Publications by authors named "Zhonghua Zhang"

184 Publications

Skin depletion of Kif3a resembles the pediatric atopic dermatitis transcriptome profile.

Hum Mol Genet 2021 Nov 23. Epub 2021 Nov 23.

Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.

Skin deficiency of kinesin family member 3A causes disrupted skin barrier function and promotes development of atopic dermatitis (AD). It is not known how well Kif3aK14∆/∆ mice approximate the human AD transcriptome. To determine the skin transcriptomic profile of Kif3aK14∆/∆ mice and compare it with other murine AD models and human AD, we performed RNA-seq of full-thickness skin and epidermis from 3- and 8-week-old Kif3aK14∆/∆ mice and compared the differentially expressed genes (DEGs) with transcriptomic datasets from mite-induced NC/Nga, flaky tail (Tmem79ma/ma Flgft/ft), and filaggrin-mutant (Flgft/ft) mice, as well as human AD transcriptome datasets including meta-analysis derived atopic dermatitis [MADAD] and the pediatric atopic dermatitis [PAD]. We then interrogated the Kif3aK14∆/∆ skin DEGs using the LINCS-L1000 database to identify potential novel drug targets for AD treatment. We identified 471 and 901 DEGs at 3 and 8 weeks of age, respectively, in the absence of Kif3a. Kif3aK14∆/∆ mice had 3.5-4.5 times more DEGs that overlapped with human AD DEGs compared to the flaky tail and Flgft/ft mice. Further, 55%, 85% and 75% of 8-week Kif3aK14∆/∆ DEGs overlapped with the MADAD and PAD non-lesional and lesional gene lists, respectively. Kif3aK14∆/∆ mice spontaneously develop a human AD-like gene signature, which better represents pediatric non-lesional skin compared to other mouse models including flaky tail, Flgft/ft and NC/Nga. Thus, Kif3aK14∆/∆ mice may model pediatric skin that is a precursor to the development of lesions and inflammation, and hence may be a useful model to study AD pathogenesis.
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http://dx.doi.org/10.1093/hmg/ddab342DOI Listing
November 2021

Ionomic and Metabolomic Analyses Reveal Different Response Mechanisms to Saline-Alkali Stress Between Community and Community.

Front Plant Sci 2021 30;12:774284. Epub 2021 Nov 30.

Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin, China.

Soil salinization imposes severe stress to plants, inhibits plant growth, and severely limits agricultural productivity and land utilization. The response of a single plant to saline-alkali stress has been well investigated. However, the plant community that usually works as a group to defend against saline-alkali stress was neglected. To determine the functions of plant community, in our current work, () community and () community, two communities that are widely distributed in Hulun Buir Grassland in Northeastern China, were selected as research objects. Ionomic and metabolomic were applied to compare the differences between community and community from the aspects of ion transport and phenolic compound accumulation, respectively. Ionomic studies demonstrated that many macroelements, including potassium (K) and calcium (Ca), were highly accumulated in community whereas microelement manganese (Mn) was highly accumulated in community. In community, transportation of K to aboveground parts of plants helps to maintain high K and low Na concentrations whereas the accumulation of Ca triggers the salt overly sensitive (SOS)-Na system to efflux Na. In community, enrichment of Mn in roots elevates the level of Mn-superoxide dismutase (SOD) and increases the resistance to saline-alkali stress. Metabolomic studies revealed the high levels of C6C1-compounds and C6C3C6-compounds in community and also the high levels of C6C3-compounds in community. C6C1-compounds function as signaling molecules to defend against stress and may stimulate the accumulation of C6C3C6-compounds. C6C3-compounds contribute to the elimination of free radicals and the maintenance of cell morphology. Collectively, our findings determine the abundance of phenolic compounds and various elements in community and community in Hulun Buir Grassland and we explored different responses of community and community to cope with saline-alkali stress. Understanding of plant response strategies from the perspective of community teamwork may provide a feasible and novel way to transform salinization land.
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http://dx.doi.org/10.3389/fpls.2021.774284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8670416PMC
November 2021

Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits.

Nat Commun 2021 12 13;12(1):7246. Epub 2021 Dec 13.

Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, 200234, Shanghai, China.

Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome. Population genomic analyses provide insights into spinach genetic diversity and population differentiation. Genome-wide association studies of 20 agronomical traits identify numerous significantly associated regions and candidate genes for these traits. Domestication sweeps in the spinach genome are identified, some of which are associated with important traits (e.g., leaf phenotype, bolting and flowering), demonstrating the role of artificial selection in shaping spinach phenotypic evolution. This study provides not only insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding.
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http://dx.doi.org/10.1038/s41467-021-27432-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8668906PMC
December 2021

Immunoadsorption Improves Remission Rates of Patients with Antineutrophil Cytoplasmic Antibody-Associated Vasculitis and Severe Kidney Involvement.

Am J Nephrol 2021 7;52(12):899-908. Epub 2021 Dec 7.

Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Introduction: The role of plasma exchange in treatment of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) with severe kidney involvement is controversial. It is urgent to find effective treatments to improve prognosis of AAV patients. In this retrospective study, the outcomes of immunoadsorption (IA) onto protein A in AAV patients with severe kidney involvement were evaluated.

