Sharifi, Ahmad Reza

[["dc.bibliographiccitation.firstpage","873"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Genes"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Hosseini, Shahrbanou"],["dc.contributor.author","Schmitt, Armin Otto"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Brenig, Bertram"],["dc.contributor.author","Simianer, Henner"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Gültas, Mehmet"],["dc.date.accessioned","2021-08-12T07:45:56Z"],["dc.date.available","2021-08-12T07:45:56Z"],["dc.date.issued","2021"],["dc.description.abstract","The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish."],["dc.description.abstract","The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.3390/genes12060873"],["dc.identifier.pii","genes12060873"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/88580"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-448"],["dc.relation.eissn","2073-4425"],["dc.relation.orgunit","Abteilung Tierzucht und Haustiergenetik"],["dc.rights","CC BY 4.0"],["dc.title","In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish (Danio rerio)"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","377"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Animal Genetics"],["dc.bibliographiccitation.lastpage","389"],["dc.bibliographiccitation.volume","41"],["dc.contributor.author","Qanbari, Saber"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Lichtner, Peter"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T08:40:33Z"],["dc.date.available","2018-11-07T08:40:33Z"],["dc.date.issued","2010"],["dc.description.abstract","P>The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding."],["dc.identifier.doi","10.1111/j.1365-2052.2009.02016.x"],["dc.identifier.isi","000279717800005"],["dc.identifier.pmid","20096028"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19260"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0268-9146"],["dc.title","A genome-wide scan for signatures of recent selection in Holstein cattle"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","13332"],["dc.bibliographiccitation.issue","23"],["dc.bibliographiccitation.journal","Ecology and Evolution"],["dc.bibliographiccitation.lastpage","13343"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Hosseini, Shahrbanou"],["dc.contributor.author","Simianer, Henner"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Brenig, Bertram"],["dc.contributor.author","Herzog, Sebastian"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.date.accessioned","2021-06-01T10:50:10Z"],["dc.date.available","2021-06-01T10:50:10Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1002/ece3.5788"],["dc.identifier.eissn","2045-7758"],["dc.identifier.issn","2045-7758"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16873"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/86556"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.notes.intern","Merged from goescholar"],["dc.notes.intern","Merged from goescholar"],["dc.relation.eissn","2045-7758"],["dc.relation.issn","2045-7758"],["dc.relation.orgunit","Fakultät für Physik"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Efficient phenotypic sex classification of zebrafish using machine learning methods"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","341"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Hosseini, Shahrbanou"],["dc.contributor.author","Ngoc-Thuy Ha, Ngoc-Thuy Ha"],["dc.contributor.author","Simianer, Henner"],["dc.contributor.author","Falker-Gieske, Clemens"],["dc.contributor.author","Brenig, Bertram B."],["dc.contributor.author","Franke, Andre"],["dc.contributor.author","Hörstgen-Schwark, Gabriele"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Herzog, Sebastian"],["dc.contributor.author","Sharifi, Ahmad R."],["dc.date.accessioned","2019-07-09T11:51:19Z"],["dc.date.available","2019-07-09T11:51:19Z"],["dc.date.issued","2019"],["dc.description.abstract","Abstract Background Elevated water temperature, as is expected through climate change, leads to masculinization in fish species with sexual plasticity, resulting in changes in population dynamics. These changes are one important ecological consequence, contributing to the risk of extinction in small and inbred fish populations under natural conditions, due to male-biased sex ratio. Here we investigated the effect of elevated water temperature during embryogenesis on sex ratio and sex-biased gene expression profiles between two different tissues, namely gonad and caudal fin of adult zebrafish males and females, to gain new insights into the molecular mechanisms underlying sex determination (SD) and colour patterning related to sexual attractiveness. Results Our study demonstrated sex ratio imbalances with 25.5% more males under high-temperature condition, resulting from gonadal masculinization. The result of transcriptome analysis showed a significantly upregulated expression of male SD