Molecular phylogenetic analysis of Tulipa (Liliaceae) from Aksu-Zhabagly Nature Reserve

Barcodes are conserved sequences of genomic, plastid and mitochondrial DNA that can be utilized to uniquely identify an unidentified specimen to its species when conventional identification methods are inapplicable. Among prokaryotic and eukaryotic species, nuclear ribosomal internal transcribed spacer (ITS) sections are one of the most often utilized DNA markers in DNA barcoding and phylogenetic research. In addition to the ribosomal genes, the plastid genes are the most suitable for identifying plant species. The Aksu-Zhabagly Nature Reserve is the oldest nature reserve in Central Asia and is home to 1,312 vascular plant species, 44 of which are categorized as threatened or endangered in Kazakhstan's red data book. In this study, a collection of specimens of uncommon tulip species was compiled, along with their morphological identification and DNA barcoding. The ITS region and parts of the matK and ycf1b genes of tulip plastid DNA were sequenced. The evolutionary link between species of tulips was investigated. Phylogenetic study predicted two Tulipa subclades. Tulipa species have substantially preserved MatK genes. Tulips' ycf1b gene has evolved more slowly than other Liliaceae family members. Nuclear and plastid DNA sequences investigated Tulipa species evolutionary relationships. The findings about the ITS region of nuclear DNA were more definite. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging

Electro-impulse Method of Surface Cleaning

This article is focused on the qualitative assessment of the electro-impulse method of surface cleaning efficiency. Heat exchanger tubes are cleaned under the action of blast waves created by the high voltage discharge in the liquid. The article presents dependences of degree of surface purification on the impulse voltage at switching device and on spark rat

Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis

This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP). It also contains a built-in program to design oligonucleotide sets both for long sequence assembly by ligase chain reaction and for design of amplicons that tile across a region(s) of interest. The software calculates the melting temperature for the standard and degenerate oligonucleotides including locked nucleic acid (LNA) and other modifications. It also provides analyses for a set of primers with the prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity as well as a primer dilution and resuspension calculator. The program consists of various bioinformatical tools for analysis of sequences with the GC or AT skew, CG% and GA% content, and the purine–pyrimidine skew. It also analyzes the linguistic sequence complexity and performs generation of random DNA sequence as well as restriction endonucleases analysis. The program allows to find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It performs efficient and complete detection of various repeat types with visual display. The FastPCR software allows the sequence file batch processing that is essential for automation. The program is available for download at http://primerdigital.com/fastpcr.html, and its online version is located at http://primerdigital.com/tools/pcr.html.Peer reviewe

Дослідження впливу підводного електричного вибуху на вибірковість руйнування кварцової сировини

The work is devoted to the study of the effect of an electric explosion on the selectivity of the destruction of quartz raw materials. The object of the study is quartz ore of the Nadyrbay deposit of the Republic of Kazakhstan. An electrohydroimpulse plant for crushing and grinding quartz raw materials has been developed and assembled. Using the electrohydroimpulse method, the granulometric composition of quartz can be adjusted. This makes it possible to adjust the magnitude of the voltage in the discharge channel and time. In this technology, quartz ore processing was carried out with an increase in the discharge voltage of the storage from 14 kV to 25 kV, the length of the interelectrode distance from 8 to 12, the capacitance of the capacitor 0.5 µF, 0.75 µF and the processing time of 5 min. Using the electrohydroimpulse method, quartz ore particles with an initial fraction of 5 mm, 10 mm and 1 mm were crushed to 0.8. The results of the grinding of quartz raw materials with the influence of an underwater electric explosion in a liquid medium allowed us to determine the degree of grinding of the material. The obtained results can be used in the course of studying the characteristics of crushing and grinding of ores. In the food industry, quartz sand within 0.25–0.5 millimeters can be used as a filler to create filters for water purification, as well as products from oil, industrial effluents, etc. Particles ranging in size from 0.5 to 1 millimeter can be used for rough processing of metal, stone and glass. The structural and quantitative analysis of powdered quartzite samples was made using a scanning electron microscope and the stoichiometry of the elements was calculatedРобота присвячена вивченню впливу електричного вибуху на вибірковість руйнування кварцової сировини. Об'єктом дослідження є кварцова руда родовища Надирбай Республіки Казахстан. Для дроблення та подрібнення кварцової сировини розроблена та зібрана електрогідроімпульсна установка. За допомогою електрогідроімпульсного методу можна регулювати гранулометричний склад кварцу. Це дозволяє регулювати величину напруги в розрядному каналі та час. За даною технологією проводилася переробка кварцової руди зі збільшенням напруги розряду накопичувача з 14 кВ до 25 кВ, довжини міжелектродної відстані з 8 до 12, ємністю конденсатора 0,5 мкФ, 0,75 мкФ і часом обробки 5 хв. З використанням електрогідроімпульсного методу частинки кварцової руди з початковою фракцією 5 мм, 10 мм та 1 мм подрібнювали до 0,8. Результати подрібнення кварцової сировини з впливом підводного електричного вибуху в рідкому середовищі дозволили визначити ступінь подрібнення матеріалу. Отримані результати можуть бути використані при вивченні особливостей дроблення і подрібнення руд. У харчовій промисловості кварцовий пісок розміром 0,25–0,5 міліметра може використовуватися в якості наповнювача для створення фільтрів очищення води, а також продуктів з нафти, промислових стоків тощо. Частинки розміром від 0,5 до 1 міліметра можуть бути використані для грубої обробки металу, каменю та скла. За допомогою скануючого електронного мікроскопа було проведено структурно-кількісний аналіз зразків порошкоподібного кварциту та розраховано стехіометрію елементі

