Terence Crofts

The Obama Hope poster, but it's a frog and it says "Hop"

I saw a tragically AI-generated version of this poster, so I have recreated a 100% human-made version for all your protest sign needs.

Joey Mannarino in a dark brown tailored jacket. The low armhole is causing his jacket to lift.

Someone in an inflatable frog costume. The high armhole allows them to raise their arm without disturbing the rest of the garment

a high armhole allows for freer and more comfortable movement

A reminder that the my department has an ongoing faculty search! Would love to have more colleagues here!

A promotional flyer for a webinar in the CSU Bioinformatics Webinar Series. On the left side, it shows the date and time: “26 Sep | 12 PM PST.” It includes instructions to join via Zoom with Meeting ID: 886 2442 3158 and a QR code above. On the right, there is a photo of Dr. Elinne Becket, Associate Professor in the Department of Biological Sciences at California State University San Marcos, sitting outdoors with plants and trees in the background. Below, the title of the talk is displayed: “The Soup that Blue up Twitter.” The description explains that Dr. Becket will discuss the shared curiosity of science, open science, and a story from February 2023 when leftover beef soup prepared by her mom turned bright blue. Scientists and people on Twitter collaborated to investigate, leading to a global effort among microbiologists and chemists. At the bottom, there are links to learn more about upcoming webinars at www.informatics.sdsu.edu and Dr. Becket’s website: https://elinneb.wixsite.com/becketlab

Giving a webinar on #BlueSoup this Friday, in case anyone wants to pop in during their lunch!

Assistant Professor of Plant Pathology University of California, Davis is hiring. Apply now!

My department at UC Davis is hiring a mycologist, broadly interpreted. Please repost, share, and consider applying. recruit.ucdavis.edu/JPF07339

Illinois Governor JB Pritzker has signed an executive order which permits pharmacists and other medical personnel to administer vaccines recommended by state officials, no prior prescription needed. The order also requires insurance companies to cover the vaccines.

And thanks to Lauren Quinn @lquinnphd.bsky.social for her fantastic write-up of our paper!

@illinoisresearch.bsky.social

aces.illinois.edu/news/researc...

🙌Congrats to Hayden and Elizabeth for their co-first author publication and thanks to our collaborators Erica Hartmann at Northwestern and Frank Oliaro at the Shedd aquarium (and to Zymo research @zymoresearch.bsky.social for the sample human fecal material!)

Why does this matter🤷‍♂️?

We think it is important to find resistance genes from other environments before they reach the clinic🏥or farm🐮. Functional metagenomics allows us to do this, and our method, by using less DNA more efficiently, opens up many new microbiome samples!

a pikachu wearing a detective hat is holding a magnifying glass . Alt: a pikachu wearing a detective hat is holding a magnifying glass .

Notably, simply sequencing metagenomic DNA would not have let us discover these functions, highlighting the importance of the *functional* aspect of functional metagenomic libraries in finding new resistance genes

With just ~30 and ~100 ng of DNA, both microbiomes gave good libraries!

We used antibiotic selections💊 to link unannotated❓MFS transporters from the aquarium to tetracycline resistance and a new acetyltransferase (we call it SatB) from the swab to streptothricin resistance.

We used our approach to tackle a pair of low biomass microbiomes that would usually be difficult to study via functional metagenomics: an aquarium microbiome🐟and a fecal swab💩.

We show that we can start with 10- to 100-fold ⬇️input metagenomic DNA (10s to 100s of nanograms) and still make ~gigabase libraries without needing to rely on potentially biasing DNA amplification.

Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes | mSystems Bacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.

We previously found that METa assembly libraries can be made with ⬆️efficiency than classic methods resulting in libraries containing 100s of gigabases of DNA.

Here, we answered 'what about making libraries from limited samples?' 🤏

journals.asm.org/doi/10.1128/...

