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1.
Nature ; 602(7898): 657-663, 2022 02.
Article in English | MEDLINE | ID: mdl-35016194

ABSTRACT

The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A-F)-a grouping that is highly concordant with knowledge-based structural classifications3-5. Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A-D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309)6 and group F (for example, CR3022)7, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Immune Evasion/immunology , Neutralization Tests , SARS-CoV-2/immunology , Angiotensin-Converting Enzyme 2/metabolism , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/therapeutic use , Antibodies, Neutralizing/classification , Antibodies, Viral/classification , COVID-19/immunology , COVID-19/virology , COVID-19 Vaccines/immunology , Cells, Cultured , Convalescence , Epitopes, B-Lymphocyte/chemistry , Epitopes, B-Lymphocyte/immunology , Humans , Immune Sera/immunology , Models, Molecular , Mutation , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology , Spike Glycoprotein, Coronavirus/metabolism
2.
PLoS Pathog ; 20(5): e1012230, 2024 May.
Article in English | MEDLINE | ID: mdl-38776321

ABSTRACT

While macrophage is one of the major type I interferon (IFN-I) producers in multiple tissues during viral infections, it also serves as an important target cell for many RNA viruses. However, the regulatory mechanism for the IFN-I response of macrophages to respond to a viral challenge is not fully understood. Here we report ADAP, an immune adaptor protein, is indispensable for the induction of the IFN-I response of macrophages to RNA virus infections via an inhibition of the conjugation of ubiquitin-like ISG15 (ISGylation) to RIG-I. Loss of ADAP increases RNA virus replication in macrophages, accompanied with a decrease in LPS-induced IFN-ß and ISG15 mRNA expression and an impairment in the RNA virus-induced phosphorylation of IRF3 and TBK1. Moreover, using Adap-/- mice, we show ADAP deficiency strongly increases the susceptibility of macrophages to RNA-virus infection in vivo. Mechanically, ADAP selectively interacts and functionally cooperates with RIG-I but not MDA5 in the activation of IFN-ß transcription. Loss of ADAP results in an enhancement of ISGylation of RIG-I, whereas overexpression of ADAP exhibits the opposite effect in vitro, indicating ADAP is detrimental to the RNA virus-induced ISGylation of RIG-I. Together, our data demonstrate a novel antagonistic activity of ADAP in the cell-intrinsic control of RIG-I ISGylation, which is indispensable for initiating and sustaining the IFN-I response of macrophages to RNA virus infections and replication.


Subject(s)
Adaptor Proteins, Signal Transducing , DEAD Box Protein 58 , Interferon Type I , Macrophages , Mice, Knockout , RNA Virus Infections , Ubiquitins , Animals , Macrophages/virology , Macrophages/metabolism , Macrophages/immunology , Mice , RNA Virus Infections/immunology , RNA Virus Infections/metabolism , Ubiquitins/metabolism , Ubiquitins/genetics , DEAD Box Protein 58/metabolism , Interferon Type I/metabolism , Adaptor Proteins, Signal Transducing/metabolism , Adaptor Proteins, Signal Transducing/genetics , Cytokines/metabolism , Mice, Inbred C57BL , Humans , Receptors, Immunologic/metabolism , Interferon-beta/metabolism , RNA Viruses/immunology , Interferon Regulatory Factor-3/metabolism
3.
Nucleic Acids Res ; 52(9): 4969-4984, 2024 May 22.
Article in English | MEDLINE | ID: mdl-38452206

