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Pereira CR, Neia RC, Silva SB, Williamson CHD, Gillece JD, O'Callaghan D, Foster JT, Oliveira IRC, Filho JSSB, Lage AP, Azevedo VAC, Dorneles EMS. Comparison of Brucella abortus population structure based on genotyping methods with different levels of resolution. J Microbiol Methods 2023:106772. [PMID: 37343840 DOI: 10.1016/j.mimet.2023.106772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/16/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
Numerous genotyping techniques based on different principles and with different costs and levels of resolution are currently available for understanding the transmission dynamics of brucellosis worldwide. We aimed to compare the population structure of the genomes of 53 Brazilian Brucella abortus isolates using eight different genotyping methods: multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphism (SNP) detection (parSNP and NASP) from whole genomes. The strains were isolated from six different Brazilian states between 1977 and 2008 and had previously been analyzed using MLVA8, MLVA11, and MLVA16. Their whole genomes were sequenced, assembled, and subjected to MSLT9 MLST21, cgMLST, and SNP analyses. All the genotypes were compared by hierarchical grouping method based on the average distances between the correlation matrices of each technique. MLST9 and MLST21 had the lowest level of resolution, both revealing only four genotypes. MLVA8, MLVA11, and MLVA16 had progressively increasing levels of resolution as more loci were analyzed, identifying 6, 16, and 44 genotypes, respectively. cgMLST showed the highest level of resolution, identifying 45 genotypes, followed by the SNP-based methods, both of which had 44 genotypes. In the assessed population, MLVA was more discriminatory than MLST and was easier and cheaper to perform. SNP techniques and cgMLST provided the highest levels of resolution and the results from the two methods were in close agreement. In conclusion, the choice of genotyping technique can strongly affect one's ability to make meaningful epidemiological conclusions but is dependent on available resources: while the VNTR based techniques are more indicated to high prevalence scenarios, the WGS methods are the ones with the best discriminative power and therefore recommended for outbreaks investigation.
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Affiliation(s)
- Carine R Pereira
- Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Raquel C Neia
- Faculdade de Ciências Básicas, Universidade Federal Fluminense, Nova Friburgo, Rio de Janeiro, Brazil
| | - Saulo B Silva
- Escola de Ciências da Saúde, Univali, Itajaí, Santa Catarina, Brazil
| | | | - John D Gillece
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David O'Callaghan
- Bacterial Virulence and Infectious Disease, University of Montpellier, Nimes, France
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Izabela R C Oliveira
- Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Júlio S S B Filho
- Departamento de Estatística, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Andrey P Lage
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco A C Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine M S Dorneles
- Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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2
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Rocha BGS, Picoli CC, Gonçalves BOP, Silva WN, Costa AC, Moraes MM, Costa PAC, Santos GSP, Almeida MR, Silva LM, Singh Y, Falchetti M, Guardia GDA, Guimarães PPG, Russo RC, Resende RR, Pinto MCX, Amorim JH, Azevedo VAC, Kanashiro A, Nakaya HI, Rocha EL, Galante PAF, Mintz A, Frenette PS, Birbrair A. Tissue-resident glial cells associate with tumoral vasculature and promote cancer progression. Angiogenesis 2023; 26:129-166. [PMID: 36183032 DOI: 10.1007/s10456-022-09858-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/08/2022] [Indexed: 11/01/2022]
Abstract
Cancer cells are embedded within the tissue and interact dynamically with its components during cancer progression. Understanding the contribution of cellular components within the tumor microenvironment is crucial for the success of therapeutic applications. Here, we reveal the presence of perivascular GFAP+/Plp1+ cells within the tumor microenvironment. Using in vivo inducible Cre/loxP mediated systems, we demonstrated that these cells derive from tissue-resident Schwann cells. Genetic ablation of endogenous Schwann cells slowed down tumor growth and angiogenesis. Schwann cell-specific depletion also induced a boost in the immune surveillance by increasing tumor-infiltrating anti-tumor lymphocytes, while reducing immune-suppressor cells. In humans, a retrospective in silico analysis of tumor biopsies revealed that increased expression of Schwann cell-related genes within melanoma was associated with improved survival. Collectively, our study suggests that Schwann cells regulate tumor progression, indicating that manipulation of Schwann cells may provide a valuable tool to improve cancer patients' outcomes.
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Affiliation(s)
- Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bryan O P Gonçalves
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Michele M Moraes
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Milla R Almeida
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luciana M Silva
- Department of Cell Biology, Ezequiel Dias Foundation, Belo Horizonte, MG, Brazil
| | - Youvika Singh
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Marcelo Falchetti
- Department of Microbiology and Immunology, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | - Pedro P G Guimarães
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Remo C Russo
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of Western Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Kanashiro
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA
| | | | - Edroaldo L Rocha
- Department of Microbiology and Immunology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Paul S Frenette
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA.
- Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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3
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Picoli CC, Martins PR, Wong XLC, Righi T, Guimarães PPG, Pinto MCX, Amorim JH, Azevedo VAC, Pereira SR, Kanashiro A, Cruz FC, Resende RR, Mintz A, Frenette PS, Birbrair A. Whole bone subcutaneous transplantation as a strategy to study precisely the bone marrow niche. Stem Cell Rev Rep 2022; 19:906-927. [PMID: 36585572 DOI: 10.1007/s12015-022-10496-9] [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] [Accepted: 12/15/2022] [Indexed: 01/01/2023]
Abstract
Hematopoietic stem cells are maintained in a specialized microenvironment, known as the 'niche', within the bone marrow. Understanding the contribution of cellular and molecular components within the bone marrow niche for the maintenance of hematopoietic stem cells is crucial for the success of therapeutic applications. So far, the roles of crucial mechanisms within the bone marrow niche have been explored in transgenic animals in which genetic modifications are ubiquitously introduced in the whole body. The lack of precise tools to explore genetic alterations exclusively within the bone marrow prevents our determination of whether the observed outcomes result from confounding effects from other organs. Here, we developed a new method - 'whole bone subcutaneous transplantation'- to study the bone marrow niche in transgenic animals precisely. Using immunolabeling of CD45.1 (donor) vs. CD45.2 (recipient) hematopoeitic stem cells, we demonstrated that hematopoeitic stem cells from the host animals colonize the subcutaneously transplanted femurs after transplantation, while the hematopoietic stem cells from the donor disappear. Strikinlgy, the bone marrow niche of these subcutaneously transplanted femurs remain from the donor mice, enabling us to study specifically cells of the bone marrow niche using this model. We also showed that genetic ablation of peri-arteriolar cells specifically in donor femurs reduced the numbers of hematopoietic stem cells in these bones. This supports the use of this strategy as a model, in combination with genetic tools, to evaluate how bone marrow niche specific modifications may impact non-modified hematopoietic stem cells. Thus, this approach can be utilized for genetic manipulation in vivo of specific cell types only within the bone marrow. The combination of whole bone subcutaneous transplantation with rodent transgenic models will facilitate a more precise, complex and comprehensive understanding of existing problems in the study of the hematopoietic stem cell bone marrow niche.
