Case report: A novel 10.8-kb deletion identified in the β-globin gene through the long-read sequencing technology in a Chinese family with abnormal hemoglobin testing results

BackgroundThalassemia is a common inherited hemoglobin disorder caused by a deficiency of one or more globin subunits. Substitution variants and deletions in the HBB gene are the major causes of β-thalassemia, of which large fragment deletions are rare and difficult to be detected by conventional polymerase chain reaction (PCR)-based methods.Case reportIn this study, we reported a 26-year-old Han Chinese man, whose routine blood parameters were found to be abnormal. Hemoglobin testing was performed on the proband and his family members, of whom only the proband's mother had normal parameters. The comprehensive analysis of thalassemia alleles (CATSA, a long-read sequencing-based approach) was performed to identify the causative variants. We finally found a novel 10.8-kb deletion including the β-globin (HBB) gene (Chr11:5216601-5227407, GRch38/hg38) of the proband and his father and brother, which were consistent with their hemoglobin testing results. The copy number and exact breakpoints of the deletion were confirmed by multiplex ligation-dependent probe amplification (MLPA) and gap-polymerase chain reaction (Gap-PCR) as well as Sanger sequencing, respectively.ConclusionWith this novel large deletion found in the HBB gene in China, we expand the genotype spectrum of β-thalassemia and show the advantages of long-read sequencing (LRS) for comprehensive and precise detection of thalassemia variants

Restoration of autophagy by puerarin in ethanol-treated hepatocytes via the activation of AMP-activated protein kinase

a b s t r a c t We investigated the effects of puerarin, the major isoflavone in Kudzu roots, on the regulation of autophagy in ethanol-treated hepatocytes. Incubation in ethanol (100 mM) for 24 h reduced cell viability by 20% and increased the cellular concentrations of cholesterol and triglycerides by 40% and 20%, respectively. Puerarin stimulation significantly recovered cell viability and reduced cellular lipid accumulation to a level comparable to that in untreated control cells. Ethanol incubation reduced autophagy significantly as assessed by microtubule-associated protein1 light chain 3 (LC3) expression using immunohistochemistry and immunoblot analysis. The reduced expression of LC3 was restored by puerarin in a dose-dependent manner in ethanol-treated cells. The effect of puerarin on mammalian targets of rapamycin (mTOR), a key regulator of autophagy, was examined in ethanol-treated hepatocytes. Immunoblotting revealed that puerarin significantly induced the phosphorylation of 5 0 AMP-activated protein kinase (AMPK), thereby suppressing the mTOR target proteins S6 ribosomal protein and 4E-binding protein 1. These data suggest that puerarin restored the viability of cells and reduced lipid accumulation in ethanol-treated hepatocytes by activating autophagy via AMPK/mTOR-mediated signaling

Morphological diversity of single neurons in molecularly defined cell types.

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits

Novel B and N Sites of One-Dimensional Boron Nitride Fiber: Efficient Performance and Mechanism in the Formaldehyde Capture Process

Identification of adsorption centers with atomic levels of adsorbents is crucial to study the adsorption of formaldehyde (HCHO), especially for an in-depth understanding of the mechanism of HCHO capture. Herein, we investigate the HCHO adsorption performance of one-dimensional (1D) nano-porous boron nitride (BN) fiber, and explore the adsorption mechanism by density functional theory (DFT) calculations, including adsorption energy change and Bader charge change, and experimental study as well. Research shows that the 1D nanoporous BN fiber possesses a high concentration of Lewis pairs, which act as Lewis acid and Lewis base sites associated with the fiber's electron-deficient and electron-rich features. It is worth noting that the HCHO removal efficiency of a typical sample is as high as 91%. This work may open the door to the field of adsorption of other pollutants by constructing Lewis pairs in the future

Nontargeted metabolomics analysis of follicular fluid in patients with endometriosis provides a new direction for the study of oocyte quality

Abstract Endometriosis is a common, estrogen‐dependent chronic gynecological disease that endangers the reproductive system and systemic metabolism of patients. We aimed to investigate the differences in metabolic profiles in the follicular fluid between infertile patients with endometriosis and controls. A total of 25 infertile patients with endometriosis and 25 infertile controls who were similar in age, BMI, fertilization method and ovulation induction treatment were recruited in this study. Metabolomics analysis of follicular fluid was performed by two methods of high‐performance liquid chromatography tandem mass spectrometry. There were 36 upregulated and 17 downregulated metabolites in the follicular fluid of patients in the endometriosis group. KEGG pathway analysis revealed that these metabolites were enriched in phenylalanine, tyrosine and tryptophan biosynthesis, aminoacyl‐tRNA biosynthesis, phenylalanine metabolism and pyrimidine metabolism pathways. A biomarker panel consisting of 20 metabolites was constructed by random forest, with an accuracy of 0.946 and an AUC of 0.988. This study characterizes differences in follicular fluid metabolites and associated pathway profiles in infertile patients with endometriosis. These findings can provide a better comprehensive understanding of the disease and a new direction for the study of oocyte quality, as well as potential metabolic markers for the prognosis of endometriosis

Novel B and N Sites of One-Dimensional Boron Nitride Fiber: Efficient Performance and Mechanism in the Formaldehyde Capture Process

Identification of adsorption centers with atomic levels of adsorbents is crucial to study the adsorption of formaldehyde (HCHO), especially for an in-depth understanding of the mechanism of HCHO capture. Herein, we investigate the HCHO adsorption performance of one-dimensional (1D) nano-porous boron nitride (BN) fiber, and explore the adsorption mechanism by density functional theory (DFT) calculations, including adsorption energy change and Bader charge change, and experimental study as well. Research shows that the 1D nanoporous BN fiber possesses a high concentration of Lewis pairs, which act as Lewis acid and Lewis base sites associated with the fiber's electron-deficient and electron-rich features. It is worth noting that the HCHO removal efficiency of a typical sample is as high as 91%. This work may open the door to the field of adsorption of other pollutants by constructing Lewis pairs in the future

