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卷 55, 编号 4 (2019)
- 年: 2019
- 文章: 14
- URL: https://journals.rcsi.science/1022-7954/issue/view/11857
General Genetics
Full Transcriptome Profiling of the Liver of Fat-, Fructose- and Cholesterol-Fed C57Black/6J Mice
摘要
C57black/6J female mice were fed an isocaloric diet with excess fat, fructose, cholesterol, or combinations of them for 62 days. In their liver, the differential expression of 30 003 genes was studied by full-chip transcriptional profiling on an Agilent One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, version 6.8, and the relative levels of mRNA for the genes Gpr19, P2ry12, Gnb1, Csf2rb, Gm38450, Pgm3, Prom2, and Adgrv1 were also evaluated by real-time RT-PCR. To determine the metabolic pathways (KEGG), which are the targets of the applied dietary influences, we analyzed the transcriptome data by bioinformatics methods in the R programming environment. We revealed a specific effect of experimental diets on the metabolic pathways of JAK-STAT and MAPK kinases, VEGF and TOR signaling pathways, and a family of transcription factors PPAR. It reflects the changes occurring in the liver in intracellular signaling, inflammation and angiogenesis. The consequences of such changes may be the development of insulin resistance and fatty hepatosis. For the first time, we revealed experimentally a specific effect of all kinds of diets on metabolic pathways of amino acid metabolism of aspartate, glutamate, alanine, proline, histidine, and arginine. Using real-time RT-PCR, we analyzed the samples derived from the groups of animals that received excess fat with fructose or cholesterol. We detected the coordinated changes in expression levels of the Gpr19, Adgrv1, and Csf2rb genes, reflecting the integrated shifts in the cytokine production profiles and the neurohormonal regulation of metabolic processes.
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Artificial Selection for Reduced Fitness in Panmictic Populations of Drosophila melanogaster
摘要
We investigated the evolution of the panmictic experimental populations of Drosophila melanogaster under the influence of artificial selection for reduced fitness. Slowly developing flies were selected among offspring from parents with low sexual activity and low fecundity. As result of this selection carried out for 16 generations, there was a strong decline in the various components of fitness. Our results confirm the results of the experiments by Kaidanov and his staff. The more rapid decrease in fitness observed by us seems to be due to the use of panmictic populations instead of inbred lines. Thus, the resulting fly selection observed in our studies likely reflects a preexisting genetic variation, rather than new mutations.
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Genetics of Microorganisms
Molecular-Genetic Polymorphism of Puccinia triticina in Southern Dagestan Relating to the Center of the Common Evolution between Agent Causing Leaf Rust and Wheat
摘要
Intraspecific genetic polymorphism of leaf rust caused by Puccinia triticina Erikss. was evaluated on the basis of the virulence, microsatellite loci (SSR), and single nucleotide polymorphism (SNP) of isolates collected in Southern Dagestan from species of Triticum L. sp. and Aegilops L. sp. Existence of pathogen population differentiation according to the results of virulence and microsatellite analysis indicates the existence of several genetically differing groups of isolates within the Derbent population. Derbent isolates and reference isolates of P. triticina from durum and common wheat that originated from different countries were characterized by a high degree of phylogenetic relationship by SNP markers. Ethiopian durum isolates in contrast were separated in a single clade.
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Phylogenetic Analysis of Yersinia pestis Strains of the Caucasian Subspecies from the Foci of the Caucasus and Transcaucasia according to the Whole Genome Sequencing Data
摘要
We have investigated the population structure of Yersinia pestis spp. caucasica strains from natural plague foci located in the Caucasus and Transcaucasia. According to the data of a whole genome SNP analysis of 28 strains of the Caucasian subspecies, seven of which are sequenced by us, and taking into account 1625 identified core SNPs, the presence of several phylogenetic lines and populations of Yersinia pestis ssp. caucasica corresponding to the geographical distribution of the strains has been determined. Strains of Y. pestis Caucasian subspecies include three separate clusters, the first of which is represented by strains from the East Caucasian high-mountain plague focus. Their genome has revealed 80 unique SNPs, which indicates their greatest antiquity and the long-standing divergence of this branch from the common stem of the evolution of Caucasian strains. The genomes of strains of two other clusters also differ in a large number of individual SNPs, 32 and 36, respectively. One of them includes strains from the Pre-Sevan mountain, Zangezur-Karabakh mountain, and Pre-Araks low-mountain foci with the grouping within the cluster of three separate subclusters: Pre-Sevan (IIa), Zangezur-Karabakh (IIb), and Zangezur-Karabakh-Pre-Araks (IIc). Another one, the third cluster of the Caucasian subspecies, consists of strains from the northwestern part of the Caucasus highlands (Gyumri and Javakheti-Akhalkalaki foci). Using PCR with hybridization-fluorescent registration of results and whole genome sequencing, two clinical strains of Y. pestis were shown to belong to the Caucasian subtype, which confirms the ability of this subspecies to cause plague in humans.
