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Qualify Arg-Met and electrostimulated community causal mechanisms (batch 37) #1437

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38 changes: 19 additions & 19 deletions docs/communities/Ecoli_K12_MG1655_Arg_Met_CrossFeeding_Coculture.html
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Expand Up @@ -583,7 +583,7 @@ <h2>Ecological Interactions</h2>
<h3>ΔargA-ΔmetJ methionine cross-feeding</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The ΔargA-ΔmetJ member overproduces methionine that supports the methionine-requiring ΔmetA-ΔargR partner.</p>
<p class="prewrap interaction-description">The delta-argA/delta-metJ mutant overproduces methionine supporting the methionine-requiring delta-metA/delta-argR partner under the tested amino-acid limitation. Both strains are E. coli K-12 MG1655 derivatives. Reciprocal growth dependence does not resolve the release route or single-cell export flux, and supplemented cultures need not remain obligately mutualistic.</p>


<p><strong>Source Taxon:</strong> Escherichia coli K-12 MG1655 ΔargA-ΔmetJ</p>
Expand Down Expand Up @@ -657,7 +657,7 @@ <h4>Evidence</h4>
<h3>ΔmetA-ΔargR arginine cross-feeding</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The ΔmetA-ΔargR member overproduces arginine that supports the arginine-requiring ΔargA-ΔmetJ partner.</p>
<p class="prewrap interaction-description">The delta-metA/delta-argR mutant supplies arginine supporting the arginine-requiring delta-argA/delta-metJ partner under the tested amino-acid limitation. The same canonical taxon ID represents distinct engineered genotypes, not one organism acting on itself. Supplementation can remove partner dependence; this is not universal obligate exchange across media.</p>


<p><strong>Source Taxon:</strong> Escherichia coli K-12 MG1655 ΔmetA-ΔargR</p>
Expand Down Expand Up @@ -731,7 +731,7 @@ <h4>Evidence</h4>
<h3>Arg-Met obligate mutualism increases cell noise</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The reciprocal Arg/Met exchange formed a two-way positive, obligate mutualistic cross-feeding system and increased single-cell fluorescence noise in each strain population relative to mono-cultures.</p>
<p class="prewrap interaction-description">In the tested nutrient-limited Arg/Met coculture, reciprocal exchange was associated with higher single-cell fluorescent-reporter coefficient of variation than in supplemented monocultures. Mean amino-acid matching controls supported a heterogeneity interpretation. Reporter amino-acid sensitivity and experimental context matter: this is not a direct measurement of intrinsic transcriptional noise, a universal protein-noise effect or evidence that noise causes community collapse. MUTUALISM denotes the restricted reciprocal-growth model, not every supplementation condition.</p>



Expand Down Expand Up @@ -760,17 +760,6 @@ <h3>Arg-Met obligate mutualism increases cell noise</h3>



<p><strong>Biological Processes:</strong></p>
<ul>

<li>
biological process involved in interspecies interaction between organisms
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
</li>

</ul>




Expand Down Expand Up @@ -814,7 +803,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(3)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -842,6 +831,21 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
How do nutrient heterogeneity and reporter sensitivity mediate the Arg/Met fluorescence response?
</h3>
<p class="prewrap">Existing nodes are qualified, not an exhaustive mechanism graph. The primary main body supports assessing additional structure for reporter sensitivity and manipulated nutrient, strain-ratio and spatial heterogeneity. Mixed preincubations are not a direct spatial nutrient map, and modeled diffusion/uptake is not measured micro-scale flux. Intrinsic/extrinsic noise remains unresolved. Keep distinct Arg-Trp and BL21/environmental-isolate experiments outside this record. One-community Edison dry run is complete, but no provider job was submitted; expansion remains needs_research under #1436 pending specific spend authorization. Preserve the existing supplement/protocol and alternative-pair gaps.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#ΔargA-ΔmetJ methionine cross-feeding</code>, <code>ecological_interactions#ΔmetA-ΔargR arginine cross-feeding</code>, <code>ecological_interactions#Arg-Met obligate mutualism increases cell noise</code></p>




</div>

</section>
Expand Down Expand Up @@ -1369,10 +1373,6 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("biological process involved in interspecies interaction between organisms");


var evidenceCount = 2;

nodes.push({
Expand Down
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