Relevant bibliographies by topics / Ontologie genowe

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Academic literature on the topic 'Ontologie genowe'

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Published: 24 April 2022

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Journal articles on the topic "Ontologie genowe"

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Dwinell, M. R., E. A. Worthey, M. Shimoyama, B. Bakir-Gungor, J. DePons, S. Laulederkind, T. Lowry, et al. "The Rat Genome Database 2009: variation, ontologies and pathways." Nucleic Acids Research 37, Database (January 1, 2009): D744—D749. http://dx.doi.org/10.1093/nar/gkn842.

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Legaz-García, María del Carmen, José Antonio Miñarro-Giménez, Marisa Madrid, Marcos Menárguez-Tortosa, Santiago Torres Martínez, and Jesualdo Tomás Fernández-Breis. "Linking Genome Annotation Projects with Genetic Disorders using Ontologies." Journal of Medical Systems 36, S1 (November 2012): 11–23. http://dx.doi.org/10.1007/s10916-012-9890-7.

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Ringwald, Martin, Joel E. Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, and Carol J. Bult. "Mouse Genome Informatics (MGI): latest news from MGD and GXD." Mammalian Genome 33, no. 1 (October 26, 2021): 4–18. http://dx.doi.org/10.1007/s00335-021-09921-0.

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AbstractThe Mouse Genome Informatics (MGI) database system combines multiple expertly curated community data resources into a shared knowledge management ecosystem united by common metadata annotation standards. MGI’s mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease. MGI is the authoritative source for mouse gene, allele, and strain nomenclature and is the primary source of mouse phenotype annotations, functional annotations, developmental gene expression information, and annotations of mouse models with human diseases. MGI maintains mouse anatomy and phenotype ontologies and contributes to the development of the Gene Ontology and Disease Ontology and uses these ontologies as standard terminologies for annotation. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI’s two major knowledgebases. Here, we highlight some of the recent changes and enhancements to MGD and GXD that have been implemented in response to changing needs of the biomedical research community and to improve the efficiency of expert curation. MGI can be accessed freely at http://www.informatics.jax.org.
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Wong, Hector R., Thomas P. Shanley, Bhuvaneswari Sakthivel, Natalie Cvijanovich, Richard Lin, Geoffrey L. Allen, Neal J. Thomas, et al. "Genome-level expression profiles in pediatric septic shock indicate a role for altered zinc homeostasis in poor outcome." Physiological Genomics 30, no. 2 (July 2007): 146–55. http://dx.doi.org/10.1152/physiolgenomics.00024.2007.

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Human septic shock involves multiple genome-level perturbations. We have conducted microarray analyses in children with septic shock within 24 h of intensive care unit admission, using whole blood-derived RNA. Based on sequential statistical and expression filters, there were 2,482 differentially regulated gene probes (1,081 upregulated and 1,401 downregulated) between patients with septic shock ( n = 42) and controls ( n = 15). Both gene lists encompassed several biologically relevant gene ontologies and canonical pathways. Notably, many of the genes downregulated in the patients with septic shock, relative to the controls, participate in gene ontologies related to metal or zinc homeostasis. Comparison of septic shock survivors ( n = 33) and nonsurvivors ( n = 9) demonstrated differential regulation of 63 gene probes. Among the 63 gene probes differentially regulated between septic shock survivors and nonsurvivors, two isoforms of metallothionein (MT) demonstrated increased expression in the nonsurvivors. Consistent with the ability of MT to sequester zinc in the intracellular compartment, nonsurvivors had lower serum zinc levels compared with survivors. In a corroborating study of murine sepsis, MT-null mice demonstrated a survival advantage compared with wild-type mice. These data represent the largest reported cohort of pediatric patients with septic shock that has undergone genome-level expression profiling based on microarray. The data are biologically plausible and demonstrate that genome-level alterations of zinc homeostasis may be prevalent in clinical pediatric septic shock.
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Shimoyama, Mary, Victoria Petri, Dean Pasko, Susan Bromberg, Wenhua Wu, Jiali Chen, Nataliya Nenasheva, Anne Kwitek, Simon Twigger, and Howard Jacob. "Using Multiple Ontologies to Integrate Complex Biological Data." Comparative and Functional Genomics 6, no. 7-8 (2005): 373–78. http://dx.doi.org/10.1002/cfg.498.

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The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease.
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Jaiswal, Pankaj, Doreen Ware, Junjian Ni, Kuan Chang, Wei Zhao, Steven Schmidt, Xiaokang Pan, et al. "Gramene: Development and Integration of Trait and Gene Ontologies for Rice." Comparative and Functional Genomics 3, no. 2 (2002): 132–36. http://dx.doi.org/10.1002/cfg.156.

