Research
Our research group is interested in understanding the molecular interactions that define prokaryotes using the Systems Biology approach. We intend to use diverse high-throughput ‘omic’ technologies, analyze and integrate experimental data using bioinformatics tools and formulate models that describe and predict the behavior of a cell. The integration and exploration of the data and model will raise new hypothesis which will be experimentally tested – validating or refuting the proposed model. This iterative cycle requires the interdisciplinar collaboration between biologists, computer scientist and mathematicians.
To understand and organism as a whole, we are using the archaea Halobacterium salinarum NRC-1 as a model. This unicellular prokaryote thrives in conditions of extreme salinity, it has a compact genome and is easily cultivated and manipulated in the laboratory. It is a fascinating microbe, with potential applications in biotechnology, studies in astrobiology, besides it’s role as a model archaea in Systems Biology: six years after the completion of the genome, there is a global gene regulatory network available for Halobacterium salinarum NRC-1.
Despite the high descriptive and predictive capacity of the proposed model, it does not yet encompass details regarding molecular mechanisms. Our group intends to work on integrating mechanism details into global gene regulation models, which requires overcoming both experimental and bioinformatics challenges. Currently, we are working on characterizing non-coding RNAs in H. salinarum and their influence on gene regulation. It is expected that inserting molecular mechanism details into global gene regulatory models will boost efforts in Synthetic Biology to engineer biological systems.
Key Concepts
Systems Biology
System Biology is the branch of science that seeks to understand biological organisms at all levels, since the characterization of its constituent parts (genes, RNAs, proteins, metabolites), the elucidation of the interconnections between the different members of the network of gene regulation until the comprehension of the organism as a whole.
Biological systems are dynamic, using complex cellular circuits to implement various functions, how to grow, differentiate and reproduce. High-throughput technologies that exploit data from transcriptome, proteome, protein-protein, protein-DNA, protein-RNA interactions, among others, represent powerful tools for the systemic analysis. However, each of these individual data sets do not reflect a global view of cell behavior, since that complexity of living organisms is an emergent property, inherent not only genes, RNAs, proteins or metabolites, but is a consequence of their actions and interactions.
Extremophiles
In the harshest environments of our planet, in places like volcanoes, we imagine an extremely hot and toxic place, unlikely to harbor any life. In salt deserts the image is the same. However, this first impression can be misleading, these environments have been showing to be filled with life, populated by organisms that are denominated extremophiles.
Extremophiles are very peculiar organisms in many aspects. The harsh environments they live are diverse: we can find extremophiles in sulfuric acid (acidophiles), living underneath thick ice (psycrophiles) and some that live under a high salt concentration (halophiles), among other examples. Another interesting aspect of these organisms is how they have adapted their metabolism and physiology to survive and thrive in these environments. Extremophiles, for their ability to survive in extreme conditions, are great candidates for the studies of origin and evolution of life in the Astrobiology field, also providing new hypotheses on the habitability of exoplanets.
The majority of extremophiles can be classified in two of the three domains of life, Bacteria and Archaea, both being represented by procaryotic organisms, the Eukaryota domain comprehends fewer extremophiles. A classic examples of extremophile in Bacteria is Thermus aquaticus, which can survive at high temperatures and was an important participant in the evolution of Molecular Biology, providing a DNA polymerase able to handle higher temperatures used in PCR techniques. Deinococcus radiodurans which is extremely resistant against radiation, vacuum, cold and acids is called a poliextremophile.
Bioinformatics
Bioinformatics is a multidisciplinary field that applies knowledge of computer science, mathematics and physics to solve problems from biological research fields such as molecular biology and biochemistry.
Through bioinformatics, several methods have been developed to better understand the molecular processes that occur in living organisms. Today, researchers have databases to store a volume of information never imagined before and algorithms to handle large-scale data produced by techniques such as next-generation sequencing and mass spectrometry. Moreover, bioinformatics uses statistical and computational techniques to help undertastand the large volume of data and provide greater explanatory power of biological processes .
Gene Expression Regulation
How the cells of your body become differentiated and perform different functions? How humans have become the most complex organisms so far discovered? What governs the ability of living organisms to respond to stimuli and to adapt to inhospitable environments? What makes life possible?
The answers to these questions fall on one of the most basic characteristic of living organisms, the regulation of gene expression. Cells with the same gene content can specialize and play distinct roles. In addition, external or internal stimuli can alter the function of a cell or even trigger systemic responses.
This cascade of changes undergone by cells during cellular differentiation, or before a stimulus is due to activation of genes that control other genes, whose activities are associated with activation or repression of various biological processes (replication, transcription, translation, cell death , DNA repair, cell cycle and energy production).
