Hola, el 17 de diciembre di una charla virtual invitado por mis compañeros de la Estación Experimental de Aula Dei-CSIC titulada "Pangenomas para dummies: ejemplos en plantas, aplicaciones y retos".
La charla quedó grabada y puedes escucharla de nuevo en
Hasta pronto,
Bruno
Hola,
estos días está transcurriendo CASP14, la edición 14 del certámen de predicción de estructura de proteínas. La última vez que hablamos de CASP en este blog fue en esta entrada del año pasado. Por recordar un poco, en CASP participan grupos de investigación de todo el mundo que tratan de modelar un conjunto de secuencias de proteínas cuyas estructuras se han resuelto experimentalmente, pero que solamente se publican despúes de la temporada de predicción. Por tanto, los grupos y su algoritmos trabajan relativamente a ciegas en esas predicciones.
Digo relativamente porque en realidad se apoyan en la creciente colección de estructuras conocidas del PDB, del orden 10E5, y en las millones de secuencias de proteínas conocidas (del orden 10E8). Por esa razón unas secuencias son más fáciles, porque se parecen a otras conocidas, y otras más difíciles, porque no se parecen demasiado a nada conocido.
En la edición CASP14 había un total de 92 secuencias de aminoácidos, cada una correspondiente a un dominio. La siguiente figura, obtenida de https://predictioncenter.org/casp14/zscores_final.cgi resume los resultados, mostrando que los dos mejores grupos de la última década (Baker y Zhang) han sido ampliamente superados por AlphaFold2 (columna de la izquierda, del que ya habíamos hablado aquí):
Qué opinan los expertos? Aquí tenéis por ejemplo a Torsten Schwede , Mohammed AlQuraishi o a Alfonso Valencia.
Supongo que no estará de más esperar a CASP15 para comprobar que este progreso se mantiene en el tiempo, pero por ahora parece que lo han resuelto. Solamente nos queda exigir a DeepMind, la matriz de AlphaFold2, que libere su predictor para fines académicos y de esa manera devuelvan a la comunidad lo que de ella han extraído en estos últimos años.
Un saludo,
Bruno
PD Nota importante: como recuerda Alfonso Valencia en https://twitter.com/Alfons_Valencia/status/1333682759366303745, no es lo mismo predecir la estructura que la reacción de plegamiento
Hi, Carlos Cantalapiedra and me recently put together teaching material about scripting in the linux terminal.
The material can be found at repository https://github.com/eead-csic-compbio/scripting_linux_shell
There are five sessions and the goal is for you to learn the basics of the Linux shell and scripting for data sciences such as genomics and plant breeding:
| session | title | required time | URL | |
|---|---|---|---|---|
| 0 | Setup | prior to course | session 0 | |
| 1 | Linux basics and files | 2h | session 1 | |
| 2 | Processes and scripts | 2h | session 2 | |
| 3 | Parsing with regular expressions | 2h | session 3 | |
| 4 | Perl one-liners | 2h | session 4 | |
| 5 | Advanced scripts | 2h | session 5 |
Figure of the standard streams, taken from https://en.wikipedia.org/wiki/Standard_streams
If you spot errors please send pull requests, hope this helps some of you out there,
Bruno
PD si prefieres aprender en español echa un vistazo a https://github.com/vinuesa/intro2linux
Hola,
hoy quería comentar un artículo reciente de Bozovic et al, donde observan el alosterismo de un dominio PDZ al unirse a su péptido ligando (ver más aquí). Lo que me ha llamado más la atención de este trabajo es que combinando medidas experimentales y simulaciones de dinámica molecular, definen poblaciones de conformaciones y cronometran las transiciones, de manera que al final proponen un modelo que parece un autómata finito, como los que se usan en teoría de la computación o para explicar expresiones regulares.
Al final, resulta que las herramientas desarrolladas hace décadas en las ciencias de la computación sirven hoy para describir poblaciones de proteínas. O dicho de otro modo, esta proteína computa,
hasta luego,
Bruno
Hi, this year's Plant Genomes in a Changing Environment was virtual with hashtag #PlantGenomes20. Check the full program here. I post here my notes on the talks I was able to attend, either live or on the recorded videos, in case they're useful for anyone out there.
Giles Oldroyd (Sainbury lab, UK) talked about a pathway conserved in plants forming intracellular endosymbiotic mycorrhizaephytes. The pathway is not found in species forming exclusively extracellular symbioses, such as ectomycorrhizae, and those forming associations with cyanobacteria. This is described at https://www.nature.com/articles/s41477-020-0613-7. Receptors used with potential symbionts are the same used to recognize chitin and peptide-glicans of pathogens. Symbiotic potential decreases when there's enough nutriends at hand.
Figure from https://www.biorxiv.org/content/10.1101/804591v1.full
N Marmiroli (SITEIA.PARMA, Italy) presented a poster about the https://simbaproject.eu, where they are testing in plots in Italy and Germany the application of Plant Growth-Promoting Microbes to wheat, maize, tomato and potato under abiotic stress conditions.
