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  1. Article ; Online: Bacterial diversity and prevalence of antibiotic resistance genes in the oral microbiome.

    Almeida, Viviane de Sousa Moreira / Azevedo, Jailton / Leal, Helena Ferreira / Queiroz, Artur Trancoso Lopo de / da Silva Filho, Hermes Pedreira / Reis, Joice Neves

    PloS one

    2020  Volume 15, Issue 9, Page(s) e0239664

    Abstract: Objectives: This study aims to describe the oral microbiome diversity and prevalence of ARGs in periodontal health and disease.: Background: The human oral cavity harbors a complex microbial community known as the oral microbiome. These organisms are ...

    Abstract Objectives: This study aims to describe the oral microbiome diversity and prevalence of ARGs in periodontal health and disease.
    Background: The human oral cavity harbors a complex microbial community known as the oral microbiome. These organisms are regularly exposed to selective pressures, such as the usage of antibiotics, which drive evolution and acquisition of antibiotic resistance genes (ARGs). Resistance among oral bacteria jeopardizes not only antibiotic therapy for oral infections, but also extra-oral infections caused by bacterial translocation.
    Methods: We carried out a cross-sectional investigation. Saliva and subgingival plaque samples were collected during a clinical exam. 16S rRNA gene sequencing was performed to assess microbial diversity. Resistance genes were identified through PCR assays.
    Results: Of the 110 participants, only 22.7% had healthy periodontium, while the majority was diagnosed with gingivitis (55.4%) and chronic periodontitis (21.8%). The composition of the oral microbiota differed from healthy and diseased samples, being Streptococcus spp. and Rothia spp. predominant in periodontal disease. Regarding ARGs, 80 (72.7%) samples were positive for at least one of genes screened, erm being the most frequent variant (58.2%), followed by blaTEM (16.4%), mecA (2.7%), pbp2b and aac(6 ') (1.8%). Neither genes coding resistance to carbapenems nor metronidazole were detected.
    Conclusions: Our findings indicate that there are no significant differences in terms of taxonomic enrichment between healthy and diseased oral microbiomes. However, samples retrieved from healthy patients had a more diverse microbial community, whereas diseased samples have lower taxonomic diversity. We have also identified clinically relevant ARGs, providing baseline information to guide antibiotic prescription in dentistry.
    MeSH term(s) Adolescent ; Adult ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacterial Proteins/genetics ; Cross-Sectional Studies ; Dental Plaque/microbiology ; Dental Plaque/pathology ; Drug Resistance, Bacterial/genetics ; Female ; Gingivitis/diagnosis ; Gingivitis/microbiology ; Humans ; Male ; Microbiota ; Middle Aged ; Mouth/microbiology ; Periodontitis/diagnosis ; Periodontitis/microbiology ; Periodontium/pathology ; RNA, Ribosomal, 16S/chemistry ; RNA, Ribosomal, 16S/metabolism ; Saliva/microbiology ; Streptococcus/genetics ; Streptococcus/isolation & purification ; Young Adult
    Chemical Substances Bacterial Proteins ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2020-09-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0239664
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The sound of silent RNA in tuberculosis and the lncRNA role on infection.

    Rocha, Eduardo Fukutani / Vinhaes, Caian Leal / Araújo-Pereira, Mariana / Mota, Tiago Feitosa / Gupte, Akshay N / Kumar, Nathella Pavan / Arriaga, Maria Belen / Sterling, Timothy R / Babu, Subash / Gaikwad, Sanjay / Karyakarte, Rajesh / Mave, Vidya / Kulkarni, Vandana / Paradkar, Mandar / Viswanathan, Vijay / Kornfeld, Hardy / Gupta, Amita / Andrade, Bruno Bezerril / Queiroz, Artur Trancoso Lopo de

    iScience

    2023  Volume 27, Issue 1, Page(s) 108662

    Abstract: Tuberculosis (TB) is one of the leading causes of death worldwide, and Diabetes Mellitus is one of the major comorbidities (TB/DM) associated with the disease. A total of 103 differentially expressed ncRNAs have been identified in the TB and TB/DM ... ...

    Abstract Tuberculosis (TB) is one of the leading causes of death worldwide, and Diabetes Mellitus is one of the major comorbidities (TB/DM) associated with the disease. A total of 103 differentially expressed ncRNAs have been identified in the TB and TB/DM comparisons. A machine learning algorithm was employed to identify the most informative lncRNAs: ADM-DT, LINC02009, LINC02471, SOX2-OT, and GK-AS1. These lncRNAs presented substantial accuracy in classifying TB from HC (AUCs >0.85) and TB/DM from HC (AUCs >0.90) in the other three countries. Genes with significant correlations with the five lncRNAs enriched common pathways in Brazil and India for both TB and TB/DM. This suggests that lncRNAs play an important role in the regulation of genes related to the TB immune response.
    Language English
    Publishing date 2023-12-08
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.108662
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Selective Suppression of Cellular Immunity and Increased Cytotoxicity in Skin Lesions of Disseminated Leishmaniasis Uncovered by Transcriptome-Wide Analysis.