Methods: Clinical data of 60 patients with AAV and severe kidney involvement were analyzed. Patients received cyclophosphamide or rituximab for remission induction, among which 16 were additionally treated with IA. Remission, end-stage kidney disease (ESKD), death, and relapse were compared.

Results: Of 60 patients, 56 patients (93.3%) were positive for myeloperoxidase (MPO)-ANCA. At diagnosis, the estimated glomerular filtration rate and Birmingham Vasculitis Activity Score (BVAS) was 13.0 (7.7, 18.7) mL/min/1.73 m2 and 11.1 ± 3.4, respectively. After 3-17 days (mean 10.4 days) of induction treatment, the disease activity decreased more obviously in the IA group (p = 0.022) than the control group. IA showed superior over standard regimen in clearance of MPO-ANCA within 3-31 days (median 11 days) after treatment (78.4% vs. 9.3%, p = 0.005). After a median follow-up of 20.2 months, remission was achieved more quickly (p = 0.035) and higher (hazard ratio (HR) = 2.3, 95% confidence interval (CI): 1.1∼7.2, p = 0.033) in the IA group than the control group. IA therapy showed an advantage in reducing death (HR = 0.2, 95% CI: 0.1∼0.9, p = 0.032). There was no difference in developing into ESKD in both groups (HR = 0.7, 95% CI: 0.3∼2.0, p = 0.504). Multivariate Cox regression analysis indicated that early-stage remission was an independent predictor for ESKD (HR = 0.03, 95% CI: 0.003∼0.25, p = 0.001) and death (HR = 0.07, 95% CI: 0.01∼0.51, p = 0.009).

Conclusion: IA treatment induces quicker and higher remission and lower mortality in AAV patients with severe kidney involvement. The early remission independently predicts the outcomes for these patients.
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http://dx.doi.org/10.1159/000519608DOI Listing
December 2021

Deletion of a cyclin-dependent protein kinase inhibitor, CsSMR1, leads to dwarf and determinate growth in cucumber (Cucumis sativus L.).

Theor Appl Genet 2021 Nov 29. Epub 2021 Nov 29.

College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.

Key Message: A 7.9 kb deletion which contains a cyclin-dependent protein kinase inhibitor leads to determinate growth and dwarf phenotype in cucumber. Plant architecture is a composite character which are mainly defined by shoot branching, internode elongation and shoot determinacy. Ideal architecture tends to increase the yield of plants, just like the case of "Green Revolution" increased by the application of semi-dwarf cereal crop varieties in 1960s. Cucumber (Cucumis sativus L.) is an important vegetable cultivated worldwide, and suitable architecture varieties were selected for different production systems. In this study, we obtained a novel dwarf mutant with strikingly shortened plant height and determinate growth habit. By bulked segregant analysis and map-based cloning, we delimited the dw2 locus to a 56.4 kb region which contain five genes. Among all the variations between WT and dw2 within the 56.4 kb region, a 7.9 kb deletion which resulted in complete deletion of CsaV3_5G035790 in dw2 was co-segregated with the dwarf phenotype. Haplotype analysis and gene expression analysis suggest that CsaV3_5G035790 encoding a cyclin-dependent protein kinase inhibitor (CsSMR1) be the candidate gene responsible for the dwarf phenotype in dw2. RNA-seq analysis shows that several kinesin-like proteins, cyclins and reported organ size regulators are expressed differentially between WT and dw2, which may account for the reduced organ size in dwarf plants. Additionally, the down-regulation of CsSTM and CsWOX9 in dw2 resulted in premature termination of shoot apical meristem development, which eventually reduces the internode number and plant height. Identification and characterization of the CsSMR1 provide a new insight into cucumber architecture modification to be applied to mechanized production system.
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http://dx.doi.org/10.1007/s00122-021-04006-7DOI Listing
November 2021

StWRKY13 promotes anthocyanin biosynthesis in potato (Solanum tuberosum) tubers.

Funct Plant Biol 2021 Dec;49(1):102-114

Key Laboratory of Horticultural Plant Biology, Ministry of Education, and Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.

Although the role of WRKY transcription factors (TFs) in colour formation has been reported in several species, their function in potato (Solanum tuberosum L.) anthocyanin biosynthesis remains unclear. In this study, the potato WRKY gene StWRKY13 was isolated and characterised. Expression analysis revealed a significantly higher StWRKY13 expression in chromatic tubers than in yellow ones. Transient activation assays showed that StWRKY13 could enhance the role of StAN2 in promoting anthocyanin biosynthesis in tobacco (Nicotiana tabacum L.). Over-expressing the StWRKY13 gene promoted anthocyanin biosynthesis in potato tubers. Further investigations indicated that StWRKY13 could interact with the StCHS, StF3H, StDFR, and StANS gene promoters and significantly enhance their activities. Our findings showed that StWRKY13 could promote anthocyanin biosynthesis by activating StCHS, StF3H, StDFR, and StANS transcription in potato tubers, thereby supporting the theoretical basis for anthocyanins formation in coloured potato tubers.
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http://dx.doi.org/10.1071/FP21109DOI Listing
December 2021

Complete chloroplast genome of (phyllanthaceae), a promising underutilized species.

Mitochondrial DNA B Resour 2021 11;6(12):3362-3363. Epub 2021 Nov 11.

Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China.

is a high economic value for the exploitation and utilization of wild fruit tree species with edible and medicinal values in Southeast Asia. In this study, the complete chloroplast genome sequence of was assembled and characterized. The chloroplast genome was 161,089 bp in length, consisting of a large single copy (LSC) of 89,515 bp and a small single copy (SSC) region of 18,826 bp, which were separated by a pair of 26,374 bp inverted repeat (IR) regions. The overall GC content was 36.71%. A total of 132 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were identified. A low intraspecies variation within was found with 22 single nucleotide polymorphisms (SNPs) and 17 insertions and deletions (INDELs). Phylogenetic tree reconstructed by 14 chloroplast genomes revealed that clusters together with species of , , and .
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http://dx.doi.org/10.1080/23802359.2021.1997105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592581PMC
November 2021

Formation, lithium storage properties, and mechanism of nanoporous germanium fabricated by dealloying.

J Chem Phys 2021 Nov;155(18):184702

Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education), School of Materials Science and Engineering, Shandong University, Jingshi Road 17923, Jinan 250061, People's Republic of China.

Germanium (Ge) has become a promising anode material for lithium-ion batteries (LIBs) due to its high theoretical capacity and decent electron/ion conductivity, but it exhibits inferior lifespan caused by dramatic volume variations during the (de)lithiation process. Herein, hierarchically, nanoporous Ge (np-Ge) was fabricated by the combination of selective phase corrosion with chemical dealloying. As an anode for LIBs, the np-Ge electrode exhibits marvelous cycling stability with capacity retentions of 1060.0 mA h g at 0.2 A g and 767.1 mA h g at 1 A g after 100 cycles. Moreover, the electrode shows excellent rate capability with a capacity retention of 844.2 mA h g at 5 A g. Noticeably, the (de)lithiation mechanisms of np-Ge and porous Si-Ge (p-SiGe) were unveiled by operando X-ray diffraction.
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http://dx.doi.org/10.1063/5.0067237DOI Listing
November 2021

Enhanced ATP and antioxidant levels for cAMP biosynthesis by Arthrobacter sp. CCTCC 2013431 with polyphosphate addition.

Biotechnol Lett 2021 Dec 21;43(12):2223-2231. Epub 2021 Oct 21.

School of Life Science and Technology, Henan Institute of Science and Technology, 90 Hualan Road, Xinxiang, 453003, Henan Province, China.

Objectives: When citrate and pyruvate were utilized to strengthen ATP generation for high cAMP production, oxidative stress became more severe in cells resulting in lower cell viability and cAMP formation at the late fermentation phase. To further improve cAMP biosynthesis, the effects of polyphosphate on cAMP fermentation performance together with intracellular ATP and oxidation levels were investigated under high oxidative stress condition and then high efficient cAMP fermentation process based on polyphosphate and salvage synthesis was developed and studied.

Results: With 2 g/L-broth sodium hexametaphosphate added at 24 h was determined as the optimal condition for cAMP production by Arthrobacter sp. CCTCC 2013431 in shake flasks. Under high oxidative stress condition caused by adding 15 mg/L-broth menadione, cAMP contents and cell viability were improved greatly due to hexametaphosphate addition and also exceeded those of control (without hexametaphosphate and menadione added) when fermentations were conducted in a 7 L bioreactor. Meanwhile, ATP levels and antioxidant capacity were improved obviously by hexametaphosphate as well. Moreover, a fermentation process with hexametaphosphate and hypoxanthine coupling added was developed by which cAMP concentration reached 7.25 g/L with an increment of 87.1% when compared with only hypoxanthine added batch and the high ROS contents generated from salvage synthesis were reduced significantly.

Conclusion: Polyphosphate could improve intracellular ATP levels and antioxidant capacity significantly under high oxidative stress condition resulting in enhanced cell viability and cAMP fermentation production no matter by de novo synthesis or salvage synthesis.
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http://dx.doi.org/10.1007/s10529-021-03197-9DOI Listing
December 2021

Current Design Strategies for Rechargeable Magnesium-Based Batteries.

ACS Nano 2021 Oct 11;15(10):15594-15624. Epub 2021 Oct 11.

Qingdao Industrial Energy Storage Research Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.

As a next-generation electrochemical energy storage technology, rechargeable magnesium (Mg)-based batteries have attracted wide attention because they possess a high volumetric energy density, low safety concern, and abundant sources in the earth's crust. While a few reviews have summarized and discussed the advances in both cathode and anode materials, a comprehensive and profound review focusing on the material design strategies that are both representative of and peculiar to the performance improvement of rechargeable Mg-based batteries is rare. In this mini-review, all nine of the material design strategies and approaches to improve Mg-ion storage properties of cathode materials have been comprehensively examined from both internal and external aspects. Material design concepts are especially highlighted, focusing on designing "soft" anion-based materials, intercalating solvated or complex ions, expanding the interlayer of layered cathode materials, doping heteroatoms into crystal lattice, size tailoring, designing metastable-phase materials, and developing organic materials. To achieve a better anode, strategies based on the artificial interlayer design, efficient electrolyte screening, and alternative anodes exploration are also accumulated and analyzed. The strategy advances toward Mg-S and Mg-Se batteries are summarized. The advantages and disadvantages of all-collected material design strategies and approaches are critically discussed from practical application perspectives. This mini-review is expected to provide a clear research clue on how to rationally improve the reliability and feasibility of rechargeable Mg-based batteries and give some insights for the future research of Mg-based batteries as well as other multivalent-ion battery chemistries.
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http://dx.doi.org/10.1021/acsnano.1c06530DOI Listing
October 2021

Mechanistic Insights into the Intercalation and Interfacial Chemistry of Mesocarbon Microbeads Anode for Potassium Ion Batteries.

