InvPT++: Inverted Pyramid Multi-Task Transformer for Visual Scene Understanding.

Multi-task scene understanding aims to design models that can simultaneously predict several scene understanding tasks with one versatile model. Previous studies typically process multi-task features in a more local way, and thus cannot effectively learn spatially global and cross-task interactions, which hampers the models' ability to fully leverage the consistency of various tasks in multi-task learning. To tackle this problem, we propose an Inverted Pyramid multi-task Transformer, capable of modeling cross-task interaction among spatial features of different tasks in a global context. Specifically, we first utilize a transformer encoder to capture task-generic features for all tasks. And then, we design a transformer decoder to establish spatial and cross-task interaction globally, and a novel UP-Transformer block is devised to increase the resolutions of multi-task features gradually and establish cross-task interaction at different scales. Furthermore, two types of Cross-Scale Self-Attention modules, i.e., Fusion Attention and Selective Attention, are proposed to efficiently facilitate cross-task interaction across different feature scales. An Encoder Feature Aggregation strategy is further introduced to better model multi-scale information in the decoder. Comprehensive experiments on several 2D/3D multi-task benchmarks clearly demonstrate our proposal's effectiveness, establishing significant state-of-the-art performances. The codes are publicly available https://github.com/prismformore/Multi-Task-Transformer/tree/main/InvPT.

Phase 1 study of safety and preliminary efficacy of intranasal transplantation of human neural stem cells (ANGE-S003) in Parkinson's disease.

BACKGROUND: Intranasal transplantation of ANGE-S003 human neural stem cells showed therapeutic effects and were safe in preclinical models of Parkinson's disease (PD). We investigated the safety and tolerability of this treatment in patients with PD and whether these effects would be apparent in a clinical trial. METHODS: This was a 12-month, single-centre, open-label, dose-escalation phase 1 study of 18 patients with advanced PD assigned to four-time intranasal transplantation of 1 of 3 doses: 1.5 million, 5 million or 15 million of ANGE-S003 human neural stem cells to evaluate their safety and efficacy. RESULTS: 7 patients experienced a total of 14 adverse events in the 12 months of follow-up after treatment. There were no serious adverse events related to ANGE-S003. Safety testing disclosed no safety concerns. Brain MRI revealed no mass formation. In 16 patients who had 12-month Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) data, significant improvement of MDS-UPDRS total score was observed at all time points (p<0.001), starting with month 3 and sustained till month 12. The most substantial improvement was seen at month 6 with a mean reduction of 19.9 points (95% CI, 9.6 to 30.3; p<0.001). There was no association between improvement in clinical outcome measures and cell dose levels. CONCLUSIONS: Treatment with ANGE-S003 is feasible, generally safe and well tolerated, associated with functional improvement in clinical outcomes with peak efficacy achieved at month 6. Intranasal transplantation of neural stem cells represents a new avenue for the treatment of PD, and a larger, longer-term, randomised, controlled phase 2 trial is warranted for further investigation.

Using a golf specific functional movement screen to predict golf performance in collegiate golfers.

Background: This study aims to examine the relationship between functional movements and golf performance using the Golf Specific Functional Movement Screen (GSFMS). Methods: This cross-sectional study included a total of 56 collegiate golfers (aged 20.89 ± 0.99 years, height of 174.55 ± 7.76 cm, and weight 68.48 ± 9.30 kg) who met the criteria, and were recruited from Hainan Normal University in June 2022. The participants' golf motor skills (1-yard putt, 10-yard putt, 25-yard chip, 130/100-yard set shot, driver, and 9-hole stroke play) were tested and the GSFMS (e.g., pelvic tilt, pelvic rotation, and torso rotation) was used. Results: There were significant weak or moderate correlations between the variables. Furthermore, a multiple linear regression analysis found that pelvic rotation and lower-body rotation abilities can significantly predict golf skill levels, which collectively explain 31.2% of the variance in golf skill levels among collegiate golfers (Adjusted R2 = 0.312, F = 2.663, p < 0.05). Standardised ß values indicate that pelvic rotation (ß = 0.398) has a more substantial impact on golf skill levels than lower-body rotation (ß = 0.315). Conclusions: This study found the weak to moderate correlations between the GSFMS and golf performance, and pelvic rotation and lower-body rotation abilities, thus predicting golf skills. Our findings provide novel insights into the relationship between functional abilities and comprehensive skill performance within the context of the Gray Cook's Movement Pyramid model, and provide theoretical support and practical reference for collegiate golf motor-skill learning and sports injury prevention.

