Parental histone transfer caught at the replication fork.

In eukaryotes, DNA compacts into chromatin through nucleosomes1,2. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin3,4. Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A-H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3-H4 tetramer, while the vacant H2A-H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3-H4 dimer and extends across the tetramerization interface of the H3-H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3-H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.

Coefficient of spatial variance of choroidal thickness on swept-source optical coherence tomography in healthy eyes.

PURPOSE: This study aims to introduce the coefficient of spatial variance of choroidal thickness to describe the choroidal variation and investigate its associated factors in healthy eyes. METHODS: This retrospective cross-sectional study included 1031 eyes from 1031 subjects who received a swept-source optical coherence tomography examination. The mean choroidal thickness in the macular 6 × 6 mm region and 900 subregions of 0.2 × 0.2 mm were computed using the embedded algorithm. Before analysis, potential segmentation and magnification errors were corrected. The coefficient of spatial variance was defined as the standard deviation divided by the mean (multiplied by 100%) of the choroidal thicknesses across 900 grids. Potential factors associated with the coefficient of spatial variance were assessed using multiple linear regression. RESULTS: The mean choroidal thickness of the entire 6 × 6 mm macular region was 204.50 ± 72.88 µm. The mean coefficient of spatial variance was 26.58 ± 8.24%, ranging from 11.00 to 61.58%. Statistical analysis revealed that the means choroidal thickness (ß = - 0.08, R2 = 0.42, p < 0.001) and anterior chamber depth (ß = - 2.39, R2 = 0.05, p = 0.06) were associated with the coefficient of spatial variance. CONCLUSION: Our study first incorporated the coefficient of spatial variance to represent the spatial variation of the choroidal thickness and observed that the greater thinning of the choroid is correlated with a more pronounced spatial variation.

Respiratory control minimizes diaphragmatic contraction and dry cough during pulsed-field ablation of atrial fibrillation.

AIMS: Pulsed-field ablation (PFA) is a promising new ablation modality to treat atrial fibrillation. However, PFA can cause varying degrees of diaphragmatic contraction and dry cough, especially under conscious sedation. This prospective study presents a method to minimize the impact of PFA on diaphragmatic contraction and dry cough during the procedure. METHODS AND RESULTS: Twenty-eight patients underwent PFA for pulmonary vein (PV) and superior vena cava isolation under conscious sedation. Each patient received two groups of ablations in each vein: the control group allowed PFA application during any phase of respiratory cycle, while the test group used respiratory control, delivering PFA energy only at the end of expiration. A rating score system was developed to assess diaphragmatic contraction and dry cough. A total of 1401 control ablations and 4317 test ablations were performed. The test group had significantly lower scores for diaphragmatic contraction (P < 0.01) and dry cough (P < 0.001) in all PVs compared to the control group. The average relative reductions in scores for all PVs were 33-47% for diaphragmatic contraction and 67-83% for dry cough. The percentage of ablations with scores ≧2 for diaphragmatic contraction decreased significantly from 18.5-28.0% in the control group to 0.4-2.6% in the test group (P < 0.001). For dry cough, the percentage decreased from 11.9-43.7% in the control group to 0.7-2.1% in the test group. CONCLUSION: Pulsed-field ablation application at the end of expiration can reduce the severity of diaphragmatic contraction and eliminate moderate and severe dry cough during PV isolation performed under conscious sedation.

Control of phosphorus release from sediment by iron/aluminum co-modified zeolite: efficiency, mechanism, and response of microbial communities in sediment.

