Transcriptional coupling of distant regulatory genes in living embryos.

The prevailing view of metazoan gene regulation is that individual genes are independently regulated by their own dedicated sets of transcriptional enhancers. Past studies have reported long-range gene-gene associations1-3, but their functional importance in regulating transcription remains unclear. Here we used quantitative single-cell live imaging methods to provide a demonstration of co-dependent transcriptional dynamics of genes separated by large genomic distances in living Drosophila embryos. We find extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases. Regulatory interconnectivity depends on promoter-proximal tethering elements, and perturbations in these elements uncouple transcription and alter the bursting dynamics of distant genes, suggesting a role of genome topology in the formation and stability of co-transcriptional hubs. Transcriptional coupling is detected throughout the fly genome and encompasses a broad spectrum of conserved developmental processes, suggesting a general strategy for long-range integration of gene activity.

Control of noncoding RNA production and histone levels by a 5' tRNA fragment.

Small RNAs derived from mature tRNAs, referred to as tRNA fragments or "tRFs," are an emerging class of regulatory RNAs with poorly understood functions. We recently identified a role for one specific tRF-5' tRF-Gly-GCC, or tRF-GG-as a repressor of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs-snoRNAs, scaRNAs, and snRNAs-that are dependent on Cajal bodies for stability and activity. Among these noncoding RNAs, regulation of the U7 snRNA by tRF-GG modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, on activity of a histone 3' UTR reporter, and ultimately on MERVL regulation could all be suppressed by manipulating U7 RNA levels. We additionally show that the related RNA-binding proteins hnRNPF and hnRNPH bind directly to tRF-GG, and are required for Cajal body biogenesis, positioning these proteins as strong candidates for effectors of tRF-GG function in vivo. Together, our data reveal a conserved mechanism for 5' tRNA fragment control of noncoding RNA biogenesis and, consequently, global chromatin organization.

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains.

Modern multiomic technologies can generate deep multiscale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make analyses and integration of high-dimensional omic datasets challenging. Here we present Significant Latent Factor Interaction Discovery and Exploration (SLIDE), a first-in-class interpretable machine learning technique for identifying significant interacting latent factors underlying outcomes of interest from high-dimensional omic datasets. SLIDE makes no assumptions regarding data-generating mechanisms, comes with theoretical guarantees regarding identifiability of the latent factors/corresponding inference, and has rigorous false discovery rate control. Using SLIDE on single-cell and spatial omic datasets, we uncovered significant interacting latent factors underlying a range of molecular, cellular and organismal phenotypes. SLIDE outperforms/performs at least as well as a wide range of state-of-the-art approaches, including other latent factor approaches. More importantly, it provides biological inference beyond prediction that other methods do not afford. Thus, SLIDE is a versatile engine for biological discovery from modern multiomic datasets.

Corner-Sharing Tetrahedrally Coordinated W-V Dual Active Sites on Cu2 V2 O7 for Photoelectrochemical Water Oxidation.

The sluggish four-electron oxygen evolving reaction is one of the key limitations of photoelectrochemical water decomposition. Optimizing the binding of active sites to oxygen in water and promoting the conversion of *O to *OOH are the key to enhancing oxygen evolution reaction. In this work, W-doped Cu2 V2 O7 (CVO) constructs corner-sharing tetrahedrally coordinated W-V dual active sites to induce the generation of electron deficiency active centers, promote the adsorption of ─OH, and accelerate the transformation of *O to *OOH for water splitting. The photocurrent obtained by the W-modified CVO photoanode is 0.97 mA cm-2 at 1.23 V versus RHE, which is much superior to that of the reported CVO. Experimental and theoretical results show that the excellent catalytic performance may be attributed to the formation of synergistic dual active sites between W and V atoms, and the introduction of W ions reduces the charge migration distance and prolongs the lifetime of photogenerated carriers. Meanwhile, the electronic structure in the center of the d-band is modulated, which leads to the redistribution of the electron density in CVO and lowers the energy barrier for the conversion of the rate-limiting step *O to *OOH.

Enhancing clinical utility: deep learning-based embryo scoring model for non-invasive aneuploidy prediction.

