Showing papers by "University of Costa Rica published in 2011"

Global Human Footprint on the Linkage between Biodiversity and Ecosystem Functioning in Reef Fishes

Abstract: Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a nonsaturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world’s coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas.

Beta ensembles, stochastic Airy spectrum, and a diffusion

Abstract: We prove that the largest eigenvalues of the beta ensembles of random matrix theory converge in distribution to the low-lying eigenvalues of the random Schrodinger operator − d2 dx2 + x+ 2 √ β bx restricted to the positive half-line, where b ′ x is white noise. In doing so we extend the definition of the Tracy-Widom(β) distributions to all β > 0, and also analyze their tails. Last, in a parallel development, we provide a second characterization of these laws in terms of a one-dimensional diffusion. The proofs rely on the associated tridiagonal matrix models and a universality result showing that the spectrum of such models converge to that of their continuum operator limit. In particular, we show how Tracy-Widom laws arise from a functional central limit theorem.

Climate change and growth scenarios for California wildfire

Abstract: Large wildfire occurrence and burned area are modeled using hydroclimate and landsurface characteristics under a range of future climate and development scenarios. The range of uncertainty for future wildfire regimes is analyzed over two emissions pathways (the Special Report on Emissions Scenarios [SRES] A2 and B1 scenarios); three global climate models (Centre National de Recherches Meteorologiques CM3, Geophysical Fluid Dynamics Laboratory CM2.1 and National Center for Atmospheric Research PCM1); three scenarios for future population growth and development footprint; and two thresholds for defining the wildland-urban interface relative to housing density. Results were assessed for three 30-year time periods centered on 2020, 2050, and 2085, relative to a 30-year reference period centered on 1975. Increases in wildfire burned area are anticipated for most scenarios, although the range of outcomes is large and increases with time. The increase in wildfire burned area associated with the higher emissions pathway (SRES A2) is substantial, with increases statewide ranging from 36% to 74% by 2085, and increases exceeding 100% in much of the forested areas of Northern California in every SRES A2 scenario by 2085.

Snake venomics of African spitting cobras: toxin composition and assessment of congeneric cross-reactivity of the pan-African EchiTAb-Plus-ICP antivenom by antivenomics and neutralization approaches.

Abstract: Venomic analysis of the venoms of Naja nigricollis, N. katiensis, N. nubiae, N. mossambica, and N. pallida revealed similar compositional trends. The high content of cytotoxins and PLA(2)s may account for the extensive tissue necrosis characteristic of the envenomings by these species. The high abundance of a type I α-neurotoxin in N. nubiae may be responsible for the high lethal toxicity of this venom (in rodents). The ability of EchiTAb-Plus-ICP antivenom to immunodeplete and neutralize the venoms of African spitting cobras was assessed by antivenomics and neutralization tests. It partially immunodepleted 3FTx and PLA(2)s and completely immunodepleted SVMPs and CRISPs in all venoms. The antivenom neutralized the dermonecrotic and PLA(2) activities of all African Naja venoms, whereas lethality was eliminated in the venoms of N. nigricollis, N. mossambica, and N. pallida but not in those of N. nubiae and N. katiensis. The lack of neutralization of lethality of N. nubiae venom may be of medical relevance only in relatively populous areas of the Saharan region. The impaired activity of EchiTAb-Plus-ICP against N. katiensis may not represent a major concern. This species is sympatric with N. nigricollis in many regions of Africa, although very few bites have been attributed to it.

An evolutionary strategy for a stealthy intracellular Brucella pathogen

Abstract: Brucella is an intracellular bacterial pathogen that causes abortion and infertility in mammals and leads to a debilitating febrile illness that can progress into a long lasting disease with severe complications in humans. Its virulence depends on survival and replication properties in host cells. In this review, we describe the stealthy strategy used by Brucella to escape recognition of the innate immunity and the means by which this bacterium evades intracellular destruction. We also discuss the development of adaptive immunity and its modulation during brucellosis that in course leads to chronic infections. Brucella has developed specific strategies to influence antigen presentation mediated by cells. There is increasing evidence that Brucella also modulates signaling events during host adaptive immune responses.

Genetic Analysis Workshop 17 mini-exome simulation.

