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1.
Blood ; 2024 Aug 16.
Article in English | MEDLINE | ID: mdl-39158067

ABSTRACT

Menin inhibitors that disrupt Menin-MLL interaction hold promise for treating specific acute myeloid leukemia subtypes, including KMT2A rearrangements (KMT2A-r), yet resistance remains a challenge. Here, through systematic chromatin-focused CRISPR screens, along with genetic, epigenetic, and pharmacologic studies in a variety of human and mouse KMT2A-r AML models, we uncover a potential resistance mechanism independent of canonical Menin-MLL targets. We show that a group of non-canonical Menin targets, which are bivalently co-occupied by active Menin and repressive H2AK119ub marks, are typically downregulated following Menin inhibition. The loss of Polycomb Repressive Complex 1.1 (PRC1.1) subunits, such as PCGF1 or BCOR, leads to Menin inhibitor resistance by epigenetic reactivation of these non-canonical targets, including MYC. Genetic and pharmacological inhibition of MYC can resensitize PRC1.1-deficent leukemia cells to Menin inhibition. Moreover, we demonstrate that leukemia cells with the loss of PRC1.1 subunits exhibit reduced monocytic gene signatures and are susceptible to the BCL2 inhibition, and combinational treatment of venetoclax overcomes the resistance to Menin inhibition in PRC1.1-deficient leukemia cells. These findings highlight the important roles of PRC1.1 and its regulated non-canonical Menin targets in modulating Menin inhibitor response and provide potential strategies to treat leukemias with compromised PRC1.1 function.

2.
Proc Natl Acad Sci U S A ; 120(1): e2214897120, 2023 01 03.
Article in English | MEDLINE | ID: mdl-36574702

ABSTRACT

During exocytosis, the fusion of secretory vesicle with plasma membrane forms a pore that regulates release of neurotransmitter and peptide. Heterogeneity of fusion pore behavior has been attributed to stochastic variation in a common exocytic mechanism, implying a lack of biological control. Using a fluorescent false neurotransmitter (FFN), we imaged dense core vesicle (DCV) exocytosis in primary mouse adrenal chromaffin cells by total internal reflection fluorescence microscopy at millisecond resolution and observed strikingly divergent modes of release, with fast events lasting <30 ms and slow events persisting for seconds. Dual imaging of slow events shows a delay in the entry of external dye relative to FFN release, suggesting exclusion by an extremely narrow pore <1 nm in diameter. Unbiased comprehensive analysis shows that the observed variation cannot be explained by stochasticity alone, but rather involves distinct mechanisms, revealing the bimodal nature of DCV exocytosis. Further, loss of calcium sensor synaptotagmin 7 increases the proportion of slow events without changing the intrinsic properties of either class, indicating the potential for independent regulation. The identification of two distinct mechanisms for release capable of independent regulation suggests a biological basis for the diversity of fusion pore behavior.


Subject(s)
Chromaffin Cells , Dense Core Vesicles , Mice , Animals , Synaptotagmins/metabolism , Exocytosis/physiology , Cell Membrane/metabolism , Chromaffin Cells/metabolism , Secretory Vesicles/metabolism , Membrane Fusion/physiology , Calcium/metabolism
3.
Brief Bioinform ; 24(6)2023 09 22.
Article in English | MEDLINE | ID: mdl-37833839

ABSTRACT

Microsatellite instability (MSI) is a hypermutator phenotype caused by DNA mismatch repair deficiency. MSI has been reported in various human cancers, particularly colorectal, gastric and endometrial cancers. MSI is a promising biomarker for cancer prognosis and immune checkpoint blockade immunotherapy. Several computational methods have been developed for MSI detection using DNA- or RNA-based approaches based on next-generation sequencing. Epigenetic mechanisms, such as DNA methylation, regulate gene expression and play critical roles in the development and progression of cancer. We here developed MSI-XGNN, a new computational framework for predicting MSI status using bulk RNA-sequencing and DNA methylation data. MSI-XGNN is an explainable deep learning model that combines a graph neural network (GNN) model to extract features from the gene-methylation probe network with a CatBoost model to classify MSI status. MSI-XGNN, which requires tumor-only samples, exhibited comparable performance with two well-known methods that require tumor-normal paired sequencing data, MSIsensor and MANTIS and better performance than several other tools. MSI-XGNN also showed good generalizability on independent validation datasets. MSI-XGNN identified six MSI markers consisting of four methylation probes (EPM2AIP1|MLH1:cg14598950, EPM2AIP1|MLH1:cg27331401, LNP1:cg05428436 and TSC22D2:cg15048832) and two genes (RPL22L1 and MSH4) constituting the optimal feature subset. All six markers were significantly associated with beneficial tumor microenvironment characteristics for immunotherapy, such as tumor mutation burden, neoantigens and immune checkpoint molecules such as programmed cell death-1 and cytotoxic T-lymphocyte antigen-4. Overall, our study provides a powerful and explainable deep learning model for predicting MSI status and identifying MSI markers that can potentially be used for clinical MSI evaluation.


