Snu Nini

Optimizing primer selection for microbial diversity studies in freshwater lakes: a comprehensive evaluation of 16S rRNA, 18S rRNA, and ITS gene regions This study identified the best performing DNA primers targeting ribosomal or ITS markers for studying bacteria, eukaryotic microbes, and fungi in lakes, wh

Optimizing primer selection for microbial diversity studies in freshwater lakes: a comprehensive evaluation of 16S rRNA, 18S rRNA, and ITS gene regions url: academic.oup.com/femsec/artic...

Biological Laboratory | LEGO® Ideas This is a two-floor realistic Biological Laboratory building. In this design, I try to tell stories about biologists, introduce biology concepts to general publ…

I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗
beta.ideas.lego.com/product-idea...

MemPrO: A Predictive Tool for Membrane Protein Orientation Membrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi...

🌟 New Tool Alert!

We present MemPrO – a toolkit for orienting and building membrane protein systems:

✅ Membrane protein orientation 
✅ Mixed membrane building 
✅ Double membranes & curvature 
✅ Peptidoglycan cell wall support

🔗 github.com/pstansfeld/mempro 
📖 pubs.acs.org/doi/10.1021/...

What is better than one? Two connected papers!

#NewResearch

S protein of Streptococcus pneumoniae activates PBP1a and coordinates with a wider GpsB-associated multi-protein complex to regulate peptidoglycan remodelling and cell division.

#MicroSky 🦠

www.nature.com/articles/s41...

New tools unlock #Bdellovibrio bacteriovorus’s predatory secrets 🦠. By combining inducible gene expression with #CRISPRi-mediated depletion for precise control of essential genes, @lalouxlab.bsky.social uncovered new insights into its unique lifecycle and cell division.
buff.ly/FcDzAY4

"jewel of the collection"

Just when she was starting to doubt whether it is all in vein. There was this person who said, "it's all very nice". In those exact words.
The simple words has so much power when people try to be kind!

Deciphering microbial spatial organization: insights from synthetic and engineered communities Abstract. Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between communi

Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...

A timeless model for writing a research summary.

1/2

Type VI secretion system activity at lethal antibiotic concentrations leads to overestimation of weapon potency Competition assays are a mainstay of modern microbiology, offering a simple and cost-effective means to quantify microbe–microbe interactions in vitro. Here, we demonstrate a key weakness of this meth...

Does your lab perform killing assays?
TL;DR: we’ve identified a problem that can bias the outcome of killing assays, making antagonism look stronger than it really is.
Adding a simple extra step can mitigate this bias!

Out now at #MicrobioJ www.microbiologyresearch.org/content/jour...

1/n

Peptidoglycan–outer membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.

www.nature.com/articles/s41... #microsky 🦠 model in which the entire cell envelope, including the periplasm, collectively enables Gram-negative bacteria to overcome osmotic challenges

Two photos of Sri Lankan flameback woodpeckers on tree trunks. On left: a yellow-backed flameback (Dinopium benghalense) in northern Sri Lanka. On right: a red-backed flameback (Dinopium psarodes) in southern Sri Lanka. Both birds have red crests on top of the head, black and white stripes on the head and neck, brightly coloured backs, and stiff black tails that help to hold them upright on the tree trunks.

Like woodpeckers?
Like pretty colors?
Like genomics of pretty colors in woodpeckers?
Then this is for you!

"Biochemical and Genomic Underpinnings of Carotenoid Colour Variation Across a Hybrid Zone Between South Asian Flameback Woodpeckers"

Lead author: Rashika Ranasinghe

doi.org/10.1111/mec....

Mathematical modelling for biologists - Modelling concepts in biological research Mathematical modelling for biologists - Modelling concepts in biological research

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...

Including both molecular and epidemiological examples

If you’re interested in learning more about protein folding and misfolding, I’ve created a convenient reading list with a few essential papers:

scholar.google.com/citations?us...

scholar.google.com/citations?us...

Being free and open-source, this is how you can support #tidyplots ❤️

tidyplots.org

#rstats #dataviz #phd

A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily - Nature Communications This study reveals that an outer membrane protein from the predator Bdellovibrio bacteriovorus forms a pentameric assembly that traps a lipid monolayer within. This allows the discovery of two superfa...

Check out these amazing lipid-monolayer-trapping oligomeric OMPs published by @lalouxlab.bsky.social and Lovering Labs. The BAM complex in these bugs must be wild!

www.nature.com/articles/s41...

Biochemistry Focus EXR webinar series New Insights into ER Chaperone Function and Ribosome Quality Control Pathways in Caner Therapy Thursday 26 June 14.00-15.00 BST

Register now for our next webinar on 26 June! Don't miss a deep dive into the exciting use of native mass spectrometry to uncover BiP molecular chaperone function and how Ribosome Quality Control can be a hidden ally of cancer cells against chemotherapy🧪: register.gotowebinar.com/register/838...

Phage DisCo: targeted discovery of bacteriophages by co-culture | mSystems In this work, we describe a targeted phage discovery method that allows immediate isolation of phages with specific traits. Currently, to find a phage with specific properties, huge libraries of phage...

The latest work from my lab, Phage Disco, a method
@ellie-rand.bsky.social
developed for targeted discovery of bacteriophages based on the bacterial receptor, defense system, or other component they interact with, is now live in mSystems
journals.asm.org/doi/10.1128/...

You can also design in Colab now: colab.research.google.com/github/patri...

AMRrules encodes in a simple table format: In this species, if we find this gene/mutation, then we expecte this drug phenotype, based on this evidence.

AMRrules encode organism-specific rules for interpreting AMR genotype calls: if I find this gene/mutation in this organism, what does it mean for clinical resistance?

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations!

These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs.

Save and share the post!

Apps are great.... until they lead to a crash course in the soft skills of survival. (TMI: I once overheard someone say that purifying her protein would make her happy but making the relationship work would make her happier. They broke up. The protein? purified with a codon optimized plasmid)

🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩‍💻

📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!

#bioinformatics #opensource #STEMeducation

YouTube video by MD TV Doctor Must Save His Daughter's Partner From a Deadly Infection | Pure Genius | MD TV

Predatory bacteria making it into Hollywood!
youtu.be/Gp6FKWkNV5Y?...

For a good start into 2025 we offer a small treat 🎁 (preprint) to quantitative proteomics and predatory bacteria 🦠 researchers. Our predatory proteome of B.bacteriovorus offers high temporal resolution (based on n=5 biological repeats!) for a better understanding of the killing process. #MicroSky

As an international student I put all eggs in one basket and applied to my dream PhD in the US and got rejected after the interviews. They did not mention fund cuts as the reason. Bt I suspect that. It took me a while bt I picked myself up (I think) to go forward!

Yup! This is not talked about enough and there is no answer for that. For me it's if "A" happens by "X" it will be "B". If it's "C", then "D" and "E". Anyways no regrets!

The moment my MSc PI professor, decided to give me a chance to join his group. I was an international student, only female graduate student of the group. This opened a whole new world for me. He gave me the confidence to dream.

Color blind friendly palettes for data visualizations with categories A discussion of color blind friendly palettes for labeling unique catergories in data visualization.

Having a color-blind colleague is a good reminder that we need to be more careful when designing figures for scientific publication 🧪
My lab has found this page especially useful for selecting color palettes, used in combination with different symbols: thenode.biologists.com/data-visuali...

Cool, nice chart! I have made a similar one showing also commercialization and resistance.
Interestingly, resistance was sometimes observed before market introduction.

bsky.app/profile/dani...