Synthesis and testing of photoaffinity probes for the site-selectivechemical modifications of the 5-HT3 receptor

The 5-HT3 receptor (5-HT3R) is an important ion channel responsible for the transmission of nerve impulses in the central nervous system.1 It is difficult to characterize transmembrane dynamic receptors with classical structural biology approaches like crystallization and x-ray. The use of photoaffinity probes is an alternative approach to identify regions in the protein that are important for the binding of small molecules. Therefore we synthesized a small library of photoaffinity probes by conjugating photophores via various linkers to granisetron which is a known antagonist of the 5-HT3R. We were able to obtain several compounds with diverse linker lengths and different photolabile moieties that show nanomolar binding affinities for the orthosteric binding site. Furthermore we established a stable h5-HT3R expressing cell line and a purification protocol to yield the receptor in a high purity. Currently we are investigating the photo crosslinking of these ligands with the 5-HT3R.

Synthesis and testing of photoaffinity probes for the site-selective chemical modifications of the 5-HT3 receptor

The 5-HT3 receptor (5-HT3R) is an important ion channel responsible for the transmission of nerve impulses in the central nervous system.[1] It is difficult to characterize transmembrane dynamic receptors with classical structural biology approaches like crystallization and x-ray. The use of photoaffinity probes is an alternative approach to identify regions in the protein that are important for the binding of small molecules. Therefore we synthesized a small library of photoaffinity probes by conjugating photolabile building blocks via various linkers to granisetron which is a known antagonist of the 5-HT3R. We were able to obtain several compounds with diverse linker lengths and different photo-labile moieties that show nanomolar binding affinities for the orthosteric binding site. Further on we developed a stable 5-HT3R overexpressing cell line and a purification method to yield the receptor in a high purity. Currently we are investigating crosslinking experiments and subsequent MS – analysis.

Synthesis and testing of photoaffinity probes for the site-selectivechemical modifications of the 5-HT3 receptor

The 5-HT3 receptor (5-HT3R) is an important ion channel responsible for the transmission of nerve impulses in the central nervous system.1 It is difficult to characterize transmembrane dynamic receptors with classical structural biology approaches like crystallization and x-ray. The use of photoaffinity probes is an alternative approach to identify regions in the protein that are important for the binding of small molecules. Therefore we synthesized a small library of photoaffinity probes by conjugating photophores via various linkers to granisetron which is a known antagonist of the 5-HT3R. We were able to obtain several compounds with diverse linker lengths and different photolabile moieties that show nanomolar binding affinities for the orthosteric binding site. Furthermore we established a stable h5-HT3R expressing cell line and a purification protocol to yield the receptor in a high purity. Currently we are investigating the photo crosslinking of these ligands with the 5-HT3R.

Synthesis and testing of photoaffinity probes for the site-selective chemical modifications of the 5-HT3 receptor

The 5-HT3 receptor (5-HT3R) is an important ion channel responsible for the transmission of nerve impulses in the central nervous system.1 It is difficult to characterize transmembrane dynamic receptors with classical structural biology approaches like crystallization and x-ray. The use of photoaffinity probes is an alternative approach to identify regions in the protein that are important for the binding of small molecules. Therefore we synthesized a small library of photoaffinity probes by conjugating photophores via various linkers to granisetron which is a known antagonist of the 5-HT3R. We were able to obtain several compounds with diverse linker lengths and different photolabile moieties that show nanomolar binding affinities for the orthosteric binding site. Furthermore we established a stable h5-HT3R expressing cell line and a purification protocol to yield the receptor in a high purity. Currently we are investigating the photo crosslinking of these ligands with the 5-HT3R.