Subject(s)
Colorectal Neoplasms , Microsatellite Instability , Humans , Colorectal Neoplasms/genetics , Microsatellite Repeats , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , DNA Methylation , Neural Networks, Computer , DNA/metabolism , RNA/metabolism , Tumor Microenvironment , DNA-Binding Proteins/metabolism , Transcription Factors/metabolism
4.
Nano Lett ; 24(35): 11043-11050, 2024 Sep 04.
Article in English | MEDLINE | ID: mdl-39162252

ABSTRACT

Coupled nanomechanical resonators have unveiled fascinating physical phenomena, including phonon-cavity coupling, coupled energy decay pathway, avoided crossing, and internal resonance. Despite these discoveries, the mechanisms and control techniques of nonlinear mode coupling phenomena with internal resonances require further exploration. Here, we report on the observation of stochastic switching between the two resonance states with coupled 1:1 internal resonance, for resonant two-dimensional (2D) molybdenum disulfide (MoS2) nanoelectromechanical systems (NEMS), which is directly driven to the critical coupling regime without parametric pumping. We further demonstrate that the probability of state switching is linearly tunable from ∼0% to ∼100% by varying the driving voltage. Furthermore, we gradually increase the white noise amplitude and show that the probability of obtaining the higher-energy state decreases, and the stochastic switching phenomenon eventually disappears. The results provide insights into the dynamics of coupled NEMS resonators and open up new possibilities for sensing and stochastic computing.

5.
Plant Physiol ; 193(4): 2788-2805, 2023 Nov 22.
Article in English | MEDLINE | ID: mdl-37725401

ABSTRACT

High temperature induces stomatal opening; however, uncontrolled stomatal opening is dangerous for plants in response to high temperature. We identified a high-temperature sensitive (hts) mutant from the ethyl methane sulfonate (EMS)-induced maize (Zea mays) mutant library that is linked to a single base change in MITOGEN-ACTIVATED PROTEIN KINASE 20 (ZmMPK20). Our data demonstrated that hts mutants exhibit substantially increased stomatal opening and water loss rate, as well as decreased thermotolerance, compared to wild-type plants under high temperature. ZmMPK20-knockout mutants showed similar phenotypes as hts mutants. Overexpression of ZmMPK20 decreased stomatal apertures, water loss rate, and enhanced plant thermotolerance. Additional experiments showed that ZmMPK20 interacts with MAP KINASE KINASE 9 (ZmMKK9) and E3 ubiquitin ligase RPM1 INTERACTING PROTEIN 2 (ZmRIN2), a maize homolog of Arabidopsis (Arabidopsis thaliana) RIN2. ZmMPK20 prevented ZmRIN2 degradation by inhibiting ZmRIN2 self-ubiquitination. ZmMKK9 phosphorylated ZmMPK20 and enhanced the inhibitory effect of ZmMPK20 on ZmRIN2 degradation. Moreover, we employed virus-induced gene silencing (VIGS) to silence ZmMKK9 and ZmRIN2 in maize and heterologously overexpressed ZmMKK9 or ZmRIN2 in Arabidopsis. Our findings demonstrated that ZmMKK9 and ZmRIN2 play negative regulatory roles in high-temperature-induced stomatal opening. Accordingly, we propose that the ZmMKK9-ZmMPK20-ZmRIN2 cascade negatively regulates high-temperature-induced stomatal opening and balances water loss and leaf temperature, thus enhancing plant thermotolerance.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Zea mays/genetics , Zea mays/metabolism , Mitogen-Activated Protein Kinases/genetics , Mitogen-Activated Protein Kinases/metabolism , Temperature , Plant Stomata/physiology , Water/metabolism
6.
Biomacromolecules ; 25(4): 2222-2242, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38437161

