estructuras del PDB parecidas en secuencia (REST)

Hola,
hace unos días un usuario preguntaba en la lista de usuarios del Protein Data Bank (PDB) cómo usar la interfaz de servicios REST, documentada en https://www.rcsb.org/pdb/software/rest.do, para hacer búsquedas BLAST.

Mientras otro usuario compartía un script escrito en Python3, llamado sequenceSimilarity.py, que requiere mmtf-pyspark para hacer consultas PSI-BLAST en tiempo real contra el PDB, a mi me llamó la atención la simplicidad del servicio sequenceCluster, que para cualquier cadena de una estructura depositada en el PDB permite obtener el clúster de secuencias con un porcentaje de identidad controlado por el usuario:

https://www.rcsb.org/pdb/rest/sequenceCluster?cluster=70&structureId=9ant.A

Esto devuelve una lista de cadenas de estructuras PDB en formato XML que podemos procesar por ejemplo como se explica en

https://developer.atlassian.com/server/fisheye-crucible/writing-a-rest-client-in-perl

Hasta luego, buen verano,
Bruno

updated footprintDB motifs

Hi,
I have just updated the format of footprintDB motifs used in RSAT (www.rsat.eu), which can de downloaded from http://floresta.eead.csic.es/footprintdb/download. This was done to ensure compatibility with compare-matrices in RSAT. Now, motifs look this:

AC  AY750993/VRN1/EEADannot
XX
ID  AY750993:VRN1:EEADannot
XX
NA  AY750993
XX
DE  AY750993
XX
OS  Hordeum vulgare cv Strider
XX
BF  10127;
XX
P0      A      C      G      T
01     19     72      7      2      C
02     10     71      7     12      C
03     57     17     14     12      a
04     56      6     32      6      r
05     94      2      4      0      A
06     84      1      3     12      A
07     79      7      7      7      A
08     57      4      9     30      w
09     24      0     76      0      G
10     15      0     85      0      G
XX
LN  http://floresta.eead.csic.es/footprintdb/index.php?motif=AY750993:VRN1:EEADannot
XX
RN  [1];
RL  Deng W, Casao Mc, Wang P, Sato K, Hayes PM, Jean Finnegan E, Trvaskis B (2015) Direct links between the vernalization response and other key 
traits of cereal crops. Nat Comm 6:5882
RN  [2];
RX  PUBMED: 24234003
RL  Sebastian, A., Contreras-Moreira, B. footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bio
informatics 30, 258-65 (2014).
XX

Note that the ID field was added and that a URL pointing to the relevant database entry identified with it is attached. The accession code replaces ':' with '/' to ensure that downstream RSAT analyses can be carried out just fine,
cheers,
Bruno

Identificar tránscritos no codificantes

Hola,
recientemente he leído diferentes trabajos sobre cómo solamente una fracción de los tránscritos totales humanos realmente son codificantes. Estas observaciones tienen consecuencias prácticas que supongo se pueden extrapolar a otras especies.

1. Cómo identificar la isoforma principal de un gen
La base de datos APPRIS (http://appris-tools.org) aplica una serie de filtros para identificar las isoformas principales de cada gen humano en base a la combinación de varios criterios (leer artículo):

• conservación de la estructura de exones
• evolución no neutral
• alineamiento sin inserciones con estructuras homólogas
• conservación de residuos funcionales
• alineamiento completo con secuencias de otros vertebrados

Anotación de 3 isoformas según APPRIS, tomada de https://academic.oup.com/nar/article/46/D1/D213/4561658

2. Como identificar un transcrito no codificante
Una vez hemos ensamblado tránscritos de uno o más tejidos o condiciones puede ser útil clasificarlos como codificantes o no. En un trabajo nuestro (leer aquí) lo hacíamos con CPC y el script transcripts2cdsCPP.pl de GET_HOMOLOGUES-EST. Ahora, un trabajo reciente (leer aquí) propone los siguientes criterios, que comento en algunos casos:

• El tránscrito debe abarcar al menos un intrón y tener un nivel de expresión > 1 tránscrito por millón (TPM).
• Si sólo comprende un exón debe expresarse al menos igual que los  tránscritos mejor descritos (TPM > 13.87 en humanos).
• No debe estar contenido en otro tránscrito.
• Debe codificar un marco de lectura (ORF) de al menos 60 aminoácidos. OJO: esto podría dejar fuera proteínas pequeñas importantes.
• El ORF no debe solapar con elementos repetidos/transposones (LINe, LTR, etc) ni loci rRNA.
• El E-valor producido por BLASTX al comparar el transcrito con proteínas de mamíferos en GenBank y UniProt debe ser < 10E-15. OJO: el E-valor cambiará a medida que crezcan las bases de datos, este criterio debería expresarse mejor como cobertura o bit score. Ver siguiente criterio.
• El mejor ORF del tránscrito debe alinear al menos el 75% de otras proteínas conocidas, para eliminar pseudogenes, que suelen estar truncados.
• Si dos tránscritos de hebras contrarias solapan, nos quedaremos con el que se parezca a proteínas con función conocida.

Espero que esto os sea útil, un saludo,
Bruno

curso: proteínas dúctiles y sus aplicaciones

Hola,

hoy quiero difundir un curso de verano de 3 días, que dirigen nuestras colegas Inma Yruela y Patricia Ferreira, "Nuevos Retos en Biología Molecular: las proteínas dúctiles y sus aplicaciones".

