Microbial cycling of marine high molecular weight dissolved organic matter

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2016Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) – a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean.Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599) and the Gordon and Betty Moore Foundation (grant #492.01, #3777, and #3298)

Microbial cycling of marine high molecular weight dissolved organic matter

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2016Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) – a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean.Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599) and the Gordon and Betty Moore Foundation (grant #492.01, #3777, and #3298)

Influence of Culture and Nutritional Conditions on Self-Flocculation of a Kloeckera apiculata Wine Strain

U radu je ispitan utjecaj uvjeta okoline na kontrolu spontane flokulacije kvasca Kloeckera apiculata mc1, izoliranog iz argentinskoga grožđa, koji dokazano poboljšava aromu vina. Povećanje temperature izravno je utjecalo na flokulaciju, omogućavajući veće povezivanje zimolektina, određenih pomoću fluorescentne probe BSA-Gal-FITC i kvantificiranih Scatchardovim modelom. Miješanje je pozitivno utjecalo na flokulaciju kvasca, a nije povećalo indeks hidrofobnosti. Flokulaciju je ubrzao dodatak glukoze, fruktoze i etanola podlozi od kvasca i dušičnih baza, bez naknadnog dodavanja aminokiselina ili amonijeva sulfata. Dodatak asimilativnog dušika bez izvora energije negativno je utjecao na flokulaciju. Tijekom proizvodnje vina flokulacija se može kontrolirati podešavanjem uvjeta okoline, kao što su temperatura i hranjive tvari, radi optimiranja procesa i kakvoće gotovog proizvoda. Pomoću parametara flokulacije može se predvidjeti ponašanje vinskoga kvasca Kloeckera apiculata mc1 tijekom fermentacije.The current work examines the environmental conditions to control the expression of self-flocculation of Kloeckera apiculata mc1 isolated from Argentinian grapes with proven beneficial effect on wine aroma. Temperature had a direct effect on the expression of flocculation resulting in an increase in the number of zymolectin sites determined with a BSA-Gal-FITC probe and quantified with the Scatchard plot. Agitation had a positive effect on yeast flocculation and the effect did not correlate with an increase in the hydrophobic index. The addition of glucose, fructose or ethanol to yeast nitrogen base medium without amino acids or ammonium sulphate stimulated flocculation. Assimilative nitrogen sources had a negative impact on flocculation in the absence of an energy source. During winemaking, control of flocculation by environmental factors such as temperature and the presence of nutrients could be applied in order to optimize the fermentation process and hence the quality of the final product. Knowledge of the effect of different parameters on flocculation of the wine yeast K. apiculata mc1 allows prediction of the behaviour of this yeast during fermentation

Isolation and Characterization of Bacteria That Degrade Phosphonates in Marine Dissolved Organic Matter

Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.Gordon and Betty Moore Foundation (Award GBMF3298)Simons Foundation (Grant 329108

Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sosa, O. A., Burrell, T. J., Wilson, S. T., Foreman, R. K., Karl, D. M., & Repeta, D. J. Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean. Limnology and Oceanography, (2020), doi:10.1002/lno.11463.In oligotrophic ocean regions, dissolved organic phosphorus (DOP) plays a prominent role as a source of phosphorus (P) to microorganisms. An important bioavailable component of DOP is phosphonates, organophosphorus compounds with a carbon‐phosphorus (C‐P) bond, which are ubiquitous in high molecular weight dissolved organic matter (HMWDOM). In addition to being a source of P, the degradation of phosphonates by the bacterial C‐P lyase enzymatic pathway causes the release of trace hydrocarbon gases relevant to climate and atmospheric chemistry. In this study, we investigated the roles of phosphate and phosphonate cycling in the production of methane (CH4) and ethylene (C2H4) in the western North Atlantic Ocean, a region that features a transition in phosphate concentrations from coastal to open ocean waters. We observed an inverse relationship between phosphate and the saturation state of CH4 and C2H4 in the water column, and between phosphate and the relative abundance of the C‐P lyase marker gene phnJ . In phosphate‐depleted waters, methylphosphonate and 2‐hydroxyethylphosphonate, the C‐P lyase substrates that yield CH4 and C2H4, respectively, were readily degraded in proportions consistent with their abundance and bioavailability in HMWDOM and with the concentrations of CH4 and C2H4 in the water column. We conclude that phosphonate degradation through the C‐P lyase pathway is an important source and a common production pathway of CH4 and C2H4 in the phosphate‐depleted surface waters of the western North Atlantic Ocean and that phosphate concentration can be an important control on the saturation state of these gases in the upper ocean.We thank the captain and crew of the R/V Neil Armstrong and chief scientist Benjamin Van Mooy for supporting and leading research at sea. Chiara Santinelli and Eric Grabowski provided analyses of dissolved organic carbon. This research was funded by NSF Chemical Oceanography award OCE‐1634080 to D.J.R. Additional support was provided by the Gordon and Betty Moore Foundation grant 3794 to D.M.K. and grant 6000 to D.J.R., and the Simons Collaboration on Ocean Processes and Ecology (SCOPE) program grant 329108 to D.M.K., E.F.D., and D.J.R

