Making complex things simpler: modern tools to edit the plant genome

There are several technologies for plant genome editing, of which the most simple and universal is CRISPR/Cas. Currently, this technology is widely used for gene knockout, deleting genome fragments and inserting exogenous sequences in the plant genome. For each of these applications, many different types of genetic tools have been developed that are used by various research groups to solve specific problems. The CRISPR/Cas technology for plant genome editing is at an early stage of optimization, which is reflected by the ongoing search for the most effective, simple and flexible techniques. As a result, experimental work has to be preceded by a rather long and laborious process of selecting a genetic tool that will be optimal for a specific experimental task. In our review we describe the main variants of the CRISPR/Cas technology used to edit a plant genome. We classify them in terms of experimental tasks solved, major components and technology performance. In the first half of the review a detailed description of two major components of CRISPR/Cas technology – nuclease and guide RNA – is given, the effect of structural features of these elements on editing efficiency is analyzed. Experimental data on the relationship between editing efficiency and nucleotide sequence of guide RNA are generalized. We also give the characteristic for different variants of nucleases used for plant genome editing and discuss their benefits for different experimental purposes. In the second half of the review various strategies for expression of CRISPR/Cas elements in plant cells, in particular, advantages and disadvantages of stable transformation and transient expression, are discussed. The effect of various regulatory elements of genes encoding nuclease and guide RNA on editing efficiency is described. Special emphasis is placed on the techniques of increasing targeted gene replacement efficiency

Prospects For the Use of Loop Isothermal Amplification in the Diagnosis of Particularly Dangerous Infectious Diseases Caused by the Viruses of the Pathogenicity Group I

Dangerous viral infectious diseases pose a serious threat to human life and health, as their uncontrolled spread leads to the development of major outbreaks and epidemics. Rapid and accurate detection of the pathogen is an essential component of the fight against infectious diseases. This review is devoted to loop-mediated isothermal amplification (LAMP), which is one of the simplest and most reliable methods of molecular-genetic research that meets modern requirements. The simplicity of the analysis and registration of the obtained results, which is necessary under conditions with minimal laboratory capacities, makes it possible to consider this type of diagnostic technology as the most promising, which allows us to identify genetic markers (DNA or RNA) of pathogens of dangerous infectious diseases in the shortest possible time. Objective of the review is to summarize and systematize the data available to date on the use of LAMP for detecting RNA of dangerous infectious diseases caused by the Ebola,Marburg and Lassa viruses. The paper discusses the basic principles of the loop isothermal amplification reaction, the components that make up the reaction mixture and are used for the analysis, as well as methods for detecting the results obtained. When studying the information available in the literature sources about the advantages and disadvantages of LAMP, it is shown that in many cases, isothermal amplification is not inferior in sensitivity and specificity to the main molecular-genetic diagnostic methods currently used. Modifications that can be used for accelerated diagnostics of RNA-containing viruses are also considered

Highly Effective xMAP Multiplex Assay for the Detection and Identification of Hemorrhagic Fever Agents, Including Ebola Virus

Developed has been the oligonucleotide liquid biochip based on xMAP technology, designed for the laboratory detection of particularly dangerous viral pathogens such as Ebola and Marburg filoviruses, and Machupo , Junin, and Lassa arenaviruses. The suggested approach allows for the detection of up to 100 viral genome equivalents in a sample. The sensitivity and specificity of oligonucleotide biochip is 100 % when the laboratory panels of positive and negative samples are used. These results indicate that the xMAP multiplexing for the detection and identification of tropical hemorrhagic fever agents, including Ebola virus, is not inferior to the conventional method such as real-time RT-PCR and can be applied for evaluation of viral load, and further on can easily be expanded for both the analysis of new viral agents and for the detection of critical mutations in viral genomes

Ultrasound examination with contrast in the diagnosis of inflammatory bowel disease. The results of the pilot study

Aim. Assessment of diagnostic significance of informativeness and security of ultrasonography with contrast enhancement drug SonoVue in the diagnosis of Crohn's disease (CD) and ulcerative colitis (UC). Materials and methods. The pilot conducted a prospective study which involved 15 patients with inflammatory bowel disease (IBD). All patients gave written consent to participate in the study and processing of personal data. The study included adult patients with an established diagnosis of UC and CD, with proven clinical activity of the disease. Activity was evaluated based on clinical and laboratory data on the scale of best (CDAI >150) for patients with CD and on a scale of Trulove-Witts (2-3 stage) and the Mayo index (DAI) for patients with UC. All the patients underwent colonoscopy with biopsy, ultrasound examination of abdominal cavity organs with the study of the vascularization of the intestinal wall (color Doppler, power Doppler, contrast study). Results. The use of contrast showed additional features in the instrumental evaluation of activity of inflammatory process, identification of complications and assessment of prognosis. Conclusion. The results of ultrasound of the bowel with contrast can be used to assess the activity and stage of disease in patients with UC or CD

ОНТОЛОГИЧЕСКИЙ ПОДХОД К ПРОЕКТИРОВАНИЮ БИЛЛИНГОВЫХ СИСТЕМ

The principles and approach to ontologies application in billing and other OSS/BSS systems, advantages of such an approach are described. Ontology of billing system is designed, classes and relations are described. Designed model was implemented using Protégé, and was verified on the correctness and consistency.Рассмотрены принципы и подход к применению онтологий в биллинговых системах и других системах OSS/BSS, выделены преимущества такого подхода. Построена онтология системы биллинга, выделены классы и отношения. Разработанная модель онтологии реализована средствами Protégé. Осуществлена проверка разработанной онтологии на корректность и непротиворечивость

