Evaluating the capability of soybean peptides as calcium ion carriers: a study through sequence analysis and molecular dynamics simulations.

Calcium homeostasis imbalance in the body can lead to a variety of chronic diseases. Supplement efficiency is essential. Peptide calcium chelate, a fourth-generation calcium supplement, offers easy absorption and minimal side effects. Its effectiveness relies on peptide's calcium binding capacity. However, research on amino acid sequences in peptides with high calcium binding capacity (HCBC) is limited, affecting the efficient identification of such peptides. This study used soybean peptides (SP), separated and purified by gel chromatography, to obtain HCBC peptide (137.45 µg mg-1) and normal peptide (≤95.78 µg mg-1). Mass spectrometry identified the sequences of these peptides, and an analysis of the positional distribution of characteristic amino acids followed. Two HCBC peptides with sequences GGDLVS (271.55 µg mg-1) and YEGVIL (272.54 µg mg-1) were discovered. Molecular dynamics showed that when either aspartic acid is located near the N-terminal's middle, or glutamic acid is near the end, or in cases of continuous Asp or Glu, the binding speed, probability, and strength between the peptide and calcium ions are superior compared to those at other locations. The study's goal was to clarify how the positions of characteristic amino acids in peptides affect calcium binding, aiding in developing peptide calcium chelates as a novel calcium supplement.

Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.

The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.

Causal relationship between serum metabolites and juvenile idiopathic arthritis: a mendelian randomization study.

BACKGROUND: Juvenile Idiopathic Arthritis (JIA) is a condition that occurs when individuals under the age of 16 develop arthritis that lasts for more than six weeks, and the cause is unknown. The development of JIA may be linked to serum metabolites. Nevertheless, the association between JIA pathogenesis and serum metabolites is unclear, and there are discrepancies in the findings across studies. METHODS: In this research, the association between JIA in humans and 486 serum metabolites was assessed using genetic variation data and genome-wide association study. The identification of causal relationships was accomplished through the application of univariate Mendelian randomization (MR) analysis. Various statistical methods, including inverse variance weighted and MR-Egger, were applied to achieve this objective. To ensure that the findings from the MR analysis were trustworthy, a number of assessments were carried out. To ensure the accuracy of the obtained results, a range of techniques were utilised including the Cochran Q test, examination of the MR-Egger intercept, implementation of the leave-one-out strategy, and regression analysis of linkage disequilibrium scores. In order to identify the specific metabolic pathways associated with JIA, our primary objective was to perform pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes. RESULTS: Two-sample summary data MR analyses and sensitivity analyses showed that five metabolites were significantly causally associated with JIA, including two risk factors-kynurenine (odds ratio [OR]: 16.39, 95% confidence interval [CI]: 2.07-129.63, p = 5.11 × 10- 6) and linolenate (OR: 16.48, 95% CI: 1.32-206.22, p = 0.030)-and three protective factors-3-dehydrocarnitine (OR: 0.32, 95% CI: 0.14-0.72, p = 0.007), levulinate (4-oxovalerate) (OR: 0.40, 95% CI: 0.20-0.80, p = 0.010), and X-14,208 (phenylalanylserine) (OR: 0.68, 95% CI: 0.51-0.92, p = 0.010). Furthermore, seven metabolic pathways, including α-linolenic acid metabolism and pantothenate and CoA biosynthesis, are potentially associated with the onset and progression of JIA. CONCLUSION: Five serum metabolites, including kynurenine and 3-dehydrocarnitine, may be causally associated with JIA. These results provide a theoretical framework for developing effective JIA prevention and screening strategies.

Dietary inflammatory index, dietary total antioxidant capacity, and frailty among older Chinese adults.

