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Hul LM, Ibelli AMG, Savoldi IR, Marcelino DEP, Fernandes LT, Peixoto JO, Cantão ME, Higa RH, Giachetto PF, Coutinho LL, Ledur MC. Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens. Sci Rep 2021; 11:17965. [PMID: 34504189 PMCID: PMC8429632 DOI: 10.1038/s41598-021-97306-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Locomotor problems are among one of the main concerns in the current poultry industry, causing major economic losses and affecting animal welfare. The most common bone anomalies in the femur are dyschondroplasia, femoral head separation (FHS), and bacterial chondronecrosis with osteomyelitis (BCO), also known as femoral head necrosis (FHN). The present study aimed to identify differentially expressed (DE) genes in the articular cartilage (AC) of normal and FHS-affected broilers by RNA-Seq analysis. In the transcriptome analysis, 12,169 genes were expressed in the femur AC. Of those, 107 genes were DE (FDR < 0.05) between normal and affected chickens, of which 9 were downregulated and 98 were upregulated in the affected broilers. In the gene-set enrichment analysis using the DE genes, 79 biological processes (BP) were identified and were grouped into 12 superclusters. The main BP found were involved in the response to biotic stimulus, gas transport, cellular activation, carbohydrate-derived catabolism, multi-organism regulation, immune system, muscle contraction, multi-organism process, cytolysis, leukocytes and cell adhesion. In this study, the first transcriptome analysis of the broilers femur articular cartilage was performed, and a set of candidate genes (AvBD1, AvBD2, ANK1, EPX, ADA, RHAG) that could trigger changes in the broiler´s femoral growth plate was identified. Moreover, these results could be helpful to better understand FHN in chickens and possibly in humans.
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Affiliation(s)
- Ludmila Mudri Hul
- grid.412329.f0000 0001 1581 1066Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, PR 85040-080 Brazil
| | - Adriana Mércia Guaratini Ibelli
- grid.412329.f0000 0001 1581 1066Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, PR 85040-080 Brazil ,Embrapa Suínos e Aves, Concórdia, SC 89715-899 Brazil
| | - Igor Ricardo Savoldi
- grid.412287.a0000 0001 2150 7271Programa de Pós-Graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, SC 89815-630 Brazil
| | | | | | - Jane Oliveira Peixoto
- grid.412329.f0000 0001 1581 1066Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Guarapuava, PR 85040-080 Brazil ,Embrapa Suínos e Aves, Concórdia, SC 89715-899 Brazil
| | | | - Roberto Hiroshi Higa
- grid.460200.00000 0004 0541 873XEmbrapa Informática Agropecuária, Campinas, SP 70770-901 Brazil
| | | | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Departamento de Zootecnia, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves, Concórdia, SC 89715-899 Brazil ,grid.412287.a0000 0001 2150 7271Programa de Pós-Graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, SC 89815-630 Brazil
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Buzanskas ME, Grossi DDA, Ventura RV, Schenkel FS, Chud TCS, Stafuzza NB, Rola LD, Meirelles SLC, Mokry FB, Mudadu MDA, Higa RH, da Silva MVGB, de Alencar MM, Regitano LCDA, Munari DP. Candidate genes for male and female reproductive traits in Canchim beef cattle. J Anim Sci Biotechnol 2017; 8:67. [PMID: 28852499 PMCID: PMC5569548 DOI: 10.1186/s40104-017-0199-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2023] Open
Abstract
Background Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals. Results Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction. Conclusions Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s40104-017-0199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba (UFPB), Areia, Paraíba 58397-000 Brazil
| | | | | | - Flavio Schramm Schenkel
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, ON N1G 2W1 Canada
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Luciana Diniz Rola
- Departamento de Zootecnia, Núcleo de Pesquisa e Conservação de Cervídeos, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | | | - Fabiana Barichello Mokry
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, São Paulo 13565-905 Brazil
| | | | | | | | | | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
