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Feng, J.

Publications and source records attributed to Feng, J..

At least 91 records · Page 5Linked to original sources

CBAM-ResNet34-based classification and evaluation method for developmental processes of greenhouse strawberries

Strawberries, known for their economic significance and rich nutritional value, are cultivated extensively worldwide. However, a host of workers need to be employed every year to identify and categorize the developmental stages of the strawberries in the greenhouses, which is not only time-consuming, inefficient, increasing the cultivation cost, but also difficult to guarantee the classification accuracy. Meanwhile, affected by the complicated background, occlusions, and color interference, the features of strawberries are proven challenging to be extracted via the traditional neural networks due to serious gradient disappearance. Therefore, an improved CBAM-ResNet34- based classification evaluation method for developmental processes of greenhouse strawberries is investigated. The procedure of this method is as follows: firstly, the developmental stages of greenhouse strawberries are classified by experts into four stages: Stage I (initial stage), Stage II (green and white fruit stage), Stage III (early ripening stage), and Stage IV (fully ripe stage). The 627, 640, 604, and 340 strawberry images for these four stages are captured. Subsequently, the images are divided into training, validation, as well as testing sets and then undergo image pre- processing, expansion, and augmentation. Whereafter, the 7x7 convolution kernel in the first layer of the network is replaced by three consecutive 3x3 convolution cores to eliminate the redundant weights and unnecessary model parameters, and the BasicBlocks configuration is adjusted. Finally, the CBAM attention mechanism is added to each BasicBlock so as to pinpoint the spatial position of the strawberries and extract their major features such as shape, size, and color. Comparison experiments with the conventional deep neural networks LeNet5, AlexNet, VGG16, ResNet18, ResNet34, and every improved part of CBAM-ResNet34 demonstrated that when the learning rate is 0.001, the Dropout rate is 0.3, and the Adams weight decay parameter is 0.001, the accuracies for validation and testing sets can reach to 92.36% and 87.56% with F1 scores of 0.92, 0.87, 0.85 and 0.88.

plant biology↗

The mechanisms by which miRNAs critically contribute to differential roles of Nrf1 and Nrf2 in modulating the epithelial-mesenchymal transformation of hepatocellular carcinoma

Accumulation of various genetics and epigenetics alterations are accepted to result in the initiation and progression of hepatocellular carcinoma (HCC), and its high metastasis is viewed as a critical bottleneck leading to its treatment failure. Amongst them, the abnormal expression of several microRNAs arising from lack of antioxidant transcription factor Nrf2 (encoded by Nfe2l2) leads to cancer metastasis. However, much less known is about regulation of microRNAs by Nrf1 (encoded by Nfe2l1), even though it acts as an essential determinon of cell homeostasis by governing the transcriptional expression of those driver genes contributing to the epithelial-mesenchymal transition (EMT) involved in its metastasis. In this study, distinctive EMT phenotypes were unveiled to result from specific knockout of Nrf1 and Nrf2 in HepG2 cells, as accompanied by differential migratory and invasive capabilities. The Nrf1-/--leading EMT results from a significantly decrease in the epithelial CDH1 expression, plus another increased expression of the mesenchymal CDH2. Such distinct phenotypes of Nrf1-/- from Nrf2-/- cell lines were also attributable to differential regulation of two key microRNAs, i.e., miR3187-3P and miR1247-5p. Further experiments unraveled that Nrf1 activates the expression of miR-3187-3p, directly targeting for the inhibition of SNAI1, leading to CDH1 activation but CDH2 inhibition insomuch as to prevent the process of EMT. By contrast, Nrf2 inhibits the expression of miR1247-5p, relieving its inhibitory effect on MMP15 and MMP17 to promote the EMT. Collectively, these demonstrate that the EMT of liver cancer cells is likely prevented by Nrf1 via the miR3187-3P signaling to the SNAI1-CDH1/2 axis, but conversely promoted by Nrf2 through the miR1247-5p-MMP15/17 signaling axis.

molecular biology↗

Up sampled PSF enables high accuracy 3D super-resolution imaging with sparse sampling rate

