SMARTdb: An Integrated Database for Exploring Single-cell Multi-omics Data of Reproductive Medicine.

Single-cell multi-omics sequencing has greatly accelerated reproductive research in recent years, and the data are continually growing. However, utilizing these data resources is challenging for wet-lab researchers. A comprehensive platform for exploring single-cell multi-omics data related to reproduction is urgently needed. Here, we introduce the single-cell multi-omics atlas of reproduction (SMARTdb), an integrative and user-friendly platform for exploring molecular dynamics of reproductive development, aging, and disease, which covers multi-omics, multi-species, and multi-stage data. We curated and analyzed single-cell transcriptomic and epigenomic data of over 2.0 million cells from 6 species across the entire lifespan. A series of powerful functionalities are provided, such as "Query gene expression", "DIY expression plot", "DNA methylation plot", and "Epigenome browser". With SMARTdb, we found that the male germ cell-specific expression pattern of RPL39L and RPL10L is conserved between human and other model animals. Moreover, DNA hypomethylation and open chromatin may collectively regulate the specific expression pattern of RPL39L in both male and female germ cells. In summary, SMARTdb is a powerful platform for convenient data mining and gaining novel insights into reproductive development, aging, and disease. SMARTdb is publicly available at https://smart-db.cn.

Production of high calorific value hydrogen-rich combustible gas by supercritical water gasification of straw assisted by machine learning.

This article reveals the basic laws of straw supercritical water gasification (SCWG) and provides basic experimental data for the effective utilization of straw. The paper studied the impact of three operational conditions on the production of high-calorific value hydrogen-rich combustible gases through SCWG of straw within a quartz tube reactor. The findings reveal that elevated reaction temperatures, extended residence times, and reduced feedstock concentrations favor the SCWG of straw. When combustible gas contains carbon dioxide, the maximum low heating value (LHV) of the gas is 21 MJ/Nm3. Upon removing carbon dioxide, the LHV of the gas reached 38 MJ/Nm3. Subsequently, a machine learning (ML) model was developed to forecast gas yield and LHV during the SCWG process. The results demonstrate that the model exhibits robust generalization capabilities. ML can be extensively applied to forecast biomass SCWG processes across various operational conditions.

Unveiling neurodevelopmental changes in multisensory integration while controlling attention.

It is well-accepted that multisensory integration (MSI) undergoes protracted maturation from childhood to adulthood. However, existing evidence may have been confounded by potential age-related differences in attention. To unveil neurodevelopmental changes in MSI while matching top-down attention between children and adults, we recorded event-related potentials of healthy children aged 7 to 9 years and young adults in the visual-to-auditory attentional spreading paradigm wherein attention and MSI could be measured concurrently. The absence of children versus adults differences in the visual selection negativity component and behavioral measures of auditory interference first demonstrates that the child group could maintain top-down visual attention and ignore task-irrelevant auditory information to a similar extent as adults. Then, the stimulus-driven attentional spreading quantified by the auditory negative difference (Nd) component was found to be overall absent in the child group, revealing the children's largely immature audiovisual binding process. These findings furnish strong evidence for the protracted maturation of MSI per se from childhood to adulthood, hence providing a new benchmark for characterizing the developmental course of MSI. In addition, we also found that the representation-driven attentional spreading measured by another Nd was present but less robust in children, suggesting their substantially but not fully developed audiovisual representation coactivation process.

Protocol for adeno-associated virus-mediated optogenetic activation of olfactory output neurons in neonatal mice.

Optogenetic manipulation has proven a powerful tool for investigating the mechanisms underlying the function of neuronal networks, but implementing the technique on mammals during early development remains challenging. Here, we present a comprehensive workflow to specifically manipulate mitral/tufted cells (M/TCs), the output neurons in the olfactory circuit, mediated by adeno-associated virus (AAV) transduction and light stimulation in neonatal mice and monitor neuronal and network activity with in vivo electrophysiology. This method represents an efficient approach to elucidate functional brain development. For complete details on the use and execution of this protocol, please refer to Chen et al.1,2,3.

Preconfigured architecture of the developing mouse brain.