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Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation.
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Lan, Ning, Gaetano T. Montelione, and Mark Gerstein. "Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level." Current Opinion in Chemical Biology 7, no. 1 (February 2003): 44–54. http://dx.doi.org/10.1016/s1367-5931(02)00020-0.

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Tian, Dongmei, Pei Wang, Bixia Tang, Xufei Teng, Cuiping Li, Xiaonan Liu, Dong Zou, Shuhui Song, and Zhang Zhang. "GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals." Nucleic Acids Research 48, no. D1 (September 30, 2019): D927—D932. http://dx.doi.org/10.1093/nar/gkz828.

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Abstract GWAS Atlas (https://bigd.big.ac.cn/gwas/) is a manually curated resource of genome-wide variant-trait associations for a wide range of species. Unlike existing related resources, it features comprehensive integration of a high-quality collection of 75 467 variant-trait associations for 614 traits across 7 cultivated plants (cotton, Japanese apricot, maize, rapeseed, rice, sorghum and soybean) and two domesticated animals (goat and pig), which were manually curated from 254 publications. We integrated these associations into GWAS Atlas and presented them in terms of variants, genes, traits, studies and publications. More importantly, all associations and traits were annotated and organized based on a suite of ontologies (Plant Trait Ontology, Animal Trait Ontology for Livestock, etc.). Taken together, GWAS Atlas integrates high-quality curated GWAS associations for animals and plants and provides user-friendly web interfaces for data browsing and downloading, accordingly serving as a valuable resource for genetic research of important traits and breeding application.
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Schoof, Heiko. "Towards Interoperability in Genome Databases: The MAtDB (MIPSArabidopsis thalianaDatabase) Experience." Comparative and Functional Genomics 4, no. 2 (2003): 255–58. http://dx.doi.org/10.1002/cfg.278.

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Increasing numbers of whole-genome sequences are available, but to interpret them fully requires more than listing all genes. Genome databases are faced with the challenges of integrating heterogenous data and enabling data mining. In comparison to a data warehousing approach, where integration is achieved through replication of all relevant data in a unified schema, distributed approaches provide greater flexibility and maintainability. These are important in a field where new data is generated rapidly and our understanding of the data changes. Interoperability between distributed data sources allows data maintenance to be separated from integration and analysis. Simple ways to access the data can facilitate the development of new data mining tools and the transition from model genome analysis to comparative genomics. With the MIPSArabidopsis thalianagenome database (MAtDB, http://mips.gsf.de/proj/thal/db) our aim is to go beyond a data repository towards creating an integrated knowledge resource. To this end, theArabidopsisgenome has been a backbone against which to structure and integrate heterogenous data. The challenges to be met are continuous updating of data, the design of flexible data models that can evolve with new data, the integration of heterogenous data, e.g. through the use of ontologies, comprehensive views and visualization of complex information, simple interfaces for application access locally or via the Internet, and knowledge transfer across species.
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Wang, Shur-Jen, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Rajni Nigam, Melinda R. Dwinell, and Mary Shimoyama. "Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database." Physiological Genomics 48, no. 8 (August 1, 2016): 589–600. http://dx.doi.org/10.1152/physiolgenomics.00046.2016.

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Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality.
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Dissertations / Theses on the topic "Ontologie genowe"

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Chen, Eric Chun-Hung. "Fractionation Resistance of Duplicate Genes Following Whole Genome Duplication in Plants as a Function of Gene Ontology Category and Expression Level." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/32789.

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With the proliferation of plant genomes being sequenced, assembled, and annotated, duplicate gene loss from whole genome duplication events, also known in plants as frac- tionation, has shown to have a different pattern from the classic gene duplication models described by Ohno in 1970. Models proposed more recently, the Gene Balance and Gene Dosage hypotheses, try to model this pattern. These models, however, disagree with each other on the relative importance of gene function and gene expression. In this thesis we explore the effects of gene function and gene expression on duplicate gene loss and retention. We use gene sequence similarity and gene order conservation to construct our gene fam- ilies. We applied multiple whole genome comparison methods across various plants in rosids, asterids, and Poaceae in looking for a general pattern. We found that there is great consistency across different plant lineages. Genes categorized as metabolic genes with low level of expression have relatively low fractionation resistance, losing duplicate genes readily, while genes categorized as regulation and response genes with high level of expression have relatively high fractionation resistance, retaining more duplicate gene pairs or triples. Though both gene function and gene expression have important effects on retention pattern, we found that gene function has a bigger effect than gene expression. Our results suggest that both the Gene Balance and Gene Dosage models account to some extent for fractionation resistance.
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Teixeira, Marcus Vinícius Carneiro. "Gerenciamento de anotações de biosseqüências utilizando associações entre ontologias e esquemas XML." Universidade Federal de São Carlos, 2008. https://repositorio.ufscar.br/handle/ufscar/384.