OBJECTIVES: Frailty is an age-related syndrome associated with poor health outcomes. Studies in developed countries indicate that the dietary inflammatory index (DII) and dietary total antioxidant capacity (DTAC) are important dietary factors influencing the risk of frailty in older adults. However, few studies have explored the association between DII, DTAC, and frailty among older Chinese adults. The objective of the current study was to examine whether DII and DTAC were associated with pre-frailty or frailty among older Chinese adults. DESIGN: A cross-sectional study. SETTING: Community-based. PARTICIPANTS: We included 6414 participants aged ≥60 years. MEASUREMENTS: Dietary intake was assessed using a validated food frequency questionnaire (FFQ). The DII and energy-adjusted DII (E-DII) were calculated using food parameters. DTAC was estimated using two widely adopted antioxidant scores: DTAC based on ferric reducing antioxidant power and dietary antioxidant quality score (DAQS) obtained from vitamins (vitamins A, C, and E) and minerals (zinc and selenium) with antioxidant functions. Frailty was assessed using the frailty index (FI) calculated from 28 health-related deficits. Individuals were classified as robust (FI ≤ 0.10), pre-frailty (FI > 0.10 to <0.25), or frailty (FI ≥ 0.25). Multiple logistic regression models were used to evaluate the associations of DII and DTAC with pre-frailty and frailty. RESULTS: After adjusting for confounding factors, individuals in the highest DII quintile (Q5) were more likely to have pre-frailty (odds ratio [OR] = 1.56; 95% confidence interval [CI]: 1.25-1.93; P for trend <0.001) than those in the lowest Q1. A similar positive association was detected for E-DII and pre-frailty. A significant association was found between DII and frailty. Compared with the lowest Q1, the highest Q5 of DTAC was negatively correlated with pre-frailty (OR = 0.66; 95% CI: 0.52-0.84; P for trend <0.001) and frailty (OR = 0.71; 95% CI: 0.50-0.1.03; P for trend <0.001). The DAQS yielded results similar to pre-frailty results (OR = 0.72; 95% CI: 0.58-0.89; P < 0.001). There was no evidence suggesting an association between DAQS and frailty. CONCLUSIONS: More proinflammatory diets were linked to higher pre-frailty risk, whereas higher levels of dietary antioxidants were associated with lower pre-frailty and frailty risk among older Chinese adults.

Unraveling the genetic architecture of congenital vertebral malformation with reference to the developing spine.

Congenital vertebral malformation, affecting 0.13-0.50 per 1000 live births, has an immense locus heterogeneity and complex genetic architecture. In this study, we analyze exome/genome sequencing data from 873 probands with congenital vertebral malformation and 3794 control individuals. Clinical interpretation identifies Mendelian etiologies in 12.0% of the probands and reveals a muscle-related disease mechanism. Gene-based burden test of ultra-rare variants identifies risk genes with large effect sizes (ITPR2, TBX6, TPO, H6PD, and SEC24B). To further investigate the biological relevance of the genetic association signals, we perform single-nucleus RNAseq on human embryonic spines. The burden test signals are enriched in the notochord at early developmental stages and myoblast/myocytes at late stages, highlighting their critical roles in the developing spine. Our work provides insights into the developmental biology of the human spine and the pathogenesis of spine malformation.

CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements.

BACKGROUND: The CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable elements (TEs) have stimulated research interest in manipulating these elements to understand their functions. However, designing single guide RNAs (sgRNAs) that are specific and efficient for TE manipulation is a significant challenge, given their sequence repetitiveness and high copy numbers. While various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer for TE manipulation has yet to be established. RESULTS: We present CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn/ , and currently tailored to the human and mouse genomes. CRISPR-TE identifies all potential sgRNAs for TEs and provides a comprehensive solution for efficient TE targeting at both the single copy and subfamily levels. Our analysis shows that sgRNAs targeting TEs can more effectively target evolutionarily young TEs with conserved sequences at the subfamily level. CONCLUSIONS: CRISPR-TE offers a versatile framework for designing sgRNAs for TE targeting. CRISPR-TE is publicly accessible at https://www.crisprte.cn/ as an online web service and the source code of CRISPR-TE is available at https://github.com/WanluLiuLab/CRISPRTE/ .

Decreased expression of TXNIP is associated with poor prognosis and immune infiltration in kidney renal clear cell carcinoma.