In the adult brain, structural and functional parameters, such as synaptic sizes and neuronal firing rates, follow right-skewed and heavy-tailed distributions. While this organization is thought to have significant implications, its development is still largely unknown. Here, we address this knowledge gap by investigating a large-scale dataset recorded from the prefrontal cortex and the olfactory bulb of mice aged 4-60 postnatal days. We show that firing rates and spike train interactions have a largely stable distribution shape throughout the first 60 postnatal days and that the prefrontal cortex displays a functional small-world architecture. Moreover, early brain activity exhibits an oligarchical organization, where high-firing neurons have hub-like properties. In a neural network model, we show that analogously right-skewed and heavy-tailed synaptic parameters are instrumental to consistently recapitulate the experimental data. Thus, functional and structural parameters in the developing brain are already extremely distributed, suggesting that this organization is preconfigured and not experience dependent.

Mechanistic insights and catalytic enhancement of phenolic wastewater supercritical water gasification: A combined experiment and density functional theory study.

Supercritical water gasification technology provides a favorable technology to achieve pollution elimination and resource utilization of phenolic wastewater. In this study, the reaction mechanism of phenolic wastewater supercritical water gasification was investigated using a combination of experimental and computational methods. Five reaction channels were identified to elucidate the underlying pathway of phenol decomposition. Importantly, the rate-determining step was found to be the dearomatization reaction. By integrating computational and experimental analyses, it was found that phenol decomposition via the path with the lowest energy barrier generates cyclopentadiene, featuring a dearomatization barrier of 70.97 kcal/mol. Additionally, supercritical water plays a catalytic role in the dearomatization process by facilitating proton transfer. Based on the obtained reaction pathway, alkali salts (Na2CO3 and K2CO3) are employed as a catalyst to diminish the energy barrier of the rate-determining step to 40.00 kcal/mol and 37.14 kcal/mol. Alkali salts catalysis significantly improved carbon conversion and pollutant removal from phenolic wastewater, increasing CGE from 58.44% to 93.55% and COD removal efficiency from 94.11% to 99.79%. Overall, this study provides a comprehensive understanding of the decomposition mechanism of phenolic wastewater in supercritical water.

Sulfur migration mechanism of pig manure in supercritical water: A combined experimental and DFT study.

Pig manure (PM) is a high concentration organic waste rich in sulfur, and its biofuel contains various sulfur-containing pollutants, which reduces the safety of the products. Supercritical water (SCW) can dissolve most organic matter, which is a technology worthy of further study. In order to reduce sulfur pollution in the process of PM resource utilization and better control the conversion path of sulfur, it is necessary to explore the migration mechanism of sulfur in the whole PM-SCW gasification process. The experimental results indicated that H2S was the only gaseous product. Only inorganic compounds (S2-, S2O32- and SO42-) were detected in the liquid. Sulfur in the solid mainly included thiol/thioether, thiophene and sulfone. The influence of different reaction conditions (temperature, residence time, PM concentration and catalysts) on sulfur migration was studied in a batch reactor. It was worth noting that the catalysts had a significant effect on H2S absorption. The lowest H2S yield was 3.2 * 10-4 mol/kg and more than 70% of the sulfur was distributed in the liquid under the condition of addition of K2CO3. While, the RTH2110 fixed most of the sulfur of PM (the maximum value reached 50.94%) in the solid. Thus, adding the catalysts flexibly can choose composition of the products. Furthermore, six possible pathways of sulfur migration in the solid were designed and the kinetic parameters were calculated by density functional theory (DFT). The results provided a basis for controlling sulfur in PM. Subsequently, the sulfur migration pathways during PM-SCW gasification process were comprehensively summarized through the combination of experiment and DFT. It provided a method for sulfur treatment in PM, which had guiding significance for the realization of pollution-free treatment of PM.

IP3R1-mediated MAMs formation contributes to mechanical trauma-induced hepatic injury and the protective effect of melatonin.

