A membrane-associated MHC-I inhibitory axis for cancer immune evasion.

Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of T cell immunity involving aberrant major histocompatibility complex class I (MHC-I) antigen presentation (AP). To map such mechanisms of resistance, we identified key MHC-I regulators using specific peptide-MHC-I-guided CRISPR-Cas9 screens in AML. The top-ranked negative regulators were surface protein sushi domain containing 6 (SUSD6), transmembrane protein 127 (TMEM127), and the E3 ubiquitin ligase WWP2. SUSD6 is abundantly expressed in AML and multiple solid cancers, and its ablation enhanced MHC-I AP and reduced tumor growth in a CD8+ T cell-dependent manner. Mechanistically, SUSD6 forms a trimolecular complex with TMEM127 and MHC-I, which recruits WWP2 for MHC-I ubiquitination and lysosomal degradation. Together with the SUSD6/TMEM127/WWP2 gene signature, which negatively correlates with cancer survival, our findings define a membrane-associated MHC-I inhibitory axis as a potential therapeutic target for both leukemia and solid cancers.

Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics.

The latest breakthroughs in spatially resolved transcriptomics technology offer comprehensive opportunities to delve into gene expression patterns within the tissue microenvironment. However, the precise identification of spatial domains within tissues remains challenging. In this study, we introduce AttentionVGAE (AVGN), which integrates slice images, spatial information and raw gene expression while calibrating low-quality gene expression. By combining the variational graph autoencoder with multi-head attention blocks (MHA blocks), AVGN captures spatial relationships in tissue gene expression, adaptively focusing on key features and alleviating the need for prior knowledge of cluster numbers, thereby achieving superior clustering performance. Particularly, AVGN attempts to balance the model's attention focus on local and global structures by utilizing MHA blocks, an aspect that current graph neural networks have not extensively addressed. Benchmark testing demonstrates its significant efficacy in elucidating tissue anatomy and interpreting tumor heterogeneity, indicating its potential in advancing spatial transcriptomics research and understanding complex biological phenomena.

3DCNAS: A universal method for predicting the location of fluorescent organelles in living cells in three-dimensional space.

Cellular biology research relies on microscopic imaging techniques for studying the complex structures and dynamic processes within cells. Fluorescence microscopy provides high sensitivity and subcellular resolution but has limitations such as photobleaching and sample preparation challenges. Transmission light microscopy offers a label-free alternative but lacks contrast for detailed interpretation. Deep learning methods have shown promise in analyzing cell images and extracting meaningful information. However, accurately learning and simulating diverse subcellular structures remain challenging. In this study, we propose a method named three-dimensional cell neural architecture search (3DCNAS) to predict subcellular structures of fluorescence using unlabeled transmitted light microscope images. By leveraging the automated search capability of differentiable neural architecture search (NAS), our method partially mitigates the issues of overfitting and underfitting caused by the distinct details of various subcellular structures. Furthermore, we apply our method to analyze cell dynamics in genome-edited human induced pluripotent stem cells during mitotic events. This allows us to study the functional roles of organelles and their involvement in cellular processes, contributing to a comprehensive understanding of cell biology and offering insights into disease pathogenesis.

Innovative methods for microplastic characterization and detection: Deep learning supported by photoacoustic imaging and automated pre-processing data.

Plastic products' widespread applications and their non-biodegradable nature have resulted in the continuous accumulation of microplastic waste, emerging as a significant component of ecological environmental issues. In the field of microplastic detection, the intricate morphology poses challenges in achieving rapid visual characterization of microplastics. In this study, photoacoustic imaging technology is initially employed to capture high-resolution images of diverse microplastic samples. To address the limited dataset issue, an automated data processing pipeline is designed to obtain sample masks while effectively expanding the dataset size. Additionally, we propose Vqdp2, a generative deep learning model with multiple proxy tasks, for predicting six forms of microplastics data. By simultaneously constraining model parameters through two training modes, outstanding morphological category representations are achieved. The results demonstrate Vqdp2's excellent performance in classification accuracy and feature extraction by leveraging the advantages of multi-task training. This research is expected to be attractive for the detection classification and visual characterization of microplastics.

Multi-aspect simulation insight on thermolysis mechanism and interaction of NTO/HMX-based plastic-bonded explosives: a new conception of the mixed explosive model.

