Alejandro Maass

University of Chile · Departamento de Ingeniería Matemática, Centro de Modelamiento Matemático, Centro para la Regulación del Genoma

Background To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated...

Background Neotropical annual killifish are able to survive in seasonal ponds due to their ability to undergo embryonic diapauses in the dry season and grow, reproduce and die in the span of a few months during the rainy season. The genus group Austrolebias is endemic to the South American basins and shows remarkable speciation and genetic plastici...

Constraint-based modeling has risen as an alternative for characterizing the metabolism of communities. Adaptations of Flux Balance Analysis have been proposed to model metabolic interactions in most cases, considering a unique optimal flux distribution derived from the maximization of biomass production. However, these approaches do not consider t...

We develop a geometric framework to address asymptoticity and nonexpansivity in topological dynamics. Our framework can be applied when the acting group is second countable and locally compact. As an application, we show extensions of Schwartzman's theorem in this context. Also, we get new results when the acting groups is ${\mathbb Z}^d$: any half...

In this work we study the role distortion plays on automorphisms groups of expansive dynamical systems. We begin by generalizing results from subshifts, linking distortion and non-expansivity, to arbitrary expansive systems, and explore the subset of symmetrically distorted automorphisms. Due to the generalization, we are able to determine that exp...

Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. a...

Significance In the current changing climate, it is essential to improve crop production and resilience under dry and nutrient-poor conditions. Desert plants have naturally evolved to flourish under such conditions. Therefore, understanding the underlying mechanisms for their adaptation can potentially help to ensure food security. The Atacama Dese...

Extensive use of antibiotics has been the primary treatment for the Salmonid Rickettsial Septicemia, a salmonid disease caused by the bacterium Piscirickettsia salmonis. Occurrence of antibiotic resistance has been explored in various P. salmonis isolates using different assays; however, P. salmonis is a nutritionally demanding intracellular facult...

We study directional mean dimension of $\mathbb{Z}^k$-actions (where $k$ is a positive integer). On the one hand, we show that there is a $\mathbb{Z}^2$-action whose directional mean dimension (considered as a $[0,+\infty]$-valued function on the torus) is not continuous. On the other hand, we prove that if a $\mathbb{Z}^k$-action is continuum-wise...

It has been recently proved that the automorphism group of a minimal subshift with non-superlinear word complexity is virtually $\mathbb {Z}$ [Cyr and Kra. The automorphism group of a shift of linear growth: beyond transitivity. Forum Math. Sigma 3 (2015), e5; Donoso et al . On automorphism groups of low complexity subshifts. Ergod. Th. & Dynam. Sy...

We describe an ecosystem for teaching data science (DS) to engineers that blends theory, methods, and applications, developed at the Faculty of Physical and Mathematical Sciences (FCFM is its Spanish acronym), Universidad de Chile, over the last three years. This initiative has been motivated by the increasing demand for DS qualifications both from...

We describe an ecosystem for teaching data science (DS) to engineers which blends theory, methods, and applications, developed at the Faculty of Physical and Mathematical Sciences, Universidad de Chile, over the last three years. This initiative has been motivated by the increasing demand for DS qualifications both from academic and professional en...

Piscirickettsiasalmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with numerous negative impacts in the Chilean salmon farming industry. Although transcriptomic studies of P. salmonis and its host have been performed, dual host–pathogen proteomic approaches during infection are still missing. Considering...

Minimal Cantor systems of finite topological rank (that can be represented by a Bratteli-Vershik diagram with a uniformly bounded number of vertices per level) are known to have dynamical rigidity properties. We establish that such systems, when they are expansive, define the same class of systems, up to topological conjugacy, as primitive and reco...

Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with numerous negative impacts in the Chilean salmon farming industry. Although transcriptomic studies of P. salmonis and its host have been performed, dual host-pathogen proteomic approaches during infection are still missing. Considering...

It has been recently proved that the automorphism group of a minimal subshift with non-superlineal word complexity is virtually $\mathbb{Z}$. In this article we extend this result to a broader class proving that the automorphism group of a minimal S-adic subshift of finite alphabet rank is virtually $\mathbb{Z}$. The proof relies on a fine combinat...

Background Berry size is considered as one of the main selection criteria in table grapes breeding programs, due to the consumer preferences. However, berry size is a complex quantitive trait under polygenic control, and its genetic determination of berry weight is not yet fully understood. The aim of this work was to perform marker discovery using...

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Background: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder vari...

The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microb...