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Plant Genetics
Inheritance of Marker Genes among Progeny of Interspecific Tomato Hybrids Expressing the recA Escherichia coli Gene
摘要
In interspecific hybrids a decrease in genetic exchanges between chromosomes from different species and negative interactions between functionally incompatible loci limit genetic variation among the progeny. Earlier the fraction of crossover genotypes was increased in intraspecific hybrids of the cultivated tomato Solanum lycopersicum with the expression of the recA Escherichia coli gene. In this research transgenic hybrids between S. lycopersicum and some wild tomato species were obtained in order to study the effect of recA gene expression on the frequency of crossovers in the progeny of interspecific hybrids. Interspecific hybrids showed negative interactions between the loci of the cultivated tomato and the S. cheesmaniae, S. pimpinellifolium, and S. habrochaites species. In the latter case it resulted in semilethal necrosis. The recA gene expression in interspecific hybrids with S. cheesmaniae partially compensates among the F2 progeny the deficiency of recessive genotypes at the Wv:wv locus of chromosome 2. In general, the fractions of crossover genotypes in the F2 progeny were higher in transgenic interspecific hybrids than in control non-transgenic hybrids of the same combination of crossing, but lower than in intraspecific S. lycopersicum hybrids.
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Development of Nuclear Microsatellite Markers with Long (Tri-, Tetra-, Penta-, and Hexanucleotide) Motifs for Three Larch Species Based on the de novo Whole Genome Sequencing of Siberian Larch (Larix sibirica Ledeb.)
摘要
Siberian larch (Larix sibirica Ledeb.) is one of the major boreal tree species in Eurasia and has a considerable economic and ecological value. Despite that importance, the development and use of microsatellite markers in this species remain limited. Microsatellite markers are considered to be a valuable tool for estimation of population diversity and structure. Availability of a draft reference assembly of the Siberian larch genome allowed us to identify 1015 microsatellite loci or simple sequence repeats (SSRs) with tri-, tetra-, penta-, and hexanucleotide motifs. For 60 of them PCR primers were designed and tested for amplification in L. sibirica and for their within-genus transferability to L. gmelinii (Rupr.) Rupr. and L. cajanderi Mayr. Here, we present a set of 14 reliable and polymorphic new nuclear SSR markers that can be used for further population genetic studies, breeding programs, and timber origin identification.
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Animal Genetics
Hybrid Zone between the Sok and Serov Chromosomal Races of the Common Shrew Sorex araneus (Lipotyphla, Mammalia) in European Russia
摘要
Analysis of the frequencies of karyotypic variants in the hybrid zone between the Sok and Serov chromosomal races of the common shrew Sorex araneus revealed that the zone has a complex configuration. A large part of the contact zone is located in a monotonous mid taiga zone, where there are no significant barriers to limit dispersion of shrews. Another part of the zone runs along the Pechora River (Komi Republic). Analysis of distribution of the diagnostic chromosomes on a transect along the Pechora River showed that the hybrid zone could be described by opposing metacentric clines. Individuals of both pure Sok and Serov races, as well as F1 hybrids, were found only on the left bank of the Pechora River. The right bank was occupied only by the Serov race, and F1 hybrids were rare there. The observed number of interracial hybrids in the center of the zone does not differ from that expected in the case of random breeding. This allows us to define this zone as unimodal. The standard width of the zone is about 40 km. This is considerably higher than all known cases of hybrid zones with the same level of karyotypic differences between parental races: two pairs of diagnostic metacentric chromosomes with monobrachial homology. We discuss possible causes of this phenomenon.