BACKGROUND: The best method for selecting embryos ploidy is preimplantation genetic testing for aneuploidies (PGT-A). However, it takes more labour, money, and experience. As such, more approachable, non- invasive techniques were still needed. Analyses driven by artificial intelligence have been presented recently to automate and objectify picture assessments. METHODS: In present retrospective study, a total of 3448 biopsied blastocysts from 979 Time-lapse (TL)-PGT cycles were retrospectively analyzed. The "intelligent data analysis (iDA) Score" as a deep learning algorithm was used in TL incubators and assigned each blastocyst with a score between 1.0 and 9.9. RESULTS: Significant differences were observed in iDAScore among blastocysts with different ploidy. Additionally, multivariate logistic regression analysis showed that higher scores were significantly correlated with euploidy (p < 0.001). The Area Under the Curve (AUC) of iDAScore alone for predicting euploidy embryo is 0.612, but rose to 0.688 by adding clinical and embryonic characteristics. CONCLUSIONS: This study provided additional information to strengthen the clinical applicability of iDAScore. This may provide a non-invasive and inexpensive alternative for patients who have no available blastocyst for biopsy or who are economically disadvantaged. However, the accuracy of embryo ploidy is still dependent on the results of next-generation sequencing technology (NGS) analysis.

Silver Nanoparticle-Loaded Titanium-Based Metal-Organic Framework for Promoting Antibacterial Performance by Synergistic Chemical-Photodynamic Therapy.

The abuse of antibiotics leads to an increasing emergence of drug-resistant bacteria, which not only causes a waste of medical resources but also seriously endangers people's health and life safety. Therefore, it is highly desirable to develop an efficient antibacterial strategy to reduce the reliance on traditional antibiotics. Antibacterial photodynamic therapy (aPDT) is regarded as an intriguing antimicrobial method that is less likely to generate drug resistance, but its efficiency still needs to be further improved. Herein, a robust titanium-based metal-organic framework ACM-1 was adopted to support Ag nanoparticles (NPs) to obtain Ag NPs@ACM-1 for boosting antibacterial efficiency via synergistic chemical-photodynamic therapy. Apart from the intrinsic antibacterial nature, Ag NPs largely boost ROS production and thus improve aPDT efficacy. As a consequence, Ag NPs@ACM-1 shows excellent antibacterial activity under visible light illumination, and its minimum bactericidal concentrations (MBCs) against E. coli, S. aureus, and MRSA are as low as 39.1, 39.1, and 62.5 µg mL-1, respectively. Moreover, to expand the practicability of Ag NPs@ACM-1, two (a dense and a loose) Ag NPs@ACM-1 films were readily fabricated by simply dispersing Ag NPs@ACM-1 into heated aqueous solutions of edible agar and sequentially cooling through heating or freeze-drying, respectively. Notably, these two films are mechanically flexible and exhibit excellent antibacterial activities, and their antimicrobial performances can be well retained in their recyclable and remade films. As agar is nontoxic, degradable, inexpensive, and ecosustainable, the dense and loose Ag NPs@ACM-1 films are potent to serve as recyclable and degradable antibacterial plastics and antibacterial dressings, respectively.

Association between physical activity and diet quality of obese and non-obese MAFLD.

BACKGROUND AND AIM: Clinical data on the prevalence of metabolic-associated fatty liver disease (MAFLD) in obese and non-obese individuals within a diverse US population is scarce. Furthermore, the influence of physical activity (PA) and dietary quality (DQ) on MAFLD risk remains unclear. This study aims to assess the prevalence and clinical features of MAFLD and examine the relationship between PA and DQ with the risk of developing MAFLD. METHODS AND RESULTS: A cross-sectional analysis of data from the 2017-2018 National Health and Nutrition Examination Survey (NHANES) was conducted. The overall MAFLD prevalence was 41.9%, with 28.6% of participants being obese and 13.4% non-obese. Among those with MAFLD, 67.1% (95% confidence interval (CI): 59.1%-75.1%) were obese, and 32.9% (95% CI: 29.1%-36.7%) were non-obese. Non-obese MAFLD was more frequent in Asians (27.2%), while obese MAFLD was more prevalent in Blacks (66.3%). Metabolic comorbidities were more common in individuals with obese MAFLD, who also exhibited more advanced fibrosis. A high-quality diet (HQD) and increased PA were linked to reduced odds of both obese and non-obese MAFLD (odds ratio (OR) and 95% CI: 0.67 [0.51-0.88] and 0.57 [0.47-0.69]; 0.62 [0.43-0.90] and 0.63 [0.46-0.87], respectively). PA and HQD significantly decreased the risk of obese and non-obese MAFLD (OR and 95% CI: 0.46 [0.33-0.64] and 0.42 [0.31-0.57]). CONCLUSION: A substantial proportion of the US population is affected by both obese and non-obese MAFLD. A strong association exists between a lower risk of both types of MAFLD and adherence to an HQD and engagement in PA.

A new 3,4-dinorsteroid from the marine sponge Cliona sp.

A new steroid, 2a-oxa-2-oxo-5ß-hydroxy-3,4-dinor-24-methylcholesta-22E-ene (1), together with 10 known ones (2-11), was isolated from the marine sponge Cliona sp. The structures of these compounds were determined by the spectroscopic methods (UV, IR, MS, and NMR) and X-ray diffraction analysis. Compound 1 was the third example of 3,4-dinorsteroid with a hemiketal at C-5 that was isolated from the natural source. In addition, the antibacterial activities of these compounds were also evaluated. However, none of them exhibited significant inhibition effects.

(+)- and (-)-Tedanine, a pair of new enantiomeric indolone alkaloids from the marine sponge Tedania sp.

(+)- and (-)-Tedanine [(+)-1 and (-)-1], a pair of new enantiomeric indolone alkaloids, along with nine compounds (2-10) were isolated from the marine sponge Tedania sp. The structures of (+)-1 and (-)-1 including absolute configurations were determined by spectroscopic analysis and quantum chemical calculation. Compounds (+)-1 and (-)-1 were the first examples of indolone alkaloids isolated from this genus. In addition, the cytotoxic and antibacterial activities of these compounds were also evaluated.

[Expression and significance of hypoxia-inducible factor 1α and Bcl-2/adenovirus E1B19kDa-interacting protein 3 in children with traumatic brain injury]. / ç¼ºæ°§è¯±å¯¼å› å­1α、Bcl-2/è ºç— æ¯’E1B19kDa相互作用蛋白3在儿童创伤性脑损伤中的表达及意义.

OBJECTIVES: To dynamically observe the changes in hypoxia-inducible factor 1α (HIF-1α) and Bcl-2/adenovirus E1B19kDa-interacting protein 3 (BNIP3) in children with traumatic brain injury (TBI) and evaluate their clinical value in predicting the severity and prognosis of pediatric TBI. METHODS: A prospective study included 47 children with moderate to severe TBI from January 2021 to July 2023, categorized into moderate (scores 9-12) and severe (scores 3-8) subgroups based on the Glasgow Coma Scale. A control group consisted of 30 children diagnosed and treated for inguinal hernia during the same period, with no underlying diseases. The levels of HIF-1α, BNIP3, autophagy-related protein Beclin-1, and S100B were compared among groups. The predictive value of HIF-1α, BNIP3, Beclin-1, and S100B for the severity and prognosis of TBI was assessed using receiver operating characteristic (ROC) curves. RESULTS: Serum levels of HIF-1α, BNIP3, Beclin-1, and S100B in the TBI group were higher than those in the control group (P<0.05). Among the TBI patients, the severe subgroup had higher levels of HIF-1α, BNIP3, Beclin-1, and S100B than the moderate subgroup (P<0.05). Correlation analysis showed that the serum levels of HIF-1α, BNIP3, Beclin-1, and S100B were negatively correlated with the Glasgow Coma Scale scores (P<0.05). After 7 days of treatment, serum levels of HIF-1α, BNIP3, Beclin-1, and S100B in both non-surgical and surgical TBI patients decreased compared to before treatment (P<0.05). ROC curve analysis indicated that the areas under the curve for predicting severe TBI based on serum levels of HIF-1α, BNIP3, Beclin-1, and S100B were 0.782, 0.835, 0.872, and 0.880, respectively (P<0.05), and for predicting poor prognosis of TBI were 0.749, 0.775, 0.814, and 0.751, respectively (P<0.05). CONCLUSIONS: Serum levels of HIF-1α, BNIP3, and Beclin-1 are significantly elevated in children with TBI, and their measurement can aid in the clinical assessment of the severity and prognosis of pediatric TBI.

Collective Quantum Magnetism in Nitrogen-Doped Nanographenes.

The emergence of quantum magnetism in nanographenes provides ample opportunities to fabricate purely organic devices for spintronics and quantum information. Although heteroatom doping is a viable way to engineer the electronic properties of nanographenes, the synthesis of doped nanographenes with collective quantum magnetism remains elusive. Here, a set of nitrogen-doped nanographenes (N-NGs) with atomic precision are fabricated on Au(111) through a combination of imidazole [2+2+2]-cyclotrimerization and cyclodehydrogenation reactions. High-resolution scanning probe microscopy measurements reveal the presence of collective quantum magnetism for nanographenes with three radicals, with spectroscopic features which cannot be captured by mean-field density functional theory calculations but can be well reproduced by Heisenberg spin model calculations. In addition, the mechanism of magnetic exchange interaction of N-NGs has been revealed and compared with their counterparts with pure hydrocarbons. Our findings demonstrate the bottom-up synthesis of atomically precise N-NGs which can be utilized to fabricate low-dimensional extended graphene nanostructures for realizing ordered quantum phases.

Obstructive sleep apnea-increased DEC1 regulates systemic inflammation and oxidative stress that promotes development of pulmonary arterial hypertension.

Obstructive sleep apnea (OSA), characterized by chronic intermittent hypoxia (CIH), is a common risk factor for pulmonary arterial hypertension (PAH). As a hypoxia-induced transcription factor, differentially expressed in chondrocytes (DEC1) negatively regulates the transcription of peroxisome proliferative activated receptor-γ (PPARγ), a recognized protective factor of PAH. However, whether and how DEC1 is associated with PAH pathogenesis remains unclear. In the present study, we found that DEC1 was increased in lungs and pulmonary arterial smooth muscle cells (PASMCs) of rat models of OSA-associated PAH. Oxidative indicators and inflammatory cytokines were also elevated in the blood of the rats. Similarly, hypoxia-treated PASMCs displayed enhanced DEC1 expression and reduced PPARγ expression in vitro. Functionally, DEC1 overexpression exacerbated reactive oxygen species (ROS) production and the expression of pro-inflammatory cytokines (such as TNFα, IL-1ß, IL-6, and MCP-1) in PASMCs. Conversely, shRNA knockdown of Dec1 increased PPARγ expression but attenuated hypoxia-induced oxidative stress and inflammatory responses in PASMCs. Additionally, DEC1 overexpression promoted PASMC proliferation, which was drastically attenuated by a PPARγ agonist rosiglitazone. Collectively, these results suggest that hypoxia-induced DEC1 inhibits PPARγ, and that this is a predominant mechanism underpinning oxidative stress and inflammatory responses in PASMCs during PAH. DEC1 could be used as a potential target to treat PAH.

Neuroprotection of exercise: P2X4R and P2X7R regulate BDNF actions.

The neurotrophin brain-derived neurotrophic factor (BDNF), which acts as a transducer, is responsible for improving cerebral stroke, neuropathic pain, and depression. Exercise can alter extracellular nucleotide levels and purinergic receptors in central nervous system (CNS) structures. This inevitably activates or inhibits the expression of BDNF via purinergic receptors, particularly the P2X receptor (P2XR), to alleviate pathological progression. In addition, the significant involvement of sensitive P2X4R in mediating increased BDNF and p38-MAPK for intracerebral hemorrhage and pain hypersensitivity has been reported. Moreover, archetypal P2X7R blockade induces mouse antidepressant-like behavior and analgesia by BDNF release. This review summarizes BDNF-mediated neural effects via purinergic receptors, speculates that P2X4R and P2X7R could be priming molecules in exercise-mediated changes in BDNF, and provides strategies for the protective mechanism of exercise in neurogenic disease.

Two New Pairs of Enantiomeric Butenolides from the Marine Sponge Suberties sp.

Two new pairs of enantiomeric butenolides, (+)- and (-)-suberiteslide A, (+)- and (-)-subertieslide B had been obtained from the marine sponge Suberties sp. The structures with absolute configurations of these compounds were unequivocally determined by spectroscopic analyses and ECD (Electronic Circular Dichroism) method. It was the first separation of butenolides from the marine sponges of genus Suberites. Additionally, the anti-inflammatory, antibacterial and cytotoxic activities of these compounds were evaluated. The result indicated that only (-)-subertieslide B showed weak anti-inflammatory activity with the IC50 value of 40.8 µM.

A new chlorobenzoate derivative from the red alga Solieria sp.

A new chlorobenzoate derivative, solieriate (1), together with six known compounds (2-7), were isolated from the red alga Solieria sp. The structures of 1-7 were determined by comprehensive spectroscopic methods and X-ray diffraction analysis. Compound 1 is the first example of halogenated derivative isolated from this genus. In addition, 1 exhibited moderate antibacterial activity on A. baumannii with MIC value of 64 µg/ml.

Spongimides A and B, two new alkaloids from the marine sponge Spongia sp.

Two new alkaloids, spongimides A (1) and B (2), along with five known ones (3-7), were isolated from the marine sponge Spongia sp. The structures of 1 and 2 were determined by the spectroscopic methods (UV, IR, MS, and NMR) and X-ray diffraction analysis. Compounds 1, 3, and 4 were the first examples of 2,4-imidazolidinediones isolated from this genus. In addition, the cytotoxic and antibacterial activities of compounds 1 and 2 were also evaluated.

Two new halogenated metabolites from the red alga Laurencia sp.

Two new halogenated metabolites, laurenhalogens A (1) and B (2), along with four known ones (3-6), were isolated from the red alga Laurencia sp. The structures of 1 and 2 were determined by the means of UV, IR, MS, NMR and X-ray diffraction analysis. In addition, the antibacterial activities of 1-6 were also evaluated.

Comparison of mitochondrial genetic variation of Taenia hydatigena cysticerci from China and Mongolia.

Parasitic infection is one of the many challenges facing livestock production globally. Cysticercosis tenuicollis is a common parasitic disease in domestic and wild ruminants (intermediate host) caused by the larval stage of Taenia hydatigena that primarily infects dogs (definitive host). Although genetic studies on this parasite exist, only a few describe the genetic variation of this parasite in Mongolia. Our aim was thus, to identify the mitochondrial differences in ovine isolates of Cysticercus tenuicollis entering China from Mongolia and comparison with existing Chinese isolates from sheep and goats based on the recently described PCR-RFLP method and mitochondrial genes of NADH dehydrogenase subunit 4 (nad4) and the NADH dehydrogenase subunit 5 (nad5). Sixty-nine isolates were collected during routine veterinary meat inspections from sheep that originated from Mongolia, at the modern slaughterhouses in Erenhot City, Inner Mongolia. Additional 114 cysticerci were also retrieved from sheep and goats from northern (Inner Mongolia Autonomous Region, Ningxia Hui Autonomous Region, and Gansu Province), western (Tibet Autonomous Region), and southern (Jiangxi Province and Guangxi Province) China. The PCR-RFLP approach of the nad5 showed nine mitochondrial subclusters A1, A2, A3, A5, A8, A9, A10, A11, and B of T. hydatigena isolates from sheep and goats from Mongolia and China. Meanwhile, haplogroup A1 RFLP profile was more widespread than other variants. These data supplements existing information on the molecular epidemiology of T. hydatigena in China and Mongolia and demonstrate the occurrence of similar genetic population structures in both countries.

Remodeling of occluded internal carotid artery in vessel wall magnetic resonance imaging.

OBJECTIVE: The purpose of the present study was to investigate the remodeling pattern of the extracranial occluded internal carotid artery (OICA) by vessel wall magnetic resonance imaging (VWI). METHODS: Thirty-nine atherosclerotic OICAs from 32 consecutive cases underwent 3-Tesla VWI to acquire pre- and post-contrast T1-weighted two-dimensional fluid-attenuated inversion recovery fast spin echo sequences. 25 symptomatic CAs exhibited ipsilateral downstream cerebral ischemia or ophthalmic artery embolism within last three months. The 14 remaining CAs were asymptomatic. Twenty-four CAs from 22 patients with atherosclerosis but no stenosis were recruited as control group. The outer wall area (OWA) was calculated based on the outer contour of the carotid artery drawn on the pre-contrast VWI. Negative remodeling was defined as a lower OWA compared to that of control group. RESULTS: Clinical characteristics including age, sex and vascular risk factors showed no significant difference between the occluded and control group. However, the OWA was lower in the occluded group than in the control group (0.63 versus 0.90 cm2, p = 0.004). For all OICAs, the OWA was larger in symptomatic cases than asymptomatic cases (0.71 versus 0.49cm2, p = 0.025). Using a cutoff value of 0.44, the sensitivity and specificity of OWA for detecting symptomatic OICA were 0.88 and 0.57, respectively. Heterogeneous signal intensity and enhancement were more often observed at the proximal than the distal segment of occlusion (p < 0.001). The inter-observer agreement regarding the evaluation of VWI characteristics was desirable (κ = 0.805 ∼ 0.847). CONCLUSIONS: Negative remodeling is prevalent in OICA, especially in asymptomatic cases.