Sabanci-Ecology-1-Biodiv-General-20090322

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					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
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.
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
1.1.1.Genetic
Diversity
1.2. Genetic Diversity
                                                                                                  Definition Genetische Diversität




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:

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 genome
                                                              Arabidopsis Segmentally duplicated regions
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

         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
                                                                                             classic reading
                                                                                             C.+ S.Somerville




                                                              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
Functional classification of predicted genes in Arabidopsis
Sequence identity of Arabidopsis and rice calculated from 64
randomly selected proteins with known probable functions
Somerville 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 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 - 92
DOI: 10.1126/science.1068037

supplementary material
http://www.sciencemag.org/cgi/content/
full/sci;296/5565/79/DC1
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
                                             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,
Bennetzen, J. (2002)                                             H.B., Lin, L.F., & Wang, X.Y. (2009)
                                                                 Comparative Genomics of Grasses Promises a Bountiful
THE RICE GENOME: Opening the Door to
                                                                 Harvest. Plant Physiology, 149, 1, pp 125-131
Comparative Plant Biology. Science, 296,                         http://www.botanischergarten.ch/Africa-Harvest-
5565, pp 60-63                                                   Sorghum-Lit-1/Paterson-Comparative-Genomics-
http://www.botanischergarten.ch/Genomics/B                       Grasses-2009.pdf
ennetzen-Opening-Door-Rice-2002.pdf
                                                                  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
                                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/Marguli
              s-Biodiversity-Molecular-1992.pdf
                                                  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/Margu
lis-Biodiversity-Molecular-1992.pdf
                           Evolution
                           in perspective
                           of the cell




red line: important step
                           Margulis, L. (1992)
in evolution               BIODIVERSITY - MOLECULAR
                           BIOLOGICAL DOMAINS,
                           SYMBIOSIS AND KINGDOM
                           ORIGINS.

                           Biosystems, 27, 1, pp 39-51
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
                                                                           Rice gene function prediction classifications
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
                                                                                     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.




                                            Genom-Vergleich Reis-Mais
Functional classification of rice genes




                                          Science, Vol 296, Issue 5565, 79-92 , 5 April 2002
Future of Genomics




                     ELSI: ethical, legal, social implications
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., &
                                                                                Figure 1 Murine gene expression quantitative trait loci (eQTL)
Friend, S. (2003)                                                               distributions and the molecular basis for fat pad mass (FPM) in a
Genetics of gene expression surveyed in maize, mouse and man. Nature, 422, pp
297-302
                                                                                murine F2 cross. a, Percentage of eQTL in 2-cM bins spanning the
Supplementary Information accompanies the paper on Nature’s website             murine autosomal chromosomes at two LOD score thresholds.
(ç http://www.nature.com/nature) and
http://www.botanischergarten.ch/Genomics/Schadt-et-al-Nature-2002.pdf
                                                                                                                                    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
                                                                                              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                                                                    Correlation of genes in maize
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
                                                         Alba, Kaninchen mit Quallengen
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

                                                                                                           Genetische Variation, Bsp. Manfred Eigen
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
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 like
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
                                                                                     Langfristige Risiken, Vergleich mit Gentechnik
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
  Gamma Field
  for radiation
    breeding

        100m
       radius

      89 TBq
      Co-60
    source at
    the center
    Shielding
     dike 8m                  Better spaghettis, whisky 1800 new plants
       high                   http://www-naweb.iaea.org/nafa/index.html


                              Irfaq, M. & Nawab, K. (2001)
                              Effect of Gamma Irradiation on Some Morphological
Institute of                  Characteristics of Three Wheat (Triticum aestivum L.)
                              Cultivars. OnLine Journal of Biological Sciences, 1, 10, pp
Radiation Breeding            935-937
Ibaraki-ken, JAPAN            http://www.botanischergarten.ch/Mutations/Irfaq-Radiation-
http://www.irb.affrc.go.jp/   Triticum-2001.pdf
Real Frankenfood

Worldwide:

all pasta is made
from
radiation mutated
durum wheat
Triticum durum




               Real Frankenfood
                                                                         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
                                                                                                Radiated spagetti genomes
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 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
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
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              New View of Gene Activity
Epigenetics, a rising science in molecular biology
http://en.wikipedia.org/wiki/Epigenetics



                                                 Explanation of
                                                 Epigenetics
                                                 through 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%2Fthegreatbeyon
 d%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 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
1.2. Biodiversity
in 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. Distribution of species
Nature Insight Biodiversity: Species richness in major groups of organisms
Purvis, 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. Artenvielfalt: Artenzahl der wichtigsten Organismengruppen
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
Afrika and




                http://homepage.univie.ac.at/christian.puff/images/AFMAD_Regions_White.jpg
Madagaskar:
Regional
centres of
endemism
(sensu White)

explanation:
Cape and
Madagaskar
are part of
the old
southern
super-
continent
Gondwana,
see
animation
next slide
Reverse animation
of the continental drift
after the old
Gondwanaland, click
to full page mode
If it does not work
for the animated
picture, go to:

http://kartoweb.itc.nl/go
ndwana/gondwana_gif.
html
Mist Forest of the Jamaican
Blue Mountains,

with Tillandsia campanulata
and a rich epiphyte flora
one tree species harbouring
hundreds of flowering plants,
like orchids etc.,
mosses, lichens and funghi
and lots of still unknown
microorganisms

				
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