Effect of Ionizing Radiation on the Transcript Variants Expression of p21 Gene

PURPOSE

CDK1A is one of the most important genes that have different key roles in cell lines. This gene has several transcript variants. Investigating of expression of each one actually can be so important because any one of them may have a separate unknown role in cancer cells so can be used to increase therapeutic efficacy.

METHODS

A549, MDA-MB-231 and Hek-AD cell lines were used in this study. Firstly, three primers for variants of p21 gene were designed by Snapgene and BLAST software. Secondly, the variants expression was checked for each cell lines by RT-qPCR technique, separately. Then the variants that expressed in the cells were selected for more investigation. Finally 2 Gy irradiation was used to evaluate the effect of that on variants expression.

RESULTS

The results show that for all cell lines, primer num1 and 3 expressed before any stimuli. After irradiation, for MDA-MB-231 and A549, the expression of primer num3 was decreased, while for Hek-AD no change was observed. The primer num1 expression after the irradiation was different for the cells, V1 expression was decreased in A549 by fold of 0.03 while expression of this for MDA-MB-231 cells was not changed after 2Gy irradiation.

CONCLUSION

It is very necessary to pay attention to the function of each splice variant as well as the response to external stimuli. Understanding the role of each variant in a gene is critical and researchers can use that to improve radiotherapy as well.

Phenotypic Response to Light Versus Shade Associated with DNA Methylation Changes in Snapdragon Plants (Antirrhinum majus)

The phenotypic plasticity of plants in response to change in their light environment, and in particularly, to shade is a schoolbook example of ecologically relevant phenotypic plasticity with evolutionary adaptive implications. Epigenetic variation is known to potentially underlie plant phenotypic plasticity. Yet, little is known about its role in ecologically and evolutionary relevant mechanisms shaping the diversity of plant populations in nature. Here we used a reference-free reduced representation bisulfite sequencing method for non-model organisms (epiGBS) to investigate changes in DNA methylation patterns across the genome in snapdragon plants (Antirrhinum majus L.). We exposed plants to sunlight versus artificially induced shade in four highly inbred lines to exclude genetic confounding effects. Our results showed that phenotypic plasticity in response to light versus shade shaped vegetative traits. They also showed that DNA methylation patterns were modified under light versus shade, with a trend towards global effects over the genome but with large effects found on a restricted portion. We also detected the existence of a correlation between phenotypic and epigenetic variation that neither supported nor rejected its potential role in plasticity. While our findings imply epigenetic changes in response to light versus shade environments in snapdragon plants, whether these changes are directly involved in the phenotypic plastic response of plants remains to be investigated. Our approach contributed to this new finding but illustrates the limits in terms of sample size and statistical power of population epigenetic approaches in non-model organisms. Pushing this boundary will be necessary before the relationship between environmentally induced epigenetic changes and phenotypic plasticity is clarified for ecologically relevant mechanisms with evolutionary implications.

Ionizing Radiation Alters the Transition/Transversion Ratio in the Exome of Human Gingiva Fibroblasts

Little is known about the mutational impact of ionizing radiation (IR) exposure on a genome-wide level in mammalian tissues. Recent advancements in sequencing technology have provided powerful tools to perform exome-wide analyses of genetic variation. This also opened up new avenues for studying and characterizing global genomic IR-induced effects. However, genotypes generated by next generation sequencing (NGS) studies can contain errors, which may significantly impact the power to detect signals in common and rare variant analyses. These genotyping errors are not explicitly detected by the standard Genotype Analysis ToolKit (GATK) and Variant Quality Score Recalibration (VQSR) tool and thus remain a potential source of false-positive variants in whole exome sequencing (WES) datasets. In this context, the transition-transversion ratio (Ti/Tv) is commonly used as an additional quality check. In case of IR experiments, this is problematic when Ti/Tv itself might be influenced by IR treatment. It was the aim of this study to determine a suitable threshold for variant filters for NGS datasets from irradiated cells in order to achieve high data quality using Ti/Tv, while at the same time being able to investigate radiation-specific effects on the Ti/Tv ratio for different radiation doses. By testing a variety of filter settings and comparing the obtained results with publicly available datasets, we observe that a coverage filter setting of depth (DP) 3 and genotype quality (GQ) 20 is sufficient for high quality single nucleotide variants (SNVs) calling in an analysis combining GATK and VSQR and that Ti/Tv values are a consistent and useful indicator for data quality assessment for all tested NGS platforms. Furthermore, we report a reduction in Ti/Tv in IR-induced mutations in primary human gingiva fibroblasts (HGFs), which points to an elevated proportion of transversions among IR-induced SNVs and thus might imply that mismatch repair (MMR) plays a role in the cellular damage response to IR-induced DNA lesions.

Cytological Effect of Gamma Radiation on Selected Mutants of Wheat <i>Triticum aestivum</i> L. in M3 Generation

BACKGROUND AND OBJECTIVE

Wheat (Triticum aestivum L.) offers some unique opportunities for the induction and exploitation of agronomic value. The use of gamma radiation has been proven to be an effective method to induce genetic variation in crops. We aimed to determine genetically stable mutants of wheat which could be utilized for breeding purposes.

MATERIALS AND METHODS

We did a cytological investigation of induced mutant's behavior and chiasma frequency. Selected mutant types induced in dry and soaked seeds were treated with different doses of gamma rays. Each treated sample and control were subjected to cytological examination of the fixed pollen mother cells in various meiotic stages.

