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1.
Aging Dis ; 12(7): 1835-1849, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34631224

RESUMO

Recent evidence indicates that collateral circulation is critical for the outcome of ischemic stroke. DL-3-n-butylphthalide (NBP), a synthesized compound based on an extract from seeds of celery Apium graveolens Linn, has been used as a therapeutic drug, showing multiple neuroprotective and regenerative activities. A potential effect of NBP on collateral arterial regulation is unknown. We examined the effects of NBP on arteriogenesis of collateral arteries in vitro and a mouse ischemic stroke model. In cultures of mouse iPS cell-derived vascular progenitors, NBP (10 µM) significantly increased α-smooth muscle actin (αSMA)/CD-31 co-labeled cells and the expression of newly formed vasculature marker PDGFRα. A sensorimotor cortex ischemia was induced in transgenic mice expressing αSMA-GFP that allowed direct observation of arterial vasculatures in brain regions. NBP (80 mg/kg) was intranasally delivered 1 hr after stroke and once daily for 14 days. To label proliferating cells, 5-Bromo-2'-deoxyuridine (BrdU, 50 mg/kg, i.p.) was administrated every day from 3 days after stroke. Western blotting of peri-infarct tissue detected increased expressions of VEGF, Ang-1 and reduced nNOS level in NBP-treated mice. The NBP treatment significantly increased αSMA/BrdU co-labeled cells, the diameter of ipsilateral collaterals, and arterial area in ischemic and peri-infarct regions examined 14 days after stroke. Examined 3 days after stroke, NBP prevented functional deficits in the cylinder test and corner test. The NBP treatment of 14 days improved the local cerebral blood flow (LCBF) and functional performance in multiple tests. Thus, NBP promotes collateriogenesis, short and long-term structural and functional improvements after ischemic stroke.

2.
Fish Physiol Biochem ; 2021 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-34633578

RESUMO

At present, due to the influence of global warming, seasonal change, diurnal variation, and eutrophication of the water body, hypoxia has become one of the major factors limiting the stable development of cobia (Rachycentron canadum) culture. In this study, the miRNAs involved in hypoxia stress were screened, and the target genes of miRNAs were annotated and analyzed. The results showed that a total of 184 conservative microRNA (miRNA) and 121 newly predicted miRNA were obtained by sequencing the liver of control (C) and hypoxic (dissolved oxygen, DO (2.64 ± 0.25) mg/L; 3 h) (S) groups. The pathways involved in energy metabolism included starch and sucrose metabolism (ko00500), glycosaminoglycan degradation (ko00531), and galactose metabolism (ko00052). The results indicate that the body maintains physiological activities by regulating some important pathways at the transcriptional level under hypoxia stress, such as the conversion of aerobic metabolism and anaerobic metabolism, the reduction of energy consumption, and the promotion of red blood cell proliferation to maintain the homeostasis of the body.

3.
Front Genet ; 12: 737965, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34603396

RESUMO

Liver hepatocellular carcinoma (LIHC) is a primary malignancy, and there is a lack of effective treatment for advanced patients. Although numerous studies exist to reveal the carcinogenic mechanism of LIHC, few studies have integrated multi-omics data to systematically analyze pathogenesis and reveal potential therapeutic targets. Here, we integrated genomic variation data and RNA-seq profiles obtained by high-throughput sequencing to define high- and low-genomic instability samples. The mutational landscape was reported, and the advanced patients of LIHC were characterized by high-genomic instability. We found that the tumor microenvironment underwent metabolic reprograming driven by mutations accumulate to satisfy tumor proliferation and invasion. Further, the co-expression network identifies three mutant long non-coding RNAs as potential therapeutic targets, which can promote tumor progression by participating in specific carcinogenic mechanisms. Then, five potential prognostic markers (RP11-502I4.3, SPINK5, CHRM3, SLC5A12, and RP11-467L13.7) were identified by examining the association of genes and patient survival. By characterizing the immune landscape of LIHC, loss of immunogenicity was revealed as a key factor of immune checkpoint suppression. Macrophages were found to be significantly associated with patient risk scores, and high levels of macrophages accelerated patient mortality. In summary, the mutation-driven mechanism and immune landscape of LIHC revealed by this study will serve precision medicine.

