Effect of fat concentration on protein digestibility of Chinese sausage.

Chinese sausage is a popular traditional Chinese meat product, but its high-fat content makes consumers hesitant. The purpose of this study is to compare the nutritional differences of Chinese sausages with different fermentation times (0, 10, 20, 30 d) and fat content (the initial content was 11.59% and 20.14%) during digestion. The comparison of digestion degree, protein structure, and peptide composition between different sausages were studied through in vitro simulated digestion. Chinese sausages with high-fat content had higher α-helix, ß-turn, and random coil, making them easier to digest. The fermentation process made this phenomenon more pronounced. The high-fat sausage fermented for 10 d showed the highest release of primary amino acids (about 9.5%), which was about 3.5% higher than the low-fat sausage under the same conditions. The results of peptidomics confirmed the relevant conclusions. After gastric digestion, the types of peptides in the digestive fluid of high-fat sausages were generally more than those in low-fat sausages, while after intestinal digestion, the opposite results were observed. The type of peptide reached its peak after fermentation for 20 d. These findings are of obvious significance for selecting the appropriate fermentation time and fat content of Chinese sausages.

Optimisation and characterization of double emulsion derived from rice starch, rice protein isolates and rice bran oil.

This study focused on the development and evaluation of a stable emulsion system using rice starch, protein isolates, and bran oil as food ingredients. This was performed using a one-factor-at-a-time (OFAT) experimental strategy, which was subsequently refined using response surface modeling (RSM), and the emulsion was then characterized. The resulting quadratic polynomial model effectively captured all the responses, with regression coefficients exceeding 0.90. The emulsion activity index, emulsion stability index, and droplet size were 86.29 %, 93.44 %, and 100.59 nm, respectively. Turbidity was significantly influenced by particle size, with the double emulsion (sample B) exhibiting higher turbidity index (43,250.34 ± 0.046) than the reference sample (29,433.303 ± 0.018). The viscosity of the emulsion increased with the addition of the protein isolates. This inferred that a stable emulsion system derived from rice could serve a multifunctional purpose as carriers, fillers, and binders to enhance the physical, functional and sensory properties of foods.

Effect of probiotic Bacillus cereus DM423 on the flavor formation of fermented sausage.

Insufficient protein and fat hydrolysis capacity of lactic acid bacteria (LAB) limit the flavor formation of fermented sausage. Bacillus is known for its substantial expression of proteases and lipases. However, its application in meat fermentation remains underexplored. In this study, a strain of probiotic Bacillus cereus (B. cereus DM423) was employed as a co-starter to improve the quality of Lactiplantibacillus plantarum (L. plantarum HH-LP56) fermented sausage. The addition of DM423 did not interfere with regular fermentation, but it significantly improved the flavor, as measured by electronic tongue and electronic nose. Further analyses using SDS-PAGE and thin-layer chromatography observed enhanced hydrolysis of protein and fat in sausages in which DM423 was involved in fermentation. GC-IMS identified DM423 mediated upregulation of various flavor compounds, including esters, ketones, furans, and branched-chain fatty acids. In addition, genomic de novo sequencing revealed that DM423 carried an abundance of genes associated with proteolysis, lipolysis, and the production of flavor substances, whereas HH-LP56 lacked these genes. Overall, this study finds that B. cereus DM423 can promote flavor formation in fermented sausages. It may illuminate a promising direction for the development of sausage co-starters from a wider microbial pool.

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells.

The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

Flavor evolution of normal- and low-fat Chinese sausage during natural fermentation.

