Re-run the functional analysis on the updated list of proteins to recreate networks.

  • Both ASCA and hierarchical clustering identify proteins based on their NSAF values
  • Chi Sq. proportions test identifies proteins based on their sum of total number of spectra

How should the networks be colored?

  • if it’s just same day fold change, that doesn’t account for those identified by ASCA or hierarchical clustering
  • it seems like there should be some kind of combined metric by which to color the nodes
    • ASCA and hierarchical clustering would not be weighted per time point as the chi sq. test.
    • find the average of the Magnitude log2 foldchange of totnumspec ratios + magnitude log2 foldchange of NSAF values
      • summing magnitude log2 foldchange NSAF values and totnumspec ratios would combine both metrics that different statistics assessed
      • computing the average would eqiulibrate NSAF values and totnumspec ratios so one metric does not weigh more than the other
  • different processes are affected

Black clade (up-reg day 3 23C): - Dynein: - - HTS: cleave cytoskeleton proteins; transport and binding related

Structure: - Actin - Titin: muscle elasticity and stability; (4000-5000 range; Ig domain; and 24000-26000 = fibronectine type III and Ig like domains) - Tektin: cytoskel proteins found in cilia and flagella as structural components of outer microtubles - Fibropellin: extracellular matrix formation - Chitinase: immunity effector (https://www.ncbi.nlm.nih.gov/pubmed/17056114) - EEF2: protein elongation factor essential for protein synthesis; it is the target of some bacterial toxins (pseudomonas, diptheria; https://en.wikipedia.org/wiki/EEF2) - Carnosine synthase: ATP + histidine + beta-alanine = ADP + phosphate + carnosine (https://en.wikipedia.org/wiki/Carnosine_synthase); carnosine = ROS scavenger, - GST: can conjugate xenobiotics to GSH and detoxify cell environments - Cilia and FLagella associated proteins (https://www.sciencedirect.com/science/article/pii/S0006291X17317692?via%3Dihub) - Alpha protein kinase vwkA: myosin related (https://www.uniprot.org/uniprot/Q6B9X6) - perlucin-like: promotes growth of calium carbonate (https://www.uniprot.org/uniprot/P82596) - SCO-spondin: neural development(https://www.uniprot.org/uniprot/A2VEC9) - twitchin: muscle related (https://www.uniprot.org/uniprot/Q23551) - tubulin - myosin

*** are their cilia being disorganized??? (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007914/)

***Do proteins work better at higher temperature so animal does not need to produce as much protein to perform the same level of activity? (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767513/)

DARKRED CLADE (up in 29C later in dev.):

  • Growth related proteins:
    • Svep1; Sushi protein (EGF domain, vWF-A domain); Required for assembling actin at ring canals in developing egg chambers. Probably interacts with other developmental proteins involved in nurse cell/oocyte transport through the ring canals.
    • TTN (900-2000aa range; Ig like domain)
    • PPP2R1A: The PR65 subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. Upon interaction with GNA12 promotes dephosphorylation of microtubule associated protein TAU/MAPT. Required for proper chromosome segregation and for centromeric localization of SGO1 in mitosis
    • SSPO (spondin): cell aggregation, development
    • C1QL4: neural development
    • Sodium/calcium exchanger regulatory protein 1 (lipid binding/transport)
    • Chloride intracellular channel exc-4: chloride ion channels; required for regulating the size of the tube lumen as it grows
  • Structural protein
    • Actin3
    • Actinin
    • ARPC2; Actin related protein complex
    • collagen
    • Dynein heavy chain 5
    • Filamin A: actin binding, actin organization
    • PDLIM7: May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation
  • Metabolism
    • NME2; nucleoside triphosphate synthesis
    • UAP1 (UDP-N-acetylhexosamine pyrophosphorylase)
    • Calumenin: regulation of carboxylation on glutamate, may modulate calcium release from sarcoplasmic reticulum
    • Sarcoplasmic calcium binding protein: associated with muscles
    • catalase: protects against hydrogen peroxide
    • CNDP2: production of lactoyl amino acids
    • Rho GDP-dissociation inhibitor 1
      • protein homeostasis
    • Elongation factor 1-alpha: protein synthesis; promotes the GTP dependent binding of tRNA to ribosome
    • enolase: glycolysis
    • FABP: lipid transporter
    • GST-a, oxidises GST
  • Proteomics paper
  • WGBS geoduck hemolymph; FASTQC, Trim, Bismark align to 10K contig genome
    • start script on Mox
    • what is the coverage?
  • Sea lice project
    • decide what method
      • RRBS for salmon
      • WGBS for sea lice (1 lane/animal)
        • or pool?