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Made available in DSpace on 2016-06-02T19:05:31Z (GMT). No. of bitstreams: 1 2080.pdf: 1369419 bytes, checksum: 4100f6c7c0400bc50f4f2f9a28621613 (MD5) Previous issue date: 2008-05-26
Universidade Federal de Sao Carlos
Bioinformatics aims at providing computational tools to the development of genome researches. Among those tools are the annotations systems and the Database Management Systems (DBMS) that, associated to ontologies, allow the formalization of both domain conceptual and the data scheme. The data yielded by genome researches are often textual and with no regular structures and also requires scheme evolution. Due to these aspects, semi-structured DBMS might offer great potential to manipulate those data. Thus, this work presents architecture for biosequence annotation based on XML databases. Considering this architecture, a special attention was given to the database design and also to the manual annotation task performed by researchers. Hence, this architecture presents an interface that uses an ontology-driven model for XML schemas modeling and generation, and also a manual annotation interface prototype that uses molecular biology domain ontologies, such as Gene Ontology and Sequence Ontology. These interfaces were proven by Bioinformatics and Database experienced users, who answered questionnaires to evaluate them. The answers presented good assessments to issues like utility and speeding up the database design. The proposed architecture aims at extending and improving the Bio-TIM, an annotation system developed by the Database Group from the Computer Science Department of the Federal University from São Carlos (UFSCar).
A Bioinformática é uma área da ciência que visa suprir pesquisas de genomas com ferramentas computacionais que permitam o seu desenvolvimento tecnológico. Dentre essas ferramentas estão os ambientes de anotação e os Sistemas Gerenciadores de Bancos de Dados (SGBDs) que, associados a ontologias, permitem a formalização de conceitos do domínio e também dos esquemas de dados. Os dados produzidos em projetos genoma são geralmente textuais e sem uma estrutura de tipo regular, além de requerer evolução de esquemas. Por suas características, SGBDs semi-estruturados oferecem enorme potencial para tratar tais dados. Assim, este trabalho propõe uma arquitetura para um ambiente de anotação de biosseqüências baseada na persistência dos dados anotados em bancos de dados XML. Neste trabalho, priorizou-se o projeto de bancos de dados e também o apoio à anotação manual realizada por pesquisadores. Assim, foi desenvolvida uma interface que utiliza ontologias para guiar a modelagem de dados e a geração de esquemas XML. Adicionalmente, um protótipo de interface de anotação manual foi desenvolvido, o qual faz uso de ontologias do domínio de biologia molecular, como a Gene Ontology e a Sequence Ontology. Essas interfaces foram testadas por usuários com experiências nas áreas de Bioinformática e Banco de Dados, os quais responderam a questionários para avaliá-las. O resultado apresentou qualificações muito boas em diversos quesitos avaliados, como exemplo agilidade e utilidade das ferramentas. A arquitetura proposta visa estender e aperfeiçoar o ambiente de anotação Bio-TIM, desenvolvido pelo grupo de Banco de Dados do Departamento de Computação da Universidade Federal de São Carlos (UFSCar).
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Mungall, Christopher. "Next-generation information systems for genomics." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5020.

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The advent of next-generation sequencing technologies is transforming biology by enabling individual researchers to sequence the genomes of individual organisms or cells on a massive scale. In order to realize the translational potential of this technology we will need advanced information systems to integrate and interpret this deluge of data. These systems must be capable of extracting the location and function of genes and biological features from genomic data, requiring the coordinated parallel execution of multiple bioinformatics analyses and intelligent synthesis of the results. The resulting databases must be structured to allow complex biological knowledge to be recorded in a computable way, which requires the development of logic-based knowledge structures called ontologies. To visualise and manipulate the results, new graphical interfaces and knowledge acquisition tools are required. Finally, to help understand complex disease processes, these information systems must be equipped with the capability to integrate and make inferences over multiple data sets derived from numerous sources. RESULTS: Here I describe research, design and implementation of some of the components of such a next-generation information system. I first describe the automated pipeline system used for the annotation of the Drosophila genome, and the application of this system in genomic research. This was succeeded by the development of a flexible graphoriented database system called Chado, which relies on the use of ontologies for structuring data and knowledge. I also describe research to develop, restructure and enhance a number of biological ontologies, adding a layer of logical semantics that increases the computability of these key knowledge sources. The resulting database and ontology collection can be accessed through a suite of tools. Finally I describe how the combination of genome analysis, ontology-based database representation and powerful tools can be combined in order to make inferences about genotype-phenotype relationships within and across species. CONCLUSION: The large volumes of complex data generated by high-throughput genomic and systems biology technology threatens to overwhelm us, unless we can devise better computing tools to assist us with its analysis. Ontologies are key technologies, but many existing ontologies are not interoperable or lack features that make them computable. Here I have shown how concerted ontology, tool and database development can be applied to make inferences of value to translational research.
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Dockter, Rhyan B. "Genome Snapshot and Molecular Marker Development in Penstemon (Plantaginaceae)." BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2512.