ABSTRACT

Recent strides in molecular pathology have unveiled distinctive alterations at the molecular level throughout the onset and progression of diseases. Enhancing the in vivo visualization of these biomarkers is crucial for advancing disease classification, staging, and treatment strategies. Peptide-based molecular probes (PMPs) have emerged as versatile tools due to their exceptional ability to discern these molecular changes with unparalleled specificity and precision. In this Perspective, we first summarize the methodologies for crafting innovative functional peptides, emphasizing recent advancements in both peptide library technologies and computer-assisted peptide design approaches. Furthermore, we offer an overview of the latest advances in PMPs within the realm of biological imaging, showcasing their varied applications in diagnostic and therapeutic modalities. We also briefly address current challenges and potential future directions in this dynamic field.


Subject(s)
Molecular Probes , Peptides , Peptides/chemistry , Diagnostic Imaging/methods , Biomarkers
7.
Biomacromolecules ; 25(5): 2953-2964, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38652682

ABSTRACT

Endoscopic submucosal dissection (ESD) is an effective method for resecting early-stage tumors in the digestive system. To achieve a low injection pressure of the injected fluid and continuous elevation of the mucosa following injection during the ESD technique, we introduced an innovative injectable sodium-alginate-based drug-loaded microsphere (Cipro-ThSA) for ESD surgery, which was generated through an emulsion reaction involving cysteine-modified sodium alginate (ThSA) and ciprofloxacin. Cipro-ThSA microspheres exhibited notable adhesiveness, antioxidant activity, and antimicrobial properties, providing a certain level of postoperative wound protection. In vitro cell assays confirmed the decent biocompatibility of the material. Lastly, according to animal experiments involving submucosal elevation of porcine colons, Cipro-ThSA microspheres ensure surgically removable lift height while maintaining the mucosa for approximately 246% longer than saline, which could effectively reduce surgical risks while providing sufficient time for operation. Consequently, the Cipro-ThSA microsphere holds great promise as a novel submucosal injection material, in terms of enhancing the operational safety and effectiveness of ESD surgery.


Subject(s)
Alginates , Endoscopic Mucosal Resection , Microspheres , Alginates/chemistry , Animals , Swine , Endoscopic Mucosal Resection/methods , Humans , Ciprofloxacin/administration & dosage , Ciprofloxacin/chemistry , Ciprofloxacin/pharmacology , Cysteine/chemistry
8.
J Sep Sci ; 47(14): e2400065, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39054584

ABSTRACT

A novel zwitterionic polymer grafted silica stationary phase, Sil-PZIC, was prepared by bonding poly(ethylene maleic anhydride) molecules on the surface of silica via multiple binding sites, followed by ammonolysis of maleic anhydride through a nucleophilic substitution reaction with ethylenediamine. The stationary phase was characterized by solid-state 13C nuclear magnetic resonance, zeta potential, and elemental analysis and the results show the successful encapsulation of zwitterionic polymer on the surface of silica. The chromatographic performance of Sil-PZIC was investigated by using nucleosides and nucleic bases as test analytes The variation of retention and separation performance of these model compounds were investigated by varying the chromatographic conditions such as the components of mobile phase, salt concentration, and pH. The results show that the retention of the Sil-PZIC phase was dominated by a hydrophilic partitioning mechanism accompanied by secondary interactions such as electrostatic and hydrogen bonding. In addition, saccharides and Amadori compounds were also well separated on the Sil-PZIC, indicating that the Sil-PZIC column has potential application for separation of the polar compound.

