When I read a paper, I usually have no idea what's going on until I
read a bunch of other papers on the same topic. I suppose this is
because it's hard for me to determine what pieces of information are
interesting or important in a paper that is outside of my field
(unfortunately, I don't have a field yet...so everything is outside of
my field).
Anyhow, I actually found this paper quite interesting. Firstly, I
thought it was cool to read more about Giardia and Giardiasis ("beaver
fever"). Giardia's life cycle is so interesting! It can live in
beavers, cattle, dogs, rodents, and bighorn sheep in addition to
humans. Ingestion of as few as 10 cysts can cause an infection. After
ingestion, the host's acidic stomach stimulates excystation, which
produces 2 trophozoites. These are little guys with tails that swim
down to the duodenum & proximal jejunum, where they attach using an
"adhesive disk." Their growth is stimulated by bile, carbs, and low
oxygen, and they may cause GI distress (unknown mechanism) in 1-2 weeks
of infection. One article from 2004 claimed that they may secrete
anti-inflammatory signals (unknown mechanism).
In any case, I also learned that an international collaboration
beginning in the 1990s, and really kicking off in 2000, resulted in
analysis of 3 ancient genomes: Trypanosoma cruzi, Trypanosoma brucei,
and Leishmania major ("Tritryps"). Another review, written in 2004,
presented evidence that RNAi machinery was present in several types of
protozoa, but its function was unknown. I think this is interesting
because this means RNAi (and possibly other types of noncoding RNAs)
are not unique to humans. This also gives an example of how RNAi
machinery is used for survival in a hostile environment.
In the introduction, the authors state that Giardia's genome codes
for more than 190 VSP genes, but they were only able to amplify 8 of
them by RT-PCR with degenerate primers. They used this nuclear run-on
assay, which I am not totally sure I understand (Fig 1a). My best
guess is that they take the nucleus out of a trophozoite and add some
transcription machinery and labeled nucleotides in vitro. Only open or
active areas of the genome will be transcribed in vitro. They used
this mixture of RNA to probe a membrane with little blobs ("slot
blotting") of DNA encoding 8 different VSPs. This experiment tells you
that particular genes are potentially transcribed in vivo.
A blurry Fig 1b is evidence that there is one dominant total RNA
transcript (or many RNA transcripts of the same size) that contains the
3' conserved region of VSPs.
In effect, the data I see so far
is supportive of their hypothesis, but not exceedingly strong. There's
a lot of supplementary data, but it's got the same issues as the data
in the article ("articular data?"): blurry blots that don't rule out
alternative hypotheses.
Wow, this is dense. That's all I have for now.
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