Difference between revisions of "Needs Analysis Workshop/Chalk talks"

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(→‎Notes from chalk talks:)
Line 5: Line 5:
 
** ostariophysi most important group of freshwater fish
 
** ostariophysi most important group of freshwater fish
 
* '''Arhat Abzhanov''':
 
* '''Arhat Abzhanov''':
 +
** works on craniofacial evolution
 
** drivers and evolution of cranial development
 
** drivers and evolution of cranial development
−
** beak development and diversification among Galapagos finches
+
** variation; beak development and diversification (morphs) among Galapagos finches
 
** comparative relationships of developmental pathways of interacting and regulatory genes
 
** comparative relationships of developmental pathways of interacting and regulatory genes
 
* '''Hans Hofman''':
 
* '''Hans Hofman''':
Line 12: Line 13:
 
** variation at the population and species level, such as ecology, biogeography, natural history, etc
 
** variation at the population and species level, such as ecology, biogeography, natural history, etc
 
** how to link these two through, for example, a data repository
 
** how to link these two through, for example, a data repository
−
** how to implement the ability for open-ended queries
+
** how to implement the ability for open-ended queries (when we don't know what questions might be)
 
** how to connect this to development time, plasticity, genotype/environment interactions
 
** how to connect this to development time, plasticity, genotype/environment interactions
 
* '''Toby Kellogg''':
 
* '''Toby Kellogg''':
 
** grasses have about 10,000 species, e.g., rice, maize
 
** grasses have about 10,000 species, e.g., rice, maize
 
** which meristem-specific genes have been conserved or evolutionarily changed
 
** which meristem-specific genes have been conserved or evolutionarily changed
−
** challenge: how to get from a list of genes to the 3'UTR to use for in-situs for same or different species
+
** challenge: how to get from a list of candidate genes (involved in floresence) to the 3'UTR to use for in-situs for same or different species?
 
** designing primers for an entire clade based on a multiple alignment
 
** designing primers for an entire clade based on a multiple alignment
−
** automating the pipeline is major challenge
+
** automating the pipeline is desire and major challenge
 
* '''Austin Mast''':
 
* '''Austin Mast''':
 
** MorphBank
 
** MorphBank
 +
** Images provide greater information than what we can put into words
 
** Slide-server interface
 
** Slide-server interface
 
** bulk annotation, 'tile' layout
 
** bulk annotation, 'tile' layout
−
* '''Elizabeth Jokusch''':
+
* '''Elizabeth Jockusch''':
−
** beetle antennae: scape (1), pedicel (1), flagellum (typically 9 segments, but many exceptions)
+
** beetle devo-evo; antennae divided into: scape (1), pedicel (1), flagellum (typically 9 segments, but many exceptions)
 
** Tribolium: flagellum -> funicle and club, with variable number of segments
 
** Tribolium: flagellum -> funicle and club, with variable number of segments
−
** using RNAi to induce changes (phenotypes) in these
+
** candidate genes; using RNAi to induce changes (phenotypes) in 5 sp of Tribolium
−
** e.g. reduced number of antenna segments, fusions of antenna segments, deletions
+
** e.g. reduced number of antenna segments, why? e.g. fusions of antenna segments, deletions, failure to form? (empirical devo Q's)
−
** how to code these phenotypes so one can ask for broader patterns, non-randomness
+
** how to code these phenotypes so one can ask for broader patterns, non-randomness?
 
* '''Chuck Kimmel''':
 
* '''Chuck Kimmel''':
−
** role of cells in skeletal shape forming
+
** Important: role of cells in forming skeletal shape  
 
** what are the activities of cells controlled by developmental genes
 
** what are the activities of cells controlled by developmental genes
 
** devo hypothesis: modular assembly?
 
** devo hypothesis: modular assembly?
 
** what is the broad nature of shape diversity (of, e.g., certain bones)
 
** what is the broad nature of shape diversity (of, e.g., certain bones)
 
** evo hyothesis: a missing module?
 
** evo hyothesis: a missing module?
−
** how could a database help with the shape transformation
+
** how could a database help with the shape transformation; how to code cells and cell activity into process?  Retrieval of hypotheses vs. facts
 
* '''Günter Wagner''':
 
* '''Günter Wagner''':
 
