Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription.

Repetitive satellite DNAs, divergent in nucleic-acid sequence and size across eukaryotes, provide a physical site for centromere assembly to orchestrate chromosome segregation during the cell cycle. These non-coding DNAs are transcribed by RNA polymerase (RNAP) II and the transcription has been shown to play a role in chromosome segregation, but a little is known about the regulation of centromeric transcription, especially in higher organisms with tandemly-repeated-DNA-sequence centromeres. Using RNA interference knockdown, chemical inhibition and AID/IAA degradation, we show that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite on centromeres in human cells. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation on centromeres. Interestingly, in response to DNA double-stranded breaks (DSBs) induced by chemotherapy drugs or CRSPR/Cas9, α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner. These DSB-induced α-satellite RNAs were predominantly derived from the α-satellite high-order repeats of human centromeres and forms into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, our findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.

Effectiveness and safety of interferon α-2a combined with phototherapy for patients with early-stage mycosis fungoides - a single-arm prospective study in 13 patients.

Background: Mycosis fungoides (MF) is the most common type of cutaneous T-cell lymphoma.Objectives: This study was conducted to evaluate efficacy and safety of interferon (IFN) α-2a combined with phototherapy for early-stage MF.Methods: Thirteen patients with early-stage MF received subcutaneous injections of IFN α-2a at 3 million IU combined with phototherapy three times per week for 6 months. Treatment efficacy was measured by changes in body surface area (BSA) score and modified severity-weighted assessment tool (mSWAT) score at 1, 3, and 6 months after treatment. Histopathologic examinations of skin lesions were performed before and after treatment.Results: After 3 months of treatment, all 13 patients achieved a partial response, and BSA and mSWAT scores were significantly lower than those at baseline (p < 0.001). After 6 months, BSA and mSWAT scores were significantly lower than those at baseline (p < 0.001) and after 3 months (p < 0.05). Eleven patients achieved complete remission and two patients achieved a partial response (overall response rate, 100%). Histopathologic examination showed a significant decrease in the number of atypical lymphocytes in both epidermis and dermis. No severe adverse effects occurred.Conclusion: IFN α-2a in combination with phototherapy may be an effective and safe alternative modality for early-stage MF.

Different effects of pea protein on the properties and structures of starch gel at low and high solid concentrations.

In the context of starch-protein composite gels, the influence of protein on gel formation significantly shapes the textural attributes of starch gels, leading to distinct outcomes. This study aimed to evaluate how different ratios of pea protein (PP) affect the properties and structures of starch-protein composite gels at low (10 wt%) and high (40 wt%) solid concentrations. The addition of PP had opposite effects on the two gels. Compared to the pure starch gel, the low-concentration composite gel (LCG) with 20 % PP experienced a 48.90 ± 0.33 % reduction in hardness, and the storage modulus (G') decreased from 14,100 Pa to 5250 Pa, indicating a softening effect of PP on LCG. Conversely, the hardness of the high-concentration composite gel (HCG) with 20 % PP exhibited a 62.19 ± 0.03 % increase in hardness, and G' increased from 12,100 Pa to 41,700 Pa, highlighting the enhancing effect of PP on HCG. SEM and fluorescence microscopy images showed that PP induced uneven network sizes in LCG, while HCG with a PP content of 20 %, PP, together with starch, formed a three-dimensional network. This study provides valuable insights and guidance for the design and production of protein-enriched starch gel products with different textural properties.

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.

Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's critical roles in progenitors. Upf2 knockout (KO) prolongs the cell cycle of radial glia progenitor cells, promotes their transition into intermediate progenitors, and leads to reduced upper-layer neurons. CRISPRi screening identified Trp53 knockdown rescuing Upf2KO progenitors without globally reversing NMD inhibition, implying marginal contributions of most NMD targets to the cell cycle defect. Integrated functional genomics shows that NMD degrades selective TRP53 downstream targets, including Cdkn1a, which, without NMD suppression, slow the cell cycle. Trp53KO restores the progenitor cell pool and rescues the microcephaly of Upf2KO mice. Therefore, one physiological role of NMD in the developing brain is to degrade selective TRP53 targets to control progenitor cell cycle and brain size.