Groundwater Cr(VI) contamination and remediation: a review from 1999 to 2022.

Hexavalent chromium (Cr(VI)) contamination of groundwater has traditionally been an environmental issue of great concern due to its bioaccumulative and highly toxic nature. This paper presents a review and bibliometric analysis of the literature on the interest area "Cr(VI) in groundwater" published in the Web of Science Core Collection from 1999 to 2022. First, information on 203 actual Cr(VI)-contaminated groundwater sites around the world was summarized, and the basic characteristics of the sources and concentrations of contamination were derived. 68.95% of the sites were due to human causes and 56.43% of these sites had Cr(VI) concentrations in the range of 0 - 10 mg/L. At groundwater sites with high Cr(VI) contamination due to natural causes, 75.00% of the sites had Cr(VI) concentrations less than 0.2 mg/L. A total of 936 papers on "Cr(VI) in groundwater" were retrieved for bibliometric analysis: interest in research on Cr(VI) in groundwater has grown rapidly in recent years; 59.4% of the papers were published in the field of environmental sciences. A systematic review of the progress of studies on the Cr(VI) removal/remediation based on reduction, adsorption and biological processes is presented. Out of 666 papers on Cr(VI) removal/remediation, 512, 274, and 75 papers dealt with the topics of reduction, adsorption, and bioremediation, respectively. In addition, several studies have demonstrated the potential applicability of natural attenuation in the remediation of Cr(VI)-contaminated groundwater. This paper will help researchers to understand and investigate methodological strategies to remove Cr(VI) from groundwater in a more targeted and effective manner.

MCTformer+: Multi-Class Token Transformer for Weakly Supervised Semantic Segmentation.

This paper proposes a novel transformer-based framework to generate accurate class-specific object localization maps for weakly supervised semantic segmentation (WSSS). Leveraging the insight that the attended regions of the one-class token in the standard vision transformer can generate class-agnostic localization maps, we investigate the transformer's capacity to capture class-specific attention for class-discriminative object localization by learning multiple class tokens. We present the Multi-Class Token transformer, which incorporates multiple class tokens to enable class-aware interactions with patch tokens. This is facilitated by a class-aware training strategy that establishes a one-to-one correspondence between output class tokens and ground-truth class labels. We also introduce a Contrastive-Class-Token (CCT) module to enhance the learning of discriminative class tokens, enabling the model to better capture the unique characteristics of each class. Consequently, the proposed framework effectively generates class-discriminative object localization maps from the class-to-patch attentions associated with different class tokens. To refine these localization maps, we propose the utilization of patch-level pairwise affinity derived from the patch-to-patch transformer attention. Furthermore, the proposed framework seamlessly complements the Class Activation Mapping (CAM) method, yielding significant improvements in WSSS performance on PASCAL VOC 2012 and MS COCO 2014. These results underline the importance of the class token for WSSS. The codes and models are publicly available here.

High-efficiency self-focusing metamaterial grating coupler in silicon nitride with amorphous silicon overlay.

Efficient fiber-chip coupling interfaces are critically important for integrated photonics. Since surface gratings diffract optical signals vertically out of the chip, these couplers can be placed anywhere in the circuit allowing for wafer-scale testing. While state-of-the-art grating couplers have been developed for silicon-on-insulator (SOI) waveguides, the moderate index contrast of silicon nitride (SiN) presents an outstanding challenge for implementing efficient surface grating couplers on this platform. Due to the reduced grating strength, a longer structure is required to radiate the light from the chip which produces a diffracted field that is too wide to couple into the fiber. In this work, we present a novel grating coupler architecture for silicon nitride photonic integrated circuits that utilizes an amorphous silicon (α-Si) overlay. The high refractive index of the α-Si overlay breaks the coupler's vertical symmetry which increases the directionality. We implement subwavelength metamaterial apodization to optimize the overlap of the diffracted field with the optical fiber Gaussian mode profile. Furthermore, the phase of the diffracted beam is engineered to focalize the field into an SMF-28 optical fiber placed 55 µm above the surface of the chip. The coupler was designed using rigorous three-dimensional (3D) finite-difference time-domain (FDTD) simulations supported by genetic algorithm optimization. Our grating coupler has a footprint of 26.8 × 32.7 µm2 and operates in the O-band centered at 1.31 µm. It achieves a high directionality of 85% and a field overlap of 90% with a target fiber mode size of 9.2 µm at the focal plane. Our simulations predict a peak coupling efficiency of - 1.3 dB with a 1-dB bandwidth of 31 nm. The α-Si/SiN grating architecture presented in this work enables the development of compact and efficient optical interfaces for SiN integrated photonics circuits with applications including optical communications, sensing, and quantum photonics.

