Chromosome-scale genome assembly of sweet cherry(Prunus avium L.)cv.Tieton obtained using long-read and Hi-C sequencing

Sweet cherry(Prunus avium)is an economically significant fruit species in the genus Prunus.However,in contrast to other important fruit trees in this genus,only one draft genome assembly is available for sweet cherry,which was assembled using only Illumina short-read sequences.The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies.A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed.A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated,representing~190x and 136x coverage,respectively,of the sweet cherry genome.The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb.Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59%of the bases in the assembled genome.Genome annotation revealed that more than half of the genome(59.40%)was composed of repetitive sequences,and 40,338 protein-coding genes were predicted,75.40%of which were functionally annotated.With the chromosomescale assembly,we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry.Four auxin-responsive genes(two GH3s and two SAURs)were induced in the late stage of fruit development,indicating that auxin is crucial for the sweet cherry ripening process.In addition,772 resistance genes were identified and functionally predicted in the sweet cherry genome.The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.

Yellow Fever: A Re-Emerging Threat

Yellow fever (YF) is arguably one of the most notorious infectious diseases in the world. The disease is not only fatal to the human but also several primate species many of which are endangered by now. YF is caused by the yellow fever virus (YFV). While YFV was one of the most feared infectious diseases in the 18th and 19th century, the overall disease burden has been greatly reduced through an effective vector (mosquito) control and the development of the live-attenuated vaccine, YFV-17D. However, recent outbreaks in previously non-endemic areas have risen intense awareness among scientists and the public and remind us that YFV cannot be forgotten and containing it needs to remain a global health priority. Notably, the 11 imported yellow fever cases to China;hence the whole Asia-Pacific region, in 2016 alone, highlight that YFV may pose a threat to a large population which is intensified by increasing human migration and an extremely low vaccination rate. This paper assesses the possibility of a new round of epidemics of YFV, indicating that the virus should indeed be recognized as a re-emerging threat, and offers suggestions on how to prevent it. Stricter vaccine regulation and border check should be applied, as well as further research into alternative vaccines. More attention and efforts should be paid to fighting against the disease.

Engineered Hybrid Materials with Smart Surfaces for Effective Mitigation of Petroleum-Originated Pollutants

The generation and controlled or uncontrolled release of hydrocarbon-contaminated industrial wastewater effluents to water matrices are a major environmental concern.The contaminated water comes to surface in the form of stable emulsions,which sometimes require different techniques to mitigate or separate effectively.Both the crude emulsions and hydrocarbon-contaminated wastewater effluents contain suspended solids,oil/grease,organic matter,toxic elements,salts,and recalcitrant chemicals.Suitable treatment of crude oil emulsions has been one of the most important challenges due to the complex nature and the substantial amount of generated waste.Moreover,the recovery of oil from waste will help meet the increasing demand for oil and its derivatives.In this context,functional nanostructured materials with smart surfaces and switchable wettability properties have gained increasing attention because of their excellent performance in the separation of oil–water emulsions.Recent improvements in the design,composition,morphology,and fine-tuning of polymeric nanostructured materials have resulted in enhanced demulsification functionalities.Herein,we reviewed the environmental impacts of crude oil emulsions and hydrocarbon-contaminated wastewater effluents.Their effective treatments by smart polymeric nanostructured materials with wettability properties have been stated with suitable examples.The fundamental mechanisms underpinning the efficient separation of oil–water emulsions are discussed with suitable examples along with the future perspectives of smart materials.

Tyrosylprotein sulfotransferase suppresses ABA signaling via sulfation of SnRK2.2/2.3/2.6

Phytohormone abscisic acid(ABA)plays vital roles in stress tolerance,while long-term overactivation of ABA signaling suppresses plant growth and development.However,the braking mechanism of ABA responses is not clear.Protein tyrosine sulfation catalyzed by tyrosylprotein sulfotransferase(TPST)is a critical post-translational modification.Through genetic screening,we identified a tpst mutant in Arabidopsis that was hypersensitive to ABA.In-depth analysis revealed that TPST could interact with and sulfate SnRK2.2/2.3/2.6,which accelerated their degradation and weakened the ABA signaling.Taken together,these findings uncovered a novel mechanism of desensitizing ABA responses via protein sulfation.

