Alejandro Maass

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

PhD Mathematics

About

257
Publications
37,854
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
5,831
Citations
Additional affiliations
September 1990 - present
University of Chile
Position
  • Professor (Full)

Publications

Publications (257)
Article
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...
Article
The Atacama Desert in Chile—hyperarid and with high–ultraviolet irradiance levels—is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre–Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environme...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Preprint
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Data
Differentially expressed genes in E. faecalis wild type and Δfur. The table shows the differentially expressed genes obtained from the RNAseq experiments.
Data
Global transcriptional regulatory network activated by iron deficiency or excess in E. faecalis wild type and Δfur.
Data
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.
Data
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.
Article
Full-text available
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...
Article
Full-text available
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...
Data
Supplementary material. Additional results, methods and figures. (PDF)
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...