The most prevalent and insidious type of kidney cancer is kidney clear cell carcinoma (KIRC). Thioredoxin-interacting protein (TXNIP) encodes a thioredoxin-binding protein involved in cellular energy metabolism, redox homeostasis, apoptosis induction and inflammatory responses. However, the relationship between TXNIP, immune infiltration and its prognostic value in KIRC remains unclear. Thus, the present study evaluated the potential for TXNIP as a prognostic marker in patients with KIRC. Data from The Cancer Genome Atlas were used to assess relative mRNA expression levels of TXNIP in different types of cancer. The protein expression levels of TXNIP were evaluated using the Human Protein Atlas. Enrichment analysis of genes co-expressed with TXNIP was performed to assess relevant biological processes that TXNIP may be involved in. CIBERSORT was used to predict the infiltration of 21 tumor-infiltrating immune cells (TIICs). Univariate and multivariate Cox regression analyses were used to assess the relationship between TXNIP expression and prognosis. Single-cell RNA-sequencing datasets were used to evaluate the mRNA expression levels of TXNIP in certain immune cells in KIRC. The CellMiner database was used to analyze the relationship between TXNIP mRNA expression and drug sensitivity in KIRC. The results from the present study demonstrated that TXNIP expression was significantly decreased in KIRC tissue compared with that in normal tissue, as confirmed by western blotting and reverse transcription-quantitative PCR. In addition, downregulated TXNIP expression was significantly associated with poor prognosis, a high histological grade and an advanced stage. The Cell Counting Kit-8 assay demonstrated that TXNIP overexpression significantly suppressed tumor cell proliferation. Univariate and multivariate Cox regression analyses indicated that TXNIP served as a separate prognostic factor in KIRC. Moreover, TXNIP expression was significantly correlated with the accumulation of several TIICs and its overexpression significantly downregulated the mRNA expression levels of CD25 and cytotoxic T-lymphocyte-associated protein 4, immune cell surface markers in CD4+ T lymphocytes. In conclusion, TXNIP may be used as a possible biomarker to assess unfavorable prognostic outcomes and identify immunotherapy targets in KIRC.

Alterations in the sequence and bioactivity of food-derived oligopeptides during simulated gastrointestinal digestion and absorption: a review.

Food-derived oligopeptides (FOPs) exhibit various bioactivities. However, little was known about their sequence changes in the gastrointestinal tract and the effect of changes on bioactivities. FOPs' sequence features, changes and effects on bioactivities have been summarised. The sequence length of FOPs decreases with increased exposure of hydrophobic and basic amino acids at the terminal during simulated gastrointestinal digestion. A decrease in bioactivities after simulated intestinal absorption has correlated with a decrease of Leu, Ile, Arg, Tyr, Gln and Pro. The sequence of FOPs that pass readily through the intestinal epithelium corresponds to transport modes, and FOPs whose sequences remain unchanged after transport are the most bioactive. These include mainly dipeptides to tetrapeptides, consisting of numerous hydrophobic and basic amino acids, found mostly at the end of the peptide chain, especially at the C-terminal. This review aims to provide a foundation for applications of FOPs in nutritional supplements and functional foods.

Clinical significance of DTX2 expression in clear cell renal cell carcinoma tissues and its effect on renal cancer cell proliferation, migration and invasion based on TCGA database / 中国肿瘤生物治疗杂志

