Environmental Microbiol meets Synthetic Biology in Southern Europe (opinions/pontifications are mine only). Long live P. putida 💪!
#SinCienciaNoHayFuturo
When you do not know what to do in a Microbiology Lab:
1970s 👉🏻 make a growth curve
1980s 👉🏻 make a mutant
1990s 👉🏻 sequence the gene
2000s 👉🏻 make omics
2010s 👉🏻 sequence everything
2020s 👉🏻 AI everything
What will be next 🤔?
Los Biólogos Moleculares del
@CSIC
y universidades llevamos *3 semanas* insistiendo que los PCR son el camino y nos hemos ofrecido (somos unos miles) con nuestros centros de investigación para montar unidades de diagnóstico ¿cúando/dónde empezamos?
Bravo Mariano Barbacid diciendo lo que muchos (todos?) los Biólogos Moleculares pensamos en estos momentos! Ojalá a él le hagan más caso que a los demás!
Vaya pedazo de líder, no los que tenemos por aquí! La Primera Ministra de Nueva Zelanda se baja el sueldo (ella y su Gobierno) un 20% en solidaridad con los afectados por la crisis COVID ¿Os animáis
@sanchezcastejon
y Ptes autonómicos?
Another blow to the Central Dogma? Same DNA sequence can originate very different proteins if the RNA is later recoded. This is unlike splicing, quite awesome. I doubt that only octopuses & similar make it, looks like a cool trick for transient adaptation
Our dear friend and colleague Joseph (Pepe) Casadesús passed away earlier today. He was a legend of Spanish microbiology, an amazing mentor of many young researchers and an inspiration for the whole community. He will be sorely missed RIP.
The advantage of having a PM with a scientific background: she understands what she talks about and can effectively communicate it. I wish we had more science-trained politicians in my country for dealing with COVID19 and way less politologists & philosophers!
Proud of joining the March for Science 2019 this morning in Madrid led by young researchers. There is no future without Science! Evidence, not politics! Science, not silence 💪🏻!
El procedimiento para compra de ordenadores en el
@csic
mediante lotes centralizados en plan soviético y otras restricciones absurdas es absolutamente grotesco. No se si viene del CSIC o de más arriba, pero esta situación que afecta directamente al trabajo es deplorable ☹️
Biology is programmable—but not with the same principles that we apply to computers. Hints: 1. The central dogma makes mistakes at every step, 2. Parameters are context & environment-dependent, 3. Biological hardware is made of soft materials, 4. Cells grow. Think differently 🤔!
I must admit that I feel a bit unsettled by bioinformaticians & computer scientists (maybe by physicists as well?) jumping without a blink from one biological question to another—in contrast with researchers who spend their whole life trying to understand just one thing … 🤔
Es una irrespondabilidad crear la expectativa de una vacuna a final de año, incluso citando fechas y núm de dosis cuando aún no hay datos sobre el grado de protección de los distintos prototipos en marcha. Ojalá me equivoque 🙏🏻! Mientras tantos, los casos en Madrid desbocados ☹️
🔴 Fernando Simón: "Para vacunar a todo el mundo no va a haber vacunas inmediatamente pero sí que hay altas probabilidades de que a final de año empiece a haber más cantidad de vacuna para que se empiece a vacunar".
➡
Ahora en positivo. Sugerencias basadas en la experiencia (y espero que constructivas) para los que buscan entrar en un Labo y tienen que dirigirse al jefe/a del grupo para explorar la posibilidad. Buena suerte!
Woow! The
@institutpasteur
in Paris is looking for a new Director. One of the most important and influential positions one biologist (in particular, one microbiologist) can dream of. Speaking French desirable, but not essential 👇
During an ongoing move I found this gem in an old drawer at home: The original DNaseI & OH* footprint of the Fur protein of E. coli on the aerobactin promoter, which 1st identified the sequence of *iron boxes* in prok genomes. Done in UC Berkeley with technology of the mid-80s 😱
I am taking stock of examples where natural evolution and human design reach the same solution to a given challenge. This one will surely be in the top group: Functioning ‘mechanical gears’ seen in nature for the first time 😱!