Reactive molecular dynamics (RMDs) calculations were used to determine, for the first time, the process of thermolysis of the mixed explosives, including 3-nitro-1,2,4-triazol-5-one (NTO) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazoline (HMX). Significantly, this is the first time that a layered model for mixed explosives, which is an extreme innovation of mixed explosive models was adopted. It is shown that a large amount of NO2 in the HMX and OH groups generated by the decomposition of HNO2 has a favorable effect on the thermolysis of NTO, as further validated by a reduction in the activation energy of NTO/HMX. The amount of H2O and N2 in the resulting products increased significantly, but the amount of NH3 changed slightly. The analysis results correspond to the change in chemical bonds. Whenever there is an increase in temperature, the time for the maximum number of clusters to appear is shortened accordingly. In addition, the acidity of NTO has been considered. An independent gradient model based on Hirshfeld partition (IGMH) and atoms in molecule (AIM) analysis of NTO/HMX was implemented. The relatively strong hydrogen bonds indicate that HMX can inhibit the acidity of NTO and is beneficial for the wide application of NTO/HMX-based plastic-bonded explosives (PBXs).

Electrochemical biosensor based on antibody-modified Au nanoparticles for rapid and sensitive analysis of influenza A virus.

To cope with the easy transmissibility of the avian influenza A virus subtype H1N1, a biosensor was developed for rapid and highly sensitive electrochemical immunoassay. Based on the principle of specific binding between antibody and virus molecules, the active molecule-antibody-adapter structure was formed on the surface of an Au NP substrate electrode; it included a highly specific surface area and good electrochemical activity for selective amplification detection of the H1N1 virus. The electrochemical test results showed that the BSA/H1N1 Ab/Glu/Cys/Au NPs/CP electrode was used for the electrochemical detection of the H1N1 virus with a sensitivity of 92.1 µA (pg/mL)-1 cm2, LOD of 0.25 pg/ml, linear ranges of 0.25-5 pg/mL, and linearity of (R 2 = 0.9846). A convenient H1N1 antibody-based electrochemical electrode for the molecular detection of the H1N1 virus will be of great use in the field of epidemic prevention and raw poultry protection. Supplementary Information: The online version contains supplementary material available at 10.1007/s11581-023-04944-w.

Multiple Parallel Fusion Network for Predicting Protein Subcellular Localization from Stimulated Raman Scattering (SRS) Microscopy Images in Living Cells.

Stimulated Raman Scattering Microscopy (SRS) is a powerful tool for label-free detailed recognition and investigation of the cellular and subcellular structures of living cells. Determining subcellular protein localization from the cell level of SRS images is one of the basic goals of cell biology, which can not only provide useful clues for their functions and biological processes but also help to determine the priority and select the appropriate target for drug development. However, the bottleneck in predicting subcellular protein locations of SRS cell imaging lies in modeling complicated relationships concealed beneath the original cell imaging data owing to the spectral overlap information from different protein molecules. In this work, a multiple parallel fusion network, MPFnetwork, is proposed to study the subcellular locations from SRS images. This model used a multiple parallel fusion model to construct feature representations and combined multiple nonlinear decomposing algorithms as the automated subcellular detection method. Our experimental results showed that the MPFnetwork could achieve over 0.93 dice correlation between estimated and true fractions on SRS lung cancer cell datasets. In addition, we applied the MPFnetwork method to cell images for label-free prediction of several different subcellular components simultaneously, rather than using several fluorescent labels. These results open up a new method for the time-resolved study of subcellular components in different cells, especially cancer cells.

Quantitative insights into tightly and loosely bound water in hydration shells of amino acids.

The hydration of amino acids closely correlates the hydration of peptides and proteins and is critical to their biological functions. However, complete and quantitative understanding about the hydration of amino acids is lacking. Here, tightly and loosely bound water of 20 zwitterionic amino acids are quantitatively distinguished and determined by Raman spectroscopy with multivariate curve resolution (Raman-MCR) and differential scanning calorimetry (DSC). The total hydration water obtained from Raman-MCR and the tightly bound water determined by DSC have certain relevance, but they do not exactly correspond. In particular, Pro, Arg and Lys exhibit larger number of tightly bound water molecules (4.02-6.59), showing a significant influence on the onset transition temperature and the melting enthalpy values of water molecules, which provides direct evidence for their unique functions associated with biological water. Asn, Ser, Thr, Met, His and Glu have a smaller number of tightly bound water molecules (0.30-1.31), whilst the other remaining 11 amino acids only contain loosely bound water molecules. Four exceptional amino acids Ile, Leu, Phe and Val show fewer tightly bound water molecules but a higher number of loosely bound water molecules. As for the hydration shell structure, most amino acids except Pro and Trp enhance tetrahedral water structure and H-bonds relative to pure water and at least 1.9% of the hydration water molecules associated with the amino acids show non-hydrogen-bonded OH defects. This work combines two effective experimental techniques to reveal the hydration water structure and quantitatively analyze two kinds of bound water molecules of 20 amino acids.

