Ed Banigan
@irate-physicist.bsky.social
📤 147
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biophysicist
pinned post!
Excited to share our preprint w/Gordana Wutz, Iain Davidson, Leonid Mirny, Jan-Michael Peters
www.biorxiv.org/content/10.1...
Evidence that PDS5A/B limits NIPBL-cohesin life w/effects on CTCF boundaries & chrm compartments, +mechanisms of compartment-extrusion interplay & cohesin regulation by PDS5
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PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes
Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heter...
https://www.biorxiv.org/content/10.1101/2025.08.30.673243
21 days ago
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Excited to share our preprint w/Gordana Wutz, Iain Davidson, Leonid Mirny, Jan-Michael Peters
www.biorxiv.org/content/10.1...
Evidence that PDS5A/B limits NIPBL-cohesin life w/effects on CTCF boundaries & chrm compartments, +mechanisms of compartment-extrusion interplay & cohesin regulation by PDS5
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PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes
Cohesin-NIPBL complexes extrude genomic DNA into loops that are constrained by CTCF boundaries. This process has important regulatory functions and weakens the separation between euchromatic and heter...
https://www.biorxiv.org/content/10.1101/2025.08.30.673243
21 days ago
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Elphege Nora Lab at UCSF
24 days ago
Excitingly, the lab of Jan-Michael Peters just reported largely concordant findings: The PDS5:NIPBL balance in cells tunes the rate/velocity of cohesin loop extrusion, shaping chromosomes from loops to compartments đźš…âž°
www.biorxiv.org/content/10.1...
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paper with
@erbash.bsky.social
now published in
@narjournal.bsky.social
academic.oup.com/nar/article/...
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about 1 month ago
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Nidhi Subbaraman
about 2 months ago
Update: A Trump administration effort to block all funding that flows to outside health researchers was scrapped Tuesday evening after senior White House officials intervened
www.wsj.com/politics/pol...
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Max Kozlov
about 2 months ago
The NIH can’t award ANY grants to outside researchers under new WH restriction, reports
@wsj.com
. The pause came in the form of a footnote from OMB Director Vought, in a document that doles out federal funds to the NIH. Prelude to rescissions, especially after his comments over the weekend?
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Trump Administration Puts New Chokehold on Billions in Health-Research Funding
The National Institutes of Health can’t award grants to outside researchers under a new White House restriction.
https://www.wsj.com/politics/policy/trump-administration-puts-new-chokehold-on-billions-in-health-research-funding-19660215?st=YWVyJH&reflink=desktopwebshare_permalink
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Ligesh Theeyancheri, Jen Schwarz, and I have a new preprint out presenting a nonequilibrium mechanism that can spatially segregate dense polymer from less compacted polymer, e.g., heterochromatin and euchromatin.
arxiv.org/abs/2507.17883
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Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euc...
https://arxiv.org/abs/2507.17883
2 months ago
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Ligesh Theeyancheri, Jen Schwarz, and I have a new preprint out presenting a nonequilibrium mechanism that can spatially segregate dense polymer from less compacted polymer, e.g., heterochromatin and euchromatin.
arxiv.org/abs/2507.17883
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Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction
During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euc...
https://arxiv.org/abs/2507.17883
2 months ago
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Flavia Corsi
2 months ago
Happy to share my postdoc work—our new preprint is out! 🧬 It’s been a privilege to lead this project. I'm immensely grateful to Anton
@golobor.bsky.social
for being such an inspiring and supportive supervisor. Also truly thankful to
@danielgerlich.bsky.social
for his guidance and collaboration.
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A little belated posting, but we (Emily Navarrete, Leonid Mirny, me) have an updated preprint in collaboration the Ines Drinnenberg, Héloïse Muller, José Gil Jr, + others on the strange and striking compartmentalization of silkworm chromatin:
www.biorxiv.org/content/10.1...
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Unique territorial and compartmental organization of chromosomes in the holocentric silkworm
Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is “secluded” from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms—compartmentalization and loop extrusion—can be repurposed to create new 3D genome architectures. ### Competing Interest Statement The authors have declared no competing interest.
https://www.biorxiv.org/content/10.1101/2023.09.14.557757v3
3 months ago
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Elzo de Wit lab @ NKI
3 months ago
(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators:
doi.org/10.1093/nar/...
