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  • 1
    Online Resource
    Online Resource
    High Throughput Isolation and Data Independent Acquisition Mass Spectrometry (DIA-MS) of Urinary Extracellular Vesicles to Improve Prostate Cancer Diagnosis
    MDPI AG ; 2022
    In:  Molecules Vol. 27, No. 23 ( 2022-11-23), p. 8155-
    Details
    In: Molecules, MDPI AG, Vol. 27, No. 23 ( 2022-11-23), p. 8155-
    Abstract: Proteomic profiling of extracellular vesicles (EVs) represents a promising approach for early detection and therapeutic monitoring of diseases such as cancer. The focus of this study was to apply robust EV isolation and subsequent data-independent acquisition mass spectrometry (DIA-MS) for urinary EV proteomics of prostate cancer and prostate inflammation patients. Urinary EVs were isolated by functionalized magnetic beads through chemical affinity on an automatic station, and EV proteins were analyzed by integrating three library-base analyses (Direct-DIA, GPF-DIA, and Fractionated DDA-base DIA) to improve the coverage and quantitation. We assessed the levels of urinary EV-associated proteins based on 40 samples consisting of 20 cases and 20 controls, where 18 EV proteins were identified to be differentiated in prostate cancer outcome, of which three (i.e., SERPINA3, LRG1, and SCGB3A1) were shown to be consistently upregulated. We also observed 6 out of the 18 (33%) EV proteins that had been developed as drug targets, while some of them showed protein-protein interactions. Moreover, the potential mechanistic pathways of 18 significantly different EV proteins were enriched in metabolic, immune, and inflammatory activities. These results showed consistency in an independent cohort with 20 participants. Using a random forest algorithm for classification assessment, including the identified EV proteins, we found that SERPINA3, LRG1, or SCGB3A1 add predictable value in addition to age, prostate size, body mass index (BMI), and prostate-specific antigen (PSA). In summary, the current study demonstrates a translational workflow to identify EV proteins as molecular markers to improve the clinical diagnosis of prostate cancer.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules27238155
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2008644-1
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  • 2
    Online Resource
    Online Resource
    Low-Light-Level Image Super-Resolution Reconstruction Based on a Multi-Scale Features Extraction Network
    MDPI AG ; 2021
    In:  Photonics Vol. 8, No. 8 ( 2021-08-10), p. 321-
    Details
    In: Photonics, MDPI AG, Vol. 8, No. 8 ( 2021-08-10), p. 321-
    Abstract: Wide field-of-view (FOV) and high-resolution (HR) imaging are essential to many applications where high-content image acquisition is necessary. However, due to the insufficient spatial sampling of the image detector and the trade-off between pixel size and photosensitivity, the ability of current imaging sensors to obtain high spatial resolution is limited, especially under low-light-level (LLL) imaging conditions. To solve these problems, we propose a multi-scale feature extraction (MSFE) network to realize pixel-super-resolved LLL imaging. In order to perform data fusion and information extraction for low resolution (LR) images, the network extracts high-frequency detail information from different dimensions by combining the channel attention mechanism module and skip connection module. In this way, the calculation of the high-frequency components can receive greater attention. Compared with other networks, the peak signal-to-noise ratio of the reconstructed image was increased by 1.67 dB. Extensions of the MSFE network are investigated for scene-based color mapping of the gray image. Most of the color information could be recovered, and the similarity with the real image reached 0.728. The qualitative and quantitative experimental results show that the proposed method achieved superior performance in image fidelity and detail enhancement over the state-of-the-art.
    Type of Medium: Online Resource
    ISSN: 2304-6732
    URL: Article
    DOI: 10.3390/photonics8080321
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2770002-1
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  • 3
    Online Resource
    Online Resource
    Molecular Targeting of the Oncoprotein PLK1 in Pediatric Acute Myeloid Leukemia: RO3280, a Novel PLK1 Inhibitor, Induces Apoptosis in Leukemia Cells
    MDPI AG ; 2015
    In:  International Journal of Molecular Sciences Vol. 16, No. 1 ( 2015-01-07), p. 1266-1292
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 16, No. 1 ( 2015-01-07), p. 1266-1292
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms16011266
    Language: English
    Publisher: MDPI AG
    Publication Date: 2015
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. & Zucc.