Nanobar Array Assay Revealed Complementary Roles of BIN1 Splice Isoforms in Cardiac T-Tubule Morphogenesis.

Bridging integrator-1 (BIN1) is a family of banana-shaped molecules implicated in cell membrane tubulation. To understand the curvature sensitivity and functional roles of BIN1 splicing isoforms, we engineered vertical nanobars on a cell culture substrate to create high and low curvatures. When expressed individually, BIN1 isoforms with phosphoinositide-binding motifs (pBIN1) appeared preferentially at high-curvature nanobar ends, agreeing well with their membrane tubulation in cardiomyocytes. In contrast, the ubiquitous BIN1 isoform without phosphoinositide-binding motif (uBIN1) exhibited no affinity to membranes around nanobars but accumulated along Z-lines in cardiomyocytes. Importantly, in pBIN1-uBIN1 coexpression, pBIN1 recruited uBIN1 to high-curvature membranes at nanobar ends, and uBIN1 attached the otherwise messy pBIN1 tubules to Z-lines. The complementary cooperation of BIN1 isoforms (comboBIN1) represents a novel mechanism of T-tubule formation along Z-lines in cardiomyocytes. Dysregulation of BIN1 splicing, e.g., during myocardial infarction, underlied T-tubule disorganization, and correction of uBIN1/pBIN1 stoichiometry rescued T-tubule morphology in heart disease.

Bridge-Mediated Charge Separation in Isomeric N-Annulated Perylene Diimide Dimers.

The possibility and rate of charge separation (CS) in donor-bridge-acceptor molecules mainly depend on two factors: electronic coupling and solvent effects. The question of how CS occurred in two identical chromophores is fundamental, as it is particularly interesting for potential molecular electronics applications and the photosynthetic reaction centers (RCs). Conjugated bridge definitely plays a crucial role in electronic coupling. To determine the bridge-mediated charge separation dynamics between the two identical chromophores, the isomeric N-annulated perylene diimide dimers (para-BDNP and meta-BDNP) with different conjugated bridge structures have been comparatively investigated in different solvents using femtosecond transient absorption spectra (fs-TA). It is found that the charge separation is disfavored in weak polar solvent, whereas direct spectroscopic signatures of radicals are observed in polar solvents, and the rate of charge separation increases as the solvent polarity increasing. To our surprise, the rate of charge separation in m-BDNP is more than an order of magnitude slower than that in p-BDNP, although there is a larger negative ΔGCS in m-BDNP. The slow CS rate that occurred in m-BDNP mainly results from the intrinsic destructive interference of the wave function through the meta-substituted bridge. The roles of solvent effects in free energy and electronic coupling for charge separation are further identified with quantum calculations.

Solvent modulated excited state processes of push-pull molecule with hybridized local excitation and intramolecular charge transfer character.

Recently, a type of synthetic highly efficient OLED molecule based on a hybridized local excitation and charge transfer (HLCT) character has received much attention as a potential high-efficiency fluorescent OLED material. In this article, we report the relaxation dynamics of the excited states of cyano-substituted oligo α-phenylenevinylene-1,4-bis(R-cyano-4-diphenylaminostyryl)-2,5-diphenylbenzene (CNDPASDB) with HLCT character using steady-state and time-resolved spectroscopy as well as quantum chemical calculations. The dramatic dependence of the fluorescence quantum yield, radiative and non-radiative rate, as well as the excited state relaxation pathways on solvent polarity reveals that the solvation process controls the energy levels of two closely spaced electronic excited states. By employing femtosecond transient absorption spectra, the gradual transition from the LE state to the intramolecular CT state with an increase in solvent polarity is clearly resolved. In low-polarity solvents the fluorescence of CNDPASDB is mainly emission from the LE state, whereas in high-polarity solvents non-radiative decay from the CT state dominates. And in medium-polarity solvents, because of the relatively weaker solvation-induced stabilization of the CT state, its energy could be equal to or slightly lower than that of the LE state, leading to a smaller driving force for LE → CT interconversion; therefore complete LE → CT interconversion cannot take place. In this situation, LE ↔ CT intercrossed equilibration is established and the equilibrium constant is further estimated to be about 4 according to the obtained kinetics, and the equilibrium population of the CT state is about 80%. DFT/TDDFT analysis also confirmed an efficient intercrossing of LE and CT states with an increase in solvent polarity. It is found that upon increasing the solvent polarity, the hole and electron on a molecule are entirely separated, suggesting a complete CT character. These results provide guidance for understanding the relationship between solvent polarity and the HLCT process, as well as for designing and synthesizing advanced OLED materials.

