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1.
Plant J ; 2024 Mar 16.
Article in English | MEDLINE | ID: mdl-38491869

ABSTRACT

The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3 , showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.

2.
Sci Rep ; 14(1): 2161, 2024 01 25.
Article in English | MEDLINE | ID: mdl-38272942

ABSTRACT

Enterovirus D68 (EV-D68) is an emerging pathogen that has caused outbreaks of severe respiratory disease worldwide, especially in children. We aim to investigate the prevalence and genetic characteristics of EV-D68 in children from Shanghai. Nasopharyngeal swab or bronchoalveolar lavage fluid samples collected from children hospitalized with community-acquired pneumonia were screened for EV-D68. Nine of 3997 samples were EV-D68-positive. Seven of nine positive samples were sequenced and submitted to GenBank. Based on partial polyprotein gene (3D) or complete sequence analysis, we found the seven strains belong to different clades and subclades, including three D1 (detected in 2013 and 2014), one D2 (2013), one D3 (2019), and two B3 (2014 and 2018). Overall, we show different clades and subclades of EV-D68 spread with low positive rates (0.2%) among children in Shanghai between 2013 and 2020. Amino acid mutations were found in the epitopes of the VP1 BC and DE loops and C-terminus; similarity analysis provided evidence for recombination as an important mechanism of genomic diversification. Both single nucleotide mutations and recombination play a role in evolution of EV-D68. Genetic instability within these clinical strains may indicate large outbreaks could occur following cumulative mutations.


Subject(s)
Enterovirus D, Human , Enterovirus Infections , Enterovirus , Respiratory Tract Infections , Child , Humans , Molecular Epidemiology , Enterovirus D, Human/genetics , Respiratory Tract Infections/epidemiology , Enterovirus Infections/epidemiology , Phylogeny , China/epidemiology , Disease Outbreaks , Enterovirus/genetics
3.
BMC Genomics ; 24(1): 423, 2023 Jul 27.
Article in English | MEDLINE | ID: mdl-37501164

ABSTRACT

BACKGROUND: Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species. RESULTS: Here, we analyzed the abundance and dynamic evolution of LTR-RTs in 54 species from an economically and agronomically important family, Fabaceae, and also selected two representative species for further analysis in expression of associated genes, transcriptional activity and DNA methylation patterns of LTR-RTs. Annotation results revealed highly varied proportions of LTR-RTs in these genomes (5.1%~68.4%) and their correlation with genome size was highly positive, and they were significantly contributed to the variance in genome size through species-specific unique amplifications. Almost all of the intact LTR-RTs were inserted into the genomes 4 Mya (million years ago), and more than 50% of them were inserted in the last 0.5 million years, suggesting that recent amplifications of LTR-RTs were an important force driving genome evolution. In addition, expression levels of genes with intronic, promoter, and downstream LTR-RT insertions of Glycine max and Vigna radiata, two agronomically important crops in Fabaceae, showed that the LTR-RTs located in promoter or downstream regions suppressed associated gene expression. However, the LTR-RTs within introns promoted gene expression or had no contribution to gene expression. Additionally, shorter and younger LTR-RTs maintained higher mobility and transpositional potential. Compared with the transcriptionally silent LTR-RTs, the active elements showed significantly lower DNA methylation levels in all three contexts. The distributions of transcriptionally active and silent LTR-RT methylation varied across different lineages due to the position of LTR-RTs located or potentially epigenetic regulation. CONCLUSION: Lineage-specific amplification patterns were observed and higher methylation level may repress the activity of LTR-RTs, further influence evolution in Fabaceae species. This study offers valuable clues into the evolution, function, transcriptional activity and epigenetic regulation of LTR-RTs in Fabaceae genomes.


