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F. Souza L, B. de B. Pereira H, M. da Rocha Filho T, A. S. Machado B, A. Moret M. New distance measure for comparing protein using cellular automata image. PLoS One 2023; 18:e0287880. [PMID: 37796771 PMCID: PMC10553295 DOI: 10.1371/journal.pone.0287880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023] Open
Abstract
One of the first steps in protein sequence analysis is comparing sequences to look for similarities. We propose an information theoretical distance to compare cellular automata representing protein sequences, and determine similarities. Our approach relies in a stationary Hamming distance for the evolution of the automata according to a properly chosen rule, and to build a pairwise similarity matrix and determine common ancestors among different species in a simpler and less computationally demanding computer codes when compared to other methods.
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Affiliation(s)
- Luryane F. Souza
- Centro de Ciências Exatas e das Tecnologias, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brazil
- Programa de Modelagem Computacional e Tecnologia Industrial, SENAI-CIMATEC, Salvador, Bahia, Brazil
| | - Hernane B. de B. Pereira
- Programa de Modelagem Computacional e Tecnologia Industrial, SENAI-CIMATEC, Salvador, Bahia, Brazil
- DEDC, UNEB, Salvador, Bahia, Brazil
| | | | - Bruna A. S. Machado
- Programa de Modelagem Computacional e Tecnologia Industrial, SENAI-CIMATEC, Salvador, Bahia, Brazil
| | - Marcelo A. Moret
- Programa de Modelagem Computacional e Tecnologia Industrial, SENAI-CIMATEC, Salvador, Bahia, Brazil
- DCET, UNEB, Salvador, Bahia, Brazil
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2
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Cao J. Functional Divergence of the N-Lobe and C-Lobe of Transferrin Gene in Pungitius sinensis (Amur Stickleback). Animals (Basel) 2022; 12:ani12243458. [PMID: 36552378 PMCID: PMC9774405 DOI: 10.3390/ani12243458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Transferrin is an important iron-binding glycosylated protein and plays key roles in iron-binding and immune response. Here, a 2037-bp open reading frame was obtained from our previous transcriptome sequencing data of Amur stickleback, which encoded a 679 amino acid putative transferrin protein harbored obvious N-lobe and C-lobe domains. The tissue-specific expression pattern showed that the transcript was detected in a variety of tissues, with the highest signal in liver. Moreover, Streptococcus iniae pathogen stimulation can increase the expression level of this transcript, implying important immune properties for organisms. Next, N-lobes and C-lobes were obtained from 45 fish species. The phylogenetic tree showed that N-lobes and C-lobes were in two different evolutionary branches, and they had different motif composition. Functional divergence indicated a higher evolutionary rate or site-specific alteration among the N-lobe and C-lobe groups. Ka/Ks value of C-lobe group was relatively higher than that of N-lobe group, indicating a faster change rate of C-lobe sequences in evolution. Moreover, some sites experiencing positive selection were also found, which may be involved in the iron- or anion-binding, pathogen resistance and diversification of transferrin protein. Differential iron-binding activity was also detected between N-lobe and C-lobe of Amur stickleback transferrin protein with Chrome Azurol S assay. Compared with the C-lobe, the N-lobe showed stronger growth inhibitory activity of Escherichia coli, implying their potential antibacterial properties. This study will give a reference for subsequent research of transferrin proteins.
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Affiliation(s)
- Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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3
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Host–Pathogen Interactions of Marine Gram-Positive Bacteria. BIOLOGY 2022; 11:biology11091316. [PMID: 36138795 PMCID: PMC9495620 DOI: 10.3390/biology11091316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Complex interactions between marine Gram-positive pathogens and fish hosts in the marine environment can result in diseases of economically important finfish, which cause economic losses in the aquaculture industry. Understanding how these pathogens interact with the fish host and generate disease will contribute to efficient prophylactic measures and treatments. To our knowledge, there are no systematic reviews on marine Gram-positive pathogens. Therefore, here we reviewed the host–pathogen interactions of marine Gram-positive pathogens from the pathogen-centric and host-centric points of view. Abstract Marine Gram-positive bacterial pathogens, including Renibacterium salmoninarum, Mycobacterium marinum, Nocardia seriolae, Lactococcus garvieae, and Streptococcus spp. cause economic losses in marine fish aquaculture worldwide. Comprehensive information on these pathogens and their dynamic interactions with their respective fish–host systems are critical to developing effective prophylactic measures and treatments. While much is known about bacterial virulence and fish immune response, it is necessary to synthesize the knowledge in terms of host–pathogen interactions as a centerpiece to establish a crucial connection between the intricate details of marine Gram-positive pathogens and their fish hosts. Therefore, this review provides a holistic view and discusses the different stages of the host–pathogen interactions of marine Gram-positive pathogens. Gram-positive pathogens can invade fish tissues, evade the fish defenses, proliferate in the host system, and modulate the fish immune response. Marine Gram-positive pathogens have a unique set of virulence factors that facilitate adhesion (e.g., adhesins, hemagglutination activity, sortase, and capsules), invasion (e.g., toxins, hemolysins/cytolysins, the type VII secretion system, and immune-suppressive proteins), evasion (e.g., free radical quenching, actin-based motility, and the inhibition of phagolysosomal fusion), and proliferation and survival (e.g., heme utilization and siderophore-mediated iron acquisition systems) in the fish host. After infection, the fish host initiates specific innate and adaptive immune responses according to the extracellular or intracellular mechanism of infection. Although efforts have continued to be made in understanding the complex interplay at the host–pathogen interface, integrated omics-based investigations targeting host–pathogen–marine environment interactions hold promise for future research.
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Carmona-Salido H, Fouz B, Sanjuán E, Carda M, Delannoy CMJ, García-González N, González-Candelas F, Amaro C. The widespread presence of a family of fish virulence plasmids in Vibrio vulnificus stresses its relevance as a zoonotic pathogen linked to fish farms. Emerg Microbes Infect 2021; 10:2128-2140. [PMID: 34702148 PMCID: PMC8635547 DOI: 10.1080/22221751.2021.1999177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Vibrio vulnificus is a pathogen of public health concern that causes either primary septicemia after ingestion of raw shellfish or secondary septicemia after wound exposure to seawater. In consequence, shellfish and seawater are considered its main reservoirs. However, there is one aspect of its biology that is systematically overlooked: its association with fish in its natural environment. This association led in 1975 to the emergence of a zoonotic clade within phylogenetic lineage 2 following successive outbreaks of vibriosis in farmed eels. Although this clade is now worldwide distributed, no new zoonotic clades were subsequently reported. In this work, we have performed phylogenetic, genomic and functional studies to show that other zoonotic clades are in fact present in 4 of the 5 lineages of the species. Further, we associate these clades, most of them previously but incompletely described, with the acquisition of a family of fish virulence plasmids containing genes essential for resistance to the immune system of certain teleosts of interest in aquaculture. Consequently, our results provide several pieces of evidence about the importance of this species as a zoonotic agent linked to fish farms, as well as on the relevance of these artificial environments acting as drivers that accelerate the evolution of the species.
