Comprehensive assessment of three crayfish culture modes: From production performance to environmental sustainability.

Integrated agriculture-aquaculture has emerged as a promising ecological development model. Crayfish, a popular aquaculture species, are traditionally reared either in monoculture ponds (mono-C) or in rice-crayfish polyculture system (poly-RC). In this study, we introduced a novel polyculture system by combining fruit tree with crayfish (poly-FC), aiming to compare these three crayfish culture modes in terms of production performance and ecological sustainability. The results indicated that crayfish reared in the two polyculture modes exhibited significantly higher specific growth rate and condition factor compared to those in mono-C. Crayfish cultured in poly-FC also showed better muscle quality and higher levels of crude fat and flavor or essential amino acids. Isotope mixing model showed that feed and benthic animals were the primary food sources of crayfish in mono-C, whereas aquatic plants, fruit litter or rice contributed more to those in polyculture modes. For greenhouse gas emissions, poly-FC mode emitted almost no CO2 and N2O even favored negative CH4 emission, while poly-RC and mono-C modes showed positive emissions of CH4 and CO2, respectively. Supported by metagenomics, the sink of CH4 in poly-FC was probably due to the lower mcr abundance but the higher pmo abundance in water. The low production and emission of N2O in poly-FC might result from the low-abundant Nitrospirae_bacterium and its coding gene norC in sediment, consistent with the lower denitrification rate but the higher NO3- concentration than mono-C. Overall, our findings reveal the superiority of polyculture of fruit tree with crayfish in terms of production performance and greenhouse gas emissions in the system.

Pancreatic agenesis and altered m6A methylation in the pancreas of PDX1-mutant cynomolgus macaques.

As an essential transcriptional activator, PDX1 plays a crucial role in pancreatic development and ß-cell function. Mutations in the PDX1 gene may lead to type 4 maturity-onset diabetes of the young (MODY4) and neonatal diabetes mellitus. However, the precise mechanisms underlying MODY4 remain elusive due to the paucity of clinical samples and pronounced differences in pancreatic architecture and genomic composition between humans and existing animal models. In this study, three PDX1-mutant cynomolgus macaques were generated using CRISPR/Cas9 technology, all of which succumbed shortly postpartum, exhibiting pancreatic agenesis. Notably, one tri-allelic PDX1-mutant cynomolgus macaque (designated as M4) developed a pancreas, whereas the two mono-allelic PDX1-mutant cynomolgus macaques displayed no anatomical evidence of pancreatic formation. RNA sequencing of the M4 pancreas revealed substantial molecular changes in both endocrine and exocrine functions, indicating developmental delay and PDX1 haploinsufficiency. A marked change in m6A methylation was identified in the M4 pancreas, confirmed through cultured PDX1-mutant islet organoids. Notably, overexpression of the m6A modulator METTL3 restored function in heterozygous PDX1-mutant islet organoids. This study highlights a novel role of m6A methylation modification in the progression of MODY4 and provides valuable molecular insights for preclinical research.

Self-Polymerized Tough and High-Entanglement Zwitterionic Functional Hydrogels.

Zwitterionic hydrogels exhibit great potential in biomedical applications due to their antifouling properties and biocompatibility. However, the single-network structure of pure zwitterionic hydrogels leads to a low toughness and strength, limiting their application in biomedical fields. In this work, a high entanglement sulfobetaine methacrylate-dopamine hydrogel (SBMA-DA-PE) with low cross-linker content and high monomer concentration is prepared by using a dopamine oxidative radical polymerization method. Compared to a regular zwitterionic hydrogel, the SBMA-DA-PE hydrogel exhibits a 5-fold increase in tensile fracture stress and a 10-fold increase in compressive fracture stress. The SBMA-DA-PE hydrogel possesses excellent mechanical properties (the maximum compressive stress ≥4.85 MPa, the maximum compressive strain ≥90%). Besides, the non-covalent interactions between catechol or ortho-quinones within the SBMA-DA-PE hydrogel, combined with strong intermolecular electrostatic interactions, endow the SBMA-DA-PE hydrogel with great self-healing capabilities and fatigue resistance. The SBMA-DA-PE hydrogel demonstrates low swellability and possesses good antifouling properties. Furthermore, the good printability and conductivity of the tough SBMA-DA-PE hydrogel endows it with new possibilities for developing biological 3D scaffolds and electronic devices. Overall, this work provides new insights into the preparation of zwitterionic hydrogels with high mechanical strength and multi-functionality for biomedical applications.

