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Allende, C., Sohn, E., & Little, C. (2015). Treelink: data integration, clustering and visualization of phylogenetic trees. BMC Bioinformatics, 16, 6 pp.
Abstract: Background: Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Results: Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Conclusion: Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www. treelinkapp. com.
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Balocchi, F., Galleguillos, M., Rivera, D., Stehr, A., Arumi, J. L., Pizarro, R., et al. (2023). Forest hydrology in Chile: Past, present, and future. J. Hydrol., 616, 128681.
Abstract: This paper reviews the current knowledge of hydrological processes in Chilean temperate forests which extend along western South America from latitude 29 degrees S to 56 degrees S. This geographic region includes a diverse range of natural and planted forests and a broad sweep of vegetation, edaphic, topographic, geologic, and climatic set-tings which create a unique natural laboratory. Many local communities, endangered freshwater ecosystems, and downstream economic activities in Chile rely on water flows from forested catchments. This review aims to (i) provide a comprehensive overview of Chilean forest hydrology, to (ii) review prior research in forest hydrology in Chile, and to (iii) identify knowledge gaps and provide a vision for future research on forest hydrology in Chile. We reviewed the relation between native forests, commercial plantations, and other land uses on water yield and water quality from the plot to the catchment scale. Much of the global understanding of forests and their relationship with the water cycle is in line with the findings of the studies reviewed here. Streamflow from forested catchments increases after timber harvesting, native forests appear to use less water than plantations, and streams draining native forest yield less sediment than streams draining plantations or grassland/shrublands. We identified 20 key knowledge gaps such as forest groundwater systems, soil-plant-atmosphere interactions, native forest hydrology, and the effect of forest management and restoration on hydrology. Also, we found a paucity of research in the northern geographic areas and forest types (35-36 degrees S); most forest hydrology studies in Chile (56%) have been conducted in the southern area (Los Rios Region around 39-40 degrees S). There is limited knowledge of the geology and soils in many forested areas and how surface and groundwater are affected by changes in land cover. There is an opportunity to advance our understanding using process-based investigations linking field studies and modeling. Through the establishment of a forest hydrology science “society” to coor-dinate efforts, regional and national-scale land use planning might be supported. Our review ends with a vision to advance a cross-scale collaborative effort to use new nation-wide catchment-scale networks Long-term Ecosystem Research (LTER) sites, to promote common and
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Little, C., Felzensztein, C., Gimmon, E., & Munoz, P. (2015). The business management of the Chilean salmon farming industry. Mar. Pol., 54, 108–117.
Abstract: This study reviews and explores the salmon farming industry management in an emerging economy context, in the light of environmental responsibility, restorative justice and moral reengagement. Strategic information were gathered, performing in-depth interviews with CEOs and other key senior executives, to analyze the managerial behavior regarding environmental care and moral engagement to industry production standards. The results reveal issues related to firms and government roles on setting industry standards and enforcing them. Firms required to be perceived as renewed in order to receive help from the government and convince the market on their IPOs. Government lack of technical strength and capacity to reestablish order forced the industry firms association to propose a new regulatory standard. But this new order seems not to be satisfactory and this industry will continue to be on the verge of a crisis. (C) 2015 Elsevier Ltd. All rights reserved.
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Mancilla, R. A., Little, C., & Amoroso, A. (2018). Efficient Bioconversion of High Concentration Phytosterol Microdispersion to 4-Androstene-3,17-Dione (AD) by Mycobacterium sp B3805. Appl. Biochem. Biotechnol., 185(2), 494–506.
