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  1. Article ; Online: Non-coding regulatory sRNAs from bacteria of the Burkholderia cepacia complex.

    Matos, Gonçalo R / Feliciano, Joana R / Leitão, Jorge H

    Applied microbiology and biotechnology

    2024  Volume 108, Issue 1, Page(s) 280

    Abstract: Small non-coding RNAs (sRNAs) are key regulators of post-transcriptional gene expression in bacteria. Hundreds of sRNAs have been found using in silico genome analysis and experimentally based approaches in bacteria of the Burkholderia cepacia complex ( ... ...

    Abstract Small non-coding RNAs (sRNAs) are key regulators of post-transcriptional gene expression in bacteria. Hundreds of sRNAs have been found using in silico genome analysis and experimentally based approaches in bacteria of the Burkholderia cepacia complex (Bcc). However, and despite the hundreds of sRNAs identified so far, the number of functionally characterized sRNAs from these bacteria remains very limited. In this mini-review, we describe the general characteristics of sRNAs and the main mechanisms involved in their action as regulators of post-transcriptional gene expression, as well as the work done so far in the identification and characterization of sRNAs from Bcc. The number of functionally characterized sRNAs from Bcc is expected to increase and to add new knowledge on the biology of these bacteria, leading to novel therapeutic approaches to tackle the infections caused by these opportunistic pathogens, particularly severe among cystic fibrosis patients. KEY POINTS: •Hundreds of sRNAs have been identified in Burkholderia cepacia complex bacteria (Bcc). •A few sRNAs have been functionally characterized in Bcc. •Functionally characterized Bcc sRNAs play major roles in metabolism, biofilm formation, and virulence.
    MeSH term(s) Humans ; Bacteria ; Burkholderia cepacia complex/genetics ; Cystic Fibrosis ; Virulence
    Language English
    Publishing date 2024-04-02
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-024-13121-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2229: Show issues Location:
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  2. Article ; Online: Transnational Biographies, Cosmopolitanism and Police Reform

    Gonçalo R. Gonçalves

    Iberoamericana. América Latina - España - Portugal, Vol 17, Iss 64, Pp 35-

    Cristóvão Morais Sarmento and the Portuguese Police at the End of Nineteenth Century

    2017  Volume 55

    Abstract: This article relates the transnational biography of Christóvão Morais Sarmento, Police Commissioner in Lisbon between 1867 and 1906, to understand the role of cosmopolitanism in the reform of the Portuguese public security system and the functioning of ... ...

    Abstract This article relates the transnational biography of Christóvão Morais Sarmento, Police Commissioner in Lisbon between 1867 and 1906, to understand the role of cosmopolitanism in the reform of the Portuguese public security system and the functioning of Lisbon's police. The result of a transnational biographical experience – not only on their individual pathway but also on family ties – Morais Sarmento cosmopolitanism is an essential element to understand the changing contours of public security policies and building an organizational culture within the Portuguese police.
    Keywords Police ; Biography ; Cosmopolitanism ; Public security ; Portugal ; History of Portugal ; DP501-900.22 ; History of Spain ; DP1-402 ; Latin America. Spanish America ; F1201-3799 ; French literature - Italian literature - Spanish literature - Portuguese literature ; PQ1-3999 ; Social Sciences ; H
    Language English
    Publishing date 2017-03-01T00:00:00Z
    Publisher Iberoamericana / Vervuert
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: 2014 Curt Stern Award: Adventures in human genetics.

    Abecasis, Gonçalo R

    American journal of human genetics

    2015  Volume 96, Issue 3, Page(s) 363–366

    MeSH term(s) Awards and Prizes ; Cardiovascular Diseases/genetics ; Cholesterol, LDL/blood ; Genetic Loci ; Genetics, Medical/history ; Genome, Human ; History, 21st Century ; Humans ; Societies, Scientific
    Chemical Substances Cholesterol, LDL
    Language English
    Publishing date 2015-02-26
    Publishing country United States
    Document type Autobiography ; Historical Article ; Lecture ; Portrait ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1016/j.ajhg.2015.02.006
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  4. Book: Sequencing 10,000s of human genomes

    Abecasis, Gonçalo R

    analytical challenges and opportunities

    (Sayer lecture)

    2016  

    Abstract: CIT): Dr. Abecasis is a world-renowned leader in the design of computational and statistical tools for analyzing the increasingly large data sets produced by genetic and genomic studies. He has led large projects seeking to better understand the role of ...

    Institution National Institutes of Health (U.S.),
    Author's details Dr. Gonçalo R. Abecasis
    Series title Sayer lecture
    Abstract (CIT): Dr. Abecasis is a world-renowned leader in the design of computational and statistical tools for analyzing the increasingly large data sets produced by genetic and genomic studies. He has led large projects seeking to better understand the role of complex disease susceptibility genes associated with a range of common disorders from macular degeneration to cardiovascular disease.
    MeSH term(s) Macular Degeneration/genetics ; Genome, Human ; Genomics/methods ; Sequence Analysis
    Language English
    Size 1 online resource (1 streaming video file (1 hr., 7 min.)) :, color, sound.
    Document type Book
    Note Closed-captioned. ; Access restricted to HHS only.
    Database Catalogue of the US National Library of Medicine (NLM)

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  5. Article ; Online: Iododerma Mimicking Cutaneous Muir-Torre Syndrome in a Patient with Rectosigmoid Transition Cancer - Case Report.

    Kondo, Rogerio N / Petrus, Antônio C / Silva, Gonçalo R / de Medeiros, Rodrigo A / Faidiga, Mariana de Castro / Franco, Isadora / Nabut, Naja

    Indian journal of dermatology

    2023  Volume 68, Issue 5, Page(s) 589

    Language English
    Publishing date 2023-07-08
    Publishing country India
    Document type Journal Article
    ZDB-ID 416069-1
    ISSN 1998-3611 ; 0019-5154
    ISSN (online) 1998-3611
    ISSN 0019-5154
    DOI 10.4103/ijd.ijd_577_22
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  6. Article ; Online: Biological role of the bidirectional interaction between epithelial-mesenchymal transition and PD-L1 expression in head and neck squamous cell carcinomas: A systematic review.

    Morais, H-G / Costa, C-S / Gonçalo, R-I / Carlan, L-M / Morais, E-F / Galvão, H-C / Freitas, R-D

    Medicina oral, patologia oral y cirugia bucal

    2023  Volume 28, Issue 4, Page(s) e395–e403

    Abstract: Background: Squamous cell carcinoma (SCC) is the most common head and neck malignant neoplasm. Despite progress in antineoplastic treatment for SCC, there are still high morbidity and mortality rates. Over the years, several tumor biomarkers have been ... ...

    Abstract Background: Squamous cell carcinoma (SCC) is the most common head and neck malignant neoplasm. Despite progress in antineoplastic treatment for SCC, there are still high morbidity and mortality rates. Over the years, several tumor biomarkers have been suggested to predict the prognosis of patients with oral SCC. Studies point to a bidirectional association between the epithelial-mesenchymal transition (EMT) and the expression of PD-L1 with the aggressive biological behavior of the neoplastic cell. Thus, this systematic review aimed to explore the biological roles and mechanisms underlying the interaction between EMT and PD-L1 expression in head and neck SCC-derived cell lines.
    Material and methods: An electronic search was performed in the PubMed/Medline, Web of Science, Science Direct, Scopus, Embase, and Cochrane Collaboration Library databases. Articles evaluating the in vitro relationship between EMT/PD-L1 interaction and the biological behavior of head and neck SCC cell lines were selected for this systematic review. The quality of evidence was assessed using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) criteria.
    Results: After applying the previously established inclusion/exclusion criteria, 9 articles were included in the qualitative synthesis. The present systematic review suggests the existence of a bidirectional interaction between EMT and PD-L1 expression, which is related to alterations in the cell cycle, proliferation, apoptosis, and cell survival, affecting the migration and invasion ability of tumor cells.
    Conclusions: Combined targeting of the two pathways may be potentially effective for immunotherapy in head and neck SCC.
    MeSH term(s) Humans ; Squamous Cell Carcinoma of Head and Neck ; Epithelial-Mesenchymal Transition ; B7-H1 Antigen ; Carcinoma, Squamous Cell/pathology ; Head and Neck Neoplasms
    Chemical Substances B7-H1 Antigen
    Language English
    Publishing date 2023-07-01
    Publishing country Spain
    Document type Systematic Review ; Journal Article
    ZDB-ID 2171573-7
    ISSN 1698-6946 ; 1698-4447
    ISSN (online) 1698-6946
    ISSN 1698-4447
    DOI 10.4317/medoral.25810
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    Zs.A 5809: Show issues Location:
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  7. Book ; Online: Differentiable Causal Discovery Under Latent Interventions

    Faria, Gonçalo R. A. / Martins, André F. T. / Figueiredo, Mário A. T.

    2022  

    Abstract: Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and ... ...

    Abstract Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, \textit{i.e.}, interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.
    Keywords Computer Science - Machine Learning ; Statistics - Methodology
    Subject code 006
    Publishing date 2022-03-04
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Genotype Imputation from Large Reference Panels.

    Das, Sayantan / Abecasis, Gonçalo R / Browning, Brian L

    Annual review of genomics and human genetics

    2018  Volume 19, Page(s) 73–96

    Abstract: Genotype imputation has become a standard tool in genome-wide association studies because it enables researchers to inexpensively approximate whole-genome sequence data from genome-wide single-nucleotide polymorphism array data. Genotype imputation ... ...

    Abstract Genotype imputation has become a standard tool in genome-wide association studies because it enables researchers to inexpensively approximate whole-genome sequence data from genome-wide single-nucleotide polymorphism array data. Genotype imputation increases statistical power, facilitates fine mapping of causal variants, and plays a key role in meta-analyses of genome-wide association studies. Only variants that were previously observed in a reference panel of sequenced individuals can be imputed. However, the rapid increase in the number of deeply sequenced individuals will soon make it possible to assemble enormous reference panels that greatly increase the number of imputable variants. In this review, we present an overview of genotype imputation and describe the computational techniques that make it possible to impute genotypes from reference panels with millions of individuals.
    MeSH term(s) Computer Simulation ; Genome-Wide Association Study/methods ; Genotype ; Humans ; Models, Genetic ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2018-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2037670-4
    ISSN 1545-293X ; 1527-8204
    ISSN (online) 1545-293X
    ISSN 1527-8204
    DOI 10.1146/annurev-genom-083117-021602
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  9. Article ; Online: On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes.

    Pinto, Daniela / Gonçalo, Raquel / Louro, Mariana / Silva, Marta Sousa / Hernandez, Guillem / Cordeiro, Tiago N / Cordeiro, Carlos / São-José, Carlos

    Microbiology spectrum

    2022  Volume 10, Issue 4, Page(s) e0103722

    Abstract: Bacteriophages (phages) and other viruses are extremely efficient in packing their genetic information, with several described cases of overlapping genes encoded in different open reading frames (ORFs). While less frequently reported, specific cases ... ...

    Abstract Bacteriophages (phages) and other viruses are extremely efficient in packing their genetic information, with several described cases of overlapping genes encoded in different open reading frames (ORFs). While less frequently reported, specific cases exist in which two overlapping ORFs are in frame and share the stop codon. Here, we studied the occurrence of this genetic arrangement in endolysins, the phage enzymes that cut the bacterial cell wall peptidoglycan to release the virion progeny. After screening over 3,000 endolysin sequences of phages infecting Gram-positive bacteria, we found evidence that this coding strategy is frequent in endolysin genes. Our bioinformatics predictions were experimentally validated by demonstrating that two polypeptides are indeed produced from these genes. Additionally, we show that in some cases the two polypeptides need to interact and multimerize to generate the active endolysin. By studying in detail one selected example, we uncovered a heteromeric endolysin with a 1:5 subunit stoichiometry that has never been described before. Hence, we conclude that the occurrence of endolysin genes encoding two polypeptide isoforms by in-frame overlapping ORFs, as well as their organization as enzymatic complexes, appears more common than previously thought, therefore challenging the established view of endolysins being mostly formed by single, monomeric polypeptide chains.
    MeSH term(s) Bacteria ; Bacteriophages/genetics ; Cell Wall ; Endopeptidases/chemistry ; Endopeptidases/genetics ; Peptidoglycan
    Chemical Substances Peptidoglycan ; Endopeptidases (EC 3.4.-) ; endolysin (EC 3.4.99.-)
    Language English
    Publishing date 2022-07-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.01037-22
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  10. Article ; Online: Mendelian Randomization Study of ACLY and Cardiovascular Disease.

    Damask, Amy / Paulding, Charles / Baras, Aris / Carey, David / Abecasis, Goncalo R

    The New England journal of medicine

    2020  Volume 383, Issue 7, Page(s) e50

    MeSH term(s) Cardiovascular Diseases ; Genetic Predisposition to Disease ; Humans ; Mendelian Randomization Analysis
    Language English
    Publishing date 2020-07-08
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc1908496
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