Baylink Lab

A view out the window

Snow outside

First major snowfall of the year in #CougarCountry! Perfect for writing papers and grants.

Photo of Bruce holding his award.

A big congratulations to future #IDsky physician-scientist Bruce Redden for his research presentation award at this year's ABRCMS. Lots of time and practice went into that presentation! Such a great meeting for the next generation of researchers to network & share discoveries! 🦠🧪 #medsky #medsky

Photo of the Baylink lab group that attended ASMNW.

ASM NW was wonderful this year! In addition to the great science, this trainee-focused meeting plays such an important role in providing the next generation of scientists, microbiologists, and clinicians an opportunity to learn, network, and share their own research.

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#BLAST A great lab to investigate bacterial locomotion and signal transduction!

#microsky
#idsky

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You can also stop reviewing for that journal and not publish there yourself.

Of course there will be real scientific disagreements that an editor will need to make a judgement call for the appropriate course of action. Yours doesn’t sound like such a case.

Beautiful!

Good question. It is a cycle. Ticks feed on an infected animal and acquire the bacteria (from ingesting the blood), and then pass it on to other animals/humans.

Absolutely! In general, motile bacteria can literally swim circles around phagocytes...

Borrelia burgdorferi initiates early transcriptional re-programming in macrophages that supports long-term suppression of inflammation Author summary Lyme disease, caused by the spirochete Borrelia burgdorferi (Bb), is a long-term infection whose inflammatory manifestations are primarily due to an exuberant immune response to the pat...

I am sure it is complicated and situation dependent, but this study covers some of those topics:

journals.plos.org/plospathogen...

Unfortunately (as I am sure you know) many people are affected - a great reason for us to keep investigating potential new and more effective treatments.

An image that shows white wiggly lines that illustrate the paths of swimming bacteria.

The video captures frames every 1 s over a few minutes. The attached image shows a 'max' projection over 30 minutes that illustrates the path of their movement similar to a time-lapse.

You’ve heard of #Lymedisease, but have you ever seen the bacteria that causes it? 🦠 Borrelia burgdorferi, the spiral-shaped culprit transmitted by ticks, swims with a creepy wriggling motion and uses #chemotaxis to navigate. Both fascinating... and disgusting #Microsky 🧪 #IDsky @shawlab.bsky.social

Registration is open! Come join us at the sensory transduction in microorganisms GRC! Spread the word! www.grc.org/sensory-tran...

🚨 Postdoctoral Position 🚨

Investigate molecular mechanisms of protein homeostasis in Salmonella during infection! Strong background in biochemistry/molecular biology encouraged.

📩 Send CV, publications, and statement to Eduardo A. Groisman at Yale:

eduardo.groisman@yale.edu
🧪 #microsky 🦠 #BLAST

Extreme armour in the world’s oldest ankylosaur - Nature The ankylosaurian dinosaur Spicomellus afer possessed a tail weapon and uniquely elaborate dermal armour.

Link to new article in Nature:

Extreme armour in the world’s oldest ankylosaur
🧪🦖🦕
www.nature.com/articles/s41...

I’m Arden, and my lab is trying to develop new antibiotics to treat bacterial infections!

The lab is based at Washington State University in Pullman - Go Cougs!

Impact of erroneous user input on AlphaFold 3 modeling of variant sites. Overlays show variant sites between the KatASS1 crystal structure (yellow) and AlphaFold three models generated with: (A–D) single-site mutations (green); (E–H) a single distant Trp insertion at the N-terminus (light purple) or C-terminus (dark purple); and (I–L) the correct sequence modeled with incorrect oligomeric states: monomer (light orange), dimer (orange), and trimer (dark orange). (M–P) Root-mean-square deviation (RMSD) calculations for all heavy atoms when comparing the AlphaFold three models to the crystal structure.

Lots of new-to-protein-structure folks are using AF3, which is great! However, non-experts might be inclined to feed AF3 incorrect information, such as modeling a monomer when the biologically-relevant state is a dimer. We found this can decrease model accuracy due to missing tertiary interactions.

Antibiotic resistance and immunogenicity are impacted by small variations in protein sequence but it isn't feasible to experimentally determine structures for the many thousands of variants that exist in nature. In this particular system AF3 generated extremely accurate models for variant sites.

AlphaFold 3 accurately models natural variants of Helicobacter pylori catalase KatA | Microbiology Spectrum Experimental structure determination is rarely performed for natural protein variants possessing only minor amino acid differences from published structures, even though small substitutions can signif...

We had a crystal structure of Helicobacter catalase collecting dust, so decided to turn it into an Alphafold test case for modeling natural protein variants, i.e. proteins with small sequence differences.

Study published here: journals.asm.org/eprint/J45UR...

Comparisons of crystal structure and AlphaFold 3 models of KatASS1. (A) Overlay of crystal structure KatASS1 (two chains, yellow) and crystal structures of KatA26659 (light gray, four chains). Variant sites are noted in pink. (B–E) Poses of variant residues within KatASS1, as indicated. KatASS1 crystal structure chains are shown in yellow and KatA26995 crystal structure chains in light gray. Green mesh is mFo-DFc omit map electron density at 3.5 σ averaged over the two non-crystallographic symmetry (NCS) chains, and dark blue mesh is 2mFo-DFc NCS-averaged electron density at 1.0 σ of the final model. (F) Overlay of the KatASS1 crystal structure (yellow) with three AlphaFold 3 models (light blue, blue, and dark blue) using native sequence and tetramer oligomerization as input parameters. (G–J). Overlay of each variant residue comparing crystal structure (yellow) positions to AlphaFold three predictions (blue). (K). Global root-mean-square-deviation (RMSD) values for each structure and model in relation to crystal structure KatASS1 chain A.

Wonderful how Alphafold has opened up protein structure prediction to non-experts but you still have to feed it correct information (like oligomeric state!). A small test case shows AF3 makes excellent guesses on natural variants but inaccuracies occur from dubious user inputs.

#microsky #IDsky 🧪🦠

🚨 2 funded #PhD positions (ERC Adv Grant) in the Moissl-Eichinger Lab, Graz! Study Methanobrevibacter as a keystone in the gut microbiome.
💡 Omics, modeling, synthetic consortia
📅 Deadline: Sept 10, 2025
🌍 Int’l applicants welcome!
Application link below.
#microbiomesky #archaeasky #microsky

How China’s bold talent recruitment has shaped science Many Chinese researchers have received enviable benefits and positions after returning from training abroad.

Talent recruitment programmes have enticed many researchers to return to China. But how successful have they been? I spoke with several researchers who have analysed these trends and assessed their impact on China's research ecosystem 🧪

Well now Im learning new things about indole! When we work with the bottle in dry format it is a bit pungent but not so bad as 💩

Disease-causing bacteria can deal with stink as long as they get a meal New WSU research shows gut pathogens like Salmonella will brave a toxic chemical to reach nutrients, offering insights for treating infections.

Some behind-the-scenes insight on the research for non-experts. And FYI, the 'stinky' indole for poo we studied here is actually a major ingredient in lots of perfumes. Turns out it smells better at low concentrations!

news.wsu.edu/press-releas...

Study published here:

elifesciences.org/reviewed-pre...

Shown is Dr. Baylink holding a tiny glass needle known as a microcapillary. This was used to study chemotaxis by injecting chemical effectors into a pond of motile bacteria and monitoring their responses through microscopy.

In our new study in @elife.bsky.social
with the cheeky title "Navigating Contradictions" we used these tiny glass needles to study chemotaxis & learn how Salmonella and other gut pathogens make decisions when they encounter conflicting stimuli.

#microsky #IDsky 🦠🧪 #gastrosky

tinyurl.com/yckdn8v6

Beautiful

Wow, well done!

Lab website: sites.rutgers.edu/ann-stock-lab/. Applicants can apply at
jobs.rutgers.edu/postings/254... and by email to stock@cabm.rutgers.edu

🚨 Postdoc Opportunity – Rutgers University!
Join Ann Stock’s lab to study how Bacteroides regulate fiber and glycan metabolism via hybrid two-component systems.
Structural + regulatory biology | CryoEM, crystallography, gene regulation
🔗 Apply | 🔬 Lab
📧 stock@cabm.rutgers.edu #postdoc #microsky 🧪🦠