Effect of lox-sites of the Cre lox recombination system on promoterless bar gene expression in transgenic plants

We demonstrate that localization of lox site between the right border of T-DNA and promoterless bar gene (RB-lox-bar-) led to its highly efficient expression in transgenic plants of Nicotiana tabacum and N. africana. Plasmid vectors used in gene integration experiments contained neomycin phosphotransferase II (npt II) gene under nos promoter as well. Transgenic plants were selected according to their capacity to grow on the medium with kanamycin and then they were tested on the selective medium containing phosphinothricin. 80% of transgenic plants expressed bar gene at the level similar to that in plants transformed with the bar gene under widely used constitutive promoter. Transformation of plants with the plasmid vector containing only promoterless bar gene near T-DNA right border (RB-bar-) and with the vector containing lox site and promoterless bar gene in the middle of the construction (-lox-bar-) led to obtaining no more than 4.5% of transgenic plants resistant to phosphinothricin. PCR analyses confirmed both the absence of tandem repeats and of plasmid recombination resulting in transference of bar gene under promoter in plasmid vector. Nos-terminator situated between the lox site and the right border of T-DNA did not decrease bar gene expression.     

Peculiarities of Regeneration and Genetic Variability of <Emphasis Type="Italic">Crambe koktebelica</Emphasis> and <Emphasis Type="Italic">Crambe tataria</Emphasis> Plants in vitro

The regenerative capability of three types of explants was studied on media with different compositions of growth regulators with the purpose of selecting optimal conditions of fast reproduction of endangered Crambe species that could be used as a relevant source of genetic material for the improvement of industrially valuable plants. PCR-analysis of genotypes of C. koktebelica and C. tataria plants was conducted to identify the influence of in vitro cultivation on the genetic stability of plants. The highest regeneration rates were observed with the use of petiole explants on MS medium with BA and NAA. The absence of somaclonal variability in C. koktebelica and C. tataria in vitro regenerated plants was demonstrated.     

Screening of plant cell culture collection for efficient host species for Agrobacterium-mediated transient expression

Agrobacterium-mediated transient expression is an approach for short-time expression of heterologous genes in plant systems. During the last decade transient expression was regarded as a potent protocol for high scale production of foreign proteins in plants including pharmaceutically valuable proteins. In vitro grown plant cell cultures represent a suitable system for accumulation of heterologous proteins under controlled conditions. Since host characteristics may strongly influence transient expression efficiency, we performed screening of undifferentiated cell cultures for transient expression ability using GUS as a reporter. Analysis of 248 plant species belonging to 49 families from the National Germplasm Bank of the World Flora of the Institute of Cell Biology and Genetic Engineering (Kyiv, Ukraine) allowed for selection of about 50 plant species exhibiting detectable β-glucuronidase activity.     

Artemisia tilesii Ledeb hairy roots establishment using Agrobacterium rhizogenes-mediated transformation

An efficient and rapid protocol for the establishment of Artemisia tilesii “hairy” root culture is reported. Leaf explants of aseptically growing plants were cocultured with Agrobacterium rhizogenes A4 wild strain or A. rhizogenes carrying the plasmids with nptII and ifn-α2b genes. Root formation on the explants started in 5–6 days after their cocultivation with bacterial suspension. Prolongation of explant cultivation time on the medium without cefotaxime led to stimulation of root growth. The effects of sucrose concentration as well as of the levels of synthetic indole-3-butyric acid (IBA) and native growth regulator Emistim on the stimulation of A. tilesii “hairy” root growth were studied. Maximum stimulating effect both for the control and for transgenic roots was observed in case of root cultivation on the media supplemented with IBA—up to 7.95- and 9.1-fold biomass increase, respectively. Cultivation on the medium with 10 μl/L Emistime has also led to the control roots growth stimulation (up to 2.75-fold). Emistime at 5 μl/L concentration led to 5.46-fold mass increase in only one “hairy” root line. Higher sucrose content (40 g/L) stimulated growth of two hairy root lines but had no effect on growth of the control roots.     

Content of myosin-activating protein kinases in myocardium of patients with dilated cardiomyopathy and in the animal heart

The skeletal myosin light chain kinase (skMLCK) was identified in human and chicken embryo myocardium but not in embryo and adult rat heart using western blotting. The content of skMLCK and myosin-activating protein kinases: RhaA-activated protein kinase (ROCK), integrin-linked protein kinase (ILK), and zipper-interacting protein kinase (ZIPK) was compared in normal human myocardium and the hearts of patients with dilated cardiomyopathy (DCM). It was demonstrated that the content of skMLCK, ROCK and ILK increases in DCM whereas the content of ZIPK decreases. The results obtained may reflect compensatory processes in cardiomyocytes in DMC, which are aimed at increasing their viability and contractility.     

Genetic transformation of Nicotiana africana Merxm. with plasmids containing lox recombination

An efficient genetic transformation method for african tobacco Nicotiana africana Merxm. has been established. African tobacco is a valuable source for cytoplasmic male sterility (CMS) and nuclear encoded resistance to potato virus Y (PVY). N. africana transgenic plants have been obtained using both Agrobacterium-mediated and direct transformation of leaf explants with gold particle bombardment using particle inflow gun. Plasmid vectors containing phosphinothricin resistance gene (bar gene) coding region without promoter and independent 35S promoter between lox sites (lox-bar-35S-lox) and nptII gene were used. Transgenic plants were selected according to growth capacity on the selective medium containing 50 mg/l kanamycin. PCR analyses of kanamycin-resistant plants confirmed the presence of nptII and bar genes in their genome. Agrobacterium-mediated transformation of root explants has proved to be the most efficient transformation method for N. africana.     

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Background

Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F_ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.

Results

Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F_ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F_ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F_ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.

Conclusions

Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-876) contains supplementary material, which is available to authorized users.     

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Background

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns.

Methods

By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation.

Results

For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1.

Conclusions

The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.     

Using methods of plant biotechnology for conservation and study of the world flora biodiversity

Ex situ germplasm bank of plant species of world flora has been created at the Institute of Cell Biology and Genetic Engineering of the National Academy of Sciences of Ukraine as a result of investigations in the fields of botany and plant biotechnology. At present the bank contains more than 4000 samples in seed bank and more than 2000 cell lines in in vitro bank. The germplasm bank which has been put on the List of scientific objects of national property of Ukraine is the basis of elaboration ofbiotechnological methods of plant biodiversity preservation and of plant material screening for biologically active substances.     

Concentrations of myosin-activating protein kinases in the myocardium of patients with dilated cardiomyopathy and in animal heart

Skeletal myosin light chain kinase in the myocardia of various animal species was identified by immunoblotting. The myocardial concentrations of this protein and myosin-activating protein kinases (RhoA-activated kinase, integrin-linked kinase, and zipper-interacting kinase) were compared in healthy humans and patients with dilated cardiomyopathy. Skeletal myosin light chain kinase was detected in the human and chicken embryo hearts, rather than in the embryonic and adult rat hearts. In the myocardium of patients with dilated cardiomyopathy, the concentrations of myosin light chain kinase, RhoA-activated kinase, and integrin-linked kinase increase and the concentration of zipper-interacting kinase decreases. The results obtained are likely to characterize compensatory processes in cardiomyocytes in dilated cardiomyopathy that are aimed at increasing their viability and contractility.