
Chemical Compounds ◽  
External Factors ◽  
Human Diseases ◽  
Epigenetic Mechanisms ◽  
Epigenetic Variability ◽  
Current State ◽  
Population Epigenetics

The review critically examines the current state of population epigenetics. Possible mechanisms of intergenerational inheritance of epigenetic and epigenomic modifications as a condition of population epigenetics reality are examined. Special attention is paid to the role of external factors, including diet and various chemical compounds as modulators of the epigenome, and the possible inheritance of epigenetic variability characteristics under the influence of such environmental factors. The role of epigenetic mechanisms in the etiology and susceptibility to complex human diseases is considered.

scholarly journals Yeast Augmented Network Analysis (YANA): a new systems approach to identify therapeutic targets for human genetic diseases

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 121 ◽  
Author(s):  
David J. Wiley ◽  
Ilona Juan ◽  
Hao Le ◽  
Xiaodong Cai ◽  
Lisa Baumbach ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Gene Networks ◽  
Disease Gene ◽  
Systems Approach ◽  
Genetic Interaction ◽  
Muscular Atrophy ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
Human Diseases ◽  
Genetic Modifiers

Genetic interaction networks that underlie most human diseases are highly complex and poorly defined. Better-defined networks will allow identification of a greater number of therapeutic targets.Here we introduce our Yeast Augmented Network Analysis (YANA) approach and test it with the X-linked spinal muscular atrophy (SMA) disease gene UBA1. First, we express UBA1 and a mutant variant in fission yeast and use high-throughput methods to identify fission yeast genetic modifiers of UBA1. Second, we analyze available protein-protein interaction network databases in both fission yeast and human to construct UBA1 genetic networks. Third, from these networks we identified potential therapeutic targets for SMA. Finally, we validate one of these targets in a vertebrate (zebrafish) SMA model. This study demonstrates the power of combining synthetic and chemical genetics with a simple model system to identify human disease gene networks that can be exploited for treating human diseases.

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