Comparison of systematic and combined biopsy for the detection of prostate cancer.

ABSTRACT: Systematic prostate biopsy has limitations, such as overdiagnosis of clinically insignificant prostate cancer and underdiagnosis of clinically significant prostate cancer. Magnetic resonance imaging (MRI)-guided biopsy, a promising alternative, might improve diagnostic accuracy. To compare the cancer detection rates of systematic biopsy and combined biopsy (systematic biopsy plus MRI-targeted biopsy) in Asian men, we conducted a retrospective cohort study of men who underwent either systematic biopsy or combined biopsy at two medical centers (Queen Mary Hospital and Tung Wah Hospital, Hong Kong, China) from July 2015 to December 2022. Descriptive statistics were calculated, and univariate and multivariate logistic regression analyses were performed. The primary and secondary outcomes were prostate cancer and clinically significant prostate cancer. A total of 1391 participants were enrolled. The overall prostate cancer detection rates did not significantly differ between the two groups (36.3% vs 36.6%, odds ratio [OR] = 1.01, 95% confidence interval [CI]: 0.81-1.26, P = 0.92). However, combined biopsy showed a significant advantage in detecting clinically significant prostate cancer (Gleason score ≥ 3+4) in patients with a total serum prostate-specific antigen (tPSA) concentration of 2-10 ng ml-1 (systematic vs combined: 11.9% vs 17.5%, OR = 1.58, 95% CI: 1.08-2.31, P = 0.02). Specifically, in the transperineal biopsy subgroup, combined biopsy significantly outperformed systematic biopsy in the detection of clinically significant prostate cancer (systematic vs combined: 12.6% vs 24.0%, OR = 2.19, 95% CI: 1.21-3.97, P = 0.01). These findings suggest that in patients with a tPSA concentration of 2-10 ng ml-1, MRI-targeted biopsy may be of greater predictive value than systematic biopsy in the detection of clinically significant prostate cancer.

Ventral subiculum promotes wakefulness through several pathways in male mice.

The ventral subiculum (vSUB), the major output structure of the hippocampal formation, regulates motivation, stress integration, and anxiety-like behaviors that rely on heightened arousal. However, the roles and underlying neural circuits of the vSUB in wakefulness are poorly known. Using in vivo fiber photometry and multichannel electrophysiological recordings in mice, we found that the vSUB glutamatergic neurons exhibited high activities during wakefulness. Moreover, activation of vSUB glutamatergic neurons caused an increase in wakefulness and anxiety-like behaviors and induced a rapid transition from sleep to wakefulness. In addition, optogenetic stimulation of vSUB glutamatergic terminals and retrograde-targeted chemogenetic activation of vSUB glutamatergic neurons revealed that vSUB promoted arousal by innervating the lateral hypothalamus (LH), nucleus accumbens (NAc) shell, and prefrontal cortex (PFC). Nevertheless, local microinjection of dopamine D1 or D2/D3 receptor antagonist blocked the wake-promoting effect induced by chemogenetic activation of vSUB pathways. Finally, chemogenetic inhibition of vSUB glutamatergic neurons decreased arousal. Altogether, our findings reveal a prominent contribution of vSUB glutamatergic neurons to the control of wakefulness through several pathways.

Yiqigubiao pill treatment regulates Sirtuin 5 expression and mitochondrial function in chronic obstructive pulmonary disease.

