DanBIF Conference on Molecular Biodiversity March 11 - 12, 2004 Venue: Festsal at Geocenter Copenhagen, Øster Voldgade 10, DK-1350 Copenhagen K, Denmark Organiser: DanBIF, Danish National Node of GBIF, Global Biodiversity Information Facility Presentations: Welcome & Introduction: The three main levels of biodiversity (Molecular, Organismic, Ecological); Why is molecular biodiversity important to GBIF/DanBIF? Professor Henrik Enghoff Director, Natural History Museum of Denmark, University of Copenhagen. email: [email protected] Abstract: Biodiversity is an immensely complex concept but can be construed as being organised according to three main "axes": Organismic biodiversity deals with entire animals, plants, fungi and micro- organisms and includes such aspects as morphology, distribution, phylogeny, naming, preservation of specimens in collections. Molecular biodiversity focuses on DNA, RNA and proteins and is the main subject of the present conference. Ecological biodiversity is about such things as, e.g., communities and interactions between species. Although research along each of the three main axes can give wonderful results, it is in the conceptual planes defined by two or in the conceptual space defined by all three of the axes that the really exciting discoveries are most likely to be made. GBIF has chosen initially to focus on the organismic level of biodiversity. However, when Denmark presented her bid to host the GBIF secretariat, much emphasis was put on exploring the interaction between organismic and molecular biodiversity. The present conference, arranged by DanBIF – GBIF's Danish node – represents an attempt to stimulate collaboration between molecular and organismic biodiversity researchers. Session 1 – What is molecular biodiversity? - Presentation of the three molecular levels. Molecular Biodiversity – more than a GenBank reference? Professor Peter Arctander Department of Evolutionary Biology, University of Copenhagen, Denmark. email: [email protected] Abstract: GenBank references generally include taxonomic and bibliographic information, a DNA sequence and often a protein sequence. Comparing sequences from different individuals is useful for characterising relationships and thus are useful as markers. Over the past fifteen years the use of comparative sequence analysis has been refined to explore a wide spectrum of relationships, from individual relationships to deep phylogenies and are now routinely used in most biological and medical disciplines. With the massive increase in data available for molecular studies and the corresponding changes in our views of molecular processes a more comprehensive classification of molecular diversity is needed. The human genome sequence has revealed less than 25,000 protein coding genes. In a mouse to human comparison only about 300 protein coding genes are found to be different. If we compare humans to our closest relative, the chimpanzee, we find about 1% difference between their DNA sequences, and 99% of these differences are found in non-protein coding regions. Vertebrate genomes have about twice the number of genes found in invertebrates, and this increase is primarily due to duplication of existing genes. Diversity is thus not only due to differences in protein coding genes or new genes; evidence is accumulating for the role of non protein coding DNA. The protein coding information in the exons comprises about 1.8% of human DNA, while more than half of our DNA is transcribed. Diversity generating mechanisms like alternative splicing is estimated from 74% of the human genes, together with other modifications the potential variation of the protein output is enormous. The vast majority of the genetic output is however non protein coding RNA (ncRNA), and it is becoming evident that ncRNA is centrally involved in the regulation and interpretation of genomic information and in the creation of molecular and phenotypic diversity. To fully understand cellular functions, it is important to understand each transcript (protein coding or not) in the context of a complex regulatory network. The emerging “modern RNA world” and molecular networks are perhaps the most important new research frontiers in molecular diversity studies Molecular markers alone, and differences in the DNA of protein coding genes, is not sufficient to describe molecular diversity. Genomic information, transcript information, protein variation and variation in the networks that drive complex cells function, and allow multicellular development, are all needed for an understanding of molecular biodiversity. As opposed to the marker based descriptions, this could be seen more as functional molecular diversity and thus come closer to uniting genotype and phenotype. The current impressive effort in collecting organism data is of paramount importance especially for conservation, nature management and traditional biological sciences. Understanding and characterising molecular diversity is likely also to become important in medicine, molecular engineering and, of course, molecular genetics. Introtype DNA sequences and what they do not tell us about chemical differentiation and biodiversity. Professor Jens Chr. Frisvad BioCentrum-DTU, Mycology Group, Technical University of Denmark. email: [email protected] Abstract: DNA sequences as such are important for establishing molecular clocks and an estimate of the tokogeny of organisms. Zuckerkandl and Pauling (1965) called molecules such as DNA and proteins for semantic molecules, because similarities in their sequences of nucleic acids and amino acids respectively, may give us hints on the phylogeny of species. As such the chemical world of nucleotides, amino acids, tricarboxylic acid cycle members etc. are common to all prokaryotes and eukaryotes and could be called biouniformity or biosimilarity. Until now most of bioinformatics has dealt with the sequences of macromolecules, and regulation and quantification of all these basic processes (genomics, transcriptomics, proteomics, metabolomics, fluxomics). This basic apparatus in all organisms can be called the introtype and the metabolism has been called the primary or general metabolism. Because of some non-lethal mutations in genes for these general processes, data from the introtype may give us estimates on a molecular clock, but in general the introtype tell us nothing about evolution. Despite this Carl Woese and most other biologists use ribosomal DNA or household gene sequences to establish estimates of phylogenies. Enter differentiation, which accounts for all the biodiversity on this planet (the extrotype). Differentiation and the following interaction between different organisms and between organisms and different abiotic conditions on the planet paves the way for evolution and ecology. For example animals have a single set of metabolic pathways, while the prokaryotes may account for more than 2 20 fundamentally different ones to cope with extreme environments. One part of differentiation concerns isolate or individual differences (fingerprint differentiation). Selection in this variation and genetic and ecological drift is the cause of speciation according to neodarwinists and in this system populations, races, varieties, subspecies and species are merging into each other. One extreme is described by Hubbell (2001), who has suggested a neutral theory (as opposed to the niche assembly theory) where the point mutation mode of speciation is considered very likely and the different systematic levels are like fractals. In contrast we believe that essential differentiation features (building up the the aristotype or the recognome) are of paramount importance for evolution and ecology, backed up by characters based on propagation, nutrition, ecophysiology and resistance. Such functional characters are often invariant, homoplastic or autapomorphic, but ecologically extremely significant, and therefore of use for classification. Classification should be based on such differentiation features, but also cladification, which is in need of new methods to show symbiogenesis and interactions between species. In the fungal kingdom the so called secondary metabolites (= extrolites) are of great importance for systematics. Paradoxically the episemantides (extrolites in our notation) of Zuckerkandl and Pauling (1965) are those that evolution is based on and hardly the semantides, which are just indirect indicators of history. - Hubbell SP (2001) The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton. - Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. Journal of Theoretical Biology 8: 357-366. Evidence of Hidden Transcriptome and Strategies Employed to Regulate Expression of RNA Transcripts. Vice President for Biological Sciences, Dr. Thomas R. Gingeras Affymetrix, Inc., Santa Clara, California, USA. email: [email protected] Abstract: The regulation of gene expression is accomplished at several points from the initiation of synthesis of RNA to post-translational modification and localization of the protein products. Two early control points where the expression of RNA is regulated are at the assembly of transcription factors in a promoter region required for the initiation/repression of RNA synthesis and in the transport of processed (spliced and polyadenylated) RNAs from the nucleus to the cytoplasm. Using high density arrays which interrogate the non-repetitive sequences of human chromosomes 21 and 22 at 35 base pair resolution