TURQUOISE4 (down-reg on day 3):

  • ITI4 (inter-alpha-trypsin inhibitor): Type II acute-phase protein (APP) involved in inflammatory responses to trauma. May also play a role in liver development or regeneration
  • RS27A-ubiquitinated (ribosome 40S protein)
  • Mitochondria eating protein
  • EGF-like proteins:
    • Gigasin
    • VWDE (von Willebrand factor D and EGF domain)
    • EGF like domain containing protein 1
  • Fibronectin containing protein (glycoprotein involved in lots of processes)
  • Hemicentin: Promotes cleavage furrow maturation during cytokinesis in preimplantation embryos. May play a role in the architecture of adhesive and flexible epithelial cell junctions. May play a role during myocardial remodeling by imparting an effect on cardiac fibroblast migration
  • TTN: 7000aa -8000aa range; this is an Ig like domain
  • KCP (Kielin/chordin-like protein): Enhances bone morphogenetic protein (BMP) signaling in a paracrine manner. In contrast, it inhibits both the activin-A and TGFB1-mediated signaling pathways
  • Collagen
  • Spectrin beta chain: cytoskeletal scaffolding protein that coordinates; degraded by caspase and or calpain (some calpain and caspace proteins are upreg. on Day 3, CASP10.4, CASP7.21, BRAFLDRAFT66705, contig049136, contig022851, CAN5.1,
  • FAT4: Cadherins are cell-cell interaction molecules. FAT4 plays a role in the maintenance of planar cell polarity as well as in inhibition of YAP1-mediated neuroprogenitor cell proliferation and differentiation
  • Methionine sulfoxide reductase
  • ATP synthase subunit d(mitochondrial)
  • MUC1: adhesion and anti-adhesion protein for protection -NPC2: intracellular cholestorol transporter
  • Neurofascin: cell adhesion, ankyrin-binding
  • PIF: essential organic matrix component for normal growth of nacreous layer; aragonite crystallization initiation
  • FKBP14: accelerates the folding of proteins during protein synthesis

Animals develop faster at higher temperatures

These animals developed larger, they have more protein. Protein accretion is due to protein synthesis. We find proteins in energy generating processes, nucleoside triphosphate synthesis and glycolysis, and protein synthesis pathyways to show increased abundance in larvae reared at 29C as opposed to 23C, confirming these previous observations.

Bivalves can adjust the componenets of energy balance to maintain positive scope for growth (have energy available for growth and reproduction in the form of body weight).

Temperature accelerated development in eel (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555698/)

Is it possible that both silos are facing the same abiotic and biotic stress, only the higher temp allows the larvae to have more efficient enzymes to deal with it?

If larval dispersal varies with temperature, you would expect to see broad population mixing at colder temperatures and more local, distinct populations at warmer temperatures

Lorgeril et al. (immune suppression by OsHV-1 viral infection):

  • early response: resistant oyster shows DE of genes involved in apoptosis and cell homeostasis under viral infection
  • late response: susceptible oyster shows massive response
    • expression of inhibitors of apoptosis

Delisle et al. : temp modulates disease susceptibility of gigas and virulence of OsHV-1:

  • 29C reduces virulence of OsHV-1 and increases survival

TO DO:

  • Update tables
  • Update code

http://whenisgood.net/syngnkg/results/eb5q77s

eb5q77s

recently observed