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chloe

@ChloeFishman

graduate fellow at Rockefeller University - previously Gladstone Institutes-UCSF, Georgetown/NASA

Joined February 2021
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🚨 Episode 6 of #FromBenchtoPodcast is live! 🎙️👩🏻‍🔬 Tune in as @ChloeFishman and I dive into the fascinating world of #PhageTherapy, the importance of #Mentorship, and a touch of #Astrobiology! 🦠👩🏻‍🚀 Don’t miss this exciting conversation @NatureBiotech open.spotify.com/episode/64h…
From Bench to Podcast: Chloe Fishman

From Bench to Podcast: Chloe Fishman

Forum · Episode

open.spotify.com
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First, phages helped us to modify bacterial genomes (lambda-red), now bacterial defense related elements- retrons- help to modify phage genomes - so cool. Will be very interesting to use this method- ordering oligs for cloning:)
Sorek Lab (@SorekLab) profile pictureSorek Lab@SorekLab9 Sep 2024
A new retron-based method from the innovative @seth_shipman lab now allows making multiple mutations in a phage genome in a single, easy process - from point mutations to small insertions and deletions Read the overview by @IlyaOsterman nature.com/articles/s41587-0…
Image from Sorek Lab (@SorekLab)
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A new retron-based method from the innovative @seth_shipman lab now allows making multiple mutations in a phage genome in a single, easy process - from point mutations to small insertions and deletions Read the overview by @IlyaOsterman nature.com/articles/s41587-0…
Image from Sorek Lab (@SorekLab)
Seth Shipman (@seth_shipman) profile pictureSeth Shipman@seth_shipman5 Sep 2024
Multiplexed editing of phage genomes using retrons, now published at @NatureBiotech with lots of new bells and whistles. @ChloeFishman @katecrawdaddy @BhattaraiKline @Darshini_Poola @thekarenzhang @alex_gonzadel @matromont nature.com/articles/s41587-0…
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Multiplexed editing of phage genomes using retrons, now published at @NatureBiotech with lots of new bells and whistles. @ChloeFishman @katecrawdaddy @BhattaraiKline @Darshini_Poola @thekarenzhang @alex_gonzadel @matromont nature.com/articles/s41587-0…
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Continuous multiplexed phage genome editing using recombitrons go.nature.com/3yUNYTi
Image from Nature Biotechnology (@NatureBiotech)
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Immense gratitude to Luciano (@MarraffiniLab) for his support, @daltonbanh for his invaluable guidance, and @ChloeFishman for daily laughter and inspiration. Studying bacTIRial ;) immunity with you all has been one of the greatest joys of my life. biorxiv.org/content/10.1101/…
A bacterial TIR-based immune system senses viral capsids to initiate defense

A bacterial TIR-based immune system senses viral capsids to initiate defense

Toll/interleukin-1 receptor (TIR) domains are present in immune systems that protect prokaryotes from viral (phage) attack. In response to infection, TIRs can produce a cyclic adenosine diphosphate...

biorxiv.org
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Multiple packaging simulations produced globally different conformations of the packaged genome, suggesting that the packaging process itself gives mature virions individual traits encoded by the topology of its genome.
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New preprint! Simultaneous multi-site editing of individual genomes using retron arrays. We're trying to make it easier to make multiple, non-adjacent, precise mutations to a genome without long cycles of editing, isolating , and editing again. biorxiv.org/content/10.1101/…
Simultaneous multi-site editing of individual genomes using retron arrays

Simultaneous multi-site editing of individual genomes using retron arrays

Our understanding of genomics is limited by the scale of our genomic technologies. While libraries of genomic manipulations scaffolded on CRISPR gRNAs have been transformative, these existing...

biorxiv.org
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“The microbes we found in Hawaii could be similar to microbes that once lived on Mars, or even microbes that live there today,” says @ChloeFishman. Fishman is now an RA at Gladstone. Read more about her work prior to joining our team. ⬇️ go.nasa.gov/3my45Qe
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Learn more about @NASAExpeditions and how studying life on Earth helps @NASA search for life on Mars: go.nasa.gov/4397plv
Four scientists hike across the Maua Loa volcano in Hawaii, trekking across dark rubble piles of rocks that form when lava cools quickly. Dense fog almost reaches the ground as they traverse the open landscape.

