Interplay between RNA interference and heat shock response systems in Drosophila melanogaster.

The genome expression pattern is strongly modified during the heat shock response (HSR) to form an adaptive state. This may be partly achieved by modulating microRNA levels that control the expression of a great number of genes that are embedded within the gene circuitry. Here, we investigated the cross-talk between two highly conserved and universal house-keeping systems, the HSR and microRNA machinery, in Drosophila melanogaster We demonstrated that pronounced interstrain differences in the microRNA levels are alleviated after heat shock (HS) to form a uniform microRNA pattern. However, individual strains exhibit different patterns of microRNA expression during the course of recovery. Importantly, HS-regulated microRNAs may target functionally similar HS-responsive genes involved in the HSR. Despite the observed general downregulation of primary microRNA precursor expression as well as core microRNA pathway genes after HS, the levels of many mature microRNAs are upregulated. This indicates that the regulation of miRNA expression after HS occurs at transcriptional and post-transcriptional levels. It was also shown that deletion of all hsp70 genes had no significant effect on microRNA biogenesis but might influence the dynamics of microRNA expression during the HSR.

A sustained deficiency of mitochondrial respiratory complex III induces an apoptotic cell death through the p53-mediated inhibition of pro-survival activities of the activating transcription factor 4.

Generation of energy in mitochondria is subjected to physiological regulation at many levels, and its malfunction may result in mitochondrial diseases. Mitochondrial dysfunction is associated with different environmental influences or certain genetic conditions, and can be artificially induced by inhibitors acting at different steps of the mitochondrial electron transport chain (ETC). We found that a short-term (5 h) inhibition of ETC complex III with myxothiazol results in the phosphorylation of translation initiation factor eIF2α and upregulation of mRNA for the activating transcription factor 4 (ATF4) and several ATF4-regulated genes. The changes are characteristic for the adaptive integrated stress response (ISR), which is known to be triggered by unfolded proteins, nutrient and metabolic deficiency, and mitochondrial dysfunctions. However, after a prolonged incubation with myxothiazol (13-17 h), levels of ATF4 mRNA and ATF4-regulated transcripts were found substantially suppressed. The suppression was dependent on the p53 response, which is triggered by the impairment of the complex III-dependent de novo biosynthesis of pyrimidines by mitochondrial dihydroorotate dehydrogenase. The initial adaptive induction of ATF4/ISR acted to promote viability of cells by attenuating apoptosis. In contrast, the induction of p53 upon a sustained inhibition of ETC complex III produced a pro-apoptotic effect, which was additionally stimulated by the p53-mediated abrogation of the pro-survival activities of the ISR. Interestingly, a sustained inhibition of ETC complex I by piericidine did not induce the p53 response and stably maintained the pro-survival activation of ATF4/ISR. We conclude that a downregulation of mitochondrial ETC generally induces adaptive pro-survival responses, which are specifically abrogated by the suicidal p53 response triggered by the genetic risks of the pyrimidine nucleotide deficiency.

Hyperfine splitting in positronium to O(α(7)m(e)): one photon annihilation contribution.

We present the complete result for the O(α7me) one photon annihilation contribution to the hyperfine splitting of the ground state energy levels in positronium. Numerically it increases the prediction of quantum electrodynamics by 217±1 kHz.

[Spatial organization of house-keeping genes in interphase nuclei].

Spatial organization of the eukaryotic genome is tightly connected to its functioning. In particular, the interaction of gene promoters with remote enhancer elements in active chromatin hubs, as well as the recruitment of genes to the common transcription factories plays an important role in regulation of gene transcription. Most of works related to the analysis of spatial interaction of genome regulatory elements relies on models of tissue-specific genes. Meanwhile, it remains unclear to which extent the spatial organization of chromosomes is guided by house-keeping genes that are transcribed in most of cell types and outnumber the transcribed tissue-specific genes. To address this question, we used the 4C technique to characterize genome-wide the spatial contacts of the chicken house-keeping genes CARHSP1 and TRAP1 situated on chromosome 14. The promoters of these genes had an increased frequency of interaction with chromosome regions enriched in CpG islands and binding motifs for the ubiquitous transcription factor Sp1, both of which mark promoters of house-keeping genes, and overall with transcriptionally active regions. By contrast, the analysis of interaction of a gene poor region of chromosome 14 revealed no such preferences. The evidence for the interaction of house-keeping gene promoters were also obtained in independent cytological experiments aimed at visualization of non-methylated CpG islands in individual nuclei of human cells, which showed clustering of CpG islands in the nuclear space. Altogether, the results of our work suggest that the interaction of house-keeping genes constitutes an important factor that determines the spatial organization of interphase chromosomes.

[Structure and evolution of junctions between inverted repeat and small single copy regions of chloroplast genome in non-core Caryophyllales].

