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Campos LRS, Trefflich S, Morais DAA, Imparato DO, Chagas VS, Albanus RD, Dalmolin RJS, Castro MAA. Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses. Mol Biol Evol 2024; 41:msae019. [PMID: 38306290 PMCID: PMC10873778 DOI: 10.1093/molbev/msae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. In this study, we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analyses. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.
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Affiliation(s)
- Leonardo R S Campos
- Bioinformatics Multidisciplinary Environment–BioME, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Sheyla Trefflich
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment–BioME, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Danilo O Imparato
- Bioinformatics Multidisciplinary Environment–BioME, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Vinicius S Chagas
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | | | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment–BioME, IMD, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Biochemistry, CB, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
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2
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Zhang R, Zeng M, Zhang X, Zheng Y, Lv N, Wang L, Gan J, Li Y, Jiang X, Yang L. Therapeutic Candidates for Alzheimer's Disease: Saponins. Int J Mol Sci 2023; 24:10505. [PMID: 37445682 DOI: 10.3390/ijms241310505] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Drug development for Alzheimer's disease, the leading cause of dementia, has been a long-standing challenge. Saponins, which are steroid or triterpenoid glycosides with various pharmacological activities, have displayed therapeutic potential in treating Alzheimer's disease. In a comprehensive review of the literature from May 2007 to May 2023, we identified 63 references involving 40 different types of saponins that have been studied for their effects on Alzheimer's disease. These studies suggest that saponins have the potential to ameliorate Alzheimer's disease by reducing amyloid beta peptide deposition, inhibiting tau phosphorylation, modulating oxidative stress, reducing inflammation, and antiapoptosis. Most intriguingly, ginsenoside Rg1 and pseudoginsenoside-F11 possess these important pharmacological properties and show the best promise for the treatment of Alzheimer's disease. This review provides a summary and classification of common saponins that have been studied for their therapeutic potential in Alzheimer's disease, showcasing their underlying mechanisms. This highlights the promising potential of saponins for the treatment of Alzheimer's disease.
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Affiliation(s)
- Ruifeng Zhang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Miao Zeng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaolu Zhang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yujia Zheng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Nuan Lv
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Luming Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jiali Gan
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yawen Li
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xijuan Jiang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin Yang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
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3
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de Souza ID, Reis CF, Morais DAA, Fernandes VGS, Cavalcante JVF, Dalmolin RJS. Ancestry analysis indicates two different sets of essential genes in eukaryotic model species. Funct Integr Genomics 2021; 21:523-531. [PMID: 34279742 DOI: 10.1007/s10142-021-00794-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 11/28/2022]
Abstract
Essential genes are so-called because they are crucial for organism perpetuation. Those genes are usually related to essential functions to cellular metabolism or multicellular homeostasis. Deleterious alterations on essential genes produce a spectrum of phenotypes in multicellular organisms. The effects range from the impairment of the fertilization process, disruption of fetal development, to loss of reproductive capacity. Essential genes are described as more evolutionarily conserved than non-essential genes. However, there is no consensus about the relationship between gene essentiality and gene age. Here, we identified essential genes in five model eukaryotic species (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus) and estimate their evolutionary ancestry and their network properties. We observed that essential genes, on average, are older than other genes in all species investigated. The relationship of network properties and gene essentiality convey with previous findings, showing essential genes as important nodes in biological networks. As expected, we also observed that essential orthologs shared by the five species evaluated here are old. However, all the species evaluated here have a specific set of young essential genes not shared among them. Additionally, these two groups of essential genes are involved with distinct biological functions, suggesting two sets of essential genes: (i) a set of old essential genes common to all the evaluated species, regulating basic cellular functions, and (ii) a set of young essential genes exclusive to each species, which perform specific essential functions in each species.