genes (e.g. dmrt1, amh, cyp11c1 and sept8b) and downregulation of female SD genes (e.g. zp2.1, vtg1, cyp19a1a and bmp15) in male gonads compared to female gonads. Contrary to expectations, we found highly differential expression of colour pattern (CP) genes in the gonads, suggesting the ‘neofunctionalisation’ of those genes in the zebrafish reproduction system. However, in the caudal fin, no differential expression of CP genes was identified, suggesting the observed differences in colouration between males and females in adult fish may be due to post-transcriptional regulation of key enzymes involved in pigment synthesis and distribution. Conclusions Our study demonstrates male-biased sex ratio under high temperature condition and support a polygenic SD (PSD) system in laboratory zebrafish. We identify a subset of pathways (tight junction, gap junction and apoptosis), enriched for SD and CP genes, which appear to be co-regulated in the same pathway, providing evidence for involvement of those genes in the regulation of phenotypic sexual dimorphism in zebrafish."],["dc.identifier.doi","10.1186/s12864-019-5722-1"],["dc.identifier.pmid","31060508"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16103"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59925"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio)"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Frontiers in Cell and Developmental Biology"],["dc.bibliographiccitation.volume","10"],["dc.contributor.affiliation","Hosseini, Shahrbanou; \r\n1\r\nMolecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany"],["dc.contributor.affiliation","Trakooljul, Nares; \r\n5\r\nResearch Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany"],["dc.contributor.affiliation","Hirschfeld, Marc; \r\n1\r\nMolecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany"],["dc.contributor.affiliation","Wimmers, Klaus; \r\n5\r\nResearch Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Genomics Unit, Dummerstorf, Germany"],["dc.contributor.affiliation","Simianer, Henner; \r\n4\r\nCenter for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany"],["dc.contributor.affiliation","Tetens, Jens; \r\n2\r\nFunctional Breeding Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany"],["dc.contributor.affiliation","Sharifi, Ahmad Reza; \r\n4\r\nCenter for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany"],["dc.contributor.affiliation","Brenig, Bertram; \r\n1\r\nMolecular Biology of Livestock and Molecular Diagnostics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany"],["dc.contributor.author","Hosseini, Shahrbanou"],["dc.contributor.author","Trakooljul, Nares"],["dc.contributor.author","Hirschfeld, Marc"],["dc.contributor.author","Wimmers, Klaus"],["dc.contributor.author","Simianer, Henner"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Brenig, Bertram"],["dc.date.accessioned","2022-08-04T07:53:42Z"],["dc.date.available","2022-08-04T07:53:42Z"],["dc.date.issued","2022-07-15"],["dc.date.updated","2022-07-29T05:41:30Z"],["dc.description.abstract","The plasticity of sexual phenotype in response to environmental conditions results in biased sex ratios, and their variation has an effect on population dynamics. Epigenetic modifications can modulate sex ratio variation in species, where sex is determined by genetic and environmental factors. However, the role of epigenetic mechanisms underlying skewed sex ratios is far from being clear and is still an object of debate in evolutionary developmental biology. In this study, we used zebrafish as a model animal to investigate the effect of DNA methylation on sex ratio variation in sex-biased families in response to environmental temperature. Two sex-biased families with a significant difference in sex ratio were selected for genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). The results showed significant genome-wide methylation differences between male-biased and female-biased families, with a greater number of methylated CpG sites in testes than ovaries. Likewise, pronounced differences between testes and ovaries were identified within both families, where the male-biased family exhibited a higher number of methylated sites than the female-biased family. The effect of temperature showed more methylated positions in the high incubation temperature than the control temperature. We found differential methylation of many reproduction-related genes (e.g., sox9a, nr5a2, lhx8a, gata4) and genes involved in epigenetic mechanisms (e.g., dnmt3bb.1, dimt1l, hdac11, h1m) in both families. We conclude that epigenetic modifications can influence the sex ratio variation in zebrafish families and may generate skewed sex ratios, which could have a negative consequence for population fitness in species with genotype-environment interaction sex-determining system under rapid environmental changes."