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Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.
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Zeng, Jia. "The evolutionary significance of DNA methylation in human genome." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50308.

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In eukaryotic genomes ranging from plants to mammals, DNA methylation is a major epigenetic modification of DNA by adding a methyl group exclusively to cytosine residuals. In mammalian genomes such as humans, these cytosine bases are usually followed by guanine. Although it does not change the primary DNA sequence, this covalent modification plays critical roles in several regulatory processes and can impact gene activity in a heritable fashion. What is more important, DNA methylation is essential for mammalian embryonic development and aberrant DNA methylation is implicated in several human diseases, in particular in neuro-developmental syndromes (such as the fragile X and Rett syndromes) and cancer. These biological significances disclose the importance of understanding genomic patterns and function role of DNA methylation in human, as a initial step to get to know the epigenotype and its manner in connecting the phenotype and genotype. Two key papers back in 1975 independently suggested that methylation of CpG dinucleotides in vertebrates could be established de novo and inherited through somatic cell divisions by protein machineries of DNA methyltransferases that recognizes hemi-methylated CpG palindromes. They also indicated that the methyl group could be recognized by DNA-binding proteins and that DNA methylation directly silences gene expression. After almost four decades, several key points in these foundation papers are proved to be true. Take the mammalian genome for example, there are several findings indicating the epigenetic repression of gene expression by DNA methylation. These include X-chromosome inactivation, gene imprinting and suppressing the proliferation of transposable elements and repeat elements of viral or retroviral origin. In addition to these, many novel roles of DNA methylation have also been revealed. For example, DNA methylation can regulate alternative splicing by preventing CTCF, an evolutionarily conserved zinc-finger protein, binding to DNA. By using the technique of fluorescence resonance energy transfer (FRET) and fluorescence polarization, DNA methylation has also been shown to increase nucleosome compaction through DNA-histone contacts. What is more important, DNA methylation is essential for mammalian embryonic development and aberrant change of DNA methylation has been related to disease such as cancer. However, it is also notable there are several lines of evidence contradicting the relationship between DNA methylation and gene silencing. For example, comparison of DNA methylation levels in human genome on the active and inactive X chromosomes showed reduced methylation specifically over gene bodies on inactive X chromosomes. Not only in human, DNA methylation is found to be usually targeted to the transcription units of actively transcribed genes in invertebrate species. These results prove that the function of DNA methylation is challenging to be unravel. Besides, due to the development of sequencing technique, whole genome DNA methylation profiles have been detected in diverse species. Comparing genomic patterns of DNA methylation shows considerable variation among taxa, especially between vertebrates and invertebrates. However, even though extensive studies reveal the patterns and functions of DNA methylation in different species, in the mean time, they also highlight the limits to our understanding of this complex epigenetic system. During my Ph.D., in order to perform in-depth studies of DNA methylation in diverse animals as a way to understand the complexity of DNA methylation and its functions, I dedicated my efforts in investigating and analyzing the DNA methylation profiles in diverse species, ranging from insects to primates, including both model and non-model organisms. This dissertation, which constitutes an important part of my research, mainly focuses on the DNA methylation profile in primates including human and chimpanzee. In general, I will use three chapters to elucidate my work in generating and interpreting the whole genome DNA methylation data. Firstly, we generated nucleotide-resolution whole-genome methylation maps of the prefrontal cortex of multiple humans and chimpanzees, then comprehensive comparative studies for these DNA methylation maps have been performed, by integrating data on gene expression as well. This work demonstrates that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and also potentially contribute to the human-specific traits, such as evolution of disease vulnerabilities. Secondly , we performed global analyses of CpG islands (CGIs) methylation across multiple methylomes of distinctive cellular origins in human. The results from this work show that the human CpG islands can be distinctly classified into different clusters solely based upon the DNA methylation profiles, and these CpG islands clusters reflect their distinctive nature at many biological levels, including both genomic characteristics and evolutionary features. Moreover, these CpG islands clusters are non-randomly associated with several important biological phenomena and processes such as diseases, aging, and gene imprinting. These new findings shed lights in deciphering the regulatory mechanisms of CpG islands in human health and diseases. At last, by utilizing the DNA methylome from human sperm and genetic map generated from the International HapMap Consortium project, we investigated the hypothesis suggesting a potential role of germ line DNA methylation in affecting meiotic recombination, which is essential for successful meiosis and various evolutionary processes. Even thought the results imply that DNA methylation is a important factor affecting regional recombination rate, the strength of correlation between these two is not as strong as the previous report. Besides, high-throughput analyses indicate that other epigenetic modifications, tri-methylation of histone 3 lysine 4 and histone 3 lysine 27 are also global features at the recombination hotspots, and may interact with methylation to affect the recombination pattern simultaneously. This work suggests epigenetic mechanisms as additional factors affecting recombination, which cannot be fully explained by the DNA sequence itself. In summary, I hope the results from these work can expand our knowledge regarding the common and variable patterns of DNA methylation in different taxa, and shed light about the function role and its major change during animal evolution.
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Pichler, Rafaela. "Annäherung an die Bildsprache : Ontologien als Hilfsmittel für Bilderschliessung und Bildrecherche in Kunstbilddatenbanken /." Chur : Hochschule für Technik und Wirtschaft, Arbeitsbereich Informationswissenschaft, 2007. http://sfx.ethz.ch/sfx_locater?sid=ALEPH:EBI01&genre=journal&issn=1660-945X&volume=18.