Abstract: The data set simulated for Genetic Analysis Workshop 17 was designed to mimic a subset of data that might be produced in a full exome screen for a complex disorder and related risk factors in order to permit workshop participants to investigate issues of study design and statistical genetic analysis. Real sequence data from the 1000 Genomes Project formed the basis for simulating a common disease trait with a prevalence of 30% and three related quantitative risk factors in a sample of 697 unrelated individuals and a second sample of 697 individuals in large, extended pedigrees. Called genotypes for 24,487 autosomal markers assigned to 3,205 genes and simulated affection status, quantitative traits, age, sex, pedigree relationships, and cigarette smoking were provided to workshop participants. The simulating model included both common and rare variants with minor allele frequencies ranging from 0.07% to 25.8% and a wide range of effect sizes for these variants. Genotype-smoking interaction effects were included for variants in one gene. Functional variants were concentrated in genes selected from specific biological pathways and were selected on the basis of the predicted deleteriousness of the coding change. For each sample, unrelated individuals and family, 200 replicates of the phenotypes were simulated.

Meson Transition Form Factors in Light-Front Holographic QCD

Abstract: We study the photon-to-meson transition form factors (TFFs) F{sub M{gamma}}(Q{sup 2}) for {gamma}{gamma}* {yields} M using light-front holographic methods. The Chern-Simons action, which is a natural form in 5-dimensional anti-de Sitter (AdS) space, leads directly to an expression for the photon-to-pion TFF for a class of confining models. Remarkably, the predicted pion TFF is identical to the leading order QCD result where the distribution amplitude has asymptotic form. The Chern-Simons form is local in AdS space and is thus somewhat limited in its predictability. It only retains the q{bar q} component of the pion wavefunction, and further, it projects out only the asymptotic form of the meson distribution amplitude. It is found that in order to describe simultaneously the decay process {pi}{sup 0} {yields} {gamma}{gamma} and the pion TFF at the asymptotic limit, a probability for the q{bar q} component of the pion wavefunction P{sub q{bar q}} = 0.5 is required; thus giving indication that the contributions from higher Fock states in the pion light-front wavefunction need to be included in the analysis. The probability for the Fock state containing four quarks (anti-quarks) which follows from analyzing the hadron matrix elements, P{sub q{bar q}q{bar q}} {approx} 10%, agrees with the analysis of the pion elastic form factor using light-front holography including higher Fock components in the pion wavefunction. The results for the TFFs for the {eta} and {eta}{prime} mesons are also presented. The rapid growth of the pion TFF exhibited by the BABAR data at high Q{sup 2} is not compatible with the models discussed in this article, whereas the theoretical calculations are in agreement with the experimental data for the {eta} and {eta}{prime} TFFs.

Structure and serpentinization of the subducting Cocos plate offshore Nicaragua and Costa Rica

Abstract: The Cocos plate experiences extensional faulting as it bends into the Middle American Trench (MAT) west of Nicaragua, which may lead to hydration of the subducting mantle. To estimate the along strike variations of volatile input from the Cocos plate into the subduction zone, we gathered marine seismic refraction data with the R/V Marcus Langseth along a 396 km long trench parallel transect offshore of Nicaragua and Costa Rica. Our inversion of crustal and mantle seismic phases shows two notable features in the deep structure of the Cocos plate: (1) Normal oceanic crust of 6 km thickness from the East Pacific Rise (EPR) lies offshore Nicaragua, but offshore central Costa Rica we find oceanic crust from the northern flank of the Cocos Nazca (CN) spreading center with more complex seismic velocity structure and a thickness of 10 km. We attribute the unusual seismic structure offshore Costa Rica to the midplate volcanism in the vicinity of the Galapagos hot spot. (2) A decrease in Cocos plate mantle seismic velocities from ∼7.9 km/s offshore Nicoya Peninsula to ∼6.9 km/s offshore central Nicaragua correlates well with the northward increase in the degree of crustal faulting outboard of the MAT. The negative seismic velocity anomaly reaches a depth of ∼12 km beneath the Moho offshore Nicaragua, which suggests that larger amounts of water are stored deep in the subducting mantle lithosphere than previously thought. If most of the mantle low velocity zone can be interpreted as serpentinization, the amount of water stored in the Cocos plate offshore central Nicaragua may be about 2.5 times larger than offshore Nicoya Peninsula. Hydration of oceanic lithosphere at deep sea trenches may be the most important mechanism for the transfer of aqueous fluids to volcanic arcs and the deeper mantle.

