Sign in

Nilesh Banavali

@nilesh-banavali.bsky.social
181 followers 188 following 167 posts

Research Scientist, Molecular dynamics, Cryo-EM, Ribosomes, Antibiotics, Nucleic acid structure and dynamics, Biochemical reaction mechanisms, Protein splicing, Other interesting/funny topics

PostsRepliesMedia
Reposted by Nilesh Banavali
Jon Paczkowski🌹 @paczkowskilab.bsky.social · 8h
🦠Interested in a PhD or MS in all things microbiology? Apply to join us at the Wadsworth Center and the University at Albany Department of Biomedical Sciences!
113
Reposted by Nilesh Banavali
pilarcossio.bsky.social @pilarcossio.bsky.social · 14/10/2026
1/5 Cryo-EM gives high-resolution RNA structures, but only when high Mg²⁺ freezes out their motion. At physiological conditions, RNAs are dynamic and 3D reconstruction fails. Can we still learn their folding equilibria? New preprint: yes, straight from the raw particle images👇
14818
Reposted by Nilesh Banavali
Siân Owen @sianowen.bsky.social · 14/10/2026
Applying to PhD programs? Consider UAlbany's Biomedical Sciences program! We're keen to recruit students interested in molecular microbiology, virology, structural & comp biology. We're a close-knit department invested in our trainees, and Albany is fun & affordable. Please share!! shorturl.at/buMsZ
Promotional graphic featuring UAlbany and Wadsworth Center imagery, highlighting interdisciplinary research, supportive mentorship, and opportunities in research
288
Reposted by Nilesh Banavali
Meade Krosby @meadekrosby.bsky.social · 08/07/2026
Timeline cleanse: American pikas calling to each other in the Canadian Rockies. Sound on to hear the loud “MEEP!” made by these potato sized alpine mammals. They’re way off under those cliffs but the calls travel. *this is likely a niche post, but it’s one of my favorite sounds in the world.
591724296
Nilesh Banavali @nilesh-banavali.bsky.social · 11/10/2026
Fall Catskills view from Ashokan reservoir
Fall view of Catskills from Ashokan reservoir
000
Reposted by Nilesh Banavali
cryoEM papers @cryoempapers.bsky.social · 11/10/2026
Ab initio CryoEM maps minimizing preferred orientation problems in heterogeneous mixtures: ReconSIREN www.biorxiv.org/content/10.64898/2026.10.03.756391v1 #cryoEM
054
Reposted by Nilesh Banavali
James Fraser @fraserlab.com · 10/10/2026
I hear so much about the growing power of predictive biology, especially in drug discovery and "co-folding". I want to see people put their GPU budget where their mouth is!
CYP3A4
13612
Reposted by Nilesh Banavali
Green Lab JHMI @greenlab.bsky.social · 09/10/2026
U should check DIS out! In our new paper (and sequel to our RIOK3 story), we find that rRNA oligo(U) tailing and DIS3L2-mediated decay drive 40S ribosome degradation 💫 www.cell.com/molecular-ce...
cell.com
Oligo(uridine) tailing and exonucleolytic decay drive 40S ribosome degradation in response to stress
40S ribosomes are degraded in diverse stress conditions. Diehl et al. find that in response to stress, TUT7 is recruited to ubiquitylated 40S ribosomes and adds 3′ oligo(U) tails to the 18S rRNA. Iter...
1159
Reposted by Nilesh Banavali
Green Lab JHMI @greenlab.bsky.social · 09/10/2026
And here’s a beautiful complementary story from the lab of @colinwu.bsky.social!! www.cell.com/molecular-ce...
cell.com
40S ribosome remodeling triggers 18S rRNA U-tailing and DIS3L2-dependent decay
Translational perturbations trigger ubiquitination and turnover of 40S ribosomes, yet how these events are coupled remains unclear. Shah et al. reveal that RIOK3 remodels ubiquitinated 40S subunits, e...
0117
Reposted by Nilesh Banavali
Przemek Dutka @przemekdut.bsky.social · 08/10/2026
Our latest development is now on bioRxiv: cryoSHIELDs — amphipathic peptide additives that make cryo-EM grid prep far more reliable. Tested across 24 protein systems, they enabled the first ABCC6 structure and GPCR–G protein structures at just 0.1–0.5 mg/mL! www.biorxiv.org/content/10.6...
