Cis-regulatory control of the SM50 gene, an early marker of skeletogenic lineage specification in the sea urchin embryo

The SM50 gene encodes a minor matrix protein of the sea urchin embryo spicule. We carried out a detailed functional analysis of a cis-regulatory region of this gene, extending 440 bp upstream and 120 bp downstream of the transcription start site, that had been shown earlier to confer accurate skeletogenic expression of an injected expression vector. The distal portion of this fragment contains elements controlling amplitude of expression, while the region from −200 to +105 contains spatial control elements that position expression accurately in the skeletogenic lineages of the embryo. A systematic mutagenesis analysis of this region revealed four adjacent regulatory elements, viz two copies of a positively acting sequence (element D) that are positioned just upstream of the transcription start site; an indispensable spatial control element (element C) that is positioned downstream of the start site; and further downstream, a second positively acting sequence (element A). We then constructed a series of synthetic expression constructs. These contained oligonucleotides representing normal and mutated versions of elements D, C, and A, in various combinations. We also changed the promoter of the SM50 gene from a TATA-less to a canonical TATA box form, without any effect on function. Perfect spatial regulation was also produced by a final series of constructs that consisted entirely of heterologous enhancers from the CyIIIa gene, the SV40 early promoter, and synthetic D, C, and A elements. We demonstrate that element C exercises the primary spatial control function of the region we analyzed. We term this a ‘locator’ element. This differs from conventional ‘tissue-specific enhancers’ in that while it is essential for expression, it has no transcriptional activity on its own, and it requires other, separable, positive regulatory elements for activity. In the normal configuration these ancillary positive functions are mediated by elements A and D. Only positively acting control elements were observed in the SM50 regulatory domain throughout this analysis

A Monte Carlo simulation of ion transport at finite temperatures

We have developed a Monte Carlo simulation for ion transport in hot background gases, which is an alternative way of solving the corresponding Boltzmann equation that determines the distribution function of ions. We consider the limit of low ion densities when the distribution function of the background gas remains unchanged due to collision with ions. A special attention has been paid to properly treat the thermal motion of the host gas particles and their influence on ions, which is very important at low electric fields, when the mean ion energy is comparable to the thermal energy of the host gas. We found the conditional probability distribution of gas velocities that correspond to an ion of specific velocity which collides with a gas particle. Also, we have derived exact analytical formulas for piecewise calculation of the collision frequency integrals. We address the cases when the background gas is monocomponent and when it is a mixture of different gases. The developed techniques described here are required for Monte Carlo simulations of ion transport and for hybrid models of non-equilibrium plasmas. The range of energies where it is necessary to apply the technique has been defined. The results we obtained are in excellent agreement with the existing ones obtained by complementary methods. Having verified our algorithm, we were able to produce calculations for Ar$^+$ ions in Ar and propose them as a new benchmark for thermal effects. The developed method is widely applicable for solving the Boltzmann equation that appears in many different contexts in physics.Comment: 14 page

Synthesis, determination of the absolute configuration of tonkinelin, and inhibitory action with bovine heart mitochondrial complex I

ArticleBIOORGANIC & MEDICINAL CHEMISTRY. 15(8): 3026-3031 (2007)journal articl

Anti-inflammatory sesquiterpenes from Curcuma zedoaria

This is a preprint of an article whose final and definitive form has been published in the NATURAL PRODUCT RESEARCH © 2006 copyright Taylor & Francis; NATURAL PRODUCT RESEARCH is available online at: http://www.informaworld.com/openurl?genre=article&issn=1478-6419&volume=20&issue=7&spage=680ArticleNATURAL PRODUCT RESEARCH. 20(7): 680-685 (2006)journal articl

Experimental benchmark of kinetic simulations of capacitively coupled plasmas in molecular gases

