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Silveira GO, Coelho HS, Pereira ASA, Miyasato PA, Santos DW, Maciel LF, Olberg GGG, Tahira AC, Nakano E, Oliveira MLS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs are essential for Schistosoma mansoni pairing-dependent adult worm homeostasis and fertility. PLoS Pathog 2023; 19:e1011369. [PMID: 37146077 DOI: 10.1371/journal.ppat.1011369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/17/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
The trematode parasite Schistosoma mansoni causes schistosomiasis, which affects over 200 million people worldwide. Schistosomes are dioecious, with egg laying depending on the females' obligatory pairing with males. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential that have been involved in other species with reproduction, stem cell maintenance, and drug resistance. In S. mansoni, we recently showed that the knockdown of one lncRNA affects the pairing status of these parasites. Here, we re-analyzed public RNA-Seq data from paired and unpaired adult male and female worms and their gonads, obtained from mixed-sex or single-sex cercariae infections, and found thousands of differentially expressed pairing-dependent lncRNAs among the 23 biological samples that were compared. The expression levels of selected lncRNAs were validated by RT-qPCR using an in vitro unpairing model. In addition, the in vitro silencing of three selected lncRNAs showed that knockdown of these pairing-dependent lncRNAs reduced cell proliferation in adult worms and their gonads, and are essential for female vitellaria maintenance, reproduction, and/or egg development. Remarkably, in vivo silencing of each of the three selected lncRNAs significantly reduced worm burden in infected mice by 26 to 35%. Whole mount in situ hybridization experiments showed that these pairing-dependent lncRNAs are expressed in reproductive tissues. These results show that lncRNAs are key components intervening in S. mansoni adult worm homeostasis, which affects pairing status and survival in the mammalian host, thus presenting great potential as new therapeutic target candidates.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Helena S Coelho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Adriana S A Pereira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Patrícia A Miyasato
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Daisy W Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Lucas F Maciel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Giovanna G G Olberg
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Eliana Nakano
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, São Paulo, Brazil
| | | | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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2
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Cabral L, Persinoti GF, Paixão DAA, Martins MP, Morais MAB, Chinaglia M, Domingues MN, Sforca ML, Pirolla RAS, Generoso WC, Santos CA, Maciel LF, Terrapon N, Lombard V, Henrissat B, Murakami MT. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 2022; 13:629. [PMID: 35110564 PMCID: PMC8810776 DOI: 10.1038/s41467-022-28310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy. Here, Cabral et al., perform a multi-omics analysis of the gut microbiome of capybara, the largest living rodent, unveiling enzymatic mechanisms for the breakdown of lignocellulosic biomass, and report two undescribed families of carbohydrate-active enzymes.
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Affiliation(s)
- Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
| | - Douglas A A Paixão
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariana A B Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mariana Chinaglia
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mauricio L Sforca
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Wesley C Generoso
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Clelton A Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Lucas F Maciel
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Nicolas Terrapon
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Vincent Lombard
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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3
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Maciel LF, Morales-Vicente DA, Verjovski-Almeida S. Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma japonicum. Noncoding RNA 2020; 6:E15. [PMID: 32244675 PMCID: PMC7344908 DOI: 10.3390/ncrna6020015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/19/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023] Open
Abstract
Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification of protein-coding genes and pathways, whose expression levels were related to sexual development. However, this work did not include an analysis of long non-coding RNAs (lncRNAs). Here, we applied a pipeline to identify and annotate lncRNAs in 66 S. japonicum RNA-Seq publicly available libraries, from different life-cycle stages. We also performed co-expression analyses to find stage-specific lncRNAs possibly related to sexual maturation. We identified 12,291 S. japonicum expressed lncRNAs. Sequence similarity search and synteny conservation indicated that some 14% of S. japonicum intergenic lncRNAs have synteny conservation with S. mansoni intergenic lncRNAs. Co-expression analyses showed that lncRNAs and protein-coding genes in S. japonicum males and females have a dynamic co-expression throughout sexual maturation, showing differential expression between the sexes; the protein-coding genes were related to the nervous system development, lipid and drug metabolism, and overall parasite survival. Co-expression pattern suggests that lncRNAs possibly regulate these processes or are regulated by the same activation program as that of protein-coding genes.
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Affiliation(s)
- Lucas F. Maciel
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo SP 05503-900, Brazil (D.A.M.-V.)
- Programa Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo SP 05508-900, Brazil
| | - David A. Morales-Vicente
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo SP 05503-900, Brazil (D.A.M.-V.)