ABSTRACT

Proteasome-mediated degradation of chromatin-bound NF-κB is critical in terminating the transcription of pro-inflammatory genes and can be triggered by Set9-mediated lysine methylation of the RelA subunit. However, the E3 ligase targeting methylated RelA remains unknown. Here, we find that two structurally similar substrate-recognizing components of Cullin-RING E3 ligases, WSB1 and WSB2, can recognize chromatin-bound methylated RelA for polyubiquitination and proteasomal degradation. We showed that WSB1/2 negatively regulated a subset of NF-κB target genes via associating with chromatin where they targeted methylated RelA for ubiquitination, facilitating the termination of NF-κB-dependent transcription. WSB1/2 specifically interacted with methylated lysines (K) 314 and 315 of RelA via their N-terminal WD-40 repeat (WDR) domains, thereby promoting ubiquitination of RelA. Computational modeling further revealed that a conserved aspartic acid (D) at position 158 within the WDR domain of WSB2 coordinates K314/K315 of RelA, with a higher affinity when either of the lysines is methylated. Mutation of D158 abolished WSB2's ability to bind to and promote ubiquitination of methylated RelA. Together, our study identifies a novel function and the underlying mechanism for WSB1/2 in degrading chromatin-bound methylated RelA and preventing sustained NF-κB activation, providing potential new targets for therapeutic intervention of NF-κB-mediated inflammatory diseases.


Subject(s)
Chromatin , Proteasome Endopeptidase Complex , Transcription Factor RelA , Ubiquitination , Humans , Chromatin/metabolism , HEK293 Cells , Lysine/metabolism , Methylation , NF-kappa B/metabolism , Proteasome Endopeptidase Complex/metabolism , Protein Binding , Proteolysis , Transcription Factor RelA/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics
4.
Plant J ; 119(2): 796-813, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38733630

ABSTRACT

Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome-wide association study of natural cucumber populations, along with map-based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow-brown fruit skin) and Zaoer-N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator-like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow-brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow-colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C-terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3'H, which encodes flavonoid 3'-hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs.


Subject(s)
Cucumis sativus , Flavonoids , Fruit , Gene Expression Regulation, Plant , Pigmentation , Plant Proteins , Transcription Factors , Cucumis sativus/genetics , Cucumis sativus/metabolism , Fruit/genetics , Fruit/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Flavonoids/metabolism , Pigmentation/genetics , Genome-Wide Association Study , Plants, Genetically Modified
5.
J Cell Mol Med ; 28(20): e70047, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39428571

ABSTRACT

Kashin-Beck disease (KBD) is a chronic degenerative, disabling disease of the bones and joints and its exact aetiology and pathogenesis remain uncertain. This study is to investigate the role of m6A modification in the pathogenesis of KBD. Combined analysis of m6A MeRIP-Seq and RNA-Seq were used to analyse human peripheral blood samples from three KBD patients and three normal controls (NC). Bioinformatic methods were used to analyse m6A-modified differential genes and RT-qPCR was performed to validate the mRNA expression of several KBD-related genes. The results indicated that the total of 16,811 genes were modified by m6A in KBD group, of which 4882 genes were differential genes. A large number of differential genes were associated with regulation of transcription, signal transduction and protein binding. KEGG analysis showed that m6A-enriched genes participated the pathways of Vitamin B6 metabolism, endocytosis and Rap 1 signalling pathway. There was a positive association between m6A abundance and levels of gene expression, that there were 6 hypermethylated and upregulated genes (hyper-up), 23 hypomethylated and downregulated genes (hypo-down) in KBD group compared with NC. In addition, the mRNA expression of levels of MMP8, IL32 and GPX1 were verified and the protein-protein interaction networks of these key factors were constructed. Our study showed that m6A modifications may play a vital role in modulating gene expression, which represents a new clue to reveal the pathogenesis of KBD.


Subject(s)
Kashin-Beck Disease , Transcriptome , Humans , Kashin-Beck Disease/genetics , Transcriptome/genetics , Male , Gene Expression Profiling , Methylation , Female , Middle Aged , Gene Expression Regulation , Computational Biology/methods , RNA, Messenger/genetics , RNA, Messenger/metabolism , Case-Control Studies , RNA Methylation , Adenosine/analogs & derivatives
6.
Plant J ; 115(2): 414-433, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37036138