Small 2021 Nov 29;17(44):e2103557. Epub 2021 Sep 29.

College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China.

Mesocarbon microbeads (MCMB) are highly desirable as anode materials for rechargeable potassium ion batteries (PIBs) due to their commercially availability, high stability and low-cost. However, their charge storage and interfacial mechanisms are still unclear. In this work, the intercalation mechanisms and the solid-electrolyte-interphase (SEI) formation of the MCMB in four different electrolytes is comprehensively studied. The MCMB anodes exhibit superior rate and cycle performances via a naked K-ions sequentially staging intercalation mechanism, realizing the complete transformation from graphite to KC . Whereas a solvated K-ions co-intercalation mechanism of the MCMB occurs in ether-based electrolytes, which might induce graphite exfoliation and result in unsatisfied specific capacity and capacity decay. Nevertheless, this co-intercalation behavior could be effectively suppressed by a highly concentrated electrolytes. Interfacial analyses unveil the distinct SEI components, which vary with the electrolyte chemistries. These SEI components also varies from surface to bulk and especially attention should be paid to the accurate control of the concentration of the fluoroethylene carbonate additives. This work provides a panoramic understanding of the intercalation and interfacial mechanisms on the MCMB anodes for PIBs.
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http://dx.doi.org/10.1002/smll.202103557DOI Listing
November 2021

Asymptotic Standard Errors of Generalized Partial Credit Model True Score Equating Using Characteristic Curve Methods.

Authors:
Zhonghua Zhang

Appl Psychol Meas 2021 Jul 12;45(5):331-345. Epub 2021 May 12.

The University of Melbourne, Carlton, Victoria, Australia.

In this study, the delta method was applied to estimate the standard errors of the true score equating when using the characteristic curve methods with the generalized partial credit model in test equating under the context of the common-item nonequivalent groups equating design. Simulation studies were further conducted to compare the performance of the delta method with that of the bootstrap method and the multiple imputation method. The results indicated that the standard errors produced by the delta method were very close to the criterion empirical standard errors as well as those yielded by the bootstrap method and the multiple imputation method under all the manipulated conditions.
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http://dx.doi.org/10.1177/01466216211013101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8361376PMC
July 2021

Facilitated magnesium atom adsorption and surface diffusion kinetics artificial bismuth-based interphases.

Chem Commun (Camb) 2021 Sep 16;57(74):9430-9433. Epub 2021 Sep 16.

Qingdao Industrial Energy Storage Research Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China.

Robust bismuth-based interphases, comprised of bismuth and bismuth oxides, were developed using galvanic replacement reactions. Facilitated Mg atom adsorption and distinct interfacial Mg atom migration were demonstrated, greatly lowering the electrochemical energy penalty (23 mV for the nucleation process and 69 mV for the growth process at 1.0 mA cm).
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http://dx.doi.org/10.1039/d1cc02048jDOI Listing
September 2021

Enhanced endogenous amino acids and energy metabolism level for cAMP biosynthesis by Arthrobacter sp. CCTCC 2013431 with citrate as cosubstrate.

Biotechnol Lett 2021 Oct 14;43(10):1989-1999. Epub 2021 Aug 14.

Collaborative Innovation Center of Modern Biological Breeding of Henan Province, Xinxiang, 453003, China.

Objectives: In our previous study, citrate was used as auxiliary energy substance for improving cAMP fermentation performance, however, the regulation mechanism of citrate on improved cAMP contents was not clear. To elucidate the regulation mechanism, cAMP fermentations with/without citrate addition were conducted in a 7 L fermentor using Arthrobacter sp. CCTCC 2013431 and assays on key enzymes activities, energy metabolism level, amino acids contents and peroxidation level were performed.

Results: With 3 g/L-broth sodium citrate added, cAMP concentration and conversion yield from glucose reached 4.34 g/L and 0.076 g/g which were improved by 30.7% and 29.8%, respectively, when compared with those of control. Citrate changed carbon flux distribution among different routes and more carbon flux was directed into pentose phosphate pathway beneficial to cAMP synthesis. Meanwhile, energy metabolism together with precursor amino acids levels were improved significantly owing to strengthened metabolic intensity of tricarboxylate cycle by exogenous citrate utilization which provided energy and substance basis for cAMP production. Moreover, higher glutamate synthesis and oxidative stress caused by citrate addition consumed excessive NADPH derived from pentose phosphate pathway by which feedback suppression for pentose phosphate pathway was relieved efficiently.