Characterization of chromoplasts and carotenoids of red- and yellow-fleshed papaya ( Carica papaya L.)

Abstract: Chromoplast morphology and ultrastructure of red- and yellow-fleshed papaya (Carica papaya L.) were investigated by light and transmission electron microscopy. Carotenoid analyses by LC–MS revealed striking similarity of nutritionally relevant carotenoid profiles in both the red and yellow varieties. However, while yellow fruits contained only trace amounts of lycopene, the latter was found to be predominant in red papaya (51% of total carotenoids). Comparison of the pigment-loaded chromoplast ultrastructures disclosed tubular plastids to be abundant in yellow papaya, whereas larger crystalloid substructures characterized most frequent red papaya chromoplasts. Exclusively existent in red papaya, such crystalloid structures were associated with lycopene accumulation. Non-globular carotenoid deposition was derived from simple solubility calculations based on carotenoid and lipid contents of the differently colored fruit pulps. Since the physical state of carotenoid deposition may be decisive regarding their bioavailability, chromoplasts from lycopene-rich tomato fruit (Lycopersicon esculentum L.) were also assessed and compared to red papaya. Besides interesting analogies, various distinctions were ascertained resulting in the prediction of enhanced lycopene bioavailability from red papaya. In addition, the developmental pathway of red papaya chromoplasts was investigated during fruit ripening and carotenogenesis. In the early maturation stage of white-fleshed papaya, undifferentiated proplastids and globular plastids were predominant, corresponding to incipient carotenoid biosynthesis. Since intermediate plastids, e.g., amyloplasts or chloroplasts, were absent, chromoplasts are likely to emerge directly from proplastids.

Potential increase in floods in California’s Sierra Nevada under future climate projections

Abstract: California’s mountainous topography, exposure to occasional heavily moisture-laden storm systems, and varied communities and infrastructures in low lying areas make it highly vulnerable to floods. An important question facing the state—in terms of protecting the public and formulating water management responses to climate change—is “how might future climate changes affect flood characteristics in California?” To help address this, we simulate floods on the western slopes of the Sierra Nevada Mountains, the state’s primary catchment, based on downscaled daily precipitation and temperature projections from three General Circulation Models (GCMs). These climate projections are fed into the Variable Infiltration Capacity (VIC) hydrologic model, and the VIC-simulated streamflows and hydrologic conditions, from historical and from projected climate change runs, allow us to evaluate possible changes in annual maximum 3-day flood magnitudes and frequencies of floods. By the end of the 21st Century, all projections yield larger-than-historical floods, for both the Northern Sierra Nevada (NSN) and for the Southern Sierra Nevada (SSN). The increases in flood magnitude are statistically significant (at p <= 0.01) for all the three GCMs in the period 2051–2099. The frequency of flood events above selected historical thresholds also increases under projections from CNRM CM3 and NCAR PCM1 climate models, while under the third scenario, GFDL CM2.1, frequencies remain constant or decline slightly, owing to an overall drying trend. These increases appear to derive jointly from increases in heavy precipitation amount, storm frequencies, and days with more precipitation falling as rain and less as snow. Increases in antecedent winter soil moisture also play a role in some areas. Thus, a complex, as-yet unpredictable interplay of several different climatic influences threatens to cause increased flood hazards in California’s complex western Sierra landscapes.

Antivenoms for Snakebite Envenomings

Abstract: Animal-derived antivenoms constitute the mainstay in the therapy of snakebite envenoming. Antivenoms are manufactured by immunizing animals, usually horses, with venoms from a single or several medically-relevant snake species. Antivenoms are constituted by either whole IgG molecules or the immunoglobulin fragments F(ab)2 and Fab, obtained by digestion with pepsin and papain, respectively. Differences in the pharmacokinetics of these active substances have pharmacodynamic implications. Novel technological possibilities may improve the quality of antivenoms in the future, as well as their microbial safety. Antivenom administration might induce early and late adverse reactions, whose possible mechanisms are discussed. Owing to the large variety in the composition of snake venoms and to the need to demonstrate neutralization of relevant snake venoms in different countries, a meticulous preclinical and clinical assessment of antivenom efficacy and safety is required before an antivenom is introduced into clinical application. The accessibility of antivenoms in low-income tropical countries is of concern and efforts should be directed at guaranteeing the access of safe and effective antivenoms at affordable prices and their correct clinical use in these countries.

