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Small secreted peptides (SSPs) are essential for defense mechanisms in plant–microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinereainfection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.

Computed tomography (CT) is widely used in clinical medicine, and low-dose CT (LDCT) has become popular to reduce potential patient harm during CT acquisition. However, LDCT aggravates the problem of noise and artifacts in CT images, increasing diagnosis difficulty. Through deep learning, denoising CT images by artificial neural network has aroused great interest for medical imaging and has been hugely successful. We propose a framework to achieve excellent LDCT noise reduction using independent operation search cells, inspired by neural architecture search, and introduce the Laplacian to further improve image quality. Employing patch-based training, the proposed method can effectively eliminate CT image noise while retaining the original structures and details, hence significantly improving diagnosis efficiency and promoting LDCT clinical applications.

In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.

Eukaryotic cells consist of numerous membrane-bound organelles, which compartmentalize cellular materials to fulfil a variety of vital functions. In the post-genomic era, it is widely recognized that identification of the subcellular organelle localization and transport mechanisms of the encoded proteins are necessary for a fundamental understanding of their biological functions and the organization of cellular activity. Multiple experimental approaches are now available to determine the subcellular localizations and dynamics of proteins. In this review, we provide an overview of the current methods and organelle markers for protein subcellular localization and trafficking studies in plants, with a focus on the organelles of the endomembrane system. We also discuss the limitations of each method in terms of protein colocalization studies.

The CLE (CLAVATA3/Embryo Surrounding Region-related) family, a group of peptides with hormone-like features, plays a pivotal role in plant growth, development, and adaptation to stress. Through homology-based blast analysis of 32 Arabidopsis thalianaCLE peptide sequences, we have identified 5, 14, and 10 CLE family members in Nicotiana tabacum, Capsicum annuum,and Solanum melongena, respectively. Chemical synthesis and functional assays of the peptides led to the discovery that NtCLE3 substantially enhances the drought resistance of these three Solanaceae crops. Our transcriptome, RT-qPCR, and antioxidant enzyme activity data showed that NtCLE3 increased antioxidant capacity and ABA synthesis in tobacco. Moreover, the recombinant protein RPNtCLE3, composed of 6*NtCLE3, preserved the capacity to foster drought resilience and proved to be a promising drought resistance regulator, which presents a more favorable alternative for field applications compared to ABA which degrades rapidly under sunlight exposure. This research unveils the prospective utility of NtCLE3 in enhancing drought tolerance in Solanaceae crops and provides new ideas for the development of novel bioregulators aimed at mitigating drought stress.

Membrane trafficking is essential for plant growth and responses to external signals. The plant unique FYVE domain-containing protein FREE1 is a component of the ESCRT complex (endosomal sorting complex required for transport). FREE1 plays multiple roles in regulating protein trafficking and organelle biogenesis including the formation of intraluminal vesicles of multivesicular body (MVB), vacuolar protein transport and vacuole biogenesis, and autophagic degradation. FREE1 knockout plants show defective MVB formation, abnormal vacuolar transport, fragmented vacuoles, accumulated autophagosomes, and seedling lethality. To further uncover the underlying mechanisms of FREE1 function in plants, we performed a forward genetic screen for mutants that suppressed the seedling lethal phenotype of FREE1-RNAitransgenic plants. The obtained mutants are termed as suppressors of free1(sof). To date, 229 putative sofmutants have been identified. Barely detecting of FREE1 protein with M3plants further identified 84 FREE1-related suppressors. Also 145 mutants showing no reduction of FREE1 protein were termed as RNAi-related mutants. Through next-generation sequencing (NGS) of bulked DNA from F2mapping population of two RNAi-related sofmutants, FREE1-RNAiT-DNA inserted on chromosome 1 was identified and the causal mutation of putative sofmutant is being identified similarly. These FREE1- and RNAi-related sofmutants will be useful tools and resources for illustrating the underlying mechanisms of FREE1 function in intracellular trafficking and organelle biogenesis, as well as for uncovering the new components involved in the regulation of silencing pathways in plants.

A novel full-conjugated 4-(2,2′:6′,2′′-terpyrid-4′-yl) benzenediazonium tetrafluoroborate (diazo-tpy) was synthesized and used for surface modification of materials, such as quartz wafers, ITO glass, silicon, and multiwalled carbon nanotubes (MWCNTs). Under UV irradiation, the diazonium group of diazo-tpy is decomposed and the residual terpyridine group is covalently anchored to the surface of substrates. The obtained tpy-modified MWCNTs (tpy-MWCNTs) have good solubility in common organic solvents. TGA and HRTEM analyses confirmed that terpyridine groups have been symmetrically grafted on MWCNTs. The thickness of the tpy-modified monolayer is about 2.3 nm, which is approximately 2 times the axial length of the 4-(2,2′:6′,2′′-terpyrid-4′-yl)phenyl group. The introduction of terpyridine groups on the surface of MWCNTs provides a coordination site to complex with metal ions. Multilayer films were fabricated from tpy-MWCNTs and ruthenium ions [Ru(III)] via the layer-by-layer self-assembled (LBL SA) technique on the tpy-modified quartz wafer, ITO glass, or silicon. The UV−vis results indicate that (1) Ru(III)-tpy-MWCNT SA multilayer films are successfully formed based on the coordination interaction between ruthenium ions and terpyridine groups, and (2) a progressive assembly occurred regularly with almost an equal amount of deposition in each cycle. The SEM image showed a highly covered Ru(III)-tpy-MWCNT film on the substrate. Moreover, the optoelectronic conversion was also studied by assembling Ru(III)-tpy-MWCNT multilayer films on ITO substrates. Under illumination, the LBL SA films on ITO showed an effective photoinduced charge transfer because of their conjugated structure and the ITO current density changed with the number of bilayers. As the number of bilayer increases, the photocurrent intensity increases and reaches its maximum (∼65 nA/cm2) at six bilayers. These results allow us to design novel materials for applications in optoelectronic devices by using LBL SA techniques.

Transient gene expression in protoplasts, which has been used in several plant species, is an important and versatile tool for rapid functional gene analysis, protein subcellular localization, and biochemical manipulations. This unit describes transient gene expression by electroporation of DNA into protoplasts of Arabidopsisor tobacco suspension‐cultured cells and by polyethylene glycol (PEG)‐mediated DNA transformation into protoplasts derived from rice leaf sheaths. PEG‐mediated DNA transformation for transient gene expression in rice protoplasts in suspension culture is also described as an alternative technique. Methods for collecting intracellular and secreted proteins are also provided. Curr. Protoc. Cell Biol. 63:2.8.1‐2.8.17. © 2014 by John Wiley & Sons, Inc.