Innate immunity

Innate immunity is the rapid, germline-encoded defence system that recognises conserved microbial features and tissue damage.

Innate immunity is the rapid defence layer shared across animals (and beyond) in the curriculum.

Claim ledger

What the evidence shows

Drawn from 8 studies in this library. Mix labels say which citation roles are present; they are not a strength score. Supports means evidence for a finding; Challenges means evidence against a stated position; Qualifies marks scope.

• ● Supporting studies only

  Multiple empirical papers in this library examine innate immunity with mechanistic biological findings.

  3 studies
  1. 1Coral gene expression in white syndromes
  2. 2How interferon throttles sterol synthesis in antiviral defense
  3. 3Immune transcriptome of bacteria-challenged sea bass

  Study comparison

  Study	Role	Design	N	Population	Outcome
  Coral gene expression in white syndromes2015	Supports	OtherRNA-seq of white-syndrome disease, adjacent, and healthy Acropora hyacinthus tissues	N=16 · Fragments from 16 colonies; analyses with n=8 per tissue group	Reef-building coral Acropora hyacinthus colonies in Palau	Differentially expressed genes separating diseased from healthy coral tissue
  How interferon throttles sterol synthesis in antiviral defense2011	Supports	Animal / in-vitroMacrophage time-series, lipidomics, IFN receptor knockouts, and murine CMV infection models	Multi-assay mouse/cell study — no single primary analytic N in stored text	Primary bone-marrow–derived macrophages and mice (including IFNAR1/Tyk2 models)	Interferon-mediated sterol-pathway down-regulation in antiviral defense
  Immune transcriptome of bacteria-challenged sea bass2010	Supports	Animal / in-vitroRNA-seq of head kidney/spleen from bacteria-challenged vs mock-challenged sea bass	Tissue RNA pooled from 15 fishes per preparation — no unpooled individual analytic N	Lateolabrax japonicus (Japanese sea bass)	Immune-related transcriptome after bacterial challenge

• ○ Limited citations

  Hundreds of DEGs separate disease from healthy; healthy vs adjacent are more similar.

  1 study
  1. 1Coral gene expression in white syndromes

• ○ Limited citations

  Infection and type I/II IFN coordinately reduce sterol-pathway transcripts and metabolites via IFNAR1/Tyk2 signaling and lowered SREBP2. Antiviral effects of pathway blockade depend on mevalonate/geranylgeraniol, not cholesterol rescue.

  1 study
  1. 1How interferon throttles sterol synthesis in antiviral defense

• ○ Limited citations

  Large transcriptome with many immune effectors and pathway annotations (hepcidin, lysozyme, RAG).

  1 study
  1. 1Immune transcriptome of bacteria-challenged sea bass

• ○ Limited citations

  OMVs carry PRR ligands (e.g., PG for NOD1/NOD2) enabling bacteria–host communication across mucus; they modulate epithelial innate responses and barrier functions.

  1 study
  1. 1How do E. coli vesicles talk to gut epithelium?

Debates

Tensions and limits

Some items are genuine disagreements on the same question. Others mark different assays, populations, or outcomes.

Timeline

How understanding moved

Study years are when the paper was published. Evidence edits are dated changes to this page's claims. Explanations are when PaperFren added a Discovery — not a claim that the science happened that day.

Papers

8 studies in this library bear on Innate immunity, ordered by citations.

• Which sensor starts IFN against SARS-CoV-2 in lung cells?

  SARS-CoV-2 triggers delayed IFN mainly via MDA5/LGP2 sensing of viral intermediates, with IRF3/IRF5/NF-κB p65 as key TFs.

  Cell reports · 2021 · 354 citations

• Was innate immunity already complex in early animals?

  Anthozoan cnidarians retain much ancestral metazoan immune/signaling complexity; flies and worms lost many components.

  Genome biology · 2007 · 265 citations

• How interferon throttles sterol synthesis in antiviral defense

  Type I interferon couples viral sensing to down-regulation of the sterol pathway’s mevalonate–isoprenoid arm, limiting viral growth.

  PLoS biology · 2011 · 239 citations

• Plant TIR domain binds viral elicitor

  Tobacco N protein’s TIR domain is critical for association with TMV p50 elicitor.

  PLoS biology · 2007 · 238 citations

• Coral gene expression in white syndromes

  White-syndrome lesions in Acropora hyacinthus show distinct innate-immunity–related expression versus healthy tissue.

  BMC genomics · 2015 · 211 citations

• Chicken β-defensin gene cluster

  Chicken genome encodes 13 β-defensin (Gal) genes in a single innate-immunity cluster.

  BMC genomics · 2004 · 181 citations

• How do E. coli vesicles talk to gut epithelium?

  Outer membrane vesicles from probiotic and commensal E. coli deliver ligands that activate NOD1-mediated immune responses in intestinal epithelial cells.

  Frontiers in microbiology · 2018 · 155 citations

• Immune transcriptome of bacteria-challenged sea bass

  Deep RNA-seq of bacteria-challenged Lateolabrax japonicus reveals innate immune genes.

  BMC genomics · 2010 · 139 citations

Questions

What is still open

1. Systems and scales differ across innate immunity studies (species, tissues, methods), so mechanisms should not be over-generalised.

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