Visualizing highly bright and uniform cellular ultrastructure by expansion-microscopy with tetrahedral DNA nanostructures.

Expansion Microscopy (ExM) is a widely used super-resolution technique that enables imaging of structures beyond the diffraction limit of light. However, ExM suffers from weak labeling signals and expansion distortions, limiting its applicability. Here, we present an innovative approach called Tetrahedral DNA nanostructure Expansion Microscopy (TDN-ExM), addressing these limitations by using tetrahedral DNA nanostructures (TDNs) for fluorescence labeling. Our approach demonstrates a 3- to 10-fold signal amplification due to the multivertex nature of TDNs, allowing the modification of multiple dyes. Previous studies have confirmed minimal distortion on a large scale, and our strategy can reduce the distortion at the ultrastructural level in samples because it does not rely on anchoring agents and is not affected by digestion. This results in a brighter fluorescence, better uniformity, and compatibility with different labeling strategies and optical super-resolution technologies. We validated the utility of TDN-ExM by imaging various biological structures with improved resolutions and signal-to-noise ratios.

Molecular Responses of Anti-VEGF Therapy in Neovascular Age-Related Macular Degeneration: Integrative Insights From Multi-Omics and Clinical Imaging.

Purpose: The purpose of this study was to investigate the molecular mechanisms underlying anti-vascular endothelial growth factor (anti-VEGF) efficacy and response variability in neovascular age-related macular degeneration (nAMD) using longitudinal proteomic and metabolomic analysis alongside three-dimensional lesion measurements. Methods: In this prospective study, 54 treatment-naive patients with nAMD underwent "3+ pro re nata" (3+PRN) anti-VEGF regimens followed for at least 12 weeks. Aqueous humors were collected pre- and post-treatment for proteomic and metabolomic analysis. Three-dimensional optical coherence tomography (OCT) and OCT angiography assessed different types of nAMD lesion volumes and areas. Results: There were 1350 proteins and 1268 metabolites that were identified in aqueous humors, with 301 proteins and 353 metabolites significantly altered during anti-VEGF treatment, enriched in pathways of angiogenesis, energy metabolism, signal transduction, and neurofunctional regulation. Sixty-seven changes of (Δ) molecules significantly correlated with at least one type of ΔnAMD lesion. Notably, proteins FGA, TALDO1, and ASPH significantly decreased during treatment, with their reductions correlating with greater lesion regression in at least two lesion types. Conversely, despite that YIPF3 also showed significant downregulation, its decrease was associated with poorer regression in total nAMD lesion and subretinal hyper-reflective material. Conclusions: This study identifies FGA, TALDO1, and ASPH as potential key molecules in the efficacy of anti-VEGF therapy, whereas YIPF3 may be a key factor in poor response. The integration of longitudinal three-dimensional lesion analysis with multi-omics provides valuable insights into the mechanisms and response variability of anti-VEGF treatment in nAMD.

Association between three-dimensional morphological features and functional indicators of neovascular age-related macular degeneration.

PURPOSE: To investigate the correlation between morphological lesions and functional indicators in eyes with neovascular age-related macular degeneration (nAMD). METHODS: This was a prospective observational study of treatment-naïve nAMD eyes. Various morphological lesions and impaired retinal structures were manually measured at baseline and month-3 in three-dimensional optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) images, including the volumes (mm3) of macular neovascularization (MNV), avascular subretinal hyperreflective material (avascular SHRM), subretinal fluid (SRF), intraretinal fluid (IRF), serous pigment epithelial detachment (sPED) and the impaired area (mm2) of ellipsoid zone (EZ), external limiting membrane (ELM) and outer nuclear layer (ONL). RESULTS: Sixty-three eyes were included. The volume of avascular SHRM showed persistent positive associations with the area of EZ damage, both at baseline, month-3, and change values (all P < 0.001). Poor BCVA (month-3) was associated with larger volumes of baseline IRF (ß = 0.377, P < 0.001), avascular SHRM (ß = 0.306, P = 0.032), and ELM impairment area (ß = 0.301, P = 0.036) in multivariate model. EZ and ELM impairment were primarily associated with baseline avascular SHRM (ß = 0.374, p = 0.003; ß = 0.388, P < 0.001, respectively), while ONL impairment primarily associated with MNV (ß = 0.475, P < 0.001). CONCLUSION: The utilization of three-dimensional measurements elucidates the intrinsic connections among various lesions and functional outcomes. In particular, avascular SHRM plays an important role in prognosis of nAMD.

