Transposable elements in fish functional genomics: technical challenges and perspectives

The recent introduction of several transposable elements in zebrafish opens new frontiers for genetic manipulation in this important vertebrate model. This review discusses transposable elements as mutagenesis tools for fish functional genomics. We review various mutagenesis strategies that were previously applied in other genetic models, such as Drosophila, Arabidopsis, and mouse, that may be beneficial if applied in fish. We also discuss the forthcoming challenges of high-throughput functional genomics in fish

Antioxidant, antimicrobial activity and mineral composition of low-temperature fractioning products of Malus domestica Borkh (common Antonovka)

The low-temperature fractionation of fruit Malus domestica Borkh (Common Antonovka) has been performed. We obtained by fractionation the biologically active products that are the dehydrated concentrate of juice and the powder of pomace fibers. Use of low temperature minimizes biological value losses during processing. These fractions of fruit Malus domestica Borkh (Common Antonovka) are experimentally studied. It is found that the fractions have high antioxidant activity and include bioflavonoids and organic and phenol carboxylic acids. Analysis of chromatograms showed availability of the identical compounds in the products of low-temperature fractionation. Sodium and potassium are part of the cells of biological systems as highly mobile ionic forms. Therefore, these elements prevail in the concentrated juice. Iron, manganese, copper, and zinc are biogenic trace elements or components of enzyme systems and are evenly distributed as in plant cell walls as well in protoplasm. It follows from the results of the study of the mineral composition that the products of the low-temperature fractioning can be used for a functional food as a result of its high content of magnesium and iron. The low-temperature fractionation of fruit Malus domestica Borkh (Common Antonovka) has antimicrobial activity against the standard strains of spoilage: Bacillus subtilis VKM-B-501, Micrococcus luteus VKM-As-2230, Aspergillus flavus VKM-F-1024, Penicillium expansion VKM-F-275, Mucor mucedo VKM- F-1257, Rhizopus stolonifer VKM- F-2005. Experimental data show that the products of low-temperature fractioning of Malus domestica Borkh (Common Antonovka) inhibit microorganism's growth. The detected composition of Malus domestica Borkh (Common Antonovka) fractions allows using these products as natural additives in food technology to maintain and increase period of storage and also for preventive nutrition

Zebrafish transgenic Enhancer TRAP line database (ZETRAP)

BACKGROUND: The zebrafish, Danio rerio, is used as a model organism to study vertebrate genetics and development. An effective enhancer trap (ET) in zebrafish using the Tol2 transposon has been demonstrated. This approach could be used to study embryogenesis of a vertebrate species in real time and with high resolution. DESCRIPTION: The information gathered during the course of systematic investigation of many ET transgenic lines have been collected and compiled in the form of an online database – the Zebrafish Enhancer TRAP lines database (ZETRAP). CONCLUSION: ZETRAP is a web-based system that provides data and information to the scientific community about the developmental, genetic and genomic aspects of transgenic zebrafish lines obtained using Tol2 transposon-mediated transgenesis. The current version (version 1.0) contains description of 27 ET lines that express EGFP in various organs and tissues, for example, heart, brain, notochord, gut, etc. It also includes information on insertion sites of the Tol2 transposon in these lines

Chemical and ecological state of the waters in the Novik Bay (Russky Island, Peter the Great Bay, Japan Sea)

Chemical and ecological state of the Novik Bay waters is described on the data of surveys conducted in summer, autumn, winter, and spring of 2014-2015. Lowered content of dissolved oxygen is noted for summer, with occasional decreasing to 5-6 mg/L that is below the standard summer value for fishery ponds. However, the oxygen content restores quickly in autumn, up to 12 mg/L, that is conditioned by hydrodynamic activity, water temperature decreasing, and phytoplankton blooming. The latter process is confirmed by high values of BOD5 (4.44-5.58 mgO2/L) in autumn. Winter conditions under the sea ice are satisfactory for marine organisms: dissolved oxygen content is > 4 mg/L in the whole water column that is close to the standard winter value for fishery ponds

Gas dynamics of stationary supersonic gas jets with inert particles exhausting into a medium with low pressure