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Knechtel, Martin, and Daniel Schuster. "Semantische Integration und Wiederverwendung von Produktontologien für offene Marktplätze im Web." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-141144.

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Tietze, Katja, and Thomas Schlegel. "On Modeling a Social Networking Service Description." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-143738.

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Yi, Gang Man. "An algorithm for identifying clusters of functionally related genes in genomes." [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1079.

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Knechtel, Martin, and Daniel Schuster. "Semantische Integration und Wiederverwendung von Produktontologien für offene Marktplätze im Web." Technische Universität Dresden, 2008. https://tud.qucosa.de/id/qucosa%3A27936.

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Books on the topic "Ontologie genowe"

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Toward a Thomist methodology. Lewiston: E. Mellen Press, 1988.

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Meizel, Katherine. Multivocality. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780190621469.001.0001.

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This book frames vocality as a particularly holistic way to investigate the voice in music, as a concept embodying all the implications with which voice is inscribed—the negotiation of sound and Self, individual and culture, medium and meaning, ontology and embodiment. Like identity, vocality is fluid, constructed and reconstructed continually; even the most iconic of singers do not simply exercise a static voice throughout a lifetime. The book highlights such singers in vocal motion, focusing on their transitions and transgressions across genre and gender boundaries, cultural borders, the lines between body and technology, between secular and religious contexts, between found voices and lost ones. And as 21st-century singers habitually perform across styles, genres, cultural contexts, histories, and identities, the author suggests that they are not only performing in multiple vocalities, but more critically, they are performing multivocality—creating and recreating identity through the process of singing with many voices, at once produced by and in resistance against neoliberal expectations. Multivocality, in its focus on the suppressions and soundings of voice in various borderlands of identity, works toward a deeper understanding of voice as a technology of the self and of culture.
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Herman, David. Narratology beyond the Human. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190850401.001.0001.

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This book aims to develop a cross-disciplinary approach to post-Darwinian narratives concerned with animals and human-animal relationships. In outlining this integrative approach to storytelling in a more-than-human setting, the study also considers the enabling and constraining effects of different narrative media, examining a range of fictional and nonfictional texts disseminated in print, comics and graphic novels, and film. Focusing on techniques employed in these media, including the use of animal narrators, alternation between human and nonhuman perspectives on events, shifts backward and forward in narrative time, the embedding of stories within stories, and others, the book explores how specific strategies for portraying nonhuman agents both emerge from and contribute to broader attitudes toward animal life. Conversely, emphasizing that stories are, in general, interwoven with cultures’ ontologies, their assumptions about what sorts of beings populate the world and how those beings’ qualities and abilities relate to the qualities and abilities ascribed to humans, promises to reshape existing frameworks for narrative inquiry. Ideas that have been foundational for the field are at stake here, including ideas about what makes narratives more or less amenable to being interpreted as narratives, about the extent to which differences of genre affect attributions of mental states to characters (human as well as nonhuman) in narrative contexts, and about the suitability of stories as a means for engaging with supraindividual phenomena unfolding over long timescales and in widely separated places, including patterns and events situated at the level of animal populations and species rather than particular creatures.
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Book chapters on the topic "Ontologie genowe"

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Kim, Ju Han. "Molecular Pathways and Gene Ontology." In Genome Data Analysis, 213–32. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-1942-6_12.