[Advances in the structure and function of MHETase].

Polyethylene terephthalate (PET) is one of the widely used plastics, but its waste pollution has become a global environmental issue. The discovery of polyethylene terephthalate hydrolase (PETase) has provided a green and environmentally friendly approach for PET degradation. However, PETase produces intermediate products that inhibit the enzyme's further activity, leading to a decrease in enzyme efficiency. Mono(2-hydroxyethyl) terephthalate hydrolase (MHETase) works synergistically with PETase to further degrade the intermediate product MHET into ethylene glycol (EG) and terephthalic acid (TPA). MHETase exhibits extremely high specificity for MHET and is crucial for the complete degradation of PET. This article comprehensively reviews MHETase from various perspectives, including its three-dimensional structure, substrate binding, and catalytic mechanism. It demonstrates the structural features and key residues associated with the enzyme's degrading activity and discusses the progress in enzyme engineering modifications. Additionally, the study envisions the development of a two-enzyme PET degradation system by combining MHETase with PETase, aiming to provide valuable references for designing and developing more efficient PET hydrolytic enzyme systems.

Targeted proteomics profiling reveals valuable biomarkers in the diagnosis of primary immune thrombocytopaenia.

The lack of biomarkers for accurate diagnosis and prognosis is a major clinical challenge of primary immune thrombocytopaenia (ITP). Using an Olink proteomics platform with a 92 immune response-related human protein panel, we analysed plasma samples from ITP patients (ITP, n = 40), patients with thrombocytopaenia secondary to other causes (Non-ITP, n = 19) and healthy controls (NC, n = 18), of a discovery cohort as well as a validation cohort (ITP, n = 36; NC, n = 20). A total of 10 differentially expressed proteins (DEPs) were identified in the ITP group compared with the non-ITP and NC groups of the discovery cohort. These include CXCL11, GZMH, ARG1, TGF-ß1, ANGPT1, CXCL12, CD40-L, PDGF subunit B, IL4 and TNFSF14. Furthermore, least absolute shrinkage and selection operator regression analysis showed some of these DEPs, such as CXCL11, TGF-ß1, ARG1 and GZMH to be significant in differentiating between patients with ITP and healthy controls (validation area under the curve = 0.87). The analysis demonstrated that the ITP group has a specific proteomic profile relative to non-ITP and NC groups. In summary, we report for the first time that Olink precision proteomics can specifically detect up-regulated inflammatory proteins as potential diagnostic biomarkers for ITP.

Development and validation of a DLLME-HPLC-FLD method for determination of aflatoxins in Chrysanthemum morifolium based on quality by design principles.

INTRODUCTION: Aflatoxins, potent carcinogens produced by Aspergillus species, present significant health risks and commonly contaminate herbal products such as Chrysanthemum morifolium. Detecting these toxins in C. morifolium proves challenging due to the complex nature of the herbal matrix and the fluctuating levels of toxins found in different samples. OBJECTIVES: This study aimed to develop and optimize a novel method for the detection of aflatoxins in C. morifolium using dispersive liquid-liquid microextraction combined with high-performance liquid chromatography-fluorescence detection based on quality by design principles. METHODOLOGY: The method involved determining critical method attributes and parameters through the Plackett-Burman design, followed by optimization using the Box-Behnken design. Monte Carlo simulation was employed to establish a design space, which was experimentally verified. Method validation was performed to confirm accuracy, precision, and stability. RESULTS: The developed method exhibited excellent linearity (R2 > 0.9991) for aflatoxins B1, B2, G1, and G2 across a range of concentrations, with recovery rates between 85.52% and 102.01%. The validated method effectively quantified aflatoxins in C. morifolium under different storage conditions, highlighting the impact of temperature and storage time on aflatoxin production. CONCLUSION: This study successfully established a reliable and effective method for the detection of aflatoxins in C. morifolium, highlighting the importance of strict storage conditions to reduce aflatoxin contamination. Using a quality by design framework, the method demonstrated robustness and high analytical performance, making it suitable for routine quality control of herbal products.

