Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 1986. / Vita. / Includes bibliographical references (leaves 208-215). / A study of the remineralization of organic carbon was conducted in the organic-rich sediments of Buzzards Bay, MA. Major processes affecting the carbon chemistry in sediments are reflected by changes in the stable carbon isotope ratios of dissolved inorganic carbon (XCO2) in sediment pore water. Six cores were collected seasonally over a period of two years. The following species were measured in the pore waters: JC02, &'3 C-2CO2, P04, JH 2S, Alk, DOC, and Ca. Measurements of pore water collected seasonally show large gradients with depth, which are larger in summer than in winter. The 613C (PDB) of IC02 varies from 1.3 o/oo in the bottom water to approximately -10 o/oo at 30 cm. During all seasons, there was a trend towards more negative values with depth in the upper 8 cm due to the remineralization of organic matter. There was a trend toward more positive values below 8 cm, most likely due to biological irrigation of sediments with bottom water. Below 16-20 cm, a negative gradient was re-established which indicates a return to remineralization as the main process affecting pore water chemistry. Using the XC02 depth profile, it was estimated that 67-85 gC/m 2 are oxidized annually and 5 gC/m 2-yr are buried. The amount of carbon oxidized represented remineralization occurring within the sediments. This estimate indicated that approximately 20% of the annual primary productivity reached the sediments. The calculated remineralization rates varied seasonally with the high of 7.5 x 10-' mol/L-sec observed in August 84 and the low (0.6 x 10-) in December 83. The calculated remineralization rates were dependent on the amount of irrigation in the sediments; if the irrigation parameter is known to ±20%, then the remineralization rates are known to this certainty also. The amount of irrigation in the sediments was estimated using the results of a seasonal study of 2 2 2Rn/ 22 'Ra disequilibria at the same study site (Martin, 1985). Estimates of the annual remineralization in the sediments using solid-phase data indicated that the solid-phase profiles were not at steady-state concentrations. The isotopic signature of 2C02 was used as an indicator of the processes affecting IC02 in pore water. During every month, the oxidation of organic carbon to C02 provided over half of the carbon added to the IC02 pool. However, in every month, the 6'"C of XCO2 added to the pore water in the surface sediments was greater than -15 o/oo, significantly greater than the 613C of solid-phase organic carbon in the sediments (-20.6 o/oo). The 613C of IC02 added to the pore water in the sediments deeper than 7 cm was between -20 and -21 o/oo, similar to the organic carbon in the sediments. Possible explanations of the 1 3C-enrichment observed in the surface sediments were: a) significant dissolution of CaC0 3 (613C = +1.7 o/oo) b) the addition of significant amounts of carbonate ion from bottom water to pore water c) an isotopic difference between the carbon oxidized in the sediments and that remaining in the sediments. The effect of CaC0 3 dissolution was quantified using measured dissolved Ca profiles and was not large enough to explain the observed isotopic enrichment. An additional source of 13C-enriched carbon was bottom water carbonate ion. In every month studied, there was a net flux of 2C0 2 from pore water to bottom water. The flux of pore water 2C02 to bottom water ranged from a minimum of 10 x 10-12 mol/cm 2 -sec in December 83 to a maximum of 50 x 10-12 mol/cm2-sec in August 84. However, because the pH of bottom water was about 8 while that of the pore water was less than or equal to 7, the relative proportion of the different species of inorganic carbon (H2CO, HCO-, C0~) was very different in bottom water and pore water. Thus, while there was a net flux of IC0 2 from pore water to bottom water, there was a flux of carbonate ion from bottom water to pore water. Because bottom water JC02 was more 13C-enriched than pore water JC0 2, the transfer of bottom water carbonate ion to pore water was a source of 13C-enriched carbon to the pore water. If the &'3C of CO2 added to the pore water from the oxidation of organic carbon was -20.6 o/oo, then the flux of C3% from bottom water to pore water must have been 10-30% of the total flux of 2C02 from pore water to bottom water. This is consistent with the amount calculated from the observed gradient in carbonate ion. Laboratory experiments were conducted to determine whether the 613C of C02 produced from the oxidation of organic carbon (613C-OCOX) was different from the 613C of organic carbon in the sediments (613C-SOC). In the laboratory experiments, mud from the sampling site was incubated at a constant temperature. Three depths were studied (0-3, 10-15, and 20-25 cm). For the first study (IEl), sediment was stirred to homogenize it before packing into centrifuge tubes for incubation. For the second study (IE2), sediment was introduced directly into glass incubation tubes by subcoring. The second procedure greatly reduced disturbance to the sediment. Rates of C02 production were calculated from the concentrations of 2C02 measured over up to 46 days. In both studies, the values of Re in the deeper intervals were about 10% of the surface values. This was consistent with the field results, although the rates decreased more rapidly in the field. In all cases, the remineralization rates during the beginning of IEl were much greater than those at the beginning of IE2. The sediment for IEl was collected in February 84. The measured value of Rc in the surface sediment of the laboratory experiment (24 x 10- mol/L-sec) was much greater than the value of Rc observed in the field in another winter month, December 83 (.62 x 10~9). The sediment for IE2 was collected in August 85. The measured values of Re in the surface sediment (6.6-12 x 10~9 mol/L-sec) were consistent with the field values from August 84 (7.5 x 10-9). The XC02 results indicated that IE2 reproduced field conditions more accurately than IEl did. The isotopic results from the experiments strongly suggested that 613C-OCOX in the surface sediments (-17.8 o/oo ± 1.9 o/oo) was greater than 6'3C-SOC (-20.6 ± 0.2 o/oo). The magnitude of the observed fractionation was small enough that the observed values of 613C-C02 in the pore waters could be explained by fractionated oxidation coupled with the diffusion of carbonate ion from bottom water to pore water. The observed fractionation was most likely due to the multiple sources of organic carbon to coastal sediments. A study of the natural levels of radiocarbon in these sediments indicated that the carbon preserved in the sediments is approximately 30% terrestrial while the rest is from phytoplankton. / by Ann P. McNichol. / Ph.D.

