Mostrando entradas con la etiqueta meeting. Mostrar todas las entradas
Mostrando entradas con la etiqueta meeting. Mostrar todas las entradas

3 de julio de 2023

My notes on Plant Biology Europe 2023 at Marseille

Hi, in this and following posts I will be sharing my notes of the sessions of the Plant Biology Europe 2023 at Marseille: https://europlantbiology2023.org

day2 day3 day4

Note: access here the slides of the "Learning to build and interrogate the pangenome of Brachypodium distachyon" talk.

03072023 

Uncovering the hidden half of plants: discovering novel ways roots sense and adapt to heterogeneous environments. Malcolm Bennet.

Talks about xerobranching (https://pubmed.ncbi.nlm.nih.gov/30270188), a mechanism to control root branching in water-deprived soil layers. This is initially controlled by phloem-produced ABA [compamion cells] that travels to the root and triggers an auxin response in the epidermis [plasmodesmata] (https://doi.org/10.1126/science.add3771). They have used air-gap experiments to show this is conserved across angiosperms.

In the 2nd part of the talk he talks about how soil compaction inhibits root growth and produces actually wider roots. However, in mutants unsensitive to ethylene, roots can actually overcome compaction. It seems that growth arrest is actually an ethylene response. Plants sense compaction by gauging gaseous ethylene diffusion in the soil (root radar signal). He is asked whether growing through compact soil actually damages the root. His answer is that natural variability suggests that damage is not the main driver or these mechanisms.

He goes on to stress we need to consider plant + soil + microbes to answer any root questions, so we should all talk to soil and microbe scientists.

 

A central role of root symbionts: the plant response to environmental stresses. Raffaella Balestrini.

Explains how strigogalactones produce by the root trigger the fungus infection during mycorrhiza establishment. Transcriptional landscape changes before -> after, revealing that [plant, fungus]  redundant transcripts encoding P-transporters ate upregulated. She shows experiments with Lotus japonica + Gigaspora. She moves to explain that AM symbiosis increases drought resilience, but it’s a process we still know little about, as responses depend on genotype interactions. She mentions https://doi.org/10.1126/science.aaz5192 and https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.18281. She explains that infection in tomato affects also stomata density.

They are now working in a consortium that will produce tomato seeds coated with priming chemicals [including salicylic acid, which affect spore germination] and fungal spores to maximize stress resilience of adult plants.  She mentions https://doi.org/10.1016/j.tplants.2022.06.004 .

 

Fusing genome simulation and crop models for computer-aided breeding in future environments – Arnaud DESBIEZ-PIAT

Talks about training genomic prediction models with 10-cross validation as part of a virtual breeding platform. They get the genotypes ranked correctly, but has a 3d biass in anthesis date. Explores the effect of simulated and real recombination and models (rrBLUP vs Bayes) on the correlation of traits. He says that automatic phenotyping of germination rates is very hard. The goal is to keep genetic gain > errors.

Pervasive Under-Dominance in Gene Expression Underlying Emergent Growth Trajectories in Arabidopsis thaliana Hybrids– Wei YUAN

As Daniela Ristova, uses Biorender.com to make summaries. In her experiments comparing F1 hybrids to inbreds she finds less additive genes than dominant ones [hybrids have larger rosette areas]. She finds that promoters with more rare alleles have lower expression [allele freq as a proxy of deleteriousness], with hybrids with less rare alleles performing best. Paper soon out in Genome Biol?

Reconsidering photoperiod-sensitivity (PS) for maize adaption to climate change– Justine DROUAULT

Hypothesis: tropical maize could be re-introduced into temperate maize to increase adaptation in the face of climate change. She shows that selection towards PS indirectly selected also for other traits, such as plant height, etc. She classifies haplotypes according to their PS. She finds that tropical genotypes can reduce thermal time to flowering, but effect depends on background genotype.

Plasticity of root permeability for nutrient acquisition. Marie Barberon.

She explains the plastic role of suberin diffusion barrier in the root, citing https://www.pnas.org/doi/10.1073/pnas.2101730118.  A set of at least 4 MYB factors control (ectopic) suberization: 41,53,92,93. They cannot do single-cell as they cannot produce viable protoplasts of their root cells.

Polygenic selection and the evolution of gene expression in Arabidopsis Iyrata. Juliette de Meaux.