Single-molecule localization microscopy (SMLM) provides nanoscale imaging, but pixel integration of acquired SMLM images limited the choice of sample rate which restricts the information content conveyed within each image. We propose an up-sampled point spread function (PSF) inverse modeling method for large-pixel single molecule localization, enabling precise 3D super-resolution imaging with sparse sampling rate. Our approach could reduce data volume or expand the field of view by nearly an order of magnitude, while maintaining high localization accuracy, greatly improving the imaging throughput with limited pixels offered by the existing cameras.

biophysics↗

Neuron-astrocyte Coupling in Lateral Habenula Mediates Depressive-like Behaviors

The lateral habenular (LHb) neurons and astrocytes have been strongly implicated in depression etiology but it was not clear how the two dynamically interact during depression onset. Here, using multi-brain-region calcium photometry recording in freely-moving mice, we discover that stress induces a unique, bimodal neuronal response and a most rapid astrocytic response in the LHb. LHb astrocytic calcium requires the 1A-adrenergic receptor, and depends on a recurrent neural network between the LHb and locus coeruleus (LC). Through the gliotransmitter glutamate and ATP/Adenosine, LHb astrocytes mediate the second-wave activation of local LHb neurons as well as release of norepinephrine (NE). Activation or inhibition LHb astrocytic calcium signaling facilitates or prevents stress-induced depressive-like behaviors respectively. These results identify a stress-induced positive feedback loop in the LHb-LC axis, with astrocytes being a critical signaling relay. The identification of this prominent neuron-glia interaction may shed light on stress management and depression prevention.

neuroscience↗

Dentate Gyrus Norepinephrine Ramping Facilitates Aversive Contextual Processing

Dysregulation in aversive contextual processing is believed to affect several forms of psychopathology, including post-traumatic stress disorder (PTSD). The dentate gyrus (DG) is an important brain region in contextual discrimination and disambiguation of new experiences from prior memories. The DG also receives dense projections from the locus coeruleus (LC), the primary source of norepinephrine (NE) in the mammalian brain, which is active during stressful events. However, how noradrenergic dynamics impact DG-dependent function during contextual discrimination and pattern separation remains unclear. Here, we report that aversive contextual processing in mice is linked to linear elevations in tonic norepinephrine release dynamics within the DG and report that this engagement of prolonged norepinephrine release is sufficient to produce contextual disambiguation, even in the absence of a salient aversive stimulus. These findings suggest that spatiotemporal ramping characteristics of LC-NE release in the DG during stress likely serve an important role in driving contextual processing.

neuroscience↗

Biocontrol efficiency and mechanism of novel Streptomyces luomodiensis SCA4-21 against banana Fusarium wilt

The soil-borne fungi Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes banana Fusarium wilt, which seriously threats global banana production. Biocontrol has been considered viable alternative method to manage banana Fusarium wilt. In previous study, we found that novel S. luomodiensis SCA4-21 exhibited antifungal activity. Here, we revealed that the extracts of strain SCA4-21 significantly inhibited the growth of Foc TR4 hyphae and spore germination, severely disrupting the ultrastructure of Foc TR4 hyphal cells and spore morphology. These extracts also exhibited broad-spectrum antifungal activity against eight other phytopathogenic fungi. Furthermore, we demonstrated that strain SCA4-21 produce 32 volatile organic compounds, including five antifungal compounds. In a pot experiment, we discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, achieving a biocontrol efficiency of 59.3%, and promoted the growth of banana seedlings. Additionally, this inoculation significantly enhanced the abundances of beneficial bacterial genera Streptomyces, Bacillus, Sphingomonas, and Massilia, as well as fungal genera Mortierella, Purpureocillium, Gibellulopsis, and Xenomyrothecium, while significantly reduced the abundances of pathogenic bacteria genus Pantoea and fungal genus Fusarium, in the banana rhizosphere soil. Moreover, the inoculation of strain SCA4-21 significantly increased the enrichment of pathways such as carbohydrate metabolism, amino acid metabolism, and metabolism of terpenoids and polyketides. Therefore, we postulated that strain SCA4-21 may synergistically combat banana Fusarium wilt by producing antifungal compounds and enriching beneficial bacteria and fungi. Our findings present a promising biocontrol agent for the management of banana Fusarium wilt. IMPORTANCEBanana (Musa spp.) is one of the most popular fruit crops and the fourth largest food crop in developing countries within tropical and subtropical regions. However, the emergence and rapid spread of strain Foc TR4 seriously hinder the development of banana industry. Currently, there is no effective control measure available. Biological control holds potential due to its safety and effectiveness. Here, we found that the extracts of S. luomodiensis SCA4-21 exhibited significant inhibitory effects on the hyphal growth and spore germination of Foc TR4, as well as severe destructive effects on its cell morphology and ultrastructure, and broad-spectrum antifungal activity. We also discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, reduced the incidence index of banana Fusarium wilt, promoted the growth of banana seedlings, and enhances beneficial microbes and metabolic pathways, suggesting that strain SCA4-21 is a promising biocontrol agent.