Ent-eudesmane sesquiterpenoids with anti-neuroinflammatory activity from the marine-derived fungus Eutypella sp. F0219.

In this study, twenty-three ent-eudesmane sesquiterpenoids (1-23) including fifteen previously undescribed ones, named eutypelides A-O (1-15) were isolated from the marine-derived fungus Eutypella sp. F0219. Their planar structures and relative configurations were established by HR-ESIMS and extensive 1D and 2D NMR investigations. The absolute configurations of the previously undescribed compounds were determined by single-crystal X-ray diffraction analyses, modified Mosher's method, and ECD calculations. Structurally, eutypelide A (1) is a rare 1,10-seco-ent-eudesmane, whereas 2-15 are typically ent-eudesmanes with 6/6/-fused bicyclic carbon nucleus. The anti-neuroinflammatory activity of all isolated compounds (1-23) was accessed based on their ability to NO production in LPS-stimulated BV2 microglia cells. Compound 16 emerged as the most potent inhibitor. Further mechanistic investigation revealed that compound 16 modulated the inflammatory response by decreasing the protein levels of iNOS and increasing ARG 1 levels, thereby altering the iNOS/ARG 1 ratio and inhibiting macrophage polarization. qRT-PCR analysis showed that compound 16 reversed the LPS-induced upregulation of pro-inflammatory cytokines, including iNOS, TNF-α, IL-6, and IL-1ß, at both the transcriptional and translational levels. These effects were linked to the inhibition of the NF-κB pathway, a key regulator of inflammation. Our findings suggest that compound 16 may be a potential structure basis for developing neuroinflammation-related disease therapeutic agents.

Anterior segment features in neovascular glaucoma: An ultrasound biomicroscopy study.

PURPOSES: To investigate the features of the anterior segment structures in neovascular glaucoma (NVG) and analyze its differences from primary angle-closure glaucoma (PACG). METHODS: This study included patients who were first diagnosed with monocular NVG and PACG at the Affiliated Eye Hospital of Nanchang University during August 2019 to June 2022. Ultrasound biomicroscopy (UBM) was used to measure the anterior segment parameters of those eyes, including anterior chamber depth (ACD), anterior chamber width (ACW), anterior chamber area (ACA), iris area (IA), maximum iris thickness (ITMAX), middle iris thickness (ITMID), iris curvature (IC), lens vault (LV), angle opening distance (AOD500), trabecular iris angle (TIA500), trabecular-iris space area (TISA500) and peripheral anterior synechia (PAS) length. RESULTS: In this study, paired samples t-test showed that IA [1.170(0.324) mm2], ITMAX [0.368(0.079) mm], ITMID [0.280(0.062) mm] and IC [0.147(0.037) mm] of NVG were smaller than F-NVG [2.058(0.195) mm2, 0.611(0.045) mm, 0.415(0.049) mm and 0.272(0.077) mm], the AOD500, TIA500, and TISA500 of NVG were also smaller than F-NVG. Independent samples t-test showed that ACD [2.349(0.350) mm] and ACA [16.326(3.547) mm2] of NVG were larger than PACG [1.971(0.240) mm, 12.030(1.860) mm2], but the IA [1.170(0.324) mm2], ITMAX [0.368(0.079) mm], ITMID [0.280(0.062) mm], IC [0.147(0.037) mm] and LV [0.436(0.172 mm)] were smaller than PACG [1.740(0.294) mm2, 0.548(0.084) mm, 0.404(0.065) mm, 0.283(0.060) mm and 0.737(0.196) mm]. Among the 16 patients with 360° angle-closure NVG, the PAS length was 0.834 (0.326) mm, which exceeded the Schwalbe line. CONCLUSION: In NVG, the iris is atrophied, thinned, and straight, while the ACD is normal or slightly shallow. In 360° angle-closure NVG, the PAS length exceeds the Schwalbe line, presenting a pseudo angle phenomenon and a hockey stick sign. Notably, the anterior segment structure morphology of NVG exhibit differences from those of PACG.