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Urbinati I, Stafuzza NB, Oliveira MT, Chud TCS, Higa RH, Regitano LCDA, de Alencar MM, Buzanskas ME, Munari DP. Selection signatures in Canchim beef cattle. J Anim Sci Biotechnol 2016; 7:29. [PMID: 27158491 PMCID: PMC4858954 DOI: 10.1186/s40104-016-0089-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization. Electronic supplementary material The online version of this article (doi:10.1186/s40104-016-0089-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismael Urbinati
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Marcos Túlio Oliveira
- Departamento de Tecnologia, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | | | | | | | - Marcos Eli Buzanskas
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
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Cardoso FF, Gomes CCG, Sollero BP, Oliveira MM, Roso VM, Piccoli ML, Higa RH, Yokoo MJ, Caetano AR, Aguilar I. Genomic prediction for tick resistance in Braford and Hereford cattle. J Anim Sci 2016; 93:2693-705. [PMID: 26115257 DOI: 10.2527/jas.2014-8832] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the main animal health problems in tropical and subtropical cattle production is the bovine tick, which causes decreased performance, hide devaluation, increased production costs with acaricide treatments, and transmission of infectious diseases. This study investigated the utility of genomic prediction as a tool to select Braford (BO) and Hereford (HH) cattle resistant to ticks. The accuracy and bias of different methods for direct and blended genomic prediction was assessed using 10,673 tick counts obtained from 3,435 BO and 928 HH cattle belonging to the Delta G Connection breeding program. A subset of 2,803 BO and 652 HH samples were genotyped and 41,045 markers remained after quality control. Log transformed records were adjusted by a pedigree repeatability model to estimate variance components, genetic parameters, and breeding values (EBV) and subsequently used to obtain deregressed EBV. Estimated heritability and repeatability for tick counts were 0.19 ± 0.03 and 0.29 ± 0.01, respectively. Data were split into 5 subsets using k-means and random clustering for cross-validation of genomic predictions. Depending on the method, direct genomic value (DGV) prediction accuracies ranged from 0.35 with Bayes least absolute shrinkage and selection operator (LASSO) to 0.39 with BayesB for k-means clustering and between 0.42 with BayesLASSO and 0.45 with BayesC for random clustering. All genomic methods were superior to pedigree BLUP (PBLUP) accuracies of 0.26 for k-means and 0.29 for random groups, with highest accuracy gains obtained with BayesB (39%) for k-means and BayesC (55%) for random groups. Blending of historical phenotypic and pedigree information by different methods further increased DGV accuracies by values between 0.03 and 0.05 for direct prediction methods. However, highest accuracy was observed with single-step genomic BLUP with values of 0.48 for -means and 0.56, which represent, respectively, 84 and 93% improvement over PBLUP. Observed random clustering cross-validation breed-specific accuracies ranged between 0.29 and 0.36 for HH and between 0.55 and 0.61 for BO, depending on the blending method. These moderately high values for BO demonstrate that genomic predictions could be used as a practical tool to improve genetic resistance to ticks and in the development of resistant lines of this breed. For HH, accuracies are still in the low to moderate side and this breed training population needs to be increased before genomic selection could be reliably applied to improve tick resistance.
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Mokry FB, Buzanskas ME, de Alvarenga Mudadu M, do Amaral Grossi D, Higa RH, Ventura RV, de Lima AO, Sargolzaei M, Conceição Meirelles SL, Schenkel FS, da Silva MVGB, Méo Niciura SC, de Alencar MM, Munari D, de Almeida Regitano LC. Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. BMC Genomics 2014; 15 Suppl 7:S6. [PMID: 25573652 PMCID: PMC4243187 DOI: 10.1186/1471-2164-15-s7-s6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies. Results The maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size. Conclusions This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.
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Tizioto PC, Decker JE, Taylor JF, Schnabel RD, Mudadu MA, Silva FL, Mourão GB, Coutinho LL, Tholon P, Sonstegard TS, Rosa AN, Alencar MM, Tullio RR, Medeiros SR, Nassu RT, Feijó GLD, Silva LOC, Torres RA, Siqueira F, Higa RH, Regitano LCA. Genome scan for meat quality traits in Nelore beef cattle. Physiol Genomics 2013; 45:1012-20. [PMID: 24022219 DOI: 10.1152/physiolgenomics.00066.2013] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.