9.
BMC Urol ; 24(1): 101, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38689249

ABSTRACT

BACKGROUND: To introduce the surgical technique and our team's extensive experience with tunnel method in laparoscopic adrenalectomy. METHODS: From July 2019 to June 2022, we independently designed and conducted 83 cases of " Tunnel Method Laparoscopic Adrenalectomy," a prospective study. There were 45 male and 38 female patients, ages ranged from 25 to 73 years(mean: 44.6 years).The cases included 59 adrenal cortical adenomas, 9 pheochromocytomas, 6 cysts, 4 myelolipomas, 1 ganglioneuroma, and 4 cases of adrenal cortical hyperplasia. In terms of anatomical location, there were 39 cases on the left side, 42 on the right side, and 2 bilateral cases. Tumor diameters ranged from 0.6 to 5.9 cm(mean: 2.9 cm). Utilizing ultrasound monitoring, percutaneous puncture was made either directly to the target organ or its vicinity, and the puncture path was manually marked. Then, under the direct view of a single-port single-channel laparoscope, the path to the target organ in the retroperitoneum or its vicinity was further delineated and separated. This approach allowed for the insertion of the laparoscope and surgical instruments through the affected adrenal gland, thereby separating the surface of the target organ to create sufficient operational space for the adrenalectomy. RESULTS: All 83 surgeries were successfully completed. A breakdown of the surgical approach reveals that 51 surgeries were done using one puncture hole, 25 with two puncture holes, and 7 with three puncture holes. The operation time ranged from 31 to 105 min (mean: 47 min), with a blood loss of 10 to 220mL (mean: 40 mL). Notably, there were no conversions to open surgery and no intraoperative complications. Postoperative follow-up ranged from 6 to 28 months, during which after re-examination using ultrasound, CT, and other imaging methods, there were no recurrences or other complications detected. CONCLUSIONS: The completion of the tunnel method laparoscopic adrenalectomy represents a breakthrough, transitioning from the traditional step-by-step separation of retroperitoneal tissues to reach the target organ in conventional retroperitoneoscopic surgery. This method directly accesses the target organ, substantially reducing the damage and complications associated with tissue separation in retroperitoneoscopic surgery, As a result, it provides a new option for minimally invasive surgery of retroperitoneal organs and introduces innovative concepts to retroperitoneoscopic surgery.


Subject(s)
Adrenalectomy , Laparoscopy , Humans , Adrenalectomy/methods , Female , Male , Middle Aged , Prospective Studies , Laparoscopy/methods , Adult , Aged , Retroperitoneal Space/surgery , Adrenal Gland Neoplasms/surgery , Adrenal Gland Neoplasms/diagnostic imaging
10.
BMC Ophthalmol ; 24(1): 70, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38360631

ABSTRACT

BACKGROUND: Studies on the factors affecting vault after posterior chamber phakic Implantable Collamer Lens (ICL) have been carried out, but most of them are single-centered and subjective selections of parameters. The present study aimed to systematically analyze the factors for vault. METHODS: A systematic review of case series, case-control, and cohort studies derived from the articles published in PubMed, the Cochrane Library, Embase, Web of Science, CNKI, CBM, Wanfang and VIP, as well as ClinicalTrials, which were conducted to search for studies on factors of vault using four core terms: phakic intraocular lenses, vault, risk factor and observational study, from January 01, 1997, to February 20, 2023. The included studies were meta-analyzed quantitatively and described qualitatively. Subsequently, meta-regression and subgroup analysis were used. RESULTS: We identified 13 studies (1,607 subjects), and 14 factors were considered. Meta-analysis showed that anterior chamber depth (ACD), horizontal corneal white-to-white (hWTW), ICL-size, and age are dual effects of the abnormal vaults; anterior chamber volume (ACV) and lens thickness (LT) are a one-way effect; while axial length (AL), ICL- spherical equivalent (ICL-SE) and Km are insignificant. In addition, descriptive analysis of anterior chamber angle (ACA), horizontal sulcus to sulcus (hSTS), ciliary processes height (T value), crystalline lens rise (CLR), and gender showed that all factors except gender tend to have significant effects on vault. Sensitivity analysis showed stable combined results. Country and design respectively affect the heterogeneity in ACD and ICL-size at low vault, while design affects the heterogeneity in ACD at high vault. No publication bias exists. CONCLUSIONS: Vault after ICL is related to multiple factors, especially anterior segmental biologic parameters, and they are weighted differently. We hope to provide a reference for the selection and adjustment of ICL.