A viscoelastic-stochastic model of cell adhesion considering matrix morphology and medium viscoelasticity.

Quantitative investigation of the adhesive behavior between cells and the extracellular matrix (ECM) through molecular bonds is essential for cell culture and bio-medical engineering in vitro. Cell adhesion is a complex multi-scale behavior that includes temporal and spatial scales. However, the influence of the cell and matrix creep effect and the complex spatial morphology characteristics of the matrix on the cell adhesion mechanism is unclear. In the present study, an idealized theoretical model has been considered, where the adhesion of cells and the matrix is simplified into a planar strain problem of homogeneous viscoelastic half-spaces. Furthermore, a new viscoelastic-stochastic model that considers the morphological characteristics of the matrix, the viscoelasticity of the cell and the viscoelasticity of the substrate was developed under the action of a constant external force. The model characterizes the matrix topographical features by fractal dimension (FD), interprets the effects of FD and medium viscoelasticity on the molecular bond force and the receptor-ligand bond re-association rate and reveals a new mechanism for the stable adhesion of molecular bond clusters by Monte Carlo simulation. Based on this model, it was identified that the temporal and spatial distribution of molecular bond force was affected by the matrix FD and the lifetime and stability of the molecular bond cluster could be significantly improved by tuning the FD. At the same time, the viscoelastic creep effect of the cell and matrix increased the re-association rate of open bonds and could expand the window of stable adhesion more flexibly.

PD-1 blockade combined with chemotherapy and bevacizumab in DNA mismatch repair-proficient/microsatellite stable colorectal liver metastases.

Background: Single-agent immunotherapy is less effective in patients with DNA mismatch repair-proficient/microsatellite stable (pMMR/MSS) metastatic colorectal cancer (mCRC). Whether pMMR/MSS mCRC patients benefit from combination immunotherapy remains unclear. This study aimed to evaluate the efficacy and safety of anti-programmed cell death protein 1 (PD-1) therapy combined with chemotherapy and bevacizumab in pMMR/MSS colorectal liver metastases (CRLM) patients. Methods: A total of 12 patients with pMMR/MSS CRLM treated at The Sixth Affiliated Hospital of Sun Yat-sen University were enrolled. All patients were treated with at least 4 doses of PD-1 monoclonal antibody combined with chemotherapy and bevacizumab as neoadjuvant/adjuvant therapy. Results: A total of 10 of the 12 patients received the combined therapies before primary tumor resection; the disease control rate (DCR) was 100% (10/10), and the objective response rate (ORR) was 70% (7/10). The ORR of liver metastases was 75% (9/12). Pathological complete response (pCR) was achieved in 1 primary tumor patient and 2 patients with hepatic lesions. A total of 5 patients underwent simultaneous resection of the primary tumor and liver metastases; 9 patients underwent microwave ablation for liver metastases. A total of 7 patients were assessed as having no evidence of disease (NED) with a median progression-free survival (PFS) interval of 9.2 (1.5-15.8) months after multimodality treatments for both primary and metastatic lesions. No severe immune-related adverse events (irAEs) and operational complications were observed. Conclusions: PD-1 blockade combined with chemotherapy and bevacizumab might be safe and effective for patients with pMMR/MSS CRLM. This treatment strategy might lead to better tumor regression and a higher chance of achieving NED.

Revealing salt concentration for microbial balance and metabolite enrichment in secondary fortified fermented soy sauce: A multi-omics perspective.