@#[摘 要] 目的：基于TCGA数据库分析Deltex E3泛素连接酶2（DTX2）在肾透明细胞癌（ccRCC）组织中的表达水平及临床意义，探讨DTX2对ccRCC细胞增殖、迁移和侵袭的影响。方法：利用TIMER数据库分析DTX2在泛癌组织中的表达水平，通过UALCAN数据库进一步验证ccRCC组织和癌旁组织中DTX2 mRNA和蛋白表达差异。使用UALCAN数据库中的TCGA-ccRCC队列数据集，分析ccRCC中DTX2表达与患者临床病理特征的相关性。通过K-M plot数据库分析DTX2表达与ccRCC患者预后的相关性。利用DAVID数据库对DTX2相关基因进行GO和KEGG通路富集分析。通过qPCR法检测DTX2基因在人胚肾293（HEK293）细胞和ccRCC细胞A498、Caki-1中的表达水平。利用siRNA技术分别将DTX2 siRNA及其阴性对照质粒转入A498、Caki-1细胞，采用CCK-8法、平板克隆实验、划痕实验及Transwell侵袭实验分别检测敲低DTX2对细胞增殖、迁移和侵袭的影响。结果：TCGA数据库分析结果表明，与癌旁组织相比，ccRCC组织中DTX2 mRNA和蛋白均呈高表达（均P<0.01）。DTX2表达水平与ccRCC患者的病理分期、临床分级、不同亚型和淋巴结转移相关联（均P<0.01），DTX2高表达与患者的不良预后具有相关性（均P<0.01）。GO功能和KEGG通路富集分析结果显示，DTX2表达相关基因主要参与蛋白酶体介导的泛素依赖性蛋白质分解代谢等生物学过程，并主要富集到了mTOR信号通路等与肿瘤的相关信号通路中（均P<0.05）。体外细胞实验结果表明，A498和Caki-1细胞中DTX2表达水平高于HEK293细胞；敲低DTX2表达可显著降低A498和Caki-1细胞的增殖、迁移及侵袭能力（均P<0.01）。结论：DTX2在ccRCC组织和细胞中呈高表达，其高表达患者的预后较差。敲低DTX2表达可抑制ccRCC细胞增殖、迁移和侵袭，DTX2有望成为ccRCC新的生物标志物和治疗靶点。

Additive interactions between obesity and insulin resistance on hypertension in a Chinese rural population.

BACKGROUND: Adiposity and insulin resistance (IR) are closely associated with hypertension; however, the role of interactions between obesity phenotypes and IR in hypertension is unclear. This study aimed to evaluate the interactions of body mass index (BMI), waist circumference (WC), and body fat percentage (BF%) with IR on hypertension risk. METHODS: We analyzed data from 4888 participants (mean age 57 years, 41.2% men) in the China Northwest Natural Population Cohort, Ningxia Project. BMI, WC, and BF% were determined using bioelectrical impedance analysis devices. IR was estimated using a homeostasis model assessment index (HOMA-IR). Multivariable-adjusted logistic regression was used to evaluate the association between HOMA-IR and hypertension risk. We calculated the relative excess risk and attributable proportion with their 95% confidence intervals (CIs) to assess whether adiposity phenotypes modified the effect of HOMA-IR on hypertension risk. RESULTS: The crude prevalence of hypertension was 52.2%. The multivariable-adjusted odds ratio of HOMA-IR was 1.80 (95% CI: 1.23-2.65) for the risk of hypertension in the highest versus the lowest quartiles, but this association became marginal in models further adjusting for BMI, WC, and BF% (P for trend = 0.056). Relative excess risk and attributable proportion for interaction between high HOMA-IR and high BF% were 0.32 (0.04-0.59) and 0.33 (0.06-0.60), respectively. Additionally, high truncal and leg BF% and high HOMA-IR accounted for the hypertension risk in women, but not in men. We did not observe any significant interactions between BMI or WC and HOMA-IR on hypertension. CONCLUSION: BF% modified the association between IR and increased risk of hypertension in women with high truncal and leg BF%, but not in men.

Beneficial effects of flavonoids on animal models of atherosclerosis: A systematic review and meta-analysis.

Atherosclerosis is the main cause of cardiovascular diseases that seriously endanger human health. The existing treatment drugs are effective, but they have some side effects. Accumulating evidence suggests that flavonoids have attracted wide attention due to their multiple cardioprotective effects and fewer side effects. PubMed, Web of Science database, Embase, and Cochrane Library were searched for studies evaluating the effects of flavonoids against atherosclerosis. 119 studies published from August 1954 to April 2023 were included. Random-effects models were performed for synthesis. Compared with the control group, flavonoids significantly reduced longitudinal and cross-sectional plaque area. The findings indicated that flavonoids significantly reduced the concentrations of serum TC, TG, and LDL-C and increased serum HDL-C concentrations. Besides, flavonoids reduced the levels of circulating pro-inflammatory factors, including TNF-α, IL-1ß, and IL-6, and increased the serum IL-10 level. This study provides evidence for the potential cardiovascular benefits of flavonoids.