RESULTS

The percentage of the total abnormal cells significantly increased in one mutant and significantly decreased in the other mutant. The percentage of total abnormal cells did not diminish from the first to the second meiotic division. The types of meiotic anomalies found included laggards (56.51%), univalent (9.43%), stickiness (45.45%) and bridges (19.32%). There were genotypic differences in the frequency of occurrence of multivalent (trivalent and quadrivalents). A marked reduction in the number of rod and ring bivalent/cell in some genotypes were noticed. The frequency of chiasmata per pollen mother cell was reduced subsequently. Depression index of mutants was negative compared with controls or treatments except for a few genotypes.

CONCLUSION

Selected mutants of wheat tend to be cytologically stable and can therefore, be utilized for breeding purposes.

Chronic radiation exposure as an ecological factor: Hypermethylation and genetic differentiation in irradiated Scots pine populations

Genetic and epigenetic changes were investigated in chronically irradiated Scots pine (Pinus sylvestris L.) populations from territories that were heavily contaminated by radionuclides as result of the Chernobyl Nuclear Power Plant accident. In comparison to the reference site, the genetic diversity revealed by electrophoretic mobility of AFLPs was found to be significantly higher at the radioactively contaminated areas. In addition, the genome of pine trees was significantly hypermethylated at 4 of the 7 affected sites.

Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments

Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.

Genetic effects in children exposed in prenatal period to ionizing radiation after the Chornobyl nuclear power plant accident

AIM

To study the genetic effects in children exposed to radiation in utero as a result of the Chornobyl nuclear power plant accident accounting the total radiation doses and equivalent radiation doses to the red bone marrow.

MATERIALS AND METHODS

Incidence of minor developmental anomalies was studied in children exposed to radiation in utero (study group) and in the control group (1144 subjects surveyed in total). Cytogenetic tests using the method of differential G-banding of chromosomes were conducted in 60 children of both study and control groups (10-12-year-olds) and repeatedly in 39 adolescents (15-17-year-olds).

RESULTS

A direct correlation was found between the number of minor developmental anomalies and fetal dose of radiation, and a reverse one with fetal gestational age at the time of radiation exposure. Incidence of chromosomal damage in somatic cells of 10-12-year-old children exposed prenatally was associated with radiation dose to the red bone marrow. The repeated testing has revealed that an increased level of chromosomal aberrations was preserved in a third of adolescents.

CONCLUSION

The persons exposed to ionizing radiation at prenatal period should be attributed to the group of carcinogenic risk due to persisting increased levels of chromosome damage. This article is a part of a Special Issue entitled "The Chornobyl Nuclear Accident: Thirty Years After".

Absolute quantification of acetylation and phosphorylation of the histone variant H2AX upon ionizing radiation reveals distinct cellular responses in two cancer cell lines

Histone modifications change upon the cellular response to ionizing radiation, and their cellular amounts could reflect the DNA damage response activity. We previously reported a sensitive and reliable method for the absolute quantification of γH2AX within cells, using liquid chromatography-tandem mass spectrometry (LC/MS/MS). The technique has broad adaptability to a variety of biological systems and can quantitate different modifications of histones. In this study, we applied it to quantitate the levels of γH2AX and K5-acetylated H2AX, and to compare the radiation responses between two cancer cell lines: HeLa and U-2 OS. The two cell lines have distinct properties in terms of their H2AX modifications. HeLa cells have relatively high γH2AX (3.1 %) against the total H2AX even in un-irradiated cells, while U-2 OS cells have an essentially undetectable level (nearly 0 %) of γH2AX. In contrast, the amounts of acetylated histones are lower in HeLa cells (9.3 %) and higher in U-2 OS cells (24.2 %) under un-irradiated conditions. Furthermore, after ionizing radiation exposure, the time-dependent increases and decreases in the amounts of histone modifications differed between the two cell lines, especially at the early time points. These results suggest that each biological system has distinct kinase/phosphatase and/or acetylase/deacetylase activities. In conclusion, for the first time, we have succeeded in simultaneously monitoring the absolute amounts of phosphorylated and acetylated cellular H2AX after ionizing radiation exposure. This multi-criteria assessment enables precise comparisons of the effects of radiation between any biological systems.

Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat

Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r (2) of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals.

The receptor-like kinase ERECTA contributes to the shade-avoidance syndrome in a background-dependent manner

BACKGROUND AND AIMS

Plants growing at high densities perceive a decrease in the red to far-red (R/FR) ratio of incoming light. These changes in light quality trigger a suite of responses collectively known as the shade-avoidance syndrome (SAS) including hypocotyl and stem elongation, inhibition of branching and acceleration of flowering.

METHODS

Quantitative trait loci (QTLs) were mapped for hypocotyl length to end-of-day far-red (EOD), a simulated shade-avoidance response, in recombinant inbred line (RIL) populations of Arabidopsis thaliana seedlings, derived from Landsberg erecta (Ler) and three accessions (Columbia, Col; Nossen, No-0; and Cape Verde Islands, Cvi-0).

KEY RESULTS

Five loci were identified as being responsible for the EOD response, with a positive contribution of Ler alleles on the phenotype independently of the RIL population. Quantitative complementation analysis and transgenic lines showed that PHYB is the candidate gene for EODRATIO5 in the Ler × Cvi-0 RIL population, but not for two co-localized QTLs, EODRATIO1 and EODRATIO2 mapped in the Ler × No-0 and Ler × Col RIL populations, respectively. The ERECTA gene was also implicated in the SAS in a background-dependent manner. For hypocotyl length EOD response, a positive contribution of erecta alleles was found in Col and Van-0, but not in Ler, Cvi-0, Hir-1 or Ws. Furthermore, pleiotropic effects of ERECTA in the EOD response were also detected for petiole and lamina elongation, hyponastic growth, and flowering time.

