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1.
Nat Methods ; 21(2): 247-258, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38200227

ABSTRACT

RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA targets are still lacking, especially when the interaction is dynamic or samples are limited. Here we present an assay of reverse transcription-based RBP binding site sequencing (ARTR-seq), which relies on in situ reverse transcription of RBP-bound RNAs guided by antibodies to identify RBP binding sites. ARTR-seq avoids ultraviolet crosslinking and immunoprecipitation, allowing for efficient and specific identification of RBP binding sites from as few as 20 cells or a tissue section. Taking advantage of rapid formaldehyde fixation, ARTR-seq enables capturing the dynamic RNA binding by RBPs over a short period of time, as demonstrated by the profiling of dynamic RNA binding of G3BP1 during stress granule assembly on a timescale as short as 10 minutes.


Subject(s)
RNA , Reverse Transcription , RNA/genetics , RNA/metabolism , DNA Helicases/metabolism , Poly-ADP-Ribose Binding Proteins/genetics , Poly-ADP-Ribose Binding Proteins/metabolism , RNA Helicases/genetics , RNA Helicases/metabolism , RNA Recognition Motif Proteins/genetics , RNA Recognition Motif Proteins/metabolism , RNA-Binding Proteins/metabolism , Binding Sites/genetics , Protein Binding
2.
Plant Cell ; 36(2): 298-323, 2024 Jan 30.
Article in English | MEDLINE | ID: mdl-37847093

ABSTRACT

The high-yielding Green Revolution varieties of cereal crops are characterized by a semidwarf architecture and lodging resistance. Plant height is tightly regulated by the availability of phosphate (Pi), yet the underlying mechanism remains obscure. Here, we report that rice (Oryza sativa) R2R3-type Myeloblastosis (MYB) transcription factor MYB110 is a Pi-dependent negative regulator of plant height. MYB110 is a direct target of PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) and regulates OsPHR2-mediated inhibition of rice height. Inactivation of MYB110 increased culm diameter and bending resistance, leading to enhanced lodging resistance despite increased plant height. Strikingly, the grain yield of myb110 mutants was elevated under both high- and low-Pi regimes. Two divergent haplotypes based on single nucleotide polymorphisms in the putative promoter of MYB110 corresponded with its transcript levels and plant height in response to Pi availability. Thus, fine-tuning MYB110 expression may be a potent strategy for further increasing the yield of Green Revolution cereal crop varieties.


Subject(s)
Edible Grain , Oryza , Edible Grain/genetics , Oryza/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Crops, Agricultural , Phosphates/metabolism
3.
Plant J ; 118(2): 506-518, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38169508

ABSTRACT

Thermosensitive genic female sterility (TGFS) is a promising property to be utilized for hybrid breeding. Here, we identified a rice TGFS line, tfs2, through an ethyl methyl sulfone (EMS) mutagenesis strategy. This line showed sterility under high temperature and became fertile under low temperature. Few seeds were produced when the tfs2 stigma was pollinated, indicating that tfs2 is female sterile. Gene cloning and genetic complementation showed that a point mutation from leucine to phenylalanine in HEI10 (HEI10tfs2), a crossover formation protein, caused the TGFS trait of tfs2. Under high temperature, abnormal univalents were formed, and the chromosomes were unequally segregated during meiosis, similar to the reported meiotic defects in oshei10. Under low temperature, the number of univalents was largely reduced, and the chromosomes segregated equally, suggesting that crossover formation was restored in tfs2. Yeast two-hybrid assays showed that HEI10 interacted with two putative protein degradation-related proteins, RPT4 and SRFP1. Through transient expression in tobacco leaves, HEI10 were found to spontaneously aggregate into dot-like foci in the nucleus under high temperature, but HEI10tfs2 failed to aggregate. In contrast, low temperature promoted HEI10tfs2 aggregation. This result suggests that protein aggregation at the crossover position contributes to the fertility restoration of tfs2 under low temperature. In addition, RPT4 and SRFP1 also aggregated into dot-like foci, and these aggregations depend on the presence of HEI10. These findings reveal a novel mechanism of fertility restoration and facilitate further understanding of HEI10 in meiotic crossover formation.