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Affiliation(s)
- P C Tizioto
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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7
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Mokry FB, Higa RH, de Alvarenga Mudadu M, Oliveira de Lima A, Meirelles SLC, Barbosa da Silva MVG, Cardoso FF, Morgado de Oliveira M, Urbinati I, Méo Niciura SC, Tullio RR, Mello de Alencar M, Correia de Almeida Regitano L. Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach. BMC Genet 2013; 14:47. [PMID: 23738659 PMCID: PMC3680339 DOI: 10.1186/1471-2156-14-47] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/23/2013] [Indexed: 12/17/2022] Open
Abstract
Background Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal’s life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality. Results The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism. Conclusions These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.
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Affiliation(s)
- Fabiana Barichello Mokry
- Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, km 235, PO BOX 676, 13565-905, São Carlos, Brazil.
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Abstract
In this work, we present a method for predicting hot spot residues by using a set of structural and evolutionary parameters. Unlike previous studies, we use a set of parameters which do not depend on the structure of the protein in complex, so that the predictor can also be used when the interface region is unknown. Despite the fact that no information concerning proteins in complex is used for prediction, the application of the method to a compiled dataset described in the literature achieved a performance of 60.4%, as measured by F-Measure, corresponding to a recall of 78.1% and a precision of 49.5%. This result is higher than those reported by previous studies using the same data set.
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Affiliation(s)
- Roberto Hiroshi Higa
- Departamento de Engenharia de Computação e Automação Industrial, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, Campinas, SP Brazil
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9
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Abstract
Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).
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Affiliation(s)
- R H Higa
- Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, Campinas, SP, Brasil.
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Neshich G, Mazoni I, Oliveira SRM, Yamagishi MEB, Kuser-Falcão PR, Borro LC, Morita DU, Souza KRR, Almeida GV, Rodrigues DN, Jardine JG, Togawa RC, Mancini AL, Higa RH, Cruz SAB, Vieira FD, Santos EH, Melo RC, Santoro MM. The Star STING server: a multiplatform environment for protein structure analysis. Genet Mol Res 2006; 5:717-22. [PMID: 17183482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Star STING is the latest version of the STING suite of programs and corresponding database. We report on five important aspects of this package that have acquired some new characteristics, designed to add key advantages to the whole suite: 1) availability for most popular platforms and browsers, 2) introduction of the STING_DB quality assessment, 3) improvement in algorithms for calculation of three STING parameters, 4) introduction of five new STING modules, and 5) expansion of the existing modules. Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/, http://trantor.bioc.columbia.edu/SMS, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://www.ar.embnet.org/SMS.
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Affiliation(s)
- G Neshich
- Núcleo de Bioinformática Estrutural, Embrapa Informática Agropecuária, Campinas, SP, Brasil.
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Higa RH, Cruz SABD, Kuser PR, Yamagishi MEB, Fileto R, Oliveira SRDM, Mazoni I, Santos EHD, Mancini AL, Neshich G. Building multiple sequence alignments with a flavor of HSSP alignments. Genet Mol Res 2006; 5:127-37. [PMID: 16755504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Homology-derived secondary structure of proteins (HSSP) is a well-known database of multiple sequence alignments (MSAs) which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB. It is also used by STING and (Java)Protein Dossier to calculate and present relative entropy as a measure of the degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and (Java)Protein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we need a new method for building alignments having a flavor of HSSP alignments (myMSAr). The present study describes a new method and its corresponding databank (SH2QS--database of sequences homologue to the query [structure-having] sequence). Our main interest in making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless of whether it has a corresponding structure deposited in the PDB. In this study, we compare the measurement of residue conservation provided by corresponding alignments produced by HSSP and SH2QS. As a case study, we also present two biologically relevant examples, the first one highlighting the equivalence of analysis of the degree of residue conservation by using HSSP or SH2QS alignments, and the second one presenting the degree of residue conservation for a structure modeled in a computer, which , as a consequence, does not have an alignment reported by HSSP.
