Reversal of handedness in DNA: A stable link between RU and LZ helices

Two types of left-handed zig-zag (LZ) helices were obtained following stereochemical guideline. They are referred to as LZ1 and LZ2 helices. LZ1 helices have conformations similar to those found in the single crystals of d(C-G)3 and d(C-G)25,6. Z-character is more prominent in LZ2 than in LZ1 helix. The conformations of a stable link between RU and LZ helical fragments are given. The link involves inverted stacking arrangement of the bases: a characteristic feature of all RL models proposed by us

Multiaction learning automata possessing ergodicity of the mean

Multiaction learning automata which update their action probabilities on the basis of the responses they get from an environment are considered in this paper. The automata update the probabilities according to whether the environment responds with a reward or a penalty. Learning automata are said to possess ergodicity of the mean if the mean action probability is the state probability (or unconditional probability) of an ergodic Markov chain. In an earlier paper [11] we considered the problem of a two-action learning automaton being ergodic in the mean (EM). The family of such automata was characterized completely by proving the necessary and sufficient conditions for automata to be EM. In this paper, we generalize the results of [11] and obtain necessary and sufficient conditions for the multiaction learning automaton to be EM. These conditions involve two families of probability updating functions. It is shown that for the automaton to be EM the two families must be linearly dependent. The vector defining the linear dependence is the only vector parameter which controls the rate of convergence of the automaton. Further, the technique for reducing the variance of the limiting distribution is discussed. Just as in the two-action case, it is shown that the set of absolutely expedient schemes and the set of schemes which possess ergodicity of the mean are mutually disjoint.

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.The ISME Journal advance online publication, 13 March 2014; doi:10.1038/ismej.2014.25.

Amide catalysed facile isomerization of 5,6-dihydroisoquinolines: synthesis of stable 1,2-dihydroisoquinolines

Stable 1,2-dihydroisoquinolines have been synthesized by an amide catalysed novel isomerization reaction of 5,6-dihydroisoquinolines.

Stable Dispersions of Metal Oxide Nanowires and Nanoparticles in Water, Dimethylformamide and Toluene

In view of the important need to generate well-dispersed inorganic nanostructures in various solvents, we have explored the dispersion of nanostructures of metal oxides such as TiO2, Fe3O4 and ZnO in solvents of differing polarity in the presence of several surfactants. The solvents used are water, dimethylformamide (DMF) and toluene. The surfactant-solvent combinations yielding the best dispersions are reported alongwith some of the characteristics of the nanostructures in the dispersions. The surfactants which dispersed TiO2 nanowires in water were polyethylene oxide (PEO), Triton X-100 (TX-100), polyvinyl alcohol (PVA) and sodium bis(2-ethylhexyl) sulphosuccinate (AOT). TiO2 nanoparticles could also be dispersed with AOT and PEO in water, and with AOT in toluene. In DMF, PVA, PEO and TX-100 were found to be effective, while in toluene, only AOT gave good dispersions. Fe3O4 nanoparticles were held for long periods of time in water by PEO, AOT, PVA and polyethylene glycol (PEG), and by AOT in toluene. In the case of ZnO nanowires, the best surfactant-solvent combinations were found to be, PEO, sodium dodecyl sulphate (SIDS) and AOT in water and AOT, PEG, PVA, PEO and TX-100 in DMF In toluene, stable dispersions of ZnO nanowires were obtained with PEO. We have also been able to disperse oxide nanostructures in non-polar solvents by employing a hydrophobic silane coating on the surface.

Isotopic fingerprints in surficial waters : Stable isotope methods applied in hydrogeological studies