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Affiliation(s)
- Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Xiao Lin Casey Wong
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA
| | - Thamires Righi
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA.,Department of Pharmacology, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Pedro P G Guimarães
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of West Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Alexandre Kanashiro
- Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA
| | - Fabio Cardoso Cruz
- Department of Pharmacology, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Paul S Frenette
- Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Department of Dermatology, University of Wisconsin-Madison, Medical Sciences Center, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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4
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Costa PAC, Silva WN, Prazeres PHDM, Picoli CC, Guardia GDA, Costa AC, Oliveira MA, Guimarães PPG, Gonçalves R, Pinto MCX, Amorim JH, Azevedo VAC, Resende RR, Russo RC, Cunha TM, Galante PAF, Mintz A, Birbrair A. Chemogenetic modulation of sensory neurons reveals their regulating role in melanoma progression. Acta Neuropathol Commun 2021; 9:183. [PMID: 34784974 PMCID: PMC8594104 DOI: 10.1186/s40478-021-01273-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 07/27/2021] [Accepted: 10/10/2021] [Indexed: 02/08/2023] Open
Abstract
Sensory neurons have recently emerged as components of the tumor microenvironment. Nevertheless, whether sensory neuronal activity is important for tumor progression remains unknown. Here we used Designer Receptors Exclusively Activated by a Designer Drug (DREADD) technology to inhibit or activate sensory neurons' firing within the melanoma tumor. Melanoma growth and angiogenesis were accelerated following inhibition of sensory neurons' activity and were reduced following overstimulation of these neurons. Sensory neuron-specific overactivation also induced a boost in the immune surveillance by increasing tumor-infiltrating anti-tumor lymphocytes, while reducing immune-suppressor cells. In humans, a retrospective in silico analysis of melanoma biopsies revealed that increased expression of sensory neurons-related genes within melanoma was associated with improved survival. These findings suggest that sensory innervations regulate melanoma progression, indicating that manipulation of sensory neurons' activity may provide a valuable tool to improve melanoma patients' outcomes.
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Affiliation(s)
- Pedro A. C. Costa
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Walison N. Silva
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Pedro H. D. M. Prazeres
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Caroline C. Picoli
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Gabriela D. A. Guardia
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP Brasil
| | - Alinne C. Costa
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Mariana A. Oliveira
- grid.8430.f0000 0001 2181 4888Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Pedro P. G. Guimarães
- grid.8430.f0000 0001 2181 4888Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Ricardo Gonçalves
- grid.8430.f0000 0001 2181 4888Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Mauro C. X. Pinto
- grid.411195.90000 0001 2192 5801Departamento de Farmacologia, Universidade Federal de Goiás, Goiânia, GO Brasil
| | - Jaime H. Amorim
- grid.472638.c0000 0004 4685 7608Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, BA Brasil
| | - Vasco A. C. Azevedo
- grid.8430.f0000 0001 2181 4888Departamento de Genetica, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Rodrigo R. Resende
- grid.8430.f0000 0001 2181 4888Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Remo C. Russo
- grid.8430.f0000 0001 2181 4888Departamento de Fisiologia e Biofísica, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brasil
| | - Thiago M. Cunha
- grid.11899.380000 0004 1937 0722Departamento de Farmacologia, Universidade de São Paulo, Ribeirão Preto, SP Brasil
| | - Pedro A. F. Galante
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sirio-Libanes, Sao Paulo, SP Brasil
| | - Akiva Mintz
- grid.239585.00000 0001 2285 2675Department of Radiology, Columbia University Medical Center, New York, NY USA
| | - Alexander Birbrair
- Departamento de Patologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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5
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Santos GSP, Costa AC, Picoli CC, Rocha BGS, Sulaiman SO, Radicchi DC, Pinto MCX, Batista ML, Amorim JH, Azevedo VAC, Resende RR, Câmara NOS, Mintz A, Birbrair A. Sympathetic nerve-adipocyte interactions in response to acute stress. J Mol Med (Berl) 2021; 100:151-165. [PMID: 34735579 PMCID: PMC8567732 DOI: 10.1007/s00109-021-02157-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/28/2020] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
Psychological stress predisposes our body to several disorders. Understanding the cellular and molecular mechanisms involved in the physiological responses to psychological stress is essential for the success of therapeutic applications. New studies show, by using in vivo inducible Cre/loxP-mediated approaches in combination with pharmacological blockage, that sympathetic nerves, activated by psychological stress, induce brown adipocytes to produce IL-6. Strikingly, this cytokine promotes gluconeogenesis in hepatocytes, that results in the decline of tolerance to inflammatory organ damage. The comprehension arising from this research will be crucial for the handling of many inflammatory diseases. Here, we review recent advances in our comprehension of the sympathetic nerve-adipocyte axis in the tissue microenvironment.