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The First Attempt at Studying the Species Diversity of Fish in Lake Khanka Using DNA Barcoding Techniques
摘要
Lake Khanka is the largest lake in the northeastern part of Asia, being a valuable part of the resources of freshwater fisheries. Lake Khanka has a low value of endemism owing to the recent origin and connection to large river systems of the Amur and Ussuri. The list of fish species present in the lake has been constantly updated owing to invasions that occur both unintentionally and because of the introduction of hydrobionts to maximize the potential of natural productivity. In this regard, the Lake Khanka is a suitable testing ground for the development and implementation of complex methods for monitoring species diversity. The cases of invasion have become more frequent in the lake recently. Moreover, the introduction of some fish species for stabilization of relationships among communities and exhaustive utilization of the natural productivity is now being carried out, which makes challenging the development and implementation of powerful techniques for monitoring of the local fauna species diversity. For the first time, we present a complex approach to the solution of that problem. We collected 64 fish specimens from 16 species representing four families of ray-finned fishes and analyzed their taxonomy and species diversity using both classic methods and DNA barcoding techniques. Specimens have been genotyped based on the mitochondrial Co-1 gene marker. The mean values of K2P-corrected intraspecific genetic distances were 0.15 ± 0.01%; the distances between different species within the same genera were 4.08 ± 0.01%. Phylogenetic analysis revealed monophyletic origin of all species clusters with high support (98–100% of bootstrap values). Thus, reciprocal complement of morphological and genetic techniques for the purpose of species delimitation and high effectiveness of DNA barcoding in application for documentation of species diversity in Lake Khanka has been demonstrated. New molecular genetic data generally are in agreement with taxonomic relationships previously shown for these fish taxa, but an additional investigation is required to verify the composition of genus Acheilognathus in Lake Khanka.
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Relationship of Bovine Lymphocyte Antigen Genes with Clinical Mastitis Disease Using SSCP Technique
摘要
BoLA-A and BoLA-DRB3 are in class I and II genes of bovine lymphocyte antigen of immune system respectively which cattle express per haplotype. The aim of this study was to evaluate relationship of BoLA-A and BoLA-DRB3 polymorphisms with clinical mastitis disease using SSCP technique. In the current study, blood sampling was carried out from Holstein cattle (n = 50 susceptible and n = 50 resistant to clinical mastitis) and a random sampling was conducted from Iranian native cattle (Sarabi; n = 50). Amplification of exon 2 of BoLA-DRB3 and BoLA-A genes by specific primers was used for SSCP technique. SSCP technique successfully able to detect some pattern is related to clinical mastitis disease in BoLA-DRB3.2 region as well as genotype pattern of C was observed significantly (P < 0.05) in susceptible Holstein cattle in compared to others pattern. Also, B and Q genotypes patterns of SSCP were detected only in susceptible cattle. Also, SSCP results were showed 17 genotypes pattern in Holstein and 17 different genotypes pattern in Sarabi cattle in BoLA-DRB3.2 gene. Thus, our finding indicated that Sarabi breed comprises completely different allelic in the BoLA-DRB3.2 region compared to Holstein breed. Moreover, results of this study revealed that exon 2 of BoLA-A showed lack of polymorphism in both studied breed. This is the first study on characterization of exon 2 of BoLA-Agene using SSCP technique in bovine.
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A Study on the Effect of Prolactin Gene Variants on Milk Production Traits of Holstein Cattle
摘要
Recent studies aiming to improve the daily milk production of cattle using both genetic and environmental factors are extremely important. The aim of this study is to determine the possible relationships between daily milk production and polymorphic distribution of exon 3 region of the prolactin (PRL) gene, which is an important marker for selection. With this purpose, 155 Holstein cows were included in the study, and the demographic data of the cattle were recorded. Venous blood was collected from the jugular vein of cows in 2 tubes of 2 mL each containing EDTA for DNA isolation. Genomic DNA were isolated from these whole blood samples. The prolactin gene region of the cattle were identified using PCR/RFLP and Sanger DNA sequencing method. The genotype, allele frequencies and Hardy–Weinberg equilibrium were calculated using Arlequin version 3.5.1.3 package software. Accordingly, it was found that cows with genotype AA had statistically higher milk yield as compared to those with genotype AB and BB. Missense mutation, frameshift and silent mutations were detected in the prolactin gene exon 3. It was also found that cows with missense mutation had statistically lower milk fat percentage as compared to the others. Consequently, the effects of genotypic distribution and mutation in the prolactin gene on the milk production of Holstein cows, which is a special breed in terms of milk productivity, have been revealed.