INTRODUCTION: There is a high morbidity and mortality rate in mechanical trauma (MT)-induced hepatic injury. Currently, the molecular mechanisms underlying liver MT are largely unclear. Exploring the underlying mechanisms and developing safe and effective medicines to alleviate MT-induced hepatic injury is an urgent requirement. The aim of this study was to reveal the role of mitochondria-associated ER membranes (MAMs) in post-traumatic liver injury, and ascertain whether melatonin protects against MT-induced hepatic injury by regulating MAMs. METHODS: Hepatic mechanical injury was established in Sprague-Dawley rats and primary hepatocytes. A variety of experimental methods were employed to assess the effects of melatonin on hepatic injury, apoptosis, MAMs formation, mitochondrial function and signaling pathways. RESULTS: Significant increase of IP3R1 expression and MAMs formation were observed in MT-induced hepatic injury. Melatonin treatment at the dose of 30 mg/kg inhibited IP3R1-mediated MAMs and attenuated MT-induced liver injury in vivo. In vitro, primary hepatocytes cultured in 20% trauma serum (TS) for 12 h showed upregulated IP3R1 expression, increased MAMs formation and cell injury, which were suppressed by melatonin (100 µmol/L) treatment. Consequently, melatonin suppressed mitochondrial calcium overload, increased mitochondrial membrane potential and improved mitochondrial function under traumatic condition. Melatonin's inhibitory effects on MAMs formation and mitochondrial calcium overload were blunted when IP3R1 was overexpressed. Mechanistically, melatonin bound to its receptor (MR) and increased the expression of phosphorylated ERK1/2, which interacted with FoxO1 and inhibited the activation of FoxO1 that bound to the IP3R1 promoter to inhibit MAMs formation. CONCLUSION: Melatonin prevents the formation of MAMs via the MR-ERK1/2-FoxO1-IP3R1 pathway, thereby alleviating the development of MT-induced liver injury. Melatonin-modulated MAMs may be a promising therapeutic therapy for traumatic hepatic injury.

Azonia-Naphthalene: A Cationic Hydrophilic Building Block for Stable N-Type Organic Mixed Ionic-Electronic Conductors.

Conjugated polymers that can efficiently transport both ionic and electronic charges have broad applications in next-generation optoelectronic, bioelectronic, and energy storage devices. To date, almost all the conjugated polymers have hydrophobic backbones, which impedes efficient ion diffusion/transport in aqueous media. Here, we design and synthesize a novel hydrophilic polymer building block, 4a-azonia-naphthalene (AN), drawing inspiration from biological systems. Because of the strong electron-withdrawing ability of AN, the AN-based polymers show typical n-type charge transport behaviors. We find that cationic aromatics exhibit strong cation-π interactions, leading to smaller π-π stacking distance, interesting ion diffusion behavior, and good morphology stability. Additionally, AN enhances the hydrophilicity and ionic-electronic coupling of the polymer, which can help to improve ion diffusion/injection speed, and operational stability of organic electrochemical transistors (OECTs). The integration of cationic building blocks will undoubtedly enrich the material library for high-performance n-type conjugated polymers.

Directional transformation and migration pathways of nitrogen during pig manure supercritical water gasification.

Nitrogen is a valuable nutrient element in pig manure. This work focuses on investigating the distribution, directional transformation, and migration pathways to facilitate the recovery of nitrogen from supercritical water gasification products. Results indicated that no nitrogen-containing gas was detected and 12.65 % of nitrogen remained in solid products. 82.49 % of nitrogen migrated into liquid products, which are predominated by ammonia. Catalysts were employed to promote the conversion of solid nitrogen to liquid nitrogen and organic nitrogen to ammonia. Finally, 85 % of nitrogen is enriched into liquid products and ammonia predominated the liquid nitrogen. The percentage of ammonia increased to 97.51 % at 620 °C in the presence of potassium carbonate. The migration pathways indicated that nitrogen was transformed into ammonia by various intermediates such as indole. The rest of the nitrogen remained in solid products with stable quaternary-nitrogen. These findings provide valuable insights into nitrogen management and recovery.

Assessing Left Ventricular Systolic Function in Patients with Pregnancy-Induced Hypertension Using Three-Dimensional Speckle Tracking Technology.