Abstract: Low solubility of sterols in aqueous media limits efficient steroid production mediated by biocatalytic microorganisms such as Mycobacterium. Sterol emulsion technologies have been developed with low success rates, largely due to the complexity of generating stable and bioavailable particles. In this study, several aqueous dispersions of sterols in-water of different particle sizes were bioconverted to 4-androstene-3,17-dione (AD) in a solvent-free environment, using a classic microorganism Mycobacterium sp. B3805 as a model system. According to our results, the high concentration (20 g/L) phytosterol dispersions with the smallest particle size tested (370 nm) achieved up to 54% (7.4 g/L) AD production yield in 11 days. Moreover, the use of 0.1 biomass/sterols ratio in a complex bioconversion media containing yeast extract, and a 1:1 glucose/microdispersion ratio in the presence of the surfactant DK-Ester P-160 (HLB16), allowed homogenization and increased microdispersion stability, thus achieving the best results using emulsion technologies to date.
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Perez-Pantoja, D., Leiva-Novoa, P., Donoso, R. A., Little, C., Godoy, M., Pieper, D. H., et al. (2015). Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134. Appl. Environ. Microbiol., 81(12), 3914–3924.
Abstract: Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.
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Rubilar, P., Hirmas, M., Matute, I., Browne, J., Little, C., Ruz, G. A., et al. (2022). Seroprevalence and estimation of the impact of SARS-CoV-2 infection in older adults residing in Long-term Care Facilities in Chile. Medwave, 22(3), 002553.
Abstract: Introduction
Older adults are at a higher risk of severe illness and death from COVID-19. This vulnerability increases in those who live in long-term care facilities due to overcrowding, greater physical dependence, and contact with health workers. Evidence on the impact of the pandemic on these establishments in low- and middle-income countries has been scant. This study aims to determine the seroprevalence of SARS-CoV-2 in older people residing in long-term care facilities and estimate the impact of infection after the first wave of the pandemic.
Methods
A cross-sectional design with 2099 residents in three regions of Chile was carried out between September and November 2020. Measurement of antibodies was performed with a rapid test. The impact of SARS-CoV-2 infection was estimated with seropositive residents, those who had a history of positive polymerase chain reaction tests, and those who died from COVID-19. Bivariate analysis with the region, sex, age, history of COVID-19, physical dependence, and serological results were performed. In addition, we performed a correlation analysis between the seroprevalence of the centers by the municipality and the rate of confirmed cases.
Results
The seroprevalence of SARS-CoV-2 antibodies in the three regions was 14.7% (95% confidence interval: 13.2 to 16.3%), the infection impact was 46.4%, and the fatality rate was 19.6%. A significant correlation was found between the seroprevalence of older adults residing in long-term care facilities and the cumulative incidence by municipalities.
Conclusions
The seroprevalence of older adults residing in long-term care facilities was higher than the general population. The high impact of infection among this population at the end of the first wave of the COVID-19 pandemic is similar to other countries. The centers' environment is directly related to COVID-19 infection. Morbidity and mortality monitoring systems should be implemented promptly to establish prevention and control measures.
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Tolorza, V., Poblete-Caballero, D., Banda, D., Little, C., Leal, C., & Galleguillos, M. (2022). An operational method for mapping the composition of post-fire litter. Remote Sens. Lett., 13(5), 511–521.
Abstract: Recent increase in the frequency and spatial extent of wildfires motivates the quick recognition of the affected soil properties over large areas. Digital Soil Mapping is a valuable approach to map soil attributes based on remote sensing and field observations. We predicted the spatial distribution of post-fire litter composition in a 40,600 ha basin burned on the 2017 wildfire of Chile. Remotely sensed data of topography, vegetation structure and spectral indices (SI) were used as predictors of random forest (RF) models. Litter sampled in 60 hillslopes after the fire provided training and validation data. Predictors selected by the Variable Selection Using Random Forests (VSURF) algorithm resulted in models for litter composition with acceptable accuracy (coefficient of determination, R (2) = 0.51-0.64, Normalized Root Mean Square Error, NRMSE = 16.9-22.1, percentage bias, pbias = -0.35%-0.5%). Modelled litter parameters decrease in concentration respect to the degree of burn severity, and the pre-fire biomass. Because pre-fire vegetation was conditioned by land cover and by a previous (2 years old) wildfire event, our results highlight the cumulative effect of severe wildfires in the depletion of litter composition.
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