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Affiliation(s)
- Héctor Carmona-Salido
- Departamento de Microbiología y Ecología, & Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València. Burjassot, Valencia, Spain
| | - Belén Fouz
- Departamento de Microbiología y Ecología, & Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València. Burjassot, Valencia, Spain
| | - Eva Sanjuán
- Departamento de Microbiología y Ecología, & Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València. Burjassot, Valencia, Spain
| | - Miguel Carda
- Departamento de Microbiología y Ecología, & Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València. Burjassot, Valencia, Spain
| | | | - Neris García-González
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology I2SysBio (UV-CSIC), Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology I2SysBio (UV-CSIC), Valencia, Spain.,CIBER in Epidemiology and Public Health, Madrid, Spain
| | - Carmen Amaro
- Departamento de Microbiología y Ecología, & Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València. Burjassot, Valencia, Spain
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Mu Z, Yu T, Liu X, Zheng H, Wei L, Liu J. FEGS: a novel feature extraction model for protein sequences and its applications. BMC Bioinformatics 2021; 22:297. [PMID: 34078264 PMCID: PMC8172329 DOI: 10.1186/s12859-021-04223-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 05/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Feature extraction of protein sequences is widely used in various research areas related to protein analysis, such as protein similarity analysis and prediction of protein functions or interactions. RESULTS In this study, we introduce FEGS (Feature Extraction based on Graphical and Statistical features), a novel feature extraction model of protein sequences, by developing a new technique for graphical representation of protein sequences based on the physicochemical properties of amino acids and effectively employing the statistical features of protein sequences. By fusing the graphical and statistical features, FEGS transforms a protein sequence into a 578-dimensional numerical vector. When FEGS is applied to phylogenetic analysis on five protein sequence data sets, its performance is notably better than all of the other compared methods. CONCLUSION The FEGS method is carefully designed, which is practically powerful for extracting features of protein sequences. The current version of FEGS is developed to be user-friendly and is expected to play a crucial role in the related studies of protein sequence analyses.
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Affiliation(s)
- Zengchao Mu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Ting Yu
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, China
| | - Xiaoping Liu
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Beijing, China
| | - Hongyu Zheng
- Department of Radiation Oncology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Leyi Wei
- School of Software, Shandong University, Jinan, China.
| | - Juntao Liu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China.
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Mapping sequence to feature vector using numerical representation of codons targeted to amino acids for alignment-free sequence analysis. Gene 2020; 766:145096. [PMID: 32919006 DOI: 10.1016/j.gene.2020.145096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/16/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022]
Abstract
The phylogenetic analysis based on sequence similarity targeted to real biological taxa is one of the major challenging tasks. In this paper, we propose a novel alignment-free method, CoFASA (Codon Feature based Amino acid Sequence Analyser), for similarity analysis of nucleotide sequences. At first, we assign numerical weights to the four nucleotides. We then calculate a score of each codon based on the numerical value of the constituent nucleotides, termed as degree of codons. Accordingly, we obtain the degree of each amino acid based on the degree of codons targeted towards a specific amino acid. Utilizing the degree of twenty amino acids and their relative abundance within a given sequence, we generate 20-dimensional features for every coding DNA sequence or protein sequence. We use the features for performing phylogenetic analysis of the set of candidate sequences. We use multiple protein sequences derived from Beta-globin (BG), NADH dehydrogenase subunit 5 (ND5), Transferrins (TFs), Xylanases, low identity (<40%) and high identity (⩾40%) protein sequences (encompassing 533 and 1064 protein families) for experimental assessments. We compare our results with sixteen (16) well-known methods, including both alignment-based and alignment-free methods. Various assessment indices are used, such as the Pearson correlation coefficient, RF (Robinson-Foulds) distance and ROC score for performance analysis. While comparing the performance of CoFASA with alignment-based methods (ClustalW, ClustalΩ, MAFFT, and MUSCLE), it shows very similar results. Further, CoFASA shows better performance in comparison to well-known alignment-free methods, including LZW-Kernal, jD2Stat, FFP, spaced, and AFKS-D2s in predicting taxonomic relationship among candidate taxa. Overall, we observe that the features derived by CoFASA are very much useful in isolating the sequences according to their taxonomic labels. While our method is cost-effective, at the same time, produces consistent and satisfactory outcomes.
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Xin M, Vechtova P, Shaliutina-Kolesova A, Fussy Z, Loginov D, Dzyuba B, Linhart O, Boryshpolets S, Rodina M, Li P, Loginova Y, Sterba J. Transferrin Identification in Sterlet ( Acipenser ruthenus) Reproductive System. Animals (Basel) 2019; 9:ani9100753. [PMID: 31575042 PMCID: PMC6826671 DOI: 10.3390/ani9100753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 01/06/2023] Open
Abstract
Transferrins are a superfamily of iron-binding proteins and are recognized as multifunctional proteins. In the present study, transcriptomic and proteomic methods were used to identify transferrins in the reproductive organs and sperm of out-of-spawning and spermiating sterlet (Acipenser ruthenus) males. The results showed that seven transferrin transcripts were identified in the transcriptome of sterlet, and these transcripts were qualified as two different transferrin genes, serotransferrin and melanotransferrin, with several isoforms present for serotransferrin. The relative abundance of serotransferrin isoforms was higher in the kidneys and Wolffian ducts in the spermiating males compared to out-of-spawning males. In addition, transferrin was immunodetected in sterlet seminal plasma, but not in sterlet spermatozoa extract. Mass spectrometry identification of transferrin in seminal plasma but not in spermatozoa corroborates immunodetection. The identification of transferrin in the reproductive organs and seminal plasma of sterlet in this study provides the potential function of transferrin during sturgeon male reproduction.
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Affiliation(s)
- Miaomiao Xin
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
- Sino-Czech Joint Laboratory of Fish Conservation and Biotechnology: Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Pavlina Vechtova
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
- Biology Centre of Academy of Sciences of the Czech Republic, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.
| | - Anna Shaliutina-Kolesova
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Zoltan Fussy
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
| | - Dmitry Loginov
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
- Biology Centre of Academy of Sciences of the Czech Republic, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.
| | - Borys Dzyuba
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Otomar Linhart
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Serhii Boryshpolets
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Marek Rodina
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
| | - Ping Li
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Zatisi 728/II, 389 25 Vodnany, Czech Republic.
- Marine College, Shandong University (Weihai), Weihai 264209, Shandong, China.
| | - Yana Loginova
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
| | - Jan Sterba
- Institute of Chemistry, Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.
- Biology Centre of Academy of Sciences of the Czech Republic, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.
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Mu Z, Yu T, Qi E, Liu J, Li G. DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information. BMC Bioinformatics 2019; 20:351. [PMID: 31221087 PMCID: PMC6587251 DOI: 10.1186/s12859-019-2943-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/10/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on graphical representation is one of the most effective and efficient ways. However, most existing methods suffer limitations from their method design. RESULTS We introduce DCGR, a novel method for extracting features from protein sequences based on the chaos game representation, which is developed by constructing CGR curves of protein sequences according to physicochemical properties of amino acids, followed by converting the CGR curves into multi-dimensional feature vectors by using the distributions of points in CGR images. Tested on five data sets, DCGR was significantly superior to the state-of-the-art feature extraction methods. CONCLUSION The DCGR is practically powerful for extracting effective features from protein sequences, and therefore important in similarity analysis of protein sequences, study of protein-protein interactions and prediction of protein functions. It is freely available at https://sourceforge.net/projects/transcriptomeassembly/files/Feature%20Extraction .