Trevor Nolan (Duke U, USA) talked about their efforts in harmonizing single cell mRNA sequencing data from 110K cells to construct an atlas for the developing Arabidopsis thaliana root. Read more at https://www.biorxiv.org/content/10.1101/2020.06.29.178863v1
Francesco Licausi (Oxford U, UK) described the strategies of flooding tolerance in plants, which can be used to breed flooding varieties of crops. Flooding is a composite stress, he focus on two components: oxygen sensing and responses to oxidative stress, which are mediated among others by NAC transcription factors such as ANAC017, read more at https://onlinelibrary.wiley.com/doi/full/10.1111/pce.13037 and https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14975
Steve Long (Lancaster U, UK) shared his knowledge on breeding for incresing photosynthesis efficienty. This figure is from a 2010 review https://www.annualreviews.org/doi/10.1146/annurev-arplant-042809-112206, but still quite impressive:
Alexander Borowsky (U California, Riverside, USA) uses their own coexpression network pipeline (Wisecaver 2019) and the Taiji pipeline to analyze their ATACseq data in order to find key transcription factors regulating responses to water logging and water deficit in rice. They plan to do validation work using CRISPR to confirm their results.
Julia Bailey-Serres (U California, Riverside, USA) gave a keynote with two parts. While the second was related to A Borowsky0s talk, on the first part, she and her team looked at the transcriptional regulation of responses to submergence/flooding by comparing 4 different species (rice, Medicago truncatula, domesticated tomato and its dryland-adapted wild relative Solanum pennellii). By combining RNA-seq and ATACseq data and different computational analyses they found 68 Submerged Upregulated oRthologous Families (SURFs) upregulated in both monocots and dicots, with hypoxia-responsive promoter element (HRPE) motifs being abundant in rice but scarce in promoters of SURFs in dryland-adapted S. pennellii. This piece of work is described at https://science.sciencemag.org/content/365/6459/1291
Figure from https://science.sciencemag.org/content/365/6459/1291
They have really nive figure, shown below, where DNA motifs instead of transcription factors are the vertices of the graph. Despite the differences observed in the network across species, 4 motifs seem to be highly conserved:
Figure from https://science.sciencemag.org/content/365/6459/1291
Klaas Vandepoele (VIB-Ugent Center for Plant Systems Biology, Belgium) and his team have been doing a conceptually similar analysis, with RNA-seq from A. thaliana, Populus trichocarpa and maize, in order to identify gene triplets with conserved leaf expression pattern which are conserved across monocots and dicots. They validate their results by phenotyping A. thaliana mutants in the glass house. Their work has been published at https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13223. He also mentions this paper https://pubmed.ncbi.nlm.nih.gov/31748815 which describes modules of genes involved in cell proliferation in the leaf.
Jeff Habben (Corteva, USA) describes their extensive field trials in low and high-yielding locations, mostly across the US, to check whether different transgenic lines that overexpress maize transcription factor zmm28 (MADS-box) have higher and more stable yields. Their work is described in detail at https://www.pnas.org/content/116/47/23850
Facundo Romani (CONICET, Argentina) explains how liverwort Marchantia polymorpha defends itself against hervibores by accumulating terpenes in oil bodies, a process controlled by HD-ZIP transcription factor MpC1HDZ. This work is described at https://www.sciencedirect.com/science/article/abs/pii/S0960982220307685
Sandra Knapp (Natural History Museum-London, UK) , a plant taxonomist, talks about diversity of Solanaceae (nightshades), starting with potatoes.
Source: Sandra Knapp
She discusses how we usually think of aridification as something bad but according tho their work in Australia (https://onlinelibrary.wiley.com/doi/full/10.1111/jse.12638) it seems to be certainly a driver of diversification. She suggests we should be looking at plant lineages that have this pattern to prepare for climate change. One possible way would be to learn from resistant weeds in order to create resistant crops (https://www.sciencedirect.com/science/article/abs/pii/S0304423818307994). This is aligned with the work of Dana MacGregor, which also had a talk in this session.
She terminates by acknowledging the collective effort of people studying nightshades around the world (http://solanaceaesource.org) and a warning about the excess of P/N consum by agriculture and the current rates of extinction, that cause an unsustainable loss of diversity.
Michael Purugganan (New York University, USA) talks about the domestication of rice (which tokk 4K years) and molecular studies to understand the geographic spread of primarily japonica rice in Asia. His two main figures are:
Figure from https://pubmed.ncbi.nlm.nih.gov/28087768/
Tal Dahan Meir (Weizmann Institute of Science, Israel) spoke about a long term observation seris of a wild Emmer wheat population in Isreal. Unfortunately I could not see the most relevant slides in the saved video, but het talk reminded me of the Eviatar Nevo's talk last year at the Brachypodium conference (see https://www.youtube.com/watch?v=UhNzH39zLbk).
Guy Naamati (Ensembl Plants, EMBL-EBI, UK) presented a poster about the wheat Pan Genome and status at Ensembl Plant. The programmatic access recipes mentioned in the poster can be found at https://github.com/Ensembl/plant_tools/tree/master/demo_scripts