Terence Crofts on X: "I am thrilled that my METa assembly paper with collaborators @ericamhartmann and @alexmcfarland_ is online now at @mSystemsJ: https://t.co/Na6iDJTnYV We show that functional metagenomic libraries (FMLs) can be made using 20-fold less DNA and with 80-fold greater efficiency 1/n https://t.co/3MO7IgScNY" / X I am thrilled that my METa assembly paper with collaborators @ericamhartmann and @alexmcfarland_ is online now at @mSystemsJ: https://t.co/Na6iDJTnYV We show that functional metagenomic libraries (FMLs) can be made using 20-fold less DNA and with 80-fold greater efficiency 1/n https://t.co/3MO7IgScNY

We make🛠️these libraries via METa assembly (previous twitter thread👇) using tagmentation to fragment DNA/add mosaic end tags on all fragments. This lets us use assembly cloning to *efficiently* ligate fragments into plasmids with a mosaic ends cloning site.

x.com/TerenceCroft...

A screenshot of an mSystems paper titled "Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes"

🚨 New Crofts lab paper🚨

Functional metagenomic libraries let us study bacterial genes 🧫🧬 from microbiomes💩, even if they've never been annotated with a function before 📒. However, these libraries often require more metagenomic DNA than is available from some samples.

Once Donald Trump gets the citizens of this nation comfortable with the current atrocities committed under the color of law – what comes next?

Assistant Professor - Plant Resilience to Climate Change - Department of Plant and Microbial Biology University of California, Berkeley is hiring. Apply now!

Our department (Berkeley PMB) is hiring an asst. prof. in Plant Resilience to Climate Change! aprecruit.berkeley.edu/JPF05049

Governor Pritzker speaks behind the podium.

In the coming days, we expect to see what's playing out in LA and DC happen in Chicago.

These efforts are not about fighting crime or making communities safer.

This is about Donald Trump testing his power and producing political drama to cover up his own corruption.

The Sears Tower looking insanely creepy during a blackout, including the impression of a scary face topped by a crown of spikes. It looks like a giant humanoid evil robot or a demonic Minecraft creature.

"It's ok, honey. The Sears Tower experiencing a blackout won't hurt you!"

The Sears Tower experiencing a blackout:

Check out this new preprint from my group + @campbell-thelab.bsky.social on precision fMRI in PD by ⭐️ grad student @jakechernicky.bsky.social

#neuroskyence #neuroimaging #MedSky #psychscisky #scicomm #neuroscience #parkinsons

Assessment and verification of commercially available pressure cookers for laboratory sterilization Laboratory science requires careful maintenance of sterile reagents and tools as well as the sterilization of waste prior to disposal. However, steam autoclaves typically used for this purpose may not...

Swenson 2018 tested a few pressure cookers for this and found instant pot can kill spores pretty well. I’ve been using one in lab without any issues for a couple of years

pmc.ncbi.nlm.nih.gov/articles/PMC...

My God, what an awful idea. I’m glad it’s been rolled back.

(5/5)

🚨 It’s time to flood the zone.

NIH scientists just took a huge risk speaking out. Now it’s our turn.

📜 Read the Bethesda Declaration
✍️ Sign the Public Letter of Support
👯‍♀️Follow NIHers doing the work: @nihvigils.bsky.social

Read and sign here 👉 www.standupforscience.net/bethesda-dec...

I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs.

Plant, Bacterial, Archaeal Non-model Bioeng
Custom Lab Hardware
Turn Key Genetic Design

Please repost for reach 💚

Bakta Web – rapid and standardized genome annotation on scalable infrastructures Abstract. The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensiv

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue
doi.org/10.1093/nar/...

Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)

alright i have my laptop, guess i'm livetweeting the dire wolf preprint.

so a quick reminder: this is not yet peer-reviewed, so there's some different expectations re: quality.

also let's be clear, i'm a hella biased reader, bc i don't trust the hype they're courting

ASM stands firm in its commitment to diversity, equity and inclusion, as such efforts are critical to advancing the microbial sciences for everyone. Read our statement: asm.org/Press-Releas...

Well the award for most cowardly, boot-lickingest academic society has squarely gone to the American Society of Microbiology, who has taken down features of various non-white scientists. Absolutely pathetic behavior. Those articles are now coming up as “under review”. Truly sickening cowardice here.