Subject(s)
Anterior Chamber , Myopia , Phakic Intraocular Lenses , Humans , Myopia/surgery , Myopia/physiopathology , Lens Implantation, Intraocular/methods , Risk Factors , Visual Acuity/physiology , Axial Length, Eye/pathology
11.
Adv Exp Med Biol ; 1459: 379-403, 2024.
Article in English | MEDLINE | ID: mdl-39017853

ABSTRACT

Myocyte enhancer factor 2 (MEF2) is a key transcription factor (TF) in skeletal, cardiac, and neural tissue development and includes four isoforms: MEF2A, MEF2B, MEF2C, and MEF2D. These isoforms significantly affect embryonic development, nervous system regulation, muscle cell differentiation, B- and T-cell development, thymocyte selection, and effects on tumorigenesis and leukemia. This chapter describes the multifaceted roles of MEF2 family proteins, covering embryonic development, nervous system regulation, and muscle cell differentiation. It further elucidates the contribution of MEF2 to various blood and immune cell functions. Specifically, in B-cell precursor acute lymphoblastic leukemia (BCP-ALL), MEF2D is aberrantly expressed and forms a fusion protein with BCL9, CSF1R, DAZAP1, HNRNPUL1, and SS18. These fusion proteins are closely related to the pathogenesis of leukemia. In addition, it specifically introduces the regulatory effect of MEF2D fusion protein on the proliferation and growth of B-cell acute lymphoblastic leukemia (B-ALL) cells. Finally, we detail the positive feedback loop between MEF2D and IRF8 that significantly promotes the progression of acute myeloid leukemia (AML) and the importance of the ZMYND8-BRD4 interaction in regulating the IRF8 and MYC transcriptional programs. The MEF2D-CEBPE axis is highlighted as a key transcriptional mechanism controlling the block of leukemic cell self-renewal and differentiation in AML. This chapter starts with the structure and function of MEF2 family proteins, specifically summarizing and analyzing the role of MEF2D in B-ALL and AML, mediating the complex molecular mechanisms of transcriptional regulation and exploring their implications for human health and disease.


Subject(s)
MEF2 Transcription Factors , MEF2 Transcription Factors/metabolism , MEF2 Transcription Factors/genetics , Humans , Animals , Interferon Regulatory Factors/genetics , Interferon Regulatory Factors/metabolism , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/metabolism , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology , Cell Differentiation/genetics , Gene Expression Regulation, Leukemic , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/metabolism , Cell Proliferation/genetics
12.
Pestic Biochem Physiol ; 201: 105862, 2024 May.
Article in English | MEDLINE | ID: mdl-38685239

ABSTRACT

Phomopsis longicolla, a causal agent of soybean root rot, stem blight, seed decay, pod and stem canker, which seriously affects the yield and quality of soybean production worldwide. The phenylpyrrole fungicide fludioxonil exhibits a broad spectrum and high activity against phytopathogenic fungi. In this study, the baseline sensitivity of 100 P. longicolla isolates collected from the main soybean production areas of China to fludioxonil were determined. The result showed that the EC50 values of all the P. longicolla isolates ranged from 0.013 to 0.035 µg/ml. Furthermore, 12 fludioxonil-resistance (FluR) mutants of P. longicolla were generated from 6 fludioxonil-sensitive (FluS) isolates. and the resistance factors (RF) of 12 FluR mutants were >3500. Sequence alignment showed that multiple mutation types were found in PlOS1, PlOS4 or/and PlOS5 of FluR mutants. All the FluR mutants exhibited fitness penalty in mycelial growth, conidiation, virulence and osmo-adaptation. Under fludioxonil or NaCl treatment condition, the glycerol accumulation was significantly increased in FluS isolates, but was slightly increased in FluR mutants, and the phosphorylation level of most FluR mutants was significantly decreased when compared to the FluS isolates. Additionally, positive cross-resistance was observed between fludioxonil and procymidone but not fludioxonil and pydiflumetofen, pyraclostrobin or fluazinam. This is first reported that the baseline sensitivity of P. longicolla to fludioxonil, as well as the biological and molecular characterizations of P. longicolla FluR mutants to fludioxonil. These results can provide scientific directions for controlling soybean diseases caused by P. longicolla using fludioxonil.