New Insights into the Dependence of CPEB3 Ribozyme Cleavage on Mn²⁺ and Mg²⁺

CPEB3 ribozyme is a self-cleaving RNA that occurs naturally in mammals and requires divalent metal ions for efficient activity. Ribozymes exhibit preferences for specific metal ions, but the exact differences in the catalytic mechanisms of various metal ions on the CPEB3 ribozyme remain unclear. Our findings reveal that Mn2+ functions as a more effective cofactor for CPEB3 ribozyme catalysis compared to Mg2+, as confirmed by its stronger binding affinity to CPEB3 by EPR. Cleavage assays of CPEB3 mutants and molecular docking analyses further showed that excessive Mn2+ ions can bind to a second binding site near the catalytic site, hindering CPEB3 catalytic efficiency and contributing to the Mn2+ bell-shaped curve. These results implicate a pivotal role for the local nucleobase–Mn2+ interactions in facilitating RNA folding and modulating the directed attack of nucleophilic reagents. Our study provides new insights and experimental evidence for exploring the divalent cation dependent cleavage mechanism of the CPEB3 ribozyme

Quantitative Simulation of Gas Hydrate Formation and Accumulation with 3D Petroleum System Modeling in the Shenhu Area, Northern South China Sea

Gas hydrates have been considered as a new energy that could replace conventional fossil resources in the future because of their high energy density, environmental friendliness, and enormous reserves. To further analyze the potential distribution of gas hydrate stability zones (GHSZ) and the formation of a gas hydrate system in the Shenhu area of the South China Sea (SCS), a 3D petroleum simulation model (PSM) was built from 3D seismic interpretations and all available geological data. Based on the thermal calibration of the 3D model, the evolution of the GHSZ, hydrocarbon generation and migration, and the formation and accumulation of gas hydrates were simulated for the first time in the area. Thermal simulation shows that the methane source of gas hydrate originated from shallow biogenic gas and deep thermogenic gas. Most areas are dominated by shallow biogenic gas, while, only about 3% of the deep thermogenic gas derived from Enping Formation source rock and contributed to the gas hydrate formation within a few areas in the southeast. The thermogenic gas migrated vertically into the GHSZ through connecting faults, mud diapir, and/or gas chimney to form gas hydrate. The source rocks of the Wenchang Formation, a deep thermogenic gas source, began to enter the main hydrocarbon generation window at 28.4 Ma. The Enping source rock began to generate oil from 25 Ma on and gas from 16 Ma on. Since 5.3 Ma, most areas of the source rocks have generated a gas window, and only the shallower parts in the east still in the oil window, which had lasted until now. The shallow biogenic gas source rocks from the Hanjiang, Yuehai, and Wanshan formations generated gas in different periods, respectively. The Qionghai Formation began to generate hydrocarbon from 0.3 Ma and until now. Other results show that the GHSZ developed mainly during the Quaternary and Neogene (Wanshan Formation) and the GHSZ is thicker in the southern area and thinner in the northern part with a positive correlation with water depth. Starting at 11.6 Ma, the GHSZ developed in the Hanjiang Formation in the south of the Shenhu area and gradually expanded to the north to cover most of the study area at 5.3 Ma during the Yuehai Formation. From 1.8 Ma on, the GHSZ covered the entire study area. At the same time, the GHSZ in the Hanjiang Formation disappeared because of the change in temperature and pressure. At present, the GHSZ in the Yuehai Formation has disappeared, while the Quaternary and Wanshan are the two main formations for GHSZ development. The formation and distribution of gas hydrates are fundamentally controlled by the space-time coupling between the hydrocarbon generation and expulsion time and distribution of the GHSZ. The simulation results of gas hydrate accumulation and distribution were verified by drilling results and the matching rate is 84%. This is the first time that 3D simulation was successfully conducted with PSM technology in the Shenhu area and it provides important guidance for gas hydrate study in other areas of the SCS

<i>Bacillus thuringiensis</i> Crystal Protein Cry6Aa Triggers <i>Caenorhabditis elegans</i> Necrosis Pathway Mediated by Aspartic Protease (ASP-1)

<div><p>Cell death plays an important role in host-pathogen interactions. Crystal proteins (toxins) are essential components of <i>Bacillus thuringiensis</i> (Bt) biological pesticides because of their specific toxicity against insects and nematodes. However, the mode of action by which crystal toxins to induce cell death is not completely understood. Here we show that crystal toxin triggers cell death by necrosis signaling pathway using crystal toxin Cry6Aa-<i>Caenorhabditis elegans</i> toxin-host interaction system, which involves an increase in concentrations of cytoplasmic calcium, lysosomal lyses, uptake of propidium iodide, and burst of death fluorescence. We find that a deficiency in the necrosis pathway confers tolerance to Cry6Aa toxin. Intriguingly, the necrosis pathway is specifically triggered by Cry6Aa, not by Cry5Ba, whose amino acid sequence is different from that of Cry6Aa. Furthermore, Cry6Aa-induced necrosis pathway requires aspartic protease (ASP-1). In addition, ASP-1 protects Cry6Aa from over-degradation in <i>C</i>. <i>elegans</i>. This is the first demonstration that deficiency in necrosis pathway confers tolerance to Bt crystal protein, and that Cry6A triggers necrosis represents a newly added necrosis paradigm in the <i>C</i>. <i>elegans</i>. Understanding this model could lead to new strategies for nematode control.</p></div