Refining Euclidean Obfuscatory Nodes Helps: A Joint-Space Graph Learning Method for Graph Neural Networks.

Many graph neural networks (GNNs) are inapplicable when the graph structure representing the node relations is unavailable. Recent studies have shown that this problem can be effectively solved by jointly learning the graph structure and the parameters of GNNs. However, most of these methods learn graphs by using either a Euclidean or hyperbolic metric, which means that the space curvature is assumed to be either constant zero or constant negative. Graph embedding spaces usually have nonconstant curvatures, and thus, such an assumption may produce some obfuscatory nodes, which are improperly embedded and close to multiple categories. In this article, we propose a joint-space graph learning (JSGL) method for GNNs. JSGL learns a graph based on Euclidean embeddings and identifies Euclidean obfuscatory nodes. Then, the graph topology near the identified obfuscatory nodes is refined in hyperbolic space. We also present a theoretical justification of our method for identifying obfuscatory nodes and conduct a series of experiments to test the performance of JSGL. The results show that JSGL outperforms many baseline methods. To obtain more insights, we analyze potential reasons for this superior performance.

Using UAV-Based Temporal Spectral Indices to Dissect Changes in the Stay-Green Trait in Wheat.

Stay-green (SG) in wheat is a beneficial trait that increases yield and stress tolerance. However, conventional phenotyping techniques limited the understanding of its genetic basis. Spectral indices (SIs) as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy. Here, we applied SIs to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field seasons. Four SIs (normalized difference vegetation index, green normalized difference vegetation index, normalized difference red edge index, and optimized soil-adjusted vegetation index) were normalized to develop relative stay-green scores (RSGS) as the SG indicators. An RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci (QTL) harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate genes. Among them, 15 QTL overlapped or were adjacent to known SG-related QTL/genes, while the remaining QTL were novel. Notably, a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100, TracesCS6B03G0356400, and TracesCS2B03G1299500 are increasing following the Green Revolution, further validating the feasibility of the pipeline. This study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.

Co-training based prediction of multi-label protein-protein interactions.

Prediction of protein-protein interaction (PPI) types enhances the comprehension of the underlying structural characteristics and functions of proteins, which gives rise to a multi-label classification problem. The nominal features describe the physicochemical characteristics of proteins directly, establishing a more robust correlation with the interaction types between proteins than ordered features. Motivated by this, we propose a multi-label PPI prediction model referred to as CoMPPI (Co-training based Multi-Label prediction of Protein-Protein Interaction). This approach aims to maximize the utility of both ordered and nominal features extracted from protein sequences. Specifically, CoMPPI incorporates graph convolutional network (GCN) and 1D convolution operation to process the complementary subsets of features individually, leveraging both local and contextualized information in a more efficient way. In addition, two multi-type PPI datasets were constructed to eliminate the duplication in previous datasets. We compare the performance of CoMPPI with three state-of-the-art methods on three datasets partitioned using distinct schemes (Breadth-first search, Depth-first search, and Random), CoMPPI consistently outperforms the other methods across all cases, demonstrating improvements ranging from 3.81% to 32.40% in Micro-F1. The subsequent ablation experiment confirms the efficacy of employing the co-training framework for multi-label PPI prediction, indicating promising avenues for future advancements in this domain.

Gelatin-Based Hydrogel Functionalized with Dopamine and Layered Double Hydroxide for Wound Healing.

Hydrogels with adhesion properties and a wetted structure are promising alternatives to traditional wound dressing materials. The insufficiency of gelatin hydrogels in terms of their adhesive and mechanical strength limits their application in wound dressings. This work presents the design and preparation of a gelatin-based hydrogel functionalized with dopamine (DA) and layered double hydroxide (LDH). The combination of DA and LDH improves the hydrogel's adhesion properties in terms of interfacial adhesion and inner cohesion. Hydrogels with 8% DA and 4% LDH attained the highest adhesion strength of 266.5 kPa, which increased to 295.5 and 343.3 kPa after hydrophobically modifying the gelatin with octanoyl and decanoyl aldehydes, respectively. The gelatin-based hydrogels also demonstrated a macroporous structure, excellent biocompatibility, and a good anti-inflammatory effect. The developed hydrogels accelerated wound healing in Sprague Dawley rat skin full-thickness wound models.

