Reform of Practical Teaching of “Linux Operating System Fundamentals” Under the Background of Emerging Engineering Education

With the advancement of the construction of emerging engineering education,the reform of practical teaching has become an important task of higher engineering education.This article takes the course“Linux Operating System Fundamentals”as an example to explore practical teaching reform in the context of emerging engineering education.By analyzing the current situation and problems in course practical teaching,we proposed practical teaching reforms such as online experiments,practical content updates,project-based engineering practices,and diversified evaluation models,and designed corresponding implementation plans.Practice has proved that this reform can improve students’learning interest and engineering practical skills,and cultivate outstanding engineers with innovative spirit and practical skills.

DR5 is a Suitable System for Studying the Auxin Response in the Poncirus trifoliata-Xanthomonas axonopodis pv.citri Interaction

The local auxin distribution characteristics in the roots,stems,and leaves of stably transformed plantlets of trifoliate orange(Poncirus trifoliata)with auxin reporter system DR5::GUS-YFP were elucidated in this research.The auxin response maxima could be observed in the apex of the root tip,primary phloem of the tender stem,and the margin of the young leaves according to the activity of theβ-glucuronidase(GUS)reporter gene triggered by the auxin responsive DR5 promoter.Auxin responses in the apex of the root tips increased when treated with synthetic auxin 1-naphthylacetic acid(NAA),but decreased when treated with the auxin polar transportation inhibitor 2,3,5-triiodobenzoic acid(TIBA).These results indicated that the DR5 reporter system worked in P.trifoliata for auxin distribution and response observation.Trifoliate orange is highly susceptible to citrus canker disease.Auxin accumulation was observed visually in the invasion sites of the detached leaves inoculated with Xanthomonas axonopodis pv.citri(Xac)by GUS staining;the upregulated expression of the YFP,GH3.1,GH3.9,and SAUR genes assessed by quantitative real-time PCR(qRT-PCR)also identified auxin accumulation in the inoculated tissues following Xac infection.Overall,these findings indicated that the plantlets of P.trifoliata engineered with the auxin reporter gene provided a promising system for studying auxin responses during Xac infection.

Exploration on the Practice System of Computer Software Course under the New Engineering

The rapid development of information technology and the new economy is a challenge to the training of computer technology and engineering professionals. The cultivation of engineering talents in Computer Engineering under the new engineering is an important part of the construction and exploration of new engineering in universities. According to the teaching reform of computer specialty in the new engineering construction, starting from the practice of curriculum system of software, mainly discusses the basic ideas of practice teaching reform of the course of computer software, software engineering practice curriculum system and practice curriculum system implementation method. The basic ideas of teaching reform practice in the course of the software include: expanding computer professional students' knowledge, strengthening students' computer science and software engineering knowledge and engineering practice ability, strengthening the frontiers of computer science and technology guide. Software practice course system is divided into three levels, including basic language course, engineering basic professional practice course and the professional practice course of engineering application direction. The implementation method of engineering application practice curriculum system is discussed in detail, such as strengthening university-enterprise cooperation, introducing teachers of social training institutions and guiding students to participate in subject competition and innovation projects.

Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis

The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Here,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell resolution.We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis seedlings.We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers.We further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity.In addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs.The analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://biobigdata.nju.edu.cn/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.

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.

A predictive model for ethylene-mediated auxin and cytokinin patterning in the Arabidopsis root

The interaction between auxin and cytokinin is important in many aspects of plant development.Experimental measurements of both auxin and cytokinin concentration and reporter gene expression clearly show the coexistence of auxin and cytokinin concentration patterning in Arabidopsis root development.However,in the context of crosstalk among auxin,cytokinin,and ethylene,little is known about how auxin and cytokinin concentration patterns simultaneously emerge and how they regulate each other in the Arabidopsis root.This work utilizes a wide range of experimental observations to propose a mechanism for simultaneous patterning of auxin and cytokinin concentrations.In addition to revealing the regulatory relationships between auxin and cytokinin,this mechanism shows that ethylene signaling is an important factor in achieving simultaneous auxin and cytokinin patterning,while also predicting other experimental observations.Combining the mechanism with a realistic in silico root model reproduces experimental observations of both auxin and cytokinin patterning.Predictions made by the mechanism can be compared with a variety of experimental observations,including those obtained by our group and other independent experiments reported by other groups.Examples of these predictions include patterning of auxin biosynthesis rate,changes in PIN1 and PIN2 patterns in pin3,4,7 mutants,changes in cytokinin patterning in the pls mutant,PLS patterning,and various trends in different mutants.This research reveals a plausible mechanism for simultaneous patterning of auxin and cytokinin concentrations in Arabidopsis root development and suggests a key role for ethylene pattern integration.

