Reconstructing Past Climate by Using Proxy Data and a Linear Climate Model

Thesis (Master's)--University of Washington, 2016-06

Chemical composition and stable sulfur isotope record of Black Sea sediments

The main terminal processes of organic matter mineralization in anoxic Black Sea sediments underlying the sulfidic water column are sulfate reduction in the upper 2-4 m and methanogenesis below the sulfate zone. The modern marine deposits comprise a ca. 1-m-deep layer of coccolith ooze and underlying sapropel, below which sea water ions penetrate deep down into the limnic Pleistocene deposits from >9000 years BP. Sulfate reduction rates have a subsurface maximum at the SO4[2-]-CH4 transition where H2S reaches maximum concentration. Because of an excess of reactive iron in the deep limnic deposits, most of the methane-derived H2S is drawn downward to a sulfidization front where it reacts with Fe(III) and with Fe2+ diffusing up from below. The H2S-Fe2+ transition is marked by a black band of amorphous iron sulfide above which distinct horizons of greigite and pyrite formation occur. The pore water gradients respond dynamically to environmental changes in the Black Sea with relatively short time constants of ca. 500 yr for SO4[2-] and 10 yr for H2S, whereas the FeS in the black band has taken ca. 3000 yr to accumulate. The dual diffusion interfaces of SO4[2-]-CH4 and H2S-Fe2+ cause the trapping of isotopically heavy iron sulfide with delta34S = +15 to +33 per mil at the sulfidization front. A diffusion model for sulfur isotopes shows that the SO4[2-] diffusing downward into the SO4[2-]-CH4 transition has an isotopic composition of +19 per mil, close to the +23 per mil of H2S diffusing upward. These isotopic compositions are, however, very different from the porewater SO4[2-] (+43 per mil) and H2S (-15 per mil) at the same depth. The model explains how methane-driven sulfate reduction combined with a deep H2S sink leads to isotopically heavy pyrite in a sediment open to diffusion. These results have general implications for the marine sulfur cycle and for the interpretation of sulfur isotopic data in modern sediments and in sedimentary rocks throughout earth's history.

‘Genetic Coding’ Reconsidered : An Analysis of Actual Usage

I thank George Pandarakalam for research assistance; Hans-Jörg Rheinberger for hosting my stay at the Max Planck Institute for History of Science, Berlin; and Sahotra Sarkar and referees of this journal for offering detailed comments. Funded by the Wellcome Trust (WT098764MA).

‘Genetic Coding’ Reconsidered : An Analysis of Actual Usage

I thank George Pandarakalam for research assistance; Hans-Jörg Rheinberger for hosting my stay at the Max Planck Institute for History of Science, Berlin; and Sahotra Sarkar and referees of this journal for offering detailed comments. Funded by the Wellcome Trust (WT098764MA).

El color en los códices prehispánicos del México Central: identificación material, cualidad plástica y valor estético

Este artículo investiga algunos de los valores plásticos y estéticos que presidieron la selección y la preparación de las materias colorantes empleadas para iluminar los códices creados por los nahuas del México Central durante el Posclásico Tardío. Estos códices son interesantes porque análisis arqueométricos y exámenes codicológicos recientes han permitido conocer la materialidad de su capa pictórica, así como las características formales y el comportamiento de los colores en estas obras. Uno de los aportes trascendentales de estos estudios ha sido averiguar que la paleta cromática que sirvió para pintar los códices del México Central era principalmente de origen orgánico, lo que contrasta con la naturaleza de los pigmentos detectados en restos de pintura mural y en esculturas creadas por los nahuas que son sobre todo minerales. El objetivo de este artículo es reflexionar sobre las razones de esas diferencias y demostrar que el uso de los colorantes orgánicos en los códices respondía a un fin plástico específico que concordaba con el canon estético imperante en la sociedad náhuatl.

The interplay between neuronal activity and actin dynamics mimic the setting of an LTD synaptic tag

Persistent forms of plasticity, such as long-term depression (LTD), are dependent on the interplay between activity-dependent synaptic tags and the capture of plasticity-related proteins. We propose that the synaptic tag represents a structural alteration that turns synapses permissive to change. We found that modulation of actin dynamics has different roles in the induction and maintenance of LTD. Inhibition of either actin depolymerisation or polymerization blocks LTD induction whereas only the inhibition of actin depolymerisation blocks LTD maintenance. Interestingly, we found that actin depolymerisation and CaMKII activation are involved in LTD synaptic-tagging and capture. Moreover, inhibition of actin polymerisation mimics the setting of a synaptic tag, in an activity-dependent manner, allowing the expression of LTD in non-stimulated synapses. Suspending synaptic activation also restricts the time window of synaptic capture, which can be restored by inhibiting actin polymerization. Our results support our hypothesis that modulation of the actin cytoskeleton provides an input-specific signal for synaptic protein capture.

Unexpected seasonality in quantity and composition of Amazon rainforest air reactivity.

The hydroxyl radical (OH) removes most atmospheric pollutants from air. The loss frequency of OH radicals due to the combined effect of all gas-phase OH reactive species is a measureable quantity termed total OH reactivity. Here we present total OH reactivity observations in pristine Amazon rainforest air, as a function of season, time-of-day and height (0?80 m). Total OH reactivity is low during wet (10 s1) and high during dry season (62 s1). Comparison to individually measured trace gases reveals strong variation in unaccounted for OH reactivity, from 5 to 15% missing in wet-season afternoons to mostly unknown (average 79%) during dry season. During dry-season afternoons isoprene, considered the dominant reagent with OH in rainforests, only accounts for B20% of the total OH reactivity. Vertical profiles of OH reactivity are shaped by biogenic emissions, photochemistry and turbulent mixing. The rainforest floor was identified as a significant but poorly characterized source of OH reactivity.

Variabilidade da concentração média de CO2 acima da floresta Amazônica durante a noite associada a distintos regimes turbulentos.

Estudou-se a Camada Limite Noturna ? CLN sobre área de floresta tropical primária a nordeste do Estado do Amazonas, no Observatório Amazônico da Torre Alta ? OATA ou Amazon Tall Tower Observatory ? ATTO. Foi aplicada a metodologia disponível na literatura que permitiu a caracterização da CLN em três regimes turbulentos: 1º) de turbulência fraca, com velocidade média do vento baixa; 2º) de turbulência forte, com velocidade do vento alta e, 3º) turbulência intermitente e condições de não estacionariedade. Existem variações sazonais nos valores de ?c? e ao passar de um regime para outro. Foram investigadas algumas das principais características estatísticas das concentrações de CO2 ? ?c? de cada um dos regimes turbulentos. ?c? aumenta levemente com a elevação do valor de uma escala característica de velocidade turbulenta, VTKE, até um valor limiar, VL, a partir do qual tem-se um aumento súbito nos valores de ?c?. Esses resultados têm importantes consequências para a parametrização de grandezas meteorológicas na CLN e modelagem do escoamento atmosférico na interface floresta-atmosfera.

Scalar turbulent behavior in the roughness sublayer of an Amazonian forest.

An important current problem in micrometeorology is the characterization of turbulence in the roughness sublayer (RSL), where most of the measurements above tall forests are made. There, scalar turbulent fluctuations display significant departures from the predictions of Monin?Obukhov similarity theory (MOST). In this work, we analyze turbulence data of virtual temperature, carbon dioxide, and water vapor in the RSL above an Amazonian forest (with a canopy height of 40 m), measured at 39.4 and 81.6 m above the ground under unstable conditions. We found that dimensionless statistics related to the rate of dissipation of turbulence kinetic energy (TKE) and the scalar variance display significant departures from MOST as expected, whereas the vertical velocity variance follows MOST much more closely. Much better agreement between the dimensionless statistics with the Obukhov similarity variable, however, was found for the subset of measurements made at a low zenith angle Z, in the range 0°  <  |Z|  <  20°. We conjecture that this improvement is due to the relationship between sunlight incidence and the ?activation?deactivation? of scalar sinks and sources vertically distributed in the forest. Finally, we evaluated the relaxation coefficient of relaxed eddy accumulation: it is also affected by zenith angle, with considerable improvement in the range 0°  <  |Z|  <  20°, and its values fall within the range reported in the literature for the unstable surface layer. In general, our results indicate the possibility of better stability-derived flux estimates for low zenith angle ranges.

