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1.
Article in English | MEDLINE | ID: mdl-38752799

ABSTRACT

An ideal vehicle with a high transfection efficiency is crucial for gene delivery. In this study, a type of cationic carbon dot (CCD) known as APCDs were first prepared with arginine (Arg) and pentaethylenehexamine (PEHA) as precursors and conjugated with oleic acid (OA) for gene delivery. By tuning the mass ratio of APCDs to OA, APCDs-OA conjugates, namely, APCDs-0.5OA, APCDs-1.0OA, and APCDs-1.5OA were synthesized. All three amphiphilic APCDs-OA conjugates show high affinity to DNA through electrostatic interactions. APCDs-0.5OA exhibit strong binding with small interfering RNA (siRNA). After being internalized by Human Embryonic Kidney (HEK 293) and osteosarcoma (U2OS) cells, they could distribute in both the cytoplasm and the nucleus. With APCDs-OA conjugates as gene delivery vehicles, plasmid DNA (pDNA) that encodes the gene for the green fluorescence protein (GFP) can be successfully delivered in both HEK 293 and U2OS cells. The GFP expression levels mediated by APCDs-0.5OA and APCDs-1.0OA are ten times greater than that of PEI in HEK 293 cells. Furthermore, APCDs-0.5OA show prominent siRNA transfection efficiency, which is proven by the significantly downregulated expression of FANCA and FANCD2 proteins upon delivery of FANCA siRNA and FANCD2 siRNA into U2OS cells. In conclusion, our work demonstrates that conjugation of CCDs with a lipid structure such as OA significantly improves the gene transfection efficiency, providing a new idea about the designation of nonviral carriers in gene delivery systems.

2.
Bioact Mater ; 37: 378-392, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38689658

ABSTRACT

Posttraumatic osteoarthritis (PTOA) patients are often diagnosed by X-ray imaging at a middle-late stage when drug interventions are less effective. Early PTOA is characterized by overexpressed matrix metalloprotease 13 (MMP13). Herein, we constructed an integrated diagnosis and treatment micelle modified with MMP13 enzyme-detachable, cyanine 5 (Cy5)-containing PEG, black hole quencher-3 (BHQ3), and cRGD ligands and loaded with siRNA silencing MMP13 (siM13), namely ERMs@siM13. ERMs@siM13 could be cleaved by MMP13 in the diseased cartilage tissues to detach the PEG shell, causing cRGD exposure. Accordingly, the ligand exposure promoted micelle uptake by the diseased chondrocytes by binding to cell surface αvß3 integrin, increasing intracellular siM13 delivery for on-demand MMP13 downregulation. Meanwhile, the Cy5 fluorescence was restored by detaching from the BHQ3-containing micelle, precisely reflecting the diseased cartilage state. In particular, the intensity of Cy5 fluorescence generated by ERMs@siM13 that hinged on the MMP13 levels could reflect the PTOA severity, enabling the physicians to adjust the therapeutic regimen. Finally, in the murine PTOA model, ERMs@siM13 could diagnose the early-stage PTOA, perform timely interventions, and monitor the OA progression level during treatment through a real-time detection of MMP13. Therefore, ERMs@siM13 represents an appealing approach for early-stage PTOA theranostics.

3.
Int J Ophthalmol ; 17(4): 676-685, 2024.
Article in English | MEDLINE | ID: mdl-38638258

ABSTRACT

AIM: To identify different metabolites, proteins and related pathways to elucidate the causes of proliferative diabetic retinopathy (PDR) and resistance to anti-vascular endothelial growth factor (VEGF) drugs, and to provide biomarkers for the diagnosis and treatment of PDR. METHODS: Vitreous specimens from patients with diabetic retinopathy were collected and analyzed by Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analyses based on 4D label-free technology. Statistically differentially expressed proteins (DEPs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway representation and protein interactions were analyzed. RESULTS: A total of 12 samples were analyzed. The proteomics results showed that a total of 58 proteins were identified as DEPs, of which 47 proteins were up-regulated and 11 proteins were down-regulated. We found that C1q and tumor necrosis factor related protein 5 (C1QTNF5), Clusterin (CLU), tissue inhibitor of metal protease 1 (TIMP1) and signal regulatory protein alpha (SIRPα) can all be specifically regulated after aflibercept treatment. GO functional analysis showed that some DEPs are related to changes in inflammatory regulatory pathways caused by PDR. In addition, protein-protein interaction (PPI) network evaluation revealed that TIMP1 plays a central role in neural regulation. In addition, CD47/SIRPα may become a key target to resolve anti-VEGF drug resistance in PDR. CONCLUSION: Proteomic analysis is an approach of choice to explore the molecular mechanisms of PDR. Our data show that multiple proteins are differentially changed in PDR patients after intravitreal injection of aflibercept, among which C1QTNF5, CLU, TIMP1 and SIRPα may become targets for future treatment of PDR and resolution of anti-VEGF resistance.

