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Plant Ecology klaus.ammann@ips.unibe.ch Sabanci University Spring 2009

Plant Ecology klaus.ammann@ips.unibe.ch Sabanci University Spring 2009 Lecturer: Prof. em. Dr. Klaus Ammann, University of Bern, Switzerland Chapter 1: Weeks 1 – 3 Document: Sabanci-Ecology-1-Biodiv-General.ppt Sabanci-Ecology-2-Patterns-Protection.ppt

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Plant Ecology klaus.ammann@ips.unibe.ch Sabanci University Spring 2009

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  1. Plant Ecologyklaus.ammann@ips.unibe.ch Sabanci University Spring 2009 Lecturer: Prof. em. Dr. Klaus Ammann, University of Bern, Switzerland Chapter 1: Weeks 1 – 3 Document: Sabanci-Ecology-1-Biodiv-General.ppt Sabanci-Ecology-2-Patterns-Protection.ppt Biodiversity Basics and Protection of Biodiversity precondition of understanding ecology and human life on earth Chapter 2: Week 4 Document: Sabanci-Ecology-3-Pollination.ppt Knowledge in pollination ecology helps to understand plant systematics and ecology Chapter 3: Weeks 5 – 6 Document: Sabanci-Ecology-4-Bioprospecting.ppt Bioprospection as a typical link between economy and protection Chapter 4: Weeks 7 – 9 Document: Sabanci-Ecology-5-Vegetation-Ecology.ppt Vegetation ecology related to climate Chapter 5: Weeks 10-14 Single Documents to be uploaded Case histories: Seed distribution, Biofortified Sorghum in Africa, Biology of Cryptogams Rain Forests Jamaica, Step Vegetation Worldwide, Alpine Vegetation and Glacial History, European Plant Geography, Vegetation of Tenerife, Canary Islands.

  2. 1.1. What is Biodiversity ?

  3. 1.1. What is Biodiversity? Link to the United Nations Convention of Biodiversity (CBD) website http://www.biodiv.org/default.shtml Link to the United Nations Convention of Biodiversity (CBD) website of Turkey http://biodiversity-chm.eea.europa.eu/news/turkish-website-cbd Biodiversity is a composite of Biology and Diversity. Normally it is used for the description of the number and diversity of taxa of living organisms. In the broadest sense of the word it is meaning: „Life on Planet Earth“ Biodiversity may also mean diversity of genes, species or ecosystems 1.1. Definition Biodiversität

  4. 1.1.1.Genetic Diversity

  5. 1.2. Genetic Diversity Inherited variation within and outside populations of organisms. Ultimately this means variation in the arrangement of the four base pairs in the sequence as components of nucleic acids, which build the genetic code. The following 5 slides from: Definition Genetische Diversität The Arabidopsis Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 6814, pp 796-815 http://dx.doi.org/10.1038/35048692 AND http://www.nature.com/nature/journal/v408/n6814/suppinfo/408796a0_S1.html AND http://www.botanischergarten.ch/Genomics/Arabidopsis-Initiative-Genome-2000.pdf

  6. Present state of Arabidopsis Sequencing: Somerville Science 1999 Arabidopsis Sequencing 1999

  7. Arabidopsis Segmentally duplicated regions Figure 4 Segmentally duplicated regions in the Arabidopsis genome

  8. Arabidopsis Chromosomes, Sequencing 2000 Representation of the Arabidopsis chromosomes. Each chromosome is represented as a coloured bar. Sequenced portions are red, telomeric and centromeric regions are light blue, heterochromatic knobs are shown black and the rDNA repeat regions are magenta. Nature 408, p. 797 2000

  9. The Arabidopsis Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 6814, pp 796-815 http://dx.doi.org/10.1038/35048692 AND http://www.nature.com/nature/journal/v408/n6814/suppinfo/408796a0_S1.html AND http://www.botanischergarten.ch/Genomics/Arabidopsis-Initiative-Genome-2000.pdf