4.
Biomed Res Int ; 2021: 9921195, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34604388

RESUMO

Hepatocellular carcinoma (HCC) is one of the most common and lethal malignancies worldwide. Although there have been extensive studies on the molecular mechanisms of its carcinogenesis, FDA-approved drugs for HCC are rare. Side effects, development time, and cost of these drugs are the major bottlenecks, which can be partially overcome by drug repositioning. In this study, we developed a computational framework to study the mechanisms of HCC carcinogenesis, in which drug perturbation-induced gene expression signatures were utilized for repositioning of potential drugs. Specifically, we first performed differential expression analysis and coexpression network module analysis on the HCC dataset from The Cancer Genome Atlas database. Differential gene expression analysis identified 1,337 differentially expressed genes between HCC and adjacent normal tissues, which were significantly enriched in functions related to various pathways, including α-adrenergic receptor activity pathway and epinephrine binding pathway. Weighted gene correlation network analysis (WGCNA) suggested that the number of coexpression modules was higher in HCC tissues than in normal tissues. Finally, by correlating differentially expressed genes with drug perturbation-related signatures, we prioritized a few potential drugs, including nutlin and eribulin, for the treatment of hepatocellular carcinoma. The drugs have been reported by a few experimental studies to be effective in killing cancer cells.

5.
Preprint em Inglês | bioRxiv | ID: ppbiorxiv-465476

RESUMO

Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.

6.
Preprint em Inglês | bioRxiv | ID: ppbiorxiv-464595

RESUMO

Spike-mediated entry of SARS-CoV-2 into human airway epithelial cells is an attractive therapeutic target for COVID-19. In addition to protein receptors, the SARS-CoV-2 spike (S) protein also interacts with heparan sulfate, a negatively charged glycosaminoglycan (GAG) attached to certain membrane proteins on the cell surface. This interaction facilitates the engagement of spike with a downstream receptor to promote viral entry. Here, we show that Mitoxantrone, an FDA-approved topoisomerase inhibitor, targets a spike-GAG complex to compromise the fusogenic function of spike in viral entry. As a single agent, Mitoxantrone inhibits the infection of an authentic SARS-CoV-2 strain in a cell-based model and in human lung EpiAirway 3D tissues. Gene expression profiling supports the plasma membrane as a major target of Mitoxantrone but also underscores an undesired activity targeting nucleosome dynamics. We propose that Mitoxantrone analogs bearing similar GAG-binding activities but with reduced affinity for DNA topoisomerase may offer an alternative therapy to overcome breakthrough infections in the post-vaccine era.

7.
Preprint em Inglês | bioRxiv | ID: ppbiorxiv-463106

RESUMO

Effective small molecule therapies to combat the SARS-CoV-2 infection are still lacking as the COVID-19 pandemic continues globally. High throughput screening assays are needed for lead discovery and optimization of small molecule SARS-CoV-2 inhibitors. In this work, we have applied viral pseudotyping to establish a cell-based SARS-CoV-2 entry assay. Here, the pseudotyped particles (PP) contain SARS-CoV-2 spike in a membrane enveloping both the murine leukemia virus (MLV) gag-pol polyprotein and luciferase reporter RNA. Upon addition of PP to HEK293-ACE2 cells, the SARS-CoV-2 spike protein binds to the ACE2 receptor on the cell surface, resulting in priming by host proteases to trigger endocytosis of these particles, and membrane fusion between the particle envelope and the cell membrane. The internalized luciferase reporter gene is then expressed in cells, resulting in a luminescent readout as a surrogate for spike-mediated entry into cells. This SARS-CoV-2 PP entry assay can be executed in a biosafety level 2 containment lab for high throughput screening. From a collection of 5,158 approved drugs and drug candidates, our screening efforts identified 7 active compounds that inhibited the SARS-CoV-2-S PP entry. Of these seven, six compounds were active against live replicating SARS-CoV-2 virus in a cytopathic effect assay. Our results demonstrated the utility of this assay in the discovery and development of SARS-CoV-2 entry inhibitors as well as the mechanistic study of anti-SARS-CoV-2 compounds. Additionally, particles pseudotyped with spike proteins from SARS-CoV-2 B.1.1.7 and B.1.351 variants were prepared and used to evaluate the therapeutic effects of viral entry inhibitors.