The driving force behind this study has been the need to develop and apply methods for investigating the hydrogeochemical processes of significance to water management and artificial groundwater recharge. Isotope partitioning of elements in the course of physicochemical processes produces isotopic variations to their natural reservoirs. Tracer property of the stable isotope abundances of oxygen, hydrogen and carbon has been applied to investigate hydrogeological processes in Finland. The work described here has initiated the use of stable isotope methods to achieve a better understanding of these processes in the shallow glacigenic formations of Finland. In addition, the regional precipitation and groundwater records will supplement the data of global precipitation, but as importantly, provide primary background data for hydrological studies. The isotopic composition of oxygen and hydrogen in Finnish groundwaters and atmospheric precipitation was determined in water samples collected during 1995 2005. Prior to this study, no detailed records existed on the spatial or annual variability of the isotopic composition of precipitation or groundwaters in Finland. Groundwaters and precipitation in Finland display a distinct spatial distribution of the isotopic ratios of oxygen and hydrogen. The depletion of the heavier isotopes as a function of increasing latitude is closely related to the local mean surface temperature. No significant differences were observed between the mean annual isotope ratios of oxygen and hydrogen in precipitation and those in local groundwaters. These results suggest that the link between the spatial variability in the isotopic composition of precipitation and local temperature is preserved in groundwaters. Artificial groundwater recharge to glaciogenic sedimentary formations offers many possibilities to apply the isotopic ratios of oxygen, hydrogen and carbon as natural isotopic tracers. In this study the systematics of dissolved carbon have been investigated in two geochemically different glacigenic groundwater formations: a typical esker aquifer at Tuusula, in southern Finland and a carbonate-bearing aquifer with a complex internal structure at Virttaankangas, in southwest Finland. Reducing the concentration of dissolved organic carbon (DOC) in water is a primary challenge in the process of artificial groundwater recharge. The carbon isotope method was used to as a tool to trace the role of redox processes in the decomposition of DOC. At the Tuusula site, artificial recharge leads to a significant decrease in the organic matter content of the infiltrated water. In total, 81% of the initial DOC present in the infiltrated water was removed in three successive stages of subsurface processes. Three distinct processes in the reduction of the DOC content were traced: The decomposition of dissolved organic carbon in the first stage of subsurface flow appeared to be the most significant part in DOC removal, whereas further decrease in DOC has been attributed to adsorption and finally to dilution with local groundwater. Here, isotope methods were used for the first time to quantify the processes of DOC removal in an artificial groundwater recharge. Groundwaters in the Virttaankangas aquifer are characterized by high pH values exceeding 9, which are exceptional for shallow aquifers on glaciated crystalline bedrock. The Virttaankangas sediments were discovered to contain trace amounts of fine grained, dispersed calcite, which has a high tendency to increase the pH of local groundwaters. Understanding the origin of the unusual geochemistry of the Virttaankangas groundwaters is an important issue for constraining the operation of the future artificial groundwater plant. The isotope ratios of oxygen and carbon in sedimentary carbonate minerals have been successfully applied to constrain the origin of the dispersed calcite in the Virttaankangas sediments. The isotopic and chemical characteristics of the groundwater in the distinct units of aquifer were observed to vary depending on the aquifer mineralogy, groundwater residence time and the openness of the system to soil CO2. The high pH values of > 9 have been related to dissolution of calcite into groundwater under closed or nearly closed system conditions relative to soil CO2, at a low partial pressure of CO2.

Stable expression of silencing-suppressor protein enhances the performance and longevity of an engineered metabolic pathway

Transgenic engineering of plants is important in both basic and applied research. However, the expression of a transgene can dwindle over time as the plant's small (s)RNA-guided silencing pathways shut it down. The silencing pathways have evolved as antiviral defence mechanisms, and viruses have co-evolved viral silencing-suppressor proteins (VSPs) to block them. Therefore, VSPs have been routinely used alongside desired transgene constructs to enhance their expression in transient assays. However, constitutive, stable expression of a VSP in a plant usually causes pronounced developmental abnormalities, as their actions interfere with endogenous microRNA-regulated processes, and has largely precluded the use of VSPs as an aid to stable transgene expression. In an attempt to avoid the deleterious effects but obtain the enhancing effect, a number of different VSPs were expressed exclusively in the seeds of Arabidopsis thaliana alongside a three-step transgenic pathway for the synthesis of arachidonic acid (AA), an ω-6 long chain polyunsaturated fatty acid. Results from independent transgenic events, maintained for four generations, showed that the VSP-AA-transformed plants were developmentally normal, apart from minor phenotypes at the cotyledon stage, and could produce 40% more AA than plants transformed with the AA transgene cassette alone. Intriguingly, a geminivirus VSP, V2, was constitutively expressed without causing developmental defects, as it acts on the siRNA amplification step that is not part of the miRNA pathway, and gave strong transgene enhancement. These results demonstrate that VSP expression can be used to protect and enhance stable transgene performance and has significant biotechnological application.

A single point mutation disrupts the capsid assembly in Sesbania Mosaic Virus resulting in a stable isolated dimer

Protein-protein interactions play a Crucial role in Virus assembly and stability. With the view of disrupting capsid assembly and capturing smaller oligomers, interfacial residue mutations were carried Out in the coat protein gene of Sesbania Mosaic Virus, a T=3 ss (+) RNA plant virus. A single point mutation of a Trp 170 present at the five-fold interface of the virus to a charged residue (Glu or Lys) arrested assembly of virus like particles and resulted in stable Soluble dimers of the capsid Protein. The X-ray crystal structure of one of the isolated dimer mutants - rCP Delta N65W170K was determined to a resolution of 2.65 angstrom. Detailed analysis of the dimeric mutant protein structure revealed that a number of Structural changes take place, especially in the loop and interfacial regions during the course of assembly. The isolated chiller was ``more relaxed'' than the dimer found in the T=3 or T=1 capsids. The isolated dimer does not bind Ca2+ ion and consequently four C-terminal residues are disordered. The FG loop, which interacts with RNA in the Virus, has different conformations in the isolated dimer and the intact Virus Suggesting its flexible nature and the conformational changes that accompany assembly. The isolated choler mutant was much less stable when compared to the assembled capsids, suggesting the importance of inter-subunit interactions and Ca2+ mediated interactions in the stability of the capsids. With this study, SeMV becomes the first icosahedral virus for which X-ray crystal Structures of T=3, T=1 capsids as well as a smaller oligomer of the capsid protein have been determined.