CONCLUSIONS

The results show that the analysis of multiple mapping populations leads to a better understanding of the SAS genetic architecture. Moreover, the background- and trait-dependent contribution of ERECTA in the SAS suggest that its function in shaded natural environments may be relevant for some populations in different phases of plant development. It is proposed that ERECTA is involved in canalization processes buffering the genetic variation of the SAS against environmental light fluctuations.

[Variability of DNA simple sequence repeats in peripheral blood of humans subjected to prolonged exposures of ionizing radiation]

Long-term post-radiation changes in the level of microsatellite DNA polymorphism in peripheral blood of the male "Mayak" employees (Ozyorsk, Russia), who had been exposed to prolonged gamma-irradiation during professional activities, were studied. DNA samples were obtained from the Radiobiology Repository of Human Tissue (Southern-Urals Biophysics Institute FMBA) and used as templates for arbitrarily primed PCR. Comparative analysis of the obtained samples of DNA fragments showed a significant increase in the number of high-molecular fragments and reduction in the number of amplified low molecular weight DNA fragments in comparison with the control. However, a direct correlation of the level of DNA polymorphism with the accumulated total dose of radiation was not found. The study of the polymorphism of microsatellite DNA repeats can be used for qualitative assessment of the levels of genetic variability.

[Dynamics and ecological-genetic variability of cytogenetic disturbances in Scots pine populations experiencing technogenic impact]

Scots pine (Pinus sylvestris L.) populations in the vicinity of nuclear industry facilities were monitored. Aberrant cells occurrence in root meristem of germinated seeds from the impacted pine populations was found to be significantly above the reference level during all six years of observations. In the reference population, changes of cytogenetic disturbances with time appeared to be cyclic while in the impacted populations, technogenic stress was strong enough to destroy the natural regularities. The increase in cytogenetic disturbances was accompanied by growth of fluctuations magnitude; deviations of basic oscillation parameters from the reference values rose along with technogenic impact level. Variability in cytogenetic response increased under technogenic stress. Inter-family component of variability predominated, though its contribution slightly decreased in impacted populations. A tendency for destabilization of a repetition coefficient dynamics was found under technogenic impact. A portion of the seeds was exposed to 15 Gy of gamma-rays, and higher radio-resistance in the impacted populations was observed. In the reference population, a family-related analysis of cytogenetic variability components after acute y-exposure revealed significant contributions of "family" and "germination conditions" factors as well as their interactions. On the contrary, in populations existing under chronic stress, considerable modifications in the structure of ecological-genetic variability were found, their degree increasing with technogenic impact severity.

[Increased genomic instability in somatic cells of the progeny of female mice exposed to acute X-radiation in the preconceptional period]

The level of genome instability (GI) was studied in the progeny of female mice exposed in the preconceptional period to radiation doses of 0.5, 1, and 2 Gy in comparison to that in the progeny of the same parent pairs born before irradiation of the females. To assess the level of genome instability, we analyzed polymorphism of DNA fragments from postmitotic (blood and brain) and proliferating (spleen and tail tip) tissues amplified by AP-PCR (PCR amplification with an arbitrary primer). It was found that polymorphism of the spectrum of AP-PCR products, which is a multilocus genetic marker (MGM), in the genome of somatic cells in the progeny of female mice exposed to 2 Gy was higher than in the progeny of male mice exposed to the same doses. In the progenies of female mice born before and after irradiation, tissue-specific variations in the level of DNA polymorphism were detected. The maximum value of this polymorphism (with respect to the frequency of "nonparental bands") was determined for peripheral blood DNA in comparison with the other tissues. Estimations of the MGM polymorphism with the AP-PCR method demonstrate an increased level of genome instability in somatic cells of offsprings from female mice exposed to a single acute dose of X-rays (0.5, 1, and 2 Gy) in the pre-conceptional period. Radiation-induced transgenerational genome instability with an increase in the dose of preconceptional irradiation of female mice was more pronounced in DNA of the postmitotic tissues (blood and brain DNA) than in DNA of the proliferating tissues (spleen and tail tip epithelium).

Cycloheximide suppresses radiation-induced apoptosis in MOLT-4 cells with Arg72 variant of p53 through translational inhibition of p53 accumulation

The human T-cell leukemia cell line MOLT-4 is highly radiosensitive, and thus it is often used as a model of p53-dependent radiation-induced apoptosis. Two branches of the p53-mediated apoptotic pathway are reported: "transcription-dependent" and "transcription-independent." However, the relative contribution of each in different types of cells is not yet clearly defined. Moreover, recent studies have shown that the codon 72 polymorphic variants of p53 show different sensitivities to apoptosis signals. The Arg72 variant has a more potent apoptosis-inducing activity in mitochondria than the Pro72 variant. Here, we initially investigated the codon 72 polymorphism of p53 in MOLT-4 cells. Analysis of the p53 exon 4 genomic DNA sequence, which includes codon 72, revealed that MOLT-4 cells are homozygous for the allele encoding Arg72. We next investigated the involvement of the transcription-independent function of p53 using an RNA synthesis inhibitor, actinomycin D (ActD), and a protein synthesis inhibitor, cycloheximide (CHX), and found that the apoptosis was suppressed by CHX but not by ActD. We also revealed that the suppressive effect of CHX on apoptosis was specifically mediated by p53, using a p53-knockdown MOLT-4 transfectant. Furthermore, the suppressive effect of CHX on apoptosis was highly correlated with the suppression of p53 protein accumulation, and less correlated with the suppression of p53 target genes expression. These results indicated that p53 transactivation is not necessary to induce apoptosis, and that p53 protein accumulation itself is both necessary and sufficient to do so.

Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different partitioning patterns under elevated [CO2]

This study compared the leaf transcription profiles, physiological characteristics and primary metabolites of two Populus tremuloides genotypes (clones 216 and 271) known to differ in their responses to long-term elevated [CO2] (e[CO2]) at the Aspen free-air CO2 enrichment site near Rhinelander, WI, USA. The physiological responses of these clones were similar in terms of photosynthesis, stomatal conductance and leaf area index under e[CO2], yet very different in terms of growth enhancement (0-10% in clone 216; 40-50% in clone 271). Although few genes responded to long-term exposure to e[CO2], the transcriptional activity of leaf e[CO2]-responsive genes was distinctly different between the clones, differentially impacting multiple pathways during both early and late growing seasons. An analysis of transcript abundance and carbon/nitrogen biochemistry suggested that the CO2-responsive clone (271) partitions carbon into pathways associated with active defense/response to stress, carbohydrate/starch biosynthesis and subsequent growth. The CO2-unresponsive clone (216) partitions carbon into pathways associated with passive defense (e.g. lignin, phenylpropanoid) and cell wall thickening. This study indicates that there is significant variation in expression patterns between different tree genotypes in response to long-term exposure to e[CO2]. Consequently, future efforts to improve productivity or other advantageous traits for carbon sequestration should include an examination of genetic variability in CO2 responsiveness.

The intergenic region of Arabidopsis thaliana cab1 and cab2 divergent genes functions as a bidirectional promoter

Genetic engineering plays a unique role in fundamental plant biology studies and in improving crop traits. These efforts often necessitate introduction and expression of multiple genes using promoters from a very limited repertoire. Current common practice of expressing multiple genes is the repeated use of the same or similar promoters. This practice causes more frequent transgene silencing due to a high degree of sequence homology and a greater chance of rearrangement among repeatedly used promoter sequences. Therefore, availability and use of natural bidirectional promoters to minimize gene silencing and achieve desirable expression pattern of transgenes is a critical issue in the field of plant genetic engineering. Here we describe the use of a single natural bidirectional promoter to drive the expression of two reporter genes in onion epidermal cells and in transgenic tobacco plants. We show that (1) the promoter drives the simultaneous expression of GUS and GFP reporter genes after transient expression and stable transformation, (2) the transcription is equally strong in both directions, (3) immediate upstream regions in each direction control transcription independently from each other, and (4) the reporter genes are expressed in leaves and stems but not in roots, as expected from the fact that the endogenous promoter controls the expression of two photosynthetic genes in Arabidopsis. Hence, use of bidirectional promoters in heterologous background provides a means to express multiple genes in transgenic plants and aids genetic engineering-based crop improvement.

[The dynamics of variability of the genotype of experimental populations of Drosophila melanogaster by chronic radiation exposure]

The reaction on the irradiation in a dose 3 Gy of experimental populations of Drosophila melanogaster, differing on mobile genetic element patterns, chronically irradiated in low doses ionising radiation was investigated. Received results testify that the effect of radioadaptation is found out only in populations with an initial genotype and is not revealed at populations containing P-mobile elements. It is shown, that in chronically irradiated populations D. melanogaster with an initial genotype, decrease in frequency recessive lethal mutations after a sharp irradiation in a dose 3 Gy is observed. The analysis of frequency of dominant lethal mutations and gonads atrophy such tendency has not revealed. It is supposed, that the mechanisms participating in formation of the adaptive answer, induced with an irradiation and transpositions activity of mobile elements differ.

Phenogenetic response of silver birch populations and half-sib families to elevated ozone and ultraviolet-B radiation at juvenile age

Phenogenetic response of silver birch populations and half-sib families to separate and combined elevated ozone (O(3)) concentrations and ultraviolet-B (UV-B) radiation dozes was studied at juvenile age in the climatic chambers. Significant population and family effects were found for seedling height, lamina width, and leaf damage. The exposure to UV-B radiation decreased genetic variation at the stage of seed germination. Complex exposure to UV-B and O(3) caused an increase of genetic variation at the stage of intensive seedling growth: seedling height genetic variation in separate treatments increased from 23.7-38.6 to 33.7-65.7%, the increase for lamina width was from 10.2-13.9 to 13.6-31.8%. Different populations and families demonstrated differing response to elevated complex UV-B and O(3) exposure. Changes of genetic intra-population variation were population-specific. Such changes in genetic variation under the impact of stressors can alter adaptation, stability, and competitive ability of regenerating populations in a hardly predictive way.

The Arabidopsis homeodomain-leucine zipper II gene family: diversity and redundancy

The Arabidopsis genome contains 10 genes belonging to the HD-Zip II family including ATHB2 and HAT2. Previous work has shown that ATHB2 is rapidly and strongly induced by light quality changes that provoke the shade avoidance response whereas HAT2 expression responds to auxin. Here, we present a genome-wide analysis of the HD-Zip II family. Phylogeny reconstruction revealed that almost all of the HD-Zip II genes can be subdivided into 4 clades (alpha-delta), each clade comprising 2-3 paralogs. Gene expression studies demonstrated that all the gamma and delta genes are regulated by light quality changes. Kinetics of induction, low R/FR/high R/FR reversibility and auxin response analyses strongly suggested that HAT1, HAT3 and ATHB4, as ATHB2, are under the control of the phytochrome system whereas HAT2 is up-regulated by low R/FR as a consequence of the induction of the auxin signaling pathway provoked by FR-rich light. Root and shoot digital in situ revealed that gamma and delta genes are also tightly regulated during plant development with both distinct and overlapping patterns. Phenotypes of gain of function and dominant negative lines demonstrated that one or more of the HD-Zip II gamma genes negatively regulate cell proliferation during leaf development in a high R/FR light environment. Finally, target gene analysis using a chimeric transcription factor (HD-Zip2-V-G), known to activate ATHB2 target genes in a glucocorticoid-dependent manner, revealed that all the 10 HD-Zip II genes can be recognized by the HD-Zip 2 domain in vivo, implying an intricate negative feedback network.