14726
Reposted by Nilesh Banavali
Randall Munroe @xkcd.com · 08/10/2026
Juice xkcd.com/3308/
4-panel comic. (1) [Two people, one with a ponytail, sitting and typing at terminals opposite each other. A sign on the wall reads “Juice Mission Control,” with JUICE in huge letters.] PERSON 1: Jupiter Icy Moons Exploder checkin is complete. All systems nominal. (2) PERSON 2 with ponytail. [People turn to look at each other.] PERSON 1: What? PERSON 2: Jupiter Icy Moons *Explorer*. (3) [Person 1 turns back to his terminal.] (4) PERON 1: Control, everything is fine, but I need to schedule an urgent spacecraft update. [Person 2 facepalms] PERSON 2: Oh no.
383412517
Nilesh Banavali @nilesh-banavali.bsky.social · 08/10/2026
Structure of human GCN1-ABCF3 bound to collided di-ribosomes - a sensor for amino acid starvation www.biorxiv.org/content/10.6...
biorxiv.org
Molecular Architecture of the Human GCN1–ABCF3 Ribosome Collision Sensor
The Integrated Stress Response is a critical eukaryotic signaling pathway that maintains cellular proteostasis. During amino acid scarcity, the yeast kinase Gcn2 (GCN2 in humans) and its activators Gc...
021
Nilesh Banavali @nilesh-banavali.bsky.social · 08/10/2026
60S ribosome degrades when it is not released from the ER translocon www.biorxiv.org/content/10.6...
biorxiv.org
Failure to release from the ER translocon induces 60S ribosome degradation
Ribosome malfunction has toxic consequences, but how mammalian cells select ribosomal subunits for degradation remains poorly understood. Here, we develop a pulse-chase CRISPR screening strategy to id...
011
Reposted by Nilesh Banavali
Nature @nature.com · 08/10/2026
Nature research paper: RNA catalysis emerges from dynamic structural ensembles go.nature.com/4hzV4jr
go.nature.com
RNA catalysis emerges from dynamic structural ensembles - Nature
RNase P RNA forms shifting active and inactive conformers whose catalytic activity depends on Mg2+-driven tertiary-interaction dynamics, which are modulated by binding of accessory proteins.
093
Reposted by Nilesh Banavali
erzbergerlab.bsky.social @erzbergerlab.bsky.social · 08/10/2026
Ribosome remodeling drives translation adaptation during viral infection and cellular stress: Molecular Cell www.cell.com/molecular-ce...
cell.com
Ribosome remodeling drives translation adaptation during viral infection and cellular stress
Tsai et al. discover that ribosome composition is reprogrammed in response to intrinsic and external cellular perturbations, which supports ribosome remodeling as a conserved mechanism that enables ad...
01110
Reposted by Nilesh Banavali
Harmit Singh Malik @harmitmalik.bsky.social · 07/10/2026
One stop codon to evade two divergent immune systems www.fredhutch.org/content/www/... Great writeup by Ashley Person @fredhutch.org Original paper by @tamanash.bsky.social here: www.science.org/doi/10.1126/...
fredhutch.org
One stop codon to evade two divergent immune systems
A recent study reveals how a single stop codon helps alphaviruses evade immune defenses in both mosquitoes and humans
15015
Reposted by Nilesh Banavali
Sarah Andersen @sarahseeandersen.bsky.social · 07/10/2026
The image is of a four panel comic.
In panel one, we see a crow’s face. It says, “I AM DEATH’S MESSENGER”.
In panel two, we see the same crow’s face. It continues, “YOUR TIME IS NEAR”.
In panel four, we see the crow awkwardly hopping away from a stick figure.
In panel five, we see the grim reaper with the crow perched on his hand. The grim reaper says, “So you should probably fly away dramatically instead.”