Intramolecular charge transfer and solvation dynamics of push-pull dyes with different π-conjugated linkers.

The solvation-dependent excited state dynamics of two push-pull fluorophores with donor-π-acceptor (D-π-A) structures were investigated using steady-state and ultrafast transient absorption (TA) spectroscopy, backed by theoretical calculations. Identical D and A groups were present in both dyes, which differed only in the structure of their central π-conjugated linkers. Dye 1 features a p-phenylenediethynyl linker, while dye 2 contains a 2,5-diethynylthiophene linker. From the steady-state spectra, no appreciable shifts in absorption bands were observed, whereas large red-shifts in emission were seen with increasing solvent polarity, which indicated that the excited states were more polar than the ground state. Theoretical calculations support charge transfer from the triphenylamine (TPA) donor to the pentafluorosulfanyl (SF5) acceptor viaπ-conjugated linkers to form an intramolecular charge transfer (ICT) state. TA spectra revealed that a solvation-stabilized conformationally relaxed intramolecular charge transfer (ICT') state was formed in polar solvents, but only an ICT state was observed in nonpolar solvent. The SE band was quenched within 1 ps in high-polarity solvent, which corresponds to the low fluorescence quantum yield. It can be concluded that the dye with the p-phenylenediethynyl π-linker (i.e., dye 1) exhibits a larger degree of ICT than the thiophene analogue (i.e., dye 2). These findings demonstrate how solvation can fine-tune the photophysical properties of push-pull dyes, and this study highlights the importance of π-conjugated linkers in the excited state ICT process.

Insights into the effect of donor ability on photophysical properties of dihydroindeno[2,1-c]fluorene-based imide derivatives.

The photophysical properties of dihydroindeno[2,1-c]fluorene-based imide (DHIFI) derivatives were investigated by steady-state and time-resolved spectroscopy as well as quantum chemical calculations. The hybridized local excited and charge transfer state (HLCT) was introduced to interpret the intercrossing of localized excited (LE) and charge transfer (CT) states. The large extent of CT in the HLCT state of a molecule with a strong electron donor (dimethylaniline) at the terminal site results in strong interaction between the dipole moments of the excited state and polar solvents. Time-resolved spectroscopy results show the formation of a stabilized ICT state in several picoseconds, which results in fluorescence quenching and less possibility of intersystem crossing to the triplet state. In contrast, a molecule with a weak electron donor (benzene) displays less fluorescence quenching. The slowing down of geometry relaxation in the weak-electron-donor molecule increases the possibility of ISC to the triplet state from the unrelaxed HLCT state.

Probing Laser-Induced Heterogeneous Microenvironment Changes in Room-Temperature Ionic Liquids.

Modulating the heterogeneous microenvironment in room-temperature ionic liquids (RTILs) by external stimuli is an important approach for understanding and designing external field-induced chemical reactions in natural and applied systems. Here, we report for the first time the redistribution of oxygen molecules related to microstructure changes in RTILs induced by an external laser field, which is probed simultaneously by the triplet-state dynamics of porphyrin. A remarkably long-lived triplet state of porphyrin is observed with changes of microstructures after irradiation, suggesting that charge-shifted O2 molecules are induced by the external field and/or rearranged intrinsic ions move from nonpolar domains into the polar domains of RTILs through electrostatic interactions. The results suggest that heterogeneous systems like ionic liquids in the presence of external stimuli can be designed for reaction systems associated with not only O2 but also for CO2 , CS2 , etc. and many other similar solvent molecules for many promising applications.

Intramolecular Charge Transfer and Solvation of Photoactive Molecules with Conjugated Push-Pull Structures.