Subject(s)
Infertility , Oryza , Crossing Over, Genetic , Point Mutation , Oryza/genetics , Plant Breeding
4.
Exp Cell Res ; 442(2): 114270, 2024 Oct 01.
Article in English | MEDLINE | ID: mdl-39389337

ABSTRACT

Weightlessness osteoporosis, which progresses continuously and has limited protective effects, has become one of the major problems that need to be solved in manned spaceflight. Our study aims to investigate the regulatory role of PHF8 in disuse osteoporosis by observing the expression of PHF8 in bone marrow mesenchymal stem cells (BMSCs) under simulated weightlessness conditions. Therefore, we used the model of ground-based microgravity simulated by disuse osteoporosis patients and tail suspension in mice to simulate microgravity in vivo, and measured the expression of PHF8 in bone tissue. Subsequently, we used the 2D gyroscope to simulate the weightless effect on bone marrow mesenchymal stem cells. In the weightless condition, we detected the proliferation, apoptosis, osteogenesis, and osteogenic differentiation functions of BMSCs. We also detected the expression of osteogenic-related transcription factors after knocking down and overexpressing PHF8. Our results show that the weightless effect can inhibit the proliferation, osteogenesis, and osteogenic differentiation functions of BMSCs, while enhancing their apoptosis; and overexpression of PHF8 can partially alleviate the osteoporosis caused by simulated weightlessness, providing new ideas and clues for potential drug targets to prevent weightlessness and disuse osteoporosis.


Subject(s)
Cell Differentiation , Cell Proliferation , Histone Demethylases , Mesenchymal Stem Cells , Osteogenesis , Osteoporosis , Osteoporosis/pathology , Osteoporosis/metabolism , Osteoporosis/genetics , Animals , Mesenchymal Stem Cells/metabolism , Mice , Osteogenesis/genetics , Osteogenesis/physiology , Histone Demethylases/metabolism , Histone Demethylases/genetics , Apoptosis , Humans , Weightlessness , Mice, Inbred C57BL , Cells, Cultured , Male , Transcription Factors/metabolism , Transcription Factors/genetics
5.
Genes Dev ; 31(12): 1228-1242, 2017 06 15.
Article in English | MEDLINE | ID: mdl-28724614

ABSTRACT

Androgen receptor (AR) signaling reprograms cellular metabolism to support prostate cancer (PCa) growth and survival. Another key regulator of cellular metabolism is mTOR, a kinase found in diverse protein complexes and cellular localizations, including the nucleus. However, whether nuclear mTOR plays a role in PCa progression and participates in direct transcriptional cross-talk with the AR is unknown. Here, via the intersection of gene expression, genomic, and metabolic studies, we reveal the existence of a nuclear mTOR-AR transcriptional axis integral to the metabolic rewiring of PCa cells. Androgens reprogram mTOR-chromatin associations in an AR-dependent manner in which activation of mTOR-dependent metabolic gene networks is essential for androgen-induced aerobic glycolysis and mitochondrial respiration. In models of castration-resistant PCa cells, mTOR was capable of transcriptionally regulating metabolic gene programs in the absence of androgens, highlighting a potential novel castration resistance mechanism to sustain cell metabolism even without a functional AR. Remarkably, we demonstrate that increased mTOR nuclear localization is indicative of poor prognosis in patients, with the highest levels detected in castration-resistant PCa tumors and metastases. Identification of a functional mTOR targeted multigene signature robustly discriminates between normal prostate tissues, primary tumors, and hormone refractory metastatic samples but is also predictive of cancer recurrence. This study thus underscores a paradigm shift from AR to nuclear mTOR as being the master transcriptional regulator of metabolism in PCa.


Subject(s)
Gene Expression Regulation, Neoplastic/genetics , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/physiopathology , Receptors, Androgen/metabolism , Signal Transduction , TOR Serine-Threonine Kinases/metabolism , Androgens/metabolism , Cell Nucleus/metabolism , DNA/metabolism , Disease Progression , Humans , Male , Protein Binding , TOR Serine-Threonine Kinases/genetics , Transcription, Genetic
6.
BMC Bioinformatics ; 25(1): 135, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38549073

