Project proposals

1. Microbe-induced plant phenotypic plasticity (Aaron Lit)

- plasticity when exposed to different environmental stress
- microbes show certain types of plasticity
o 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
o Investigate signals by growing different strains of PGPR
o Nutrient poor soil, measure phenotypic plasticity: different
physical traits
2. 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
o If HGT occurred by this, observe the different DNA uptake
efficiency
3. 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
o 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 gut
5. 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 WT
6. 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
o surface proteins that undergo variation, alter its DNA
during replication to cut out certain sites to create
different proteins
o bacteria can select for different phenotypes
- selection for certain phenotypes under different hormonal
conditions
7. Morphology of mitochondria in eukaryotic cells (Rachel)
- reticular, fragmented, intermediated
- take mtDNA (transcriptome profiling) and investigate how these
are influencing cells

8. Symbiosis between gut and commensals (Frances Wu)

- if homeostasis plays a role in affecting gut development
9. 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 acids
10.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-differentiation
11.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 Drosophila
13.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?
o Foxd3 into ocellus if so
14.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
o Identifying Msx, Pax3 binding sites in FoxD3 regulatory
region
o Use gel-shift assay
- Verification of enhancer activity
15.From fins to limbs (Devon Denisson)
- determining HoxD 5 genes
16.Heart evolution, four chambered (Haneih Barkhodari)
- Tbx5gene required for the formation of septum
17.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
o RNA-seq
o Analysis of gene expression profile to determine any
variation in expression patterns

18.Are genes that undergo polyphenism a potential target for evolution

and eventual speciation? (Scotti)
- positive selection for polyphonic traits eliminating plasticity
19.Evolution of temperature- dependent sex determination (Patrick
Boyd)
- what genes have evolved to cause TSD
- C. elegans as model organism
20.Origin of polyphonic traits (Justin Devera)
- poly color variation (20, 28oC)
- how to identify color polyphenism genes?
o QTL to identify color-determining genes
21.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
o RNA seq of mRNA expression in heads and jaws of
cannibalistic morphs vs. wild-type
o Run mutagenesis screen to find constitutive cannibalistic
for candidate genes
22.Finding the genetic basis of polyphenism (Rahim)
- light intensity
- eggs have genome to become green or brown
o determined the switch mechanism
- use microarrays to narrow down when and where the switch
mechanism is triggered
- 6th phase polyphenic path is decided
23.C. remanei heat response: general?
- if during development not exposed to lethal response, they seem
to adapt well
- proteins controlling not related to heat
24.Polyphenism in beetle horn development
- what molecular mechanisms allow for horn development to arise
in species?
-