Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.

Post-transcriptional Gene Silencing Induced by Short Interfering RNAs in Cultured Transgenic Plant Cells

Short interfering RNA (siRNA) is widely used for studyingpost-transcriptional gene silencing and holds great promise as a tool for both identifying functionof novel genes and validating drug targets. Two siRNA fragments (siRNA-a and -b), which weredesigned against different specific areas of coding region of the same target green fluorescentprotein (GFP) gene, were used to silence GFP expression in cultured gfp transgenic cells of rice(Oryza sativa L.; OS), cotton (Gossypium hirsutum L.; GH), Eraser fir [Abies fraseri (Pursh) Poir;AF], and Virginia pine (Pinus virginiana Mill.; PV). Differential gene silencing was observed in thebombarded transgenic cells between two siRNAs, and these results were consistent with theinactivation of GFP confirmed by laser scanning microscopy, Northern blot, and siRNA analysis intested transgenic cell cultures. These data suggest that siRNA-mediated gene inactivation can be thesiRNA specific in different plant species. These results indicate that siRNA is a highly specifictool for targeted gene knockdown and for establishing siRNA-mediated gene silencing, which could bea reliable approach for large-scale screening of gene function and drug target validation.

Celebrating Plant Cells:A Special Issue on Plant Cell Biology

A special issue on plant cell biology is long overdue for JIPB! In the last two decades or so, the plant biology community has been thrilled by explosive discoveries regarding the molecular and genetic basis of plant growth, development, and responses to the environment, largely owing to recent maturation of model systems like Arabidopsis thaliana and the rice Oryza sativa, as well as the rapid development of high throughput technologies associated with qenomics and proteomics.

Mechanical Response of Single Plant Cells to Cell Poking:A Numerical Simulation Model

Cell poking is an experimental technique that is widely used to study the mechanical properties of plant cells. A full understanding of the mechanical responses of plant cells to poking force Is helpful for experimental work. The aim of this study was to numerically investigate the stress distribution of the cell wall, cell turgor, and deformation of plant cells in response to applied poking force. Furthermore, the locations damaged during poking were analyzed. The model simulates cell poking, with the cell treated as a spherical, homogeneous, isotropic elastic membrane, filled with incompressible, highly viscous liquid. Equilibrium equations for the contact region and the non-contact regions were determined by using membrane theory. The boundary conditions and continuity conditions for the solution of the problem were found. The forcedeformation curve, turgor pressure and tension of the cell wall under cell poking conditions were obtained. The tension of the cell wall circumference was larger than that of the meridian. In general, maximal stress occurred at the equator around. When cell deformation increased to a certain level, the tension at the poker tip exceeded that of the equator. Breakage of the cell wall may start from the equator or the poker tip, depending on the deformation. A nonlinear model is suitable for estimating turgor, stress, and stiffness, and numerical simulation is a powerful method for determining plant cell mechanical properties.

Determination of volumetric elastic moduli of plant leaf cells based on pressure-volume curves

Volumetric elastic modulus （VEM） is an important parameter in biophysics and biomechanics of plants for in particular understanding cell growth. This paper proposes a new relation that can be used for precisely determining VEM. With the aid of this relation, it shows that the exponential approximation of the pressure-volume relationship adopted in most of the literatures in this field may lead to serious errors on VEM.

Plant regeneration of protoplasts isolated from suspension cells derived from leaf blale of Oryza sative

We used the leaf blade of rice (cultivars were Nonghu 6, Sugeng 2, Huyou 2 and Hanfeng) as initial material for protoplast culture, and a great number of regenerated plants were obtained. Rice seeds were sterilized and germinated. The immature leaves were cut into 3-5 mm pieces when the third or forth leaf appeared. Leaf pieces were inoculated on MS medium with 2,4-D 4 mg/1, NAA 2mg/1 and IAA Img/1. After 2 wk culture, calli were induced and subcultured once or twice for multiplication. 3-5 g calli were transferred to the modified MS liquid medium with 2,4-D 2 mg/1 and KT 0.5mg/1 for suspension culture. Embryogenic cell suspension was established after 2 mo culture. The effect of the growth period of suspension cells on the

