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Posts by E. Rodríguez-Robles

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

2 weeks ago 211 113 6 7
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A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n

2 months ago 500 210 10 28

Xeno amino acid alphabets form peptides with familiar secondary structure www.biorxiv.org/content/10.64898/2026.01...

2 months ago 1 1 0 0
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Feel like doing a SynBio PhD in Spain? Check this offer, many fellowships available 👉🏻 lifehub.csic.es/synbio-cofund/

2 months ago 20 21 0 0

Great new story from Sophie Helaine and Molly Sargen!

www.helainelab.com

2 months ago 35 18 0 0
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Engineering Fluoroacetate Dehalogenase by Growth‐Based Selections on Non‐Natural Organofluorides We present a high-throughput selection system to engineer fluoroacetate dehalogenases (FAcDs). By challenging E. coli populations that produce diverse FAcD libraries to grow on non-natural organofluo....

🥳🥳🥳 Our study on engineering enzymes to break C–F bonds is out in @angewandtechemie.bsky.social. Congrats to the brilliant & dedicated @suzannejansen.bsky.social for taking this step toward the remediation of #PFAS & other contaminating organofluorides!
onlinelibrary.wiley.com/doi/10.1002/...

2 months ago 9 6 0 0
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...

Fresh off the lab press! 📰 Scientists from FfAME, Tohoku Univ., and JAMSTEC report a prebiotic route to form long RNA from compounds containing 1-3 carbon, 0-4 hydrogen and 1-3 nitrogen atoms, in geological environments that occurred on early Earth ~4.3 billion years ago. 🔗 doi.org/10.1073/pnas...

4 months ago 1 1 0 0
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Apply for #EMBOSynBio! 🥼🧪

The course offers hands-on experience with cutting-edge SynBio tools, supported by lectures covering the whole engineering cycle and its convergence toward a deeper understanding of biology.

30 Jun – 6 Jul 2026
EMBL Heidelberg
s.embl.org/syn26-01-bl

4 months ago 4 5 1 1

The future is not in the training set.

4 months ago 55 13 3 1

Active learning guides automated discovery of DNA delivery via electroporation for non-model microbes www.biorxiv.org/content/10.1101/2025.11....

5 months ago 1 1 0 0
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Really cool study from Katrin Lang lab

6 months ago 0 0 0 0
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When less is more: Counterintuitive stoichiometriesand cellular abundances are essential for ABC transporters’ function Unexpected stoichiometries in E. coli ABC importers reveal design principles linking protein abundance to transporter function.

When less is more: Counterintuitive stoichiometriesand cellular abundances are essential for ABC transporters’ function www.science.org/doi/10.1126/...

10 months ago 0 2 0 0

Directed evolution of a plant Rubisco chaperone with altered client recognition | PNAS www.pnas.org/doi/abs/10.1...

7 months ago 0 0 0 0
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Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨New paper out in @natcomms.nature.com!!

Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬

👉 www.nature.com/articles/s41...

9 months ago 185 85 4 4
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De-novo promoters emerge more readily from random DNA than from genomic DNA Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab!

"De-novo promoters emerge more readily from random DNA than from genomic DNA"

This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

7 months ago 170 59 4 1
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Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates Uncurbed exponential proliferation might not always be required for genetically modified microorganisms, and might even cause unpredictable liabilities in their behavior and impact. We therefore const...

E. Coli with linear growth 🦠🤯 #micdosky "linear proliferation for a finite number of generations" where only one daughter cell continues to divide, with split cyaA making cAMP only in one daughter cell. www.biorxiv.org/content/10.1...

7 months ago 15 7 0 0
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An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....

#NatMicroPicks

Synthetic evolution overdrive 🦠🔧🚅

A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.

#SynBio #MicroSky

www.science.org/doi/10.1126/...

8 months ago 28 11 0 2
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A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research

A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon
research.pasteur.fr/en/job/a-two...

8 months ago 42 48 0 0
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A 2 yr postdoc position at the Bacterial
Genome Plasticity Unit of the Institut Pasteur (Paris) led by @amazeld.bsky.social in collaboration with Pierre-Alexandre Kaminski, funded by the French National Research Agency 👇

8 months ago 11 16 1 0
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Escherichia coli ribosomes support translation of (R) and (S) β2-hydroxyacids in vitro: a structural and biochemical study The ribosomal incorporation of backbone-modified amino acid analogs into peptides and proteins enables the programmed synthesis of sequence-defined biopolymers with tunable properties. However, the su...

Check out our latest preprint describing two structures of ribosomes complexed with the two enantiomers of a β2-hydroxy acid. Our structures show that despite stereochemical differences, both are ultimately well positioned for bond formation within the ribosome!
chemrxiv.org/engage/chemr...