4.
J Clin Ultrasound ; 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38655706

ABSTRACT

PURPOSE: To analyze the influence of RV dysfunction evaluated by Free-angle M-mode (FAM) TAPSE Z-score on retrograde ductus arteriosus flow (RDAF) in fetuses with Ebstein anomaly (EA). METHODS: A retrospective cohort study of 30 EA and 60 normal fetuses were enrolled. The EA group was divided into two groups: with RDAF (EA-RDAF group) and without RDAF (EA-NRDAF group). FAM was used to measure TAPSE of EA and normal fetuses, and Z-scores were calculated. The differences of FAM-TAPSE Z-score, gestational week (GW), maternal age (MA), and mitral valve-tricuspid valve distance (MTD) between three groups were compared. The correlation and binary logistic regression between FAM-TAPSE Z-score, GW, MA, MTD, and RDAF were analyzed. RESULTS: FAM-TAPSE Z-score was significantly lower in EA-RDAF group compared to other groups (p < 0.05). FAM-TAPSE Z-score, GW, and MA were negatively correlated with RDAF (p < 0.05), but no correlation was found between TR, MDT, and RDAF (p > 0.05). Multivariate logistic regression showed that FAM-TAPSE Z-score was an independent influencing factor for RDAF (OR = 0.102, p < 0.05). CONCLUSION: RV dysfunction is an independent factor leading to RDAF in EA fetus, which provides a feasible theoretical basis for further study on improvement of RV function through intrauterine treatment to delay and prevent the RDAF, to avoid death cycle and improve live-birth rate.

6.
Ultrasonics ; 140: 107305, 2024 May.
Article in English | MEDLINE | ID: mdl-38554667

ABSTRACT

During aircraft operations, the impact events experienced by the aircraft may cause damage to the structure, thus posing a safety hazard. Therefore, an accurate determination of where the impact occurred and the time history of the impact force can provide an important basis for assessing the condition of the aircraft. However, modern aircraft structures are often large and complex, and relying on dense arrays of sensors for monitoring adds additional weight to the aircraft and reduces the economics of aircraft operation. This paper proposes a region-to-point monitoring strategy. First, a Convolutional Neural Network (CNN) model with region localization capability is trained using the sparse sensor array acquisition data. Then, the weighted center algorithm is used to determine the specific location where the impact occurs, in which the added fuzzy genetic algorithm can provide the ability to adjust weights to improve localization accuracy adaptively. As for the impact force prediction, this paper adopts a model based on a Convolutional Neural Network-Gated Recurrent Unit combined with a Squeeze-Excitation attention mechanism (CNN-GRU-SE), which is capable of predicting the impact force occurring in the flat plate and reinforced structure region of the aircraft under different energy conditions. Finally, the impact of incorporating a transfer learning approach on model performance and training cost is investigated for fuselage regions with different structures.