Tendrá lugar en Jaca del 11 al 13 de julio, y participamos varios profesores invitados. Hay 4 bolsas de viaje disponibles. Más información en la dirección:

https://cursosextraordinarios.unizar.es/curso/2018/nuevos-retos-en-biologia-molecular-las-proteinas-ductiles-y-sus-aplicaciones

(cartel actualizado 02052018)

Hasta pronto,
Bruno

PD: el enlace al material que usaremos en mi sesión es http://www.eead.csic.es/compbio/material/alineafilog

notes on 1st Spanish Simposium on Physiology & Cereal Breeding (and II)

My notes on the second and final day of the 1st Spanish Simposium on Physiology & Cereal Breeding: http://networks.iamz.ciheam.org/cerealsnetwork/en/summaries.html

Omar Vergara-Diaz, Univ.Barcelona

He presents preliminary results on yield predictive models in water stress and control conditions based on metabolite profiles of leaves and spikes of field-grown wheat inferred from hyperspectral readings. He has recently presented this results at http://adsabs.harvard.edu/abs/2017AGUFM.B51A1782V.

Shawn Kefauver, Univ. Barcelona & CIMMYT Africa

He talks about methods of proximal UVA phenotyping/scanning maize using complex image processing software (MosaicTool, a plugin for FIJI, see more at this presentation in Spanish: https://ruralcat.gencat.cat/documents/20181/68301/Aplicacions%20i%20reptes%20dels%20drons%20en%20el%20fenotipatge1508158117144). 

Inès Zouari, INAT, Tunisia

She presents results on drought stress impact on durum wheat. Her work involves the development and use of drought (susceptibility and tolerance) indices, which were evaluated to ascertain their value in breeding. She concludes that selection must be based on different combinations of indices depending on whether breeding targets irrigated or rainfed materials. In all cases the number of spikes and high biomass seem diagnostic as traits to be selected.

John Foulkes, University of Nottingham-UK

His keynote is about exploring genetic diversity for rooting traits and tolerance of water & N stresses in wheat. He starts by explaining what N-use efficiency (NUE) is. He mentions that deep roots help plants under drought and that is reflected in C12/13 isotope ratios. He also mentions RootNav (http://www.plant-image-analysis.org/software/rootnav) and ImageJ (https://imagej.nih.gov/ij) which they have used to study root phenotypes (crown root angle, root length density) in lab experiments, observing high heritabilities in DH populations and significant association to yield in rainfed trials. He shows nice pics of aerenchyma formation in roots under drought.

Marta Lopes, CIMMYT, Turkey

She talks about winter wheat physiology and the optimization of resilience to a changing environment in rainfed crop systems of Turkey and Iran. She shows field data on grain yield when plots are exposed to heat spells and drought before and after heading. She mentions an article recently published in FPS, but I could not find, sorry. During questions, she explains that there is a database of CIMMYT genotypes so that anyone can query and order seeds.

Mariona Martínez-Subira, Univ. Lleida

She talks about her work, in collaboration with CSIC and SemillasBatlle, synthesis of bioactive compounds (beta-glucans, arabinoxylans) in barley during grain filling in response to late abiotic stress. She reports that growth under plastics reproduces terminal heat stress and that stress affects the composition of bioactive compounds.

Rubén Vicente, presents work done at Univ. Barcelona

Talks about C and N metabolism in laminar and non-laminar photosynthetic organs under contrasting water regimes in low- and high-yielding durum wheat cultivars (Sebastian & Pelayo) grown in ITACyL, Valladolid for 3 seasons. Under water stress they observe reduction of biomass, grain yield and senescence.

Damiano Martignano, CRAG, Barcelona

His talk describes approaches for Cas9 genome editing in Sorghum, which he applies to brassinosteroids (BS) engineering. He builds on previous observations in Arabidopsis thaliana showing that increasing BS receptors increases performance under drought. He mentions also the uzu mutant in barley, which is related. His protocol takes 10-14 weeks. They are producing NILs from Iberian landraces obtained from INIA. They are building a facility to perform high-throughput phenotyping (DroughtSpotter and PHENOSPEX).

David Soba, Univ. Navarra

He talks about the effect of elevated [CO2] on durum wheat grain quality during grain filling. Concludes that yield is increased, as well as gluten proteins. In contrats, free amino acids are reduced.

Elena Prats, IAS-CSIC, Córdoba

She delivers a keynote on the physiological dysfunctions of stomata (lock-up) under fungal infection and drought which affect both resistance to disease and drought responses. She explains a series of experiments in which plants were supplied with ABA and exposed to fungi, that allowed her team to conclude that infection does affect the stomatal movements. This behavior is part of what has been called hypersensitive response, which has been described in https://academic.oup.com/jxb/article/59/3/501/573771.

Francisco Ciudad- Bautista, ITACyL, Valladolid

Reports on the current incidence of fly Oscinella frit, which affects both wheat and barley, in Castilla y León, Spain. He shows fly curves and pictures of larvae and pupae in grains and explains how the symptoms can be distinguished from other diseases.

Yésica Pallavicini, ITACyL

She presents preliminary results on the use of aerial platforms and spectral indices to monitor the spread of  yellow rust in bread wheat along the growing season.