Diversidad genética y distribución regional de cepas de Mycobacterium bovis del ganado en México

The molecular fingerprints of 878 isolates of Mycobacterium bovis from cattle, mostly dairy cattle, collected from cattle between 2009 and 2010 in different regions of Mexico were obtained by spoligotyping. Seventy-two percent (72 %) of the spoligotypes fell into nine clusters, and 27 % of the isolates fell into only two spoligotypes; 149 were orphan spoligotypes. The two predominant spoligotypes, arbitrarily designated as SP1 and SP2, were found in almost all States in Mexico, especially in central Mexico, where a concentration of dairy cattle is known. In spite of the wide distribution of spoligotypes observed, some show high regional preference, especially those in geographically distant regions. Only a few spoligotypes show patterns completely different from those shown by the most frequent spoligotypes, suggesting strange sources of infection or the formation of new genetic lines derived from non-lethal mutations. Most States with predominantly high dairy cattle populations showed similar spoligotypes, suggesting exchange of animals between regions. Some spoligotypes are common to dairy and beef cattle, suggesting transmission between populations, most probably due to the movement of dairy cattle to non-dairy regions.Se obtuvieron patrones moleculares (espoligotipos) de 878 aislados de Mycobacterium bovis de ganado de diferentes regiones de México entre los años 2009 y 2010. Setenta y dos por ciento (72 %) de los espoligotipos cayeron en nueve grupos y 27 % de los aislados dentro de sólo dos espoligotipos; 149 fueron espoligotipos individuales. Los dos espoligotipos predominantes, arbitrariamente identificados como SP1 y SP2, se distribuyen en la mayor parte del territorio nacional, en especial en la zona centro de México en ganado especializado en producción de leche. A pesar de la amplia distribución geográfica de los espoligotipos de mayor frecuencia, algunos muestran cierta localización, en especial los encontrados en zonas geográficas distantes, como es el caso de Chihuahua y Baja California. Aunque pocos, algunos espoligotipos muestran patrones moleculares distintos a los mostrados por los espoligotipos de mayor frecuencia, sugiriendo fuentes de infección desconocida. La mayoría de los Estados con ganadería predominantemente lechera muestran espoligotipos comunes, lo que sugiere intercambio regional frecuente de ganado. Algunos espoligotipos son comunes en ganado para leche y ganado para carne, lo que sugiere transmisión entre estas dos poblaciones; se desconoce, sin embargo, si los animales de carne infectados provienen de explotaciones extensivas o si son de engordas ubicadas dentro de la explotación lechera. Se propone la tipificación rutinaria de aislados de M. bovis obtenidos en todos los laboratorios de diagnóstico y mejorar la captura de información epidemiológica de los casos, para hacer mejores conclusiones epidemiológicas de la distribución espacial de las cepas de este agente en el territorio nacional

Influence of taste disorders on dietary behaviors in cancer patients under chemotherapy

<p>Abstract</p> <p>Objectives</p> <p>To determine the relationship between energy and nutrient consumption with chemosensory changes in cancer patients under chemotherapy.</p> <p>Methods</p> <p>We carried out a cross-sectional study, enrolling 60 subjects. Cases were defined as patients with cancer diagnosis after their second chemotherapy cycle (n = 30), and controls were subjects without cancer (n = 30). Subjective changes of taste during treatment were assessed. Food consumption habits were obtained with a food frequency questionnaire validated for Mexican population. Five different concentrations of three basic flavors --sweet (sucrose), bitter (urea), and a novel basic taste, umami (sodium glutamate)-- were used to measure detection thresholds and recognition thresholds (RT). We determine differences between energy and nutrient consumption in cases and controls and their association with taste DT and RT.</p> <p>Results</p> <p>No demographic differences were found between groups. Cases showed higher sweet DT (6.4 vs. 4.4 μmol/ml; p = 0.03) and a higher bitter RT (100 vs. 95 μmol/ml; <it>p </it>= 0.04) than controls. Cases with sweet DT above the median showed significant lower daily energy (2,043 vs.1,586 kcal; p = 0.02), proteins (81.4 vs. 54 g/day; <it>p </it>= 0.01), carbohydrates (246 vs.192 g/day; <it>p </it>= 0.05), and zinc consumption (19 vs.11 mg/day; <it>p </it>= 0.01) compared to cases without sweet DT alteration. Cases with sweet DT and RT above median were associated with lower completion of energy requirements and consequent weight loss. There was no association between flavors DT or RT and nutrient ingestion in the control group.</p> <p>Conclusion</p> <p>Changes of sweet DT and bitter RT in cancer patients under chemotherapy treatment were associated with lower energy and nutrient ingestion. Taste detection and recognition thresholds disorders could be important factors in malnutrition development on patients with cancer under chemotherapy treatment.</p

Future research directions on the "elusive" white shark

White sharks, Carcharodon carcharias, are often described as elusive, with little information available due to the logistical difficulties of studying large marine predators that make long-distance migrations across ocean basins. Increased understanding of aggregation patterns, combined with recent advances in technology have, however, facilitated a new breadth of studies revealing fresh insights into the biology and ecology of white sharks. Although we may no longer be able to refer to the white shark as a little-known, elusive species, there remain numerous key questions that warrant investigation and research focus. Although white sharks have separate populations, they seemingly share similar biological and ecological traits across their global distribution. Yet, white shark’s behavior and migratory patterns can widely differ, which makes formalizing similarities across its distribution challenging. Prioritization of research questions is important to maximize limited resources because white sharks are naturally low in abundance and play important regulatory roles in the ecosystem. Here, we consulted 43 white shark experts to identify these issues. The questions listed and developed here provide a global road map for future research on white sharks to advance progress toward key goals that are informed by the needs of the research community and resource managers

Doctorado en educación: temas y conceptos

1 documento en PDF de 11 páginas.Los escritos reunidos aquí presentan varios rasgos comunes, que les dan derecho a formar parte de la primera publicación del Doctorado en Educación. El primero de ellos, el rigor documental y argumentativo. Sus autores muestran un sólido manejo de los temas que enfrental, se percibe su reflexión y apropiación crítica, lo que les permite exponerlos de forma sistemática y profunda, desde una perspectiva propia, a veces retadora y siempre propositiva. Otro rasgo es la apertura, en el sentido de que los autores no pretenden dar la última palabra, sino aportar al campo del saber educativo; abrir nuevas puertas a la investigación, al diálogo y a la reflexión académica. También salta a la vista la trans- e interdisciplinariedad de los contenidos, sino en los modos y perspectivas desde donde abordan sus objetos de estudio. El último rasgo que quiero destacar es la actualidad de los asuntos tratados, actualidad que proviene de la relevancia de los temas, de su íntima relación con elementos esenciales de la educación: su finalidad, sus agentes, sus instituciones y sus procesos, lo cual explica su permanencia en la investigación educativa.Presentación, Ciro Hernando Parra Moreno La formación doctoral en Colombia, Marina Camargo Abello Naturaleza de las instituciones educativas, Rafael Alvira Domínguez Finalidad de la Universidad: reflexión necesaria, Javier Bermúdez Aponte La Universidad, escuela al servicio de la verdad, Luz Yolanda Sandoval Estupiñán, Alfredo Rodríguez Sedano La vida y el reto contemporáneo de educar para la paz, María Elvira Martínez A. Teorías sociales contemporáneas en educación, Marta Ardila Debates en torno a la educación familiar desde una perspectiva pedagógica, Aurora Bernal Martínez de Soria, Sandra Patricia Varela Londoño Alfabetización y construcción de subjetividad, Rosa Julia Guzmán Rodríguez Educomunicación en entornos digitales: mirada desde la comunicación no verbal, Andrés Chiappe, Hugo Rozo, Eduardo Menjivar, María Alejandra Corchuelo, Maite Alarcón Retos para la formación del tutor en modalidad virtual, Cristina Hennig Manzuoli Juego serio: modelo teórico para su diseño y producción, Oscar Boude Figueredo, Edgar Andrés Sosa"Presentación, Ciro Hernando Parra Moreno La formación doctoral en Colombia, Marina Camargo Abello Naturaleza de las instituciones educativas, Rafael Alvira Domínguez Finalidad de la Universidad: reflexión necesaria, Javier Bermúdez Aponte La Universidad, escuela al servicio de la verdad, Luz Yolanda Sandoval Estupiñán, Alfredo Rodríguez Sedano La vida y el reto contemporáneo de educar para la paz, María Elvira Martínez A. Teorías sociales contemporáneas en educación, Marta Ardila Debates en torno a la educación familiar desde una perspectiva pedagógica, Aurora Bernal Martínez de Soria, Sandra Patricia Varela Londoño Alfabetización y construcción de subjetividad, Rosa Julia Guzmán Rodríguez Educomunicación en entornos digitales: mirada desde la comunicación no verbal, Andrés Chiappe, Hugo Rozo, Eduardo Menjivar, María Alejandra Corchuelo, Maite Alarcón Retos para la formación del tutor en modalidad virtual, Cristina Hennig Manzuoli Juego serio: modelo teórico para su diseño y producción, Oscar Boude Figueredo, Edgar Andrés Sosa