ABSTRACT

Sensory plastids are important in plant responses to environmental changes. Previous studies show that MutS HOMOLOG 1 (MSH1) perturbation in sensory plastids induces heritable epigenetic phenotype adjustment. Previously, the PsbP homolog DOMAIN-CONTAINING PROTEIN 3 (PPD3), a protein of unknown function, was postulated to be an interactor with MSH1. This study investigates the relationship of PPD3 with MSH1 and with plant environmental sensing. The ppd3 mutant displays a whole-plant phenotype variably altered in growth rate, flowering time, reactive oxygen species (ROS) modulation and response to salt, with effects on meristem growth. Present in both chloroplasts and sensory plastids, PPD3 colocalized with MSH1 in root tips but not in leaf tissues. The suppression or overexpression of PPD3 affected the plant growth rate and stress tolerance, and led to a heritable, heterogenous 'memory' state with both dwarfed and vigorous growth phenotypes. Gene expression and DNA methylome data sets from PPD3-OX and derived memory states showed enrichment in growth versus defense networks and meristem effects. Our results support a model of sensory plastid influence on nuclear epigenetic behavior and ppd3 as a second trigger, functioning within meristem plastids to recalibrate growth plasticity.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Plastids/genetics , Plastids/metabolism , Chloroplasts/metabolism , Epigenesis, Genetic , Gene Expression Regulation, Plant , MutS DNA Mismatch-Binding Protein/genetics , MutS DNA Mismatch-Binding Protein/metabolism
7.
J Am Chem Soc ; 2024 Oct 30.
Article in English | MEDLINE | ID: mdl-39475252

ABSTRACT

New methods for the enantioselective synthesis of N-alkylated indoles and their derivatives are of great interest because indoles are pivotal structural elements in biologically active molecules and natural products. They are also versatile intermediates in organic synthesis. Among well-established asymmetric hydroamination methods, the asymmetric hydroamination with indole-based substrates is a formidable challenge. This observation is likely due to the reduced nucleophilicity of the indole nitrogen. Herein, a unique nickel-catalyzed enantio- and branched-selective hydroamination of 2-azadienes with indoles and structurally related N-heterocycles is reported for the generation of enantioenriched N,N-aminals. Salient features of this reaction include good yields, mild reaction conditions, high enantioselectivities, and broad substrate scope (60 examples, up to 96% yield and 99% ee). The significance of this approach with indoles and other N-heterocycles is demonstrated through structural modification of natural products and drug molecules and the preparation of enantioenriched N-alkylated indole core structures. Mechanistic studies reveal that olefin insertion into a Ni-H bond in the hydroamination is the enantio-determining step and oxidative addition of the N-H bond may be the turnover-limiting step.

8.
EMBO J ; 39(2): e102201, 2020 01 15.
Article in English | MEDLINE | ID: mdl-31762063

ABSTRACT

The innate immune sensor NLRP3 assembles an inflammasome complex with NEK7 and ASC to activate caspase-1 and drive the maturation of proinflammatory cytokines IL-1ß and IL-18. NLRP3 inflammasome activity must be tightly controlled, as its over-activation is involved in the pathogenesis of inflammatory diseases. Here, we show that NLRP3 inflammasome activation is suppressed by a centrosomal protein Spata2. Spata2 deficiency enhances NLRP3 inflammasome activity both in the macrophages and in an animal model of peritonitis. Mechanistically, Spata2 recruits the deubiquitinase CYLD to the centrosome for deubiquitination of polo-like kinase 4 (PLK4), the master regulator of centrosome duplication. Deubiquitination of PLK4 facilitates its binding to and phosphorylation of NEK7 at Ser204. NEK7 phosphorylation in turn attenuates NEK7 and NLRP3 interaction, which is required for NLRP3 inflammasome activation. Pharmacological or shRNA-mediated inhibition of PLK4, or mutation of the NEK7 Ser204 phosphorylation site, augments NEK7 interaction with NLRP3 and causes increased NLRP3 inflammasome activation. Our study unravels a novel centrosomal regulatory pathway of inflammasome activation and may provide new therapeutic targets for the treatment of NLRP3-associated inflammatory diseases.


