View source for NifH detection/quantification (qPCR, RT-qPCR; nifH database)


* [[Page authors|Page authors]]: [[Christian Furbo Reeder]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Chreaa | Christian Furbo Reeder]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Approach:''' gene quantification
|-
| '''Context:''' ''Molecular''
|-
| '''Spatial scale:'''
|-
| '''Temporal scale:''' Days, Seasons
|-
| '''Units:''' gene copies, transcripts
|-
| '''Community captured:''' diazotrophs (potential or active)
|-
| '''Co-measurements:''' 
|}
</div>
<div style="clear:both"></div>

== Method Overview ==
Quantification of nifH is typically performed using quantitative PCR (qPCR) to measure nifH gene copy numbers, providing an estimate of diazotroph abundance. Reverse transcription qPCR (RT-qPCR) targets nifH transcripts, enabling assessment of gene expression and thus potential nitrogenase activity

== Output ==
* nifH gene copy numbers (qPCR)
* nifH transcript abundance (RT-qPCR)
* Gene- or transcript-based estimates of nitrogen fixation potential

=== Scale of measurement ===
* Molecular / gene-expression level
* Quantitative
* Community-integrated signal

=== Data generated ===
* Ct (cycle threshold) values
* Standard curves for absolute quantification
* Gene or transcript copy number estimates
* Metadata-linked abundance or expression tables

=== Units & currency ===
* nifH gene copies L<sup>−1</sup> or g<sup>−1</sup>
* nifH transcripts L<sup>−1</sup> or g<sup>−1</sup>
* Relative expression (normalized units)
* Fold change (RT-qPCR)

=== Sample size ===
* Varies by study design
* Includes biological replication and controls

=== Repositories & databases ===

== Limitations ==
* Gene copy number does not equal nitrogen fixation rate

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

Protocols:
* Standard nifH qPCR and RT-qPCR protocols
* SYBR Green or probe-based detection methods
* Custom laboratory SOPs optimized for primer sets and environmental matrices

=== Common calculations/conversions ===
* Gene copies = Ct-based quantification using standard curves
* Normalization to volume, mass, or biomass
* Conversion of transcript abundance to relative expression levels

== References ==

[[Category:Main Pages|Model types]]