Rho GTPases and their regulators such as guanosine exchange factors (GEFs) and GTPase activating proteins (GAPs) represent an important class of molecules controlling dendritic spine plasticity. Although they are typically described as cytoskeletal modulators, roles for the GTPases in endocytosis and cell polarity establishment have also been defined. The neuronal proteins a1- and a2-chimaerins belong to a group of Rac and Cdc42 GAPs that inactivate these GTPases; in addition to a GAP domain, the a-chimaerins share a phosphokinase C (PKC)-like C1 domain but have distinct N-terminal domains (NTDs). My project has explored the importance of specific domains of a1-chimaerin both in induction of a morphological cellular protrusion collapse phenotype ('circularisation') and in interactions with partner proteins that may help to explain the phenotype. The results described in my thesis show that a1-chimaerin possesses a previously undescribed C-terminal domain (CTD) that is indispensable for the ability of the protein to induce collapse of protrusions, and consequent circularisation, in various cell types; moreover, an intact CTD is also important for association of a1-chimaerin with its known effector EphA4, and potentially with other undefined membrane proteins, in a C1-domain- dependent manner. In addition, my results show that a1-chimaerin associates via its NTD with the Src kinase Fyn, and via its C1 domain with the NR2A subunit of the NMDA receptor. Further experiments explored a1-chimaerin effects on EphA4 and NMDA receptor cell surface expression, as well as binding to other putative partners - including the adaptor protein p35 and the polarity protein PAR6. Finally, I have shown that inhibition of a pathway involving the Rho-associated coiled-coil containing protein kinase (ROCK) reverts circularisation induced by a1- chimaerin, and that a blocking peptide based on the CTD may be employed to partially counteract the phenotype. These results uncover a novel domain in a1-chimaerin that may have a crucial importance for the induction of cellular process collapse by a1-chimaerin with a potential relevance to the EphA4-induced dendritic spine retraction, EphA4 receptor endocytosis, and cell surface expression of NR2A-containing NMDA receptors. This suggests a model of a multi-protein signalling complex involving a1-chimaerin that coordinates cellular process remodelling, and that is likely to be important both for adult neuronal circuit plasticity and for neurodegenerative diseases.