** evolution of limbs, gene duplication in teleosts, internal development of human
 
** evolution of limbs, gene duplication in teleosts, internal development of human
Line 43: Line 45:
 
** what to compare to in organisms that don't have a particular cell type? e.g. myelinated cells comparing to lampreys (which have only glial cells)
 
** what to compare to in organisms that don't have a particular cell type? e.g. myelinated cells comparing to lampreys (which have only glial cells)
 
* '''David Stern''' (Tuesday):
 
* '''David Stern''' (Tuesday):
−
** trait differences between Drosophila species
+
** parsing out categories of morphological features (morphology, physiology, behavior, etc.); trait differences between Drosophila species
 +
** list of mutations that cause phenotypic differences
 +
** experimental evidence for the role of mutation
 
** database of evolutionary mutations and their phenotypes fixed through drift or selection (EvolGen)
 
** database of evolutionary mutations and their phenotypes fixed through drift or selection (EvolGen)
 
* '''Hopi Hoekstra''' (Tuesday):
 
* '''Hopi Hoekstra''' (Tuesday):
 +
** genetic basis for variation
 +
** classify phenotypic variation (pigment, morphology (e.g. tail length), behavior)
 
** Peromyscus trait evolution
 
** Peromyscus trait evolution

Revision as of 15:53, 25 September 2007

Notes from chalk talks:

  • John Lundberg:
    • ~30,000 teleost species
    • ostariophysi most important group of freshwater fish
  • Arhat Abzhanov:
    • works on craniofacial evolution
    • drivers and evolution of cranial development
    • variation; beak development and diversification (morphs) among Galapagos finches
    • comparative relationships of developmental pathways of interacting and regulatory genes
  • Hans Hofman:
    • individual variation in gene expression, pathways, physiology, anatomy, behaviour, etc
    • variation at the population and species level, such as ecology, biogeography, natural history, etc
    • how to link these two through, for example, a data repository
    • how to implement the ability for open-ended queries (when we don't know what questions might be)
    • how to connect this to development time, plasticity, genotype/environment interactions
  • Toby Kellogg:
    • grasses have about 10,000 species, e.g., rice, maize
    • which meristem-specific genes have been conserved or evolutionarily changed
    • challenge: how to get from a list of candidate genes (involved in floresence) to the 3'UTR to use for in-situs for same or different species?
    • designing primers for an entire clade based on a multiple alignment
    • automating the pipeline is desire and major challenge
  • Austin Mast:
    • MorphBank
    • Images provide greater information than what we can put into words
    • Slide-server interface
    • bulk annotation, 'tile' layout
  • Elizabeth Jockusch:
    • beetle devo-evo; antennae divided into: scape (1), pedicel (1), flagellum (typically 9 segments, but many exceptions)
    • Tribolium: flagellum -> funicle and club, with variable number of segments
    • candidate genes; using RNAi to induce changes (phenotypes) in 5 sp of Tribolium
    • e.g. reduced number of antenna segments, why? e.g. fusions of antenna segments, deletions, failure to form? (empirical devo Q's)
    • how to code these phenotypes so one can ask for broader patterns, non-randomness?
  • Chuck Kimmel:
    • Important: role of cells in forming skeletal shape
    • what are the activities of cells controlled by developmental genes
    • devo hypothesis: modular assembly?
    • what is the broad nature of shape diversity (of, e.g., certain bones)
    • evo hyothesis: a missing module?
    • how could a database help with the shape transformation; how to code cells and cell activity into process? Retrieval of hypotheses vs. facts
  • Günter Wagner:
    • evolution of limbs, gene duplication in teleosts, internal development of human
    • following the genes to the taxa they lead to
    • comparative cell morphology and cell physiology
    • what to compare to in organisms that don't have a particular cell type? e.g. myelinated cells comparing to lampreys (which have only glial cells)
  • David Stern (Tuesday):
    • parsing out categories of morphological features (morphology, physiology, behavior, etc.); trait differences between Drosophila species
    • list of mutations that cause phenotypic differences
    • experimental evidence for the role of mutation
    • database of evolutionary mutations and their phenotypes fixed through drift or selection (EvolGen)
  • Hopi Hoekstra (Tuesday):
    • genetic basis for variation
    • classify phenotypic variation (pigment, morphology (e.g. tail length), behavior)
    • Peromyscus trait evolution
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