  10. The Arabidopsis Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 6814, pp 796-815 http://dx.doi.org/10.1038/35048692 AND http://www.nature.com/nature/journal/v408/n6814/suppinfo/408796a0_S1.html AND http://www.botanischergarten.ch/Genomics/Arabidopsis-Initiative-Genome-2000.pdf

  11. Functional classification of predicted genes in Arabidopsis Somerville, C. & Somerville, S. (1999) Plant Functional Genomics. Science, 285, 5426, pp 380-383 http://www.sciencemag.org/cgi/content/abstract/285/5426/380 AND http://www.botanischergarten.ch/Genomics/Somervilles-Plant-Functional-Genomics-1999.pdf C.+ S.Somerville classic reading

  12. Sequence identity of Arabidopsis and rice calculated from 64 randomly selected proteins with known probable functionsSomerville Science 1999, see previous slide Sequence identity Arabidopsis - Rice

  13. COVER Photograph of the Honghe Hani rice terraces in Yunnan Province, China. In this issue, two separate research groups report draft sequences of two strains of rice--japonica and indica. In addition, the Editorial, News Focus, Letters, and Perspectives highlight the significance of the rice genome to the world's population The biology of rice, the world's indispensable grain, comes into sharper focus with the publication in Science of two draft sequences of the rice genome -- one by a publicly funded group led by the Beijing Genomics Institute; the other by the private firm Syngenta. The 5 April 2002 issue of Science celebrates the publication of these landmark papers with a collection of research, news, and features that help place the achievement in context. Science 5 April 2002:Vol. 296. no. 5565, pp. 79 - 92DOI: 10.1126/science.1068037 supplementary material http://www.sciencemag.org/cgi/content/full/sci;296/5565/79/DC1

  14. Going with the Grain Two separate research groups report high-quality draft sequences of the rice genome that are expected to facilitate advances in the agriculture of this critical food grain. Yu et al. (p. 79) sequenced the indica variety of rice, and Goff et al. (p. 92) sequenced the japonica variety of rice. Comparisons will show how these two popular rice strains have diverged. The rice genome also provides a useful road map for investigating the larger genomes of related cereal grains such as wheat and maize [see also the report by Seki (p. 141) on Arabidopisis complementary DNA clones]. Related pieces include a pull-out wall chart that gives a summary of important aspects of rice genome research, the editorial discussing the agreements that govern accessibility to some of the data, and letters to the editor that call for continuing with the sequencing of rice to the point of a final, complete sequence. In the Perspectives, Bennetzen, as well as Ronald and Leung, discuss the implications for genomic and agricultural sciences, Cantrell and Reeves discuss the implications that sequencing the rice genome holds for promoting worldwide food security, and Serageldin discusses the interplay between worldwide economic development and food security. News stories discuss the background on what many of the various rice genome-sequencing groups have been doing, the Celera-type agreements that are governing release of the data for the Goff et al. paper, and a profile of the Chinese group that authored the Yu et al. paper. Normile, D. & Pennisi, E. (2002) Rice: Boiled down to bare essentials. Science, 296, 5565, pp 32-36 http://www.botanischergarten.ch/Genomics/Normile-Rice-Boiled-Down-2002.pdf Bennetzen, J. (2002) THE RICE GENOME: Opening the Door to Comparative Plant Biology. Science, 296, 5565, pp 60-63 http://www.botanischergarten.ch/Genomics/Bennetzen-Opening-Door-Rice-2002.pdf

