1
|
Zuvanov L, Basso Garcia AL, Correr FH, Bizarria R, Filho APDC, da Costa AH, Thomaz AT, Pinheiro ALM, Riaño-Pachón DM, Winck FV, Esteves FG, Margarido GRA, Casagrande GMS, Frajacomo HC, Martins L, Cavalheiro MF, Grachet NG, da Silva RGC, Cerri R, Ramos RTJ, de Medeiros SDS, Tavares TV, Corrêa dos Santos RA. The experience of teaching introductory programming skills to bioscientists in Brazil. PLoS Comput Biol 2021; 17:e1009534. [PMID: 34762646 PMCID: PMC8584955 DOI: 10.1371/journal.pcbi.1009534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners. Here, we describe the conception, organization, and implementation of the Brazilian Python Workshop for Biological Data. This workshop has been organized by graduate and undergraduate students and supported, mostly in administrative matters, by experienced faculty members since 2017. The workshop was conceived for teaching bioscientists, mainly students in Brazil, on how to program in a biological context. The goal of this article was to share our experience with the 2020 edition of the workshop in its virtual format due to the Coronavirus Disease 2019 (COVID-19) pandemic and to compare and contrast this year's experience with the previous in-person editions. We described a hands-on and live coding workshop model for teaching introductory Python programming. We also highlighted the adaptations made from in-person to online format in 2020, the participants' assessment of learning progression, and general workshop management. Lastly, we provided a summary and reflections from our personal experiences from the workshops of the last 4 years. Our takeaways included the benefits of the learning from learners' feedback (LLF) that allowed us to improve the workshop in real time, in the short, and likely in the long term. We concluded that the Brazilian Python Workshop for Biological Data is a highly effective workshop model for teaching a programming language that allows bioscientists to go beyond an initial exploration of programming skills for data analysis in the medium to long term.
Collapse
Affiliation(s)
- Luíza Zuvanov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University, Rio Claro, Brazil
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, Brazil
| | | | | | - Andréa T. Thomaz
- School of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Ana Lucia Mendes Pinheiro
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Flavia Vischi Winck
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Franciele Grego Esteves
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, Brazil
| | | | | | | | - Leonardo Martins
- Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Mariana Feitosa Cavalheiro
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Genomics for Climate Change Research Center, University of Campinas, Campinas, Brazil
| | | | - Raniere Gaia Costa da Silva
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, Special Administrative Region, People’s Republic of China
| | - Ricardo Cerri
- Department of Computer Science, Federal University of São Carlos, São Carlos, Brazil
| | | | | | - Thayana Vieira Tavares
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Renato Augusto Corrêa dos Santos
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
- Institute of Biology, State University of Campinas, Campinas, Brazil
- * E-mail:
| |
Collapse
|
2
|
Costa-Leonardo AM, da Silva IB, Janei V, Poiani SB, Dos Santos-Pinto JRA, Esteves FG, Palma MS. Correction to: Salivary glands in workers of Ruptitermes spp. (Blattaria, Isoptera, Termitidae, Apicotermitinae): a morphological and preoteomic approach. Cell Tissue Res 2021; 384:791. [PMID: 34021775 DOI: 10.1007/s00441-021-03475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Maria Costa-Leonardo
- Laboratório de Cupins, Departamento de Biologia Geral E Aplicada, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil. .,Centro de Estudos de Insetos Sociais‑CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil.