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Kim, Ju Han. "Network Biology, Sequence, Pathway and Ontology Informatics." In Genome Data Analysis, 175–87. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-1942-6_10.

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Kim, Ju Han. "Gene Ontology and Biological Pathway-Based Analysis." In Genome Data Analysis, 121–34. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-1942-6_7.

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Enea, Roberto, Maria Teresa Pazienza, and Andrea Turbati. "GENOMA: GENeric Ontology Matching Architecture." In Lecture Notes in Computer Science, 303–15. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-24309-2_23.

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Rance, Bastien, Jean-François Gibrat, and Christine Froidevaux. "An Adaptive Combination of Matchers: Application to the Mapping of Biological Ontologies for Genome Annotation." In Lecture Notes in Computer Science, 113–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02879-3_10.

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Martínez Ferrandis, Ana Ma, Oscar Pastor López, and Giancarlo Guizzardi. "Applying the Principles of an Ontology-Based Approach to a Conceptual Schema of Human Genome." In Conceptual Modeling, 471–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-41924-9_40.

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Librelotto, Giovani Rubert, José Carlos Mombach, Marialva Sinigaglia, Éder Simão, Heleno Borges Cabral, and Mauro A. A. Castro. "An Ontology to Integrate Transcriptomics and Interatomics Data Involved in Gene Pathways of Genome Stability." In Advances in Bioinformatics and Computational Biology, 164–67. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-03223-3_18.

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Meier, Michael, and Megan J. Wilson. "Using RNA-Seq for Transcriptome Profiling of Botrylloides sp. Regeneration." In Methods in Molecular Biology, 599–615. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_32.

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AbstractThe decrease in sequencing costs and technology improvements has led to the adoption of RNA-sequencing to profile transcriptomes from further non-traditional regeneration model organisms such as the colonial ascidian Botrylloides leachii. The relatively unbiased way in which transcripts are identified and quantified makes this technique suitable to detect large-scale changes in expression, and the identification of novel transcripts and isoforms. Of particular interest to many researchers is the discovery of differentially expressed transcripts across different treatment conditions or stages of regeneration. This protocol describes a workflow starting from processing raw sequencing reads, mapping reads, assembly of transcripts, and measuring their abundance, creating lists of differentially expressed genes and their biological interpretation using gene ontologies. All programs used in this protocol are open-source software tools and freely available.
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Collmer, C. W., M. Lindeberg, and Alan Collmer. "Gene Ontology (GO) for Microbe–Host Interactions and Its Use in Ongoing Annotation of Three Pseudomonas syringae Genomes via the Pseudomonas–Plant Interaction (PPI) Web Site." In Pseudomonas syringae Pathovars and Related Pathogens – Identification, Epidemiology and Genomics, 221–28. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6901-7_23.

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Saripalle, Rishi Kanth, Steven A. Demurjian, Michael Blechner, and Thomas Agresta. "HOD2MLC." In Application Development and Design, 659–85. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-3422-8.ch028.

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Ontologies have gained increasing usage to augment an application with domain knowledge, particularly in healthcare, where they represent knowledge ranging from: bioinformatics data such as protein, gene, etc. to biomedical informatics such as diseases, diagnosis, symptoms, etc. However, the current ontology development efforts and process are data intensive and construction based, creating ontologies for specific applications/requirements, rather than designing an abstract ontological solution(s) that can be reusable across the domain using a well-defined design process. To address this deficiency, the work presented herein positions ontologies as software engineering artifact that allows them to be placed into the position to share the captured domain conceptualization and its vocabulary involving disparate domain backgrounds, that can then be created, imported, exported and re-used using different frameworks, tools and techniques. Towards this end, the authors propose an agile software process for ontologies referred to as the Hybrid Ontology Design & Development Model with Lifecycle, HOD2MLC. To place HOD2MLC into a proper perspective, they explore, compare, and contrast it to existing ontology design and development alternatives with respect their various phases as related to the authors' work and phases in varied SDP models.
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Conference papers on the topic "Ontologie genowe"

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McPherson, Jeffrey D., Ian R. Grosse, Sundar Krishnamurty, Jack C. Wileden, Elizabeth R. Dumont, and Michael A. Berthaume. "Integrating Biological and Engineering Ontologies." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-13527.