Inspiring talk on how her group is taking advantage of the Arabidopsis genomes (thaliana, halleri and lyrata) to study gene dominance. She starts by explaining that most genetic variance is deleterious and probably cannot be removed due to drift and the inability of selection to eliminate it. She shows that genes that show dominance display less Ks (more constrained) and that, conversely, additive genes, with smaller phenotypic effects, show larger Ks values (https://europepmc.org/article/ppr/ppr453330). She refers to https://www.nature.com/articles/s41467-021-23558-2, where they compare sterile hybrids of those species to classify cis variation. In outlokk, she favors future focus on many genes with small additive effect but large collective weight.

Changes in competitive ability over the course of durum wheat domestication are mediated by plant functional traits– Taïna LEMOINE

She studies Triticum monococcum, T. dicoccoides, T. turgidum landraces and T. turgidum elite varieties to measure their i) performance and ii) trait plasticity in the face of stress. She finds that domesticated materials performs better overall, but in terms of individual trait plasticity, wild material show larger variability, which suggests that breeding with a view of individual traits can still make gains from wild materials.

Horizontal gene transfer in Hordeum species– Marek SZECÓWKA

Hordeum species acquired DNA from panicoid sources via at least 9 events 5-1My ago. These lineages diverged 50Myr ago (https://pubmed.ncbi.nlm.nih.gov/33484020/). He asks how many accessory genes are from panicoids and what are their roles. So he chops Hordeum  genomes in 1Kb bits which are then mapped onto reference panicoid genomes, requiring at least 500b matches (BLASTN, 175b for BLASTX) and high % identity. He then requires >=70% identity and fragments >=5Kb for further analysis.  

They have also tracked panicoid TEs in Hordeum genomes and they seem to follow the segments and chromosomes previously shortlisted. They behave effectively as additional confirmation. They have built consensus panicoid TE library for this work.


25 de marzo de 2014

XII Jornadas de Bioinformática / XII Symposium on Bioinformatics

Hola,
hoy damos difusión a las pŕoximas Jornadas de Bioinformática, el mayor evento científico sobre biología computacional en España. Esta es la información que tengo de momento:


The XII Symposium on Bioinformatics (XII Jornadas de Bioinformática) will take place on 21-24 September in Sevilla, Spain, at cicCartuja (CSIC-US). 

The 21st will be the student symposium, and the main conference will start on Monday the 22nd. The URL for the meeting is: 


http://www.bioinformaticsconference2014.org/

(programme/committees are still preliminar, but will be updated periodically)
With the aim of encouraging the participation of younger bioinformaticians this year’s symposium main theme is “Bioinformatics: The New Breed”.Abstracts topics include but are not limited to:
  • Integrative Biology (NGS, -omics technologies...)
  • Structural Bioinformatics and function prediction
  • Algorithms, method, and tools development
  • Metagenomics
  • Medical Informatics 

    Abstract submission closes Thursday, July 31, 2014 

PD 25 de Agosto: nuestro laboratorio presentará dos charlas seleccionadas en las secciones de Metagenómica y Estructura y Función. Además Álvaro Sebastián, colaborador habitual del blog presentará un libro de texto sobre Bioinformática en español, en la sección The Unworkshop format.

29 de diciembre de 2011

Jornadas Bioinformáticas JBI 2012 (XI Edición)

Aprovecho esta última entrada del año para dar difusión a las Jornadas de Bioinformática JBI 2012. Como muchos sabréis, este congreso es el principal punto de encuentro anual de nuestra comunidad en la península ibérica, así que nuestro laboratorio también estará en Barcelona del 23 al 25 de Enero. El programa completo de las jornadas se puede descargar en este enlace.
http://sgu.bioinfo.cipf.es/jbi2012


Este año presentaremos parte de nuestro trabajo reciente:

"Genome-wide clustering of transcription factors by comparison of predicted protein-DNA interfaces"

donde explicamos y evaluamos la anotación de interfaces de reconocimiento de DNA en secuencias de proteínas por medio de diferentes aproximaciones como BLAST, TFmodeller, DP-Bind y DISIS.