Bioinformatic methods in applied genomic research

Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex human dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simultaneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR. This work was done under the supervision of Prof. Christine Nardini, at the “CAS-MPG Partner Institute for Computational Biology” of Shangai, China (co-founded by the Max Planck Society and the Chinese Academy of Sciences jointly) The third topic concerns the development of a new method to overcome the variety of PCR technologies routinely adopted to characterize unknown flanking DNA regions of a viral integration locus of the human genome after clinical gene therapy. This new method is entirely based on next generation sequencing and it reduces the time required to detect insertion sites, decreasing the complexity of the procedure. This work was done in collaboration with the group of Dr. Manfred Schmidt at the Nationales Centrum für Tumorerkrankungen (Heidelberg, Germany) supervised by Dr. Annette Deichmann and Dr. Ali Nowrouzi. Furthermore I add as an Appendix the description of a R package for gene network reconstruction that I helped to develop for scientific usage (http://www.bioconductor.org/help/bioc-views/release/bioc/html/BUS.html).

El rol de las redes de apoyo transnacional en la evolución del régimen de trata de personas en la región del mekong, 2004-2015

Con el fin de la unipolaridad no sólo se fortalecieron mecanismos de gobernanza global como los Regímenes Internacionales, sino también se fortalecieron actores no estatales. A pesar de la importancia que tomaron estos dos elementos aún no existe una teoría que explique exhaustivamente la relación que existe entre ellos. Es por lo anterior que, la investigación busca responder de qué manera el rol de las Redes de Apoyo Transnacional ha incidido en la evolución del régimen de tráfico de personas en la Región del Mekong. Asimismo tiene como objetivo comprender las relación entre el Régimen y las Redes de Apoyo Transnacional a través de la formulación de un caso de estudio basado en metodologías cualitativas, específicamente, en el análisis teórico-constructivista y el análisis de contenido de documentos producidos por actores estatales y no estatales.

Healing wounds institutional strength, peacebuilding, and productive entrepreneurship – exploratory analysis on 23 departments of Colombia

Este estudio presenta un análisis exploratorio sobre la correlación entre la fortaleza institucional, las condiciones de paz, y el emprendimiento en una muestra de 23 departamentos en Colombia usando datos de 2014. Para llevar a cabo este objetivo se propusieron y construyeron tres índices siguiendo definiciones conceptuales seminales o estándares de evaluación internacional, a saber: 1) El Índice de Fortaleza Institucional, 2) El Índice de Construcción de Paz (construido a partir del índice de paz negativa y el índice de paz positiva) y 3) El Índice de Emprendimiento Productivo. Los resultados no muestran una correlación significativa entre todos los tres índices. Por un lado, existe una correlación significativa (p<0.05) entre los índices de fortaleza institucional y emprendimiento productivo. Por otro lado, existen correlaciones negativas no significativas entre los índices de paz positiva y fortaleza institucional, emprendimiento productivo y paz positiva y emprendimiento productivo y construcción de paz. En un segundo acercamiento, la población de los departamentos fue la variable con mayor número de correlaciones significativas (p<0.01) entre variables relacionadas con emprendimiento productivo, empleo, producto interno bruto, sofisticación industrial, innovación (patentes) y crimen. Finalmente, se discuten las conclusiones y las futuras investigaciones.