  15. Friends and relations. Phylogenetic relationships among multicellular organisms whose genomes have been sequenced or are currently being sequenced. Rice is the first cereal to have its genome sequenced. The genome sequence of the model plant Arabidopsis was largely completed in 2000. These two genome sequences will enable a detailed comparison between monocotyledonous and dicotyledonous flowering plants to be made. Species in dark blue are those with completed sequences or drafts that have been published; sequencing of genomes for species in turquoise is ongoing. Ma, millions of years ago As of 2009, several major crops have fully sequenced genomes, the latest one from Sorghum: Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A., Schmutz, J., Spannagl, M., Tang, H.B., Wang, X.Y., Wicker, T., Bharti, A.K., Chapman, J., Feltus, F.A., Gowik, U., Grigoriev, I.V., Lyons, E., Maher, C.A., Martis, M., Narechania, A., Otillar, R.P., Penning, B.W., Salamov, A.A., Wang, Y., Zhang, L.F., Carpita, N.C., Freeling, M., Gingle, A.R., Hash, C.T., Keller, B., Klein, P., Kresovich, S., McCann, M.C., Ming, R., Peterson, D.G., Mehboob ur, R., Ware, D., Westhoff, P., Mayer, K.F.X., Messing, J., & Rokhsar, D.S. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 7229, pp 551-556 http://www.botanischergarten.ch/Africa-Harvest-Sorghum-Lit-1/Paterson-Sorghum-bicolor-genome-2009.pdf Paterson, A.H., Bowers, J.E., Feltus, F.A., Tang, H.B., Lin, L.F., & Wang, X.Y. (2009) Comparative Genomics of Grasses Promises a Bountiful Harvest. Plant Physiology, 149, 1, pp 125-131 http://www.botanischergarten.ch/Africa-Harvest-Sorghum-Lit-1/Paterson-Comparative-Genomics-Grasses-2009.pdf Bennetzen, J. (2002) THE RICE GENOME: Opening the Door to Comparative Plant Biology. Science, 296, 5565, pp 60-63 http://www.botanischergarten.ch/Genomics/Bennetzen-Opening-Door-Rice-2002.pdf

  16. new star added on April 5, 2009 red line: the important step in evolution Margulis, L. (1992) BIODIVERSITY - MOLECULAR BIOLOGICAL DOMAINS, SYMBIOSIS AND KINGDOM ORIGINS. Biosystems, 27, 1, pp 39-51 http://www.botanischergarten.ch/Evolution/Margulis-Biodiversity-Molecular-1992.pdf

  17. new star added on April 5, 2009 Red line: the important step in evolution Margulis, L. (1992) BIODIVERSITY - MOLECULAR BIOLOGICAL DOMAINS, SYMBIOSIS AND KINGDOM ORIGINS. Biosystems, 27, 1, pp 39-51 http://www.botanischergarten.ch/Evolution/Margulis-Biodiversity-Molecular-1992.pdf

  18. new star added on April 5, 2009 red line: the important step in evolution Margulis, L. (1992) BIODIVERSITY - MOLECULAR BIOLOGICAL DOMAINS, SYMBIOSIS AND KINGDOM ORIGINS. Biosystems, 27, 1, pp 39-51 http://www.botanischergarten.ch/Evolution/Margulis-Biodiversity-Molecular-1992.pdf

  19. Evolution in perspective of the cell red line: important step in evolution Margulis, L. (1992) BIODIVERSITY - MOLECULAR BIOLOGICAL DOMAINS, SYMBIOSIS AND KINGDOM ORIGINS. Biosystems, 27, 1, pp 39-51

  20. Rice gene function prediction classifications Rice gene prediction classifications. HMLgenes300 were classified with Interpro and GO software (27-29); the categories generated are shown Science, Vol 296, Issue 5565, 92-100 , 5 April 2002 Normile, D. & Pennisi, E. (2002) THE RICE GENOME: Rice: Boiled Down to Bare Essentials. Science, 296, 5565, pp 32-36 http://www.sciencemag.org/cgi/content/summary/296/5565/32?ck=nck AND

