CRISPR/Cas9-mediated generation of a mutant library of cotton CDPK gene family for identifying insect-resistant genes.

Calcium-dependent protein kinases (CDPKs) are pivotal signaling transduction enzymes in plants, especially responsive to diverse stress, including herbivory. In this study, through comprehensive analysis of CDPK gene family in upland cotton, we showed that GhCPKs are widely expressed in multiple tissues of cotton and positively respond to various biotic and abiotic stress. We developed a strategy for screening insect-resistant genes based on the CRISPR/Cas9 mutant library of GhCPKs. The library contains 82 members of the GhCPKs using 246 sgRNAs to generate 518 independent T0 plants. The coverage rate of target genes reached to 86.18%, the genome editing rate reached to 89.49%, and the editing heritability reached 82%. Through field insect bioassay, 14 GhCPK mutants resistant or susceptible to insect were identified. The most obvious insect-resistant mutant, cpk33/74 (simultaneously knocking out the homologous genes GhCPK33 and GhCPK74), was selected for further study. Oral secretions (OS) from Spodoptera litura induced a rapid influx of Ca2+ in cpk33/74 leaves, resulting in a significant increase in jasmonic acid (JA) content. S-adenosylmethionine synthase (SAMS) is an important protein involved in plant stress response, protein interaction experiments provided evidence of interactions between GhCPK33 and GhCPK74 with GhSAMS1 and GhSAM2, respectively. Additionally, silencing GhSAMS1 and GhSAM2 in cotton using VIGS resulted in decreased defense against S. litura. This study provides an effective strategy for constructing a mutant library of gene families in polyploid plant species and valuable insights into the role of CDPKs in the interaction between plants and herbivorous insects.

Using a smartphone-based self-management platform to study sex differences in Parkinson's disease: multicenter, cross-sectional pilot study.

BACKGROUND: Patient-reported outcome (PRO) is a distinct and indispensable dimension of clinical characteristics and recent advances have made remote PRO measurement possible. Sex difference in PRO of Parkinson's disease (PD) is hardly extensively researched. METHODS: A smartphone-based self-management platform, offering remote PRO measurement for PD patients, has been developed. A total of 1828 PD patients, including 1001 male patients and 827 female patients, were enrolled and completed their PRO submission through this platform. RESULTS: Sex differences in PROs have been identified. The female group had a significantly lower height, weight, and body mass index (BMI) than the male group (P < 0.001). For motor symptoms, a higher proportion of patients reporting dyskinesia was observed in the female group. For non-motor symptoms, there is a higher percentage (P < 0.001) as well as severity (P = 0.016) of depression in the female group. More male patients reported hyposmia, lisp, drooling, dysuria, frequent urination, hypersexuality, impotence, daytime sleepiness, and apathy than females (P < 0.05). In contrast, more female patients reported headache, palpation, body pain, anorexia, nausea, urinal incontinence, anxiety, insomnia (P < 0.05) than males. CONCLUSIONS: We provide evidence for sex differences in PD through the data collected from our platform. These results highlighted the importance of gender in clinical decision-making, and also support the feasibility of remote PRO measurement through a smartphone-based self-management platform in patients with PD.

Disease progression in proposed brain-first and body-first Parkinson's disease subtypes.

A new Parkinson's disease (PD) subtyping model has been recently proposed based on the initial location of α-synuclein inclusions, which divides PD patients into the brain-first subtype and the body-first subtype. Premotor RBD has proven to be a predictive marker of the body-first subtype. We found compared to PD patients without possible RBD (PDpRBD-, representing the brain-first subtype), PD patients with possible premotor RBD (PDpRBD+, representing the body-first subtype) had lower Movement Disorders Society Unified Parkinson's Disease Rating Scale part III (MDS UPDRS-III) score (p = 0.022) at baseline but presented a faster progression rate (p = 0.009) in MDS UPDRS-III score longitudinally. The above finding indicates the body-first subtype exhibited a faster disease progression in motor impairments compared to the brain-first subtype and further validates the proposed subtyping model.