Insight into DNA substrate specificity of PARP1-catalysed DNA poly(ADP-ribosyl)ation

DNA-dependent poly(ADP-ribose) polymerases (PARPs) PARP1, PARP2 and PARP3 act as DNA break sensors signalling DNA damage. Upon detecting DNA damage, these PARPs use nicotine adenine dinucleotide as a substrate to synthesise a monomer or polymer of ADP-ribose (MAR or PAR, respectively) covalently attached to the acceptor residue of target proteins. Recently, it was demonstrated that PARP1–3 proteins can directly ADP-ribosylate DNA breaks by attaching MAR and PAR moieties to terminal phosphates. Nevertheless, little is still known about the mechanisms governing substrate recognition and specificity of PARP1, which accounts for most of cellular PARylation activity. Here, we characterised PARP1-mediated DNA PARylation of DNA duplexes containing various types of breaks at different positions. The 3′-terminal phosphate residue at double-strand DNA break ends served as a major acceptor site for PARP1-catalysed PARylation depending on the orientation and distance between DNA strand breaks in a single DNA molecule. A preference for ADP-ribosylation of DNA molecules containing 3′-terminal phosphate over PARP1 auto-ADP-ribosylation was observed, and a model of DNA modification by PARP1 was proposed. Similar results were obtained with purified recombinant PARP1 and HeLa cell-free extracts. Thus, the biological effects of PARP-mediated ADP-ribosylation may strongly depend on the configuration of complex DNA strand breaks

Розробка технології одержання водовугільного палива

The object of the study is coal sludge and coal fines of the Shubarkol deposit and the Kuznetsk coal basin (Republic of Kazakhstan) for the production of coal-water fuel, which allows replacing liquid and gaseous expensive products. The resulting fuel (after treatment of coal seams and burial) from industrial waste should not harm the environment, which requires certain economic investments. For crushing coal and coal sludge in the crushing and grinding unit, an electrohydroimpulse device for fine grinding of materials was used, consisting of a control unit with a protection system, a pulse capacitor and a high-voltage generator (capacitor bank capacity 0.75 µF, pulse discharge voltage 15–30 kV, length of the interelectrode distance 7–10 mm). After grinding, fine coal particles rise to the surface of the water, and impurities settle at the bottom of the device, which allows enriching the product (flotation). Surface structures and coal fraction sizes were obtained using a Tescan Mira 3 scanning electron microscope. The main characteristics of coal-water fuel during vortex combustion were: the diameter of the fraction 0–250 microns – 63–74 %, process water – 36–24 %, special additive – 1–2 %. Coal-water fuel is similar to liquid fuel, and when transferring heat-generating plants to combustion of suspension, no significant changes in the design of boilers (units) are required. This makes it easy to mechanize and automate the processes of receiving, feeding and burning fuel, and the vortex combustion technology at a temperature of 950–1050 °C guarantees fuel efficiency of more than 97 %. The given optimal parameters of electrohydroimpulse technology when introduced into production will allow not only grinding, but also enriching the coal productОб'єктом дослідження є вугільні шлами та вугільний дріб'язок Шубаркольського родовища і Кузнецького вугільного басейну (Республіка Казахстан) для виробництва водовугільного палива, що дозволяє замінити дорогі рідкі та газоподібні продукти. Одержуване паливо (після обробки вугільних пластів та захоронення) з промислових відходів не повинно завдавати шкоди навколишньому середовищу, що вимагає певних економічних вкладень. Для подрібнення вугілля та вугільного шламу в дробильно-подрібнювальному агрегаті використовувалась електрогідроімпульсна установка для тонкого подрібнення матеріалів, що складається з блоку управління з системою захисту, імпульсного конденсатора і високовольтного генератора (ємність конденсаторної батареї 0,75 мкФ, імпульсна розрядна напруга 15-30 кВ, міжелектродна відстань 7-10 мм). Після подрібнення дрібні частинки вугілля піднімаються на поверхню води, а домішки осідають на дні пристрою, що забезпечує збагачення продукту (флотацію). Структури поверхні та розміри вугільних фракцій були отримані за допомогою скануючого електронного мікроскопа Tescan Mira 3. Основні характеристики водовугільного палива при вихровому спалюванні становили: діаметр фракції 0-250 мкм – 63-74 %, технічна вода – 36-24 %, спеціальна добавка – 1-2 %. Водовугільне паливо аналогічно рідкому паливу, що при переведенні теплогенеруючих установок на спалювання суспензії не вимагає істотних змін у конструкції котлів (агрегатів). Це полегшує механізацію та автоматизацію процесів прийому, подачі і спалювання палива, а технологія вихрового спалювання при температурі 950-1050 °C гарантує паливний ККД понад 97 %. Наведені оптимальні параметри електрогідроімпульсної технології при впровадженні у виробництво забезпечують не тільки подрібнення, а й збагачення вугільного продукт