Effects of dietary selenium deficiency and supplementation on liver in grazing sheep: insights from transcriptomic and metabolomic analysis.

Background: Mineral elements play a crucial role in supporting the life activities and physiological functions of animals. However, numerous studies have revealed that in some geographical areas and certain grazing situations, grazing livestock frequently suffers from mineral element deficiencies due to the loss of mineral elements from grassland forages, such as selenium (Se). To shed fresh light on this issue, this study aims to investigate the impact of dietary Se deficiency and supplementation on the liver of grazing sheep in these challenging conditions. Method: This study involved 28 grazing Mongolian Wu Ranke sheep with an average body weight of about 32.20 ± 0.37 kg, which were divided into the Se treatment group and the control group. The Se treatment group was fed with the low-Se diet for 60 days and then continued to be fed with the high-Se diet for 41 days. The liver concentration of minerals, transcriptomic analysis, and untargeted metabolomic analysis were conducted to assess the impact of Se deficiency and supplementation on the liver of grazing sheep. Results: Dietary Se deficiency and supplementation significantly reduced and elevated liver concentration of Se, respectively (p < 0.05). Gene functional enrichment analysis suggested that dietary Se deficiency might impair protein synthesis efficiency, while Se supplementation was found to enhance liver protein synthesis in grazing sheep. AGAP1, ERN1, MAL2, NFIC, and RERG were identified as critical genes through the weighted gene correlation network analysis, the quantitative real-time polymerase chain reaction, and the receiver operating characteristic curve validation that could potentially serve as biomarkers. Metabolomics analysis revealed that dietary Se deficiency significantly reduced the abundance of metabolites such as 5-hydroxytryptamine, while dietary Se supplementation significantly elevated the abundance of metabolites such as 5-hydroxytryptophan (p < 0.05). Conclusion: Integrative analysis of the transcriptome and metabolome revealed that dietary Se deficiency led to reduced hepatic antioxidant and anti-inflammatory capacity, whereas Se supplementation increased the hepatic antioxidant and anti-inflammatory capacity in grazing Wu Ranke sheep. These findings provide new insights into the effects of dietary Se deficiency and supplementation on the liver of grazing sheep, potentially leading to improved overall health and well-being of grazing livestock.

Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs.

Detecting multiple targets in living cells is important in cell biology. However, multiplexed fluorescence imaging beyond two-to-three targets remains a technical challenge. Herein, we introduce a multiplexed imaging strategy, 'sequential Fluorogenic RNA Imaging-Enabled Sensor' (seqFRIES), which enables live-cell target detection via sequential rounds of imaging-and-stripping. In seqFRIES, multiple orthogonal fluorogenic RNA aptamers are genetically encoded inside cells, and then the corresponding cell membrane permeable dye molecules are added, imaged, and rapidly removed in consecutive detection cycles. As a proof-of-concept, we have identified in this study four fluorogenic RNA aptamer/dye pairs that can be used for highly orthogonal and multiplexed imaging in living bacterial and mammalian cells. After further optimizing the cellular fluorescence activation and deactivation kinetics of these RNA/dye pairs, the whole four-color semi-quantitative seqFRIES process can be completed in ∼20 min. Meanwhile, seqFRIES-mediated simultaneous detection of critical signalling molecules and mRNA targets was also achieved within individual living cells. We expect our validation of this new seqFRIES concept here will facilitate the further development and potential broad usage of these orthogonal fluorogenic RNA/dye pairs for multiplexed and dynamic live-cell imaging and cell biology studies.