Conclusion: Citrate promoted cAMP fermentation production by Arthrobacter sp. CCTCC 2013431 due to enhanced precursor amino acids, energy metabolism level and relieved feedback suppression for pentose phosphate pathway.
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http://dx.doi.org/10.1007/s10529-021-03170-6DOI Listing
October 2021

Facile Preparation of MoS Nanocomposites for Efficient Potassium-Ion Batteries by Grinding-Promoted Intercalation Exfoliation.

Small 2021 Aug 16;17(34):e2102263. Epub 2021 Jul 16.

Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications (NUPT), Nanjing, 210023, China.

Efficient exfoliations of bulk molybdenum disulfide (MoS ) into few-layered nanosheets in pure phase are highly attractive because of the promising applications of the resulted 2D materials in diversified optoelectronic devices. Here, a new exfoliation method is presented to prepare semiconductive 2D hexagonal phase (2H phase) MoS -cellulose nanocrystal (CNC) nanocomposites using grinding-promoted intercalation exfoliation (GPIE). This method with facile grinding of the bulk MoS and CNC powder followed by conventional liquid-phase exfoliation in water can not only efficiently exfoliate 2H-MoS nanosheets, but also produce the 2H-MoS /CNC 2D nanocomposites simultaneously. Interestingly, the intercalated CNC sandwiched in MoS nanosheets increases the interlayer spacing of 2H-MoS , providing perfect conditions to accommodate the large-sized ions. Therefore, these nanocomposites are good anode materials of potassium-ion batteries (KIBs), showing a high reversible capacity of 203 mAh g at 200 mA g after 300 cycles, a good reversible capacity of 114 mAh g at 500 mA g , and a low decay of 0.02% per cycle over 1500 cycles. With these impressive KIB performances, this efficient GPIE method will open up a new avenue to prepare pure-phase MoS and promising 2D nanocomposites for high-performance device applications.
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http://dx.doi.org/10.1002/smll.202102263DOI Listing
August 2021

The Taxus genome provides insights into paclitaxel biosynthesis.

Nat Plants 2021 08 15;7(8):1026-1036. Epub 2021 Jul 15.

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.
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http://dx.doi.org/10.1038/s41477-021-00963-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8367818PMC
August 2021

Sugars promote graft union development in the heterograft of cucumber onto pumpkin.

Hortic Res 2021 Jul 1;8(1):146. Epub 2021 Jul 1.

Institute of Vegetables and Flowers, Chinese Academy of Agriculture Sciences, Beijing, 100081, China.

The use of heterografts is widely applied for the production of several important commercial crops, but the molecular mechanism of graft union formation remains poorly understood. Here, cucumber grafted onto pumpkin was used to study graft union development, and genome-wide tempo-spatial gene expression at the graft interface was comprehensively investigated. Histological analysis suggested that resumption of the rootstock growth occurred after both phloem and xylem reconnection, and the scion showed evident callus production compared with the rootstock 3 days after grafting. Consistently, transcriptome data revealed specific responses between the scion and rootstock in the expression of genes related to cambium development, the cell cycle, and sugar metabolism during both vascular reconnection and healing, indicating distinct mechanisms. Additionally, lower levels of sugars and significantly changed sugar enzyme activities at the graft junction were observed during vascular reconnection. Next, we found that the healing process of grafted etiolated seedlings was significantly delayed, and graft success, xylem reconnection, and the growth of grafted plants were enhanced by exogenous glucose. This demonstrates that graft union formation requires the correct sugar content. Furthermore, we also found that graft union formation was delayed with a lower energy charge by the target of rapamycin (TOR) inhibitor AZD-8055, and xylem reconnection and the growth of grafted plants were enhanced under AZD-8055 with exogenous glucose treatment. Taken together, our results reveal that sugars play a positive role in graft union formation by promoting the growth of cucumber/pumpkin and provide useful information for understanding graft union healing and the application of heterografting in the future.
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http://dx.doi.org/10.1038/s41438-021-00580-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245404PMC
July 2021

Complete chloroplast genome of a semi-mangrove plant (Malvaceae).

Mitochondrial DNA B Resour 2021 Jun 14;6(7):1904-1905. Epub 2021 Jun 14.

College of Environmental and Life Sciences, Nanning Normal University, Nanning, China.

is a semi-mangrove species that is widely distributed in tropical and subtropical coastal areas around the world. Here, the complete chloroplast (cp) genome sequence of was assembled and characterized. The cp genome was 161,748 bp in length, consisting of a large single copy (LSC) region of 89,190 bp and a small single copy (SSC) region of 19,616 bp, which were separated by a pair of 26,471 bp inverted repeat (IR) regions. The overall GC content was 36.88%. A total of 131 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified. Phylogenetic tree reconstructed by 15 complete cp genomes revealed that was sister to the congeneric species .
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http://dx.doi.org/10.1080/23802359.2021.1935337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204996PMC
June 2021

Uniform Magnesium Electrodeposition via Synergistic Coupling of Current Homogenization, Geometric Confinement, and Chemisorption Effect.

Adv Mater 2021 Jul 31;33(26):e2100224. Epub 2021 May 31.

Qingdao Industrial Energy Storage Research Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China.

