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{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! PSII D1 expression (psbA) |- | '''Approach:''' RT-qPCR or ddPCR of psbA transcripts |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' minute..."

2026-05-11T23:22:00Z

Created page with "{{BreadcrumbsPrimaryProduction}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! PSII D1 expression (psbA) |- | '''Approach:''' RT-qPCR or ddPCR of psbA transcripts |- | '''Context:''' incubation, lab |- | '''Spatial scale:''' point sample |- | '''Temporal scale:''' minute..."

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{{BreadcrumbsPrimaryProduction}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
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<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! PSII D1 expression (psbA)
|-
| '''Approach:''' RT-qPCR or ddPCR of psbA transcripts
|-
| '''Context:''' incubation, lab
|-
| '''Spatial scale:''' point sample
|-
| '''Temporal scale:''' minutes to hours
|-
| '''Units:''' transcripts L<sup>-1</sup> or relative abundance
|-
| '''Community captured:''' bulk to group-specific
|-
| '''Co-measurements:''' FRRf (variable fluorescence); O<sub>2</sub> production (Clark electrode)
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

psbA encodes the D1 reaction centre protein of photosystem II (PSII), which is the primary target for photodamage and is rapidly turned over under high-light conditions. Because D1 repair is tightly coupled to PSII electron transport, psbA transcript abundance has been used as a proxy for PSII activity and the transcriptional response to changing irradiance. Transcripts are quantified by RT-qPCR or ddPCR using degenerate or group-specific primers, following the same nucleic acid extraction and reverse transcription workflow as for rbcL<ref name="Zeidner2003">Zeidner, G., Preston, C. M., DeLong, E. F., Massana, R., Post, A. F., Scanlan, D. J., & Béjà, O. (2003). Molecular diversity among marine picophytoplankton as revealed by ''psbA'' analyses. ''Environmental Microbiology'', 5(3), 212–216. https://doi.org/10.1046/j.1462-2920.2003.00403.x</ref>.

When combined with PSII fluorescence-based measurements (FRRf) or direct O<sub>2</sub> production assays, psbA expression can be linked to photosynthetic electron transport rates and used to infer D1 protein synthesis and repair rates.

=== Scale of measurement ===

Each filtered sample provides a point measurement. psbA transcripts respond rapidly to changes in irradiance (timescale of minutes to hours), making the time of day of collection a critical variable. The method captures a snapshot of the transcriptional state at the moment of sampling.

=== Data generated ===

psbA transcript concentrations (transcripts L<sup>-1</sup>) or relative expression (normalized to a reference gene). The ratio of psbA to reference gene expression is used to assess transcriptional upregulation or downregulation relative to a control treatment.

=== Units & currency ===

Units are transcripts L<sup>-1</sup> or relative abundance. The currency is cDNA copies.

=== Sample size ===

Typical samples are ~1 L in volume.

=== Repositories & databases ===

== Limitations ==

psbA transcript levels change on timescales of minutes in response to irradiance shifts, making sampling time critical and requiring rapid, standardized sample collection to avoid ex-situ artifacts. Degenerate primer biases apply as for rbcL. A single gene copy per genome is assumed. Transcript levels report transcriptional activity but do not directly indicate the rate of D1 protein synthesis or repair without additional data on translation efficiency and protein turnover.

== Example Applications & Protocols ==

=== Classic examples ===
* Zeidner et al. (2003) ''Molecular diversity among marine picophytoplankton as revealed by ''psbA'' analyses'' <ref name="Zeidner2003" />

=== Recent applications ===
*

=== Common calculations/conversions ===
* Relative expression: ΔΔCt method — compare psbA Ct to reference gene Ct across treatments: fold change = 2<sup>−ΔΔCt</sup>.

== References ==

[[Category:Main Pages|Model types]]

PsbA - Revision history