| | - Iago Bueno da Silva
- Laboratório de Cupins, Departamento de Biologia Geral E Aplicada, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil
| | - Vanelize Janei
- Laboratório de Cupins, Departamento de Biologia Geral E Aplicada, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil
| | - Silvana Beani Poiani
- Centro de Estudos de Insetos Sociais‑CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Centro de Estudos de Insetos Sociais‑CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil
| | - Franciele Grego Esteves
- Centro de Estudos de Insetos Sociais‑CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil
| | - Mario Sérgio Palma
- Centro de Estudos de Insetos Sociais‑CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506‑900, Brazil
| |
Collapse
|
3
|
Costa-Leonardo AM, da Silva IB, Janei V, Poiani SB, Dos Santos-Pinto JRA, Esteves FG, Palma MS. Salivary glands in workers of Ruptitermes spp. (Blattaria, Isoptera, Termitidae, Apicotermitinae): a morphological and preoteomic approach. Cell Tissue Res 2021; 385:603-621. [PMID: 33961129 DOI: 10.1007/s00441-021-03469-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Salivary glands are omnipresent in termites and occur in all developmental stages and castes. They function to produce, store, and secrete compounds, ranging from a feeding function to defensive mechanisms. Here, we provide a complete morphological overview of the salivary glands in the soldierless species Ruptitermes reconditus and R. xanthochiton, and the first proteomic profile of the salivary glands in a Neotropical Apicotermitinae representative, R. reconditus. Salivary glands from both species were composed of several acini, roughly spherical structures composed of two types of central cells (type I and II) and peripheral parietal cells, as well as transporting ducts and two salivary reservoirs. Central cells were richly supplied with electron-lucent secretory vesicles and rough endoplasmic reticulum, a feature of protein-secreting cells. Parietal cells of Ruptitermes spp. had conspicuous characteristics such as electron-lucent secretory vesicles surrounded by mitochondria and well-developed microvilli. Moreover, different individuals showed variation in the secretory cycle of salivary acini, which may be related to polyethism. Ultrastructural analysis evidenced a high synthesis of secretion and also the occurrence of lysosomes and autophagic structures in central cells. Proteomic analysis of the salivary glands revealed 483 proteins divided into functional groups, highlighting toxins/defensins and compounds related to alarm communication and colony asepsis. Soldierless termites are quite successful, especially due to morphological adaptations of the workers, including unknown modifications of exocrine glands. Thus, according to our morphological and proteomic findings, we discuss the potential roles of the salivary gland secretion in different social aspects of the sampled species.
Collapse
Affiliation(s)
- Ana Maria Costa-Leonardo
- Laboratório de Cupins, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil. .,Centro de Estudos de Insetos Sociais-CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil.
| | - Iago Bueno da Silva
- Laboratório de Cupins, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Vanelize Janei
- Laboratório de Cupins, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Silvana Beani Poiani
- Centro de Estudos de Insetos Sociais-CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Centro de Estudos de Insetos Sociais-CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Franciele Grego Esteves
- Centro de Estudos de Insetos Sociais-CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Mario Sérgio Palma
- Centro de Estudos de Insetos Sociais-CEIS, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| |
Collapse
|
4
|
Esteves FG, Dos Santos-Pinto JRA, Ferro M, Sialana FJ, Smidak R, Rares LC, Nussbaumer T, Rattei T, Bilban M, Bacci Júnior M, Lubec G, Palma MS. Revealing the Venomous Secrets of the Spider's Web. J Proteome Res 2020; 19:3044-3059. [PMID: 32538095 DOI: 10.1021/acs.jproteome.0c00086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Orb-weaving spiders use a highly strong, sticky and elastic web to catch their prey. These web properties alone would be enough for the entrapment of prey; however, these spiders may be hiding venomous secrets in the web, which current research is revealing. Here, we provide strong proteotranscriptomic evidence for the presence of toxin/neurotoxin-like proteins, defensins, and proteolytic enzymes on the web silk from Nephila clavipes spider. The results from quantitative-based transcriptomic and proteomic approaches showed that silk-producing glands produce an extensive repertoire of toxin/neurotoxin-like proteins, similar to those already reported in spider venoms. Meanwhile, the insect toxicity results demonstrated that these toxic components can be lethal and/or paralytic chemical weapons used for prey capture on the web, and the presence of fatty acids in the web may be a responsible mechanism opening the way to the web toxins for accessing the interior of prey's body, as shown here. Comparative phylogenomic-level evolutionary analyses revealed orthologous genes among two spider groups, Araneomorphae and Mygalomorphae, and the findings showed protein sequences similar to toxins found in the taxa Scorpiones and Hymenoptera in addition to Araneae. Overall, these data represent a valuable resource to further investigate other spider web toxin systems and also suggest that N. clavipes web is not a passive mechanical trap for prey capture, but it exerts an active role in prey paralysis/killing using a series of neurotoxins.
