Exciting news! The pre-print for our paper, “Diverse and abundant viruses exploit conjugative plasmids” is finally out! Join me on this thread to hear more about this mysterious group of phages with rather unique lifestyle preferences. 1/
This sounds almost too easy to be true, but it works! Since the determinant of phage susceptibility can be horizontally transferred 🤯, many of these phages have a broad host range. If we add fluorescence to it, it’s even easier to see, and we get Phage DisCo! 🪩 6/
I don’t have words to describe how proud I am to hood Dr. Natalia Quinones-Olvera
@nquinoneso
today. I could not have asked for a more brilliant student to start the lab, and am excited to see where her career in science leads!
Great to see the amazing Mische Holland at
#SACNAS2019
. Mische spent this past summer working in the
@baym
lab, through the Summer Institute in Biomedical Informatics. If you want to know more about summer research opportunities
@HarvardGSAS
, come to booth 1534!
This project has been a blast! What’s up with these strange phages? What does all of this mean for plasmid conjugation? And what other overlooked treasures await to be found in this world of mobile genetics elements? Thank you for reading, and stay tuned for our next adventures.
Hello
#SACNAS2020
! I’m a PhD student in the Systems, Synthetic and Quantitative Biology program. We have a virtual booth at the Graduate School Expo, together with the Biophysics program. :) Visit us if you want to talk about grad school and summer programs!
@HMS_SysBio
@sacnas
So we started screening as many samples as we could, looking for phages that depend on IncP conjugative plasmids (like RP4). This is
@implosian
and me, showing off our samples. Our favorite samples: compost and wastewater. 7/
Hello
#SACNAS2019
! I’m a Mexican PhD student at
@HarvardGSAS
in the Systems, Synthetic and Quantitative Biology program. Visit booth 1534 if you want to talk about grad school and summer programs!
@HMS_SysBio
@sacnas
Exciting news! The pre-print for our paper, “Diverse and abundant viruses exploit conjugative plasmids” is finally out! Join me on this thread to hear more about this mysterious group of phages with rather unique lifestyle preferences. 1/
These phages have zero accessory genome, and exactly the same gene content, but they can differ by a large number of SNPs. These ones, for example, only differ by ~500 SNPs, but they can have strikingly different host preferences! Look: 11/
Why? Well, because they had A LOT of plasmid-dependent phages. Like, in wastewater(!) there are almost as many plasmid-dependent phages as E. coli phages, and way more than S. enterica or P. putida phages (the hosts we were using in our assay.) 8/
Finally, we revisited the phages that depend on the F plasmid. We found members of all the known groups, and even a completely new, tailed(!) plasmid-dependent phage!
@microMcCully
here, introducing the wonderful FtMidnight, showing there’s even more diversity to be found! 13/
This work represents many years of hard work of my co-first author
@implosian
and me, my advisor
@baym
, lab mates
@microMcCully
and
@EllieRand3
,
@maxgmarin
, and many awesome students that passed through the lab: Alice, Remi, Kay, Cleo, Rachel, and Jillian. Thank you! 2/
@adrinjalali
@github
It's a shame that GitHub doesn't provide a solution to this. They should make the icons distinct! As a temporary solution, hopefully this can help:
If they are so abundant, why haven’t we heard about them from metagenomic studies? Well, we think they’re just not getting through. They seem hard to recover even from samples where we know they are present at high abundance. 12/
There were so many, that we were worried about finding names for all of them, so we decided to go for “PRD” + a color name. We have some wonderful ones like PRDchartreuse, PRDaquamarine, and my favorite: PRDcerulean 😊. 10/
Plasmid-dependent phages use proteins in plasmids as receptors to infect bacteria. You might have heard of some of them, like M13 (a filamentous phage), MS2 (a tailless, tiny 3.5kb RNA phage), and PRD1 (also tailless, lipid-containing phage). 3/
All the phages we were finding belong to the Tectiviridae family, and are closely related to PRD1. Not only were we finding them in large amounts but also, in more diversity than all the previously isolated phages of this group. 9/
The species-specific phages will make plaques in only one of the two hosts, while the plasmid-dependent phages would be able to kill both because both strains are carrying the correct plasmid-encoded receptor. 5/
They are definitely an exotic bunch, and the thing is, we only know a few of them. We wanted to find more! So this was the plan: Let’s grow two different bacterial species in the same soft-agar lawn, both carrying the same plasmid. 4/
@CSMFHT
Awesome! Thanks :) I just saw the meme and went down the Wikipedia rabbit hole and ended up googling “How did Numa Pompilius die?” 😂
Hurrah for meme-fact-checking threads!
