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Chilean native species as source of natural polyphenols
(CABI, 2013) Fredes, Carolina; Montenegro, Gloria; Céspedes, Carlos L.; Sampietro, Diego A.; Sigler, David; Rai, Mahendra
This chapter discusses the traditional uses of native medicinal plants from Chile and provides tabulated data on Chilean medicinal plants, including the parts used and their effects, in order to analyse compounds that could be responsible for these medicinal effects. It presents scientific evidence supporting biological activity associated with the presence of polyphenols in Chilean plants. The determination of polyphenols in Chilean plants and their antioxidant capacity are described. The main factors affecting polyphenol content in plants are also mentioned, i.e. genotype, environment, storage and processing, and stage of harvest.
Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner
(2016) Gutiérrez, Fernando I.; Rodríguez Valenzuela, Felipe.; Ibarra, Ignacio L.; Melo Ledermann, Francisco Javier; Devos, Damien P.
Abstract Background The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete Protein Data Bank (PDB), at the multi-chain level, has been released. However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available. The availability of such a tool is critical for a sustainable boosting of biological discovery. Results Here we report on the development of a new method for the fast and flexible comparison of protein structure chains. The method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm. The unique features of this new approach are the integration and trade-off balancing of the following: 1) speed, 2) accuracy and 3) global and semiglobal flexible structure alignment by integration of local substructure matching. The comparison, and matching with competitive accuracy, of one medium sized (250-aa) query structure against the complete PDB database (216,322 protein chains) takes about 8 min using an average desktop computer. The method is at least 2–3 orders of magnitude faster than other tested tools with similar accuracy. We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures. We finally provide a series of examples to illustrate the usefulness of this method and its application in biological discovery. Conclusions The method is able to detect partial structure matching, rigid body shifts, conformational changes and tolerates substantial structural variation arising from insertions, deletions and sequence divergence, as well as structural convergence of unrelated proteins.Abstract Background The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete Protein Data Bank (PDB), at the multi-chain level, has been released. However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available. The availability of such a tool is critical for a sustainable boosting of biological discovery. Results Here we report on the development of a new method for the fast and flexible comparison of protein structure chains. The method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm. The unique features of this new approach are the integration and trade-off balancing of the following: 1) speed, 2) accuracy and 3) global and semiglobal flexible structure alignment by integration of local substructure matching. The comparison, and matching with competitive accuracy, of one medium sized (250-aa) query structure against the complete PDB database (216,322 protein chains) takes about 8 min using an average desktop computer. The method is at least 2–3 orders of magnitude faster than other tested tools with similar accuracy. We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures. We finally provide a series of examples to illustrate the usefulness of this method and its application in biological discovery. Conclusions The method is able to detect partial structure matching, rigid body shifts, conformational changes and tolerates substantial structural variation arising from insertions, deletions and sequence divergence, as well as structural convergence of unrelated proteins.Abstract Background The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete Protein Data Bank (PDB), at the multi-chain level, has been released. However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available. The availability of such a tool is critical for a sustainable boosting of biological discovery. Results Here we report on the development of a new method for the fast and flexible comparison of protein structure chains. The method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm. The unique features of this new approach are the integration and trade-off balancing of the following: 1) speed, 2) accuracy and 3) global and semiglobal flexible structure alignment by integration of local substructure matching. The comparison, and matching with competitive accuracy, of one medium sized (250-aa) query structure against the complete PDB database (216,322 protein chains) takes about 8 min using an average desktop computer. The method is at least 2–3 orders of magnitude faster than other tested tools with similar accuracy. We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures. We finally provide a series of examples to illustrate the usefulness of this method and its application in biological discovery. Conclusions The method is able to detect partial structure matching, rigid body shifts, conformational changes and tolerates substantial structural variation arising from insertions, deletions and sequence divergence, as well as structural convergence of unrelated proteins.Abstract Background The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete Protein Data Bank (PDB), at the multi-chain level, has been released. However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available. The availability of such a tool is critical for a sustainable boosting of biological discovery. Results Here we report on the development of a new method for the fast and flexible comparison of protein structure chains. The method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm. The unique features of this new approach are the integration and trade-off balancing of the following: 1) speed, 2) accuracy and 3) global and semiglobal flexible structure alignment by integration of local substructure matching. The comparison, and matching with competitive accuracy, of one medium sized (250-aa) query structure against the complete PDB database (216,322 protein chains) takes about 8 min using an average desktop computer. The method is at least 2–3 orders of magnitude faster than other tested tools with similar accuracy. We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures. We finally provide a series of examples to illustrate the usefulness of this method and its application in biological discovery. Conclusions The method is able to detect partial structure matching, rigid body shifts, conformational changes and tolerates substantial structural variation arising from insertions, deletions and sequence divergence, as well as structural convergence of unrelated proteins.