Collapse
Affiliation(s)
- Franciele Grego Esteves
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, University of São Paulo State (UNESP), Rio Claro, SP 13506-900, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, University of São Paulo State (UNESP), Rio Claro, SP 13506-900, Brazil
| | - Milene Ferro
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, University of São Paulo State (UNESP), Rio Claro, SP 13506-900, Brazil
| | - Fernando J Sialana
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Roman Smidak
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Lucaciu Calin Rares
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Thomas Nussbaumer
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Thomas Rattei
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Mauricio Bacci Júnior
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, University of São Paulo State (UNESP), Rio Claro, SP 13506-900, Brazil
| | - Gert Lubec
- Paracelsus Medical University, A 5020 Salzburg, Austria
| | - Mario Sergio Palma
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, University of São Paulo State (UNESP), Rio Claro, SP 13506-900, Brazil
| |
Collapse
|
5
|
Perez-Riverol A, Musacchio-Lasa A, Fernandes LGR, dos Santos-Pinto JRA, Esteves FG, Bazon ML, Zollner RDL, Palma MS, Brochetto-Braga MR. Improved production of the recombinant phospholipase A1 from Polybia paulista wasp venom expressed in bacterial cells for use in routine diagnostics. 3 Biotech 2020; 10:217. [PMID: 32355591 DOI: 10.1007/s13205-020-02202-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/09/2020] [Indexed: 12/27/2022] Open
Abstract
Phospholipase A1 (PLA1) is one of the three major allergens identified in the venom of P. paulista (Hymenoptera: Vespidae), a clinically relevant wasp from southeastern Brazil. The recombinant form of this allergen (rPoly p 1) could be used for the development of molecular diagnostic of venom allergy. Early attempts to produce rPoly p 1 using Escherichia coli BL21 (DE3) cells rendered high yields of the insoluble rPoly p 1 but with low levels of solubilized protein recovery (12%). Here, we aimed to improve the production of rPoly p 1 in E. coli by testing different conditions of expression, solubilization of the inclusion bodies and protein purification. The results showed that the expression at 16 °C and 0.1 mM of IPTG increased the production of rPoly p 1, still in the insoluble form, but with high solubilized protein yields after incubation with citrate-phosphate buffer with 0.15 M NaCl, 6 M urea, pH 2.6 at 25 ºC for 2 h. The venom allergen was also cloned in pPICZαA vector for soluble expression as a secreted protein in Pichia pastoris X-33 cells, rendering almost undetectable levels (nanograms) in the culture supernatant. In contrast, a sevenfold increase of the solubilized and purified rPoly p 1 yields (1.5 g/L of fermentation broth) was obtained after improved production in E. coli. The identity of the protein was confirmed with an anti-His antibody and MS spectra. Allergen-specific IgE (sIgE)-mediated recognition was evaluated in immunoblotting with sera of allergic patients (n = 40). Moreover, rPoly p 1 showed high levels of diagnostic sensitivity (95%). The optimized strategy for rPoly p 1 production described here, will provide the amounts of allergen necessary for the subsequent protein refolding, immunological characterization steps, and ultimately, to the development of molecular diagnostic for P. paulista venom allergy.
Collapse
|
6
|
de Almeida NEC, Esteves FG, Dos Santos-Pinto JRA, Peres de Paula C, da Cunha AF, Malavazi I, Palma MS, Rodrigues-Filho E. Digestion of Intact Gluten Proteins by Bifidobacterium Species: Reduction of Cytotoxicity and Proinflammatory Responses. J Agric Food Chem 2020; 68:4485-4492. [PMID: 32195585 DOI: 10.1021/acs.jafc.0c01421] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Celiac disease (CD) is a chronic illness characterized by an inflammatory process triggered by gluten protein intake. Recent evidence has suggested that the lower relative abundance of bifidobacteria in the intestinal lumen may be associated with CD. Herein, we assessed the effect of the Bifidobacterium species Bifidobacterium bifidum, Bifidobacterium longum, Bembidion breve, Bifidobacterium animalis alone, and also a Bifidobacterium consortium on the digestion of intact gluten proteins (gliadins and glutenins) and the associated immunomodulatory responses elicited by the resulting peptides. The cytotoxicity and proinflammatory responses were evaluated through the activation of NF-kB p65 and the expression of cytokines TNF-α and IL-1β in Caco-2 cell cultures exposed to gluten-derived peptides. The peptides induced a clear reduction in cytotoxic responses and proinflammatory marker levels compared to the gluten fragments generated during noninoculated gastrointestinal digestion. These results highlight the possible use of probiotics based on bifidobacteria as a prospective treatment for CD.