Unevenly distributed magnesium (Mg) electrodeposits have emerged as a major obstacle for Mg-metal batteries. A comprehensive design matrix is reported for 3D magnesiophilic hosts, which regulate the uniform Mg electrodeposition through a synergistic coupling of homogenizing current distribution, geometric confinement, and chemisorptive interaction. Vertically aligned nitrogen- and oxygen-doped carbon nanofiber arrays on carbon cloth (denoted as "[email protected]") are developed as a proof of concept. The evenly arranged short nanoarray architecture helps to homogenize the surface current density and the microchannels built in this 3D host allow the preferential nucleation of Mg due to their geometrical confinement effect. Besides, the nitrogen-/oxygen-doped carbon species exhibit strong chemisorptive interaction toward Mg atoms, providing preferential nucleation sites as demonstrated by first-principle calculation results. Electrochemical analysis reveals a peculiar yet highly reversible microchannel-filling growth behavior of Mg metals, which empowers the delicately designed [email protected] host with the ability to deliver a reduced nucleation overpotential of 429 mV at 10.0 mA cm and an elongated Mg plating/stripping cycle life (110 cycles) under high current density of 10.0 mA cm . The proposed design matrix can be extended to other metal anodes (such as lithium and zinc) for high-energy-density batteries.
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http://dx.doi.org/10.1002/adma.202100224DOI Listing
July 2021

Characterization of underutilized root starches from eight varieties of ramie (Boehmeria nivea) grown in China.

Int J Biol Macromol 2021 Jul 21;183:1475-1485. Epub 2021 May 21.

Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China. Electronic address:

Ramie root is an underutilized starch source. In this study, eight ramie varieties were investigated for starch properties. Starch content ranged from 18.6% to 50.1% in dry root. Starches from different varieties showed similar morphology including ellipsoidal, spherical and truncated granules with size D[4,3] from 10.1 to 14.1 μm. Starch had amylose content from 20.8% to 28.5%. All ramie varieties had B-type starches with relative crystallinity from 24.8% to 27.1%, ordered degree from 0.724 to 0.897 and lamellar thickness from 9.1 to 9.6 nm. Starches had gelatinization peak temperature from 70.5 to 73.8 °C and enthalpy from 14.9 to 15.8 J/g. Starches had swelling power and water solubility from 27.9 to 31.9 g/g and from 11.7% to 15.5%, respectively, at 95 °C, and exhibited different pasting properties with breakdown viscosity from 36 to 377 mPa s and setback viscosities from 1295 to 1863 mPa s. Starch pastes exhibited pseudoplastic behavior and different rheological properties. Native, gelatinized and retrograded starches had resistant starch from 81.7% to 83.9%, from 1.7% to 5.1% and from 5.6% to 13.3%, respectively. The eight varieties were divided into 3 groups according to starch properties. This study is helpful for selecting suitable ramie variety as starch source.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.05.126DOI Listing
July 2021

Electrospun cobalt Prussian blue analogue-derived nanofibers for oxygen reduction reaction and lithium-ion batteries.

J Colloid Interface Sci 2021 Oct 21;599:280-290. Epub 2021 Apr 21.

School of Applied Physics and Materials, Wuyi University, Jiangmen, China; Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education), School of Materials Science and Engineering, Shandong University, Jinan, China. Electronic address:

Electrospinning is an effective technique to fabricate one-dimensional materials. In this study, cobalt-embedded carbon nanofibers ([email protected]) are obtained via carbonization of electrospun cobalt Prussian blue analogue (Co-Co PBA) under nitrogen atmosphere. The [email protected] have metallic cobalt surrounded by graphitic carbon shells and possess high specific surface area, rich porosity, high graphitic degree, and rational nitrogen doping. The structure merits endow them with excellent electrocatalytic performances for oxygen reduction reaction (ORR): an onset potential of 0.867 V vs. RHE and 0.784 V vs. RHE at j =  - 3 mA cm with a four-electron transfer process. Through a further mild oxidation process, we obtain CoO nanoparticles-embedded nitrogen-doped carbon ([email protected]) with spindle-like morphology. When working as the anode materials for lithium-ion batteries (LIBs), [email protected] show high specific capacity, good stability, and excellent rate capability. The [email protected] anode delivers a discharge specific capacity of 1404 mA h g after 100 cycles at a current density of 100 mA g and about 500 mA h g after 500 cycles at 2000 mA g. The diffusion- and capacitive-controlled processes both contribute to the charge storage of the [email protected] electrode. This study provides a new strategy to fabricate the excellent electrocatalysts for ORR and anode materials for LIBs via facile electrospinning.
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http://dx.doi.org/10.1016/j.jcis.2021.04.102DOI Listing
October 2021

Gain-of-function of the 1-aminocyclopropane-1-carboxylate synthase gene ACS1G induces female flower development in cucumber gynoecy.

Plant Cell 2021 04;33(2):306-321

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China.