    MDPI AG ; 2020
    In:  Forests Vol. 11, No. 3 ( 2020-03-20), p. 350-
    Details
    In: Forests, MDPI AG, Vol. 11, No. 3 ( 2020-03-20), p. 350-
    Abstract: The objective of this research was to study the differences in endogenous hormone levels and the genes related to reproductive development in Chinese pinenut (Pinus koraiensis) trees of different ages. The apical buds of P. koraiensis were collected from 2-, 5-, 10-, 15-, and 30-year-old plants and also from grafted plants. There were three replicates from each group used for transcriptome sequencing. After assembly and annotation, we identified the differentially expressed genes (DEGs) and performed enrichment analysis, pathway analysis, and expression analysis of the DEGs in each sample. The results showed that unigenes related to reproductive development, such as c64070.graph_c0 and c68641.graph_c0, were expressed at relatively low levels at young ages, and that the relative expression gradually increased with increasing plant age. In addition the highest expression levels were reached around 10 and 15 years of age, after which they gradually decreased. Moreover, some unigenes, such as c61855.graph_c0, were annotated as abscisic acid hydroxylase genes, and the expression of c61855.graph_c0 gradually declined with increasing age in P. koraiensis.
    Type of Medium: Online Resource
    ISSN: 1999-4907
    URL: Article
    DOI: 10.3390/f11030350
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2527081-3
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  • 5
    Online Resource
    Online Resource
    Fabrication of Silicon Nanowires by Metal-Assisted Chemical Etching Combined with Micro-Vibration
    MDPI AG ; 2023
    In:  Materials Vol. 16, No. 15 ( 2023-08-05), p. 5483-
    Details
    In: Materials, MDPI AG, Vol. 16, No. 15 ( 2023-08-05), p. 5483-
    Abstract: In this work, we design a micro-vibration platform, which combined with the traditional metal-assisted chemical etching (MaCE) to etch silicon nanowires (SiNWs). The etching mechanism of SiNWs, including in the mass-transport (MT) and charge-transport (CT) processes, was explored through the characterization of SiNW’s length as a function of MaCE combined with micro-vibration conditions, such as vibration amplitude and frequency. The scanning electron microscope (SEM) experimental results indicated that the etching rate would be continuously improved with an increase in amplitude and reached its maximum at 4 μm. Further increasing amplitude reduced the etching rate and affected the morphology of the SiNWs. Adjusting the vibration frequency would result in a maximum etching rate at a frequency of 20 Hz, and increasing the frequency will not help to improve the etching effects.
    Type of Medium: Online Resource
    ISSN: 1996-1944
    URL: Article
    DOI: 10.3390/ma16155483
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2487261-1
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  • 6
    Online Resource
    Online Resource
    Epigallocatechin Gallate Attenuates Gentamicin-Induced Nephrotoxicity by Suppressing Apoptosis and Ferroptosis
    MDPI AG ; 2022
    In:  Molecules Vol. 27, No. 23 ( 2022-12-05), p. 8564-
    Details
    In: Molecules, MDPI AG, Vol. 27, No. 23 ( 2022-12-05), p. 8564-
    Abstract: Gentamicin (GEN) is a kind of aminoglycoside antibiotic with the adverse effect of nephrotoxicity. Currently, no effective measures against the nephrotoxicity have been approved. In the present study, epigallocatechin gallate (EG), a useful ingredient in green tea, was used to attenuate its nephrotoxicity. EG was shown to largely attenuate the renal damage and the increase of malondialdehyde (MDA) and the decrease of glutathione (GSH) in GEN-injected rats. In NRK-52E cells, GEN increased the cellular ROS in the early treatment phase and ROS remained continuously high from 1.5 H to 24 H. Moreover, EG alleviated the increase of ROS and MDA and the decrease of GSH caused by GEN. Furthermore, EG activated the protein levels of nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1). After the treatment of GEN, the protein level of cleaved-caspase-3, the flow cytometry analysis and the JC-1 staining, the protein levels of glutathione peroxidase 4 (GPX4) and SLC7A11, were greatly changed, indicating the occurrence of both apoptosis and ferroptosis, whereas EG can reduce these changes. However, when Nrf2 was knocked down by siRNA, the above protective effects of EG were weakened. In summary, EG attenuated GEN-induced nephrotoxicity by suppressing apoptosis and ferroptosis.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules27238564