Objective: This study investigates the clinical utility of three-dimensional speckle tracking technology in assessing left ventricular systolic function in pregnancy-induced hypertension syndrome (PIH). Methods: We retrospectively enrolled 70 patients with diagnosed PIH treated at our institution between July 2019 and August 2021 as the study group. A total of 70 healthy pregnant women undergoing routine antenatal examinations at the same institution during the same period were included in the control group. Two-dimensional conventional echocardiography measured left ventricular parameters in both groups. Three-dimensional speckle tracking technology analyzed Left Ventricular Global Longitudinal Peak Strain (LVGLS), Left Ventricular Global Radial Peak Strain (LVGRS), and Left Ventricular Global Circumferential Peak Strain (LVGCS). Differences in left ventricular systolic function and pregnancy outcomes were compared. Results: In the study group, LVEDD, LVPWTd, and IVSTd (47.67±4.88, 10.68±1.21, 11.24±1.03) exceeded those in the control group (45.21±5.65, 8.17±0.98, 8.91±0.37). LVEF (62.12±5.63) was lower than the control group (65.25±5.17) (all P < .05). LVGLS, LVGCS, and LVGAS in the study group (-15.66±1.07, -20.17±2.89, -23.17±3.43) were higher than the control group (-20.14±1.27, -25.17±1.36, -37.68±3.29), while LVGRS (30.29±3.61) was lower than the control group (34.18±4.08) (all P < .05). The study group had 72.86% natural deliveries and 27.14% cesarean sections; the control group had 31.43% natural deliveries and 68.57% cesarean sections (all P < .05). Weeks of delivery and birth weight in the study group (36.87±1.23, 2.71±0.41) were lower than the control group (38.96±1.54, 3.41±0.78) (both P < .05). Conclusions: Compared to traditional methods, three-dimensional speckle tracking technology more sensitively detects left ventricular strain and rotation in PIH patients. It holds clinical relevance in early left ventricular dysfunction detection, effectively mitigating adverse pregnancy outcomes and warranting clinical adoption and application.

Olfactory bulb activity shapes the development of entorhinal-hippocampal coupling and associated cognitive abilities.

The interplay between olfaction and higher cognitive processing has been documented in the adult brain; however, its development is poorly understood. In mice, shortly after birth, endogenous and stimulus-evoked activity in the olfactory bulb (OB) boosts the oscillatory entrainment of downstream lateral entorhinal cortex (LEC) and hippocampus (HP). However, it is unclear whether early OB activity has a long-lasting impact on entorhinal-hippocampal function and cognitive processing. Here, we chemogenetically silenced the synaptic outputs of mitral/tufted cells, the main projection neurons in the OB, during postnatal days 8-10. The transient manipulation leads to a long-lasting reduction of oscillatory coupling and weaker responsiveness to stimuli within developing entorhinal-hippocampal circuits accompanied by dendritic sparsification of LEC pyramidal neurons. Moreover, the transient silencing reduces the performance in behavioral tests involving entorhinal-hippocampal circuits later in life. Thus, neonatal OB activity is critical for the functional LEC-HP development and maturation of cognitive abilities.

Number of segments with motion abnormalities is better correlated with infarct size in acute myocardial infarction.

BACKGROUND: The relationship between the number of segments with motion abnormalities (SMA) on the bull's-eye plots of speckle-tracking echocardiography (STE) and myocardial infarct size (MIS) on late gadolinium-enhanced cardiac MRI (LGE-cMRI) has not been well characterized. This study aimed to determine MIS using the number of SMA in patients with acute myocardial infarction (MI). METHODS: Left ventricular two-dimensional STE and LGE-cMRI were performed in 380 patients with ST-segment elevation MI within 48 h and 5-6 days after primary percutaneous intervention, respectively. RESULTS: Patients with impaired global and regional myocardial strain, work and greater number of SMA had significantly larger infarcts ( P  < 0.05). Multivariate logistic regression analysis that included myocardial strain, work, and number of SMA showed that total number of SMA [odds ratio (OR) = 1.976; 95% confidence interval (CI): 1.539-2.538, P  < 0.0001], the number of segments with paradoxalic systolic movements (SPSM, OR = 3.703; 95% CI: 2.112-6.493, P  < 0.0001) were independent risk factors of large MIS (>19%). The area under receiver operating characteristic curve (AUC) of 0.904 (0.866~0.942) for total number of SMA was superior to that for global longitudinal strain (GLS, AUC = 0.813, 0.761~0.865), global work efficiency (GWE, AUC = 0.794, 0.730~0.857) and number of SPSM (AUC = 0.851, 0.804-0.899) to predict a large MIS ( P  < 0.05). The optimal cutoff value of total number of SMA was 7, with a sensitivity of 85.31%, a specificity of 81.48%, and an accuracy of 83.27%. CONCLUSION: Total number of SMA is better associated with infarct size, which provided an incremental prognostic value above established prognostic parameters such as GLS and GWE.