The efficiency of iron/aluminum co-modified zeolite (FeAl-Z) covering and amendment for controlling the internal loading of phosphorus (P) from sediment to the overlying water (OW) and its controlling mechanism were explored. The response of the composition of sedimentary microbial communities in sediment and their function to the FeAl-Z capping and amendment was also examined. FeAl-Z showed good removal performance for phosphate in aqueous solution. The maximum phosphate adsorption quantity for FeAl-Z at pH 7 attained 11.2 mg P/g. The release of sediment endogenous phosphorus to OW can be successfully restrained by the FeAl-Z covering and amendment, and the suppression ability of FeAl-Z covering was stronger than that of FeAl-Z amendment. Under the capping or amendment condition, FeAl-Z can effectively inactivate the labile phosphorus measured by diffusion gradient in thin film (DGT-LP) in the overlying water and surface sediment. The added FeAl-Z transformed redox-sensitive phosphorus (BD-P) to metal oxide-bound phosphorus (NaOH-IP) and residual phosphorus (Res-P) in sediment, which increased the stability of inorganic phosphorus in the sediment. The passivation of soluble reactive phosphorus (SRP) and DGT-LP in the surface sediment by FeAl-Z significantly contributed to the inhibition of sediment endogenous phosphorus release to OW by the FeAl-Z capping, and the passivation of SRP, DGT-LP and mobile phosphorus in the surface sediment played a pivotal role in the control of sediment internal phosphorus release by the FeAl-Z amendment. The FeAl-Z amendment and capping did not increase the liberation risk of Fe from sediment, and the microorganisms in the sediments under the conditions of FeAl-Z amendment and covering still can perform good ecological functions. Results of this research demonstrate that FeAl-Z capping has high application potential in the control of phosphorus transfer from sediment to OW.

Contrasting effects of MgAl- and MgFe-based layered double hydroxides on phosphorus mobilization and microbial communities in sediment.

The effects of two types of layered double hydroxides (LDH) in-situ treatment on sediment phosphorus (P) mobilization and microbial community's structure were studied comparatively. The results presented that magnesium/aluminum-based (MA) and magnesium/iron (MF)-based LDH displayed great phosphate uptake ability in aqueous solution in a broad pH range of 3-8. The maximum phosphate sorption capacity of MA was 64.89 mg/g, around four times greater than that of MF (14.32 mg/g). Most of phosphate bound by MA and MF is hard to re-liberate under reduction and ordinary pH (5-9) conditions. In the in-situ remediation, the MA and MF capping/amendment both prevented P migration from the sediment to the overlying water (OL-water) under long-term anaerobic conditions, and MA had a better interception efficiency compared to MF in the same application mode. MA amendment significantly reduced mobile P (Mob-P) content in sediment and could remain its stable Mob-P inactivation capacity over a wide pH range. On the contrary, MF amendment increased Mob-P content in sediment and exhibited a variable ability to inactivate Mob-P under elevated pH conditions. MF can decrease Mob-P content at pH of 7 and 11 but increase Mob-P content at pH of 8-10. Under resuspension conditions, MA and MF capping groups still maintained low P levels in OL-water, while MA capping simultaneously showed a certain degree of resistance to sediment resuspension, but it had a weaker stabilizing effect for sediment than MF. Microbial community analysis manifested neither MA nor MF addition observably altered the sediment microbial diversity, but impacted the functional microorganisms' abundance and reshaped the microbial community's structure, intervening the sediment-P stabilization. Viewed from environmental friendliness, control efficiency, stability of P fixation capacity, and application convenience, MA capping wrapped by fabric is more suitable for addressing internal P loading in eutrophic lakes and holds great potential application.

Effects of lysine and threonine on milk yield, amino acid metabolism, and fecal microbiota of Yili lactating mares.