8.
Front Plant Sci ; 12: 721203, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34691102

RESUMO

Multiplex genome-editing (MGE) technologies are recently developed versatile bioengineering tools for modifying two or more specific DNA loci in a genome with high precision. These genome-editing tools have greatly increased the feasibility of introducing desired changes at multiple nucleotide levels into a target genome. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) [CRISPR/Cas] system-based MGE tools allow the simultaneous generation of direct mutations precisely at multiple loci in a gene or multiple genes. MGE is enhancing the field of plant molecular biology and providing capabilities for revolutionizing modern crop-breeding methods as it was virtually impossible to edit genomes so precisely at the single base-pair level with prior genome-editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Recently, researchers have not only started using MGE tools to advance genome-editing applications in certain plant science fields but also have attempted to decipher and answer basic questions related to plant biology. In this review, we discuss the current progress that has been made toward the development and utilization of MGE tools with an emphasis on the improvements in plant biology after the discovery of CRISPR/Cas9. Furthermore, the most recent advancements involving CRISPR/Cas applications for editing multiple loci or genes are described. Finally, insights into the strengths and importance of MGE technology in advancing crop-improvement programs are presented.

9.
Sci Rep ; 11(1): 20244, 2021 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-34642373

RESUMO

Due to the increase in computing power, it is possible to improve the feature extraction and data fitting capabilities of DNN networks by increasing their depth and model complexity. However, the big data and complex models greatly increase the training overhead of DNN, so accelerating their training process becomes a key task. The Tianhe-3 peak speed is designed to target E-class, and the huge computing power provides a potential opportunity for DNN training. We implement and extend LeNet, AlexNet, VGG, and ResNet model training for a single MT-2000+ and FT-2000+ compute nodes, as well as extended multi-node clusters, and propose an improved gradient synchronization process for Dynamic Allreduce communication optimization strategy for the gradient synchronization process base on the ARM architecture features of the Tianhe-3 prototype, providing experimental data and theoretical basis for further enhancing and improving the performance of the Tianhe-3 prototype in large-scale distributed training of neural networks.

11.
mSystems ; : e0136820, 2021 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-34546068

RESUMO

Rice paddy soil-associated microbiota participate in biogeochemical processes that underpin rice yield and soil sustainability, yet continental-scale biogeographic patterns of paddy soil microbiota remain elusive. The soil bacteria of four typical Chinese rice-growing regions were characterized and compared to those of nonpaddy soils. The paddy soil bacteria were significantly less diverse, with unique taxonomic and functional composition, and harbored distinct cooccurrence network topology. Both stochastic and deterministic processes shaped soil bacteria assembly, but paddy samples exhibited a stronger deterministic signature than nonpaddy samples. Compared to other environmental factors, climatic factors such as mean monthly precipitation and mean annual temperature described most of the variance in soil bacterial community structure. Cooccurrence network analysis suggests that the continental biogeographic variance in bacterial community structure was described by the competition between two mutually exclusive bacterial modules in the community. Keystone taxa identified in network models (Anaerolineales, Ignavibacteriae, and Deltaproteobacteria) were more sensitive to changes in environmental factors, leading us to conclude that environmental factors may influence paddy soil bacterial communities via these keystone taxa. Characterizing the uniqueness of bacterial community patterns in paddy soil (compared to nonpaddy soils) at continental scales is central to improving crop productivity and resilience and to sustaining agricultural soils. IMPORTANCE Rice fields provide food for over half of the world's human population. The ecology of paddy soil microbiomes is shaped by human activities, which can have a profound impact on rice yield, greenhouse gas emissions, and soil health. Investigations of the soil bacteria in four typical Chinese rice-growing regions showed that (i) soil bacterial communities maintain highly modularized species-to-species network structures; (ii) community patterns were shaped by the balance of integrated stochastic and deterministic processes, in which homogenizing selection and dispersal limitation dominate; and (iii) deterministic processes and climatic and edaphic factors influence community patterns mainly by their impact on highly connected nodes (i.e., keystone taxa) in networks. Characterizing the unique ecology of bacterial community patterns in paddy soil at a continental scale may lead to improved crop productivity and resilience, as well as sustaining agricultural soils.