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As methods for engineering data acquisition improve, methods for storing, generating knowledge from, and sharing that data for efficient reuse have become more important. Knowledge management in the engineering community can greatly benefit from advancements made in knowledge management in biology. The biological community has already made progress in knowledge management through projects such as the Gene Ontology and CellML, and it behooves the engineering community to learn from their successes. Engineering and biology overlap in the field of biosimulation, (i.e. finite-element analysis of biological systems, see www.biomesh.org) which gives an opportunity to integrate successful ontologies from the biology community into the engineering community. Previous research has led to the creation of the Biomesh project, which is a collection of biological finite element (FE) models. These FE models relate to a particular anatomical structure of an organism, and to the set of biological material properties associated with the models. Thus, knowledge management for this application requires knowledge integration from three distinct fields: engineering (materials and models), anatomy, and biological classification. The existing e-Design Framework offers the Engineering Analysis Models ontology and Materials ontology to store knowledge about materials and FE models. Similarly, the existing Minimal Anatomical Terms ontology and the NCBI Organismal Classification taxonomy were used to store information about anatomy and biological classification, respectively. In this paper these ontologies are interlinked in a single, synergistic ontology to expose and integrate knowledge in a transparent manner between previously disparate domains. A case study is presented to demonstrate the usefulness of the approach in which knowledge from a biological material and FE model are methodically stored in the new ontology, and the organismal classification and anatomical structure of the model are immediately exposed to the user.
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Witherell, Paul, Sundar Krishnamurty, Ian Grosse, and Jack Wileden. "Semantic Relatedness Measures for Identifying Relationships in Product Development Processes." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-87624.

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The Semantic Web, especially in relation to ontologies, provides a structured, formal framework for knowledge interoperability. This trait has been exploited by both the biomedical community in development of the Human Gene Ontology [1] and also by geographers in development of geospatial ontologies [2]. Using semantic relatedness techniques, researchers from both communities have been able to develop and integrate comprehensive knowledge bases. Beyond knowledge integration, semantic relatedness techniques have also been able to provide each community with a unique insight into relationships between concepts in their respective domains. In the engineering community, semantic relatedness techniques promise to provide similar insight into product development processes. This paper explores the application of semantic relatedness techniques to ontologies as a means towards improved knowledge management in product development processes. Several different semantic relatedness techniques are reviewed, including a recently developed meronomic technique specific to domain ontologies. Three of these techniques are adopted to create a semantic relatedness measure specifically designed to identify and rank underlying relationships that exist between aspects of the product development process. Four separate case studies are then presented to evaluate the relative accuracy of the developed algorithm and then determine its effectiveness in exposing underlying relationships.
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Masseroli, Marco, Marco Tagliasacchi, and Davide Chicco. "Semantically improved genome-wide prediction of Gene Ontology annotations." In 2011 11th International Conference on Intelligent Systems Design and Applications (ISDA). IEEE, 2011. http://dx.doi.org/10.1109/isda.2011.6121802.

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Papadimitriou, Georgios, Zeyn Saigol, and David M. Lane. "Enabling fault recovery and adaptation in mine-countermeasures missions using ontologies." In OCEANS 2015 - Genova. IEEE, 2015. http://dx.doi.org/10.1109/oceans-genova.2015.7271535.

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HVIDSTEN, T. R., J. KOMOROWSKI, A. K. SANDVIK, and A. LÆGREID. "PREDICTING GENE FUNCTION FROM GENE EXPRESSIONS AND ONTOLOGIES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2000. http://dx.doi.org/10.1142/9789814447362_0030.

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KARP, P. D., S. PALEY, C. J. KRIEGER, and P. ZHANG. "AN EVIDENCE ONTOLOGY FOR USE IN PATHWAY/GENOME DATABASES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0019.

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Beck, Tim, Gudmundur A. Thorisson, and Anthony J. Brookes. "Applying ontologies and exploring nanopublishing in a genome-wide association study database." In the 4th International Workshop. New York, New York, USA: ACM Press, 2012. http://dx.doi.org/10.1145/2166896.2166897.

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Visconti, Alessia, Francesca Cordero, Marco Botta, and Raffaele A. Calogero. "Gene Ontology Rewritten for Computing Gene Functional Similarity." In 2010 International Conference on Complex, Intelligent and Software Intensive Systems (CISIS). IEEE, 2010. http://dx.doi.org/10.1109/cisis.2010.30.

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Kustra, R., and A. Zagdanski. "Incorporating Gene Ontology in Clustering Gene Expression Data." In Proceedings. 19th IEEE International Symposium on Computer-Based Medical Systems. IEEE, 2006. http://dx.doi.org/10.1109/cbms.2006.100.