Non-invasive screening of bladder cancer using digital microfluidics and FLIM technology combined with deep learning.

Non-invasive screening for bladder cancer is crucial for treatment and postoperative follow-up. This study combines digital microfluidics (DMF) technology with fluorescence lifetime imaging microscopy (FLIM) for urine analysis and introduces a novel non-invasive bladder cancer screening technique. Initially, the DMF was utilized to perform preliminary screening and enrichment of urine exfoliated cells from 54 participants, followed by cell staining and FLIM analysis to assess the viscosity of the intracellular microenvironment. Subsequently, a deep learning residual convolutional neural network was employed to automatically classify FLIM images, achieving a three-class prediction of high-risk (malignant), low-risk (benign), and minimal risk (normal) categories. The results demonstrated a high consistency with pathological diagnosis, with an accuracy of 91% and a precision of 93%. Notably, the method is sensitive for both high-grade and low-grade bladder cancer cases. This highly accurate non-invasive screening method presents a promising approach for bladder cancer screening with significant clinical application potential.

PI3K inhibitor idelalisib enhances the anti-tumor effects of CDK4/6 inhibitor palbociclib via PLK1 in B-cell lymphoma.

Relapsed or refractory diffuse large B cell lymphoma (DLBCL) and mantle cell lymphoma (MCL) patients still faced with poor survival, representing an unmet clinical need. In-depth research into the disease's pathogenesis and the development of targeted treatment strategies are urgently needed. Here, we conducted a comprehensive bioinformatic analysis of gene mutation and expression using data from our center and public databases. Cell cycle-related genes especially for CDKN2A/B-CDK4/6/CCND1 machinery altered frequently in DLBCL and MCL. Clinically, high CDK4 and CDK6 expression were correlated with poor prognosis of DLBCL and MCL patients. Furthermore, we also validated the pharmacological efficacy of CDK4/6 inhibitor palbociclib and its synergy effect with PI3K inhibitor idelalisib utilizing in vitro cell lines and in vivo cell-derived xenograft (CDX) and patient-derived xenograft (PDX) mouse models. Our results provided sufficient pre-clinical evidence to support the potential combination of palbociclib and idelalisib for DLBCL and MCL patients.

A portable electrochemical DNA sensor for sensitive and tunable detection of piconewton-scale cellular forces.

Cell-generated forces are a key player in cell biology, especially during cellular shape formation, migration, cancer development, and immune response. A new type of label-free smartphone-based electrochemical DNA sensor is developed here for cellular force measurement. When cells apply tension forces to the DNA sensors, the rapid rupture of DNA duplexes allows multiple redox reporters to reach the electrode and generate highly sensitive electrochemical signals. The sensitivity of these portable sensors can be further enhanced by incorporating a CRISPR-Cas12a system. Meanwhile, the threshold force values of these DNA-based sensors can be rationally tuned based on the force application geometries and also DNA intercalating agents. Overall, these highly sensitive, portable, cost-efficient, and easy-to-use electrochemical sensors can be powerful tools for detecting different cell-generated molecular forces.

Adaptively leverage multiple real-world data sources for treatment effect estimation based on similarity.

The incorporation of real-world data (RWD) into medical product development and evaluation has exhibited consistent growth. However, there is no universally adopted method of how much information to borrow from external data. This paper proposes a study design methodology called Tree-based Monte Carlo (TMC) that dynamically integrates patients from various RWD sources to calculate the treatment effect based on the similarity between clinical trial and RWD. Initially, a propensity score is developed to gauge the resemblance between clinical trial data and each real-world dataset. Utilizing this similarity metric, we construct a hierarchical clustering tree that delineates varying degrees of similarity between each RWD source and the clinical trial data. Ultimately, a Gaussian process methodology is employed across this hierarchical clustering framework to synthesize the projected treatment effects of the external group. Simulation result shows that our clustering tree could successfully identify similarity. Data sources exhibiting greater similarity with clinical trial are accorded higher weights in treatment estimation process, while less congruent sources receive comparatively lower emphasis. Compared with another Bayesian method, meta-analytic predictive prior (MAP), our proposed method's estimator is closer to the true value and has smaller bias.

