SGNet: Folding Symmetrical Protein Complex with Deep Learning

Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of large homo-oligomeric assemblies exhibit internal symmetry, posing a major challenge in structure determination. The performances of existing deep learning methods are limited since the symmetrical protein assembly usually has a long sequence, making structural computation infeasible. In addition, multiple identical subunits in symmetrical protein complex cause the issue of supervision ambiguity in label assignment, requiring a consistent structure modeling for the training. To tackle these problems, we propose a protein folding framework called SGNet to model protein-protein interactions in symmetrical assemblies. SGNet conducts feature extraction on a single subunit and generates the whole assembly using our proposed symmetry module, which largely mitigates computational problems caused by sequence length. Thanks to the elaborate design of modeling symmetry consistently, we can model all global symmetry types in quaternary protein structure prediction. Extensive experimental results on a benchmark of symmetrical protein complexes further demonstrate the effectiveness of our method

Efficient Generation of Non-Integration and Feeder-Free Induced Pluripotent Stem Cells from Human Peripheral Blood Cells by Sendai Virus

Background/Aims: Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, disease modeling, and drug development. Thus, generation of non-integration and feeder-free iPSCs is highly desirable for clinical applications. Peripheral blood mononuclear cells (PBMCs) are an attractive resource for cell reprogramming because of their properties of easy accessibility and the limited invasiveness of blood collection. However, derivation of iPSCs is technically demanding due to the low reprogramming efficiency and nonadherent features of PBMCs. Methods: iPSCs were generated from PBMCs using non-integrative Sendai viruses carrying the reprogramming factors Oct4, Sox2, Klf4, and cMyc. The derived iPSCs were fully characterized at the levels of gene and protein, and then they were transplanted into immunocompromised mice for evaluation of in vivo differentiation potential. Three types of extracellular substrates (Geltrex, vitronectin, and rhLaminn-521) were tested for their influences on cell reprogramming under feeder-free conditions. We also sought to establish approaches to efficient cell recovery post-thaw and single cell passaging of iPSCs employing Rock inhibitors. Results: iPSCs were efficiently generated from PBMCs under feeder-free conditions. The derived iPSCs proved to be pluripotent and transgene-free. Furthermore, they demonstrated multi-lineage differentiation potentials when transplanted into immunocompromised mice. Among the three substrates, Geltrex and rhLaminin-521 could effectively support the initial cell reprogramming process, but vitronectin failed. However, the vitronectin, similar to Geltrex and rhLaminin-521, could effectively maintain cell growth and expansion of passaged iPSCs. In addition, RevitaCell supplement (RVC) was more potent on cell recovery post-thaw than Y-27632. And RVC and Y-27632 could significantly increase the cell survival when the cells were passaged in single cells, and they showed comparable effectiveness on cell recovery. Conclusion: We have successfully derived non-integration and feeder-free human iPSCs from peripheral blood cells, and established effective strategies for efficient cell recovery and single cell passaging. This study will pave the way to the derivation of clinical-grade human iPSCs for future clinical applications

EMID: An Emotional Aligned Dataset in Audio-Visual Modality

In this paper, we propose Emotionally paired Music and Image Dataset (EMID), a novel dataset designed for the emotional matching of music and images, to facilitate auditory-visual cross-modal tasks such as generation and retrieval. Unlike existing approaches that primarily focus on semantic correlations or roughly divided emotional relations, EMID emphasizes the significance of emotional consistency between music and images using an advanced 13-dimension emotional model. By incorporating emotional alignment into the dataset, it aims to establish pairs that closely align with human perceptual understanding, thereby raising the performance of auditory-visual cross-modal tasks. We also design a supplemental module named EMI-Adapter to optimize existing cross-modal alignment methods. To validate the effectiveness of the EMID, we conduct a psychological experiment, which has demonstrated that considering the emotional relationship between the two modalities effectively improves the accuracy of matching in abstract perspective. This research lays the foundation for future cross-modal research in domains such as psychotherapy and contributes to advancing the understanding and utilization of emotions in cross-modal alignment. The EMID dataset is available at https://github.com/ecnu-aigc/EMID

Enhancement of plasmid-mediated stable gene expression by woodchuck hepatitis virus post-transcriptional regulatory element (WPRE) in human embryonic kidney (HEK293) cells

Influence of random integration site on the expression of transgene in mammalian cells makes it a major challenge to achieve high productivity of recombinant proteins. Optimization of expression vector is one of the most popular strategies to resolve this problem. Among this, woodchuck hepatitis virus  post-transcriptional regulatory element (WPRE) is a possible enhancer of gene expression in mammalian  cells that promotes efficient export of unspliced (RNA) into the cytoplasm, as has been proved in  transient transfection. In this study, WPRE was evaluated for enhancing stable gene expression levels in two industrial cell lines, human embryonic kidney (HEK293) and CHO-S, using the enhanced green fluorescent protein (EGFP), prourokinase (pro-UK) and protein C (PC) as the reporter gene. Based on the mean fluorescence intensity (MFI), WPRE exerted a clear positive effect on gene expression in HEK293 cells with an increase of EGFP expression level by approximately 2.5- to 3-fold independent of the  promoter used in plasmid vector. In contrast, in Chinese hamster ovary (CHO)-S cells, only a marginal effect on plasmid-mediated EGFP expression by WPRE was observed. The measurable increase of EGFP expression at the protein level was paralleled by an increase of EGFP RNA. Further test of the effect of WPRE on plasmid-mediated gene expression with two therapeutic proteins showed substantial increase of stable pro-UK and PC expression only in HEK293 by about 2.2-fold and 6.1-fold, respectively. The data of PC expression levels obtained from the random HEK293 cell clones transfected with WPRE-containing or lacking vector further demonstrated the enhancement of stable plasmid-mediated gene expression by WPRE in HEK293 cells. These results in stable transfectants show the positive effect of WPRE on transgene expression is cell-type dependent and promoter-independent, and provide valuable information to improve vectors for efficient and stable gene expression in HEK293 cells.Key words: Mammalian cells, plasmid vector, stable gene expression, protein therapeutics, woodchuck hepatitis virus post-transcriptional regulatory element (WPRE)