61137002754
Reposted by Nilesh Banavali
cryoEM papers @cryoempapers.bsky.social · 06/10/2026
Long-form hibernation-promoting factor coordinates 100S assembly and translational repression www.biorxiv.org/content/10.64898/2026.10.02.756224v1 #cryoEM
001
Reposted by Nilesh Banavali
Merriam-Webster @merriam-webster.com · 05/10/2026
The SPEAKER implies. The LISTENER infers. The DUDE abides.
6548321128
Reposted by Nilesh Banavali
Massimo (mirror) @rainmaker1973-m.bsky.social · 05/10/2026
How to digitalize a camera film Repost of @EIRancheroLoco: Original post
0247
Reposted by Nilesh Banavali
Gwênlyn Glusman (she/her) ☸️ @gwenlyn.bsky.social · 04/10/2026
I have modernized and enhanced the NSF COA generator tool. Results now update dynamically • Published under more than one name? Covered! • Other people share your name? No problem! • You prefer searching by ORCID? Go ahead! Give it a try. Feedback, bug reports, feature requests are MOST welcome! 🧪
05327
Reposted by Nilesh Banavali
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 03/10/2026
A type VI secretion ADP-ribosyltransferase Rhs toxin selectively modifies charged tRNAThr(GGU) anticodon loops to block ACC codon decoding academic.oup.com/nar/article/...
academic.oup.com
A type VI secretion ADP-ribosyltransferase Rhs toxin selectively modifies charged tRNAThr(GGU) anticodon loops to block ACC codon decoding
Abstract. The type VI secretion system (T6SS) is a sophisticated machine that uses a contractile mechanism to deliver antibacterial toxins into neighboring
051
Reposted by Nilesh Banavali
Diorge Souza @diorgeps.bsky.social · 02/10/2026
Finally out! Our work uncovers evolutionary links between bacterial and archaeal ribosome hibernation and eukaryotic energy sensing, through the archaeal hibernation factor AHA link.springer.com/article/10.1...
link.springer.com
A conserved archaeal protein with evolutionary links to bacterial ribosome hibernation and eukaryotic energy sensing - The EMBO Journal
Ribosome hibernation helps cells survive stress by reversibly silencing translation and preserving ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation rem...
14316
Reposted by Nilesh Banavali
cryoEM papers @cryoempapers.bsky.social · 02/10/2026
CryoConvNeXt enables robust identification of low-abundance molecular species in experimental cryo-EM data pubmed.ncbi.nlm.nih.gov/42818773/ #cryoEM
053
Reposted by Nilesh Banavali
Science Magazine @science.org · 30/09/2026
In Science, researchers present the Virtual Biotech, an AI system to inform drug-development decisions. By combining diverse biomedical and clinical evidence in a unified platform, the system may help identify therapeutic opportunities that would otherwise be missed. scim.ag/4h0KTnJ
scim.ag
The Virtual Biotech: A multi-agent AI framework for therapeutic discovery and development
Drug development requires evidence integration across biological scales and modalities, but relevant tools are fragmented. We introduce the Virtual Biotech, an organization of artificial intelligence ...
1134
Reposted by Nilesh Banavali
Faine Greenwood @faineg.com · 30/09/2026
GOAT OR BIRD????
This is even better than the
"what color is this dress" dress.
Goat?
or Bird?
2071830480
Reposted by Nilesh Banavali
Wes Craven Glizzies @ywfyf.com · 29/09/2026
I saw a leaf with legs on my way home today.
Green leaf bug on a curb
371729143
Reposted by Nilesh Banavali
Brian Stevenson Ph.D. spirochete lab @bstevensonlab.bsky.social · 28/09/2026
The Insect Epiphany: How Our Six-Legged Allies Shape Human Culture Free zoom presentation October 8, 7:00PM Central time Information and registration: www.aldoleopold.org/news-and-eve...
aldoleopold.org
Upcoming Programs and Events | Aldo Leopold Foundation
Stay updated on upcoming programs and events at the Aldo Leopold Foundation. Browse our calendar, learn more, and register for events to secure your spot.