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2008644-1
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  • 7
    Online Resource
    Online Resource
    A Missense Mutation c.1132G 〉 A in Fumarate Hydratase (FH) Leads to Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) Syndrome and Insights into Clinical Management in Uterine Leiomyomata
    MDPI AG ; 2023
    In:  Genes Vol. 14, No. 3 ( 2023-03-18), p. 744-
    Details
    In: Genes, MDPI AG, Vol. 14, No. 3 ( 2023-03-18), p. 744-
    Abstract: Background: HLRCC syndrome is a hereditary cancer predisposition syndrome caused by heterozygous germline pathogenic variant of the fumarate hydratase (FH) gene and characterized by cutaneous leiomyomas (CL), uterine leiomyomas (UL), and renal cell carcinoma (RCC). Loss of function variant of FH gene inactivates the Kreb’s cycle enzyme activity and predisposes individuals with such variant to the development of HLRCC. Methods: Next-generation sequencing (NGS) and Sanger confirmation were given to family members accessible. Following that, a functional study in vitro was performed to further confirm the pathogenicity of the variant. FH-Wild type (FH-WT) and FH-mutant (FH-MUT) (E378K) plasmid were constructed and transfected into 293T and uterine leiomyoma cell lines, respectively. Proliferation assessment was executed to show how this mutation affects the growth of uterine leiomyoma. qPCR and Western blotting were performed to investigate the change of transcription and translation of FH with mutation (E378K), and FH enzyme assay activity were tested in 293T cells with mutation and wild-type plasmids. Results: Here, we presented two families with the same missense variant (c.1132G 〉 A) that has not been reported as a germline mutation in hereditary uterine leiomyomas before and classified as VUS in gene databases. Our in vitro experiments supported the pathogenicity of this missense variant, especially in uterine leiomyomata. Conclusions: According to the American College of Medical Genetics (ACMG) guideline, the E378K variant was classified as likely pathogenic (with evidence PS4_support, PS3_support, PM2_support, PP1, PP3 and PP4 evidence). Further insights into clinical management in uterine leiomyomata were discussed and should be practiced in gynecological clinical settings.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes14030744
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2527218-4
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  • 8
    Online Resource
    Online Resource
    Greater Biofilm Formation and Increased Biodegradation of Polyethylene Film by a Microbial Consortium of Arthrobacter sp. and Streptomyces sp.
    MDPI AG ; 2020
    In:  Microorganisms Vol. 8, No. 12 ( 2020-12-12), p. 1979-
    Details
    In: Microorganisms, MDPI AG, Vol. 8, No. 12 ( 2020-12-12), p. 1979-
    Abstract: The widespread use of polyethylene (PE) mulch films has led to a significant accumulation of plastic waste in agricultural soils. The biodegradation of plastic waste by microorganisms promises to provide a cost-effective and environmentally-friendly alternative for mitigating soil plastic pollution. A large number of microorganisms capable of degrading PE have been reported, but degradation may be further enhanced by the cooperative activity of multiple microbial species. Here, two novel strains of Arthrobacter sp. and Streptomyces sp. were isolated from agricultural soils and shown to grow with PE film as a sole carbon source. Arthrobacter sp. mainly grew in the suspension phase of the culture, and Streptomyces sp. formed substantial biofilms on the surface of the PE film, indicating that these strains were of different metabolic types and occupied different microenvironments with contrasting nutritional access. Individual strains were able to degrade the PE film to some extent in a 90-day inoculation experiment, as indicated by decreased hydrophobicity, increased carbonyl index and CO2 evolution, and the formation of biofilms on the film surface. However, a consortium of both strains had a much greater effect on these degradation properties. Together, these results provide new insights into the mechanisms of PE biodegradation by a microbial consortium composed of different types of microbes with possible metabolic complementarities.