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Affiliation(s)
- Zengchao Mu
- School of Mathematics, Shandong University, Jinan, 250100 Shandong Province China
| | - Ting Yu
- School of Mathematics, Shandong University, Jinan, 250100 Shandong Province China
| | - Enfeng Qi
- College of Mathematics and Statistics, Guangxi Normal University, Guilin, 541001 China
| | - Juntao Liu
- School of Mathematics, Shandong University, Jinan, 250100 Shandong Province China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100 Shandong Province China
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Saw AK, Raj G, Das M, Talukdar NC, Tripathy BC, Nandi S. Alignment-free method for DNA sequence clustering using Fuzzy integral similarity. Sci Rep 2019; 9:3753. [PMID: 30842590 PMCID: PMC6403383 DOI: 10.1038/s41598-019-40452-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/28/2019] [Indexed: 12/28/2022] Open
Abstract
A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence analysis algorithms. In this study, we developed an alignment-free algorithm for faster sequence analysis. The novelty of our approach is the inclusion of fuzzy integral with Markov chain for sequence analysis in the alignment-free model. The method estimate the parameters of a Markov chain by considering the frequencies of occurrence of all possible nucleotide pairs from each DNA sequence. These estimated Markov chain parameters were used to calculate similarity among all pairwise combinations of DNA sequences based on a fuzzy integral algorithm. This matrix is used as an input for the neighbor program in the PHYLIP package for phylogenetic tree construction. Our method was tested on eight benchmark datasets and on in-house generated datasets (18 s rDNA sequences from 11 arbuscular mycorrhizal fungi (AMF) and 16 s rDNA sequences of 40 bacterial isolates from plant interior). The results indicate that the fuzzy integral algorithm is an efficient and feasible alignment-free method for sequence analysis on the genomic scale.
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Affiliation(s)
- Ajay Kumar Saw
- Institute of Advanced Study in Science and Technology, Mathematical Sciences Division, Guwahati, 781035, India
| | - Garima Raj
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India
| | - Manashi Das
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India
| | - Narayan Chandra Talukdar
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India
| | | | - Soumyadeep Nandi
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India.
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Saw AK, Tripathy BC, Nandi S. Alignment-free similarity analysis for protein sequences based on fuzzy integral. Sci Rep 2019; 9:2775. [PMID: 30808983 PMCID: PMC6391537 DOI: 10.1038/s41598-019-39477-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
Sequence comparison is an essential part of modern molecular biology research. In this study, we estimated the parameters of Markov chain by considering the frequencies of occurrence of the all possible amino acid pairs from each alignment-free protein sequence. These estimated Markov chain parameters were used to calculate similarity between two protein sequences based on a fuzzy integral algorithm. For validation, our result was compared with both alignment-based (ClustalW) and alignment-free methods on six benchmark datasets. The results indicate that our developed algorithm has a better clustering performance for protein sequence comparison.
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Affiliation(s)
- Ajay Kumar Saw
- Institute of Advanced Study in Science and Technology, Mathematical Sciences Division, Guwahati, 781035, India
| | | | - Soumyadeep Nandi
- Institute of Advanced Study in Science and Technology, Life Science Division, Guwahati, 781035, India.
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Liu XL, Wang YK, Ouyang S, Zhu YY, Li W, Hong XY, Xu HY, Zhu XP. Evolutionary conservation of transferrin genomic organization and expression characterization in seven freshwater turtles. Biochem Biophys Res Commun 2018; 506:874-882. [PMID: 30392910 DOI: 10.1016/j.bbrc.2018.10.168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 01/28/2023]
Abstract
Serum transferrin (tf), encoding an iron-binding glycoprotein, has been revealed to play important roles in iron transportation and immune response, and it also has been demonstrated to be valuable for phylogenetic analysis in vertebrates. However, the evolutionary conservation, expression profiles and positive selection of transferrin genes among freshwater turtle species remain largely unclear. Here, the genomic DNA and coding sequences of transferrin genes were cloned and characterized in seven freshwater turtles including Mauremys mutica, Mauremys sinensis, Cyclemys dentate, Mauremyssi reevesi, Heosemys grandis, Trachemys scripta and Chrysemys picta. The isolated coding sequences of turtles' tf genes were 2118 bp or 2121 bp, encoding 706 or 707 amino acids. The predicted Tf proteins of turtles share high identities with M. mutica Tf, up to 91%-98% and the M. mutica Tf has the highest identity (91%) in amino acid with the Chelomia mydas Tf, the moderate with other reptiles' Tfs (65%-59%), chicken (58%), and Human Tf (∼55%), and the lowest with zebrafish Tf (41%). Additionally, tf genes were consistently composed of 17 exons and 16 introns with the same splicing sites in introns in all the turtles examined. Moreover, 12 positive selected sites were detected in these turtles' Tf and mainly distributed on the surface of transferrin protein. Importantly, it was found that transferrin genes in all turtles examined were predominantly expressed in adult liver via real-time quantitative PCR. The molecular characterizations and expression profiles of transferrin would shed new insights into understanding the conversations and divergences of transferrin genes in turtles, even in vertebrates.
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Affiliation(s)
- Xiao-Li Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Ya-Kun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Life Science, Nanchang University, Nanchang 330031, China
| | - Shu Ouyang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Yan-Yu Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xiao-You Hong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hong-Yan Xu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| | - Xin-Ping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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Identifying anticancer peptides by using a generalized chaos game representation. J Math Biol 2018; 78:441-463. [PMID: 30291366 DOI: 10.1007/s00285-018-1279-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 08/01/2018] [Indexed: 10/28/2022]
Abstract
We generalize chaos game representation (CGR) to higher dimensional spaces while maintaining its bijection, keeping such method sufficiently representative and mathematically rigorous compare to previous attempts. We first state and prove the asymptotic property of CGR and our generalized chaos game representation (GCGR) method. The prediction follows that the dissimilarity of sequences which possess identical subsequences but distinct positions would be lowered exponentially by the length of the identical subsequence; this effect was taking place unbeknownst to researchers. By shining a spotlight on it now, we show the effect fundamentally supports (G)CGR as a similarity measure or feature extraction technique. We develop two feature extraction techniques: GCGR-Centroid and GCGR-Variance. We use the GCGR-Centroid to analyze the similarity between protein sequences by using the datasets 9 ND5, 24 TF and 50 beta-globin proteins. We obtain consistent results compared with previous studies which proves the significance thereof. Finally, by utilizing support vector machines, we train the anticancer peptide prediction model by using both GCGR-Centroid and GCGR-Variance, and achieve a significantly higher prediction performance by employing the 3 well-studied anticancer peptide datasets.
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13
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Abstract
Advances in sequencing technologies led to rapid increase in the number and diversity of biological sequences, which facilitated development in the sequence research. In this paper, we present a new method for analyzing protein sequence similarity. We calculated the spectral radii of 20 amino acids (AAs) and put forward a novel 2-D graphical representation of protein sequences. To characterize protein sequences numerically, three groups of features were extracted and related to statistical, dynamics measurements and fluctuation complexity of the sequences. With the obtained feature vector, two models utilizing Gaussian Kernel similarity and Cosine similarity were built to measure the similarity between sequences. We applied our method to analyze the similarities/dissimilarities of four data sets. Both proposed models received consistent results with improvements when compared to that obtained by the ClustalW analysis. The novel approach we present in this study may therefore benefit protein research in medical and scientific fields.