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Gladstone, Julia. "Exploring the Key Informational, Ethical and Legal Concerns to the Development of Population Genomic Databases for Pharmacogenomic Research." In InSITE 2005: Informing Science + IT Education Conference. Informing Science Institute, 2005. http://dx.doi.org/10.28945/2880.

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The completion of a high quality comprehensive sequence of the human genome has lead to the discovery of genetic links to complex diseases and the development of target drugs. Population genetic databases (PGDs) are a powerful resource to the systematic study of the genetic component of disease; in the quest to understand the impact of genetic factors on drug response data from laboratory experiments, computational methods and clinical studies must be integrated. The establishment of a pharmacogenomics knowledge base entails complex information management balanced with the appropriate legal and ethical standards. This article reviews some of the ontology development challenges and examines the need to establish a legal structure which creates the proper intellectual property incentives to develop PGDs and the ethical standards that must be upheld so that the terms of informed consent are legitimate.
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Reports on the topic "Ontologie genowe"

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Mukhopadhyay, Biswarup, Brett M. Tyler, Joao Setubal, and T. M. Murali. Gene Ontology Terms and Automated Annotation for Energy-Related Microbial Genomes. Office of Scientific and Technical Information (OSTI), November 2017. http://dx.doi.org/10.2172/1406983.

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Levin, Ilan, Avtar K. Handa, Avraham Lalazar, and Autar K. Mattoo. Modulating phytonutrient content in tomatoes combining engineered polyamine metabolism with photomorphogenic mutants. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7587724.bard.

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Fruit constitutes a major component of our diet, providing fiber, vitamins, minerals, and many other phytonutrients that promote good health. Fleshy fruits, such as tomatoes, already contain high levels of several of these ingredients. Nevertheless, efforts have been invested in increasing and diversifying the content of phytonutrients, such as carotenoids and flavonoids, in tomato fruits. Increasing levels of phytonutrients, such as lycopene, is highly justified from the perspective of the lycopene extraction industry due to cost effectiveness reasons. Diversifying phytonutrients, in particular those that contribute to fruit color, could potentially provide an array of attractive colors to our diet. Our major goal was to devise a novel strategy for developing tomato fruits with enhanced levels of phytochemicals known to promote good health with special emphasis on lycopene content. A further important goal was to analyze global gene expression of selected genetic lines produced throughout this study in order is to dissect the molecular mechanisms regulating phytonutrients accumulation in the tomato fruit. To achieve these goals we proposed to: 1. combine, by classical breeding, engineered polyamine metabolism with photomorphogenic high pigment mutants in order generate tomato plant with exceptionally high levels of phytonutrients; 2. use gene transfer technology for genetic introduction of key genes that promote phytonutrient accumulation in the tomato fruit, 3. Analyze accumulation patterns of the phytonutrients in the tomato fruit during ripening; 4. Analyze global gene expression during fruit ripening in selected genotypes identified in objectives 1 and 2, and 5. Identify and analyze regulatory mechanisms of chloroplast disassembly and chromoplast formation. During the 3 years research period we have carried out most of the research activities laid out in the original proposal and our key conclusions are as follows: 1. the engineered polyamine metabolism strategy proposed by the US collaborators can not increase lycopene content either on its own or in combination with an hp mutant (hp-2ᵈᵍ); 2. The hp-2ᵈᵍ affects strongly the transcriptional profile of the tomato fruit showing a strong tendency for up- rather than down-regulation of genes, 3. Ontology assignment of these miss-regulated genes revealed a consistent up-regulation of genes related to chloroplast biogenesis and photosynthesis in hp-2ᵈᵍ mutants throughout fruit development; 4. A tendency for up-regulation was also usually observed in structural genes involved in phytonutrientbiosynthesis; however this up-regulation was not as consistent. 5. Microscopic observations revealed a significantly higher number of chloroplasts in pericarp cells of mature-green hp-2ᵈᵍ/hp-2ᵈᵍ fruits in comparison to their normal fully isogenic counterparts. 6. The relative abundance of chloroplasts could be observed from early stages of fruit development. Cumulatively these results suggest that: 1. the overproduction of secondary metabolites, characterizing hp-2ᵈᵍ/hp-2ᵈᵍ fruits, is more due to chloroplast number rather then to transcriptional activation of structural genes of the relevant metabolic pathways, and 2. The molecular trigger increasing metabolite levels in hp-2ᵈᵍ mutant fruits should be traced at early stage of fruit development.
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