Genome Finland

Genome Finland
Author: Ilpo Helén
Publisher: Helsinki University Press
Total Pages: 310
Release: 2024-06-27
Genre: Medical
ISBN: 9523691074

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Genome Finland tells a story of genomic medicine in Finland from the study of rare Finnish diseases in the 1960s and 1970s to the implementation of personalized medicine in the 2020s. The main focus is on the 21st century – the period after the Human Genome Project – and on the establishment of new infrastructures to support genomic medicine, such as biobanks. The book opens up the reasoning and discussions as well as the settings and events through which Finnish medical genetics reached the top level of international biomedicine in the late 1990s, biobanks and biobank research evolved during the 2000s and 2010s, and large transnational public-private partnership projects utilising massive amounts of genome and patient data started to dominate also Finnish research into the 2020s. In particular, Genome Finland examines and exposes the connections between biomedical science, ‘knowledge-based’ economy and business, and innovation policy in Finland during the past decades.

Genome Finland

Genome Finland
Author: Ilpo Helén
Publisher:
Total Pages: 0
Release: 2024-06-27
Genre: Medical
ISBN: 9789523691063

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Genome Finland tells a story of genomic medicine in Finland and examines and exposes the connections between biomedical science, 'knowledge-based' economy and business, and innovation policy.

Genome-Scale Algorithm Design

Genome-Scale Algorithm Design
Author: Veli Mäkinen
Publisher: Cambridge University Press
Total Pages: 470
Release: 2023-10-12
Genre: Computers
ISBN: 1009341219

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Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials
Author: Maria Lundström
Publisher: Linköping University Electronic Press
Total Pages: 52
Release: 2018-11-07
Genre:
ISBN: 917685194X

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Crop plants have undergone a multitude of genetic changes during and following their domestication. The spread of agriculture brought the crops to new geographic regions exposing them to new environments and selection pressures along the way. This gave rise to many local variants with traits favoured both by agricultural practices and the environment. Agriculture was introduced in Fennoscandia (Norway, Sweden, Finland and Denmark) around 4000 BC. The composition of the archaeobotanical record gives some clues as to which species were cultivated, but macroscale analyses rarely reach beyond that. Therefore, methods like genetic analysis are necessary to expand our knowledge about the history of crop cultivation. Under optimal conditions, DNA can survive in biological samples for several hundred thousand years. The preservation of plant specimens in the Fennoscandian climate has, however, rarely been explored. This thesis therefore attempts to dive deeper into the Fennoscandian cultivation history through genetic analyses of aged plant materials from both museum collections and archaeological sources. Cereal grains from a range of preservation conditions were evaluated to find which ones might be of interest for genetic investigations. Desiccated materials gave the highest success rates, in agreement with previous studies. Waterlogged materials appeared to contain small amounts of endogenous DNA, whereas genetic analysis of charred cereals failed completely in all samples. Population structure was investigated in 17-19th century materials of both barley and rye from Sweden and Finland. Northern and southern populations of Finnish six-row barley were distinct from one another. In southern Sweden, genetic analysis suggested conserved population structure extending over 200 years. The genetic composition of rye also seemed mostly conserved, but rye did not show geographic population structure across the investigated region in Sweden and Finland. A long-standing question in Fennoscandian crop history has been the interpretation of historical written records mentioning Brassica (cole crops, turnips and mustards), as well as the species identity of archaeobotanical finds of Brassica seeds. Thus, Next Generation Sequencing (NGS) was applied to identify which Brassica types that were cultivated in 17th century Kalmar, Sweden. The analysis corroborated morphological species classification in two of the investigated subfossil seeds, whereas no conclusions could be drawn from the remaining samples. The genome coverages were too low to allow subspecies identification. Wheat has been cultivated in Fennoscandia since the introduction of agriculture but has increased dramatically in importance over the last century. The functional allele of the wheat nutrition gene NAM-B1 was found to be particularly prominent in Fennoscandian wheats, likely associated with its effect on grain maturation time. Here the evolutionary history of NAM-B1 was investigated to see if it could truly be considered a domestication gene as suggested in a previous study. By studying extant landrace materials of Mediterranean tetraploid wheat, it was found that the non-functional allele showed signs indicative of a selective sweep. This selection did not, however, appear to have occurred during domestication. In conclusion, aged plant specimens from both museum and archaeological contexts could contribute greatly to our knowledge about historical cultivation, extending the investigated period into the mid 17th century. Subfossil and waterlogged archaeobotanical materials do contain endogenous DNA, suggesting that they are better suited for genetic analysis than charred ones, at least as far as cereals are concerned. There is potential for classifying archaeological Brassica remains using NGS, even though further optimisation of sample and library preparation may be necessary. And finally, despite NAM-B1 showing signs of selection it should not be considered a domestication gene in tetraploid wheat.