循环热风低温干燥系统湿空气冷凝特性分析

基于能量梯级利用热力系统耦合理论,集成了一种适合热敏性农副产品烘干的新型空气干燥循环系统,系统可得到热敏性干燥产品,同时回收湿空气冷凝废热用于有机朗肯循环(ORC)系统对外做功。对关键部件湿空气冷凝器建立传热传质数学模型并经实验验证,考察了关键操作参数对系统脱水速率及节能效果的影响。结果表明,湿空气湿度是影响该系统凝水和节能的最关键参数,该系统凝水及节能特性均随湿空气湿度提高而改善;当干燥箱出口湿空气含湿量温度一定时,新型空气干燥循环凝水量主要受到干燥箱出口空气流量的影响,系统的凝水量和换热量均随湿空气质量流量增加先增加后降低,在0.10~0.15 kg/s出现极大值;系统净输出功随ORC底循环蒸发温度提高显著增加。本系统下的热敏性农副产品烘干建议选择低空气流速、低烘干温度,推荐的ORC底循环蒸发温度为313~323 K。

Regulation of the stability and ABA import activity of NRT1.2/NPF4.6 by CEPR2-mediated phosphorylation in Arabidopsis

Abscisic acid(ABA)transport plays an important role in systemic plant responses to environmental factors.However,it remains largely unclear about the precise regulation of ABA transporters in plants.In this study,we show that the C-terminally encoded peptide receptor 2(CEPR2)directly interacts with the ABA transporter NRT1.2/NPF4.6.Genetic and phenotypic analyses revealed that NRT1.2/NPF4.6 positively regulates ABA response and that NRT1.2/NPF4.6 is epistatically and negatively regulated by CEPR2.Further biochemical assays demonstrated that CEPR2 phosphorylates NRT1.2/NPF4.6 at serine 292 to promote its degradation under normal conditions.However,ABA treatment and non-phosphorylation at serine 292 prevented the degradation of NRT1.2/NPF4.6,indicating that ABA inhibits the phosphorylation of this residue.Transport assays in yeast and Xenopus oocytes revealed that non-phosphorylated NRT1.2/NPF4.6 had high levels of ABA import activity,whereas phosphorylated NRT1.2/NPF4.6 did not import ABA.Analyses of complemented nrt1.2 mutants that mimicked non-phosphorylated and phosphorylated NRT1.2/NPF4.6 confirmed that non-phosphorylated NRT1.2S292A had high stability and ABA import activity in planta.Additional experiments showed that NRT1.2/NPF4.6 was degraded via the 26S proteasome and vacuolar degradation pathways.Furthermore,we found that three E2 ubiquitin-conjugating enzymes,UBC32,UBC33,and UBC34,interact with NRT1.2/NPF4.6 in the endoplasmic reticulum and mediate its ubiquitination.NRT1.2/NPF4.6 is epistatically and negatively regulated by UBC32,UBC33,and UBC34 inplanta.Taken together,these results suggest that the stability and ABA import activity of NRT1.2/NPF4.6 are precisely regulated by its phosphorylation and degradation in response to environmental stress.

Regulation of the stability and ABA import activity of NRT1.2/NPF4.6 by CEPR2-mediated phosphorylation in Arabidopsis

(Molecular Plant 14,633–646;April 52021)In Figure 1D in our original manuscript,we demonstrated by the mating-based split ubiquitin system(MbSUS)assay that the functional domains of CEPR2 interact with the loop region of NRT1.2/NPF4.6(NRT1.2loop,aa 232-346).However,the sub-image of-WLU in Figure 1D was mistakenly assembled.

The Brassicaceae-specific secreted peptides,STMPs,function in plant growth and pathogen defense