ABSTRACT

Michaelis constant (KM) is one of essential parameters for enzymes kinetics in the fields of protein engineering, enzyme engineering, and synthetic biology. As overwhelming experimental measurements of KM are difficult and time-consuming, prediction of the KM values from machine and deep learning models would increase the pace of the enzymes kinetics studies. Existing machine and deep learning models are limited to the specific enzymes, i.e., a minority of enzymes or wildtype enzymes. Here, we used a deep learning framework PaddlePaddle to implement a machine and deep learning approach (GraphKM) for KM prediction of wildtype and mutant enzymes. GraphKM is composed by graph neural networks (GNN), fully connected layers and gradient boosting framework. We represented the substrates through molecular graph and the enzymes through a pretrained transformer-based language model to construct the model inputs. We compared the difference of the model results made by the different GNN (GIN, GAT, GCN, and GAT-GCN). The GAT-GCN-based model generally outperformed. To evaluate the prediction performance of the GraphKM and other reported KM prediction models, we collected an independent KM dataset (HXKm) from literatures.


Subject(s)
Deep Learning , Electric Power Supplies , Language , Neural Networks, Computer , Protein Engineering
7.
Eur J Neurosci ; 60(2): 3973-3983, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38711292

ABSTRACT

A mounting body of evidences suggests that patients with chronic heart failure (HF) frequently experience cognitive impairments, but the neuroanatomical mechanism underlying these impairments remains elusive. In this retrospective study, 49 chronic HF patients and 49 healthy controls (HCs) underwent brain structural MRI scans and cognitive assessments. Cortical morphology index (cortical thickness, complexity, sulcal depth and gyrification) were evaluated. Correlations between cortical morphology and cognitive scores and clinical variables were explored. Logistic regression analysis was employed to identify risk factors for predicting 3-year major adverse cardiovascular events. Compared with HCs, patients with chronic HF exhibited decreased cognitive scores (p < .001) and decreased cortical thickness, sulcal depth and gyrification in brain regions involved cognition, sensorimotor, autonomic nervous system (family-wise error correction, all p values <.05). Notably, HF duration and New York Heart Association (NYHA) demonstrated negative correlations with abnormal cortex morphology, particularly HF duration and thickness in left precentral gyrus (r = -.387, p = .006). Cortical morphology characteristics exhibited positive associations with global cognition, particularly cortical thickness in left pars opercularis (r = .476, p < .001). NYHA class is an independent risk factor for adverse outcome (p = .001). The observed correlation between abnormal cortical morphology and global cognition suggested that cortical morphology may serve as a promising imaging biomarker and provide insights into neuroanatomical underpinnings of cognitive impairment in patients with chronic HF.


Subject(s)
Cerebral Cortex , Cognitive Dysfunction , Heart Failure , Magnetic Resonance Imaging , Humans , Male , Heart Failure/diagnostic imaging , Heart Failure/pathology , Female , Cognitive Dysfunction/diagnostic imaging , Cognitive Dysfunction/pathology , Cognitive Dysfunction/physiopathology , Middle Aged , Cerebral Cortex/diagnostic imaging , Cerebral Cortex/pathology , Aged , Retrospective Studies , Chronic Disease
8.
Small ; 20(7): e2305336, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37797180

ABSTRACT

Despite decades of progress, developing minimally invasive bone-specific drug delivery systems (DDS) to improve fracture healing remains a significant clinical challenge. To address this critical therapeutic need, nanoparticle (NP) DDS comprised of poly(styrene-alt-maleic anhydride)-b-poly(styrene) (PSMA-b-PS) functionalized with a peptide that targets tartrate-resistant acid phosphatase (TRAP) and achieves preferential fracture accumulation has been developed. The delivery of AR28, a glycogen synthase kinase-3 beta (GSK3ß) inhibitor, via the TRAP binding peptide-NP (TBP-NP) expedites fracture healing. Interestingly, however, NPs are predominantly taken up by fracture-associated macrophages rather than cells typically associated with fracture healing. Therefore, the underlying mechanism of healing via TBP-NP is comprehensively investigated herein. TBP-NPAR28 promotes M2 macrophage polarization and enhances osteogenesis in preosteoblast-macrophage co-cultures in vitro. Longitudinal analysis of TBP-NPAR28 -mediated fracture healing reveals distinct spatial distributions of M2 macrophages, an increased M2/M1 ratio, and upregulation of anti-inflammatory and downregulated pro-inflammatory genes compared to controls. This work demonstrates the underlying therapeutic mechanism of bone-targeted NP DDS, which leverages macrophages as druggable targets and modulates M2 macrophage polarization to enhance fracture healing, highlighting the therapeutic benefit of this approach for fractures and bone-associated diseases.