Association between triglyceride glucose-body mass index and heart failure in subjects with diabetes mellitus or prediabetes mellitus: a cross-sectional study.

Background: The triglyceride glucose-body mass index (TyG-BMI) is a surrogate indicator of insulin resistance. However, the association of TyG-BMI with heart failure (HF) in individuals with diabetes mellitus or prediabetes mellitus is unknown. Methods: This study included 7,472 participants aged 20-80 years old with prediabetes or diabetes from the National Health and Nutrition Examination Survey (2007-2018). The TyG-BMI was calculated as Ln [triglyceride (mg/dL) × fasting blood glucose (mg/dL)/2] × BMI, and individuals were categorized into tertiles based on TyG-BMI levels. The relationship of TyG-BMI with HF was analyzed using multiple logistic regression models. Subgroup analyses were stratified by gender, age, hypertension, and diabetes mellitus status. Results: This cross-sectional study had 7,472 participants (weighted n = 111,808,357), including 329 HF participants. Participants with a high TyG-BMI were prone to HF. The highest tertile group with a fully adjusted model was more likely to have HF compared to the lowest tertile group (odds ratio [OR], 2.645; 95% CI, 1.529-4.576). Restricted cubic spline analysis showed a significant dose-response relationship between TyG-BMI and HF (P < 0.001). In subgroup analyses, similar results were seen in terms of age (≥50 years old), gender, hypertension, and diabetes mellitus status. Conclusion: A high TyG-BMI is significantly associated with HF risk in participants with diabetes mellitus or prediabetes mellitus.

Quantitative flood disaster loss-resilience with the multilevel hybrid evaluation model.

The severity of global flood disasters is growing, causing loss of human life and property. Building a high-resilience social system, an important means of sustainable flood control, can address these flood-related issues. Numerous studies have carried out disaster resilience evaluations and explored the correlation between flood disaster loss and intensity, but neglected to analyze the role of resilience construction in disaster loss reduction. This study proposed a research route for linking flood loss and disaster loss to quantify the relationship between the two. Take Guangdong Province, China as a study case, the mixed-effects (ME) model and multilevel hybrid evaluation model (MHEM) were established to assess disaster loss and resilience of cities, respectively. Subsequently, disaster resilience curves were built to quantitatively evaluate disaster resilience and corresponding disaster loss. The results show that (1) the ME model can concurrently build the disaster intensity-loss curves of multiple cities with high fitting accuracy. The MHEM combines multiple methods to determine the evaluation result with the highest consistency, showing high reliability. (2) The central and southern regions of Guangdong Province have low disaster loss and high resilience, while the northern regions have high disaster loss and low resilience. (3) With the improvement of disaster resistance, the reduction in disaster loss gradually decreases. Disaster loss in low-resilience cities exhibits greater randomness than that in high-resilience cities, and increasing their resilience can more significantly reduce their level of loss. This study provides a quantitative basis and available methods for comprehensive responses to natural disasters and adaptation to global climate change.

Genetic testing and diagnostic strategies of fetal skeletal dysplasia: a preliminary study in Wuhan, China.