Low molecular weight secreted peptides have recently been shown to affect multiple aspects of plant growth,development,and defense responses.Here,we performed stepwise BLAST filtering to identify unannotated peptides from the Arabidopsis thaliana protein database and uncovered a novel secreted peptide family,secreted transmembrane peptides(STMPs).These low molecular weight peptides,which consist of an N-terminal signal peptide and a transmembrane domain,were primarily localized to extracellular compartments but were also detected in the endomembrane system of the secretory pathway,including the endoplasmic reticulum and Golgi.Comprehensive bioinformatics analysis identified 10 STMP family members that are specific to the Brassicaceae family.Brassicaceae plants showed dramatically inhibited root growth uponexposure to chemically synthesized STMP1 and STMP2.Arabidopsis overexpressing STMP1,2,4,6,or 10 exhibited severely arrested growth,suggesting that STMPs are involved in regulating plant growth and development.In addition,in vitro bioassays demonstrated that STMP1,STMP2,and STMP10 have antibacterial effects against Pseudomonas syringae pv.tomato DC3000,Ralstonia solanacearum,Bacillus subtilis,and Agrobacterium tumefaciens,demonstrating that STMPs are antimicrobial peptides.These findings suggest that STMP family members play important roles in various developmental events and pathogen defense responses in Brassicaceae plants.

Function identification of Md TIR1 in apple root growth benefited from the predicted Md PPI network

Protein–protein interaction(PPI)network analysis is an effective method to identify key proteins during plant development,especially in species for which basic molecular research is lacking,such as apple(Malus domestica).Here,an MdPPI network containing 30806 PPIs was inferred in apple and its quality and reliability were rigorously verified.Subsequently,a rootgrowth subnetwork was extracted to screen for critical proteins in root growth.Because hormone-related proteins occupied the largest proportion of critical proteins,a hormonerelated sub-subnetwork was further extracted from the root-growth subnetwork.Among these proteins,auxin-related M.domestica TRANSPORT INHIBITOR RESISTANT 1(MdTIR1)served as the central,high-degree node,implying that this protein exerts essential roles in root growth.Furthermore,transgenic apple roots overexpressing an MdTIR1 transgene displayed increased primary root elongation.Expression analysis showed that MdTIR1 significantly upregulated auxin-responsive genes in apple roots,indicating that it mediates root growth in an auxin-dependent manner.Further experimental validation revealed that MdTIR1 interacted with and accelerated the degradation of MdIAA28,MdIAA43,andMdIAA46.Thus,MdTIR1-mediated degradation of MdIAAs is critical in auxin signal transduction and root growth regulation in apple.Moreover,our network analysis and high-degree node screening provide a novel research technique for more generally characterizing molecular mechanisms.

DEMETHYLATION REGULATOR 1 regulates DNA demethylation of the nuclear and mitochondrial genomes

Active DNA demethylation effectively modulates gene expression during plant development and in response to stress.However,little is known about the upstream regulatory factors that regulate DNA demethylation.We determined that the demethylation regulator 1(demr1)mutant exhibits a distinct DNA methylation profile at selected loci queried by methylation-sensitive polymerase chain reaction and globally based on whole-genome bisulfite sequencing.Notably,the transcript levels of the DNA demethylase gene REPRESSOR OF SILENCING 1(ROS1)were lower in the demr1 mutant.We established that DEMR1 directly binds to the ROS1 promoter in vivo and in vitro,and the methylation level in the DNA methylation monitoring sequence of ROS1 promoter decreased by 60%in the demr1 mutant.About 40%of the hyper-differentially methylated regions(DMRs)in the demr1 mutant were shared with the ros1-4 mutant.Genetic analysis indicated that DEMR1 acts upstream of ROS1 to positively regulate abscisic acid(ABA)signaling during seed germination and seedling establishment stages.Surprisingly,the loss of DEMR1 function also caused a rise in methylation levels of the mitochondrial genome,impaired mitochondrial structure and an early flowering phenotype.Together,our results show that DEMR1 is a novel regulator of DNA demethylation of both the nuclear and mitochondrial genomes in response to ABA and plant development in Arabidopsis.

Numerical simulation and experimental verification of silicone oil flow over magnetic fluid under applied magnetic field

Two-layer flow of magnetic fluid and non-magnetic silicone oil was simulated numerically. The continuity equation, momentum equations, kinematic equation, and magnetic potential equation were solved in two-dimensional Cartesian coordinate. PLIC (piecewise linear integration calculation) VOF (volume of fluid) scheme was employed to track the free interface. Surface tension was treated via a continuous surface force (CSF) model that ensures robustness and accuracy. The influences of applied magnetic field, inlet velocity profile, initial surface disturbance of interface and surface tension were analyzed. The computed interface shapes at different conditions were compared with experimental observation.