12.
Artigo em Inglês | MEDLINE | ID: mdl-34554612

RESUMO

The stepwise chemical reduction of molecular warped nanographene (WNG) having a negatively curved π -surface and defined C 80 H 30 composition with Cs metal used as the reducing and complexing agent allowed the isolation of three different reduced states with one, two, and three electrons added to its π -conjugated system. This provided a unique series of contorted nanosized carbanions with increasing negative charge for in-depth structural analysis of consequences of controlled electron charging of non-planar nanographenes, using X-ray crystallographic and computational tools. The 3D molecular electrostatic potential (MEP) maps identified the negative charge localization at the central part of the WNG surface where selective coordination of Cs + ions has been confirmed crystallographically. In-depth theoretical investigation revealed a complex response of WNG to the stepwise electron acquisition. The extended and contorted π -surface of WNG undergoes subtle swinging distortions that are accompanied by notable changes in the electronic structure and site-dependent aromaticity of the resulting nanosized carbanions.

13.
Pharmazie ; 76(9): 422-427, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34481532

RESUMO

MicroRNAs are emerging as important endogenous regulators of gene function and they are playing an important role in the occurrence and development of cancer. They are also regarded as robust biomarkers of cancer diagnosis and prognosis. Hepatocellular carcinoma (HCC) is a common and complex human malignancy with high mortality and morbidity in the world. MicroRNA-122 (miR-122) is a liver-specific microRNA and is closely associated with HCC metastasis, which makes miR-122 a promising target for drug design and development. In this study, we performed a cell-based screening method for discovering miR-122 activators and found that oleanolic acid (OA), a natural pentacyclic triterpene, specifically increased miR-122 expression in a concentration-dependent manner. Two HCC cell lines (HepG2 and Sk-hep-1 cells) were used to evaluate the effect of OA on cell migration and invasion abilities. The results indicated that OA attenuated the migration and invasion abilities of HCC cells by upregulating miR-122 expression. In addition, OA increased the expression of E-cadherin and decreased the expression of ß-catenin, N-cadherin and vimentin. After knocking down miR-122 with miR-122 inhibitor, we found that the effect of OA on these epithelial-to-mesenchymal transition (EMT) related molecules was significantly weakened, indicating OA exhibited anti-EMT effect by increasing the expression of miR-122. These finding may help to better understand the molecular mechanism of OA's anti-metastasis activity.

14.
Bioresour Technol ; 341: 125822, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34467889

RESUMO

This study discovered one nitrate-calcium-based anammox start-up pathway. Compared with control, the start-up time of anammox was saved by 33.3%, and the average total nitrogen removal efficiency increased from 29.6% to 53.7% during the start-up. Besides, the continuous nitrite accumulation (1.18 mg/L) and a marked increase in the relative abundance of denitrifying and anammox bacteria were observed in the only Ca(NO3)2-added group. These results suggested that calcium nitrate induced partial denitrification to provide nitrite for anammox. Additionally, the role of dissimilatory nitrate reduction to ammonium (DNRA) in the Ca(NO3)2-added systems also deserved attention, for the contribution of DNRA to nitrate removal as well as the relative abundance of DNRA bacteria were both increased for the Ca(NO3)2-added groups. These results suggested that a mutualistic symbiosis among denitrification, DNRA and anammox exists in the calcium nitrate-added systems, which may explain the reason for acceleration of anammox start-up by adding calcium nitrate.


Assuntos
Compostos de Amônio , Anaerobiose , Compostos de Cálcio , Desnitrificação , Nitratos , Nitrogênio , Oxirredução
15.
Elife ; 102021 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-34569935

RESUMO

Keratinocytes, the predominant cell type of the epidermis, migrate to reinstate the epithelial barrier during wound healing. Mechanical cues are known to regulate keratinocyte re-epithelialization and wound healing however, the underlying molecular transducers and biophysical mechanisms remain elusive. Here, we show through molecular, cellular and organismal studies that the mechanically-activated ion channel PIEZO1 regulates keratinocyte migration and wound healing. Epidermal-specific Piezo1 knockout mice exhibited faster wound closure while gain-of-function mice displayed slower wound closure compared to littermate controls. By imaging the spatiotemporal localization dynamics of endogenous PIEZO1 channels we find that channel enrichment at some regions of the wound edge induces a localized cellular retraction that slows keratinocyte collective migration. In migrating single keratinocytes, PIEZO1 is enriched at the rear of the cell, where maximal retraction occurs, and we find that chemical activation of PIEZO1 enhances retraction during single as well as collective migration. Our findings uncover novel molecular mechanisms underlying single and collective keratinocyte migration that may suggest a potential pharmacological target for wound treatment. More broadly, we show that nanoscale spatiotemporal dynamics of Piezo1 channels can control tissue-scale events, a finding with implications beyond wound healing to processes as diverse as development, homeostasis, disease and repair.