physiology↗

Genetic-Dependent Brain Signatures of Resilience: Interactions among Childhood Abuse, Genetic Risks and Brain Function

Resilience to emotional disorders is critical for adolescent mental health, especially following childhood abuse. Yet, brain signatures of resilience remain undetermined due to the differential susceptibility of the brains emotion processing system to environmental stresses. Analyzing brains responses to angry faces in a longitudinally large-scale adolescent cohort (IMAGEN), we identified two functional networks related to the orbitofrontal and occipital regions as candidate brain signatures of resilience. In girls, but not boys, higher activation in the orbitofrontal-related network was associated with fewer emotional symptoms following childhood abuse, but only when the polygenic burden for depression was high. This finding defined a genetic-dependent brain (GDB) signature of resilience. Notably, this GDB signature predicted subsequent emotional disorders in late adolescence, extending into early adulthood and generalizable to another independent prospective cohort (ABCD). Our findings underscore the genetic modulation of resilience-brain connections, laying the foundation for enhancing adolescent mental health through resilience promotion.

neuroscience↗

Regulation of Age-Related Lipid Metabolism in Ovarian Cancer

Although a lot of effort has been dedicated to ovarian cancer (OC) research, the mortality rate is still among the highest in female gynecologic malignancies. The effects of the aged tumor microenvironment are still being undermined despite age being the highest risk factor in ovarian cancer development and progression. In this study, we have conducted RNA sequencing and lipidomics analysis of gonadal adipose tissues from young and aged rat xenografts before and after ovarian cancer formation. We have found significantly higher tumor formation rates and volumes in aged OC xenograft rat models compared to their young counterparts (p<0.05), suggesting the aged adipose microenvironment (AME) is more susceptible to OC outgrowth. We have revealed significant shifts in the gene expression enrichment from groups of young vs. aged rats before tumor formation, groups of young vs. aged rats when the tumor formed, and groups of aged rats before and after tumor formation. We also observed shifts in the lipid components of the gonadal adipose tissues between young and aged rat xenografts when tumors were generated. Additionally, we found that the aged AME was associated with age-related changes in the immune cell composition, especially inflammation-related cells. The top hits showing the most differences between aged and young adipose tissues were eight genes including S100a8, S100a9, Il1rl1, Lcn2, C3, Hba-a1, Fcna, and Pnpla3, 22 lipids including multiple isoforms of free fatty acids (FFA) and triglyceride (TG), as well as four immune cells including neutrophil, myeloid dendritic cell, T cell CD4+ (non-regulatory), and mast cell activation. The functional correlation among S100a8, S100a9, neutrophil, and FFA (18:3) was also determined. Furthermore, FFA (18:3), which was shown to be downregulated in aged xenograft rats, was capable of inhibiting OC cell proliferation. In conclusion, our study suggested that aging promoted OC proliferation through changes in genes/pathways, lipid metabolism, and immune cells. Targeting the aging adipose microenvironment, particularly lipid metabolism reprogramming, holds promise as a therapeutic strategy for OC, which warrants further investigation. SignificanceAging microenvironment of OC may be regulated by S100a8 and S100a9 secreted by adipocytes, preadipocytes, or neutrophils through affecting the lipid metabolism, such as FFA (18:3).

cancer biology↗

Elucidating the Selection Mechanisms in Context-Dependent Computation through Low-Rank Neural Network Modeling