Analysis of Fluid Replacement in Two Fluidic Chambers for Oblique-Incidence Reflectivity Difference (OI-RD) Biosensor.

Optical biosensors have a significant impact on various aspects of our lives. In many applications of optical biosensors, fluidic chambers play a crucial role in facilitating controlled fluid delivery. It is essential to achieve complete liquid replacement in order to obtain accurate and reliable results. However, the configurations of fluidic chambers vary across different optical biosensors, resulting in diverse fluidic volumes and flow rates, and there are no standardized guidelines for liquid replacement. In this paper, we utilize COMSOL Multiphysics, a finite element analysis software, to investigate the optimal fluid volume required for two types of fluidic chambers in the context of the oblique-incidence reflectivity difference (OI-RD) biosensor. We found that the depth of the fluidic chamber is the most crucial factor influencing the required liquid volume, with the volume being a quadratic function of the depth. Additionally, the required fluid volume is also influenced by the positions on the substrate surface bearing samples, while the flow rate has no impact on the fluid volume.

Effects of dietary minerals deficiency and supplementation on different parts of muscle minerals content in grazing Mongolian sheep.

Objective: The objective of this study was to investigate the impact of dietary deficiency and supplementation of calcium, zinc, copper, cobalt, manganese or selenium on minerals content in the longissimus dorsi (LD), biceps femoris (BF) and triceps brachii (TB) of grazing Mongolian sheep. Methods: We randomly divided 98 sheep into 7 treatment groups and fed them specific diets for 60 days: a total mineral nutrition diet (LCG), a calcium deficiency diet (LCa), a zinc deficiency diet (LZn), a copper deficiency diet (LCu), a cobalt deficiency diet (LCo), a manganese deficiency diet (LMn) and a selenium deficiency diet (LSe). Then 7 sheep from each group were slaughtered and samples of LD, BF and TB were collected for mineral content analysis. The remaining sheep in each group were subsequently fed specific diets for an additional 41 days: a total mineral nutrition diet (SCG), a calcium supplementation diet (SCa), a zinc supplementation diet (SZn), a copper supplementation diet (SCu), a cobalt supplementation diet (SCo), a manganese supplementation diet (SMn) and a selenium supplementation diet (SSe). Afterward, all sheep were slaughtered, and muscle samples were collected and analyzed. Results: Significant findings emerged that LCa decreased sulfur (S) content in BF and increased Ca content in LD and BF, while SCa increased S and Ca content in BF and TB, respectively (P < 0.05). LZn decreased Zn, S, and potassium (K) content in LD and BF, while SZn increased Zn and S content in LD and BF, respectively (P < 0.05). LCu decreased Cu and iron (Fe) content in LD and TB, while SCu increased Fe content in TB (P < 0.05). LCo decreased phosphorus, S, K, Ca, Mn, Fe, Cu, and Zn content in LD (P < 0.05). LMn decreased Mn content and increased K content in TB, while SMn decreased K content in BF and TB (P < 0.05). LSe and SSe decreased and increased Se content in LD, BF, and TB, respectively (P < 0.05). Conclusion: Dietary mineral levels have varying effects on lamb meat minerals content. It is important to ensure an adequate intake of minerals in the diet to enhance the mineral nutrition of lamb meat.

A Novel Exploration of the Choroidal Vortex Vein System: Incidence and Characteristics of Posterior Vortex Veins in Healthy Eyes.