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Affiliation(s)
- Iara D de Souza
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Clovis F Reis
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Vítor G S Fernandes
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - João Vitor F Cavalcante
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil
| | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande Do Norte, Av. Odilon Gomes de Lima, 1722, Capim Macio, Natal, RN, 59078-400, Brazil. .,Department of Biochemistry - CB, Federal University of Rio Grande Do Norte, Campus Universitário UFRN, Lagoa Nova, Natal, RN, 59078-970, Brazil.
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4
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Viscardi LH, Imparato DO, Bortolini MC, Dalmolin RJS. Ionotropic Receptors as a Driving Force behind Human Synapse Establishment. Mol Biol Evol 2021; 38:735-744. [PMID: 32986821 PMCID: PMC7947827 DOI: 10.1093/molbev/msaa252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The origin of nervous systems is a main theme in biology and its mechanisms are largely underlied by synaptic neurotransmission. One problem to explain synapse establishment is that synaptic orthologs are present in multiple aneural organisms. We questioned how the interactions among these elements evolved and to what extent it relates to our understanding of the nervous systems complexity. We identified the human neurotransmission gene network based on genes present in GABAergic, glutamatergic, serotonergic, dopaminergic, and cholinergic systems. The network comprises 321 human genes, 83 of which act exclusively in the nervous system. We reconstructed the evolutionary scenario of synapse emergence by looking for synaptic orthologs in 476 eukaryotes. The Human–Cnidaria common ancestor displayed a massive emergence of neuroexclusive genes, mainly ionotropic receptors, which might have been crucial to the evolution of synapses. Very few synaptic genes had their origin after the Human–Cnidaria common ancestor. We also identified a higher abundance of synaptic proteins in vertebrates, which suggests an increase in the synaptic network complexity of those organisms.
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Affiliation(s)
- Lucas Henriques Viscardi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Danilo Oliveira Imparato
- Bioinformatics Multidisciplinary Environment-BioME, IMD, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment-BioME, IMD, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Department of Biochemistry, CB, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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5
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Wei Z, Nie G, Yang F, Pi S, Wang C, Cao H, Guo X, Liu P, Li G, Hu G, Zhang C. Inhibition of ROS/NLRP3/Caspase-1 mediated pyroptosis attenuates cadmium-induced apoptosis in duck renal tubular epithelial cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 273:115919. [PMID: 33497945 DOI: 10.1016/j.envpol.2020.115919] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) is an occupational and environmental pollutant, which mainly causes nephrotoxicity by damaging renal proximal tubular cells. To evaluate the effects of Cd on pyroptosis and the relationship between pyroptosis and apoptosis in duck renal tubular epithelial cells, the cells were cultured with 3CdSO4·8H2O (0, 2.5, 5.0, or 10.0 μM Cd), N-acetyl-L-cysteine (NAC) (100.0 μM), Z-YVAD-FMK (10.0 μM) or the combination of Cd and NAC or Z-YVAD-FMK for 12 h, and then cytotoxicity was assessed. The results evidenced that Cd significantly increased the releases of interleukin-18 (IL-18) and interleukin-1β (IL-1β), lactate dehydrogenase (LDH) and nitric oxide (NO), relative conductivity and cellular reactive oxygen species (ROS) level. Simultaneously, Cd also markedly upregulated NLRP3, Caspase-1, ASC, NEK7, IL-1β and IL-18 mRNA levels and NLRP3, Caspase-1 p20, GSDMD and ASC protein levels. Additionally, NAC notably improved the changes of above indicators induced by Cd. Combined treatment with Cd and Z-YVAD-FMK remarkably elevated Bcl-2 mRNA and protein levels, inhibited p53, Bax, Bak-1, Cyt C, Caspase-9 and Caspase-3 mRNA levels and p53, Bax, Bak-1, Caspase-9/cleaved Caspase-9 and Caspase-3/cleaved Caspase-3 protein levels, increased mitochondrial membrane potential (MMP), decreased apoptosis ratio and cell damage compared to treatment with Cd alone. Taken together, Cd exposure induces duck renal tubular epithelial cell pyroptosis through ROS/NLRP3/Caspase-1 signaling pathway, and inhibiting Caspase-1 dependent pyroptosis attenuates Cd-induced apoptosis.
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Affiliation(s)
- Zejing Wei
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Gaohui Nie
- School of Information Technology, Jiangxi University of Finance and Economics, No. 665 Yuping West Street, Economic and Technological Development District, Nanchang, 330032, Jiangxi, PR China
| | - Fan Yang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Shaoxing Pi
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Chang Wang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Huabin Cao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Guyue Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China
| | - Caiying Zhang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Economic and Technological Development District, Nanchang, 330045, Jiangxi, PR China.
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6
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Wang Y, Lai L, Guo W, Peng S, Liu R, Hong P, Wei G, Li F, Jiang S, Wang P, Li J, Lei H, Zhao W, Xu S. Inhibition of Ku70 in a high-glucose environment aggravates bupivacaine-induced dorsal root ganglion neurotoxicity. Toxicol Lett 2020; 318:104-113. [DOI: 10.1016/j.toxlet.2019.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022]
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7
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Trefflich S, Dalmolin RJS, Ortega JM, Castro MAA. Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194472. [PMID: 31825805 DOI: 10.1016/j.bbagrm.2019.194472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/06/2019] [Accepted: 11/30/2019] [Indexed: 01/06/2023]
Abstract
Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity, TFs are highly conserved and recognize the same DNA sequences in different organisms. One of the main factors that confer regulatory specificity is the distribution of the binding sites of the TFs along the genome, allowing the configuration of different transcriptional regulatory networks (TRNs) from the same regulator. A similar scenario occurs between tissues of the same organism, where a TRN can be rewired by epigenetic factors, modulating the accessibility of the TF to its binding sites. In this article we discuss concepts that can help to formulate testable hypotheses about the construction of regulons, exploring the presence and absence of the elements that form a TRN throughout the evolution of an ancestral lineage. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Sheyla Trefflich
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil
| | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - José Miguel Ortega
- Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba 81520-260, Brazil.
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8
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Oliveira RADC, de Andrade AS, Imparato DO, de Lima JGS, de Almeida RVM, Lima JPMS, Pasquali MADB, Dalmolin RJS. Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants. Sci Rep 2019; 9:15741. [PMID: 31673065 PMCID: PMC6823369 DOI: 10.1038/s41598-019-52299-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 08/16/2019] [Indexed: 12/14/2022] Open
Abstract
Reactive oxygen species (ROS) are byproducts of aerobic metabolism and may cause oxidative damage to biomolecules. Plants have a complex redox system, involving enzymatic and non-enzymatic compounds. The evolutionary origin of enzymatic antioxidant defense in plants is yet unclear. Here, we describe the redox gene network for A. thaliana and investigate the evolutionary origin of this network. We gathered from public repositories 246 A. thaliana genes directly involved with ROS metabolism and proposed an A. thaliana redox gene network. Using orthology information of 238 Eukaryotes from STRINGdb, we inferred the evolutionary root of each gene to reconstruct the evolutionary history of A. thaliana antioxidant gene network. We found two interconnected clusters: one formed by SOD-related, Thiol-redox, peroxidases, and other oxido-reductase; and the other formed entirely by class III peroxidases. Each cluster emerged in different periods of evolution: the cluster formed by SOD-related, Thiol-redox, peroxidases, and other oxido-reductase emerged before opisthokonta-plant divergence; the cluster composed by class III peroxidases emerged after opisthokonta-plant divergence and therefore contained the most recent network components. According to our results, class III peroxidases are in expansion throughout plant evolution, with new orthologs emerging in each evaluated plant clade divergence.
