Natalia Quinones-Olvera
@nquinoneso
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Postdoc at Zhang Lab @BroadInstitute @MIT | Previously PhD @baym Lab | Mobile Genetic Elements, Bioinformatics | Amphibious (wet + dry)
Cambridge, MA
Joined September 2016
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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/
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“We adore chaos because we love to produce order.”
@nquinoneso
and
@implosian
made a logo for our lab and it's incredible. I can't get over it
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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/
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It’s been amazing working together :’)
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!
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The Harvard PhD Program in Systems Biology is at
#ABRCMS2018
booth 812! Come talk to us about admissions, summer programs or cool science! :)
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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!
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I’m incredibly grateful for being part of this lab.
I'm thankful for the wonderful scientists in my lab past and present who make it such a pleasure to study microbes every day:
@KarelBrinda
@CristinaHerren
@nquinoneso
@magnificasian
@labrat65632
@anuraglimdi
@simonepignotti
@socialmicrobes
@DiagnosticChick
Eve Arielle & Winston
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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.
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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
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The best thing about being a scientist has to be getting to work with people that love and care so much about what they do. Today,
#PantanoMetano
parts ways after a summer of microbial adventures. Thank you
@LotGraaf
@pedrocjunger
@sheilaclare_
@lymadiaz
, what a team!
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Shoutout to
@Kaylee__Mueller
who leaves cartoons for me in the lab’s whiteboard and they make my day. ♥️
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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/
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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
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My ~60 yo mother: “I’m too old to travel with millennials, I think I’ll just stay here drinking coffee.”
Also my mother:
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Hello
@vom2023
friends!
If you want to chat about this pre-print, I’ll be presenting a poster today, at C2-032.
#vom2023
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/
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Hello,
@Chaminade_Univ
! I’m with
@KNGonzalez_PhD
at Hale Hoaloha Building. Come to talk to us about
@HarvardGSAS
: Grad school, summer program opportunities and more!
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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/
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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/
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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/
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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/
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[ Day 2 ] of my
#booklove
challange. 7 days 7 books no comments. Thanks to
@RivasElenaRivas
for the challenge. Today I tag
@maxgmarin
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@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:
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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/
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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/
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Hello
#ABRCMS2018
!
Come talk to us about the Harvard PhD Program in Systems Biology! We’re in the Exhibit Hall booth 812.
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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/
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Well, so...
@Twitter
threads seem to be broken, and half of my tweets about our new paper have disappeared. 😢
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Why did no one tell me that the LTE of celular data meant Long Term Evolution? 😂
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Dear
@MASCOLMA
, please help us solve this highly debated mystery: What does M2 stand for? (And perhaps as important: What happened to the M1?!)
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Wohoo!
Good day in the lab: first (awesome) rotation student
@nquinoneso
got the crate of custom-ordered glass from alibaba open!
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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/
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@Beat_AMR_Bugs
@ZaminIqbal
@JessicaMABlair
@LauraPiddock
Yes! This one:
Molecular mechanisms of antibiotic resistance (Blair, et. al., 2015)
I read it when I started grad school and it was super helpful. 👌🏼
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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/
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This course holds a special place in my science heart. Highly, highly, recommend!
Last call! Applications for the Microbial Diversity course are due Jan 31, 2020. There is PLENTY of financial aid. Pls share!
@MBLScience
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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/
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@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!
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Nanopore electric snapshots of an RNA tertiary folding pathway
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🤡🤡🤡
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
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@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…
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@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.)
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Poster today! 🥳 Come and hear about our (very)broad-host-range phages!
#VoM2022
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 👀
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@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!
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«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
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Nikon Small World Photomicrography Competition 2016 Winners:
1st place: Four-day-old zebrafish embryo (10x)
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Listen carefully,
to voices which are not your own,
until something starts burning.
Staying quiet is also violent.
#BlackLivesMatter
No es momento de que hables. Es hora de escuchar. Usa tu plataforma para amplificar las voces de quienes han sido silenciades.
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If you don’t feel anger,
open your eyes wide,
and look again,
and again.
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@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 :)
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@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!
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@KimDSeed
@AmeliaMcKitt
@UCBerkeley
@MariaHTNguyen
@TaniaVSilvas
I had the chance to meet
@MariaHTNguyen
at her poster. Awesome, awesome work! It’s always great to meet new phage friends. :)
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O'Rilley's Essential Copy and Pasting from Stackoverflow
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'The Charms of Statistics' from F. Galton's 'Natural Inheritance' (1889)
(right before the description of the quincunx apparatus
@cryptogenomicon
)
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@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?
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@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! ✨
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@RivasElenaRivas
@YouTube
«A los que ya no estan echaremos de menos y a ver si espabilamos los que estamos vivos.»
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@biobenkj
How to design appropriate controls! (Why is it a thing that people believe controls are only important in wet stuff? 🤷🏽♀️)
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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:
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@BanfieldLab
@nature
@themicrobeguy
@archaeaologist
@ChenLinxing
Is there a way to reproduce this analysis? The assembly method in particular?
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Awesome talk! Incredible dataset and integration of dry & wet.
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I love this!
Find locations of Rfam hits, modified nucleotides, and other features using the new sequence viewer:
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@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!
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[ Day 3 ] of my
#booklove
challange. 7 days 7 books no comments. Thanks to
@RivasElenaRivas
for the challenge.
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@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)
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@ricosushi
¿Cómo que nooo? Jajaja el sueño sería: olor a medio recién salido del autoclave por la mañana, tamal oaxaqueño por la noche.
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@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!
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💅🏼💅🏼💅🏼
(From: Tangible Things: Making History through Objects, Oxford University Press, 2015)
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@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)_/¯
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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.
@HarvardHBS
@Susie_Wolff
@anitaelberse
Read Anita's piece on Toto's leadership lessons in the latest
@HarvardBiz
here. 👇
'
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@ricosushi
Y las bacterias escucharían: “Hay medio LB, medio calientitooo. Ya llegó su rico y delicioso medio LB.”
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@johanneskoester
Hello! :) Is there a way we could buy/get
#snakemake
vinyl stickers? (We love it!)
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@IAmSciArt
These inaccuracies might not represent how life IS, but how science itself works. That is beautiful.
(Better said by
@tomscott
in this video:
)
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Spanish speakers: This is a great chance to become a wikipedian! It’s hosted
@UNAM_MX
but you can also work remotely. Give it a shot!
¡Atención profesores, profesoras, estudiantes de la
@UNAM_MX
, ya viene el Segundo Editatón
#WikiUNAM
!
@cuaedunam
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Cephalopods diversify their neuronal proteome with RNA editing
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@AAvihail
Thank you! I’m glad you liked it! I think this merits a disco party next time we meet! 🪩
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