Subject(s)
Fabaceae , Retroelements , Retroelements/genetics , Epigenesis, Genetic , Fabaceae/genetics , Evolution, Molecular , Genome, Plant , Terminal Repeat Sequences/genetics , Phylogeny
4.
Anal Methods ; 15(14): 1819-1825, 2023 04 06.
Article in English | MEDLINE | ID: mdl-36961405

ABSTRACT

A novel nanozyme of bimetallic (Ni/Co) metal-organic framework (Ni/Co-MOF) was synthesized using a simultaneous precipitation and acid etching method with a zeolitic imidazolate framework ZIF-67 as the template. The as-synthesized Ni/Co-MOF catalyst presented a three-dimensional hollow nanocage structure and exhibited excellent intrinsic oxidase-like activity. It was demonstrated that Ni/Co-MOF could directly catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) to produce a blue product (oxidized TMB, oxTMB) in the absence of H2O2. The mechanisms and kinetics of this nanozyme activity were investigated, and it was determined that the catalytic activity of Ni/Co-MOF was closely related to temperature and solution pH. Owing to its strong reducibility, ascorbic acid (AA) could reduce oxTMB, and the blue color of the reaction mixture faded over time. Therefore, a novel colorimetric platform was constructed to detect AA based on the oxidase-like activity of Ni/Co-MOF. Under optimal conditions, the absorbance of ox-TMB at 652 nm decreased linearly over the 0.015-50 µM AA range with a detection limit of 0.004 µM.


Subject(s)
Colorimetry , Metal-Organic Frameworks/chemistry , Nickel/chemistry , Cobalt/chemistry , Colorimetry/methods , Oxidoreductases/metabolism , Ascorbic Acid/chemistry
5.
mBio ; 14(2): e0328522, 2023 04 25.
Article in English | MEDLINE | ID: mdl-36786573

ABSTRACT

In the last 2 decades, pathogens originating in animals may have triggered three coronavirus pandemics, including the coronavirus disease 2019 pandemic. Thus, evaluation of the spillover risk of animal severe acute respiratory syndrome (SARS)-related coronavirus (SARSr-CoV) is important in the context of future disease preparedness. However, there is no analytical framework to assess the spillover risk of SARSr-CoVs, which cannot be determined by sequence analysis alone. Here, we established an integrity framework to evaluate the spillover risk of an animal SARSr-CoV by testing how viruses break through key human immune barriers, including viral cell tropism, replication dynamics, interferon signaling, inflammation, and adaptive immune barriers, using human ex vivo lung tissues, human airway and nasal organoids, and human lung cells. Using this framework, we showed that the two pre-emergent animal SARSr-CoVs, bat BtCoV-WIV1 and pangolin PCoV-GX, shared similar cell tropism but exhibited less replicative fitness in the human nasal cavity or airway than did SARS-CoV-2. Furthermore, these viruses triggered fewer proinflammatory responses and less cell death, yet showed interferon antagonist activity and the ability to partially escape adaptive immune barriers to SARS-CoV-2. Collectively, these animal viruses did not fully adapt to spread or cause severe diseases, thus causing successful zoonoses in humans. We believe that this experimental framework provides a path to identifying animal coronaviruses with the potential to cause future zoonoses. IMPORTANCE Evaluation of the zoonotic risk of animal SARSr-CoVs is important for future disease preparedness. However, there are misconceptions regarding the risk of animal viruses. For example, an animal SARSr-CoV could readily infect humans. Alternately, human receptor usage may result in spillover risk. Here, we established an analytical framework to assess the zoonotic risk of SARSr-CoV by testing a series of virus-host interaction profiles. Our data showed that the pre-emergent bat BtCoV-WIV1 and pangolin PCoV-GX were less adapted to humans than SARS-CoV-2 was, suggesting that it may be extremely rare for animal SARSr-CoVs to break all bottlenecks and cause successful zoonoses.