Non-Canonical Functions of the E2F/DP Pathway with Emphasis in Plants

The E2F/DP pathway is a widely conserved regulatory mechanism in pluricellular organisms.The family of E2F and DP transcription factors was originally described having a role in the transition from the G1 to the S phase of the cell cycle.However,the discovery of hundreds of possible gene targets and their involvement in many other biochemical processes,soon showed that they participated in cell development and differentiation,chromatin remodeling,DNA repair and others.The E2F/DP transcription factors can act as either activators or repressors of transcription depending on their association to other regulatory proteins,particularly the retinoblastoma protein,or even depending to their protein structure that can define their role.In plants the E2F/DP pathway also regulates endoreduplication,a process present along the life cycle,from organ elongation to root differentiation and reproduction.These transcription factors also help plant cells to respond to environmental disturbances such as those caused by different types of radiation,or by pathogens.This review focuses on the“so called”non-canonical functions of the E2F/DP family proteins in animal and plant cells,that are in fact essential activities that connect regulatory circuits among multiple metabolic pathways by means of their atypical functions.

Transient Expression of Exogenous Gene into Plant Cell Mediated by PEI Nanovector

This study was carried out to investigate the transfection effect of exogenous gene into plant protoplast cell mediated by polyethylenimine （PEI） nanovector, based on PEI gene delivery system in the field of medical science. PEI/DNA complexes were prepared by using PEI polymer to bind the plant expression plasmid, pCMl205-GFPn. The ability of PEI combining and protecting DNA was investigated by agarose gel electrophoresis retardation assay. The surface characteristics of PEI/DNA complexes were observed with transmission electron microscope. The transfection efficiency of Arabidopsis thaliana protoplasts mediated by PEI/DNA complexes at different N/P ratios was analyzed based on observation of transient expression of green fluorescent protein with confocal laser scanning microscope. PEI could bind and condense DNA, and form stable 100-200 nm PEI/DNA complexes when the proportion of PEl and DNA is in the range of 5：1-1：4. Transfection efficiency of PEI/DNA complexes increased with N/P ratios in range of N/P〈5 and reached the highest at N/P=5, and began to decrease beyond N/P〉5 as higher toxicity to cells. The transfection efficiency of PEI/DNA complexes at N/P=5 was higher than PEG. This study confirmed that PEI nanovector could effectively mediate foreign gene entering into A. thaliana protoplast cell to obtain transient expression, which may be developed as a hopeful and novel transgenic method combined with plant protoplast regeneration.

Synthesis of Fluorescent Carbon Quantum Dots and Their Application in the Plant Cell Imaging

Carbon quantum dots(CQDs) exhibit tremendous advantages for plant growth study due to its strong fluorescence and good biocompatibility. The fluorescent CQDs were synthesized by the onestep microwave method with the raw materials of citric acid(CA) and urea(UR), and expressed a unique green fluorescence with the optimal excitation wavelength of over 400 nm through adjusting the doping of N elements. It is demonstrated that CQDs can act as deliver media in plant and fluorescent probes for plant cell imaging through directly cultivated in the seedlings of melon and wheat, respectively. Based on the effects of the fluorescent CQDs on plants growth, we can further study the mechanisms of the ions transport in plants.

Plant Cell Wall, a Challenge for Its Characterisation

The plant cell wall is a complex 3D network composed of polysaccharides, lignin and proteins. The knowledge of the structure and content of each cell wall polymer is a prerequisite to understand their functions during plant development and adaptation but also to optimise their industrial applications. The analysis of cell wall compounds is complicated by their multiple molecular interactions. In this review, we present numerous methods to purify, characterise and quantify proteins, polysaccharides and lignin from the wall. Two kinds of approaches are detailed: the first presents in vitro methods which involve the breakdown of the molecular linkages between polymers thanking to chemical, physical and/or enzymatic treatments. The second approach describes in situ methods that allow the cell wall polymer characterisation thanking to many analytical techniques coupled with microscopy. If microscopy is the common point of all of them, their development is associated with improvement of analytical techniques, increasing their power of resolution.