. A Bluetorialđź§µ:
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Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec
https://doi.org/10.1093/nar/gkaf549
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Ashamed of my PhD institution Penn deciding to ban and erase trans athletes today. Could just barely wait to get out of Pride month. Another university trying to make an impossible deal with Trump or is this what the suits wanted anyway? Gross either way
www.espn.com/college-spor...
3 months ago
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Cees Dekker
3 months ago
Latest
#CDlab
paper online now: Cohesin supercoils DNA during loop extrusion
www.cell.com/cell-reports...
This extensive study was led by Jan Michael Peters at Vienna; our lab contributed mostly modeling of plasmid supercoiling (
@romanbarth.bsky.social
‬) and single-molecule data (Richard Janissen).
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Jeremy Berg
4 months ago
Getting confirmation from several sources that the review branch at the National Institute of General Medical Sciences (NIGMS) at NIH no longer exists. I am sure this is true across many/all institutes and centers at NIH. I hope the Center for Scientific Review will be up to the task.
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Anders Sejr Hansen
4 months ago
(1/n) Thread
@matteomazzocca.bsky.social
@domenicnarducci.bsky.social
Simon Grosse-Holz
@jessematthias.bsky.social
preprint Q: how does chromatin move? Using MINFLUX, SPT & SRLCI, we track chromatin dynamics across 7 orders of magnitude in time to provide answers
www.biorxiv.org/content/10.1...
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Aykut Erbas
5 months ago
How Can Mesoscale Phases of Lamin Fibrous Structure Form on the Nuclear Surface? 🔍🧬 Lamina is a protective meshwork at the nuclear periphery, but in diseases like HGPS, its structure becomes disrupted and becomes thicker with the traces of nematically ordered lamin fibers.
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Phase behavior and dissociation kinetics of lamins in a polymer model of progeria
One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery
https://pubs.aip.org/aip/jcp/article/162/18/185101/3346472/Phase-behavior-and-dissociation-kinetics-of-lamins
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Science Magazine
5 months ago
Exclusive: National Science Foundation staff were told today that the agency’s 37 divisions—across all eight directorates—are being abolished and the number of programs within those divisions will be drastically reduced.
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Exclusive: NSF faces radical shake-up as officials abolish its 37 divisions
Changes seen as a response to presidential directives on what research to fund
https://scim.ag/3YCFvO3
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Kai Kupferschmidt
5 months ago
„Americans are living under a new regime. The question now is whether we will allow it to take root. So far, American society’s response to this authoritarian offensive has been underwhelming — alarmingly so.“ Written by political scientists who study how democracies come to an end
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Opinion | No One Has Ever Defeated Autocracy From the Sidelines
https://www.nytimes.com/2025/05/08/opinion/trump-authoritarianism-democracy.html?unlocked_article_code=1.Fk8.JhE1.lb_mzlYu3hC_&smid=url-share
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Annie Waldman
5 months ago
NEW: Whistleblower records show that the NIH axed research grants – even after a federal judge blocked the cuts with an injunction.
www.propublica.org/article/trum...
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Trump’s NIH Axed Research Grants Even After a Judge Blocked the Cuts, Internal Records Show
A lawsuit led by the Washington state attorney general offers an unprecedented view of the termination of more than 600 NIH grants, including transgender research grants threatened by Trump’s executiv...
https://www.propublica.org/article/trump-nih-cuts-transgender-research-grants
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Anders Sejr Hansen
5 months ago
(1/n) New preprint from
@claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu. Q: How do we get ultra-high-res 3D genome maps? A: New deep learning model, Cleopatra. Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.
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Carl Zimmer
5 months ago
Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10
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Anton Goloborodko
6 months ago
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
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Rules of Engagement
YouTube video by Johan Gibcus
https://www.youtube.com/watch?v=pmvOrmErhhc
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American Society for Cell Biology
6 months ago
From MBoC DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture, by Andrew Stephens, UMass Amherst, et al.
doi.org/10.1091/mbc....
#ASCB
#CellBiology
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Needhi Bhalla 💅🏽
6 months ago
They are resegregating academic science
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Jason Koebler
6 months ago
Petabytes of critical government research that is marked for possible deletion cannot be archived because of technical and legal restrictions, meaning it is very likely to be lost forever:
www.404media.co/nih-archives...
