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Bound resource loops, community profiles and treatment effects (batch99) #1790

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142 changes: 44 additions & 98 deletions docs/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.html
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Original file line number Diff line number Diff line change
Expand Up @@ -545,7 +545,7 @@ <h2>Ecological Interactions</h2>
<h3>Yeast Carbon Dioxide Provisioning</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">S. cerevisiae metabolizes glucose and releases carbon dioxide that is assimilated photosynthetically by C. reinhardtii under carbon-limited coculture conditions.</p>
<p class="prewrap interaction-description">In the sealed illuminated coculture, yeast glucose metabolism supplies carbon dioxide assimilated by the algal partner. This is the carbon arm of the authors&#39; experimentally supported reciprocal carbon/nitrogen mutualism. The source does not isolate fermentation as the only route of yeast carbon dioxide production.</p>


<p><strong>Source Taxon:</strong> Saccharomyces cerevisiae</p>
Expand Down Expand Up @@ -573,12 +573,6 @@ <h3>Yeast Carbon Dioxide Provisioning</h3>
<p><strong>Biological Processes:</strong></p>
<ul>

<li>
fermentation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006113"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006113</a>)
</li>

<li>
photosynthesis
(<a href="http://amigo.geneontology.org/amigo/term/GO:0015979"
Expand All @@ -594,7 +588,7 @@ <h3>Yeast Carbon Dioxide Provisioning</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Algal Reduced Nitrogen Provisioning
<p class="prewrap causal-description">Yeast-derived carbon dioxide is fixed photosynthetically by C. reinhardtii, sustaining the algal partner that reduces nitrite to ammonia for S. cerevisiae.</p>
<p class="prewrap causal-description">PARTIAL: yeast-derived carbon dioxide sustains the alga that supplies reduced nitrogen to yeast, closing the resource-dependence loop. Coculture and resource-availability comparisons support this reciprocal mechanism, but do not separately quantify how a change in carbon transfer changes ammonia release.</p>
</div>

</div>
Expand All @@ -619,57 +613,14 @@ <h4>Evidence</h4>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Algal Oxygen Provisioning</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">C. reinhardtii releases photosynthetic oxygen that supports aerobic yeast metabolism in the sealed coculture.</p>


<p><strong>Source Taxon:</strong> Chlamydomonas reinhardtii</p>



<p><strong>Target Taxon:</strong> Saccharomyces cerevisiae</p>



<p><strong>Metabolites:</strong>

dioxygen
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15379"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15379</a>)

</p>



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

<li>
photosynthesis
(<a href="http://amigo.geneontology.org/amigo/term/GO:0015979"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0015979</a>)
</li>

</ul>





</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Algal Reduced Nitrogen Provisioning</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">C. reinhardtii metabolizes nitrite and releases ammonia, providing reduced nitrogen that supports S. cerevisiae growth.</p>
<p class="prewrap interaction-description">Algal nitrite metabolism supplies ammonia usable by yeast in the carbon/nitrogen mutualism. The dependence is conditional on the resource environment, not an unconditional property of these species; external reduced nitrogen can remove yeast dependence on the alga.</p>


<p><strong>Source Taxon:</strong> Chlamydomonas reinhardtii</p>
Expand Down Expand Up @@ -712,7 +663,7 @@ <h3>Algal Reduced Nitrogen Provisioning</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Yeast Carbon Dioxide Provisioning
<p class="prewrap causal-description">Algal reduction of nitrite to ammonia supplies the nitrogen source that lets S. cerevisiae proliferate and keep producing carbon dioxide from glucose.</p>
<p class="prewrap causal-description">PARTIAL: algal reduced nitrogen sustains yeast growth and therefore the yeast partner supplying carbon dioxide. This reciprocal support is consistent with the reported dependence, not a measured feedback gain or a separate temporal causal experiment.</p>
</div>

</div>
Expand Down Expand Up @@ -779,6 +730,45 @@ <h2>Associated Datasets</h2>
</div>
</section>

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Is algal oxygen release a demonstrated additional benefit to yeast in this exact coculture?
</h3>
<p class="prewrap">The primary manuscript depicts oxygen release, but the reviewed main text establishes reciprocal carbon/nitrogen dependence rather than an isolated oxygen-mediated yeast benefit. The two-node resource loop is retained with PARTIAL mediation limits. The oxygen-benefit assertion is removed pending exact-system evidence. This does not assert that yeast cannot use oxygen. Broader re-evidencing remains in issue765, and cache-version/license provenance is tracked separately.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Yeast Carbon Dioxide Provisioning</code>, <code>ecological_interactions#Algal Reduced Nitrogen Provisioning</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/24994654/" rel="nofollow noreferrer">PMID:24994654</a>


</div>
<p class="snippet small prewrap">an environment requiring reciprocal carbon and nitrogen exchange</p>
<p class="muted small prewrap">The abstract supports the established reciprocal resource basis, not an oxygen-specific benefit.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1025,8 +1015,6 @@ <h3>
var processes = [];


processes.push("fermentation");

processes.push("photosynthesis");


Expand Down Expand Up @@ -1063,48 +1051,6 @@ <h3>
var metabolites = [];


metabolites.push("dioxygen");


var processes = [];


processes.push("photosynthesis");


var evidenceCount = 0;

nodes.push({
id: intId,
label: "Algal Oxygen Provisioning",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
processes: processes,
evidenceCount: evidenceCount
});


var srcKey = "Chlamydomonas reinhardtii";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}



var tgtKey = "Saccharomyces cerevisiae";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}