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2022"],["dc.identifier.doi","10.3389/fcell.2022.880779"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/112615"],["dc.language.iso","en"],["dc.relation.eissn","2296-634X"],["dc.relation.orgunit","Abteilung Functional Breeding"],["dc.relation.orgunit","Zentrum für Integrierte Züchtungsforschung"],["dc.rights","CC BY 4.0"],["dc.rights.uri","http://creativecommons.org/licenses/by/4.0/"],["dc.title","Epigenetic Regulation of Phenotypic Sexual Plasticity Inducing Skewed Sex Ratio in Zebrafish"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","346"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Animal Genetics"],["dc.bibliographiccitation.lastpage","356"],["dc.bibliographiccitation.volume","41"],["dc.contributor.author","Qanbari, Saber"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Lichtner, Peter"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T08:40:32Z"],["dc.date.available","2018-11-07T08:40:32Z"],["dc.date.issued","2010"],["dc.description.abstract","P>This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r2 statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r2 = 0.30 +/- 0.32 was observed in pairwise distances of < 25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r2 >= 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance < 100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r2. It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r2 estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to similar to 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed."],["dc.identifier.doi","10.1111/j.1365-2052.2009.02011.x"],["dc.identifier.isi","000279717800002"],["dc.identifier.pmid","20055813"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19259"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0268-9146"],["dc.title","The pattern of linkage disequilibrium in German Holstein cattle"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","435"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Reproduction in domestic animals = Zuchthygiene"],["dc.bibliographiccitation.lastpage","444"],["dc.bibliographiccitation.volume","54"],["dc.contributor.author","Hosseini, Shahrbanou"],["dc.contributor.author","Brenig, Bertram"],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.date.accessioned","2019-10-14T06:57:16Z"],["dc.date.available","2019-10-14T06:57:16Z"],["dc.date.issued","2019"],["dc.description.abstract","Ambient temperature during early stages of life has a substantial effect on physiological processes, eliciting phenotypic plasticity during zebrafish developmental stages. Zebrafish are known to possess a noteworthy ability to modify their phenotype in dependence of environmental factors. However, there is a poor understanding of the effects of temperature during embryogenesis, which influences the biological functions such as survival ability and masculinization in later developmental stages. Since the middle embryonic phase (pharyngula period) is genetically the most conserved stage in embryogenesis, it is very susceptible to embryonic lethality in developmental processes of vertebrates. Here, we tested the effect of transient perturbations (heat shock) during early development (5-24 hr post-fertilization; hpf) at 35°C compared to control group at 28°C, on survival ability of zebrafish to study the embryonic and post-embryonic mortality. We studied the variation of heat-induced masculinization among and across the families in response to high temperature. Furthermore, morphometric traits of adult zebrafish at different developmental time points were measured in order to estimate the temperature × sex interaction effect. We found the highest embryonic mortality around the gastrula and segmentation periods in both experimental groups, with significantly lower survival ability in the temperature-treated group (73.30% ± 0.58% vs. 70.19% ± 0.57%, respectively). A higher hatching success was observed in the control group (71.08% ± 0.61%) compared to the heat-induced group (67.95% ± 0.60%). A distinct reduction in survival ability was also observed in both experimental groups during the first two weeks after hatching, followed by a reduced level of changes thereafter. We found sex ratio imbalances across all families, with 25.2% more males under temperature treatment. Our study on growth performance has shown a positive effect of increased temperature on growth plasticity, with a greater impact on female fish in response to high ambient temperature."],["dc.identifier.doi","10.1111/rda.13382"],["dc.identifier.pmid","30472784"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/62486"],["dc.language.iso","en"],["dc.relation.eissn","1439-0531"],["dc.relation.issn","0936-6768"],["dc.relation.issn","1439-0531"],["dc.title","Phenotypic plasticity induced using high ambient temperature during embryogenesis in domesticated zebrafish, Danio rerio"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]