Humans and animals exhibit a remarkable ability to selectively filter out irrelevant information based on context. However, the neural mechanisms underlying this context-dependent selection process remain elusive. Recently, the issue of discriminating between two prevalent selection mechanisms-- input modulation versus selection vector modulation--with neural activity data has been highlighted as one of the major challenges in the study of individual variability underlying context-dependent decision-making (CDM). Here, we investigated these selection mechanisms through low-rank neural network modeling of the CDM task. We first showed that only input modulation was allowed in rank-one neural networks and additional dimensions of network connectivity were required to endow neural networks with selection vector modulation. Through rigorous information flow analysis, we gained a mechanistic understanding of why additional dimensions are required for selection vector modulation and how additional dimensions specifically contribute to selection vector modulation. This new understanding then led to the identification of novel neural dynamical signatures for selection vector modulation at both single neuron and population levels. Together, our results provide a rigorous theoretical framework linking network connectivity, neural dynamics and selection mechanisms, paving the way towards elucidating the circuit mechanisms when studying individual variability in context-dependent computation.

neuroscience↗

Three-dimension transcriptomics maps of whole mouse embryo during organogenesis

Understanding mammalian development heavily relies on classical animal models like the house mouse (Mus musculus). Advanced spatial transcriptomics has enabled biologists to break new ground in studies of molecular dynamics and cellular patterning during embryonic development with spatiotemporal resolution. To construct a comprehensive developmental trajectory, current three-dimensional (3D) spatial transcriptomic profiling leverages mouse embryos from gastrulation (E5.5) to organogenesis (E13.5) in continuity. However, a crucial phase for early organogenesis between E9.5 and E11.5 was deficient. To unveil the mystery of this stage, we present the 3D transcriptomics of mouse embryos at E9.5 and E11.5, with a widely applicable reconstruction workflow that bypasses sophisticated bioinformatic calculations. As our 3D atlas is generated at single-cell resolution, we demonstrate how organogenetic processes can be interpreted at different levels of granularity, from local cellular interactions to whole embryonic regionalization. We release the open-access database MOSTA3D (Mouse Organogenesis Spatiotemporal Transcriptomic Atlas in Three-dimensional) and hope a broader community will contribute to extending this framework from conception to senility in the near future.

developmental biology↗

FACT-(H3-H4) complex stimulates Pol activity to coordinate DNA synthesis with nucleosome assembly

Deficiencies in replication-coupled (RC) nucleosome assembly often lead to reduced DNA replication rate, but the precise mechanism underlying this process remains unsolved. Here, we discovered that H3-H4, but not H2A-H2B, mediates the interaction between FACT and the primase-polymerase complex DNA Pol . This interaction stimulates the DNA polymerase activity of Pol , and is indispensable for Okazaki fragment synthesis and replication fork progression. Moreover, the Pol1-N domain of Pol provides a specific binding site for FACT and H3-H4. Furthermore, CAF-1 and Rtt106-mediated replication-coupled nucleosome assembly pathways regulate this interaction. Together, we propose that the FACT-(H3-H4)-Pol interaction acts as a "Pre-Warning System" that regulates DNA replication, ensuring proper coordination between DNA synthesis and nucleosome assembly.

molecular biology↗

Cholecystokinin modulates age-dependent Thalamocortical Neuroplasticity

The thalamocortical pathways exhibit neuroplasticity not only during the critical period but also in adulthood. In this study, we investigated how cholecystokinin (CCK) modulates age-dependent thalamocortical plasticity. Our findings demonstrated that CCK is expressed in thalamocortical neurons and that high-frequency stimulation (HFS) of the thalamocortical pathway triggers the release of CCK in auditory cortex (ACx), as detected by a CCK sensor. HFS of the medial geniculate body (MGB) induced thalamocortical long-term potentiation (LTP) in wild-type young adult mice. However, knockdown of Cck expression in MGB neurons or blockade of the CCK-B receptor (CCKBR) in the ACx abolished HFS-induced LTP. Interestingly, this LTP could not be elicited in juvenile (3-week-old) or aged mice (over 18-month-old) due to distinct mechanisms: the absence of CCKBR in juveniles and the inability to release CCK in aged mice. Notably, exogenous administration of CCK into the ACx rescued LTP in aged mice and significantly improved frequency discrimination. These findings highlight the potential of CCK as a therapeutic intervention for ameliorating neuroplasticity deficits associated with thalamocortical connectivity.