Subject(s)
COVID-19 , Chiroptera , Animals , Humans , Pangolins , SARS-CoV-2 , Zoonoses , Interferons , Phylogeny
6.
Int J Mol Sci ; 23(17)2022 Sep 05.
Article in English | MEDLINE | ID: mdl-36077556

ABSTRACT

Long terminal repeat (LTR)-retrotransposons (LTR-RTs) comprise a major portion of many plant genomes and may exert a profound impact on genome structure, function, and evolution. Although many studies have focused on these elements in an individual species, their dynamics on a family level remains elusive. Here, we investigated the abundance, evolutionary dynamics, and impact on associated genes of LTR-RTs in 16 species in an economically important plant family, Cucurbitaceae. Results showed that full-length LTR-RT numbers and LTR-RT content varied greatly among different species, and they were highly correlated with genome size. Most of the full-length LTR-RTs were amplified after the speciation event, reflecting the ongoing rapid evolution of these genomes. LTR-RTs highly contributed to genome size variation via species-specific distinct proliferations. The Angela and Tekay lineages with a greater evolutionary age were amplified in Trichosanthes anguina, whereas a recent activity burst of Reina and another ancient round of Tekay activity burst were examined in Sechium edule. In addition, Tekay and Retand lineages belonging to the Gypsy superfamily underwent a recent burst in Gynostemma pentaphyllum. Detailed investigation of genes with intronic and promoter LTR-RT insertion showed diverse functions, but the term of metabolism was enriched in most species. Further gene expression analysis in G.pentaphyllum revealed that the LTR-RTs within introns suppress the corresponding gene expression, whereas the LTR-RTs within promoters exert a complex influence on the downstream gene expression, with the main function of promoting gene expression. This study provides novel insights into the organization, evolution, and function of LTR-RTs in Cucurbitaceae genomes.


Subject(s)
Evolution, Molecular , Retroelements , Genome Size , Genome, Plant , Phylogeny , Retroelements/genetics , Terminal Repeat Sequences/genetics
7.
Signal Transduct Target Ther ; 7(1): 83, 2022 03 11.
Article in English | MEDLINE | ID: mdl-35277473

ABSTRACT

SARS-CoV-2 induced marked lymphopenia in severe patients with COVID-19. However, whether lymphocytes are targets of viral infection is yet to be determined, although SARS-CoV-2 RNA or antigen has been identified in T cells from patients. Here, we confirmed that SARS-CoV-2 viral antigen could be detected in patient peripheral blood cells (PBCs) or postmortem lung T cells, and the infectious virus could also be detected from viral antigen-positive PBCs. We next prove that SARS-CoV-2 infects T lymphocytes, preferably activated CD4 + T cells in vitro. Upon infection, viral RNA, subgenomic RNA, viral protein or viral particle can be detected in the T cells. Furthermore, we show that the infection is spike-ACE2/TMPRSS2-independent through using ACE2 knockdown or receptor blocking experiments. Next, we demonstrate that viral antigen-positive T cells from patient undergone pronounced apoptosis. In vitro infection of T cells induced cell death that is likely in mitochondria ROS-HIF-1a-dependent pathways. Finally, we demonstrated that LFA-1, the protein exclusively expresses in multiple leukocytes, is more likely the entry molecule that mediated SARS-CoV-2 infection in T cells, compared to a list of other known receptors. Collectively, this work confirmed a SARS-CoV-2 infection of T cells, in a spike-ACE2-independent manner, which shed novel insights into the underlying mechanisms of SARS-CoV-2-induced lymphopenia in COVID-19 patients.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , SARS-CoV-2/metabolism , T-Lymphocytes/metabolism , Animals , Caco-2 Cells , Chlorocebus aethiops , Humans , Vero Cells
8.
Viruses ; 13(12)2021 12 11.
Article in English | MEDLINE | ID: mdl-34960752