Subject(s)
Centrosome/immunology , Deubiquitinating Enzyme CYLD/metabolism , Inflammasomes/immunology , NIMA-Related Kinases/metabolism , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Protein Serine-Threonine Kinases/metabolism , Proteins/physiology , Animals , Centrosome/metabolism , Cytokines/metabolism , Deubiquitinating Enzyme CYLD/genetics , Disease Models, Animal , Inflammasomes/metabolism , Macrophages/immunology , Macrophages/metabolism , Macrophages/pathology , Mice , Mice, Inbred C57BL , Mice, Knockout , NIMA-Related Kinases/genetics , NLR Family, Pyrin Domain-Containing 3 Protein/genetics , Peritonitis/immunology , Peritonitis/metabolism , Peritonitis/pathology , Phosphorylation , Protein Serine-Threonine Kinases/genetics , Signal Transduction , Ubiquitination
9.
Funct Integr Genomics ; 24(4): 116, 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38910225

ABSTRACT

Chloroplasts are not only critical photosynthesis sites in plants, but they also participate in plastidial retrograde signaling in response to developmental and environmental signals. MEcPP (2-C-Methyl-D-erythritol-2,4-cyclopyrophosphate) is an intermediary in the methylerythritol phosphate (MEP) pathway in chloroplasts. It is a critical precursor for the synthesis of isoprenoids and terpenoid derivatives, which play crucial roles in plant growth and development, photosynthesis, reproduction, and defense against environmental constraints. Accumulation of MEcPP under stressful conditions triggers the expression of IMPα-9 and TPR2, contributing to the activation of abiotic stress-responsive genes. In this correspondence, we discuss plastidial retrograde signaling in support of a recently published paper in Molecular Plant (Zeng et al. 2024). We hope that it can shed more insight on the retrograde signaling cascade.


Subject(s)
Chloroplasts , Stress, Physiological , Chloroplasts/metabolism , Gene Expression Regulation, Plant , Signal Transduction , Arabidopsis/genetics , Arabidopsis/metabolism , Erythritol/metabolism , Erythritol/analogs & derivatives , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Sugar Phosphates/metabolism , MAP Kinase Kinase Kinase 5/metabolism , MAP Kinase Kinase Kinase 5/genetics
10.
Hum Genet ; 2024 Oct 24.
Article in English | MEDLINE | ID: mdl-39446226

ABSTRACT

Preaxial polydactyly (PPD) is a congenital limb malformation, previously reported to be caused primarily by variants in the ZRS and upstream preZRS regions. This study investigated genetic variations associated with PPD, focusing on point variants and copy number variations (CNVs) in the ZRS and preZRS regions. Comprehensive genetic analyses were conducted on 102 patients with PPD, including detailed clinical examinations and Sanger sequencing of the ZRS and preZRS regions. Additionally, real-time quantitative PCR (qPCR) was used to detect CNVs in the ZRS region. The evolutionary conservation and population frequencies of identified variants were also evaluated. Six point variants were identified, among which four are likely pathogenic novel variants: 93G > T (g.156584477G > T), 106G > A (g.156584464G > A), 278G > A (g.156584292G > A), and 409A > C (g.156585378A > C). Additionally, qPCR analysis revealed that 66.67% of patients exhibited ZRS duplications. Notably, these duplications were also present in cases with newly identified potential pathogenic point variants. These findings suggest the possible interaction of point variants in ZRS and preZRS through a common pathogenic mechanism, leading jointly to PPD. The findings expand the variant spectrum associated with non-syndromic polydactyly and highlight that, despite different classifications, anterior polydactyly caused by variants in ZRS and nearby regions may share common pathogenic mechanisms. The incorporation of various variant types in genetic screening can effectively enhance the rate of pathogenic variant detection and contribute to the cost-effectiveness of genetic testing for limb developmental defects, thereby promoting healthy births.