Interpretable Machine Learning-Based Prediction Model for Concrete Cover Separation of FRP-Strengthened RC Beams.

This study focuses on the prediction of concrete cover separation (CCS) in reinforced concrete beams strengthened by fiber-reinforced polymer (FRP) in flexure. First, machine learning models were constructed based on linear regression, support vector regression, BP neural networks, decision trees, random forests, and XGBoost algorithms. Secondly, the most suitable model for predicting CCS was identified based on the evaluation metrics and compared with the codes and the researcher's model. Finally, a parametric study based on SHapley Additive exPlanations (SHAP) was carried out, and the following conclusions were obtained: XGBoost is best-suited for the prediction of CCS and codes, and researchers' model accuracy needs to be improved and suffers from over or conservative estimation. The contributions of the concrete to the shear force and the yield strength of the reinforcement are the most important parameters for the CCS, where the shear force at the onset of CCS is approximately proportional to the contribution of the concrete to the shear force and approximately inversely proportional to the yield strength of the reinforcement.

Enhancing ecosystem productivity and stability with increasing canopy structural complexity in global forests.

Forest canopy structural complexity (CSC) plays a crucial role in shaping forest ecosystem productivity and stability, but the precise nature of their relationships remains controversial. Here, we mapped the global distribution of forest CSC and revealed the factors influencing its distribution using worldwide light detection and ranging data. We find that forest CSC predominantly demonstrates significant positive relationships with forest ecosystem productivity and stability globally, although substantial variations exist among forest ecoregions. The effects of forest CSC on productivity and stability are the balanced results of biodiversity and resource availability, providing valuable insights for comprehending forest ecosystem functions. Managed forests are found to have lower CSC but more potent enhancing effects of forest CSC on ecosystem productivity and stability than intact forests, highlighting the urgent need to integrate forest CSC into the development of forest management plans for effective climate change mitigation.

Carbon storage through China's planted forest expansion.

China's extensive planted forests play a crucial role in carbon storage, vital for climate change mitigation. However, the complex spatiotemporal dynamics of China's planted forest area and its carbon storage remain uncaptured. Here we reveal such changes in China's planted forests from 1990 to 2020 using satellite and field data. Results show a doubling of planted forest area, a trend that intensified post-2000. These changes lead to China's planted forest carbon storage increasing from 675.6 ± 12.5 Tg C in 1990 to 1,873.1 ± 16.2 Tg C in 2020, with an average rate of ~ 40 Tg C yr-1. The area expansion of planted forests contributed ~ 53% (637.2 ± 5.4 Tg C) of the total above increased carbon storage in planted forests compared with planted forest growth. This proactive policy-driven expansion of planted forests has catalyzed a swift increase in carbon storage, aligning with China's Carbon Neutrality Target for 2060.

Association between the insufficient improvement of the quantitative flow ratio and worsening outcomes in ST-segment elevated myocardial infarction: a multicentre prospective cohort study.

Background: Improved coronary physiological function after percutaneous coronary intervention (PCI) has been shown to improve prognosis in stable ischaemic heart disease, but has not yet been explored in ST-segment elevated myocardial infarction (STEMI). The study sought to determine whether an improvement in the quantitative flow ratio (QFR) could improve the prognosis of STEMI patients undergoing primary PCI. Methods: Patients diagnosed with STEMI who were receiving primary PCI were recruited for the study. Those with thrombolysis in myocardial infarction (TIMI) flow <2 after wiring were excluded. The ΔQFR was calculated using the following formula: ΔQFR = post-PCI QFR - pre-stent QFR. The primary endpoint was the composite event, including recurrent myocardial infarction (MI) and acute heart failure (AHF). Results: In total, 515 STEMI patients with a median follow-up of 364 days were enrolled in the study. Based on the cut-off value from the receiver operator characteristic (ROC) curve, the patients were divided into the following two groups: the lower ΔQFR group (≤0.25, N=332); and the normal ΔQFR group (>0.25, N=183). Patients with a lower ΔQFR had a relatively higher rate of MI/AHF (10.5% vs. 4.4%, P=0.019) and AHF (7.2% vs. 2.7%, P=0.044). A lower ΔQFR was significantly associated with a higher incidence of MI/AHF [hazard ratio (HR) =2.962, 95% confidence interval (CI): 1.358-6.459, P=0.006, respectively] after adjusting for potential confounders. Pre-stent angiographic microvascular resistance [odds ratio (OR) =1.027, 95% CI: 1.022-1.033, P<0.001] and the stent-to-vessel diameter ratio <1.13 (OR =1.766, 95% CI: 1.027-3.071, P=0.04) were independent predictors of a lower ΔQFR. Conclusions: An insufficient improvement in the QFR contributes to worsening outcomes and might be a useful tool for risk stratification in STEMI.