neuroscience↗

Expression and characterization of the complete cyanophage genome PP in the heterologous host Synechococcus elongatus PCC 7942

Cyanophages are considered a promising biological management option for treating cyanobacterial blooms. Broadening the host range of cyanophages and/or shortening the lysis cycle by designing and synthesizing artificial cyanophages are potential strategies to enhance their effectiveness and efficiency. However, the rescue of artificial cyanophage genomes remains unexplored. In this study, we achieved the integration of a full-length cyanophage genome, PP, which originally infects Plectonema boryanum FACHB-240, into the model cyanobacterium Synechococcus elongatus PCC 7942. Since the integration of these large fragments ([~]42 kb) into cyanobacteria depended on conjugation via Escherichia coli, the toxic open reading frames (ORFs) of PP to E. coli were first identified, leading to the identification of toxic ORF6, ORF11, and ORF22. The original PP genome was then rearranged, and the three toxic ORFs were controlled using a tandem induction switch. The full length of the PP genome was integrated into the genome of S. elongatus PCC 7942 via two rounds of homologous recombination. Interestingly, compared to the control strain, the integration of the PP genome decreased photosynthesis and carbon fixation in S. elongatus PCC 7942, exhibiting cyanophage-like behavior. Transcriptomic analysis revealed that 32 of the 41 ORFs of the PP genome were transcribed in S. elongatus PCC 7942, significantly altering the energy metabolism and carbon fixation pathways. These influences were further demonstrated using metabolomics. This study provides a comprehensive approach for the artificial design and integration of cyanophage genomes in cyanobacteria, laying the foundation for their real rescue in the future.

synthetic biology↗

TCMNP: a data processing and visualization database and R package for traditional Chinese medicine network pharmacology

BackgroundNetwork pharmacology is pivotal for the study of the mechanism of action of traditional Chinese medicine (TCM). However, there are currently some challenges in data processing and visualization for traditional Chinese medicine network pharmacology (TCMNP). We develop the R-environment-based software database and package TCMNP. MethodsTCMNP is designed for the analysis and visualization of compositions in TCM compounds, herbs, ingredients, corresponding targets and pathway enrichment. Data analysis and visualization in R using "dplyr", "clusterProfiler", "ggplot2", and "circlize" packages, as well as functions of our own making. ResultsTCMNP is designed for the analysis and visualization of compositions in TCM compounds, herbs, ingredients, corresponding targets and pathway. The TCMNP database contains 571 kinds of TCM herbs, 17,118 ingredients, 10,013 diseases, and 15,956 targets. TCMNP simplifies the data analysis process and realizes a complete set of process operations from Chinese herbal compound composition, component and target automatic screening, enrichment analysis visualization, protein interaction and TF and target gene screening. Its built-in functions of various types provide a tidy interface for the visualization of TCM network pharmacology. TCMNP database is freely available at https://tcmlab.top/tcmr. TCMNP package is freely available at https://github.com/tcmlab/TCMNP. ConclusionThe TCMNP database and package provide a comprehensive overview of the interconnections between components of a TCM compound and its potential effects on disease treatment. TCMNP database is available for free at https://tcmlab.top/tcmr/. TCMNP package is available for free at https://github.com/tcmlab/TCMNP. We anticipate that TCMNP will help to explore the mechanism of TCM to treat diseases.

bioinformatics↗

Metabolic conservation by protein quality control in Campylobacter jejuni underlies the antibiotic tolerance

Bacterial persistence enables survival during lethal antibiotic exposure and is implicated in recurrent infections, yet the physiology underlying bacterial persistence in many pathogens remains poorly defined. Here we show that exposure of Campylobacter jejuni to ampicillin or ciprofloxacin generates an antibiotic-persistent subpopulation. Rather than undergoing global metabolic shutdown, persister cells adopted a metabolically constrained state characterized by selective maintenance of oxidative phosphorylation and bioenergetic metabolism through coordinated proteostasis control. The ATP-dependent protease ClpP was essential for entry into this persistent state. Loss of ClpP disrupted proteostasis of the electron transport chain, specifically impaired bd-like terminal oxidase integrity, and reduced survival in vivo and in macrophages. These findings identify ClpP-dependent maintenance of redox and bioenergetic homeostasis as critical determinants of C. jejuni persistence and highlight metabolic remodeling as a defining feature of antibiotic tolerance. These insights may inform future therapeutic strategies aimed at disrupting persistence and improving antibiotic efficacy.