7.
J Clin Ultrasound ; 2024 Mar 14.
Article in English | MEDLINE | ID: mdl-38485265

ABSTRACT

PURPOSE: This study was designed to investigate the application value of the atrial septum excursion index (ASEI) in fetuses with isolated restrictive foramen ovale (RFO) or redundant foramen ovale flap (RFOF) and the outcomes of these fetuses. METHODS: This was a retrospective study. Healthy pregnant women who were examined by antenatal fetal echocardiography from January 1, 2019 to December 31, 2021, at Sir Run Run Shaw Hospital were enrolled. One hundred seventy-seven (177) fetuses were categorized into three groups by diagnosis: (1) RFOF (n = 33), (2) RFO (n = 21), and (3) normal (n = 123). Fetal echocardiographic features and postnatal outcomes were collected. RESULTS: The median ASEIs were 0.50 (range, 0.41-0.65) in the control group, 0.76 (range, 0.67-0.88) in the RFOF group and 0.31 (range, 0.14-0.35) in the RFO group, and the differences were significant (p < 0.001). The ratios of right atrium/left atrium, right ventricle/left ventricle, and pulmonary artery diameter to aorta diameter (PA/AO) and the pulmonary annulus Z-scores were greater in fetuses with RFOF and RFO than in the controls (p < 0.05). Twenty-seven of 33 fetuses (87.9%) with RFOF and 19 of 21 fetuses (90.5%) with RFO had good outcomes after birth. CONCLUSION: The ASEI may be a new tool for quantitatively assessing the mobility of foramen ovale flaps in fetuses with isolated RFOF or RFO.

8.
Article in English | MEDLINE | ID: mdl-38504565

ABSTRACT

BACKGROUND: The dysregulation of the innate immune system plays a crucial role in the development of Diabetic Retinopathy (DR). To gain an insight into the underlying mechanism of DR, it is essential to identify specific biomarkers associated with immune cell infiltration. METHODS: In this study, we retrieved the GSE94019 and GSE60436 datasets from the Gene Expression Omnibus (GEO) database. By utilizing CIBERSORT, MCPcounter, and xCell algorithms, we conducted a comprehensive analysis of the immune cell infiltration landscape in DR. The limma package was employed to identify Differentially Expressed Necroptosis-related Genes (DENRGs). Subsequently, enrichment analysis was performed to investigate the potential functions of the DENRGs. To identify the core DENRGs, the CytoHubba plug-in in Cytoscape software was utilized. The expression levels of these core DENRGs were verified in an independent dataset. RESULTS: Our analysis identified 213 DENRGs, and among them, Platelet-derived Growth Factor subunit A (PDGFA) was identified as a core DENRG. Notably, the expression of PDGFA was found to be upregulated in DR, and this finding was further validated in the GSE102485 dataset. Additionally, the results of GSVA and GSEA revealed that in the high PDGFA group, there was activation of pathways related to inflammation and the immune system. Moreover, analysis of immune infiltration demonstrated a significant association between PDGFA gene expression and the infiltration levels of specific immune cells, including basophils, macrophages M1, macrophages, neutrophils, monocytes, NK cells, and B cells. CONCLUSION: The involvement of neutrophils in the development and progression of DR is suggested. PDGFA has emerged as a potential marker and is linked to the infiltration of immune cells in DR. These findings shed new light on the underlying mechanisms of DR.

9.
J Hazard Mater ; : 133749, 2024 Feb 08.
Article in English | MEDLINE | ID: mdl-38383276

ABSTRACT

The superoxide radical (•O2-)-mediated peroxymonosulfate (PMS)-based photo-Fenton-like reaction enables highly selective water decontamination. Nevertheless, the targeted construction of •O2--mediated photo-Fenton-like system has been challenging. Herein, we developed an electron-rich/-poor dual sites driven •O2--mediated cascade photo-Fenton-like system by modulating electron density. Experimental and theoretical results demonstrated that PMS was preferentially adsorbed on electron-poor Co site. This adsorption promoted O-O bond cleavage of PMS to generate hydrogen peroxide (H2O2), which then migrated to electron-rich O site to extract eg electrons for O-H bond cleavage, rather than competing with PMS for Co site. The developed versatile cascade reaction system could selectively eliminate contaminants with low n-octanol/water partition constants (KOW) and dissociation constants (pKa) and remarkably resist inorganics (Cl-, H2PO4- and NO3-), humic acid (HA) and even real water matrices (tap water and secondary effluent). This finding provided a novel and plausible strategy to accurately and efficiently generate •O2- for the selective water decontamination.

