Regional risks of artificial forestation in the steppe zone of Kazakhstan (case study of the green belt of Astana)

This article deals with results of research on artificial forest in a green zone around the city of Astana. The authors of the article established temporary sample plots where condition, capacity for survival, and growth of trees were observed by standard techniques adapted to conditions of the forest-steppe subzone of Northern Kazakhstan. The reasons for the unsatisfactory condition of the planted forest were found and recommendations on improvement were made. The conclusion was drawn that to establish forest plantations it is necessary to select such species of trees and shrubs that will be resistant in specific conditions to the negative factors of urban lands. A possibility of replanting adult trees to intensify reforestation was also studied. The authors analyzed the dynamics of Silver birch preservation in 2011-2017. The Mann-Whitney-Wilcoxon U test was used to prove the presence of differences between the types of trees' average preservations. Based on the data thus obtained, it was concluded that the forest plantations created by the different methods differed significantly in terms of the preservation rate, as well as in the heights and diameters of the trees. Forecasts of tree preservations in 2018 were made using moving average and linear regression methods. The best forecasts were chosen in terms of the mean relative absolute error of approximation. The results confirmed an initial hypothesis predicting significant differences between the methods used for artificial reforestation: the non-replanted trees are expected to have the highest rate of preservation, whereas the trees replanted to a low location, the lowest preservation rate. The prediction of the preservation rate of forest plantations of Silver birch created by the different methods will allow reducing the risks when conducting forestry activities on artificial reforestation. Regional features must be taken into account in the development of recommendations for a comprehensive system of measures which are based on the scientific forestry techniques to ensure optimum reforestation

Phantasus, a web application for visual and interactive gene expression analysis

Transcriptomic profiling became a standard approach to quantify a cell state, which led to the accumulation of huge amount of public gene expression datasets. However, both reuse of these datasets or analysis of newly generated ones requires significant technical expertise. Here, we present Phantasus: a user-friendly web application for interactive gene expression analysis which provides a streamlined access to more than 96,000 public gene expression datasets, as well as allows analysis of user-uploaded datasets. Phantasus integrates an intuitive and highly interactive JavaScript-based heatmap interface with an ability to run sophisticated R-based analysis methods. Overall Phantasus allows users to go all the way from loading, normalizing, and filtering data to doing differential gene expression and downstream analysis. Phantasus can be accessed online at https://alserglab.wustl.edu/phantasus or can be installed locally from Bioconductor (https://bioconductor.org/packages/phantasus). Phantasus source code is available at https://github.com/ctlab/phantasus under an MIT license

Site-Selective Artificial Ribonucleases: Oligonucleotide Conjugates Containing Multiple Imidazole Residues in the Catalytic Domain

Design of site-selective artificial ribonucleases (aRNases) is one of the most challenging tasks in RNA targeting. Here, we designed and studied oligonucleotide-based aRNases containing multiple imidazole residues in the catalytic part and systematically varied structure of cleaving constructs. We demonstrated that the ribonuclease activity of the conjugates is strongly affected by the number of imidazole residues in the catalytic part, the length of a linker between the catalytic imidazole groups of the construct and the oligonucleotide, and the type of anchor group, connecting linker structure and the oligonucleotide. Molecular modeling of the most active aRNases showed that preferable orientation(s) of cleaving constructs strongly depend on the structure of the anchor group and length of the linker. The inclusion of deoxyribothymidine anchor group significantly reduced the probability of cleaving groups to locate near the cleavage site, presumably due to a stacking interaction with the neighbouring nucleotide residue. Altogether the obtained results show that dynamics factors play an important role in site-specific RNA cleavage. Remarkably high cleavage activity was displayed by the conjugates with the most flexible and extended cleaving construct, which presumably provides a better opportunity for imidazole residues to be correctly positioned in the vicinity of scissile phosphodiester bond

RNase T1 mimicking artificial ribonuclease

Recently, artificial ribonucleases (aRNases)—conjugates of oligodeoxyribonucleotides and peptide (LR)4-G-amide—were designed and assessed in terms of the activity and specificity of RNA cleavage. The conjugates were shown to cleave RNA at Pyr-A and G–X sequences. Variations of oligonucleotide length and sequence, peptide and linker structure led to the development of conjugates exhibiting G–X cleavage specificity only. The most efficient catalyst is built of nonadeoxyribonucleotide of unique sequence and peptide (LR)4-G-NH2 connected by the linker of three abasic deoxyribonucleotides (conjugate pep-9). Investigation of the cleavage specificity of conjugate pep-9 showed that the compound is the first single-stranded guanine-specific aRNase, which mimics RNase T1. Rate enhancement of RNA cleavage at G–X linkages catalysed by pep-9 is 108 compared to non-catalysed reaction, pep-9 cleaves these linkages only 105-fold less efficiently than RNase T1 (kcat_RNase T1/kcat_pep-9 = 105)

Genetic and biochemical characterization of staphylococci occurring in Novosibirsk, Russia

