GRE

GRE
 
            The Graduate Program in Biology of Host-Pathogen Interactions will receive PhD candidates interested in applying for the USP and FAPESP Joint Initiative. For more information please click on the link: http://www.prpg.usp.br/index.php/pt-br/gre-2/usp-gre-2.
 
            Eligible advisors for this particular initiative and their respective research lines are listed below.
 
 
Prof. Ariel Mariano Silber
The biological role of amino acids and their metabolites in Trypanosoma cruzi.
Several studies have described the relevance of the amino acids in the biology of several protozoa parasites such as Trypanosoma cruzi, the etiological agent of Chagas disease. Besides their role in protein synthesis and energy metabolism, amino acids are also involved in different biological processes in the parasite. Among them, it is worth mentioning the differentiation between stages, the energetic support to the host-cell invasion, the establishment of the infection and the resistance to different stresses the parasite faces during its life cycle, such as osmotic, thermal, oxidative and nutritional. Until now, different roles of several amino acids were evaluated individually, but an integrated and systematic view of the role of main amino acid metabolic pathways and their interactions is still lacking. Taking into account this gap, this project aims: (1) To develop a metabolic chart for the amino acids with focus on that having a role in the bioenergetic of T. cruzi, including the identification of auxothrophies for these metabolites. (2) To evaluate their intervention on: i) the induction of ATP synthesis, production of H2O2, respiratory burst and mitochondrial membrane potential, ii) differentiation, iii) support of the host-cells invasion, iv) resistance to osmotic, oxidative, thermal, nutritional, acidic stress as well as toxicity due to NH4+ accumulation, v) the modulation of cell cycle, autophagy and the programmed cell-death triggered by metabolic stress. (3) To evaluate the roles of enzymes participating of the metabolism of those amino acids having activities described in (2), as well as the effect of their chemical inhibition or overexpression, on different aspects of the biology of the parasite mentioned in (2). (4) To perform a comparative study of the different metabolic pathways activity among different stages by targeted metabolomics. (5) To develop knock-out lineages by CRISPR/Cas9 for the most relevant enzymes among those of the amino acids metabolism for different aspects of the biology of the parasite mentioned in (2) to evaluate their possible effects related to their therapeutic potential. To evaluate by metabolomics the effect of the gene suppression or the treatment of inhibitors on the metabolic profile of the cells. (6) To evaluate the impact of the amino acids metabolism on the management of the excess of NH4+ and the production of amino sugars and glycoconjugates.
 
Prof. Carsten Wrenger
Drug discovery against human infectious diseases
            Infectious diseases are a threat to humanity and currently their causative pathogens are spreading geographically due to globalization and the development of drug resistance. Drug resistance is currently occurring against almost all pathogens and therefore there is an urgent need to discover new therapeutic targets and/or new classes of targets. In this project, the focus will be on the discovery of new pro-drugs exploring the biosynthesis pathways of B1/B6 vitamins from human pathogens: Plasmodium falciparum, the parasite responsible for causing severe malaria, and the multi-resistant bacterium Staphylococcus aureus MRSA. Compounds will be identified and designed according to evaluations based on the crystallographic structures of the respective enzymes involved in the biosynthesis of vitamins B1/B6, aiming the incorporation of the compounds into the pathogen. Therefore the new compounds will seek to poison the vitamin-dependent enzymes as cofactors. Complementary assays will involve the use of human cell lines as well as their respective transgenic lines over expressing nuclear receptors for xenobiotics, in order to report possible interactions with the host.
 
Prof. Célia Regina da Silva Garcia
Functional Genomics in Plasmodium
The elucidation of cell cycle and development control mechanisms of Plasmodium, the etiological agent of malaria, is crucial for development of new strategies for disease control. In this way, different ways of control either cell cycle or parasite development are propose to be studied in this project.
Since our data generated in recent last years, including the identification of serpentine receptors, known in participating in a variety of cell processes, usually known as drug targets, will be better analyzed. Characterizing the RACK protein (receptor of activated protein kinase C) is also very important, whereas protein kinase C has not been found in Plasmodium falciparum.
 Moreover, the melatonin signaling pathway has bring us information about the participation of ubiquitin-proteasome system and protein kinase 7 as molecular effectors. Finally, detoxification mechanisms of heme in malaria parasites through hemeoxigenase will also be here evaluated.
These proposed sub-projects enclose a range of cellular processes that participate in   development and proliferation control of malaria parasite responsible for the most severe form of the disease, Plasmodium falciparum providing a contribution to knowledgement of diverse biological processes that enclose signaling pathways, gene expression control, cellular metabolism and others that participate in an indirect way.
 
