Single-cell RNA sequencing reveals the landscape of maize root tips and assists in identification of cell type-specific nitrate-response genes

The root system is fundamental for maize growth and yield.Characterizing its heterogeneity and cell type-specific response to nitrate at the single-cell level will shed light on root development and nutrient uptake.We profiled the transcriptomes of>7000 cells derived from root tips of maize seedlings grown on media with or without nitrate,and identified 11 major cell types or tissues and 85 cell type-specific nitrate-response genes,including several known nitrate metabolic genes.A pseudotime analysis showed a continuous pseudotime series with the beginning at meristematic zone cells and showed that the root hair cell was derived by differentiation of a subset of epidermal cells.Interspecies comparison of root cells between maize and rice revealed the conservation and divergence of the root cell types and identified 57,216,and 80 conserved orthologous genes in root hair,endodermis,and phloem cells respectively.This study provides a global view of maize root tip developmental processes and responses to nitrate at the single-cell level.The genes described in the present work could serve as targets for further genetic analyses and accurate regulation of gene expression and phenotypic variation in specific cell types or tissues.

Overexpression of the Wounding-Responsive Gene AtMYB15 Activates the Shikimate Pathway in Arabidopsis

The MYB transcription factor genes play important roles in many developmental processes and various defense responses of plants. The shikimate pathway is a major biosynthetic pathway for the production of three aromatic amino acids and other aromatic compounds that are involved in multiple responses of plants, including protection against UV and defense. Herein, we describe the characterization of the R2R3-MYB gene AtMYB15as an activator of the shikimate pathway in Arabidopsis. The AtMYB15 protein is nuclear localized and a transcriptional activation domain is found in its C-terminal portion. Northern blots showed that AtMYB15 is an early wounding-inducible gene. Resutls of microarray analysis, confirmed using quantitative real-time polymerase chain reaction, showed that overexpression of AtMYB15 in transgenic plants resulted in elevated expression of almost all the genes involved in the shikimate pathway. Bioinformatics analysis showed that one or more AtMYB15-binding AC elements were detected in the promoters of these upregulated genes. Furthermore, these genes in the shikimate pathway were also found to be induced by wounding. These data suggest an important role of AtMYB15as a possible direct regulator of the Arabidopsis shikimate pathway in response to wounding.

OS1 functions in the allocation of nutrients between the endosperm and embryo in maize seeds

Uncovering the genetic basis of seed develop-ment will provide useful tools for improving both crop yield and nutritional value, However, the genetic regulatory networks of maize (Zea mays) seed development remain largely unknown. The maize opaque endosperm and small germ 1 (osl) mutant has opaque endosperm and a small embryo,Here, we cloned OSi1 and show that it encodes a putative transcription factor containing an RWP-RK domain-Transcriptional analysis indicated that OSi1 expression is elevated in early endosperm development, especially in the basal endosperm transfer layer (BETL), conducting zone (CZ), and central starch endospcrm (CSE) cells. RNA sequencing (RNA-Seq) analysis of the osi mutant revealed sharp downregulation of certain genes in specific cell types, including ZmMRP-1 and Megl in BETL cells and a majority of zein-and starch-related genes in CSE cells. Using a haploid induction system, we show that wild-type endosperm could rescue the smaller size of osi embryo, which suggests that nutrients are allocated by tho wild type endosperm. Therefore, our dsta imply that the network regulated by 051 accomplishes a key step in nutrient allocation between endosperm and embryo within maize seeds. Identification of this network will help uncover the mechanisms regulating the nutritional balance between endosperm and embryo.

Preparation of freestanding palladium nanosheets modified with gold nanoparticles at edges

Electronic adjustment is one of the most commonly used strategies to improve the catalytic performance of heterogeneous catalysts. We prepared hexagonal ultrathin Pd nanosheets with edges modified by gold nanoparticles （Au@Pd nanosheets） using galvanic replacement method. By virtue of the electronic interactions between the Pd nanosheets and Au nanoparticles, the Au@Pd nanosheets exhibited excellent catalytic performances in the carbonylation of iodobenzene by carbon monoxide. The novel nanocomposites could be applied as model catalysts to explore electronic effects in catalysis.