Background: Chronic obstructive pulmonary disease (COPD) is a heterogeneous group of pathophysiological bases of airway inflammation and its anti-inflammatory response. Aberrant mitochondrial signaling and mitochondrial dysfunction underlie the pathomechanisms leading to COPD. This study aims to investigate the effects of the Yiqigubiao (YQGB) pill, a traditional Chinese medicine (TCM), on Sirtuin 5 (SIRT5) and mitochondrial function in patients with COPD. Methods: Thirty-four patients with COPD were randomized into oral YQGB or placebo groups concurrent with a 24-week routine treatment. The pulmonary function was assessed by examining the levels of forced expiratory volume in one second (FEV1)/forced vital capacity (FVC), FEV1, and FVC. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were used to detect SIRT5 expression in mitochondria isolated from peripheral blood. Flow cytometry was used to detect changes in mitochondrial membrane potential and reactive oxygen species (ROS) in peripheral blood lymphocytes. Human bronchial epithelial (HBE) cells stimulated by cigarette smoke extract (CSE) were treated with YQGB. After SIRT5 was knocked down in cells, the changes in mitochondrial membrane potential, levels of adenosine triphosphate (ATP), and ROS were detected. Results: YQGB treatment significantly improved lung function in patients with COPD. The expression of SIRT5 and the mitochondrial membrane potential significantly increased and ROS decreased in patients with COPD after YQGB treatment. The CSE decreased cell proliferation and SIRT5 expression, which was alleviated after YQGB treatment. Furthermore, SIRT5 was knocked down in CSE-stimulated HBE cells, and its expression was elevated upon YQGB treatment. The knockdown of SIRT5 significantly altered the CSE-stimulation-induced dysregulation of mitochondrial membrane potential, ATP levels, and ROS. This was also restored after YQGB treatment. Conclusions: YQGB treatment can elevate SIRT5 expression, restore mitochondrial function in COPD, and exert protective effects.

Analysis of tissue tropism of GCRV-II infection in grass carp using a VP35 monoclonal antibody.

Grass carp, one of the major freshwater aquaculture species in China, is susceptible to grass carp reovirus (GCRV). GCRV is a non-enveloped RNA virus and has a double-layered capsid, causing hemorrhagic disease and high mortalities in infected fish. However, the tropism of GCRV infection has not been investigated. In this study, monoclonal antibodies against recombinant VP35 protein were generated in mice and characterized. The antibodies exhibited specific binding to the N terminal region (1-155 aa) of the recombinant VP35 protein expressed in the HEK293 cells, and native VP35 protein in the GCRV-II infected CIK cells. Immunofluorescent staining revealed that viruses aggregated in the cytoplasm of infected cells. In vivo challenge experiments showed that high levels of GCRV-II viruses were present in the gills, intestine, spleen and liver, indicating that they are the major sites for virus infection. Our study showed that the VP35 antibodies generated in this study exhibited high specificity, and are valuable for the development of diagnostic tools for GCRV-II infection.

Epigenetic regulation of high light-induced anthocyanin biosynthesis by histone demethylase IBM1 in Arabidopsis.

In plant species, anthocyanin accumulation is specifically regulated by light signaling. Although the CONSTITUTIVELY PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA-105 (COP1/SPA) complex is known to control anthocyanin biosynthesis in response to light, the precise mechanism underlying this process remains largely unknown. Here, we report that Increase in BONSAI Methylation 1 (IBM1), a JmjC domain-containing histone demethylase, participates in the regulation of light-induced anthocyanin biosynthesis in Arabidopsis. The expression of IBM1 was induced by high light (HL) stress, and loss-of-function mutations in IBM1 led to accelerated anthocyanin accumulation under HL conditions. We further identified that IBM1 is directly associated with SPA1/3/4 chromatin in vivo to establish a hypomethylation status on H3K9 and DNA non-CG at these loci under HL, thereby releasing their expression. Genetic analysis showed that quadruple mutants of IBM1 and SPA1/3/4 resemble spa134 mutants. Overexpression of SPA1 in ibm1 mutants complements the mutant phenotype. Our results elucidate the significance and mechanism of IBM1 histone demethylase in the epigenetic regulation of anthocyanin biosynthesis in Arabidopsis under HL conditions.

Decreasing circ_0014614 promotes the differentiation of bone marrow flineage cells into megakaryocytes in essential thrombocythemia via activiation of miR-138-5p/caspase3 axis.