Unisexual flowers provide a useful system for studying plant sex determination. In cucumber (Cucumis sativus L.), three major Mendelian loci control unisexual flower development, Female (F), androecious [a; 1-aminocyclopropane-1-carboxylate {ACC} synthase 11, acs11], and Monoecious (M; ACS2), referred to here as the Female, Androecious, Monoecious (FAM) model, in combination with two genes, gynoecious (g, the WIP family C2H2 zinc finger transcription factor gene WIP1) and the ethylene biosynthetic gene ACC oxidase 2 (ACO2). The F locus, conferring gynoecy and the potential for increasing fruit yield, is defined by a 30.2-kb tandem duplication containing three genes. However, the gene that determines the Female phenotype, and its mechanism, remains unknown. Here, we created a set of mutants and revealed that ACS1G is responsible for gynoecy conferred by the F locus. The duplication resulted in ACS1G acquiring a new promoter and expression pattern; in plants carrying the F locus duplication, ACS1G is expressed early in floral bud development, where it functions with ACO2 to generate an ethylene burst. The resulting ethylene represses WIP1 and activates ACS2 to initiate gynoecy. This early ACS1G expression bypasses the need for ACS11 to produce ethylene, thereby establishing a dominant pathway for female floral development. Based on these findings, we propose a model for how these ethylene biosynthesis genes cooperate to control unisexual flower development in cucumber.
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http://dx.doi.org/10.1093/plcell/koaa018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136878PMC
April 2021

Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber.

Hortic Res 2021 Mar 1;8(1):40. Epub 2021 Mar 1.

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.

Cucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in "defense response," and C. hystrix harbored 104 nucleotide-binding site-encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber-C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.
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http://dx.doi.org/10.1038/s41438-021-00475-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7917098PMC
March 2021

CircKIF2A contributes to cell proliferation, migration, invasion and glycolysis in human neuroblastoma by regulating miR-129-5p/PLK4 axis.

Mol Cell Biochem 2021 Jun 25;476(6):2513-2525. Epub 2021 Feb 25.

Department of Pediatric Surgery, Heze Municipal Hospital, Family Committee of the Municipal Party Committee, Tianxiang Road, Heze City, 274000, Shangdong Province, China.

Multiple circular RNAs (circRNAs) have been identified to act as essential mediators in diverse human cancers. However, the roles of circRNAs in neuroblastoma (NB) are largely unknown. In this study, we aimed to explore the function of circKIF2A in NB. Quantitative real-time polymerase chain reaction was executed to detect the levels of circKIF2A, KIF2A mRNA, miR-129-5p and polo-like kinase 4 (PLK4) mRNA. Actinomycin D assay and RNase R digestion assay were conducted to analyze the feature of circKIF2A. 3-(4, 5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay, transwell assay and specific kits were utilized to evaluate cell proliferation, metastasis and glycolysis, respectively. Western blot assay was performed to examine the protein levels of matrix metalloproteinase 2 (MMP2), MMP9 and PLK4. Bioinformatics analysis, RNA pull-down assay and dual-luciferase reporter assay were conducted to analyze the relationship between miR-129-5p and circKIF2A or PLK4. Murine xenograft model assay was done to investigate the role of circKIF2A in NB in vivo. CircKIF2A level was increased in NB tissue samples and cell lines. Silencing of circKIF2A impeded NB cell proliferation, migration, invasion and glycolysis. For mechanism analysis, circKIF2A could positively modulate PLK4 expression via sponging miR-129-5p. Moreover, miR-129-5p inhibition reversed the inhibitory effects of circKIF2A silencing on the behaviors of NB cells. MiR-129-5p overexpression weakened the malignant biological behaviors of NB cells by targeting PLK4. Additionally, circKIF2A knockdown hampered tumorigenesis in vivo. CircKIF2A knockdown suppressed cell proliferation, migration, invasion and glycolysis via downregulating PLK4 expression through miR-129-5p.
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http://dx.doi.org/10.1007/s11010-021-04096-3DOI Listing
June 2021

Asymptotic Standard Errors of Parameter Scale Transformation Coefficients in Test Equating Under the Nominal Response Model.

Authors:
Zhonghua Zhang

Appl Psychol Meas 2021 Mar 21;45(2):134-138. Epub 2020 Oct 21.

The University of Melbourne, Victoria, Australia.

Researchers have developed a characteristic curve procedure to estimate the parameter scale transformation coefficients in test equating under the nominal response model. In the study, the delta method was applied to derive the standard error expressions for computing the standard errors for the estimates of the parameter scale transformation coefficients. This brief report presents the results of a simulation study that examined the accuracy of the derived formulas and compared the performance of this analytical method with that of the multiple imputation method. The results indicated that the standard errors produced by the delta method were very close to the criterion standard errors as well as those yielded by the multiple imputation method under all the simulation conditions.
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http://dx.doi.org/10.1177/0146621620965740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876637PMC
March 2021

Tailoring P2/P3 Biphases of Layered Na MnO by Co Substitution for High-Performance Sodium-Ion Battery.

Small 2021 Feb 27;17(7):e2007103. Epub 2021 Jan 27.

Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education), School of Materials Science and Engineering, Shandong University, Jingshi Road 17923, Jinan, 250061, P. R. China.