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Affiliation(s)
- Raffael Azevedo de Carvalho Oliveira
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal, Brazil.,Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Abraão Silveira de Andrade
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Danilo Oliveira Imparato
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | - João Paulo Matos Santos Lima
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal, Brazil.,Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Matheus Augusto de Bittencourt Pasquali
- Institute of Tropical Medicine, Federal University of Rio Grande do Norte, Natal, Brazil.,Food Engineering Unit, UAEALI, UFCG, Campina Grande, Brazil.,Graduate Program in Natural Resources, PPGRN, UFCG, Campina Grande, Brazil
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment - IMD, Federal University of Rio Grande do Norte, Natal, Brazil. .,Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil.
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9
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Ali H, Galal O, Urata Y, Goto S, Guo CY, Luo L, Abdelrahim E, Ono Y, Mostafa E, Li TS. The potential benefits of nicaraven to protect against radiation-induced injury in hematopoietic stem/progenitor cells with relative low dose exposures. Biochem Biophys Res Commun 2014; 452:548-53. [DOI: 10.1016/j.bbrc.2014.08.112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/21/2014] [Indexed: 12/01/2022]
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10
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Ferreira RM, Rybarczyk-Filho JL, Dalmolin RJS, Castro MAA, Moreira JCF, Brunnet LG, de Almeida RMC. Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PLoS One 2013; 8:e56579. [PMID: 23468868 PMCID: PMC3582557 DOI: 10.1371/journal.pone.0056579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 01/14/2013] [Indexed: 12/31/2022] Open
Abstract
Whole genome protein-protein association networks are not random and their topological properties stem from genome evolution mechanisms. In fact, more connected, but less clustered proteins are related to genes that, in general, present more paralogs as compared to other genes, indicating frequent previous gene duplication episodes. On the other hand, genes related to conserved biological functions present few or no paralogs and yield proteins that are highly connected and clustered. These general network characteristics must have an evolutionary explanation. Considering data from STRING database, we present here experimental evidence that, more than not being scale free, protein degree distributions of organisms present an increased probability for high degree nodes. Furthermore, based on this experimental evidence, we propose a simulation model for genome evolution, where genes in a network are either acquired de novo using a preferential attachment rule, or duplicated with a probability that linearly grows with gene degree and decreases with its clustering coefficient. For the first time a model yields results that simultaneously describe different topological distributions. Also, this model correctly predicts that, to produce protein-protein association networks with number of links and number of nodes in the observed range for Eukaryotes, it is necessary 90% of gene duplication and 10% of de novo gene acquisition. This scenario implies a universal mechanism for genome evolution.
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Affiliation(s)
- Ricardo M. Ferreira
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Rodrigo J. S. Dalmolin
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mauro A. A. Castro
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- National Institute of Science and Technology for Complex Systems, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - José C. F. Moreira
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Leonardo G. Brunnet
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rita M. C. de Almeida
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- National Institute of Science and Technology for Complex Systems, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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11
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Overlooking evolution: a systematic analysis of cancer relapse and therapeutic resistance research. PLoS One 2011; 6:e26100. [PMID: 22125594 PMCID: PMC3219640 DOI: 10.1371/journal.pone.0026100] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 09/19/2011] [Indexed: 01/06/2023] Open
Abstract
Cancer therapy selects for cancer cells resistant to treatment, a process that is fundamentally evolutionary. To what extent, however, is the evolutionary perspective employed in research on therapeutic resistance and relapse? We analyzed 6,228 papers on therapeutic resistance and/or relapse in cancers and found that the use of evolution terms in abstracts has remained at about 1% since the 1980s. However, detailed coding of 22 recent papers revealed a higher proportion of papers using evolutionary methods or evolutionary theory, although this number is still less than 10%. Despite the fact that relapse and therapeutic resistance is essentially an evolutionary process, it appears that this framework has not permeated research. This represents an unrealized opportunity for advances in research on therapeutic resistance.
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12
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Dalmolin RJS, Castro MAA, Rybarczyk Filho JL, Souza LHT, de Almeida RMC, Moreira JCF. Evolutionary plasticity determination by orthologous groups distribution. Biol Direct 2011; 6:22. [PMID: 21586164 PMCID: PMC3117832 DOI: 10.1186/1745-6150-6-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 05/17/2011] [Indexed: 12/29/2022] Open
Abstract
Background Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution of gene families in non-exclusively closely related species can provide insights on how plastic or how conserved a given gene family is. Here, we analyze the abundance and diversity of all Eukaryotic Clusters of Orthologous Groups (KOG) present in STRING database, resulting in a total of 4,850 KOGs. This dataset comprises 481,421 proteins distributed among 55 eukaryotes. Results We propose an index to evaluate the evolutionary plasticity and conservation of an orthologous group based on its abundance and diversity across eukaryotes. To further KOG plasticity analysis, we estimate the evolutionary distance average among all proteins which take part in the same orthologous group. As a result, we found a strong correlation between the evolutionary distance average and the proposed evolutionary plasticity index. Additionally, we found low evolutionary plasticity in Saccharomyces cerevisiae genes associated with inviability and Mus musculus genes associated with early lethality. At last, we plot the evolutionary plasticity value in different gene networks from yeast and humans. As a result, it was possible to discriminate among higher and lower plastic areas of the gene networks analyzed. Conclusions The distribution of gene families brings valuable information on evolutionary plasticity which might be related with genetic plasticity. Accordingly, it is possible to discriminate among conserved and plastic orthologous groups by evaluating their abundance and diversity across eukaryotes. Reviewers This article was reviewed by Prof Manyuan Long, Hiroyuki Toh, and Sebastien Halary.
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Affiliation(s)
- Rodrigo J S Dalmolin
- Department of Biochemistry, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Rio Grande do Sul, Brazil.
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13
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Nowick K, Stubbs L. Lineage-specific transcription factors and the evolution of gene regulatory networks. Brief Funct Genomics 2010; 9:65-78. [PMID: 20081217 DOI: 10.1093/bfgp/elp056] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nature is replete with examples of diverse cell types, tissues and body plans, forming very different creatures from genomes with similar gene complements. However, while the genes and the structures of proteins they encode can be highly conserved, the production of those proteins in specific cell types and at specific developmental time points might differ considerably between species. A full understanding of the factors that orchestrate gene expression will be essential to fully understand evolutionary variety. Transcription factor (TF) proteins, which form gene regulatory networks (GRNs) to act in cooperative or competitive partnerships to regulate gene expression, are key components of these unique regulatory programs. Although many TFs are conserved in structure and function, certain classes of TFs display extensive levels of species diversity. In this review, we highlight families of TFs that have expanded through gene duplication events to create species-unique repertoires in different evolutionary lineages. We discuss how the hierarchical structures of GRNs allow for flexible small to large-scale phenotypic changes. We survey evidence that explains how newly evolved TFs may be integrated into an existing GRN and how molecular changes in TFs might impact the GRNs. Finally, we review examples of traits that evolved due to lineage-specific TFs and species differences in GRNs.
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Affiliation(s)
- Katja Nowick
- Department of Cell and Developmental Biology, Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Drive, Urbana, IL 61802, USA
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Castro MAA, Filho JLR, Dalmolin RJS, Sinigaglia M, Moreira JCF, Mombach JCM, de Almeida RMC. ViaComplex: software for landscape analysis of gene expression networks in genomic context. ACTA ACUST UNITED AC 2009; 25:1468-9. [PMID: 19369498 DOI: 10.1093/bioinformatics/btp246] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867, 2007; Nucleic Acids Res., 36, 6269-6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm. AVAILABILITY (http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex).
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Affiliation(s)
- Mauro A A Castro
- Unidade de Bioinformática, Departamento de Bioquímica, Instituto de Física, Núcleo de Bioinformática, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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