Fertility differences between two wild-type Drosophila melanogaster lines correlate with differences in the expression of the Jheh1 gene, which codes for an enzyme degrading juvenile hormone

Juvenile hormone plays a "status quo" role in Drosophila melanogaster larvae, preventing the untimely metamorphosis, and performs a gonadotropic function in imagoes, ensuring the ovaries' preparedness for vitellogenesis. The decreased level of juvenile hormone results in reproductive disorders in D. melanogaster females including a delay in the oviposition onset and a fertility decrease. Another factor that can affect the insect reproduction is an infection with the maternally inherited symbiotic α-proteobacterium Wolbachia. The present study is devoted to the analysis of the expression of two juvenile hormone metabolism genes encoding enzymes of its synthesis and degradation, juvenile hormone acid O-methyltransferase ( jhamt) and juvenile hormone epoxide hydrase (Jheh1), respectively, in four wild-type D. melanogaster lines, two of them being infected with Wolbachia. Lines w153 and Bi90 were both derived from an individual wild-caught females infected with Wolbachia, while lines w153T and Bi90T were derived from them by tetracycline treatment and are free of infection. Line Bi90 is known to be infected with the Wolbachia strain wMel, and line w153, with the Wolbachia strain wMelPlus belonging to the wMelCS genotype. It was found that infection with either Wolbachia strain does not affect the expression of the studied genes. At the same time, it was shown that the w153 and w153T lines differ from the Bi90 and Bi90T lines by an increased level of the Jheh1 gene expression and do not differ in the jhamt gene expression level. Analysis of the fertility of these four lines showed that it does not depend on Wolbachia infection either, but differs between lines with different nuclear genotypes: in w153 and w153T, it is significantly lower than in lines Bi90 and Bi90T. The data obtained allow us to reasonably propose that the inter-line D. melanogaster polymorphism in the metabolism of the juvenile hormone is determined by its degradation (not by its synthesis) and correlates with the fertility level.

The Effect of Genotype Combinations of Wolbachia and Its Drosophila melanogaster Host on Fertility, Developmental Rate and Heat Stress Resistance of Flies

The best-known effect of the intracellular bacterium Wolbachia is its mostly negative influence on the reproduction of the host. However, there is evidence of a positive influence of Wolbachia on the host's resistance to stress, pathogens, and viruses. Here, we analyzed the effects of two Wolbachia strains belonging to wMel and wMelCS genotypes on D. melanogaster traits, such as fertility, survival under acute heat stress, and developmental rate. We found that D. melanogaster lines under study differ significantly in the above-mentioned characteristics, both when the natural infection was preserved, and when it was eliminated. One of Wolbachia strains, wMel, did not affect any of the studied traits. Another strain, wMelPlus, had a significant effect on the development time. Moreover, this effect is observed not only in the line in which it was discovered but also in the one it was transferred to. When transferred to a new line, wMelPlus also caused changes in survival under heat stress. Thus, it could be concluded that Wolbachia-Drosophila interaction depends on the genotypes of both the host and the symbiont, but some Wolbachia effects could depend not on the genotypes, but on the fact of recent transfer of the symbiont.

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder

Bacillus strains are ubiquitous in the environment and are widely used in the microbiological industry as valuable enzyme sources, as well as in agriculture to stimulate plant growth. The Bacillus genus comprises several closely related groups of species. The rapid classification of these remains challenging using existing methods. Techniques based on MALDI-TOF MS data analysis hold significant promise for fast and precise microbial strains classification at both the genus and species levels. In previous work, we proposed a geometric approach to Bacillus strain classification based on mass spectra analysis via the centroid method (CM). One limitation of such methods is the noise in MS spectra. In this study, we used a denoising autoencoder (DAE) to improve bacteria classification accuracy under noisy MS spectra conditions. We employed a denoising autoencoder approach to convert noisy MS spectra into latent variables representing molecular patterns in the original MS data, and the Random Forest method to classify bacterial strains by latent variables. Comparison of the DAE-RF with the CM method using the artificially noisy test samples showed that DAE-RF offers higher noise robustness. Hence, the DAE-RF method could be utilized for noise-robust, fast, and neat classification of Bacillus species according to MALDI-TOF MS data.

A GC-MS Chemotaxonomic Study on Lipophilic Compounds in the Bark of S. aucuparia subsp. sibirica Trees from the Population Growing in Akademgorodok, Novosibirsk (Russia)

Determination of chemotypes and of their role in the polymorphism of populations is an important field in the research on secondary metabolites of plants. In the present study, by gas chromatography coupled with mass spectrometry, the composition of bark extracts from rowan S. aucuparia subsp. sibirica was determined for 16 trees growing within Akademgorodok of Novosibirsk, with bark samples collected both in winter and summer. Among 101 fully or partially identified metabolites, there are alkanes, alkenes, linear alcohols, fatty acids and their derivatives, phenols and their derivatives, prunasin and its parent and derivative compounds, polyprenes and their derivatives, cyclic diterpenes, and phytosterols. These compounds were grouped according to their biosynthesis pathways. Cluster analysis revealed two groups among the bark samples collected in winter and three groups among bark samples collected in summer. The key determinants of this clustering are the biosynthesis of metabolites via the cyanogenic pathway (especially potentially toxic prunasin) and their formation via the phytosterol pathway (especially potentially pharmacologically useful lupeol). It follows from the results that the presence of chemotypes having sharply different profiles of metabolites in a population from a small geographic area invalidates the practice of general sampling to obtain averaged data when a population is described. From the standpoint of possible industrial use or plant selection based on metabolomic data, it is possible to select specific sets of samples containing a minimal amount of potentially toxic compounds and the largest amount of potentially useful substances.

Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley

Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.

[Geometric Approach to Phylogeographic Analysis Molecular Genetic Sequences: Principal Components and Dendrograms]

Currently, the search for manifestations of selection under the influence of the environment in molecular sequences is usually carried out within closely related species or at the intraspecific level. It is believed that at high taxonomic levels this is unpromising due to phylogenetic relationship. Cytochrome b amino acid sequences of 67 rodent and lagomorph species with known geographic coordinates were digitized using the AAindex database. Based on more than 200 thousand characters, the principal components were obtained. A well-known statistical method, which has not been previously used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and intertaxon variability and analyze them separately. The subfamily level was selected. For the second principal component (17.05% of intertaxon variability), a correlation with latitude was found (r = 0.561; n = 67; p < E-5). The clear division into two groups, revealed by the first principal component (39.48% of intertaxon variability), which does not coincide with the taxonomic one, indicates a possible physicochemical underlying cause for the differences between them. This requires further research.

Effects of Positive Fighting Experience and Its Subsequent Deprivation on the Expression Profile of Mouse Hippocampal Genes Associated with Neurogenesis

The hippocampus is known as the brain region implicated in visuospatial processes and processes associated with learning and short- and long-term memory. An important functional characteristic of the hippocampus is lifelong neurogenesis. A decrease or increase in adult hippocampal neurogenesis is associated with a wide range of neurological diseases. We have previously shown that in adult male mice with a chronic positive fighting experience in daily agonistic interactions, there is an increase in the proliferation of progenitor neurons and the production of young neurons in the dentate gyrus (in hippocampus), and these neurogenesis parameters remain modified during 2 weeks of deprivation of further fights. The aim of the present work was to identify hippocampal genes associated with neurogenesis and involved in the formation of behavioral features in mice with the chronic experience of wins in aggressive confrontations, as well as during the subsequent 2-week deprivation of agonistic interactions. Hippocampal gene expression profiles were compared among three groups of adult male mice: chronically winning for 20 days in the agonistic interactions, chronically victorious for 20 days followed by the 2-week deprivation of fights, and intact (control) mice. Neurogenesis-associated genes were identified whose transcription levels changed during the social confrontations and in the subsequent period of deprivation of fights. In the experimental males, some of these genes are associated with behavioral traits, including abnormal aggression-related behavior, an abnormal anxiety-related response, and others. Two genes encoding transcription factors (Nr1d1 and Fmr1) were likely to contribute the most to the between-group differences. It can be concluded that the chronic experience of wins in agonistic interactions alters hippocampal levels of transcription of multiple genes in adult male mice. The transcriptome changes get reversed only partially after the 2-week period of deprivation of fights. The identified differentially expressed genes associated with neurogenesis and involved in the control of a behavior/neurological phenotype can be used in further studies to identify targets for therapeutic correction of the neurological disturbances that develop in winners under the conditions of chronic social confrontations.

Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient

In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.

Creation of an Online Platform for Identification of Microorganisms: Peak Picking or Full-Spectrum Analysis

Identification of microorganisms by MALDI-TOF mass spectrometry is a very efficient method with high throughput, speed, and accuracy. However, it is significantly limited by the absence of a universal database of reference mass spectra. This problem can be solved by creating an Internet platform for open databases of protein spectra of microorganisms. Choosing the optimal mathematical apparatus is the pivotal issue for this task. In our previous study we proposed the geometric approach for processing mass spectrometry data, which represented a mass spectrum as a vector in a multidimensional Euclidean space. This algorithm was implemented in a Jacob4 stand-alone package. We demonstrated its efficiency in delimiting two closely related species of the Bacillus pumilus group. In this study, the geometric approach was realized as R scripts which allowed us to design a Web-based application. We also studied the possibility of using full spectra analysis (FSA) without calculating mass peaks (PPA), which is the logical development of the method. We used 74 microbial strains from the collections of ICiG SB RAS, UNIQEM, IEGM, KMM, and VGM as the models. We demonstrated that the algorithms based on peak-picking and analysis of complete data have accuracy no less than that of Biotyper 3.1 software. We proposed a method for calculating cut-off thresholds based on averaged intraspecific distances. The resulting database, raw data, and the set of R scripts are available online at https://icg-test.mydisk.nsc.ru/s/qj6cfZg57g6qwzN.

Young «oil site» of the Uzon Caldera as a habitat for unique microbial life

BACKGROUND

The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks.

RESULTS

The study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities.

CONCLUSIONS

There were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.

Genetic loci determining potato starch yield and granule morphology revealed by genome-wide association study (GWAS)

Background

It is well-documented that (bio)chemical reaction capacity of raw potato starch depends on crystallinity, morphology and other chemical and physical properties of starch granules, and these properties are closely related to gene functions. Preparative yield, amylose/amylopectin content, and phosphorylation of potato tuber starch are starch-related traits studied at the genetic level. In this paper, we perform a genome-wide association study using a 22K SNP potato array to identify for the first time genomic regions associated with starch granule morphology and to increase number of known genome loci associated with potato starch yield.