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Affiliation(s)
- Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sheu O Sulaiman
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Debora C Radicchi
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Laboratory of Neuropharmacology, Federal University of Goiás, Goiânia, GO, Brazil
| | - Miguel L Batista
- Laboratory of Adipose Tissue Biology, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil.,Department of Biochemistry, Boston University School of Medicine, Boston, USA
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of Western Bahia, BA, Barreiras, Brazil
| | - Vasco A C Azevedo
- Cellular and Molecular Genetics Laboratory, Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Niels O S Câmara
- Laboratory of Transplantation Immunobiology, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, SP, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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6
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Ribeiro SP, Reis AB, Dáttilo W, Silva AVCDECE, Barbosa EAG, Coura-Vital W, Góes-Neto A, Azevedo VAC, Fernandes GW. From Spanish Flu to Syndemic COVID-19: long-standing sanitarian vulnerability of Manaus, warnings from the Brazilian rainforest gateway. AN ACAD BRAS CIENC 2021; 93:e20210431. [PMID: 34378637 DOI: 10.1590/0001-3765202120210431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/19/2021] [Indexed: 12/24/2022] Open
Abstract
A second deadlier wave of COVID-19 and the causes of the recent public health collapse of Manaus are compared with the Spanish flu events in that city, and Brazil. Historic sanitarian problems, and its hub position in the Brazilian airway network are combined drivers of deadly events related to COVID-19. These drivers were amplified by misleading governance, highly transmissible variants, and relaxation of social distancing. Several of these same factors may also have contributed to the dramatically severe outbreak of H1N1 in 1918, which caused the death of 10% of the population in seven months. We modelled Manaus parameters for the present pandemic and confirmed that lack of a proper social distancing might select the most transmissible variants. We succeeded to reproduce a first severe wave followed by a second stronger wave. The model also predicted that outbreaks may last for up to five and half years, slowing down gradually before the disease disappear. We validated the model by adjusting it to the Spanish Flu data for the city, and confirmed the pattern experienced by that time, of a first stronger wave in October-November 1918, followed by a second less intense wave in February-March 1919.
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Affiliation(s)
- Sérvio P Ribeiro
- Universidade Federal de Ouro Preto, Núcleo de Pesquisas em Ciências Biológicas - NUPEB, St. Três, 408-462, Bauxita, 35400-000 Ouro Preto, MG, Brazil.,Universidade Federal de Ouro Preto, Laboratory of Ecology of Diseases and Forests, Departamento de Biodiversidade, Evolução e Meio Ambiente, St. Quatro, 786, Bauxita, 35400-000 Ouro Preto, MG, Brazil.,Universidade Federal de Minas Gerais, Laboratory of Physiology of Hematophagous Insects, Departamento de Parasitologia, Ave. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Alexandre B Reis
- Universidade Federal de Ouro Preto, Núcleo de Pesquisas em Ciências Biológicas - NUPEB, St. Três, 408-462, Bauxita, 35400-000 Ouro Preto, MG, Brazil.,Universidade Federal de Ouro Preto, Laboratory of Imunopatology, Departamento de Análises Clínicas, St. Três, 408-462, Bauxita, 35400-000 Ouro Preto, MG, Brazil
| | - Wesley Dáttilo
- Instituto de Ecología AC, Red de Ecoetología, Carretera Antigua a Coatepec, 351, El Haya, Xalapa, Veracruz, 91070 Mexico
| | - Alcides V C DE Castro E Silva
- Universidade Federal de Ouro Preto, Laboratory of Complexity Science, Departamento de Física, St. Quatro, 786, Bauxita, 35400-000 Ouro Preto, MG, Brazil
| | - Eduardo Augusto G Barbosa
- Centro Federal de Educação Tecnológica de Minas Gerais, Programa de Pós-Graduação em Modelagem Matemática e Computacional, 30510-000 Belo Horizonte, MG, Brazil
| | - Wendel Coura-Vital
- Universidade Federal de Ouro Preto, Núcleo de Pesquisas em Ciências Biológicas - NUPEB, St. Três, 408-462, Bauxita, 35400-000 Ouro Preto, MG, Brazil.,Universidade Federal de Ouro Preto, Laboratory of Epidemiology and Citology, Departamento de Análises Clínicas, St. Nove, 27, Bauxita, 35400-000 Ouro Preto, MG, Brazil
| | - Aristóteles Góes-Neto
- Universidade Federal de Minas Gerais, Laboratory of Molecular and Computational Biology of Fungi, Departamento de Microbiologia, Ave. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Vasco A C Azevedo
- Universidade Federal de Minas Gerais, Laboratory of Cell and Molecular Genetics, Departamento de Genética, Ecologia e Evolução, Ave. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Geraldo Wilson Fernandes
- Universidade Federal de Minas Gerais, Laboratory of Evolutionary Ecology and Biodiversity, Departamento de Genética, Ecologia e Evolução, Ave. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
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7
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Melo RT, Galvão NN, Guidotti-Takeuchi M, Peres PABM, Fonseca BB, Profeta R, Azevedo VAC, Monteiro GP, Brenig B, Rossi DA. Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil. Front Microbiol 2021; 12:674147. [PMID: 34220757 PMCID: PMC8253257 DOI: 10.3389/fmicb.2021.674147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.
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Affiliation(s)
- Roberta T Melo
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Newton N Galvão
- Ministry of Agriculture, Livestock and Supply, Rio de Janeiro, Brazil
| | | | - Phelipe A B M Peres
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Belchiolina B Fonseca
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme P Monteiro
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Daise A Rossi
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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8
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Coimbra-Campos LMC, Silva WN, Baltazar LM, Costa PAC, Prazeres PHDM, Picoli CC, Costa AC, Rocha BGS, Santos GSP, Oliveira FMS, Pinto MCX, Amorim JH, Azevedo VAC, Souza DG, Russo RC, Resende RR, Mintz A, Birbrair A. Circulating Nestin-GFP + Cells Participate in the Pathogenesis of Paracoccidioides brasiliensis in the Lungs. Stem Cell Rev Rep 2021; 17:1874-1888. [PMID: 34003465 DOI: 10.1007/s12015-021-10181-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
Multiple infectious diseases lead to impaired lung function. Revealing the cellular mechanisms involved in this impairment is crucial for the understanding of how the lungs shift from a physiologic to a pathologic state in each specific condition. In this context, we explored the pathogenesis of Paracoccidioidomycosis, which affects pulmonary functioning. The presence of cells expressing Nestin-GFP has been reported in different tissues, and their roles as tissue-specific progenitors have been stablished in particular organs. Here, we explored how Nestin-GFP+ cells are affected after lung infection by Paracoccidioides brasiliensis, a model of lung granulomatous inflammation with fibrotic outcome. We used Nestin-GFP transgenic mice, parabiosis surgery, confocal microscopy and flow cytometry to investigate the participation of Nestin-GFP+ cells in Paracoccidioides brasiliensis pathogenesis. We revealed that these cells increase in the lungs post-Paracoccidioides brasiliensis infection, accumulating around granulomas. This increase was due mainly to Nestin-GPF+ cells derived from the blood circulation, not associated to blood vessels, that co-express markers suggestive of hematopoietic cells (Sca-1, CD45 and CXCR4). Therefore, our findings suggest that circulating Nestin-GFP+ cells participate in the Paracoccidioides brasiliensis pathogenesis in the lungs.