16.
Molecules ; 26(18)2021 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-34577182

RESUMO

Despite remarkable progress in photoconversion efficiency, the toxicity of lead-based hybrid perovskites remains an important issue hindering their applications in consumer optoelectronic devices, such as solar cells, LED displays, and photodetectors. For that reason, lead-free metal halide complexes have attracted great attention as alternative optoelectronic materials. In this work, we demonstrate that reactions of two aromatic diamines with iodine in hydroiodic acid produced phenylenediammonium (PDA) and N,N-dimethyl-phenylenediammonium (DMPDA) triiodides, PDA(I3)2⋅2H2O and DMPDA(I3)I, respectively. If the source of bismuth was added, they were converted into previously reported PDA(BiI4)2⋅I2 and new (DMPDA)2(BiI6)(I3)⋅2H2O, having band gaps of 1.45 and 1.7 eV, respectively, which are in the optimal range for efficient solar light absorbers. All four compounds presented organic-inorganic hybrids, whose supramolecular structures were based on a variety of intermolecular forces, including (N)H⋅⋅⋅I and (N)H⋅⋅⋅O hydrogen bonds as well as I⋅⋅⋅I secondary and weak interactions. Details of their molecular and supramolecular structures are discussed based on single-crystal X-ray diffraction data, thermal analysis, and Raman and optical spectroscopy.

17.
Inorg Chem ; 60(19): 14844-14853, 2021 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-34524808

RESUMO

The monoanion of triphenylene (C18H12, 1) was generated in THF using several alkali metals (Na, K, Rb, and Cs) as reducing agents and crystallized with the corresponding cations in the presence of 18-crown-6 ether. The UV-vis spectroscopy points to the metal-dependent coordination environment of the triphenylene monoanion-radicals, 1·-, in solution. The X-ray diffraction characterization confirmed the formation of a solvent-separated ion pair (SSIP) with sodium ions, [{Na+(18-crown-6)(THF)2}(1·-)] (2), and three contact-ion pair (CIP) complexes formed by larger alkali metal ions, [{K+(18-crown-6)}(1·-)] (3), [{Rb+(18-crown-6)}(1·-)] (4), and [{Cs+(18-crown-6)}(1·-)] (5). Structural analysis of the series reveals a notable geometry perturbation of the triphenylene framework in 2 caused by one-electron acquisition, which is further enhanced by direct metal binding in 3-5. This has been correlated with the aromaticity changes and charge redistribution upon one-electron reduction of 1, as revealed by the computational studies. The EPR spectroscopy and magnetic susceptibility measurements confirm antiferromagnetic interactions corresponding to an S = 1/2 system in the solid state. The magnetic behavior of 3-5 correlates with the arrangement of triphenylene radicals in the crystal structures. All three compounds exhibit antiferromagnetic (AFM) interactions between S = 1/2 radicals in the solid state, but the exchange coupling in 4 and 5 is notably stronger than that in 3, which leads to AFM ordering at 3.8 K in 4 and at 2.0 K in 5. The magnetic phase transitions in 4 and 5 can be interpreted as originating from interactions between the chains of the AFM-coupled S = 1/2 radicals.