The genetic basis of adaptive pigmentation variation in Drosophila melanogaster

In a broad survey of Drosophila melanogaster population samples, levels of abdominal pigmentation were found to be highly variable and geographically differentiated. A strong positive correlation was found between dark pigmentation and high altitude, suggesting adaptation to specific environments. DNA sequence polymorphism at the candidate gene ebony revealed a clear association with the pigmentation of homozygous third chromosome lines. The darkest lines sequenced had nearly identical haplotypes spanning 14.5 kb upstream of the protein-coding exons of ebony. Thus, natural selection may have elevated the frequency of an allele that confers dark abdominal pigmentation by influencing the regulation of ebony.

Transmission of Genomic Instability from a Single Irradiated Human Chromosome to the Progeny of Unirradiated Cells

Ionizing radiation can induce chromosome instability that is transmitted over many generations after irradiation in the progeny of surviving cells, but it remains unclear why this instability can be transmitted to the progeny. To acquire knowledge about the transmissible nature of genomic instability, we transferred an irradiated human chromosome into unirradiated mouse recipient cells by microcell fusion and examined the stability of the transferred human chromosome in the microcell hybrids. The transferred chromosome was stable in all six microcell hybrids in which an unirradiated human chromosome had been introduced. In contrast, the transferred chromosome was unstable in four out of five microcell hybrids in which an irradiated human chromosome had been introduced. The aberrations included changes in the irradiated chromosome itself and rearrangements with recipient mouse chromosomes. Thus the present study demonstrates that genomic instability can be transmitted to the progeny of unirradiated cells by a chromosome exposed to ionizing radiation, implying that the instability is caused by the irradiated chromosome itself and also that the instability is induced by the nontargeted effect of radiation.

Environmental pollution affects genetic diversity in wild bird populations

Many common environmental pollutants, together with nuclear radiation, are recognized as genotoxic. There is, however, very little information on pollution-related genetic effects on free-living animal populations, especially in terrestrial ecosystems. We investigated whether genetic diversity in two small insectivorous passerines, the great tit (Parus major) and the pied flycatcher (Ficedula hypoleuca), was changed near point sources of heavy metals (two copper smelters) or radioactive isotopes (nuclear material reprocessing plant). We measured concentration of heavy metals and nucleotide diversity in mitochondrial DNA in feather samples taken from nestlings in multiple polluted areas and at control sites. In both species, heavy metal concentrations - especially of arsenic - were increased in feathers collected at smelter sites. The P. major population living near a smelter showed significantly higher nucleotide diversity than a control population in an unpolluted site, suggesting increased mutation rates in a polluted environment. On the contrary, F. hypoleuca showed reduced nucleotide diversity at both smelter sites but increased nucleotide diversity near the source of radioactivity. Our results show that heavy metal pollution and low level nuclear radiation affect the nucleotide diversity in two free-living insectivorous passerines. We suggest that the different response in these two species may be due to their different ability to handle toxic compounds in the body.

Alterations of DNA Copy Number and Expression in Genes Involved in Cell Cycle Regulation and Apoptosis Signal Pathways in γ-Radiation-Sensitive SX9 Cells and -Resistant SR-1 Cells

In the present study, genomic differences related to sensitivity to radiation were examined by comparative genomic hybridization and GeneChip 45K microarray in SX9 cells (radiation-sensitive) and their parental line, SR-1 (radiation-resistant). SX9 cells have defective DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activity. DNA-PKcs is a DNA double-strand break repair protein that maintains chromosomal stability through nonhomologous end joining. However, the molecular basis of the radiation sensitivity of SX9 cells is unclear. Flow cytometry analysis showed that SR-1 and SX9 cells had a larger G2/M-phase population at 12 h after 4 Gy gamma irradiation, while only SR-1 cells progressed to G1/S at 24-36 h. SX9 and SR-1 cells had similar patterns of DNA copy number alteration, but the gains were observed on chromosome 9 (cent-E2), 11 (cent-A3), and 12 (C1-E) only in SX9 cells. Expression of genes located on those regions is higher in SX-9 cells than in SR1 cells, and the regions include genes associated with apoptosis and cell cycle regulation. Time-course data for gene expression at 0, 1, 3, 6 and 12 h after 4 Gy gamma irradiation revealed that the genes whose expression was altered in SX9 cells but not in SR-1 cells are in 16 clusters. Three of these clusters included genes for cell cycle regulation: JNK, PKC (PRKC) and ceramide cascade protein. These results suggest that amplification and altered expression of genes associated with cell cycle and apoptosis regulators in DNA-PK-deficient SX9 cells affect the differences in response to gamma radiation between SX9 and SR-1 cells.

Genetic variation in radiation-induced expression phenotypes

Studies have demonstrated that natural variation in the expression level of genes at baseline is extensive, and the determinants of this variation can be mapped by a genetic-linkage approach. In this study, we used lymphoblastoid cells to explore the variation in radiation-induced transcriptional changes. We found that, among normal individuals, there is extensive variation in transcriptional response to radiation exposure. By studying monozygotic twins, we demonstrated that there is evidence of a heritable component to this variation. The postradiation variation in the expression level of several genes, including the ferredoxin reductase gene (FDXR) and the cyclin-dependent kinase inhibitor 1A gene (CDKN1A), is significantly greater (P<.001) among twin pairs than within twin pairs. The induction of FDXR by radiation showed a bimodal distribution. Our findings have important implications for understanding the genetic basis of radiation response, which has remained largely unknown due to the lack of family material needed for genetic studies. Our approach, which uses expression phenotypes in cell lines, allows us to expose cells from family members to radiation. Similar study design can be applied to dissect the genetic basis of other complex human traits.

