Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix.

Cell type specific (CTS) analysis is essential to reveal biological insights obscured in bulk tissue data. However, single-cell (sc) or single-nuclei (sn) resolution data are still cost-prohibitive for large-scale samples. Thus, computational methods to perform deconvolution from bulk tissue data are highly valuable. We here present EPIC-unmix, a novel two-step empirical Bayesian method integrating reference sc/sn RNA-seq data and bulk RNA-seq data from target samples to enhance the accuracy of CTS inference. We demonstrate through comprehensive simulations across three tissues that EPIC-unmix achieved 4.6% - 109.8% higher accuracy compared to alternative methods. By applying EPIC-unmix to human bulk brain RNA-seq data from the ROSMAP and MSBB cohorts, we identified multiple genes differentially expressed between Alzheimer's disease (AD) cases versus controls in a CTS manner, including 57.4% novel genes not identified using similar sample size sc/snRNA-seq data, indicating the power of our in-silico approach. Among the 6-69% overlapping, 83%-100% are in consistent direction with those from sc/snRNA-seq data, supporting the reliability of our findings. EPIC-unmix inferred CTS expression profiles similarly empowers CTS eQTL analysis. Among the novel eQTLs, we highlight a microglia eQTL for AD risk gene AP3B2, obscured in bulk and missed by sc/snRNA-seq based eQTL analysis. The variant resides in a microglia-specific cCRE, forming chromatin loop with AP3B2 promoter region in microglia. Taken together, we believe EPIC-unmix will be a valuable tool to enable more powerful CTS analysis.

Construction and Properties of Oil-Loaded Soybean Protein Isolate/Polysaccharide-Based Meat Analog Fibers.

Rationally designing the fibrous structure of artificial meat is a challenge in enriching the organoleptic quality of meat analogs. High-quality meat analog fibers have been obtained by wet-spinning technique in our previous study, whereas introducing oil droplets will further achieve their fine design from the insight of microstructure. Herein, in this current work, oil was introduced to the soybean protein isolate/polysaccharide-based meat analog fibers by regulating the oil droplets' size and content, which, importantly, controlled the spinning solution characterization as well as structure-related properties of the meat analog fiber. Results showed that the oil dispersed in the matrix as small droplets with regular shapes, which grew in size as the oil content increased. Considering the effect of oil droplets' size and content on the spinnability of the spinning solution, the mechanical stirring treatment was chosen as the suitable treatment method. Importantly, increasing the oil content has the potential to enhance the juiciness of meat analog fibers through improvements in water-holding capacity and alterations in water mobility. Overall, the successful preparation of oil-loaded plant-based fiber not only mimicked animal muscle fiber more realistically but also provided a general platform for adding fat-soluble nutrients and flavor substances.

Construction of a soybean protein isolate/polysaccharide-based whole muscle meat analog: Physical properties and freeze-thawing stability study.

A growing interest has arisen in recreating real meat by mimicking its texture characteristics and muscle fiber structure. Our previous work successfully created meat analog fiber based on soybean protein isolate (SPI) and sodium alginate (SA) with the wet-spinning method. In this work, we analyzed the microstructure, texture profile, and water retainability of the assembled plant-based whole muscle meat analog (PMA) made of SPI/SA-based meat analog fiber and systematically studied the effect of different combinations and contents of transglutaminase (TG), salt, and soybean oil on the rheological behavior of the formulated adhesive. The estimated optimal condition that has the most similar texture characteristic with real chicken breast meat is: for every 1:1 mass ratio of simulated plant meat fibers to the adhesive, add 0.1 % TG enzyme addition in the adhesive and 100 mM NaCl addition. The physical behavior of PMA during cryopreservation was investigated through freeze-thaw cycles and freezing times. The addition of a small amount of oil and salt can efficiently prevent the PMA through freezing conditions which is comparable with the addition of D-Trehalose (TD). Overall, this study not only created a plant-based whole muscle meat analog product that is similar in texture to real chicken breast meat but also provided a new direction for constructing fiber-rich structure protein-based muscle meat analogs and their further commercialization.