Issues related to the development of tools for mathematical modeling of stationary supersonic flows of an ideal compressible gas with inert particles are considered. A mathematical model is constructed that describes the flow of an inviscid compressible gas with inert particles in a jet flowing from an axisymmetric nozzle into a flooded space. Provided that the flow is supersonic along one of the spatial coordinates, the Euler equations are hyperbolic along this coordinate. For numerical calculations of the gas flow field, the finite volume method and the marching method are used. For integration over the marching direction, the three-step Runge–Kutta scheme is used. The procedure for calculating the flows includes the reconstruction of the values of the desired functions on the faces of the control volumes from the average values over the control volumes and the solution of the problem of the decay of an arbitrary discontinuity (the Riemann problem). The Lagrangian method of test particles is used to describe the dispersed phase. The effects of the reverse influence of particles on the flow of the carrier gas are not taken into account. The effects of viscosity and rarefaction of the gas flow are taken into account only when the gas interacts with particles. Calculation of the trajectories of inert particles is carried out in a known flow field of the carrier gas. The motion trajectories of discrete inclusions in jet flows with strong underexpansion are presented. The influence of the particle size and the coordinates of the particle entry point into the flow on the features of their transfer by the jet stream are discussed. Efficient means of numerical simulation of stationary supersonic flows of an ideal compressible gas with particles in nozzles and jets have been developed. The calculation results are of interest for studying supersonic gas suspension flows around bodies and for calculating oblique shock waves

Ecological characteristic of water in the Eastern Bosporus Strait by oxygen parameters

Spatial distribution and seasonal variability of the basic ecological parameters for marine water, as dissolved oxygen content, biochemical oxygen demand, and permanganate oxidizability are considered for the Eastern Bosporus Strait (Peter the Great Bay, Japan Sea) on the data obtained in autumn, spring and summer seasons of 2013-2014, with special attention to the Ajax and Paris Bights of Russky Island on the southern coast of the Strait, changed significantly after construction of new university campus and marine aquarium. Normal oxygen regime is observed over the whole strait in autumn, but cases of low dissolved oxygen content, close to the minimal permissible level, are revealed in spring and summer. This phenomenon is an important feature of environmental conditions in the Strait in the warm period. It is possibly reasoned by general pollution of marine environments by sewage water, high water temperature, and relatively high concentration of suspended matter caused by active water circulation in the narrow strait and heavy rains. However, there is no any specific anthropogenic impact on the oxygen content in the Ajax and Paris Bights

A multifunctional mutagenesis system for analysis of gene function in zebrafish

Since the sequencing of the human reference genome, many human disease-related genes have been discovered. However, understanding the functions of all the genes in the genome remains a challenge. The biological activities of these genes are usually investigated in model organisms such as mice and zebrafish. Large-scale mutagenesis screens to generate disruptive mutations are useful for identifying and understanding the activities of genes. Here, we report a multifunctional mutagenesis system in zebrafish using the maize Ds transposon. Integration of the Ds transposable element containing an mCherry reporter for protein trap events and an EGFP reporter for enhancer trap events produced a collection of transgenic lines marking distinct cell and tissue types, and mutagenized genes in the zebrafish genome by trapping and prematurely terminating endogenous protein coding sequences. We obtained 642 zebrafish lines with dynamic reporter gene expression. The characterized fish lines with specific expression patterns will be made available through the European Zebrafish Resource Center (EZRC), and a database of reporter expression is available online (http://fishtrap.warwick.ac.uk/). Our approach complements other efforts using zebrafish to facilitate functional genomic studies in this model of human development and disease

Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of nearinfrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.Peer reviewe

BEN domain protein Elba2 can functionally substitute for linker histone H1 in Drosophila in vivo

Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo. Although the Elba2 gene is not essential, its mutation causes a disruption of normal internucleosomal spacing of chromatin and reduced nuclear compaction in syncytial embryos. Elba2 protein is distributed ubiquitously in polytene chromosomes and strongly colocalizes with H1. In H1-depleted animals, ectopic expression of Elba2 rescues the increased lethality and ameliorates abnormalities of chromosome architecture and heterochromatin functions. We also demonstrate that ectopic expression of BigH1 similarly complements the deficiency of H1 protein. Thus, in organisms that do not express redundant H1 isoforms, the structural and biological functions performed by canonical linker histones in later development, may be shared in early embryos by weakly homologous proteins, such as BigH1, or even unrelated, non-homologous proteins, such as Elba2