Microbial diversity in the Mediterranean hypersaline deep-sea lake Tyro

1. Purpose of the research Characterization of bacterial and viral diversity of brine Tyro using molecular methods of identification. 2. Procedures For bacteria: 1. Amplification or multiplication of 16S rRNA gene (one of the most conservative gene) by polymerase chain reaction (PCR). 2. Agarose gel electrophoresis and purification of PCR product 3. Ligation of purified PCR product into the vector pGEM-T 4. Transformation of plasmids containing an insert into competent cells E.coli XB1 5. Blue-white selection (we need white colonies, they contain the insert of interest) 6. Isolation of plasmids containing an insert of interest 7. Sequencing of inserts 8. Bioinformatics analysis: matching homologues from GeneBank database, construction of phylogenetic trees, statistical analysis. For viruses: The same methods were used for gp23 gene, which code a major head protein of T-even bacteriophages; to amplify gp23 gene a special set of primers was used, along with a standard cloning protocol described above. 3. Data 1) Two libraries of clones were obtained during analysis: lake Tyro (24 operational taxonomic units (OTUs), 10 classes) and sea water (6 OTUs, 2 classes of eubacteria). 2) The most abundant classes were: gamma-, delta-, epsilon- Proteobacteria, which is in agreement with previous reports about bacteria in brines of Mediterranean Sea. 3) The number of clones was not sufficient to obtain stable estimates of diversity, the analysis require additional data. 4) The diversity of bacteria was unexpectedly high in brine but not in the seawater, due to higher and more diverse ion composition. 5) Most of the detected bacteria in the deep-sea lake belonged to the previously undescribed (18,75%) bacteria or had unusual metabolism (43,75%). 4. Conclusions The analysis demonstrated unexpectedly high diversity of halophilic bacteria inhabiting Tyro lake. Most of bacteria presented in brine water had unique and uncommon characteristics based on information about its closest relatives. Therefore, the deep-sea hypersaline lakes of Mediterranean Sea have great potential for further investigations. Preliminary results of diversity of viruses of Tyro lake were obtained during analysis, more complete description is coming soon.

Basalt prism of Santa Maria Regla river, Huasca, Mexico

The purpose: To study the basaltic prisms to understand their formation. Tasks: To study chemical and mineral composition, textures and density of basalts of central and peripheral parts of prisms, to reveal the possible difference as a consequence of the formation of Benard sells. Basalt prisms have 6-5-4-face shape with a diameter 10 -50 cm and height of 30-40m. They are divided by transverse fracture in blocks of 20-50 cm. Prismatic jointing of basalts widespread throughout the world. There are many theories about its origin. We decided to collect data to identify the most appropriate of these. We suppose that if the hypothesis about the role of Benard cells is correct then the properties of basalt in the central and peripheral parts of the prisms must be different. If we consider the center of the prism as the center of the cell, where the hot matter rise, spreading out to the periphery and lower in the peripheral part, it is likely that the density of basalt forming in the center must be lower than at the periphery and later crystallization should lead to a slightly more acidic basalt in the middle. We determined the density of basalts of different parts of prisms. And the density of central part basalts was equal to 2.502g/sm3 and of peripheral part basalts was equal to 2.907g/sm3. X-ray fluorescence analysis showed that basalt of central part contain 12,91% Si and of peripheral part only 10,17%. Basalt of central part is depleted of Fe, Mn, Ti, Mg compared with of peripheral. We investigated samples and thin sections of basalts under the microscope MIN-8. For basalts of peripheral part flow texture expressed by the orientation of the microlites are characteristic. In the central part flow texture are poorly expressed but we can see many phenocrysts. Our data reveal a significant and expected difference between the basalts of central and peripheral parts of prism, that are the evidences in favor of the hypothesis about the role of Benard cells in the formation of basalt prismatic jointing.

First photochromic diarylethenes with cyclohexenone ethene "bridge"

Photochromism is determined as reversible transformation between two chemical species, induced by action of light [1]. Herewith, initial form and photoinduced isomer have different properties, first of all, spectral. The phenomenon is attractive for the design of hi-tech materials for different applications, including optical memory elements and molecular switches. Diarylethenes are the most promising class of organic photochromic compounds due to outstanding thermal stability of both isomers and high photostability [2, 3]. Photochromism of diarylethenes explained by reversible electrocyclic reaction of hexatriene system, provoked by UV light, back reaction is induced by visible light. In this work we have proposed a new class of photochromic diarylethenes with cyclohexenone ethene “bridge” 4. The key stage of the synthesis is “one-pot” reaction of ketoesters 1 and chalkones 2 in ethanol in the presence of sodium ethoxide that includes Michael reaction and subsequent intramolecular condensation of the resulting product. The final decarboxylation of semi-product 3 results in target diarylethenes 4. We have prepared a wide range of photochromic diarylethenes with thiophene, oxazole, imidazole and benzene derivatives as aryl moieties. The spectral characteristics of compounds obtained have also been discussed.