Novel Polyurethane Based, Fully Flexible, High-Performance Piezoresistive Sensor for Real-Time Pressure Monitoring.

Flexible piezoresistive pressure sensors are garnering substantial attention, in line with advancements in biointegrated and wearable electronics. However, a significant portion of piezoresistive pressure sensors suffer from the trade-off between sensitivity and pressure range. Moreover, the current piezoresistive sensors generally rely on a rigid metallic electrode, severely deteriorating their long-term durability. Herein, a fully flexible piezoresistive sensor coupling polyurethane (PU) based electrode and active sensing element is proposed to circumvent the aforementioned problems. By rationally regulating the double-permeable conductive networks within the PU matrix, an elastomeric electrode and sensing element are implemented, respectively. The assembled heterostructured configurations enable impressive sensitivity up to 7.023 kPa-1, broad pressure detection (up to 420 kPa), an ultralow pressure sensing limit (0.1 Pa), and extraordinary operation stability over 80000 cyclic pressings along with fast response/relaxation times (60 ms/80 ms). Additionally, the fully flexible sensor is capable of both real-time detection of physiological signals and mimicking keyboards, implying its viability as a high-performance pressure sensor.

Protocol to test for the formation of ternary protein complexes in vivo or in vitro using a two-step immunoprecipitation approach.

Co-immunoprecipitation (coIP) is an experimental technique to study protein-protein interactions (PPIs). However, single-step coIP can only be used to identify the interaction between two proteins and does not solve the interaction testing of ternary complexes. Here, we present a protocol to test for the formation of ternary protein complexes in vivo or in vitro using a two-step coIP approach. We describe steps for cell culture and transfection, elution of target proteins, and two-step coIP including western blot analyses. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Risk factor analysis and nomogram development and verification for medullary carcinoma of the colon using SEER database.

Medullary Carcinoma of the Colon (MCC) is a rare histological subtype of colon cancer, and there is currently no recognized optimal treatment plan for it, with its prognosis remaining unclear. The aim of this study is to analyze the independent prognostic factors for MCC patients and develop and validate nomograms to predict overall survival (OS). A total of 760 patients newly diagnosed with MCC from 2004 to 2020 were selected from the Surveillance, Epidemiology, and End Results (SEER) database. All patients were randomly allocated to a training group and a validation group in a 7:3 ratio. Univariate and multivariable Cox regression analyses were conducted to identify prognostic factors and construct nomograms. The nomogram prediction model was evaluated and validated using receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA). The study found that elderly women are more susceptible to MCC, and the ascending colon and cecum are the most common sites of involvement. MCC is poorly differentiated, with stages II and III being the most common. Surgery is the primary treatment for MCC. The prognosis for patients with stage IV MCC is poor, with a median survival time of only 10 months. Independent prognostic factors for MCC include age, N stage, M stage, surgery, chemotherapy, and tumor size. Among them, age < 75 years and completion of chemotherapy were protective factors for colon medullary carcinoma, while N2 (HR = 2.18, 95%CI 1.40-3.38), M1 (HR = 3.31, 95%CI 2.01-5.46), no surgery (HR = 27.94, 95%CI 3.69-211.75), and tumor diameter > 7 cm (HR = 1.66, 95%CI 1.20-2.30) were risk factors for colon medullary carcinoma. The results of ROC, AUC, calibration curves, and DCA demonstrate that the nomogram prediction model exhibits good predictive performance. We have updated the demographic characteristics of colon medullary carcinoma and identified age, N staging, M staging, surgery, chemotherapy and tumor size as independent prognostic factors for colon medullary carcinoma. Additionally, we have established nomograms for prognostic prediction. These nomograms can provide personalized predictions and serve as valuable references for clinical decision-making.

LPS and ATP-induced Death of PMA-differentiated THP-1 Macrophages and its Validation.