Purpose: The purpose of this study was to investigate the incidence and characteristics of posterior vortex veins (PVVs) in healthy eyes and explore their relationship with age and refractive status. Methods: This retrospective cross-sectional analysis encompassed 510 eyes from 255 consecutive healthy participants. Wide-field optical coherence tomography angiography (WF-OCTA) imaging was used to assess the presence of PVVs. Eyes were classified according to refractive status (emmetropia, low and moderate myopia, and high myopia) and age (minors and adults). The incidence and characteristics of eyes with PVVs were analyzed. Results: Participants (mean age = 30.60 ± 21.12 years, 47.4% men) showed a mean refractive error of -2.83 ± 3.10 diopters (D; range = -12.00 to +0.75). PVVs were observed in 16.1% (82/510) of eyes. Of these, 39% (32/82) had PVVs in one eye and 61% (50/82) in both eyes. The mean number of PVVs per eye was 1.65 ± 1.05 (range = 1-6). PVVs are mainly around the optic disc (78%, 64/82) of eyes with PVVs and less in the macular area (6.1%, 5/82) or elsewhere (15.9%, 13/82). PVV incidence correlated with refractive status: 10.3% (22/213) in emmetropia, 16.6% (31/187) in low and moderate myopia, and 26.4% (29/110) in high myopia (P = 0.001), but not with age. Refractive status was the key predictor of PVV occurrence (odds ratio [OR] = 1.45, 95% confidence interval [CI] = 1.02-2.06, P = 0.038). Conclusions: This study confirms PVVs' presence in healthy eyes, highlighting their inherent existence and susceptibility to alterations due to refractive conditions. These findings enhance our understanding of the vortex vein system and its distribution within the eyes.

Transcriptomics and metabolomics analysis reveal the dietary copper deficiency and supplementation effects of liver gene expression and metabolite change in grazing sheep.

BACKGROUND: The appropriate mineral nutrients are essential for sheep growth and reproduction. However, traditional grazing sheep often experience mineral nutrient deficiencies, especially copper (Cu), due to inadequate mineral nutrients from natural pastures. RESULTS: The results indicated that dietary Cu deficiency and supplementation significantly reduced and elevated liver concentration of Cu, respectively (p < 0.05). FOXO3, PLIN1, ACTN2, and GHRHR were identified as critical genes using the weighted gene co-expression network analysis (WGCNA), quantitative real-time polymerase chain reaction (qRT-PCR), and receiver operating characteristic curve (ROC) validation as potential biomarkers for evaluating Cu status in grazing sheep. Combining these critical genes with gene functional enrichment analysis, it was observed that dietary Cu deficiency may impair liver regeneration and compromise ribosomal function. Conversely, dietary Cu supplementation may enhance ribosomal function, promote lipid accumulation, and stimulate growth and metabolism in grazing sheep. Metabolomics analysis indicated that dietary Cu deficiency significantly decreased the abundance of metabolites such as cholic acid (p < 0.05). On the other hand, dietary Cu supplementation significantly increased the abundance of metabolites such as palmitic acid (p < 0.05). Integrative analysis of the transcriptome and metabolome revealed that dietary Cu deficiency may reduce liver lipid metabolism while Cu supplementation may elevate it in grazing sheep. CONCLUSIONS: The Cu content in diets may have an impact on hepatic lipid metabolism in grazing sheep. These findings provide new insights into the consequences of dietary Cu deficiency and supplementation on sheep liver and can provide valuable guidance for herders to rationalize the use of mineral supplements.

Enhancing the photodynamic effect of curcumin through modification with TiO2 nanoparticles and cationic polymers.