P-type layered oxide is a promising cathode candidate for sodium-ion batteries (SIBs), but faces the challenge of simultaneously realizing high rate capability and long cycle life. Herein, Co-substituted Na MnO nanosheets with tunable P2/P3 biphase structures are synthesized by a novel dealloying-annealing strategy. The optimized P2/P3-Na Mn Co Al O cathode delivers an excellent rate capability of 83 mA h g at a high current density of 1700 mA g (10 C), and an outstanding cycling stability over 500 cycles at 1000 mA g . This excellent performance is attributed to the unique P2/P3 biphases with stable crystal structures and fast Na diffusion between open prismatic Na sites. Moreover, operando X-ray diffraction is applied to explore the structural evolution of Na Mn Co Al O during the Na extraction/insertion processes, and the P2-P2' phase transition is effectively suppressed. Operando Raman technique is utilized to explore the structural superiority of P2/P3 biphase cathode compared with pure P2 or P3 phase. This work highlights precisely tailoring the phase composition as an effective strategy to design advanced cathode materials for SIBs.
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http://dx.doi.org/10.1002/smll.202007103DOI Listing
February 2021

Structural and technological determinants of carbon intensity reduction of China's electricity generation.

Environ Sci Pollut Res Int 2021 Mar 12;28(11):13469-13486. Epub 2020 Nov 12.

Australia-China Relations Institute, University of Technology Sydney, Sydney, 2007, Australia.

Electricity generation is the largest sector with decarbonization potential for China and the world. Based on the new emission factors, this paper aims to identify the structural and technological determinants of provincial carbon intensity in the electricity generation sector (CIE) using the multiplicative LMDI-II method. Results demonstrate that (1) China's overall CIE decreases by 7.3% in 2001-2015, and the research period can be divided into four stages according to CIE changes (i.e., rapid growth, rapid decline, slow growth, and transition). The CIE in the 12th FYP estimated in this paper, 24.9% lower than that using the emission factors from IPCC, is closer to China's actual situation. (2) There exists huge heterogeneity in the determinants of provincial CIE changes in four stages. CIE growth in the Northwest and Northeast is caused by the coal-dominated energy structure. CIE growth in the Southwest is attributed to the electricity structure effect, while that of the Coast region is caused by the geographic distribution effect. The electricity efficiency effect is attributed to the CIE growth for these regions and the Southwest should also place focus on the electricity trade effect. The impact of electricity trade-related factors depends on the region being a net exporter or importer of electricity. (3) To achieve carbon intensity reduction targets, 30 provinces are categorized into four types based on various combinations of structural and technological determinants. The findings provide insights into capturing future emission-mitigating focus as well as defining the emission-mitigating responsibilities between electricity exporters and importers in China.
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http://dx.doi.org/10.1007/s11356-020-11429-0DOI Listing
March 2021

A Robust Strategy for Engineering FeS/C Hybrid Nanocages Reinforced by Defect-Rich MoS Nanosheets for Superior Potassium-Ion Storage.

ACS Nano 2020 Nov 4;14(11):16046-16056. Epub 2020 Nov 4.

College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.

Metal sulfides have attracted tremendous research interest for developing high-performance electrodes for potassium-ion batteries (PIBs) for their high theoretical capacities. Nevertheless, the practical application of metal sulfides in PIBs is still unaddressed due to their intrinsic shortcomings of low conductivity and severe volume changes during the potassiation/depotassiation process. Herein, robust FeS/C hybrid nanocages reinforced by defect-rich MoS nanosheets (FeS/[email protected]) were designed, which possess abundant multichannel and active sites for potassium-ion transportation and storage. Kinetic analysis and theoretical calculation verify that the introduction of defect-rich MoS nanosheets dramatically promotes the potassium-ion diffusion coefficient. The measurements revealed the potassium-ion storage mechanism in the FeS/[email protected] composite. Benefitting from the tailored structural design, the FeS/[email protected] hybrid nanocages show high reversible capacity, exceptional rate property, and superior cyclability.
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http://dx.doi.org/10.1021/acsnano.0c07733DOI Listing
November 2020

Isolation and Characterization of a Variant Psedorabies Virus HNXY and Construction of rHNXY-∆/∆.

Animals (Basel) 2020 Oct 4;10(10). Epub 2020 Oct 4.

College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China.

The outbreak of pseudorabies in China, caused by more virulent pseudorabies virus (PRV) than the classical strains, has led to considerable economic losses. In this study, PRV strain HNXY was isolated from the Henan province of China in 2015 from the pig farm with severe reproductive failure in sows and a high mortality in piglets. The 50% tissue culture infectious doses (TCID) of HNXY in Vero cells were examined to be 10/mL, and the neutralisation titer against Bartha-K61 was significantly higher than against HNXY when tested with the serum from Bartha-K61 vaccinated pigs. The 50% lethal doses (LD) of HNXY to six-week-old BALB/c mice and two-month-old PRV-free pigs were both 10 TCID. HNXY was classified as genotype II, and numerous amino acid variations were found in gB, gE, gC, gD, TK, and RR1 proteins, compared with PRV from other countries or those prevalent in China before 2012. The attenuated rHNXY-∆TK/∆gE was further constructed, which presented significantly smaller plaques than HNXY, as well as the similar growth kinetics. rHNXY-∆/∆ was confirmed to be non-pathogenic to six-week-old BALB/c mice and zero-day-old piglets. This study isolated updated PRV promising to develop into a new vaccine candidate.
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http://dx.doi.org/10.3390/ani10101804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7600349PMC
October 2020

Haplotype-resolved genome analyses of a heterozygous diploid potato.

Nat Genet 2020 10 28;52(10):1018-1023. Epub 2020 Sep 28.

Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.
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http://dx.doi.org/10.1038/s41588-020-0699-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527274PMC
October 2020
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