AIMC Topic: Plant Proteins

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AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface.

Nature communications
Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs of seven tomato pathogens for interacting with six def...

Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks.

BMC bioinformatics
BACKGROUND: Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de novo from sequence is difficu...

Predicting functions of maize proteins using graph convolutional network.

BMC bioinformatics
BACKGROUND: Maize (Zea mays ssp. mays L.) is the most widely grown and yield crop in the world, as well as an important model organism for fundamental research of the function of genes. The functions of Maize proteins are annotated using the Gene Ont...

Ab initio GO-based mining for non-tandem-duplicated functional clusters in three model plant diploid genomes.

PloS one
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds-related FNTDC...

Multi-feature fusion for deep learning to predict plant lncRNA-protein interaction.

Genomics
Long non-coding RNAs (lncRNAs) play key roles in regulating cellular biological processes through diverse molecular mechanisms including binding to RNA binding proteins. The majority of plant lncRNAs are functionally uncharacterized, thus, accurate p...

JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants.

BMC genomics
BACKGROUND: Jatropha curcas is an oil-bearing plant, and has seeds with high oil content (~ 40%). Several advantages, such as easy genetic transformation and short generation duration, have led to the emergence of J. curcas as a model for woody energ...

Application of Ultrasound-Ultrafiltration-Assisted alkaline isoelectric precipitation (UUAAIP) technique for producing alfalfa protein isolate for human consumption: Optimization, comparison, physicochemical, and functional properties.

Food research international (Ottawa, Ont.)
A new Ultrasound-Ultrafiltration-Assisted Alkaline Isoelectric Precipitation (UUAAIP) technique was employed for producing alfalfa protein isolate from alfalfa leaves. A five-factor-three-level Box-Behnken Design (BBD) was used to optimize the UUAAIP...

Nutritional and technological properties of a quinoa (Chenopodium quinoa Willd.) spray-dried powdered extract.

Food research international (Ottawa, Ont.)
The relevance of an appropriate nutrition requires innovation in the design of food ingredients. The goal of this work was to obtain a powdered extract of quinoa by using spray-drying. To this aim, quinoa flour was suspended in water to obtain a solu...

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne).

PloS one
Perennial ryegrass (Lolium perenne) is a forage and amenity grass species widely cultivated in temperate regions worldwide. As such, perennial ryegrass populations are exposed to a range of environmental conditions and stresses on a seasonal basis an...

Fuzzy controller based E-nose classification of Sitophilus oryzae infestation in stored rice grain.

Food chemistry
Fuzzy controller artmap based algorithms via E-nose selective metal oxides sensor (MOS) data was applied for classification of S. oryzae infestation in rice grains. The screened defuzzified data of selective sensors was further applied to detect S. o...