VvbHLH036, a basic helix-loop-helix transcription factor regulates the cold tolerance of grapevine.

Cold stress is an adverse environmental factor that limits the growth and productivity of horticulture crops such as grapes (Vitis vinifera). In this study, we identified a grapevine cold-induced basic helix-loop-helix (bHLH) transcription factor (VvbHLH036). Overexpression and CRISPR/Cas9-mediated knockout (KO) of VvbHLH036 enhanced and decreased cold tolerance in grapevine roots, respectively.

Comparative transcriptome analysis of Cyperus esculentus and C. rotundus with contrasting oil contents in tubers defines genes and regulatory networks involved in oil accumulation.

Plant vegetative organs present great potential for lipid storage, with tubers of Cyperus esculentus as a unique example. To investigate the genome and transcriptomic features of C. esculentus and related species, we sequenced and assembled the C.

Inhibition of flowering by gibberellins in the woody plant Jatropha curcas is restored by overexpression of JcFT.

Jatropha curcas (J. curcas) is a perennial oil-seed plant with vigorous vegetative growth but relatively poor reproductive growth and low seed yield. Gibberellins (GAs) promotes flowering in most annual plants but inhibits flowering in many woody plants, including J.

scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer.

Transformer-based models have revolutionized single cell RNA-seq (scRNA-seq) data analysis. However, their applicability is challenged by the complexity and scale of single-cell multi-omics data. Here a novel single-cell multi-modal/multi-task transformer (scmFormer) is proposed to fill up the existing blank of integrating single-cell proteomics with other omics data.

IRON MAN interacts with Cu-DEFICIENCY INDUCED TRANSCRIPTION FACTOR 1 to maintain copper homeostasis.

Copper (Cu) is essential for plant growth and development. IRON MAN (IMA) is a family of small peptides that can bind both iron (Fe) and Cu ions. It was reported that IMAs mediate Fe homeostasis in Arabidopsis thaliana.

Identification of HpMYB1 inducing anthocyanin accumulation in Hippeastrum Hybridum tepals by RNA-seq.

Background: Cultivated Hippeastrum × hybridum is a popular ornamental plant with large and colorful flowers, long flowering duration, and high commercial value. As its main ornamental feature, its flower color is related to the anthocyanin content in the tepals. However, the molecular regulatory mechanisms of anthocyanin biosynthesis in H.

Identification of the () Family Involved in the Adaptation of (Pall.) Kuntze to Saline-Alkaline and Drought Habitats.

(Pall.) Kuntze (Aizoaceae, 2n = 2x = 32), a vegetable used for both food and medicine, is a halophyte that is widely distributed in the coastal areas of the tropics and subtropics. Saline-alkaline soils and drought stress are two major abiotic stressors that significantly affect the distribution of tropical coastal plants.

A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress.

Kiwifruit is a perennial fruit tree with high nutritional and economic value; however, various pathogen stresses have resulted in reductions in its yield and quality. Pentatricopeptide repeat proteins (PPRs), characterized by tandem repetitions of 35 amino acid motifs, play roles in RNA editing, mRNA stability, and splicing. They may also regulate plant development and growth.

JcSEUSS1 negatively regulates reproductive organ development in perennial woody Jatropha curcas.

Overexpression of JcSEUSS1 resulted in late flowering, reduced flower number, wrinkled kernels, and decreased seed yield in Jatopha curcas, while downregulation of JcSEUSS1 increased flower number and seed production. The seed oil of Jatropha curcas is suitable as an ideal alternative for diesel fuel, yet the seed yield of Jatropha is restricted by its small number of female flowers and low seed setting rate. Therefore, it is crucial to identify genes that regulate flowering and seed set, and hence improve seed yield.

Physiological and metabolomic analyses reveal that FeO nanoparticles ameliorate cadmium and arsenic toxicity in Panax notoginseng.

Heavy metal(loid)-contaminated available arable land seriously affects crop development and growth. Engineered nanomaterials have great potential in mitigating toxic metal(loid) stress in plants. However, there are few details of nanoparticles (NPs) involved in Panax notoginseng response to cadmium (Cd) and arsenic (As).

EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors.

Reconstructing functional gene regulatory networks (GRNs) is a primary prerequisite for understanding pathogenic mechanisms and curing diseases in animals, and it also provides an important foundation for cultivating vegetable and fruit varieties that are resistant to diseases and corrosion in plants. Many computational methods have been developed to infer GRNs, but most of the regulatory relationships between genes obtained by these methods are biased. Eliminating indirect effects in GRNs remains a significant challenge for researchers.

Light induces an increasing release of benzyl nitrile against diurnal herbivore Ectropis grisescens Warren attack in tea (Camellia sinensis) plants.

Herbivore-induced plant volatiles (HIPVs) are critical compounds that directly or indirectly regulate the tritrophic interactions among herbivores, natural enemies and plants. The synthesis and release of HIPVs are regulated by many biotic and abiotic factors. However, the mechanism by which multiple factors synergistically affect HIPVs release remains unclear.

Optimization of Heterotrophic Culture Conditions for the Algae WBG-1 to Produce Proteins.

The aim of this study was to improve the protein content and yield of heterotrophic microalgal cultivation and establish a simple, economical, and efficient method for microalgal protein production using the novel green alga, WBG-1, which has not been previously reported for heterotrophic cultivation. Through batch heterotrophic cultivation of this alga, we observed that glucose was the optimal carbon source, while it could not use sucrose as a carbon source. Biomass production and protein content were significantly reduced when sodium acetate was used as the carbon source.

ERF5 enhances protocorm-like body regeneration via enhancement of STM expression in Dendrobium orchid.

Orchid plants develop protocorms upon germination and produce protocorm-like structures called protocorm-like bodies (PLBs) from protocorms and somatic cells via tissue culture. Protocorm-like bodies have broad technical application potential in the orchid industry and their regeneration is a distinct developmental process in the plant kingdom. However, little is known about this unparalleled developmental program.

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage.

Background: Plants sustain intimate relationships with diverse microbes. It is well-recognized that these plant-associated microbiota shape individual performance and fitness of host plants, but much remains to be explored regarding how they exert their function and maintain their homeostasis.

Results: Here, using pink lady (Heterotis rotundifolia) as a study plant, we investigated the phenomenon of microbiota-mediated nitrogen fixation and elucidated how this process is steadily maintained in the root mucilage microhabitat.

Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth.

Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN).

STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data.

Motivation: Single-cell RNA-sequencing (scRNA-seq) technologies provide an opportunity to infer cell-specific gene regulatory networks (GRNs), which is an important challenge in systems biology. Although numerous methods have been developed for inferring GRNs from scRNA-seq data, it is still a challenge to deal with cellular heterogeneity.

Results: To address this challenge, we developed an interpretable transformer-based method namely STGRNS for inferring GRNs from scRNA-seq data.

Tung tree stearoyl-acyl carrier protein Δ9 desaturase improves oil content and cold resistance of and .

The seed oil of tung tree is rich in a-eleostearic acid (ESA), which endows tung oil with the characteristic of an excellently dry oil. The stearoyl-acyl carrier protein δ9 desaturase (SAD) is a rate-limiting enzyme that converts the stearic acid to the oleic acid, the substrate for the production of the α-ESA. However, the function of the two predicted and genes in the tung tree has not been determined.

Epigenetic modifications: Allusive clues of lncRNA functions in plants.

Long non-coding RNAs (lncRNAs) have been verified as flexible and important factors in various biological processes of multicellular eukaryotes, including plants. The respective intricate crosstalk among multiple epigenetic modifications has been examined to some extent. However, only a small proportion of lncRNAs has been functionally well characterized.

Dissecting the effect of ethylene in the transcriptional regulation of chilling treatment in grapevine leaves.

Ethylene (ETH) plays important roles in various development programs and stress responses in plants. In grapevines, ETH increased dramatically under chilling stress and is known to positively regulate cold tolerance. However, the role of ETH in transcriptional regulation during chilling stress of grapevine leaves is still not clear.