Subject(s)
Fracture Healing , Nanoparticle Drug Delivery System , Fracture Healing/physiology , Macrophages/metabolism , Bone and Bones , Peptides/metabolism
9.
Plant Biotechnol J ; 22(7): 2020-2032, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38421616

ABSTRACT

P/TGMS (Photo/thermo-sensitive genic male sterile) lines are crucial resources for two-line hybrid rice breeding. Previous studies revealed that slow development is a general mechanism for sterility-fertility conversion of P/TGMS in Arabidopsis. However, the difference in P/TGMS genes between rice and Arabidopsis suggests the presence of a distinct P/TGMS mechanism in rice. In this study, we isolated a novel P/TGMS line, ostms19, which shows sterility under high-temperature conditions and fertility under low-temperature conditions. OsTMS19 encodes a novel pentatricopeptide repeat (PPR) protein essential for pollen formation, in which a point mutation GTA(Val) to GCA(Ala) leads to ostms19 P/TGMS phenotype. It is highly expressed in the tapetum and localized to mitochondria. Under high temperature or long-day photoperiod conditions, excessive ROS accumulation in ostms19 anthers during pollen mitosis disrupts gene expression and intine formation, causing male sterility. Conversely, under low temperature or short-day photoperiod conditions, ROS can be effectively scavenged in anthers, resulting in fertility restoration. This indicates that ROS homeostasis is critical for fertility conversion. This relationship between ROS homeostasis and fertility conversion has also been observed in other tested rice P/TGMS lines. Therefore, we propose that ROS homeostasis is a general mechanism for the sterility-fertility conversion of rice P/TGMS lines.


Subject(s)
Fertility , Homeostasis , Oryza , Plant Infertility , Plant Proteins , Pollen , Reactive Oxygen Species , Oryza/genetics , Oryza/metabolism , Reactive Oxygen Species/metabolism , Fertility/genetics , Pollen/genetics , Pollen/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Infertility/genetics , Gene Expression Regulation, Plant , Temperature , Light , Photoperiod
10.
J Virol ; 97(12): e0151323, 2023 Dec 21.
Article in English | MEDLINE | ID: mdl-38032198

ABSTRACT

IMPORTANCE: The precise regulation of the innate immune response is essential for the maintenance of homeostasis. MAVS and STING play key roles in immune signaling pathways activated by RNA and DNA viruses, respectively. Here, we showed that DHCR24 impaired the antiviral response by targeting MAVS and STING. Notably, DHCR24 interacts with MAVS and STING and inhibits TRIM21-triggered K27-linked ubiquitination of MAVS and AMFR-triggered K27-linked ubiquitination of STING, restraining the activation of MAVS and STING, respectively. Together, this study elucidates how one cholesterol key enzyme orchestrates two antiviral signal transduction pathways.


Subject(s)
Adaptor Proteins, Signal Transducing , Immunity, Innate , Membrane Proteins , Oxidoreductases Acting on CH-CH Group Donors , Animals , Humans , Mice , Adaptor Proteins, Signal Transducing/metabolism , Hydroxysteroids , Membrane Proteins/metabolism , Oxidoreductases , Oxidoreductases Acting on CH-CH Group Donors/genetics , Oxidoreductases Acting on CH-CH Group Donors/metabolism , Ubiquitination , Cell Line
11.
Plant Physiol ; 191(2): 1066-1083, 2023 02 12.
Article in English | MEDLINE | ID: mdl-36477345