Methods

A set of 90 potato (Solanum tuberosum L.) varieties from the ICG “GenAgro” collection (Novosibirsk, Russia) was harvested, 90 samples of raw tuber starch were obtained, and DNA samples were isolated from the skin of the tubers. Morphology of potato tuber starch granules was evaluated by optical microscopy and subsequent computer image analysis. A set of 15,214 scorable SNPs was used for the genome-wide analysis. In total, 53 SNPs were found to be significantly associated with potato starch morphology traits (aspect ratio, roundness, circularity, and the first bicomponent) and starch yield-related traits.

Results

A total of 53 novel SNPs was identified on potato chromosomes 1, 2, 4, 5, 6, 7, 9, 11 and 12; these SNPs are associated with tuber starch preparative yield and granule morphology. Eight SNPs are situated close to each other on the chromosome 1 and 19 SNPs—on the chromosome 2, forming two DNA regions—potential QTLs, regulating aspect ratio and roundness of the starch granules. Thirty-seven of 53 SNPs are located in protein-coding regions. There are indications that granule shape may depend on starch phosphorylation processes. The GWD gene, which is known to regulate starch phosphorylation—dephosphorylation, participates in the regulation of a number of morphological traits, rather than one specific trait. Some significant SNPs are associated with membrane and plastid proteins, as well as DNA transcription and binding regulators. Other SNPs are related to low-molecular-weight metabolite synthesis, and may be associated with flavonoid biosynthesis and circadian rhythm-related metabolic processes. The preparative yield of tuber starch is a polygenic trait that is associated with a number of SNPs from various regions and chromosomes in the potato genome.

SNPs associated with barley resistance to isolates of Pyrenophora teres f. teres

BACKGROUND

Net blotch caused by Pyrenophra teres f. teres is a major foliar disease of barley. Infection can result in significant yield losses of susceptible cultivars of up to 40%. Of the two forms of net blotch (P. teres f. teres and P. teres f. maculata), P. teres f. teres (net form of net blotch) is the dominant one in Russia. The goal of the current study was to identify genomic regions associated with seedling resistance to several pathotypes of the net form of net blotch in Siberian spring barley genotypes. For this, a genome-wide association study of a Siberian barley collection, genotyped with 50 K Illumina SNP-chip, was carried out.

RESULTS

Seedling resistance of 94 spring barley cultivars and lines to four Pyrenophora teres f. teres isolates (S10.2, K5.1, P3.4.0, and A2.6.0) was investigated. According to the Tekauz rating scale, 25, 21, 14, and 14% of genotypes were highly resistant, and 19, 8, 9, and 16% of genotypes were moderate-resistant to the isolates S10.2, K5.1, P3.4.0, and A2.6.0, respectively. Eleven genotypes (Alag-Erdene, Alan-Bulag, L-259/528, Kedr, Krymchak 55, Omsky golozyorny 2, Omsky 13709, Narymchanin, Pallidum 394, Severny and Viner) were resistant to all studied isolates. Nine additional cultivars (Aley, Barkhatny, Belogorsky, Bezenchuksky 2, Emelya, G-19980, Merit 57, Mestny Primorsky, Slavaynsky) were resistant to 3 of the 4 isolates. The phenotyping and genotyping data were analysed using several statistical models: GLM + Q, GLM + PCA, GLM + PCA + Q, and the MLM + kinship matrix. In total, 40 SNPs in seven genomic regions associated with net blotch resistance were revealed: the region on chromosome 1H between 57.3 and 62.8 cM associated with resistance to 2 isolates (to P3.4.0 at the significant and K5.1 at the suggestive levels), the region on chromosome 6H between 52.6 and 55.4 cM associated with resistance to 3 isolates (to P3.4.0 at the significant and K5.1 and S10.2 at the suggestive levels), three isolate-specific significant regions (P3.4.0-specific regions on chromosome 2H between 71.0 and 74.1 cM and on chromosome 3H between 12.1 and 17.4 cM, and the A2.6.0-specific region on chromosome 3H between 50.9 and 54.8 cM), as well as two additional regions on chromosomes 2H (between 23.2 and 23.8 cM, resistant to S10.2) and 3 (between 135.6 and 137.5 cM resistant to K5.1) with suggestive SNPs, coinciding, however, with known net blotch resistance quantitative trait loci (QTLs) at the same regions.

CONCLUSIONS

Seven genomic regions on chromosomes 1H, 2H, 3H, and 6H associated with the resistance to four Pyrenophora teres f. teres isolates were identified in a genome-wide association study of a Siberian spring barley panel. One novel isolate-specific locus on chromosome 3 between 12.1 and 17.4 cM was revealed. Other regions identified in the current study coincided with previously known loci conferring resistance to net blotch. The significant SNPs revealed in the current study can be converted to convenient PCR markers for accelerated breeding of resistant barley cultivars.

The differences in brain stem transcriptional profiling in hypertensive ISIAH and normotensive WAG rats

BACKGROUND

The development of essential hypertension is associated with a wide range of mechanisms. The brain stem neurons are essential for the homeostatic regulation of arterial pressure as they control baroreflex and sympathetic nerve activity. The ISIAH (Inherited Stress Induced Arterial Hypertension) rats reproduce the human stress-sensitive hypertensive disease with predominant activation of the neuroendocrine hypothalamic-pituitary-adrenal and sympathetic adrenal axes. RNA-Seq analysis of the brain stems from the hypertensive ISIAH and normotensive control WAG (Wistar Albino Glaxo) rats was performed to identify the differentially expressed genes (DEGs) and the main central mechanisms (biological processes and metabolic pathways) contributing to the hypertensive state in the ISIAH rats.