  21. Genom-Vergleich Reis-Mais Rice-maize synteny. Maize markers were mapped to the rice genome in silico. Maize map and sequence information were derived from MaizeDB (610 markers) and GenBank, respectively. Maize chromosomes are indicated along the vertical black lines; positions of specific markers and bins are defined by horizontal lines. Rice chromosomes are represented by numbered, colored rectangles. Significant homology (at least 80% identity, over 100 continuous base pairs, between a maize chromosomal region and a particular rice region) is indicated by a colored rectangle to the right of the maize chromosome. For a more detailed version of this map, see Website link. Yu, J., Hu, S., Wang, J., Wong, G.K.-S., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., Cao, M., Liu, J., Sun, J., Tang, J., Chen, Y., Huang, X., Lin, W., Ye, C., Tong, W., Cong, L., Geng, J., Han, Y., Li, L., Li, W., Hu, G., Huang, X., Li, W., Li, J., Liu, Z., Li, L., Liu, J., Qi, Q., Liu, J., Li, L., Li, T., Wang, X., Lu, H., Wu, T., Zhu, M., Ni, P., Han, H., Dong, W., Ren, X., Feng, X., Cui, P., Li, X., Wang, H., Xu, X., Zhai, W., Xu, Z., Zhang, J., He, S., Zhang, J., Xu, J., Zhang, K., Zheng, X., Dong, J., Zeng, W., Tao, L., Ye, J., Tan, J., Ren, X., Chen, X., He, J., Liu, D., Tian, W., Tian, C., Xia, H., Bao, Q., Li, G., Gao, H., Cao, T., Wang, J., Zhao, W., Li, P., Chen, W., Wang, X., Zhang, Y., Hu, J., Wang, J., Liu, S., Yang, J., Zhang, G., Xiong, Y., Li, Z., Mao, L., Zhou, C., Zhu, Z., Chen, R., Hao, B., Zheng, W., Chen, S., Guo, W., Li, G., Liu, S., Tao, M., Wang, J., Zhu, L., Yuan, L., & Yang, H. (2002) A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica). Science, 296, 5565, pp 79-92 http://www.sciencemag.org/cgi/content/abstract/296/5565/79 and http://www.botanischergarten.ch/Rice/Yu-et-al-Draft-Rice-Genome-2002.pdf

  22. Genom-Vergleich Reis-Mais Maize QTLs mapped to the rice genome. (A) Rice-maize comparative QTL mapping. Portions of maize chromosomes, represented by numbered, colored rectangles, that show sequence similarity (at least 80% identity over 100 continuous base pairs) with specific regions of the top of rice chromosome 1 are shown. The rice map is from the IRGSP. Genetic distance is indicated by the numbers to the left of the rice chromosome (e.g., 1004.2 means 4.2 cM from the tip of chromosome 1); specific markers that map to this region are indicated to the right. Regions from maize chromosomes 1, 2, and 7 show similarity with the tip of rice chromosome 1 as shown, and maize QTLs in these regions are indicated. The region represented by the thick black line comprises ~650 kbp in rice; each colored block represents varying amounts of maize DNA. (B) Detailed example of rice-maize comparative QTL mapping. Grain yield QTL 21 is mapped to maize map bin 1.03 between cDNA markers csu 710 and csu 392, and is syntenic with rice chromosome 3. Additional markers from the same maize bin confirm microsynteny in this target region, which contains ~220 candidate genes and 120 SSR markers in rice. Dotted lines connect homologous genes with the indicated BLAST expectation values.

  23. Functional classification of rice genes Science, Vol 296, Issue 5565, 79-92 , 5 April 2002

  24. Future of Genomics ELSI: ethical, legal, social implications

  25. Prometheus Unbound: Revolutionary Advances in Biological Technologies

  26. Gene expression maize, mouse and man Schadt, E., Monks, S., Drake TA, Lusisk, J., Chek, N., Colinayok, V., Ruff, T., Milligan, S., Lamb, J., Cavet, G., Linsley, P., Mao, M., Stoughton, R., & Friend, S. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, pp 297-302 Supplementary Information accompanies the paper on Nature’s website (ç http://www.nature.com/nature) and http://www.botanischergarten.ch/Genomics/Schadt-et-al-Nature-2002.pdf Figure 1 Murine gene expression quantitative trait loci (eQTL) distributions and the molecular basis for fat pad mass (FPM) in a murine F2 cross. a, Percentage of eQTL in 2-cM bins spanning the murine autosomal chromosomes at two LOD score thresholds.