It is awesome how the basic design of the Gilson pipettes has remained identical for ~ 40 yrs. They seem to be the only pieces of equipment that a time traveller could easily recognize in Labs distant by various decades. Any attempt at further improvement has failed miserably 💪🏻
Es grotesco que el
@csic
, que tiene a los mayores especialistas españoles en qRT-PCR, esté subcontratando empresas privadas para hacer diagnósticos COVID a su propia gente. Ha habido tiempo desde Marzo para solucionar las acreditaciones, protocolos etc ¿no?
#encasadeherrero
De verdad que no lo entiendo—tampoco lo entendí en Marzo. Purificar Taq polimerasa es súperfacil. Cualquier estudiante de Biol Mol saber preparar buffers. Los primers PCR llegan de un día a otro. Hay miles de máquinas y de gente. Dónde está el problema?
The best lectures for me are not those where the speaker overwhelms the audience with an avalanche of results & high IF pubs. Instead I like those in which the speaker tells his/her story to a level that can be fully understood & the audience is encouraged to give useful feedback
Querido
@sanidadgob
¿podríais decidir de una **** vez qué vais a hacer con las segundas dosis para los millones que han recibido la vacuna AZ? Es incomprensible que tras semanas y abundantes datos estemos así ... ☹️
It is often frustrating to see academic positions advertised publicly & encouraging applications just for the sake of fulfilling a legal requirement while in reality the job is already designed to be filled by an specific individual ☹️
I wrote yesterday 5 emails to 5 diff Labs around the World kindly requesting published strains that would be useful for our projects. All 5 PIs—some of whom I had never met before—answered in no time that they would send the bugs immediately. This is the way science should work!
Bonnie Bassler & Pete Greenberg receiving today the Prize Princess of Asturias for Scientific Research—the top Spanish award in this domain—for their pioneering work on bacterial quorum sensing. 1st time Mol Micro makes it to this public & well publicized recognition in Spain 👏!
For two years in a row the Nobel for Chemistry has gone to Biology (in fact, to Microbiology), not to Chemistry proper. Does this mean that Biology is the frontier of Chemistry these days? Is Biology just programmable, information-capturing Chemistry 🤔? Happy to be a chemist 💪🏻!
Denmark is packed with Pseudomonas aficionados! No wonder a Conference on this amazing bacterial genus had to be held sooner or later in Copenhagen … and it will finally happen in 2024! Chaired by the one and only
@PabloINik
👏
Programming surface-displayed nanobodies & T6SS for engineering a bacterial *kiss of death* to get rid of undesirable folks in the microbiome. An amazing collaboration with Joseph Mougous stemming from his sabbatical in our Lab of
@CNB_CSIC
Young, well-trained researchers in Madrid downtown in their way to the Spanish Parliament for demanding a significant (albeit still comparatively modest) increase in Reseach funding (1.2 ➡️2.0 % GNP)
#MarchaporlaCiencia
#EnMarcha190
Woow! The MPI for Terrestrial Microbiology & Marburg Uni offer 3 independent research group leader positions in the *general* area of Microbiology. Great opportunity for those who wish to start their own career in a key Bio hub in Europe
After 15 yr of amazing technological developments, the top Microb Biotech challenge cannot be other than 1st mitigating & then reverting climate change through a partnership with the global env microbiome & the power of Synth Biol. Some thoughts on this 👇
Ron Milo
@WeizmannScience
did it again 👇 Autotrophic growth of E. coli on CO2 as sole C source. True, with a little help of formate to generate reductive currency, but still an awesome breakthrough 👏
This Perspective in
@PLOSBiology
stems from a Twitter discussion in Oct 2023 on whether beyond a given level of complexity, Biology can be understood mechanistically—or we'd better focus on ML-based identification of patterns & setting of probabilities 😱
Everything you wished to know about .... CRISPR Tools To Control Gene Expression in Bacteria ... by someone who knows what he is talking
@dbikard
👇
It is in fact regrettable that only 1st & last author positions are considered for appointments, grants etc. This state of affairs discourages collaborations, deter folks from working with others & create lifelong enemities. I am glad that this has *never* been an issue in my Lab
The constant changes of names in bacterial families, genera & species not only generate an enormous confusion (in particular re past literature) but also irritates many microbiologists & cause a considerable loss of reputation to the whole field of Taxonomy ☹️
This is remarkable (and probably a pain in the *** also): you kill a gene with CRISPR but the encoded product still manages to get expressed. The phenomenon is tactfully described as *biological plasticity* 👇
This is super-interesting! Non-conjugative/non-mobile plasmids can pass from one host to another as a stowaway cargo in a phage capside 😱! One selfish element parasiting another👇
New paper out! Superspread of antimicrobial resistance genes through plasmid-phage cooperation.