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo SP 05508-900, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo SP 05503-900, Brazil (D.A.M.-V.)
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo SP 05508-900, Brazil
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4
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Maciel LF, Morales-Vicente DA, Silveira GO, Ribeiro RO, Olberg GGO, Pires DS, Amaral MS, Verjovski-Almeida S. Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages. Front Genet 2019; 10:823. [PMID: 31572441 PMCID: PMC6752179 DOI: 10.3389/fgene.2019.00823] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/09/2019] [Indexed: 01/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) (>200 nt) are expressed at levels lower than those of the protein-coding mRNAs, and in all eukaryotic model species where they have been characterized, they are transcribed from thousands of different genomic loci. In humans, some four dozen lncRNAs have been studied in detail, and they have been shown to play important roles in transcriptional regulation, acting in conjunction with transcription factors and epigenetic marks to modulate the tissue-type specific programs of transcriptional gene activation and repression. In Schistosoma mansoni, around 10,000 lncRNAs have been identified in previous works. However, the limited number of RNA-sequencing (RNA-seq) libraries that had been previously assessed, together with the use of old and incomplete versions of the S. mansoni genome and protein-coding transcriptome annotations, have hampered the identification of all lncRNAs expressed in the parasite. Here we have used 633 publicly available S. mansoni RNA-seq libraries from whole worms at different stages (n = 121), from isolated tissues (n = 24), from cell-populations (n = 81), and from single-cells (n = 407). We have assembled a set of 16,583 lncRNA transcripts originated from 10,024 genes, of which 11,022 are novel S. mansoni lncRNA transcripts, whereas the remaining 5,561 transcripts comprise 120 lncRNAs that are identical to and 5,441 lncRNAs that have gene overlap with S. mansoni lncRNAs already reported in previous works. Most importantly, our more stringent assembly and filtering pipeline has identified and removed a set of 4,293 lncRNA transcripts from previous publications that were in fact derived from partially processed mRNAs with intron retention. We have used weighted gene co-expression network analyses and identified 15 different gene co-expression modules. Each parasite life-cycle stage has at least one highly correlated gene co-expression module, and each module is comprised of hundreds to thousands lncRNAs and mRNAs having correlated co-expression patterns at different stages. Inspection of the top most highly connected genes within the modules’ networks has shown that different lncRNAs are hub genes at different life-cycle stages, being among the most promising candidate lncRNAs to be further explored for functional characterization.
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Affiliation(s)
- Lucas F Maciel
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Programa Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - David A Morales-Vicente
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Gilbert O Silveira
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Raphael O Ribeiro
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Giovanna G O Olberg
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - David S Pires
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Murilo S Amaral
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Expressão Gênica em Eucariotos, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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5
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Carrazoni T, Nguyen C, Maciel LF, Delgado-Cañedo A, Stewart BA, Lange AB, Dal Belo CA, Carlini CR, Orchard I. Jack bean urease modulates neurotransmitter release at insect neuromuscular junctions. Pestic Biochem Physiol 2018; 146:63-70. [PMID: 29626993 DOI: 10.1016/j.pestbp.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/09/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Plants have developed a vast range of mechanisms to compete with phytophagous insects, including entomotoxic proteins such as ureases. The legume Canavalia ensiformis produces several urease isoforms, of which the more abundant is called Jack Bean Urease (JBU). Previews work has demonstrated the potential insecticidal effects of JBU, by mechanisms so far not entirely elucidated. In this work, we investigated the mechanisms involved in the JBU-induced activity upon neurotransmitter release on insect neuromuscular junctions. METHODS Electrophysiological recordings of nerve and muscle action potentials, and calcium imaging bioassays were employed. RESULTS AND CONCLUSION JBU (0.28 mg/animal/day) in Locusta migratoria 2nd instar through feeding and injection did not induce lethality, although it did result in a reduction of 20% in the weight gain at the end of 168 h (n = 9, p ≤ 0.05). JBU (0.014 and 0.14 mg) injected direct into the locust hind leg induced a dose and time-dependent decrease in the amplitude of muscle action potentials, with a maximum decrease of 70% in the amplitude at the highest dose (n = 5, p ≤ 0.05). At the same doses JBU did not alter the amplitude of action potentials evoked from motor neurons. Using Drosophila 3rd instar larvae neuromuscular preparations, JBU (10-7 M) increased the occurrence of miniature Excitatory Junctional Potentials (mEJPs) in the presence of 1 mM CaCl2 (n = 5, p ≤ 0.05). In low calcium (0.4 mM) assays, JBU (10-7 M) was not able to modulate the occurrence of the events. In Ca2+-free conditions, with EGTA or CoCl2, JBU induced a significant decrease in the occurrence of mEPJs (n = 5, p ≤ 0.05). Injected into the 3rd abdominal ganglion of Nauphoeta cinerea cockroaches, JBU (1 μM) induced a significant increase in Ca2+ influx (n = 7, p ≤ 0.01), similar to that seen for high KCl (35 mM) condition. Taken together the results confirm a direct action of JBU upon insect neuromuscular junctions and possibly central synapses, probably by disrupting the calcium machinery in the pre-synaptic region of the neurons.
