@FdlC61

Plasmid Biology

 Santander, Spain
castillo.dicom.unican.es/Intergenomics/index.html
Joined February 2015
  • Tweets82
  • Following299
  • Followers436
3Media
Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model biorxiv.org/content/10.64898… Awesome tool for interrogating plasmids and other MGEs. There is so much we ignore about non-coding RNAs in plasmid biology!

Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model

Prokaryotic genomes encode a vast repertoire of noncoding elements such as ribozymes, riboswitches, and CRISPR RNAs. The sequence-level diversity of these intergenic elements precludes alignment-ba...

biorxiv.org
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Olivier Borkowski@O_BorkowskiOct 22
biorxiv.org/content/10.64898…

Design of synthetic activators for programmable gene expression

Transcription factors control gene expression by recruiting transcriptional coactivators through intrinsically disordered transcriptional activation domains (TADs), whose weak and promiscuous...

biorxiv.org
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Microbiology Society@MicrobioSocOct 21
Applications of transposon-insertion sequencing for understanding bacterial physiology. Published Open Access and fee-free in MGen using a Publish and Read agreement: doi.org/10.1099/mgen.0.00179… #MGen #PublishAndRead
fig 1. Applications of Tn-seq. Overview of the transposon (Tn) library construction process, depicting one Tn per cell integrating into the chromosome at random. Following sequencing of Tn-genomic DNA junctions, the Tn insertion site is mapped to a reference genome and these frequencies are counted, producing a graph of Tn insertion frequency across the genome for each nt position. These graphs represent a pool of mutants and a stretch of no insertions is indicative of an essential gene or domain. The library can be grown under different conditions, and changes in mutant frequency, inferred from changes in Tn–gDNA sequencing data, are indicative of positive or negative fitness effects. Abbreviations: AbR, antibiotic resistance selection marker; Ess., essential; GOF, gain of function; IR, inverted repeat; LOF, loss of function; NE, non-essential.

ALT fig 1. Applications of Tn-seq. Overview of the transposon (Tn) library construction process, depicting one Tn per cell integrating into the chromosome at random. Following sequencing of Tn-genomic DNA junctions, the Tn insertion site is mapped to a reference genome and these frequencies are counted, producing a graph of Tn insertion frequency across the genome for each nt position. These graphs represent a pool of mutants and a stretch of no insertions is indicative of an essential gene or domain. The library can be grown under different conditions, and changes in mutant frequency, inferred from changes in Tn–gDNA sequencing data, are indicative of positive or negative fitness effects. Abbreviations: AbR, antibiotic resistance selection marker; Ess., essential; GOF, gain of function; IR, inverted repeat; LOF, loss of function; NE, non-essential.

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Tominaga K. (tomiken)@pacyc1841Oct 20
Identification and genetic characterization of megabase-scale plasmids of Enterobacteriaceae | Nature Communications nature.com/articles/s41467-0…

Identification and genetic characterization of megabase-scale plasmids of Enterobacteriaceae

Nature Communications - Here, the authors report the identification and characterization of large, up to 1.58 million base-pair-long plasmids in gut microbiomes worldwide, showing that while most...

nature.com
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That was seven years ago. This time, the world is in more trouble, including Spain, but the wishes remain the same.
Fernando de la Cruz@FdlC6112 Oct 2019
Today we celebrate the national day in Spain, also celebrated in other countries, commemorating Columbus arrival in America. I am proud of Spain. But I wish we invest more in Science and Technology. It will be good for our country and for the world. I´ll do my best to help!
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Plasmid copy number control offers a versatile tool in synthetic biology applications: Trends in Biotechnology cell.com/trends/biotechnolog…

Plasmid copy number control offers a versatile tool in synthetic biology applications

Plasmids are central tools in biotechnology, yet their copy number is often treated as fixed. This study shows that plasmid copy number can be dynamically controlled to tune gene expression, growth,...

cell.com
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Three examples to backup my post below?
Itai Yanai
@ItaiYanaiOct 10
1. CRISPR came from basic research on bacteria. 2. Optogenetics started with a discovery in algae. 3. The GFP protein comes from jellyfish. The biggest breakthroughs all trace to scientists follow their curiosity. This is one huge reason why we must keep funding basic research!
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I completely agree with Salis´s thread. We need "alive" labs to run the many side experiments that occur to individual scientists when they examine the results of a previous experiment. In his words, automation will mean "the death knell of biotech innovation".
Howard Salis@hsalisOct 11
We all want more measurements with faster turnaround, but there is a drawback to automating labs that is not often discussed: it will stymie innovation. Here’s why: … /1
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Very interesting paper!! After a plasmid expands in a community by antibiotic selection we need effective countermeasures to eliminate it from the infected populations. A variety of such countermeasures exists in the bacterial arsenal. I suggest conjugation inhibitors.
Lingchong You@lingchongyouOct 8
1/ Even bacterial communities can get caught in a bad romance they just can't get over. A brief encounter with antibiotics can leave a lasting ecological memory of resistance plasmids persisting for weeks after the drug is gone. @DukeBiodesign @DukeUBME nature.com/articles/s41467-0…