RESULTS

The study revealed 224 DEGs. Their annotation in databases showed that 22 of them were associated with hypertension and blood pressure (BP) regulation, and 61 DEGs were associated with central nervous system diseases. In accordance with the functional annotation of DEGs, the key role of hormonal metabolic processes and, in particular, the enhanced biosynthesis of aldosterone in the brain stem of ISIAH rats was proposed. Multiple DEGs associated with several Gene Ontology (GO) terms essentially related to modulation of BP were identified. Abundant groups of DEGs were related to GO terms associated with responses to different stimuli including response to organic (hormonal) substance, to external stimulus, and to stress. Several DEGs making the most contribution to the inter-strain differences were detected including the Ephx2, which was earlier defined as a major candidate gene in the studies of transcriptional profiles in different tissues/organs (hypothalamus, adrenal gland and kidney) of ISIAH rats.

CONCLUSIONS

The results of the study showed that inter-strain differences in ISIAH and WAG brain stem functioning might be a result of the imbalance in processes leading to the pathology development and those, exerting the compensatory effects. The data obtained in this study are useful for a better understanding of the genetic mechanisms underlying the complexity of the brain stem processes in ISIAH rats, which are a model of stress-sensitive form of hypertension.

Starch phosphorylation associated SNPs found by genome-wide association studies in the potato (Solanum tuberosum L.)

Background

The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures and shear rates and has higher water capacity. The genetic improvement of phosphate content in potato starch by selection or engineering would allow the production of phosphorylated starch in a natural, environmentally friendly way without chemicals. The aim of the current research is to identify genomic SNPs associated with starch phosphorylation by carrying out a genome-wide association study in potatoes.

Results

A total of 90 S. tuberosum L. varieties were used for phenotyping and genotyping. The phosphorus content of starch in 90 potato cultivars was measured and then statistically analysed. Principal component analysis (PCA) revealed that the third and eighth principal components appeared to be sensitive to variation in phosphorus content (p = 0.0005 and p = 0.002, respectively). PC3 showed the correlation of starch phosphorus content with allelic variations responsible for higher phosphorylation levels, found in four varieties. Similarly, PC8 indicated that hybrid 785/8–5 carried an allele associated with high phosphorus content, while the Impala and Red Scarlet varieties carried alleles for low phosphorus content. Genotyping was carried out using an Illumina 22 K SNP potato array. A total of 15,214 scorable SNPs (71.7% success rate) was revealed. GWAS mapping plots were obtained using TASSEL based on several statistical models, including general linear models (GLMs), with and without accounting for population structure, as well as MLM. A total of 17 significant SNPs was identified for phosphorus content in potato starch, 14 of which are assigned to 8 genomic regions on chromosomes 1, 4, 5, 7, 8, 10, and 11. Most of the SNPs identified belong to protein coding regions; however, their allelic variation was not associated with changes in protein structure or function.

Conclusions

A total of 8 novel genomic regions possibly associated with starch phosphorylation on potato chromosomes 1, 4, 5, 7, 8, 10, and 11 was revealed. Further validation of the SNPs identified and the analysis of the surrounding genomic regions for candidate genes will allow better understanding of starch phosphorylation biochemistry. The most indicative SNPs may be useful for developing diagnostic markers to accelerate the breeding of potatoes with predetermined levels of starch phosphorylation.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0729-9) contains supplementary material, which is available to authorized users.

Quantitative characteristics of pubescence in wheat (Triticum aestivum L.) are associated with photosynthetic parameters under conditions of normal and limited water supply

Density and length of leaf pubescence are important factors of diversity in the response to water deficiency among wheat genotypes. Many studies evidence an important protective value of leaf hairiness in plants, especially under the conditions of drought, thermal loads and increased solar radiation. However, the physiological and adaptive roles of such traits in cereals, including cultivated plants, have not been sufficiently studied to date. The aim of this work was to study the association of morphological characteristics of leaves with parameters of gas exchange and chlorophyll fluorescence in wheat lines carrying a genetically different leaf hairiness. Isogenic and inter-varietal substitution wheat lines were used, carrying various combinations of dominant and recessive alleles of the known genes. A quantitative assessment of the pubescence was carried out in contrasting watering conditions to establish the physiological role of this trait in adaptation to drought. With the help of a portable system for studying the gas exchange and chlorophyll fluorescence, ten parameters of photosynthesis were studied, as well as morphological features of leaves and shoot biomass. It was found that gas exchange parameters are inversely proportional to the density and length of trichomes. In drought conditions, the trichome density increased and the length of trichomes decreased under the observed decrease in the level of gas exchange. A similar dependence was observed for the level of non-photochemical quenching of chlorophyll fluorescence. Under optimal conditions, the poorly haired cultivars exhibited a higher biomass than the densely haired. However, under water deficiency they significantly reduced the biomass and showed a low value of the tolerance index.

Identification of 50 K Illumina-chip SNPs associated with resistance to spot blotch in barley

BACKGROUND

Spot blotch, caused by Cochliobolus sativus, is one of the most widespread and harmful diseases in barley. Identification of genetic loci associated with resistance to C. sativus is of importance for future marker-assisted selection. The goal of the current study was to identify loci conferring seedling resistance to two different pathotypes of C. sativus in the Siberian spring barley core collection.