Emiliania huxleyi endures N-limitation with an efficient metabolic budgeting and effective ATP synthesis
(2014) Rokitta, Sebastian D.; Dassow, Peter von; Rost, Björn.; John, Uwe.
Abstract Background Global change will affect patterns of nutrient upwelling in marine environments, potentially becoming even stricter regulators of phytoplankton primary productivity. To better understand phytoplankton nutrient utilization on the subcellular basis, we assessed the transcriptomic responses of the life-cycle stages of the biogeochemically important microalgae Emiliania huxleyi to nitrogen-limitation. Cells grown in batch cultures were harvested at ‘early’ and ‘full’ nitrogen-limitation and were compared with non-limited cells. We applied microarray-based transcriptome profilings, covering ~10.000 known E. huxleyi gene models, and screened for expression patterns that indicate the subcellular responses. Results The diploid life-cycle stage scavenges nitrogen from external organic sources and -like diatoms- uses the ornithine-urea cycle to rapidly turn over cellular nitrogen. The haploid stage reacts similarly, although nitrogen scavenging is less pronounced and lipid oxidation is more prominent. Generally, polyamines and proline appear to constitute major organic pools that back up cellular nitrogen. Both stages induce a malate:quinone-oxidoreductase that efficiently feeds electrons into the respiratory chain and drives ATP generation with reduced respiratory carbon throughput. Conclusions The use of the ornithine-urea cycle to budget the cellular nitrogen in situations of limitation resembles the responses observed earlier in diatoms. This suggests that underlying biochemical mechanisms are conserved among distant clades of marine phototrophic protists. The ornithine-urea cycle and proline oxidation appear to constitute a sensory-regulatory system that monitors and controls cellular nitrogen budgets under limitation. The similarity between the responses of the life-cycle stages, despite the usage of different genes, also indicates a strong functional consistency in the responses to nitrogen-limitation that appears to be owed to biochemical requirements. The malate:quinone-oxidoreductase is a genomic feature that appears to be absent from diatom genomes, and it is likely to strongly contribute to the uniquely high endurance of E. huxleyi under nutrient limitation.
Enhancement of Peroxidase Stability Against Oxidative Self-Inactivation by Co-immobilization with a Redox-Active Protein in Mesoporous Silicon and Silica Microparticles
(2016) Sahare, P.; Osorio Román, Igor; Ayala, M.; Vazquez-Duhalt, R.; Pal, U.; Loni, A.; Canham, L. T.; Agarwal, V.