Synthesis of photo-crosslinking probes and their application for the site-selective chemical modification of the 5-HT3 receptor

The 5-HT3 receptor (5-HT3R) is an important ion channel responsible for the transmission of nerve impulses in the CNS and PNS that is activated by the endogenous agonist serotonin (5-hydroxytryptamine, 5-HT). 5-HT3R is the only serotonin receptor belonging to the Cys-loop superfamily of neurotransmitter receptors. Different structural biology approaches can be applied, such as crystallization and x-ray analysis. Nonetheless, characterizing the exact ligand binding site(s) of these dynamic receptors is still challenging. The use of photo-crosslinking probes is an alternative validated approach allowing identification of regions in the protein that are important for the binding of small molecules. We designed our probes based on the core structure of the 5-HT3R antagonist granisetron, a FDA approved drug used for the treatment of chemotherapy-induced nausea and vomiting. We synthesized a small library of photo-crosslinking probes by conjugating diazirines and benzophenones via various linkers to granisetron. We were able to obtain several compounds with diverse linker lengths and different photo-crosslinking moieties that show nanomolar binding affinity for the orthosteric binding site. Furthermore we established a stable h5-HT3R expressing cell line and a purification protocol to yield the receptor in a high purity. Several experiments showed unambiguously that we are able to photo-crosslink our probes with the receptor site-specifically. The functionalised protein was analysed by Western blot and MS-analysis. This yielded the exact covalent modification site, corroborating current ligand binding models derived from mutagenesis and docking studies.

Calcium concentrations and isotopic composition in carbonates and porefluids from ODP Hole 130-807A

The calcium isotopic compositions (d44Ca) of 30 high-purity nannofossil ooze and chalk and 7 pore fluid samples from ODP Site 807A (Ontong Java Plateau) are used in conjunction with numerical models to determine the equilibrium calcium isotope fractionation factor (a_s-f) between calcite and dissolved Ca2+ and the rates of post-depositional recrystallization in deep sea carbonate ooze. The value of a_s-f at equilibrium in the marine sedimentary section is 1.0000+/-0.0001, which is significantly different from the value (0.9987+/-0.0002) found in laboratory experiments of calcite precipitation and in the formation of biogenic calcite in the surface ocean. We hypothesize that this fractionation factor is relevant to calcite precipitation in any system at equilibrium and that this equilibrium fractionation factor has implications for the mechanisms responsible for Ca isotope fractionation during calcite precipitation. We describe a steady state model that offers a unified framework for explaining Ca isotope fractionation across the observed precipitation rate range of ~14 orders of magnitude. The model attributes Ca isotope fractionation to the relative balance between the attachment and detachment fluxes at the calcite crystal surface. This model represents our hypothesis for the mechanism responsible for isotope fractionation during calcite precipitation. The Ca isotope data provide evidence that the bulk rate of calcite recrystallization in freshly-deposited carbonate ooze is 30-40%/Myr, and decreases with age to about 2%/Myr in 2-3 million year old sediment. The recrystallization rates determined from Ca isotopes for Pleistocene sediments are higher than those previously inferred from pore fluid Sr concentration and are consistent with rates derived for Late Pleistocene siliciclastic sediments using uranium isotopes. Combining our results for the equilibrium fractionation factor and recrystallization rates, we evaluate the effect of diagenesis on the Ca isotopic composition of marine carbonates at Site 807A. Since calcite precipitation rates in the sedimentary column are many orders of magnitude slower than laboratory experiments and the pore fluids are only slightly oversaturated with respect to calcite, the isotopic composition of diagenetic calcite is likely to reflect equilibrium precipitation. Accordingly, diagenesis produces a maximum shift in d44Ca of +0.15? for Site 807A sediments but will have a larger impact where sedimentation rates are low, seawater circulates through the sediment pile, or there are prolonged depositional hiatuses.