Subject(s)
Ascomycota , Dioxoles , Drug Resistance, Fungal , Fungicides, Industrial , Pyrroles , Pyrroles/pharmacology , Fungicides, Industrial/pharmacology , Drug Resistance, Fungal/genetics , Dioxoles/pharmacology , Ascomycota/drug effects , Ascomycota/genetics , Ascomycota/metabolism , Mutation , Fungal Proteins/genetics , Fungal Proteins/metabolism , Plant Diseases/microbiology , Glycine max/microbiology , Glycine max/drug effects
13.
Nano Lett ; 23(20): 9375-9382, 2023 Oct 25.
Article in English | MEDLINE | ID: mdl-37788247

ABSTRACT

In resonant nanoelectromechanical systems (NEMS), the quality (Q) factor is essential for sensing, communication, and computing applications. While a large vibrational amplitude is useful for increasing the signal-to-noise ratio, the damping in this regime is more complex because both linear and nonlinear damping are important, and an accurate model for Q has not been fully explored. Here, we demonstrate that by combining the time-domain ringdown and frequency-domain resonance measurements, we extract the accurate Q for two-dimensional (2D) MoS2 and MoTe2 NEMS resonators at different vibration amplitudes. In particular, in the transition region between linear and nonlinear damping, Q can be precisely extracted by fitting to the ringdown characteristics. By varying AC driving, we tune the Q by ΔQ/Q = 269% and extract the nonlinear damping coefficient. We develop the dissipation model that well captures the linear to nonlinear damping, providing important insights for accurately modeling and optimizing Q in 2D NEMS resonators.

14.
J Xray Sci Technol ; 32(3): 493-512, 2024.
Article in English | MEDLINE | ID: mdl-38189738

ABSTRACT

In the medical field, computed tomography (CT) is a commonly used examination method, but the radiation generated increases the risk of illness in patients. Therefore, low-dose scanning schemes have attracted attention, in which noise reduction is essential. We propose a purposeful and interpretable decomposition iterative network (DISN) for low-dose CT denoising. This method aims to make the network design interpretable and improve the fidelity of details, rather than blindly designing or using deep CNN architecture. The experiment is trained and tested on multiple data sets. The results show that the DISN method can restore the low-dose CT image structure and improve the diagnostic performance when the image details are limited. Compared with other algorithms, DISN has better quantitative and visual performance, and has potential clinical application prospects.


Subject(s)
Algorithms , Image Processing, Computer-Assisted , Radiation Dosage , Tomography, X-Ray Computed , Tomography, X-Ray Computed/methods , Humans , Image Processing, Computer-Assisted/methods , Signal-To-Noise Ratio , Phantoms, Imaging
15.
J Xray Sci Technol ; 32(4): 1061-1077, 2024.
Article in English | MEDLINE | ID: mdl-38669513

ABSTRACT

BACKGROUND: Recently, X-rays have been widely used to detect complex structural workpieces. Due to the uneven thickness of the workpiece and the high dynamic range of the X-ray image itself, the detailed internal structure of the workpiece cannot be clearly displayed. OBJECTIVE: To solve this problem, we propose an image enhancement algorithm based on a multi-scale local edge-preserving filter. METHODS: Firstly, the global brightness of the image is enhanced through logarithmic transformation. Then, to enhance the local contrast, we propose utilizing the gradient decay function based on fuzzy entropy to process the gradient and then incorporate the gradient into the energy function of the local edge-preserving filter (LEP) as a constraint term. Finally, multiple base layers and detail layers are obtained through filtering multi-scale decomposition. All detail layers are enhanced and fused using S-curve mapping to improve contrast further. RESULTS: This method is competitive in both quantitative indices and visual perception quality. CONCLUSIONS: The experimental results demonstrate that the proposed method significantly enhances various complex workpieces and is highly efficient.


Subject(s)
Algorithms , Entropy , Fuzzy Logic , Image Processing, Computer-Assisted/methods , Radiographic Image Enhancement/methods , Humans
16.
Plant Mol Biol ; 111(3): 291-307, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36469200