032
Reposted by Nilesh Banavali
cryoEM papers @cryoempapers.bsky.social · 26/09/2026
The CAHRA Challenge: A Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms pubmed.ncbi.nlm.nih.gov/42779743/ #cryoEM
053
Reposted by Nilesh Banavali
joe dobbs @joedobbs.bsky.social · 25/09/2026
Our work investigating the cooperation between gene expression machines is now online @cellpress.bsky.social. Check it out if you're interested in high-throughput #cryoET, transcription and translation, or using structural biology to quantify gene expression in cells! 🔬 www.cell.com/cell/fulltex...
cell.com
Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries
Cryo-electron tomography (cryo-ET) resolves and quantifies an almost complete view of bacterial translation, revealing how gene expression machineries coordinate across the processes of transcription,...
28426
Reposted by Nilesh Banavali
Robert Arkowitz @robertarkowitz.bsky.social · 26/09/2026
In-cell structures visualize human pre-ribosome assembly in the nucleolus | Science www.science.org/doi/10.1126/...
science.org
In-cell structures visualize human pre-ribosome assembly in the nucleolus
In eukaryotes, ribosome biogenesis initiates within the nucleolus, a hallmark multilayered compartment of the nucleus. Structures of pre-ribosomes have been characterized ex situ, but their assembly p...
0112
Reposted by Nilesh Banavali
Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
1023696
Reposted by Nilesh Banavali
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 25/09/2026
Fluorescent proteins misreport ribosome abundance under translation inhibition www.biorxiv.org/content/10.6...
biorxiv.org
Fluorescent proteins misreport ribosome abundance under translation inhibition
Fluorescent proteins are widely used as quantitative reporters of protein abundance in living cells. Here we show that this relationship can break down under translation inhibition: the cellular ribos...
031
Reposted by Nilesh Banavali
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 25/09/2026
An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites www.biorxiv.org/content/10.6...
biorxiv.org
An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites
Millions of RNA sequences are readily available, but the structures that determine their function are not. Picornaviruses initiate translation through Internal Ribosome Entry Sites (IRESes), RNA eleme...
053
Reposted by Nilesh Banavali
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 25/09/2026
Sparsomycin inhibits translation through a conserved mechanism across all domains of life academic.oup.com/nar/article/...
academic.oup.com
Sparsomycin inhibits translation through a conserved mechanism across all domains of life
Abstract. Sparsomycin (SPA) is a broad-spectrum inhibitor of protein synthesis with activity across all three domains of life. Although SPA has long been k
054
Reposted by Nilesh Banavali
IU Biology @iubiology.bsky.social · 20/08/2026
Congratulations to IU biology postdoc Kayla Simanek in the van Kessel lab on receiving the prestigious Life Sciences Research Foundation Fellowship! @ksimanek.bsky.social 🔗 go.iu.edu/hy58UV
This is a photo of IU biology postdoc Kayla Simanek.
042
Reposted by Nilesh Banavali
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 20/09/2026
Bacterial growth rate in populations and single cells 🦠💫 www.nature.com/articles/s41... beautiful review by Petra Levin and Jue Wang
nature.com
Bacterial growth rate in populations and single cells - Nature Microbiology
In this Perspective, Levin and Wang give a brief history of bacterial growth rate and discuss how it is connected to nutrient availability and macromolecule synthesis, with a focus on (p)ppGpp as a ce...
083
Reposted by Nilesh Banavali
Robert Arkowitz @robertarkowitz.bsky.social · 20/09/2026
millenniumproblems.bio
millenniumproblems.bio
The Millennium Problems for Biology
A working catalogue of twelve open problems in biology — each a concrete, testable target for the field.
352
Reposted by Nilesh Banavali
c0nc0rdance @c0nc0rdance.bsky.social · 06/02/2025
A Pirate Ribosome's first love is the C ... (GU). (🧑‍🎨: Science Fried Art)
Pirate ribosome:  a brown ribosome cartoon wears a pirate hat with skull and crossbones and eyepatch, and a long string of ARG amino acids is on the nascent chain, while an mRNA consisting of CGU repeats is labeled from 5' to 3'.
514630
Reposted by Nilesh Banavali
soneya-majumdar.bsky.social @soneya-majumdar.bsky.social · 17/09/2026
www.nature.com/articles/s41...
nature.com
Reimagining research papers as interactive and reliable AI agents - Nature
Paper2Agent converts research papers into interactive artificial intelligence agents by turning manuscripts, code and data into model context protocol-based tool-invoking systems that reproduce origin...