Composition and origin of sediments at DSDP Site 54-424

The sediments recovered on Deep Sea Drilling Project Leg 54 appear to be mixtures of the normal pelagic sediments of the area and hydrothermally produced manganese and iron phases. The latter are mineralogically and chemically very similar to phases recovered from surficial sampling of the mounds. The hydrothermal nontronite which is approximately 15 meters thick in the three holes is essentially free of carbonate or detrital contaminants. The basal sediments are similar to the carbonate oozes presently being deposited in the region, but are enriched in Mn and Fe. This enrichment appears to be the result of hydrothermal deposition that took place at or near the spreading center and may not be associated with the mounds formation. Three different hypotheses for the formation of the nontronite layer and the mounds deposits are considered. An initial deposition of a widespread nontronite layer and subsequent diapiric-like movement of the layer into carbonates could account for the observed stratigraphy; however, if this be correct, analogous deposits should be present in other DSDP sites. The second hypothesis - replacement of the normal sediments by nontronite - may be feasible, but the high purity of the nontronite requires dissolution and removal of refractory elements. The third hypothesis, metal deposition in an advancing oxidation gradient, is compatible with submersible observations of the mounds; however, it can account only for the high purity of the nontronite by very rapid deposition of the hydrothermal phases.

Agricultural pesticide in sediment cores from the Lac de Saint-André, France

Agricultural pesticide use has increased worldwide during the last several decades, but the long-term fate, storage, and transfer dynamics of pesticides in a changing environment are poorly understood. Many pesticides have been progressively banned, but in numerous cases, these molecules are stable and may persist in soils, sediments, and ice. Many studies have addressed the question of their possible remobilization as a result of global change. In this article, we present a retro-observation approach based on lake sediment records to monitor micropollutants and to evaluate the long-term succession and diffuse transfer of herbicides, fungicides, and insecticide treatments in a vineyard catchment in France. The sediment allows for a reliable reconstruction of past pesticide use through time, validated by the historical introduction, use, and banning of these organic and inorganic pesticides in local vineyards. Our results also revealed how changes in these practices affect storage conditions and, consequently, the pesticides' transfer dynamics. For example, the use of postemergence herbicides (glyphosate), which induce an increase in soil erosion, led to a release of a banned remnant pesticide (dichlorodiphenyltrichloroethane, DDT), which had been previously stored in vineyard soil, back into the environment. Management strategies of ecotoxicological risk would be well served by recognition of the diversity of compounds stored in various environmental sinks, such as agriculture soil, and their capability to become sources when environmental conditions change.

137Cs and 90Sr depositions, and 137Cs/90Sr ratios of samples from the Kraton-3 underground nuclear explosion site, Russia

Strontium-90 activity concentrations in surface soils and areal deposition densities have been studied at a site contaminated by an accidental release to atmosphere from the underground nuclear explosion 'Kraton-3' conducted near the Polar Circle (65.9°N, 112.3°E) within the territory of the former USSR in 1978. In 2001-2002, the ground surface contamination at 14 plots studied ranged from 20 to 15000 kBq/m**2, which significantly exceeds the value of 0.44 kBq/m**2 deduced for three background plots. The zone with substantial radiostrontium contamination extends, at least, 2.5 km in a north-easterly direction from the borehole. The average 137Cs/90Sr ratio in the ground contamination originated from the 'Kraton-3' fallout was estimated to be 0.55, which is significantly different from the ratio of 2.05 evaluated for background plots contaminated mostly from global fallout. Although vertical migration of 90Sr in all undisturbed soil profiles studied is more rapid than that for 137Cs, the depth of percolation of both radionuclides into the ground is mostly limited to the top 10-20 cm, which may be explained, primarily, by permafrost conditions. The horizontal migration rate of radiostrontium in the aqueous phase exceeds the radiocaesium migration rate by many times. This phenomenon seems to be a reason for the significant enrichment of the soil surface layers by radiostrontium at some sites, with variations occurring in accordance with small-scale irregularities of landscape.