Cracking the Genome

Cracking the Genome
Author: Kevin Davies
Publisher: JHU Press
Total Pages: 358
Release: 2002-10
Genre: Medical
ISBN: 9780801871405

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This newly updated edition sheds light on the secrets of the sequence, highlighting the myriad ways in which genomics will impact human health for generations to come.

Ecology, Genetics and Evolution of Metapopulations

Ecology, Genetics and Evolution of Metapopulations
Author: Ilkka A. Hanski
Publisher: Academic Press
Total Pages: 717
Release: 2004-05-17
Genre: Science
ISBN: 0080530699

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Ecology, Genetics and Evolution of Metapopulations is acollection of specially commissioned articles that looks at fragmented habitats, bringing together recent theoretical advances and empirical studies applying the metapopulation approach. Several chapters closely integrate ecology with genetics and evolutionary biology, and others illustrate how metapopulation concepts and models can be applied to answer questions about conservation, epidemiology, and speciation. The extensive coverage of theory from highly regarded scientists and the many substantive applications in this one-of-a-kind work make it invaluable to graduate students and researchers in a wide range of disciplines. Provides a comprehensive and authoritative account of all aspects of metapopulation biology, integrating ecology, genetics, and evolution Developed by recognized experts, including Hanski who won the Balzan Prize for Ecological Sciences Covers novel applications of the metapopulation approach to conservation

Genome-wide view on the physiology of vitamin D

Genome-wide view on the physiology of vitamin D
Author: Carsten Carlberg
Publisher: Frontiers E-books
Total Pages: 195
Release: 2014-12-05
Genre: Physiology
ISBN: 2889193497

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The main physiological actions of the biologically most active metabolite of vitamin D, 1a,25-dihydroxyvitamin D3(1a,25(OH)2D3), are calcium and phosphorus uptake and transport and thereby controlling bone formation. Other emergent areas of 1a,25(OH)2D3 action are in the control of immune functions, cellular growth and differentiation. This fits both with the widespread expression of the VDR and the above described consequences of vitamin D deficiency. Transcriptome-wide analysis indicated that per cell type between 200 and 600 genes are primary targets of vitamin D. Since most of these genes respond to vitamin D in a cell-specific fashion, the total number of vitamin D targets in the human genome is far higher than 1,000. This is supported by the genome-wide view on VDR binding sites in human lymphocytes, monocytes, colon and hepatic cells. All genomic actions of 1a,25(OH)2D3 are mediated by the transcription factor vitamin D receptor (VDR) that has been the subject of intense study since the 1980’s. Thus, vitamin D signaling primarily implies the molecular actions of the VDR. In this research topic, we present in 15 chapters different perspectives on the action of vitamin D and its receptor, such as the impact of the genomewide distribution of VDR binding loci, ii) the transcriptome- and proteome-wide effects of vitamin D, iii) the role of vitamin D in health, iv) tissue-specific functions of vitamin D and v) the involvement of vitamin D in different diseases, such as infections, autoimmune diseases, diabetes and different types of cancer.