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Massive, Unarchivable Datasets of Cancer, Covid, and Alzheimer's Research Could Be Lost Forever
Days before Robert F. Kennedy Jr. announced that 10,000 HHS staffers would lose their jobs, a message appeared on NIH research repository sites saying they were "under review."
https://www.404media.co/nih-archives-repositories-marked-for-review-for-potential-modification/
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Jeremy Berg
6 months ago
Reach out to your Senators with your concerns and suggestions. HELP committee…
www.help.senate.gov/about/members
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Unacceptable. As long as Musk/Trump admin act outside of law and Constitution, this is meaningless bullshit. Vote no.
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7 months ago
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Jonathan M. Katz
7 months ago
“The president of the United States is illegally impounding critical research funds in an attempt to silence members of the Columbia community. As a university committed to free inquiry, free expression and the rule of law, we categorically reject these efforts and will see him in court.”
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Markus Deserno
7 months ago
Straight up political influence interfering with science. This cannot end well. Your grant didn’t get canceled yet? Maybe next time! If your research could show that the world isn’t upside down like Trump claims it is, you’ll be a target. We cannot have science contradicting the king.
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Drug Monkey
7 months ago
These grants survived intense scientific competition and scrutiny by expert peer scientists. It’s a sham to suggest they are unworthy. Pure bigotry to revoke them.
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maybe sacrilegious for a transplanted yankees fan, but david ortiz is right
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7 months ago
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Usha Lee McFarling
7 months ago
SCOOP: The National Academies of Science, Engineering, and Medicine, arguably the nation's most powerful scientific organization, is bending to political pressure and removing terms like "health equity" from pending reports. Members are not happy. Story by me:
www.statnews.com/2025/02/20/n...
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National Academies is altering pending reports to appease Trump administration, some members say
Words such as “health equity” are being replacing with vaguer terms, and 100 members sent a letter of protest to NASEM leaders.
https://www.statnews.com/2025/02/20/national-academies-altering-pending-reports-to-appease-trump-administration-members-say/
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Jeremy Berg
7 months ago
“What is happening is that they’re basically blocking the process, just by an administrative, legal means, rather than by ordering staff not to make grants,” said Jeremy Berg, who directed the National Institute of General Medical Sciences at the N.I.H. for eight years... 2/n
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Jeremy Berg
7 months ago
New York Times article now up on Federal Register stuff.
www.nytimes.com/2025/02/21/s...
1/n
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Trump Administration Stalls Scientific Research Despite Court Ruling (Gift Article)
Using an arcane law, officials have effectively delayed funding from the National Institutes of Health, leaving medical studies in jeopardy.
https://www.nytimes.com/2025/02/21/science/nih-research-funding-delays.html?unlocked_article_code=1.yk4.qNQA.zVPAsVztAZ3p&smid=url-share
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@PhysGenCenter
7 months ago
Next Friday Feb. 28 @ 12pm CT, Andrew Stephens, PhD of UMass presents the Monthly Seminar on Physical Genomics: "Transcription Inhibition Suppresses Nuclear Blebbing And Rupture, Independent Of Nuclear Rigidity" Registration is free at
tinyurl.com/mr2s7fpy
#chromatin
#northwestern
#dna
#genomics
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Welcome to bluesky
@erbash.bsky.social
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7 months ago
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extrusion and extrusion barriers by archaeal SMC complexes?!
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7 months ago
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A bright spot in the midst of this ongoing disaster: new work in collab w/ Aykut Erbas + his former student Goktug Attar Heterochromatin stiffens cell nuclei, but how? What is the physical mechanism of chromatin-based force response? We use polymer sims...
www.biorxiv.org/content/10.1...
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Peripheral heterochromatin tethering is required for chromatin-based nuclear mechanical response
The cell nucleus is a mechanically responsive structure that governs how external forces affect chromosomes. Chromatin, particularly transcriptionally inactive heterochromatin, resists nuclear deformations through its mechanical response. However, chromatin also exhibits liquid-like properties, casting ambiguity on the physical mechanisms of chromatin-based nuclear elasticity. To determine how heterochromatin strengthens nuclear mechanical response, we performed polymer physics simulations of a nucleus model validated by micromechanical measurements and chromosome conformation capture data. The attachment of peripheral heterochromatin to the lamina is required to transmit forces directly to the chromatin and elicit its elastic response. Thus, increases in heterochromatin levels increase nuclear rigidity by increasing the linkages between chromatin and the lamina. Crosslinks within heterochromatin, such as HP1α proteins, can also stiffen nuclei, but only if chromatin is peripherally tethered. In contrast, heterochromatin affinity interactions that may drive liquid-liquid phase separation do not contribute to nuclear rigidity. When the nucleus is stretched, gel-like peripheral heterochromatin can bear stresses and deform, while the more fluid-like interior euchromatin is less perturbed. Thus, heterochromatin's internal structure and stiffness may regulate nuclear mechanics via peripheral attachment to the lamina, while also enabling nuclear mechanosensing of external forces and external measurement of the nucleus' internal architecture. ### Competing Interest Statement The authors have declared no competing interest.