Cell death is a fundamental process in all living organisms. The protocol establishes a lipopolysaccharide (LPS) and adenosine triphosphate (ATP)-induced phorbol-12-myristate-13-acetate (PMA)-differentiated lipid deposition in human monocyte (THP-1) macrophage model to observe cell death. LPS combined with ATP is a classic inflammatory induction method, often used to study pyroptosis, but apoptosis and necroptosis also respond to stimulation by LPS/ATP. Under normal circumstances, phosphatidylserine is only localized in the inner leaflet of the plasma membrane. However, in the early stages of pyroptosis, apoptosis, and necroptosis, the cell membrane remains intact and exposed to phosphatidylserine, and in the later stages, the cell membrane loses its integrity. Here, flow cytometry was used to analyze Annexin V and 7-Aminoactinomycin D (AAD) double staining to detect the cell death from the whole cells. The results show that substantial cells died after stimulation with LPS/ATP. Using scanning electron microscopy, we observe the possible forms of cell death in individual cells. The results indicate that cells may undergo pyroptosis, apoptosis, or necroptosis after stimulation with LPS/ATP. This protocol focuses on observing the death of macrophages after stimulation with LPS/ATP. The results showed that cell death after LPS and ATP stimulation is not limited to pyroptosis and that apoptosis and necrotic apoptosis can also occur, helping researchers better understand cell death after LPS and ATP stimulation and choose a better experimental method.

"Ion-imprinting" strategy towards metal sulfide scavenger enables the highly selective capture of radiocesium.

Highly selective capture of radiocesium is an urgent need for environmental radioactive contamination remediation and spent fuel disposal. Herein, a strategy is proposed for construction of "inorganic ion-imprinted adsorbents" with ion recognition-separation capabilities, and a metal sulfide Cs2.33Ga2.33Sn1.67S8·H2O (FJSM-CGTS) with "imprinting effect" on Cs+ is prepared. We show that the K+ activation product of FJSM-CGTS, Cs0.51K1.82Ga2.33Sn1.67S8·H2O (FJMS-KCGTS), can reach adsorption equilibrium for Cs+ within 5 min, with a maximum adsorption capacity of 246.65 mg·g-1. FJMS-KCGTS overcomes the hindrance of Cs+ adsorption by competing ions and realizes highly selective capture of Cs+ in complex environments. It shows successful cleanup for actual 137Cs-liquid-wastes generated during industrial production with removal rates of over 99%. Ion-exchange column filled with FJMS-KCGTS can efficiently treat 540 mL Cs+-containing solutions (31.995 mg·L-1) and generates only 0.12 mL of solid waste, which enables waste solution volume reduction. Single-crystal structural analysis and density functional theory calculations are used to visualize the "ion-imprinting" process and confirm that the "imprinting effect" originates from the spatially confined effect of the framework. This work clearly reveals radiocesium capture mechanism and structure-function relationships that could inspire the development of efficient inorganic adsorbents for selective recognition and separation of key radionuclides.

A photothermal aptasensor based on rolling circle amplification-enriched DNAzyme for portable detection of ochratoxin A in grape juice.

Aptasensors for detection of ochratoxin A (OTA) have been extensively studied, but the majority of them require costly and large-scale equipment as signal readers. Herein, a photothermal aptasensor capable of portable detection of OTA through a thermometer was developed on basis of aptamer structural switching and rolling circle amplification (RCA)-enriched DNAzyme. Oligonucleotides and alkaline phosphatase (ALP) modified magnetic beads were prepared. The binding of aptamers to OTA led to the release of ALP labeled complementary DNA. After magnetic separation, ALP catalyzed the padlock dephosphorylation, inhibiting the subsequent RCA reaction. This process converted the OTA concentration into the amount of the photothermal reagent oxTMB produced from the catalytic reaction induced by RCA-enriched DNAzyme. Under the optimal conditions, the detection limit (LOD) of this aptasensor was 2.28 nM in a clean buffer, while the LOD reached 2.43 nM in 2 % grape juice. The good performance of the photothermal aptasensor makes it possible to measure OTA pollution in low resource environments.

A transthyretin-like protein acts downstream of miR397 and LACCASE to regulate grain yield in rice.