Dynamic Effects of Cerium on Syntheses of Soluble Protein and Taxol in Suspension Culture of Taxus Chinensis Var. Mairei Cells

The dynamic effects of Ce4+ on the syntheses of soluble protein and taxol in suspension cultures of Taxus chinensis var. mairei cells were studied. The phenomena of 'partition' and 'bifurcation' were observed in studying the dynamic effect of Ce4+ on soluble protein synthesis and cell activity. That is, Ce4+ of low concentration improves the soluble protein synthetic strength and cell activity, while Ce4+ of high concentration is harmful to protein synthesis and cell activity. In addition, Ce4+ of appropriate concentration enhances taxol synthesis.

Enhancement of the transfection efficiency of DNA into Crocus sativus L. cells via PEI nanoparticles

Over the past decade, several natural and synthetic cationic polymers have been utilized for gene delivery into cells. Among them, polyethylenimine(PEI) was used for gene therapy successfully. The present study investigated the effect of PEI and ultrasound waves on ssD NA delivery into saffron cells. Gel retardation, dynamic light scattering(DLS) and scanning electron microscopy(SEM) assays were employed to determine the physicochemical properties of PEI/f-DNA polyplex(complex of PEI and fluorescently labeled DNA). Moreover, the cytotoxicity of PEI, PEI/f-DNA polyplex and ultrasound were investigated on saffron cells at different concentrations. The gel retardation results indicated that the formation and neutralization of the PEI/f-DNA polyplex were completed at N/P=5. The particle size distribution of the polyplexes was from 50 to 122 nm. The experimental results revealed that the cytotoxicity of the PEI/f-DNA polyplex was lower than that of PEI alone, hence the cells showed both dose-and exposure duration-dependent responses. Furthermore, the viability of saffron cells declined extremely after 5 and 10 min sonication but this reduction was not significant at 2 min exposure duration. The results also indicated that the combined utilization of ultrasound and PEI nanoparticles increased the transfection efficiency of saffron cells up to two times higher than those obtained by PEI or ultrasound separately.

Physiological Response of the Resurrection Fern Subjected to Environmental Stress as Shown by Plant Cell Membrane Integrity

Resurrection fern has a unique ability to maintain cell wall integrity when the plant cell is desiccated. It uses proteins such as late embryogenesis proteins and heat shock proteins to maintain their cellular functions. The purpose of this experiment is to determine the effects of environmental stressors on the physiological response of the resurrection fern (Pleopeltis polypodioides). The physiological response of resurrection fern plants was subjected to various temperatures (-50°C, 0°C, 25°C, and 50°C) for 7 days. Results indicated that there was a significant difference between hydrated and desiccated ferns based on the temperature. Additionally, electrolyte leakage measurements confirmed cell damage following exposure to temperature extremes of -50°C and 50°C.

Summary of the Frontier Introduction of Preparation of Secondary Metabolites in Plant Cell Culture

Plant cell culture technology is a technology that applies the research results of cell engineering to produce plant biological products at the cellular level.In recent years,the secondary metabolites of plants have attracted more and more attention.The use of plant cell culture technology is a fast and efficient method of producing secondary metabolites.