  27. Schadt, E.E., Monks, S.A., Drake, T.A., Lusis, A.J., Che, N., Colinayo, V., Ruff, T.G., Milligan, S.B., Lamb, J.R., Cavet, G., Linsley, P.S., Mao, M., Stoughton, R.B., & Friend, S.H. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, 6929, pp 297-302 http://dx.doi.org/10.1038/nature01434 AND http://www.nature.com/nature/journal/v422/n6929/suppinfo/nature01434_S1.html AND http://www.botanischergarten.ch/Genomics/Schadt-Maize-Mice-Man-2003.pdf

  28. Correlation of genes in maize seemingly uncorrelated genes in maize do correlate after all: pattern in plots evident eQTL: expressed Quantitative Trait Loci Figure 4 Genes with no overall correlation with respect to expression demonstrate interesting patterns of genetic interaction. The scatter plot shows the mean log10 ratio for two Zea mays genes that are uncorrelated overall, each with a significant eQTL (LOD of 24.3 for the gene on the x axis and 24.9 for the gene on the y axis) falling on two separate chromosomes. Patterns are apparent in the plot despite the overall random correlation, as the four groups in each quadrant of the plot are correlated. The least squares regression line is shown for each quadrant, with the correlation coefficient values and corresponding P-values given in parentheses. EST, expressed sequence tag. HC, Helminthosporium carbonum. Schadt et al. 2003

  29. Alba, Kaninchen mit Quallengen Fluorescing rabbit ALBA a well known example of biotech art as a provokation Comments under http://www.ekac.org/ shellyfish gene in rabbit Eduardo Kac, Professor at Chicago School of Art, Project Genesis

  30. Genetische Variation, Bsp. Manfred Eigen Genetic Variation calculated on Permutations of base pairs Based on gene and chromosome mutation: The number of possible permutations is gigantic, calculated for a minimal genome of a virus: 1000 base pairs 41000, ≈ to 10602 possibilities of variations, please note that the total volume of the universe based on the view of the universe as a sphere with a diameter of ten billion light years, is estimated to ca. 1084 cm2 hitherto estimated in the universe is aequivalent to circa 1075 genes. Eigen, M. (1987) Stufen zum Leben. Die fruehe Evolution im Visier der Molekularbiologie Piper Verlag, Muenchen, Zuerich, IS: ISBN 3-492-03169-2, pp

  31. It is still stupendous, that only 1% of the genetic material is expressed morphologically. a lot of genetic material is still unknown in ist functions. the roughly 109 genes known to be distributed in all biota of Earth, contribute in very different ways to biodiversity, and the quantification of this contribution is still largely unknown Genetische Variation, Bsp. Manfred Eigen

  32. Universalität der wichtigen Gene Most of the functionally important genes are distributed universally: Humans are built to 99,6% of the same funktionally important genes as chimpanzees fundamentally important genes for the main physiological processes of organisms show little variation, and if there are differences, they are important and show dramatic effects on the species. This also means that in cases a very few genes can be the cause of great variation (2 examples immune systems of mammals, inflorescence characters of flowering plants).

  33. Genetic Diversity Turkey is at the crossroads of two important Vavilovian gene centers: -The Mediterranean and the Near East- each important for the origin of field crops as well as horticultural plants. Some of the cultivated plant species originating in Turkey are Linum, Allium, Hordeum, Secale, Triticum, Avena, Cicer, Lens, Pisum, Vitis, Amygladus, Prunus, Beta, etc. There are 5 "micro-gene centre" in Turkey (Harlan 1951): Thrace-Aegean Region: bread wheat, durum wheat, Poulardwheat, club wheat, einkorn wheat, lentil chickpea, melon, vetch, lupine, and clover. Southern-Southeastern Anatolia: emmer wheat, einkorn wheat, Aegilops speltoides, squash, water melon, cucumber, bean, lentil, broad bean, grapevine, and forage plants. Samsun, Tokat, Amasya: numerous genera and species of fruits, broad bean, bean, lentil, and several forage legumes. Kayseri and environs: almond, apple, pea, fruit species, grapevine, lentil, chickpea, alfalfa, and sainfoin. Agri and environs: apple, apricot, cherry, sour cherry, forage legumes and watermelon.

