Dispersión horizontal y vertical en un modelo idealizado de la circulación inducida por el viento

Horizontal and vertical dispersion in an idealized wind-driven circulation model

José Rodrigo Barrientos Valencia (2023, [Tesis de maestría])

El estudio de la dispersión de materia flotante en el océano es fundamental para abordar problemas contemporáneos, como la contaminación por desechos y la distribución de nutrientes. Sin embargo, la distribución superficial horizontal no captura completamente la complejidad del problema, ya que muchos contaminantes, incluidos los plásticos, tienden a hundirse debido a la desintegración o a la adhesión de materiales que alteran su densidad. Este estudio se centra en la dispersión horizontal y vertical de trazadores pasivos en un océano turbulento impulsado por el viento. Se utilizan partículas sintéticas que son advectadas por un modelo Lagrangiano resolviendo la trayectoria de cada partícula mediante un método Runge-Kutta de 4 ◦ orden. Se exploran cuatro mecanismos de dispersión: (i) corrientes geostróficas a gran escala según el modelo clásico de Stommel, (ii) velocidad de Ekman, (iii) difusividad turbulenta debida a movimientos de submesoescala (simulados con una caminata aleatoria), y (iv) efectos inerciales relacionados con el tamaño y la flotabilidad del trazador. El estudio se divide en dos partes: primero, se examina la dispersión horizontal en superficie, y después se aborda el caso tridimensional mediante la inmersión de trazadores por bombeo de Ekman. Los principales resultados son: 1) con la deriva superficial de Ekman, las partículas convergen hacia una región alrededor del centro del giro de Stommel; sin embargo, dicha convergencia disminuye a medida que aumentan los efectos de la turbulencia; 2) considerando los efectos inerciales, aumentar la flotabilidad o el tamaño de las partículas provoca una convergencia mayor que la producida por la deriva de Ekman; 3) al incluir la velocidad vertical negativa, una baja difusividad turbulenta permite que los trazadores alcancen mayores profundidades porque permanecen más tiempo en regiones de mayor hundimiento.

The study of floating material dispersion in the ocean is crucial for addressing contemporary issues such as waste pollution and nutrient distribution. However, the horizontal surface distribution does not fully capture the complexity of the problem. Many pollutants, including plastics, tend to sink due to the disintegration or adhesion of materials altering their density. This study focuses on the horizontal and vertical dispersion of passive tracers in a turbulent, wind-driven ocean. Synthetic particles are advected using a Lagrangian model, with each particle’s trajectory solved using a fourth-order Runge-Kutta method. Four dispersion mechanisms are explored: (i) large-scale geostrophic currents based on the Stommel’s classical model, (ii) Ekman velocity, (iii) turbulent diffusivity due to submesoscale motions (simulated with a random walk), and (iv) inertial effects related to the tracer’s size and buoyancy. The study is divided into two parts: first, horizontal dispersion at the surface is examined, and then the three-dimensional scenario is addressed by immersing tracers through Ekman pumping. The key findings are as follows: 1) with surface Ekman drift, particles converge around the center of the Stommel gyre; however, this convergence decreases as turbulence effects increase; 2) considering inertial effects, increasing buoyancy or particle size results in greater convergence than that caused by Ekman drift; 3) when the vertical velocity is included, a low turbulent diffusivity allows tracers to reach greater depths because they remain longer times in regions of greater sinking.

circulación de Stommel, deriva de Ekman, partículas inerciales, dispersión de partículas, bombeo de Ekman Stommel circulation, Ekman drift, inertial particles, particle dispersion, Ekman pumping CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA FÍSICA (VE R 5603 .04) OCEANOGRAFÍA FÍSICA (VE R 5603 .04)

Phylogenetic relationships of Pseudo-nitzschia subpacifica (Bacillariophyceae) from the Mexican Pacific, and its production of domoic acid in culture

Sonia Quijano (2020, [Artículo])

Pseudo-nitzschia is a cosmopolitan genus, some species of which can produce domoic acid (DA), a neurotoxin responsible for the Amnesic Shellfish Poisoning (ASP). In this study, we identified P. subpacifica for the first time in Todos Santos Bay and Manzanillo Bay, in the Mexican Pacific using SEM and molecular methods. Isolates from Todos Santos Bay were cultivated under conditions of phosphate sufficiency and deficiency at 16°C and 22°C to evaluate the production of DA. This toxin was detected in the particulate (DAp) and dissolved (DAd) fractions of the cultures during the exponential and stationary phases of growth of the cultures. The highest DA concentration was detected during the exponential phase grown in cells maintained in P-deficient medium at 16°C (1.14 ± 0.08 ng mL-1 DAd and 4.71 ± 1.11 × 10−5 ng cell-1 of DAp). In P-sufficient cultures DA was higher in cells maintained at 16°C (0.25 ± 0.05 ng mL-1 DAd and 9.41 ± 1.23 × 10−7 ng cell-1 of DAp) than in cells cultured at 22°C. Therefore, we confirm that P. subpacifica can produce DA, especially under P-limited conditions that could be associated with extraordinary oceanographic events such as the 2013–2016 "Blob" in the northeastern Pacific Ocean. This event altered local oceanographic conditions and possibly generated the presence of potential harmful species in areas with economic importance on the Mexican Pacific coast. © 2020 Quijano-Scheggia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

domoic acid, domoic acid, kainic acid, Article, cell growth, controlled study, diatom, Mexico, morphology, nonhuman, Pacific Ocean, phylogeny, plant cell, plant growth, Pseudo nitzschia, toxin analysis, cell culture technique, classification, diatom, CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Effects of geostrophic kinetic energy on the distribution of mesopelagic fish larvae in the southern Gulf of California in summer/fall stratified seasons

FERNANDO CONTRERAS CATALA (2016, [Artículo])

Effects of geostrophic kinetic energy flux on the three-dimensional distribution of fish larvae of mesopelagic species (Vinciguerria lucetia, Diogenichthys laternatus, Benthosema panamense and Triphoturus mexicanus) in the southern Gulf of California during summer and fall seasons of stronger stratification were analyzed. The greatest larval abundance was found at sampling stations in geostrophic kinetic energy-poor areas (<7.5 J/m3), where the distribution of the dominant species tended to be stratified. Larvae of V. lucetia (average abundance of 318 larvae/10m2) and B. panamense (174 larvae/10m2) were mostly located in and above the pycnocline (typically ∼ 40 m depth). In contrast, larvae of D. laternatus (60 larvae/10m2) were mainly located in and below the pycnocline. On the other hand, in sampling stations from geostrophic kinetic energy-rich areas (> 21 J/m3), where mesoscale eddies were present, the larvae of the dominant species had low abundance and were spread more evenly through the water column, in spite of the water column stratification. For example, in a cyclonic eddy, V. lucetia larvae (34 larvae/10m2) extended their distribution to, at least, the limit of sampling 200 m depth below the pycnocline, while D. laternatus larvae (29 larvae/10m2) were found right up to the surface, both probably as a consequence mixing and secondary circulation in the eddy. Results showed that the level of the geostrophic kinetic energy flux affects the abundance and the three-dimensional distribution of mesopelagic fish larvae during the seasons of stronger stratification, indicating that areas with low geostrophic kinetic energy may be advantageous for feeding and development of mesopelagic fish larvae because of greater water column stability. © 2016 Contreras-Catala et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, autumn, Benthosema panamense, Diogenichthys laternatus, environmental factor, environmental parameters, fish, geographic distribution, geostrophic kinetic energy, hydrography, larva, nonhuman, population abundance, population dispersion, pop CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Synthetic libraries of shark vNAR domains with different cysteine numbers within the CDR3

OLIVIA CABANILLAS BERNAL (2019, [Artículo])

The variable domain of New Antigen Receptors (vNAR) from sharks, present special characteristics in comparison to the conventional antibody molecules such as: small size (12–15 kDa), thermal and chemical stability and great tissue penetration, that makes them a good alternative source as therapeutic or diagnostic agents. Therefore, it is essential to improve techniques used for the development and selection of vNAR antibodies that recognize distinct antigens. The development of synthetic antibody libraries offers a fast option for the generation of antibodies with the desired characteristics. In this work three synthetic antibody libraries were constructed; without cysteines (Cys), with one Cys and with two Cys residues within its CDR3, with the objective of determining whether the presence or absence of Cys in the CDR3 favors the isolation of vNAR clones from a synthetic library. The libraries were validated selecting against six mammalian proteins. At least one vNAR was found for each of the antigens, and a clone coming from the library without Cys in the CDR3 was selected with all the antigens. In vitro angiogenesis assay with the isolated anti-VEGF antibodies, suggest that these vNARs are capable of inhibiting in vitro angiogenesis. In silico analysis of anti-VEGF antibodies showed that vNARs from synthetic libraries could rival antibodies with affinity maturation by in silico modeling. © 2019 Cabanillas-Bernal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

aquaporin 1, carcinoembryonic antigen, cysteine, fibroblast growth factor 2, glycophorin A, leukemia inhibitory factor, vasculotropin, vasculotropin antibody, angiogenesis inhibitor, antibody, cysteine, lymphocyte antigen receptor, vasculotropin A, a BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOFÍSICA BIOFÍSICA

Rapid effects of marine reserves via larval dispersal

Richard Cudney Bueno (2009, [Artículo])

Marine reserves have been advocated worldwide as conservation and fishery management tools. It is argued that they can protect ecosystems and also benefit fisheries via density-dependent spillover of adults and enhanced larval dispersal into fishing areas. However, while evidence has shown that marine reserves can meet conservation targets, their effects on fisheries are less understood. In particular, the basic question of if and over what temporal and spatial scales reserves can benefit fished populations via larval dispersal remains unanswered. We tested predictions of a larval transport model for a marine reserve network in the Gulf of California, Mexico, via field oceanography and repeated density counts of recently settled juvenile commercial mollusks before and after reserve establishment. We show that local retention of larvae within a reserve network can take place with enhanced, but spatially-explicit, recruitment to local fisheries. Enhancement occurred rapidly (2 yrs), with up to a three-fold increase in density of juveniles found in fished areas at the downstream edge of the reserve network, but other fishing areas within the network were unaffected. These findings were consistent with our model predictions. Our findings underscore the potential benefits of protecting larval sources and show that enhancement in recruitment can be manifested rapidly. However, benefits can be markedly variable within a local seascape. Hence, effects of marine reserve networks, positive or negative, may be overlooked when only focusing on overall responses and not considering finer spatially-explicit responses within a reserve network and its adjacent fishing grounds. Our results therefore call for future research on marine reserves that addresses this variability in order to help frame appropriate scenarios for the spatial management scales of interest. © 2009 Cudney-Bueno et al.

article, environmental monitoring, fishery, larva, marine environment, marine species, Mexico, mollusc, nonhuman, oceanography, prediction, animal, biology, environmental protection, food industry, geography, growth, development and aging, larva, met CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA