Regulon active landscape reveals cell development and functional state changes of human primary osteoblasts in vivo.

BACKGROUND: While transcription factor (TF) regulation is known to play an important role in osteoblast development, differentiation, and bone metabolism, the molecular features of TFs in human osteoblasts at the single-cell resolution level have not yet been characterized. Here, we identified modules (regulons) of co-regulated genes by applying single-cell regulatory network inference and clustering to the single-cell RNA sequencing profiles of human osteoblasts. We also performed cell-specific network (CSN) analysis, reconstructed regulon activity-based osteoblast development trajectories, and validated the functions of important regulons both in vivo and in vitro. RESULTS: We identified four cell clusters: preosteoblast-S1, preosteoblast-S2, intermediate osteoblasts, and mature osteoblasts. CSN analysis results and regulon activity-based osteoblast development trajectories revealed cell development and functional state changes of osteoblasts. CREM and FOSL2 regulons were mainly active in preosteoblast-S1, FOXC2 regulons were mainly active in intermediate osteoblast, and RUNX2 and CREB3L1 regulons were most active in mature osteoblasts. CONCLUSIONS: This is the first study to describe the unique features of human osteoblasts in vivo based on cellular regulon active landscapes. Functional state changes of CREM, FOSL2, FOXC2, RUNX2, and CREB3L1 regulons regarding immunity, cell proliferation, and differentiation identified the important cell stages or subtypes that may be predominantly affected by bone metabolism disorders. These findings may lead to a deeper understanding of the mechanisms underlying bone metabolism and associated diseases.

Functional Enrichment Analysis Identifying Regulatory Information Associated with Human Fracture.

Dozens of loci associated with fracture have been identified by genome-wide association studies (GWASs). However, most of these variants are located in the noncoding regions including introns, long terminal repeats, and intergenic regions. Although combining regulation information helps to identify the causal SNPs and interpret the involvement of these variants in the etiology of human fracture, regulation information which was truly associated with fracture was unknown. A novel functional enrichment method GARFIELD (GWAS Analysis of Regulatory of Functional Information Enrichment with LD correction) was applied to identify fracture-associated regulation information, including transcript factor binding sites, expression quantitative trait loci (eQTLs), chromatin states, enhancer, promoter, dyadic, super enhancer and Epigenome marks. Fracture SNPs were significantly enriched in exon (Bonferroni correction, p value < 7.14 × 10-3) at two GWAS p value thresholds through GARFIELD. High level of fold-enrichment was observed in super enhancer of monocyte and the enhancer of chondrocyte (Bonferroni correction, p value < 4.45 × 10-3). eQTLs of 44 tissues/cells and 10 transcription factors (TFs) were identified to be associated with human fracture. These results provide new insight into the etiology of human fracture, which might increase the identification of the causal SNPs through the fine-mapping study combined with functional annotation, as well as polygenic risk score.

Integrative analysis of multi-omics data to detect the underlying molecular mechanisms for obesity in vivo in humans.

BACKGROUND: Obesity is a complex, multifactorial condition in which genetic play an important role. Most of the systematic studies currently focuses on individual omics aspect and provide insightful yet limited knowledge about the comprehensive and complex crosstalk between various omics levels. SUBJECTS AND METHODS: Therefore, we performed a most comprehensive trans-omics study with various omics data from 104 subjects, to identify interactions/networks and particularly causal regulatory relationships within and especially those between omic molecules with the purpose to discover molecular genetic mechanisms underlying obesity etiology in vivo in humans. RESULTS: By applying differentially analysis, we identified 8 differentially expressed hub genes (DEHGs), 14 differentially methylated regions (DMRs) and 12 differentially accumulated metabolites (DAMs) for obesity individually. By integrating those multi-omics biomarkers using Mendelian Randomization (MR) and network MR analyses, we identified 18 causal pathways with mediation effect. For the 20 biomarkers involved in those 18 pairs, 17 biomarkers were implicated in the pathophysiology of obesity or related diseases. CONCLUSIONS: The integration of trans-omics and MR analyses may provide us a holistic understanding of the underlying functional mechanisms, molecular regulatory information flow and the interactive molecular systems among different omic molecules for obesity risk and other complex diseases/traits.

Gardenia (Gardenia jasminoides Ellis) fruit: a critical review of its functional nutrients, processing methods, health-promoting effects, comprehensive application and future tendencies.

Gardenia fruit (GF) is the mature fruit of Gardenia jasminoides Ellis, boasting a rich array of nutrients and phytochemicals. Over time, GF has been extensively utilized in both food and medicinal contexts. In recent years, numerous studies have delved into the chemical constituents of GF and their associated pharmacological activities, encompassing its phytochemical composition and health-promoting properties. This review aims to provide a critical and comprehensive summary of GF research, covering nutrient content, extraction technologies, and potential health benefits, offering new avenues for future investigations and highlighting its potential as an innovative food resource. Additionally, the review proposes novel industrial applications for GF, such as utilizing gardenia yellow/red/blue pigments in the food industry and incorporating it with other herbs in traditional Chinese medicine. By addressing current challenges in developing GF-related products, this work provides insights for potential applications in the cosmetics, food, and health products industries. Notably, there is a need for the development of more efficient extraction methods to harness the nutritional components of GF fully. Further research is needed to understand the specific molecular mechanisms underlying its bioactivities. Exploring advanced processing techniques to create innovative GF-derived products will show great promise for the future.

Advances on delta 5-unsaturated-polymethylene-interrupted fatty acids: Resources, biosynthesis, and benefits.

Though the knowledge on delta 5-unsaturated-polymethylene-interrupted fatty acids (Δ5-UPIFAs) is being updated, the issue of their integration still exists within the field. Thus, this review systematically summarizes the sources, biosynthesis and metabolism, analytical methods, preparation, and health-promoting roles of Δ5-UPIFAs. In plants, the content of Δ5-UPIFAs is higher, which is an ideal source. In animals, although the content of Δ5-UPIFAs is not high, there are many species, which is the possible source of some special Δ5-UPIFAs. At present, although the extraction of Δ5-UPIFAs is mainly from plants, the fermentation by organisms, especially for genetically modified microorganisms engineering maybe be a substitue of pepration of Δ5-UPIFAs. Δ5-UPIFAs have been proved to possess multi-beneficial effects, such as lipid lowering, anti-inflammation and so on, so it has a certain potential application value. However, related knowledge of the underlying molecular mechanisms regarding Δ5-UPIFAs limited, and how Δ5-UPIFAs work is not clear. Further clinical and human studies about Δ5-UPIFAs are also needed. Studies on tapping new resources, developing structured lipide rich in Δ5-UPIFA and enhancing delivery were quite deficient. This review emphasizes the further directions on Δ5-UPIFAs with scientific suggestions to pay more attention to the applications of Δ5-UPIFAs in food, pharmaceutical and cosmetic industries.

Synthesis, Crystal Structure, and Nonlinear-Optical Properties of a Diamond-Like Chalcogenide Cu2GeS3.

Metal sulfides with diamond-like (DL) structures generally exhibit excellent mid-IR nonlinear-optical (NLO) properties. Here, Cu2GeS3 (CGS) as a member of the DL chalcogenides was synthesized by a high-temperature solid-state method, and the optical properties were carefully studied experimentally and theoretically. The results revealed that CGS has a large second harmonic generation (0.8 × AgGaSe2) and a moderate birefringence of 0.067 at 1064 nm. In addition, the linear and NLO properties of the A2MS3 (A = Cu, Li; M = Ge, Si) series of compounds were evaluated and compared with the help of first-principles calculations.

Perfectly Encoding π-Conjugated Anions in the RE5 (C3 N3 O3 )(OH)12 (RE=Y, Yb, Lu) Family with Strong Second Harmonic Generation Response and Balanced Birefringence.

Nonlinear optical (NLO) crystal, which simultaneously exhibits strong second-harmonic-generation (SHG) response and desired optical anisotropy, is a core optical material accessible to the modern optoelectronics. Accompanied by strong SHG effect in a NLO crystal, a contradictory problem of overlarge birefringence is ignored, leading to low frequency doubling efficiency and poor beam quality. Herein, a series of rare earth cyanurates RE5 (C3 N3 O3 )(OH)12 (RE=Y, Yb, Lu) were successfully characterized by 3D electron diffraction technique. Based on a "three birds with one stone" strategy, they enable the simultaneous fulfillment of strong SHG responses (2.5-4.2× KH2 PO4 ), short UV cutoff (ca. 220 nm) and applicable birefringence (ca. 0.15 at 800 nm) by the introduction of rare earth coordination control of π-conjugated (C3 N3 O3 )3- anions. These findings provide high-performance short-wavelength NLO materials and highlight the exploration of cyanurates as a new research area.

Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants.

MOTIVATION: Although genome-wide association studies (GWASs) have identified thousands of variants for various traits, the causal variants and the mechanisms underlying the significant loci are largely unknown. In this study, we aim to predict non-coding variants that may functionally affect translation initiation through long-range chromatin interaction. RESULTS: By incorporating the Hi-C data, we propose a novel and powerful deep learning model of artificial intelligence to classify interacting and non-interacting fragment pairs and predict the functional effects of sequence alteration of single nucleotide on chromatin interaction and thus on gene expression. The changes in chromatin interaction probability between the reference sequence and the altered sequence reflect the degree of functional impact for the variant. The model was effective and efficient with the classification of interacting and non-interacting fragment pairs. The predicted causal SNPs that had a larger impact on chromatin interaction were more likely to be identified by GWAS and eQTL analyses. We demonstrate that an integrative approach combining artificial intelligence-deep learning with high throughput experimental evidence of chromatin interaction leads to prioritizing the functional variants in disease- and phenotype-related loci and thus will greatly expedite uncover of the biological mechanism underlying the association identified in genomic studies. AVAILABILITY AND IMPLEMENTATION: Source code used in data preparing and model training is available at the GitHub website (https://github.com/biocai/DeepHiC). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

NaN(SiMe3)2/CsTFA Copromoted Aminobenzylation/Cyclization of 2-Isocyanobenzaldehydes with Toluene Derivatives or Benzyl Compounds: One-Pot Access to Dihydroquinazolines and Quinazolines.

A NaN(SiMe3)2/CsTFA copromoted aminobenzylation/cyclization reaction of 2-isocyanobenzaldehydes with toluene derivatives or benzyl compounds has been developed. The reaction works with a broad range of toluene derivatives and benzyl compounds, and provides a simple and efficient strategy for the synthesis of 4-benzyl-substitued dihydroquinazoline and quinazoline derivatives from easily available acyclic starting materials in a single step. Further applications, including synthesis of quinazoline, dihydroindolo[1,2-c]quinazoline, and dihydro-8H-isoquinolino[2,3-c]quinazoline, demonstrated the tremendous potential of the tandem reaction.

Growth, Structure, and Optical Properties of a Nonlinear Optical Niobium Borate Crystal CsNbOB2O5 with Distorted NbO5 Square Pyramids.

In this paper, a revised structure determination of an already known compound CsNbOB2O5 with new structural insights was performed and the detailed characterization of its optical properties was reported for the first time. CsNbOB2O5 was synthesized by spontaneous crystallization. It crystallizes in the Pmn21 space group, and the unit lattice parameters are a = 7.5220(7) Å, b = 3.9881(4) Å, c = 9.7167(9) Å, and Z = 2. In the structure of CsNbOB2O5, a [NbO5] square pyramid and [B2O5] unit are linked to constitute an infinitely extended two-dimensional ∞2[NbOB2O5] layer via sharing oxygen atoms. Between these two-dimensional layers, there are no covalent bonds perpendicular to their planes based on Mulliken bond order analysis. CsNbOB2O5 has a wide band gap (4.52 eV) and a large second-harmonic-generation (SHG) response (1.2 × KDP) and demonstrates type-I phase-matchable behavior. First-principles simulations reveal that the birefringence is approximately 0.10. Moreover, SHG-weighted charge density analysis shows that the primary source of the nonlinearity of the title compound is the distorted NbO5 square pyramids.

Building core-shell FeSe2@C anode electrode for delivering superior potassium-ion batteries.

Inferior electrical conductivity and large volume variation are two disadvantages of metal selenides. In this work, we have designed a core-shell structure of FeSe2@C composite with low cost using facile hydrothermal method. The FeSe2particles as the 'core' and the carbon layer as the 'shell' displayed good synergistic effect that attributed to alleviate volume expansion of electrode and improving the electrical conductivity, which achieved the fast potassium storage. The core-shell structural FeSe2@C electrode achieved 286 mA h g-1at 1 A g-1over 1000 cycles with 99.8% coulombic efficiency and delivered excellent rate capacity with 273 mA h g-1at 2 A g-1, which was ascribed to dispersed FeSe2particles and the strong carbon shell coating. This work will provide the basis for the further development of the application of metal selenides in the field of flexible electrodes.

Cd7SiAs6, a Nonchalcopyrite Arsenide with a Strong Nonlinear-Optical Response.

A new arsenide, Cd7SiAs6, has been successfully synthesized and characterized. It is the first arsenide that adopts a nonchalcopyrite structure and possesses a strong nonlinear-optical (NLO) response. In the structure, the CdAs3 trigonal planar unit, a kind of π-conjugated planar NLO-active group, was identified for the first time. Furthermore, theoretical calculations reveal that the CdAs3 planar unit contributes more to the NLO effect than the CdAs4 tetrahedron does. The result may provide valuable insights for the future exploration of IR NLO materials, especially for application above 10 µm.

Dietary fibers fractionated from gardenia (Gardenia jasminoides Ellis) husk: structure and in vitro hypoglycemic effect.

BACKGROUND: Gardenia (Gardenia jasminoides Ellis) husk rich in dietary fiber is a byproduct of fructus processing, and commonly discarded as waste. The husk was fractionated by sequential extraction into four fractions: water-soluble fiber (W-SF), acid-soluble fiber (Ac-SF), alkali-soluble fiber (Al-SF) and insoluble residue fiber (IRF). The aim of this study was to investigate the differences in structure and in vitro hypoglycemic effect of these fibers. RESULTS: Monosaccharide composition and Fourier transform infrared spectra showed that the major component might be pectin for W-SF and Ac-SF, xylan as well as pectin for Al-SF and cellulose for IRF. These fibers offered excellent water-holding capacity and swelling capacity, except that IRF was only slightly swellable in water. W-SF exhibited significantly higher capacities to adsorb glucose (2.408 mmol g-1 at a glucose concentration of 200 mmol L-1 ) and inhibit α-amylase activity (29.48-49.45% inhibition rate at a concentration of 4-8 mg mL-1 ), probably caused by the higher viscosity and hydration properties; while Ac-SF, Al-SF and IRF (especially Al-SF) were more effective in retarding the glucose diffusion across a dialysis membrane (34.97-41.67% at 20-30 min), which might be attributed to particle size and specific surface area. All the fibers could quench the intrinsic fluorescence of α-amylase to some degree. CONCLUSIONS: Dietary fiber from gardenia husk, especially W-SF, can be used as a potential hypoglycemic ingredient in diabetic functional foods. © 2020 Society of Chemical Industry.

FAM134B Attenuates Seizure-Induced Apoptosis and Endoplasmic Reticulum Stress in Hippocampal Neurons by Promoting Autophagy.

Autophagy plays a critical role in epileptic neuronal injury, and recent studies have demonstrated that FAM134B plays an important role in regulating autophagy. However, the effect of FAM134B on epileptic neuronal injury remains unclear. In this study, we investigated the role of FAM134B in neuronal apoptosis and endoplasmic reticulum (ER) stress using the hippocampal neuronal culture model of acquired epilepsy (AE) in vitro. We found that in this model, the level of autophagy significantly increased, indicated by an elevated LC3-II/LC3-I ratio. FAM134B overexpression using lentiviral vectors enhanced autophagy, whereas FAM134B downregulation using lentiviral vectors impaired this process. In addition, the ER Ca2+ concentration was decreased and the intracellular level of reactive oxygen species was increased in this model. FAM134B overexpression was sufficient to reverse these changes. Moreover, FAM134B overexpression attenuated ER stress as shown by a decrease in the expression of C/-EBP homologous protein and glucose-regulated protein 78, and neuronal apoptosis induced by seizure, while FAM134B downregulation caused the opposite effects. Further, pre-treatment with the selective autophagy inhibitor 3-methyladenine abolished the effects of FAM134B on ER stress and neuronal apoptosis. Altogether, we demonstrate that FAM134B is an important regulator of AE-induced ER stress and neuronal apoptosis by controlling autophagy function.

Antioxidant activity and absorption of cyanidin-3-O-glucoside liposomes in GES-1 cells in vitro.

The use of anthocyanins are limited by their chemical properties. Recent evidence suggests Cyanidin-3-O-glucoside (C3 G) liposomes via the ethanol injection method exhibit improved stability. In the current study, the characterization and cell absorption of C3 G liposomes were explored via transmission electron microscopy and flow cytometry. The internalization of the C3 G liposomes across the gastric epithelial cell monolayer (GES-1 cells) were investigated. Results showed that the particle size and encapsulation efficiency were 234 ± 9.35 nm and 75.0% ± 0.001, respectively. The total antioxidant capacity (T-AOC) and malondialdehyde (MDA) content were used to evaluate the antioxidant activity of C3 G liposomes. The C3 G liposomes can obviously increased T-AOC and decreased the MDA content.Collectively, C3 G liposomes protected human GES-1 cells from gastric mucosal injury induced by H2O2 by activating the related antioxidant pathway. Our research could provide a new effective treatment strategy for the absorption of stomach drugs.Abbreviations: C3G: Cyanidin-3-O-glucoside; LP: Liposome; GES-1 cells: Human gastric epithelial cell lines; FBS: Fetal Bovine Serum; PBS: Phosphate-buffered saline; PC: Phosphatidylcholine; CH: Cholesterol; MDA: Malondialdehyde; TEM: Transmission electron microscope; FCM: Flow cytometry; FITC: Fluorescein isothiocyanate; DAPI: 4', 6-diamidino-2phenylidole; FT-IR: Fourier Transform infrared spectroscopy; PFA: Paraformaldehyde.

A new compound heterozygous mutation in adult-onset Krabbe disease.

Purpose: Krabbe disease (KD) or globoid cell leukodystrophy is an autosomal recessive lysosomal disorder caused by a lack of the lysosomal enzyme galactocerebrosidase (GALC) because of mutations in GALC. Patients with KD exhibit a wide spectrum of clinical symptoms; therefore, their diagnosis can be challenging. We report the clinical features and gene mutations in a 48-year-oldpatient with adult-onset KD.Methods: We collected and analyzed clinical data of the patientwith a diagnosis of KD. Gene mutations were identified by whole exome sequencing.Results: We describe a case of adult-onset KD caused by a novel compound heterozygous mutation; a missense mutation, c. 1901 T > C (p. L634S); and a novel nonsense mutation, c.1005C > G (p. Y335X), in GALC. The disease onset started when the patient was 40 years old, and manifested as typical paralytic paraplegia. Magnetic resonance imaging indicated demyelination of the white matter, which is consistent with the typical symptoms of adult-onset KD. Biochemical analysis revealed GALC activity to be 1.5 nmol/17 h/mg protein, confirming its deficiency and KD diagnosis.Conclusions: Our findings provide evidence of a novel mutation, providing additional information toward to the GALC mutation database.

Role of the mitochondrial calcium uniporter in Mg2+-free-induced epileptic hippocampal neuronal apoptosis.

PURPOSE: Mitochondrial Ca2+ overload is closely associated with seizure-induced neuronal damage. The mitochondrial calcium uniporter (MCU) plays a crucial role in regulating mitochondrial Ca2+ homeostasis. However, the role of the MCU in seizure-induced neuronal damage remains elusive. Materials and methods: In this study, the hippocampal neuronal culture (HNC) model of acquired epilepsy (AE) was used to investigate the role of the MCU in seizure-induced neuronal injury. Results: We found an increase in mitochondrial Ca2+ concentration in the HNC model of AE. The MCU inhibitor, Ru360, significantly reduced the rate of seizure-induced cell apoptosis and mitochondrial reactive oxygen species (ROS) production; whereas, the MCU agonist, spermine, exacerbated these processes. In addition, Ru360 significantly attenuated seizure-induced endoplasmic reticulum (ER) stress, which is characterized by the expression of glucose-regulated protein 78 (GRP78) and C/-EBP homologous protein (CHOP), while spermine had the opposite effect. We also found that pre-treatment with the mitochondria-targeted antioxidant, mitoquinone, decreased GRP78 and CHOP expression. Moreover, knockdown of CHOP using CHOP-specific small interfering RNA reduced neuronal seizure-induced apoptosis. Conclusions: Taken together, our data indicate that MCU inhibition has a neuroprotective effect against seizure-induced neuronal damage and that this mechanism may involve reduction of ROS-mediated ER stress.

Facile Growth of an Ultraviolet Hydroisocyanurate Crystal with Strong Nonlinearity and a Wide Phase-Matching Region from π-Conjugated (HC3N3O3)2- Groups.

Mixed-alkali-metal hydroisocyanurate nonlinear-optical crystal RbLi(HC3N3O3)·2H2O was grown by a facile aqueous solution method. It exhibits a short phase-matching wavelength (λPM = 239 nm) and a strong second-harmonic-generation response (deff = 2.1KDP) benefitting from the well-aligned planar π-conjugated (HC3N3O3)2- anions, as confirmed by the first-principles calculations. Moreover, solar blind ultraviolet radiation can be reached using the title crystal via a fourth-harmonic-generation technique of a Nd-based laser, i.e., 1064 nm/4 = 266 nm.

Parallel Alignment of π-Conjugated Anions in Hydroisocyanurates Enhancing Optical Anisotropy.

Birefringent crystals with optical anisotropy, which are employed to modulate the polarization of light, play a vital role in many fields of the optical industry. In this Communication, two mixed alkali metal hydroisocyanurates, RbLi(H2C3N3O3)2·2H2O (I) and CsLi(H2C3N3O3)2·2H2O (II), were synthesized by a simple aqueous solution method, and they feature layered structures composed of ∞2[H2C3N3O3]- ribbons through hydrogen bonds with the separation of water molecules and alkali cations. They exhibit a simultaneously short ultraviolet cutoff and giant birefringence, resulting from the perfect parallel alignment of π-conjugated (H2C3N3O3)- anions. Interestingly, the first-principles calculations elucidated that the electronic states and optical properties are slightly different owing to the distinct p-π interaction between alkaline metals and the (H2C3N3O3)- group despite the isostructural crystallographic lattice.

Ba2M(C3N3O3)2 (M = Sr, Pb): Band Engineering from p-π Interaction via Homovalent Substitution in Metal Cyanurates Containing Planar π-Conjugated Groups.

The two new metal cyanurates Ba2M(C3N3O3)2 (M = Sr, Pb) were successfully grown by a solid-state cyclotrimerization reaction. The electronic energy bands of Ba2M(C3N3O3)2 are totally divergent in spite of their same structures and similar interlayer distances. Theoretical calculations show the narrowing band gap of Ba2Pb(C3N3O3)2 stems from the strong interaction between Pb 6p orbitals and anti-π orbitals in (C3N3O3)3- groups.