Increasing grain yield is a major goal of breeders due to the rising global demand for food. We previously reported that the miR397-LACCASE (OsLAC) module regulates brassinosteroid (BR) signaling and grain yield in rice (Oryza sativa). However, the precise roles of laccase enzymes in the BR pathway remain unclear. Here, we report that OsLAC controls grain yield by preventing the turnover of TRANSTHYRETIN-LIKE (OsTTL), a negative regulator of BR signaling. Overexpressing OsTTL decreased BR sensitivity in rice, while loss-of-function of OsTTL led to enhanced BR signaling and increased grain yield. OsLAC directly binds to OsTTL and regulates its phosphorylation-mediated turnover. The phosphorylation site Ser226 of OsTTL is essential for its ubiquitination and degradation. Overexpressing the dephosphorylation-mimic form of OsTTL (OsTTLS226A) resulted in more severe defects than did overexpressing OsTTL. These findings provide insight into the role of an ancient laccase in BR signaling and suggest that the OsLAC-OsTTL module could serve as a target for improving grain yield.

Improvement of nucleotide content of Cordyceps tenuipes by Schisandra chinensis: fermentation process optimization and application prospects.

Nucleotides are important components and the main indicators for judging Cordyceps quality. In this paper, the mixed fermentation process of Schisandra chinensis and Cordyceps tenuipes was systematically studied, and it was proposed that the fermentation products aqueous extract (S-ZAE) had antioxidant activity and anti-AChE ability. Herein, the results of a single factor showed that S. chinensis, yeast extract, inoculum amount, and pH had significant effects on nucleotide synthesis. The fermentation process optimization results were 3% glucose, 0.25% KH2PO4, 2.1% yeast extract, and S. chinensis 0.49% (m/v), the optimal fermentation conditions were 25℃, inoculum 5.8% (v/v), pH 3.8, 6 d. The yield of total nucleotides in the scale-up culture was 0.64 ± 0.027 mg/mL, which was 10.6 times higher than before optimization. S-ZAE has good antioxidant and anti-AChE activities (IC50 0.50 ± 0.050 mg/mL). This fermentation method has the advantage of industrialization, and its fermentation products have the potential to become good functional foods or natural therapeutic agents.

Effect of non-metal doping on the optoelectronic properties of ZrS2/ZrSe2 heterostructure under strain: a first-principles study.

CONTEXT: In this paper, we systematically studied the effects of non-metallic element (B, C, N, O, F) doping and biaxial stretching on the photoelectric properties of ZrS2/ZrSe2 heterostructures by using the first-principles calculation method based on density functional theory. The results show that the p-type doping is realized by B, C, and N atom doping, and the n-type doping is realized by O and F atom doping. The doping of B and C atoms produces impurity energy levels in the band gap, which affects the conductivity of the heterostructure. The band gap of N and O atom-doped heterostructures increases under tensile strain, but it is still a direct band gap. The analysis of the optical properties of the heterostructures shows that the doping of non-metallic atoms can adjust the optical absorption rate and reflectivity of the heterostructures. Under the action of tensile strain, the optical properties of the doped heterostructures have changed significantly in the low-energy region. This article provides a theoretical basis for the future application of ZrS2/ZrSe2 heterostructures. METHOD: This paper uses the first-principles calculation method based on density functional theory. The PBE exchange-correlation functional based on generalized gradient approximation (GGA) is selected for the specific calculation, and the crystal structure is geometrically optimized by the ultrasoft pseudopotential method. It is verified that when the cutoff energy of the ZrS2/ZrSe2 heterostructure is 500 eV, the K-point grid is selected to be 10 × 10 × 2 with the lowest energy, so the cutoff energy is selected to be 500 eV. The K-point grid is selected to be 10 × 10 × 2. The convergence limits for structural optimization are as follows: the maximum force between atoms is 0.01 eV/Å, the convergence threshold of the maximum energy change is set to 10-9 eV/atom, and the convergence threshold of the maximum displacement is 0.001 Å. In order to avoid the influence of atomic periodic motion between different atomic layers, a vacuum layer of 20 Å is added in the vertical direction. Considering the interaction of vdW between the interfaces, the DFT-D2 method is used to verify. The optical properties were calculated by the random phase approximation method, and the K-point grid was selected as 12 × 12 × 2.