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Affiliation(s)
- Roberto Hiroshi Higa
- Centro Nacional de Pesquisa em Informática Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
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12
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Mancini AL, Higa RH, Oliveira A, Dominiquini F, Kuser PR, Yamagishi MEB, Togawa RC, Neshich G. STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. Bioinformatics 2004; 20:2145-7. [PMID: 15073001 DOI: 10.1093/bioinformatics/bth203] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Amino acid contacts in terms of atomic interactions are essential factors to be considered in the analysis of the structure of a protein and its complexes. Consequently, molecular biologists do require specific tools for the identification and visualization of all such contacts. Graphical contacts (GC) and interface forming residue graphical contacts (IFRgc) presented here, calculate atomic contacts among amino acids based on a table of predefined pairs of the atom types and their distances, and then display them using number of different forms. The inventory of currently listed contact types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge-charge interactions, aromatic stacking and disulfide bonds. Such extensive catalog of the interactions, representing the forces that govern protein folding, stability and binding, is the key feature of these two applications. GC and IFRgc are part of STING Millennium Suite. AVAILABILITY http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org//SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS (Options: Graphical Contacts and IFR Graphical Contacts).
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Affiliation(s)
- A L Mancini
- Núcleo de Bioinformática, Centro Nacional de Pesquisa Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
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Higa RH, Montagner AJ, Togawa RC, Kuser PR, Yamagishi MEB, Mancini AL, Pappas G, Miura RT, Horita LG, Neshich G. ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics 2004; 20:1983-5. [PMID: 15044236 DOI: 10.1093/bioinformatics/bth185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SUMMARY A web-based application to analyze protein amino acids conservation-Consensus Sequence (ConSSeq) is presented. ConSSeq graphically represents information about amino acid conservation based on sequence alignments reported in homology-derived structures of proteins. Beyond the relative entropy for each position in the alignment, ConSSeq also presents the consensus sequence and information about the amino acids, which are predominant at each position of the alignment. ConSSeq is part of the STING Millennium Suite and is implemented as a Java Applet. AVAILABILITY http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/consseq/, http://trantor.bioc.columbia.edu/SMS/STINGm/consseq/, http://mirrors.rcsb.org//SMS/STINGm/consseq/, http://www.es.embnet.org/SMS/STINGm/consseq/ and http://www.ar.embnet.org/SMS/STINGm/consseq/
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Affiliation(s)
- R H Higa
- Núcleo de Bioinformática, Centro Nacional de Pesquisa Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
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Higa RH, Oliveira AG, Horita LG, Miura RT, Inoue MK, Kuser PR, Mancini AL, Yamagishi MEB, Togawa RC, Neshich G. Defining 3D residue environment in protein structures using SCORPION and FORMIGA. Bioinformatics 2004; 20:1989-91. [PMID: 15044232 DOI: 10.1093/bioinformatics/bth190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Two web-based applications to analyze amino acids three-dimensional (3D) local environment within protein structures-SCORPION and FORMIGA-are presented. SCORPION and FORMIGA produce a graphical presentation for simple statistical data showing the frequency of residue occurrence within a given sphere (defined here as the 3D contacts). The center of that sphere is placed at the Calpha and at the last heavy atom in the side chain of the selected amino acid. Further depth of detail is given in terms of a secondary structure to which the profiled amino acid belongs. Results obtained with those two applications are relevant for estimating the importance of the amino acid 3D local environment for protein folding and stability. Effectively, SCORPION and FORMIGA construct knowledge-based force fields. The difference between SCORPION and FORMIGA is in that the latter operates on protein interfaces, while the former only functions for a single protein chain. Both applications are implemented as stand-alone components of STING Millennium Suite. AVAILABILITY http://sms.cbi.cnptia.embrapa.br/SMS, http://trantor.bioc.columbia.edu/SMS, http://mirrors.rcsb.org/SMS, http://www.es.embnet.org/SMS and http://www.ar.embnet.org/SMS. [options: Scorpion, Formiga]
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Affiliation(s)
- R H Higa
- Núcleo de Bioinformática, Centro Nacional de Pesquisa Agropecuária, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
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