This study examined the impact of varying salt concentrations on microbiota, physicochemical properties, and metabolites in a secondary fortified fermentation process using multi-omics techniques. It aimed to determine the influence of salt stress on microbiota shifts and metabolic activities. The findings demonstrated that moderate salt reduction (MS) was found to enhance moromi's flavor and quality, while mitigating the negative effects of excessive low salt (LS). MS samples had 1.22, 1.13, and 2.92 times more amino acid nitrogen (AAN), non-volatiles, and volatiles, respectively, than high salt (HS) samples. In contrast, lactic acid and biogenic amines in LS samples were 1.56 g/100 g and 4115.11 mg/kg, respectively, decreasing to 0.15 g/100 g and 176.76 mg/kg in MS samples. Additionally, the contents of ethanol and small peptides increased in MS due to the growth of specific functional microorganisms such as Staphylococcus gallinarum, Weissella confusa, and Zygosaccharomyces rouxii, while food-borne pathogens were inhibited. Network analysis revealed that the core microbial interactions were enhanced in MS samples, promoting a balanced fermentation environment. Redundancy analysis (RDA) and correlation analyses underscored that the physicochemical properties significantly impacted bacterial community structure and the correlations between key microbes and flavor compounds. These findings provided a theoretical foundation for developing innovative reduced-salt fermentation techniques, contributing to the sustainable production of high-quality soy sauce.

Experimental Study on the Process and Performance of Laser-Assisted Vascular Anastomosis Based on Response Surface Methodology.

The selection of an appropriate vascular anastomosis process has an important impact on the surgical treatment of coronary artery disease. In this paper, a laser-assisted vascular anastomosis process test was carried out based on the response surface experimental method, and the interaction of laser process parameters on the bursting pressure strength and thermal damage of the anastomotic incision was analyzed, and the relationship model between process parameters and anastomotic performance of the vascular incision tissues was established, and the optimal welding process parameters were obtained. The results show that the laser power has a significant effect on the bursting pressure strength of the anastomotic incision; the interaction of laser power and scanning speed has a substantial impact on the thermal damage of the anastomotic incision; and the anastomotic incision has the best comprehensive performance when the laser power is 6.2 W, the scanning speed is 206 mm/s, and the defocus is 2 mm.

PSD-ELGAN: A pseudo self-distillation based CycleGAN with enhanced local adversarial interaction for single image dehazing.

Compared to pixel-level content loss, domain-level style loss in CycleGAN-based dehazing algorithms just imposes relatively soft constraints on the intermediate translated images, resulting in struggling to accurately model haze-free features from real hazy scenes. Furthermore, globally perceptual discriminator may misclassify real hazy images with significant scene depth variations as clean style, thereby resulting in severe haze residue. To address these issues, we propose a pseudo self-distillation based CycleGAN with enhanced local adversarial interaction for image dehazing, termed as PSD-ELGAN. On the one hand, we leverage the characteristic of CycleGAN to generate pseudo image pairs during training. Knowledge distillation is employed in this unsupervised framework to transfer the informative high-quality features from the self-reconstruction network of real clean images to the dehazing generator of paired pseudo hazy images, which effectively improves its haze-free feature representation ability without increasing network parameters. On the other hand, in the output of dehazing generator, four non-uniform image patches severely affected by residual haze are adaptively selected as input samples. The local discriminator could easily distinguish their hazy style, thereby further compelling the dehazing generator to suppress haze residues in such regions, thus enhancing its dehazing performance. Extensive experiments show that our PSD-ELGAN can achieve promising results and better generality across various datasets.

Sucrose contributed to the biofilm formation of Tetragenococcus halophilus and changed the biofilm structure.

Based on the previous research results that the addition of sucrose in the medium improved the biofilm formation of Tetragenococcus halophilus, the influence of sucrose on biofilm formation was explored. Moreover, the influence of exogenous expression of related genes sacA and galE from T. halophilus on the biofilm formation of L. lactis NZ9000 was investigated. The results showed that the addition of sucrose in the medium improved the biofilm formation, the resistance of biofilm cells to freeze-drying stress, and the contents of exopolysaccharides (EPS) and eDNA in the T. halophilus biofilms. Meanwhile, the addition of sucrose in the medium changed the monosaccharide composition of EPS and increased the proportion of glucose and galactose in the monosaccharide composition. Under 2.5% (m/v) salt stress condition, the expression of gene sacA promoted the biofilm formation and the EPS production of L. lactis NZ9000 with the sucrose addition in the medium and changed the EPS monosaccharide composition. The expression of gene galE up-regulated the proportion of rhamnose, galactose, and arabinose in the monosaccharide composition of EPS, and down-regulated the proportion of glucose and mannose. This study will provide a theoretical basis for regulating the biofilm formation of T. halophilus, and provide a reference for the subsequent research on lactic acid bacteria biofilms.

