Project proposals

1. Microbe-induced plant phenotypic plasticity (Aaron Lit) plasticity when exposed to different environmental stress microbes show certain types of plasticity increasing flowering number or fruit production what types of signals do microbes communicate with the plant? How does the plant respond to those signals Does microbe-induced plasticity cause an adaptive advantage Investigate signals by growing different strains of PGPR Nutrient poor soil, measure phenotypic plasticity: different physical traits2. Horizontal gene transfer can affect eukaryotic evolution (Katherine Chen) important for transition, occupying niches genes derived from viruses (moss), parsimonious explanation: contributes to essential processes (ie. glycolysis) uptaken by spore germination or fertiziliation of development of embryo Proposed: transofmraiton of algae to evaluate DNA uptake frequency If HGT occurred by this, observe the different DNA uptake efficiency3. Pathogenic receptors important in immune response (Carlos Acosta) why is there a skew in selection of TLR over MyD TLR4 affinity for MyD and Trif Conserved regions?4. Evolution of gut microbe in response to new food source (Crispin Herrick) metabolic aspect of gut microbes extract Drosophila gut microbes and compare phylogenies restrict diet to new unusual food source not found in fly gut5. adaptive immune system in jawed vertebrates (Sophia) novel future of the jawed vertebrates required RAG genes (recombination genes) brought in through transposon adaptive vs. innate: why they work just fine T-cels that regulate commensals Gnotobiotic Rag1 models: known microbes in the organism and compare with WT6. Infertility in host-pathogen relationships many STDs cause infertility; does not allow host to divert resources from the pathogens, host stays alive gonorrhea; scars tissues such as fallopian tube and testicles surface proteins that undergo variation, alter its DNA during replication to cut out certain sites to create different proteins bacteria can select for different phenotypes selection for certain phenotypes under different hormonal conditions7. Morphology of mitochondria in eukaryotic cells (Rachel) reticular, fragmented, intermediated take mtDNA (transcriptome profiling) and investigate how these are influencing cells8. Symbiosis between gut and commensals (Frances Wu) if homeostasis plays a role in affecting gut development9. GPR-40, 41, 43 (Jodi So) GPR-40 binds long chain fatty acids GPR41, 43 only binds to short chain fatty acids (gut bacteria) In Xenopus, it was indiscriminate to the length of the fatty acids10. Evolution of limb regeneration in vertebrates (Nick Donde) what genes account for the variation in limb regenerative ability in vertebrates? Are these the same genes with evolved novel activities or different genes altogether? Previously identified genes: Shh, Sox2, Wnt signaling genes such as Axin1 Look at relative expression of these genes In newt muscles cells, Pax7 was identified and shown to be involved in post-amputation de-differentiation11. Origins of the vertebrate placodes (Bryan Bach) unique to vertebrates (cranial ectodermal placodes) develop into cranial nerves and sensory organs of the head bottom-up approach: ChIP-seq top-down approach: Six3, islet follow fate map 12. Evolution of declined regeneration capacity (Steven Reich) blocking Wnt signaling: weird spike Wnt regeneration enhancer in Drosophila13. Evolution of the neural crest gene regulatory network (Emilie Dalbram) tunicate Ciona: neural crest identified (rudimentary) elaboration of ancestral chordate gene network instead of a de novo evolution Hoxb5 Foxd3 (neural crest important aspect) Is the Hoxb5 homolog conserved in Ciona? Foxd3 into ocellus if so14. AmphiFoxD gene and vertebrate FoxD genes (Kyu Chang) amphioxus: 1 copy, vertebrate: 5 copies Foxd3 has new critical function in NC Amphi cant induce expression in NC, in vertebrate, gained new enhancers Identifying Msx, Pax3 binding sites in FoxD3 regulatory region Use gel-shift assay Verification of enhancer activity15. From fins to limbs (Devon Denisson) determining HoxD 5 genes16. Heart evolution, four chambered (Haneih Barkhodari) Tbx5gene required for the formation of septum17. identifying modifier genes involved in sex-linked polyphenism (Rosheen Birdie) in Manducta sexta: color polyphenism is poly genic determine loci of modifier genes involved in sex-linked polyphenism expression pattenrs of modifier genes RNA-seq Analysis of gene expression profile to determine any variation in expression patterns18. Are genes that undergo polyphenism a potential target for evolution and eventual speciation? (Scotti) positive selection for polyphonic traits eliminating plasticity19. Evolution of temperature- dependent sex determination (Patrick Boyd) what genes have evolved to cause TSD C. elegans as model organism20. Origin of polyphonic traits (Justin Devera) poly color variation (20, 28oC) how to identify color polyphenism genes? QTL to identify color-determining genes21. The genetic basis of cannibalistic polyphenism in Pelobates fuscus (Liam OConnell) 2 weeks from zygote to adult cannibalistic growth, its jaws are more developed, past its increased size turning on of early jaw development salinity, release of hormones candidate gene approach RNA seq of mRNA expression in heads and jaws of cannibalistic morphs vs. wild-type Run mutagenesis screen to find constitutive cannibalistic for candidate genes22. Finding the genetic basis of polyphenism (Rahim) light intensity eggs have genome to become green or brown determined the switch mechanism use microarrays to narrow down when and where the switch mechanism is triggered 6th phase polyphenic path is decided23. C. remanei heat response: general? if during development not exposed to lethal response, they seem to adapt well proteins controlling not related to heat24. Polyphenism in beetle horn development what molecular mechanisms allow for horn development to arise in species?