Curcumin (CUR), a natural compound extracted from turmeric, has shown potential as a photosensitizer in photodynamic therapy (PDT). The aim of this work was to enhance the efficacy of CUR by modifying it using titanium dioxide (TiO2) nanoparticles and a cationic polymer called Sofast to create a nanocomposite TiO2-CUR-Sofast (TCS). Compared to unmodified CUR, TCS exhibited a broadening toward longer wavelength in the absorption wavelength within the 400-550 nm range, leading to improved CUR absorption. Cellular uptake efficiency of TCS was also enhanced, and it demonstrated nearly 4.7-fold higher reactive oxygen species (ROS) generation than CUR. Furthermore, TCS displayed the ability to attach to the cell membrane and enter cells within a 30-min incubation period. Upon irradiation, TCS exhibited remarkable cytotoxicity, resulting in a significant reduction in the viability of various cancer cells. Autofluorescence lifetime imaging of intracellular reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) enzymes indicated that cancer cells treated with TCS and irradiation undergo a metabolic pathway shift from oxidative phosphorylation to glycolysis. These findings highlight the potential of TCS as an effective PDT agent for cancer treatment.

MultiClassMetabo: A Superior Classification Model Constructed Using Metabolic Markers in Multiclass Metabolomics.

Multiclass metabolomics has become a popular technique for revealing the mechanisms underlying certain physiological processes, different tumor types, or different therapeutic responses. In multiclass metabolomics, it is highly important to uncover the underlying biological information on biosamples by identifying the metabolic markers with the most associations and classifying the different sample classes. The classification problem of multiclass metabolomics is more difficult than that of the binary problem. To date, various methods exist for constructing classification models and identifying metabolic markers consisting of well-established techniques and newly emerging machine learning algorithms. However, how to construct a superior classification model using these methods remains unclear for a given multiclass metabolomic data set. Herein, MultiClassMetabo has been developed for constructing a superior classification model using metabolic markers identified in multiclass metabolomics. MultiClassMetabo can enable online services, including (a) identifying metabolic markers by marker identification methods, (b) constructing classification models by classification methods, and (c) performing a comprehensive assessment from multiple perspectives to construct a superior classification model for multiclass metabolomics. In summary, MultiClassMetabo is distinguished for its capability to construct a superior classification model using the most appropriate method through a comprehensive assessment, which makes it an important complement to other available tools in multiclass metabolomics. MultiClassMetabo can be accessed at http://idrblab.cn/multiclassmetabo/.

A prospective observation of influence of anti-VEGF on optic disc vasculature in nAMD patients.

BACKGROUND: This study aims to investigate the short-term changes in relatively normal retinal vessels following anti-vascular endothelial growth factor (anti-VEGF) therapy in nAMD patients, an area that currently represents a research gap. METHODS: In this prospective study, we enrolled patients newly diagnosed with neovascular age-related macular degeneration (nAMD) and received standardized monthly anti-VEGF therapy for three months. Follow-ups were conducted at baseline and 1-week, 1-month, 2-months and 3-months post first injection. Assessment indicators included radial peripapillary capillary vascular density (RPC-VD) and retinal nerve fiber layer (RNFL) thickness in different optic disk regions using optical coherence tomography angiography, as well as intraocular pressure (IOP). RESULTS: 68 nAMD patients (68 eyes) were included in this study. Significant reductions of RPC-VD and increases of RNFL thickness primarily in the nasal regions were observed 1-week post anti-VEGF (adjusted P < 0.05). Significant negative correlations were found between 1-week changes in RPC-VD and RNFL thickness in the nasal sectors (P < 0.05). From 1 to 3 months post-injection, RPC-VD and RNFL thickness essentially returned to baseline levels. Throughout the follow-up periods, IOP remained stable (P > 0.05). CONCLUSION: Anti-VEGF treatments transiently influence the relatively normal retinal vessels, which might lead to nerve fiber edema, predominantly on the nasal side of the optic disk.

Persistent Placoid Maculopathy: Lichen-like Lesions Growing between Retinal Pigment Epithelium and Bruch's Membrane.