An L-type calcium channel blocker nimodipine exerts anti-fibrotic effects by attenuating TGF-ß1 induced calcium response in an in vitro model of thyroid eye disease.

BACKGROUND: Thyroid eye disease (TED) is a vision-threatening autoimmune disorder. Orbital tissue fibrosis leading to intractable complications remains a troublesome issue in TED management. Exploration of novel therapeutic targets and agents to ameliorate tissue fibrosis is crucial for TED. Recent work suggests that Ca2+ signaling participates in tissue fibrosis. However, whether an alteration of Ca2+ signaling has a role in fibrogenesis during TED remains unclear. In this study, we aimed to investigate the role of Ca2+ signaling in the fibrogenesis process during TED and the potential therapeutic effects of a highly selective inhibitor of the L-type calcium channel (LTCC), nimodipine, through a TGF-ß1 induced in vitro TED model. METHODS: Primary culture of orbital fibroblasts (OFs) were established from orbital adipose connective tissues of patients with TED and healthy control donors. Real-time quantitative polymerase chain reaction (RT-qPCR) and RNA sequencing were used to assess the genes expression associated with LTCC in OFs. Flow cytometry, RT-qPCR, 5-ethynyl-2'-deoxyuridine (EdU) proliferation assay, wound healing assay and Western blot (WB) were used to assess the intracellular Ca2+ response on TGF-ß1 stimulation, and to evaluate the potential therapeutic effects of nimodipine in the TGF-ß1 induced in vitro TED model. The roles of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and signal transducer and activator of transcription 1 (STAT1) in fibrogenesis during TED were determined by immunohistochemistry, WB, flow cytometry and co-immunoprecipitation assay. Selective inhibitors were used to explore the downstream signaling pathways. RESULTS: LTCC inhibitor nimodipine blocked the TGF-ß1 induced intracellular Ca2+ response and further reduced the expression of alpha-smooth muscle actin (α-SMA), collagen type I alpha 1 (Col1A1) and collagen type I alpha 2 (Col1A2) in OFs. Besides, nimodipine inhibited cell proliferation and migration of OFs. Moreover, our results provided evidence that activation of the CaMKII/STAT1 signaling pathway was involved in fibrogenesis during TED, and nimodipine inhibited the pro-fibrotic functions of OFs by down-regulating the CaMKII/STAT1 signaling pathway. CONCLUSIONS: TGF-ß1 induces an LTCC-mediated Ca2+ response, followed by activation of CaMKII/STAT1 signaling pathway, which promotes the pro-fibrotic functions of OFs and participates in fibrogenesis during TED. Nimodipine exerts potent anti-fibrotic benefits in vitro by suppressing the CaMKII/STAT1 signaling pathway. Our work deepens our understanding of the fibrogenesis process during TED and provides potential therapeutic targets and alternative candidate for TED.

CD4+ T cells with convergent TCR recombination reprogram stroma and halt tumor progression in adoptive therapy.

Cancers eventually kill hosts even when infiltrated by cancer-specific T cells. We examined whether cancer-specific T cell receptors of CD4+ T cells (CD4TCRs) from tumor-bearing hosts can be exploited for adoptive TCR therapy. We focused on CD4TCRs targeting an autochthonous mutant neoantigen that is only presented by stroma surrounding the MHC class II-negative cancer cells. The 11 most common tetramer-sorted CD4TCRs were tested using TCR-engineered CD4+ T cells. Three TCRs were characterized by convergent recombination for which multiple T cell clonotypes differed in their nucleotide sequences but encoded identical TCR α and ß chains. These preferentially selected TCRs destroyed tumors equally well and halted progression through reprogramming of the tumor stroma. TCRs represented by single T cell clonotypes were similarly effective only if they shared CDR elements with preferentially selected TCRs in both α and ß chains. Selecting candidate TCRs on the basis of these characteristics can help identify TCRs that are potentially therapeutically effective.