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14
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Fu D, Bridle A, Leef M, Norte Dos Santos C, Nowak B. Hepatic expression of metal-related genes and gill histology in sand flathead (Platycephalus bassensis) from a metal contaminated estuary. MARINE ENVIRONMENTAL RESEARCH 2017; 131:80-89. [PMID: 28943068 DOI: 10.1016/j.marenvres.2017.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/12/2017] [Accepted: 09/16/2017] [Indexed: 06/07/2023]
Abstract
Hepatic gene expression and gill histology were measured in sand flathead (Platycephalus bassensis) from a metal polluted estuary. The gene expression analyses were conducted on fish from two most polluted sites and a reference site. The metal-related genes were metal-regulatory transcription factor 1 (MTF1), transferrin (TF), ferriportin1 (FPN1), ferritin and metallothionein. The transcripts of MTF1, TF, and FPN1 were significantly higher in the liver of fish caught at polluted sites, suggesting these genes are potential biomarkers for environmental exposure to metal. Strong correlations were found between the transcripts of these three genes. Four types of gill lesions such as hyperplasia and lamellar fusion, epitheliocystis, telangiectasis, and deformed filament were observed in sampled fish. There was significant difference in the prevalence of epitheliocystis and telangiectasis between the fish from the polluted areas and reference area. Gill parasites were less prevalent in the flathead from polluted sites. The gill histopathological results indicated both pollutants and infections could contribute to gill lesions.
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Affiliation(s)
- Dingkun Fu
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia.
| | - Andrew Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
| | - Melanie Leef
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
| | - Catarina Norte Dos Santos
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
| | - Barbara Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
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15
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Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix. Sci Rep 2017; 7:46237. [PMID: 28393857 PMCID: PMC5385872 DOI: 10.1038/srep46237] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/14/2017] [Indexed: 11/08/2022] Open
Abstract
We develop a novel position-feature-based model for protein sequences by employing physicochemical properties of 20 amino acids and the measure of graph energy. The method puts the emphasis on sequence order information and describes local dynamic distributions of sequences, from which one can get a characteristic B-vector. Afterwards, we apply the relative entropy to the sequences representing B-vectors to measure their similarity/dissimilarity. The numerical results obtained in this study show that the proposed methods leads to meaningful results compared with competitors such as Clustal W.
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16
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Xu C, Sun D, Liu S, Zhang Y. Protein sequence analysis by incorporating modified chaos game and physicochemical properties into Chou's general pseudo amino acid composition. J Theor Biol 2016; 406:105-15. [PMID: 27375218 DOI: 10.1016/j.jtbi.2016.06.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 06/17/2016] [Accepted: 06/25/2016] [Indexed: 11/27/2022]
Abstract
In this contribution we introduced a novel graphical method to compare protein sequences. By mapping a protein sequence into 3D space based on codons and physicochemical properties of 20 amino acids, we are able to get a unique P-vector from the 3D curve. This approach is consistent with wobble theory of amino acids. We compute the distance between sequences by their P-vectors to measure similarities/dissimilarities among protein sequences. Finally, we use our method to analyze four datasets and get better results compared with previous approaches.
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Affiliation(s)
- Chunrui Xu
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
| | - Dandan Sun
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
| | - Shenghui Liu
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai 264209, China.
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17
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El-Lakkani A, Lashin M. An efficient method for measuring the similarity of protein sequences. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2016; 27:363-370. [PMID: 27103219 DOI: 10.1080/1062936x.2016.1174735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/01/2016] [Indexed: 06/05/2023]
Abstract
An accurate numerical descriptor for protein sequence is introduced. It is basically a set of each three successive amino acids in the sequence (triplet), starting from left to right, in addition to the distances between each two successive amino acids in the triplet such that the summation of these distances does not exceed 8. This numerical descriptor combines two features the amino acid composition and the position of each amino acid relative to the other nearby amino acids. This numerical descriptor is used to measure the similarity between protein sequences in three sets: NADH dehydrogenase subunit 5 (ND5) proteins of different species, 24 transferrin proteins from vertebrates and 12 proteins of baculoviruses. High correlation coefficient values between our results and the results of ClustalW program are obtained. These values are higher than the values obtained in many other related works.
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Affiliation(s)
- A El-Lakkani
- a Faculty of Science, Department of Biophysics , Cairo University , Giza , Egypt
| | - M Lashin
- a Faculty of Science, Department of Biophysics , Cairo University , Giza , Egypt
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18
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Wang ZS, Qi ZT, Zhang QH, Qiu M, Huang JT, Zhao WH, Guo XJ. The cDNA sequence of the transferrin gene in tongue sole (Cynoglosus semilaevis) and its transcriptional changes under acute hypoxic stress. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2012.e74] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Pajuelo D, Lee CT, Roig FJ, Hor LI, Amaro C. Novel host-specific iron acquisition system in the zoonotic pathogenVibrio vulnificus. Environ Microbiol 2015; 17:2076-89. [DOI: 10.1111/1462-2920.12782] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/08/2015] [Accepted: 01/13/2015] [Indexed: 12/17/2022]
Affiliation(s)
- David Pajuelo
- Estructura de Investigación Interdisciplinar en Biotecnología y Medicina (ERI BIOTECMED); Department of Microbiology and Ecology; University of Valencia; Dr. Moliner 50 Valencia 46100 Spain
| | - Chung-Te Lee
- Department of Microbiology and Immunology; Institute of Basic Medical Sciences; Tainan 701 Taiwan
| | - Francisco J. Roig
- Estructura de Investigación Interdisciplinar en Biotecnología y Medicina (ERI BIOTECMED); Department of Microbiology and Ecology; University of Valencia; Dr. Moliner 50 Valencia 46100 Spain
| | - Lien-I. Hor
- Department of Microbiology and Immunology; Institute of Basic Medical Sciences; Tainan 701 Taiwan
- College of Medicine; National Cheng-Kung University; Tainan 701 Taiwan
| | - Carmen Amaro
- Estructura de Investigación Interdisciplinar en Biotecnología y Medicina (ERI BIOTECMED); Department of Microbiology and Ecology; University of Valencia; Dr. Moliner 50 Valencia 46100 Spain
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20
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Liu L, Li C, Bai F, Zhao Q, Wang Y. An optimization approach and its application to compare DNA sequences. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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El-Lakkani A, Mahran H. An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical representation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:125-137. [PMID: 25650529 DOI: 10.1080/1062936x.2014.995700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A new two-dimensional graphical representation of protein sequences is introduced. Twenty concentric evenly spaced circles divided by n radial lines into equal divisions are selected to represent any protein sequence of length n. Each circle represents one of the different 20 amino acids, and each radial line represents a single amino acid of the protein sequence. An efficient numerical method based on the graph is proposed to measure the similarity between two protein sequences. To prove the accuracy of our approach, the method is applied to NADH dehydrogenase subunit 5 (ND5) proteins of nine different species and 24 transferrin sequences from vertebrates. High values of correlation coefficient between our results and the results of ClustalW are obtained (approximately perfect correlations). These values are higher than the values obtained in many other related works.