ABSTRACT

KEY MESSAGE: We identified a dosage-dependent dominant negative form of Sar1c, which confirms the essential role of COPII system in mediating ER export of storage proteins in rice endosperm. Higher plants accumlate large amounts of seed storage proteins (SSPs). However, mechanisms underlying SSP trafficking are largely unknown, especially the ER-Golgi anterograde process. Here, we showed that a rice glutelin precursor accumulation13 (gpa13) mutant exhibited floury endosperm and overaccumulated glutelin precursors, which phenocopied the reported RNAi-Sar1abc line. Molecular cloning revealed that the gpa13 allele encodes a mutated Sar1c (mSar1c) with a deletion of two conserved amino acids Pro134 and Try135. Knockdown or knockout of Sar1c alone caused no obvious phenotype, while overexpression of mSar1c resulted in seedling lethality similar to the gpa13 mutant. Transient expression experiment in tobacco combined with subcellular fractionation experiment in gpa13 demonstrated that the expression of mSar1c affects the subcellular distribution of all Sar1 isoforms and Sec23c. In addition, mSar1c failed to interact with COPII component Sec23. Conversely, mSar1c competed with Sar1a/b/d to interact with guanine nucleotide exchange factor Sec12. Together, we identified a dosage-dependent dominant negative form of Sar1c, which confirms the essential role of COPII system in mediating ER export of storage proteins in rice endosperm.


Subject(s)
Oryza , Seed Storage Proteins , Seed Storage Proteins/metabolism , Oryza/genetics , Protein Transport/genetics , Glutens/genetics , Endoplasmic Reticulum/metabolism
17.
Bioinformatics ; 38(16): 4027-4029, 2022 08 10.
Article in English | MEDLINE | ID: mdl-35771644

ABSTRACT

SUMMARY: Characterizing biomarkers based on microbiome profiles has great potential for translational medicine and precision medicine. Here, we present microbiomeMarker, an R/Bioconductor package implementing commonly used normalization and differential analysis (DA) methods, and three supervised learning models to identify microbiome markers. microbiomeMarker also allows comparison of different methods of DA and confounder analysis. It uses standardized input and output formats, which renders it highly scalable and extensible, and allows it to seamlessly interface with other microbiome packages and tools. In addition, the package provides a set of functions to visualize and interpret the identified microbiome markers. AVAILABILITY AND IMPLEMENTATION: microbiomeMarker is freely available from Bioconductor (https://www.bioconductor.org/packages/microbiomeMarker). Source code is available and maintained at GitHub (https://github.com/yiluheihei/microbiomeMarker). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Microbiota , Software , Biomarkers
18.
Plant Cell ; 32(3): 758-777, 2020 03.
Article in English | MEDLINE | ID: mdl-31949008

ABSTRACT

Dense vesicles (DVs) are vesicular carriers, unique to plants, that mediate post-Golgi trafficking of storage proteins to protein storage vacuoles (PSVs) in seeds. However, the molecular mechanisms regulating the directional targeting of DVs to PSVs remain elusive. Here, we show that the rice (Oryza sativa) glutelin precursor accumulation5 (gpa5) mutant is defective in directional targeting of DVs to PSVs, resulting in discharge of its cargo proteins into the extracellular space. Molecular cloning revealed that GPA5 encodes a plant-unique phox-homology domain-containing protein homologous to Arabidopsis (Arabidopsis thaliana) ENDOSOMAL RAB EFFECTOR WITH PX-DOMAIN. We show that GPA5 is a membrane-associated protein capable of forming homodimers and that it is specifically localized to DVs in developing endosperm. Colocalization, biochemical, and genetic evidence demonstrates that GPA5 acts in concert with Rab5a and VPS9a to regulate DV-mediated post-Golgi trafficking to PSVs. Furthermore, we demonstrated that GPA5 physically interacts with a class C core vacuole/endosome tethering complex and a seed plant-specific VAMP727-containing R-soluble N-ethylmaleimide sensitive factor attachment protein receptor complex. Collectively, our results suggest that GPA5 functions as a plant-specific effector of Rab5a required for mediating tethering and membrane fusion of DVs with PSVs in rice endosperm.