})();

(function() {
var intId = "interaction:2";
var intType = "CROSS_FEEDING";
var metabolites = [];


metabolites.push("nitrite");

metabolites.push("ammonia");
Expand Down Expand Up @@ -1162,7 +1108,7 @@ <h3>
var svg = d3.select("#network-svg");
var width = container.clientWidth - 32;
// Dynamic height based on node count: minimum 500px, add 40px per node
var nodeCount = 5;
var nodeCount = 4;
var height = Math.max(500, 400 + nodeCount * 20);
svg.attr("width", width).attr("height", height);

Expand Down
55 changes: 49 additions & 6 deletions docs/communities/Saccharomyces_Met14_Trp4_FLO1_Resveratrol_Coculture.html
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Expand Up @@ -596,6 +596,11 @@ <h2>Ecological Interactions</h2>
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>

Expand All @@ -605,7 +610,7 @@ <h2>Ecological Interactions</h2>
<h3>Met-Trp4 Coauxotrophic Cross-Feeding</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The two engineered S. cerevisiae auxotrophs require one another for growth in SM medium; the Met-Trp4 pair couples a met14-deficient cell-1 lineage with a trp4-deficient cell-2 lineage in a defined cross-feeding coculture.</p>
<p class="prewrap interaction-description">The Met-Trp4 coauxotrophic yeast pair forms a mutually dependent growth system in the tested medium lacking the complementary required nutrients. This growth relationship is distinct from the resveratrol pathway handoff and does not by itself establish enhanced product titer or unconditional dependence in supplemented environments.</p>



Expand Down Expand Up @@ -651,7 +656,7 @@ <h4>Evidence</h4>
<h3>Resveratrol Pathway Division of Labor</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The met14 cell-1 partner runs module A to convert L-tyrosine into the p-coumaric acid intermediate, which is then routed to the trp4 cell-2 partner carrying module B for conversion into resveratrol.</p>
<p class="prewrap interaction-description">The existing met14 module-A and trp4 module-B partners divide the resveratrol pathway around p-coumaric acid. The reported module assignment and product/intermediate measurements support the intended metabolic handoff, but do not directly quantify intercellular transfer flux or show that it alone explains the FLO1-associated production increment.</p>


<p><strong>Source Taxon:</strong> Saccharomyces cerevisiae 007 met14 module A FLO1 cell 1</p>
Expand Down Expand Up @@ -679,7 +684,7 @@ <h3>Resveratrol Pathway Division of Labor</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> FLO1 Adhesion-Enhanced Resveratrol Production
<p class="prewrap causal-description">The divided module A/module B pathway supplies the p-coumaric-acid handoff used by the FLO1 Met-Trp4 A-B bioproduction coculture.</p>
<p class="prewrap causal-description">PARTIAL: the divided pathway supplies the precursor-to-product route in the tested FLO1 coculture, enabling resveratrol synthesis. It does not independently explain the increase over the no-FLO1 control; adhesion-dependent transfer efficiency was not isolated as the mediator.</p>
</div>

</div>
Expand Down Expand Up @@ -709,9 +714,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>FLO1 Adhesion-Enhanced Resveratrol Production</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Adding the FLO1 adhesion system to the Met-Trp4 A-B division-of-labor coculture increased resveratrol production compared with the no-FLO1 Met-Trp4 A-B coculture, the corresponding FLO1 noncross-feeding control, and the full-pathway monoculture control.</p>
<p class="prewrap interaction-description">The tested Met-Trp4 A-B:FLO1 coculture produced more resveratrol than its no-FLO1 counterpart, the corresponding FLO1 noncross-feeding control and the full-pathway monoculture. This is an aggregate production endpoint, not by itself a mutualistic fitness measurement. The higher titer co-occurred with precursor accumulation and lower biomass in this configuration; it does not establish more efficient precursor conversion or a universal benefit of adhesion across yeast pairs.</p>



Expand Down Expand Up @@ -770,6 +774,45 @@ <h4>Evidence</h4>

<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
How much of the FLO1-associated titer increment is mediated by intercellular precursor transfer?
</h3>
<p class="prewrap">The production comparison and coauxotrophic mutualism are supported, but neither an endpoint titer nor pathway assignment independently measures transfer efficiency or reciprocal fitness. The source explicitly leaves aggregate morphology and metabolic exchange for further study. Preserve the one existing direction as PARTIAL, without restoring the previously removed growth-background arrow.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Met-Trp4 Coauxotrophic Cross-Feeding</code>, <code>ecological_interactions#Resveratrol Pathway Division of Labor</code>, <code>ecological_interactions#FLO1 Adhesion-Enhanced Resveratrol Production</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/41491832/" rel="nofollow noreferrer">PMID:41491832</a>


</div>
<p class="snippet small prewrap">Systematic investigation of aggregate morphology and its impact on metabolic exchange represents an important direction for future research</p>
<p class="muted small prewrap">The authors distinguish their demonstrated production endpoint from unresolved exchange mechanisms.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1104,7 +1147,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:2";
var intType = "MUTUALISM";
var intType = "UNKNOWN";
var metabolites = [];

var processes = [];
Expand Down
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