Prof. Luís Carlos de Souza Ferreira
Antigen discovery and development of serological diagnostic methods and vaccine strategies against Zika virus (ZIKV)
            The main objective of this funding research project is to fund research on the Zika Virus (ZIKV) currently underway at the USP Virology (LV) and Vaccine Development Laboratory (LDV). The work is centered on four main points, namely: I) generation and use of recombinant antigens derived from ZIKV for use in vaccine strategies and development of specific serological diagnostic methods; II) development of different in vitro and in vivo experimental models, as well as markers, that allow to evaluate and monitor the ZIKV-induced immunity and the protective immunity conferred by vaccine formulations; III) development and testing of vaccine formulations aimed to the control of ZIKV infection, including different antigens, adjuvants, and inoculation pathways; and (iv) development of specific serological tests using recombinant antigens derived from ZIKV. The work will be performed in a partnership with different research groups at USP and abroad, with emphasis in Butantan Institute, Fiocruz and Pasteur Institute. LV and LDV have experience in antigen development, development of vaccine formulations and diagnostic tests against Dengue Virus (DENV) and other viruses and pathogens. The proposed work is supported by the experience of the proposing groups in recent years. In addition, results obtained in the context of the project have already resulted in publications, patent applications and scientific discoveries that have been used by different research institutions in Brazil and abroad. The expected results will bring important impacts both to a better understanding of the serology of the ZIKV infection and to research that results in the development of vaccine formulations that can be used in humans. We hope that the results to be achieved will have significant academic impact and will result in the development of technologies with short and medium term applications in the country.
 
Prof. Marcelo Urbano Ferreira
The scientific basis for the elimination of residual malaria in Brazilian Amazon
            With 143,910 laboratory-confirmed cases and 41 malaria-related deaths in 2014, Brazil has now the lowest malaria burden in 35 years, with transmission virtually limited to the Amazon Basin. The focal nature of malaria transmission in Brazil suggests that elimination efforts will require a careful prioritization of a few residual malaria pockets. We combine classical epidemiological approaches, to characterize risk factors and intervention targets, with population genetics/genomics analyses of parasites with the ultimate goal of improving current strategies for malaria control and elimination in Brazil. Our field-based studies in the main endemic area of Brazil (Juruá Valley, close to the border with Peru, which accounts for 20% of all infections in this country) are complemented with mathematical modeling of different malaria elimination scenarios. We focus on two main challenges for malaria elimination: (a) the presence of asymptomatic infections with low-level parasitemias that are often below the detection threshold of available diagnostic techniques, creating a large and undetected reservoir of infection, and (b) the maintenance of high vector densities resulting from new man-made mosquito breeding sites (fish ponds opened across Juruá Valley for commercial aquaculture).
 
Dr. Maria Carolina Quartim Barbosa Elias Sabbaga
How do common and diverged features of the replicative stress response shape the biology of TriTryp parasites?
            Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp. (tritryps) present different in their life cycles as well as in their strategy for vertebrate infection. These differences in core biology are influenced by the ability of the parasites to maintain and alter their genome, leading to adaptive changes in gene expression. Gene expression is organized almost exclusively as polycistronic transcription, where every gene is expressed from one of a small number of a multigene units meaning that RNA Polymerase needs to traverse unusually long distances. The nature of transcription in each genome must predispose the parasites to pronounced replication stress due to collision between the replication and transcription machineries, leading to DNA replication fork stalling. In such stress conditions, the halted DNA fork is recognized by kinases ATM and ATR, which initiate a signaling cascade that mediates the appropriate response to the blockade. The nature of the replication stress signaling or the mechanisms of response are not the same in the tritryps and differences in genome architecture in the tritryps may be related to differing strategies used to resolve replication stress due to clashes with transcription. Specifically, it might be predicted that T. brucei activates dormant origins in conditions of stress, whereas T. cruzi and Leishmania resolve the stalled forks using recombination/amplification. We aim to determine if replication-transcription clashes are the main cause of the different genome architectures, and to reveal and compare the strategies used to resolve a stalled DNA replication forks in the parasites.
 
Prof. Sirlei Daffre and Prof. Andréa Cristina Fogaça
Molecular characterization of the interactions among ticks, rickettsiae and vertebrate hosts
            Ticks have parasitic habit of life, feeding obligatory on blood and/or lymph of vertebrates. As a result of hematophagy, these arthropods transmit a wide variety of pathogens. Among the tick-borne rickettsial diseases, we highlight Bovine Anaplasmosis (BA) and Brazilian Spotted Fever (BSF). BA is a severe disease that affects cattle, being caused by Anaplasma marginale and transmitted by Rhipicephalus microplus in Brazil. Despite the veterinary and economic importance, there is no commercial vaccine for the control of either R. microplus or BA. Similarly, there is no vaccine for prevention of BSF, the most severe rickettsial disease that affects humans. In our country, the etiologic agent of BSF, Rickettsia rickettsii, is transmitted by ticks of the genus Amblyomma. This project aims to elucidate the molecular factors involved in the interaction among ticks and rickettsiae with the participation of a consistent network of researchers with complementary expertises. The generated data may reveal new targets for the development of vaccines for the control of both ticks and BA and BSF. In addition, we propose to investigate the susceptibility of A. marginale to antimicrobial components, enabling a more effective control of BA through chemoprophylaxis which is more frequently used in combination with vaccination.