El tema principal de las jornadas será "Arquitectura genómica, anotación y diseño", sobre el cual se discutirán los diferentes avances en la integración de los campos de la Biología, Medicina e Informática en el campo de la Genómica. Además se tratarán los siguientes temas:
- Análisis de datos de secuenciación de alto rendimiento (NGS)
- Bioinformática estructural
- Algoritmos de biología computacional y computación de alto rendimiento
- Análisis de sequencias, filogenética y evolución
- Bases de datos, herramientas y tecnologías en biología computacional
- Bioinformática en transcriptómica y proteómica
- Biología de sistemas

ENGLISH:

The XIth Spanish Symposium on Bioinformatics (JBI2012) will take place in January 23-25, 2012 in Barcelona, Spain. Co-organised by the Spanish Institut of Bioinformatics and the Portuguese Bioinformatics Network and hosted by the Barcelona Biomedical Research Park (PRBB). The full program can be downloaded from this link.

This year, the reference topic is “Genome Architecture, Annotation and Design” for which the conference will provide the opportunity to discuss the state of the art for the integration of the fields of biology, medicine and informatics. We invite you to submit your work and share your experiences in the following topics of interest including, but not limited to:

- Analysis of high throughput data  (NGS)
- Structural Bioinformatics
- Algorithms for computational biology and HPC
- Sequence analysis, phylogenetics and evolution
- Databases, Tools and technologies for computational biology
-  Bioinformatics in Transcriptomics and Proteomics
- System and Synthetic Biology

Our contribution to the congress:

Genome-wide clustering of transcription factors by comparison of predicted protein-DNA interfaces

Transcription Factors (TFs) play a central role in gene regulation by binding to DNA target sequences, mostly in promoter regions. However, even for the best annotated genomes, only a fraction of these critical proteins have been experimentally characterized and linked to some of their target sites. The dimension of this problem increases in multicellular organisms, which tend to have large collections of TFs, sometimes with redundant roles, that result of whole-genome duplication events and lineage-specific expansions. In this work we set to study the repertoire of Arabidopsis thaliana TFs from the perspective of their predicted interfaces, to evaluate the degree of DNA-binding redundancy at a genome scale. First, we critically compare the performance of a variety of methods that predict the interface residues of DNA-binding proteins, those responsible for specific recognition, and measure their sensitivity and specificity. Second, we apply the best predictors to the complete A.thaliana repertoire and build clusters of transcription factors with similar interfaces. Finally, we use our in-house footprintDB to benchmark to what extent TFs in the same cluster specifically bind to similar DNA sites. Our results indicate that there is substantial overlap of DNA binding specificities in most TF families. This observation supports the use of interface predictions to construct reduced representation of TF sets with common DNA binding preferences.


13 de septiembre de 2010

Jornadas Bioinformáticas JBI 2010 (X Edición), nuestro laboratorio estará allí...

Las Jornadas Bioinformáticas son la cita anual obligada para los bioinformáticos españoles. Este año se celebrará su décima edición del 27 al 29 de Octubre en Torremolinos (Málaga). La organización de las mismas corre a cargo de la Universidad de Málaga, el Instituto Nacional de Bioinformática y la Red Portuguesa de Bioinformática. Este año el tema central es "La bioinformática aplicada a la medicina personalizada", sobre el cual se discutirá la integración de los campos de la biología, medicina e informática para el desarrollo de terapias más específicas y efectivas. Sin embargo, éste no será el único tema a tratar, también se compartirán resultados y experiencias en otros campos:
- Análisis de datos en técnicas de alto rendimiento como la secuenciación de nueva generación.
- Bioinformática estructural
- Algoritmos de biología computacional y técnicas de computación de alto rendimiento
- Análisis de secuencias, filogenética y evolución
- Bases de datos, herramientas y tecnologías de biología computacional
- Bioinformática en transcriptómica y proteómica
- Biología sintética y de sistemas

IN ENGLISH:


The Xth Spanish Symposium on Bioinformatics (JBI2010) will take place in October 27-29, 2010 in Torremolinos-Málaga, Spain. Co-organised by the National Institute of Bioinformatics-Spain and the Portuguese Bioinformatics Network and hosted by the University of Malaga (Spain).