New approach to the synthesis of functionalized fluoroalkenes

Fluorine has a big influence on physical, chemical and biological properties of organic structures. Organofluorine compounds are widely used in modern medical chemistry to develop new drugs. Insertion of fluorine atom into organic molecules can improve their reactivity in biological systems, increase their metabolic stability, lipophilicity and permeability through membranes. As a consequence, in recent years, the percentage of drugs containing one or more fluorine atoms has increased rapidly up to 40%. The fluoroallylic fragment is also able to change properties of bioactive molecules. Its introduction into such structures as inhibitors of histonedeacetylase, inhibitors of matrix metalloproteinase, asparagine, glutamine, etc. increases their biological activity and electronic properties. We propose a new method for the synthesis of functionalized fluoroalkenes, based on the generation of fluoroallyl nucleophiles from silyl- and boronyl-substituted fluorocyclopropanes and their further usage in the allylation of carbonyl compounds or their derivatives. Due to the fact that the cyclopropanation of alkenyl boronates is not possible under conditions of alkaline dehydrohalogenation of dibromofluoromethane, we have developed a new method for the preparation of silyl- and boronyl-substituted cyclopropanes, which consist of carbene cyclopropanation of multiple C=C bonds by sodium dibromofluoroacetate catalyzed by (IPr)AgCl. The new method is effective for the cyclopropanation of not only boronyl- and silyl-substituted olefins, but also for low-reactivity alkenes, such as monoalkyl substituted alkenes, allyl alcohol ethers and α,β-unsaturated carbonyl compounds. The conditions for isomerization of silyl- and boronyl-substituted fluorohalocyclopropanes in the presence of catalytic amounts of copper (I) bromide in acetonitrile was selected. It was shown that the regioselectivity of the process is determined by the thermodynamic control. Thus, the formation of fluorovinylsilanes or fluorovinylboranes in the isomerization of α-silyl- or α-boronyl-gem-bromofluorophenylcyclopropanes and fluoroallylsilanes upon isomerization of β-silyl-gem-bromofluorophenylcyclopropanes was observed. Thus, new types of fluorinated reagents were obtained that are not previously described in the literature (...)

Light as energy source in chemical reaction. New synthesis of valuable dithienylacetylenes

Photochromism (from Greek φωζ photo “light” and χρωμα chroma “colour”) is determined as reversible transformation between two chemical species, induced by action of light [1]. Herewith, initial form and photoinduced isomer have different physical and chemical properties. The phenomenon is attractive for the design of hi-tech materials, including optical memory elements and molecular switches. Diarylethenes is the most promising class of organic photochromic compounds due to outstanding thermal stability of both isomers and high photostability [2]. The size of so-called ethene bridge significantly affects the photochromic reaction. The photochromic diarylethenes with 4-, 5-, and 6-membered cyclic ethene bridge are known, but there is no example with 3-membered bridge. In this study we report a new approach towards dithienylacetylenes 3 that include the synthesis of diarylcyclopropenones 2 via Friedel-Crafts alkylation of heterocyclic compounds 1 with tetrachlorocyclopropene and following UV-irradiation. It was found that the diarylethenes 2 do not display photochromic properties, but they undergo quantitative photoelimination of carbon monoxide upon UV-irradiation resulting in dithienylacetylene 3. Thus, we have proposed a new synthetic two-step approach to dithienylacetylenes 3 [3], which could be useful synthons in synthesis of photochromic diarylethenes with various ethene bridges.

[3+3]-annelation of cyclic nitronates with enol diazoacetates

The purpose of this research is to prevent the desertification by using my original “agar sheets”. The dry regions, in other words, the desert has already occupied about forty percent of the surface of the earth (Figure 1). In addition, it is said that land of seven million hectares turn into desert every year. However, we can reproduce the green-bosomed earth by using appropriate means, because this desertification originated in excessive farming, excessive pasturing, and deforestation caused by human beings. I learned “Cape Erimo’s Green Construction Method”, which has succeeded in planting trees in the coast of Japan by using seaweed, and this method led me to use the agar to prevent the desertification, which is a familiar Japanese food made from seaweed. I think that it is possible to prevent the desertification of any conditioned lands by using my original “agar sheets.”

