Lightnews — Scholar-powered news

Reposted by Sofya Garushyants

Zamin Iqbal @zaminiqbal.bsky.social · 12d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

14 150 300

Reposted by Sofya Garushyants

Joshua Weitz @joshuasweitz.bsky.social · 15d

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished.

jamanetwork.com/journals/jam...

Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability

This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.

jamanetwork.com

11 22

Reposted by Sofya Garushyants

Georgii "Yegor" Bazykin @gbazykin.bsky.social · 20d

Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...

Careers | Emory University | Atlanta GA

faculty-emory.icims.com

27 14

Reposted by Sofya Garushyants

Julius Brennecke @juliusbrennecke.bsky.social · 21d

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.

But how does piRNA-guided target interaction translate into silencing?

PhD student Júlia Portell Montserrat has an intriguing answer

www.cell.com/molecular-ce...

2 41 89

Reposted by Sofya Garushyants

Franklin Nobrega @fnobrega.bsky.social · 22d

Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu.

www.biorxiv.org/content/10.1...

YprA family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...

www.biorxiv.org

6 21

Sofya Garushyants @garushyants.bsky.social · 21d

YprA is a helicase popping up in multiple defense systems. In our new preprint (led by Ryan Bell), we investigate YprA clades and describe new defense systems. Importantly, ARMADA II synergizes with Druantia III; and Zorya II, Druantia III, and ARMADA II often travel together on various MGEs.

YprA family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helic...

www.biorxiv.org

7

Sofya Garushyants @garushyants.bsky.social · 21d

Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today

Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics | mBio

The virus-host arms race is a major component of the evolutionary process in all organisms that drove the evolution of a broad variety of immune mechanisms. In the last few years, over 200 distinct an...

journals.asm.org

5 11

Sofya Garushyants @garushyants.bsky.social · 23d

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

1 91 70

Reposted by Sofya Garushyants

Emmanuele Severi @emmseveri.bsky.social · Aug 31

www.biorxiv.org/content/10.1...

#phagesky #phage

Gabija restricts phages that antagonize a conserved host DNA repair complex

Anti-bacteriophage systems like restriction-modification and CRISPR-Cas have DNA substrate specificity mechanisms that enable identification of invaders. How Gabija, a highly prevalent nuclease-helica...

www.biorxiv.org

16 17

Reposted by Sofya Garushyants

Siân Owen @sianowen.bsky.social · Aug 28

An inspiring read!
academic.oup.com/genetics/adv...
A beautiful historical perspective on Ester Lederberg's legacy from @ccwendling.bsky.social & @zacharybailey.bsky.social

Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg

Abstract. Esther Miriam Lederberg's brilliant scientific lifework, from the discovery of phage lambda, bacterial conjugation, and replica plating, provided

academic.oup.com

2 26 46

Reposted by Sofya Garushyants

Karthik Anantharaman @karthik-a.bsky.social · Aug 27

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

www.nature.com

2 36 72

Reposted by Sofya Garushyants

Sorek Lab @soreklab.bsky.social · Aug 25

Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR

The first viral sponges to inhibit Pycsar and type IV Thoeris

Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings

15 48

Reposted by Sofya Garushyants

George Bouras @gbouras13.bsky.social · Aug 8

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

www.biorxiv.org/content/10.1...

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

www.biorxiv.org

5 65 130

Reposted by Sofya Garushyants

Richard Neher @neher.io · Aug 23

It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.

We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.

[1/6]

www.biorxiv.org/content/10.1...

The Actinobacteriophage Database | Home

phagesdb.org

1 17 37

Reposted by Sofya Garushyants

Indrek Kalvet @ikalvet.bsky.social · Aug 22

RFdiffusion2 is now live!
github.com/RosettaCommo...

You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!

1 18 39

Reposted by Sofya Garushyants

Current Research in Microbial Sciences @microbesinfect.bsky.social · Aug 22

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti- #phage defense

www.cell.com/molecular-ce... #bacteriophage #MicroSky

1 6 14

Reposted by Sofya Garushyants

Vivek Mutalik @vivekmutalik.bsky.social · Aug 10

😮 Cool work from Sylvain Moineau

#phage #phagesky

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

Strengthening phage resistance of Streptococcus thermophilus by leveraging complementary defense systems - Nature Communications

A study by Leprince et al. shows the effectiveness of Streptococcus thermophilus defense systems against dairy phages, their synergy with CRISPR-Cas, and the absence of fitness cost under lab or indus...

www.nature.com

9 24

Reposted by Sofya Garushyants

Zeynep Baharoglu @zeynepbaharoglu.bsky.social · Jul 14

Really cool link between tRNA copy number and bacterial cell wall 🦠 #rnasky #microsky academic.oup.com/nar/article/...

Coupling tRNAGly gene redundancy with staphylococcal cell wall integrity, antibiotic susceptibility, and virulence potential

Abstract. Redundancy in transfer RNA (tRNA) gene copies across species remains poorly understood and, in many cases, largely unexplored. In Staphylococcus

academic.oup.com

2 3 10

Reposted by Sofya Garushyants

Sorek Lab @soreklab.bsky.social · Jul 14

Preprint: “Structural modeling reveals viral proteins that manipulate host immune signaling”

Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules

Congrats Nitzan Tal!

www.biorxiv.org/content/10.1...

1 34 78

Reposted by Sofya Garushyants

Jeremy Berg @jeremymberg.bsky.social · Jul 6

When I was offered the position of Director of NIGMS in 2003, I had a range of experiences as an applicant, a grantee, and a study section member (and chair), but actually knew relatively little about how NIH operated.

1/n

1 4 40

Sofya Garushyants @garushyants.bsky.social · Jun 25

Happy to be part of this fascinating project studying why some mutant mtDNA in baker's yeast outcompete wt mtDNA journals.plos.org/plosgenetics...

Inheritance bias of deletion-harbouring mtDNA in yeast: The role of copy number and intracellular selection

Author summary Eukaryotic cells contain multiple copies of mitochondrial DNA (mtDNA), which encode essential mitochondrial proteins required for cell functioning. However, some mtDNA molecules can acq...

journals.plos.org

1

Reposted by Sofya Garushyants

Claus Wilke @clauswilke.com · Jun 17

New preprint: Modeling protein expression with explicit tRNA dynamics. We find that there's an optimum level of codon usage bias that maximizes expression. We also find charged rare tRNAs get fully depleted in late-stage bacteriophage T7 infection.
www.biorxiv.org/content/10.1...

1 3 7

Sofya Garushyants @garushyants.bsky.social · Jun 12

I had exactly the same thought yesterday after watching the budget meeting in the Senate... And also it is a good time to read "It can't happen here"

1 1

Sofya Garushyants @garushyants.bsky.social · Jun 11

Happy to be part of this effort to understand evolution of gene order in prokaryotic genomes. For different groups of closely related genomes (ATGCs) genome rearrangement to gene flux ratio in order of 0.1 pointing to the tremendous role of gene gain/loss www.pnas.org/doi/10.1073/...

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

1 4

Reposted by Sofya Garushyants

Science Magazine @science.org · Jun 9

Breaking news: Staff at the National Institutes of Health have issued a declaration calling on their director to depoliticize the agency and reverse spending cuts.

NIH staff and biomedical community sound alarm about agency politicization, funding slowdown

In test of NIH director’s support of dissent, NIH staff sign Bethesda Declaration urging reversal of grant cuts and freezes

scim.ag

9 160 410