Multicopy Plasmid Transduction.
Free full article:
All explained in this Figure 👇
Un secreto a voces: los microorganismos marinos (no los bosques) son los mayores captadores de CO2 y emisores de O2. De hecho, son (casi) nuestros únicos aliados para combatir el
#CambioClim
ático a escala global (ya lo hicieron varias veces en el pasado) 👇
El pulmón de la Tierra no es el Amazonas, ¡es el océano! Más del 50% del oxígeno se produce en el océano, a través de la fotosíntesis a través de millones de algas miscroscópicas (fitoplancton) #ÓrbitaLaikaMares
I am puzzled that despite availability of dozens of tightly regulated promoters inducible by cheap & innocuous effectors, so many of the SynBio folk still adore lac-based promoters and IPTG in their experiments, even for large-scale production 🤷
First updated Lab picture after a long confinement with a total lack of social life and many changes in between. Autumn in the surroundings of the
@CNB_CSIC
at the
@UAM_Madrid
is beautiful, isn't it 😍?
Freaking out 😱! RNA vaccines containing N1-methylpseudouridine elicit immune responses in vivo not only to the encoded protein(s) but also to products of frequent mistranslation caused eg by frameshifting (thanx Antoine Danchin for flagging this!)
Querido
@CSIC
, por favor terminad de una vez por todas el contrato de exclusividad con
@halconviajes
. Ineficientes, + caros, no hay con quien hablar al otro lado, pésima atención al solicitante ¿Quién se beneficia de todo esto? Ciertamente NO los investigadores o el personal CSIC
Every paper on HGT starts wth a dramatic statement on how horrible the phenomenon is 'cause of spreading of antibiotic resistances. But HGT is in fact a key driver of adaptation to changing environments & we could domesticate it for our own sake eg for large-scale bioremediation
Mariano Esteban, Premio Castilla y León de Investigación Nuestro Director
@CNB_CSIC
durante muchos años ha vuelto al foco público por la vacuna COVID pero esto es poco comparado con su lucha incesante por la Biotecnología española dentro y fuera del país
Hmm … it seems that bioengineering is not piece of cake 😅: Trace impurities in sodium phosphate influences the physiological activity of E. coli in M9.
¿Porqué el
@csic
(y creo que toda la Administracion Pública) nos obliga a contratar viajes y hoteles con Halcon Viajes? ¿Quién se beneficia de esto? Ciertamente, no los investigadores: más burocracia, más tiempo perdido y ningún ahorro que veamos ... ☹️
June 10 is the National Day of Portugal to commemorate the death of their great poet Luís de Camões. No celebration of battles, conquests or independence wars—perhaps the only country not to do so. But honouring a poet. Fraternal hugs to all my portuguese friends and colleagues!
