RESUMO
Assessing marker genes from all cell clusters can be time-consuming and lack systematic strategy. Streamlining this process through a unified computational platform that automates identification and benchmarking will greatly enhance efficiency and ensure a fair evaluation. We therefore developed a novel computational platform, cellMarkerPipe ( https://github.com/yao-laboratory/cellMarkerPipe ), for automated cell-type specific marker gene identification from scRNA-seq data, coupled with comprehensive evaluation schema. CellMarkerPipe adaptively wraps around a collection of commonly used and state-of-the-art tools, including Seurat, COSG, SC3, SCMarker, COMET, and scGeneFit. From rigorously testing across diverse samples, we ascertain SCMarker's overall reliable performance in single marker gene selection, with COSG showing commendable speed and comparable efficacy. Furthermore, we demonstrate the pivotal role of our approach in real-world medical datasets. This general and opensource pipeline stands as a significant advancement in streamlining cell marker gene identification and evaluation, fitting broad applications in the field of cellular biology and medical research.
Assuntos
Análise de Célula Única , Software , Transcriptoma , Análise de Célula Única/métodos , Humanos , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Biomarcadores , Marcadores GenéticosRESUMO
Assessing marker genes from all cell clusters can be time-consuming and lack systematic strategy. Streamlining this process through a unified computational platform that automates identification and benchmarking will greatly enhance efficiency and ensure a fair evaluation. We therefore developed a novel computational platform, cellMarkerPipe (https://github.com/yao-laboratory/cellMarkerPipe), for automated cell-type specific marker gene identification from scRNA-seq data, coupled with comprehensive evaluation schema. CellMarkerPipe adaptively wraps around a collection of commonly used and state-of-the-art tools, including Seurat, COSG, SC3, SCMarker, COMET, and scGeneFit. From rigorously testing across diverse samples, we ascertain SCMarker's overall reliable performance in single marker gene selection, with COSG showing commendable speed and comparable efficacy. Furthermore, we demonstrate the pivotal role of our approach in real-world medical datasets. This general and opensource pipeline stands as a significant advancement in streamlining cell marker gene identification and evaluation, fitting broad applications in the field of cellular biology and medical research.
RESUMO
Electromechanical phenomena in two-dimensional (2D) materials can be related to sizable electric polarizations and switchable spontaneous ferroelasticity, allowing them to be used as miniaturized electronic and memory devices. Even in a parent centrosymmetric (nonpolar) ferroelastic (FE) material, non-zero polarization can be produced around the FE domain wall, owing to the strain-gradient-induced flexoelectricity. Compared with the negligibly weak flexoelectric effect in bulk compounds, significant electric polarizations can be expected in 2D FE materials that sustain a large elastic strain and a strain gradient. Using first-principles calculations, we predict that spontaneous 2D ferroelasticity and domain-wall flexoelectricity can be simultaneously realized in synthetic HgX2 (X = Br or I) monolayers. The FE phase renders three oriented variants, which form FE domain walls with a large strain gradient and the associated domain-wall flexoelectric polarizations. Our thermodynamic stability analysis and kinetic barrier simulations allow us to manipulate the domain-wall flexoelectricity via applied mechanical stress, thereby enabling future electromechanical applications in nanoelectronics.
RESUMO
Domain features and domain walls in lead halide perovskites (LHPs) have attracted broad interest due to their potential impact on optoelectronic properties of this unique class of solution-processable semiconductors. Using nonpolarized light and simple imaging configurations, ferroelastic twin domains and their switchings through multiple consecutive phase transitions are directly visualized. This direct optical contrast originates from finite optical reflections at the wall interface between two compositionally identical, orientationally different, optically anisotropic domains inside the material bulk. The findings show these domain walls serve as internal reflectors and steer energy transport inside halide perovskites optically. First-principles calculations show universal low domain-wall energies and modest energy barriers of domain switching, confirming their prevalent appearance, stable presence, and facile moving observed in the experiments. The generality of ferroelasticity in halide perovskites stems from their soft bonding characteristics. This work shows the feasibility of using LHP twin domain walls as optical guides of internal photoexcitations, capable of nonvolatile on-off switching and tunable positioning endowed by their universal ferroelasticity.