001
Reposted by Nilesh Banavali
Hauke Hillen @haukehillen.bsky.social · 11/09/2026
Happy to share our new preprint on the structure of the human mitochondrial RNA degradosome, a central player in organellar RNA metabolism! Work led by graduate student @paulafprado.bsky.social in our group. www.biorxiv.org/content/10.6... 🧵 1/9
19134
Reposted by Nilesh Banavali
Alan Brown @alanbrownhms.bsky.social · 10/09/2026
Millions of beating cilia keep airways clean. At the base of each is the transition zone (TZ), a gate that controls which proteins enter and leave. In our paper out today in Science, we used cryo-FIB-ET to image the TZ inside human airway cells www.science.org/doi/10.1126/...
science.org
In situ structure of the human ciliary transition zone links linker defects to primary ciliary dyskinesia
The ciliary transition zone (TZ) regulates ciliary proteome composition, yet its molecular architecture, protein content, and contribution to motile ciliopathies remain poorly defined. We applied in situ cryo-electron tomography and subtomogram averaging ...
211945
Nilesh Banavali @nilesh-banavali.bsky.social · 10/09/2026
Cover framed, put outside lab, and posed next to.
Me posing with a Biochemistry cover poster from a paper by us.
000
Reposted by Nilesh Banavali
Dani cRabaiotti 🦀 @danirabaiotti.bsky.social · 10/02/2024
Welcome to the Science feed! Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/ Mod introductory posts linked below⬇️ Use the test tube emoji on posts you want to appear in the feed🧪 Please like the feed and make sure you follow our feed rules:
Science Feed Rules:
🧪 No misinformation
🧪 Keep posts relevant to science
🧪 Use alt text
🧪 Credit images
🧪 Give context to links to external sites
🧪 Have fun!
1091316392360
Reposted by Nilesh Banavali
The Royal Society @royalsociety.org · 27/08/2026
Professor Lewis E Kay FRS is awarded the Royal Medal (Biological) 2026 for his remarkable contribution to understand and quantify protein dynamics and their relevance to protein function. #RSMedals royalsociety.org/medals-and-prizes/…
A man in a black shirt and glasses smiles at the camera. You can see a computer screen and framed certificates in the background.
4228
Reposted by Nilesh Banavali
The Royal Society @royalsociety.org · 28/08/2026
The Francis Crick Medal and Lecture 2027 is awarded to Dr Thi Hoang Duong (Kelly) Nguyen for her ground-breaking discoveries into the molecular mechanisms of telomere maintenance. #RSMedals royalsociety.org/medals-and-prizes/…
A woman in a blue top with a small colourful pattern smiles at the camera in front of a white background.
3529
Reposted by Nilesh Banavali
The Royal Society @royalsociety.org · 27/08/2026
Professor Dame Janet M Thornton DBE FMedSci FRS is awarded the Croonian Medal and Lecture 2027 for her pioneering work in protein structural and functional bioinformatics. #RSMedals royalsociety.org/medals-and-prizes/…
A scientist sits at a desk in front of a computer display with complicated graphics on the screen. She is turned slightly and smiling at the camera.
54814
Reposted by Nilesh Banavali
The Royal Society @royalsociety.org · 27/08/2026
Professor Bonnie Bassler is awarded the Copley Medal for her discovery of the universality of chemical communication in bacteria and for her idea that interfering with this communication could form the basis of novel anti-bacterials. #RSMedals royalsociety.org/medals-and-prizes/…
A woman with dark hair and a light blue shirt smiles at the camera in front of a bright white background.
413836
Reposted by Nilesh Banavali
ContempraInn 🌹 @contemprainn.bsky.social · 07/09/2026
Studies show that watching a beaver eating cabbage lowers stress levels by 15% so enjoy 😊
22357521136
Nilesh Banavali @nilesh-banavali.bsky.social · 06/09/2026
A late summer day at the million dollar beach in Lake George.
A late summer day at the million dollar beach in Lake George.
020