Lightnews — Scholar-powered news

Reposted by Ben Neely

Colin Carlson

@colincarlson.bsky.social

Yesterday, we sent this message to the @viralemergence.org team, bringing a (hopefully temporary) end to our project three years into what started as a decade of planned work. /1

Hi everyone,

I wanted to share some sad news about the future of the Verena program.

As you know, in September, NSF delayed our annual payment indefinitely, and asked us to keep spending closer and closer to zero until they could “justify” another payment. We began to run out of funds at some universities this month, and will be fully spent out by late spring, so the goal was to get paid in December. We’ve been working with our program officer to make this happen, but sadly, we’ve learned we’re not getting an increment again, and there’s no clarity on when or how much we will be paid in the remainder of the grant (through September 1, 2027).

Because of this, the Executive Committee has made the difficult decision to essentially shut the BII down until / unless something changes. What that means is an indefinite end to all programs (e.g., seminar), training activities (integration workshops, trainee corner), and evaluation. On research, what’s able to continue will have to be navigated by each investigator; our goal is to work together to push out all the impactful science we’ve spent three years collecting and analyzing data for, but we also know that priorities may shift around to keep people employed.

If we’re lucky, Congress will pass a budget that lets us continue doing something like what we planned, and we’ll pick that back up when Zoe and Collin are back in April. Until then, Verena will continue to exist as a community where we can collaborate (and give and receive support!), and we’re working to find funding sources that can pick up from where the BII left off.

On a personal note: it’s been the privilege of a lifetime to work with all of you, and an unbelievably lucky thing to get to run an NSF center in my 20s. I’ve loved this project, and I hope it’s made as much of a difference in your lives as it has in mine.

In case I don’t see you later: happy holidays, be well, and so long and thanks for all the viruses.

Best,
Colin

December 5, 2025 at 2:30 PM

Ben Neely

@benneely.com

#AminoAcidAdvent Day 2: Serine (Ser; S)

Is one of 6 where the first letter is unique, and one of two with hydroxyl side chains... so it is polar. Some people love it as one of the phospho musketeers.

I didn't know it was first described in silk protein:
babel.hathitrust.org/cgi/pt?id=hv...

December 5, 2025 at 12:45 PM

Ben Neely

@benneely.com

#AminoAcidAdvent Day 1: Proline

The kinkiest of amino acids (NSFW!), synthesized from glutamic acid, and some even call it the simplest "enzyme". Regardless, its a pro move to include the hydroxyproline variable mod if your abundant proteins have collagen domains... really, do this.

December 4, 2025 at 12:50 PM

Ben Neely

@benneely.com

Alright, back from turkey and a few weeks before winter break, can we get a Proteomics Old Time Radio Hour planned, @ucdproteomics.bsky.social and @leannewg.bsky.social?

Step 1, platform. Clubhouse still rocking?

December 4, 2025 at 11:21 AM

Reposted by Ben Neely

Lindsay K Pino

@lindsaykpino.com

Small thread on biotech in Seattle before I head out to Boston:

Sentiments in WA life science startup scene = very disappointed in the lack of SBIR renewal to fuel good startup ideas/commercialization efforts, and the number of clinical trials moving from the US to China, Australia, Canada.

December 3, 2025 at 1:16 AM

Ben Neely

@benneely.com

BPC-157, a 15 amino acid peptide in the news… how is proteomics not more mainstream in pop sci?!!!!

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

Emerging Use of BPC-157 in Orthopaedic Sports Medicine: A Systematic Review

Background: Body protection compound-157 (BPC-157) is a naturally occurring gastric peptide that promotes mucosal integrity and homeostasis. Preclinical studies show its potential for promoting healing in musculoskeletal injuries such as fractures, ...

pmc.ncbi.nlm.nih.gov

December 3, 2025 at 11:52 AM

Reposted by Ben Neely

Brett Phinney

@ucdproteomics.bsky.social

This is our loading buffer on our Exploris 480 /U3000 system today. Coming to Nature Methods ASAP: The Proteomics S.P.I.D.E.R. Method (Suitability Protocol Integrating Dead Eight-legged Reference)

December 2, 2025 at 10:18 PM

Ben Neely

@benneely.com

Not science/PSA: I only recently learned Lego sets retire. So big sale on Blacktron means it’s likely gone when it’s out. I only had a few blacktron as a kid (and still have a small ship my kids found), but I remember the Christmas I got the M tron Magnetizer. It was epic!!! youtu.be/53SoOuf7yD8?...

MEGA CORE MAGNETIZER ~ A Pinnacle of LEGO Space? ~ M:Tron Retrospective

YouTube video by TrikBrix

youtu.be

December 2, 2025 at 10:26 PM

Ben Neely

@benneely.com

This super fun proteomics article from @davidteschner.bsky.social et al. came out last spring in JPR, but just found the repo thanks to @magnuspalmblad.bsky.social. Definitely need to poke around a bit more in this.

pubs.acs.org/doi/full/10....
github.com/theGreatHerr...

Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data

Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform is a prominent commercial tool for this purpose, particularly in bottom-up acquisition scenarios. ...

pubs.acs.org

December 1, 2025 at 3:31 PM

Reposted by Ben Neely

TabletopGamingDeals

@tabletopgamedeals.bsky.social

Dungeon Crawler Carl Hardcover

62% off, only $11.38

Find out what the hype is all about, or share the love!

#ad amzn.to/4a7gX6z

December 1, 2025 at 12:02 PM

Ben Neely

@benneely.com

Really not science: so I adored prairie home companion but had never seen anything like it live. Until right now.

www.shortwavekitsch.com

November 30, 2025 at 10:18 PM

Ben Neely

@benneely.com

Not science: this college football season has been a wild ride, from coaches leaving to rivalry games this weekend to how conference championships shaped up. Toss in some Kiffin and it’s insane, and we aren’t even at CFP yet. Great time for [some] fans and all neutrals. Of course, GO DAWGS!!!

November 30, 2025 at 5:32 PM

Ben Neely

@benneely.com

Listening to In Our Time on slime moulds and all I can think about is proteomics and of course @edwardmarcotte.bsky.social.

www.bbc.co.uk/programmes/m...

BBC Radio 4 - In Our Time, Slime Moulds

Melvyn Bragg and guests discuss the remarkable world of slime mould.

www.bbc.co.uk

November 25, 2025 at 5:21 AM

Ben Neely

@benneely.com

This “major update to ProteomicsDB” is definitely worth a look. academic.oup.com/nar/advance-...

Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale

Abstract. Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanism

academic.oup.com

November 22, 2025 at 4:49 AM

Ben Neely

@benneely.com

We wrapped up #THEProteomicsShow Alt Proteomics season with Tim Cleland @paleoproteomicist.bsky.social talking paleoproteomics with me and Ben @proteomicsnews.bsky.social. Won't lie, this season was a blast talking about less typical "proteomics". Find it wherever you find fine podcasts or here.

Ep 94 - Alt Proteomics - Dr. Timothy Cleland by The Proteomics Show

For the final episode of the US HUPO sponsored "Alt Proteomics" series highlighting alternative proteomics things, Ben and Ben sit down to talk with Dr. Timothy Cleland, Smithsonian Institution.Keywor...

creators.spotify.com

November 18, 2025 at 7:13 PM

Reposted by Ben Neely

BF Francis Ouellette

@bffo.bsky.social

From the @narjournal.bsky.social #NARDatabaseIssue | EMBL's European Bioinformatics Institute (EMBL-EBI) in 2025 | #Bioinformatics #OpenData #OpenScience #Proteomics #Genomics #Bioimaging 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/advance-...

EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2025

Abstract. The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolec

academic.oup.com

November 15, 2025 at 2:38 PM

Reposted by Ben Neely

Ronald Beavis ❌

@ronbeavis.bsky.social

Since I didn't get anything back yesterday, I'll ask again:

Is there an existing terminology to refer to the two proximal flanking IDRs associated with a named structured domain?

November 16, 2025 at 2:00 PM

Ben Neely

@benneely.com

Core: yeah that RIN value really is too low for us to get anything meaningful.

… mammoth you say, no problem!

NPR @npr.org · 21d

Scientists have extracted the oldest RNA molecules out of a wooly mammoth, gaining a snapshot into the processes at work in the extinct mammal's body just before it died. n.pr/4patABW

Scientists pull ancient RNA from a wooly mammoth's body

Scientists have extracted the oldest RNA molecules out of a wooly mammoth, gaining a snapshot into the processes at work in the extinct mammal's body just before it died.

n.pr

November 14, 2025 at 9:12 PM

Ben Neely

@benneely.com

In case you missed the live #THEProteomicsShow with me and Ben Orsburn @proteomicsnews.bsky.social, it was pretty fun. HUGE thanks to the organizers of #HUPO2025 for inviting us, and for Ken Weke (Univ. of Victoria) for being our guest. Definitely check it out wherever you get podcasts, or here:

The Proteomics Show • A podcast on Spotify for Creators

Ben Orsburn and Ben Neely co-host a podcast series in a “fireside chat” format with prestigious proteomics researchers. The guests are great, the hosts are questionable.

anchor.fm

November 14, 2025 at 2:03 PM

Ben Neely

@benneely.com

Not science: after months of not really reading (aka stress), I am late to the Dungeon Crawler Carl series and loving it. Squid Games + Hunger Games + Hitchhiker's Guide + DnD + who knows what else = this LitRPG masterpiece, and I can't put it down (read book 1 on trip). Lotsa stars/thumbs from me.

November 13, 2025 at 1:40 PM

Ben Neely

@benneely.com

Good news: only 370 emails made it through to my inbox. That is still alot of emails.

Bad news: if it is important, I hope they write me again, cause I am not going through 370 emails anytime soon, if at all.