ABSTRACT

Patients with COVID-19 generally raise antibodies against SARS-CoV-2 following infection, and the antibody level is positively correlated to the severity of disease. Whether the viral antibodies exacerbate COVID-19 through antibody-dependent enhancement (ADE) is still not fully understood. Here, we conducted in vitro assessment of whether convalescent serum enhanced SARS-CoV-2 infection or induced excessive immune responses in immune cells. Our data revealed that SARS-CoV-2 infection of primary B cells, macrophages and monocytes, which express variable levels of FcγR, could be enhanced by convalescent serum from COVID-19 patients. We also determined the factors associated with ADE, and found which showed a time-dependent but not viral-dose dependent manner. Furthermore, the ADE effect is not associated with the neutralizing titer or RBD antibody level when testing serum samples collected from different patients. However, it is higher in a medium level than low or high dilutions in a given sample that showed ADE effect, which is similar to dengue. Finally, we demonstrated more viral genes or dysregulated host immune gene expression under ADE conditions compared to the no-serum infection group. Collectively, our study provides insight into the understanding of an association of high viral antibody titer and severe lung pathology in severe patients with COVID-19.


Subject(s)
Antibody-Dependent Enhancement/immunology , Leukocytes/virology , SARS-CoV-2/pathogenicity , COVID-19/immunology , Cells, Cultured , Gene Expression Profiling , Humans , Immune Sera/immunology , Leukocytes/metabolism , Receptors, IgG/metabolism , Virus Replication/immunology
9.
Org Lett ; 23(21): 8522-8526, 2021 11 05.
Article in English | MEDLINE | ID: mdl-34662135

ABSTRACT

α-Amino azines are widely found in pharmaceuticals and ligands. Herein, we report a practical method for accessing this class of compounds via photocatalyzed hydroarylation of azine-substituted enamides with the in situ-generated aryl thianthrenium salts as the radical precursor. This reaction features a broad substrate scope, good functional group tolerance, and mild conditions and is suitable for the late-stage installation of α-amino azines in complex structures.

10.
Ying Yong Sheng Tai Xue Bao ; 32(8): 2693-2702, 2021 Aug.
Article in Chinese | MEDLINE | ID: mdl-34664441

ABSTRACT

We investigated the effects of different biochar application patterns on soil nutrient contents and element transformation, with soil samples being collected from two five-year field experiments in Phaeozem and Luvisol amended with biochar at annual low-rate (AL, 22.5 t·hm-2·a-1) and intervalic high-rate (IH, 112.5 t·hm-2·5 a-1). Changes of soil total carbon (C), nitrogen (N) and phosphorus (P) contents as well as the related enzyme activities were measured under different biochar application patterns to provide fundamental information for the straw utilization and soil fertility improvement in agroecosystem. Results showed that total C and organic N contents in AL treatment were significantly higher than those in IH treatment in Phaeozem soil. Compared with the control, the decreases of dehydrogenase activity in AL treatment was more pronounced than that in IH treatment in Phaeozem soil, and the increases of protease activity in IH treatment was pronounced than that in AL treatment in Luvisol. Compared with Luvisol soil, the application of biochar had stronger effect on total soil C and organic N contents in Phaeozem soil. Application of biochar significantly increased the activities of soil dehydrogenase and protease in Luvisol soil, but decreased the activity of soil dehydrogenase. Soil types and biochar application patterns interacted to affect soil C and N contents, microbial metabolic activity, N- and P-related enzyme activities. In summary, soil types and biochar addition affected soil properties and microbial characteristics, which would provide important information for straw application and soil management.