Characterisation of Recombinant Human Erythropoietin Obtained from CHOpE—Erythropoietin Producing Strain of Chinese Hamster Ovary Cells

Development and implementation in clinical practice of recombinant human erythropoietins (rhEPOs) remain a priority task today. Additional studies were performed in order to obtain clinical trial authorisation for rhEPO tablets for oral use. The studies were aimed to demonstrate the suitability of the erythropoietin producer strain based on Chinese hamster ovary cells (CHOpE) for the production of rhEPO, and the compliance of the substance characteristics with the requirements for erythropoietin (EPO).The aim of the study was to characterise the rhEPO substance obtained from the CHOpE strain cells in accordance with the requirements for EPO.Materials and methods: the rhEPO substance was obtained by culturing the strain of Chinese hamster ovary cells—CHOpE. The expression construct of the producer strain was evaluated using methods for determination of nucleotide and amino acid sequences. The Sanger method was used to perform sequencing of the nucleotide sequence encoding the human EPO gene. The amino acid sequences of the rhEPO molecule C- and N-termini were determined by the Edman method. The copy number of the EPO gene in CHOpE cells was determined by real-time polymerase chain reaction. The properties of the rhEPO substance were evaluated in accordance with the requirements for EPO. Isoelectric focusing, peptide mapping, and polyacrylamide gel electrophoresis were used for identification of the rhEPO substance. The ratio of isoform composition was determined by capillary electrophoresis. Dimer impurities and high molecular weight related substances were determined by high-pressure liquid chromatography. The content of protein and residual nucleic acids was determined by spectrophotometry. The concentration of the rhEPO substance was assessed by enzyme immunoassay.The results of the study confirmed genetic stability of the CHOpE producer strain and demonstrated identity of N- and C-terminal amino acid sequences of the rhEPO molecule to those of the natural EPO. The CHOpE producer strain was used to obtain a rhEPO substance which is homogenous and does not contain impurities of EPO oligomeric forms. Dimers and high molecular weight related substances account for less than 0.5%. The rhEPO molecular weight ranges from 32 to 38 kDa, and the isoelectric point is within 2.8—4.15. The study identified the peaks of isoforms 1–8, the isoform composition of the rhEPO substance corresponds to that of EPO. It was determined that 1 mol of the substance contains 13.75 mols of sialic acids.Conclusions: the study confirmed the suitability of the CHOpE producer strain for the production of rhEPO. The obtained rhEPO substance meets requirements for EPO

Development of DNA-Biochip for Identification of Influenza A Virus Subtypes

Developed was the DNA-biochip to identify subtypes of influenza A virus, pathogenic for humans. Microchip was capable of detecting H1, H3, H5-subtypes of hemagglutinin (including H1-subtype of pandemic A/H1N1(2009) influenza virus ) and neuraminidase subtypes N1,N2 of influenza virus. This microchip was successfully tested on the strains of A/H5N1 highly pathogenic avian influenza virus, A/H1N1(2009) pandemic influenza virus, A/H1N1 and A/H3N2 seasonal influenza viruses

Molecular Genetic Analysis of the Complete Genome of Tick-Borne Encephalitis Virus (Siberia Subtype): Modern Kolarovo-2008 Isolate

Determined is the complete genome sequence of Kolarovo-2008 strain (Siberia subtype) of Tick-borne encephalitis virus (TBEV), isolated from a tick in the suburbs of the Tomsk city. Nucleotide sequence analysis testifies of the fact that the level of genetic differences within the Siberian subtype of TBEV amounts to 10 % of the nucleotide sequence and to 7 % of amino-acid sequence for certain virus genes. 3'-HTO of the genome of Siberian subtype has the highest rate of variability and the homology level ranging from 65 to 97 %. Kolarovo-2008 and Vasilchenko (isolated in Novosibirsk in 1969) strains have the highest level of genome homology. The level of dissimilarity between the two Tomsk strains is substantially higher: the total number of amino-acid substitutions in Tomsk Zausaev and Kolarovo-2008 strains equals to 124, and 3'HTO level of homology is 79 %. Identified genetic variability of the Siberian subtype of TBEV is of a great importance for further development and enhancement of tick-borne encephalitis virus diagnostics

Development of the Multiplex Real-Time PCR for Marburg, Ebola, and Lassa Viruses Identification

Presented are the data on the development and approbation of the method of Marburg, Ebola, and Lassa viruses identification based on real-time multiplex PCR with hybridization-fluorescent detection. This method is meant for the differential diagnostics of hemorrhagic fevers caused by these viruses. Displayed are the results of determination of multiplex PCR analytical sensitivity and specific activity

Analysis of Ebola virus Zaire 2014 isolates

Analysis of 5 Ebola virus Zaire 2014 isolates passaged in cell cultures or in mice, demonstrated presence of unique mutations in the genome RNA in some cases. All identified nucleotide substitutions are singular, stochastically located, synonymous or fall within non-coding regions. Variability level of nucleotide sequences is equal to 0.005-0.01 %, suggesting extremely high genetic stability of Ebola virus Zaire, the causative agent of the outbreak. Confirmed is suppression of non-synonymous mutations accumulation in ebolavirus variants in the course of time. Detected are alterations in glycosilation sites and mucin-like domain of ebolavirus glycoprotein