Abstract The study of the stability enhancement of a peroxidase immobilized onto mesoporous silicon/silica microparticles is presented. Peroxidases tend to get inactivated in the presence of hydrogen peroxide, their essential co-substrate, following an auto-inactivation mechanism. In order to minimize this inactivation, a second protein was co-immobilized to act as an electron acceptor and thus increase the stability against self-oxidation of peroxidase. Two heme proteins were immobilized into the microparticles: a fungal commercial peroxidase and cytochrome c from equine heart. Two types of biocatalysts were prepared: one with only covalently immobilized peroxidase (one-protein system) and another based on covalent co-immobilization of peroxidase and cytochrome c (two-protein system), both immobilized by using carbodiimide chemistry. The amount of immobilized protein was estimated spectrophotometrically, and the characterization of the biocatalyst support matrix was performed using Brunauer–Emmett–Teller (BET), scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX), and Fourier transform infrared (FTIR) analyses. Stability studies show that co-immobilization with the two-protein system enhances the oxidative stability of peroxidase almost four times with respect to the one-protein system. Thermal stability analysis shows that the immobilization of peroxidase in derivatized porous silicon microparticles does not protect the protein from thermal denaturation, whereas biogenic silica microparticles confer significant thermal stabilization.Abstract The study of the stability enhancement of a peroxidase immobilized onto mesoporous silicon/silica microparticles is presented. Peroxidases tend to get inactivated in the presence of hydrogen peroxide, their essential co-substrate, following an auto-inactivation mechanism. In order to minimize this inactivation, a second protein was co-immobilized to act as an electron acceptor and thus increase the stability against self-oxidation of peroxidase. Two heme proteins were immobilized into the microparticles: a fungal commercial peroxidase and cytochrome c from equine heart. Two types of biocatalysts were prepared: one with only covalently immobilized peroxidase (one-protein system) and another based on covalent co-immobilization of peroxidase and cytochrome c (two-protein system), both immobilized by using carbodiimide chemistry. The amount of immobilized protein was estimated spectrophotometrically, and the characterization of the biocatalyst support matrix was performed using Brunauer–Emmett–Teller (BET), scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX), and Fourier transform infrared (FTIR) analyses. Stability studies show that co-immobilization with the two-protein system enhances the oxidative stability of peroxidase almost four times with respect to the one-protein system. Thermal stability analysis shows that the immobilization of peroxidase in derivatized porous silicon microparticles does not protect the protein from thermal denaturation, whereas biogenic silica microparticles confer significant thermal stabilization.
Introducción al visón norte-americano (Neovison vison): impacto de un carnívoro invasor sobre las aves de una de las zonas más "prístinas" del planeta
(University of North Texas, 2014) Ibarra Eliessetch, Jose Tomas; Anderson, Cristopher B.; Rozzi, Ricardo; Jiménez, Jaime E.
La creciente dispersión de organismos por parte del ser humano a través de barreras naturales que antes parecían insuperables, tales como océanos, cordilleras, desiertos, ríos y zonas climáticamente hostiles, se ha convertido en un fenómeno global con causas y consecuencias tanto ecológicas como socio-culturales a escala local. Incluso lugares relativamente libres de otros impactos antrópicos no han escapado a la introducción, naturalización y expansión de especies foráneas. Por ejemplo, a partir de la investigación de largo plazo implementada en el archipiélago Cabo de Hornos con la creación del Parque Etnobotánico Omora, desde el año 2000, se ha registrado que esta zona austral y remota del continente americano también ha experimentado la llegada y establecimiento de numerosas especies exóticas (Anderson et al. 2006). A su vez, la introducción de esta nueva lora y fauna sería un relejo de una "mentalidad exótica" que prioriza y muchas veces valora más a las especies no-nativas, principalmente de origen europeo o norteamericano (Rozzi et al. 2003), siendo así la homogeneización biótica, en parte, una consecuencia última de la homogeneización cultural. Los nuevos hallazgos de especies exóticas en la zona más austral del continente americano provocan una relexión acerca del papel, tanto académico como social, que pueden jugar los sitios de investigación a largo plazo como el Parque Omora (Anderson et al. 2010). Si evaluamos la aseveración de que el bosque subantártico es una de las ecorregiones más prístinas del planeta, encontramos que este "reconocimiento" se puede fechar a una publicación en la prestigiosa revista Proceedings of the National Academy of Sciences del año 2003. Un grupo de investigadores de la organización Conservation International, con sede en Nueva York, estableció que esta ecorregión, junto a otras 23 áreas, era una de las últimas "wilderness areas" del planeta. Esta identificación se basó en tres criterios que se pueden medir con sensores remotos e información demográica, siendo ellos: i) un alto porcentaje de cobertura vegetacional intacta, ii) una baja densidad humana, y iii) una gran extensión de la ecorregión (Mittermeier et al. 2003). Además, los autores destacaron el alto porcentaje de áreas protegidas en la región (> 50% de su supericie total).