Collapse
Affiliation(s)
| | - Franciele Grego Esteves
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Carla Peres de Paula
- Department of Genetics and Evolution, Biotechnology Graduate Program (PPGBiotec), Federal University of São Carlos, São Carlos, São Paulo 13565-905, Brazil
| | - Anderson Ferreira da Cunha
- Department of Genetics and Evolution, Biotechnology Graduate Program (PPGBiotec), Federal University of São Carlos, São Carlos, São Paulo 13565-905, Brazil
| | - Iran Malavazi
- Department of Genetics and Evolution, Biotechnology Graduate Program (PPGBiotec), Federal University of São Carlos, São Carlos, São Paulo 13565-905, Brazil
| | - Mario Sergio Palma
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Edson Rodrigues-Filho
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos, São Paulo 13565-905, Brazil
| |
Collapse
|
7
|
Costa-Leonardo AM, da Silva IB, Poiani SB, Dos Santos-Pinto JRA, Esteves FG, da Silva LHB, Palma MS. Proteomic-components provide insights into the defensive secretion in termite workers of the soldierless genus Ruptitermes. J Proteomics 2019; 213:103622. [PMID: 31863930 DOI: 10.1016/j.jprot.2019.103622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/03/2019] [Accepted: 12/14/2019] [Indexed: 12/11/2022]
Abstract
Termite soldiers constitute the defensive frontline of the colonies, despite workers also perform such tasks, especially within the Neotropical Apicotermitinae, in which all species are soldierless. Workers of the genus Ruptitermes display an extreme form of defense, characterized by body rupture and release of a sticky secretion. Previous observations suggested that such behavior may be advantageous against enemies, but the chemical composition of this secretion has been neglected. Here we firstly provide the proteomic profile of the defensive secretion of Ruptitermes reconditus and Ruptitermes pitan workers. Additionally, the mechanisms of action of this behavior was evaluated through different bioassays. A total of 446 proteins were identified in R. reconditus and 391 proteins in R. pitan, which were classified into: toxins, defensins and proteolytic enzymes; sticky components/ alarm communication; proteins related to detoxification processes; proteins involved in folding/conformation and post-translational modifications; housekeeping proteins; and uncharacterized/hypothetical proteins. According to the bioassays, the self-sacrifice is triggered by a physical stimulus, and the defensive secretion may cause immobility and death of the opponents. Assuming that termites are abundant in the tropics and therefore exposed to predators, suicidal behaviors seem to be advantageous, since the loss of an individual benefit the whole colony. SIGNIFICANCE: Although recent studies have reported the biochemical composition of different weapons in soldiered species of termites, such efforts had not been applied to sordierless taxa up until now. Thus, this is the first report of the defensive mechanisms in soldierless termite species based on proteomic analysis. The diversity of compounds, which included toxin-like and mucin-like proteins, reflect the mechanisms of action of the defensive secretion released by termite workers, which may cause immobility and death of the opponents. Our findings may contribute to the knowledge regarding the development of defensive strategies in termites, especially in groups which lost the soldier caste during the evolution.
Collapse
Affiliation(s)
- Ana Maria Costa-Leonardo
- Laboratório de Cupins, Departamento de Biologia, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP 13506-900, Brazil; Center for the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, Univ Estadual Paulista, UNESP, Rio Claro, São Paulo, Brazil.
| | - Iago Bueno da Silva
- Laboratório de Cupins, Departamento de Biologia, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP 13506-900, Brazil
| | - Silvana Beani Poiani
- Center for the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, Univ Estadual Paulista, UNESP, Rio Claro, São Paulo, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Center for the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, Univ Estadual Paulista, UNESP, Rio Claro, São Paulo, Brazil
| | - Franciele Grego Esteves
- Center for the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, Univ Estadual Paulista, UNESP, Rio Claro, São Paulo, Brazil
| | - Luiza Helena Bueno da Silva
- Laboratório de Cupins, Departamento de Biologia, Instituto de Biociências, Univ Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro, SP 13506-900, Brazil
| | - Mario Sergio Palma
- Center for the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, Univ Estadual Paulista, UNESP, Rio Claro, São Paulo, Brazil
| |
Collapse
|
8
|
de Souza CL, Dos Santos-Pinto JRA, Esteves FG, Perez-Riverol A, Fernandes LGR, de Lima Zollner R, Palma MS. Revisiting Polybia paulista wasp venom using shotgun proteomics - Insights into the N-linked glycosylated venom proteins. J Proteomics 2019; 200:60-73. [PMID: 30905720 DOI: 10.1016/j.jprot.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
The partial proteome of Polybia paulista wasp venom was previously reported elsewhere using a gel-dependent approach and resulted in the identification of a limited number of venom toxins. Here, we reinvestigated the P. paulista venom using a gel-free shotgun proteomic approach; the highly dynamic range of this approach facilitated the detection and identification of 1673 proteins, of which 23 venom proteins presented N-linked glycosylation as a posttranslational modification. Three different molecular forms of PLA1 were identified as allergenic proteins, and two of these forms were modified by N-linked glycosylation. This study reveals an extensive repertoire of hitherto undescribed proteins that were classified into the following six different functional groups: (i) typical venom proteins; (ii) proteins related to the folding/conformation and PTMs of toxins; (iii) proteins that protect toxins from oxidative stress; (iv) proteins involved in chemical communication; (v) housekeeping proteins; and (vi) uncharacterized proteins. It was possible to identify venom toxin-like proteins that are commonly reported in other animal venoms, including arthropods such as spiders and scorpions. Thus, the findings reported here may contribute to improving our understanding of the composition of P. paulista venom, its envenoming mechanism and the pathologies experienced by the victim after the wasp stinging accident. BIOLOGICAL SIGNIFICANCE: The present study significantly expanded the number of proteins identified in P. paulista venom, contributing to improvements in our understanding of the envenoming mechanism produced by sting accidents caused by this wasp. For example, novel wasp venom neurotoxins have been identified, but no studies have assessed the presence of this type of toxin in social wasp venoms. In addition, 23 N-linked glycosylated venom proteins were identified in the P. paulista venom proteome, and some of these proteins might be relevant allergens that are immunoreactive to human IgE.