Nanoarchitectonics of Injectable Biomimetic Conjugates for Cartilage Protection and Therapy Based on Degenerative Osteoarthritis Progression.

Osteoarthritis (OA) is a common age-related degenerative disease characterized by changes in the local tissue environment as inflammation progresses. Inspired by the wind-dispersal mechanism of dandelion seeds, this study develops responsive biomimetic microsphere-drug conjugate for OA therapy and protection. The conjugate integrates dibenzaldehyde polyethylene glycol (DFPEG) with chitosan and polyethylene glycol diacrylate (PEGDA) through dynamic covalent bonds to form a dual-network hydrogel microsphere. Based on the progression of OA, the conjugate with the surface-anchored cyclic peptide cortistatin-14 (CST-14) achieves targeted drug therapy and a self-regulating hydrogel network. In cases of progressing inflammation (pH < 5), CST-14 dissociates from the microsphere surface (viz. the drug release rate increased) and inhibits TNF-α signaling to suppress OA. Concurrently, the monomer DFPEG responsively detaches from the hydrogel network and scavenges reactive oxygen species (ROS) to protect the cartilage tissue. The ROS scavenging of DFPEG is comparable to that of coenzyme Q10 and vitamin C. The degraded PEGDA microspheres provide tissue lubrication through reused conjugates. The rat OA model successfully achieved a synergistic therapeutic effect greater than the additive effect (1 + 1 > 2). This strategy offers an approach for anchoring amine-containing drugs and has marked potential for OA treatment and protection.

The Blood-Brain Barrier in Both Humans and Rats: A Perspective From 3D Imaging.

Background: The blood-brain barrier (BBB) is part of the neurovascular unit (NVU) which plays a key role in maintaining homeostasis. However, its 3D structure is hardly known. The present study is aimed at imaging the BBB using tissue clearing and 3D imaging techniques in both human brain tissue and rat brain tissue. Methods: Both human and rat brain tissue were cleared using the CUBIC technique and imaged with either a confocal or two-photon microscope. Image stacks were reconstructed using Imaris. Results: Double staining with various antibodies targeting endothelial cells, basal membrane, pericytes of blood vessels, microglial cells, and the spatial relationship between astrocytes and blood vessels showed that endothelial cells do not evenly express CD31 and Glut1 transporter in the human brain. Astrocytes covered only a small portion of the vessels as shown by the overlap between GFAP-positive astrocytes and Collagen IV/CD31-positive endothelial cells as well as between GFAP-positive astrocytes and CD146-positive pericytes, leaving a big gap between their end feet. A similar structure was observed in the rat brain. Conclusions: The present study demonstrated the 3D structure of both the human and rat BBB, which is discrepant from the 2D one. Tissue clearing and 3D imaging are promising techniques to answer more questions about the real structure of biological specimens.

Zürich II Statement on Per- and Polyfluoroalkyl Substances (PFASs): Scientific and Regulatory Needs.

Per- and polyfluoroalkyl substances (PFASs) are a class of synthetic organic chemicals of global concern. A group of 36 scientists and regulators from 18 countries held a hybrid workshop in 2022 in Zürich, Switzerland. The workshop, a sequel to a previous Zürich workshop held in 2017, deliberated on progress in the last five years and discussed further needs for cooperative scientific research and regulatory action on PFASs. This review reflects discussion and insights gained during and after this workshop and summarizes key signs of progress in science and policy, ongoing critical issues to be addressed, and possible ways forward. Some key take home messages include: 1) understanding of human health effects continues to develop dramatically, 2) regulatory guidelines continue to drop, 3) better understanding of emissions and contamination levels is needed in more parts of the world, 4) analytical methods, while improving, still only cover around 50 PFASs, and 5) discussions of how to group PFASs for regulation (including subgroupings) have gathered momentum with several jurisdictions proposing restricting a large proportion of PFAS uses. It was concluded that more multi-group exchanges are needed in the future and that there should be a greater diversity of participants at future workshops.