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Affiliation(s)
- A El-Lakkani
- a Department of Biophysics, Faculty of Science , Cairo University , Giza , Egypt
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22
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Khrustaleva AM, Klovach NV, Gritsenko OF, Seeb JE. Intra- and interpopulation variability of southwestern Kamchatka sockeye salmon Oncorhynchus nerka inferred from the data on single nucleotide polymorphism. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414070096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Chen JH, Wang CH, Li YL, Wang HM, Zhang XJ, Yan BL. cDNA cloning and expression characterization of serum transferrin gene from oriental weatherfish Misgurnus anguillicaudatus. JOURNAL OF FISH BIOLOGY 2014; 84:885-896. [PMID: 24673686 DOI: 10.1111/jfb.12307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 11/16/2013] [Indexed: 06/03/2023]
Abstract
In this study, the cDNA coding serum transferrin (stf) of Misgurnus anguillicaudatus (mastf) was cloned. mastf cDNA is composed of 2326 bp with a 2007 bp open reading frame encoding 668 amino acids. The deduced Mastf protein consists of a signal peptide, two lobes (N and C-lobes) and signature motifs of transferrin (Tf) family. The results of tissue distribution indicated that mastf mRNA was predominantly expressed in the liver. The results indicate that the mastf expression increased significantly in liver, blood, spleen and head kidney after the challenge with Aeromonas sobria, acting as a positive acute protein, suggesting that mastf is related to the immune response. The cloning and expression analysis of mastf further demonstrates the evolutionary conservation of Stf and immune function in vertebrates.
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Affiliation(s)
- J H Chen
- Jiangsu Key Laboratory of Marine Biotechnology, Huaihai Institute of Technology, Lianyungang 222005, China; Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, Shanghai 200090, China; Jiangsu Province R & D Institute of Marine Resources, Huaihai Institute of Technology, Lianyungang 222005, China
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24
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Huang DS, Yu HJ. Normalized feature vectors: a novel alignment-free sequence comparison method based on the numbers of adjacent amino acids. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:457-467. [PMID: 23929869 DOI: 10.1109/tcbb.2013.10] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Based on all kinds of adjacent amino acids (AAA), we map each protein primary sequence into a 400 by ((L-1)) matrix (M). In addition, we further derive a normalized 400-tuple mathematical descriptors (D), which is extracted from the primary protein sequences via singular values decomposition (SVD) of the matrix. The obtained 400-D normalized feature vectors (NFVs) further facilitate our quantitative analysis of protein sequences. Using the normalized representation of the primary protein sequences, we analyze the similarity for different sequences upon two data sets: 1) ND5 sequences from nine species and 2) transferrin sequences of 24 vertebrates. We also compared the results in this study with those from other related works. These two experiments illustrate that our proposed NFV-AAA approach does perform well in the field of similarity analysis of sequence.
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Affiliation(s)
- De-Shuang Huang
- School of Electronics and Information Engineering, Tongji University, 4800 Caoan Road, Shanghai 201804, China
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25
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Mohd-Padil H, Mohd-Adnan A, Gabaldón T. Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates. Mol Biol Evol 2012; 30:894-905. [PMID: 23258311 PMCID: PMC3603312 DOI: 10.1093/molbev/mss325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transferrin is a protein super-family involved in iron transport, a central process in cellular homeostasis. Throughout the evolution of vertebrates, transferrin members have diversified into distinct subfamilies including serotransferrin, ovotransferrin, lactoferrin, melanotransferrin, the inhibitor of carbonic anhydrase, pacifastin, and the major yolk protein in sea urchin. Previous phylogenetic analyses have established the branching order of the diverse transferrin subfamilies but were mostly focused on the transferrin repertoire present in mammals. Here, we conduct a comprehensive phylogenetic analysis of transferrin protein sequences in sequenced vertebrates, placing a special focus on the less-studied nonmammalian vertebrates. Our analyses uncover a novel transferrin clade present across fish, sauropsid, and amphibian genomes but strikingly absent from mammals. Our reconstructed scenario implies that this novel class emerged through a duplication event at the vertebrate ancestor, and that it was subsequently lost in the lineage leading to mammals. We detect footprints of accelerated evolution following the duplication event, which suggest positive selection and early functional divergence of this novel clade. Interestingly, the loss of this novel class of transferrin in mammals coincided with the divergence by duplication of lactoferrin and serotransferrin in this lineage. Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups.
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Affiliation(s)
- Hirzahida Mohd-Padil
- School of Biosciences & Biotechnology, Faculty of Science Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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26
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Sun Y, Zhu Z, Wang R, Sun Y, Xu T. Miiuy croaker transferrin gene and evidence for positive selection events reveal different evolutionary patterns. PLoS One 2012; 7:e43936. [PMID: 22957037 PMCID: PMC3434209 DOI: 10.1371/journal.pone.0043936] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 07/26/2012] [Indexed: 01/12/2023] Open
Abstract
Transferrin (TF) is a protein that plays a central role in iron metabolism. This protein is associated with the innate immune system, which is responsible for disease defense responses after bacterial infection. The clear link between TF and the immune defense mechanism has led researchers to consider TF as a candidate gene for disease resistance. In this study, the Miichthys miiuy (miiuy croaker) TF gene (MIMI-TF) was cloned and characterized. The gene structure consisted of a coding region of 2070 nucleotides divided into 17 exons, as well as a non-coding region that included 16 introns and spans 6757 nucleotides. The deduced MIMI-TF protein consisted of 689 amino acids that comprised a signal peptide and two lobes (N- and C-lobes). MIMI-TF expression was significantly up-regulated after infection with Vibrio anguillarum. A series of model tests implemented in the CODEML program showed that TF underwent a complex evolutionary process. Branch-site models revealed that vertebrate TF was vastly different from that of invertebrates, and that the TF of the ancestors of aquatic and terrestrial organisms underwent different selection pressures. The site models detected 10 positively selected sites in extant TF genes. One site was located in the cleft between the N1 and N2 domains and was expected to affect the capability of TF to bind to or release iron indirectly. In addition, eight sites were found near the TF exterior. Two of these sites, which could have evolved from the competition for iron between pathogenic bacteria and TF, were located in potential pathogen-binding domains. Our results could be used to further investigate the function of TF and the selective mechanisms involved.
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Affiliation(s)
- Yueyan Sun
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Zhihuang Zhu
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Rixin Wang
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Yuena Sun
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
| | - Tianjun Xu
- Laboratory for Marine Living Resources and Molecular Engineering, College of Marine Science, Zhejiang Ocean University, Zhoushan, China
- * E-mail:
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27
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Liu L, Li D, Bai F. A relative Lempel-Ziv complexity: Application to comparing biological sequences. Chem Phys Lett 2012; 530:107-112. [PMID: 32226089 PMCID: PMC7094452 DOI: 10.1016/j.cplett.2012.01.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 01/24/2012] [Indexed: 11/17/2022]
Abstract
One of the main tasks in biological sequence analysis is biological sequence comparison. Numerous efficient methods have been developed for sequence comparison. Traditional sequence comparison is based on sequence alignment. In this report, we propose a novel alignment-free method based on the relative Lempel-Ziv complexity to compare biological sequences. The vertebrate transferring genomes and the spike protein sequences are prepared and tested to evaluate the validity of the method. We use this method to build phylogenetic tree of two groups of the sequences. The result demonstrates that our method is powerful and efficient.