RESULTS

A total of 96 spring barley cultivars and lines were phenotyped at the seedling stage with two C. sativus isolates (Kr2 and Ch3). According to the Fetch-Steffenson rating scale 16%/17% of genotypes were resistant and 26%/30% were moderate-resistant to the Kr2/Ch3 isolates respectively. A total of 94 genotypes were analyzed with the barley 50 K Illumina Infinium iSELECT assay. From 44,040 SNPs, 40,703 were scorable, from which 39,140 were polymorphic. 27,319 SNPs passed filtering threshold and were used for association mapping. Data analysis by GLM revealed 48 and 41 SNPs for Kr2 and Ch3 isolates, respectively. After application of 5% Bonferroni multiple test correction, only 3 and 27 SNPs were identified, respectively. A total of three genomic regions were associated with the resistance. The region on chromosome 3H associated with Ch3-resistance was expanded between markers SCRI_RS_97417 and JHI-Hv50k-2016-158003 and included 11 SNPs, from which JHI-Hv50k-2016-157070, JHI-Hv50k-2016-156842 had the lowest p-values. These two SNPs were also significant in case of Kr2 isolate. The region on chromosome 2H included 16 loci (7 of them with the lowest p-values were tightly linked to BOPA2_12_11504). Three loci corresponding to this region had suggestive p-values in case of Kr2 tests, so the locus on chromosome 2H may also contribute to resistance to Kr2 isolate. The third region with significant p-value in case of Kr2 tests was identified on chromosome 1H at the locus JHI-Hv50k-2016-33568.

CONCLUSIONS

Three genomic regions associated with the resistance to one or both isolates of C. sativus were identified via screening of the Siberian spring barley core collection. Comparison of their location with QTLs revealed previously either with biparental mapping populations studies or with GWAS of distinct germplasm and other isolates, demonstrated that resistance to isolates Kr2 and Ch3 is conferred by known spot blotch resistance loci. Information on SNPs related can be used further for development of DNA-markers convenient for diagnostics of resistance-associated alleles in barley breeding programs.

Molecular determinants of the adrenal gland functioning related to stress-sensitive hypertension in ISIAH rats

Background

The adrenals are known as an important link in pathogenesis of arterial hypertensive disease. The study was directed to the adrenal transcriptome analysis in ISIAH rats with stress-sensitive arterial hypertension and predominant involvement in pathogenesis of the hypothalamic-pituitary-adrenal and sympathoadrenal systems.

Results

The RNA-Seq approach was used to perform the comparative adrenal transcriptome profiling in hypertensive ISIAH and normotensive WAG rats. Multiple differentially expressed genes (DEGs) related to different biological processes and metabolic pathways were detected.

The discussion of the results helped to prioritize the several DEGs as the promising candidates for further studies of the genetic background underlying the stress-sensitive hypertension development in the ISIAH rats. Two of these were transcription factor genes (Nr4a3 and Ppard), which may be related to the predominant activation of the sympathetic-adrenal medullary axis in ISIAH rats. The other genes are known as associated with hypertension and were defined in the current study as DEGs making the most significant contribution to the inter-strain differences. Four of them (Avpr1a, Hsd11b2, Agt, Ephx2) may provoke the hypertension development, and Mpo may contribute to insulin resistance and inflammation in the ISIAH rats.

Conclusions

The study strongly highlighted the complex nature of the pathogenesis of stress-sensitive hypertension. The data obtained may be useful for identifying the common molecular determinants in different animal models of arterial hypertension, which may be potentially used as therapeutic targets for pharmacological intervention.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3354-2) contains supplementary material, which is available to authorized users.

The gene-expression profile of renal medulla in ISIAH rats with inherited stress-induced arterial hypertension

Background

The changes in the renal function leading to a reduction of medullary blood flow can have a great impact on sodium and water homeostasis and on the long-term control of arterial blood pressure. The RNA-Seq approach was used for transcriptome profiling of the renal medulla from hypertensive ISIAH and normotensive WAG rats to uncover the genetic basis of the changes underlying the renal medulla function in the ISIAH rats being a model of the stress-sensitive arterial hypertension and to reveal the genes which possibly may contribute to the alterations in medullary blood flow.

Results

Multiple DEGs specifying the function of renal medulla in ISIAH rats were revealed. The group of DEGs described by Gene Ontology term ‘oxidation reduction’ was the most significantly enriched one. The other groups of DEGs related to response to external stimulus, response to hormone (endogenous) stimulus, response to stress, and homeostatic process provide the molecular basis for integrated responses to homeostasis disturbances in the renal medulla of the ISIAH rats. Several DEGs, which may modulate the renal medulla blood flow, were detected. The reduced transcription of Nos3 pointed to the possible reduction of the blood flow in the renal medulla of ISIAH rats.

Conclusions

The generated data may be useful for comparison with those from different models of hypertension and for identifying the common molecular determinants contributing to disease manifestation, which may be potentially used as new pharmacological targets.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0462-6) contains supplementary material, which is available to authorized users.

Genome-wide transcriptome analysis of hypothalamus in rats with inherited stress-induced arterial hypertension

Background

The hypothalamus has an important role in the onset and maintenance of hypertension and stress responses. Rats with inherited stress-induced arterial hypertension (ISIAH), reproducing the human stress-sensitive hypertensive state with predominant involvement of the neuroendocrine hypothalamic-pituitary-adrenal and sympathoadrenal axes, were used for analysis of the hypothalamus transcriptome.

