On classification of groups generated by 3-state automata over a 2-letter alphabet

We show that the class of groups generated by 3-state automata over a 2-letter alphabet has no more than 122 members. For each group in the class we provide some basic information, such as short relators, a few initial values of the growth function, a few initial values of the sizes of the quotients by level stabilizers (congruence quotients), and hystogram of the spectrum of the adjacency operator of the Schreier graph of the action on level 9. In most cases we provide more information, such as whether the group is contracting, self-replicating, or (weakly) branch group, and exhibit elements of infinite order (we show that no group in the class is an infinite torsion group). A GAP package, written by Muntyan and Savchuk, was used to perform some necessary calculations. For some of the examples, we establish that they are (virtually) iterated monodromy groups of post-critically finite rational functions, in which cases we describe the functions and the limit spaces. There are exactly 6 finite groups in the class (of order no greater than 16), two free abelian groups (of rank 1 and 2), and only one free nonabelian group (of rank 3). The other examples in the class range from familiar (some virtually abelian groups, lamplighter group, Baumslag-Solitar groups BS(1±3), and a free product C2 ∗ C2 ∗ C2) to enticing (Basilica group and a few other iterated monodromy groups)

Mitochondrial genomes of kinorhyncha: TrnM duplication and new gene orders within animals

© 2016 Popova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the earlybranching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia

Захист атмосфери від забруднення при емісії небезпечних речовин на залізничному транспорті