The structure of junction between inverted repeat (IR) and small single copy (SSC) regions of chloroplast genome in the representatives of non-core Caryophyllales is investigated in this work. It was found that for two families - Polygonaceae and Plumbaginaceae - the extension of inverted region is characteristic. This extension is due to the duplication the part of ycf1 gene that is partly located in the small single copy region in plants with typical structure of IR/SSC junctions. Comparison of the position of IR/SSC junctions in different species of Polygonaceae has shown that their exact position is not correlated with the affinity of these species inferred from molecular and morphological data. Possible mechanisms leading to the change in position of IR/SSC junctions observed in this work are discussed.

Heavy-flavor contribution to Bhabha scattering.

We evaluate the last missing piece of the two-loop QED corrections to the high-energy electron-positron scattering cross section originating from the vacuum polarization by heavy fermions. The calculation is performed within a new approach applicable to a wide class of perturbative problems with mass hierarchy. The result is crucial for the high-precision physics program at existing and future e(+) e(-) colliders.

[Interaction of the BRACTEA gene with the TERMINAL FLOWER1, LEAFY, and APETALA1 genes during inflorescence and flower development in Arabidopsis thaliana].

The major Arabidopsis thaliana genes controlling the shoot architecture are TERMINAL FLOWER1 (TFL1), APETALA1 (AP1), and LEAFY (LFY). The BRACTEA (BRA) gene also codes for one of the key regulators of inflorescence development. The bra tfl1-11, bra lfy-5, and bra ap1-20 double mutants were analyzed morphologically, and expression of the TFL1, AP1, and LFY genes was studied in the bra mutant and wild-type plants. The BRA gene was found to positively regulate the TFL1 and AP1 genes after floral initiation, determining more than 70% of their total expression level. In floral meristem, the BRA gene prevented AP1 expression, restricting AP1 transcription to the perianth zone. Since flowers were completely converted into vegetative shoots in the bra lfy-5 double mutant, it was assumed that the BRA and LFY genes function redundantly and independently in floral initiation. The results demonstrate that BRA is one of the genes that determine the balance between maintenance of proliferative activity in apical meristem and floral development in its peripheral region; such a balance is necessary for indeterminate inflorescence development.

[Unusual alternations of floral organs in Paeonia: structure and possible mechanism of formation].

Morphological analysis of flowers was carried out in Paeonia cultivars. Some unusual alternations of floral organs were described: sepal-(petal-stamen) x N-carpel, where 2 < or = n < or = 4 (appearance of an additional zone of petal and stamen formation in the medial flower part). The identity of floral organs was not affected in the flowers with this unusual alternation. It was shown on the basis of mathematical simulation of the genes responsible for flower development that these alternations may be determined by increased pool of stem cells, which may lead to delayed termination of flower development.

Phylogeny of flowering plants by the chloroplast genome sequences: in search of a "lucky gene".

One of the most complicated remaining problems of molecular-phylogenetic analysis is choosing an appropriate genome region. In an ideal case, such a region should have two specific properties: (i) results of analysis using this region should be similar to the results of multigene analysis using the maximal number of regions; (ii) this region should be arranged compactly and be significantly shorter than the multigene set. The second condition is necessary to facilitate sequencing and extension of taxons under analysis, the number of which is also crucial for molecular phylogenetic analysis. Such regions have been revealed for some groups of animals and have been designated as "lucky genes". We have carried out a computational experiment on analysis of 41 complete chloroplast genomes of flowering plants aimed at searching for a "lucky gene" for reconstruction of their phylogeny. It is shown that the phylogenetic tree inferred from a combination of translated nucleotide sequences of genes encoding subunits of plastid RNA polymerase is closest to the tree constructed using all protein coding sites of the chloroplast genome. The only node for which a contradiction is observed is unstable according to the different type analyses. For all the other genes or their combinations, the coincidence is significantly worse. The RNA polymerase genes are compactly arranged in the genome and are fourfold shorter than the total length of protein coding genes used for phylogenetic analysis. The combination of all necessary features makes this group of genes main candidates for the role of "lucky gene" in studying phylogeny of flowering plants.

[Determination of type and spatial pattern formation of flower organs: dynamic model of development].

The mathematical model imitating floral organ spatial pattern formation (positioning) was developed. Computer experiments performed on its basis demonstrated that organ spatial pattern formation in typical crucifer flower occurred in successive order: medial sepals, carpels, lateral sepals, long stamens, petals and short stamens. The positioning was advanced in two directions, acropetally in the perianth and basipetally in the stamens and carpels. The organ type specifying and positioning take place non-simultaneously in different floral areas. The organ type specifying passed ahead of organ primordial spatial pattern formation. The modeling of flower development of several mutants demonstrated that arabidopsis genes AP2 and AG in addition to specifying floral organ types also determine the particular zones in the floral meristem for futur organ development. The AG gene controls the formation of basipetal patterning zones where the reproductive organs develop, AP2 maintains the proliferative activity in the floral meristem that form acropetal patterning zones where perianth organ develop.