Induced mutations in cassava using somatic embryos and the identification of mutant plants with altered starch yield and composition

A cyclic somatic embryogenic system was used to induce mutations in cassava variety PRC 60a in vitro. Globular-stage somatic embryos were selected as suitable experimental materials, and 50 Gy of gamma-rays was determined to be the optimal dose for inducing mutations. During subsequent field trials, more than 50% of the regenerated mutant lines varied morphologically from wild-type plants. Consequently, we used this approach to induce genetic variability for obtaining novel cassava cultivars. Among the different mutant lines obtained, lines S14 and S15 showed large morphological variations. In 10-month-old S14 and S15 mutant lines, storage root yield was reduced 17-fold and 60-fold, respectively, compared to wild-type plants, while the storage roots of S15 mutant plants also exhibited an almost 50% decrease in starch content and a significant reduction (30%) in amylose content. These two features were observed throughout the different developmental stages of the storage roots in S15 plants.

Extensive phenotypic variation in early flowering mutants of Arabidopsis

Flowering time, the major regulatory transition of plant sequential development, is modulated by multiple endogenous and environmental factors. By phenotypic profiling of 80 early flowering mutants of Arabidopsis, we examine how mutational reduction of floral repression is associated with changes in phenotypic plasticity and stability. Flowering time measurements in mutants reveal deviations from the linear relationship between the number of leaves and number of days to bolting described for natural accessions and late flowering mutants. The deviations correspond to relative early bolting and relative late bolting phenotypes. Only a minority of mutants presents no detectable phenotypic variation. Mutants are characterized by a broad release of morphological pleiotropy under short days, with leaf characters being most variable. They also exhibit changes in phenotypic plasticity across environments for florigenic-related responses, including the reaction to light and dark, photoperiodic behavior, and Suc sensitivity. Morphological pleiotropy and plasticity modifications are differentially distributed among mutants, resulting in a large diversity of multiple phenotypic changes. The pleiotropic effects observed may indicate that floral repression defects are linked to global developmental perturbations. This first, to our knowledge, extensive characterization of phenotypic variation in early flowering mutants correlates with the reports that most factors recruited in floral repression at the molecular genetic level correspond to ubiquitous regulators. We discuss the importance of functional ubiquity for floral repression with respect to robustness and flexibility of network biological systems.

[Evaluation of the effect of pollen irradiation on karyotype variability in M2 cotton plants]

The karyotypes of biomorphologically abnormal cotton (Gossypium hirsutum L.) plants obtained in M2 after pollination with pollen irradiated at dose rates 10, 15, 20, and 25 Gy were studied. Various genomic and chromosomal mutations were detected in 57 M2 families. The primary monosomics isolated in M2 were found to be cytologically more stable and more viable, since they had higher meiotic indices, pollen fertility, and seed formation. In M2, a decrease in the number of plants with multiple karyotype aberrations and interchromosomal exchanges with high frequency of multivalent formation was observed. The multivalents had diverse patterns and types of chromosome segregation and translocation complexes. Their pollen fertility was higher than in translocants found in M1. Desynapsis often occurred in M2, including plants with chromosome deficiency or rearrangements. The variation in the number of univalents in various cells was found to result from different expression of synaptic genes. The results indicate stabilization of karyotypes, increase in cytologic stability and viability, and the absence of sterility in aberrant plants.

Cytokine polymorphisms play a role in susceptibility to ultraviolet B-induced modulation of immune responses after hepatitis B vaccination

UVB exposure can alter immune responses in experimental animals and humans. In an earlier human volunteer study, we demonstrated that hepatitis B-specific humoral and cellular immunity after vaccination on average were not significantly affected by UVB exposure. However, it is known that individuals differ in their susceptibility to UVB-induced immunomodulation, and it was hypothesized that polymorphisms in specific cytokines may play a role in this susceptibility. In this respect, we previously demonstrated that immune responses after hepatitis B vaccination are influenced by the minor allelic variant of IL-1 beta in the general population. For all volunteers, single nucleotide polymorphisms were determined for the following UV response-related cytokines: IL-1 receptor antagonist (+2018), IL-1 alpha (+4845), IL-1 beta (+3953), TNF-alpha (-308), and TNF-alpha (-238). Exposure to UVB significantly suppressed Ab responses to hepatitis B in individuals with the minor variant for the IL-1 beta polymorphism. Increased minimal erythema dose values (just perceptible), which resulted in higher absolute UVB exposures, were observed in the same individuals. There were no associations observed between UVB-induced immunomodulation and the other cytokine polymorphisms examined. This study indicates that individual susceptibility to UVB radiation needs to be considered when studying the effects of UVB in humans.

Genetic consequences of radioactive contamination by the Chernobyl fallout to agricultural crops

The genetic consequences of radioactive contamination by the fallout to agricultural crops after the accident at the Chernobyl NPP in 1986 have been studied. In the first, acute, period of this accident, when the absorbed dose was primarily due to external beta- and gamma-irradiation, the radiation injury of agricultural crops, according to the basic cytogenetic tests, resembled the effect produced by acute gamma-irradiation at comparable doses. The yield of cytogenetic damage in leaf meristem of plants grown in the 10-km zone of the ChNPP in 1987-1989 (the period of chronic, lower level radiation exposure) was shown to be enhanced and dependent on the level of radioactive contamination. The rate of decline with time in cytogenetic damage induced by chronic exposure lagged considerably behind that of the radiation exposure. Analysis of genetic variability in three sequential generations of rye and wheat revealed increased cytogenetic damage in plants exposed to chronic irradiation during the 2nd and 3rd years.