Both FA- and mPEG-conjugated chitosan nanoparticles for targeted cellular uptake and enhanced tumor tissue distribution

Tianjin Key Laboratory of Biomedical Materials; Xiamen Science and Technology project [3502Z20114007]; Fujian Provincial Health Department [2009-2-79]Both folic acid (FA)- and methoxypoly(ethylene glycol) (mPEG)- conjugated chitosan nanoparticles (NPs) had been designed for targeted and prolong anticancer drug delivery system. The chitosan NPs were prepared with combination of ionic gelation and chemical cross-linking method, followed by conjugation with both FA and mPEG, respectively. FA-mPEG-NPs were compared with either NPs or mPEG-/FA-NPs in terms of their size, targeting cellular efficiency and tumor tissue distribution. The specificity of the mPEG-FA-NPs targeting cancerous cells was demonstrated by comparative intracellular uptake of NPs and mPEG-/FA-NPs by human adenocarcinoma HeLa cells. Mitomycin C (MMC), as a model drug, was loaded to the mPEG-FA-NPs. Results show that the chitosan NPs presented a narrow-size distribution with an average diameter about 200 nm regardless of the type of functional group. In addition, MMC was easily loaded to the mPEG-FA-NPs with drug-loading content of 9.1%, and the drug releases were biphasic with an initial burst release, followed by a subsequent slower release. Laser confocal scanning imaging proved that both mPEG-FA-NPs and FA-NPs could greatly enhance uptake by HeLa cells. In vivo animal experiments, using a nude mice xenograft model, demonstrated that an increased amount of mPEG-FA-NPs or FA-NPs were accumulated in the tumor tissue relative to the mPEG-NPs or NPs alone. These results suggest that both FA-and mPEG-conjugated chitosan NPs are potentially prolonged drug delivery system for tumor cell-selective targeting treatments

TRH Analog, Taltirelin Protects Dopaminergic Neurons From Neurotoxicity of MPTP and Rotenone

Dopaminergic neurons loss is one of the main pathological characters of Parkinson’s disease (PD), while no suitable neuroprotective agents have been in clinical use. Thyrotropin-releasing hormone (TRH) and its analogs protect neurons from ischemia and various cytotoxins, but whether the effect also applies in PD models remain unclear. Here, we showed that Taltirelin, a long-acting TRH analog, exhibited the neuroprotective effect in both cellular and animal models of PD. The in vitro study demonstrated that Taltirelin (5 μM) reduced the generation of reactive oxygen species (ROS) induced by MPP+ or rotenone, alleviated apoptosis and rescued the viability of SH-SY5Y cells and rat primary midbrain neurons. Interestingly, SH-SY5Y cells treated with Taltirelin also displayed lower level of p-tau (S396) and asparagine endopeptidase (AEP) cleavage products, tau N368 and α-synuclein N103 fragments, accompanied by a lower intracellular monoamine oxidase-B (MAO-B) activity. In the subacute MPTP-induced and chronic rotenone-induced PD mice models, we found Taltirelin (1 mg/kg) significantly improved the locomotor function and preserved dopaminergic neurons in the substantia nigra (SN). In accordance with the in vitro study, Taltirelin down-regulated the levels of p-tau (S396), p-α-synuclein (S129) tau N368 and α-synuclein N103 fragments in SN and striatum. Together, this study demonstrates that Taltirelin may exert neuroprotective effect via inhibiting MAO-B and reducing the oxidative stress and apoptosis, preventing AEP activation and its subsequent pathological cleavage of tau and α-synuclein, thus provides evidence for Taltirelin in protective treatment of PD

TRH Analog, Taltirelin Improves Motor Function of Hemi-PD Rats Without Inducing Dyskinesia via Sustained Dopamine Stimulating Effect

Thyrotropin-releasing hormone (TRH) and its analogs are able to stimulate the release of the endogenic dopamine (DA) in the central nervous system. However, this effect has not been tested in the Parkinson’s disease (PD), which is characterized by the DA deficiency due to the dopaminergic neurons loss in the substantia nigra. Here, we investigated the therapeutic effect of Taltirelin, a long-acting TRH analog on 6-hydroxydopamine-lesioned hemi-Parkinsonian rat model. 1–10 mg/kg Taltirelin i.p. administration significantly improved the locomotor function and halted the electrophysiological abnormities of PD animals without inducing dyskinesia even with high-dose for 7 days treatment. Microdialysis showed that Taltirelin gently and persistently promoted DA release in the cortex and striatum, while L-DOPA induced a sharp rise of DA especially in the cortex. The DA-releasing effect of Taltirelin was alleviated by reserpine, vanoxerine (GBR12909) or AMPT, indicating a mechanism involving vesicular monoamine transporter-2 (VMAT-2), dopamine transporter (DAT) and tyrosine hydroxylase (TH). The in vivo and in vitro experiments further supported that Taltirelin affected the regulation of TH expression in striatal neurons, which was mediated by p-ERK1/2. Together, this study demonstrated that Taltirelin improved motor function of hemi-PD rats without inducing dyskinesia, thus supporting a further exploration of Taltirelin for PD treatment