RESUMO
Semimetallic two-dimensional (2D) Dirac materials beyond graphene, especially 2D materials with robust Dirac points against the spin-orbit coupling (SOC), are still highly sought. Herein, we theoretically demonstrate the InBi monolayer as a long-sought 2D Dirac material whose exotic Dirac Fermionic states cannot be gapped out by SOC. The InBi monolayer with the litharge crystal structure possesses not only 4-fold band degeneracy, linear energy dispersion, and ultrahigh Fermi velocity in the order of 105 m/s, but also spontaneous ferroelasticity that can lead to the orthorhombic lattice deformation and semimetallic electronic structure. Specifically, the symmetry protected spin-orbit Dirac points in 2D InBi are located at the Brillouin Zone (BZ) boundary and near the Fermi level in energy. More importantly, with coexisting spin-orbit Dirac points and spontaneous ferroelasticity, the InBi monolayer exhibits an additional advantage for engineering Dirac Fermionic states by ferroelastic (FE) strain. Energy levels of Dirac points are strongly coupled to FE strain, and the semimetallic electronic structure of the InBi monolayer is also susceptible to the FE strain induced carrier self-doping effect. Depending on the strain orientation within the InBi monolayer, electron and hole Fermi pockets will develop along the two planar directions, leading to the characteristic transport coefficients (as evidenced by our transport simulations based on Boltzmann formalism) for future experimental detection. FE strain tunable Dirac Fermionic states together with the carrier self-doping effect will benefit future development of ultrathin electronic devices with both high carrier mobility and controllable charge conductivities.
RESUMO
Deciphering the atomic and electronic structures of interfaces is key to developing state-of-the-art perovskite semiconductors. However, conventional characterization techniques have limited previous studies mainly to grain-boundary interfaces, whereas the intragrain-interface microstructures and their electronic properties have been much less revealed. Herein using scanning transmission electron microscopy, we resolved the atomic-scale structural information on three prototypical intragrain interfaces, unraveling intriguing features clearly different from those from previous observations based on standalone films or nanomaterial samples. These intragrain interfaces include composition boundaries formed by heterogeneous ion distribution, stacking faults resulted from wrongly stacked crystal planes, and symmetrical twinning boundaries. The atomic-scale imaging of these intragrain interfaces enables us to build unequivocal models for the ab initio calculation of electronic properties. Our results suggest that these structure interfaces are generally electronically benign, whereas their dynamic interaction with point defects can still evoke detrimental effects. This work paves the way toward a more complete fundamental understanding of the microscopic structure-property-performance relationship in metal halide perovskites.
RESUMO
Perinereis aibuhitensis peptide (PAP) is a decapeptide (Ile-Glu-Pro-Gly-Thr-Val-Gly-Met-Met-Phe, IEPGTVGMMF) with anticancer activity that was purified from an enzymatic hydrolysate of Perinereis aibuhitensis. In the present study, the anticancer effect of PAP on H1299 cell proliferation was investigated. Our results showed that PAP promoted apoptosis and inhibited the proliferation of H1299 cells in a time- and dose-dependent manner. When the PAP concentration reached 0.92 mM, more than 95% of treated cells died after 72 h of treatment. Changes in cell morphology were further analyzed using an inverted microscope and AO/EB staining and flow cytometry was adopted for detecting apoptosis and cell cycle phase. The results showed that the early and late apoptosis rates of H1299 cells increased significantly after treatment with PAP and the total apoptosis rate was significantly higher than that of the control group. Moreover, after treatment with PAP, the number of cells in the S phase of cells was significantly reduced and the ability for the cells to proliferate was also reduced. H1299 cells were arrested in the G2/M phase and cell cycle progression was inhibited. Furthermore, the results of western blotting showed that nm23-H1 and vascular endothelial growth factor (VEGF) protein levels decreased in a dose-dependent manner, while the pro-apoptotic protein and anti-apoptotic protein ratios and the level of apoptosis-related caspase protein increased in a dose-dependent manner. In conclusion, our results indicated that PAP, as a natural marine bioactive substance, inhibited proliferation and induced apoptosis of human lung cancer H1299 cells. PAP is likely to be exploited as the functional food or adjuvant that may be used for prevention or treatment of human non-small cell lung cancer in the future.
