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Three-dimensional gold and its alloyed nanoporous structures possess high surface areas and strong local electric fields, rendering them ideal substrates for plasmonic molecular detection. Despite enhancing plasmonic properties and altering molecular interactions, the effect of alloy composition on molecular detection capability has not yet been explored. Here, we report molecular interactions between nanoporous gold alloys and charged molecules by controlling the alloy composition. We demonstrate enhanced adsorption of negatively charged molecules onto the alloy surface due to positively charged gold atoms and a shifted d-band center through charge transfer between gold and other metals. Despite similar EM field intensities, nanoporous gold with silver (Au/Ag) achieves SERS enhancement factors (EF) up to 6 orders of magnitude higher than those of other alloys for negatively charged molecules. Finally, nanoporous Au/Ag detects amyloid-beta at concentrations as low as approximately 1 fM, with SERS EF up to 10 orders of magnitude higher than that of a monolayer of Au nanoparticles.
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A comprehensive analysis of site-specific protein O-glycosylation is hindered by the absence of a consensus O-glycosylation motif, the diversity of O-glycan structures, and the lack of a universal enzyme that cleaves attached O-glycans. Here, we report the development of a robust O-glycoproteomic workflow for analyzing complex biological samples by combining four different strategies: removal of N-glycans, complementary digestion using O-glycoprotease (IMPa) with/without another protease, glycopeptide enrichment, and mass spectrometry with fragmentation of glycopeptides using stepped collision energy. Using this workflow, we cataloged 474 O-glycopeptides on 189 O-glycosites derived from 79 O-glycoproteins from human plasma. These data revealed O-glycosylation of several abundant proteins that have not been previously reported. Because many of the proteins that contained unannotated O-glycosylation sites have been extensively studied, we wished to confirm glycosylation at these sites in a targeted fashion. Thus, we analyzed selected purified proteins (kininogen-1, fetuin-A, fibrinogen, apolipoprotein E, and plasminogen) in independent experiments and validated the previously unknown O-glycosites.
Assuntos
Glicoproteínas , Proteoma , Proteômica , Fluxo de Trabalho , Humanos , Glicosilação , Glicoproteínas/metabolismo , Glicoproteínas/química , Proteômica/métodos , Proteoma/metabolismo , Proteoma/análise , Glicopeptídeos/análise , Glicopeptídeos/química , Glicopeptídeos/metabolismo , Cininogênios/metabolismo , Cininogênios/química , Polissacarídeos/metabolismo , Apolipoproteínas E/metabolismo , Apolipoproteínas E/química , Fibrinogênio/metabolismo , Fibrinogênio/química , alfa-2-Glicoproteína-HS/metabolismo , alfa-2-Glicoproteína-HS/análiseRESUMO
Hybridization of microbial cells with inorganic nanoparticles that could dramatically improve cellular functions such as electron transfer has been realized by the random attachment or stochastic entry of the nanoparticles. Clearly, the selective growth of inorganic nanoparticles on target functional organelles is ideal for such hybridization. Here, we report the selective growth of gold nanocrystals in the intermembrane space (IMS) of Escherichia coli by exploiting the electron transport chain (ETC). We systematically show that gold ions are permeated through porins in the outer membrane of E. coli and further reduced to gold nanocrystals by the ETC in live E. coli. We directly observe that the resulting gold nanocrystals exist only in the IMS by transmission electron microscopy measurements of cross-sectioned E. coli. Molecular dynamics simulations suggest that once gold ions are reduced to small nuclei by the ETC, the nuclei can be stably physisorbed onto ETC complexes, further supporting the ETC-mediated growth. Finally, we show that the ATP synthesis of E. coli where gold nanocrystals are formed in the IMS is up to 9 times higher than that of E. coli alone. We believe that our work can significantly contribute to not only improving microbial metabolic functions for biological energy conversion but also restoring physiological dysfunctions of microbial cells for biomedicine.
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Escherichia coli , Nanopartículas , Ouro/química , Elétrons , ÍonsRESUMO
Neural differentiation is crucial for advancing our understanding of the nervous system and developing treatments for neurological disorders. The advanced methods and the ability to manipulate the alignment, proliferation, and differentiation of stem cells are essential for studying neuronal development and synaptic interactions. However, the utilization of human induced pluripotent stem cells (iPSCs) for disease modeling of neurodegenerative conditions may be constrained by the prolonged duration and uncontrolled cell differentiation required for functional neural cell differentiation. Here, we developed a microfluidic chip to enhance the differentiation and maturation of specific neural lineages by placing aligned microelectrodes on the glass surface to regulate the neural differentiation of human iPSCs. The utilization of electrical stimulation (ES) in conjunction with neurotrophic factors (NF) significantly enhanced the efficiency in generating functional neurons from human iPSCs. We also observed that the simultaneous application of NF and ES to human iPSCs promoted their differentiation and maturation into functional neurons while increasing synaptic interactions. Our research demonstrated the effect of combining NF and ES on human iPSC-derived neural differentiation.