BACKGROUND: Fetal skeletal dysplasia is a diverse group of degenerative diseases of bone and cartilage disorders that can lead to movement disorder and even death. This study aims to evaluate the diagnostic yield of sonographic examination and genetic testing for fetal skeletal dysplasia. METHODS: From September 2015 to April 2021, the study investigated 24 cases with suspected short-limb fetuses, which were obtained from Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology. To identify the causative gene, multiple approaches (including karyotype analysis, copy number variations and whole exome sequencing) were performed on these fetuses. And further segregation analysis of the candidate variant was performed in parents by using Sanger sequencing. RESULTS: ① Out of 24 cases, likely pathogenic variants in FGFR3, FBN2, COL1A2, CUL7 and DYNC2H1 were detected in 6 cases; pathogenic variants in FGFR3, IMPAD1 and GORAB were identified in other 6 cases; and variants in WNT1, FBN1, OBSL1, COL1A1, DYNC2H1 and NEK1, known as Variant of Undetermined Significance, were found in 4 cases. There were no variants detected in the rest 8 cases by the whole exome sequencing. ② Of 24 cases, 12 (50%) were found to carry variants (pathogenic or likely pathogenic) in seven genes with 12 variants. Four fetuses (16.7%) had variants of uncertain significance. CONCLUSION: Genetic testing combining with ultrasound scanning enhances the accurate diagnosis of fatal skeletal dysplasia in utero, and then provides appropriate genetic counseling.

Lanthanide-grafted hollow bipyridine-based periodic mesoporous organosilicas as chemical sensors.

We have synthesized a co-condensed hollow ethane-bipyridine periodic mesoporous organosilica (HEt-bpy-PMO) as a host material to anchor lanthanides for the purpose of developing a multifunctional chemical sensor. The host material was grafted with lanthanide chloride salts or complexes. The luminescence properties of the developed series of hybrid materials were studied in detail in the solid-state and after dispersing in water. The Eu3+ or Tb3+ singly incorporated materials were investigated for their use as ion sensors, showing ions selectivity towards Cu2+, Co2+ and Fe3+. Additionally, the Eu3+ or Tb3+ incorporated materials showed obvious luminescence quenching behavior towards acetone compared to other organic solvents, indicating excellent acetone sensing selectivity.

Associations between Low-Carbohydrate Diets and Low-Fat Diets with Frailty in Community-Dwelling Aging Chinese Adults.

Frailty is a major health issue associated with aging. Diet affects frailty status; however, studies on the associations between the low-carbohydrate diet (LCD) score, low-fat diet (LFD) score and frailty in older Chinese adults are scarce. This study aimed to examine the associations between the LCD score, LFD score and risk of frailty in older Chinese adults. We analyzed data from 6414 participants aged ≥ 60 years from the China Northwest Natural Population Cohort: Ningxia Project. Frailty was measured using the frailty index (FI), calculated from 28 items comprising diseases, behavioral disorders and blood biochemistry and classified as robust, pre-frail and frail. LCD and LFD scores were calculated using a validated food frequency questionnaire (FFQ). Multiple logistic regression models were used to evaluate associations between LCD, LFD scores and frail or pre-frail status after adjusting for confounders. Participants' mean age was 66.60 ± 4.15 years, and 47.8% were male. After adjusting for age, sex, educational level, drinking, smoking, BMI, physical activity and total energy, compared to the lowest quartile (Q1: reference), the odds ratios (ORs) for pre-frail and frail status in the highest quartile (Q4) of LCD score were 0.73 (95% confidence intervals: 0.61-0.88; p for trend = 0.017) and 0.73 (95%CI: 0.55-0.95; p for trend = 0.035), respectively. No significant associations were observed between LFD score and either pre-frail or frail status. Our data support that lower-carbohydrate diets were associated with lower pre-frail or frail status, particularly in females, while diets lower in fat were not significantly associated with the risk of either pre-frail or frail status in older Chinese adults. Further intervention studies are needed to confirm these results.

Selenium-enriched peptides identified from selenium-enriched soybean protein hydrolysate: protective effects against heat damage in Caco-2 cells.