A national-scale assessment of land subsidence in China's major cities.

China's massive wave of urbanization may be threatened by land subsidence. Using a spaceborne synthetic aperture radar interferometry technique, we provided a systematic assessment of land subsidence in all of China's major cities from 2015 to 2022. Of the examined urban lands, 45% are subsiding faster than 3 millimeters per year, and 16% are subsiding faster than 10 millimeters per year, affecting 29 and 7% of the urban population, respectively. The subsidence appears to be associated with a range of factors such as groundwater withdrawal and the weight of buildings. By 2120, 22 to 26% of China's coastal lands will have a relative elevation lower than sea level, hosting 9 to 11% of the coastal population, because of the combined effect of city subsidence and sea-level rise. Our results underscore the necessity of enhancing protective measures to mitigate potential damages from subsidence.

Bacitracin-resistant Staphylococcus aureus induced in chicken gut and in vitro under bacitracin exposure.

It is common knowledge that prolonged and excessive use of antibiotics can lead to antimicrobial resistance. However, the characteristics and mechanism of resistant-bacteria induced by clinically recommended and prophylactic dose drugs remain largely unclear. This study aimed to observe the trends of drug resistance of the bacitracin-susceptible Staphylococcus aureus strain FS127 under exposure to bacitracin (BAC), which were induced in vitro and in chicken gut. Antimicrobial susceptibility testing was used to detect the susceptibility of S. aureus induced in vitro and in the chicken gut to gentamicin, chloramphenicol, tetracycline, doxycycline, penicillin and chloramphenicol. The research results showed that bacitracin could induce drug resistance in S. aureus both in vitro and in vivo. The bacitracin-resistance rate of S. aureus isolated from chicken gut was positively correlated with the dose and time of bacitracin administration. The findings revealed that bacitracin-resistant S. aureus induced in vivo had enhanced susceptibility to chloramphenicol but no such change in vitro. Meanwhile, RT-qPCR assay was used to detect the expression levels of vraD, braD, braR and bacA in typical strains with different bacitracin-resistance levels. It was found that BacA may play a key role in the bacitracin resistance of S. aureus. In conclusion, this work reveals the characteristics and mechanism of bacitracin-resistant S. aureus induced by bacitracin in vivo and in vitro respectively.

Comprehensive analysis of MAPK gene family in upland cotton (Gossypium hirsutum) and functional characterization of GhMPK31 in regulating defense response to insect infestation.