Understanding and improving the chemical vapor deposition process for solar grade silicon production

Esta Tesis Doctoral se centra en la investigación del proceso de producción de polisilicio para aplicaciones fotovoltaicas (FV) por la vía química; mediante procesos de depósito en fase vapor (CVD). El polisilicio para la industria FV recibe el nombre de silicio de grado solar (SoG Si). Por un lado, el proceso que domina hoy en día la producción de SoG Si está basado en la síntesis, destilación y descomposición de triclorosilano (TCS) en un reactor CVD -denominado reactor Siemens-. El material obtenido mediante este proceso es de muy alta pureza, pero a costa de un elevado consumo energético. Así, para alcanzar los dos principales objetivos de la industria FV basada en silicio, bajos costes de producción y bajo tiempo de retorno de la energía invertida en su fabricación, es esencial disminuir el consumo energético de los reactores Siemens. Por otro lado, una alternativa al proceso Siemens considera la descomposición de monosilano (MS) en un reactor de lecho fluidizado (FBR). Este proceso alternativo tiene un consumo energético mucho menor que el de un reactor Siemens, si bien la calidad del material resultante es también menor; pero ésta puede ser suficiente para la industria FV. A día de hoy los FBR deben aún abordar una serie de retos para que su menor consumo energético sea una ventaja suficiente comparada con otras desventajas de estos reactores. En resumen, la investigación desarrollada se centra en el proceso de depósito de polysilicio por CVD a partir de TCS -reactor Siemens-; pero también se investiga el proceso de producción de SoG Si en los FBR exponiendo las fortalezas y debilidades de esta alternativa. Para poder profundizar en el conocimiento del proceso CVD para la producción de polisilicio es clave el conocimiento de las reacciones químicas fundamentales y cómo éstas influencian la calidad del producto resultante, al mismo tiempo que comprender los fenómenos responsables del consumo energético. Por medio de un reactor Siemens de laboratorio en el que se llevan a cabo un elevado número de experimentos de depósito de polisilicio de forma satisfactoria se adquiere el conocimiento previamente descrito. Se pone de manifiesto la complejidad de los reactores CVD y de los problemas asociados a la pérdidas de calor de estos procesos. Se identifican las contribuciones a las pérdidas de calor de los reactores CVD, éstas pérdidas de calor son debidas principalmente a los fenómenos de radiación y, conducción y convección vía gases. En el caso de los reactores Siemens el fenómeno que contribuye en mayor medida al alto consumo energético son las pérdidas de calor por radiación, mientras que en los FBRs tanto la radiación como el calor transferido por transporte másico contribuyen de forma importante. Se desarrolla un modelo teórico integral para el cálculo de las pérdidas de calor en reactores Siemens. Este modelo está formado a su vez por un modelo para la evaluación de las pérdidas de calor por radiación y modelos para la evaluación de las pérdidas de calor por conducción y convección vía gases. Se ponen de manifiesto una serie de limitaciones del modelo de pérdidas de calor por radiación, y se desarrollan una serie de modificaciones que mejoran el modelo previo. El modelo integral se valida por medio un reactor Siemens de laboratorio, y una vez validado se presenta su extrapolación a la escala industrial. El proceso de conversión de TCS y MS a polisilicio se investiga mediante modelos de fluidodinámica computacional (CFD). Se desarrollan modelados CFD para un reactor Siemens de laboratorio y para un prototipo FBR. Los resultados obtenidos mediante simulación son comparados, en ambos casos, con resultados experimentales. Los modelos desarrollados se convierten en herramientas para la identificación de aquellos parámetros que tienen mayor influencia en los procesos CVD. En el caso del reactor Siemens, ambos modelos -el modelo integral y el modelado CFD permiten el estudio de los parámetros que afectan en mayor medida al elevado consumo energético, y mediante su análisis se sugieren modificaciones para este tipo de reactores que se traducirían en un menor número de kilovatios-hora consumidos por kilogramo de silicio producido. Para el caso del FBR, el modelado CFD permite analizar el efecto de una serie de parámetros sobre la distribución de temperaturas en el lecho fluidizado; y dicha distribución de temperaturas está directamente relacionada con los principales retos de este tipo de reactores. Por último, existen nuevos conceptos de depósito de polisilicio; éstos se aprovechan de la ventaja teórica de un mayor volumen depositado por unidad