11 months ago 6 4 0 0
THE SECRETARY OF EDUCATION
WASHINGTON, DC 20202
May 5, 2025
Dr. Alan Garber
Office of the President
Harvard University
Massachusetts Hall
Cambridge, MA 02138
Dr. Garber,
The Federal Government has a sacred responsibility to be a wise and important steward of American taxpayer dollars. Harvard University, despite amassing a largely tax-free $53.2 billion dollar endowment (larger than the GDP of 100 countries), receives billions of dollars of taxpayer largess each year. Receiving such taxpayer funds is a privilege, not a right. Yet instead of using these funds to advance the education of its students, Harvard is engaging in a systemic pattern of violating federal law. Where do many of these "students" come from, who are they, how do they get into Harvard, or even into our country—and why is there so much HATE? These are questions that must be answered, among many more, but the biggest question of all is, why will Harvard not give straightforward answers to the American public?
Harvard University has made a mockery of this country's higher education system. It has invited foreign students, who engage in violent behavior and show contempt for the United States of America, to its campus. In every way, Harvard has failed to abide by its legal obligations, its ethical and fiduciary duties, its transparency responsibilities, and any semblance of academic rigor. It had scrapped standardized testing requirements and a normalized grading system. This year Harvard was forced to adopt an embarrassing "remedial math" program for undergraduates.
Why is it, we ask, that Harvard has to teach simple and basic mathematics, when it is supposedly so hard to get into this "acclaimed university"? Who is getting in under such a low standard when others, with fabulous grades and a great understanding of the highest levels of mathematics, are being rejected?
Harvard has even been embroiled in humiliating plagiarism scandals, exposed clearly and plainly in the media, with respect to your then…

THE SECRETARY OF EDUCATION WASHINGTON, DC 20202 May 5, 2025 Dr. Alan Garber Office of the President Harvard University Massachusetts Hall Cambridge, MA 02138 Dr. Garber, The Federal Government has a sacred responsibility to be a wise and important steward of American taxpayer dollars. Harvard University, despite amassing a largely tax-free $53.2 billion dollar endowment (larger than the GDP of 100 countries), receives billions of dollars of taxpayer largess each year. Receiving such taxpayer funds is a privilege, not a right. Yet instead of using these funds to advance the education of its students, Harvard is engaging in a systemic pattern of violating federal law. Where do many of these "students" come from, who are they, how do they get into Harvard, or even into our country—and why is there so much HATE? These are questions that must be answered, among many more, but the biggest question of all is, why will Harvard not give straightforward answers to the American public? Harvard University has made a mockery of this country's higher education system. It has invited foreign students, who engage in violent behavior and show contempt for the United States of America, to its campus. In every way, Harvard has failed to abide by its legal obligations, its ethical and fiduciary duties, its transparency responsibilities, and any semblance of academic rigor. It had scrapped standardized testing requirements and a normalized grading system. This year Harvard was forced to adopt an embarrassing "remedial math" program for undergraduates. Why is it, we ask, that Harvard has to teach simple and basic mathematics, when it is supposedly so hard to get into this "acclaimed university"? Who is getting in under such a low standard when others, with fabulous grades and a great understanding of the highest levels of mathematics, are being rejected? Harvard has even been embroiled in humiliating plagiarism scandals, exposed clearly and plainly in the media, with respect to your then…

running the institution in a totally chaotic way. Harvard alumnus and highly successful hedge fund manager Bill Ackman noted that, under her leadership, Harvard has become "a political advocacy organization for one party."
Ackman has called for the resignation of Pritzker, concluding that the "[t)he mismanagement here is Penny Pritzker" and noting that any serious corporation would have removed her after a litany of recent failings and the fact that, incredibly, "Harvard is not in a good financial position." According to Ackman, one of the world's foremost finance experts, Harvard's so-called S53 billion endowment is "massively overstated as far as what it's really worth," and Harvard has irresponsibly taken out $8 billion in debt.
If this is true, it is concerning evidence of Harvard's disastrous mismanagement, indicating an urgent need for massive reform-not continued taxpayer investment. If Harvard prefers not to change, then Harvard should have no problem using its overflowing endowment to fund its bloated bureaucracy.
At its best, a university should fulfill the highest ideals of our Nation, and enlighten the thousands of hopeful students who walk through its magnificent gates. But Harvard has betrayed this ideal.
Perhaps most alarmingly, Harvard has failed to abide by the United States Supreme Court's ruling demanding that it end its racial preferencing, and continues to engage in ugly racism in its undergraduate and graduate schools, and even within the Harvard Law Review itself. Our universities should be bastions of merit that reward and celebrate excellence and achievement.
They should not be incubators of discrimination that encourage resentment and instill grievance and racism into our wonderful young Americans.
The above concerns are only a fraction of the long list of Harvard's consistent violations of its own legal duties. Given these and other concerning allegations, this letter is to inform you that Harvard should no longer seek GRANTS from the fede…