KEY MESSAGE: The transcriptomic, phenotypic and metabolomic analysis of transgenic plants overexpressing GhMPK31 in upland cotton revealed the regulation of H2O2 burst and the synthesis of defensive metabolites by GhMPK31. Mitogen-activated protein kinases (MAPKs) are a crucial class of protein kinases, which play an essential role in various biological processes in plants. Upland cotton (G. hirsutum) is the most widely cultivated cotton species with high economic value. To gain a better understanding of the role of the MAPK gene family, we conducted a comprehensive analysis of the MAPK gene family in cotton. In this study, a total of 55 GhMPK genes were identified from the whole genome of G. hirsutum. Through an investigation of the expression patterns under diverse stress conditions, we discovered that the majority of GhMPK family members demonstrated robust responses to abiotic stress, pathogen stress and pest stress. Furthermore, the overexpression of GhMPK31 in cotton leaves led to a hypersensitive response (HR)-like cell death phenotype and impaired the defense capability of cotton against herbivorous insects. Transcriptome and metabolomics data analysis showed that overexpression of GhMPK31 enhanced the expression of H2O2-related genes and reduced the accumulation of defensive related metabolites. The direct evidence of GhMPK31 interacting with GhRBOHB (H2O2-generating protein) were found by Y2H, BiFC, and LCI. Therefore, we propose that the increase of H2O2 content caused by overexpression of GhMPK31 resulted in HR-like cell death in cotton leaves while reducing the accumulation of defensive metabolites, ultimately leading to a decrease in the defense ability of cotton against herbivorous insects. This study provides valuable insights into the function of MAPK genes in plant resistance to herbivorous insects.

Molecular basis for substrate transport of Mycobacterium tuberculosis ABC importer DppABCD.

The type I adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter DppABCD is believed to be responsible for the import of exogenous heme as an iron source into the cytoplasm of the human pathogen Mycobacterium tuberculosis (Mtb). Additionally, this system is also known to be involved in the acquisition of tri- or tetra-peptides. Here, we report the cryo-electron microscopy structures of the dual-function Mtb DppABCD transporter in three forms, namely, the apo, substrate-bound, and ATP-bound states. The apo structure reveals an unexpected and previously uncharacterized assembly mode for ABC importers, where the lipoprotein DppA, a cluster C substrate-binding protein (SBP), stands upright on the translocator DppBCD primarily through its hinge region and N-lobe. These structural data, along with biochemical studies, reveal the assembly of DppABCD complex and the detailed mechanism of DppABCD-mediated transport. Together, these findings provide a molecular roadmap for understanding the transport mechanism of a cluster C SBP and its translocator.

In pursuit of feedback activation: New insights into redox-responsive hydropersulfide prodrug combating oxidative stress.

Redox-responsive hydropersulfide prodrugs are designed to enable a more controllable and efficient hydropersulfide (RSSH) supply and to thoroughly explore their biological and therapeutic applications in oxidative damage. To obtain novel activation patterns triggered by redox signaling, we focused on NAD(P)H: quinone acceptor oxidoreductase 1 (NQO1), a canonical antioxidant enzyme, and designed NQO1-activated RSSH prodrugs. We also performed a head-to-head comparison of two mainstream structural scaffolds with solid quantitative analysis of prodrugs, RSSH, and metabolic by-products by LC-MS/MS, confirming that the perthiocarbamate scaffold was more effective in intracellular prodrug uptake and RSSH production. The prodrug was highly potent in oxidative stress management against cisplatin-induced nephrotoxicity. Strikingly, this prodrug possessed potential feedback activation properties by which the delivered RSSH can further escalate the prodrug activation via NQO1 upregulation. Our strategy pushed RSSH prodrugs one step further in the pursuit of efficient release in biological matrices and improved druggability against oxidative stress.

An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality.

Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.

Unveiling camouflaged and partially occluded colorectal polyps: Introducing CPSNet for accurate colon polyp segmentation.

BACKGROUND: Segmenting colorectal polyps presents a significant challenge due to the diverse variations in their size, shape, texture, and intricate backgrounds. Particularly demanding are the so-called "camouflaged" polyps, which are partially concealed by surrounding tissues or fluids, adding complexity to their detection. METHODS: We present CPSNet, an innovative model designed for camouflaged polyp segmentation. CPSNet incorporates three key modules: the Deep Multi-Scale-Feature Fusion Module, the Camouflaged Object Detection Module, and the Multi-Scale Feature Enhancement Module. These modules work collaboratively to improve the segmentation process, enhancing both robustness and accuracy. RESULTS: Our experiments confirm the effectiveness of CPSNet. When compared to state-of-the-art methods in colon polyp segmentation, CPSNet consistently outperforms the competition. Particularly noteworthy is its performance on the ETIS-LaribPolypDB dataset, where CPSNet achieved a remarkable 2.3% increase in the Dice coefficient compared to the Polyp-PVT model. CONCLUSION: In summary, CPSNet marks a significant advancement in the field of colorectal polyp segmentation. Its innovative approach, encompassing multi-scale feature fusion, camouflaged object detection, and feature enhancement, holds considerable promise for clinical applications.