BACKGROUND: Circular RNAs (circRNA) are pivotal in hematological diseases. Previous study showed that circ_0014614 (circDAP3) was significantly underexpressed in bone marrow-derived exosomes from essential thrombocythemia (ET) patients, affecting the differentiation of bone marrow lineage cells into megakaryocytes. METHODS: Fluorescence in situ hybridization (FISH) was used to display circ_0014614's primary cytoplasmic location in K562 cells. Cytoscape software was used to predict the circRNA-miRNA-mRNA networks, and their expression at the cellular level was detected by Quantitative reverse transcription-polymerase chain reaction (qRT-PCR). qRT-PCR was utilized to detect the expression levels of circ_0014614，miR-138-5p and caspase3 mRNA. Western blot was used to determine the protein levels of GATA-1, RUNX-1, NF-E2, CD41 and caspase3. The proliferation of K562 cells was assessed using the Cell Counting Kit-8 (CCK-8) Assay. Furthermore, the interplay between miR-138-5p and circ_0014614 or caspase3 was elucidated through a Dual-luciferase reporter assay. RESULTS: FISH assay indicated circ_0014614's primary cytoplasmic location in K562 cells. In ET bone marrow and K562 cells, circ_0014614 and caspase3 were down-regulated, whereas miR-138-5p saw a significant surge. Overexpressing circ_0014614 curtailed K562 cells' proliferation and differentiation. Further, circ_0014614 targeted miR-138-5p, with heightened miR-138-5p levels counteracting circ_0014614's inhibition. MiR-138-5p further targeted caspase3, and caspase3 silencing neutralized suppressed miR-138-5p's effects on K562 cell differentiation. CONCLUSION: Circ_0014614 was down-regulated in ET bone marrow and bone marrow lineage cells, and upregulating circ_0014614 can inhibit bone marrow lineage cells' proliferation and differentiation into megakaryocytes. Mechanistically, circ_0014614 functioned as ceRNA via sponging miR-138-5p and alleviated the inhibitory effect of miR-138-5p on its target caspase3, which potentially deters tumor activity in ET.

Quality Changes and Fungal Microbiota Dynamics in Stored Jujube Fruits: Insights from High-Throughput Sequencing for Food Preservation.

Postharvest rot is an urgent problem affecting the storage of winter jujube. Therefore, the development of new technologies for efficient and safe preservation is very important. This study aimed to elucidate the fungal microbiota found on the epidermis of jujube during the storage period using high-throughput sequencing, as well as to monitor the changes in quality indexes throughout this period. Through internal transcribed spacer (ITS) sequencing, we identified two phyla (Basidiomycota and Ascomycota) and six genera (Cryptococcus, Bulleromyces, Sporidiobolus, Alternaria, Pseudozyma, and Sporobolomyces), which potentially contribute to the spoilage and deterioration of jujube, referred to as "core fungal taxa". A high correlation was further found between preservation indices (including decay rate, firmness, and total soluble solids) and the growth of multiple core fungi over time. These findings will provide insights and a theoretical basis for further research on preservation techniques related to biological control during date fruit storage.

Systematic Review and Meta-analysis of the Association Between Malnutrition and Risk of Depression in the Elderly.

Objective: To explore the association between malnutrition and risk of depression in the elderly. Methods: Relevant studies were searched in PubMed, Web of Science, the Cochrane Library, Scopus, and Embase from the establishment of the database to August 17, 2023. Two researchers independently screened the literature, extracted data, and evaluated the risk of bias in the included studies. Stata16.0 software was used for meta-analysis. Results: A total of 8 observational studies were identified with 11 112 participants, of which 2771 elderly patients had depression. The meta-pooled results showed a significant correlation between nutritional status and depression risk (odds ratio (OR) = 2.03, 95% CI = (1.47, 2.81), P < 0.001). Subgroup analysis found that the malnutrition scores of different study types and the diagnostic methods of depression and malnutrition were correlated with the risk of depression. Conclusion: Malnutrition was associated with depression risk in the elderly. Further large-scale multicenter studies should be conducted to test and verify the results.

Imageable Brachytherapy with Chelator-Free Radiolabeling Hydrogel.