ABSTRACT

Pomegranate (Punica granatum) flowers are classified as bisexual flowers and functional male flowers. Functional male flowers have sterile pistils that show abnormal ovule development. In previous studies, we identified INNER NO OUTER (INO), CRABS CLAW (CRC), and BELL1 (BEL1), which were specifically expressed in bisexual and functional male flowers. However, the functions of ovule identity genes and the mechanism underlying ovule sterility in pomegranate remain unknown. Here, we found that the integument primordia formed and then ceased developing in the ovules of functional male flowers with a vertical diameter of 8.1-13.0 mm. Megaspore mother cells were observed in bisexual flowers when the vertical diameters of flowers were 10.1-13.0 mm, but not in functional male flowers. We analyzed the expression patterns of ovule-related genes in pomegranate ovule sterility and found that PgCRC mRNA was highly expressed at a critical stage of ovule development in bisexual flowers. Ectopic expression of PgCRC and PgINO was sufficient to increase seed number in transgenic lines. PgCRC partially complemented the Arabidopsis (Arabidopsis thaliana) crc mutant, and PgINO successfully rescued the seeds set in the Arabidopsis ino mutant. The results of yeast two-hybrid assays, bimolecular fluorescence complementation assays, and genetic data analyses showed that PgCRC and PgINO directly interact with PgBEL1. Our results also showed that PgCRC and PgINO could not interact directly with MADS-box proteins and that PgBEL1 interacted with SEPALLATA proteins. We report the function of PgCRC and PgINO in ovule and seed development and show that PgCRC and PgINO interact with PgBEL1. Thus, our results provide understanding of the genetic regulatory networks underlying ovule development in pomegranate.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Pomegranate , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Transcription Factors/metabolism , Pomegranate/genetics , Pomegranate/metabolism , Ovule/genetics , Ovule/metabolism , Flowers , Seeds/genetics , Seeds/metabolism , Gene Expression Regulation, Plant
12.
Plant Cell Environ ; 2024 Oct 23.
Article in English | MEDLINE | ID: mdl-39440542

ABSTRACT

Photoperiod/thermo-sensitive genic male sterility (P/TGMS) is critical for rice two-line hybrid system. Previous studies showed that slow development of pollen is a general mechanism for sterility-to-fertility conversion of TGMS in Arabidopsis. However, whether this mechanism still exists in rice is unknown. Here, we identified a novel rice TGMS line, ostms16, which exhibits abnormal pollen exine under high temperature and fertility restoration under low temperature. In mutant, a single base mutation of OsTMS16, a fatty acyl-CoA reductase (FAR), reduced its enzyme activity, leading to defective pollen wall. Under high temperature, the mOsTMS16M549I couldn't provide sufficient protection for the microspores. Under low temperature, the enzyme activity of mOsTMS16M549I is closer to that of OsTMS16, so that the imperfect exine could still protect microspore development. These results indicated whether the residual enzyme activity in mutant could meet the requirement in different temperature is a determinant factor for fertility conversion of P/TGMS lines. Additionally, we previously found that res2, the mutant of a polygalacturonase for tetrad pectin wall degradation, restored multiple TGMS lines in Arabidopsis. In this study, we proved that the osres2 in rice restored the fertility of ostms16, indicating the slow development is also suitable for the fertility restoration in rice.

13.
Opt Express ; 32(6): 9255-9275, 2024 Mar 11.
Article in English | MEDLINE | ID: mdl-38571164

ABSTRACT

Dwell time scheduling is a critical stage of deterministic polishing for ultra-precision fabrication of optics. Recently the dwell time algorithms for deterministic polishing have been widely studied. Nevertheless, there exist some shortcomings when those methods were applied in the industry, including low computational efficiency, large memory consumption, insufficiently-considered dynamic constraints, poor smoothness of the feedrate profile, and reliance on non-open CNC interpolator. To overcome those deficiencies, this work proposes a highly-efficient dwell time algorithm under the dynamic constraints of machine tools. The method calculates the initial dwell time density (DTD) sequence through non-blind deconvolution algorithm, and provides the feasible set of DTD profiles based on trigonometric-spline model. And the DTD repairing tactics are developed based on a self-adaptive offset algorithm under confined feedrate and acceleration. Finally, a C1-continuous DTD profile satisfying dynamic constraints is generated. A real-time interpolator based on trigonometric-spline DTD profile is developed. The simulation results show that the proposed method generates a C1-continuous feedrate profile rigidly respecting dynamic constraints, and preserves the ideal dwell time gradient distribution, achieving a more ideal residual error with high computational efficiency compared with the previous methods. The comparative experiments demonstrate that the proposed method performs better in suppressing the multi-frequency errors compared with the previous methods, and achieves high computational efficiency. The algorithm is applicable to highly-precise and highly-efficient fabrication of large-aperture optical components.