ResNet incorporating the fusion data of RGB & hyperspectral images improves classification accuracy of vegetable soybean freshness.

The freshness of vegetable soybean (VS) is an important indicator for quality evaluation. Currently, deep learning-based image recognition technology provides a fast, efficient, and low-cost method for analyzing the freshness of food. The RGB (red, green, and blue) image recognition technology is widely used in the study of food appearance evaluation. In addition, the hyperspectral image has outstanding performance in predicting the nutrient content of samples. However, there are few reports on the research of classification models based on the fusion data of these two sources of images. We collected RGB and hyperspectral images at four different storage times of VS. The ENVI software was adopted to extract the hyperspectral information, and the RGB images were reconstructed based on the downsampling technology. Then, the one-dimensional hyperspectral data was transformed into a two-dimensional space, which allows it to be overlaid and concatenated with the RGB image data in the channel direction, thereby generating fused data. Compared with four commonly used machine learning models, the deep learning model ResNet18 has higher classification accuracy and computational efficiency. Based on the above results, a novel classification model named ResNet-R &H, which is based on the residual networks (ResNet) structure and incorporates the fusion data of RGB and hyperspectral images, was proposed. The ResNet-R &H can achieve a testing accuracy of 97.6%, which demonstrates a significant enhancement of 4.0% and 7.2% compared to the distinct utilization of hyperspectral data and RGB data, respectively. Overall, this research is significant in providing a unique, efficient, and more accurate classification approach in evaluating the freshness of vegetable soybean. The method proposed in this study can provide a theoretical reference for classifying the freshness of fruits and vegetables to improve classification accuracy and reduce human error and variability.

Non-invasive methods for heart rate measurement in fish based on photoplethysmography.

Heart rate is a crucial physiological indicator for fish, but current measurement methods are often invasive or require delicate manipulation. In this study, we introduced two non-invasive and easy-to-operate methods based on photoplethysmography, namely reflectance-type photoplethysmography (PPG) and remote photoplethysmography (rPPG), which we applied to the large yellow croaker (Larimichthys crocea). PPG showed perfect synchronization with electrocardiogram (ECG), with a Pearson's correlation coefficient of 0.99999. For rPPG, the results showed good agreement with ECG. Under active provision of green light, the Pearson's correlation coefficient was 0.966, surpassing the value of 0.947 under natural light. Additionally, the root mean square error was 0.810, which was lower than the value of 1.30 under natural light, indicating not only that the rPPG method had relatively high accuracy but also that green light may have the potential to further improve its accuracy.

Prognostic value of optical flow ratio for cardiovascular outcomes in patients after percutaneous coronary stent implantation.

Background: The relationship between the optical flow ratio (OFR) and clinical outcomes in patients with coronary artery disease (CAD) after percutaneous coronary stent implantation (PCI) remains unknown. Objective: To examine the correlation between post-PCI OFR and clinical outcomes in patients with CAD following PCI. Methods: Patients who underwent optical coherence tomography (OCT) guided PCI at Guangdong Provincial People's Hospital were retrospectively and continuously enrolled. Clinical data, post-PCI OCT characteristics, and OFR measurements were collected and analyzed to identify predictors of target vessel failure (TVF) after PCI. Results: Among 354 enrolled patients, 26 suffered TVF during a median follow-up of 484 (IQR: 400-774) days. Post-PCI OFR was significantly lower in the TVF group than in the non-TVF group (0.89 vs. 0.93; P = 0.001). In multivariable Cox regression analysis, post-PCI OFR (HR per 0.1 increase: 0.60; 95% CI: 0.41-0.89; P = 0.011), large stent edge dissection (HR: 3.85; 95% CI: 1.51-9.84; P = 0.005) and thin-cap fibroatheroma (TCFA) (HR: 2.95; 95% CI: 1.19-7.35; P = 0.020) in the non-stented segment were independently associated with TVF. In addition, the inclusion of post-PCI OFR to baseline characteristics and post-PCI OCT findings improved the predictive power of the model to distinguish subsequent TVF after PCI (0.838 vs. 0.796; P = 0.028). Conclusion: The post-PCI OFR serves as an independent determinant of risk for TVF in individuals with CAD after PCI. The inclusion of post-PCI OFR assessments, alongside baseline characteristics and post-PCI OCT findings, substantially enhances the capacity to differentiate the subsequent manifestation of TVF in CAD patients following PCI.

Tree mortality during long-term droughts is lower in structurally complex forest stands.

Increasing drought frequency and severity in a warming climate threaten forest ecosystems with widespread tree deaths. Canopy structure is important in regulating tree mortality during drought, but how it functions remains controversial. Here, we show that the interplay between tree size and forest structure explains drought-induced tree mortality during the 2012-2016 California drought. Through an analysis of over one million trees, we find that tree mortality rate follows a "negative-positive-negative" piecewise relationship with tree height, and maintains a consistent negative relationship with neighborhood canopy structure (a measure of tree competition). Trees overshadowed by tall neighboring trees experienced lower mortality, likely due to reduced exposure to solar radiation load and lower water demand from evapotranspiration. Our findings demonstrate the significance of neighborhood canopy structure in influencing tree mortality and suggest that re-establishing heterogeneity in canopy structure could improve drought resiliency. Our study also indicates the potential of advances in remote-sensing technologies for silvicultural design, supporting the transition to multi-benefit forest management.

Structural insights into trehalose capture and translocation by mycobacterial LpqY-SugABC.

The human pathogen, Mycobacterium tuberculosis (Mtb) relies heavily on trehalose for both survival and pathogenicity. The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the only trehalose import pathway in Mtb. Conformational dynamics of ABC transporters is an important feature to explain how they operate, but experimental structures are determined in a static environment. Therefore, a detailed transport mechanism cannot be elucidated because there is a lack of intermediate structures. Here, we used single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the Mycobacterium smegmatis (M. smegmatis) trehalose-specific importer LpqY-SugABC complex in five different conformations. These structures have been classified and reconstructed from a single cryo-EM dataset. This study allows a comprehensive understanding of the trehalose recycling mechanism in Mycobacteria and also demonstrates the potential of single-particle cryo-EM to explore the dynamic structures of other ABC transporters and molecular machines.

Molecular recognition of trehalose and trehalose analogues by Mycobacterium tuberculosis LpqY-SugABC.

Trehalose plays a crucial role in the survival and virulence of the deadly human pathogen Mycobacterium tuberculosis (Mtb). The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the sole pathway for trehalose to enter Mtb. The substrate-binding protein, LpqY, which forms a stable complex with the translocator SugABC, recognizes and captures trehalose and its analogues in the periplasmic space, but the precise molecular mechanism for this process is still not well understood. This study reports a 3.02-Å cryoelectron microscopy structure of trehalose-bound Mtb LpqY-SugABC in the pretranslocation state, a crystal structure of Mtb LpqY in a closed form with trehalose bound and five crystal structures of Mtb LpqY in complex with different trehalose analogues. These structures, accompanied by substrate-stimulated ATPase activity data, reveal how LpqY recognizes and binds trehalose and its analogues, and highlight the flexibility in the substrate binding pocket of LpqY. These data provide critical insights into the design of trehalose analogues that could serve as potential molecular probe tools or as anti-TB drugs.