Reactivity of styrylmalonates as synthetic equivalents of Donor–acceptor cyclopropanes with aldehydes in the presence of BF3•Et2O

Donor–acceptor cyclopropanes (DACs), which can act as sources of 1,2- and 1,3-zwitterions in the presence of Lewis acids, are widely used in organic synthesis for the preparation of various carbo- and heterocyclic compounds, including natural compounds and their analogues. To date, many types of DACs reactivity have been identified. However, the chemistry of styrylmalonates (isomers of DACs, which can be easily generated from DACs) is almost undescribed and has a powerful synthetic potential. The use of styrylmalonates as synthetic equivalents of DACs allows us cardinally change the known reaction pathways of DACs. In this work, a new strategy for cascade assembly of substituted pyrenes based on the reactions of styrylmalonates with aldehydes in the presence of BF3•Et2O has been developed. Generation of formal 1,2-zwitterionic intermediates owing to complexation of dicarboxylate groups with BF3•Et2O is the driving force of the reaction discovered. This method makes it possible to assemble pyrenes or 5,6-dihydro-2H-pyran-2-ones in one synthetic stage from readily available starting compounds with high regio- and diastereoselectivity, and use these pyrenes in futher reactions. We’ve optimized conditions of the reaction and synthesized a number of various substituted pyrenes. Moreover, the reaction shows good results with various aromatic and heteroaromatic substituents. Pyrenes can be easily purified by crystallization. Every product was obtained selectively and determined by full set of physical-chemical methods, including X-ray analysis. 5,6-dihydro-2H-pyran-2-one skeleton is found in various natural compounds demonstrating a broad spectrum of biological activity, such as antiviral and antineoplastic.

Interaction of the unsaturated sulfones with azinium ylides

1. Introduction In Japan the energy self-efficiency is very low: only 6%. Hydrogen (H2) has been expected as a new and alternative energy source to imported one, such as petroleum resources. Now hydrogen energy comes into the practical use in the field of the fuel cell. Hydrogen must be extracted from other sources, for example, water, fossil fuel, and so on. Hydrogen is obtained from water by using electronic or thermal or photo energy in most cases, whereas it is well-known that hydrogen is given by the oxidation reaction of silicon in alkaline aqueous solution: Si + 2OH- + H2O → SiO32- + 2H2 Free silicon (Si) is not only used in the steel refining, aluminum-casting in the field of fine chemical industries but also is used as a material in semiconductor electronics. However, a lot of used silicon is thrown away as a waste, being not reused and recycled. In this study we try to apply a waste silicon to obtain hydrogen based on the above reaction. The purpose of the study is to develop a safe and convenient manufacturing method to generate hydrogen for an energy source of the fuel cell.

Co-evolution of transcription factors and their binding sites in DNA

The synthesis of RNA using DNA (transcription) can be regulated by special proteins - transcription factors (TF) by binding to specific DNA regions - binding sites (BSTF). The purpose of the project is building a phylogenetic tree of orthologous groups of the each studying TF subfamilies, compare it with the tree of the corresponding BSTF motifs belonging to one orthologous group, find some common parts.

Direct reductive amination of camphor

Terpenoids are an irreplaceable class of natural products. The camphoryl group is an important moiety in the structure of chiral ligands for asymmetric synthesis catalysis or it can be used as an auxiliary group in asymmetric synthesis.[1] The usage of fenchone based molecules for asymmetric catalysis and synthesis is less common because of the difficulty of fenchone modifications due to steric hindrance. Camphor is a readily available starting molecule for the preparation of different compounds with biological activity. For example, camphor diimines demonstrate antiviral activity.[2] Fenchonyl amine-based molecules are potential therapeutic agents for the treatment of Alzheimer’s disease. Amines are a crucial class of organic compounds with multiple academic and industrial applications. There are a plethora of synthetic approaches towards amines synthesis and modifications, reductive amination being one of the most powerful and useful methods. However, the reductive amination of camphor and fenchone remains a challenge. A standard approach to reductive amination with amines other than ammonia and methylamine includes two steps: preparation of azomethines or Schiff bases in the presence of strong Lewis acids and their reduction with more or less conventional reducing agents. The synthesis of fenchonyl amines is even more challenging. There is no universal approach, and almost every manuscript reports some particular protocol different from others. In most cases, the first stage of this process requires quite harsh conditions. For example, the preparation of a Schiff base from camphor and 1-phenylethylamine requires 5-10 days of heating at 150°C.[3] Schiff bases of other primary amines could be prepared under similarly harsh conditions. Preparation of enamines is possible using titanium tetrachloride as a catalyst. The reduction also might be challenging. Sodium borohydride or sodium cyanoborohydride was described as suitable for this goal in several reports.[4] To the best of our knowledge, no papers describe any general approach for the direct reductive amination of camphor or fenchone. There is only one example of camphor direct reductive amination without an external hydrogen source using carbon monoxide as a reducing agent. This protocol is very efficient but its application is limited by the necessity of carbon monoxide and high-pressure equipment for the reaction setup.