The most common insect in the world\u2019s laboratories, the drosophila, or fruit fly\u00a0 \u2013 Drosophila melanogaster, commonly seen around ripe bananas\u00a0 \u2013 has just gone through a rereading. In October last year, a team from the School of Medicine at the University of S\u00e3o Paulo (USP), at Ribeir\u00e3o Preto, completed a piece of research that discovered 91 new genes for the insect and generated sequences that help define the transcription template \u2013 the set of an organism\u2019s ribonucleic acids (RNAs) forming its genetic code. As a result, the way is paved for more accurate analyses of how genes act and interrelate in the drosophila.<\/p>\n
Studied for around 90 years, the insect, measuring at most half a centimeter, has been used in the attempt to understand human diseases and malfunctions, and it lies at the base of genetic evolution. It was adopted as a laboratory model because it has large chromosomes, easily visible under the microscope, and it reproduces relatively rapidly \u2013\u00a0 from ten to twelve days.<\/p>\n
Global research<\/strong> Nonetheless, in complex organisms, reading the genome sequence alone does not enable correct identification of all the genes. In these organisms, parts of the DNA that constitute the gene are withdrawn during the formation of the messenger gene \u2013 the molecule that carries the information to be translated into the formation of the protein. Hence, there is the need to obtain the sequences present in the RNA. To do this, the Californian group BDGP uses the ESTs (Expressed Sequence Tags) technique, which leads to readings of the ends of the messenger RNA.<\/p>\n The Brazilian team of 15 researchers, however \u2013 by suggestion from the scientific board of FAPESP, which financed the research \u2013 employed a new technique in studies of this type: Open Reading Expressed Sequence Tags, known by the acronym Orestes. Created in Brazil and used in the Human Cancer Genome research, also financed by FAPESP in partnership with Ludwig Institute of S\u00e3o Paulo, this technique was developed by researchers at this institute, who passed it on to USP at Ribeir\u00e3o Preto. The Orestes technique differs from the classic method of studying the drosophila because it does not give priority to reading the ends, but to the central parts of the RNA sequences \u2013 where the genetic code information that is translated into proteins tends to be concentrated.<\/p>\n Valuable path<\/strong> In record time, from April to September, the team obtained and analyzed 10,092 readings of Orestes sequences of the drosophila. \u201cWith the help of the researchers at the Ludwig Institute and the Ribeir\u00e3o Preto Hemocenter, our team was responsible for executing the entire process: extracting the RNA, generating profiles, cloning, producing, and analyzing the sequences\u201d, says the researchers.<\/p>\n The team\u2019s analyses validated 91 new genes. Based on the similarity to the proteins of other organisms, half of these genes were written down as codifiers of proteins with various functions \u2013 regulatory, enzymatic, and structural, for example.<\/p>\n Other 133 sequences were also identified, deriving from regions not classified as genes based on the analysis of the genome sequence.<\/p>\n \u201cWe detected uncharacterized gene fragments as well as sequences for which there is no EST, absolutely new material in terms of the expressed sequencing of the drosophila\u201d, says Maria Lu\u00edsa. In other words: the way was paved for carrying out more accurate analyses of the role of these new genes in the organism.<\/p>\n Fast-track study<\/strong> In Maria Lu\u00edsa\u2019s opinion, it is possible to speed this up without impairing quality. \u201cBased on the data obtained in this pilot experiment, we believe that the Orestes method can supplement the data produced by other projects\u201d, she says. Based on the experience acquired in the Human Cancer Genome project, she calculates that about 10,000 Orestes a month can be done with a capillary sequencer \u2013 a sort of latest model, luxury car in laboratory sequencers.<\/p>\n Regardless of approach used, the importance of sequencing the drosophila genome is clear: by analogy, it enables better understanding of the human genome. Of the 280 human genes associated with diseases or deformations, 177 have already been detected in the insect\u2019s chromosomes. They are the so-called orthologous genes \u2013 that have similarities that may be functional, and accordingly enable a more accurate approach to genetic phenomena.<\/p>\n Many mutations<\/strong> In October, the BDGP released the second version of the genome sequence, with new sequences and filling in 330 of the gaps left behind. And, according to the more recent report by the Berkeley group, the final version of the genome sequence will be available by mid-year. Maria Lu\u00edsa believes that, with this material, they will be in a position to produce a more correct list of the expected genes.