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Affiliation(s)
| | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ludmila M Baltazar
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro H D M Prazeres
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Fabrício M S Oliveira
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Laboratory of Neuropharmacology and Neurochemistry, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of West Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Cellular and Molecular Genetics Laboratory, Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Danielle G Souza
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Remo C Russo
- Laboratory of Pulmonary Immunology and Mechanics, Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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9
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Sena IFG, Rocha BGS, Picoli CC, Santos GSP, Costa AC, Gonçalves BOP, Garcia APV, Soltani-Asl M, Coimbra-Campos LMC, Silva WN, Costa PAC, Pinto MCX, Amorim JH, Azevedo VAC, Resende RR, Heller D, Cassali GD, Mintz A, Birbrair A. C(3)1-TAg in C57BL/6 J background as a model to study mammary tumor development. Histochem Cell Biol 2021; 156:165-182. [PMID: 34003355 DOI: 10.1007/s00418-021-01995-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2021] [Indexed: 02/06/2023]
Abstract
Diagnosis and prognosis of breast cancer is based on disease staging identified through histopathological and molecular biology techniques. Animal models are used to gain mechanistic insights into the development of breast cancer. C(3)1-TAg is a genetically engineered mouse model that develops mammary cancer. However, carcinogenesis caused by this transgene was characterized in the Friend Virus B (FVB) background. As most genetic studies are done in mice with C57BL/6 J background, we aimed to define the histological alterations in C3(1)-TAg C57BL/6 J animals. Our results showed that C3(1)-TAg animals with C57BL/6 J background develop solid-basaloid adenoid cystic carcinomas with increased fibrosis, decreased area of adipocytes, and a high proliferative index, which are triple-negative for progesterone, estrogen, and human epidermal growth factor receptor 2 (HER2) receptors. Our results also revealed that tumor development is slower in the C57BL/6 J background when compared with the FVB strain, providing a better model to study the different stages in breast cancer progression.
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Affiliation(s)
- Isadora F G Sena
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bryan O P Gonçalves
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Paula V Garcia
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maryam Soltani-Asl
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Laboratory of Neuropharmacology and Neurochemistry, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of West Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Cellular and Molecular Genetics Laboratory, Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Debora Heller
- Hospital Israelita Albert Einstein, São Paulo, Brazil.,Cruzeiro Do Sul University, São Paulo, Brazil
| | - Geovanni D Cassali
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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10
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Sanches RCO, Tiwari S, Ferreira LCG, Oliveira FM, Lopes MD, Passos MJF, Maia EHB, Taranto AG, Kato R, Azevedo VAC, Lopes DO. Immunoinformatics Design of Multi-Epitope Peptide-Based Vaccine Against Schistosoma mansoni Using Transmembrane Proteins as a Target. Front Immunol 2021; 12:621706. [PMID: 33737928 PMCID: PMC7961083 DOI: 10.3389/fimmu.2021.621706] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Schistosomiasis remains a serious health issue nowadays for an estimated one billion people in 79 countries around the world. Great efforts have been made to identify good vaccine candidates during the last decades, but only three molecules reached clinical trials so far. The reverse vaccinology approach has become an attractive option for vaccine design, especially regarding parasites like Schistosoma spp. that present limitations for culture maintenance. This strategy also has prompted the construction of multi-epitope based vaccines, with great immunological foreseen properties as well as being less prone to contamination, autoimmunity, and allergenic responses. Therefore, in this study we applied a robust immunoinformatics approach, targeting S. mansoni transmembrane proteins, in order to construct a chimeric antigen. Initially, the search for all hypothetical transmembrane proteins in GeneDB provided a total of 584 sequences. Using the PSORT II and CCTOP servers we reduced this to 37 plasma membrane proteins, from which extracellular domains were used for epitope prediction. Nineteen common MHC-I and MHC-II binding epitopes, from eight proteins, comprised the final multi-epitope construct, along with suitable adjuvants. The final chimeric multi-epitope vaccine was predicted as prone to induce B-cell and IFN-γ based immunity, as well as presented itself as stable and non-allergenic molecule. Finally, molecular docking and molecular dynamics foresee stable interactions between the putative antigen and the immune receptor TLR 4. Our results indicate that the multi-epitope vaccine might stimulate humoral and cellular immune responses and could be a potential vaccine candidate against schistosomiasis.
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Affiliation(s)
- Rodrigo C. O. Sanches
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Sandeep Tiwari
- Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Laís C. G. Ferreira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Flávio M. Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Marcelo D. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Maria J. F. Passos
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Eduardo H. B. Maia
- Laboratório de Química Farmacêutica Medicinal, Universidade Federal de São João del-Rei, Divinópolis, Brazil
- Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Divinópolis, Brazil
| | - Alex G. Taranto
- Laboratório de Química Farmacêutica Medicinal, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Rodrigo Kato
- Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vasco A. C. Azevedo
- Programa de Pós-Graduação em Bioinformática, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Debora O. Lopes
- Laboratório de Biologia Molecular, Universidade Federal de São João del-Rei, Divinópolis, Brazil
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11
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Araújo DS, De-Paula RB, Tomé LMR, Quintanilha-Peixoto G, Salvador-Montoya CA, Del-Bem LE, Badotti F, Azevedo VAC, Brenig B, Aguiar ERGR, Drechsler-Santos ER, Fonseca PLC, Góes-Neto A. Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames. Mitochondrion 2021; 58:1-13. [PMID: 33582235 DOI: 10.1016/j.mito.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/08/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/07/2023]
Abstract
The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.
