Metabolism

Metabolism is the network of chemical reactions that extract energy and build or break down molecules in living systems.

Metabolic regulation connects molecular networks to organismal energy and disease biology.

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 metabolism with mechanistic biological findings.

  3 studies
  1. 1What can a wild Medicago genome teach about stress tolerance?
  2. 2Aloe vera medicinal pathway transcriptome
  3. 3How does ZFP36 reshape metabolism after growth signals?

  Study comparison

  Study	Role	Design	N	Population	Outcome
  What can a wild Medicago genome teach about stress tolerance?2021	Supports	Computational / modellingDe novo assembly/annotation of Medicago ruthenica with stress-trait comparisons to cultivated legumes	~914 Mb estimated genome; PacBio/Illumina assembly resource — not a sample-N study	Wild Medicago ruthenica	Genome features linked to stress tolerance for alfalfa improvement
  Aloe vera medicinal pathway transcriptome2018	Supports	Computational / modellingIllumina RNA-seq de novo Trinity assembly of Aloe vera root and leaf transcriptomes	Two tissues; ~43,443 root and ~43,178 leaf CDS — transcriptome resource, not a sample-N study	Aloe vera root and leaf tissues	Annotated transcriptome resources linked to secondary-metabolite pathways
  How does ZFP36 reshape metabolism after growth signals?2023	Supports	Animal / in-vitroZFP36 eCLIP, Eno2 decay, metabolomics, and endothelial Zfp36 loss in retinal angiogenesis	MEF and in-vivo angiogenesis assays — no single primary analytic N in stored text	Mouse embryonic fibroblasts and neonatal retinal vasculature models	ZFP36-mediated decay of metabolic mRNAs including Eno2

• ○ Limited citations

  Highly complete genome assembly; wild species retains tolerance traits diluted by domestication for yield; useful for breeding stress-tolerant alfalfa.

  1 study
  1. 1What can a wild Medicago genome teach about stress tolerance?

• ○ Limited citations

  ~43k CDS per tissue with extensive annotation tied to secondary-metabolite pathways.

  1 study
  1. 1Aloe vera medicinal pathway transcriptome

• ○ Limited citations

  ZFP36 family members are acute growth-factor immediate-early genes; they bind many metabolic mRNAs and promote Eno2 mRNA decay; loss elevates ENO2/PEP and alters the metabolome; regulation appears in neonatal retinal angiogenesis.

  1 study
  1. 1How does ZFP36 reshape metabolism after growth signals?

• ○ Limited citations

  MEP pathway contributes to ginsenoside biosynthesis; IspD predicted as a key MEP enzyme; tissue patterns match ginsenoside distribution.

  1 study
  1. 1Does the MEP pathway feed ginsenoside production?

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 Metabolism, ordered by citations.

• What extreme physiologies does the painted turtle genome encode?

  The western painted turtle genome informs evolution of extreme anoxia and freeze tolerance in a slowly evolving vertebrate lineage.

  Genome biology · 2013 · 237 citations

• What can a wild Medicago genome teach about stress tolerance?

  A highly complete Medicago ruthenica genome provides genetic resources for environmental-stress tolerance missing from yield-focused cultivated alfalfa.

  BMC biology · 2021 · 54 citations

• How does ZFP36 reshape metabolism after growth signals?

  Growth factors induce ZFP36, which binds and decays metabolic enzyme/transporter mRNAs—especially Eno2—tuning glycolytic metabolism.

  Cell reports · 2023 · 45 citations

• Does the MEP pathway feed ginsenoside production?

  Transcriptomics implicates the chloroplastic MEP pathway—highlighting IspD—in ginsenoside biosynthesis beyond the classic MVA route.

  BMC genomics · 2019 · 42 citations

• Salmon fat-cell differentiation transcriptome

  Atlantic salmon adipose SVF cells progress through proliferative then adipogenic expression programs.

  BMC genomics · 2010 · 42 citations

• Folliculin tunes mTORC1 toward TFE3

  FLCN–RagC signaling makes mTORC1 substrate-selective for TFE3 phosphorylation under amino-acid cues.

  PLoS biology · 2022 · 41 citations

• How do Cryptosporidium oocysts survive outside hosts?

  Oocyst transcriptomes reveal metabolic features that help Cryptosporidium parvum endure environmental stresses without nutrient supply.

  BMC genomics · 2012 · 38 citations

• Aloe vera medicinal pathway transcriptome

  De novo root and leaf transcriptomes highlight saponin and anthraquinone metabolism genes.

  BMC genomics · 2018 · 33 citations

Questions

What is still open

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

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