Effect of Ultrasound and Salt on Structural and Physical Properties of Sodium Alginate/Soy Protein Isolates Composite Fiber.

Recently, there has been a growing interest in advancing plant-based or cultured meat substitutes as environmentally and ethically superior alternatives to traditional animal-derived meat. In pursuit of simulating the authentic meat structure, a composite fiber composed primarily of soy protein isolates (SPIs) was fashioned, employing a fiber-based plant-based analog meat construct. To refine the spinning process and enhance fiber quality, we employed ultrasound treatment, a physical modification technique, to scrutinize its influence on SPI protein structure. This inquiry extended to the examination of the interplay between sodium alginate (SA) and SPI, as well as the impact of salt ions on the SA and ultrasound soy protein isolates (USPI) interaction. A comprehensive exploration encompassing ultrasound treatments and salt concentrations within the composite solution, along with their repercussions on composite fiber characterization, with a rise in negative zeta potential value, states the ultrasound treatment fosters protein aggregation. Moreover, the introduction of salt augments protein aggregation as salt content escalates, ultimately resulting in a reduced structural viscosity index and improved spinnability. The presence of Ca2+ ions during the coagulation process leads to interactions with SA. The involvement of ultrasound prompts the exposure of hydrophilic amino acid segments in the protein to water, leading to the development of a more porous structure. Solely under the influence of ultrasound, the fiber exhibits 5% higher water-holding capacity and superior mechanical properties while maintaining comparable thermal stability.

Associations between 24-h Movement Behavior and Internet Addiction in Adolescents: A Cross-Sectional Study.

OBJECTIVE: This study aimed to explore the relationship between 24-h activity behavior and Chinese adolescents' Internet addiction. METHODS: A survey of 2045 adolescents (56.5% boys) was conducted, and adolescents' 24-h movement behavior and Internet addiction were measured via a questionnaire. Descriptive statistics were used to analyze the basic situation of the respondents; chi-square analysis was used to compare gender differences, and logistic regression was used to analyze the relationship between 24-h exercise guide entries and Internet addiction. RESULTS: From the number of 24-h movement behavior guides, 25.3% of the children did not meet the recommended amount of any kind of activity behavior guide, while 50.4% and 21.7% of the children reached the recommended amount of one and two activity behavior guidelines, respectively; only 3.2% of the children met the recommended amount of all three activity behavior guidelines. Adolescents who did not meet the recommended 24-h activity behavior guidelines were more likely to have Internet addiction (OR = 8.46, 95 CI = 3.06-23.36), and were more likely to have one item (OR = 4.50, 95 CI = 1.64-12.39) or two items (OR = 3.12, 95 CI = 1.11-8.74). CONCLUSIONS: Physical activity, static behavior, and sleep may all have a greater impact on adolescents' Internet addiction, among which physical activity has a greater impact on adolescents' Internet addiction. Different combinations of 24-h movement behavior have different effects on adolescents' Internet addiction.

Dietary fiber extracted from pomelo fruitlets promotes intestinal functions, both in vitro and in vivo.

Pomelo fruitlets contain various active substances that are easily collected and processed. Here, the biological effects of pomelo fruitlet dietary fiber were investigated in vivo and in vitro. Total dietary fiber (TDF), soluble dietary fiber (SDF), and insoluble dietary fiber (IDF) values of pomelo fruitlets were 75.64 ± 3.65 %, 10.10 ± 1.39 %, and 62.48 ± 3.68 %, respectively. The main monosaccharides identified were rhamnose, arabinose, galactose, and glucose. All fibers scavenged free 2,2'-diphenyl-1-picrylhydrazyl radicals and reduced ferric cations. The water-holding, oil-holding, and swelling capacities of the fibers retarded glucose diffusion, inhibited α-amylase, and influenced cholesterol micelle formation. In a mouse model of alloxan-induced diabetes, SDF improved glucose tolerance, controlled blood glucose, and reduced serum insulin better than TDF or IDF. All fiber types decreased the total cholesterol content and the prevalence of Bacteroidetes, Proteobacteria, and Ruminococcaceae, but increased the abundance of Firmicutes, Lactobacillus, and Prevotellaceae in hyperglycemic mice.

