Transcriptome Analysis Reveals Genes Responsive to Three Low-Temperature Treatments in .

Cold stress impedes the growth and development of plants, restricts the geographical distribution of plant species, and impacts crop productivity. In this study, we analyzed the transcriptome to identify differentially expressed genes (DEGs) in 14-day-old plantlets exposed to temperatures of 0 °C, 4 °C, and 10 °C for 24 h, compared to the 22 °C control group. Among the top 50 cold-induced genes at each temperature, we identified 31 genes that were common across all three low temperatures, with nine genes common to 0-4 °C, eight genes to 4-10 °C, and two genes to 0-10 °C.

Marine oil spill detection and segmentation in SAR data with two steps Deep Learning framework.

Marine oil spills pose significant ecological and economic threats worldwide, requiring effective decision-making tools. In this study, the optimal parameters, and configurations for Deep Learning models in oil spill classification and segmentation using Sentinel-1 SAR imagery were identified. First, a new Sentinel-1 image dataset was created.

Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp.

Fungi of the Trichoderma genus are called "biostimulants" because they promote plant growth and development and induce disease resistance. We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma virens. The transcriptional landscape of the plant during the interaction with these fungi showed a reduction in functions such as reactive oxygen species production, defense mechanisms against pathogens, and hormone signaling.

Dietary Supplementation with Popped Amaranth Modulates the Gut Microbiota in Low Height-for-Age Children: A Nonrandomized Pilot Trial.

Amaranth has been recognized as a nutraceutical food because it contains high-quality proteins due to its adequate amino acid composition that covers the recommended requirements for children and adults. Since pre-Hispanic times, amaranth has been consumed as popped grain; the popping process improves its nutritive quality and improves its digestibility. Popped amaranth consumption has been associated with the recovery of malnourished children.

Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria.

Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked.

Oil spills: Detection and concentration estimation in satellite imagery, a machine learning approach.

The method's development to detect oil-spills, and concentration monitoring of marine environments, are essential in emergency response. To develop a classification model, this work was based on the spectral response of surfaces using reflectance data, and machine learning (ML) techniques, with the objective of detecting oil in Landsat imagery. Additionally, different concentration oil data were used to obtain a concentration-estimation model.

Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato.

Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete subsp. (), one of the most devastating bacterial pathogens of this crop.

The nutrient-improvement bacteria selected by Agave lechuguilla T. and their role in the rhizosphere community.

Agave lechuguilla has one of the widest distributions among other agave species in the Chihuahuan Desert. Their capacity to grow in poorly developed soils and harsh conditions has been related to their association with plant growth-promoting rhizobacteria. In this work, we explored how soil properties and plant growth stage influence the composition of the rhizobacterial communities, their interactions, and the enzymatic activity and abundance of nitrogen-fixing bacteria and organic phosphorus-mineralizing bacteria in two subregions of the Chihuahuan Desert.

Immunoproteomic identification of allergenic proteins in pecan (Carya illinoinensis) pollen.

Pecan (C. illinoinensis) pollen is an important cause of allergic respiratory disease. Pecan is distributed worldwide as shade, ornamental or cultivation tree.

DNA-MBF1 study using molecular dynamics simulations : On the road to understanding the heat stress response in DNA-protein interactions in plants.

Regulatory factor MBF1 is highly conserved between species and has been described as a cofactor and transcription factor. In plants, several reports associate MBF1 with heat stress response. Nevertheless, the specific physical processes involved in the MBF1-DNA interaction are still far from clearly understood.

Secretome Analysis of - Interaction Unveils New Roles for the Plant Glutamate:Glyoxylate Aminotransferase GGAT1 in Plant Growth Induced by the Fungus and Resistance against .

The establishment of plant-fungus mutualistic interaction requires bidirectional molecular crosstalk. Therefore, the analysis of the interacting organisms secretomes would help to understand how such relationships are established. Here, a gel-free shotgun proteomics approach was used to identify the secreted proteins of the plant and the mutualistic fungus during their interaction.

Target-Decoy MineR for determining the biological relevance of variables in noisy datasets.

Motivation: Machine learning algorithms excavate important variables from big data. However, deciding on the relevance of identified variables is challenging. The addition of artificial noise, 'decoy' variables, to raw data, 'target' variables, enables calculating a false-positive rate and a biological relevance probability for each variable rank.

Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides.

Extracellular RNA has been proposed to mediate communication between cells and organisms however relatively little is understood regarding how specific sequences are selected for export. Here, we describe a specific Argonaute protein (exWAGO) that is secreted in extracellular vesicles (EVs) released by the gastrointestinal nematode Heligmosomoides bakeri, at multiple copies per EV. Phylogenetic and gene expression analyses demonstrate exWAGO orthologues are highly conserved and abundantly expressed in related parasites but highly diverged in free-living genus Caenorhabditis.

Elucidating the Distribution of Plant Metabolites from Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging.

Secondary metabolites of plants have important biological functions, which often depend on their localization in tissues. Ideally, a fresh untreated material should be directly analyzed to obtain a realistic view of the true sample chemistry. Therefore, there is a large interest for ambient mass-spectrometry-based imaging (MSI) methods.

miR-182 Regulates Slit2-Mediated Axon Guidance by Modulating the Local Translation of a Specific mRNA.

During brain wiring, cue-induced axon behaviors such as directional steering and branching are aided by localized mRNA translation. Different guidance cues elicit translation of subsets of mRNAs that differentially regulate the cytoskeleton, yet little is understood about how specific mRNAs are selected for translation. MicroRNAs (miRNAs) are critical translational regulators that act through a sequence-specific mechanism.

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle.

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode's genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.

The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p.

Background: IL-4-driven alternative macrophage activation and proliferation are characteristic features of both antihelminthic immune responses and wound healing in contrast to classical macrophage activation, which primarily occurs during inflammatory responses. The signaling pathways defining the genome-wide microRNA expression profile as well as the cellular functions controlled by microRNAs during alternative macrophage activation are largely unknown. Hence, in the current work we examined the regulation and function of IL-4-regulated microRNAs in human and mouse alternative macrophage activation.

Improving microRNA target prediction with gene expression profiles.

Background: Mammalian genomes encode for thousands of microRNAs, which can potentially regulate the majority of protein-coding genes. They have been implicated in development and disease, leading to great interest in understanding their function, with computational methods being widely used to predict their targets. Most computational methods rely on sequence features, thermodynamics, and conservation filters; essentially scanning the whole transcriptome to predict one set of targets for each microRNA.