Plant Ecology klaus.ammann@ips.unibe.chSabanci University Spring 2009Lecturer: Prof. em. Dr. Klaus Ammann, University of Bern, SwitzerlandChapter 1: Weeks 1 – 3 Document: Sabanci-Ecology-1-Biodiv-General.ppt

Sabanci-Ecology-2-Patterns-Protection.pptBiodiversity Basics and Protection of Biodiversityprecondition of understanding ecology and human life on earth

Chapter 2: Week 4 Document: Sabanci-Ecology-3-Pollination.pptKnowledge in pollination ecology helps to understand plant systematics and ecology

Chapter 3: Weeks 5 – 6 Document: Sabanci-Ecology-4-Bioprospecting.pptBioprospection as a typical link between economy and protection

Chapter 4: Weeks 7 – 9 Document: Sabanci-Ecology-5-Vegetation-Ecology.pptVegetation ecology related to climate

Chapter 5: Weeks 10-14 Single Documents to be uploadedCase histories: Seed distribution, Biofortified Sorghum in Africa, Biology of CryptogamsRain Forests Jamaica, Step Vegetation Worldwide, Alpine Vegetation and Glacial History,European Plant Geography, Vegetation of Tenerife, Canary Islands.

1.1. What is Biodiversity ?

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

1.1.1.Genetic Diversity

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

Present state of Arabidopsis Sequencing: Somerville Science 1999

Arabidopsis Sequencing 1999

Figure 4 Segmentally duplicated regions in the Arabidopsis genomeArabidopsis Segmentally duplicated regions

Representation of the Arabidopsis chromosomes. Each chromosome isrepresented as a coloured bar. Sequenced portions are red, telomeric and centromericregions are light blue, heterochromatic knobs are shown black and the rDNA repeatregions are magenta.

Nature 408, p. 7972000

Arabidopsis Chromosomes, Sequencing 2000

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

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

Functional classification of predicted genes in Arabidopsis

C.+ S.Somervilleclassic reading

So

mer

vill

e, C

. &

So

mer

vill

e, S

. (1

999)

Pla

nt

Fun

ctio

nal G

enom

ics.

Sci

ence

, 28

5, 5

426,

pp

380

-383

ht

tp:/

/ww

w.s

cien

cem

ag.o

rg/c

gi/c

ont

ent/

abst

ract

/285

/542

6/38

0 A

ND

ht

tp:/

/ww

w.b

ota

nisc

herg

arte

n.ch

/Gen

omic

s/S

om

ervi

lles-

Pla

nt-F

unc

tion

al-

Gen

omic

s-19

99.

pdf

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

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 populationThe 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 materialhttp://www.sciencemag.org/cgi/content/full/sci;296/5565/79/DC1

Going with the GrainTwo separate research groups report high-quality draft sequences of the rice genomethat are expected to facilitate advances in the agriculture of this critical food grain. Yu etal. (p. 79) sequenced the indica variety of rice, and Goff et al. (p. 92) sequenced thejaponica variety of rice. Comparisons will show how these two popular rice strains havediverged. The rice genome also provides a useful road map for investigating the largergenomes 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 wallchart that gives a summary of important aspects of rice genome research, the editorialdiscussing the agreements that govern accessibility to some of the data, and letters to theeditor that call for continuing with the sequencing of rice to the point of a final, completesequence. In the Perspectives, Bennetzen, as well as Ronald and Leung, discuss theimplications for genomic and agricultural sciences, Cantrell and Reeves discuss theimplications that sequencing the rice genome holds for promoting worldwide foodsecurity, and Serageldin discusses the interplay between worldwide economicdevelopment and food security. News stories discuss the background on what many of thevarious rice genome-sequencing groups have been doing, the Celera-type agreements thatare governing release of the data for the Goff et al. paper, and a profile of the Chinesegroup 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.pdfBennetzen, 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

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

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 agoAs 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

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

red line: theimportant stepin evolution

new star addedon April 5, 2009

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

new star addedon April 5, 2009

Red line: the important step inevolution

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

red line: the important stepin evolution

new star added on April 5, 2009

Evolution in perspectiveof the cell

Margulis, L. (1992)BIODIVERSITY - MOLECULAR BIOLOGICAL DOMAINS, SYMBIOSIS AND KINGDOM ORIGINS.

Biosystems, 27, 1, pp 39-51

red line: important stepin evolution

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

Rice gene function prediction classifications

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

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.

Genom-Vergleich Reis-Mais

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

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.

Genom-Vergleich Reis-Mais

Science,

Vol

296

, Iss

ue 5

565,

79-

92 ,

5 A

pril

2002

Functional classification of rice genes

EL

SI: e

thic

al, l

egal

, soc

ial i

mpl

icat

ions

Future of Genomics

Prometheus Unbound: Revolutionary Advances in Biological Technologies

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.