Collapse
Affiliation(s)
- Caroline Lacerra de Souza
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil.
| | - Franciele Grego Esteves
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil
| | - Amilcar Perez-Riverol
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil
| | - Luís Gustavo Romani Fernandes
- Laboratory of Translational Immunology, Faculty of Medicine, University of Campinas (UNICAMP), Cidade Universitária "Zeferino Vaz", Campinas, SP 13083887, Brazil
| | - Ricardo de Lima Zollner
- Laboratory of Translational Immunology, Faculty of Medicine, University of Campinas (UNICAMP), Cidade Universitária "Zeferino Vaz", Campinas, SP 13083887, Brazil
| | - Mario Sergio Palma
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil.
| |
Collapse
|
9
|
dos Santos-Pinto JRA, Esteves FG, Sialana FJ, Ferro M, Smidak R, Rares LC, Nussbaumer T, Rattei T, Bilban M, Bacci Júnior M, Palma MS, Lübec G. A proteotranscriptomic study of silk-producing glands from the orb-weaving spiders. Mol Omics 2019; 15:256-270. [DOI: 10.1039/c9mo00087a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A proteotranscriptomic approach provides a biochemical basis for understanding the intricate spinning process and complex structural features of spider silk proteins.
Collapse
Affiliation(s)
| | - Franciele Grego Esteves
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | | | - Milene Ferro
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | - Roman Smidak
- Department of Pharmaceutical Chemistry
- University of Vienna
- Austria
| | - Lucaciu Calin Rares
- Division of Computational System Biology
- Department of Microbiology and Ecosystem Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Thomas Nussbaumer
- Division of Computational System Biology
- Department of Microbiology and Ecosystem Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Thomas Rattei
- Division of Computational System Biology
- Department of Microbiology and Ecosystem Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics
- Medical University of Vienna
- Vienna
- Austria
| | - Maurício Bacci Júnior
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | - Mario Sergio Palma
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | - Gert Lübec
- Paracelsus Medical University
- A 5020 Salzburg
- Austria
| |
Collapse
|
10
|
Dos Santos-Pinto JRA, Arcuri HA, Esteves FG, Palma MS, Lubec G. Spider silk proteome provides insight into the structural characterization of Nephila clavipes flagelliform spidroin. Sci Rep 2018; 8:14674. [PMID: 30279551 PMCID: PMC6168590 DOI: 10.1038/s41598-018-33068-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 06/11/2018] [Accepted: 09/12/2018] [Indexed: 12/13/2022] Open
Abstract
The capture spiral of web from N. clavipes spider consists of a single type of spidroin - the flagelliform silk protein, a natural material representing a combination of strength and high elasticity. Flagelliform spider silk is the most extensible silk fibre produced by orb weaver spiders and the structure of this remarkable material is still largely unknown. In the present study we used a proteomic approach to elucidate the complete sequence and the post-translational modifications of flagelliform silk proteins. The long sequence of flagelliform silk protein presents 45 hydroxylated proline residues, which may contribute to explain the mechanoelastic property of these fibres, since they are located in the GPGGX motif. The 3D-structure of the protein was modelled considering the three domains together, i.e., the N- and C-terminal non-repetitive domains, and the central repetitive domain. In the resulting molecular model there is a predominance of random structures in the solid fibres of the silk protein. The N-terminal domain is composed of three α-helices and the C-terminal domain is composed of one small helical section. Proteomic data reported herein may be relevant for the development of novel approaches for the synthetic or recombinant production of novel silk-based spider polymers.