This work compared the flavor evolution of normal-fat (NF) with that of low-fat (LF) Chinese sausage during natural fermentation. Higher degree of lipid oxidation occurred in NF sausages, resulting in its faster formation of stable volatile profiles. Faster formation of esters occurred in NF sausage in the initial 10 days, whereas prolonged fermentation reduced the level of ethyl lactate-M, ethyl heptanoate, ethyl hexanoate-D and ethyl pentanoate-D. Gradual reduction of alcohols was observed in both groups, and surge in aldehydes occurred in LF samples during day 20-30 period. Faster formation of taste characteristics and larger amount of 2-methylfuran as well as 2,3-dimethylpyrazine were found in LF sausages, since more free amino acids were liberated in LF sausages. Umami and aftertaste tastes formed in the first 20 days, whereas prolonged fermentation reduced these favorable taste. These results highlight that the choice of proper fermentation duration should largely depend on the fat content in Chinese sausages.

SPICEMIX enables integrative single-cell spatial modeling of cell identity.

Spatial transcriptomics can reveal spatially resolved gene expression of diverse cells in complex tissues. However, the development of computational methods that can use the unique properties of spatial transcriptome data to unveil cell identities remains a challenge. Here we introduce SPICEMIX, an interpretable method based on probabilistic, latent variable modeling for joint analysis of spatial information and gene expression from spatial transcriptome data. Both simulation and real data evaluations demonstrate that SPICEMIX markedly improves on the inference of cell types and their spatial patterns compared with existing approaches. By applying to spatial transcriptome data of brain regions in human and mouse acquired by seqFISH+, STARmap and Visium, we show that SPICEMIX can enhance the inference of complex cell identities, reveal interpretable spatial metagenes and uncover differentiation trajectories. SPICEMIX is a generalizable analysis framework for spatial transcriptome data to investigate cell-type composition and spatial organization of cells in complex tissues.

Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.

Single-cell Hi-C (scHi-C) technologies can probe three-dimensional (3D) genome structures in individual cells. However, existing scHi-C analysis methods are hindered by the data quality and complex 3D genome patterns. The lack of computational scalability and interpretability poses further challenges for large-scale analysis. Here, we introduce Fast-Higashi, an ultrafast and interpretable method based on tensor decomposition and partial random walk with restart, enabling joint identification of cell identities and chromatin meta-interactions from sparse scHi-C data. Extensive evaluations demonstrate the advantage of Fast-Higashi over existing methods, leading to improved delineation of rare cell types and continuous developmental trajectories. Fast-Higashi can directly identify 3D genome features that define distinct cell types and help elucidate cell-type-specific connections between genome structure and function. Moreover, Fast-Higashi can generalize to incorporate other single-cell omics data. Fast-Higashi provides a highly efficient and interpretable scHi-C analysis solution that is applicable to a broad range of biological contexts.

Multiscale and integrative single-cell Hi-C analysis with Higashi.

Single-cell Hi-C (scHi-C) can identify cell-to-cell variability of three-dimensional (3D) chromatin organization, but the sparseness of measured interactions poses an analysis challenge. Here we report Higashi, an algorithm based on hypergraph representation learning that can incorporate the latent correlations among single cells to enhance overall imputation of contact maps. Higashi outperforms existing methods for embedding and imputation of scHi-C data and is able to identify multiscale 3D genome features in single cells, such as compartmentalization and TAD-like domain boundaries, allowing refined delineation of their cell-to-cell variability. Moreover, Higashi can incorporate epigenomic signals jointly profiled in the same cell into the hypergraph representation learning framework, as compared to separate analysis of two modalities, leading to improved embeddings for single-nucleus methyl-3C data. In an scHi-C dataset from human prefrontal cortex, Higashi identifies connections between 3D genome features and cell-type-specific gene regulation. Higashi can also potentially be extended to analyze single-cell multiway chromatin interactions and other multimodal single-cell omics data.

The 3D Genome Structure of Single Cells.

The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts.

Rotation equivariant and invariant neural networks for microscopy image analysis.