Staphylococci are capable of penetrating many human tissues and organs, causing superficial and deep purulent infections, respiratory and urinary tract infections, food poisoning and intoxication. Last years, coagulase­negative staphylococci were the cause of infection in many cases. Infectious agents, namely Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus hominis, were detected more often as nosocomial infections. A particular danger of these infections is a high virulence and  pathogenicity of bacterial strains and their resistance to various anti ­ biotics. Methicillin­resistant staphylococci are especially difficult to treat. The correct identification of staphylococci and their sensitivity to antibiotics are important for clinical diagnosis and appointment of adequate drug therapy. Rapid and accurate identification of Staphylococcus species and detection of their sensitivity to antibiotics is quite important. The aim of this study was to study staphylococci isolated in Novosibirsk from human, animal and environmental samples. A collection of 100 staphylococcus strains was analyzed. Staphylococcus species were identified by sequencing the 16S rRNA gene. Eleven staphylococcus species were identified. Among the strains obtained from hospitalized patients, Staphylococcus aure us dominated (79.1 %), Staphylococcus  epidermidis amounted to about 12.5 %. However, S. aureus and S. epi dermidis strains were isolated in an approximately equal proportion from community­associated samples. Identification of coagulase positive strains was performed using a standard biochemical method and by real­time PCR of the coa gene. 100 % coincidence between the presence of the gene and coagulase activity for S. aureus strains was recorded, which suggests that detection of the coa gene can be used as a correct method for S. aure us identification. A high coincidence rate (99 %) was reveal ed between the phenotypic resistance to oxacillin and the presence of the staphylococcal mecA gene. The study of staphylococci for the presence of the mecA gene can be considered as an alternative to the phenotypical method for identification of methicillin­resistant strains of staphylococci

A novel expression cassette delivers efficient production of exclusively tetrameric human butyrylcholinesterase with improved pharmacokinetics for protection against organophosphate poisoning

© 2015 Published by Elsevier B.V. Butyrylcholinesterase is a stoichiometric bioscavenger against poisoning by organophosphorus pesticides and nerve agents. The low level of expression and extremely rapid clearance of monomeric recombinant human butyrylcholinesterase (rhBChE) from bloodstream (t1/2;≈2 min) limits its pharmaceutical application. Recently (Ilyushin at al., PNAS, 2013) we described a long-acting polysialylated recombinant butyrylcholinesterase (rhBChE-CAO), stable in the bloodstream, that protects mice against 4.2 LD50 of VR. Here we report a set of modifications of the initial rhBChE expression vector to improve stability of the enzyme in the bloodstream and increase its production in CHO cells by introducing in the expression cassette: (i) the sequence of the natural human PRAD-peptide in frame with rhBChE gene via "self-processing" viral F2A peptide under control of an hEF/HTLV promoter, and (ii) previously predicted in silico MAR 1-68 and MAR X-29 sequences. This provides fully tetrameric rhBChE (4rhBChE) at 70 mg/l, that displays improved pharmacokinetics (t1/2; = 32 ± 1.2 h, MRT = 43 ± 2 h). 3D Fluorescent visualization and distribution of 125I-labeled enzyme reveals similar low level 4rhBChE and rhBChE-CAO accumulation in muscle, fat, and brain. Administered 4rhBChE was mainly catabolized in the liver and breakdown products were excreted in kidney. Injection of 1.2 LD50 and 1.1 LD50 of paraoxon to BALB/c and knockout BChE-/- mice pre-treated with 4rhBChE (50 mg/kg) resulted in 100% and 78% survival, respectively, without perturbation of long-term behavior. In contrast, 100% mortality of non-pre-treated mice was observed. The high expression level of 4rhBChE in CHO cells permits consideration of this new expression system for manufacturing BChE as a biopharmaceutical

Вариабельность гематологических показателей у коров в зависимости от физиологического статуса

The object of the study was Holstein cows of the second-fourth milk secretion and first-calf cows of different production groups formed depending on the physiological status of the animals. The most pronounced hematological changes were observed in sexually mature cows during the first three months of milk secretion. After fawning, the number of erythrocytes, lymphocytes, and hemoglobin decreased. The concentration of bloodforming elements in the groups with a first-calf cow was significantly higher than in sexually mature cows. The level of erythrocytes and hemoglobin in first-calf cows reaches its maximum value at the beginning of milk secretion. Sexually mature cows after the first month of milk secretion were statistically significantly superior to first-calf cows at the beginning of milk secretion in terms of granulocyte content. Cows, in the first days of milk secretion, had the most fantastic range of variability in the scope of erythrocytes, leukocytes, and hemoglobin, which reflects the individual response of the body to significant changes in physiological status. At the same time, the first-calf cows at the beginning of milk secretion had the most stable level of these hematological indices. Dry cows, as a rule, occupied an intermediate position regarding the variability of the content of blood form elements. Thus, assessing the hematological profile of cows of different production groups helps specialists make targeted adjustments to rations and housing conditions, effectively manage genetic resources and obtain high profits.Объектом исследования являлись коровы голштинской породы второй-четвертой лактаций и первотелки разных производственных групп, сформированных в зависимости от физиологического статуса животных. Наиболее выраженные гематологические изменения наблюдались у половозрелых коров в первые три месяца лактации. После отела у животных отмечалось снижение количества эритроцитов, лимфоцитов, содержания гемоглобина. В группах с первотелками концентрация форменных элементов крови была достоверно больше по сравнению с половозрелыми коровами. При этом уровень эритроцитов и гемоглобина у первотелок достигает максимального значения в начале лактации. Половозрастные коровы после первого месяца лактации по содержанию гранулоцитов статистически значимо преобладали над первотелками в начале лактации. У коров в первые дни лактации наблюдался наибольший размах изменчивости содержания эритроцитов, лейкоцитов, гемоглобина, что отражает индивидуальную реакцию организма на значимые изменения физиологического статуса. При этом у первотелок в начале лактации уровень данных гематологических показателей был наиболее стабильным. Сухостойные коровы по вариабельности содержания форменных элементов крови, как правило, занимали промежуточное положение. Таким образом, оценка гематологического профиля коров разных производственных групп помогает специалистам производить направленную корректировку рационов и условий содержания, эффективно управлять генетическими ресурсами и получать высокие прибыли