Fitness through the enteric and sexual cycle: does disrupting a gene cost the parasite oocysts.
The third curated table in the map, and it exists for a reason worth stating precisely. The sweeps
that closed this slot looked for a pooled screen through the enteroepithelial stages and correctly
found none -- the sexual cycle runs only in a felid, and nobody has put a barcoded library through a
cat. But the slot asks whether disrupting a gene changes fitness in the gut, and a pooled screen is
only one instrument that answers it. Feeding one knockout to a cat and counting the oocysts it sheds
answers the same question one gene at a time, and four labs have done it.
The bar
A row exists only if a defined gene disruption was carried through the feline stage and the
enteric outcome was measured -- oocysts counted, or the sporulation rate scored. Read from
primary open-access text. A paper that says the cat experiment "should be carried out" does not
count, and one that says oocysts were seen but "the numbers were not quantified" does not either;
both were found and both were left out.
Why the unchanged rows are the most valuable ones here
Four of the ten rows are unchanged, and they come from a deletion of all four LEA genes at once.
That is not a weaker result than a single knockout -- it is a stronger one. When a joint deletion of
a paralogue cluster leaves oocyst yield alone (30 against 34 million from paired kittens), no member
of the cluster is individually required, and redundancy cannot be hiding the phenotype. A single
knockout of one LEA gene could not have established that.
What background is for, again
The AAH2 row measured in a delta-aah1 background is a genetic-interaction result, and the double
mutant is indistinguishable from delta-aah1 alone -- so reading a severe defect onto AAH2 from it
would be wrong. background says so per row, exactly as it does in drug_sensitivity.
The graded outcomes are deliberate
abolished, reduced and unchanged are not one scale collapsed into three bins; they are what the
assays distinguish. HAP2 sheds a few mis-shapen oocysts that never sporulate, which is not the same
event as Grx5 shedding a third as many that sporulate poorly, and neither is AAH1 shedding four logs
fewer. The magnitudes live in evidence because they are not comparable across cats, strains and
inocula -- one numeric column here would invent a precision the experiments do not have.
@dataclass(frozen=True)
classEnteric:
One gene carried through the enteric cycle, and everything needed to check it.
MEASUREMENTS =
(Enteric(gene='TGME49_227100', product='glutaredoxin 5', outcome='reduced', sporulation='reduced', background='parental', strain='Pru (type II)', pmid='PMC12942651', evidence='cats fed tissue cysts orally; total oocysts over the shedding period 2.5e7 in Pru against 8e6 in the deletion, ~70% down, and sporulation ~80% against ~30%. A complemented line was built, so the phenotype is tied to the locus'), Enteric(gene='TGME49_287510', product='aromatic amino acid hydrolase AAH1', outcome='reduced', sporulation='not measured', background='parental', strain='ME49 dhxg::Luc', pmid='28288194', evidence='~1e3 total oocysts per animal against 1e6-1e7 for wild type, in two of two cats. Sporulation could not be scored because the yield was too low to quantify'), Enteric(gene='TGME49_212740', product='aromatic amino acid hydrolase AAH2', outcome='reduced', sporulation='reduced', background='parental', strain='ME49 dhxg::Luc', pmid='28288194', evidence='milder and variable: much lower in two of three cats, the third only ~10-fold down to ~1e5. Sporulation 75-80% for wild type against ~60%'), Enteric(gene='TGME49_212740', product='aromatic amino acid hydrolase AAH2', outcome='reduced', sporulation='not measured', background='dAAH1', strain='ME49 dhxg::Luc', pmid='28288194', evidence="the double deletion's oocyst yield is severe (~1e3 per animal) but indistinguishable from delta-aah1 alone, so this row carries no evidence that AAH2 adds to the defect"), Enteric(gene='TGME49_285940', product='male gamete fusion factor HAP2, putative', outcome='reduced', sporulation='abolished', background='parental', strain='CZ clone H3', pmid='30728393', evidence='oocysts fell below reliable enumeration (<1,600 per two-day faecal sample against 11 +/- 6 million for the parental line), were mis-shapen, and showed no diploidy by ploidy qPCR, so fertilisation did not occur. Sporulation was 0% at every timepoint against 45/69/82% for the parental. The authors report a second mutation in an intron of TGME49_223060 in this line and argue it is unlikely to contribute'), Enteric(gene='TGME49_276850', product='LEA domain-containing protein LEA850', outcome='unchanged', sporulation='unchanged', background='dLEA cluster (all four)', strain='ME49 dhpt luc+', pmid='36809045', evidence='paired kittens yielded 30 million oocysts from wild type against 34 million from the cluster deletion, with no morphological difference and no excystation or invasion defect'), Enteric(gene='TGME49_276860', product='LEA domain-containing protein LEA860', outcome='unchanged', sporulation='unchanged', background='dLEA cluster (all four)', strain='ME49 dhpt luc+', pmid='36809045', evidence='as LEA850: the four-gene deletion left oocyst yield alone'), Enteric(gene='TGME49_276870', product='LEA domain-containing protein LEA870', outcome='unchanged', sporulation='unchanged', background='dLEA cluster (all four)', strain='ME49 dhpt luc+', pmid='36809045', evidence='as LEA850: the four-gene deletion left oocyst yield alone'), Enteric(gene='TGME49_276880', product='LEA domain-containing protein LEA880', outcome='unchanged', sporulation='unchanged', background='dLEA cluster (all four)', strain='ME49 dhpt luc+', pmid='36809045', evidence='as LEA850. Sporulation was ~65% against ~85%, which the authors place inside the 60-90% range they see normally, so it is recorded as unchanged rather than reduced'))
deftable() -> pandas.DataFrame:
One row per gene, summarising every enteric measurement made on it.