Brain-derived neurotrophic factor contributes to neurogenesis after intracerebral hemorrhage: a rodent model and human study.

Background and purpose: Intracerebral hemorrhage (ICH) enhances neurogenesis in the subventricular zone (SVZ); however, the mechanism is not fully understood. We investigated the role of brain-derived neurotrophic factor (BDNF) in post-ICH neurogenesis in a rodent model and in patients with ICH using cerebrospinal fluid (CSF). Methods: A rat model of ICH was constructed via stereotaxic injection of collagenase into the left striatum. Patients with ICH receiving an external ventricular drain were prospectively enrolled. CSF was collected from rats and patients at different post-ICH times. Primary cultured rat neural stem cells (NSCs) were treated with CSF with or without BDNF-neutralized antibody. Immunohistochemistry and immunocytochemistry were used to detect NSC proliferation and differentiation. The BDNF concentration in CSF was quantified using enzyme-linked immunosorbent assays (ELISA). Results: In the rat model of ICH, the percentage of proliferating NSCs and neuroblasts in SVZ was elevated in bilateral hemispheres. The cultured rat NSCs treated with CSF from both rats and patients showed an increased capacity for proliferation and differentiation toward neuroblasts. BDNF concentration was higher in CSF collected from rats and patients with ICH than in controls. Blocking BDNF decreased the above-noted promotion of proliferation and differentiation of cultured NSCs by CSF treatment. In patients with ICH, the BDNF concentration in CSF and the neurogenesis-promoting capacity of post-ICH CSF correlated positively with ICH volume. Conclusion: BDNF in CSF contributes to post-ICH neurogenesis, including NSC proliferation and differentiation toward neuroblasts in a rat model and patients with ICH.

Ischemia/reperfusion-induced MiD51 upregulation recruits Drp1 to mitochondria and contributes to myocardial injury.

The translocation of Drp1 from the cytosol to mitochondria leads to Drp1 activation and mitochondrial fission in myocardial ischemia/reperfusion (MI/R). However, the molecular mechanism underlying mitochondrial Drp1 translocation remains poorly understood. Mitochondrial Drp1 recruitment relies on 4 binding partners including MiD49, MiD51, Mff and Fis1. This study was to elucidate which one facilitate mitochondrial Drp1 translocation and its role in MI/R injury. MI/R was induced by ligating the left anterior descending coronary artery for 30 min and subsequent reperfusion for 3 h. Primary neonatal cardiomyocytes were subjected to hypoxia for 2 h and reoxygenation for 4 h. SiRNA or Adeno-associated virus (AAV) expressing shRNA was used to knock down the key binding partner in vitro or in vivo respectively. The expression of MiD51 rather than other binding partners (MiD49, Mff or Fis1) was increased after MI/R. MiD51 knockdown inhibited hypoxia/reoxygenation (H/R) or ischemia/reperfusion (I/R)-induced mitochondrial Drp1 translocation. SiRNA-induced knockdown of MiD51 suppressed mitochondrial oxidative stress, improved mitochondrial function and alleviate cellular injury in H/R cardiomyocytes. AAV-mediated knockdown of MiD51 reduced myocardial injury and improved cardiac function in the I/R hearts, while mitochondrial Drp1 translocation and cardiac function were not affected by MiD51 knockdown in the hearts without I/R. MiD51 is identified as the binding partner that promotes mitochondrial Drp1 translocation and contributes to MI/R injury. Inhibition of MiD51 may be a potential therapeutic target to alleviate MI/R injury.

Aging-induced pseudouridine synthase 10 impairs hematopoietic stem cells.