A prediction model for CO2/CO adsorption performance on binary alloys based on machine learning.

Despite the rapid development of computational methods, including density functional theory (DFT), predicting the performance of a catalytic material merely based on its atomic arrangements remains challenging. Although quantum mechanics-based methods can model 'real' materials with dopants, grain boundaries, and interfaces with acceptable accuracy, the high demand for computational resources no longer meets the needs of modern scientific research. On the other hand, Machine Learning (ML) method can accelerate the screening of alloy-based catalytic materials. In this study, an ML model was developed to predict the CO2 and CO adsorption affinity on single-atom doped binary alloys based on the thermochemical properties of component metals. By using a greedy algorithm, the best combination of features was determined, and the ML model was trained and verified based on a data set containing 78 alloys on which the adsorption energy values of CO2 and CO were calculated from DFT. Comparison between predicted and DFT calculated adsorption energy values suggests that the extreme gradient boosting (XGBoost) algorithm has excellent generalization performance, and the R-squared (R2) for CO2 and CO adsorption energy prediction are 0.96 and 0.91, respectively. The errors of predicted adsorption energy are 0.138 eV and 0.075 eV for CO2 and CO, respectively. This model can be expected to advance our understanding of structure-property relationships at the fundamental level and be used in large-scale screening of alloy-based catalysts.

A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.

Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear. Here, we apply a chemical-crosslinking assisted proximity capture (CAP-C) method to elucidate the fine-scale chromatin landscape, revealing chromatin interactions within gene bodies closely associated with RNA polymerase II (Pol II) densities across initiation, pausing, and termination sites. We observe dynamic changes in chromatin interactions alongside Pol II activity alterations during cold stress, suggesting local chromatin dynamics may regulate Pol II activity. Notably, cold stress does not affect large-scale chromatin conformations. We further identify a comprehensive promoter-promoter interaction (PPI) network across the genome, potentially facilitating co-regulation of gene expression in response to cold stress. Our study deepens the understanding of chromatin conformation-associated gene regulation in plant response to cold.

Correlation of Peripheral Blood Inflammatory Indicators to Prognosis After Intravenous Thrombolysis in Acute Ischemic Stroke: A Retrospective Study.

Purpose: According to many previous studies, neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR) and hypersensitive C-reactive protein (CRP) are commonly used as important indicators to assess the prognosis of intravenous thrombolysis in AIS patients. Based on this, we used two novel biomarkers C-NLR (CRP/neutrophil-to-lymphocyte ratio) and C-LMR (CRP×lymphocyte-to-monocyte ratio) to investigate their correlation with 90-day outcomes in AIS patients after intravenous thrombolysis. Patients and Methods: A total of 204 AIS patients who received intravenous thrombolysis at the Stroke Center of Jiangsu Province Hospital of Chinese Medicine from January 2021 to December 2022 were retrospectively included. All patients were followed up 90 days after thrombolysis to assess their prognosis. Patients with a modified Rankin scale score (mRS) of 3-6 were included in the unfavorable outcome group, and those with a score of 0-2 were included in the favorable outcome group. Logistic regression analysis, receiver operating characteristic (ROC) curve, and Kaplan-Meier survival curve were used to investigate the association between C-NLR, C-LMR, and 90-day prognosis in AIS patients treated with early intravenous thrombolysis. Results: C-NLR (OR=1.586, 95% CI=1.098~2.291, P=0.014) and C-LMR (OR=1.099, 95% CI=1.025~1.179, P=0.008) were independent risk factors for 90-day prognosis of AIS patients treated with early intravenous thrombolysis. The higher C-NLR and C-LMR were associated with unfavorable prognosis. Conclusion: C-NLR and C-LMR can be used as biomarkers to predict prognosis of AIS patients treated with early intravenous thrombolysis.