The alpaca is a small South American camelid (SAC) that is an important production animal in Peru, especially among the highly impoverished communities of the high Andes, and raised for its fiber and meat. Alpacas are highly reliant on the microbes within their digestive tracts to digest the plant material they consume; volatile fatty acids (VFAs) are released as a byproduct of this microbial fermentation and used as a major source of energy by the alpaca. To explore optimal parameters for alpaca microbiome analysis, performed 16S rRNA gene surveys on alpaca C1 and fecal samples that had been extracted using one of three different DNA extraction methods (PowerFecal® DNA Isolation Kit (MO BIO); ZR Fecal DNA MiniPrep™ (Zymo); and a non-commercial extraction method called salting out) and amplified using one of two different polymerase enzyme mixes (AccuPrime™ Pfx SuperMix and 5 PRIME HotMasterMix). We found that choice of polymerase enzyme had a profound effect on the recovered microbiome, with the majority of 5 PRIME-amplified fecal samples failing to amplify. Extraction method had an effect on the recovered microbiome of fecal samples (but not C1 samples), with samples extracted using the MO BIO kit and the salting out method recovering different communities. The Zymo extraction kit returned microbial communities comparable to each of the other extraction methods. These results suggested that the AccuPrime enzyme and either the MO BIO or Zymo kits were optimal for alpaca gut microbiome analysis. We also performed two 16S rRNA gene surveys, the first from alpacas fed either a grass hay (GH) or alfalfa hay (AH) diet, and the second a C1 survey of alpacas fed two-week periods of mixed grass hay plus one of four supplements. We discovered body site and diet effects on the microbiota of alpacas fed either the GH or AH diet, with samples grouping by general body site (C1, small intestine, and distal intestine) and diet. However, we found no significant effect on the C1 microbiome of alpacas administered grain supplements. To study how energy extraction related to the microbiome, we correlated OTUs from GH/AH-fed alpaca with C1 VFA abundances. We discovered no significant correlations, and a 16S survey of low body condition (LBC) and good body condition (GBC) alpacas showed no difference in C1 microbial communities. We concluded that the microbiota of the alpaca digestive tract follow trends seen in microbiome studies of ruminants, but found no evidence of a relationship between body condition, energy extraction, and the C1 microbiome in alpacas.

Les instabilités fluides peuvent dégrader le confinement du plasma au sein des tokamaks. Étant données les échelles spatio-temporelles, on choisit les modèles fluides obtenus à partir de la dérivation des modèles cinétiques. On dérive plusieurs modèles hiérarchiques de la MagnétoHydroDynamique (MHD) et en particulier les modèles de la MHD réduite du Current Hole et de l'équilibre de Grad-Shafranov. Une des difficulté de l'ensemble de ces modèles est de respecter l'équation modélisant l'absence de monopôles magnétiques. Pour assurer cette condition en tout point du domaine, le champ magnétique est réécrit avec un potentiel vecteur. L'utilisation de potentiels fait apparaître des équations faisant intervenir des dérivées d'ordre supérieurs. La stratégie numérique développée est l'utilisation de la méthode des éléments finis avec des éléments C1 de Bell. Sur un maillage non structuré, ces éléments ont l'intérêt de présenter une base réduite définir exclusivement avec des variables aux noeuds du maillage. Les modèles de MHD réduite du Current Hole et de Grad-Shafranov ont été résolus avec ces éléments. La résolution du cas test de Grad-Shafranov avec les conditions de bords exactes a permis d'obtenir l'ordre optimale de 5. La résolution du système du Current Hole avec ces éléments, validée par l'obtention du paramètre η1/3, a permis l'observation de développement d'instabilités en dents de scies.

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Es geht um die Verbesserung verschiedener Infektions- und Transfektionsprotokolle zur in vitro Arbeit mit Cryptosporidium parvum in der Zellkultur. Des weiteren wurden Mausdarmorganoide ohne Hilfe eines Mikroinjektors mit C. parvum Sporozoiten infiziert. Außerdem wurde ein Protein (Trap-C1) von C. parvum welches ein putativer Virulenzfaktor ist, molekularbiologisch untersucht.

We consider reduced Hsieh-Clough-Tocher basis functions with respect to a splitting into subtriangles at the barycenter of the original triangular element. This article gives a proof that the second derivatives of those functions, which in general may jump at the subtriangle boundaries, do not jump at the barycenter.:1 Introduction 2 Shape functions 3 Transformation of second derivatives 4 Second derivatives at the barycenter

Reduced Hsieh-Clough-Tocher elements are triangular C1-elements with only nine degrees of freedom. Simple formulas for the basis functions of reduced Hsieh-Clough-Tocher elements based on the edge vectors of the triangle have been given recently for a barycentric splitting. We generalise these formulas to the case of an arbitrary splitting point.:1 Introduction 2 Basic definitions 3 Mapping to the reference triangle 4 Construction of the rHCT shape functions

We consider reduced Hsieh-Clough-Tocher basis functions with respect to a splitting into subtriangles at an arbitrary interior point of the original triangular element. This article gives a proof that the second derivatives of those functions, which in general may jump at the subtriangle boundaries, do not jump at the splitting point.:1 Introduction 2 Shape functions 3 Transformation of second derivatives 4 Second derivatives at the splitting point