A comparative investigation on the photophysical properties and solvation-related ICT dynamics of three push-pull compounds containing different donors including carbazole, triphenylamine and phenothiazine, was performed. The steady-state spectra and theoretical calculations show the charge transfers from the central donors to the acceptors at each side. The characterization of the extent of charge transfer was determined by various means, including estimation of the dipole moment, the electron density distribution of HOMO and LUMO, CDD and change in Gibb's free energy, which show the charge transfer strength to be in the order PDHP > BDHT > PDHC. This suggests that the electron-donating ability of the donor groups plays a crucial role in the charge transfer in these compounds. The TA data show the excited-state relaxation dynamics follow a sequential model: FC→ICT→ICT'→S0 , and are affected by the solvent polarity. The results presented here demonstrate that the compound with a higher degree of ICT characteristic interacts more strongly with stronger polar solvent molecules, which can accelerate the solvation and spectral evolution to lower energy levels. The A-π-D-π-A architectures with prominent ICT characteristics based on carbazole, triphenylamine and phenothiazine might be potential scaffolds for light-harvesting and photovoltaic devices. These results are of value for understanding structure-property relationships and the rational design of functional materials for photoelectric applications.

A Study of Excitation Delocalization/Localization in Multibranched Chromophores by Using Fluorescence Excitation Anisotropy Spectroscopy.

We describe a simple approach to study the excitation localization/delocalization in multibranched chromophores by using fluorescence excitation anisotropy spectroscopy at room temperature. As examples, the electronic excitations in three different multibranched chromophores (dimers) are investigated. For a weakly coupled dimer, fluorescence anisotropy is independent of excitation wavelength, due to localized excitation as well as the degenerate electronic excited states. In contrast, in the case of a strongly coupled dimer, owing to excitonic splitting, a redistribution of the excitation energy is demonstrated by the dependence of anisotropy spectra on the excitation wavelength, which leads to significant deviation from the anisotropy signal of localized excitation. In particular, based on the law of additivity for anisotropy, the degree of delocalized excitation can be simply estimated for a given dimer.

Photophysical properties of octupolar triazatruxene-based chromophores.

The photophysical properties of three octupolar chromophores containing planar triazatruxene (TAT) as the central electron donor with different electron-withdrawing groups in the tribranched arrangement have been systematically investigated by means of steady state and transient spectroscopy. The multidimensional intramolecular charge transfer (ICT) properties of these tribranched chromophores related to the observed two-photon absorption (TPA) properties are explored by estimating the TPA essential factors (Mge and Δµge). Besides the large Stokes shift between steady state absorption and fluorescence spectra in different polar solvents, photoinduced ICT was further demonstrated by quantum-chemical calculations and transient absorption measurements. Both quantum calculations and spectral experiments show that a multidimensional ICT occurs from the electron-rich core to the electron-deficient periphery of these TAT derivatives. The results of solvation effects and the dynamics of the excited states show that the excited states of these three chromophores tend to exhibit an excitation localization on one of the dipolar branches, which is beneficial to achieve large Mge and Δµge, thus leading to enhanced TPA properties.

Enhanced fluorescence of [[5'-(4-hydroxyphenyl)[2,2'-bithiophen]-5-yl]methylene]-propanedinitrile (NIAD-4): solvation induced micro-viscosity enhancement.

Excited state solvation plays a very important role in modulating the emission behavior of fluorophores upon excitation. Here, the solvation effects on the local micro-environment around a fluorophore are proposed by investigating the fantastic emission behavior of a novel amyloid fibril marker, NIAD-4, in different alcoholic and aprotic solvents. In alcoholic solvents, high solvent viscosity causes an obvious enhancement of fluorescence because of the restriction of torsion of NIAD-4, where the formation of a non-fluorescent twist intramolecular charge transfer (TICT) state is suppressed. In aprotic solvents, high solvent polarity leads to a remarkable redshift of the emission spectra suggesting strong solvation. Surprisingly, an abnormal fluorescence enhancement of NIAD-4 is observed with increasing solvent polarity of the aprotic solvents, whereas solvent viscosity plays little role in influencing the fluorescence intensity. We conclude that such an abnormal phenomenon is originated from a solvation induced micro-viscosity enhancement around the fluorophore upon excitation which restricts the torsion of NIAD-4. Femtosecond transient absorption results further prove such a micro-viscosity increasing mechanism. We believe that this solvation induced micro-viscosity enhancement effect on fluorescence could widely exist for most donor-π-acceptor (D-π-A) compounds in polar solvents, which should be carefully taken into consideration when probing the micro-viscosity in polar environments, especially in complex bioenvironments.

Excited-State Deactivation of Branched Phthalocyanine Compounds.

The excited-state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis- and trisphthalocyanines) are studied by using steady-state and femtosecond transient absorption spectral measurements, where the excited-state energy-transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis-Pc). In trisphthalocyanine (tris-Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre-associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady-state spectra also show a face-to-face conformation in bis-Pc, whereas in tris-Pc, two of the three phthalocyanine branches form a pre-associated face-to-face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure-property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems.