Published in april 2013
The University of Campinas (Unicamp) has set up a laboratory that combines in a single location state-of-the-art equipment designed for research in genomics, bioinformatics, proteomics and cell biology. Located in the university’s Science and Technology Park and patterned along the lines of university research facilities abroad, the Central High Performance Technologies Laboratory (LaCTAD) seeks to ensure a high level of quality in the research conducted at Unicamp and in São Paulo State –– the facilities are made available to researchers from other institutions. “The university has signed two significant agreements as a result of the laboratory’s existence. This unit will be very useful for research into the proposed areas and will give a major boost to Brazilian science,” asserted Unicamp’s President, Fernando Ferreira Costa, at the inaugural ceremony.
FAPESP invested approximately R$5.5 million in the purchase of laboratory equipment under the Multi-user Equipment Program (EMU), while building construction and the hiring of staff were left to the university. “It is notable that Unicamp has invested almost as much as FAPESP, and that LaCTAD has a well-demonstrated cost structure and institutional support critical to hiring employees in bioinformatics and technical support staff with doctorates,” said Carlos Henrique de Brito Cruz, FAPESP’s scientific director, who attended the opening of the laboratory on March 1. The proposed creation of LaCTAD was submitted as part of the notice of request for proposals of FAPESP’s Multi-user Equipment Program in 2009. In 2011 the offer of services in temporary facilities in teaching and research units was initiated.
Three modern sequencers have been acquired for work in the field of genomics. There are two models. One is the Illumina HiSeq 2500, which enables complex sequencing studies through its ability to produce a large number of genome sequences for bioinformatic analysis. The other model is the ABI 3730XL DNA Analyzer, made by Applied Biosystems, which does not produce as many sequences as the other model, but has the ability to map a larger number of base pairs. “It’s not easy to find a scientific study in the life sciences published by a leading journal that does not contain some element of gene sequencing or changes in the genome, and doesn’t use such data to design the research or plan the experiments,” says Ronaldo Pilli, Unicamp’s Dean of Research. “This equipment is improving the quality of research carried out at Unicamp.” Providing bioinformatic services, another LaCTAD purpose, is supported by a bank of computers that includes IBM servers and HP machines. “We have invested in the training of human resources by offering bioinformatics courses every semester,” says Dean Pilli. About 160 students have already been trained.
One of the ongoing projects at the facility is led by Professor Iscia Lopes-Cendes of the Department of Medical Genetics at Unicamp’s School of Medical Sciences. She is using one of the LaCTAD sequencers in a research project on the molecular mechanisms in the development of epilepsy, which seeks to identify gene expression in the brain tissues of rats. Selected neuronal groups in the hippocampus of animal models that have been induced to present the disease are subjected to deep sequencing in a search for transcripts (messenger RNA) that may be relevant for differentiating the pathological from the normal state. “As this involves deep sequencing, we needed a fast sequencer and we even helped to upgrade its software with funding from our research project,” she says.
Professor Gláucia Mendes de Souza of the University of São Paulo (USP) Chemistry Institute, who conducts research and is one of the coordinators of FAPESP’s Program for Research on Bioenergy (BIOEN), also used the services of the Unicamp facility in sequencing a sugarcane reference genome. “LaCTAD is providing sequences obtained by using the Illumina sequencer, which complement the sequences we determined with the Roche 454 sequencer. We have one 454 at USP, but not an Illumina, hence the importance of the services they provide,” says Professor Mendes de Souza. Paulo Arruda of Unicamp’s Institute of Biology has also been using the LaCTAD services. A project of his doctoral student Vagner Katsumi Okura involves constructing and sequencing the bacterial artificial chromosome (BAC) library of sugarcane. BAC libraries are fundamental tools for characterizing chromosomal regions that contain genes of interest. A second research project, by doctoral student Pedro Barreto, is investigating how plants regulate mitochondrial biogenesis. The mitochondrion is an organelle responsible for cell bioenergetics. “There is a reasonable knowledge base about mitochondrial biogenesis in mammals, but little is known about it in plants,” says Arruda, whose work envisions sequencing plant RNAs that overexpress the mitochondrial uncoupling protein (UCP1).
In the field of proteomics, LaCTAD has liquid chromatography equipment, which can analyze and purify proteins, as well as a calorimeter, which is used to determine the thermodynamic parameters of biochemical interactions. A mass spectrometer, model Xevo Q-TOF MS, belonging to Unicamp’s Chemistry Institute will be made available to LaCTAD’s users until the laboratory purchases its own equipment. As far as the field of cell biology is concerned, the laboratory is equipped with a Leica confocal microscope capable of producing high resolution fluorescence images of a variety of biological samples of materials. Another piece of equipment is a Bio-Rad multiplex immunoassay instrument, which is capable of quickly and accurately assaying dosages of hormones or cytokines, the molecules involved in emitting the signals between cells during immune responses. “We are organizing an international workshop on cell biology to be held in May. We’re going to hear from outside experts who are conducting the same type of work in the life sciences in a central laboratory so that we can exchange experiences and improve our services. The idea is to generate greater momentum for LaCTAD in cell biology,” says Dean Pilli.