Brachytherapy stands as an essential clinical approach for combating locally advanced tumors. Here, an injectable brachytherapy hydrogel is developed for the treatment of both local and metastatic tumor. Fe-tannins nanoparticles are efficiently and stably radiolabeled with clinical used therapeutic radionuclides (such as 131I, 90Y, 177Lu and 225Ac) without a chelator, and then chemically cross-linked with 4-ArmPEG-SH to form brachytherapy hydrogel. Upon intratumoral administration, magnetic resonance imaging (MRI) signal from ferric ions embedded within the hydrogel directly correlates with the retention dosage of radionuclides, which can real-time monitor radionuclides emitting short-range rays in vivo without penetration limitation during brachytherapy. The hydrogel's design ensures the long-term tumor retention of therapeutic radionuclides, leading to the effective eradication of local tumor. Furthermore, the radiolabeled hydrogel is integrated with an adjuvant to synergize with immune checkpoint blocking therapy, thereby activating potent anti-tumor immune responses and inhibiting metastatic tumor growth. Therefore, this work presents an imageable brachytherapy hydrogel for real-time monitoring therapeutic process, and expands the indications of brachytherapy from treatment of localized tumors to metastatic tumors. This article is protected by copyright. All rights reserved.

Layerwised multimodal knowledge distillation for vision-language pretrained model.

The transformer-based model can simultaneously learn the representation for both images and text, providing excellent performance for multimodal applications. Practically, the large scale of parameters may hinder its deployment in resource-constrained devices, creating a need for model compression. To accomplish this goal, recent studies suggest using knowledge distillation to transfer knowledge from a larger trained teacher model to a small student model without any performance sacrifice. However, this only works with trained parameters of the student model by using the last layer of the teacher, which makes the student model easily overfit in the distillation procedure. Furthermore, the mutual interference between modalities causes more difficulties for distillation. To address these issues, the study proposed a layerwised multimodal knowledge distillation for a vision-language pretrained model. In addition to the last layer, the intermediate layers of the teacher were also used for knowledge transfer. To avoid interference between modalities, we split the multimodality into separate modalities and added them as extra inputs. Then, two auxiliary losses were implemented to encourage each modality to distill more effectively. Comparative experiments on four different multimodal tasks show that the proposed layerwised multimodality distillation achieves better performance than other KD methods for vision-language pretrained models.

Innovative tumor interstitial fluid-triggered carbon dot-docetaxel nanoassemblies for targeted drug delivery and imaging of HER2-positive breast cancer.

In this study, we have developed an innovative pH-triggered nanomedicine delivery system, targeting HER2-positive breast cancer cells for effective low-cost, imaging-guided drug delivery and precise therapy. The key feature of this system lies in its unique tumor interstitial fluid microenvironment-responsive drug release behavior which achieved tumor site-specific drug delivery. Our in vitro experiments demonstrated that the carbon dot-integrated material achieves more efficient DTX release (96.13 % at 72 h) in the tumor interstitial fluid microenvironment (pH 6.5), thereby boosting drug concentration at the tumor site and enhancing therapeutic efficacy. Further cell experiments confirmed the system's significant inhibitory effect on HER2-positive tumor cells SKBR3 in a pH 6.5 environment, and apoptosis assays indicating a notable increase in early cell apoptosis (from 8.39 % to 24.61 % compared with pH 7.4). Furthermore, the integration of HER2 aptamer within the carbon dot-based system enables targeted recognition and binding to tumor cells, ensuring more precise delivery of DTX while minimizing potential side effects. Crucially, the carbon dots in this system emit superior red fluorescence (the QY = 47.64 % excited at 535 nm compared with Rodamine 6G), enabling real-time visualization of the drug delivery process. This feature provides valuable feedback on treatment effectiveness, facilitating necessary adjustments. The small size (1.88 ± 0.48 nm) of carbon dots significantly improved their ability to penetrate biological barriers, while their low toxicity (no significant cell toxicity under 350 µg/mL) contributed to the formulation's outstanding biocompatibility. Overall, this carbon dot-enhanced drug delivery system offers immense potential for enhancing drug efficacy, minimizing side effects, and providing real-time treatment monitoring, thus proposing a innovate strategy for breast cancer therapy.

Elucidation of Palmarumycin Spirobisnaphthalene Biosynthesis Reveals a Set of Previously Unrecognized Oxidases and Reductases.

