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Record W2037002397 · doi:10.1242/jeb.121012

Ammonia excretion: <i>C. elegans</i> style

2015· article· en· W2037002397 on OpenAlexaboutno aff
Kathryn Knight

Bibliographic record

VenueJournal of Experimental Biology · 2015
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenetics, Aging, and Longevity in Model Organisms
Canadian institutionsnot available
Fundersnot available
KeywordsCaenorhabditis elegansExcretionAmmoniaUreaBiologyChemistryGeneBiochemistry

Abstract

fetched live from OpenAlex

For such a tiny animal, Caenorhabditis elegans must be one of the best understood creatures on the planet. Its development has been painstakingly scrutinized cell by cell and its 100 million base pair genome has been deconstructed in fine detail; yet little is known about the physiology of these microscopic soil dwellers that reside in the water film surrounding soil particles. ‘It's not just a worm in a fridge’, chuckles Dirk Weihrauch from the University of Manitoba, Canada, who adds that he is always keen to learn about how animals from exotic environments dispose of toxic nitrogenous waste. Yet, it wasn't even clear whether the nematodes excrete ammonia or urea. So, Weihrauch and his student Aida Adlimoghaddam rolled up their sleeves and decided to get to grips with nitrogen excretion in this super-star model organism (p. 675).Caenorhabditis elegans usually dine on bacteria in soil, so Adlimoghaddam and Ann-Karen Brassinga made sure that the lab worms were well fed with nutritious E. coli before collecting the nematodes’ waste for 1 day. Analysing the media that was the worms’ home, the duo found that instead of producing costly urea, they were excreting ammonia.Next, Adlimoghaddam tested whether the worms were expressing the genes encoding proteins that are known to participate in nitrogen excretion in other animals. As Weihrauch explains, the Na+/K+-ATPase enzyme pumps ammonium ions across the cell membranes of various animals, while the V-type H+-ATPase produces a pH gradient across membranes that ammonia can diffuse along, and Rhesus proteins form channels that ammonia gas travels through. When Adlimoghaddam looked for evidence of expression of each of these proteins by measuring mRNA expression of the C. elegans equivalents, she found that the worms expressed them all.However, Weihrauch wanted to know more about the worms’ excretion mechanism, even though it was impossible to measure directly the transport processes in the minute animals. So he and Adlimoghaddam resorted to measuring the ammonia excreted by large numbers of the animals bathed in drugs that targeted specific proteins in ammonia excretion in other organisms to find out which participated in ammonia excretion. The duo discovered that inhibiting the V-ATPase, carbonic anhydrase (which provides protons to fuel the V-ATPase) and the worm's microtubule network all reduced ammonia excretion. The drug targeting the Na+/K+-ATPase (ouabain) had no effect on ammonia excretion, suggesting that it was unable to access the pump in the cell membrane. However, when Jason Treberg directly tested whether Na+/K+-ATPase could transport ammonium, the protein successfully transported the ions, so it also contributes to excretion.Next Mélanie Boeckstaens and Anna-Maria Marini tested whether one of the worm Rhesus channel proteins – CeRhr-1 – actually transports ammonia. Inserting the channel into yeast mutants that were unable to import ammonia – which is essential for their survival – the duo found that the mutant yeast carrying the CeRhr-1 protein survived. So CeRhr-1 is an ammonia transporter.Tying all of their results together, Weihrauch concludes that C. elegans excrete ammonia through their skin using two mechanisms. The first – known as ammonia trapping – occurs when the V-ATPase, fuelled by protons provided by the carbonic anhydrase, creates a pH gradient across the cell membrane allowing the gas to diffuse through Rhesus proteins to cross membranes in the skin. In the second mechanism, ammonium is transported in lipid vesicles through the cell's microtubule network to the external membrane, ready for excretion. And Weihrauch is excited to have discovered the ammonia trapping mechanism in such an ancient animal, saying: ‘Ammonia excretion mechanisms… evolved early on’.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.001
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.009
Threshold uncertainty score0.030

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0000.001
Meta-epidemiology (narrow)0.0010.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0010.001
Scholarly communication0.0010.001
Open science0.0020.001
Research integrity0.0010.002
Insufficient payload (model declined to judge)0.0090.007

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.019
GPT teacher head0.283
Teacher spread0.263 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations0
Published2015
Admission routes1
Has abstractyes

Explore more

Same venueJournal of Experimental Biology→Same topicGenetics, Aging, and Longevity in Model Organisms→French-language works237,207→