Acyl carrier protein OsMTACP2 confers rice cold tolerance at the booting stage.

Low temperatures occurring at the booting stage in rice (Oryza sativa L.) often result in yield loss by impeding male reproductive development. However, the underlying mechanisms by which rice responds to cold at this stage remain largely unknown. Here, we identified MITOCHONDRIAL ACYL CARRIER PROTEIN 2 (OsMTACP2), the encoded protein of which mediates lipid metabolism involved in the cold response at the booting stage. Loss of OsMTACP2 function compromised cold tolerance, hindering anther cuticle and pollen wall development, resulting in abnormal anther morphology, lower pollen fertility, and seed setting. OsMTACP2 was highly expressed in tapetal cells and microspores during anther development, with the encoded protein localizing to both mitochondria and the cytoplasm. Comparative transcriptomic analysis revealed differential expression of genes related to lipid metabolism between the wild type and the Osmtacp2-1 mutant in response to cold. Through a lipidomic analysis, we demonstrated that wax esters, which are the primary lipid components of the anther cuticle and pollen walls, function as cold-responsive lipids. Their levels increased dramatically in the wild type but not in Osmtacp2-1 when exposed to cold. Additionally, mutants of two cold-induced genes of wax ester biosynthesis, ECERIFERUM1 and WAX CRYSTAL-SPARSE LEAF2, showed decreased cold tolerance. These results suggest that OsMTACP2-mediated wax ester biosynthesis is essential for cold tolerance in rice at the booting stage.

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization.

Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.

Discovery of Trifluorobutene Amide Derivatives as Potential Nematicides: Design, Synthesis, Nematicidal Activity Evaluation, SAR, and Mode of Action Study.

Plant-parasitic nematodes are one of the major threats to crop protection. However, only limited nematicides are currently available and are confronted with a growing resistance problem, which necessitates the development of novel nematicides. In this study, a series of trifluorobutene amide derivatives was synthesized through the strategy of amide bond reversal, and their nematicidal activity against Meloidogyne incognita was evaluated. The bioassay showed that compounds C2, C10, and C18 and some analogues thereof exhibited good nematicidal activity. Among them, the derivatives of compound C2 containing a benzene ring [C26 (R = 2-CH3) and C33 (R = 2-Cl)] exhibited excellent bioactivity against M. incognita in vitro. The LC50/72h values reached 14.13 and 14.71 mg·L-1, respectively. Moreover, analogues of compounds C10 and C18 containing a thiophene ring [C43 (R = 5-CH3), C44 (R = 4-CH3), and C50 (R = 5-Cl)] exhibited significant bioactivity against M. incognita in vivo with inhibition rates of 68.8, 65.5, and 69.8% at 2.5 mg·L-1 in a matrix, respectively. Meanwhile, C44 and C50 also showed excellent control effects against M. incognita in both cups and microplots. The structure-activity relationship (SAR) of synthesized compounds was discussed in detail. Comparative molecular field analysis (CoMFA) was also conducted to develop the SAR profile. The preliminary mode of action investigation showed that compound C33 exhibited strong inhibition on egg hatching, motility, feeding behavior, and growth of Caenorhabditis elegans. At the same time, the impact of active compounds on biochemical indicators related to oxidative stress showed that compound C33 influenced the production of ROS (reactive oxygen species), and the accumulation of lipofuscin and lipids on C. elegans.

An inducible CRISPR activation tool for accelerating plant regeneration.

The inducible CRISPR activation (CRISPR-a) system offers unparalleled precision and versatility for regulating endogenous genes, making it highly sought after in plant research. In this study, we developed a chemically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system. We systematically compared different induction strategies and achieved high efficiency in target gene activation. We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration. Further experiments showed that induced activation of these morphogenic genes can accelerate regeneration and improve regeneration efficiency in both eudicot and monocot plants, including alfalfa, woodland strawberry, and sheepgrass. Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.

Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5.

Light plays a central role in plant growth and development, providing an energy source and governing various aspects of plant morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play a role in rapidly responding to changes in environmental signals. However, the mechanism underlying post-transcriptional regulation during initial light exposure of young, etiolated seedlings remains elusive. In this study, we used FLEP-seq2, a Nanopore-based sequencing technique, to analyze nuclear RNAs in Arabidopsis (Arabidopsis thaliana) seedlings under different light conditions and found numerous light-responsive PTS introns. We also used single-nucleus RNA sequencing (snRNA-seq) to profile transcripts in single nucleus and investigate the distribution of light-responsive PTS introns across distinct cell types. We established that light-induced PTS introns are predominant in mesophyll cells during seedling de-etiolation following exposure of etiolated seedlings to light. We further demonstrated the involvement of the splicing-related factor A. thaliana PROTEIN ARGININE METHYLTRANSFERASE 5 (AtPRMT5), working in concert with the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a critical repressor of light signaling pathways. We showed that these two proteins orchestrate light-induced PTS events in mesophyll cells and facilitate chloroplast development, photosynthesis, and morphogenesis in response to ever-changing light conditions. These findings provide crucial insights into the intricate mechanisms underlying plant acclimation to light at the cell-type level.

Blocking miR528 function promotes tillering and regrowth in switchgrass.

MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA-seq analysis, combined with in situ hybridization assay revealed that up-regulation of two miR528 targets coding for Cu/Zn-SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528-SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528-SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation-mediated crop improvement.

Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance.

Alkaline soils pose an increasing problem for agriculture worldwide, but using stress-tolerant plants as green manure can improve marginal land. Here, we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and, when used as a green manure, substantially improves alkaline soil. To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume, we generated the first telomere-to-telomere genome assembly of S. cannabina spanning ∼2,087 Mb. The assembly included all centromeric regions, which contain centromeric satellite repeats, and complete chromosome ends with telomeric characteristics. Further genome analysis distinguished A and B subgenomes, which diverged approximately 7.9 million years ago. Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events (>10 Mb) and a significant, transposon-driven size expansion of the chromosome 5A homoeolog. We further identified four specific alkali-induced phosphate transporter genes in S. cannabina; these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil. Our work highlights the significance of S. cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.

Stent fracture after transjugular intrahepatic portosystemic shunt placement using the bare metal stent/stent-graft combination technique.

BACKGROUND: A transjugular intrahepatic portosystemic shunt (TIPS) is widely placed to treat portal hypertension. Because the Viatorr® stent (W. L. Gore and Associates, Flagstaff, AZ, United States) is not available in all hospitals in China, the bare metal stent (BMS)/stent-graft combination technique is still popular for TIPS construction. Stent fracture is a complication after TIPS placement using this technique, with limited available literature focusing on it. AIM: To assess the incidence of stent fracture after TIPS placement using the BMS/ stent-graft combination technique and to identify the risk factors for stent fracture. We proposed technique modifications to improve the clinical results of TIPS placement with the BMS/stent-graft combination technique. METHODS: We retrospectively analyzed the computed tomography (CT) data of all patients with portal hypertension who underwent the TIPS procedure between June 2011 and December 2021 in a single center. Patients implanted with the BMS/stent graft and had follow-up imaging data available were included. We identified patients with stent fracture and analyzed their characteristics. Multivariable logistic regression was applied to identify the potential predictors of stent fracture. RESULTS: Of the 68 included patients, stent fracture occurred in seven (10.3%) patients. Based on CT images, the stent fractures were categorized into three types. Our study consisted of four (57.1%) type I fractures, one (14.3%) type II fracture, one (14.3%) type IIIa fracture, and one (14.3%) type IIIb fracture. After adjusting for covariates, multivariable logistic regression revealed that the risk factors for stent fracture were the implantation of a greater number of stents [adjusted odds ratio (aOR) = 22.2, 95% confidence interval (CI): 1.2-415.4, P = 0.038] and a larger proximal sagittal stent bending angle (aOR = 1.1, 95%CI: 1.0-1.3, P = 0.020). CONCLUSION: Stent fracture occurred in approximately 10% of patients with portal hypertension who underwent TIPS with the BMS/stent-graft combination technique. The number of implanted stents and stent bending angle at the inferior vena cava end were predictors of stent fracture, which suggests that the incidence of stent fracture could potentially be reduced by procedural modifications.

Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe.

Leymus chinensis, a dominant perennial grass in the Eurasian Steppe, is well known for its remarkable adaptability and forage quality. Hardly any breeding has been done on the grass, limiting its potential in ecological restoration and forage productivity. To enable genetic improvement of the untapped, important species, we obtained a 7.85-Gb high-quality genome of L. chinensis with a particularly long contig N50 (318.49 Mb). Its allotetraploid genome is estimated to originate 5.29 million years ago (MYA) from a cross between the Ns-subgenome relating to Psathyrostachys and the unknown Xm-subgenome. Multiple bursts of transposons during 0.433-1.842 MYA after genome allopolyploidization, which involved predominantly the Tekay and Angela of LTR retrotransposons, contributed to its genome expansion and complexity. With the genome resource available, we successfully developed a genetic transformation system as well as the gene-editing pipeline in L. chinensis. We knocked out the monocot-specific miR528 using CRISPR/Cas9, resulting in the improvement of yield-related traits with increases in the tiller number and growth rate. Our research provides valuable genomic resources for Triticeae evolutionary studies and presents a conceptual framework illustrating the utilization of genomic information and genome editing to accelerate the improvement of wild L. chinensis with features such as polyploidization and self-incompatibility.

Mutation in Polycomb repressive complex 2 gene OsFIE2 promotes asexual embryo formation in rice.

Prevention of autonomous division of the egg apparatus and central cell in a female gametophyte before fertilization ensures successful reproduction in flowering plants. Here we show that rice ovules of Polycomb repressive complex 2 (PRC2) Osfie1 and Osfie2 double mutants exhibit asexual embryo and autonomous endosperm formation at a high frequency, while ovules of single Osfie2 mutants display asexual pre-embryo-like structures at a lower frequency without fertilization. Earlier onset, higher penetrance and better development of asexual embryos in the double mutants compared with those in Osfie2 suggest that the autonomous endosperm facilitated asexual embryo development. Transcriptomic analysis showed that male genome-expressed OsBBM1 and OsWOX8/9 were activated in the asexual embryos. Similarly, the maternal alleles of the paternally expressed imprinted genes were activated in the autonomous endosperm, suggesting that the egg apparatus and central cell convergently adopt PRC2 to maintain the non-dividing state before fertilization, possibly through silencing of the maternal alleles of male genome-expressed genes.

A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice.

Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.

Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules.

Abnormal high temperature (HT) caused by global warming threatens plant survival and food security, but the effects of HT on plant organ identity are elusive. Here, we show that Class II TEOSINTE BRANCHED 1/CYCLOIDEA/ PCF (TCP) transcription factors redundantly protect ovule identity under HT. The duodecuple tcp2/3/4/5/10/13/17/24/1/12/18/16 (tcpDUO) mutant displays HT-induced ovule conversion into carpelloid structures. Expression of TCP4 in tcpDUO complements the ovule identity conversion. TCP4 interacts with AGAMOUS (AG), SEPALLATA3 (SEP3), and the homeodomain transcription factor BELL1 (BEL1) to strengthen the association of BEL1 with AG-SEP3. The tcpDUO mutant synergistically interacts with bel1 and the ovule identity gene seedstick (STK) mutant stk in tcpDUO bel1 and tcpDUO stk. Our findings reveal the critical roles of Class II TCPs in maintaining ovule identity under HT and shed light on the molecular mechanisms by which ovule identity is determined by the integration of internal factors and environmental temperature.