    Ramos, Pablo Ivan Pereira / Cristal, Juqueline Rocha / Khouri, Ricardo / Boaventura, Viviane / Azevedo, Lucas Gentil / Correia, Thaizza Cavalcante / Sharma, Rohit / Cardoso, Cristina R de Barros / Pinzan, Camila Figueiredo / de Noronha, Almério Libório Lopes / Van Weyenbergh, Johan / Queiroz, Artur Trancoso Lopo de / de Oliveira, Camila I / Barral-Netto, Manoel / Barral, Aldina

    The Journal of investigative dermatology

    2021  Volume 141, Issue 10, Page(s) 2542–2546.e5

    MeSH term(s) Humans ; Immunity, Cellular ; Leishmaniasis, Cutaneous/immunology ; Leishmaniasis, Cutaneous/pathology ; Skin/pathology ; Th1 Cells/immunology ; Th2 Cells/immunology ; Transcriptome
    Language English
    Publishing date 2021-04-03
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 80136-7
    ISSN 1523-1747 ; 0022-202X
    ISSN (online) 1523-1747
    ISSN 0022-202X
    DOI 10.1016/j.jid.2021.03.017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Follow up of a robust meta-signature to identify Zika virus infection in Aedes aegypti: another brick in the wall.

    Fukutani, Eduardo / Rodrigues, Moreno / Kasprzykowski, José Irahe / Araujo, Cintia Figueiredo de / Paschoal, Alexandre Rossi / Ramos, Pablo Ivan Pereira / Fukutani, Kiyoshi Ferreira / Queiroz, Artur Trancoso Lopo de

    Memorias do Instituto Oswaldo Cruz

    2018  Volume 113, Issue 6, Page(s) e180053

    Abstract: The mosquito Aedes aegypti is the main vector of several arthropod-borne diseases that have global impacts. In a previous meta-analysis, our group identified a vector gene set containing 110 genes strongly associated with infections of dengue, West Nile ... ...

    Abstract The mosquito Aedes aegypti is the main vector of several arthropod-borne diseases that have global impacts. In a previous meta-analysis, our group identified a vector gene set containing 110 genes strongly associated with infections of dengue, West Nile and yellow fever viruses. Of these 110 genes, four genes allowed a highly accurate classification of infected status. More recently, a new study of Ae. aegypti infected with Zika virus (ZIKV) was published, providing new data to investigate whether this "infection" gene set is also altered during a ZIKV infection. Our hypothesis is that the infection-associated signature may also serve as a proxy to classify the ZIKV infection in the vector. Raw data associated with the NCBI/BioProject were downloaded and re-analysed. A total of 18 paired-end replicates corresponding to three ZIKV-infected samples and three controls were included in this study. The nMDS technique with a logistic regression was used to obtain the probabilities of belonging to a given class. Thus, to compare both gene sets, we used the area under the curve and performed a comparison using the bootstrap method. Our meta-signature was able to separate the infected mosquitoes from the controls with good predictive power to classify the Zika-infected mosquitoes.
    MeSH term(s) Aedes/virology ; Animals ; Mosquito Vectors/virology ; Transcriptome ; Zika Virus/genetics ; Zika Virus/isolation & purification ; Zika Virus Infection/transmission
    Language English
    Publishing date 2018-05-28
    Publishing country Brazil
    Document type Journal Article
    ZDB-ID 953293-6
    ISSN 1678-8060 ; 0074-0276
    ISSN (online) 1678-8060
    ISSN 0074-0276
    DOI 10.1590/0074-02760180053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Description of microsporidia in simulids: molecular and morphological characterization of microsporidia in the larvae of Simulium pertinax Kollar (Diptera: Simuliidae).

    Carvalho, Isabel Maria Vicente Guedes de / Queiroz, Artur Trancoso Lopo de / Moraes, Rosiane Brito de / Gil, Helio Benites / Alves, Rafael / Viviani, Andréa de Barros Pinto / Becnel, James John / Araujo-Coutinho, Carlos José Pereira da Cunha de

    Revista da Sociedade Brasileira de Medicina Tropical

    2015  Volume 47, Issue 5, Page(s) 624–631

    Abstract: Introduction: Microsporidia constitute the most common black fly pathogens, although the species' diversity, seasonal occurrence and transmission mechanisms remain poorly understood. Infections by this agent are often chronic and non-lethal, but they ... ...

    Abstract Introduction: Microsporidia constitute the most common black fly pathogens, although the species' diversity, seasonal occurrence and transmission mechanisms remain poorly understood. Infections by this agent are often chronic and non-lethal, but they can cause reduced fecundity and decreased longevity. The objective of this study was to identify microsporidia infecting Simulium (Chirostilbia) pertinax (Kollar, 1832) larvae from Caraguatatuba, State of São Paulo, Brazil, by molecular and morphological characterization.
    Methods: Larvae were collected at a single point in a stream in a rural area of the city and were kept under artificial aeration until analysis. Polydispyrenia spp. infection was characterized by the presence of at least 32 mononuclear spores measuring 6.9 ± 1.0 × 5.0 ± 0.7 µm in persistent sporophorous vesicles. Similarly, Amblyospora spp. were characterized by the presence of eight uninucleate spores measuring 4.5 × 3.5 µm in sporophorous vesicles.
    Results: The molecular analysis confirmed the presence of microsporidian DNA in the 8 samples (prevalence of 0.51%). Six samples (Brazilian larvae) were related to Polydispyrenia simulii and Caudospora palustris reference sequences but in separate clusters. One sample was clustered with Amblyospora spp. Edhazardia aedis was the positive control taxon.
    Conclusions: Samples identified as Polydispyrenia spp. and Amblyospora spp. were grouped with P. simulii and Amblyospora spp., respectively, corroborating previous results. However, the 16S gene tree showed a considerable distance between the black fly-infecting Amblyospora spp. and the mosquito-infecting spp. This distance suggests that these two groups are not congeneric. Additional genomic region evaluation is necessary to obtain a coherent phylogeny for this group.
    MeSH term(s) Animals ; Larva/microbiology ; Microsporidia/classification ; Microsporidia/genetics ; Microsporidia/isolation & purification ; Phylogeny ; Polymerase Chain Reaction ; Seasons ; Simuliidae/classification ; Simuliidae/microbiology
    Language English
    Publishing date 2015-01-20
    Publishing country Brazil
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1038126-0
    ISSN 1678-9849 ; 0037-8682
    ISSN (online) 1678-9849
    ISSN 0037-8682
    DOI 10.1590/0037-8682-0165-2014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil.

    Queiroz, Artur Trancoso Lopo de / Santos, Luciane Amorim / Moreau, Domingos Ramon / Oliveira, Tulio de / Watkins, David I / Galvão-Castro, Bernardo / Alcantara, Luiz Carlos Junior

    The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases

    2007  Volume 11, Issue 1, Page(s) 27–30

    Abstract: Genetic analysis of HIV-1 is essential to improve treatment strategies and select epitopes for vaccine programs. The objective of this study was to determine whether known CD4+ and CD8+ epitopes were present in Brazilian HIV-1 strains. We used previously ...

    Abstract Genetic analysis of HIV-1 is essential to improve treatment strategies and select epitopes for vaccine programs. The objective of this study was to determine whether known CD4+ and CD8+ epitopes were present in Brazilian HIV-1 strains. We used previously described CD8+ and CD4+ epitopes from the Los Alamos laboratory to search for these epitopes in the Brazilian sequences using the HIVbase program and we compared the frequency results with the analyses using physical-chemical profile tools from Network Protein Sequence Analysis (NPSA), and the SYFPEITHI program. Furthermore, this analysis was carried out with the Prosite tool using the GeneDoc program and ds/dn analyses using the Synonymous Nonsynonymous Analysis Program (SNAP). The HIVbase epitope mapping demonstrated that 30 CD8+ and 6 CD4+ epitopes were present in the Brazilian sequences at a high frequency. Only two of these epitopes were heavily glycosylated. Interestingly, ds/dn analyses showed evidence of purifying selective pressure. These types of analyses could be useful for the assessment of possible vaccine efficiency in populations.
    MeSH term(s) Brazil ; CD4-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/immunology ; Epitopes/genetics ; Gene Products, env/genetics ; HIV Infections/virology ; HIV-1/classification ; HIV-1/genetics ; HIV-1/immunology ; Humans
    Chemical Substances Epitopes ; Gene Products, env
    Language English
    Publishing date 2007-05-15
    Publishing country Brazil
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041400-6
    ISSN 1678-4391 ; 1413-8670
    ISSN (online) 1678-4391
    ISSN 1413-8670
    DOI 10.1590/s1413-86702007000100008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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