11.
Anal Chem ; 96(28): 11137-11145, 2024 07 16.
Article in English | MEDLINE | ID: mdl-38953491

ABSTRACT

The Tn antigen, an immature truncated O-glycosylation, is a promising biomarker for cancer detection and diagnosis. However, reliable methods for analyzing O-GalNAcylation and complex O-glycosylation are lacking. Here, we develop a novel method, MOTAI, for the sequential analysis of O-glycosylation using different O-glycoproteases. MOTAI conjugates glycopeptides on a solid support and releases different types of O-glycosylation through sequential enzymatic digestion by O-glycoproteases, including OpeRATOR and IMPa. Because OpeRATOR has less activity on O-GalNAcylation, MOTAI enriches O-GalNAcylation for subsequent analysis. We demonstrate the effectiveness of MOTAI by analyzing fetuin O-glycosylation and Jurkat cell lines. We then apply MOTAI to analyze colorectal cancer and benign colorectal polyps. We identify 32 Tn/sTn-glycoproteins and 43 T/sT-glycoproteins that are significantly increased in tumor tissues. Gene Ontology analysis reveals that most of these proteins are ECM proteins involved in the adhesion process of the intercellular matrix. Additionally, the protein disulfide isomerase CRELD2 has a significant difference in Tn expression, and the abnormally glycosylated T345 and S349 O-glycosylation sites in cancer group samples may promote the secretion of CRELD2 and ultimately tumorigenesis through ECM reshaping. In summary, MOTAI provides a powerful new tool for the in-depth analysis of O-GalNAcylation and complex O-glycosylation. It also reveals the upregulation of Tn/sTn-glycoproteins in colorectal cancer, which may provide new insights into cancer biology and biomarker discovery.


Subject(s)
Antigens, Tumor-Associated, Carbohydrate , Humans , Glycosylation , Antigens, Tumor-Associated, Carbohydrate/metabolism , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Jurkat Cells
12.
Small ; 20(45): e2402767, 2024 Nov.
Article in English | MEDLINE | ID: mdl-39086056

ABSTRACT

Electroactive organic electrode materials exhibit remarkable potential in aqueous zinc ion batteries (AZIBs) due to their abundant availability, customizable structures, sustainability, and high reversibility. However, the research on AZIBs has predominantly concentrated on unraveling the storage mechanism of zinc cations, often neglecting the significance of anions in this regard. Herein, bipolar poly(thionine) is synthesized by a simple and efficient polymerization reaction, and the kinetics of different anions are investigated using poly(thionine) as the cathode of AZIBs. Notably, poly(thionine) is a bipolar organic polymer electrode material and exhibits enhanced stability in aqueous solutions compared to thionine monomers. Kinetic analysis reveals that ClO4 - exhibits the fastest kinetics among SO4 2-, Cl-, and OTF-, demonstrating excellent rate performance (109 mAh g-1 @ 0.5 A g-1 and 92 mAh g-1 @ 20 A g-1). Mechanism studies reveal that the poly(thionine) cathode facilitates the co-storage of both anions and cations in Zn(ClO4)2. Furthermore, the lower electrostatic potential of ClO4 - influences the strength of hydrogen bonding with water molecules, thereby enhancing the overall kinetics in aqueous electrolytes. This work provides an effective strategy for synthesizing high-quality organic materials and offers new insights into the kinetic behavior of anions in AZIBs.

13.
Plant Biotechnol J ; 22(5): 1325-1334, 2024 May.
Article in English | MEDLINE | ID: mdl-38213067

ABSTRACT

Cytoplasmic male sterility (CMS), encoded by the mitochondrial open reading frames (ORFs), has long been used to economically produce crop hybrids. However, the utilization of CMS also hinders the exploitation of sterility and fertility variation in the absence of a restorer line, which in turn narrows the genetic background and reduces biodiversity. Here, we used a mitochondrial targeted transcription activator-like effector nuclease (mitoTALENs) to knock out ORF138 from the Ogura CMS broccoli hybrid. The knockout was confirmed by the amplification and re-sequencing read mapping to the mitochondrial genome. As a result, knockout of ORF138 restored the fertility of the CMS hybrid, and simultaneously manifested a cold-sensitive male sterility. ORF138 depletion is stably inherited to the next generation, allowing for direct use in the breeding process. In addition, we proposed a highly reliable and cost-effective toolkit to accelerate the life cycle of fertile lines from CMS-derived broccoli hybrids. By applying the k-mean clustering and interaction network analysis, we identified the central gene networks involved in the fertility restoration and cold-sensitive male sterility. Our study enables mitochondrial genome editing via mitoTALENs in Brassicaceae vegetable crops and provides evidence that the sex production machinery and its temperature-responsive ability are regulated by the mitochondria.