Aged hematopoietic stem cells (HSC) exhibit compromised reconstitution capacity and differentiation-bias towards myeloid lineage, however, the molecular mechanism behind it remains not fully understood. In this study, we observed that the expression of pseudouridine (Ψ) synthase 10 is increased in aged hematopoietic stem and progenitor cells (HSPC) and enforced protein of Ψ synthase 10 (PUS10) recapitulates the phenotype of aged HSC, which is not achieved by its Ψ synthase activity. Consistently, we observed no difference of transcribed RNA pseudouridylation profile between young and aged HSPC. No significant alteration of hematopoietic homeostasis and HSC function is observed in young Pus10-/- mice, while aged Pus10-/- mice exhibit mild alteration of hematopoietic homeostasis and HSC function. Moreover, we observed that PUS10 is ubiquitinated by E3 ubiquitin ligase CRL4DCAF1 complex and the increase of PUS10 in aged HSPC is due to aging-declined CRL4DCAF1- mediated ubiquitination degradation signaling. Taken together, this study for the first time evaluated the role of PUS10 in HSC aging and function, and provided a novel insight into HSC rejuvenation and its clinical application.

Nicotinamide Adenine Dinucleotide Precursor Suppresses Hepatocellular Cancer Progression in Mice.

Targeting Nicotinamide adenine dinucleotide (NAD) metabolism has emerged as a promising anti-cancer strategy; we aimed to explore the health benefits of boosting NAD levels with nicotinamide riboside (NR) on hepatocellular carcinoma (HCC). We established three in vivo tumor models, including subcutaneous transplantation tumor model in both Balb/c nude mice (xenograft), C57BL/6J mice (allograft), and hematogenous metastatic neoplasm in nude mice. NR (400 mg/kg bw) was supplied daily in gavage. In-situ tumor growth or noninvasive bioluminescence were measured to evaluate the effect of NR on the HCC process. HepG2 cells were treated with transforming growth factor-ß (TGF-ß) in the absence/presence of NR in vitro. We found that NR supplementation alleviated malignancy-induced weight loss and metastasis to lung in nude mice in both subcutaneous xenograft and hematogenous metastasis models. NR supplementation decreased metastasis to the bone and liver in the hematogenous metastasis model. NR supplementation also significantly decreased the size of allografted tumors and extended the survival time in C57BL/6J mice. In vitro experiments showed that NR intervention inhibited the migration and invasion of HepG2 cells triggered by TGF-ß. In summary, our results supply evidence that boosting NAD levels by supplementing NR alleviates HCC progression and metastasis, which may serve as an effective treatment for the suppression of HCC progression.

In-source fragmentation of nucleosides in electrospray ionization towards more sensitive and accurate nucleoside analysis.

Nucleosides have been found to suffer in-source fragmentation (ISF) in electrospray ionization mass spectrometry, which leads to reduced sensitivity and ambiguous identification. In this work, a combination of theoretical calculations and nuclear magnetic resonance analysis revealed the key role of protonation at N3 near the glycosidic bond during ISF. Therefore, an ultrasensitive liquid chromatography-tandem mass spectrometry system for 5-formylcytosine detection was developed with 300 fold signal enhancement. Also, we established a MS1-only platform for nucleoside profiling and successfully identified sixteen nucleosides in the total RNA of MCF-7 cells. Taking ISF into account, we can realize analysis with higher sensitivity and less ambiguity, not only for nucleosides, but for other molecules with similar protonation and fragmentation behaviors.

Ultrasensitive HPLC-MS Quantification of S-(2-Succino) Cysteine Based on Ethanol/Acetyl Chloride Derivatization in Fumarate Accumulation Cells.

Succination is a nonenzymatic and irreversible post-translational modification (PTM) with important biological significance, yielding S-(2-succino) cysteine (2SC) residue. This PTM is low in abundance and often requires a large amount of protein samples for 2SC quantification. In this work, an efficient quantification method based on ethanol/acetyl chloride chemical derivatization was developed. The three carboxyl groups of 2SC were all esterified to increase hydrophobicity, greatly improving its ionization efficiency. The sensitivity was increased by 112 times; the limit of detection was reduced to 0.885 fmol, and the protein usage was reduced by at least 10 times. The established method was used to detect the overall concentration of 2SC in fumarate accumulation cells quantitatively.