10.
Pediatr Cardiol ; 45(4): 740-748, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38393337

ABSTRACT

Morphology and function in a fetal heart with severe tricuspid regurgitation remains challenging. The aim of this study was to assess cardiac morphology and function in fetuses with severe tricuspid regurgitation by fetal heart quantification (HQ) and to assess the practical value of fetal HQ. Clinical information was analyzed for 63 pregnant women who underwent fetal cardiac ultrasonography. The women were divided into those who had a fetus with severe tricuspid regurgitation (n = 20) and those with a normal fetus (n = 40). The global sphericity index (GSI), fractional area change (FAC), and global longitudinal strain (GLS) of both ventricles and the sphericity index (SI) and fractional shortening (FS) of 24 segments were quantified by fetal HQ using speckle tracking imaging. Fetuses with severe tricuspid regurgitation had a significantly lower GSI (1.14 ± 0.10 vs. 1.26 ± 0.08, p < 0.001) and a higher GSI Z-score (-0.98 ± 1.01 vs. 0.25 ± 0.87, p < 0.001) as well as a significantly lower right ventricular FAC (36.50 ± 7.34% vs. 45.19 ± 3.39%, p < 0.001), FAC Z-score (-1.02 ± 1.41 vs. 0.49 ± 0.74, p < 0.001), and GLS (-21.01 ± 5.66% vs. 45.19 ± 3.49%, p < 0.001). The SI and SI Z-score were significantly lower in segments 1-18 of the right ventricle in fetuses with severe tricuspid regurgitation (p < 0.05); furthermore, FS of segments 1-12 and 19-24 and the FS Z-score of segments 18-24 were significantly lower in fetuses with severe tricuspid regurgitation (p < 0.05). Fetal HQ is useful for evaluation of cardiac morphology and function in fetuses with severe tricuspid regurgitation and can provide important reference information for both clinical diagnosis and treatment.


Subject(s)
Tricuspid Valve Insufficiency , Humans , Female , Pregnancy , Tricuspid Valve Insufficiency/diagnostic imaging , Fetal Heart/diagnostic imaging , Heart Ventricles , Ultrasonography, Prenatal/methods
12.
IEEE Trans Cybern ; PP2024 Jan 12.
Article in English | MEDLINE | ID: mdl-38215330

ABSTRACT

EA, such as the genetic algorithm (GA), offer an elegant way to handle combinatorial optimization problems (COPs). However, limited by expertise and resources, most users lack the capability to implement evolutionary algorithms (EAs) for solving COPs. An intuitive and promising solution is to outsource evolutionary operations to a cloud server, however, it poses privacy concerns. To this end, this article proposes a novel computing paradigm called evolutionary computation as a service (ECaaS), where a cloud server renders evolutionary computation services for users while ensuring their privacy. Following the concept of ECaaS, this article presents privacy-preserving genetic algorithm (PEGA), a privacy-preserving GA designed specifically for COPs. PEGA enables users, regardless of their domain expertise or resource availability, to outsource COPs to the cloud server that holds a competitive GA and approximates the optimal solution while safeguarding privacy. Notably, PEGA features the following characteristics. First, PEGA empowers users without domain expertise or sufficient resources to solve COPs effectively. Second, PEGA protects the privacy of users by preventing the leakage of optimization problem details. Third, PEGA performs comparably to the conventional GA when approximating the optimal solution. To realize its functionality, we implement PEGA falling in a twin-server architecture and evaluate it on two widely known COPs: 1) the traveling Salesman problem (TSP) and 2) the 0/1 knapsack problem (KP). Particularly, we utilize encryption cryptography to protect users' privacy and carefully design a suite of secure computing protocols to support evolutionary operators of GA on encrypted chromosomes. Privacy analysis demonstrates that PEGA successfully preserves the confidentiality of COP contents. Experimental evaluation results on several TSP datasets and KP datasets reveal that PEGA performs equivalently to the conventional GA in approximating the optimal solution.