International audienceWe discuss the origin of uncertainties in the results of numerical simulations of low-temperature plasma sources, focusing on capacitively coupled plasmas. These sources can be operated in various gases/gas mixtures, over a wide domain of excitation frequency, voltage, and gas pressure. At low pressures, the non-equilibrium character of the charged particle transport prevails and particle-based simulations become the primary tools for their numerical description. The particle-in-cell method, complemented with Monte Carlo type description of collision processes, is a well-established approach for this purpose. Codes based on this technique have been developed by several authors/groups, and have been benchmarked with each other in some cases. Such benchmarking demonstrates the correctness of the codes, but the underlying physical model remains unvalidated. This is a key point, as this model should ideally account for all important plasma chemical reactions as well as for the plasma-surface interaction via including specific surface reaction coefficients (electron yields, sticking coefficients, etc). In order to test the models rigorously, comparison with experimental ?benchmark data? is necessary. Examples will be given regarding the studies of electron power absorption modes in O 2 , and CF 4 ?Ar discharges, as well as on the effect of modifications of the parameters of certain elementary processes on the computed discharge characteristics in O 2 capacitively coupled plasmas

An efficient synthesis of procyanidins. Rare earth metal Lewis acid catalyzed equimolar condensation of catechin and epicatechin

ArticleTETRAHEDRON LETTERS. 48(33): 5891-5894 (2007)journal articl

Electron power absorption dynamics in capacitive radio frequency discharges driven by tailored voltage waveforms in CF4

The power absorption dynamics of electrons and the electrical asymmetry effect in capacitive radio-frequency plasmas operated in CF4 and driven by tailored voltage waveforms are investigated experimentally in combination with kinetic simulations. The driving voltage waveforms are generated as a superposition of multiple consecutive harmonics of the fundamental frequency of 13.56 MHz. Peaks/valleys and sawtooth waveforms are used to study the effects of amplitude and slope asymmetries of the driving voltage waveform on the electron dynamics and the generation of a DC self-bias in an electronegative plasma at different pressures. Compared to electropositive discharges, we observe strongly different effects and unique power absorption dynamics. At high pressures and high electronegativities, the discharge is found to operate in the drift-ambipolar (DA) heating mode. A dominant excitation/ionization maximum is observed during sheath collapse at the edge of the sheath which collapses fastest. High negative-ion densities are observed inside this sheath region, while electrons are confined for part of the RF period in a potential well formed by the ambipolar electric field at this sheath edge and the collapsed (floating potential) sheath at the electrode. For specific driving voltage waveforms, the plasma becomes divided spatially into two different halves of strongly different electronegativity. This asymmetry can be reversed electrically by inverting the driving waveform. For sawtooth waveforms, the discharge asymmetry and the sign of the DC self-bias are found to reverse as the pressure is increased, due to a transition of the electron heating mode from the α-mode to the DA-mode. These effects are interpreted with the aid of the simulation results

Hadal water biogeochemistry over the Izu–Ogasawara Trench observed with a full-depth CTD-CMS

Full-depth profiles of hydrographic and geochemical properties at the Izu–Ogasawara Trench were observed for the first time using a CTD-CMS (conductivity–temperature–depth profiler with carousel multiple sampling) system. Additionally, comparative samplings were done at the northern Mariana Trench using the same methods. A well-mixed hydrographic structure below 7000 m was observed within the Izu–Ogasawara Trench. Seawater samples collected from this well-mixed hadal layer exhibited constant concentrations of nitrate, phosphate, silicate, and nitrous oxide as well as constant nitrogen and oxygen isotopic compositions of nitrate and nitrous oxide. These results agree well with previous observations of the Izu–Ogasawara hadal waters and deep-sea water surrounding the Izu–Ogasawara Trench. In turn, methane concentrations and isotopic compositions indicated spatial heterogeneity within the well-mixed hadal water mass, strongly suggesting a local methane source within the trench, in addition to the background methane originating from the general deep-sea bottom water. Sedimentary compound releases, associated with sediment re-suspensions, are considered to be the most likely mechanism for generating this significant CH4 anomaly.</p