PURPOSE: To report the novel imaging findings in persistent placoid maculopathy (PPM) from the first case series of Asian subjects. DESIGN: Retrospective observational case series. SUBJECTS: Patients with PPM from 2013 to 2023. METHODS: Medical records and multimodal images from each visit were analyzed. MAIN OUTCOME MEASURES: Imaging and follow-up findings. RESULTS: Twenty-one eyes of 16 patients were included. Mean age was 61 (range, 48-84) years old. Five patients showed bilateral involvement. Persistent placoid maculopathy lesions were unremarkable on color fundus photography, autofluorescence, and fluorescein angiography. Hypofluorescent spots with a lichen-like appearance presented in all phases of indocyanine green angiography, which were most prominent in the late phase and presented in a fused (71%) or clustered (29%) pattern. The hypofluorescence correlated with the lesions between the retinal pigment epithelium (RPE) and Bruch's membrane (BM) with moderate reflectivity on OCT, and the thickness ranged from slit-like to mound-like. The intensity of hypofluorescence sometimes varied in the same eye and correlated with the thickness of sub-RPE lesions on OCT. No abnormal blood flow signals were detected in either the sub-RPE space or choriocapillaris slab of OCT angiography across the PPM lesions. Peripapillary (5 eyes, 24%) and extra posterior pole (2 eyes, 10%) involvements were seen, the former sparing the ß zones of optic discs. Ten eyes of 7 patients were followed up (median, 26 months; range, 2-121 months). During follow-up, the lichen-like lesions spread and migrated slowly without changing the plane patterns of the first visit and were limited to sub-RPE growth. The fused lichen-like pattern sprawled around the enlarged base. The clustered lichen-like pattern gradually loosened. Ten eyes (48%, 9 eyes in the fused pattern, 1 eye in the clustered pattern) had secondary choroidal neovascularization (CNV) at the first visit, with type I (6 eyes, 5 of which were polypoidal choroidal vasculopathy) and type II (4 eyes). No new CNV developed during follow-up. CONCLUSION: Persistent placoid maculopathy lesions were located in the sub-RPE space, as determined by multimodal imaging. Spreading and migration between the RPE and BM may account for their unique lichen-like appearance and progression pattern. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Genetic abnormalities assist in pathological diagnosis and EBV-positive cell density impact survival in Chinese angioimmunoblastic T-cell lymphoma patients.

Objective: To explore the application of genetic abnormalities in the diagnosis of angioimmunoblastic T-cell lymphoma (AITL) and the reliable pathological prognostic factors. Methods: This study included 53 AITL cases, which were reviewed for morphological patterns, immunophenotypes, presence of Hodgkin and Reed-Sternberg (HRS)-like cells, and co-occurrence of B cell proliferation. The Epstein-Barr virus (EBV)-positive cells in tissues were counted, and cases were classified into "EBV encoded RNA (EBER) high-density" group if >50/HPF. Targeted exome sequencing was performed. Results: Mutation data can assist AITL diagnosis: 1) with considerable HRS-like cells (20 cases): RHOA mutated in 14 cases (IDH2 co-mutated in 3 cases, 4 cases with rare RHOA mutation), TET2 was mutated in 5 cases (1 case co-mutated with DNMT3A), and DNMT3A mutated in 1 case; 2) accompanied with B cell lymphoma (7 cases): RHOA mutated in 4 cases (1 case had IDH2 mutation), TET2 mutated in 2 cases and DNMT3A mutated in 1 case; 3) mimic peripheral T cell lymphoma, not otherwise specified (5 cases): RHOA mutated in 2 cases (IDH2 co-mutated in 1 case), TET2 mutated in 3 cases, and DNMT3A mutated in 1 case; 4) pattern 1 (1 case), RHOA and TET2 co-mutated. Besides RHOAG17V (30/35), rare variant included RHOAK18N, RHOAR68H, RHOAC83Y, RHOAD120G and RHOAG17del, IDH2R172 co-mutated with IDH2M397V in one case. There were recurrent mutations of FAT3, PCLO and PIEZO1 and genes of epigenetic remodeling, T-cell activation, APC and PI3K/AKT pathway. EBER high-density independently indicated adverse overall survival and progression-free survival (P=0.046 and P=0.008, Kaplan-Meier/log-rank). Conclusions: Over half AITL cases might be confused in diagnosis for certain conditions without mutation data. Targeted exome sequencing with a comprehensive panel is crucial to detect both hot-spot and rare mutation variants for RHOA and IDH2 and other recurrent mutated genes in addition to TET2 and DNMT3A. EBER high-density independently indicated adverse survival.

