Andrés González

Homeostatic NMDA receptor down‐regulation via brain derived neurotrophic factor and nitric oxide‐dependent signalling in cortical but not in hippocampal neurons

J. Neurochem. (2011) 118, 760–772.

Targeted metabolic reconstruction: a novel approach for the characterization of plant–pathogen interactions

Genome-scale metabolic reconstruction (GEMR), along with flux balance analysis, has been widely used to study complex metabolic networks in several microbial organisms. This approach is of particular applicability in biological systems where the lack of kinetics data is typical. This is the case of plant-pathogen interactions, where these methods open the possibility of studying host metabolic network phenotype during the interaction with pathogens. Since GEMRs are based on sequenced genomes, its applicability to organisms where genomic information is lacking is limited. Here we describe an alternative approach to GEMR: targeted metabolic reconstruction, where network reconstruction is guided by transcriptomic data instead of genomic information. This approach is being applied successfully in our laboratory for the Phytophthora infestans--Solanum tuberosum pathosystem.

Draft Genome Sequence of the Animal and Human Pathogen Malassezia pachydermatis Strain CBS 1879

ABSTRACT Malassezia pachydermatis is a basidiomycetous yeast that causes infections in humans and animals. Here, we report the genome sequence of Malassezia pachydermatis strain CBS 1879, which will facilitate the study of mechanisms underlying pathogenicity of the only non-lipid-dependent Malasezzia species.

Computational Biology in Colombia

High-throughput techniques are somewhat restricted in developing countries. However, computational resources have evolved in recent years to become available to the general public, with greater ability to solve intense computational problems at low cost. Therefore, the vast amount of information that is currently being generated and the need for finding the underpinnings of several issues in biology, have been the impetus of the computational biology area in Latin America. Colombia is no exception, as its rich genetic diversity has convened the attention of several institutions, including both governmental and academic departments, to find how, where, and when these resources could be employed to its benefit. In this review, we introduce the efforts being made throughout the country to spread the word and establish a strong network from a mid- and long-term perspective.

Sharing a Ride on the Commodities Roller Coaster

Fluctuations in commodity prices are an important driver of business cycles in small emerging market economies (EMEs). This paper documents how these fluctuations correlate strongly with the business cycle in EMEs. A commodity sector is then embedded into a multi-country EMEs business cycle model where exogenous fluctuations in commodity prices follow a common dynamic factor structure and coexist with other driving forces. The estimated model assigns to commodity shocks 42 percent of the variance in income, of which a considerable part is linked to the common factor. A further amplification mechanism is a spillover effect from commodity prices to risk premia. JEL classifications: E32, F41, F44

Efficient Infrastructure Restoration Strategies Using the Recovery Operator

Infrastructure systems are critical for societys resilience, government operation, and overall defense. Thereby, it is imperative to develop informative and computationally efficient analysis methods for infrastructure systems, which reveal system vulnerabilities and recoverability. To capture practical constraints in systems analyses, various layers of complexity play a role, including limited element capacities, restoration resources, and the presence of interdependence among systems. High-fidelity modeling such as mixed integer programming and physics-based modeling can often be computationally expensive, making time-sensitive analyses challenging. Furthermore, the complexity of recovery solutions can reduce analysis transparency. An alternative, presented in this work, is a reduced-order representation, dubbed a recovery operator, of a high-fidelity time-dependent recovery model of a system of interdependent networks. The form of the operator is assumed to be a time-invariant linear dynamic model apt for infrastructure restoration. The recovery operator is generated by applying system identification techniques to numerous disaster and recovery scenarios. The proposed compact representation provides simple yet powerful information regarding systemic recovery dynamics, and enables generating fast suboptimal recovery policies in time-critical applications.

Identification and characterization of lipid droplets in Malassezia furfur

Objective: We explored the phenotypical and genetic variability among isolates of the ubiquitous and saprophytic fungus Aspergillus fumigatus which has the remarkable ability to adapt and grow in many different niches. Due to this ability it can also cause invasive and non-invasive infections in humans and animals, for example invasive pulmonary aspergillosis (IPA) in humans and sinonasal aspergillosis (SNA) in dogs. Our main objective is to understand how this fungus adapts to different niches and to find the factors and genetic traits that influences host adaptation and development in the context of fungal infections. To address this question we have compared a set of clinical and environmental isolates at a genetic and phenotypic level. Isolates were derived from sputum or bronchoalveolar lavage from human patients at the intensive care unit who were suspected to developed IPA. In addition we cultured isolates from fungal plaques isolated from the sinus of dogs suffering with SNA using endoscopy or trephination. Methods: We have compared a set of isolates of A. fumigatus from A) humans (29 isolates from a preselected set of 9 patients), B) dogs with SNA (27 isolates form 9 patients) C) environmental isolates (27 isolates) with reference strains. Azole resistance was determined by microdilution assay antifungal susceptibility testing and tandem repeats in the promotor region of the cyp51A gene. Sequencing of calmodulin (CaM), beta-tubulin(benA) and mating type genes (MAT1-1 and 1-2) and microsatellite (STRAf) analysis were performed to detect genetic differences between isolates. Plating on different media was performed to observe differences in macro and micromorphology Results: Genotyping of the different isolates showed that each human patient carried multiple fungal genotypes. In contrast, each dog suffering from SNA appeared to be infected by only one single genotype. Remarkably, different isolates from each dogs, and having the same genotype, showed a large phenotypic variability. In particular “white isolates” with apparent reduced sporulation were frequently isolated (13 out of 27 isolates) from dogs but not in human patients or in environmental isolates. In terms of azole resistance only human isolates and one of the indoor and outdoor environmental isolates were found to be resistant. Principal component analysis using colony diameter as a proxy for growth speed suggests that canine isolates might represent a subgroup of A. fumigatus that are responsible for SNA. Conclusion: Our observations shows thatfumigatus from dogs with SNA are phenotypically very diverse in contrast to their environmental and human counterparts. Phenotypic variability seems to be generated during the chronic infection process in the sinus of the dogs. The basis of this heterogeneity might be due to genomic differences and/or epigenetic variations. We expect that appearance of the phenotypic “white isolates” in dogs is a result of within-host adaption and is triggered by environmental factors in the sinus which we address in ongoing research.Objective: Aspergillus fumigatus is the main causative agent of aspergillosis. Most infections occur in immunocompromised individuals, indicating an efficient clearance of conidia by the pulmonary defence system in immunocompetent individuals. Infections by other aspergilli like Aspergillus niger can occur, but to lesser extent. Previous studies showed that A. fumigatus and A. niger behave differently in the presence of type II alveolar A549 epithelial cells. A. fumigatus is more efficiently internalized by the A549 cells and shows a delay in germination, when compared to A. niger. The hyphae of A. fumigatus, that escaped the epithelial cells grow parallel to the epithelium, while the A. niger hyphae grow away from the epithelial cell layer. This study focusses on the gene expression of A. fumigatus and A. niger after co-cultivation with A549 cells. Our hypothesis is that the difference in lifestyle between the two aspergilli is also observed in the gene expression profiles. Methods: RNA of the co-cultivation of the A549 cells with A. fumigatus or A. niger was isolated and sequenced. The obtained RNA sequences were analysed with custom R and python scripts to obtain the differentially expressed genes and GO terms. Results: The obtained RNA sequences show big differences in the global gene expression of A. fumigatus and A. niger upon contact with A549 cells. A total of 545 and 473 genes for respectively A. fumigatus and A. niger were differently expressed when compared to growth in absence of A549 cells. Of these genes only 53 (∼10%) were shared between both species. The different response was also illustrated by the fact that only 4 GO terms were shared between the differentially expressed genes of both gene sets. Genes described in hypoxia regulation and heat shock were found up-regulated in A. fumigatus and their homologs in A. niger. The A. fumigatus thioredoxin reductase and allergen genes were found up-regulated in this fungus, but homologous genes were down-regulated in A. niger. After co-cultivation with A. fumigatus 62 genes were up and 47 genes were down-regulated in the A549 cells. Co-cultivation with A. niger resulted in 17 up and 34 down-regulated genes. GO term related with the immune response were down-regulated in the A549 cells upon exposure to A. fumigatus, but not in the case of A. niger. This is a strong indication that A. fumigatus reprograms the A549 cells to be immunologically less alert. Conclusion: Our dual transcriptome analysis supports earlier observations of a markedly difference in life style between A. fumigatus and A. niger when grown in presence of type II epithelial lung cells. These results show an important difference in gene expression, amongst others the downregulation of immune response genes in epithelial cells by A. fumigatus and not by A. niger.Objective: The form of human fungal sinusitis that most closely approximates the disease occurring in the dog is chronic erosive non-invasive fungal sinusitis. This disease is characterized by final destruction of bone in the absence of tissue invasion by the fungus and requires both removal of fungal plaques, necrotic tissue and medical therapy with antifungals. Remarkably, these fungal plaques are white indicated that asexual development does not proceed in the patients. Immune response in SNA infections has been studied via biopsy and cytokine profiling as well as transcriptomic analysis of the host tissue. However, a transcriptomic study of this fungal pathogen growing in patients causing a non-invasive infection has never being performed. We obtained fungal plaques directly from canine patients suffering from SNA and characterize the transcriptome of the causative fungus A. fumigatus in order understand gene expression in the context of the host and particularly in the field of in-host adaptation Methods: Four different fungal plaques were isolated from dogs suffering from SNA. After surgical removal using endoscope or trephination part of fungal plaques were immediately frozen in liquid nitrogen and stored at -80°C for RNA isolation and sequencing. RNA isolation was performed using RNeasy Mini Kit® from Qiagen and sequencing was performed by ServiceXS (Leiden, The Netherlands). RNA-seq analysis involved quality check with fastQC. Cleaning and trimming of reads with Fastx-toolkit. Kallisto was used for transcript quantification(TPM) with A. fumigatus Af293 (AspGD) as reference. For functional characterization of the transcriptome, highly variable expressed genes between samples were removed, and 3 subjective levels of expression were established: low (1 to 39.8 TPM), median (39.8 to 1584.8 TPM) and high (1584.8 to 79432.8 TPM), for each group an enrichment analysis was performed. Additionally a more targeted categorization of the transcriptome was done using published lists of genes involved in stress, reproduction and virulence. Results: According to the used criteria 17% of the expressed genes presented a stable expression across all 4 fungal plaques. Careful examination of this group of genes showed genes previously reported to be involved in SskA-Hog/SakA signalling pathway with some of them (bck1 and hdaA) also involved in the regulation of secondary metabolism. Interestingly, central regulators of asexual reproduction like BrlA, WetA and AbaA showed variable or null expression. A similar pattern was observed for catalases and superoxide dismutases. Finally comparison with published biofilm expression data showed that 18% of the stable expressed genes were also differentially expressed in A. fumigatus biofilm, of which approximately half of them were described to be differentially expressed in an “mature” biofilm (48 h). Conclusion: 1-To our knowledge this is the first transcriptomic study of A. fumigatus in the context of a natural non-invasive infection in dogs suffering from SNA. 2-Variability in gene expression in SNA fungal plaques could be caused by several factors like time of infection, host response, and genomic differences. 3-SNA fungal plaques resemble a non-sporulation mature biofilm, explained partially by low expression of central regulators of sporulation and the expression of some genes related to previously reported biofilm formation.Objective: Malassezia species are lipid-dependent due to the lack of cytosolic fatty acid synthase required for De novo synthesis of fatty acids (FAs) and these yeasts are part of the skin mycobiome. Pathogenicity of Malassezia has been related to several factors including the ability to produce enzymes such as esterases, lipases, lipoxygenases and proteases which enable growth on the host skin and lead to changes in sebum (skin fat) composition. The skin functions in the innate defense against pathogens due to its low water content, acidic pH, its microbiota, and antimicrobial compounds like free fatty acids. Understanding lipid dependency of Malassezia will help to understand how these yeasts establish themselves as part of the skin microbiota, which adaptation mechanisms are involved, and how, and whether, lipid metabolism impacts the shift to pathogenicity. The complex nutritional requirements of Malassezia have delayed the full comprehension of its lipid metabolism. Reconstruction of the lipid-synthesis pathways of Malassezia species in silico predicted amongst others a defect in the assimilation of palmitic acid in M. globosa, M. sympodialis, M. pachydermatis and an atypical isolate of M. furfur, but not in M. furfur. This prediction was validated by physiological characterization in chemically defined media (MM) using different lipid sources. Methods: Growth on FAs in liquid MM: Strains were first grown for 7 days at 33°C in lipid-rich mDixon medium. To prevent subsequent growth in MM due to the presence of residual lipids we performed a two-phase growth in MM. First, cells were diluted into MM containing specific lipids. After 3 days, these cells were diluted again in fresh MM with the same lipids. Growth was monitored for 7 days by determining OD600 nm and CFU by plating on mDixon plates. Results: M. furfur could assimilate palmitic acid or oleic acid as well as all Tween variants tested. The atypical M. fufur strain could assimilate only Tween 80, Tween 20, and oleic acid. M. pachydermatis, M. globosa, and M. sympodialis were able to grow in the first step in MM but not in the second step in MM with any of the lipid sources tested. Only M. furfur was able to maintain growth in MM with palmitic acid in the second growth step. Both M. pachydermatis and atypical M. furfur could sustain growth in MM with a mixture of palmitic acid and oleic acid. Conclusion: 1. A new culturing method for Malassezia spp. in chemically defined media was developed. 2. In silico predicted assimilation defects of palmitic acid for Malassezia spp. was confirmed. 3. Palmitic acid is fungicidal for a subset of Malassezia spp. but not for M. furfur. 4. FAs that induce lipid toxicity and do not affect the skin cells and microbiome harmony might have a therapeutic use.

The computational complexity of probabilistic Interdependent Network Design Problems

We present a rigorous study of the computational complexity of an Interdependent Network Design Problem (INDP) solution model, which is at the core of future infrastructure restoration studies. The paper details how each constraint in the INDP formulation adds to the overall complexity, while also revealing strategies to tame the computational demands for large interdependent networks. It is shown how some algorithms that are used to enhance the Network Design Problem (NDP) (Poss 2011), including decomposition techniques, can be cleverly adapted to the INDP model. Computational examples are based on diverse yet idealized topologies, to illustrate the sensitivity of the INDP model to input parameters and constraints, as well as the underlying topological properties of the studied systems. The present study paves the way for future approaches to improve the INDP and its Mixed-Integer Programming (MIP) model, particularly in terms of its efficiency and capability to handle large size instances, and by extension, its ability to support practical infrastructure decision making and resilience analyses.