Results

RNA-seq analysis revealed 139 genes differentially expressed in the hypothalami of hypertensive ISIAH and normotensive Wistar Albino Glaxo (WAG) rats. According to the annotation in databases, 18 of the differentially expressed genes (DEGs) were associated with arterial hypertension. The Gene Ontology (GO) functional annotation showed that these genes were related to different biological processes that may contribute to the hypertension development in the ISIAH rats. The most significantly affected processes were the following: regulation of hormone levels, immune system process, regulation of response to stimulus, blood circulation, response to stress, response to hormone stimulus, transport, metabolic processes, and endocrine system development. The most significantly affected metabolic pathways were those associated with the function of the immune system and cell adhesion molecules and the metabolism of retinol and arachidonic acid. Of the top 40 DEGs making the greatest contribution to the interstrain differences, there were 3 genes (Ephx2, Cst3 and Ltbp2) associated with hypertension that were considered to be suitable for further studies as potential targets for the stress-sensitive hypertension therapy. Seven DEGs were found to be common between hypothalamic transcriptomes of ISIAH rats and Schlager mice with established neurogenic hypertension.

Conclusions

The results of this study revealed multiple DEGs and possible mechanisms specifying the hypothalamic function in the hypertensive ISIAH rats. These results provide a basis for further investigation of the signalling mechanisms that affect hypothalamic output related to stress-sensitive hypertension development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0307-8) contains supplementary material, which is available to authorized users.

The role of environmental factors for the composition of microbial communities of saline lakes in the Novosibirsk region (Russia)

Background

Nothing is currently known about microbial composition of saline lakes of the Novosibirsk region and its dependence on physical-chemical parameters of waters. We studied the structure of microbial communities of saline lakes of the Novosibirsk region and the effect of physical-chemical parameters of waters on microbial communities of these lakes.

Results

According to the ion content, the lakes were classified either as chloride or chloride-sulfate types. Water salinity ranges from 4.3 to 290 g L⁻¹. Many diverse microbial communities were found. Filamentous and colonial Cyanobacteria of the genera Scytonema, Aphanocapsa, and/or filamentous Algae dominated in littoral communities. Spatial and temporal organization of planktonic microbial communities and the quantities of Archaea and Bacteria were investigated using fluorescent in situ hybridization. We have found that the dominant planktonic component is represented by Archaea, or, less frequently, by Bacteria. Various phylogenetic groups (Bacteria, Archaea, Algae, and Cyanobacteria) are nonuniformly distributed. The principal component analysis was used to detect environmental factors that affect microorganism abundance. We found the principal components responsible for 71.1 % of the observed variation. It was demonstrated that two-block partial least squares was a better method than principal component analysis for analysis of the data. We observed general relationships between microbial abundance and water salinity.

Conclusions

We have performed the first-ever study of the structure of the microbial communities of eleven saline lakes in the Novosibirsk region along with their physical-chemical parameters of waters. Our study demonstrates that saline lakes in the Novosibirsk region contain a unique microbial communities that may become a prolific source of microorganisms for fundamental and applied studies in various fields of ecology, microbiology, geochemistry, and biotechnology, and deserve further metagenomic investigation.

Asynchrony between Host Plant and Insects-Defoliator within a Tritrophic System: The Role of Herbivore Innate Immunity

The effects of asynchrony in the phenology of spring-feeding insect-defoliators and their host plants on insects’ fitness, as well as the importance of this effect for the population dynamics of outbreaking species of insects, is a widespread and well-documented phenomenon. However, the spreading of this phenomenon through the food chain, and especially those mechanisms operating this spreading, are still unclear. In this paper, we study the effect of seasonally declined leafquality (estimated in terms of phenolics and nitrogen content) on herbivore fitness, immune parameters and resistance against pathogen by using the silver birch Betula pendula—gypsy moth Lymantria dispar—nucleopolyhedrovirus as the tritrophic system. We show that a phenological mismatch induced by the delay in the emergence of gypsy moth larvae and following feeding on mature leaves has negative effects on the female pupal weight, on the rate of larval development and on the activity of phenoloxidase in the plasma of haemolymph. In addition, the larval susceptibility to exogenous nucleopolyhydrovirus infection as well as covert virus activation were both enhanced due to the phenological mismatch. The observed effects of phenological mismatch on insect-baculovirus interaction may partially explain the strong and fast fluctuations in the population dynamics of the gypsy moth that is often observed in the studied part of the defoliator area. This study also reveals some indirect mechanisms of effect related to host plant quality, which operate through the insect innate immune status and affect resistance to both exogenous and endogenous virus.

[Correspondence analysis and combination of molecular genetic and morphological data in zoological systematics]

A new algorithmic approach is proposed for correspondence analysis of different types of data in zoological systematics. The algorithm is tested on actual data. A high degree of correspondence is shown for morphometric and genetic distances in the tested set of species. Two directions of variation in both character spaces have clearly appeared. The first direction discriminates families; the second discriminates orders. The characters responsible for these differences have been revealed. After uniting both distance matrixes, the morphological one and the molecular genetic one, into a single matrix, and displaying the summarized distances between species on a plane, the configuration of species remained principally unchanged. The principal directions of variations were preserved and marked the differences between orders, families, and genera.