I found out that word SEVA in sanskrit (सेवा) & ensuing Hindu traditions means *selfless service to the others*. What a fortunate verbatim coincidence with the name of the
@SEVAplasmids
plaform that freely distributes vectors to the SynBio & Microbial Biotech communities 😀!
What SynBio could do for the environment & how large-scale release of remediation agents could look like I have been working on this review for quite a while, finally here it is! Thanks many friends & colleagues (Twitter included) for countless discussions
Woow! I had missed this one: Rational microbiome engineering/fortification is closer and closer to become a therapeutic tool way beyond mere fecal transplantation. Super nice contribution by van del Lelie et al
Why P. putida does so well under oxidative stress? It took time & an international team to figure it out but here it goes one key explanation Important contribution to PP Biology & Metabol by
@PabloINik
Tobi Fuhrer, Uwe Sauer
@MaxChavarriaV
&
@Alberto_SPJ
My own minimalist decalogue for writing a reasonably readable paper (mostly for non-native English speakers in the Lab). I wonder whether asking the main writer a 1€ penalty every time I detect one of these faults in a manuscript draft could improve things ... 😉
Why virtually all bacterial proteins are multimeric? Is it because it facilitates regulation? Is it essential for catalysis? Is it possible to create monomeric versions of naturally-occurring multimeric enzymes that keep full activity? Any systematic study on this 🤔?
An urgent call for action to increase microbiology literacy at all levels, from kids to global decision makers. A most important manifesto by international microbiologists led by
@KennethTimmis
The COVID mess in Madrid is taking a toll on the Lab’s morale—let alone on the work proper. Two coworkers currently quarantined. Others working <50%. Myself 100% teleworking. No new recruits for >6 m. New projects at a standstill. All of us furious with incompetent politicians 🤬
Woow! This is really something 👉🏻 A genomic catalog of Earth’s microbiomes. I see a bunch of great friends & colleagues in the Authorship, big congrats 👏
Hmm ...
@duarteoceans
shows that some typical plastics (eg PET) could in fact be massively degraded by marine bacteria, after all . That this was indeed happening was anticipated time ago by
@ricard_sole
but few believed him!
Estoy atónito e indignado por los muchos videos y declaraciones de pseudoexpertos en contra de las vacunas que circulan por Whatsapp y RRSS. Siembran dudas en familia y amigos. Maldad, ignorancia o una mezcla de las dos. ¿A quién beneficia? Incomprensible ☹️
That bacteria lack intracytoplasmic compartments is not because they are simple: just the contrary! They have evolved charge-driven macromolecular condensation for creating specialized domains & physical structures
After long-time co-existence in the Labs (& beyond, I guess 🤔), Pseudomonas has recently learnt how to eat the synthetic & dearmost reagent Tris! Fellow Mol Biologists: keep an eye on your Tris-based buffer bottles! Is there anything this bug cannot do?
There was a time when research projects were not written with the business-sounding jargon of WPs, PMs, tasks, milestones, deliverables, GANTT charts & Venn diagrams. Instead, the focus was on the ideas & the competence of the applicant to carry them out. Only
@embo
has resisted!
Interesting! 20% proteins contain errors. Phenotypic diversity of single cells is thus far superior than genetic diversity. New advantageous enzymes & reactions could be ‘invented’ and running even if not fixed in the genome. Evolutionary consequences 🤔?
