joe-wade.bsky.social
@joe-wade.bsky.social
Reposted by joe-wade.bsky.social
Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1
February 11, 2026 at 4:16 AM
Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1
Reposted by joe-wade.bsky.social
@ewarman.bsky.social has followed up on her discovery of bidirectional promoters in bacteria by defining their basic rules for regulation and links to gene expression noise...
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Bidirectional promoters in Escherichia coli: regulatory rules and implications for gene expression noise
Abstract. In prokaryotes, bidirectional promoters are pseudo-symmetrical DNA sequences that stimulate divergent transcription. Ubiquitous, and far more lik
academic.oup.com
February 6, 2026 at 3:35 PM
@ewarman.bsky.social has followed up on her discovery of bidirectional promoters in bacteria by defining their basic rules for regulation and links to gene expression noise...
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by joe-wade.bsky.social
Actuation of CRP activating region 3 by acetylation modulates V. cholerae sugar utilization and virulence https://www.biorxiv.org/content/10.64898/2026.01.27.701997v1
January 28, 2026 at 2:18 AM
Actuation of CRP activating region 3 by acetylation modulates V. cholerae sugar utilization and virulence https://www.biorxiv.org/content/10.64898/2026.01.27.701997v1
Reposted by joe-wade.bsky.social
Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second π₯°). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!
PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis
Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro
academic.oup.com
January 27, 2026 at 4:59 PM
Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out: academic.oup.com/nar/article/... (obviously the first more important than the second π₯°). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!
Reposted by joe-wade.bsky.social
New Perspective out in Advanced Science π in collaboration with @alanrice.ie for @uniofbath.bsky.social 60th anniversary special issue.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
We review nearly a decade of work asking:
how do gene regulatory networks rewire during evolution?
π§«π§΅
advanced.onlinelibrary.wiley.com/doi/10.1002/...
We review nearly a decade of work asking:
how do gene regulatory networks rewire during evolution?
π§«π§΅
Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria
This special issue marking the University of Bath's 60th anniversary offers an opportunity to reflect on nearly a decade of research into the evolution of gene regulatory networks (GRNs) from members...
advanced.onlinelibrary.wiley.com
January 23, 2026 at 2:22 PM
New Perspective out in Advanced Science π in collaboration with @alanrice.ie for @uniofbath.bsky.social 60th anniversary special issue.
advanced.onlinelibrary.wiley.com/doi/10.1002/...
We review nearly a decade of work asking:
how do gene regulatory networks rewire during evolution?
π§«π§΅
advanced.onlinelibrary.wiley.com/doi/10.1002/...
We review nearly a decade of work asking:
how do gene regulatory networks rewire during evolution?
π§«π§΅
Reposted by joe-wade.bsky.social
Reposted by joe-wade.bsky.social
Phase variable colony morphotypes of Clostridioides difficile elicit distinct host responses during acute infection https://www.biorxiv.org/content/10.64898/2026.01.09.698580v1
January 11, 2026 at 4:16 PM
Phase variable colony morphotypes of Clostridioides difficile elicit distinct host responses during acute infection https://www.biorxiv.org/content/10.64898/2026.01.09.698580v1
Reposted by joe-wade.bsky.social
A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation www.biorxiv.org/content/10.6...
A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation
DNA methylation is a widespread phenomenon in bacteria that can regulate gene expression, although the mechanisms underlying this epigenetic regulation are often poorly understood. In Clostridioides d...
www.biorxiv.org
January 2, 2026 at 1:59 PM
A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation www.biorxiv.org/content/10.6...
Reposted by joe-wade.bsky.social
π£New preprint with @rberntsson.bsky.socialπWe overturn the long-standing view that Gram-positive bacteria lack conjugative pili! We identify pili-forming proteins in a wide range of bacteria and show they're essential for the spread of #antibioticresistance #AMR π§΅1/6
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Pili are essential for conjugation also in many Gram-positive bacteria
Type IV secretion systems (T4SS) enable the spread of antibiotic resistance and other virulence factors. In Gram-positive bacteria, T4SSs have long been thought to lack VirB2-like proteins that form c...
www.biorxiv.org
December 30, 2025 at 6:03 PM
π£New preprint with @rberntsson.bsky.socialπWe overturn the long-standing view that Gram-positive bacteria lack conjugative pili! We identify pili-forming proteins in a wide range of bacteria and show they're essential for the spread of #antibioticresistance #AMR π§΅1/6
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by joe-wade.bsky.social
Tiffany Zarrella et al. provide new insights into the role of the bacterial second messenger cyclic di-adenosine monophosphate (c-di-AMP) in maintaining cell envelope homeostasis in Streptococcus pneumoniae.