  34. 1.1.2. Natural Mutation and Genetic Engineering

  35. Bedeutung der genetischen Variation The importance of genetic variation is clear: it is the basis for any view on genetic mutation. Nobel prize winner Werner Arber claims that in the evolutionary dynamics in nature is important and relatively common. It is even a pre-condition and major force of evolution

  36. Langfristige Risiken, Vergleich mit Gentechnik Each of those mutations can be seen as a potential small risk on the long run of biological evolution. In the view of molecular genetics and its analysis of mutational dynamics, there is no scientific reason to focus in a special way on genetic engineering. This is the view of Werner Arber, who was responsible for important breakthroughs in molecular geneticslike restriction enzymes, allowing to cut DNA at a precise location. Arber, W. (2002) Roots, strategies and prospects of functional genomics. Current Science, 83, 7, pp 826-828 http://www.botanischergarten.ch/Mutations/Arber-Comparison-2002.pdf Arber, W. (2004) Biological evolution: Lessons to be learned from microbial population biology and genetics. Research in Microbiology, 155, 5, pp 297-300 http://www.botanischergarten.ch/Mutations/Arber-Evolution-Lessons-2004.pdf

  37. Massenhafte Freisetzungen Nevertheless it must also be emphasized that the results of agricultural genetic engineering, the transgenic crops, can be multiplied in short time periods and can be cultivated in great quantities. But this is also clear of the results of classic breeding methods, such as chemical or radiation mutation, which has produced dozens of important crops, such as Durum wheat, used for all pasta worldwide..

  38. Gamma Field for radiation breeding 100m radius 89 TBq Co-60 source at the center Shielding dike 8m high Better spaghettis, whisky 1800 new plants http://www-naweb.iaea.org/nafa/index.html Irfaq, M. & Nawab, K. (2001) Effect of Gamma Irradiation on Some Morphological Characteristics of Three Wheat (Triticum aestivum L.) Cultivars. OnLine Journal of Biological Sciences, 1, 10, pp 935-937 http://www.botanischergarten.ch/Mutations/Irfaq-Radiation-Triticum-2001.pdf Institute of Radiation Breeding Ibaraki-ken, JAPAN http://www.irb.affrc.go.jp/

  39. Real Frankenfood Real Frankenfood Worldwide: all pasta is made from radiation mutated durum wheat Triticum durum

  40. Radiated spagetti genomes • All pasta should be labelled as • Above, since all durum wheat has radiated genomes • Sakin, M.A. & Yildirim, A. (2004) • Induced mutations for yield and its components in durum wheat (Triticum durum Desf.). Food, Agriculture & Environment, 2, 1, pp 285-290 • http://www.botanischergarten.ch/Mutations/Sakin-Mutations-Durum-2002.pdf http://nucleus.iaea.org/NUCLEUS/nucleus/Content/Applications/FICdb/FoodIrradiationClearances.jsp?module=cif

  41. 1.1.3. Epigenetics

  42. New role of Introns • Mattick, J.S. (2004) • The hidden genetic program of complex organisms. Scientific American, 291, 4, pp 60-67 • http://www.botanischergarten.ch/Genomics/Mattick-Genome-Complexity-2004.pdf

  43. Definition of RNA RNA: Short for ribonucleic acid, a nucleic acid molecule similar to DNA but containing ribose rather than deoxyribose. RNA is formed upon a DNA template. There are several classes of RNA molecules. They play crucial roles in protein synthesis and other cell activities: Messenger RNA (mRNA) is a type of RNA that reflects the exact nucleoside sequence of the genetically active DNA. mRNA carries the "message" of the DNA to the cytoplasm of cells where protein is made in amino acid sequences specified by the mRNA. Transfer RNA (tRNA) is a short-chain type of RNA present in cells. There are 20 varieties of tRNA. Each variety combines with a specific amino acid and carries it along (transfers it), leading to the formation of protein with a specific amino acid arrangement dictated by DNA. Ribosomal RNA (rRNA) is a component of ribosomes. Ribosomal RNA functions as a nonspecific site for making polypeptides. http://www.medterms.com/script/main/art.asp?articlekey=5382