running the institution in a totally chaotic way. Harvard alumnus and highly successful hedge fund manager Bill Ackman noted that, under her leadership, Harvard has become "a political advocacy organization for one party." Ackman has called for the resignation of Pritzker, concluding that the "[t)he mismanagement here is Penny Pritzker" and noting that any serious corporation would have removed her after a litany of recent failings and the fact that, incredibly, "Harvard is not in a good financial position." According to Ackman, one of the world's foremost finance experts, Harvard's so-called S53 billion endowment is "massively overstated as far as what it's really worth," and Harvard has irresponsibly taken out $8 billion in debt. If this is true, it is concerning evidence of Harvard's disastrous mismanagement, indicating an urgent need for massive reform-not continued taxpayer investment. If Harvard prefers not to change, then Harvard should have no problem using its overflowing endowment to fund its bloated bureaucracy. At its best, a university should fulfill the highest ideals of our Nation, and enlighten the thousands of hopeful students who walk through its magnificent gates. But Harvard has betrayed this ideal. Perhaps most alarmingly, Harvard has failed to abide by the United States Supreme Court's ruling demanding that it end its racial preferencing, and continues to engage in ugly racism in its undergraduate and graduate schools, and even within the Harvard Law Review itself. Our universities should be bastions of merit that reward and celebrate excellence and achievement. They should not be incubators of discrimination that encourage resentment and instill grievance and racism into our wonderful young Americans. The above concerns are only a fraction of the long list of Harvard's consistent violations of its own legal duties. Given these and other concerning allegations, this letter is to inform you that Harvard should no longer seek GRANTS from the fede…

Federal Agencies. The Administration's priorities have not changed and today's letter marks the end of new grants for the University.
These requests will advance the best interests of Harvard University, so it can reclaim its status as a respected educational institution for the future leaders of America. Thank you for your attention to this matter!
Sincerely,
Linda E. McMahon
Secretary of Education

Federal Agencies. The Administration's priorities have not changed and today's letter marks the end of new grants for the University. These requests will advance the best interests of Harvard University, so it can reclaim its status as a respected educational institution for the future leaders of America. Thank you for your attention to this matter! Sincerely, Linda E. McMahon Secretary of Education

🚨🚨 Deranged letter from Education Secretary Linda McMahon to Harvard’s president, cutting off federal funding for any new grants.

Worth reading in full. It is NUTS.

11 months ago 4580 1553 690 692
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Hydrogenase-driven ATP synthesis from air All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The universally conserved F1Fo-ATP synthase regenerates ATP...

Energy from air? No problem! In our new preprint, we reconstitute the machinery that allows microbes to endure starvation. By using the trace amounts of hydrogen in air alone, they produce plenty of chemical energy (2 ATP) to get by. The only byproduct? Water. www.biorxiv.org/content/10.1...

1 year ago 85 29 5 5
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Sustainable regeneration of 20 aminoacyl-tRNA synthetases in a reconstituted system toward self-synthesizing artificial systems An in vitro system is capable of sustainably regenerating 20 aminoacyl-tRNA synthetases toward artificial cells.

Sustainable regeneration of 20 aminoacyl-tRNA synthetases in a reconstituted system toward self-synthesizing artificial systems

www.science.org/doi/10.1126/...

1 year ago 24 9 0 0
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Engineering a genomically recoded organism with one stop codon - Nature Ochre, a strain of Escherichia coli engineered to have a single stop codon, enables reassignment of four codons for non-degenerate functions, such as incorporation of non-standard amino acids into pro...

Amazing work from Farren Isaacs team at Yale - reducing E.coli's genetic code down to only using a single stop codon. A 62 codon GRO with lots of potential for applications. www.nature.com/articles/s41...

1 year ago 91 39 0 3

Hijacking a bacterial membrane transporter for efficient genetic code expansion www.biorxiv.org/content/10.1101/2025.03....

1 year ago 3 1 0 0
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E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n
www.biorxiv.org/content/10.1...

1 year ago 135 67 2 5
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Simultaneous in vitro expression of minimal 21 transfer RNAs by tRNA array method www.biorxiv.org/content/10.1101/2025.02....

1 year ago 6 4 0 1
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CRISPR 101: Cytosine and Adenine Base Editors An overview of cytosine and adenine base transition editors, which make precise changes in DNA bases without causing double-strand breaks.

Switching an C to a T in your DNA? Sounds like you need a cytosine base editor! Learn about them in our updated CRISPR 101 blog post "Cytosine and Adenine Base Editors"!

blog.addgene.org/sin...

1 year ago 2 1 0 0
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A Direct Hit, by @holdenthorp.bsky.social @science.org
www.science.org/doi/full/10....
"This is a moment to unite."

1 year ago 900 375 24 18
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Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria We report the construction of an alternative protein priming system to recode genetic translation in Escherichia coli by designing, through trial and error, a chimeric initiator whose sequence identit...

Cys-tRNAj as a Second Translation Initiator for Priming Proteins with Cysteine in Bacteria in ACS Omega!

1 year ago 1 0 0 0