Minimal Cantor systems of finite topological rank (that can be represented by a Bratteli-Vershik diagram with a uniformly bounded number of vertices per level) are known to have dynamical rigidity properties. We establish that such systems, when they are expansive, define the same class of systems, up to topological conjugacy, as primitive and reco...

One of the more common healthcare associated infection is Chronic diarrhea. This disease is caused by the bacterium Clostridium difficile which alters the normal composition of the human gut flora. The most successful therapy against this infection is the fecal microbial transplant (FMT). They displace C. difficile and contribute to gut microbiome...

Nile tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world. Currently, the estimation of genetic merit of breeders is typically based on genealogical and phenotypic infor...

Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxid...

Piscirickettsia salmonis is the causative agent of Piscirickettsiosis, a systemic infection of salmonid fish species. P. salmonis infects and survives in its host cell, a process that correlates with the expression of virulence factors including components of the type IVB secretion system. To gain further insights into the cellular and molecular me...

Four large cryptic plasmids were identified in the salmon pathogen Piscirickettsia salmonis reference strain LF-89. These plasmids appeared highly novel, with less than 7% nucleotidic identity to the nr plasmid database. Plasmid copy number analysis revealed that they are harbored in chromosome equivalent ratios. In addition to plasmid-related gene...

Using Illumina HiSeq ™ 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) and pink (P) fruit stages of red raspberry. Transcriptome was obtained by the de-novo assembly of 298 Million high-quality reads through Trinity assembler, out of the 41,650 high quality transcripts, 18,171 coding...

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, through an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during the larva...

We introduce the notions of directional dynamical cubes and directional regionally proximal relation defined via these cubes for a minimal $\mathbb{Z}^{d}$ -system $(X,T_{1},\ldots ,T_{d})$ . We study the structural properties of systems that satisfy the so-called unique closing parallelepiped property and we characterize them in several ways. In t...

Design and selection of efficient metabolic pathways is critical for the success of metabolic engineering endeavors. Convenient pathways should not only produce the target metabolite in high yields, they also require to be thermodynamically feasible under production conditions, and prefer efficient enzymes. To support the design and selection of su...

Nile Tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world and so far, they are mainly based on conventional selection using genealogical and phenotypic information to es...

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Faster male development during grow-out phase is considered a major problem that generate heterogeneous sizes of fish at harvest. Identifying genomic regions associated with sex determination in Nile tilapia is a research topi...

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native pl...

Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations...

We introduce the notions of directional dynamical cubes and directional regionally proximal relation defined via these cubes for a minimal $\mathbb{Z}^d$-system $(X,T_1,\ldots,T_d)$. We study the structural properties of systems that satisfy the so called unique closing parallelepiped property and we characterize them in several ways. In the distal...

Wilson Disease (WD) is an autosomal recessive disorder caused by mutation in the ATP7B gene that affects copper transport in the body. ATP7B mutation damages copper transporter function, ultimately resulting in excessive copper accumulation and subsequent toxicity in both the liver and brain. Mechanisms of copper toxicity, however, are not well def...

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present...

The ferric uptake regulator (Fur) plays a major role in controlling the expression of iron homeostasis genes in bacterial organisms. In this work, we fully characterized the capacity of Fur to reconfigure the global transcriptional network and influence iron homeostasis in Enterococcus faecalis. The characterization of the Fur regulon from E. faeca...

Differentially expressed genes in E. faecalis wild type and Δfur. The table shows the differentially expressed genes obtained from the RNAseq experiments.

Global transcriptional regulatory network activated by iron deficiency or excess in E. faecalis wild type and Δfur.

Protein sequence alignments between E. faecalis Fur (EF1525) and Fur archetypes from different bacterial species. Color circles denote conserve motif involved in iron/zinc binding.

Growth curve of E. faecalis wild type and Δfur under different conditions of iron exposure (excess and deficiency) in three biological replicates (Mann–Whitney test, p < 0.05). Error bars represent standard deviation (SD) values.

Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics met...

Supplementary material. Additional results, methods and figures. (PDF)

Background Long read sequencing technologies are the ultimate solution for genome repeats, allowing near reference level reconstructions of large genomes. However, long read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes...

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slop...

The construction of affine interval exchange maps with wandering intervals that are semi-conjugate with a given self-similar interval exchange map is strongly related with the existence of the so called minimal sequences associated with local potentials, which are certain elements of the substitution subshift arising from the given interval exchang...

Background Whole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant. Results Here...

The high lignocellulolytic activity displayed by the soft-rot fungus Penicillium purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2 Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and Core Eukaryotic Genes Map...

Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on P. salmonis has grown in the last...