#MicroSky #cyclic-di-AMP
onlinelibrary.wiley.com/doi/10.1111/...
#MicroSky #cyclic-di-AMP
onlinelibrary.wiley.com/doi/10.1111/...
Cyclic DiβAMP Affects Cell Membrane Integrity of Streptococcus pneumoniae
When Streptococcus pneumoniae produces low amounts of the second messenger cyclic di-AMP (c-di-AMP), they do not survive in the presence of competence-stimulating peptide (CSP), which is used for tra...
onlinelibrary.wiley.com
July 2, 2025 at 3:01 PM
Tiffany Zarrella et al. provide new insights into the role of the bacterial second messenger cyclic di-adenosine monophosphate (c-di-AMP) in maintaining cell envelope homeostasis in Streptococcus pneumoniae.
#MicroSky #cyclic-di-AMP
onlinelibrary.wiley.com/doi/10.1111/...
#MicroSky #cyclic-di-AMP
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by joe-wade.bsky.social
1/ Our new preprint is out on biorxiv on how antibiotics bind to bacterial 30S subunits, please repost. #ribosome #antibiotics #microsky #rnasky doi.org/10.64898/202...
How medically important antimicrobials bind to the 30S ribosomal subunit in a bacterial pathogen
Ribosomes translate the genetic code in mRNA to synthesize proteins in all living organisms. Decoding of mRNA occurs in the small subunit of the ribosome and is mediated by tRNA anticodons. Regions ne...
doi.org
December 26, 2025 at 3:27 AM
1/ Our new preprint is out on biorxiv on how antibiotics bind to bacterial 30S subunits, please repost. #ribosome #antibiotics #microsky #rnasky doi.org/10.64898/202...
Reposted by joe-wade.bsky.social
High-throughput transposon mutagenesis defines the essential genome of diverse phages https://www.biorxiv.org/content/10.64898/2025.12.19.695335v1
December 20, 2025 at 11:15 PM
High-throughput transposon mutagenesis defines the essential genome of diverse phages https://www.biorxiv.org/content/10.64898/2025.12.19.695335v1
Reposted by joe-wade.bsky.social
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during Ξ» infection. Phages donβt just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during Ξ» infection. Phages donβt just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda
infection and uncover a conserved phage-encoded sRNA that activates host replication
machinery. Their findings re...
www.cell.com
December 19, 2025 at 6:43 AM
Do viruses use RNA to rewire bacteria?
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during Ξ» infection. Phages donβt just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Yes!
In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during Ξ» infection. Phages donβt just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection.
#RNA #Phage
doi.org/10.1016/j.mo...
Reposted by joe-wade.bsky.social
RNAβRNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNAβmRNA pairing url: academic.oup.com/nar/article/...
RNAβRNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNAβmRNA pairing
Abstract. Most bacterial small regulatory RNAs (sRNAs) modulate gene expression by forming complementary base pairs with target messenger RNAs (mRNAs), dep
academic.oup.com
December 14, 2025 at 4:06 AM
RNAβRNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNAβmRNA pairing url: academic.oup.com/nar/article/...
Reposted by joe-wade.bsky.social
I think some folks might be happy to see this. NIGMS MIRA R35 for EI/NI has been published. PAR-26-121 files.simpler.grants.gov/opportunitie...
PAR-26-121: Maximizing Investigators' Research Award (MIRA) (R35 - Clinical Trial Optional)
files.simpler.grants.gov
December 11, 2025 at 6:48 PM
I think some folks might be happy to see this. NIGMS MIRA R35 for EI/NI has been published. PAR-26-121 files.simpler.grants.gov/opportunitie...
Lots of opportunities to collaborate with groups here doing research and diagnostics work on infectious disease topics. Feel free to reach out if youβre interested and want to learn more.
December 11, 2025 at 5:38 PM
Lots of opportunities to collaborate with groups here doing research and diagnostics work on infectious disease topics. Feel free to reach out if youβre interested and want to learn more.