[A comparative analysis of plant hereditary variability during mutagenic treatment of the generative cells and seeds of corn]

The effect of mutagenic factors on maize generative cells during different gametogenesis stages, as well as on mature pollen and gametes causes an essential raise in frequency, widening in visible mutation spectra and seems to be more efficient than on dry seeds. Original mutations on qualitative and quantitative characters have been obtained.

[The possibilities of sensitized photomutagenesis for the induction of genetic variability in plants]

It was found that combined influence of sensitizers and laser emission on vegetation under some conditions induces marked mutagenesis. The observed synergism was analysed. The possible mechanisms of the phenomenon was considered. A unified approach was proposed to assess efficacy of sensitizer-laser pairs by fragmentation DNA. The recommendations were given for application of combined action of sensitizers and laser emission for experimental mutagenesis.

[Variability in the longevity of Drosophila imagoes under chronic irradiation at low doses]

The investigation of life span variability induced by a chronic influence of low doses gamma irradiation on the laboratory stocks of D. melanogaster, distinguishing by mobile genetic units, were carried out. Shown was the link of life span alterations in D. melanogaster with features of cytotype and genotype in tested stocks and with induced apoptotic cell death. The life span variation can be determined by a genomic destabilisation with an induction of mobile genetic elements in conditions of chronic gamma irradiation.

[Ultraviolet irradiation of soil samples as a model of the effect of stress factors on bacterial diversity in soil ecosystem]

UV irradiation is proposed for use in studying the effect of radioactive irradiation, since radioresistant bacteria are, as a rule, resistant to UV, and the mechanisms of repair of cell damage induced by UV and ionizing radiation are similar. It was found that the total number of bacteria and the number of dominant species in soil samples exposed to UV radiation decreased, indicating the unfavorable effect of UV radiation on bacterial diversity in soil ecosystems. The percentage of cells of bacteria belonging to dominant species varied significantly depending on the intensity of UV irradiation. It can be inferred that long-term irradiation of soils must impair the stability of soil ecosystems, a phenomenon that was indeed observed in the zone around the Chernobyl Nuclear Power Plant. At the same time, the UV irradiation of soil samples made it possible to reveal minor species, primarily UV-resistant pigmented bacteria. UV irradiation can probably be used as a selective factor for the isolation of radioresistant species.

[Gene instability induced by mobile genetic elements in Drosophila melanogaster]

The genetic instability of Drosophila melanogaster genes induced by the mobile genetic elements is reviewed. The main attention is paid to genetic instability depended on types of crossing. Data on the possibility of genetic instability induction by the chemical and physical (X-rays, heat-shock) agents and their complex effect are cited. It was shown that a number of agents which cause mutagenic effect realize their action by involving of mobile genetic elements.

[An analysis of the cytogenetic sequelae of chronic low-dose irradiation in plantings of agricultural crops]

There is a tendency for a decrease in the yield of cytogenetic disturbances with time elapsed from the Chernobyl accident. But an increased rate of cytogenetical damages significantly dependent on the level of radioactive contamination was observed even in several years after the incident. The rate of decline with time in cytogenetic disturbances induced by chronic exposure considerably lagged behind that of radiation exposure. Analysis of genetic changeability in three sequential generations of winter rye and wheat revealed increased cytogenetic damage in crops grown on contaminated sites during 2 and 3 years.

[Interlocus associations and their variability in cattle]

The results of analysis of interloci associations between two pairs of syntenic loci (transferrin and ceruloplasmin, receptor for vitamin D and kappa-casein) and two non-syntenic ones (amylase-1 and post-transferrin 2) in two cattle groups of Red Steppe breed (infected and uninfected by bovine leukosis virus) and in two groups of Black-and-White Holsteins (from relatively "pure" zone and from the 10 km zone of Chernobyl NPP) were presented. It is found that "linkage disequilibrium" between loci is observed independent of their synteny. The data obtained allowed the authors to suppose, that the interloci associations are rather controlled by different factors of artificial and natural selection than by the genetic linkages between genes.

[Pseudomutagenesis. The persistent increase in the level of cellular variability induced by radiation and some other agents]

Electron microscopic investigation of capillary endothelium cells in myocardium of irradiated rats revealed an unusual effect of persistent increase of probability of cell damage, similar in many relations to that described earlier for various unicellular species. New effect, unlike those traditionally studied, is characterised by non-stochastic nature, large number of the involved cells, reveals itself even after faint influences, and can be induced as well by agents other than radiation. The question is put on the probable commonness between these changes and the pseudomutagenesis which has the similar phenomenology.

[The dynamics of the allele variants of biochemical markers in generations of cattle in the exclusion zone of the Chernobyl Atomic Electric Power Station]

Analysis of the heritability of allelic variants of polymorphous genetic-biochemical systems in the cattle groups, reproduced in conditions of increased radionuclide pollution in exclusion zone of the Chernobyl AES was carried out. The disturbances of equal probability of the heritability for different allelic variants in some cattle group were revealed. It was supposed, that the appearance of the disturbances may take part in changeabilities of different gene pools under the conditions of ecological stresses. Possible mechanisms of this phenomenon were discussed.