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Affiliation(s)
- Liwei Liu
- College of Science, Dalian Jiaotong University, Dalian 116028, PR China
| | - Dongbo Li
- Department of Otolaryngology, Affiliated Xinhua Hospital of Dalian University, Dalian 116021, PR China
| | - Fenglan Bai
- College of Science, Dalian Jiaotong University, Dalian 116028, PR China
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28
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Rieger AM, Barreda DR. Antimicrobial mechanisms of fish leukocytes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:1238-45. [PMID: 21414350 DOI: 10.1016/j.dci.2011.03.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 02/06/2011] [Accepted: 03/06/2011] [Indexed: 05/22/2023]
Abstract
Early activation and coordination of innate defenses are critical for effective responses against infiltrating pathogens. Rapid engagement of immune cells provides a critical first line of defense soon after pathogen infiltration. Activation leads to a well-orchestrated set of events that sees the induction and regulation of intracellular and extracellular antimicrobial defenses. An array of regulatory mediators, highly toxic soluble molecules, degradative enzymes and antimicrobial peptides provides maximal protection against a wide range of pathogens while limiting endogenous damage to host tissues. In this review we highlight recent advances in our understanding of innate cellular antimicrobial responses of teleost fish and discuss their implications to cell survival, immunomodulation and death. The evolutionary conservation of these responses is a testament to their effectiveness against pathogen infiltration and their commitment to effective maintenance of host homeostasis. Importantly, recent developments in teleost fish systems have identified novel host defense strategies that may be unique to this lower vertebrate group or may point to previously unknown innate mechanisms that also play a significant role in higher vertebrate host immunity.
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Affiliation(s)
- Aja M Rieger
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
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29
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García-Fernández C, Sánchez JA, Blanco G. Characterization of the gilthead seabream (Sparus aurata L.) transferrin gene: genomic structure, constitutive expression and SNP variation. FISH & SHELLFISH IMMUNOLOGY 2011; 31:548-556. [PMID: 21782954 DOI: 10.1016/j.fsi.2011.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 07/01/2011] [Accepted: 07/02/2011] [Indexed: 05/31/2023]
Abstract
Transferrin (Tf) is a multi-function protein with a central role in iron metabolism, and it is this function that is associated with a role in the innate immune system response. The clear link between Tf and immune defense mechanism lead to propose Tf as a candidate gene for disease resistance. In this study, genomic and cDNA sequences of Tf gene in gilthead seabream (Sparus aurata L.) (SaTf gene), were identified and characterized. SaTf gene structure consists of a coding region of 2076 nucleotides divided into 17 exons and a no-coding region that includes 16 introns and spans 5495 nucleotides. The deduced Tf protein for gilthead seabream is composed of 691 amino acids and consists of an initial peptide and two lobes (N- and C-lobes). This gene structure is similar to that of previously described Tf genes in other fish species. RT-PCR analyses carried out in different tissues and two developmental stages showed tissue-and stage-specific Tf expression in gilthead seabream. Finally, by sequencing the transferrin genomic sequences of 20 unrelated seabreams, 31 SNPs were identified. These data allowed the estimation of the frequency of nucleotide substitution in the SaTf gene as 1SNP per 253 bp. SNPs were detected in different regions of the genomic sequence but they were mainly localized in non-coding regions, specifically, SNP frequency in non-coding regions was fifteen-fold higher than within coding regions.
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Affiliation(s)
- Carmen García-Fernández
- Laboratorio de Genética Acuícola, Departamento de Biología Funcional, Universidad de Oviedo, IUBA, 33071 Oviedo, Spain
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30
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George RD, McVicker G, Diederich R, Ng SB, MacKenzie AP, Swanson WJ, Shendure J, Thomas JH. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res 2011; 21:1686-94. [PMID: 21795384 DOI: 10.1101/gr.121327.111] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Comparison of protein-coding DNA sequences from diverse primates can provide insight into these species' evolutionary history and uncover the molecular basis for their phenotypic differences. Currently, the number of available primate reference genomes limits these genome-wide comparisons. Here we use targeted capture methods designed for human to sequence the protein-coding regions, or exomes, of four non-human primate species (three Old World monkeys and one New World monkey). Despite average sequence divergence of up to 4% from the human sequence probes, we are able to capture ~96% of coding sequences. Using a combination of mapping and assembly techniques, we generated high-quality full-length coding sequences for each species. Both the number of nucleotide differences and the distribution of insertion and deletion (indel) lengths indicate that the quality of the assembled sequences is very high and exceeds that of most reference genomes. Using this expanded set of primate coding sequences, we performed a genome-wide scan for genes experiencing positive selection and identified a novel class of adaptively evolving genes involved in the conversion of epithelial cells in skin, hair, and nails to keratin. Interestingly, the genes we identify under positive selection also exhibit significantly increased allele frequency differences among human populations, suggesting that they play a role in both recent and long-term adaptation. We also identify several genes that have been lost on specific primate lineages, which illustrate the broad utility of this data set for other evolutionary analyses. These results demonstrate the power of second-generation sequencing in comparative genomics and greatly expand the repertoire of available primate coding sequences.
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Affiliation(s)
- Renee D George
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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31
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Brieuc MSO, Naish KA. Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources. Mol Ecol Resour 2011; 11 Suppl 1:172-83. [PMID: 21429173 DOI: 10.1111/j.1755-0998.2010.02948.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studying the actions of selection provides insight into adaptation, population divergence and gene function. Next-generation sequencing produces large amounts of partial sequences, potentially facilitating efforts to detect signatures of selection based on comparisons between synonymous (d(S)) and nonsynonymous (d(N)) substitutions, and single nucleotide polymorphism assays placed in selected genes would improve the ability to study adaptation in population surveys. However, sequences generated by these technologies are typically short. In nonmodel organisms that are a focus of evolutionary studies, the lack of a reference genome that facilitates the assembly of short sequences has limited surveys of positive selection in large numbers of genes. Here, we describe a series of steps to facilitate these surveys. We provide PERL scripts to assist data analysis, and describe the use of commonly available programs. We demonstrate these approaches in six salmon species, which have partially duplicated genomes. We recommend using multiway blast to optimize the number of alignments between partial coding sequences. Reading frames should be manually detected after alignment with sequences in Genbank using the BLASTX program. We encourage the use of a phylogenetic approach to separate orthologs from paralogs in duplicated genomes. Simple simulations on a gene known to have undergone selection in salmon species, transferrin, showed that the ability to detect selection in short sequences (<600 bp) depended on the proportion of codons under selection (1-2%) within that sequence. This relationship was less relevant in longer sequences. In this exploratory study, we detected 11 genes showing evidence of positive selection.
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Affiliation(s)
- Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, 98195, USA.
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32
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Abstract
Up to now, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary sequences. In this paper, we propose a new sequence distance for efficient reconstruction of phylogenetic trees based on the distribution of length about common sub-sequences between two sequences. We describe some applications of this method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.