Weβre hiring! Weβre looking for researchers who use AI/machine learning to study infectious disease. The position is at the University at Albany, in the Biomedical Sciences Dept, which has very close ties to the Wadsworth Center. albany.interviewexchange.com/jobofferdeta...
albany.interviewexchange.com
December 11, 2025 at 5:38 PM
Weβre hiring! Weβre looking for researchers who use AI/machine learning to study infectious disease. The position is at the University at Albany, in the Biomedical Sciences Dept, which has very close ties to the Wadsworth Center. albany.interviewexchange.com/jobofferdeta...
Reposted by joe-wade.bsky.social
Assistant Professor Biomedical Sciences AI position available. Read details and apply at:
albany.interviewexchange.com/jobofferdeta...
albany.interviewexchange.com/jobofferdeta...
albany.interviewexchange.com
December 9, 2025 at 3:40 PM
Assistant Professor Biomedical Sciences AI position available. Read details and apply at:
albany.interviewexchange.com/jobofferdeta...
albany.interviewexchange.com/jobofferdeta...
Reposted by joe-wade.bsky.social
What started out as a structure-function project for an undergraduate researcher morphed into something bigger w/ @popea.bsky.social leading the way. Check out how RhlR fine tunes its response to its autoinducer to avoid producing too much pyocyanin.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
RhlR quorum-sensing receptor ligand sensitivity regulates the differential expression of phenazine genes in Pseudomonas aeruginosa
Bacteria control individualistic and group behaviors using a form of cell-cell communication called quorum sensing. Quorum sensing relies on the production of chemical signals called autoinducers and ...
www.biorxiv.org
December 9, 2025 at 2:22 PM
What started out as a structure-function project for an undergraduate researcher morphed into something bigger w/ @popea.bsky.social leading the way. Check out how RhlR fine tunes its response to its autoinducer to avoid producing too much pyocyanin.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by joe-wade.bsky.social
It is rare as an editor to get to take on an article so uniquely in your wheelhouse. Sharing some wonderful work by Guarnaccia et al. from the Perez, Ng, and Neiditch labs. #structuralbiology of #pathogens @plos.org
dx.plos.org/10.1371/jour...
dx.plos.org/10.1371/jour...
Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition
Author summary Quorum sensing, a form of bacterial cell-cell communication, regulates diverse developmental behaviors. This study investigates CqsR, a transmembrane receptor in Vibrio cholerae, the ga...
dx.plos.org
September 8, 2025 at 5:13 PM
It is rare as an editor to get to take on an article so uniquely in your wheelhouse. Sharing some wonderful work by Guarnaccia et al. from the Perez, Ng, and Neiditch labs. #structuralbiology of #pathogens @plos.org
dx.plos.org/10.1371/jour...
dx.plos.org/10.1371/jour...
Reposted by joe-wade.bsky.social
π¨The Yap Lab at Northwestern Univ is looking to fill 2 postdoc positions in 2026 to study aspects of Staphylococcus aureus antibiotic resistance and RNA synthesis-degradation. Please contact Frances Yap at frances.yap@northwestern.edu for details. sites.northwestern.edu/yaplab/. Pls repost #Microsky
Homepage | Yap Laboratory
sites.northwestern.edu
December 1, 2025 at 4:45 PM
π¨The Yap Lab at Northwestern Univ is looking to fill 2 postdoc positions in 2026 to study aspects of Staphylococcus aureus antibiotic resistance and RNA synthesis-degradation. Please contact Frances Yap at frances.yap@northwestern.edu for details. sites.northwestern.edu/yaplab/. Pls repost #Microsky
Reposted by joe-wade.bsky.social
Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli https://www.biorxiv.org/content/10.1101/2025.11.27.690950v1
November 28, 2025 at 2:16 AM
Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli https://www.biorxiv.org/content/10.1101/2025.11.27.690950v1
Reposted by joe-wade.bsky.social
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by joe-wade.bsky.social
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
Reposted by joe-wade.bsky.social
Apply through APHL to be a summer intern at the Wadsworth Center. Both basic science research and public health opportunities available.
November 19, 2025 at 3:49 PM
Apply through APHL to be a summer intern at the Wadsworth Center. Both basic science research and public health opportunities available.