Assuntos
Antineoplásicos/farmacologia , Oligopeptídeos/farmacologia , Poliquetos/química , Sequência de Aminoácidos , Animais , Antineoplásicos/isolamento & purificação , Apoptose/efeitos dos fármacos , Proteínas Reguladoras de Apoptose/efeitos dos fármacos , Proteínas Reguladoras de Apoptose/metabolismo , Caspases/metabolismo , Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Relação Dose-Resposta a Droga , Humanos , Neoplasias Pulmonares/tratamento farmacológico , Metástase Neoplásica/prevenção & controle , Oligopeptídeos/isolamento & purificação , Fator A de Crescimento do Endotélio Vascular/biossínteseRESUMO
In light of their easy processing, light weight and mechanical flexibility, ferroelectric molecular crystal with large spontaneous polarization ( Ps) is highly desired for many advanced applications. Herein, we report the first theoretical study of two-dimensional (2D) ferroelectric molecular crystals via ab initio calculations. Specifically, we show that diisopropylammonium bromide (DIPAB) based 2D ferroelectric monolayer molecular crystal with large in-plane Ps of â¼1.5 × 10-6 µC cm-1 can be achieved by slicing the bulk DIPAB along a specific plane while keeping the space group unchanged. The important roles of hydrogen bonds are also identified. Ab initio molecular dynamics simulations indicate that, with the support of a graphene substrate, the ferroelectric order of 2D DIPAB monolayer can be retained at room temperature. Lastly, we show that several other diisopropylammonium halide molecular crystals can also be used to achieve 2D all-organic ferroelectric monolayer singular molecular crystal with large in-plane Ps.
RESUMO
Anthopleura anjunae anti-tumor peptide (AAP-H) is a pentapeptide from the sea anemone Anthopleura anjunae with an amino acid sequence of Tyr-Val-Pro-Gly-Pro that is obtained by alkaline protease enzymatic hydrolysis extraction. In this study, we investigated the inhibitory effects of AAP-H on prostate cancer DU-145 cell proliferation using a methylthiazolyldiphenyl-tetrazolium bromide assay. Cell morphology was analyzed by hematoxylin-eosin staining, acridine orange/ethidium bromide fluorescence staining, Hoechst 33258 fluorescence staining, and scanning electron microscopy. The mitochondrial membrane potential was determined by flow cytometry following JC-1 staining. The cell apoptosis rate was measured by Annexin V-fluorescein isothiocyanate and propidium iodide staining followed by flow cytometric analysis, and the expression of apoptosis-associated proteins was assayed by Western blotting. The results demonstrated that AAP-H induced significant reductions in the number of viable cells and increased cell death in both a dose-dependent and time-dependent manner, with an IC50 of approximately 9.605 mM, 7.910 mM, and 2.298 mM at 24 h, 48 h, and 72 h, respectively. The morphologic characteristics of apoptotic cells were observed after treatment with AAP-H. The mitochondrial membrane potential was markedly decreased, and apoptosis increased after AAP-H treatment. Pro-apoptotic proteins, such as Bax, cytochrome-C, caspase-3, and caspase-9 were increased, but Bcl-2 was decreased. These findings suggest that AAP-H has moderate inhibitory effects on prostate cancer DU-145 cells, and the mechanism might involve the mitochondria-mediated apoptotic pathway. Therefore, AAP-H is a candidate anti-prostate cancer drug or health-care food.