Correlation between fungi and volatile compounds during different fermentation modes at the industrial scale of Merlot wines.

Elucidation of the relationship between fungal community development and dynamic changes in volatile components during fermentation is of great significance in controlling wine production. However, such studies on an industrial scale are rarely reported. In this study, fungal community succession during spontaneous fermentation (SPF) and inoculation fermentation (INF) of Merlot wine was monitored by a research strategy combining culture-dependent and culture-independent methods. The volatile compounds were monitored during SPF and INF by headspace solid-phase micro-extraction coupled with gas chromatography-mass spectrometry technology. The Spearman correlation coefficient was also used to investigate the interplay between fungal communities and volatile compounds. We found that fungal community diversity in SPF decreased as fermentation progressed but was significantly higher than that of INF. Starmerella and Kazachstania were the dominant non-Saccharomyces genera in Merlot wine during SPF. However, the presence of commercial yeasts and sulphur dioxide led to a sharp decrease or the disappearance of non-Saccharomyces genera during INF. Spearman correlation analysis revealed that all major volatiles were positively correlated with most functional microbiotas except P. fermentans, S. bacillaris, E. necator, and D. exigua in INF. In SPF, most non-Saccharomyces were negatively correlated with core volatiles, whereas K. humilis, M. laxa, P. kluyveri, and A. japonicus were positively correlated with the major volatiles, especially some higher alcohols (isopentol, heptanol) and terpenes (linalool, citronellol). S. cerevisiae was positively correlated with most of the main volatile substances except ethyl isovalerate and isoamyl acetate. These findings provide a reference for comprehending the diverse fermentation methods employed in the wine industry and improving the quality of Merlot wines.

Effects of Leymus chinensis hay and alfalfa hay on growth performance, rumen microbiota, and untargeted metabolomics of meat in lambs.

Objective: The objective of this study was to compare the effects of Leymus chinensis hay and alfalfa hay as the roughage on the rumen bacterial and the meat metabolomics in lambs. Methods: Fourteen male lambs were randomly assigned to two dietary treatments (one group was fed with concentrate and Leymus chinensis hay; another was fed with concentrate and alfalfa hay) with seven replicates per treatment. The feeding experiment lasted for 60 days. Lambs were slaughtered at the end of the feeding experiment. Growth performance, carcass performance, and weights of various viscera were determined. The longissimus dorsi and rumen contents were collected for untargeted metabolomics and 16S rDNA amplicon sequencing analysis, respectively. Results: The lambs fed with alfalfa hay showed a significantly increased in average daily gain, carcass weight, dressing percentage, loin-eye area, and kidney weight. Feeding Leymus chinensis hay and alfalfa hay diets resulted in different meat metabolite deposition and rumen bacterial communities in the lambs. The relative abundance of phyla Fibrobacteres, Bacteroidetes, and Spirochaetes were greater in the Leymus Chinensis hay group, while, the relative abundance of Firmicutes, Proteobacteria, Fusobacteria, and Verrucomicrobia were greater in the alfalfa hay group. Based on untargeted metabolomics, the main altered metabolic pathways included alanine, aspartate and glutamate metabolism, D-glutamine and D-glutamate metabolism, phenylalanine metabolism, nitrogen metabolism, and tyrosine metabolism. Several bacteria genera including BF31, Alistipes, Faecalibacterium, Eggerthella, and Anaeroplasma were significantly correlated with growth performance and meat metabolites. Conclusion: Alfalfa hay improved growth performance and carcass characteristics in lambs. Leymus chinensis hay and alfalfa hay caused different meat metabolite deposition by modifying the rumen bacterial community. These findings will be beneficial to future forage utilization for sheep growth, carcass performance, and meat quality improvement.