ALT Four scientists hike across the Maua Loa volcano in Hawaii, trekking across dark rubble piles of rocks that form when lava cools quickly. Dense fog almost reaches the ground as they traverse the open landscape.

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While in a Hawaiian lava tube, astrobiologists discovered new species of microorganisms thriving in the extreme environment! Data gathered will inform future missions to Martian lava tubes, locations some suspect life could’ve migrated to after Mars’ surface became inhospitable.
Two silhouettes of scientists are seen as the researchers lower themselves 30 feet through an opening in the ground, which formed where part of a lava tube collapsed. Wearing a headlamp, gloves, and kneed pads, they climb down the tube's rocky walls deep under the ground. Bright sunlight shines at the mouth of the lava tube but only reaches a few feet into the opening, and the scientists lower themselves into the rocky darkness.

ALT Two silhouettes of scientists are seen as the researchers lower themselves 30 feet through an opening in the ground, which formed where part of a lava tube collapsed. Wearing a headlamp, gloves, and kneed pads, they climb down the tube's rocky walls deep under the ground. Bright sunlight shines at the mouth of the lava tube but only reaches a few feet into the opening, and the scientists lower themselves into the rocky darkness.

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*Preprint Alert* This one’s in a new area for the lab: phage editing! We're using retrons to produce recombineering donors ~inside~ bacterial hosts. A wild-type phage infects the host and an edited phage comes out. biorxiv.org/content/10.1101/…
Continuous Multiplexed Phage Genome Editing Using Recombitrons

Continuous Multiplexed Phage Genome Editing Using Recombitrons

Bacteriophages, which naturally shape bacterial communities, can be co-opted as a biological technology to help eliminate pathogenic bacteria from our bodies and food supply[1][1]. Phage genome...

biorxiv.org
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I’m excited to share our new paper on the fundamental biology of RETRONS. Retrons are incredible molecular machines that produce small fragments of reverse transcribed DNA in bacteria that functions in phage defense. academic.oup.com/nar/advance… @NAR_Open @GladstoneInst @UCSF_BTS
Retron reverse transcriptase termination and phage defense are dependent on host RNase H1

Retron reverse transcriptase termination and phage defense are dependent on host RNase H1

Abstract. Retrons are bacterial retroelements that produce single-stranded, reverse-transcribed DNA (RT-DNA) that is a critical part of a newly discovered

academic.oup.com
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This week, the @NASAGoddard Instrument Field Team (GIFT) is on the Mauna Loa volcano in Hawaii, researching underground caves formed by molten lava, called lava tubes, so we can better understand them on other planets.
Image from ARCHIVED - NASA Expeditions (@NASAExpeditions)
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We are testing methods to detect those microbes and also defining where in the lava tube is a good place to find them. That way, when we go to Mars we can know how and where to look for microbial life.
Image from ARCHIVED - NASA Expeditions (@NASAExpeditions)
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Okay out of the tube again. See all that white stuff from the lava tube? It’s full of life. We are here to find out what microbes are there and how they get their energy. From chemicals? Water? Sunlight? For example some bacteria use sulfur to live & reproduce.
Image from ARCHIVED - NASA Expeditions (@NASAExpeditions)
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What gear do you need to stay safe in a lava tube? We made this handy guide
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Okay tube break to post and take a moment to share how cool this lava tube is. CAVE SCIENCE!!!
Scientist climbs down into a lava tube

ALT Scientist climbs down into a lava tube

Image from ARCHIVED - NASA Expeditions (@NASAExpeditions)
Image from ARCHIVED - NASA Expeditions (@NASAExpeditions)
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Day 3 - heading into the lava tube with the Geochemistry team. The team is collecting samples and taking measurements with a few different instruments - all with the goal of figuring out what the rocks in the lava tube are made of. Do they contain life? What kind?
Image from ARCHIVED - NASA Expeditions (@NASAExpeditions)
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Seismic waves travel through air much more slowly than they travel through rock, so theoretically, if there’s a big space filled with air underground we should be able to tell based on the time and energy of the waves we detect.
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