[Patterns of transposable elements distribution on the Drosophila melanogaster polytene chromosomes before and after selection for a quantitative trait]

The effect of selection for radius vein length on the distribution of hybridization sites of the P and hobo transposons and the mdgl and mdg2 retrotransposons on polytene chromosomes of Drosophila melanogaster salivary glands was studied. The patterns of these transposable elements (TEs) distribution were polymorphic in both the parental strain and selected strains. The similarity in mdg1 and mdg2 patterns between strains selected in one direction was closer than between strains selected in opposite directions, but the selected strains were closer to each other than to the parental strain regardless of selection direction. No mdg2 hybridization sites that would be absent in the control were found in the selected strains. There were more mdg2 and hobo hybridization sites in the strains selected in the (+) direction than in the (-) direction. The mobility of hobo copies in the strains studied correlated with the presence of its full-sized copy in the genome. The polymorphism of all TEs studied except for mdgl was greater for strains selected in the (+) direction that in the (-) direction. These facts suggest that some TEs migrate over the genome independently of selection, and others are markers of evolutionary events rather than their causes.

SNPs in the HIV-1 TATA box and the AIDS pandemic

Evolutionary trends have been examined in 146 HIV-1 forms (2662 copies, 2311 isolates) polymorphic for the TATA box using the "DNA sequence-->affinity for TBP" regression (TBP is the TATA binding protein). As a result, a statistically significant excess of low-affinity TATA box HIV-1 variants corresponding to a low level of both basal and TAT-dependent expression and, consequently, slow replication of HIV-1 have been detected. A detailed analysis revealed that the excess of slowly replicating HIV-1 is associated with the subtype E-associated TATA box core sequence "CATAAAA". Principal Component Analysis performed on 2662 HIV-1 TATA box copies in 70 countries revealed the presence of two principal components, PC1 (75.7% of the variance) and PC2 (23.3% of the variance). They indicate that each of these countries is specifically associated with one of the following trends in HIV-1 evolution: neutral drift around the normal TATA box; neutral drift around the slowly replicating TATA box core sequence (phylogenetic inertia); an adaptive increase in the frequency of the slowly replicating form.

Rats with inherited stress-induced arterial hypertension (ISIAH strain) display specific quantitative trait loci for blood pressure and for body and kidney weight on chromosome 1

1. The aim of the present study was to scan chromosome 1 in the hypertensive 'inherited stress-induced arterial hypertension' (ISIAH) rat strain for the quantitative trait loci (QTL) that control basal and stress-induced arterial blood pressure (ABP) levels and weight traits. 2. Two F(2) populations of 3-4- and 6-month-old male rats derived from a cross between the normotensive Wistar albino Glaxo (WAG) and hypertensive ISIAH rats were used in the search for the QTL. To identify the QTL for blood pressure (basal and under stress) and weight traits (bodyweight, as well as the weight of the adrenals, kidney and heart), 12 polymorphic markers covering a span of 234.6 Mb on chromosome 1 were analysed. 3. In 3-4-month-old rats, QTL were found for bodyweight in the vicinity of the D1Rat76 marker (230.6 Mb; P = 0.0019; logarithm of odds (LOD) score 3.23) and for relative kidney weight in the vicinity of the D1Rat117 marker (219.3 Mb; P = 0.000992; LOD score 3.41). No QTL for blood pressure were detected on chromosome 1 in the 3-4-month-old population. 4. In 6-month-old rats, a QTL for basal ABP in the region spanning 168.0-250.4 Mb, with two peaks around the markers D1Rat168 (204.8 Mb; P = 0.00087; LOD score 3.42) and D1Rat76 (P = 0.0006; LOD score 3.34), was described. A novel QTL was found in the D1Rat54-D1Rat168 region for stress-induced blood pressure (P = 0.0014; LOD score 3.08). 5. The results provide support for the existence of age-dependent differences in the genetic control of ABP and weight traits. Chromosome 1 was characterized by four QTL: for bodyweight and relative kidney weight in 3-4-month-old F(2) (ISIAH yen WAG) rats and basal ABP and ABP under emotional (restraint) stress conditions in 6-month-old F(2) rats. The QTL for stress-induced ABP seems to be novel and specific to the ISIAH rat strain.

A new approach to the study of genetic variability of complex characters

A new approach to multivariate genetic analysis of complex organismal traits is developed. It is based on examination of the distribution of parental strains and the F1 and F2 hybrids in a multidimensional space, and the determination of the directions corresponding to heterozygosity, epistatic and additive gene effects. The effect of heterozygosity includes variability produced by interaction between and within heterozygous loci. The additive gene effects and the remaining epistatic interactions between the homozygous loci can be visualized separately from the effects of heterozygosity by an appropriate projection of the points in multidimensional space. In all, 20 morphological, physiological and behavioural characters and 21 craniometric measures were studied in crosses between two laboratory rat strains. Linear combinations of craniometric and of morphophysiological characters with a high narrow-sense heritability could be identified. These combinations characterized the organismal stress response, which had been selected for in one of the strains. The prospects for the practical application of the new approach and also for the evaluation of the contribution of the genetic diversity to phenotypic variability in animals in natural populations are discussed.