Movilidad y ecología urbana: nuevas estrategias para la cicloinclusividad
(Centro de Políticas Públicas UC, 2020) Iturriaga del Campo, Sandra
En las últimas décadas, el fomento del uso de medios no motorizados como la bicicleta, ha sido un imperativo para descongestionar muchas ciudades, así como un factor esencial para reducir las emisiones de carbono y gases de efecto invernadero en el actual contexto de cambio climático en Chile, el uso de la bicicleta ha ido en aumento en los últimos años, y si bien ha ido de la mano con algunas leyes y disposiciones que regulan la convivencia de modos en la ciudad, aún falta mucho por abordar en el ámbito de la infraestructura cicloinclusiva. La presente investigación propone un acercamiento a la temática de la movilidad sostenible en directa relación con los principios de la ecología urbana. Se parte del supuesto que ya no basta con el fomento al uso de la bicicleta como una manera de descongestionar las ciudades, sino que se trata de avanzar en estrategias de cicloinclusividad que incorporen aspectos de la ecología y el medioambiente, abordando la oportunidad que tiene la infraestructura ciclable para aportar al cambio climático, la equidad social y la resiliencia de nuestras ciudades. Para ello, la investigación se enmarca en paradigmas de movilidad sostenible asociados a conceptos como Corredores y Vias Verdes, Greenways e Infraestructura Verde, proponiendo un campo de aplicación en el contexto nacional a partir de un conjunto de buenas prácticas, que presentamos a continuación la síntesis de esta propuesta de investigación, que integró a un conjunto de estudiantes de distintas disciplinas, para abordar las oportunidades de una nueva cultura cicloinclusiva con base en una sostenibilidad urbana
Role of Connexin Hemichannels in Neurodegeneration
(InTech, 2011) Orellana Roca, Juan Andrés; Sáez, Juan Carlos; Giaume, Christian
Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data
(Humana Press, 2018) Contreras López, Orlando; Moyano, Tomás C.; Soto, Daniela C.; Gutiérrez, Rodrigo A.
The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. Many examples of new hypothesis derived from network analyses can be found in the literature, spanning different organisms including plants and specific fields such as root developmental biology. In order to make the process of constructing a gene co-expression network more accessible to biologists, here we provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. Similar strategies have been used in previous studies to advance root developmental biology. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.
The importance of protected areas in mitigating climate change and conserving ecosystems in Latin America and the Caribbean
(Springer, 2022) Ibarra Eliessetch Jose Tomas; Bonacic Salas Cristian; Constanza, Arévalo; Laker, Jerry; Mohamed Behnassi; Himangana Gupta; Mirza Barjees Baig; Ijaz Rasool Noorka
Biodiversity conservation in a world under climate change is a significant challenge for Latin America and the Caribbean (LAC), which holds 60% of global terrestrial life. Six of the ten most biodiverse countries (Brazil, Colombia, Ecuador, Mexico, Peru, and Venezuela) are in LAC, and biodiversity hotspots are well-represented along the region’s coasts and mainland. The region has the most significant areas of tropical forest and large portions of subtropical forests, temperate steppe, and subantarctic Patagonia. Protected areas offer opportunities to conserve unique biodiversity, provide ecosystem services, and mitigate climate change effects. LAC’s contribution to carbon capture, by protecting extensive forests and other natural ecosystems, is potentially opening tremendous economic opportunities under the green economy paradigm. This chapter describes the current status of protected areas in LAC and explains how this conservation mechanism should play a mitigation role. LAC’s protected areas cover almost all types of terrestrial and marine ecosystems, and their number is increasing in the region. Although protected areas mitigate the effects of climate change on biodiversity, climate change and traditional environmental problems like deforestation, mining, and agriculture affect the viability of protected areas. Thus, their expansion and connectivity throughout the region are crucial to combat climate change and biodiversity loss. Nature is also essential to the region’s biocultural diversity, including a miriad of complex cosmovisions and traditions. In LAC’s unique ecosystems, rich biodiversity is spatially correlated with rich cultural diversity, granting opportunity for Indigenous Peoples and Local Communities to lead experiences in managing protected areas in biologically and culturally diverse ecosystems of LAC.

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