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Human Genetics
Association between Allelic Variants of IL2, IL2RA, and IL7R Genes and Multiple Sclerosis
摘要
Multiple sclerosis is a chronic progressive disease of nervous system caused by a combination of genetic and environmental factors leading to the development of a complex of autoimmune and neurodegenerative processes. We performed the analysis of association between multiple sclerosis and polymorphic markers of interleukin-2 (IL2), interleukin-2 receptor alpha chain (IL2A) and interleukin-7 receptor alpha chain (IL7R) in the group of Russians, Tatars, and Bashkirs from the Republic of Bashkortostan (N = 1620). In the total study group, we detected the association of IL7R rs10624573*I (OR = 0.79, PBonf = 0.018) and rs1494558*T (OR = 1.44, PBonf = 2.33 × 10–4) variants with multiple sclerosis. When analyzed separately according to the ethnic origin, the association with IL7R rs1494558*T (OR = 1.49, PBonf = 0.005) remained significant in the group of Russians, and the association of IL7R rs10624573*I remained significant in the group of Bashkirs (OR = 0.56, PBonf = 0.02). We performed the multilocus analysis of association using the APSampler algorithm, and found seven combinations of the alleles and/or genotypes of the studied polymorphic loci, significantly associated with multiple sclerosis, most frequently including IL7R rs1494558 and IL7R rs10624573 allelic variants.
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An Analysis of the Associations of Polymorphic Variants of the LEPR (rs1137100), LRP5 (rs3736228), and LPL (rs320) Genes with the Risk of Developing Type 2 Diabetes Mellitus
摘要
Diabetes mellitus is a hereditary predisposed multifactorial disease. However, the genetic mechanisms of its development have not been fully revealed yet. We conducted a search for associations of polymorphic variants of the LEPR (rs1137100), LRP5 (rs3736228), and LPL (rs320) genes involved in the development of obesity with the development of type 2 diabetes mellitus. The association with development of the disease was established for the T allele of the LRP5 locus (rs3736228) (p = 0.029, OR = 1.46). The rs1137100 locus (p = 0.032) of the LEPR gene was shown to be associated with the body mass index (BMI), but it was not connected with the presence of type 2 diabetes mellitus. Risk markers of development of type 2 diabetes included the T allele of the rs3736228 locus of the LRP5 gene (OR = 1.74, p = 0.012) and the G allele of the rs320 locus of the LPL gene (OR = 1.39, p = 0.027). Statistically significant association was only found in the group of nonobese patients. A decrease in the level of low-density lipoprotein was observed in individuals with the TT genotype of the LPL locus (rs320) (p = 0.04). Individuals with the GT and GG genotypes of this locus had a lower cholesterol level (p = 0.027). A decrease in the level of BMI (p = 0.012) and a decrease in the concentration of triglycerides in the blood (p = 0.00000004) were detected in carriers of the CC genotype of the LRP5 rs3736228 locus.
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Mathematical Models and Methods
Quasi Linkage Equilibrium under Weak Two-Locus Viability Selection: I. Haploid Population with Diallelic Loci
摘要
A model of weak viability selection at two diallelic loci with standardization of approaches through the use of perturbation theory is examined. The estimate of the quasi-equilibrium value for the linkage disequilibrium coefficient D is analyzed, and results in terms of average effects in quantitative genetics and in terms of the theory of singular perturbations in mathematics are obtained. The approximation of a discrete-time model of a random mating population with non-overlapping generations under weak selection by ordinary differential equations is considered. Weak selection is considered as a perturbation of the model without selection. The resulting model is singularly perturbed; that is, fast (D) and slow (allele frequencies) variables can be distinguished. The first approximation equation for quasi-equilibrium of D is obtained using the first terms of the Taylor series expansion of the model functions. It coincides with the corresponding part of the system of the first approximation of the asymptotic series for solving singularly perturbed equations. The first approximation for quasi-equilibrium of D is D* = ε(p)\(\frac{\mu }{r}\)x(1 – x) y(1 – y), ε(p) ≡ v11(p) – v12(p) – v21(p) + v22(p), where μ is the intensity of selection, r is the recombination coefficient, ε(p) is the index of epistasis nonadditivity for the viabilities \({{{v}}_{{{{i}_{{\text{1}}}}{{i}_{{\text{2}}}}}}}\), x and y are the allele frequencies of the first and second locus, respectively. The evolution of a nonequilibrium state of the population actually takes place at quasi-equilibrium (as the result of the stage of fast variable D dynamics) and current values of slow x, y.
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Short Communications
Mutations in the Insulin Signaling Pathway Genes Affect Carbohydrate Level under Heat Stress in Drosophila melanogaster Females
摘要
The effect of the following insulin signaling pathway genes on carbohydrate content under normal and heat stress conditions in Drosophila melanogaster females is studied: transcription factor Forkhead box class O (dfoxo) and insulin-like peptide DILP6 (dilp6), which is synthesized in the fat body. The hypomorphic mutations dilp641 and foxoBG01018 are shown to result in an increase in glucose and trehalose levels under normal conditions. For the first time, a sharp decline in the expression level of dilp6 and dfoxo genes caused by these mutations is demonstrated not to prevent the increase in the levels of both sugars under heat stress, but reduce the intensity of this response.
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