Subject(s)
Brassica , Infertility, Male , Male , Humans , Brassica/genetics , Transcription Activator-Like Effector Nucleases , Plant Breeding , Mitochondria/genetics , Fertility/genetics , Plant Infertility/genetics
14.
Mol Ecol ; 33(4): e17246, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38153177

ABSTRACT

Acclimatization through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms' performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant-like properties. They are light dependent with a sessile and modular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes within the colony. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally advance our understanding of how reef-building corals repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.


Subject(s)
Anthozoa , Animals , Anthozoa/genetics , Epigenome , Adaptation, Physiological , Phenotype , Transcriptome/genetics , Coral Reefs , Acclimatization/genetics
15.
Plant Physiol ; 193(2): 1001-1015, 2023 09 22.
Article in English | MEDLINE | ID: mdl-37394925

ABSTRACT

Cucumber (Cucumis sativus L.) flesh is typically colorless or pale green. Flesh with yellow or orange pigment, determined mainly by carotenoid content and composition, is mostly found in semi-wild Xishuangbanna cucumber, which has a very narrow genetic background. Here, we identified a spontaneous cucumber mutant with yellow flesh (yf-343), which accumulated more ß-cryptoxanthin and less lutein than regular cultivated European glasshouse-type cucumbers. Genetic analysis revealed that the yellow flesh phenotype was controlled by a single recessive gene. Through fine mapping and gene sequencing, we identified the candidate gene C. sativus yellow flesh 2 (Csyf2), encoding an abscisic acid (ABA) 8'-hydroxylase. Overexpression and RNAi-silencing of Csyf2 in cucumber hairy roots produced lower and higher ABA contents than in non-transgenic controls, respectively. Further, RNA-seq analysis suggested that genes related to ABA signal transduction were differentially expressed in fruit flesh between yf-343 and its wild type, BY, with white flesh. The carotenoid biosynthesis pathway was specifically enriched in fruit flesh at 30 days after pollination when yf-343 fruit flesh turns yellow. Our findings highlight a promising target for gene editing to increase carotenoid content, expanding our genetic resources for pigmented cucumber flesh breeding for improving the nutritional quality of cucumber.


Subject(s)
Cucumis sativus , Cucumis sativus/genetics , Plant Breeding , Plant Proteins/genetics , Plant Proteins/metabolism , Carotenoids/metabolism , Fruit/genetics
16.
Opt Express ; 32(3): 3308-3315, 2024 Jan 29.
Article in English | MEDLINE | ID: mdl-38297555

ABSTRACT

Mechanical strain can be used to tune the optical properties of monolayer transition metal dichalcogenides (1L-TMDs). Here, upconversion photoluminescence (UPL) from 1L-WSe2 flakes is tuned with biaxial strain induced by cruciform bending and indentation method. It is found that the peak position of UPL is redshifted by around 24 nm as the applied biaxial strain increases from 0% to 0.51%. At the same time, the UPL intensity increases exponentially for the upconversion energy difference that lies within a broad range between -157 meV to -37 meV. The observed linear and sublinear power dependence of UPL emission in 1L-WSe2 with and without biaxial strain at three different excitation wavelengths of 784 nm, 800 nm, and 820 nm indicates the multiphonon-assisted one-photon upconversion emission process. The results of strain-dependent UPL emission from 1L-TMDs pave a unique path to the advances in photon upconversion applications and optoelectronic devices.