  44. Traditional View of Gene Activity • Mattick, J.S. (2004) • The hidden genetic program of complex organisms. Scientific American, 291, 4, pp 60-67 • http://www.botanischergarten.ch/Genomics/Mattick-Genome-Complexity-2004.pdf

  45. New View of Gene Activity NEW VIEW OF GENE ACTIVITY IN EUKARYOTES Some of the intronic RNA and even some of the assembled exonic RNA may play a direct regulatory role by interacting with the DNA, other RNA molecules or proteins. By modifying protein production at various levels, these noncoding RNAs may superimpose additional genetic instructions on a cell. • Mattick, J.S. (2004) • The hidden genetic program of complex organisms. Scientific American, 291, 4, pp 60-67 • http://www.botanischergarten.ch/Genomics/Mattick-Genome-Complexity-2004.pdf

  46. Epigenetics, a rising science in molecular biology http://en.wikipedia.org/wiki/Epigenetics Explanation of Epigenetics through histones, see next slide

  47. EPIGENETICS explanation Because the phenotype of a cell or individual is affected by which of its genes are transcribed, heritable transcription states can give rise to epigenetic effects. There are several layers of regulation of gene expression. One way that genes are regulated is through the remodeling of chromatin. Chromatin is the complex of DNA and the histone proteins with which it associates. Histone proteins are little spheres that DNA wraps around. If the way that DNA is wrapped around the histones changes, gene expression can change as well. Chromatin remodeling is initiated by one of two things: The first way is post translational modification of the amino acids that make up histone proteins. Histone proteins are made up of long chains of amino acids. If the amino acids that are in the chain are changed, the shape of the histone sphere might be modified. DNA is not completely unwound during replication. It is possible, then, that the modified histones may be carried into each new copy of the DNA. Once there, these histones may act as templates, initiating the surrounding new histones to be shaped in the new manner. By altering the shape of the histones around it, these modified histones would ensure that a differentiated cell would stay differentiated, and not convert back into being a stem cell. The second way is the addition of methyl groups to the DNA, at CpG sites, to convert cytosine to 5-methylcytosine. Cytosine is the nucleotide that our cells can "read." Our cells cannot "read" methylcytosine. If DNA is conceived as an instruction manual again, changing cytosine to methylcytosine would be like changing the font on a Word document to "wingdings." The contention would be that since the cell can no longer "read" the gene, the gene is turned off. Two Stanford rappers on gene regulation from youtube, its hilarious and full of good details http://www.youtube.com/watch?v=9k_oKK4Teco&eurl=http%3A%2F%2Fblogs%2Enature%2Ecom%2Fnews%2Fthegreatbeyond%2Fbiology%5Fbiotechnology%2F&feature=player_embedded

  48. Lynn Margulis 1995, some wise closing remarks What is life? Its a linguistic trap. To answer according to the rules of grammar, we must supply a noun, a thing. But life on Earth is more like a verb. It is a material process, surfing over matter like a strange slow wave. It is a controlled artistic chaos, a set of chemical reactions so staggeringly complex that more than 4 billion years ago it began a sojourn that now, in human form, composes love letters and uses silicon computers to calculate the temperature of matter at the birth of the universe. Margulis, L.(1995), What is Life ?, accessed: 2003, IIASA "Evolution and Complexity" series, Laxenburg, Austria http://www.newworldencyclopedia.org/entry/Lynn_Margulis Margulis 5 Kingdoms of Life

  49. 1.2. Biodiversity in general

  50. Biodiversity in General Since Biodiversity is often seen as diversity of species, biodiversity is therefore nearly synonymous to abundance and richness of species. This is why global biodiversity is often described and numbers of various taxonomic groups. It is estimated that today there are ca. 1.7 mio species described, but conservative estimates name a total of 12.5 mio species, some more audacious estimates are reaching 100 mio species. Artenvielfalt

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