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Affiliation(s)
- Daniel S Araújo
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ruth B De-Paula
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luiz M R Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Eric R G R Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Paula L C Fonseca
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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12
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de Oliveira Zamprogna T, Ribeiro D, Azevedo VAC, Lara GHB, Motta RG, da Silva RC, Siqueira AK, de Nardi Júnior G, Listoni FJP, de Souza Araújo Martins L, da Silva AV, Portilho FVR, da Rocha Mota A, Rodrigues CA, de Almeida BO, Ribeiro MG. Bacteriological, cytological, and molecular investigation of Corynebacterium pseudotuberculosis, mycobacteria, and other bacteria in caseous lymphadenitis and healthy lymph nodes of slaughtered sheep. Braz J Microbiol 2020; 52:431-438. [PMID: 33185852 DOI: 10.1007/s42770-020-00403-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 11/04/2020] [Indexed: 11/27/2022] Open
Abstract
Caseous lymphadenitis (CL) in sheep is a chronic contagious disease caused by Corynebacterium pseudotuberculosis, commonly characterized by abscess formation in peripheral lymph nodes and disseminated infections. Nonetheless, other microorganisms, including with zoonotic relevance, can be isolated from CL-resembling lymph nodes. Currently, mycobacteria have been reported in visceral granulomatous lesions in small ruminants, a fact that poses a public health issue, particularly in slaughtered sheep intended for human consumption. Cytology using fine needle aspiration and microbiological culturing are suitable tests for routine diagnostic, whereas present drawbacks and molecular methods have been confirmatory. Data about the occurrence of mycobacteria in both lymph nodes with aspect of CL and apparently healthy visceral nodes of sheep slaughtered for human consumption are scarce. In this study, 197 visceral lymph nodes of sheep showed lymphadenitis and 202 healthy visceral lymph nodes of slaughtered sheep intended for human consumption were submitted to conventional bacteriological diagnosis, mycobacteria culturing, and cytological evaluation. Compatible Corynebacterium isolates were subjected to multiplex PCR targeting 16S rRNA, rpoB, and pld genes to detect C. pseudotuberculosis. Based on microbiological identification, C. pseudotuberculosis (86/197; 43.7%), streptococci γ-hemolytic (17/197; 8.6%), and Trueperella pyogenes (12/197; 6.1%) were prevalent in lymph nodes with abscesses, as opposed to staphylococci (53/202; 26.2%) in apparently healthy lymph nodes. No mycobacteria were isolated. Cytology identified 49.2% (97/197) Gram-positive pleomorphic organisms (coryneform aspect). Multiplex PCR confirmed genetic material of C. pseudotuberculosis in 74.4% (64/86) of the samples with C. pseudotuberculosis isolation and 66% (64/97) samples with cytological coryneform aspect (κ = 86.78%; 95% CI = 79.87-93.68%). These findings emphasize the prevalence of C. pseudotuberculosis in abscess formation among peripheral lymph nodes of sheep. Other bacteria were also identified in lymph nodes sampled that resembling C. pseudotuberculosis-induced infections that may difficult the diagnosis. Multiplex PCR revealed a valuable assay to detect C. pseudotuberculosis, in addition to routine methods applied to CL-diagnosis. No mycobacteria were identified in lymph nodes sampled, with and without apparent lesions. Nonetheless, due to public health impacts, this pathogen should be considered as a differential diagnosis of C. pseudotuberculosis-induced infections during inspection procedures of slaughtered sheep intended for human consumption.
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Affiliation(s)
- Thiago de Oliveira Zamprogna
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Dayana Ribeiro
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Vasco A C Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Gustavo Henrique Batista Lara
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Rodrigo Garcia Motta
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Rodrigo Costa da Silva
- School of Agrarian Sciences, University of Western São Paulo (UNOESTE), Presidente Prudente, SP, Brazil
| | - Amanda Keller Siqueira
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | - Fernando José Paganini Listoni
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Lorrayne de Souza Araújo Martins
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Aristeu Vieira da Silva
- Zoonosis and Public Health Research Group, Department of Biologial Sciences, Feira de Santana State University (UEFS), Feira de Santana, BA, Brazil
| | - Fábio Vinícius Ramos Portilho
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - André da Rocha Mota
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Carolina Aparecida Rodrigues
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Beatriz Oliveira de Almeida
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Márcio Garcia Ribeiro
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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13
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Picoli CC, Costa AC, Rocha BGS, Silva WN, Santos GSP, Prazeres PHDM, Costa PAC, Oropeza A, da Silva RA, Azevedo VAC, Resende RR, Cunha TM, Mintz A, Birbrair A. Sensory nerves in the spotlight of the stem cell niche. Stem Cells Transl Med 2020; 10:346-356. [PMID: 33112056 PMCID: PMC7900586 DOI: 10.1002/sctm.20-0284] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/28/2020] [Revised: 08/27/2020] [Accepted: 09/26/2020] [Indexed: 12/16/2022] Open
Abstract
Niches are specialized tissue microenvironments that control stem cells functioning. The bone marrow mesenchymal stem cell niche defines a location within the marrow in which mesenchymal stem cells are retained and produce new cells throughout life. Deciphering the signaling mechanisms by which the niche regulates stem cell fate will facilitate the use of these cells for therapy. Recent studies, by using state-of-the-art methodologies, including sophisticated in vivo inducible genetic techniques, such as lineage-tracing Cre/loxP mediated systems, in combination with pharmacological inhibition, provide evidence that sensory neuron is an important component of the bone marrow mesenchymal stem cell niche. Strikingly, knockout of a specific receptor in sensory neurons blocked stem cell function in the bone marrow. The knowledge arising from these discoveries will be crucial for stem cell manipulation in the future. Here, we review recent progress in our understanding of sensory nerves biology in the stem cell niche.