Collapse
Affiliation(s)
- José Roberto Aparecido Dos Santos-Pinto
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP, 13500, Brazil
| | - Helen Andrade Arcuri
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP, 13500, Brazil
| | - Franciele Grego Esteves
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP, 13500, Brazil
| | - Mario Sergio Palma
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP, 13500, Brazil.
| | - Gert Lubec
- Paracelsus Medical University, A 5020, Salzburg, Austria.
| |
Collapse
|
11
|
Pratavieira M, Menegasso ARDS, Esteves FG, Sato KU, Malaspina O, Palma MS. MALDI Imaging Analysis of Neuropeptides in Africanized Honeybee (Apis mellifera) Brain: Effect of Aggressiveness. J Proteome Res 2018; 17:2358-2369. [DOI: 10.1021/acs.jproteome.8b00098] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcel Pratavieira
- Institute of Biosciences, Department of Biology, Center of the Study of Social Insects, University of São Paulo State (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Anally Ribeiro da Silva Menegasso
- Institute of Biosciences, Department of Biology, Center of the Study of Social Insects, University of São Paulo State (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Franciele Grego Esteves
- Institute of Biosciences, Department of Biology, Center of the Study of Social Insects, University of São Paulo State (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Kenny Umino Sato
- Institute of Biosciences, Department of Biology, Center of the Study of Social Insects, University of São Paulo State (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Osmar Malaspina
- Institute of Biosciences, Department of Biology, Center of the Study of Social Insects, University of São Paulo State (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| | - Mario Sergio Palma
- Institute of Biosciences, Department of Biology, Center of the Study of Social Insects, University of São Paulo State (UNESP), Rio Claro, São Paulo 13506-900, Brazil
| |
Collapse
|
12
|
Esteves FG, Santos-Pinto JRAD, Saidemberg DM, Palma MS. Using a proteometabolomic approach to investigate the role of Dufour's gland in pheromone biosynthesis in the social wasp Polybia paulista. J Proteomics 2017; 151:122-130. [DOI: 10.1016/j.jprot.2016.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 11/28/2022]
|
13
|
Dos Santos-Pinto JRA, Garcia AMC, Arcuri HA, Esteves FG, Salles HC, Lubec G, Palma MS. Silkomics: Insight into the Silk Spinning Process of Spiders. J Proteome Res 2016; 15:1179-93. [PMID: 26923066 DOI: 10.1021/acs.jproteome.5b01056] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The proteins from the silk-producing glands were identified using both a bottom-up gel-based proteomic approach as well as from a shotgun proteomic approach. Additionally, the relationship between the functions of identified proteins and the spinning process was studied. A total of 125 proteins were identified in the major ampullate, 101 in the flagelliform, 77 in the aggregate, 75 in the tubuliform, 68 in the minor ampullate, and 23 in aciniform glands. On the basis of the functional classification using Gene Ontology, these proteins were organized into seven different groups according to their general function: (i) web silk proteins-spidroins, (ii) proteins related to the folding/conformation of spidroins, (iii) proteins that protect silk proteins from oxidative stress, (iv) proteins involved in fibrillar preservation of silks in the web, (v) proteins related to ion transport into and out of the glands during silk fiber spinning, (vi) proteins involved in prey capture and pre-digestion, and (vii) housekeeping proteins from all of the glands. Thus, a general mechanism of action for the identified proteins in the silk-producing glands from the Nephila clavipes spider was proposed; the current results also indicate that the webs play an active role in prey capture.
Collapse
Affiliation(s)
- José Roberto Aparecido Dos Santos-Pinto
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP) , Rio Claro, São Paulo 13500, Brazil.,Department of Pediatrics, Medical University of Vienna , Vienna 1090, Austria
| | - Ana Maria Caviquioli Garcia
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP) , Rio Claro, São Paulo 13500, Brazil
| | - Helen Andrade Arcuri
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP) , Rio Claro, São Paulo 13500, Brazil
| | - Franciele Grego Esteves
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP) , Rio Claro, São Paulo 13500, Brazil
| | - Heliana Clara Salles
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP) , Rio Claro, São Paulo 13500, Brazil
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna , Vienna 1090, Austria
| | - Mario Sergio Palma
- Center of Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP) , Rio Claro, São Paulo 13500, Brazil
| |
Collapse
|