13.
Environ Sci Pollut Res Int ; 31(6): 8883-8897, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38180667

ABSTRACT

Heavy metal pollutants such as Hg, As, Pb, Cr, and Cd emitted from coal and waste combustion have received widespread attention. In this study, we systematically investigated the emission characteristics of heavy metals in waste incineration and coal-fired flue gases, focused on testing the removal effect of self-made cold electrode electrostatic precipitator (CE-ESP) on heavy metals in flue gas, and made a comparative analysis with the existing air pollution control devices (APCDs). Test results from waste incineration power plant showed that each APCD showed a certain effect on the removal of heavy metals in condensable particulate matter (CPM), with an average removal efficiency of bag filter was 86%, but its effect on Hg removal was slightly worse. Under the coupled field with electrified cold electrode plate operation mode, the average removal efficiency of CE-ESP on heavy metals in CPM was as high as 93%, including 76% for Hg. The removal efficiency of heavy metals (especially Hg) in CPM increased with the increase of flue gas temperature difference between inlet and outlet of CE-ESP. Test results from this coal-fired power plant showed that heavy metals were enriched in fly ash to a higher degree than in slag, the synergistic control of heavy metals in submicron particulate matter by the dust remover was not obvious, and there was a significant correlation between each heavy metal emission factor and its content in coal. Under the temperature field with non-electric cold electrode plate operation mode, the overall effect of CE-ESP on the removal of gaseous heavy metals was better than that of particulate heavy metals. Under the conventional electric field operation mode, CE-ESP was less effective in removing particulate Cr and gaseous Hg0. Under the coupled field with electrified cold electrode plate operation mode, the average removal efficiencies of CE-ESP for particulate and gaseous heavy metals were 82.37% and 76.16%, respectively.


Subject(s)
Air Pollutants , Mercury , Metals, Heavy , Air Pollutants/analysis , Environmental Monitoring/methods , Particulate Matter/analysis , Coal Ash/analysis , Mercury/analysis , Dust , Power Plants , Incineration , Coal/analysis , Gases
14.
Echocardiography ; 41(1): e15747, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38284682

ABSTRACT

OBJECTIVES: Congenital ventricular outpouching (CVO) is a rare cardiac malformation that can manifest as congenital ventricular aneurysm (CVA) and/or congenital ventricular diverticula (CVD). In this study, we describe the prenatal features and postnatal follow-up of 27 cases of CVO. METHODS: The clinical data of 27 patients with CVO who attended Sir Run Run Shaw Hospital Affiliated to the Medical College of Zhejiang University (Zhejiang Province, China) and Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University (Zhejiang Province, China) from April 2013 to October 2022 were retrospectively analyzed. The patients were also followed up by telephone. The prenatal characteristics and postnatal outcomes of the patients with CVO were evaluated. RESULTS: CVO was detected in 26 cases prenatally, 14 (51.85%) were diagnosed with CVA, nine (33.33%) were diagnosed with CVD, three (11.11%) were equivocal for CVA/CVD, and one (3.70%) was detected with CVA postnatally. Six patients underwent follow-up fetal echocardiography approximately 4 weeks after the initial echocardiography examination, and a significant difference in CVO size was observed between the two examinations (P = .02). Eight patients (29.63%) demonstrated cardiovascular dysfunction, and the median CVO size in fetuses with and without cardiovascular dysfunction was 205 (range: 169-396) mm2 and 124 (range: 92-154.5) mm2 , respectively (P = .01). Correlation was found between CVO size and fetal cardiac dysfunction (p = .000, r = .778). Eight patients (29.63%) had cardiac/extracardiac defects. Thirteen patients were live born, 12 were terminated pregnancies, and two were lost to follow-up. The postpartum size of the CVOs remained stable in six patients, decreased in two patients, dissolved in three patients, and were surgically removed in two patients. With the exception of one patient with CVA complicated with complex congenital cardiac malformation who underwent surgical treatment after birth and who had postoperative left ventricular dysfunction (Case 1), the prognosis of all of the patients was good. CONCLUSION: CVO is often associated with cardiac malformations. The size of prenatal CVOs can increase with gestational development, and cardiovascular dysfunction is significantly related to CVO size. The postpartum prognosis of patients with CVO is good. Echocardiography plays a key role in the diagnosis of congenital ventricular outpouching. Prenatal counseling should be cautious regarding the diagnosis and the prognosis although our cases had a favorable prognosis.


Subject(s)
Heart Defects, Congenital , Ultrasonography, Prenatal , Pregnancy , Female , Humans , Retrospective Studies , Follow-Up Studies , Heart Defects, Congenital/diagnostic imaging , Fetus
15.
Nanoscale ; 16(5): 2250-2264, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38213302

ABSTRACT

Messenger RNA (mRNA)-based therapeutic agents have demonstrated significant potential in recent times, particularly in the context of the COVID-19 pandemic outbreak. As a promising prophylactic and therapeutic strategy, polypeptide-based mRNA delivery systems attract significant interest because of their low cost, simple preparation, tuneable sizes and morphology, convenient large-scale production, biocompatibility, and biodegradability. In this review, we begin with a brief discussion of the synthesis of polypeptides, followed by a review of commonly used polypeptides in mRNA delivery, including classical polypeptides and cell-penetrating peptides. Then, the challenges against mRNA delivery, including extracellular, intracellular, and clinical barriers, are discussed in detail. Finally, we highlight a range of strategies for polypeptide-based mRNA delivery, offering valuable insights into the advancement of polypeptide-based mRNA carrier development.