[Localization of genes, determining quantitative traits in wheat: amendment to the "catalog of chromosomal mapping of genes in domestic cultivars of wheat"]

An amendment to the catalog of chromosome location of genes in Russian wheat cultivars was constructed with the published data of the recent decade. The results of chromosomal localization were summarized and analyzed by methods of multivariate statistics. Chromosomes critical for 40 quantitative traits under study proved to cluster according to their homeology, i.e., by homeological groups. The hypotheses providing an explanation for this finding are considered. It is suggested that quantitative traits are similarly controlled by genes located on homeological chromosomes in common wheat, making it possible to isolate a limited number of major genes for each particular quantitative trait.

[Use of the major components methods in epidemiological studies]

When multifactorial processes are analyzed, it is most rational to use the methods of multidimensional statistical analysis, including the major components methods. This method is rather new in epidemiological surveys. Its advantage is that it may be used to get information that is difficult derived by other ways. Noteworthy is the versatility of the method, which lies in that the problems of analysis, prediction, and classification (stratification) of temporal series are solved by using actually the same techniques. How to apply the major components method are considered by using an example of investigating the general trends in the development of an epidemic tuberculous process in a specific area. Statistical data on tuberculosis morbidity in the areas of the Novosibirsk Region were employed as the initial material.

[Informative value of the major component technique in the assessment of the epidemic tuberculosis situation]

The paper describes a method for comprehensive analysis of the epidemic situation which is based on the major component technique. The algorithm proposed for comprehensive assessment is highly effective in the retrospective analysis and in the analysis of the current material which includes a great deal of various characteristics that are at first sight occasionally unrelated. The use of the algorithm is shown by the example of analyzing 19 statistical variables that characterize the epidemic situation and different aspects of the work of a tuberculosis-controlling facility in 30 districts of the Novosibirsk Region in a period of 15 years (1985-1999). During processing, the variables fall into two groups: a group of variables that characterize the quality of antituberculosis work and a group of those reflecting the epidemic situation, which were used to divide the districts of the region into several groups.

[Dynamics of major constituents of tuberculosis morbidity in the population of Novosibirsk region]

After processing the dynamic series of tuberculosis morbidity in the population of the Novosibirsk region by the smooth component methods, two major constituents were defined in morbidity dynamics. In total, they make up about half the total variability of tuberculosis morbidity. The first constituent is due to socioeconomic causes that are common for the whole region. The second one shows rather evident 10-year fluctuations. The same 10-year fluctuations are observed in the dynamics of tuberculosis morbidity among the cattle of the Novosibirsk region by out-stripping that in the population in the northern and eastern areas by 1-3 years.

[An analysis of the space-time changes in tick-borne encephalitis morbidity in Novosibirsk Province]

The authors analyzed data on space and time changes in tick-borne encephalitis (TBE) morbidity in Novosibirsk Province from 1955 to 1995 by using the method of principal components (PCs). The first PC (26.0% of total variance) was linearly represented. Judging the the loading scores, this component can be interpreted as redistribution of TBE morbidity rates between southeastern taiga foci in Salair foothills and northern forest-steppe foci in vicinity of the Ob' River valley. The second PC (22.6% of total variance) can be read as regional differences with long-term cyclic changes. The first PC correlated with the annual average temperature (r = 0.45; P < 0.05) and this correlation can be determined by global climate warming-up.

[Helminthiases among the population of northwestern Siberia. 1. Opisthorchiasis and mixed invasion in the native inhabitants of the Ob River basin and their clinical course]

The use of multifactor statistic analysis for screening population of the northern part of the Ob river basin for helminthiasis allowed the authors to reveal a significant feedback between manifested opisthorchiasis and other types of this disease course in both sexes. The main component analysis indicates that the tentatively control group of males is presented by adolescents (14-17 years old) who are likely to be infected with Opisthorchis without evidence of its clinical manifestations. The correlation analysis demonstrated also a direct relationship between the age and manifest opisthorchiasis, as well as double mixed invasion of males (r-0.15 and 0.26, p less than 0.05 and 0.01, respectively). The first three main components explain about 55% variance in the correlation matrix of initial parameters and allow to reveal the variance source, taking into account, along with differentiation of 4 groups of opisthorchiasis patients, also the age- and sex-dependent combination of opisthorchiasis with other helminthic invasions.

[Multifaceted analysis of the interactions of morphophysiologic signs and ischemic ECG changes (a population study)]

Relationships between serum lipid and lipoprotein levels, arterial blood pressure, body weight and age, on the one hand, and coronary heart disease (CHD), on the other, were investigated by means of the main constituents analysis in a Northern Khant population. The pattern of relationship between the parameters in question was similar, by the first main constituent, in males and females, and suggested their age-dependence, unrelated to CHD. The second constituent, as a sum total of the effects of another factor, showed an unbalance between body weight and blood lipids, which was correlated with CHD in males and remained indifferent with respect to CHD in females.

[Factor analysis of rat behavior in the open-field test]

Method of major components, a variety of factor analysis, was used for evaluation of rats behaviour motivational structure in the open field test. 40 outbred rats of Wistar line (20 males and females) were examined in which 22 behaviour characteristics were studied. It was shown that a greater part (60%) of rats individual behaviour variability in the open field test was determined by the action of three major components (factors), which were defined as "investigation", "fear" and "shifted activity". Factor structure was studied of main characteristics of behaviour, recorded in the open field test. The use of factor analysis allowed to carry out animals classification on the basis of their disposition in coordinates of the obtained major components.