[Effect of the ABRUPTUS/PINOID gene on expression of the LEAFY gene in Arabidopsis thaliana].

The nucleotide sequence was analyzed for the temperature-sensitive allele abruptus (abr), which distorts polar auxin transport (PAT) in the floral shoot. The mutation C-->T was found in the second exon and led to an amino acid substitution (glycin-->glutamic acid) in the conserved domain of protein kinase encoded by the ABRUPTUS/PINOID (ABR/PID) gene. RT--PCR revealed a 100-fold decrease in transcription of the LEAFY (LFY) gene in the abr mutant with high expressiveness of the mutant character; transcription of the fused LFY::GUS gene was also low in the mutant. The results agree with data of the phenotypic analysis of the abr lfy double mutant and testify to an important role of auxin gradients in regulating expression of the LFY gene.

[Basic principles of terminal flower formation].

Studies of efflorescences of the mutants bractea and terminal flower1 and double mutant bra tfl1 of Arabidoipsis thaliana (L.) Heynh. have shown that the presence of a developed leaf in the node preceding the terminal flower is a necessary condition for the formation of the terminal flower perianth. This means that perianth cannot develop in an abracteose efflorescence of terminal flower. The second necessary condition for the terminal flower formation is a sufficient level of expression of the genes responsible for floral morphogenesis. Combination of these two conditions suffices for the development of a terminal flower with perianth. Since the general principles of organization are close for most flower plants, it can be stated that if the abracteose efflorescence is terminated by a flower with perianth, this is a consequence of forcing the lateral flower into the terminal position.

[The role of gene tepal-like bract (TLB) in the separation between the bracts and perianth in Fagopyrum esculentum moench].

The morphological and genetic studies of the tlb mutant of common buckwheat Fagopyrum esculentum from the collection of the All-Russia Research Institute of Legumes and Groat Crops have demonstrated that gene TLB controls an important stage of flower development-it determines the lower boundary of simple perianths. The loss of TLB gene function leads to changes in the structure of the bract from scale-like to tepal-like. Gene TLB is assumed to limit, on the basal side, the region of the expression of genes determining the development of flower organs as petals.

[Structure of flower in Arabidopsis thaliana: spatial pattern formation]. / Struktura tsvetka Arabidopsis thaliana (L.) Heynh.: razmetka polozheniia organov.

Morphological analysis of flowers was carried out in Arabidopsis thaliana wild type plants and agamous and apetala2 mutants. No direct substitution of organs takes place in the mutants, since the number and position of organs in them do not correspond to the structure of wild type flower. In order to explain these data, a notion of spatial pattern formation in the meristem was introduced, which preceded the processes of appearance of organ primordia and formation of organs. Zones of acropetal and basipetal spatial pattern formation in the flower of wild type plants were postulated. It was shown that the acropetal spatial pattern formation alone took place in agamous mutants and basipetal spatial pattern formation alone, in apetala2 mutants. Different variants of flower structure are interpreted as a result of changes in the volume of meristem (space) and order of spatial pattern formation (time).

[The principles of data formalization for building the genetic-morphological model of shoot development in flowering plants]. / Printsipy formalizatsii dannykh dlia postroeniia genetiko-morfologicheskoi modeli razvitiia pobega tsvetkovykh rastenii.

Shoot system of a plant can be divided into elementary molecules composed of phyllome, internode, and meristem of the lateral bud. The capacity of plants for open growth is manifested as multiple reproductions of the modules. These main principles of plant structural organization can be used to formalize and integrate the data from various disciplines studying the shoot development--genetics of development, morphology, etc. At the example of model species Arabidopsis thaliana we show that the data on genetic control of shoot development can be considered in terms of individual modules reorganization. Several variants of the modules structural reorganization are allowed: reduction or transformation of phyllome, change in the internode length, and triggering active/inactive status of the lateral shoot meristem. Each variant of the module structure corresponds to specific pattern of genes activity. Such integration of the data on genetic and structural aspects of morphogenesis can form a basis for mathematical modeling of plant development.

[A novel gene Bractea (bra) controls the formation of an indeterminate bractless inflorescence in Arabidopsis thaliana]. / Novyi gen Bractea (bra), kontroliruiushchii formirovanie otkrytogo ébrakteoznogo sotsvetiia u Arabidopsis thaliana.

The morphological and genetic studies of the bra mutant of Arabidopsis thaliana (L.) Heynh. from the collection of the Department of Genetics and Breeding, Moscow State University, showed that the BRA gene controls the main stages of inflorescence development: it suppresses the development of leaflike organs subtending flowers (bracts) and inhibits the formation of the terminal flower. Inactivation of the BRA gene leads to the transition from the indeterminate bractless inflorescence characteristic of the family Cruciferaceae to the determinate bracteose inflorescence. The BRA gene plays a regulatory role and was probably involved in the conversion of the bracteose determinate inflorescence to the bractless indeterminate inflorescence during the origin of ancestral crucifers.