The Anti-Sickling Properties of Medicinal Plants, Insights in Botanical Medicine*

SCD is one of the most prevailing homogeneous inherited haemoglobinopathies causing a plethora of various clinical complications to the patients. The high mortality and morbidity severely concern the Western community, where numerous clinical trials and research for a cure are in process. In order to alleviate patients from the severe symptoms of the disease, avoiding the side effects, Botanical Medicine exhibits concrete evidence, as a gold candidate, to be the salvation to the problem. The Preferred Reporting Items for Systematic Review (PRISMA) protocol has been used to achieve extensive research on the topic, focusing on the identification and evaluation of the phytochemical properties of common medicinal plants. Meta-analysis has also been implemented on the results of published literature. Forest plots have been plotted, comparing and evaluating the results’ validity and significance. The meta-analysis results have undoubtedly demonstrated the importance and significance of the medicinal plants and their properties against various clinical complications, focusing on the pathogenicity of SCD. Surprisingly, their effectiveness to suppress haemoglobin polymerisation and increase the Fe2+/Fe3+ ratio in patients, enhanced the normal morphological erythrocytes’ appearance by suppressing the sickle shape of drepanocytes. Research made on the epidemiology of SCD associates the disease with the geographical frequency of malaria infection. Based on the natural selection theory of Charles Darwin, nature aids in the population’s survival by the endemicity of various medicinal plants in areas with increased SCD patients. Limitations to the medicinal plants’ consumptions and further therapeutic options have been discussed.

Elucidating the role of SlXTH5 in tomato fruit softening

Fruit softening in tomato(Solanum lycopersicum)is closely associated with cell wall disassembly,which is brought about through the action of a range of cell wall structure-related enzymes and other proteins such as expansins.Xyloglucan endotransglucosylase/hydrolase(XTH)(EC 2.4.1.207 and/or EC 3.2.1.151)has been proposed to be key player involved in xyloglucan metabolism.SlXTH5 showed the highest expression level among all SlXTHs during tomato ripening.In this study,the role of SlXTH5 involved in tomato softening was investigated in CRISPR-based knockout mutants of SlXTH5.Loss-of-function of SlXTH5 in transgenic tomato lines resulted in slightly firmer fruit pericarp,but significantly decreased their color index compared with azygous wild type(WT)control fruits.Increased paste viscosity was detected in CRISPR mutants,indicating that the activity of SlXTH5 is responsible for maintaining cell wall structural integrity.Immunocytochemistry studies were performed using the monoclonal antibody probe LM25 to examine the localization and distribution of xyloglucan in the pericarp cells of the CRISPR mutant fruits.The data indicated more xyloglucan was retained in the pericarp of CRISPR mutant fruit than in WT control fruit.This study revealed the link between SlXTH5 and xyloglucan metabolism and indicated the potential of manipulating SlXTH5 to regulate fruit softening.

Plant regeneration in the new era:from molecular mechanisms to biotechnology applications

Plants or tissues can be regenerated through various pathways.Like animal regeneration,cell totipotency and pluripotency are the molecular basis of plant regeneration.Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration.Specifically,plant hormones,cell division,epigenetic remodeling,and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells.Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species,with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity.Conducting multi-omics studies at the single-cell level,tracking plant regeneration processes in real-time,and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration,improve crop regeneration efficiency,and contribute to future crop design.

Enantioselective reduction of acetophenone analogues using carrot and celeriac enzymes system

The enantioselective reduction of acetophenone analogues catalyzed by carrot and celeriac was performed in moderate conversions and excellent enantiomeric excesses.The steric factors and electronic effects of the substituents at the aromatic ring were found to significantly affect the efficiency of the enantioselective reduction of acetophenone analogues,while they had a little effect on the enantioselectivity of acetophenone analogues reduction.It was also found that the conversions of acetophenone analogu...

Sweet sorghum and Miscanthus：Two potential dedicated bioenergy crops in China

Among the potential non-food energy crops,the sugar-rich C4 grass sweet sorghum and the biomass-rich Miscanthus are increasingly considered as two leading candidates.Here,we outline the biological traits of these energy crops for largescale production in China.We also review recent progress on understanding of plant cell wall composition and wall polymer features of both plant species from large populations that affect both biomass enzymatic digestibility and ethanol conversion rates under various pretreatment conditions.We finally propose genetic approaches to enhance biomass production,enzymatic digestibility and sugar-ethanol conversion efficiency of the energy crops.