A5040445041- Mathematical Dynamics and Fractals
- Cellular Automata and Applications
- semigroups and automata theory
- Genomics and Phylogenetic Studies
- Computability, Logic, AI Algorithms
- Advanced Topology and Set Theory
- Microbial Metabolic Engineering and Bioproduction
- Topological and Geometric Data Analysis
- Aquaculture disease management and microbiota
- Metal Extraction and Bioleaching
- Limits and Structures in Graph Theory
- Corrosion Behavior and Inhibition
- Fish Ecology and Management Studies
- Genetic diversity and population structure
- DNA and Biological Computing
- Geometric and Algebraic Topology
- Biofuel production and bioconversion
- Fish Biology and Ecology Studies
- Algal biology and biofuel production
- Water Quality Monitoring and Analysis
- Minerals Flotation and Separation Techniques
- Horticultural and Viticultural Research
- Identification and Quantification in Food
- Genetic and phenotypic traits in livestock
- Stochastic processes and statistical mechanics
University of Chile
2016-2025
Millennium Science Initiative
2024-2025
Center for Mathematical Modeling
2010-2024
Millennium Institute for Integrative Biology
2023-2024
Millennium Institute
2023-2024
Institute of Electrical and Electronics Engineers
2021
Signal Processing (United States)
2021
Institute of Mathematics and Mathematical Modeling
2018-2020
Pontificia Universidad Católica de Chile
2018-2019
University of O'Higgins
2019
Abstract The whole-genome duplication 80 million years ago of the common ancestor salmonids (salmonid-specific fourth vertebrate duplication, Ss4R) provides unique opportunities to learn about evolutionary fate a duplicated genome in 70 extant lineages. Here we present high-quality assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts transposon-mediated repeat expansions, were crucial post-Ss4R rediploidization process. Comparisons...
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide unified interface biomedical databases that are distributed worldwide. portal provides access numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the independently administered funded their host data federation...
The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in salmon acts as reference for other salmonids.
The genome of potato, a major global food crop, was recently sequenced. work presented here details the integration potato reference (DM) with new sequence-tagged site marker-based linkage map and other physical genetic maps closely related species tomato. Primary anchoring DM assembly accomplished by use diploid segregating population, which genotyped several types molecular markers to construct ~936 cM comprising 2469 marker loci. In silico approaches used from genotype RH89-039-16 (RH)...
The Li–Yorke definition of chaos proved its value for interval maps. In this paper it is considered in the setting general topological dynamics. We adopt two opposite points view. On one hand sufficient conditions a dynamical system are given. solve long–standing open question by proving that positive entropy implies chaos. other properties systems without pairs investigated; addition to having 0, they minimal when transitive, and property stable under factor maps, arbitrary products inverse...
Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge microbial ecology. In this work, we compared two co-occurrence networks representing soil communities from different sections of pH, temperature and humidity gradient occurring along western slope Andes Atacama Desert. doing so, topological graph alignment was used to determine impact shift environmental variables on OTUs taxonomic composition their relationships. We observed...
Abstract Background Grapevine ( Vitis vinifera L.) is the most important Mediterranean fruit crop, used to produce both wine and spirits as well table grape raisins. Wine cultivars represent two divergent germplasm pools with different origins domestication history, differential characteristics for berry size, cluster architecture chemical profile, among others. ‘Sultanina’ plays a pivotal role in modern breeding providing main source of seedlessness. This cultivar also one planted fresh...
A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication genetic variation from American European salmon populations. total 9 736 473 nonredundant SNPs were identified across a set 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K selected develop...
Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach controlling SRS in farmed Atlantic salmon. Knowledge concerning architecture trait needed before deciding on most appropriate to enhance artificial selection P. The purpose study was dissect genetic variation this pathogen 2,601 smolts were experimentally challenged against by means...
Genome-scale metabolic models have become the tool of choice for global analysis microorganism metabolism, and their reconstruction has attained high standards quality reliability. Improvements in this area been accompanied by development some major platforms databases, an explosion individual bioinformatics methods. Consequently, many recent result from "à la carte" pipelines, combining use platforms, tools biological expertise to enhance reconstruction. Although very useful, introducing...
The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens species grow there, including Atacama-endemic plants. Herein, we establish Talabre-Lejía transect (TLT) as an unparalleled natural laboratory to study plant adaptation extreme environmental conditions. We characterized climate, soil, plant, soil-microbe diversity at 22 sites (every 100 m altitude) along TLT over a 10-y period. quantified drought,...
Abstract Background Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These can use carbon dioxide directly from the air as their sole source different sources of such ammonia, nitrate, nitrite, or even air. To have a better understanding how these processes occur to determine we make them more efficient, comparative genomic analysis three bioleaching isolated mine sites Chile was performed. This study demonstrated that there...
A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence disturbed ecosystems. The study genomic variation that accounts for ecological evolutionary adaptation represent a powerful approach to extend understanding nature. Here we present chromosome-level reference genome assembly Chinook salmon ( Oncorhynchus tshawytscha ; 2.36 Gb) enabled association mapping life-history traits this species. Whole-genome re-sequencing...
Piscirickettsiosis or Salmonid Rickettsial Septicaemia (SRS) is a bacterial disease that has major economic impact on the Chilean salmon farming industry. Despite fact Piscirickettsia salmonis been recognized as fish pathogen for over 20 years, molecular strategies underlying response to infection and mechanisms of pathogenesis are poorly understood. We analysed compared head kidney transcriptional Atlantic (Salmo salar) families with different levels susceptibility P. in order reveal might...
In this article, we study the automorphism group $\text{Aut}(X,{\it\sigma})$ of subshifts $(X,{\it\sigma})$ low word complexity. particular, prove that is virtually $\mathbb{Z}$ for aperiodic minimal and certain transitive with non-superlinear More precisely, quotient relative to one generated by shift map a finite group. addition, show any can be obtained in way. The class considered includes induced substitutions, linearly recurrent even some which simultaneously exhibit superpolynomial...
Calcium/calmodulin-dependent protein kinase IV (CaMKIV) plays a key role in the regulation of calcium-dependent gene expression. The expression CaMKIV and activation CREB regulated genes are involved memory neuronal survival. We report here that: (a) bioinformatic analysis 15,476 promoters human genome predicted several Wnt target genes, being very interesting candidate; (b) promoter contains TCF/LEF transcription motifs similar to those present genes; (c) biochemical studies indicate that...
Abstract Background Data normalization is a key step in gene expression analysis by qPCR. Endogenous control genes are used to estimate variations and experimental errors occurring during sample preparation measurements. However, the transcription level of most commonly reference can vary considerably samples obtained from different individuals, tissues, developmental stages under variable physiological conditions, resulting misinterpretation performance target gene(s). This issue has been...
We have identified and characterized a spontaneous Brown Norway from Janvier rat strain (BN-J) presenting progressive retinal degeneration associated with early telangiectasia, neuronal alterations, loss of Müller glial cells resembling human macular telangiectasia type 2 (MacTel 2), which is disease unknown cause. Genetic analyses showed that the BN-J phenotype results an autosomal recessive indel novel mutation in Crb1 gene, causing dislocalization protein glia (RMG)/photoreceptor cell...
COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data quantitative prediction physicochemically biochemically feasible phenotypic states. The COBRA Toolbox is comprehensive software suite interoperable methods. It has found widespread applications in biology, biomedicine, biotechnology because its functions can be flexibly combined to implement tailored protocols any biochemical network. Version 3.0...