17.
Opt Express ; 32(11): 20136-20145, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38859130

ABSTRACT

Integrating phase-change materials in metasurfaces has emerged as a powerful strategy to realize optical devices with tunable electromagnetic responses. Here, phase-change chiral metasurfaces based on GST-225 material with the designed trapezoid-shaped resonators are demonstrated to achieve tunable circular dichroism (CD) responses in the infrared regime. The asymmetric trapezoid-shaped resonators are designed to support two chiral plasmonic resonances with opposite CD responses for realizing switchable CD between negative and positive values using the GST phase change from amorphous to crystalline. The electromagnetic field distributions of the chiral plasmonic resonant modes are analyzed to understand the chiroptical responses of the metasurface. Furthermore, the variations in the absorption spectrum and CD value for the metasurface as a function of the baking time during the GST phase transition are analyzed to reveal the underlying thermal tuning process of the metasurface. The demonstrated phase-change metasurfaces with tunable CD responses hold significant promise in enabling many applications in the infrared regime such as chiral sensing, encrypted communication, and thermal imaging.

18.
J Exp Bot ; 75(10): 2951-2964, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38426564

ABSTRACT

Vessel traits contribute to plant water transport from roots to leaves and thereby influence how plants respond to soil water availability, but the sources of variation in fine root anatomical traits remain poorly understood. Here, we explore the variations of fine root vessel traits along topological orders within and across tropical tree species. Anatomical traits were measured along five root topological orders in 80 individual trees of 20 species from a tropical forest in southwestern China. We found large variations for most root anatomical traits across topological orders, and strong co-variations between vessel traits. Within species, theoretical specific xylem hydraulic conductivity (Kth) increased with topological order due to increased mean vessel diameter, size heterogeneity, and decreased vessel density. Across species, Kth was associated with vessel fraction in low-order roots and correlated with mean vessel diameter and vessel density in high-order roots, suggesting a shift in relative anatomical contributors to Kth from the second- to fifth-order roots. We found no clear relationship between Kth and stele: root diameter ratios. Our study shows strong variations in root vessel traits across topological orders and species, and highlights shifts in the anatomical underpinnings by varying vessel-related anatomical structures for an optimized water supply.


Subject(s)
Plant Roots , Trees , Xylem , Plant Roots/anatomy & histology , Plant Roots/physiology , Trees/physiology , Trees/anatomy & histology , Xylem/physiology , Xylem/anatomy & histology , Water/metabolism , Water/physiology , Tropical Climate , China
19.
Phys Rev Lett ; 133(14): 140602, 2024 Oct 04.
Article in English | MEDLINE | ID: mdl-39423418

ABSTRACT

The accurate determination of the electronic structure of strongly correlated materials using first principle methods is of paramount importance in condensed matter physics, computational chemistry, and material science. However, due to the exponential scaling of computational resources, incorporating such materials into classical computation frameworks becomes prohibitively expensive. In 2016, Bauer et al. proposed a hybrid quantum-classical approach to correlated materials [B. Bauer et al., Hybrid quantum-classical approach to correlated materials, Phys. Rev. X 6, 031045 (2016).PRXHAE2160-330810.1103/PhysRevX.6.031045] that can efficiently tackle the electronic structure of complex correlated materials. Here, we experimentally demonstrate that approach to tackle the computational challenges associated with strongly correlated materials. By seamlessly integrating quantum computation into classical computers, we address the most computationally demanding aspect of the calculation, namely the computation of the Green's function, using a spin quantum processor. Furthermore, we realize a self-consistent determination of the single impurity Anderson model through a feedback loop between quantum and classical computations. A quantum phase transition in the Hubbard model from the metallic phase to the Mott insulator is observed as the strength of electron correlation increases. As the number of qubits with high control fidelity continues to grow, our experimental findings pave the way for solving even more complex models, such as strongly correlated crystalline materials or intricate molecules.

20.
Transgenic Res ; 2024 Sep 17.
Article in English | MEDLINE | ID: mdl-39287761

ABSTRACT

The study by Zheng et al. (2024) identifies a NAC transcription factor, SOMBRERO (SMB), localized in the root cap of Arabidopsis, which is essential for root halotropism. SMB influences root halotropism by establishing asymmetric auxin distribution in the lateral root cap (LRC) and maintaining the expression of the auxin influx carrier gene AUX1. This mechanism leads to directional root bending away from high salinity areas. The findings reveal the SMB-AUX1-auxin module as a crucial mediator in root cap signaling and root halotropic response.

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