Evolved QCD predictions for the meson-photon transition form factors

Abstract: The QCD evolution of the pion distribution amplitude (DA) ${\ensuremath{\phi}}_{\ensuremath{\pi}}(x,{Q}^{2})$ is computed for several commonly used models. Our analysis includes the nonperturbative form predicted by light-front holographic QCD, thus combining the nonperturbative bound state dynamics of the pion with the perturbative ERBL evolution of the pion DA. We calculate the meson-photon transition form factors for the ${\ensuremath{\pi}}^{0}$, $\ensuremath{\eta}$ and ${\ensuremath{\eta}}^{\ensuremath{'}}$ using the hard-scattering formalism. We point out that a widely-used approximation of replacing $\ensuremath{\phi}(x,(1\ensuremath{-}x)Q)$ with $\ensuremath{\phi}(x,Q)$ in the calculations will unjustifiably reduce the predictions for the meson-photon transition form factors. It is found that the four models of the pion DA discussed give very different predictions for the ${Q}^{2}$ dependence of the meson-photon transition form factors in the region of ${Q}^{2}g30\text{ }\text{ }{\mathrm{GeV}}^{2}$. More accurate measurements of these transition form factors at the large ${Q}^{2}$ region will be able to distinguish different models of the pion DA. The rapid growth of the large ${Q}^{2}$ data for the pion-photon transition form factor reported by the BABAR Collaboration is difficult to explain within the current framework of QCD. If the BABAR data for the pion-photon transition form factor is confirmed, it could indicate physics beyond-the-standard model, such as a weakly coupled elementary $C=+$ axial vector or pseudoscalar ${z}^{0}$ in the few GeV domain, an elementary field which would provide the coupling ${\ensuremath{\gamma}}^{*}\ensuremath{\gamma}\ensuremath{\rightarrow}{z}^{0}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{0}$ at leading twist. Our analysis thus indicates the importance of additional measurements of the pion-photon transition form factor at large ${Q}^{2}$.

Immune Response Towards Snake Venoms

Abstract: The immune response involves a complex repertoire of innate and adaptive responses to foreign agents in the organism. The present review focuses on the immune response to snake venoms, including those occurring in snakebite accidental envenomation, experimental vaccination and animal hyperimmunization for snake antivenom production. The following aspects are considered: (a) the structural characteristics of snake toxins and their relationship to immunogenicity, (b) the effects that factors such as administration route, venom dose, type of adjuvant, and individual and species characteristics of the immunized animal have on the immune response, (c) the initial venom-induced inflammatory response, (d) the process by which specific antibodies towards individual toxins are produced, and (e) the techniques currently used to evaluate the antibody response. Understanding the immune response to snake venoms is highly relevant for improving antivenom production and for gaining a more complete view of snakebite envenoming.

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

Abstract: Background A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects.

Venomic and antivenomic analyses of the Central American coral snake, Micrurus nigrocinctus (Elapidae).

Abstract: The proteome of the venom of Micrurus nigrocinctus (Central American coral snake) was analyzed by a “venomics” approach. Nearly 50 venom peaks were resolved by RP-HPLC, revealing a complex protein ...

From Dust Bowl to Dust Bowl: Soils are Still Very Much a Frontier of Science

Abstract: 2037 Soil Sci. Soc. Am. J. 75:2037–2048 Posted online 28 Sept. 2011 doi:10.2136/sssaj2011.0145 Received 18 Apr. 2011. *Corresponding author (baveyp@rpi.edu). © Soil Science Society of America, 5585 Guilford Rd., Madison WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. From Dust Bowl to Dust Bowl: Soils are Still Very Much a Frontier of Science SSSA 75th Anniversary Paper

Surface structures involved in plant stomata and leaf colonization by shiga-toxigenic Escherichia coli o157:h7