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Affiliation(s)
- Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Pedro H D M Prazeres
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Oropeza
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo A da Silva
- Department of Dentistry, University of Taubaté, Taubaté, São Paulo, Brazil
| | - Vasco A C Azevedo
- Cellular and Molecular Genetics Laboratory, Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago M Cunha
- Department of Pharmacology, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, New York, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Department of Radiology, Columbia University Medical Center, New York, New York, USA
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14
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Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh D, Ghosh P, Azevedo VAC, Dos Santos MA. Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression. Gene 2019; 726:144168. [PMID: 31759986 DOI: 10.1016/j.gene.2019.144168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/21/2019] [Accepted: 10/11/2019] [Indexed: 01/02/2023]
Abstract
Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many authors have performed feature selection or reduced the size of data matrix. In this work, we introduce a new logistic regression-based model to classify breast cancer tumor samples based on microarray expression data, including all features of gene expression and without reducing the microarray data matrix. If the user still deems it necessary to perform feature reduction, it can be done after the application of the methodology, still maintaining a good classification. This methodology allowed the correct classification of breast cancer sample data sets from Gene Expression Omnibus (GEO) data series GSE65194, GSE20711, and GSE25055, which contain the microarray data of said breast cancer samples. Classification had a minimum performance of 80% (sensitivity and specificity), and explored all possible data combinations, including breast cancer subtypes. This methodology highlighted genes not yet studied in breast cancer, some of which have been observed in Gene Regulatory Networks (GRNs). In this work we examine the patterns and features of a GRN composed of transcription factors (TFs) in MCF-7 breast cancer cell lines, providing valuable information regarding breast cancer. In particular, some genes whose αi ∗ associated parameter values revealed extreme positive and negative values, and, as such, can be identified as breast cancer prediction genes. We indicate that the PKN2, MKL1, MED23, CUL5 and GLI genes demonstrate a tumor suppressor profile, and that the MTR, ITGA2B, TELO2, MRPL9, MTTL1, WIPI1, KLHL20, PI4KB, FOLR1 and SHC1 genes demonstrate an oncogenic profile. We propose that these may serve as potential breast cancer prediction genes, and should be prioritized for further clinical studies on breast cancer. This new model allows for the assignment of values to the αi ∗ parameters associated with gene expression. It was noted that some αi ∗ parameters are associated with genes previously described as breast cancer biomarkers, as well as other genes not yet studied in relation to this disease.
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Affiliation(s)
- Francielly Morais-Rodrigues
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil.
| | - Rita Silv Erio-Machado
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Diego Lucas Neres Rodrigues
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Juan Valdez-Baez
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Vagner Fonseca
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Emmanuel James San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Lucas Gabriel Rodrigues Gomes
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Roselane Gonçalves Dos Santos
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Marcus Vinicius Canário Viana
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil; Federal University of Pará, UFPA, Brazil
| | - Joyce da Cruz Ferraz Dutra
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana Teixeira Dornelles Parise
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Doglas Parise
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Frederico F Campos
- Department of Computer Science, Federal University of Minas Gerais, Brazil Av Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | | | - José Miguel Ortega
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721172, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Vasco A C Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Brazil. Av. Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
| | - Marcos A Dos Santos
- Department of Computer Science, Federal University of Minas Gerais, Brazil Av Antônio Carlos, 6627, Belo Horizonte, MG 31270-901, Brazil
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15
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Leonel C, Sena IFG, Silva WN, Prazeres PHDM, Fernandes GR, Mancha Agresti P, Martins Drumond M, Mintz A, Azevedo VAC, Birbrair A. Staphylococcus epidermidis role in the skin microenvironment. J Cell Mol Med 2019; 23:5949-5955. [PMID: 31278859 PMCID: PMC6714221 DOI: 10.1111/jcmm.14415] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/12/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
Wound healing is a complex dynamic physiological process in response to cutaneous destructive stimuli that aims to restore the cutaneous' barrier role. Deciphering the underlying mechanistic details that contribute to wound healing will create novel therapeutic strategies for skin repair. Recently, by using state-of-the-art technologies, it was revealed that the cutaneous microbiota interact with skin immune cells. Strikingly, commensal Staphylococcus epidermidis-induced CD8+ T cells induce re-epithelization of the skin after injury, accelerating wound closure. From a drug development perspective, the microbiota may provide new therapeutic candidate molecules to accelerate skin healing. Here, we summarize and evaluate recent advances in the understanding of the microbiota in the skin microenvironment.
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Affiliation(s)
- Caroline Leonel
- Departamento de PatologiaUniversidade Federal de Minas GeraisBelo HorizonteBrasil
| | - Isadora F. G. Sena
- Departamento de PatologiaUniversidade Federal de Minas GeraisBelo HorizonteBrasil
| | - Walison N. Silva
- Departamento de PatologiaUniversidade Federal de Minas GeraisBelo HorizonteBrasil
| | | | | | - Pamela Mancha Agresti
- Departamento de Biologia GeralUniversidade Federal de Minas GeraisBelo HorizonteBrasil
| | | | - Akiva Mintz
- Department of RadiologyColumbia University Medical CenterNew YorkNew York
| | - Vasco A. C. Azevedo
- Departamento de Biologia GeralUniversidade Federal de Minas GeraisBelo HorizonteBrasil
| | - Alexander Birbrair
- Departamento de PatologiaUniversidade Federal de Minas GeraisBelo HorizonteBrasil
- Department of RadiologyColumbia University Medical CenterNew YorkNew York
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16
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Tavares GC, Carvalho AF, Pereira FL, Rezende CP, Azevedo VAC, Leal CAG, Figueiredo HCP. Transcriptome and Proteome of Fish-Pathogenic Streptococcus agalactiae Are Modulated by Temperature. Front Microbiol 2018; 9:2639. [PMID: 30450092 PMCID: PMC6224512 DOI: 10.3389/fmicb.2018.02639] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 04/30/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Streptococcus agalactiae is one of the most important pathogens associated with streptococcosis outbreaks in Nile tilapia farms worldwide. High water temperature (above 27°C) has been described as a predisposing factor for the disease in fish. At low temperatures (below 25°C), fish mortalities are not usually observed in farms. Temperature variation can modulate the expression of genes and proteins involved in metabolism, adaptation, and bacterial pathogenicity, thus increasing or decreasing the ability to infect the host. This study aimed to evaluate the transcriptome and proteome of a fish-pathogenic S. agalactiae strain SA53 subjected to in vitro growth at different temperatures using a microarray and label-free shotgun LC-HDMSE approach. Biological triplicates of isolates were cultured in BHIT broth at 22 or 32°C for RNA and protein isolation and submitted for transcriptomic and proteomic analyses. In total, 1,730 transcripts were identified in SA53, with 107 genes being differentially expressed between the temperatures evaluated. A higher number of genes related to metabolism, mainly from the phosphotransferase system (PTS) and ATP-binding cassette (ABC) transport system, were upregulated at 32°C. In the proteome analysis, 1,046 proteins were identified in SA53, of which 81 were differentially regulated between 22 and 32°C. Proteins involved in defense mechanisms, lipid transport and metabolism, and nucleotide transport and metabolism were upregulated at 32°C. A higher number of interactions were observed in proteins involved in nucleotide transport and metabolism. We observed a low correlation between the transcriptome and proteome datasets. Our study indicates that the transcriptome and proteome of a fish-adapted S. agalactiae strain are modulated by temperature, particularly showing differential expression of genes/proteins involved in metabolism, virulence factors, and adaptation.