This year, the reference topic is “Bioinformatics for personalized medicine” for which the conference will provide the opportunity to discuss the state of the art for the integration of the fields of biology, medicine and informatics. We invite you to submit your work and share your experiences in the following topics of interest including, but not limited to:
- Analysis of high throughput data    (NGS)
- Structural Bioinformatics
 - Algorithms for computational biology and HPC
 - Sequence analysis, phylogenetics and evolution
 - Databases, Tools and technologies for computational biology
-  Bioinformatics in  Transcriptomics and Proteomics
- System and Synthetic Biology



Nuestras aportaciones

Nuestro laboratorio va a participar en las Jornadas Bioinformáticas con tres contribuciones que presentaré a continuación:


3D-footprint: a database for the structural analysis of protein–DNA complexes
3D-footprint is a living database, updated and curated on a weekly basis, which provides estimates of binding specificity for all protein–DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Each complex in the database is dissected to draw interface graphs and footprint logos, and two complementary algorithms are employed to characterize binding specificity. Moreover, oligonucleotide sequences extracted from literature abstracts are reported in order to show the range of variant sites bound by each protein and other related proteins. Benchmark experiments, including comparisons with expert-curated databases RegulonDB and TRANSFAC, support the quality of structure-based estimates of specificity. The relevant content of the database is available for download as flat files and it is also possible to use the 3D-footprint pipeline to analyze protein coordinates input by the user. 3D-footprint is available at http://floresta.eead.csic.es/3dfootprint with demo buttons and a comprehensive tutorial that illustrates the main uses of this resource.


The relation between amino-acid substitutions in the interface of transcription factors and their recognized DNA motifs

Transcription Factors (TFs) play a key role in gene regulation by binding to DNA target sequences. While there is a vast literature describing computational methods to define patterns and match DNA regulatory motifs within genomic sequences, the prediction of DNA binding motifs (DBMs) that might be recognized by a particular TF is a relatively unexplored field. Numerous DNA-binding proteins are annotated as TFs in databases; however, for many of these orphan TFs the corresponding DBMs remain uncharacterized. Standard annotation practice transfer DBMs of well known TFs to those orphan protein sequences which can be confidently aligned to them, usually by means of local alignment tools such as BLAST, but these predictions are known to be error-prone. With the aim of improving these predictions, we test whether the knowledge of protein-DNA interface architectures and existing TF-DNA binding experimental data can be used to generate family-wise interface substitution matrices (ISUMs). An experiment with 85 Drosophila melanogaster homeobox proteins demonstrate that ISUMs: i) capture information about the correlation between the substitution of a TF interface residue and the conservation of the DBM; ii) are valuable to evaluate TFs alignments and iii) are better classifiers than generic amino-acid substitution matrices and that BLAST E-value when deciding whether two aligned homeobox proteins bind to the same DNA motif.


101DNA: a set of tools for Protein-DNA interface analysis

Analysis of protein-DNA interfaces has shown a great structural dependency. Despite the observation that related proteins tend to use the same pattern of amino acid and base contacting positions, no simple recognition code has been found. While protein contacts with the sugar-phosphate backbone of DNA provide stability and yield very little specificity information, contacts between amino acid side-chains and DNA bases (direct readout) apparently define specificity, in addition to some constrains defined by DNA sequence-dependent features, namely indirect readout.
Recent approaches have proposed bipartite graphs as an structural way of analysing interfaces from a protein-DNA-centric viewpoint. With this perspective in mind, we have developed a set of tools for the dissection and comparison of protein-DNA interfaces. Taking a protein-DNA complex file in PDB format as input, the software generates a 2D matrix that represents a bipartite graph of residue contacts  obtained after applying a simple distance threshold that captures all non-covalent interactions. The generated 2D matrices allow a fast and simple visual inspection of the interface and have been successfully produced for the current non-redundant set of protein-DNA complexes in the 3D-footprint database.
As a second utility to compare 2 interfaces, the 101DNA software includes an aligment tool where a dynamic programming matrix is created with the Local Affine Gap algorithm and traced back as a finite state automata. The scores between pairs of  interface amino acid residues are calculated as a function of the observed contacts with DNA nitrogen bases. This tool produces local interface alignments which are independent of the underlying protein sequence, but that faithfully represent the binding architecture. Preliminary tests show that these local alignments successfully identify binding interfaces that share striking similarity despite belonging to different protein superfamilies, and these observations support this graph-theory approach.