Your periodic reminder not to compare impact factors across disciplines:
Medical paper “invents” a way to estimate the area under a curve using rectangles.
Gets over 400 citations
@cloverfoodlab
@baym
@Longwood_LMA
😱 Woaaah, wth
@cloverfoodlab
💔😢 I was expecting something like “Oh no, that sucks! It does look dangerous, and we care about cyclists! It’s tricky, but we’ll look into it.”
Many of us biking through there work in the area and are actually the clients that sit in your tables…
@implosian
@AndreaGiometto
I highly recommend ! I was dealing with some particularly horrible pdf tables and it got the job done. (I also tried tabula-py, which worked fine for very simple cases, but starting with camelot would've saved me a lot of time.)
Really enjoying all the
#vom2022
tweets this week! Wish I was there 😢 but if YOU are, go and check out
@nquinoneso
's poster TODAY [room 3, pos 18] about our discovery of plasmid-dependent phages almost everywhere we looked for them, using a cool fluorescent plaque assay 👀
@baym
I disagree! Although the lab you join is super important, a lot of students find their friends/support groups within their program (and it's great and healthy to have that outside your lab!). Programs within Harvard certainly have very different personalities!
«Que tiemble el Estado, los cielos, las calles.
Que tiemblen los jueces y los judiciales.
Hoy a las mujeres nos quitan la calma.
Nos sembraron miedo, nos crecieron alas.»
(Canción sin miedo - Vivir Quintana)
#8M2021
@conTaminatedsci
@baym
@thebibliophile9
There's no pretty-and-native way to open a local html file in my lab iPad, so I made a Google Sheets version of your tool! Might be useful to other iPad users :)
@WishartLab
Hey! I'm excited to see that the code is downloadable as a Docker container. I tried running it with the instructions you provide, but there's no Dockerfile in the root directory, nor phastest-app/ directory. Maybe it's not the most updated download file? Thanks!
@TwitterSupport
I can’t see half of my tweets on this thread. For some people they appear as deleted, but other people can see them. What’s going on here?
@wheezenfeld
Sophia 💙💙
Thank you so much! 🥲 The pleasure has been mine! It’s been wonderful sharing time with you, can’t wait to see all the awesome places you’ll explore with your science!
May the dream fish always accompany in your magical endeavors! ✨
Hello,
@RNA3DHub
:)
I'm having trouble accessing the RNA Structure Atlas. This happens when I want to navigate into any structure page beyond the Summary:
@baym
My advice would be more like: Academically, things will go smoother in the first years if the requirements/faculty are in tune with what you're interested in doing. Socially, go to the student events during recruitment and see if you connect with them!
@mbeisen
@IBJIYONGI
@CoreyWelch_STEM
Also, it’s quite a bad situation for foreigners: Paying for it in USD with a low purchasing power makes it outrageously expensive ( >360 minimum wage hours, in my case)
@RNA3DHub
It seems to be working now! That message was from: (and others attempted were: 2qus, 3dj2, 5ddp, 5flx). I was getting it intermittently from around 2:00-7:00 pm EST. Thanks!
@phiweger
Hmm, but why would you parse the standard output, which is meant to be human-readable, instead of one of the plenty of other machine-readable output options? ¯\_(ツ)_/¯
Now that Toto Wolff is going to be a guest lecturer at HBS, maybe we should convince him to run a couple of workshops at
@harvardmed
. Many of these lessons seem relevant for teams of scientists.
@IAmSciArt
These inaccuracies might not represent how life IS, but how science itself works. That is beautiful.
(Better said by
@tomscott
in this video:
)