    Type of Medium: Online Resource
    ISSN: 2076-2607
    URL: Article
    DOI: 10.3390/microorganisms8121979
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2720891-6
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  • 9
    Online Resource
    Online Resource
    Dexmedetomidine Preserves Activity of Neurons in Primary Somatosensory Cortex Compared to Propofol and Ketamine
    MDPI AG ; 2022
    In:  Brain Sciences Vol. 12, No. 12 ( 2022-12-15), p. 1720-
    Details
    In: Brain Sciences, MDPI AG, Vol. 12, No. 12 ( 2022-12-15), p. 1720-
    Abstract: General anesthesia has been shown to induce significant changes in the functional connectivity of the cerebral cortex. However, traditional methods such as electroencephalography (EEG) or functional magnetic resonance imaging (fMRI) lack the spatial resolution to study the effects of general anesthesia on individual cortical neurons. This study aimed to use high-resolution two-photon imaging, which can provide single-neuron resolution, to investigate the characteristics of consciousness under general anesthesia. We used C57BL/6J and Thy1-GCamp6s mice and found that at similar levels of sedation, as measured by EEG, dexmedetomidine did not significantly inhibit the spontaneous activity of neuronal somata in the S1 cortex, but preserved the frequency of calcium events in neuronal spines. In contrast, propofol and ketamine dramatically inhibited the spontaneous activity of both neuronal somata and spines. The S1 cortex still responded to whisker stimulation under dexmedetomidine anesthesia, but not under propofol or ketamine anesthesia. Our results suggest that dexmedetomidine anesthesia has unique neuronal properties associated with its ability to facilitate easy awakening in the clinic. These findings provide insights into the development of more effective strategies for monitoring consciousness during general anesthesia.
    Type of Medium: Online Resource
    ISSN: 2076-3425
    URL: Article
    DOI: 10.3390/brainsci12121720
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2651993-8
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  • 10
    Online Resource
    Online Resource
    Integrated Omic Analysis of Human Plasma Metabolites and Microbiota in a Hypertension Cohort
    MDPI AG ; 2023
    In:  Nutrients Vol. 15, No. 9 ( 2023-04-25), p. 2074-
    Details
    In: Nutrients, MDPI AG, Vol. 15, No. 9 ( 2023-04-25), p. 2074-
    Abstract: Hypertension is closely related to metabolic dysregulation, which is associated with microbial dysbiosis and altered host–microbiota interactions. However, plasma metabolite profiles and their relationships to oral/gut microbiota in hypertension have not been evaluated in depth. Plasma, saliva, subgingival plaques, and feces were collected from 52 hypertensive participants and 24 healthy controls in a cross-sectional cohort. Untargeted metabolomic profiling of plasma was performed using high-performance liquid chromatography–mass spectrometry. Microbial profiling of oral and gut samples was determined via 16S rRNA and metagenomic sequencing. Correlations between metabolites and clinic parameters/microbiota were identified using Spearman’s correlation analysis. Metabolomic evaluation showed distinct clusters of metabolites in plasma between hypertensive participants and control participants. Hypertensive participants had six significantly increased and thirty-seven significantly decreased plasma metabolites compared to controls. The plasma metabolic similarity significantly correlated with the community similarity of microbiota. Both oral and gut microbial community composition had significant correlations with metabolites such as Sphingosine 1-phosphate, a molecule involved in the regulation of blood pressure. Plasma metabolites had a larger number of significant correlations with bacterial genera than fungal genera. The shared oral/gut bacterial genera had more correlations with metabolites than unique genera but shared fungal genera and metabolites did not show clear clusters. The hypertension group had fewer correlations between plasma metabolites and bacteria/fungi than controls at species level. The integrative analysis of plasma metabolome and oral/gut microbiome identified unreported alterations of plasma metabolites in hypertension and revealed correlations between altered metabolites and oral/gut microbiota. These observations suggested metabolites and microbiota may become valuable targets for therapeutic and preventive interventions of hypertension.
    Type of Medium: Online Resource
    ISSN: 2072-6643
    URL: Article
    DOI: 10.3390/nu15092074
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2518386-2
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