Subject(s)
Cell-Penetrating Peptides , Pandemics , Humans , RNA, Messenger/genetics
16.
Protein Sci ; 33(1): e4841, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37983648

ABSTRACT

The recognition of T-cell receptor (TCR) on the surface of T cell to specific epitope presented by the major histocompatibility complex is the key to trigger the immune response. Identifying the binding rules of TCR-epitope pair is crucial for developing immunotherapies, including neoantigen vaccine and drugs. Accurate prediction of TCR-epitope binding specificity via deep learning remains challenging, especially in test cases which are unseen in the training set. Here, we propose TEPCAM (TCR-EPitope identification based on Cross-Attention and Multi-channel convolution), a deep learning model that incorporates self-attention, cross-attention mechanism, and multi-channel convolution to improve the generalizability and enhance the model interpretability. Experimental results demonstrate that our model outperformed several state-of-the-art models on two challenging tasks including a strictly split dataset and an external dataset. Furthermore, the model can learn some interaction patterns between TCR and epitope by extracting the interpretable matrix from cross-attention layer and mapping them to the three-dimensional structures. The source code and data are freely available at https://github.com/Chenjw99/TEPCAM.


Subject(s)
Deep Learning , T-Lymphocytes , Receptors, Antigen, T-Cell , Protein Binding , Epitopes, T-Lymphocyte/chemistry
17.
bioRxiv ; 2023 Dec 04.
Article in English | MEDLINE | ID: mdl-38106200

ABSTRACT

The three-dimensional structure of a protein plays a fundamental role in determining its function and has an essential impact on understanding biological processes. Despite significant progress in protein structure prediction, such as AlphaFold2, challenges remain on those hard targets that Alphafold2 does not often perform well due to the complex folding of protein and a large number of possible conformations. Here we present a modified version of the AlphaFold2, called Distance-AF, which aims to improve the performance of AlphaFold2 by including distance constraints as input information. Distance-AF uses AlphaFold2's predicted structure as a starting point and incorporates distance constraints between amino acids to adjust folding of the protein structure until it meets the constraints. Distance-AF can correct the domain orientation on challenging targets, leading to more accurate structures with a lower root mean square deviation (RMSD). The ability of Distance-AF is also useful in fitting protein structures into cryo-electron microscopy maps.

19.
J Integr Plant Biol ; 65(12): 2645-2659, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37929676

ABSTRACT

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.


Subject(s)
Genome-Wide Association Study , Zea mays , Zea mays/genetics , Zea mays/microbiology , Nitrogen , Polysaccharides , Bacteria
20.
BMC Genomics ; 24(1): 661, 2023 Nov 02.
Article in English | MEDLINE | ID: mdl-37919660

ABSTRACT

Microproteins, prevalent across all kingdoms of life, play a crucial role in cell physiology and human health. Although global gene transcription is widely explored and abundantly available, our understanding of microprotein functions using transcriptome data is still limited. To mitigate this problem, we present a database, Mip-mining ( https://weilab.sjtu.edu.cn/mipmining/ ), underpinned by high-quality RNA-sequencing data exclusively aimed at analyzing microprotein functions. The Mip-mining hosts 336 sets of high-quality transcriptome data from 8626 samples and nine representative living organisms, including microorganisms, plants, animals, and humans, in our Mip-mining database. Our database specifically provides a focus on a range of diseases and environmental stress conditions, taking into account chemical, physical, biological, and diseases-related stresses. Comparatively, our platform enables customized analysis by inputting desired data sets with self-determined cutoff values. The practicality of Mip-mining is demonstrated by identifying essential microproteins in different species and revealing the importance of ATP15 in the acetic acid stress tolerance of budding yeast. We believe that Mip-mining will facilitate a greater understanding and application of microproteins in biotechnology. Moreover, it will be beneficial for designing therapeutic strategies under various biological conditions.


Subject(s)
Biotechnology , Transcriptome , Animals , Humans , Sequence Analysis, RNA , Micropeptides
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