Subject(s)
Golgi Apparatus/metabolism , Oryza/metabolism , Plant Proteins/metabolism , Seed Storage Proteins/metabolism , Endosperm/metabolism , Glutens/metabolism , Golgi Apparatus/ultrastructure , Membrane Proteins/metabolism , Models, Biological , Mutation/genetics , Phosphatidylinositol Phosphates/metabolism , Plant Proteins/chemistry , Protein Binding , Protein Multimerization , Protein Transport , Seed Storage Proteins/chemistry , Vacuoles/metabolism , Vacuoles/ultrastructure
19.
Cell Commun Signal ; 21(1): 17, 2023 01 23.
Article in English | MEDLINE | ID: mdl-36691021

ABSTRACT

BACKGROUND: The inflammatory response induced by intestinal ischaemia‒reperfusion injury (I/R) is closely associated with infectious complications and mortality in critically ill patients, and the timely and effective clearance of apoptotic cells is an important part of reducing the inflammatory response. Studies have shown that the efferocytosis by phagocytes plays an important role. Recently, studies using small intestine organoid models showed that macrophage efferocytosis could promote the repair capacity of the intestinal epithelium. However, no studies have reported efferocytosis in the repair of I/R in animal models. RESULTS: We used an in vivo efferocytosis assay and discovered that macrophage efferocytosis played an indispensable role in repairing and maintaining intestinal barrier function after I/R. In addition, the specific molecular mechanism that induced macrophage efferocytosis was Cth-ERK1/2 dependent. We found that Cth drove macrophage efferocytosis in vivo and in vitro. Overexpression/silencing Cth promoted/inhibited the ERK1/2 pathway, respectively, which in turn affected efferocytosis and mediated intestinal barrier recovery. In addition, we found that the levels of Cth and macrophage efferocytosis were positively correlated with the recovery of intestinal function in clinical patients. CONCLUSION: Cth can activate the ERK1/2 signalling pathway, induce macrophage efferocytosis, and thus promote intestinal barrier repair. Video Abstract.


Subject(s)
Cystathionine gamma-Lyase , Intestines , MAP Kinase Signaling System , Macrophages , Animals , Cystathionine gamma-Lyase/metabolism , Macrophages/metabolism , Phagocytosis , Signal Transduction , Humans , Mice , Intestines/injuries , Intestines/physiology
20.
Mol Pharm ; 20(5): 2634-2641, 2023 05 01.
Article in English | MEDLINE | ID: mdl-37043243

ABSTRACT

During the pathogenesis of heart failure with preserved ejection fraction (HFpEF), fibroblasts are activated and express the fibroblast activation protein (FAP). Targeted imaging of FAP can qualitatively and quantitatively assess the fibroblast activity. This study aimed to use [18F]AlF-NOTA-FAPI-04 (AlF = aluminum fluoride; NOTA = 1,4,7-triazacyclononane-1,4,7-triacetic acid; FAPI = FAP inhibitor) positron emission tomography/computed tomography (PET/CT) imaging to detect activated fibroblasts in a rat HFpEF model. The rat HfpEF model was established by feeding a high-fat diet plus l-NAME (Nω-nitro-l-arginine methyl ester) for 10 weeks. Blood pressure, echocardiography, and [18F]AlF-NOTA-FAPI-04 PET/CT were used to assess the progression of HfpEF. The biodistribution of [18F]AlF-NOTA-FAPI-04 in healthy rats was obtained. Cardiac tissue sections were also analyzed using Masson's, hematoxylin and eosin (H&E), and FAP immunohistochemistry (IHC) staining. The echocardiography and blood pressure data indicated that the rat HfpEF model was successfully established. [18F]AlF-NOTA-FAPI-04 PET/CT imaging showed obvious radiotracer accumulation in the left ventricular wall of the HfpEF rats from the seventh week. A biodistribution test showed that the tracer was cleared mainly via renal and intestinal excretion. Percentage of injected dose per gram tissue (% ID) of the heart and its surrounding organs was lower in normal rats, which was conducive to image analysis. Masson's and H&E stainings showed large areas of vascular and interstitial fibrosis in the HfpEF rat hearts. IHC staining also confirmed the presence of FAP-positive cardiac fibroblasts of the HfpEF rat hearts, with a good correlation with FAPI PET. Thus, [18F]AlF-NOTA-FAPI-04 PET/CT is a promising and non-invasive method to assess the progression of fibrosis in HfpEF to facilitate the clinical management.


Subject(s)
Heart Failure , Positron Emission Tomography Computed Tomography , Rats , Animals , Positron Emission Tomography Computed Tomography/methods , Heart Failure/diagnostic imaging , Tissue Distribution , Stroke Volume , Fibroblasts , Gallium Radioisotopes , Positron-Emission Tomography/methods
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