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Affiliation(s)
- Guisong Chang
- School of Mathematical Sciences, Dalian University of Technology, 116024 Dalian, People's Republic of China.
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33
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SEEB LW, TEMPLIN WD, SATO S, ABE S, WARHEIT K, PARK JY, SEEB JE. Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon. Mol Ecol Resour 2011; 11 Suppl 1:195-217. [DOI: 10.1111/j.1755-0998.2010.02966.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Zhao JP, Su XH. Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa. PLANTA 2010; 232:949-62. [PMID: 20645107 DOI: 10.1007/s00425-010-1218-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/28/2010] [Indexed: 05/16/2023]
Abstract
Some pathogenesis-related proteins (PR proteins) are subject to positive selection, while others are under negative selection. Here, we report the patterns of molecular evolution in thaumatin-like protein (TLP, PR5 protein) genes of Populus trichocarpa. Signs of positive selection were found in 20 out of 55 Populus TLPs using the likelihood ratio test and ML-based Bayesian methods. Due to the connection between the acidic cleft and the antifungal activity, the secondary structure and three-dimensional structure analyses predicted antifungal activity beta-1,3-glucanase activities in these TLPs. Moreover, the coincidence with variable basic sites in the acidic cleft and positively selected sites suggested that fungal diseases may have been the main environmental stress that drove rapid adaptive evolution in Populus.
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Affiliation(s)
- Jia Ping Zhao
- Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China.
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35
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Ding S, Dai Q, Liu H, Wang T. A simple feature representation vector for phylogenetic analysis of DNA sequences. J Theor Biol 2010; 265:618-23. [DOI: 10.1016/j.jtbi.2010.05.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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Liang GM, Jiang XP. Positive selection drives lactoferrin evolution in mammals. Genetica 2010; 138:757-62. [PMID: 20401683 DOI: 10.1007/s10709-010-9456-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2009] [Accepted: 04/06/2010] [Indexed: 01/05/2023]
Abstract
Lactoferrin (LF) is a member of the transferrin family that is abundantly expressed and secreted by glandular epithelial cells. The biological functions of LF involve in iron homeostasis regulation of the body and antibacterial activity. Previous studies demonstrated that it had a high cationic N-terminal domain that could interact with glycosaminoglycans, lipopolysaccharides and the bacterial virulence protein. Two anti-microbial peptides, lactoferricin (LFcin) and lactoferrampin (LFampin), were also isolated and identified in N-terminal of LF. Although the antibacterial mechanism was carefully studied, little was known about the molecular evolution of LF. In this study, we estimated the nonsynonymous-to-synonymous substitution ratios ( ) per site using maximum likelihood method to analyze the LF evolution. The results of omega > 1 and five identified positive selection sites of amino acid suggested that the evolution of LF gene was characterized by positive selection. Further study found that the positive selection sites were either located in the LF-bacteria binding region or the peptides of LFcin and LFampin, indicating that the selection pressure was related to LF-bacteria interaction. The identification of these sites may contribute to the mechanism of bacteria-LF interaction.
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Affiliation(s)
- Guo Ming Liang
- Animal Science Department, Huazhong Agricultural University, Wuhan, People's Republic of China
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37
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Yang L, Chang G, Zhang X, Wang T. Use of the Burrows–Wheeler similarity distribution to the comparison of the proteins. Amino Acids 2010; 39:887-98. [DOI: 10.1007/s00726-010-0547-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 02/25/2010] [Indexed: 10/19/2022]
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38
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The Burrows–Wheeler similarity distribution between biological sequences based on Burrows–Wheeler transform. J Theor Biol 2010; 262:742-9. [DOI: 10.1016/j.jtbi.2009.10.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 10/23/2009] [Accepted: 10/29/2009] [Indexed: 11/22/2022]
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39
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Sahoo P, Mohanty B, Kumari J, Barat A, Sarangi N. Cloning, nucleotide sequence and phylogenetic analyses, and tissue-specific expression of the transferrin gene in Cirrhinus mrigala infected with Aeromonas hydrophila. Comp Immunol Microbiol Infect Dis 2009; 32:527-37. [DOI: 10.1016/j.cimid.2008.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2008] [Indexed: 10/21/2022]
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40
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Jia C, Liu T, Zhang X, Fu H, Yang Q. Alignment-free Comparison of Protein Sequences Based on Reduced Amino Acid Alphabets. J Biomol Struct Dyn 2009; 26:763-9. [DOI: 10.1080/07391102.2009.10507288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Jurecka P, Irnazarow I, Westphal AH, Forlenza M, Arts JAJ, Savelkoul HFJ, Wiegertjes GF. Allelic discrimination, three-dimensional analysis and gene expression of multiple transferrin alleles of common carp (Cyprinus carpio L.). FISH & SHELLFISH IMMUNOLOGY 2009; 26:573-581. [PMID: 18824109 DOI: 10.1016/j.fsi.2008.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 08/22/2008] [Accepted: 08/22/2008] [Indexed: 05/26/2023]
Abstract
We cloned and sequenced four different transferrin (Tf) alleles (C, D, F and G) of European common carp (Cyprinus carpio carpio L.) and studied allelic diversity with respect to differences in sequence, constitutive transcription and three-dimensional structure. Most of the disulfide bonds were conserved between human and carp Tf, and modeling confirmed the overall conservation of the three-dimensional structure of carp Tf. While the iron-binding sites in the C-lobe of carp Tf were completely conserved, in the N-lobe the majority of iron-coordinating residues were not conserved. This may have a serious impact on the ability of carp Tf to bind iron with both the C- and N-lobe. In contrast to human Tf, we could not detect potential N-glycosylation sites in carp Tf, which does not seem to be a glycoprotein. Comparison of the cDNA of the four Tf alleles of carp indicated 21 polymorphic sites of which 13 resulted in non-synonymous changes. Allelic diversity did not seem to influence the overall conservation of carp Tf. Neither the iron binding sites nor the receptor binding of carp Tf seemed influenced by allelic diversity. Possibly, interaction with pathogen-associated receptors for Tf could be influenced by allelic diversity. Basal gene expression of Tf alleles D and G was especially high in carp liver. Although we could detect a higher transcription level of allele D than of Tf allele G in head kidney, thymus and spleen, the differences seem minor with respect to the very high transcription level in liver. Preliminary results with Tf-typed serum suggest a difference in the ability of Tf alleles D and G to modulate LPS-induced NO production in carp macrophages.
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Affiliation(s)
- Patrycja Jurecka
- Institute of Ichthyobiology and Aquaculture, Polish Academy of Sciences, Gołysz, 43-520 Chybie, Poland
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42
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Abstract
This study reports on the development of comparative data for the transferrin (TF) gene in cyprinid fishes, focusing on the genus Notropis. While previous studies have suggested varied patterns of adaptation influencing the diversity at this gene locus both within and among species, sequence data for (TF) in Notropis exhibit limited evidence for selection. However, there are significant effects of sequence variation associated with Notropis lutipinnis, suggesting some form of diversifying selection acting among populations of this species. Overall, the gene performs well as a second locus for phylogenetic and biogeographic inference and may help improve description of the pattern and the process of diversification in Notropis.