MOTIVATION: Neural networks have been widely used to analyze high-throughput microscopy images. However, the performance of neural networks can be significantly improved by encoding known invariance for particular tasks. Highly relevant to the goal of automated cell phenotyping from microscopy image data is rotation invariance. Here we consider the application of two schemes for encoding rotation equivariance and invariance in a convolutional neural network, namely, the group-equivariant CNN (G-CNN), and a new architecture with simple, efficient conic convolution, for classifying microscopy images. We additionally integrate the 2D-discrete-Fourier transform (2D-DFT) as an effective means for encoding global rotational invariance. We call our new method the Conic Convolution and DFT Network (CFNet). RESULTS: We evaluated the efficacy of CFNet and G-CNN as compared to a standard CNN for several different image classification tasks, including simulated and real microscopy images of subcellular protein localization, and demonstrated improved performance. We believe CFNet has the potential to improve many high-throughput microscopy image analysis applications. AVAILABILITY AND IMPLEMENTATION: Source code of CFNet is available at: https://github.com/bchidest/CFNet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ComplexContact: a web server for inter-protein contact prediction using deep learning.

ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

Effect of Nanophase Li3PO4 and Li4P2O7 on the Electrochemical Performance of LiFePO4 Cathode Materials.

The Li3PO4 modified LiFePO4/C and Li4P2O7 modified LiFePO4/C cathode materials were synthesized by in-situ synthesis method, respectively. Phase compositions and microstructures of the products were characterized by X-ray powder diffraction (XRD), scanning electronic microscope (SEM). Results indicate that Li3PO4 and Li4P2O7 can sufficiently coat on the LiFePO4 surface and does not alter LiFePO4 crystal structure. The electrochemical behavior of cathode materials was analyzed using galvanostatic measurement and cyclic voltammetry (CV). Compared with Li3PO4, the existence of Li4P2O7 can better improve the electrochemical performance of LiFePO4 cathode materials in specific capability and lithium ion diffusion of cathode materials. The charge-discharge specific capacity and apparent lithium ion diffusion coefficient increase with Li4P2O7 content and maximizes around the Li4P2O7 content is 5 wt%. The results indicated that the Li4P2O7 adding enhances the lithium ion diffusion rate of LiFePO4. However, because of the interface fracture between Li4P2O7 and LiFePO4 particles during charging and discharging process, the cycling performance of Li4P2O7 modified LiFePO4/C cathode materials is very poor.

[Experiences of nasal reconstruction with forehead flap: reports of 13 cases].

OBJECTIVE: To present the experience of nasal reconstruction with forehead flap. METHOD: nasal reconstruction with forehead flap were applied in eight nasal carcinoma cases after operation and 5 nasal trauma cases with defects. RESULT: These forehead flaps were alive in all patients, all incision healed in I stage, no post operative complications were found. The shapes of nose were satisfactory, there were no recurrence of tumor during 1 to 17 year follow up. CONCLUSION: The method can be clinically applied for its simple procedure, reliable flap's blood supply, high survival rate and satisfied result.

[Immune modulatory and therapeutic effect of BCG polysaccharides nucleic acid on perennial allergic rhinitis].

OBJECTIVE: To observe the immune modulatory and therapeutic effect of BCG polysaccharides nucleic acid (BCG-PSN) on patients with perennial allergic rhinitis. METHOD: Sixty patients with perennial allergic rhinitis were randomly divided into two groups, 30 in the test group were treated with BCG-PSN plus ketotefen and 30 in the control group were treated with ketotefen respectively. All patients were followed up and assessed for 3 months, and the blood samples were collected before treatment and 3 months after treatment for measuring the blood IgA, IgG, IgM, IgE, CD3, CD4 and CD8. RESULT: In the test group, the total effective rate was significantly higher comparable to that in the control group. After treatment of BCG-PSN, blood CD3, CD4 and CD4/CD8 were significantly increased. IgE significantly reduced (P < 0.05). CONCLUSION: BCG polysaccharides nucleic acid can modulate the cellular immunofunction of patients with perennial allergic rhinitis and can increase the curative rate on perennial allergic rhinitis.