Spirobisnaphthalenes (SBNs) are a class of highly oxygenated, fungal bisnaphthalenes containing a unique spiroketal bridge, that displayed diverse bioactivities. Among the reported SBNs, palmarumycins are the major type, which are precursors for the other type of SBNs structurally. However, the biosynthesis of SBNs is unclear. In this study, we elucidated the biosynthesis of palmarumycins, using gene disruption, heterologous expression, and substrate feeding experiments. The biosynthetic gene cluster for palmarumycins was identified to be distant from the polyketide synthase gene cluster, and included two cytochrome P450s (PalA and PalB), and one short chain dehydrogenase/reductase (PalC) encoding genes as key structural genes. PalA is an unusual, multifunctional P450 that catalyzes the oxidative dimerization of 1,8-dihydroxynaphthalene to generate the spiroketal linkage and 2,3-epoxy group. Chemical synthesis of key intermediate and in vitro biochemical assays proved that the oxidative dimerization proceeded via a binaphthyl ether. PalB installs the C-5 hydroxy group, widely found in SBNs. PalC catalyzes 1-keto reduction, the reverse 1-dehydrogenation, and 2,3-epoxide reduction. Moreover, an FAD-dependent oxidoreductase, encoded by palD, which locates outside the cluster, functions as a 1-dehydrogenase. These results provided the first genetic and biochemical evidence for the biosynthesis of palmarumycin SBNs.

Identification of ferroptosis-related key genes associated with immune infiltration in sepsis by bioinformatics analysis and in vivo validation.

OBJECTIVES: Sepsis is a life-threatening infectious disease in which an immune inflammatory response is triggered. The potential effect of ferroptosis-related genes (FRGs) in inflammation of sepsis remained unclear. We focused on identifying and validating core FRGs and their association with immune infiltration in blood from currently all patients with sepsis. METHODS: All current raw data of septic blood were obtained from Gene Expression Omnibus. After removing the batch effect merging into a complete dataset and obtaining Diferentially expressed genes (DEGs). Common cross-talk genes were identified from DEGs and FRGs. WGCNA, GO, KEGG, PPI, GESA, ROC curves, and LASSO regression analysis were performed to indentify and validate key genes based on external septic datasets. Infiltrated immune cells in 2 hub genes (MAPK14 and ACSL4) were conducted using CIBERSORT algorithm and Spearman correlation analysis. Further, the expressions of 2 core FRGs were verified in the LPS-induced ALI and cardiac injury sepsis mice. RESULTS: MAPK14 and ACSL4 were identified, mostly enriched in T cell infiltration through NOD-like receptor signaling pathway according to the high or low 2 hub genes expression. The upregulated 2 ferroptosis-related genes were validated in LPS-induced ALI and cardiac injury mice, accompanied by upregulation of the NLRP3 pathway. CONCLUSION: MAPK14 and ACSL4 could become robustly reliable and promising biomarkers for sepsis by regulating ferroptosis through the NLRP3 pathway, which is mainly associated with T-cell infiltration.

Efficient gene editing in the slow-growing, non-sporulating, melanized, endophytic fungus Berkleasmium sp. Dzf12 using a CRISPR/Cas9 system.

The endophytic fungus Berkleasmium sp. Dzf12 that was isolated from Dioscorea zingiberensis, is a proficient producer of palmarumycins, which are intriguing polyketides of the spirobisnaphthalene class. These compounds displayed a wide range of bioactivities, including antibacterial, antifungal, and cytotoxic activities. However, conventional genetic manipulation of Berkleasmium sp. Dzf12 is difficult and inefficient, partially due to the slow-growing, non-sporulating, and highly pigmented behavior of this fungus. Herein, we developed a CRISPR/Cas9 system suitable for gene editing in Berkleasmium sp. Dzf12. The protoplast preparation was optimized, and the expression of Cas9 in Berkleasmium sp. Dzf12 was validated. To assess the gene disruption efficiency, a putative 1, 3, 6, 8-tetrahydroxynaphthalene synthase encoding gene, bdpks, involved in 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis, was selected as the target for gene disruption. Various endogenous sgRNA promoters were tested, and different strategies to express sgRNA were compared, resulting in the construction of an optimal system using the U6 snRNA-1 promoter as the sgRNA promoter. Successful disruption of bdpks led to a complete abolishment of the production of spirobisnaphthalenes and melanin. This work establishes a useful gene targeting disruption system for exploration of gene functions in Berkleasmium sp. Dzf12, and also provides an example for developing an efficient CRISPR/Cas9 system to the fungi that are difficult to manipulate using conventional genetic tools.