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Affiliation(s)
- J P Wares
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Jurecka P, Irnazarow I, Stafford JL, Ruszczyk A, Taverne N, Belosevic M, Savelkoul HFJ, Wiegertjes GF. The induction of nitric oxide response of carp macrophages by transferrin is influenced by the allelic diversity of the molecule. FISH & SHELLFISH IMMUNOLOGY 2009; 26:632-638. [PMID: 18996204 DOI: 10.1016/j.fsi.2008.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 09/23/2008] [Accepted: 10/13/2008] [Indexed: 05/27/2023]
Abstract
The central role of transferrin (Tf) as an iron transporting protein has been extended by observations that modified versions of Tf also participate in the regulation of innate immunity. We report on the isolation of two carp Tf proteins (alleles D and G) to purity using rivanol precipitation and ion-exchange chromatography, and describe the activation of head kidney-derived carp macrophages by cleaved Tf. We demonstrate the superiority of the D-type over the G-type Tf in inducing nitric oxide (NO) and confirm previous observations that full-length Tf cannot induce NO in fish macrophages. We believe that cleaved Tf fragments should be considered to be "alarmins". We discuss the possibility that parasites such as Trypanoplasma borreli cleave Tf and use Tf fragments to their advantage by modulating the NO induction in carp macrophages.
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Affiliation(s)
- Patrycja Jurecka
- Polish Academy of Sciences, Institute of Ichthyobiology and Aquaculture, Gołysz, 43-520 Chybie, Poland
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44
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Elibol-Flemming B, Waldbieser GC, Wolters WR, Boyle CR, Hanson LA. Expression analysis of selected immune-relevant genes in channel catfish during Edwardsiella ictaluri infection. JOURNAL OF AQUATIC ANIMAL HEALTH 2009; 21:23-35. [PMID: 19485123 DOI: 10.1577/h08-009.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Channel catfish Ictalurus punctatus were intraperitoneally challenged with the bacterium Edwardsiella ictaluri (the causative agent of enteric septicemia of catfish), and the expression of genes presumed to function in the inducible innate defense was evaluated. End-binding protein 1 (EB1), beta1-integrin, natural-resistance-associated macrophage protein (Nramp), heat shock protein 70 (Hsp70), serum amyloid P (SAP), and transferrin gene expression profiles were determined using quantitative reverse-transcriptase-polymerase chain reaction on liver, anterior kidney, spleen, and gut. Fish were subsampled at 0, 24, 48, 72, and 96 h after bacterial or phosphate-buffered-saline injection. Posterior kidney sampling demonstrated increasing bacterial counts at 24-48 h postinjection (hpi), followed by a plateau to 96 hpi. The transferrin and SAP transcripts were liver specific. The other genes were expressed in all four tissues. In bacterially infected fish, expression of EB1 (anterior kidney, spleen, and liver), Hsp70 (anterior kidney and spleen), and Nramp (spleen and gut) significantly increased by 48 hpi. Transferrin was strongly up-regulated and SAP was downregulated by 72 hpi, indicating positive and negative acute-phase reactants, respectively. The data indicate a substantial response of innate immunity effector cells by 48 hpi, followed by suppression of bacterial growth and induction of the acute-phase response. This suggests that the 48-72-hpi time frame is critical in our model for evaluating the effectiveness of innate defenses.
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Affiliation(s)
- Banu Elibol-Flemming
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, USA
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45
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Jurecka P, Wiegertjes GF, Rakus KŁ, Pilarczyk A, Irnazarow I. Genetic resistance of carp (Cyprinus carpio L.) to Trypanoplasma borreli: Influence of transferrin polymorphisms. Vet Immunol Immunopathol 2009; 127:19-25. [DOI: 10.1016/j.vetimm.2008.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 08/21/2008] [Accepted: 09/12/2008] [Indexed: 11/15/2022]
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46
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Rozman T, Dovc P, Marić S, Kokalj-Vokac N, Erjavec-Skerget A, Rab P, Snoj A. Evidence for two transferrin loci in the Salmo trutta genome. Anim Genet 2008; 39:577-85. [PMID: 18786157 DOI: 10.1111/j.1365-2052.2008.01768.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To determine the organization of transferrin (TF) locus in the Salmo trutta genome, partial DNA and cDNA sequencing, fluorescent in situ hybridization (FISH) and Salmo salar BAC analysis were performed. TF expression levels and copy number prediction were assessed using real-time PCR. In addition to two previously reported DNA TF variant sequences of S. trutta and Salmo marmoratus (TF1), two novel variant sequences (TF2) were revealed in both species. Variant-specific sequence tags, characterizing two variants for each TF type (TF1 and TF2), were identified in genomic clones from each of the F1 hybrids between S. trutta and S. marmoratus. These clearly documented double heterozygote status at the TF loci. The real-time PCR data showed that each of the two TF types (TF1 and TF2) existed in one copy only and that the transcription of TF2 was considerably lower compared with TF1. Using FISH, hybridization signals were observed on two medium-sized acrocentric chromosomes of S. trutta karyotype. A TF type-specific PCR followed by a restriction analysis revealed the presence of two TF loci in the majority of analysed BAC clones. It was concluded that the TF gene is duplicated in the genome of S. trutta, and that the two TF loci are located adjacent to one another on the same chromosome. The differing transcription levels of TF1 and TF2 appear to depend on the corresponding promoter activity, which at least for TF2 seems to vary between different Salmo congeners.
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Affiliation(s)
- T Rozman
- Department of Animal Science, University of Ljubljana, Groblje 3, SI-1230 DomZale, Slovenia
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47
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Evolutionary analysis of the transferrin gene in Antarctic Notothenioidei: A history of adaptive evolution and functional divergence. Mar Genomics 2008; 1:95-101. [DOI: 10.1016/j.margen.2008.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2008] [Accepted: 10/23/2008] [Indexed: 01/09/2023]
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48
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Consuegra S, Johnston IA. Effect of natural selection on the duplicated lysyl oxidase gene in Atlantic salmon. Genetica 2008; 134:325-34. [DOI: 10.1007/s10709-008-9240-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
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49
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Affiliation(s)
- Tomohisa Ogawa
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, 981-8555 Japan
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50
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Cruz F, Bradley DG, Lynn DJ. Evidence of positive selection on the Atlantic salmon CD3γδ gene. Immunogenetics 2007; 59:225-32. [PMID: 17211637 DOI: 10.1007/s00251-006-0188-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 12/12/2006] [Indexed: 11/29/2022]
Abstract
Atlantic salmon are typically anadromous, spending the majority of their lifetime in oceans and returning to fresh water to breed. This diversity of environments likely results in strong selective forces shaping their genome. In this paper, we present the first genomics approach to detect positive selection operating on the Salmo salar (salmon) lineage, an important aquaculture species. We identify a panel of candidate genes that may have been subject to adaptive evolution in this species. In particular, we identify a robust signature of positive selection operating on the salmon CD3gammadelta gene, which encodes one of the protein chains essential for formation of the T-cell receptor complex and for T-cell activation. Furthermore, we identified the particular codon sites that have been subject to positive selection in fish and highlight two sites flanking an important N-glycosylation site in this molecule.
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Affiliation(s)
- Fernando Cruz
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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