Oral microbiota dysbiosis alters chronic restraint stress-induced depression-like behaviors by modulating host metabolism.

Studies have shown that the microbiota-gut-brain axis is highly correlated with the pathogenesis of depression in humans. However, whether independent oral microbiome that do not depend on gut microbes could affect the progression of depression in human beings remains unclear, neither does the presence and underlying mechanisms of the microbiota-oral-brain axis in the development of the condition. Hence this study that encompasses clinical and animal experiments aims at investigating the correlation between oral microbiota and the onset of depression via mediating the microbiota-oral-brain axis. We compared the oral microbial compositions and metabolomes of 87 patients with depressive symptoms versus 70 healthy controls. We found that the oral microbial and metabolic signatures were significantly different between the two groups. Significantly, germ-free (GF) mice transplanted with saliva from mice exposing to chronic restraint stress (CRS) displayed depression-like behavior and oral microbial dysbiosis. This was characterized by a significant differential abundance of bacterial species, including the enrichment of Pseudomonas, Pasteurellaceae, and Muribacter, as well as the depletion of Streptococcus. Metabolomic analysis showed the alternation of metabolites in the plasma of CRS-exposed GF mice, especially Eicosapentaenoic Acid. Furthermore, oral and gut barrier dysfunction caused by CRS-induced oral microbiota dysbiosis may be associated with increased blood-brain barrier permeability. Pseudomonas aeruginosa supplementation exacerbated depression-like behavior, while Eicosapentaenoic Acid treatment conferred protection against depression-like states in mice. These results suggest that oral microbiome and metabolic function dysbiosis may be relevant to the pathogenesis and pathophysiology of depression. The proposed microbiota-oral-brain axis provides a new way and targets for us to study the pathogenesis of depression.

Effect of lecithin on the complexation between different botanically sourced starches and lauric acid.

This research investigated the effect of lecithin on the complexation of lauric acid with maize starch, potato starch, waxy maize starch, and high amylose maize starch. Rapid visco analysis showed that lecithin altered the setback pattern of potato starch-lauric acid and maize starch-lauric acid mixtures but not waxy maize starch-lauric acid. Further investigation, including differential scanning calorimetry, complex index, and X-ray diffraction, showed that lecithin enhanced the complexation of maize starch, potato starch, and high amylose maize starch with lauric acid. Fourier transform infrared and Raman spectroscopy revealed increasingly ordered structures formed in maize starch-lauric acid-lecithin, potato starch-lauric acid-lecithin, and high amylose maize starch-lauric acid-lecithin systems compared to corresponding binary systems. These highly ordered complexes of maize starch, potato starch, and high amylose maize starch also demonstrated greater resistance to in vitro enzymatic hydrolysis. Waxy maize starch complexation however remained unaffected by lecithin. The results of this study show that lecithin impacts complexation between fatty acids and native starches containing amylose, with the starch source being critical. Lecithin minimally impacted the complexation of low amylose starch and fatty acids.

Long range topography by dispersion unmatched spectral-domain interferometry based on virtually imaged phased array modes.

We propose to realize a long range topography by dispersion unmatched spectral-domain interferometry based on virtually imaged phased array (VIPA) modes. By filtering the continuous spectrum of a supercontinuum source through a side-entrance Fabry-Perot etalon configured at two input angles, two groups of VIPA modes are generated. A method based on unmatched dispersion is proposed for non-aliasing reconstruction of the true depth from the interference spectrum under-sampled at two groups of VIPA modes. With the high spectral resolution provided by the VIPA modes instead of the grating-based spectrometer, only a 10 dB falloff in sensitivity over a range of 10 mm was demonstrated. The feasibility of the proposed method was confirmed by topography of a sample of gauge blocks and a model of three-dimensional (3D) printed tooth. The occlusal surface of the tooth model was further quantitatively evaluated, demonstrating its potential application in long range 3D topography.