Ecological memory of prolonged plasmid persistence after transient antibiotic exposure

Nature Communications - Zhou, Weiss and colleagues show that a brief antibiotic pulse can prolong plasmid persistence by removing plasmid-free competitors, creating an ecological memory that may...

nature.com
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Alexander Harms@AHarms485Sep 25
The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/3
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Tominaga K. (tomiken)@pacyc1841Sep 26
Entry exclusion enables selective conjugative DNA delivery in synthetic bacterial communities. | bioRxiv biorxiv.org/content/10.64898…

Entry exclusion enables selective conjugative DNA delivery in synthetic bacterial communities

Selective DNA delivery to specific members of assembled bacterial communities remains challenging. Bacterial conjugation enables efficient DNA delivery, but transfer to non-target recipients limits...

biorxiv.org
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Olivier Borkowski@O_BorkowskiSep 23
Engineering Persistent and Rewritable Genetic Memory in Bacteria through Multiscale Plasmid Competition doi.org/10.64898/2026.09.18.…
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Nature Microbiology@NatureMicrobiolSep 17
In vivo CRISPRi screens reveal Escherichia coli functional adaptations in the mouse gut dlvr.it/TVWj9t #MicroSky

In vivo CRISPRi screens reveal Escherichia coli functional adaptations in the mouse gut

Nature Microbiology - In vivo silencing of genes in E. coli strains using CRISPRi reveals specific genetic factors and metabolic adaptations that influence colonization in the mouse gut under...

nature.com
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Fernando de la Cruz retweeted
Tominaga K. (tomiken)@pacyc1841Sep 4
High-throughput recovery of integron cassettes for gene discovery screens | Nature Microbiology nature.com/articles/s41564-0…

High-throughput recovery of integron cassettes for gene discovery screens

Nature Microbiology - Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria...

nature.com
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Informational architecture organizes plasmid genomes Yuxuan Zhong, Teng Wang biorxiv.org/content/10.64898… Results indicate that plasmids propagate the infrastructure required to execute their adaptive functions, making them more efficient upon HGT.
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A nice tool for non-professional bioinformaticians and geneticists
antisense.@razoralign5 Jan 2023
gget: Efficient querying of genomic reference databases academic.oup.com/bioinformat…
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Perfect orthogonality is a chimerical dream of synthetic biology and, more specifically, in signal transduction. Accepting unavoidable signal-signal interactions as a basis for interpretation of multiplexed signals seems a clever approach.
Lingchong You@lingchongyouAug 25
1/ Let’s face it: we synthetic biologists are control freaks. We want every component to do exactly what we intend and nothing else. Our new paper asks what happens if we stop fighting biological “messiness”. @DukeBiodesign @DukeUBME nature.com/articles/s41467-0…

Engineering microbial consortia for distributed signal processing

Nature Communications - Multiplexed biosensing is often limited by crosstalk between sensors. Here, authors distribute sensing across microbial communities and use timer-resolved modelling and...

nature.com
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You et al. demonstrate that multiplexed quantitative inference works. My hope will be that it may lead to more efficient programming of bacterial interventions on diverse microbiomes.
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This is just another publication reporting data that was available, and conclusions stablished, MANY years ago, from the times of Nordstrom copy-number mutants. It is disheartening, specially since it is happening more and more often.
Tominaga K. (tomiken)@pacyc1841Aug 21
Distinct plasmid- and host-encoded mechanisms drive small plasmid copy number-mediated heteroresistance in Escherichia coli | bioRxiv biorxiv.org/content/10.64898…

Distinct plasmid- and host-encoded mechanisms drive small plasmid copy number-mediated heteroresi...

Antibiotic heteroresistance, the presence of a rare resistant subpopulation within an otherwise susceptible bacterial population, poses a significant clinical challenge. Understanding its genetic...

biorxiv.org
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Fernando de la Cruz retweeted
Niko McCarty.
@NikoMcCartyAug 17
Circuit boards made from living bacteria. Strains are engineered to act as N- or P-type transistors. Other strains pass around the signals, which are molecules instead of electrons. These strains are then printed on a plate, using a liquid handler, to build any logic you want.
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