Isolation of <i>Bacillus</i> sp. A5.3 Strain with Keratinolytic Activity

Environmental safety and economic factors necessitate a search for new ways of processing poultry farm feathers, which are 90% β-keratin and can be used as a cheap source of amino acids and peptones. In this study, feather-decomposing bacteria were isolated from a site of accumulation of rotten feathers and identified as Bacillus. Among them, the Bacillus sp. A5.3 isolate showed the best keratinolytic properties. Scanning electron microscopy indicated that Bacillus sp. A5.3 cells closely adhere to the feather surface while degrading the feather. It was found that Bacillus sp. A5.3 secretes thermostable alkaline proteolytic and keratinolytic enzymes. Zymographic analysis of the enzymatic extract toward bovine serum albumin, casein, gelatin, and β-keratin revealed the presence of proteases and keratinases with molecular weights 20–250 kDa. The proteolytic and keratinolytic enzymes predominantly belong to the serine protease family. Proteome analysis of the secreted proteins by nano-HPLC coupled with Q-TOF mass spectrometry identified 154 proteins, 13 of which are proteases and peptidases. Thus, strain Bacillus sp. A5.3 holds great promise for use in feather-processing technologies and as a source of proteases and keratinases

Development of a grinding device for producing coal powder-raw materials of coal-water fuel

This article proposes a method for grinding coal based on the use of the energy of a pulsed shock wave resulting from a spark electric discharge in a liquid. The main purpose of the scientific work is the development of an electric pulse device for producing coal powder, the main component of coal-water fuel. The diameter of the initial coal fraction averaged 3 mm, and the size of the resulting product was 250 μm. To achieve this goal, the dependence of the length of a metal rod electrode (positive electrode) on the length and diameter of its insulation is investigated. Various variants of the shape of the base (bottom) of the device acting as a negative electrode are considered, and an effective variant based on the results of coal grinding is proposed. An experimental electric pulse installation is described, the degree of coal grinding is determined depending on the geometric parameters. The optimal characteristics of the obtained coal powder have been established

Characterization of biochemical properties of an apurinic/apyrimidinic endonuclease from Helicobacter pylori.

Apurinic/apyrimidinic (AP) endonucleases play critical roles in the repair of abasic sites and strand breaks in DNA. Complete genome sequences of Helicobacter pylori reveal that this bacterial specie has a single AP endonuclease. An H. pylori homolog of Xth (HpXth) is a member of exonuclease III family, which is represented by Escherichia coli Xth. Currently, it remains unknown whether this single AP endonuclease has DNA repair activities similar to those of its counterpart in E. coli and other bacteria. We report that HpXth possesses efficient AP site cleavage, 3'-repair phosphodiesterase, and 3'-phosphatase activities but not the nucleotide incision repair function. Optimal reaction conditions for HpXth's AP endonuclease activity are low ionic strength, high Mg2+ concentration, pH in the range 7-8, and temperature 30 °C. The kinetic parameters measured under steady-state conditions showed that HpXth removes the AP site, 3'-blocking sugar-phosphate, and 3'-terminal phosphate in DNA strand breaks with good efficiency (kcat/KM = 1240, 44, and 5,4 μM-1·min-1, respectively), similar to that of E. coli Xth. As expected, the presence of HpXth protein in AP endonuclease-deficient E. coli xth nfo strain significantly reduced the sensitivity to an alkylating agent and H2O2. Mutation of active site residue D144 in HpXth predicted to be essential for catalysis resulted in a complete loss of enzyme activities. Several important structural features of HpXth were uncovered by homology modeling and phylogenetic analysis. Our data show the DNA substrate specificity of H. pylori AP endonuclease and suggest that HpXth counteracts the genotoxic effects of DNA damage generated by endogenous and host-imposed factors