FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation

For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments

Microalgal co-cultivation -recent methods, trends in omic-studies, applications, and future challenges

The burgeoning human population has resulted in an augmented demand for raw materials and energy sources, which in turn has led to a deleterious environmental impact marked by elevated greenhouse gas (GHG) emissions, acidification of water bodies, and escalating global temperatures. Therefore, it is imperative that modern society develop sustainable technologies to avert future environmental degradation and generate alternative bioproduct-producing technologies. A promising approach to tackling this challenge involves utilizing natural microbial consortia or designing synthetic communities of microorganisms as a foundation to develop diverse and sustainable applications for bioproduct production, wastewater treatment, GHG emission reduction, energy crisis alleviation, and soil fertility enhancement. Microalgae, which are photosynthetic microorganisms that inhabit aquatic environments and exhibit a high capacity for CO2 fixation, are particularly appealing in this context. They can convert light energy and atmospheric CO2 or industrial flue gases into valuable biomass and organic chemicals, thereby contributing to GHG emission reduction. To date, most microalgae cultivation studies have focused on monoculture systems. However, maintaining a microalgae monoculture system can be challenging due to contamination by other microorganisms (e.g., yeasts, fungi, bacteria, and other microalgae species), which can lead to low productivity, culture collapse, and low-quality biomass. Co-culture systems, which produce robust microorganism consortia or communities, present a compelling strategy for addressing contamination problems. In recent years, research and development of innovative co-cultivation techniques have substantially increased. Nevertheless, many microalgae co-culturing technologies remain in the developmental phase and have yet to be scaled and commercialized. Accordingly, this review presents a thorough literature review of research conducted in the last few decades, exploring the advantages and disadvantages of microalgae co-cultivation systems that involve microalgae-bacteria, microalgae-fungi, and microalgae-microalgae/algae systems. The manuscript also addresses diverse uses of co-culture systems, and growing methods, and includes one of the most exciting research areas in co-culturing systems, which are omic studies that elucidate different interaction mechanisms among microbial communities. Finally, the manuscript discusses the economic viability, future challenges, and prospects of microalgal co-cultivation methods

Advances in Microalgae Biology and Sustainable Applications

It has become more evident that many microalgae respond very differently than land plants to diverse stimuli. Therefore, we cannot reduce microalgae biology to what we have learned from land plants biology. However, we are still at the beginning of a comprehensive understanding of microalgae biology. Microalgae have been posited several times as prime candidates for the development of sustainable energy platforms, making thus the in-depth understanding of their biological features an important objective. Thus, the knowledge related to the basics of microalgae biology must be acquired and shared rapidly, fostering the development of potential applications. Microalgae biology has been studied for more than forty years now and more intensely since the 1970’s, when genetics and molecular biology approaches were integrated into the research programs. Recently, studies on the molecular physiology of microalgae have provided evidences on the particularities of these organisms, mainly in model species, such as Chlamydomonas reinhardtii. Of note, cellular responses in microalgae produce very interesting phenotypes, such as high lipid content in nitrogen deprived cells, increased protein content in cells under high CO2 concentrations, the modification of flagella structure and motility in basal body mutant strains, the different ancient proteins that microalgae uses to dissipate the harmful excess of light energy, the hydrogen production in cells under sulfur deprivation, to mention just a few. Moreover, several research groups are using high-throughput and data-driven technologies, including “omics” approaches to investigate microalgae cellular responses at a system-wide level, revealing new features of microalgae biology, highlighting differences between microalgae and land plants. It has been amazing to observe the efforts towards the development and optimization of new technologies required for the proper study of microalgae, including methods that opened new paths to the investigation of important processes such as regulatory mechanisms, signaling crosstalk, chemotactic mechanisms, light responses, chloroplast controlled mechanisms, among others. This is an exciting moment in microalgae research when novel data are been produced and applied by research groups from different areas, such as bioprocesses and biotechnology. Moreover, there has been an increased amount of research groups focused in the study of microalgae as a sustainable source for bioremediation, synthesis of bioproducts and development of bioenergy. Innovative strategies are combining the knowledge of basic sciences on microalgae into their applied processes, resulting in the progression of many applications that hopefully, will achieve the necessary degree of optimization for economically feasible large-scale applications. Advances on the areas of basic microalgae biology and novelties on the essential cellular processes were revealed. Progress in the applied science showed the use of the basic science knowledge into fostering translational research, proposing novel strategies for a sustainable world scenario. In this present e-book, articles presented by research groups from different scientific areas showed, successfully, the increased development of the microalgae research. Herewith, you will find articles ranging from bioprospecting regional microalgae species, through advances in microalgae molecular physiology to the development of techniques for characterization of biomass and the use of biomass into agriculture and bioenergy production. This e-book is an excellent source of knowledge for those working with microalgae basic and applied sciences, and a great opportunity for researchers from both areas to have an overview of the amazing possibilities we have for building an environmentally sustainable future once the knowledge is translated into novel applications

Analysis of sensitive CO2 pathways and genes related to carbon uptake and accumulation in Chlamydomonas reinhardtii through genomic scale modeling and experimental validation

The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism towards biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04% (air), 2.5%, 5%, 8% and 10% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins and starch were further quantified for the reference low (0.04%) and high (10%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time qPCR. The sensitive analysis revealed mitochondrial compartment as the major affected by high CO2 levels and glycolysis/gluconeogenesis, glyoxylate and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1) and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. Possible roles of the sensitive pathways in the biomass metabolism are discussed

FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation

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Bioinformática : Aplicaciones a la proteómica y genómica

En esta publicación intitulada “Bioinformática: aplicaciones a la genómica y proteómica” se detallan algunos de los avances más sobresalientes de los temas de genómica y proteómica, derivados de un curso internacional sobre el tema, organizado por el Colegio de Postgraduados. Estos avances incluyen aspectos de las dos ciencias ómicas, incluyendo genómica y biología estructural, código R, análisis comparativo y evolución, agrupamiento y minería de datos en R, redes de interacciones entre proteínas y proteómica bioinformática. BIOINFORMATICS : APPLICATIONS TO GENOMICS AND PROTEOMICS. ABSTRACT : In this publication entitled "Bioinformatics: applications to genomics and proteomics" are some of the most salient issues of genomics and proteomics, derived from an international course on the subject organized by the Colegio de Postgraduados, Mexico. These advances include both aspects of omics sciences, including genomics and structural biology, code R, comparative analysis and evolution, clustering and data mining in R, networks of interactions between proteins and proteomics bioinformatics.CONTENIDO: 1. Bases de la Bioinformática / Diego Mauricio Riano Pachón. – 2. Herramientas Bioinformáticas / s. a. – 3. Análisis comparativo y evolución / s. a. - 4. Introducción a R – Parte I/ Elizabeth González Estrada. – 5. Introduction to R – Part II / Adrian Alexa. – 6. Exploratory Data Analysis – Clustering gene expression data / Adrian Alexa. – 7. Tutorial Cytoscape / Fidel Ramírez. – 8. Bioinformatics for proteomics, tutorial of practice session / Flavia Vischi Wink. AGRADECIMIENTOS A: LPI 5 Biotecnología Microbiana Vegetal y Animal y LPI 15. Estadística, Modelado y Tecnologías de la Información Aplicadas a la Agrícultura y al Medio Rura