microbiology↗

ADM: Adaptive Graph Diffusion for Meta-Dimension Reduction

Dimension reduction is ubiquitous in high dimensional data analysis. Divergent data characteristics have driven the development of various techniques in this field. Although individual techniques can capture specific aspects of data, they often struggle to grasp all the intricate and complex patterns and structures. To address this limitation, we introduce ADM (Adaptive graph Diffusion for Metadimension reduction), a novel meta-dimension reduction method grounded in graph diffusion theory. ADM integrates results from diverse dimension reduction techniques to leverage the unique strength of each individual technique. By employing dynamic Markov processes, ADM simulates information propagation for each dimension reduction result, thereby transforming traditional spatial measurements into dynamic diffusion distances. Importantly, ADM incorporates an adaptive mechanism to tailor the time scale of information diffusion according to sample-specific attributes. This improvement facilitates a more thorough exploration of the datasets overall structure and allows the heterogeneity among samples.

bioinformatics↗

A host enzyme reduces non-alcoholic fatty liver disease by inactivating intestinal lipopolysaccharide

The incidence of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) has been increasing world-wide. Since gut-derived bacterial lipopolysaccharides (LPS) can travel via the portal vein to the liver and play an important role in producing hepatic pathology, it seemed possible that (1) LPS stimulates hepatic cells to accumulate lipid, and (2) inactivating LPS can be preventive. Acyloxyacyl hydrolase (AOAH), the eukaryotic lipase that inactivates LPS and oxidized phospholipids, is produced in the intestine, liver, and other organs. We fed mice either normal chow or a high-fat diet for 28 weeks and found that Aoah-/- mice accumulated more hepatic lipid than did Aoah+/+ mice. In young mice, before increased hepatic fat accumulation was observed, Aoah-/-mouse livers increased their abundance of Sterol Regulatory Element-Binding Protein 1 (SREBP1) and the expression of its target genes that promote fatty acid synthesis. Aoah-/- mice also increased hepatic expression of CD36 and Fabp3, which mediate fatty acid uptake, and decreased expression of fatty acid oxidation-related genes Acot2 and Ppar-. Our results provide evidence that increasing AOAH abundance in the gut, bloodstream and/or liver may be an effective strategy for preventing or treating MASLD.

immunology↗

Neural correlates of device-based sleep characteristics in adolescents

Understanding the brain mechanisms underlying objective sleep patterns in adolescents and their implications for psychophysiological development is a complex challenge. Here, we applied sparse canonical correlation (sCCA) analysis on 3300 adolescents from Adolescent Brain Cognitive Development (ABCD) study, integrating extensive device-based sleep characteristics and multimodal imaging data. We revealed two sleep-brain dimensions: one characterized by later being asleep and shorter duration, linked to decreased subcortical-cortical network functional connectivities; the other showed higher heart rate and shorter light sleep duration, associated with lower brain volumes and decreased functional connectivities. Hierarchical clustering based on brain dimension associated with sleep characteristics revealed three biotypes of adolescents, marked by unique sleep profiles: biotype 1 exhibited delayed and shorter sleep, coupled with higher heart rate during sleep; biotype 3 with earlier and longer sleep, accompanied by lower heart rate; and biotype 2 with intermediate pattern. This biotypic differences also extended to cognition, academic attainment, brain structure and function in a gradient order. Longitudinal analysis demonstrated consistent biotypic differences from ages 9 to14, highlighting enduring cognitive and academic advantages in biotype3. The linked sleep-brain dimensions and the associated biotypes were well replicated in a longitudinal sample of 1271 individuals. Collectively, our novel findings delineate a linkage between objective sleep characteristics and developing brain in adolescents, underscoring their significance in cognitive development and academic attainment, which could serve as references for individuals with sleep difficulties and offer insights for optimizing sleep routines to enhance better cognitive development and school achievement.

neuroscience↗