[The heterogeneity of the cytogenetic variability in the bone marrow cells of laboratory and wild rodents in the exclusion zone of the Chernobyl Atomic Electric Power Station]

Analysis of the characters of cytogenetic variabilities and correlative interrelations between them revealed the group specificities of karyotype instability in bone marrow cells of some lines of laboratory and of wild mice under the conditions of increased radionuclide pollution in the Chernobyl zone. The complex correlative interrelations between the frequencies of cytogenetic anomalies and the character of cell division (the number of metaphases, binucleated leukocytes per 1000 cells) were observed. The obtained data indicate the stimulatory influence of chronic low doses of ionizing radiation on the manifestation of spontaneous mutagenesis, which has own genotype specific characteristics.

[The genetic processes in chronically irradiated natural populations of Centaurea scabiosa L. growing in the eastern Urals radioactive trace]

The examination of chronically irradiated natural populations of C. scabiosa L. have been carried out for 30 years at the territory of the east Urals radioactive trial. By using of different tests (frequency of aberrant cells, chlorophyll mutations and mutations in Lap locus) the mutation rates in chronically irradiated populations and in the control natural populations were compared. It was shown that long-term radiation influence caused changes in population genetic structure due to induction of new allelic forms and selection of more adapted genotypes.

[The variability of different cytogenetic characteristics in groups of Black Pied cattle]

The comparative analysis of frequency of occurrence of different indications of cytogenetic variabilities in blood cells of cattle groups (relative healthy, infected by bovine leukosis virus and exposed to ionizing radiation in the Chernobyl zone) was carried out. Both genotoxic influences induced increases in frequencies of cytogenetic defects, but only ionizing radiation induced the increase of chromosome aberration frequency. The heterogeneity of all cattle groups for investigated cytogenetic characters was revealed.

Expression of AP 3, 4 and 5 isophytochromes in etiolated oat seedlings (Avena sativa L.)

Type 1 phytochrome from etiolated oat seedlings was digested with V-8 protease. Microsequencing of a 13 kDa fragment yielded a sequence of 31 amino acids. The fragment starting with the alanine residue at position 427 of the entire phytochrome amino acid sequence revealed a heterogeneity (threonine, alanine and asparagine) at position 10. This demonstrates that the phytochrome type A genes AP3, 4 and 5 are expressed as proteins.

[Monitoring the seeds of chronically irradiated indigenous populations of Plantago lanceolata L. Variability in the progeny]

The results of the morphometric study of Plantago lanceolata L. grown, in nursery, from seeds of the first and second post-accident reproductions within the thirty-kilometer zone around the crippled Chernobyl reactor show no relationship between the alterations in some quantitative indices and the variability of gamma-radiation background in places where maternal plants grow.

[Segregation of the somatic and germ-cell pathways of development in Drosophila]

Two groups of lethal mutations that are expressed only in somatic cells were isolated using the gonosomic selective method. The mutations tend to be organized in clusters along the sex chromosome. Analysis of mutation expression allowed to characterize the degree of changes in genetic diversity of somatic and germ lines in development; it is minimal in the III instar larvae and prepupae and maximal in the I and II instar larvae and pupae.

[Reproducible chromosomal instability of an established Chinese hamster cell line detectable by flow cytometry]

The karyotypes of individual cells in clones of the established Chinese hamster cell line display a highly heterogeneous pattern. Unlike situation in individual cells, the flow karyotypes of cloned cell populations are very similar. A comparison of these facts suggests that mostly the same certain chromosomal reorganizations, appearing frequently enough, may occur in the cells. As a result, the whole set of possible variants of reorganized chromosomes appear during few cell cycles, regardless of the initial cell karyotype. This hypothesis is supported by our flow cytometry data. The same small peaks corresponding to rarely met (less than 1 per cell) rear ranged chromosomes appear on flow karyotype histograms of parental cell clones and their secondary subclones. Chromosomes with random gamma or UV irradiation-induced reorganizations do not remain in the cell population, unlike certain reorganization of regular nature.

Increase in clonal variation in Chinese hamster ovary cells after treatment with mutagens

Clonal variation has been studied in CHO cells. The variant phenotype was an altered morphology of clones in agar: the parental CHO cells give rise to solid clumps of cells (wild-type colonies); occasionally, dispersed colonies arise, and the cells display an invasive growth in agar (INGA-type colonies). The frequency of this altered phenotype can be enhanced by treatment with a variety of mutagens (EMS, ENU, 4NQO, N-Ac-AAF, ultraviolet light, and X-irradiation). Enhancement was not due to a selective killing of wild-type cells or to a side-effect of cytotoxicity, which suggests that DNA damage is the cause of the altered phenotype. The INGA-trait breeds true, but most of the isolated clones have an inherent instability.

[Natural variability of Streptomyces spheroides--a producer of extracellular proteolytic enzymes possessing fibrinolytic action]

Streptomyces spheroides M 8-2 was obtained using UV irradiation of spores taken from the parent culture. It shows a high activity of exocellular proteases which are capable of fibrin hydrolysis and degradation of blood clots. On certain media, a population of S. spheroides M8-2 was shown to yield three variants differing in their morphologo-biochemical properties. During submerged cultivation, these variants produce different quantities of exocellular proteases (3 to 19 units per 1 mg of biomass) with the fibrinolytic activity. Variants I and III are most active; their proteolytic activity is 10-14 units per 1 mg of biomass, on the average, and can reach 18-19 units per 1 mg of biomass. Variants with a low activity (variant II) are accumulated when the actinomycets is kept as spores on a solid medium with corn extract and on a solid medium with fibrin. The high proteolytic activity of the strain can be preserved by selection on a diagnostic medium with fibrin taking account of the diameter of hydrolytic zones around the colonies and selecting solely the colonies of variants I and III.