Silver nanoparticles:From in vitro green synthesis to in vivo biological effects in plants

Silver nanoparticles(AgNPs)are extensively utilized in industrial,biotechnological and medical fields because of their specific physical and chemical properties,which shown small size effects,surface and interface effects,quantum scale effects.Inevitably,wastewater containing AgNPs is leached into the soil.AgNPs in soil may be absorbed by plant roots and they affect plant growth.Understanding the complex interactions between AgNPs and plants is of crucial significance since plants are essential to the ecological environment as key players in ecosystems.Most previous reports have focused on AgNP phytotoxicity rather than positive effects in the plant field.This article reviews recent studies on the important aspects about nanoparticles including the green synthesis,absorption,migration,accumulation,biotransformation,biological effects,and the underlying molecular mechanisms of AgNPs affecting plants.We provide insights into the interactions between AgNPs and plants,helping to further understand AgNP-related effects and biosafety in agricultural production,as well as the practical application of various nanomaterials in agriculture.

Crosstalk Complexities between Auxin, Cytokinin, and Ethylene in Arabidopsis Root Development： From Experiments to Systems Modeling, and Back Again

Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin, and ethylene are three important hormones that regulate many aspects of plant development. This review critically evaluates the crosstalk between the three hormones in Arabidopsis root development. We integrate a variety of experimental data into a crosstalk network, which reveals multiple layers of complexity in auxin, cytokinin, and ethylene crosstalk. In particular, data integration reveals an additional, largely overlooked link between the ethylene and cytokinin pathways, which acts through a phosphorelay mechanism. This proposed link addresses outstanding questions on whether ethylene application promotes or inhibits receptor kinase activity of the ethylene receptors. Elucidating the complexity in auxin, cytokinin, and ethylene crosstalk requires a combined experimental and systems modeling approach. We evaluate important modeling efforts for establishing how crosstalk between auxin, cytokinin, and ethylene regulates patterning in root develop- ment. We discuss how a novel methodology that iteratively combines experiments with systems modeling analysis is essential for elucidating the complexity in crosstalk of auxin, cytokinin, and ethylene in root development. Finally, we discuss the future challenges from a combined experimental and modeling perspective.

Environmental pollution by persistent toxic substances and health risk in an industrial area of China

Soil is an important environmental medium that is closely associated with humans and their health. Despite this, very few studies have measured toxicants in soils, and associated them with health risks in humans. An assessment of health effects from exposure to contaminants in soils surrounding industrial areas of chemical production and storage is important. This article aims at determining pollution characteristics of persistent toxic substances （PTS） in an industrial area in China to unravel the relationship between soil pollution by PTS and human health. One hundred and five soil samples were collected and 742 questionnaires were handed out to residents living in and around an industrial area around Bohai Bay, Tianjin in Northern China. Concentrations of organochlorine pesticides and polycyclic aromatic hydrocarbons （PAHs） were determined in soil. Mann-Whitney U and binary multivariate non- conditional logistic regression models were employed to analyze the relationship between health indicators of local residents and contaminant levels. Odds ratio （OR） and a 95% confidence interval （CI） for health incidences were also calculated. The average concentrations of DDT （73.9 ng/g）, HCH （654 ng/g） and PAHs （1225 ng/g） were relatively high in the industrial area. Residents living in the chemical industry parks were exposed to a higher levels of PTS than those living outside the chemical industry parks. This exposure was associated with a higher risk of breast cancer （OR 1.87, 95% CI 0.12-30.06）, stomach cancer （OR 1.87, 95% CI 0.26- 13.41）, dermatitis （OR 1.72, 95% CI 1.05-2.80）, gastroenteritis （OR 1.59, 95% CI 0.94-2.68）, and pneumonia （OR 1.05, 95% CI 0.58-1.89）.

DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice

R-loop structures （RNA：DNA hybrids） have important functions in many biological processes, including transcriptional regulation and genome instability among diverse organisms. DNA topoisomerase 1 （TOP1）, an essential manipulator of DNA topology during RNA transcription and DNA replication processes, can prevent R-loop accumulation by removing the positive and negative DNA supercoiling that is made by RNA polymerases during transcription. TOP1 is required for plant development, but little is known about its function in preventing co-transcriptional R-loop accumulation in various biological processes in plants. Here we show that knockdown of OsTOP1 strongly affects rice development, causing defects in root archi- tecture and gravitropism, which are the consequences of misregulation of auxin signaling and transporter genes. We found that R-loops are naturally formed at rice auxin-related gene loci, and overaccumulate when OsTOP1 is knocked down or OsTOP1 protein activity is inhibited. OsTOP1 therefore sets the accurate expression levels of auxin-related genes by preventing the overaccumulation of inherent R-loops. Our data reveal R-loops as important factors in polar auxin transport and plant root development, and highlight that OsTOP1 functions as a key to link transcriptional R-loops with plant hormone signaling, provide new in- sights into transcriptional regulation of hormone signaling in plants.

Molecular cytogenetic map visualizes the heterozygotic genome and identifies translocation chromosomes in Citrus sinensis

Citrus sinensis is the most cultivated and economically valuable Citrus species in the world,whose genome has been assembled by three generation sequencings.However,chromosome recognition remains a problem due to the small size of chromosomes,and difficulty in differentiating between pseudo and real chromosomes because of a highly heterozygous genome.Here,we employ fluorescence in situ hybridization(FISH)with 9 chromosome painting probes,30 oligo pools,and 8 repetitive sequences to visualize 18 chromosomes.Then,we develop an approach to identify each chromosome in one cell through single experiment of oligo-FISH and Chromoycin A3(CMA)staining.By this approach,we construct a high-resolution molecular cytogenetic map containing the physical positions of CMA banding and 38 sequences of FISH including centromere regions,which enables us to visualize significant differences between homologous chromosomes.Based on the map,we locate several highly repetitive sequences on chromosomes and estimate sizes and copy numbers of each site.In particular,we discover the translocation regions of chromosomes 4 and 9 in C.sinensis“Valencia.”The high-resolution molecular cytogenetic map will help improve understanding of sweet orange genome assembly and also provide a fundamental reference for investigating chromosome evolution and chromosome engineering for genetic improvement in Citrus.

The F-box protein SHORT PRIMARY ROOT modulates primary root meristem activity by targeting SEUSS-LIKE protein for degradation in rice

Root meristem activity is essential for root morphogenesis and adaptation,but the molecular mechanism regulating root meristem activity is not fully understood.Here,we identify an F-box family E3 ubiquitin ligase named SHORT PRIMARY ROOT(SHPR) that regulates primary root(PR)meristem activity and cell proliferation in rice.SHPR loss-of-function mutations impair PR elongation in rice.SHPR is involved in the formation of an SCF complex with the Oryza sativa SKP1-like protein OSK1/20.We show that SHPR interacts with Oryza sativa SEUSS-LIKE(OsSLK) in the nucleus and is required for OsSLK polyubiquitination and degradation by the ubiquitin 26S-proteasome system(UPS).Transgenic plants overexpressing OsSLK display a shorter PR phenotype,which is similar to the SHPR loss-of-function mutants.Genetic analysis suggests that SHPR promotes PR elongation in an OsSLK-dependent manner.Collectively,our study establishes SHPR as an E3 ubiquitin ligase that targets OsSLK for degradation,and uncovers a protein ubiquitination pathway as a mechanism for modulating root meristem activity in rice.