A Comparative Study of Methods for Calculating the Dislocation Density in GaN-on-Si Epitaxial Wafers.

A series of characterization methods involving high-resolution X-ray diffraction (HR-XRD), electron channel contrast imaging (ECCI), cathodoluminescence microscopy (CL), and atomic force microscopy (AFM) were applied to calculate the dislocation density of GaN-on-Si epitaxial wafers, and their performance was analyzed and evaluated. The ECCI technique, owing to its high lateral resolution, reveals dislocation distributions on material surfaces, which can visually characterize the dislocation density. While the CL technique is effective for low-density dislocations, it is difficult to accurately identify the number of dislocation clusters in CL images as the density increases. The AFM technique analyzes surface dislocation characteristics by detecting surface pits caused by dislocations, which are easily affected by sample and probe conditions. A prevalent method for assessing the crystal quality of GaN is the rocking curve of HR-XRD (ω-scan), which calculates the dislocation density based on the FWHM value of the curves. By comparing the above four dislocation characterization methods, the advantages and limitations of each method are clarified, which also verifies the applicability of DB=ß29b2 for GaN-on-Si epitaxial wafers. This provides an important reference value for dislocation characterization in GaN-on-Si materials. The accuracy evaluation of dislocation density can truly and reliably reflect crystal quality, which is conducive to further optimization. Furthermore, this study can also be applied to other heterogeneous or homogeneous epitaxial materials.

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases.

The genomes of the fungus Magnaporthe oryzae that causes blast diseases on diverse grass species, including major crops, have indispensable core-chromosomes and may contain supernumerary chromosomes, also known as mini-chromosomes. These mini-chromosomes are speculated to provide effector gene mobility, and may transfer between strains. To understand the biology of mini-chromosomes, it is valuable to be able to detect whether a M. oryzae strain possesses a mini-chromosome. Here, we applied recurrent neural network models for classifying DNA sequences as arising from core- or mini-chromosomes. The models were trained with sequences from available core- and mini-chromosome assemblies, and then used to predict the presence of mini-chromosomes in a global collection of M. oryzae isolates using short-read DNA sequences. The model predicted that mini-chromosomes were prevalent in M. oryzae isolates. Interestingly, at least one mini-chromosome was present in all recent wheat isolates, but no mini-chromosomes were found in early isolates collected before 1991, indicating a preferential selection for strains carrying mini-chromosomes in recent years. The model was also used to identify assembled contigs derived from mini-chromosomes. In summary, our study has developed a reliable method for categorizing DNA sequences and showcases an application of recurrent neural networks in predictive genomics.

DNA damage-induced proteasome phosphorylation controls substrate recognition and facilitates DNA repair.

Upon DNA damage, numerous proteins are targeted for ubiquitin-dependent proteasomal degradation, which is an integral part of the DNA repair program. Although details of the ubiquitination processes have been intensively studied, little is known about whether and how the 26S proteasome is regulated in the DNA damage response (DDR). Here, we show that human Rpn10/PSMD4, one of the three ubiquitin receptors of the 26S proteasome, is rapidly phosphorylated in response to different types of DNA damage. The phosphorylation occurs at Rpn10-Ser266 within a conserved SQ motif recognized by ATM/ATR/DNA-PK. Blockade of S266 phosphorylation attenuates homologous recombination-mediated DNA repair and sensitizes cells to genotoxic insults. In vitro and in cellulo experiments indicate that phosphorylation of S266, located in the flexible linker between the two ubiquitin-interacting motifs (UIMs) of Rpn10, alters the configuration of UIMs, and actually reduces ubiquitin chain (substrate) binding. As a result, essential DDR proteins such as BRCA1 are spared from premature degradation and allowed sufficient time to engage in DNA repair, a scenario supported by proximity labeling and quantitative proteomic studies. These findings reveal an inherent self-limiting mechanism of the proteasome that, by controlling substrate recognition through Rpn10 phosphorylation, fine-tunes protein degradation for optimal responses under stress.