de tiempo -cuando una mayor superficie de depósito está disponible- con el objetivo de reducir la energía consumida por los reactores Siemens. Estos conceptos se exploran mediante cálculos teóricos y pruebas en el reactor Siemens de laboratorio. ABSTRACT This Doctoral Thesis comprises research on polysilicon production for photovoltaic (PV) applications through the chemical route: chemical vapor deposition (CVD) process. PV polysilicon is named solar grade silicon (SoG Si). On the one hand, the besetting CVD process for SoG Si production is based on the synthesis, distillation, and decomposition of thriclorosilane (TCS) in the so called Siemens reactor; high purity silicon is obtained at the expense of high energy consumption. Thus, lowering the energy consumption of the Siemens process is essential to achieve the two wider objectives for silicon-based PV technology: low production cost and low energy payback time. On the other hand, a valuable variation of this process considers the use of monosilane (MS) in a fluidized bed reactor (FBR); lower output material quality is obtained but it may fulfil the requirements for the PV industry. FBRs demand lower energy consumption than Siemens reactors but further research is necessary to address the actual challenges of these reactors. In short, this work is centered in polysilicon CVD process from TCS -Siemens reactor-; but it also offers insights on the strengths and weaknesses of the FBR for SoG Si production. In order to aid further development in polysilicon CVD is key the understanding of the fundamental reactions and how they influence the product quality, at the same time as to comprehend the phenomena responsible for the energy consumption. Experiments conducted in a laboratory Siemens reactor prove the satisfactory operation of the prototype reactor, and allow to acquire the knowledge that has been described. Complexity of the CVD reactors is stated and the heat loss problem associated with polysilicon CVD is addressed. All contributions to the energy consumption of Siemens reactors and FBRs are put forward; these phenomena are radiation and, conduction and convection via gases heat loss. In a Siemens reactor the major contributor to the energy consumption is radiation heat loss; in case of FBRs radiation and heat transfer due to mass transport are both important contributors. Theoretical models for radiation, conduction and convection heat loss in a Siemens reactor are developed; shaping a comprehensive theoretical model for heat loss in Siemens reactors. Limitations of the radiation heat loss model are put forward, and a novel contribution to the existing model is developed. The comprehensive model for heat loss is validated through a laboratory Siemens reactor, and results are scaled to industrial reactors. The process of conversion of TCS and MS gases to solid polysilicon is investigated by means of computational fluid-dynamics models. CFD models for a laboratory Siemens reactor and a FBR prototype are developed. Simulated results for both CVD prototypes are compared with experimental data. The developed models are used as a tool to investigate the parameters that more strongly influence both processes. For the Siemens reactors, both, the comprehensive theoretical model and the CFD model allow to identify the parameters responsible for the great power consumption, and thus, suggest some modifications that could decrease the ratio kilowatts-hour per kilogram of silicon produced. For the FBR, the CFD model allows to explore the effect of a number of parameters on the thermal distribution of the fluidized bed; that is the main actual challenge of these type of reactors. Finally, there exist new deposition surface concepts that take advantage of higher volume deposited per time unit -when higher deposition area is available- trying to reduce the high energy consumption of the Siemens reactors. These novel concepts are explored by means of theoretical calculations and tests in the laboratory Siemens prototype.

A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin–CDK complex

A novel multiple affinity purification (MAFT) or tandem affinity purification (TAP) tag has been constructed. It consists of the calmodulin binding peptide, six histidine residues, and three copies of the hemagglutinin epitope. This ‘CHH’ MAFT tag allows two or three consecutive purification steps, giving high purity. Active Clb2–Cdc28 kinase complex was purified from yeast cells after inserting the CHH tag into Clb2. Associated proteins were identified using mass spectrometry. These included the known associated proteins Cdc28, Sic1 and Cks1. Several other proteins were found including the 70 kDa chaperone, Ssa1.