https://www.biorxiv.org/content/10.1101/2025.02.12.637704v1
7 months ago
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Needhi Bhalla 💅🏽
7 months ago
1) collateral damage is STILL damage 2) the NIH and the NSF are being systematically dismantled. There is nothing collateral about that 3) this administration is SPECIFICALLY attacking initiatives that broaden participation and who science benefits
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Jeremy Berg
7 months ago
Bluetorial: The rationale for the “NIH” indirect cost “plan” is based on misunderstood (unintentional or intentional) accounting and math The value of real government transparency
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Alberto Marin
7 months ago
1/n Really excited to share our latest pre-print on the role of cohesin in homology search, now available on bioRxiv!
www.biorxiv.org/content/10.1...
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Cohesin drives chromatin scanning during the RAD51-mediated homology search.
Cohesin folds genomes into chromatin loops, whose roles are under debate. We report that double strand breaks (DSB) induce de novo formation of chromatin loops, with the break positioned at the loop b...
https://www.biorxiv.org/content/10.1101/2025.02.10.637451v1
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Wallace Marshall
8 months ago
if you happen to live in a state represented by someone on the senate HELP committee, PLEASE call your senators and tell them how this will affect science (and employment) in your state! explain things to your family and friends and get them to call too!
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Carl T. Bergstrom
8 months ago
1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
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NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
https://grants.nih.gov/grants/guide/notice-files/NOT-OD-25-068.html
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Jamison Foser
8 months ago
It is long past time we as a society asked the tough questions, like, uh, “do we really need doctors?” wait that can’t be right
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David Suter
8 months ago
Genome architecture folks, this perspective is really worth your time
www.cell.com/molecular-ce...
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Cohesin as an essential disruptor of chromosome organization
Chromosomes are long strings of DNA carrying multiple genes. A chromosomal factor called cohesin creates loops of DNA proposed to be functional units of the genome. By contrast, it is proposed here th...
https://www.cell.com/molecular-cell/fulltext/S1097-2765%2825%2900044-9
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Derek Lowe
8 months ago
A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it.
www.science.org/content/blog...
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What's Happening Inside the NIH and NSF
https://www.science.org/content/blog-post/what-s-happening-inside-nih
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Katie Mack
8 months ago
It is very easy to call your representatives’ offices. They have to log your calls and the call numbers are meaningful. You don’t even have to try to convince anyone; just call and tell them your concerns. They are there to represent you. Let them know what that means.
www.usa.gov/elected-offi...
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Find and contact elected officials | USAGov
Use USAGov’s Contact Your Elected Officials tool to get contact information for your members of Congress, the president, and state and local officials.
https://www.usa.gov/elected-officials
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yes and it can become higher salience if our reps start making some noise about it too looking at you
@markey.senate.gov
@warren.senate.gov
@repauchincloss.bsky.social
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8 months ago
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Gregg Gonsalves
8 months ago
This man cannot be confirmed. This is pre-meditated murder of children.
www.politico.com/news/2025/01...
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RFK Jr.’s allies have a plan to upend childhood vaccination
Robert F. Kennedy’s Jr. advisers are sparring over how far he should go on vaccines as health secretary.
https://www.politico.com/news/2025/01/24/rfk-jr-allies-child-vaccinations-00200364?nname=playbook-pm&nid=0000015a-dd3e-d536-a37b-dd7fd8af0000&nrid=00000154-82c3-de5f-a954-cedb79610002&nlid=964328
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Aleksandra Galitsyna
8 months ago
Three-dimensional organization of amoeba Dictyostelium discoideum has fascinating features! Very prominent dots at between convergent gene positions, something never really seen for other species. More about the puzzle and how the team of my PhD colleagues resolves it:
doi.org/10.1093/nar/...
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Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum
Abstract. Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied b
https://doi.org/10.1093/nar/gkaf006
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