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Alves SIA, Ferreira VBC, Dantas CWD, da Silva ALDC, Ramos RTJ. EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison. Front Genet 2023; 14:1228552. [PMID: 37693309 PMCID: PMC10483286 DOI: 10.3389/fgene.2023.1228552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/28/2023] [Indexed: 09/12/2023] Open
Abstract
Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1-6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually-time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR.
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Affiliation(s)
- Sandy Ingrid Aguiar Alves
- Laboratory of Biological Engineering, Biological Science Institute, Park of Science and Technology, Federal University of Pará, Belém, Brazil
| | - Victor Benedito Costa Ferreira
- Laboratory of Biological Engineering, Biological Science Institute, Park of Science and Technology, Federal University of Pará, Belém, Brazil
| | | | - Artur Luiz da Costa da Silva
- Laboratory of Biological Engineering, Biological Science Institute, Park of Science and Technology, Federal University of Pará, Belém, Brazil
| | - Rommel Thiago Jucá Ramos
- Laboratory of Biological Engineering, Biological Science Institute, Park of Science and Technology, Federal University of Pará, Belém, Brazil
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Martins Balbinot K, Almeida Loureiro FJ, Chemelo GP, Alves Mesquita R, Cruz Ramos AMP, Ramos RTJ, da Costa da Silva AL, de Menezes SAF, da Silva Kataoka MS, Alves Junior SDM, Viana Pinheiro JDJ. Immunoexpression of stem cell markers SOX-2, NANOG AND OCT4 in ameloblastoma. PeerJ 2023; 11:e14349. [PMID: 36655039 PMCID: PMC9841912 DOI: 10.7717/peerj.14349] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/16/2022] [Indexed: 01/15/2023] Open
Abstract
Background Ameloblastoma (AME) is characterized by a locally invasive growth pattern. In an attempt to justify the aggressiveness of neoplasms, the investigation of the role of stem cells has gained prominence. The SOX-2, NANOG and OCT4 proteins are important stem cell biomarkers. Methodology To verify the expression of these proteins in tissue samples of AME, dentigerous cyst (DC) and dental follicle (DF), immunohistochemistry was performed and indirect immunofluorescence were performed on the human AME (AME-hTERT) cell line. Results Revealed expression of SOX-2, NANOG and OCT4 in the tissue samples and AME-hTERT lineage. Greater immunostaining of the studied proteins was observed in AME compared to DC and DF (p < 0.001). Conclusions The presence of biomarkers indicates a probable role of stem cells in the genesis and progression of AME.
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Affiliation(s)
- Karolyny Martins Balbinot
- Laboratory of Pathological Anatomy and Immunohistochemistry, Federal University of Pará, Belém, Pará, Brazil
| | | | | | - Ricardo Alves Mesquita
- Department of Oral Surgery and Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | | | - Sergio de Melo Alves Junior
- Laboratory of Pathological Anatomy and Immunohistochemistry, Federal University of Pará, Belém, Pará, Brazil
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Pinheiro KDC, Gois BVA, Nogueira WG, Araújo FA, Queiroz ALC, Cardenas-Alegria O, da Silva ALDC, Júnior AMGM, Ramos RTJ. In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes. Front Bioinform 2022; 2:931583. [PMID: 36304273 PMCID: PMC9580864 DOI: 10.3389/fbinf.2022.931583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Corynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of C. pseudotuberculosis. The similarities associated with SSRs amongst the different serum variants of C. pseudotuberculosis, biovars equi and ovis, were also evaluated, and it was possible to identify SSRs located in coding regions responsible for a VF enrolled in pathogenesis known to mediate bacterial adherence (SpaH-type pili virulence factor). Phylogenetic analyses revealed that strains sharing SSR patterns, including the possible polymorphisms identified in the same position of gene-coding regions, were displayed by strains with a common ancestor, corroborating with the Genome Tree Report of the NCBI. Statistical analysis showed that the microsatellite groups belonging to equi and ovis biovars have a significance of 0.006 (p-value) in similarity, thus indicating them as good biomarker candidates for C. pseudotuberculosis.
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Affiliation(s)
| | | | - Wylerson Guimarães Nogueira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Artur Luiz da Costa da Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | | | - Rommel Thiago Jucá Ramos
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
- *Correspondence: Rommel Thiago Jucá Ramos,
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Cruz ELDS, Loureiro FJA, Silva ALDCD, Ramos RT, Kataoka MSDS, Pinheiro JDJV, Alves Júnior SDM. Gene expression in cell lines from human ameloblastoma immortalized using hTERT and HPV16-E6/E7. Oral Dis 2021; 28:2230-2238. [PMID: 34060687 DOI: 10.1111/odi.13930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 05/10/2021] [Accepted: 05/26/2021] [Indexed: 01/09/2023]
Abstract
OBJECTIVE The aim of this study was to evaluate and compare alterations in gene expression using two distinct immortalization methods (hTERT and HPV16-E6/E7) in ameloblastoma cell lines. MATERIALS AND METHODS A primary cell culture derived from human ameloblastoma (AME-1) was established and immortalized by two different methods using a transfection processes to hTERT and HPV-E6/E7. The RNA-seq was used to verify which immortalization method had less influence on gene expression. It was performed in four steps: extraction and collection of mRNA, PCR amplification, comparison with the human reference genome, and analysis of differential expression. The genes with differentiated expression were identified and mapped. RESULTS RNA-seq revealed genetic alterations in ameloblastoma cell lines after the immortalization process, including increased expression of tumor genes like MYC, E2F1, BRAF, HRAS, and HTERT, and a decrease in tumor suppressor genes like P53, P21, and Rb. CONCLUSIONS It is possible to affirm that cell immortalization is not an inert method regarding gene regulation mechanisms and the hTERT method (AME-TERT) presented fewer changes in gene expression levels.
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Affiliation(s)
| | | | | | - Rommel Thiago Ramos
- Department of Genetics and Molecular Biology, Federal University of Pará - UFPA, Belém, Brazil
| | - Maria Sueli da Silva Kataoka
- Oral Pathology, Cell Culture Laboratory of School of Dentistry, Federal University of Pará - UFPA, Belém, Brazil
| | - João de Jesus Viana Pinheiro
- Oral Pathology, Cell Culture Laboratory of School of Dentistry, Federal University of Pará - UFPA, Belém, Brazil
| | - Sérgio de Melo Alves Júnior
- Oral Pathology, Cell Culture Laboratory of School of Dentistry, Federal University of Pará - UFPA, Belém, Brazil
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de Carvalho DC, Wanderley AV, Dos Santos AMR, Moreira FC, de Sá RBA, Fernandes MR, Modesto AAC, de Souza TP, Cohen-Paes A, Leitão LPC, Rodrigues JCG, da Silva ALDC, Guerreiro JF, Santos S, Khayat AS, de Assumpção PP, Dos Santos NPC. Characterization of pharmacogenetic markers related to Acute Lymphoblastic Leukemia toxicity in Amazonian native Americans population. Sci Rep 2020; 10:10292. [PMID: 32581388 PMCID: PMC7314857 DOI: 10.1038/s41598-020-67312-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 03/17/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Acute Lymphoblastic Leukemia (ALL) is the most common cancer in children. Differences are found among ethnic groups in the results of the treatment of pediatric ALL. In general, children with a high level of native American ancestry tend to respond less positively to ALL treatments, which may be related to specific genomic variants found in native American groups. Despite the evidence, few data are available on the distribution of the pharmacogenomic variants relevant to the treatment of ALL in traditional Amerindian populations, such the those of the Amazon region. Given this, the present study investigated 27 molecular markers related to the treatment of ALL in Amerindians from Brazilian Amazonia and compared the frequencies with those recorded previously on five continents, that are available in the 1,000 Genomes database. The variation in the genotype frequencies among populations was evaluated using Fisher's exact test. The False Discovery Rate method was used to correct the results of the multiple analyses. Significant differences were found in the frequencies of the majority of markers between the Amerindian populations and those of other regions around the world. These findings highlight the unique genetic profile of the indigenous population of Brazilian Amazonia, which may reflect a distinct therapeutic profile for the treatment of ALL in these populations.
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Affiliation(s)
| | - Alayde Vieira Wanderley
- Oncology Research Nucleus, Universidade Federal Do Pará, Belém, PA, Brazil.,Departamento de Pediatria, Ophir Loyola Hospital, Belém, PA, Brazil
| | | | | | | | | | | | | | - Amanda Cohen-Paes
- Oncology Research Nucleus, Universidade Federal Do Pará, Belém, PA, Brazil
| | | | | | - Artur Luiz da Costa da Silva
- Genomics and Bioinformatics Laboratory, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| | - João Farias Guerreiro
- Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, PA, Brazil
| | - Sidney Santos
- Oncology Research Nucleus, Universidade Federal Do Pará, Belém, PA, Brazil.,Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, PA, Brazil
| | - André Salim Khayat
- Oncology Research Nucleus, Universidade Federal Do Pará, Belém, PA, Brazil
| | - Paulo Pimentel de Assumpção
- Oncology Research Nucleus, Universidade Federal Do Pará, Belém, PA, Brazil.,João de Barros Barreto University Hospital, Universidade Federal Do Pará, Belém, PA, Brazil
| | - Ney Pereira Carneiro Dos Santos
- Oncology Research Nucleus, Universidade Federal Do Pará, Belém, PA, Brazil. .,Human and Medical Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, PA, Brazil. .,Hospital Universitário João de Barros Barreto - Núcleo de Pesquisa Em Oncologia, 2º Piso da Unidade de Alta Complexidade Em Oncologia. Av. Mundurucus, 4487, Guamá, Belém, PA, 66073-005, Brazil.
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Queiroz LL, Bendia AG, Duarte RTD, das Graças DA, da Costa da Silva AL, Nakayama CR, Sumida PY, Lima AOS, Nagano Y, Fujikura K, Kitazato H, Pellizari VH. Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau. Antonie Van Leeuwenhoek 2020; 113:707-717. [PMID: 31950303 DOI: 10.1007/s10482-020-01384-8] [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] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/02/2020] [Indexed: 11/29/2022]
Abstract
Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2456 to 2728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.
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Affiliation(s)
- Luciano Lopes Queiroz
- Institute of Oceanography, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil. .,Microbiology Graduate Program, Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil.
| | - Amanda Gonçalves Bendia
- Institute of Oceanography, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Rubens Tadeu Delgado Duarte
- Microbiology, Immunology and Parasitology Department, Federal University of Santa Catarina: CCB-MIP, Campus Trindade, PO Box 476, Florianópolis, CEP: 88040-900, Brazil
| | - Diego Assis das Graças
- Institute of Biological Science, Federal University of Pará, Rua Augusto Correa, 01, Belém, CEP: 66075-110, Brazil
| | - Artur Luiz da Costa da Silva
- Institute of Biological Science, Federal University of Pará, Rua Augusto Correa, 01, Belém, CEP: 66075-110, Brazil
| | - Cristina Rossi Nakayama
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, Rua São Nicolau, 210, Diadema, CEP: 09913-030, Brazil
| | - Paulo Yukio Sumida
- Institute of Oceanography, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Andre O S Lima
- Centro de Ciências Tecnológicas da Terra e do Mar (CTTMAR), University of Vale do Itajaí, Rua Uruguai, 458, Itajaí, SC, CEP: 88302-202, Brazil
| | - Yuriko Nagano
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Katsunori Fujikura
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiroshi Kitazato
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Vivian Helena Pellizari
- Institute of Oceanography, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
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de Sousa AL, Maués D, Lobato A, Franco EF, Pinheiro K, Araújo F, Pantoja Y, da Costa da Silva AL, Morais J, Ramos RTJ. PhageWeb - Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes. Front Genet 2018; 9:644. [PMID: 30619469 PMCID: PMC6305541 DOI: 10.3389/fgene.2018.00644] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/27/2018] [Indexed: 12/04/2022] Open
Abstract
This study developed a computational tool with a graphical interface and a web-service that allows the identification of phage regions through homology search and gene clustering. It uses G+C content variation evaluation and tRNA prediction sites as evidence to reinforce the presence of prophages in indeterminate regions. Also, it performs the functional characterization of the prophages regions through data integration of biological databases. The performance of PhageWeb was compared to other available tools (PHASTER, Prophinder, and PhiSpy) using Sensitivity (Sn) and Positive Predictive Value (PPV) tests. As a reference for the tests, more than 80 manually annotated genomes were used. In the PhageWeb analysis, the Sn index was 86.1% and the PPV was approximately 87%, while the second best tool presented Sn and PPV values of 83.3 and 86.5%, respectively. These numbers allowed us to observe a greater precision in the regions identified by PhageWeb while compared to other prediction tools submitted to the same tests. Additionally, PhageWeb was much faster than the other computational alternatives, decreasing the processing time to approximately one-ninth of the time required by the second best software. PhageWeb is freely available at http://computationalbiology.ufpa.br/phageweb.
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Affiliation(s)
| | - Dener Maués
- Institute of Exact and Natural Sciences, Federal University of Para, Belém, Brazil
| | - Amália Lobato
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Edian F. Franco
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Kenny Pinheiro
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Fabrício Araújo
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | - Yan Pantoja
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
| | | | - Jefferson Morais
- Institute of Exact and Natural Sciences, Federal University of Para, Belém, Brazil
| | - Rommel T. J. Ramos
- Institute of Biological Sciences, Federal University of Para, Belém, Brazil
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Eslabão MR, Kremer FS, Ramos RTJ, Silva ALDCD, Azevedo VADC, Pinto LDS, Silva ÉFD, Dellagostin OA. Genome of Leptospira borgpetersenii strain 4E, a highly virulent isolate obtained from Mus musculus in southern Brazil. Mem Inst Oswaldo Cruz 2018; 113:137-141. [PMID: 29236926 PMCID: PMC5722270 DOI: 10.1590/0074-02760170111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 03/17/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022] Open
Abstract
A previous study by our group reported the isolation and characterisation of Leptospira borgpetersenii serogroup Ballum strain 4E. This strain is of particular interest because it is highly virulent in the hamster model. In this study, we performed whole-genome shotgun genome sequencing of the strain using the SOLiD sequencing platform. By assembling and analysing the new genome, we were able to identify novel features that have been previously overlooked in genome annotations of other strains belonging to the same species.
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Affiliation(s)
- Marcus Redü Eslabão
- Núcleo de Biotecnologia, Universidade Federal de Pelotas, Capão do Leão, RS, Brasil
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Gomes JCM, Azevedo JSND, Veras AADO, Alves JTC, Henriques I, Correia A, Silva ALDCD, Carneiro AR. Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system ( Ria de Aveiro , Portugal). Genomics Data 2016; 8:21-4. [PMID: 27114904 PMCID: PMC4832037 DOI: 10.1016/j.gdata.2016.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/18/2016] [Accepted: 02/20/2016] [Indexed: 11/26/2022]
Abstract
The genus Psychrobacter includes Gram-negative coccobacilli that are non-pigmented, oxidase-positive, non-motile, psychrophilic or psychrotolerant, and halotolerant. Psychrobacter strain ENNN9_III was isolated from water in a polluted temperate estuarine system, contaminated with hydrocarbons and heavy metals. The genome has a G + C content of 42.7%, 2618 open reading frames (ORFs), three copies of the rRNAs operon, and 29 tRNA genes. Twenty-five sequences related to the degradation of aromatic compounds were predicted, as well as numerous genes related to resistance to metals or metal(loid)s. The genome sequence of Psychrobacter strain ENNN9_III provides the groundwork for further elucidation of the mechanisms of metal resistance and aromatic compounds degradation. Future studies are needed to confirm the usefulness of this strain for bioremediation proposes.
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Pylro VS, Roesch LFW, Ortega JM, do Amaral AM, Tótola MR, Hirsch PR, Rosado AS, Góes-Neto A, da Costa da Silva AL, Rosa CA, Morais DK, Andreote FD, Duarte GF, de Melo IS, Seldin L, Lambais MR, Hungria M, Peixoto RS, Kruger RH, Tsai SM, Azevedo V. Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects. Microb Ecol 2014; 67:237-241. [PMID: 24173537 DOI: 10.1007/s00248-013-0302-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/27/2013] [Indexed: 06/02/2023]
Abstract
The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.
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Affiliation(s)
- Victor Satler Pylro
- Microbiology Department, Federal University of Vicosa, Vicosa, Minas Gerais, 365700-000, Brazil,
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Marinotti O, Cerqueira GC, de Almeida LGP, Ferro MIT, Loreto ELDS, Zaha A, Teixeira SMR, Wespiser AR, Almeida E Silva A, Schlindwein AD, Pacheco ACL, Silva ALDCD, Graveley BR, Walenz BP, Lima BDA, Ribeiro CAG, Nunes-Silva CG, de Carvalho CR, Soares CMDA, de Menezes CBA, Matiolli C, Caffrey D, Araújo DAM, de Oliveira DM, Golenbock D, Grisard EC, Fantinatti-Garboggini F, de Carvalho FM, Barcellos FG, Prosdocimi F, May G, Azevedo Junior GMD, Guimarães GM, Goldman GH, Padilha IQM, Batista JDS, Ferro JA, Ribeiro JMC, Fietto JLR, Dabbas KM, Cerdeira L, Agnez-Lima LF, Brocchi M, de Carvalho MO, Teixeira MDM, Diniz Maia MDM, Goldman MHS, Cruz Schneider MP, Felipe MSS, Hungria M, Nicolás MF, Pereira M, Montes MA, Cantão ME, Vincentz M, Rafael MS, Silverman N, Stoco PH, Souza RC, Vicentini R, Gazzinelli RT, Neves RDO, Silva R, Astolfi-Filho S, Maciel TEF, Urményi TP, Tadei WP, Camargo EP, de Vasconcelos ATR. The genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic Acids Res 2013; 41:7387-400. [PMID: 23761445 PMCID: PMC3753621 DOI: 10.1093/nar/gkt484] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector–human and vector–parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi.
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Affiliation(s)
- Osvaldo Marinotti
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA, Institute of Technology, Broad Institute of Harvard and Massachusetts, Cambridge, MA 02141, USA, Laboratório de Bioinformática do Laboratório Nacional de Computação Científica, Petrópolis, RJ 25651-075, Brasil, Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP -Universidade Estadual Paulista, SP 14884-900, Brasil, Departamento de Biologia, Universidade Federal de Santa Maria, Santa Maria, RS 97105-900, Brasil, Departamento de Biologia Molecular e Biotecnologia, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brasil, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270901, Brasil, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA, Laboratório de Entomologia Médica IPEPATRO/FIOCRUZ, Porto Velho, RO 76812-245, Brasil, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900, Brasil, Centro de Ciências da Saúde, Universidade Estadual do Ceará, Fortaleza, CE 62042-280, Brasil, Departamento de Ciências Biológicas, Campus Senador Helvídio Nunes de Barros, Universidade Federal do Piauí, Picos, PI 60740-000, Brasil, Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA 66075-900, Brasil, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA, Informatics, The J. Craig Venter Institute, Medical Center Drive, Rockville, MD 20850, USA, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brasil, Departamento de Genética e Melhoramento, Universidade Federal de Viçosa, MG 36570-000, Brasil, Centro de Apoio Mul
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Pérez Chaparro PJ, McCulloch JA, Cerdeira LT, Al-Dilaimi A, Canto de Sá LL, de Oliveira R, Tauch A, de Carvalho Azevedo VA, Cruz Schneider MP, da Silva ALDC. Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads. J Microbiol Methods 2011; 87:208-12. [PMID: 21871929 DOI: 10.1016/j.mimet.2011.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 08/04/2011] [Accepted: 08/08/2011] [Indexed: 10/17/2022]
Abstract
Multiple Displacement Amplification (MDA) of DNA using φ29 (phi29) DNA polymerase amplifies DNA several billion-fold, which has proved to be potentially very useful for evaluating genome information in a culture-independent manner. Whole genome sequencing using DNA from a single prokaryotic genome copy amplified by MDA has not yet been achieved due to the formation of chimeras and skewed amplification of genomic regions during the MDA step, which then precludes genome assembly. We have hereby addressed the issue by using 10 ng of genomic Vibrio cholerae DNA extracted within an agarose plug to ensure circularity as a starting point for MDA and then sequencing the amplified yield using the SOLiD platform. We successfully managed to assemble the entire genome of V. cholerae strain LMA3984-4 (environmental O1 strain isolated in urban Amazonia) using a hybrid de novo assembly strategy. Using our method, only 178 out of 16,713 (1%) of contigs were not able to be inserted into either chromosome scaffold, and out of these 178, only 3 appeared to be chimeras. The other contigs seem to be the result of template-independent non-specific amplification during MDA, yielding spurious reads. Extraction of genomic DNA within an agarose plug in order to ensure circularity of the extracted genome might be key to minimizing amplification bias by MDA for WGS.
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Affiliation(s)
- Paula Juliana Pérez Chaparro
- Laboratório de Polimorfismo do DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
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Barile KADS, Silva ALDCD, Xavier JN, Assumpção MB, Corvelo TCDO. Characterization of 23S rRNA domain V mutations in gastric biopsy patients from the eastern Amazon. Mem Inst Oswaldo Cruz 2010; 105:314-7. [PMID: 20512246 DOI: 10.1590/s0074-02762010000300012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 03/05/2010] [Indexed: 01/25/2023] Open
Abstract
Resistance of Helicobacter pylori to clarithromycin is characterised by simple point mutations in the 23S ribosomal RNA (rRNA) gene and is responsible for the majority of cases of failure to eradicate this bacterium. In this paper, we characterised the variability of the 23S rRNA gene in biopsies of patients with gastric pathologies in the eastern Amazon (Northern Region of Brazil) using PCR and sequencing. A total of 49 sequences of H. pylori strains were analysed and of those, 75.6% presented nucleotide substitutions: A2142G (3.3%), T2182C (12.9%), G2224A (6.45%), T2215C (61.3%), A2192G (3.3%), G2204C (6.4%) and T2221C (6.4%). Of the mutations identified, four are known mutations related to cases of resistance and 16.1% are not yet described, revealing a high prevalence of mutations in the H. pylori 23S rRNA gene among the strains circulating in the in the eastern Amazon. The high prevalence in individuals with gastric pathologies in the Northern Region of Brazil demonstrates the need for characterising the profile of these strains to provide correct therapy for patients, considering that mutations in this gene are normally associated with resistance to the primary medication used in controlling H. pylori infection.
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de Arruda MP, Gonçalves EC, Schneider MPC, da Silva ALDC, Morielle-Versute E. An alternative genotyping method using dye-labeled universal primer to reduce unspecific amplifications. Mol Biol Rep 2009; 37:2031-6. [PMID: 19642013 DOI: 10.1007/s11033-009-9655-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [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: 04/28/2009] [Accepted: 07/21/2009] [Indexed: 11/26/2022]
Abstract
We proposed a modification the procedure of genotyping based in labeled universal primer and tailed primer. In the standard protocol, three primers are used in the same PCR reaction, a forward primer with tail added at the 5' end of the identical sequence to labeled universal primer with dye-fluorescent and a reverse primer. Unfortunately, the choice of a labeled primer characterized by a large number of complementary sequences in target genomes (which is more probable in larger genomes) result in unspecific amplifications (false positive) can cause absence or decrease amplification of the locus of interest and also false interpretation of the analysis. However, identification of possible homologies between the primer chosen for labelling and the genome is rarely possible from the available DNA data bases. In our approach, cycling is interrupted for the addition of the labeled primer only during the final cycles, thus minimizing unspecific amplification and competition between primers, resulting in the more fidelity amplification of the target regions.
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Affiliation(s)
- Maurício Papa de Arruda
- Laboratório de Chiroptera/Departamento de Zoologia e Botânica, Universidade Estadual Paulista (UNESP), Campus S.J. Rio Preto, São Paulo, Brazil.
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