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Affiliation(s)
- Thiago Carrazoni
- Universidade Federal do Rio Grande do Sul, Graduate Program in Cell and Molecular Biology, Center of Biotechnology, Porto Alegre, RS, Brazil; University of Toronto Mississauga, Department of Biology, Mississauga, ON, Canada; Pontifícia Universidade Católica do Rio Grande de Sul, Brain Institute, Porto Alegre, RS, Brazil.
| | - Christine Nguyen
- University of Toronto Mississauga, Department of Biology, Mississauga, ON, Canada
| | - Lucas F Maciel
- Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, RS, Brazil
| | | | - Bryan A Stewart
- University of Toronto Mississauga, Department of Biology, Mississauga, ON, Canada
| | - Angela B Lange
- University of Toronto Mississauga, Department of Biology, Mississauga, ON, Canada
| | | | - Celia R Carlini
- Universidade Federal do Rio Grande do Sul, Graduate Program in Cell and Molecular Biology, Center of Biotechnology, Porto Alegre, RS, Brazil; Pontifícia Universidade Católica do Rio Grande de Sul, Brain Institute, Porto Alegre, RS, Brazil.
| | - Ian Orchard
- University of Toronto Mississauga, Department of Biology, Mississauga, ON, Canada.
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Carvalho EL, Maciel LF, Macedo PE, Dezordi FZ, Abreu MET, Victória FDC, Pereira AB, Boldo JT, Wallau GDL, Pinto PM. De novo Assembly and Annotation of the Antarctic Alga Prasiola crispa Transcriptome. Front Mol Biosci 2018; 4:89. [PMID: 29359133 PMCID: PMC5766667 DOI: 10.3389/fmolb.2017.00089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Evelise L Carvalho
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Lucas F Maciel
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Pablo E Macedo
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Filipe Z Dezordi
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Maria E T Abreu
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | | | - Antônio B Pereira
- Núcleo de Estudos da Vegetação Antártica, Federal University of Pampa, São Gabriel, Brazil
| | - Juliano T Boldo
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | | | - Paulo M Pinto
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
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Santos TCO, Maciel LF, Leal KS, Bender AEN, Paiva TS, Garcias GL, Martino-Roth MG. Mutagenic potential of water from Pelotas Creek in Rio Grande do Sul, Brazil. Genet Mol Res 2009; 8:1057-66. [PMID: 19731216 DOI: 10.4238/vol8-3gmr622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Water resource degradation is one of mankind's greatest worries, as it causes direct and indirect damage to the associated biota. We initiated a water monitoring study in Pelotas Creek in 2003 in order to assess the mutagenic effect of the creek's waters. Allium cepa cells exposed to water samples and a chronically exposed macrophyte were analyzed, through evaluation of the mitotic index, mitotic anomalies, interphase anomalies, and total anomalies. Five points were chosen along the lower course of Pelotas Creek, from which water samples and floating pennywort (Hydrocotyle ranunculoides, Apiaceae) were collected in 2006 and 2007. The enteric bacterium Escherichia coli was found at all sampling points; in the physical-chemical analysis, a few variables exceeded permitted limits, pH (from 6 to 9), chloride (250 mg/L), hardness (from 10 to 200 mg CaCO(3)/L), and conductivity (100 microOmega/cm). There was an increased number of cytogenetic anomalies in exposed A. cepa cells and in the pennywort in 2006 relative to 2007, which may be explained by the increased rainfall, which was three times greater in 2007 at some stations than in 2006.Omega/cm). There was an increased number of cytogenetic anomalies in exposed A. cepa cells and in the pennywort in 2006 relative to 2007, which may be explained by the increased rainfall, which was three times greater in 2007 at some stations than in 2006.
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Affiliation(s)
- T C O Santos
- Laboratório de Genética, Centro de Ciências da Vida e da Saúde, Universidade Católica de Pelotas, Pelotas, RS, Brasil
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