Highly stable oscillator for quartz crystal thickness monitor

A highly stable oscillator used in a quartz crystal thickness monitor for monitoring the rate of evaporation and total thickness of film during thin film deposition is reported. The design aspects of the oscillator and its long term stability, which enhances the reproducibility and the performance of the thickness monitor, are discussed. The stability of the oscillator at defined conditions is tested and compared with the conventional transistorized oscillator and the IC oscillator using inverters. The oscillator is coupled to the crystal monitor and its performance is studied in an evaporation system by evaporating different materials

Characterization of single-stranded DNA-binding proteins from Mycobacteria. The carboxyl-terminal of domain of SSB is essential for stable association with its cognate RecA protein

Single-stranded DNA-binding proteins (SSB) play an important role in most aspects of DNA metabolism including DNA replication, repair, and recombination. We report here the identification and characterization of SSB proteins of Mycobacterium smegmatis and Mycobacterium tuberculosis. Sequence comparison of M. smegmatis SSB revealed that it is homologous to M. tuberculosis SSB, except for a small spacer connecting the larger amino-terminal domain with the extreme carboxyl-terminal tail. The purified SSB proteins of mycobacteria bound single-stranded DNA with high affinity, and the association and dissociation constants were similar to that of the prototype SSB. The proteolytic signatures of free and bound forms of SSB proteins disclosed that DNA binding was associated with structural changes at the carboxyl-terminal domain. Significantly, SSB proteins from mycobacteria displayed high affinity for cognate RecA, whereas Escherichia coli SSB did not under comparable experimental conditions. Accordingly, SSB and RecA were coimmunoprecipitated from cell lysates, further supporting an interaction between these proteins in vivo. The carboxyl-terminal domain of M. smegmatis SSB, which is not essential for interaction with ssDNA, is the site of binding of its cognate RecA. These studies provide the first evidence for stable association of eubacterial SSB proteins with their cognate RecA, suggesting that these two proteins might function together during DNA repair and/or recombination.

Tetragonal bismuth bilayer: A stable and robust quantum spin hall insulator

Topological insulators (TIs) exhibit novel physics with great promise for new devices, but considerable challenges remain to identify TIs with high structural stability and large nontrivial band gap suitable for practical applications. Here we predict by first-principles calculations a two-dimensional (2D) TI, also known as a quantum spin Hall (QSH) insulator, in a tetragonal bismuth bilayer (TB-Bi) structure that is dynamically and thermally stable based on phonon calculations and finite-temperature molecular dynamics simulations. Density functional theory and tight-binding calculations reveal a band inversion among the Bi-p orbits driven by the strong intrinsic spin-orbit coupling, producing a large nontrivial band gap, which can be effectively tuned by moderate strains. The helical gapless edge states exhibit a linear dispersion with a high Fermi velocity comparable to that of graphene, and the QSHphase remains robust on a NaCl substrate. These remarkable properties place TB-Bi among the most promising 2D TIs for high-speed spintronic devices, and the present results provide insights into the intriguing QSH phenomenon in this new Bi structure and offer guidance for its implementation in potential applications.

Absolute quantification of human tear lactoferrin using multiple reaction monitoring technique with stable-isotopic labeling

The mass spectrometry technique of multiple reaction monitoring (MRM) was used to quantify and compare the expression level of lactoferrin in tear films among control, prostate cancer (CaP), and benign prostate hyperplasia (BPH) groups. Tear samples from 14 men with CaP, 15 men with BPH, and 14 controls were analyzed in the study. Collected tears (2 μl) of each sample were digested with trypsin overnight at 37 °C without any pretreatment, and tear lactoferrin was quantified using a lactoferrin-specific peptide, VPSHAVVAR, both using natural/light and isotopic-labeled/heavy peptides with MRM. The average tear lactoferrin concentration was 1.01 ± 0.07 μg/μl in control samples, 0.96 ± 0.07 μg/μl in the BPH group, and 0.98 ± 0.07 μg/μl in the CaP group. Our study is the first to quantify tear proteins using a total of 43 individual (non-pooled) tear samples and showed that direct digestion of tear samples is suitable for MRM studies. The calculated average lactoferrin concentration in the control group matched that in the published range of human tear lactoferrin concentration measured by enzyme-linked immunosorbent assay (ELISA). Moreover, the lactoferrin was stably expressed across all of the samples, with no significant differences being observed among the control, BPH, and CaP groups.