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Células-Tronco Pluripotentes Induzidas , Humanos , Microfluídica , Neurônios , Diferenciação Celular , Fatores de Crescimento Neural/metabolismo , EletrodosRESUMO
Ambient temperature affects flowering time in plants, and the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a crucial role in the response to changes in ambient temperature. SVP protein stability is regulated by the 26S proteasome pathway and decreases at high ambient temperature, but the details of SVP degradation are unclear. Here, we show that SVP degradation at high ambient temperature is mediated by the CULLIN3-RING E3 ubiquitin ligase (CRL3) complex in Arabidopsis thaliana. We identified a previously uncharacterized protein that interacts with SVP at high ambient temperature and contains a BTB/POZ domain. We named this protein LATE FLOWERING AT HIGH TEMPERATURE 1 (LFH1). Single mutants of LFH1 or CULLIN3A (CUL3A) showed late flowering specifically at 27°C. LFH1 protein levels increased at high ambient temperature. We found that LFH1 interacts with CUL3A in the cytoplasm and is important for SVP-CUL3A complex formation. Mutations in CUL3A and/or LFH1 led to increased SVP protein stability at high ambient temperature, suggesting that the CUL3-LFH1 complex functions in SVP degradation. Screening E2 ubiquitin-conjugating enzymes (UBCs) using RING-BOX PROTEIN 1 (RBX1), a component of the CRL3 complex, as bait identified UBC15. ubc15 mutants also showed late flowering at high ambient temperature. In vitro and in vivo ubiquitination assays using recombinant CUL3A, LFH1, RBX1, and UBC15 showed that SVP is highly ubiquitinated in an ATP-dependent manner. Collectively, these results indicate that the degradation of SVP at high ambient temperature is mediated by a CRL3 complex comprising CUL3A, LFH1, and UBC15.
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Proteínas de Arabidopsis , Arabidopsis , Ubiquitina-Proteína Ligases , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Ligases/metabolismo , Temperatura , Ubiquitinas/metabolismo , Ubiquitina-Proteína Ligases/metabolismoRESUMO
Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.
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Ouro , Hidrodinâmica , Nanotubos , SARS-CoV-2 , Dióxido de Silício , Ouro/química , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/genética , Dióxido de Silício/química , Nanotubos/química , COVID-19/virologia , COVID-19/diagnóstico , Reação em Cadeia da Polimerase/métodos , Humanos , Limite de DetecçãoRESUMO
The utilization of multi-omics research has gained popularity in clinical investigations. However, effectively managing and merging extensive and diverse datasets presents a challenge due to its intricacy. This research introduces a Multi-Omics Analysis Sandbox Toolkit, an online platform designed to facilitate the exploration, integration, and visualization of datasets ranging from single-omics to multi-omics. This platform establishes connections between clinical data and omics information, allowing for versatile analysis and storage of both single and multi-omics data. Additionally, users can repeatedly utilize and exchange their findings within the platform. This toolkit offers diverse alternatives for data selection and gene set analysis. It also presents visualization outputs, potential candidates, and annotations. Furthermore, this platform empowers users to collaborate by sharing their datasets, analyses, and conclusions with others, thus enhancing its utility as a collaborative research tool. This Multi-Omics Analysis Sandbox Toolkit stands as a valuable asset in comprehensively grasping the influence of diverse factors in diseases and pinpointing potential biomarkers.
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NSCLC, the most common type of lung cancer, is often diagnosed late due to minimal early symptoms. Its high risk of recurrence or metastasis post-chemotherapy makes DC-based immunotherapy a promising strategy, offering targeted cancer destruction, low side effects, memory formation, and overcoming the immune evasive ability of cancers. However, the limited response to DCs pulsed with single antigens remains a significant challenge. To overcome this, we enhanced DC antigen presentation by pulsing with TAAs. Our study focused on enhancing DC-mediated immune response specificity and intensity by combinatorial pulsing of TAAs, selected for their prevalence in NSCLC. We selected four types of TAAs expressed in NSCLC and pulsed DCs with the optimal combination. Next, we administered TAAs-pulsed DCs into the LLC1 mouse model to evaluate their anti-tumor efficacy. Our results showed that TAAs-pulsed DCs significantly reduced tumor size and promoted apoptosis in tumor tissue. Moreover, TAAs-pulsed DCs significantly increased total T cells in the spleen compared to the unpulsed DCs. Additionally, in vitro stimulation of splenocytes from the TAAs-pulsed DCs showed notable T-cell proliferation and increased IFN-γ secretion. Our findings demonstrate the potential of multiple TAA pulsing to enhance the antigen-presenting capacity of DCs, thereby strengthening the immune response against tumors.
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The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.