Woow! When we thought we knew everything about CRP & catabolite repression, it turns out that a 15–amino acid (small!) protein regulates the most famous activator of E. coli 👇
A veritable roadmap for merging Syn Biology, Network Science & Ecological Theory for the sake of tackling climate change Notice the concept of *engineering microbial-based hypercycles* Congrats
@ricard_sole
& the amazing *Earth Terraforming* team he leads
La única iniciativa de abajo arriba que conozco en
@madrid
y que ha funcionado (o que ha sido escuchada por quien puede/debe hacerlo) ha sido la de la
@unicomplutense
promovida por
@1000genes
y
@birloque
Gran aplauso para los implicados 👏
Lamentable! La paranoia sobre el contacto físico empieza a ser cansina. Intercambiar bacterias besando, abrazando, dando la mano es necesario y deseable. La Tierra es un planeta microbiano y nosotros somos 50% bacterias: hay que celebrarlo, no evitarlo
After years of drought, the
@csic
offers 140 new permanent positions in a variety of centers, topics & profiles. Text of the Call (in Spanish): A few of them are on Microbiomes, Syst/Synth Biology, Plant-Microbe interaction & other Microb-related topics
Why we like Pseudomonas putida KT2440 so much 😍 . Story told with
@PabloINik
& Danilo Pérez on how a modest soil bacterium has become a biotechnological star 😱
Plasmids & MGEs are most often criminalized in the microbiol literature as culprits of AMR spreading. Quite true. However they are also the main vehicles for propagation of beneficial activities eg new catabolic activities for degradation of env pollutants
Glad to share the brand new Lab logo developed with the creative drive of our friends & colleagues of
@Scienseed
. I believe it captures everything we are passionate about: P. putida, SynBio, genetic circuits, environment, evolution, DNA, biocatalysis, sustainability ... 👇
One more year the
@SEVAplasmids
team (Sofía Fraile, Esteban Martínez & yours truly 😅) holds together for distributing standardized plasmid & transposon vectors to the SynBio community & other Mol Microbiologists & Biotechnologists … for free! No MTAs and no questions asked 💪🏻!
At last, the 4.0 update of the
@SEVAplasmids
database & repository is out 🎉 🥳 with a bunch of novelties & useful utilities for making life easier to users-to-be. Thanks all co-authors & all those who have contributed to the standard over the years!
This may look insane to outsiders but … few things are as rewarding to Mol Biologists (and other exotic species 😅) as going to the Lab in the morning and finding that a complex cloning set up the day before … worked 🎉 🎈 🎊!
MoClo really is amazing. 18 part ligation. Two colonies picked at random. Both correct. Empty backbone neg control near rightmost ladder. If I did that cloning in series, at two parts per week, that would be NINE WEEKS of work. Sequencing time!
👏👏👏 Margarita Salas, ganadora por partida doble de los Premios al Inventor Europeo 2019 💪🏻 No hay nada más práctico que una buena investigación básica 👇
Results of my first idli-making attempt. Outcome of the pilot experiment not bad at all. Consumables & hardware purchased in Amazon. Methods from the Internet & YouTube (and some memories of my last indian trip). Next challenge: preparing sambar & chutneys at home 💪🏻
Con mis muy limitados conocimientos de virología e immunología, yo diría que la *vacuna de Enjuanes* puede ser infinitamente mejor que las que se van a empezar a poner. Pero un grupo de pocas personas/ recursos no puede competir con las grandes Pharmas ☹️
El Gobierno afirma que basa sus decisiones sobre relajar el confinamiento en informes *de los expertos* ¿Son esos informes confidenciales? ¿Podríamos verlos? Deberían ser públicos ¿Quienes son esos expertos? ¿Los mismos del Comité Científico Asesor nombrado el 21 Marzo?
I often get annoyed—if not furious—when I see a paper stating novelty for a phenomenon which was known for a long time but it is now revisited with a different terminology & narrative. Of course, the earlier work is simply ignored or downplayed for the sake of claiming freshness
There is nothing I like more than merging unrelated genetic technologies in a new platform. With the invaluable help of
@AkosNyerges
,
@Yamaloon
managed to combine ssDNA recombineering with bacterial surface display of nanobodies & experimental evolution
Este video es francamente irritante. De repente
@sanchezcastejon
concluye que no hay científicos españoles de los que echar mano cuando el pais los necesita. Existir, existen, pero en general se les ignora si no dicen lo que el poder quiere ☹️ Ver caso Aznalcóllar y caso Prestige