<\/p>\n Thus, the spotlights are on the fruit fly\u2019s genetic material, and expectations rise. \u201cWhen we have all the RNAs, we will be able to produce filters with all the sequences and examine them in a deformed drosophila to try to understand the process that made it be defective\u201d, exemplifies Ricardo Gelerman Pinheiro Ramos, one of the biologists on the project undertaken in Ribeir\u00e3o Preto.<\/p>\n Breath-taking<\/strong> At the beginning of November, when the team from Ribeir\u00e3o Preto was putting the finishing touches to the article with the results of their study, researchers at Yale University analyzed the possibility of the text being published in an international scientific magazine. Maria Lu\u00edsa says that the Brazilian sequences will be deposited in the biggest database open to the public; the one maintained by the National Cancer Institute (NCBI) in the United States.<\/p>\n While waiting for replies, Maria Lu\u00edsa is drafting another project to obtain and analyze around 200,000 expressed sequences of the drosophila genome, equivalent to 20 times the volume of material handled so far. \u201cWe don\u2019t know whether one day we will fully understand the genome of an organism as complex as the drosophila. But, given its importance as an experimental model, any progress in this sense is worthwhile\u201d.<\/p>\n","protected":false},"excerpt":{"rendered":"Discovered 91 genes of the model insect thanks to a Brazilian technique ","protected":false},"author":6,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_exactmetrics_skip_tracking":false,"_exactmetrics_sitenote_active":false,"_exactmetrics_sitenote_note":"","_exactmetrics_sitenote_category":0,"footnotes":""},"categories":[159],"tags":[],"coauthors":[93],"class_list":["post-50605","post","type-post","status-publish","format-standard","hentry","category-science"],"acf":[],"_links":{"self":[{"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/posts\/50605","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/comments?post=50605"}],"version-history":[{"count":0,"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/posts\/50605\/revisions"}],"wp:attachment":[{"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/media?parent=50605"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/categories?post=50605"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/tags?post=50605"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/revistapesquisa.fapesp.br\/en\/wp-json\/wp\/v2\/coauthors?post=50605"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\nThe research by the USP team was inspired by the publication of the first version of the drosophila\u2019s genome sequence \u2013 its set of genes \u2013 with the results of\u00a0 the reading of about 120 million base pairs of the deoxyribonucleic acid molecule, DNA, the carrier of the genetic code in each cell. Announced in March 2000, the sequencing of the drosophila\u2019s genome was the outcome of a mega-operation, involving the Berkeley Drosophila Genome Project (BDGP), at the University of California, and the US company Celera Genomics. It is expected that the final gene sequence, with 180 million bases, will be released this year.<\/p>\n
\nMaria Lu\u00edsa Pa\u00e7\u00f3-Larson, coordinator of the USP study, points out another difference: the Brazilian method is a valuable path to detecting the not-very-abundant messenger RNA molecules, which are, therefore, difficult to clone using conventional techniques. Thus, the research proved the validity of the technique: \u201cWe observed that the Orestes method can produce new information on expressed sequences and it supplements what is obtained by conventional methods\u201d, says Maria Lu\u00edsa.<\/p>\n
\nThere are around 90,000 Drosophila ESTs, according to the BDGP reports. \u201cThese ESTs helped identify around 40% of the genes predicted by the genome sequencing analysis released by the BDGP in the report of March 2000\u201d, she says. To identify the remaining 60%, the BDGP began a new project to produce 200,000 ESTs at a rate of 4,000 a month.<\/p>\n
\nThere are other open questions. For a century students of the fruit fly have sought to understand how an organism with a relatively limited genome \u2013 only four pairs of chromosomes \u2013 can trigger subtle and varied responses to the environment. In the 50s, the geneticist Crodowaldo Pavan discovered local and seasonal variations in insects in 35 places in 17 Brazilian regions \u2013 there was a marked variation in the concentration of individuals, even in places close to each other. As a general rule, the environment may change little, but the drosophilae vary a great deal \u2013 one of the reasons why they became a standard study in evolutionary biology. Reading the genome provides valuable tools for these studies.<\/p>\n
\nThe importance of completing the sequencing goes well beyond genetics. The English researcher Jonathan Hodgkin pointed out recently in the magazine Nature that nowadays the world has a consistent database of genomic data, \u201csomething to take your breath away\u201d, with sufficient data to keep biologists busy for decades: \u201cNothing like it has happened before in the history of science, nor is it likely to happen again\u201d.<\/p>\n