Gene expression maize, mouse and man

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

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

seemingly uncorrelatedgenes in maizedo correlateafter all: patternin plots evident

eQTL:expressedQuantitativeTraitLoci

Correlation of genes in maize

                                             

   

Fluorescing rabbit ALBAa well known example of biotech art as a provokationComments under http://www.ekac.org/ shellyfish gene in rabbitEduardo Kac, Professor at Chicago School of Art, Project Genesis

Alba, Kaninchen mit Quallengen

Genetic Variation calculated on Permutationsof base pairsBased 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.

Genetische Variation, Bsp. Manfred Eigen

Eigen, M. (1987) Stufen zum Leben. Die fruehe Evolution im Visier der Molekularbiologie Piper Verlag, Muenchen, Zuerich, IS: ISBN 3-492-03169-2, pp

It is still stupendous, that only 1% of the geneticmaterial 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

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).

Universalität der wichtigen Gene

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.

1.1.2. Natural Mutation and Genetic Engineering

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

Bedeutung der genetischen Variation

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 genetics likerestriction enzymes, allowing to cut DNA at a precise location.

Langfristige Risiken, Vergleich mit Gentechnik

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

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..

Massenhafte Freisetzungen

Institute of Radiation Breeding Ibaraki-ken, JAPAN http://www.irb.affrc.go.jp/

100m radius

89 TBqCo-60

source at the centerShielding dike 8m

high

Gamma Field for radiation

breeding

Better spaghettis, whisky 1800 new Better spaghettis, whisky 1800 new plantsplants

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

Real Frankenfood

Real Frankenfood

Worldwide:

all pasta is made fromradiation mutateddurum wheatTriticum durum

Radiated spagetti genomes

All pasta should be labelled as Above, since all durum wheat has radiated genomesSakin, 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

1.1.3. Epigenetics

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

New role of Introns

Definition of RNARNA: 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

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

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

New View of Gene Activity

NEW VIEW OF GENEACTIVITY IN EUKARYOTESSome of the intronic RNA and evensome of the assembled exonic RNAmay play a direct regulatory role byinteracting with the DNA, other RNAmolecules or proteins. By modifyingprotein production at various levels,these noncoding RNAs maysuperimpose additional geneticinstructions on a cell.

Epigenetics, a rising science in molecular biologyhttp://en.wikipedia.org/wiki/Epigenetics

Explanation of Epigeneticsthrough histones,see next slide

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:1.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. 2.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

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 4billion 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 5 Kingdoms of Life

Margulis, L. (1995), What is Life ?, accessed: 2003, IIASA "Evolution and Complexity" series, Laxenburg, Austria http://www.newworldencyclopedia.org/entry/Lynn_Margulis

1.2. Biodiversityin general

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

1.3. Artenvielfalt: Artenzahl der wichtigsten Organismengruppen

Nature Insight Biodiversity: Species richness in major groups of organismsPurvis, A. & Hector, A. (2000) Getting the measure of biodiversity. Nature, 405, 6783, pp 212-219 http://www.botanischergarten.ch/biodiversity/Purvis-Nature-Biodiv-Measure-2000.pdf

1.3. Distrib

utio

n o

f species

In a global view, biodiversity consists predominantly on insects and micro-organisms. But the estimates have several possible errors: Relativity of species definition, limited knowledge on distribution, limited knowledge of taxonomists. It should also be clear that the sheer number does not really tell much, we should also take into account the taxonomic distance and also the various views on taxonomic hierarchies

Artenzahlen: begrenzte Aussagekraft

the naked numbers of species are not really giving a good picture on biodiversity distribution

1. taxonomic distance: a few palaeoendemic species with considerable taxonomic distance to other species can add considerably to the value of a region: Example Madagaskar.

2. synsociological relationships not reflected in species numbers: Example a tropical tree in the mist forest with thousands of endemic epiphytes (mosses, lichens, orchids, this tree contributes as a single species much more than any grass in any ecosystem

Artensummen: wenig aussagekräftig

http

://h

omep

age

.uni

vie.

ac.

at/c

hris

tian

.pu

ff/im

age

s/A

FM

AD

_Re

gion

s_W

hite

.jpg Afrika and

Madagaskar:Regional centres of endemism(sensu White)

explanation:Cape and Madagaskar are part of the old southern super-continentGondwana,see animation next slide

Reverse animationof the continental drift after the old Gondwanaland, click to full page modeIf it does not work for the animated picture, go to:

http://kartoweb.itc.nl/gondwana/gondwana_gif.html

Mist Forest of the JamaicanBlue Mountains,

with Tillandsia campanulataand a rich epiphyte floraone tree species harbouringhundreds of flowering plants,like orchids etc.,mosses, lichens and funghiand lots of still unknownmicroorganisms