MP3RNA-seq:Massively parallel 3’end RNA sequencing for high-throughput gene expression profiling and genotyping

Transcriptome deep sequencing(RNA‐seq)hasbecome a routine method for global geneexpression profiling.However,its application tolarge‐scale experiments remains limited by costand labor constraints.Here we describe amassively parallel 3′end RNA‐seq(MP3RNA‐seq)method that introduces unique samplebarcodes during reverse transcription to permitsample pooling immediately following this initialstep.MP3RNA‐seq allows for handling of hun-dreds of samples in a single experiment,at acost of about$6 per sample for libraryconstruction and sequencing.MP3RNA‐seq iseffective for not only high‐throughput geneexpression profiling,but also genotyping.Todemonstrate its utility,we applied MP3RNA‐seqto 477 double haploid lines of maize.We iden-tified 19,429 genes expressed in at least 50%ofthe lines and 35,836 high‐quality singlenucleotide polymorphisms for genotypinganalysis.Armed with these data,we performedexpression and agronomic trait quantitativetrait locus(QTL)mapping and identified 25,797expression QTLs for 15,335 genes and 21 QTLsfor plant height,ear height,and relative earheight.We conclude that MP3RNA‐seq is highlyreproducible,accurate,and sensitive forhigh‐throughput gene expression profiling andgenotyping,and should be generally applicableto most eukaryotic species.

Investigation into gas lubrication performance of porous gas bearing considering velocity slip boundary condition

Porous gas bearings(PGBs)have a proactive application in aerospace and turbomachinery.This study investigates the gas lubrication performance of a PGB with the condition of velocity slip boundary(VSB)owing to the high Knudsen number in the gas film.The Darcy-Forchheimer laws and modified Navier-Stokes equations were adopted to describe the gas flow in the porous layer and gas film region,respectively.An improved bearing experimental platform was established to verify the accuracy of the derived theory and the reliability of the numerical analysis.The effects of various parameters on the pressure distribution,flow cycle,load capacity,mass flow rate,and velocity profile are demonstrated and discussed.The results show that the gas can flow in both directions,from the porous layer to the gas film region,or in reverse.The load capacity of the PGB increases with an increase in speed and inlet pressure and decreases with an increase in permeability.The mass flow rate increases as the inlet pressure and permeability increase.Furthermore,the simulation results using VSB are in agreement with the experimental results,with an average error of 3.4%,which indicates that the model using VSB achieves a high accuracy.The simulation results ignoring the VSB overrate the load capacity by 16.42%and undervalue the mass flow rate by 11.29%.This study may aid in understanding the gas lubrication mechanism in PGBs and the development of novel gas lubricants.

Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize

Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are poorly understood. Here, we present genome-wide nucleosome maps of maize shoot and endosperm generated by sequencing the micrococcal nuclease digested nucleosomal DNA. The changes of gene transcriptional status between shoot and endosperm were accompanied by preferential nucleosome loss from the promoters and shifts in the first nucleosome downstream of the transcriptional start sites （＋1 nucleosome） and upstream of transcriptional termination sites （-1 nucleosome）. Intrinsically DNA-encoded nucleosome orga- nization was largely associated with the capacity of a gene to alter its transcriptional status among different tissues. Compared with tissue-specific genes, constitutively expressed genes showed more pronounced 5＇ and 3＇ nucleosome-depleted regions as well as further ＋1 nucleosome to transcriptional start sites and -1 nucleosome to transcriptional termination sites. Moreover, nucleosome organization was more highly correlated with the plasticity of gene transcriptional status than with its expression level when examined using in vivo and predicted nucleosome data. In addition, the translational efficiencies of tissue-specific genes appeared to be greater than those of constitutively expressed genes. Taken together, our results indicate that intrinsically DNA-encoded nucleosome organization is important, beyond its role in regulating gene expression levels, in determining the plasticity of gene transcriptional status.