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Affiliation(s)
- Guilherme C Tavares
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alex F Carvalho
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Cristiana P Rezende
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- LGCM-Laboratory of Cellular and Molecular Genetics, Biological Science Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Carlos A G Leal
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Henrique C P Figueiredo
- AQUACEN-National Reference Laboratory of Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
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17
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Parise D, Parise MTD, Viana MVC, Muñoz-Bucio AV, Cortés-Pérez YA, Arellano-Reynoso B, Díaz-Aparicio E, Dorella FA, Pereira FL, Carvalho AF, Figueiredo HCP, Ghosh P, Barh D, Gomide ACP, Azevedo VAC. First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. Stand Genomic Sci 2018; 13:21. [PMID: 30338024 PMCID: PMC6180578 DOI: 10.1186/s40793-018-0325-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 07/25/2017] [Accepted: 09/24/2018] [Indexed: 12/20/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software. The automatic genome annotation was done using the software RAST and in-house scripts for transference, followed by manual curation using Artemis software and BLAST against NCBI and UniProt databases. The six genomes are publicly available in NCBI database. The analysis of nucleotide sequence similarity and the generated phylogenetic tree led to the observation that the Mexican strains are more similar between strains from the same host, but the genetic structure is probably more influenced by transportation of animals between farms than host preference. Also, a putative drug target was predicted and in silico analysis of 46 strains showed two gene clusters capable of differentiating the biovars equi and ovis: Restriction Modification system and CRISPR-Cas cluster.
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Affiliation(s)
- Doglas Parise
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Mariana T D Parise
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Marcus V C Viana
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Adrian V Muñoz-Bucio
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Yazmin A Cortés-Pérez
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Beatriz Arellano-Reynoso
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Efrén Díaz-Aparicio
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Fernanda A Dorella
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Felipe L Pereira
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Alex F Carvalho
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Henrique C P Figueiredo
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284 USA
| | - Debmalya Barh
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721172 India
- Division of Bioinformatics and Computational Genomics, NITTE University Center for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka India
| | - Anne C P Gomide
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Vasco A C Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
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18
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Oliveira AF, Folador EL, Gomide ACP, Goes-Neto A, Azevedo VAC, Wattam AR. Cell Division in genus Corynebacterium: protein-protein interaction and molecular docking of SepF and FtsZ in the understanding of cytokinesis in pathogenic species. AN ACAD BRAS CIENC 2018; 90:2179-2188. [PMID: 29451601 DOI: 10.1590/0001-3765201820170385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/23/2017] [Indexed: 11/22/2022] Open
Abstract
The genus Corynebacterium includes species of great importance in medical, veterinary and biotechnological fields. The genus-specific families (PLfams) from PATRIC have been used to observe conserved proteins associated to all species. Our results showed a large number of conserved proteins that are associated with the cellular division process. Was not observe in our results other proteins like FtsA and ZapA that interact with FtsZ. Our findings point that SepF overlaps the function of this proteins explored by molecular docking, protein-protein interaction and sequence analysis. Transcriptomic analysis showed that these two (Sepf and FtsZ) proteins can be expressed in different conditions together. The work presents novelties on molecules participating in the cell division event, from the interaction of FtsZ and SepF, as new therapeutic targets.
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Affiliation(s)
- Alberto F Oliveira
- Departamento de Biologia Geral, Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Edson L Folador
- Centro de Biotecnologia/CBiotec, Universidade Federal da Paraíba/UFPB, s/n, Castelo Branco III, 58051-085 João Pessoa, PB, Brazil
| | - Anne C P Gomide
- Departamento de Biologia Geral, Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Aristóteles Goes-Neto
- Departamento de Microbiologia, Laboratório de Biologia Molecular e Computacional de Fungos, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Vasco A C Azevedo
- Departamento de Biologia Geral, Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, 31270-901 Belo Horizonte, MG, Brazil
| | - Alice R Wattam
- Biocomplexity Institute of Virginia Tech, 1015 Life Science Circle, Virginia Tech, 24060, Blacksburg, VA, U.S.A
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19
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Hassan SS, Jamal SB, Radusky LG, Tiwari S, Ullah A, Ali J, Behramand, de Carvalho PVSD, Shams R, Khan S, Figueiredo HCP, Barh D, Ghosh P, Silva A, Baumbach J, Röttger R, Turjanski AG, Azevedo VAC. The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets. Front Genet 2018; 9:44. [PMID: 29487617 PMCID: PMC5816920 DOI: 10.3389/fgene.2018.00044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 11/23/2017] [Accepted: 01/30/2018] [Indexed: 01/20/2023] Open
Abstract
Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the “pocketome druggability.” To this end, we first computed the “modelome” (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.
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Affiliation(s)
- Syed S Hassan
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Syed B Jamal
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Leandro G Radusky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sandeep Tiwari
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Asad Ullah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Javed Ali
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Behramand
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Paulo V S D de Carvalho
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rida Shams
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Sabir Khan
- Department of Analytical Chemistry, Institute of Chemistry, São Paulo State University, São Paulo, Brazil
| | - Henrique C P Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Vasco A C Azevedo
- PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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20
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Jamal SB, Hassan SS, Tiwari S, Viana MV, Benevides LDJ, Ullah A, Turjanski AG, Barh D, Ghosh P, Costa DA, Silva A, Röttger R, Baumbach J, Azevedo VAC. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One 2017; 12:e0186401. [PMID: 29049350 PMCID: PMC5648181 DOI: 10.1371/journal.pone.0186401] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 09/29/2017] [Indexed: 01/03/2023] Open
Abstract
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics based core-genome and core-modelome analyses. Further, using subtractive proteomics and modelomics approaches for target identification, a set of 23 proteins was selected as essential for the bacteria. Considering human as a host, eight of these proteins (glpX, nusB, rpsH, hisE, smpB, bioB, DIP1084, and DIP0983) were considered as essential and non-host homologs, and have been subjected to virtual screening using four different compound libraries (extracted from the ZINC database, plant-derived natural compounds and Di-terpenoid Iso-steviol derivatives). The proposed ligand molecules showed favorable interactions, lowered energy values and high complementarity with the predicted targets. Our proposed approach expedites the selection of C. diphtheriae putative proteins for broad-spectrum development of novel drugs and vaccines, owing to the fact that some of these targets have already been identified and validated in other organisms.
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Affiliation(s)
- Syed Babar Jamal
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Syed Shah Hassan
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Sandeep Tiwari
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcus V. Viana
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leandro de Jesus Benevides
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Asad Ullah
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, Argentina
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Daniela Arruda Costa
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Artur Silva
- Institute of Biologic Sciences, Federal University of Para, Belém, PA, Brazil
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Vasco A. C. Azevedo
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of General Biology (LGCM), Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- * E-mail:
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21
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Mariano DCB, Pereira FL, Aguiar EL, Oliveira LC, Benevides L, Guimarães LC, Folador EL, Sousa TJ, Ghosh P, Barh D, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. BMC Bioinformatics 2016; 17:456. [PMID: 28105921 PMCID: PMC5249034 DOI: 10.1186/s12859-016-1344-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. RESULTS In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. CONCLUSION Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .
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Affiliation(s)
- Diego C. B. Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Felipe L. Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edgar L. Aguiar
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Letícia C. Oliveira
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Leandro Benevides
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Luís C. Guimarães
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Edson L. Folador
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Thiago J. Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Preetam Ghosh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur WB-721172 India
| | - Henrique C. P. Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Rommel T. J. Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará Brazil
| | - Vasco A. C. Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901 Belo Horizonte, Minas Gerais Brazil
- Federal University of Minas Gerais, Institute of Biological Sciences, Antônio Carlos 6627, Pampulha, 30161-970 Belo Horizonte, Minas Gerais Brazil
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22
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Figueiredo HCP, Soares SC, Pereira FL, Dorella FA, Carvalho AF, Teixeira JP, Azevedo VAC, Leal CAG. Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout. BMC Genomics 2015; 16:1095. [PMID: 26694728 PMCID: PMC4687380 DOI: 10.1186/s12864-015-2324-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 06/25/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The genus Weissella belongs to the lactic acid bacteria and includes 18 currently identified species, predominantly isolated from fermented food but rarely from cases of bacteremia in animals. Recently, a new species, designated Weissella ceti, has been correlated with hemorrhagic illness in farm-raised rainbow trout in China, Brazil, and the USA, with high transmission and mortality rates during outbreaks. Although W. ceti is an important emerging veterinary pathogen, little is known about its genomic features or virulence mechanisms. To better understand these and to characterize the species, we have previously sequenced the genomes of W. ceti strains WS08, WS74, and WS105, isolated from different rainbow trout farms in Brazil and displaying different pulsed-field gel electrophoresis patterns. Here, we present a comparative analysis of the three previously sequenced genomes of W. ceti strains from Brazil along with W. ceti NC36 from the USA and those of other Weissella species. Results Phylogenomic and orthology-based analyses both showed a high-similarity in the genetic structure of these W. ceti strains. This structure is corroborated by the highly syntenic order of their genes and the neutral evolution inferred from Tajima’s D. A whole-genome multilocus sequence typing analysis distinguished strains WS08 and NC36 from strains WS74 and WS105. We predicted 10 putative genomic islands (GEI), among which PAIs 3a and 3b are phage sequences that occur only in WS105 and WS74, respectively, whereas PAI 1 is species specific. Conclusions We identified several genes putatively involved in the basic processes of bacterial physiology and pathogenesis, including survival in aquatic environment, adherence in the host, spread inside the host, resistance to immune-system-mediated stresses, and antibiotic resistance. These data provide new insights in the molecular epidemiology and host adaptation for this emerging pathogen in aquaculture. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2324-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Henrique C P Figueiredo
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Veterinary School, Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Pampulha, Belo Horizonte, 30161-970, MG, Brazil.
| | - Siomar C Soares
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Felipe L Pereira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Fernanda A Dorella
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Alex F Carvalho
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Júnia P Teixeira
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco A C Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute for Biological Science, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Carlos A G Leal
- AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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23
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Vasconcelos ATR, Ferreira HB, Bizarro CV, Bonatto SL, Carvalho MO, Pinto PM, Almeida DF, Almeida LGP, Almeida R, Alves-Filho L, Assunção EN, Azevedo VAC, Bogo MR, Brigido MM, Brocchi M, Burity HA, Camargo AA, Camargo SS, Carepo MS, Carraro DM, de Mattos Cascardo JC, Castro LA, Cavalcanti G, Chemale G, Collevatti RG, Cunha CW, Dallagiovanna B, Dambrós BP, Dellagostin OA, Falcão C, Fantinatti-Garboggini F, Felipe MSS, Fiorentin L, Franco GR, Freitas NSA, Frías D, Grangeiro TB, Grisard EC, Guimarães CT, Hungria M, Jardim SN, Krieger MA, Laurino JP, Lima LFA, Lopes MI, Loreto ELS, Madeira HMF, Manfio GP, Maranhão AQ, Martinkovics CT, Medeiros SRB, Moreira MAM, Neiva M, Ramalho-Neto CE, Nicolás MF, Oliveira SC, Paixão RFC, Pedrosa FO, Pena SDJ, Pereira M, Pereira-Ferrari L, Piffer I, Pinto LS, Potrich DP, Salim ACM, Santos FR, Schmitt R, Schneider MPC, Schrank A, Schrank IS, Schuck AF, Seuanez HN, Silva DW, Silva R, Silva SC, Soares CMA, Souza KRL, Souza RC, Staats CC, Steffens MBR, Teixeira SMR, Urmenyi TP, Vainstein MH, Zuccherato LW, Simpson AJG, Zaha A. Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol 2005; 187:5568-77. [PMID: 16077101 PMCID: PMC1196056 DOI: 10.1128/jb.187.16.5568-5577.2005] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2005] [Accepted: 05/19/2005] [Indexed: 11/20/2022] Open
Abstract
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.
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Affiliation(s)
- Ana Tereza R Vasconcelos
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Prédio 43421, Porto Alegre, RS, Brazil
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