Subject(s)
Nitrogen , Soil , Charcoal , Nitrogen/analysis , Nutrients , Phosphorus
11.
Hortic Res ; 8(1): 198, 2021 Sep 01.
Article in English | MEDLINE | ID: mdl-34465747

ABSTRACT

DNA methylation is a crucial regulatory mechanism in many biological processes. However, limited studies have dissected the contribution of DNA methylation to sexual differentiation in dioecious plants. In this study, we investigated the variances in methylation and transcriptional patterns of male and female flowers of garden asparagus. Compared with male flowers, female flowers at the same stages showed higher levels of DNA methylation. Both male and female flowers gained DNA methylation globally from the premeiotic to meiotic stages. Detailed analysis revealed that the increased DNA methylation was largely due to increased CHH methylation. Correlation analysis of differentially expressed genes and differentially methylated regions suggested that DNA methylation might not have contributed to the expression variation of the sex-determining genes SOFF and TDF1 but probably played important roles in sexual differentiation and flower development of garden asparagus. The upregulated genes AoMS1, AoLAP3, AoAMS, and AoLAP5 with varied methylated CHH regions might have been involved in sexual differentiation and flower development of garden asparagus. Plant hormone signaling genes and transcription factor genes also participated in sexual differentiation and flower development with potential epigenetic regulation. In addition, the CG and CHG methylation levels in the Y chromosome were notably higher than those in the X chromosome, implying that DNA methylation might have been involved in Y chromosome evolution. These data provide insights into the epigenetic modification of sexual differentiation and flower development and improve our understanding of sex chromosome evolution in garden asparagus.

13.
Cell Discov ; 6(1): 96, 2020 Dec 22.
Article in English | MEDLINE | ID: mdl-33349633

ABSTRACT

The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread to >200 countries posing a global public health concern. Patients with comorbidity, such as hypertension suffer more severe infection with elevated mortality. The development of effective antiviral drugs is in urgent need to treat COVID-19 patients. Here, we report that calcium channel blockers (CCBs), a type of antihypertensive drug that is widely used in clinics, inhibited the post-entry replication events of SARS-CoV-2 in vitro, while no in vitro anti-SARS-CoV-2 effect was observed for the two other major types of antihypertensive drugs, namely, angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers. CCB combined with chloroquine showed a significantly enhanced anti-SARS-CoV-2 efficacy. A retrospective clinical investigation on hospitalized COVID-19 patients with hypertension as the only comorbidity revealed that the CCB amlodipine besylate therapy was associated with a decreased case fatality rate. The results from this study suggest that CCB administration to COVID-19 patients with hypertension as the comorbidity might improve the disease outcome.

14.
Org Lett ; 22(19): 7768-7772, 2020 Oct 02.
Article in English | MEDLINE | ID: mdl-32966742

ABSTRACT

Vinyl sulfonium salts typically act as an electrophilic Michael acceptor, thus initiating many tandem cyclization reactions. Herein, we disclosed the novel reactivity of vinyl sulfonium salts as a radical acceptor. Using redox-active ester as an alkyl radical precursor, metal-free decarboxylative alkenylation with vinyl sulfonium salts was realized using eosin Y as a photocatalyst. This process features a broad substrate scope and tolerates with a broad range of primary, secondary, tertiary carboxylic acids.

16.
Invest Ophthalmol Vis Sci ; 61(10): 2, 2020 08 03.
Article in English | MEDLINE | ID: mdl-32744597

ABSTRACT

Purpose: Retinoblastoma is a malignant tumor of the developing retina that mostly occurs in children. Our study aimed to investigate the effect of tripartite motif-containing protein 59 (TRIM59) on retinoblastoma growth and the underlying mechanisms. Methods: We performed bioinformatic analysis of three datasets (GSE24673, GSE97508, and GSE110811) from the Gene Expression Omnibus database. Quantitative reverse-transcription PCR and immunoblotting of three retinoblastoma cell lines were conducted to verify TRIM59 as a differentially expressed gene. Specific siRNAs were used to inhibit TRIM59 expression in the HXO-Rb44 cell line. A lentiviral vector was transfected into the Y79 cell line to overexpress TRIM59. The effects of TRIM59 on retinoblastoma cell proliferation, cell cycling, and apoptosis were explored in vitro using the abovementioned cell lines. The effect of TRIM59 expression on retinoblastoma cell proliferation was evaluated in a mouse xenograft tumor model. Results: TRIM59 expression in three retinoblastoma cell lines was remarkably elevated compared with normal control. Knocking down TRIM59 expression remarkably suppressed cell proliferation and growth and promoted cell apoptosis in HXO-Rb44 cells, whereas TRIM59 overexpression promoted tumor progression in Y79 cells. Silencing TRIM59 also markedly inhibited in vivo tumor growth in the xenograft model. Mechanistic studies revealed that TRIM59 upregulated phosphorylated p38, p-JNK1/2, p-ERK1/2, and p-c-JUN expression in retinoblastoma cells. Notably, the p38 inhibitor SB203580 attenuated the effects of TRIM59 on cell proliferation, apoptosis, and the G1/S phase transition. Conclusions: TRIM59 plays an oncogenic role in retinoblastoma and exerts its tumor-promotive function by activating the p38-mitogen-activated protein kinase pathway.