Our previous study evaluated the antioxidant and anti-inflammatory activities of selenium-enriched soybean peptides (SePPs) in vivo. In this study, we purified SePPs via gel filtration chromatography and obtained five fractions (F1, F2, F3, F4 and F5), among which F3 displayed the highest antioxidant and anti-inflammatory activities. Nineteen selenium-enriched peptides were identified in F3 by mass spectrometry. Two selenium-enriched peptides with sequences ESeCQIQKL (Sep-1) and SELRSPKSeC (Sep-2) were selected for synthesis based on their score and the number of hydrophobic amino acids, acidic and basic amino acids. Both Sep-1 and Sep-2 exhibited preventive effects on the heat stress-induced impairment of intestinal epithelial cell integrity, oxidative stress and inflammatory responses in a Caco-2 cell model. Pretreatment of the cells with Sep-1 or Sep-2 for 24 h reduced intracellular reactive oxygen species (ROS) generation, prevented the disruption of tight junction (TJ) proteins, and decreased paracellular permeability. Western blot results showed that Sep-1 and Sep-2 could improve the abnormal expressions of Nrf2, Keap1, NLRP3, caspase-1 and ASC/TMS1, thereby enhancing the glutathione (GSH) redox system and reducing IL-1ß and IL-18 concentrations. Sep-1 activated the Nrf2-Keap1 signaling pathway significantly more than Sep-2. Molecular docking results indicated that Sep-1 and Sep-2 are both bound to Keap1 and NLRP3 in the form of hydrogen bonds, hydrophobic interactions and salt bridges, which interferes with Nrf2 and NLRP3 signaling. Molecular dynamics simulations suggested that more hydrogen bonds were formed during the resultant process of Sep-1 with Keap1, and the compactness and stability of the complex structure were better than those of Sep-2. These findings confirm the value of both Sep-1 and Sep-2 in the development of dietary supplements as potential alternatives for heat damage and related disease prevention.

Dissecting peri-implantation development using cultured human embryos and embryo-like assembloids.

Studies of cultured embryos have provided insights into human peri-implantation development. However, detailed knowledge of peri-implantation lineage development as well as underlying mechanisms remains obscure. Using 3D-cultured human embryos, herein we report a complete cell atlas of the early post-implantation lineages and decipher cellular composition and gene signatures of the epiblast and hypoblast derivatives. In addition, we develop an embryo-like assembloid (E-assembloid) by assembling naive hESCs and extraembryonic cells. Using human embryos and E-assembloids, we reveal that WNT, BMP and Nodal signaling pathways synergistically, but functionally differently, orchestrate human peri-implantation lineage development. Specially, we dissect mechanisms underlying extraembryonic mesoderm and extraembryonic endoderm specifications. Finally, an improved E-assembloid is developed to recapitulate the epiblast and hypoblast development and tissue architectures in the pre-gastrulation human embryo. Our findings provide insights into human peri-implantation development, and the E-assembloid offers a useful model to disentangle cellular behaviors and signaling interactions that drive human embryogenesis.

MSdb: An integrated expression atlas of human musculoskeletal system.

The global prevalence and burden of musculoskeletal (MSK) disorders are immense. Advancements in next-generation sequencing (NGS) have generated vast amounts of data, accelerating the research of pathological mechanisms and the development of therapeutic approaches for MSK disorders. However, scattered datasets across various repositories complicate uniform analysis and comparison. Here, we introduce MSdb, a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis. Overall, systematic categorizing, standardized processing, and freely accessible knowledge features MSdb a valuable resource for MSK research community.

Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network.

Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown. In this study, we identify the unexpected role of a highly expressed 2-cell (2C) embryo specific transcription factor, ZFP352, in facilitating the dissolution of the totipotency network. We find that ZFP352 has selective binding towards two different retrotransposon sub-families. ZFP352 coordinates with DUX to bind the 2C specific MT2_Mm sub-family. On the other hand, without DUX, ZFP352 switches affinity to bind extensively onto SINE_B1/Alu sub-family. This leads to the activation of later developmental programs like ubiquitination pathways, to facilitate the dissolution of the 2C state. Correspondingly, depleting ZFP352 in mouse embryos delays the 2C to morula transition process. Thus, through a shift of binding from MT2_Mm to SINE_B1/Alu, ZFP352 can trigger spontaneous dissolution of the totipotency network. Our study highlights the importance of different retrotransposons sub-families in facilitating the timely and programmed cell fates transition during early embryogenesis.