18.
Mol Biol Rep ; 48(10): 6897-6909, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34453674

RESUMO

BACKGROUND: Environmental hypoxia affects the survival and development of organisms. It is also an important environmental factor that leads to oxidative damage. Hypoxia is a condition in which tissues are deprived of oxygen; reoxygenation is the phenomenon in which hypoxic tissues are exposed to oxygen. Hypoxia-reoxygenation is vital in pathogenesis, where the production of reactive oxygen species and antioxidant disparity significantly contribute to disease progression, and it is one of the most common physiological stressors in the aquaculture industry. METHODS AND RESULTS: In this study, the full length of complementary DNA (cDNA) of the manganese superoxide dismutase (Mn-SOD) gene of healthy cobia Rachycentron canadum was analysed using rapid amplification of cDNA ends. The real-time quantitative Polymerase Chain Reaction was used to measure the expression levels of Mn-SOD mRNAs in various tissues (heart, muscle, brain, liver, kidney, gill, intestine, and spleen). The 2-ΔΔCT method was used to performed the expression analysis. The experimental data were analysed using SPSS ver. 19.0 ( https://spss.software.informer.com/19.0/ ). P < 0.05 and P < 0.01 were set as significant differences. The values were articulated as mean ± standard deviation. The Mn-SOD gene cDNA sequence was 1209 bp long, including a 684 bp open reading frame, 42 bp 5'UTR and 483 bp 3'UTR, encoding 227 amino acids. Under hypoxia-reoxygen stress, the expression of Mn-SOD in brain tissue was significantly lower than in the control group after 8 h of reoxygenation and higher than the control group after 24 h. Hypoxia and subsequent reoxygenation triggered a disturbance in antioxidant homeostasis, displayed in the modification of GPx expression/activity in the liver: GPx was improved. CONCLUSIONS: These results provide valuable information on the role of Mn-SOD regulation in oxidative stress caused by hypoxia.

19.
Angew Chem Int Ed Engl ; 60(43): 23289-23298, 2021 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-34436811

RESUMO

Multi-scale calcium (Ca2+ ) dynamics, exhibiting wide-ranging temporal kinetics, constitutes a ubiquitous mode of signal transduction. We report a novel endoplasmic-reticulum (ER)-targeted Ca2+ indicator, R-CatchER, which showed superior kinetics in vitro (koff ≥2×103  s-1 , kon ≥7×106  M-1 s-1 ) and in multiple cell types. R-CatchER captured spatiotemporal ER Ca2+ dynamics in neurons and hotspots at dendritic branchpoints, enabled the first report of ER Ca2+ oscillations mediated by calcium sensing receptors (CaSRs), and revealed ER Ca2+ -based functional cooperativity of CaSR. We elucidate the mechanism of R-CatchER and propose a principle to rationally design genetically encoded Ca2+ indicators with a single Ca2+ -binding site and fast kinetics by tuning rapid fluorescent-protein dynamics and the electrostatic potential around the chromophore. The design principle is supported by the development of G-CatchER2, an upgrade of our previous (G-)CatchER with improved dynamic range. Our work may facilitate protein design, visualizing Ca2+ dynamics, and drug discovery.

20.
Cancer Rep (Hoboken) ; : e1522, 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34383385

RESUMO

BACKGROUND: Osteosarcoma is the most common primary bone tumor. The survival rate of osteosarcoma patients has not significantly increased in the past decades. Uncovering the mechanisms of malignancy, progression, and metastasis will shed light on the development of new therapeutic targets and treatment for osteosarcoma. AIM: The aim of this study is to identify potential osteosarcoma biomarker and/or therapeutic targets by using integrated bioinformatics analysis. METHODS AND RESULTS: We utilized existing gene expression datasets to identify differential expressed genes (DEGs) that could serve as osteosarcoma biomarkers or even as therapeutic targets. We found 48 DEGs were overlapped in three datasets. Among these 48 DEGs, PSMD14 was on the top of the up-regulated gene list. We further found that higher PSMD14 expression was correlated with higher risk group (younger age group, ≤20.83 years of age), metastasis within 5 years and higher grade of tumor. Higher PSMD14 expression in osteosarcoma had positive correlation with higher infiltration of CD8+ T cells, neutrophils and myeloid dendritic cells. Kaplan-Myer survival data further revealed that higher expression of PSMD14 predicted significantly worse prognosis (p = .013). Gene set enrichment analysis was further performed for the DEGs related to PSMD14 in osteosarcoma. We found that lower PSMD14 expression group had more immune responses such as interferon γ, α responses, inflammation response etc. However, the higher PSMD14 expression group had more cell proliferation-related biological processes, such as G2M checkpoints and Myc targets. Through establishing protein-protein interaction networks using PSMD14 related DEGs, we identified 10 hub genes that were all ribosomal proteins. These hub genes may play roles in osteosarcoma tumorigenesis, progression and/or metastasis. CONCLUSION: We identified PSMD14 gene as a possible osteosarcoma biomarker, and/or a possible therapeutic target.

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