Conjugating a groove binder analogue to a styryl-quinolinium scaffold for the light-up detection of duplex and G-Quadruplex DNA with different binding modes.

The rational design of novel small molecules, which can target specific DNA sequences or secondary structural DNAs, is one of the most important goals in medicinal chemistry. Also the studies of DNA binding potency which can give fundamental insight into binding mechanisms and specificity are essential. In this paper, a N-methylated quinolinium probe NSQ functionalized with a G-Quadruplex DNA groove binder analogue was designed and synthesized. NSQ was found to express selective and sensitive for "light-up" detection of both G-Quadruplex and duplex DNAs over RNA and other biomolecules. The characteristics of NSQ and its interactions with DNAs were comprehensively evaluated by means of fluorescence, UV-Vis, circular dichroism, FID assay, DFT calculation and molecular docking. NSQ exhibited higher binding affinity to G-Quadruplex than to duplex DNA. Binding mechanism analysis indicated NSQ interacted with G-Quadruplex DNA mainly through end-stacking mode, while bound with duplex DNA into the minor groove of AT-rich regions. Further, NSQ exhibited potent in vitro anti-tumor activity, and to elucidate the cellular applications, confocal cell imaging was carried out and validated its mainly nuclear localization.

Effects of environmentally relevant concentrations of tris (2-butoxyethyl) phosphate on growth and transcription of genes involved in the GH/IGF and HPT axes in zebrafish (Danio rerio).

Tris (2-butoxyethyl) phosphate (TBOEP), as one of the most widely used organophosphate flame retardants (OPFRs), is applied in nearly all manufactured items and materials. It has been reported that TBOEP could cause developmental impairments and disrupt the endocrine regulation of fish growth during acute toxic experiments. However, concentrations to which fish were exposed in these studies were greater than environmentally relevant concentrations ever reported. This study examined effects on growth associated with exposure of zebrafish to 0, 0.1, 1 and 10 µg/L TBOEP during 20-90 days post fertilization (dpf). The changes in growth indicators and bioaccumulation of TBOEP were examined along with the transcription of related genes in the growth hormone/insulin-like growth factor (GH/IGF) axis and the hypothalamic-pituitary-thyroid (HPT) axis. The average body contents of TBOEP were higher in females than in males in all the exposure groups. Exposure to environmentally relevant concentrations of TBOEP significantly decreased body length and body mass and down-regulated expression of several genes involved in the GH/IGF and HPT axes. Exposure to TBOEP decreased plasma thyroxine (T4) content accompanied by decreased mRNA level of thyrotropin ß-subunit (tshß) in females at 60 dpf, but no effects were observed at 90 dpf. These results suggested that bioaccumulation of TBOEP and down-regulation of genes involved in the GH/IGF axis might be responsible for the observed growth inhibition in zebrafish exposed to TBOEP.

Tris (2-butoxyethyl) phosphate affects motor behavior and axonal growth in zebrafish (Danio rerio) larvae.

Tris (2-butoxyethyl) phosphate (TBOEP) is an environmental contaminant that poses serious risks to aquatic organisms and their associated ecosystem. Recently, the reproductive and developmental toxicology of TBOEP has been reported. However, fewer studies have assessed the neurotoxic effects in zebrafish (Danio rerio) larvae. In this study, zebrafish embryos were subjected to waterborne exposure of TBOEP at 0, 50, 500, 1500 and 2500 µg/L from 2 to 144-h post-fertilization (hpf). Behavioral measurements showed that TBOEP exposure reduced embryonic spontaneous movement and decreased swimming speed of larvae in response to dark stimulation. In accordance with these motor effects, TBOEP treatment reduced neuron-specific GFP expression in transgenic Tg (HuC-GFP) zebrafish larvae and inhibited the growth of secondary motoneurons, as well as decreased expression of marker genes related to central nervous system development in TBOEP treated group. Furthermore, increased concentrations of reactive oxygen species (ROS) and malondialdehyde (MDA), as well as reduction of SOD activity were detected in TBOEP exposure group. The present results showed that the alteration in motor neuron and oxidative stress could together lead to the motor behavior alterations induced by TBOEP.