Abstract: Shiga-toxigenic Escherichia coli (STEC) O157:H7 uses a myriad of surface adhesive appendages including pili, flagella, and the type 3 secretion system (T3SS) to adhere to and inflict damage to the human gut mucosa. Consumption of contaminated ground beef, milk, juices, water or leafy greens has been associated with outbreaks of diarrheal disease in humans due to STEC. The aim of this study was to investigate which of the known STEC O157:H7 adherence factors mediate colonization of baby spinach leaves and where the bacteria reside within tainted leaves. We found that STEC O157:H7 colonizes baby spinach leaves through the coordinated production of curli, the E. coli common pilus (ECP), hemorrhagic coli type 4 pilus (HCP), flagella, and T3SS. Electron microscopy analysis of tainted leaves revealed STEC bacteria in the internal cavity of the stomata, in intercellular spaces, and within vascular tissue (xylem and phloem), where the bacteria were protected from the bactericidal effect of gentamicin, sodium hypochlorite or ozonated water treatments. We confirmed that the T3S escN mutant showed a reduced number of bacteria within the stomata suggesting that T3S is required for the successful colonization of leaves. In agreement, non-pathogenic E. coli K-12 strain DH5α transformed with a plasmid carrying the LEE pathogenicity island, harboring the T3SS and effector genes, internalized into stomata more efficiently than without the LEE. This study highlights a role for pili, flagella, and T3SS in the interaction of STEC with spinach leaves. Colonization of plant stomata and internal tissues may constitute a strategy by which STEC survives in a nutrient-rich microenvironment protected from external foes and may be a potential source for human infection.

Grade Changes in Brain–Body Allometry: Morphological and Behavioural Correlates of Brain Size in Miniature Spiders, Insects and Other Invertebrates

Abstract: We use a recent wave of data to confirm that Haller's rule of brain–body allometry, for smaller species to have relatively larger brains, holds for invertebrates as well as vertebrates But different invertebrate taxa fall on several different allometric lines (grades) In the smallest animals in several grades, the brain occupies a large fraction (up to approximately 16%) of the total body mass The brain and the structures enclosing it show morphological alterations suggesting a lack of housing capacity in the head for the brain (eg the brain extends into other parts of the body such as the legs or thorax), and other structures normally enclosed in the same area are displaced Miniature animals may thus sacrifice some morphological aspects of body design to accommodate their disproportionately large CNS The smallest animals of one such group, orb web spiders, do not show signs of behavioural limitation in web construction compared with larger relatives We speculate that, because of selection resulting from the high metabolic costs of nervous tissue, grade changes may involve substantial modifications of how brains function, and help explain differences between neuron-profligate vertebrates and invertebrates having far fewer neurons (as few as approximately 200–500 neurons in two groups) Scaling problems associated with small size are of general importance, because many moderate-sized animals have very small free-living immature stages

Phospholipases A2 From Viperidae Snake Venoms: How do They Induce Skeletal Muscle Damage?

Abstract: Phospholipases A2 (PLA2s) are abundant components in snake venoms, which play important toxic roles. This review focuses on group II PLA2s endowed with myotoxic effects, present in Viperidae venoms. These PLA2s are subdivided into catalytically-active (Asp49) PLA2s, and catalytically-inactive PLA2 homologues, the latter most frequently presenting the Lys49 substitution. Both protein subgroups induce skeletal muscle necrosis, although by different mechanisms. Current evidence indicates that phospholipid hydrolysis plays a central role in the necrotizing action of Asp49 myotoxins, whereas PLA2 homologues rely on the direct membrane-destabilizing actions of their cationic C-terminal region to achieve such effect, in the absence of catalysis. Both mechanisms converge in sarcolemmal permeabilization, triggering a series of intracellular events that lead to necrosis. Most viperid PLA2 myotoxins act only locally, but those forming heterodimeric complexes such as crotoxin spread to distant muscles and induce rhabdomyolysis. This divergence between local and systemic myotoxicity might be related to differences in binding specificity to cell targets. Nevertheless, the identity of molecular targets recognized by viperid PLA2 myotoxins remains elusive. Identification of their membrane target(s), and a deeper understanding of the catalytic-dependent and -independent mechanisms that result in membrane destabilization, are two crucial, but still unclarified aspects of their myotoxic action.