Purpose. The development of numerical models for the prediction of air pollution in the emission of chemical hazardous substances in rail transport in the case of emergencies.Methodology. To solve this problem developed numerical models based on the use of the equations of mass transfer and potential flow. The equations for potential flow are used to determine the velocity field of the wind flow near the carriages and buildings. For the numerical simulations of mass transfer of the pollutant used implicit change triangle difference schemes. When constructing a difference scheme is carried out physical and geometric splitting of the transport equation in the four steps. For the numerical integration of the equation for potential flow of implicit difference scheme is used conditional approximation.Findings. The numerical models that belong to the class «operational models». These numerical models allow to take into account in conducting the computational experiment the basic physical processes that affect dispersion of hazardous chemical substances in the atmosphere taking into account the placement of various types of obstacles near place of emission. These numerical models can be applied in the development of the PLAS, when carried out serial calculations of various scenarios of emergencies in transport. The results of computational experiments to assess the size, shape, concentration of chemical substances in the case of dangerous emissions on the railroad.Originality. The effective numerical models for real-time simulated emergencies, accompanied by the emission of hazardous substances in transport.Practical value. A numerical model of the type of «operational models» to determine the size and intensity zones of chemical contamination in emergency situations in the case of transport by rail chemically hazardous substances. A numerical model using standard meteorological information and do not require special training of the user. Цель. Разработка численных моделей для прогноза загрязнения атмосферы при эмиссии химически опасных веществ на железнодорожном транспорте в случае аварийных ситуаций.Методика. Для решения поставленной задачи разработаны численные модели, основанные на применении уравнений массопереноса и потенциального течения. Уравнения для потенциального течения используются для определения поля скорости ветрового потока вблизи вагонов и зданий. Для численного интегрирования уравнения массопереноса загрязнителя использовалась неявная попеременно-треугольная разностная схема. При построении разностной схемы осуществляется физическое и геометрическое расщепление уравнения переноса на четыре шага. Неизвестное значение концентрации загрязнителя на каждом шаге расщепления определяется  по явной схеме – методу бегущего счета. Для численного интегрирования уравнения для потенциального течения применяется неявная разностная схема условной аппроксимации. На основе построенных численных моделей проведен вычислительный эксперимент по оценке уровня загрязнения атмосферы в случае эмиссии химически опасного вещества на примагистральной территории.Результаты. Разработаны численные модели, которые относятся к классу «operational models». Эти численные модели позволяют учесть при проведении вычислительного эксперимента основные физические процессы, влияющие на рассеивание химически опасных веществ в атмосфере с учетом размещения различного рода препятствий возле очага эмиссии. Построенные модели требуют небольших затрат компьютерного времени при практической реализации на компьютерах малой и средней мощности. Данные численные модели могут применяться при разработке ПЛАСа, когда проводятся серийные расчеты различных сценариев аварийных ситуаций на транспорте. Представлены результаты вычислительного эксперимента по оценке размеров, формы, концентрации химически опасного вещества в случае эмиссии на железной дороге.Научная новизна. Разработаны эффективные численные модели, позволяющие в режиме реального времени моделировать аварийные ситуации, сопровождающиеся эмиссией опасных веществ на транспорте.Практическая значимость. Разработаны численные модели типа «operational models» для определения размеров и интенсивности зон химического заражения при аварийных ситуациях в случае перевозки железнодорожным транспортом химически опасных веществ. Разработанные численные модели используют стандартную метеорологическую информацию и не требуют специальной подготовки у пользователя.Мета. Розробка чисельних моделей для прогнозу забруднення атмосфери при емісії хімічно небезпечних речовин на залізничному транспорті в разі аварійних ситуацій.Методика. Для вирішення поставленого завдання розроблені чисельні моделі, засновані на застосуванні рівнянь масопереносу і потенційної течії. Рівняння для потенційної течії використовуються для визначення поля швидкості вітрового потоку поблизу вагонів і будівель. Для чисельного інтегрування рівняння масопереносу забруднювача використовувалася неявна поперемінно-трикутна різницева схема. При побудові різницевої схеми здійснюється фізичне і геометричне розщеплення рівняння переносу на чотири кроки. Невідоме значення концентрації забруднювача на кожному кроці розщеплення визначається за явною схемою – методу біжучого рахунку. Для чисельного інтегрування рівняння для потенційної течії застосовується неявна різницева схема умовної апроксимації. На основі побудованих чисельних моделей проведено обчислювальний експеримент з оцінки рівня забруднення атмосфери у разі емісії хімічно небезпечної речовини на примагістральній території.Результати. Розроблено чисельні моделі, які відносяться до класу «operational models». Ці чисельні моделі дозволяють врахувати при проведенні обчислювального експерименту основні фізичні процеси, що впливають на розсіювання хімічно небезпечних речовин в атмосфері з урахуванням розміщення різного роду перешкод біля джерела емісії. Побудовані моделі вимагають невеликих витрат комп'ютерного часу при практичній реалізації на комп'ютерах малої та середньої потужності. Дані чисельні моделі можуть застосовуватися при розробці ПЛАСа, коли проводяться серійні розрахунки різних сценаріїв аварійних ситуацій на транспорті. Представлені результати обчислювального експерименту з оцінки розмірів, форми, концентрації хімічно небезпечної речовини у разі емісії на залізниці.Наукова новизна. Розроблено ефективні чисельні моделі, що дозволяють в режимі реального часу моделювати аварійні ситуації, що супроводжуються емісією небезпечних речовин на транспорті.Практична значимість. Розроблено чисельні моделі типу «operational models» для визначення розмірів та інтенсивності зон хімічного ураження при аварійних ситуаціях у разі перевезення залізничним транспортом хімічно небезпечних речовин. Розроблені чисельні моделі використовують стандартну метеорологічну інформацію і не вимагають спеціальної підготовки у користувача

Sodium Energetic Cycle in the Natronophilic Bacterium: Thioalkalivibrio versutus

As inhabitants of soda lakes, Thioalkalivibrio versutus are halo- and alkaliphilic bacteria that have previously been shown to respire with the first demonstrated Na+-translocating cytochrome-c oxidase (CO). The enzyme generates a sodium-motive force (Ds) as high as -270 mV across the bacterial plasma membrane. However, in these bacteria, operation of the possible Ds consumers has not been proven. We obtained motile cells and used them to study the supposed Na+ energeticcycle in these bacteria. The resulting motility was activated in the presence of the protonophore2-heptyl-4-hydroxyquinoline N-oxide (HQNO), in line with the same effect on cell respiration, andwas fully blocked by amiloride—an inhibitor of Na+-motive flagella. In immotile starving bacteria, ascorbate triggered CO-mediated respiration and motility, both showing the same dependence on sodium concentration. We concluded that, in T. versutus, Na+-translocating CO and Na+-motive flagella operate in the Na+ energetic cycle mode. Our research may shed light on the energetic reasonfor how these bacteria are confined to a narrow chemocline zone and thrive in the extreme conditions of soda lakes

Phenotypic and genomic properties of a novel deep-lineage haloalkaliphilic member of the phylum Balneolaeota from soda lakes possessing Na⁺-translocating proteorhodopsin

Stable development of a heterotrophic bacterial satellite with a peculiar cell morphology has been observed in several enrichment cultures of haloalkaliphilic benthic filamentous cyanobacteria from a hypersaline soda lake in Kulunda Steppe (Altai, Russia). The organism was isolated in pure culture (strain Omega) using sonicated cyanobacterial cells as substrate and it was identified as a deep phylogenetic lineage within the recently proposed phylum Balneolaeota. It is an obligately aerobic heterotroph utilizing proteins and peptides for growth. The cell morphology significantly varied from semicircles to long filaments depending on the growth conditions. The cultures are red-orange colored due to a presence of carotenoids. The isolate is an obligate alkaliphile with a pH range for growth from 8.5 to 10.5 (optimum at 9.5-10) and moderately salt-tolerant with a range from 0.3 to 3 M total Na+ (optimum at 1 M). The genome analysis of strain Omega demonstrated a presence of gene, encoding a proteorhodopsin forming a separate branch in the sodium-translocating proteorhodopsin family. Experiments with washed cells of Omega confirmed light-dependent sodium export. A possible physiological role of the sodium proteorhodopsin in strain Omega is discussed. Phylogenomic analysis demostrated that strain Omega forms an deep, independent branch of a new genus and family level within a recently established phylum Balneolaeota.BT/Environmental Biotechnolog

Dynamics of parameters of ultrasonic, microbiological and cytological investigations in the treatment of postoperative wound complications using magnesium containing minerals in the elderly patients.

57 patients aged over 60 years with various types of wound complications after surgery for abdominal and anterior abdominal wall were treated. Treatment of wound complications included both traditional methods and the use of packs of bishofit. Оn the third day after the start of treatment there was a significant decrease in almost all computing performance indices as compared with treatment using bishofit. On the day 7 a noticeable difference of wound cavity width by 62.88%, the volume of the wound cavity by 85.76% in patients of the second group as compared with patients of the first was noted. So,bishofit use in the form of compresses in the treatment of postoperative wound complications such as hematoma, seroma and infiltration leads to a significant reduction in wound exudation, rapid decline in the concentration of microorganisms in the wound; this reduces time of wounds healing and patients’ recovery

Sodium Energetic Cycle in the Natronophilic Bacterium: Thioalkalivibrio versutus

As inhabitants of soda lakes, Thioalkalivibrio versutus are halo- and alkaliphilic bacteria that have previously been shown to respire with the first demonstrated Na+-translocating cytochrome-c oxidase (CO). The enzyme generates a sodium-motive force (Ds) as high as -270 mV across the bacterial plasma membrane. However, in these bacteria, operation of the possible Ds consumers has not been proven. We obtained motile cells and used them to study the supposed Na+ energeticcycle in these bacteria. The resulting motility was activated in the presence of the protonophore2-heptyl-4-hydroxyquinoline N-oxide (HQNO), in line with the same effect on cell respiration, andwas fully blocked by amiloride—an inhibitor of Na+-motive flagella. In immotile starving bacteria, ascorbate triggered CO-mediated respiration and motility, both showing the same dependence on sodium concentration. We concluded that, in T. versutus, Na+-translocating CO and Na+-motive flagella operate in the Na+ energetic cycle mode. Our research may shed light on the energetic reasonfor how these bacteria are confined to a narrow chemocline zone and thrive in the extreme conditions of soda lakes.BT/Environmental Biotechnolog

Mitochondrial genomes of kinorhyncha: TrnM duplication and new gene orders within animals

© 2016 Popova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the earlybranching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia