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Article ; Online: Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.

Ferreira, Renata C / Rodrigues, Camila R / Broach, James R / Briones, Marcelo R S

International journal of molecular sciences

2024 Volume 25, Issue 7

Abstract: The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals ... ...

Abstract	The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
MeSH term(s)	Humans ; Animals ; Neanderthals/genetics ; Genome, Mitochondrial ; Mutation ; Alzheimer Disease ; Nucleotides
Chemical Substances	Nucleotides
Language	English
Publishing date	2024-03-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25073785
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Article ; Online: The epitranscriptome of Vero cells infected with SARS-CoV-2 assessed by direct RNA sequencing reveals m6A pattern changes and DRACH motif biases in viral and cellular RNAs.

Campos, João H C / Alves, Gustavo V / Maricato, Juliana T / Braconi, Carla T / Antoneli, Fernando M / Janini, Luiz Mario R / Briones, Marcelo R S

Frontiers in cellular and infection microbiology

2022 Volume 12, Page(s) 906578

Abstract: The epitranscriptomics of the SARS-CoV-2 infected cell reveals its response to viral replication. Among various types of RNA nucleotide modifications, the m6A is the most common and is involved in several crucial processes of RNA intracellular location, ... ...

Abstract	The epitranscriptomics of the SARS-CoV-2 infected cell reveals its response to viral replication. Among various types of RNA nucleotide modifications, the m6A is the most common and is involved in several crucial processes of RNA intracellular location, maturation, half-life and translatability. This epitranscriptome contains a mixture of viral RNAs and cellular transcripts. In a previous study we presented the analysis of the SARS-CoV-2 RNA m6A methylation based on direct RNA sequencing and characterized DRACH motif mutations in different viral lineages. Here we present the analysis of the m6A transcript methylation of Vero cells (derived from African Green Monkeys) and Calu-3 cells (human) upon infection by SARS-CoV-2 using direct RNA sequencing data. Analysis of these data by nonparametric statistics and two computational methods (m6anet and EpiNano) show that m6A levels are higher in RNAs of infected cells. Functional enrichment analysis reveals increased m6A methylation of transcripts involved in translation, peptide and amine metabolism. This analysis allowed the identification of differentially methylated transcripts and m6A unique sites in the infected cell transcripts. Results here presented indicate that the cell response to viral infection not only changes the levels of mRNAs, as previously shown, but also its epitranscriptional pattern. Also, transcriptome-wide analysis shows strong nucleotide biases in DRACH motifs of cellular transcripts, both in Vero and Calu-3 cells, which use the signature GGACU whereas in viral RNAs the signature is GAACU. We hypothesize that the differences of DRACH motif biases, might force the convergent evolution of the viral genome resulting in better adaptation to target sequence preferences of writer, reader and eraser enzymes. To our knowledge, this is the first report on m6A epitranscriptome of the SARS-CoV-2 infected Vero cells by direct RNA sequencing, which is the
MeSH term(s)	Animals ; Bias ; COVID-19 ; Chlorocebus aethiops ; Humans ; Nucleotides ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Sequence Analysis, RNA ; Vero Cells
Chemical Substances	Nucleotides ; RNA, Viral
Language	English
Publishing date	2022-08-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2022.906578
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Article ; Online: Whole-genome analysis of monozygotic Brazilian twins discordant for type 1 narcolepsy: a case report.

Campos, João H C / Aguilar, Ana C R / Antoneli, Fernando / Truzzi, Giselle / Briones, Marcelo R S / Ferreira, Renata C / Coelho, Fernando M S

BMC neurology

2022 Volume 22, Issue 1, Page(s) 439

Abstract: Background: Narcolepsy type 1 (NT1) is a rare and chronic neurological disease characterized by sudden sleep attacks, overwhelming daytime drowsiness, and cataplexy. When associated with a sudden loss of muscle tone (cataplexy) narcolepsy is classified ... ...

Abstract	Background: Narcolepsy type 1 (NT1) is a rare and chronic neurological disease characterized by sudden sleep attacks, overwhelming daytime drowsiness, and cataplexy. When associated with a sudden loss of muscle tone (cataplexy) narcolepsy is classified as type 1, while the absence of cataplexy indicates type 2. Genetic, degenerative, and immunological hypotheses to explain the pathophysiology of NT1 are still a matter of debate. To contribute to the understanding of NT1 genetic basis, here we describe, for the first time, a whole genome analysis of a monozygotic twin pair discordant for NT1. Case presentation: We present the case of a pair of 17-year-old male, monozygotic twins discordant for NT1. The affected twin had Epworth Sleepiness Scale (ESS) of 20 (can range from 0 to 24), cataplexy, hypnagogic hallucinations, polysomnography without abnormalities, multiple sleep latency tests (MSLT) positive for narcolepsy, a mean sleep latency of 3 min, sleep-onset REM periods SOREMPs of 5, presence of allele HLA-DQB106:02, and Hypocretin-1 level of zero pg/mL (normal values are > 200 pg/mL). The other twin had no narcolepsy symptoms (ESS of 4), normal polysomnography, MSLT without abnormalities, presence of allele HLA-DQB106:02, and Hypocretin-1 level of 396,74 pg/mL. To describe the genetic background for the NT1 discordant manifestations in this case, we present the whole-genome analysis of this monozygotic twin pair. The whole-genome comparison revealed that both twins have identical NT1 pathogenic mutations in known genes, such as HLA-DQB106:02:01, HLA-DRB111:01:02/15:03:01. The affected twin has the expected clinical manifestation while the unaffected twin has an unexpected phenotype. The unaffected twin has significantly more frameshift mutations as compared to the affected twin (108 versus 75) and mutations that affect stop codons (61 versus 5 in stop gain, 26 versus 2 in start lost). Conclusions:* The differences observed in frameshift and stop codon mutations in the unaffected twin are consistent with loss-of-function effects and protective alleles, that are almost always associated with loss-of-function rare alleles. Also, overrepresentation analysis of genes containing variants with potential clinical relevance in the unaffected twin shows that most mutations are in genes related to immune regulation function, Golgi apparatus, MHC, and olfactory receptor. These observations support the hypothesis that NT1 has an immunological basis although protective mutations in non-HLA alleles might interfere with the expression of the NT1 phenotype and consequently, with the clinical manifestation of the disease.
MeSH term(s)	Male ; Humans ; Cataplexy ; Orexins ; Brazil ; Narcolepsy/diagnosis ; Narcolepsy/genetics ; Polysomnography
Chemical Substances	Orexins
Language	English
Publishing date	2022-11-18
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2041347-6
ISSN	1471-2377 ; 1471-2377
ISSN (online)	1471-2377
ISSN	1471-2377
DOI	10.1186/s12883-022-02921-w
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Article: Evidence for Mitochondrial Genome Methylation in the Yeast

Bartelli, Thais F / Bruno, Danielle C F / Briones, Marcelo R S

Frontiers in genetics

2018 Volume 9, Page(s) 166

Abstract: The commensal ... ...

Abstract	The commensal yeast
Language	English
Publishing date	2018-05-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2018.00166
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Article: Whole-Genome Sequences and Annotation of the Opportunistic Pathogen

Bartelli, Thais Fernanda / Bruno, Danielle do Carmo Ferreira / Briones, Marcelo R S

Genome announcements

2018 Volume 6, Issue 5

Abstract: The genetic variability of the opportunistic ... ...

Abstract	The genetic variability of the opportunistic pathogen
Language	English
Publishing date	2018-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2704277-7
ISSN	2169-8287
ISSN	2169-8287
DOI	10.1128/genomeA.01475-17
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Article ; Online: Genome Sequence of a Staphylococcus epidermidis Strain (GTH12) Associated with Candida albicans SC5314 Cultured under Hypoxia at 37°C in Glycerol for 12 Weeks.

Bruno, Danielle do Carmo Ferreira / Bartelli, Thais Fernanda / Briones, Marcelo R S

Genome announcements

2018 Volume 6, Issue 25

Abstract: Polymicrobial infections with mixed-species biofilms are important health problems because of increased antimicrobial resistance and worse patient outcomes than with monomicrobial infections. Here, we present the whole-genome sequence ... ...

Abstract	Polymicrobial infections with mixed-species biofilms are important health problems because of increased antimicrobial resistance and worse patient outcomes than with monomicrobial infections. Here, we present the whole-genome sequence of
Language	English
Publishing date	2018-06-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2704277-7
ISSN	2169-8287 ; 2169-8287
ISSN (online)	2169-8287
ISSN	2169-8287
DOI	10.1128/genomeA.00533-18
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Article ; Online: A Kolmogorov-Smirnov test for the molecular clock based on Bayesian ensembles of phylogenies.

Antoneli, Fernando / Passos, Fernando M / Lopes, Luciano R / Briones, Marcelo R S

PloS one

2018 Volume 13, Issue 1, Page(s) e0190826

Abstract: Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a ... ...

Abstract	Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter λ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides a gain of power.
MeSH term(s)	Animals ; Ascomycota/classification ; Ascomycota/genetics ; Bayes Theorem ; Computer Simulation ; Cyclooxygenase 1/genetics ; DNA/genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Products, env/genetics ; Humans ; Lentivirus/classification ; Lentivirus/genetics ; Models, Genetic ; Phylogeny ; Poisson Distribution ; Primates/classification ; Primates/genetics ; Proteins/genetics ; Statistics, Nonparametric ; Time Factors
Chemical Substances	Gene Products, env ; Proteins ; DNA (9007-49-2) ; Cyclooxygenase 1 (EC 1.14.99.1)
Language	English
Publishing date	2018
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0190826
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Article ; Online: Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants.

Campos, João H C / Maricato, Juliana T / Braconi, Carla T / Antoneli, Fernando / Janini, Luiz Mario R / Briones, Marcelo R S

Viruses

2021 Volume 13, Issue 11

Abstract: The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, ... ...

Abstract	The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the
MeSH term(s)	3' Untranslated Regions ; Adenosine/analogs & derivatives ; Adenosine/metabolism ; Animals ; COVID-19/virology ; Chlorocebus aethiops ; Genome, Viral ; Humans ; Immune Evasion/genetics ; Methylation ; Nanopore Sequencing/methods ; Open Reading Frames ; RNA, Viral/metabolism ; SARS-CoV-2/genetics ; Sequence Analysis, RNA/methods ; Vero Cells
Chemical Substances	3' Untranslated Regions ; RNA, Viral ; N-methyladenosine (CLE6G00625) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2021-10-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112108
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Article: Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants

Campos, João H. C. / Maricato, Juliana T. / Braconi, Carla T. / Antoneli, Fernando / Janini, Luiz Mario R. / Briones, Marcelo R. S.

Viruses. 2021 Oct. 20, v. 13, no. 11

2021

Abstract	The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the N⁶-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced thus far are, in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because the incorporation of dNTPs hides RNA base modifications. Here, we present an initial exploration of Nanopore direct RNA sequencing to assess the m6A residues in the SARS-CoV-2 sequences of ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10 and the 3′-untranslated region. We identified fifteen m6A methylated positions, of which, six are in ORF N. Additionally, because m6A is associated with the DRACH motif, we compared its distribution in major SARS-CoV-2 variants. Although DRACH is highly conserved among variants, we show that variants Beta and Eta have a fourth position C > U change in DRACH at 28,884b that could affect methylation. This is the first report of direct RNA sequencing of a Brazilian SARS-CoV-2 sample coupled with the identification of modified bases.
Keywords	COVID-19 infection ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; etiological agents ; immune response ; methylation ; nanopores ; nucleobases ; viral genome
Language	English
Dates of publication	2021-1020
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112108
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks.

Antoneli, Fernando / Ferreira, Renata C / Briones, Marcelo R S

Mathematical biosciences

2016 Volume 276, Page(s) 82–100

Abstract: Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by ...

Abstract	Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model. We illustrate our framework with some simple examples of single-gene system and network motifs.
MeSH term(s)	Animals ; Gene Expression/genetics ; Gene Regulatory Networks/genetics ; Humans ; Models, Genetic
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126-5
ISSN	1879-3134 ; 0025-5564
ISSN (online)	1879-3134
ISSN	0025-5564
DOI	10.1016/j.mbs.2016.03.008
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