Subject(s)
Intracellular Signaling Peptides and Proteins/genetics , MAP Kinase Signaling System/physiology , Retinal Neoplasms/genetics , Retinoblastoma/genetics , Tripartite Motif Proteins/genetics , Animals , Apoptosis , Cell Cycle/physiology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Disease Models, Animal , Disease Progression , Gene Expression Regulation, Neoplastic/physiology , Genetic Vectors/genetics , Humans , Immunohistochemistry , Lentivirus/genetics , Mice, Nude , Phosphorylation , RNA, Small Interfering/genetics , Real-Time Polymerase Chain Reaction , Retinal Neoplasms/metabolism , Retinal Neoplasms/pathology , Retinoblastoma/metabolism , Retinoblastoma/pathology , Signal Transduction/physiology , Xenograft Model Antitumor Assays
17.
Cell Rep ; 30(13): 4370-4385.e7, 2020 03 31.
Article in English | MEDLINE | ID: mdl-32234474

ABSTRACT

Severe fever with thrombocytopenia syndrome (SFTS) virus (SFTSV) is an emerging tick-borne virus that carries a high fatality rate of 12%-50%. In-depth understanding of the SFTSV-induced pathogenesis mechanism is critical for developing effective anti-SFTS therapeutics. Here, we report transcriptomic analysis of blood samples from SFTS patients. We observe a strong correlation between inflammatory responses and disease progression and fatal outcome. Quantitative proteomic analysis of SFTSV infection confirms the induction of inflammation and further reveals virus-induced mitochondrial dysfunction. Mechanistically, SFTSV infection triggers BCL2 antagonist/killer 1 (BAK) upregulation and BAK/BCL2-associated X (BAX) activation, leading to mitochondrial DNA (mtDNA) oxidization and subsequent cytosolic release. The cytosolic mtDNA binds and triggers NLRP3 inflammasome activation. Notably, the BAK expression level correlates with SFTS disease progression and fatal outcome. These findings provide insights into the clinical features and molecular underpinnings of severe SFTS, which may aid in patient care and therapeutic design, and may also be conserved during infection by other highly pathogenic viruses.


Subject(s)
Bunyaviridae Infections/metabolism , DNA, Mitochondrial/metabolism , Inflammasomes/metabolism , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Phlebovirus/physiology , bcl-2 Homologous Antagonist-Killer Protein/metabolism , bcl-2-Associated X Protein/metabolism , Adult , Animals , Bunyaviridae Infections/genetics , Bunyaviridae Infections/virology , Cell Line , Disease Models, Animal , Disease Progression , Female , Humans , Inflammation/genetics , Interleukin-1beta/metabolism , Mice, Inbred C57BL , Mitochondria/metabolism , Mitochondria/pathology , Models, Biological , Myeloid Differentiation Factor 88/metabolism , NF-kappa B/metabolism , Reactive Oxygen Species/metabolism , Signal Transduction , Toll-Like Receptor 8/metabolism , Transcriptome/genetics
18.
Hortic Res ; 7(1): 48, 2020.
Article in English | MEDLINE | ID: mdl-32257234

ABSTRACT

Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome of A. setaceus to facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly of A. setaceus covering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome of A. setaceus was predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time of A. setaceus from its close relative A. officinalis of ~9.66 million years ago, and A. setaceus underwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted in A. setaceus. These findings provide new knowledge about the characteristics and evolution of the A. setaceus genome, and will facilitate comparative genetic and genomic research on the genus Asparagus.

