Enzyme assay with fluoresceinamine labeled biopolymers: Difference between revisions
Kate Evans (talk | contribs) Created page with "* Page authors: Melanie Staeubli, Grommet the Cat, PRIMO * Responsible curator: Kate Evans ---- __TOC__ <div class="model-box"> {| class="model-ib" ! What is being measured in 1 - 3 words |- | '''Approach:''' tracer quantification, remote sensing, sequencing, etc. |- | '''Context:''' ''in situ'', incubation |- | '''Spatial scale:''' mL, km<sup>2</sup> |- | '''Temporal scale:''' seconds, days, seas..." |
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* [[Page authors|Page authors]]: | {{BreadcrumbsSecondaryProduction}} | ||
* [[Responsible curator|Responsible curator]]: [[User: | |||
* [[Page authors|Page authors]]: [[PRIMO]] | |||
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]] | |||
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__TOC__ | __TOC__ | ||
<div class="model-box"> | <div class="model-box"> | ||
{| class="model-ib" | {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" | ||
! | ! Polysaccharide hydrolysis | ||
|- | |- | ||
| '''Approach:''' | | '''Approach:''' enzyme assay | ||
|- | |- | ||
| '''Context:''' | | '''Context:''' incubation, lab | ||
|- | |- | ||
| '''Spatial scale:''' | | '''Spatial scale:''' low | ||
|- | |- | ||
| '''Temporal scale:''' | | '''Temporal scale:''' low; hours to days | ||
|- | |- | ||
| '''Units:''' | | '''Units:''' mol monomer L-1 h-1 | ||
|- | |- | ||
| '''Community captured:''' | | '''Community captured:''' heterotrophs | ||
|- | |- | ||
| '''Co-measurements:''' | | '''Co-measurements:''' cell abundance | ||
|} | |} | ||
</div> | </div> | ||
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== Method Overview == | == Method Overview == | ||
= | This enzyme assay measures polysaccharide hydrolysis by time course incubations with fluorescently labeled substrate (fluoresceinamine labeled biopolymers)<ref name="Arnosti1996">Arnosti (1996). A new method for measuring polysaccharide hydrolysis rates in marine environments. ''Organic Geochemistry'', 25(1-2), 105-115. https://doi.org/10.1016/S0146-6380(96)00112-X</ref>. | ||
The assay is performed in discrete mode on bulk, size-fract, single cell samples. | |||
=== Scale of measurement === | === Scale of measurement === | ||
Typically performed on replicate samples collected at a sampling station at one point in time. Sampling effort is relatively high impairing resolution in space or time. Time course incubations last hours to days, further restricting temporal resolution. | |||
=== Data generated === | === Data generated === | ||
These measurements can provide hydrolysis rates per unit time. | |||
=== Units & currency === | === Units & currency === | ||
Units are mol monomer L-1 h-1. The currency is carbon. | |||
=== Sample size === | === Sample size === | ||
Typical samples are < 1 L in volume. | |||
== Limitations == | |||
Rate measurements to estimate Vmax, yielding potential rates. Bottle effects are likely to occur. | |||
== Example Applications & Protocols == | == Example Applications & Protocols == | ||
=== Classic examples === | === Classic examples === | ||
* | * Arnosti (1996) ''A new method for measuring polysaccharide hydrolysis rates in marine environments'' <ref name="Arnosti1996" /> | ||
=== Recent applications === | === Recent applications === | ||
* | * Martinez-Garcia et al. (2012) ''Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia'' <ref name="Martinez-Garcia2012">Martinez-Garcia et al. (2012). Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia. ''PLoS ONE'', 7(4), e35314. https://doi.org/10.1371/journal.pone.0035314</ref> | ||
== References == | == References == | ||
[[Category:Main Pages|Model types]] | [[Category:Main Pages|Model types]] | ||
Latest revision as of 11:30, 11 May 2026
Template:BreadcrumbsSecondaryProduction
| Polysaccharide hydrolysis |
|---|
| Approach: enzyme assay |
| Context: incubation, lab |
| Spatial scale: low |
| Temporal scale: low; hours to days |
| Units: mol monomer L-1 h-1 |
| Community captured: heterotrophs |
| Co-measurements: cell abundance |
Method Overview
This enzyme assay measures polysaccharide hydrolysis by time course incubations with fluorescently labeled substrate (fluoresceinamine labeled biopolymers)[1].
The assay is performed in discrete mode on bulk, size-fract, single cell samples.
Scale of measurement
Typically performed on replicate samples collected at a sampling station at one point in time. Sampling effort is relatively high impairing resolution in space or time. Time course incubations last hours to days, further restricting temporal resolution.
Data generated
These measurements can provide hydrolysis rates per unit time.
Units & currency
Units are mol monomer L-1 h-1. The currency is carbon.
Sample size
Typical samples are < 1 L in volume.
Limitations
Rate measurements to estimate Vmax, yielding potential rates. Bottle effects are likely to occur.
Example Applications & Protocols
Classic examples
- Arnosti (1996) A new method for measuring polysaccharide hydrolysis rates in marine environments [1]
Recent applications
- Martinez-Garcia et al. (2012) Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia [2]
References
- ↑ 1.0 1.1 Arnosti (1996). A new method for measuring polysaccharide hydrolysis rates in marine environments. Organic Geochemistry, 25(1-2), 105-115. https://doi.org/10.1016/S0146-6380(96)00112-X
- ↑ Martinez-Garcia et al. (2012). Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia. PLoS ONE, 7(4), e35314. https://doi.org/10.1371/journal.pone.0035314