14.
Reprod Biol Endocrinol ; 22(1): 36, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38570783

ABSTRACT

Microtubule-associated protein 1a (Map1a) is a microtubule (MT) regulatory protein that binds to the MT protofilaments in mammalian cells to promote MT stabilization. Maps work with MT cleavage proteins and other MT catastrophe-inducing proteins to confer MT dynamics to support changes in the Sertoli cell shape to sustain spermatogenesis. However, no functional studies are found in the literature to probe its role in spermatogenesis. Using an RNAi approach, coupled with the use of toxicant-induced testis (in vivo)- and Sertoli cell (in vitro)-injury models, RNA-Seq analysis, transcriptome profiling, and relevant bioinformatics analysis, immunofluorescence analysis, and pertinent biochemical assays for cytoskeletal organization, we have delineated the functional role of Map1a in Sertoli cells and testes. Map1a was shown to support MT structural organization, and its knockdown (KD) also perturbed the structural organization of actin, vimentin, and septin cytoskeletons as these cytoskeletons are intimately related, working in concert to support spermatogenesis. More importantly, cadmium-induced Sertoli cell injury that perturbed the MT structural organization across the cell cytoplasm was associated with disruptive changes in the distribution of Map1a and a surge in p-p38-MAPK (phosphorylated p38-mitogen-activated protein kinase) expression but not total p38-MAPK. These findings thus support the notion that p-p38-MAPK activation is involved in cadmium-induced Sertoli cell injury. This conclusion was supported by studies using doramapimod, a specific p38-MAPK phosphorylation (activation) inhibitor, which was capable of restoring the cadmium-induced disruptive structural organization of MTs across the Sertoli cell cytoplasm. In summary: this study provides mechanistic insights regarding restoration of toxicant-induced Sertoli cell and testis injury and male infertility.


Subject(s)
Actins , Sertoli Cells , Rats , Animals , Male , Actins/metabolism , Sertoli Cells/metabolism , Cadmium , Rats, Sprague-Dawley , Blood-Testis Barrier/metabolism , Microtubules/metabolism , Testis/metabolism , Spermatogenesis/physiology , Mammals
15.
BMC Cancer ; 24(1): 1277, 2024 Oct 15.
Article in English | MEDLINE | ID: mdl-39407127

ABSTRACT

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide, with high incidence and poor survival rates. RBP1 is highly expressed in several kinds of cancer and plays a potential prognostic factor. However, the relationship between RBP1 and HNSCC were analyzed based on The Cancer Genome Atlas (TCGA) database. MATERIALS AND METHODS: RBP1 expression and clinical information were obtained from the Cancer Genome Atlas (TCGA) database. Tumor tissue and adjacent normal tissue of 6 HNSCC patients were collected to analyze the RBP1 mRNA expression level by quantitative PCR. Cox regression analysis was used to evaluate the prognostic values of RBP1 and clinical data in HNSCC. A nomogram was also established to predict the impact of RBP1 on prognosis based on Cox multivariate results. The methylation level of RBP1 in HNSC and its prognosis were analyzed in UALACN and MethSurv. Finally, the potential biological functions of RBP1 were investigated using gene set enrichment analysis (GSEA) and single sample GSEA (ssGSEA). RESULTS: The mRNA expression levels of RBP1 were highly expressed in HNSCC tissue. The Cox analyses demonstrate that highly-expressed RBP1 is an independent prognosis marker(P < 0.05). ROC curve analysis showed that performances of RBP1 (area under the ROC curve: 0.887, sensitivity: 84.1%, specificity: 79.9%). The methylation was increased in HNSCC patients compared with normal subjects(P < 0.05) and was associated with better prognosis at sites cg06208339, cg12298268, cg12497564, cg15288618, cg20532370, cg23448348. Additionally, RBP1 expression is mildly associated with immune cell infiltration and immunological checkpoints. CONCLUSION: RBP1 is overexpressed and associated with poor patient prognosis in head and neck squamous cell carcinoma.


Subject(s)
Biomarkers, Tumor , DNA Methylation , Head and Neck Neoplasms , Squamous Cell Carcinoma of Head and Neck , Humans , Prognosis , Squamous Cell Carcinoma of Head and Neck/genetics , Squamous Cell Carcinoma of Head and Neck/mortality , Squamous Cell Carcinoma of Head and Neck/metabolism , Squamous Cell Carcinoma of Head and Neck/pathology , Male , Female , Head and Neck Neoplasms/genetics , Head and Neck Neoplasms/metabolism , Head and Neck Neoplasms/mortality , Head and Neck Neoplasms/pathology , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Middle Aged , Gene Expression Regulation, Neoplastic , Retinol-Binding Proteins, Plasma/genetics , Retinol-Binding Proteins, Plasma/metabolism , Nomograms , Aged , RNA, Messenger/genetics , RNA, Messenger/metabolism , Retinol-Binding Proteins, Cellular
16.
Theor Appl Genet ; 137(10): 221, 2024 Sep 13.
Article in English | MEDLINE | ID: mdl-39271558

ABSTRACT

KEY MESSAGE: The hybrid rice variety (Hanyou73) exhibits the maternal-like (HH7A) gene expression in roots and parental-like (HH3) gene expression in leaves to obtain both advantages of drought avoidance and drought tolerance from its two parents. BACKGROUND: Rice is one of the most important crops in the world. Rice production consumes lots of water and significantly suffers from the water deficiency and drought stress. The water-saving and drought-resistance rice (WDR) confers good drought resistance and performs well in the water-saving cultivation. MAIN FINDINGS: A hybrid WDR variety Hanyou73 (HY73) exhibited superior drought resistance compared with its parents Hanhui3 (HH3) and Huhan7A (HH7A). Studies on drought resistance related traits revealed that HY73 performed like HH3 and HH7A on drought tolerance and drought avoidance, respectively. Transcriptomes were analyzed for samples with various phytohormone treatments and abiotic stresses, in which HY73 was closer to HH3 in leaf samples while HH7A in root samples. HY73 and its parents differed largely in DEGs and GO analysis for DEGs suggested the different pathways of drought response in HH3 and HH7A. Parent-like expression analysis revealed that the higher-parent-like expression pattern was prevailing in HY73. In addition, patterns of the parent-like expression significantly transformed between abiotic-stressed/phytohormone-treated and control samples, which might help HY73 to adapt to different environments. WGCNA analysis for those parent-like expression genes revealed some drought resistant genes that should contribute to the superior drought resistance of HY73. Genetic variation on the promotor sequence was confirmed as the reason for the flexible parent-like gene expression in HY73. CONCLUSION: Our study uncovered the important roles of complementation of beneficial traits from parents and flexible gene expressions in drought resistance of HY73, which could facilitate the development of new WDR varieties.


Subject(s)
Droughts , Gene Expression Regulation, Plant , Oryza , Oryza/genetics , Oryza/physiology , Stress, Physiological/genetics , Water , Plant Roots/genetics , Plant Roots/physiology , Plant Leaves/genetics , Plant Leaves/physiology , Plant Proteins/genetics , Plant Proteins/metabolism , Phenotype , Genes, Plant , Drought Resistance
17.
Langmuir ; 2024 Oct 23.
Article in English | MEDLINE | ID: mdl-39442770

ABSTRACT

The mechanism underlying the interfacial interaction between ZnO and surface functional groups, which drives the self-assembly of ZnO nanoflowers on the cellulose nanofibril (CNF) surface, remains inadequately understood. Moreover, the ideal sites for the loading and growth of ZnO nanoflowers on the oxygen atoms (Os) of various surface functional groups on the CNF surface are not well-defined. This work addressed these gaps by systematically regulating the size and surface charge density of CNF templates through minor surface modifications and adjustments in processing cycles by using an ultrafine grinder. Physicochemical analyses demonstrated that the ZnO nanoflowers exhibited sizes (µm)/pieces/thickness (nm) of 0.86/16/20.1 for ZnO/TOCNFs, 0.88/17/20.4 for ZnO/ACNFs, and 0.89/16/20.5 for ZnO/ECNFs, respectively. Simulation calculations revealed that the interaction between Zn2+ ions and the Os of hydroxyl (-OH) groups exhibited the most favorable binding energy of -31.7 kcal/mol. These findings suggested that the surface charge density rather than specific surface functional groups primarily governs the loading and growth of ZnO nanoflowers on the CNF surface. The OS from -OH groups on the surface of CNF templates were optimal for both the loading and growth of ZnO nanoflowers. Overall, this study provides crucial theoretical insights into the design and optimization of the ZnO/CNF composites.

18.
Biomacromolecules ; 25(4): 2438-2448, 2024 04 08.
Article in English | MEDLINE | ID: mdl-38502912

ABSTRACT

The treatment of infected wounds faces substantial challenges due to the high incidence and serious infection-related complications. Natural-based hydrogel dressings with favorable antibacterial properties and strong applicability are urgently needed. Herein, we developed a composite hydrogel by constructing multiple networks and loading ciprofloxacin for infected wound healing. The hydrogel was synthesized via a Schiff base reaction between carboxymethyl chitosan and oxidized sodium alginate, followed by the polymerization of the acrylamide monomer. The resultant hydrogel dressing possessed a good self-healing ability, considerable compression strength, and reliable compression fatigue resistance. In vitro assessment showed that the composite hydrogel effectively eliminated bacteria and exhibited an excellent biocompatibility. In a model of Staphylococcus aureus-infected full-thickness wounds, wound healing was significantly accelerated without scars through the composite hydrogel by reducing wound inflammation. Overall, this study opens up a new way for developing multifunctional hydrogel wound dressings to treat wound infections.


Subject(s)
Chitosan , Hydrogels , Hydrogels/pharmacology , Wound Healing , Anti-Bacterial Agents/pharmacology , Ciprofloxacin , Bandages
19.
Eur J Haematol ; 112(1): 83-93, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37712633

ABSTRACT

OBJECTIVES: The treatment of refractory and recurrent acute myeloid leukaemia (AML) is still a challenge with poor response rates and short survival times. In an attempt to solve this problem, we constructed a tandem bispecific chimeric antigen receptor (CAR) targeting CD123 and C-type lectin-like molecule 1 (CLL-1), two different AML antigens, and verified its cytotoxic effects in vitro. METHODS: We established and cultured K562 cell lines expressing both CD123 and CLL1 antigens. Single-target CAR-T cells specific to CD123 and CLL1 were engineered, alongside tandem CD123/CLL1 bispecific CAR-T cells. Flow cytometry was used to determine cell phenotypes, transfection efficiencies, cytokine release, and CAR-T-cell proliferation, and an lactate dehydrogenase assay was used to detect the cytotoxicity of CD123/CLL-1 bispecific tandem CAR-T cells in vitro. RESULTS: Two types of tandem CAR-T cells exhibited significant killing effects on CLL-1 + CD123+ leukaemia cell lines and primary AML tumour cells. The killing efficiency of tandem CAR-T cells in the case of single antigen expression is comparable to that of single target CAR-T cells. When faced with dual target tumour cells, dual target CAR-T cells significantly surpass single target CAR-T cells. CD123/CLL-1 CAR-T cells in tandem targeted and killed CD123- and CLL-1-positive leukaemia cell lines and released a large number of cytokines. CONCLUSIONS: CD123/CLL-1 CAR-T cells in tandem can simultaneously target CD123 and CLL-1 on AML cells, demonstrating a significant ability to kill single antigens and multi-target tumour cells. This suggests that CD123/CLL-1 CAR-T cells exhibit significant advantages in the expression of multiple antigens in a wide range of target cells, which may help overcome the challenges posed by tumour heterogeneity and evasion mechanisms.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Leukemia, Myeloid, Acute , Receptors, Chimeric Antigen , Humans , Cell Line, Tumor , Cytokines/metabolism , Immunotherapy, Adoptive , Interleukin-3 Receptor alpha Subunit/genetics , Interleukin-3 Receptor alpha Subunit/metabolism , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/therapy , Leukemia, Lymphocytic, Chronic, B-Cell/metabolism , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/therapy , Leukemia, Myeloid, Acute/metabolism , Neoplasm Recurrence, Local , Receptors, Chimeric Antigen/genetics , Receptors, Chimeric Antigen/metabolism , T-Lymphocytes
20.
Org Biomol Chem ; 22(2): 348-352, 2024 Jan 03.
Article in English | MEDLINE | ID: mdl-38086690

ABSTRACT

Sulfinamides are a versatile class of compounds that find applications in both organic synthesis and pharmaceuticals. Here we developed an efficient photocatalytic approach for the convenient preparation of sulfinamides. Commercially available potassium trifluoro(organo)borates and readily available sulfinyl amines are rationally used and converted to a series of alkyl or aryl sulfinamides in moderate to high yields. The reaction allows for the gram-scale preparation of sulfinamides. Moreover, sulfonimidamides, sulfonimidate esters and sulfonyl amides could be obtained in one pot.

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