19.
Int J Ophthalmol ; 13(2): 213-219, 2020.
Article in English | MEDLINE | ID: mdl-32090029

ABSTRACT

AIM: To observe the effect of inhibiting long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) on diabetic neurodegeneration. METHODS: Thirty-six 8-week-old C57BL/6 mice were randomly divided into normal control, diabetic control, diabetic scrambled small interfering RNAs (siRNAs) and diabetic MALAT1-siRNA groups. After diabetic induction with streptozocin intraperitoneally-injection, the diabetic MALAT1-siRNA group was intravitreally injected with 1 µL 20 µmol/L MALAT1 siRNA, and the diabetic scrambled siRNA group was injected with the same amount of scrambled siRNA. Electroretinography was performed to examine photoreceptor functions 16wk after diabetes induction. MALAT1 expression was detected via real time polymerase chain reaction. Cone morphological changes were examined using immunofluorescence. Rod morphological changes were examined by determining outer nuclear layer (ONL) thickness. RESULTS: The upregulation of retinal MALAT1 expression was detected in the diabetic control mice, while MALAT1 expression in the diabetic MALAT1-siRNA mice was decreased by 91.48% compared to diabetic control mice. The diabetic MALAT1-siRNA and diabetic control mice showed lower a-wave and b-wave amplitudes than did the normal control mice in scotopic and photopic electroretinogram, while the diabetic MALAT1-siRNA mice showed higher amplitudes than diabetic control mice. Morphological examination revealed that ONL thickness in the diabetic MALAT1-siRNA and diabetic control mice was lower than normal control mice. However, ONL thickness was greater in the diabetic MALAT1-siRNA mice than diabetic control mice. Moreover, the diabetic control mice performed a sparser cone cell arrangement and shorter outer segment morphology than diabetic MALAT1-siRNA mice. CONCLUSION: Inhibiting retinal MALAT1 results in mitigative effects on the retinal photoreceptors, thus alleviating diabetic neurodegeneration.

20.
Ying Yong Sheng Tai Xue Bao ; 31(6): 1957-1962, 2020 Jun.
Article in Chinese | MEDLINE | ID: mdl-34494749

ABSTRACT

Urease in soil, as the most important enzyme catalyzing urea hydrolysis, plays an important role in nitrogen supply of grassland ecosystems. While the effects of different carbon additions on extracellular urease in grassland soil are well understood, their effects on soil intracellular urease remain unknow. Moreover, whether the responses of intracellular and extracellular urease to carbon additions are consistent need to be clarified. With a field experiment in Hulun Buir grassland of Inner Mongolia, we investigated soil intracellular and extracellular urease activities in chernozem under four treatments, including carbon-free (C0), 250 (C250), and 500 (C500) kg C·hm-2·a-1, using glucose as carbon source. Further, we analyzed their relationships with soil properties. Carbon additions significantly increased soil intracellular urease activity and its ratio to total urease activities and total urease activity, but did not affect soil extracellular urease activities. There was significant positive correlation between soil intracellular urease activity and microbial biomass, suggesting that the increases of soil intracellular urease activities were mainly caused by the increases of microbial biomass. Results of structural equation modeling (SEM) analysis showed that carbon additions indirectly increased soil intracellular urease activities by affecting microbial biomass.


Subject(s)
Carbon , Soil , Biomass , Carbon/analysis , China , Ecosystem , Nitrogen/analysis , Soil Microbiology , Urease
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