The nutritional benefits of mare milk are attracting increasing consumer interest. Limited availability due to low yield poses a challenge for widespread adoption. Although lysine and threonine are often used to enhance protein synthesis and muscle mass in horses, their impact on mare milk yield and nutrient composition remains underexplored. This study investigated the effects of lysine and threonine supplementation on 24 healthy Yili mares, mares at day 30 of lactation, over a 120-day period. The mares were divided into control and three experimental groups (six mares each) under pure grazing conditions. The control group received no amino acid supplementation, while experimental groups received varying daily doses of lysine and threonine: Group I (40 g lysine + 20 g threonine), Group II (60 g lysine + 40 g threonine), and Group III (80 g lysine + 60 g threonine). Supplementation in Group II notably increased milk yield, while Groups I and II showed higher milk fat percentages, and all experimental groups exhibited improved milk protein percentages. Additionally, blood levels of total protein, albumin, triglycerides, and glucose were reduced. Detailed analyses from Group II at peak lactation (day 60) included targeted metabolomics and microbial sequencing of milk, blood, and fecal samples. Amino acid metabolomics assessed amino acid content in mare milk and serum, while 16S rRNA gene sequencing evaluated rectal microbial composition. The results indicated that lysine and threonine supplementation significantly increased levels of threonine and creatine in the blood, and lysine, threonine, glutamine, and alanine in mare milk. Microbial analysis revealed a higher prevalence of certain bacterial families and genera, including Prevotellaceae, p_251_o5, and Rikenellaceae at the family level, and unclassified_p_251_o5, Prevotellaceae_UCG_001, and Rikenellaceae_RC9_gut_group at the genus level. Multi-omics analysis showed positive correlations between specific fecal genera and amino acids in mare milk. For instance, Prevotellaceae_UCG_003, unclassified Bacteroidetes_BS11_gut_group, and Corynebacterium were positively correlated with lysine, while unclassified Prevotellaceae was positively correlated with alanine and threonine, and Unclassified_Bacteroidales_BS11_gut_group was positively correlated with glutamine. In summary, lysine and threonine supplementation in grazing lactating mares enhanced milk production and improved milk protein and fat quality. It is recommended that herders, veterinarians, and technicians consider amino acid content in the diet of lactating mares. The optimal supplementation levels under grazing conditions for Yili horses were determined to be 60 g lysine and 40 g threonine per day. Future research should explore the molecular mechanisms by which these amino acids influence milk protein and lipid synthesis in mare mammary epithelial cells.

Preparation of Pt and bamboo charcoal co-modified TiO2 for formaldehyde sensing at room temperature.

Anatase TiO2 has evolved into one of the most attractive materials for gas sensing owing to its strong oxidation activity and excellent sensing properties. In this study, we prepared Pt and bamboo charcoal co-modified nano-TiO2 using a one-pot hydrothermal process and applied it to detect formaldehyde. The successful incorporation of the precious metal Pt and bamboo charcoal onto TiO2 was confirmed by scanning electron microscope, transmission electron microscopy, energy dispersive spectrometer, X-ray diffraction and X-ray photoelectron spectroscopy. Detailed analysis revealed a homogeneous distribution of Pt nanoparticles and bamboo charcoal on the TiO2 surface, which significantly improved the surface area and facilitated gas adsorption. These modifiers significantly enhanced the response of TiO2 to formaldehyde, for instance, the response signal increased fourfold, while the response time decreased from 91 to 68 s. The sample with 0.5@Pt and 0.5@C bamboo charcoal performed the best, showcasing the synergistic effect of metal nanoparticles and carbonaceous materials on gas-sensing properties. Our work highlighted the potential of using biomass-derived carbon to enhance the detection of formaldehyde and demonstrated the importance of material characteristics in designing effective gas sensors.

Inter-Individual Topographic Variation of Choroidal Thickness in Healthy Eyes on Swept-Source Optical Coherence Tomography.

Purpose: To investigate the topographic characters of inter-individual variations of the macular choroidal thickness (CT). Methods: This was a retrospective study. Macular CT data for 900 0.2 × 0.2-mm grids from 410 healthy eyes were collected from swept-source optical coherence tomography. Following the analysis of factors associated with mean CT, the ß-coefficients of the included associated factors in each grid were summarized for choroidal thickness changes analysis. Additionally, the coefficient of variance (CoV), coefficient of determination (CoD), and coefficient of variance unexplained (CoVU) for CT were calculated in each individual grid to investigate the inter-individual choroidal variations pattern. Results: Sex (ß = -17.26, female vs. male), age (ß = -1.61, per 1 year), and axial length (ß = -18.62, per 1 mm) were associated with mean macular CT. Females had a thinner choroid in all 900 grids (0.5-26.9 µm). As age increased, the CT noticeably decreased (8.74-19.87 µm per 10 years) in the temporal regions. With axial length elongation, the thinning (7.94-24.91 µm per 1 mm) was more evident in subfoveal and nasal regions. Both the CoV (34.69%-58.00%) and CoVU (23.05%-40.78%) were lower in the temporal regions, whereas the CoD (18.41%-39.66%) was higher in the temporal regions. Conclusions: Choroidal thinning is more predominant in the subfoveal and nasal regions with axial length elongation, but in the temporal region with aging. The inter-individual variation of CT is higher and less determined by sex, age, or axial length in the nasal regions. Translational Relevance: Topographic variation should be considered when interpreting choroidal thickness.

Differentiating Definite and Probable Ménière Disease: A Comprehensive Evaluation of Audio-Vestibular Function Testing Combined with Inner Ear MRI.

OBJECTIVES: To evaluate the differences between audio-vestibular function testing and inner ear gadolinium magnetic resonance imaging (MRI) in distinguishing definite Ménière disease (DMD) and probable Ménière disease (PMD), and to provide a reference for early clinical diagnosis and intervention. METHODS: A total of 116 patients diagnosed with DMD (n = 80) and PMD (n = 36) were enrolled. The differences in the results of pure tone audiometry, caloric test, and tympanic injection of gadolinium for contrast-enhanced MRI between the two groups were compared and analyzed. Parameters that could differentiate between the two conditions were identified, and the sensitivity and specificity and the area under the curve (AUC) of individual and combined indices in the differential diagnosis of DMD and PMD were evaluated. RESULTS: The hearing threshold and hearing asymmetry rate of the DMD group were significantly higher than those of the PMD group (p < 0.001), 98.8% and 30.6%, respectively. The abnormal rates of canal paresis (CP) and severity of endolymphatic hydrops in the DMD group were higher than those in the PMD group (p < 0.05). When combined with high-frequency hearing thresholds, hearing asymmetry, hearing curve type, endolymphatic hydrops, and abnormal CP, the diagnostic accuracy of DMD was improved compared to using high-frequency alone (p < 0.05). CONCLUSION: This study showed that PMD and DMD may represent two different stages in the development of MD disease. The comprehensive assessment of audio-vestibular function testing and inner ear MRI proves beneficial for early diagnosis, potentially contributing to the preservation of inner ear function.

Use of intracardiac echocardiography in vein of Marshall ethanol infusion for ablation of persistent atrial fibrillation.

BACKGROUND: Few methods have been reported to demonstrate real-time effects during vein of Marshall (VOM) ethanol infusion in persistent atrial fibrillation (PeAF). OBJECTIVE: This study was to evaluate the impact of left atrial (LA) monitoring using intracardiac echocardiography (ICE) during VOM ethanol infusion. METHODS: Seventy-four consecutive patients with PeAF who underwent VOM ethanol infusion followed by radiofrequency (RF) ablation were included. Patients with findings on ICE consistent with echogenic streaming in the LA and with increased myocardial local echogenicity along the VOM area were placed into one group (group A) and those without into the other group (group B). Outcomes between the 2 groups were compared. RESULTS: Forty-six patients (62%) were placed into group A. A new ethanol-induced low-voltage area in group A was larger than that in group B (8.5 cm2 [5.5-10.2 cm2] and 4.0 cm2 (2.4-6.3 cm2]; P < .001). The RF ablation time required to achieve MI block was reduced in group A patients (263.0 seconds [196.0-351.0 seconds] vs 417.0 seconds [315.0-709.5 seconds] in group B patients; P < .001). MI block was achieved in 46 patients (100%) via an endocardial approach in group A and 27 patients (96.4%) in group B (extra coronary sinus ablation in 4 patients). One patient developed clinically significant pericardial effusions and required pericardiocentesis in group B. CONCLUSION: Presence of increased myocardial local echogenicity at the ridge and consistent echogenic streaming in the LA detected by ICE-based imaging during VOM ethanol infusion suggests increased ablated tissue in that region and lower RF ablation time during ablation for PeAF.

Risk factors for diabetic retinopathy, diabetic macular edema, and sight-threatening diabetic retinopathy.

OBJECTIVE: To identify the risk factors for the development of diabetic retinopathy (DR), diabetic macular edema (DME), and sight-threatening DR (STDR) based on a city-wide diabetes screening program. RESEARCH DESIGN AND METHODS: Diabetic patients were prospectively recruited between June 2016 and December 2022. All patients underwent dilated fundus photography centered on the disc and macula or macular spectral domain optical coherence tomography (SD-OCT) scan. Complete medical history was documented. Systematic examination, blood analysis, and urinalysis were performed. Multivariate logistic regression analysis adjusting for age and sex was conducted. RESULTS: Out of 7274 diabetic patients, 6840 had gradable images, among which 3054 (42.0%) were graded as DR, 1153 (15.9%) as DME, and 1500 (20.6%) as STDR. The factors associated with DR, DME, and STDR included younger age (odds ratio [OR]: 0.96, 0.97, and 0.96 respectively), lower BMI (OR: 0.97, 0.95, and 0.95 respectively), longer duration of diabetes (OR: 1.07, 1.03, and 1.05 respectively) and positive of urinary albumin (OR: 2.22, 2.56, and 2.88 respectively). Other associated factors included elevated blood urea nitrogen (OR: 1.22, 1.28, and 1.27 respectively), higher LDL-cholesterol, lower blood hemoglobin (OR: 0.98, 0.98, and 0.98), insulin intake, presence of diabetic foot pathologies and diabetic peripheral neuropathy. We also identified novel risk factors, including high serum potassium (OR: 1.37, 1.46, and 1.55 respectively), high-serum sodium (OR: 1.02, 1.02, and 1.04 respectively). Better family income was a protective factor for DR, DME, and STDR. Alcohol consumption once a week was also identified as a protective factor for DR. CONCLUSIONS: Similar risk factors for DR, DME, and STDR were found in this study. Our data also indicates high serum sodium, high serum potassium, low blood hemoglobin, and level of family income as novel associated factors for DR, DME, and STDR, which can help with DR monitoring and management.

Evaluation of Myocilin Variant Protein Structures Modeled by AlphaFold2.

Deep neural network-based programs can be applied to protein structure modeling by inputting amino acid sequences. Here, we aimed to evaluate the AlphaFold2-modeled myocilin wild-type and variant protein structures and compare to the experimentally determined protein structures. Molecular dynamic and ligand binding properties of the experimentally determined and AlphaFold2-modeled protein structures were also analyzed. AlphaFold2-modeled myocilin variant protein structures showed high similarities in overall structure to the experimentally determined mutant protein structures, but the orientations and geometries of amino acid side chains were slightly different. The olfactomedin-like domain of the modeled missense variant protein structures showed fewer folding changes than the nonsense variant when compared to the predicted wild-type protein structure. Differences were also observed in molecular dynamics and ligand binding sites between the AlphaFold2-modeled and experimentally determined structures as well as between the wild-type and variant structures. In summary, the folding of the AlphaFold2-modeled MYOC variant protein structures could be similar to that determined by the experiments but with differences in amino acid side chain orientations and geometries. Careful comparisons with experimentally determined structures are needed before the applications of the in silico modeled variant protein structures.

Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases.

The aim of the study is to establish an online database for predicting protein structures altered in ocular diseases by Alphafold2 and RoseTTAFold algorithms. Totally, 726 genes of multiple ocular diseases were collected for protein structure prediction. Both Alphafold2 and RoseTTAFold algorithms were built locally using the open-source codebases. A dataset with 48 protein structures from Protein Data Bank (PDB) was adopted for algorithm set-up validation. A website was built to match ocular genes with the corresponding predicted tertiary protein structures for each amino acid sequence. The predicted local distance difference test-Cα (pLDDT) and template modeling (TM) scores of the validation protein structure and the selected ocular genes were evaluated. Molecular dynamics and molecular docking simulations were performed to demonstrate the applications of the predicted structures. For the validation dataset, 70.8% of the predicted protein structures showed pLDDT greater than 90. Compared to the PDB structures, 100% of the AlphaFold2-predicted structures and 97.9% of the RoseTTAFold-predicted structure showed TM score greater than 0.5. Totally, 1329 amino acid sequences of 430 ocular disease-related genes have been predicted, of which 75.9% showed pLDDT greater than 70 for the wildtype sequences and 76.1% for the variant sequences. Small molecule docking and molecular dynamics simulations revealed that the predicted protein structures with higher confidence scores showed similar molecular characteristics with the structures from PDB. We have developed an ocular protein structure database (EyeProdb) for ocular disease, which is released for the public and will facilitate the biological investigations and structure-based drug development for ocular diseases. Database URL:  http://eyeprodb.jsiec.org.