The development of a vision-based phenotypic analysis algorithm for measuring spikelet-related traits in rice

Rice (Oryza sativa) and its production is of great importance to China’s food security. To assess its yield potential and grain quality, spikelet-related traits such as the number of spikelets per spike, seed coat color, spikelet length, width and length, and width ratio (W/L ratio) can be employed as key phenotypic evidence. Nevertheless, the present methods for spikelet-related trait analysis are still largely relying on manual counting or various post-harvest grain testing equipment, which is time-consuming, prone to error, and costly. Here, we present an original phenotypic analysis algorithm that can analyze key spikelet-based traits based on images collected by high-definition cameras, photo scanners, or smartphones, under both indoor and outdoor conditions. The vision-based algorithm combines automated image processing and deep learning techniques with domain knowledge in rice spikelet measurement, which does not require any prerequisites such as threshing or post-harvest processing. Besides the number of spikelets per spike, the algorithm can quickly detect and measure complete rice spikelets from the acquired images, quantifying spikelet-related traits such as grain length, grain width, W/L ratio, circularity, and grain coat color. We chose 18 rice varieties to verify the algorithm using images collected from indoor and in-field settings. Based on the trait analysis results, we examined correlations (i.e. the coefficient of determination, R2) between the computational and manual scoring for traits such as the number of spikelets per spike and concluded significant positive correlations: R2 =0.95 (P<0.001; n=4 930 spikelets, scored from indoor images), R2=0.88 (P<0.001; n=4 191, scored from indoor rice spikelets), R2=0.86 (P<0.001; n=2 490, scored from infield images), and R2=0.85 (P<0.001; n=2 645, scored from in-field rice spikelets). Additionally, we performed correlation analysis using the W/L ratio trait and concluded strong positive correlations, R2=0.84 (P<0.001; n=1 454, scored from indoor images) and R2=0.71 (P<0.001; n=726, scored from in-field images). Both correlations indicate a mechanistic link between the algorithm-derived traits and plant specialists’ scores. The above results suggest that the work presented here is reliable for automated phenotypic analysis of spikelet-related traits in rice. Furthermore, through cluster analysis, the 18 tested rice varieties can be reliably divided into four categories based on the spikelet-related trait analysis produced by our algorithm, similar to the clustering analysis results using manual scoring. This indicates that our work can be employed to enable the identification of phenotypic variation of these rice varieties, effectively. Hence, we trust our work can have a wide range of applications to provide an original, low-cost, accurate and generalized algorithmic solution for spikelet-related trait analysis in rice, enabling biological studies in this important research domain

Roles for heterodimerization of APJ and B2R in promoting cell proliferation via ERK1/2-eNOS signaling pathway

Apelin receptor (APJ) and bradykinin B2 receptor (B2R) play an important role in many physiological processes and share multiple similar characteristics in distribution and functions in the cardiovascular system. We first identified the endogenous expression of APJ and B2R in human umbilical vein endothelial cells (HUVECs) and their co-localization on human embryonic kidney (HEK) 293 cells membrane. A suite of bioluminescence and fluorescence resonance energy transfer (BRET and FRET), proximity ligation assay (PLA), and co-immunoprecipitation (Co-IP) was exploited to demonstrate formation of functional APJ and B2R heterodimer in HUVECs and transfected cells. Stimulation with apelin-13 and bradykinin (BK) increased the phosphorylation of the endothelial nitric oxide synthase (eNOS) in HUVECs, which could be inhibited by the silencing of APJ or B2R, indicating the APJ-B2R dimer is critical for eNOS phosphorylation in HUVECs. Furthermore, the increase of NOS and extracellular signal regulated kinases1/2 (ERK1/2) phosphorylation mediated by APJ/B2R dimer can be inhibited by U0126 and U73122, respectively, suggesting that the heterodimer might activate the PLC/ERK1/2/eNOS signaling pathway, and finally leading to a significant increase in cell proliferation. Thus, we uncovered for the first time the existence of APJ-B2R heterodimer and provided a promising new target in cardiovascular therapeutics

Construction and comprehensive analysis of a curoptosis-related lncRNA signature for predicting prognosis and immune response in cervical cancer

Cuproptosis (copper-ion-dependent cell death) is an unprogrammed cell death, and intracellular copper accumulation, causing copper homeostasis imbalance and then leading to increased intracellular toxicity, which can affect the rate of cancer cell growth and proliferation. This study aimed to create a newly cuproptosis-related lncRNA signature that can be used to predict survival and immunotherapy in patients with cervical cancer, but also to predict prognosis in patients treated with radiotherapy and may play a role in predicting radiosensitivity. First of all, we found lncRNAs associated with cuproptosis between cervical cancer tumor tissues and normal tissues. By LASSO-Cox analysis, overlapping lncRNAs were then used to construct lncRNA signatures associated with cuproptosis, which can be used to predict the prognosis of patients, especially the prognosis of radiotherapy patients, ROC curves and PCA analysis based on cuprotosis-related lncRNA signature and clinical signatures were developed and demonstrated to have good predictive potential. In addition, differences in immune cell subset infiltration and differences in immune checkpoint expression between high-risk and low-risk score groups were analyzed, and we investigated the relationship between this signature and tumor mutation burden. In summary, we constructed a lncRNA prediction signature associated with cuproptosis. This has important clinical implications, including improving the predictive value of cervical cancer patients and providing a biomarker for cervical cancer

Prevention of Wogonin on Colorectal Cancer Tumorigenesis by Regulating p53 Nuclear Translocation

The tumor suppressor protein p53 plays an important role in the development and progression of colon cancer, and the subcellular organelle localization directly affects its function. Wogonin (5,7-dihydroxy-8-methoxyflavone), a mono-flavonoid extracted from root of Scutellaria baicalensis Georgi, possesses acceptable toxicity and has been used in colorectal cancer (CRC) chemoprevention in pre-clinical trials by oncologist. However, the underlying anti-colon cancer mechanisms of wogonin are not yet fully understood. In the present study, the effect of wogonin on the initiation and development of colitis-associated cancer through p53 nuclear translocation was explored. AOM-DSS CRC animal model and human CRC HCT-116 cell model were used to evaluate the in vivo and in vitro anti-colon cancer action of wogonin. We observed that wogonin showed a dramaticlly preventive effect on colon cancer. Our results showed that wogonin caused apoptotic cell death in human CRC HCT-116 cell through increased endoplasmic reticulum (ER) stress. Meanwhile, excessive ER stress facilitated the cytoplasmic localization of p53 through increasing phosphor-p53 at S315 and S376 sites, induced caspase-dependent apoptosis and inhibited autophagy. Furthermore, we verified the chemoprevention effect and toxicity of wogonin in vivo by utilizing an AOM-DSS colon cancer animal model. We found that wogonin not only reduced tumor multiplicity, preserved colon length to normal (6.79 ± 0.34 to 7.41 ± 0.56, P &lt; 0.05) but also didn’t induce side effects on various organs. In conclusion, these results explain the anti-tumor effect of wogonin in CRC and suggest wogonin as a potential therapeutic candidate for the therapeutic strategy in CRC treatment

Analysis of Genomic and Immune Intratumor Heterogeneity in Linitis Plastica via Multiregional Exome and T-Cell Receptor Sequencing

The molecular landscape and the intratumor heterogeneity (ITH) architecture of gastric linitis plastica (LP) are poorly understood. We performed whole-exome sequencing (WES) and T-cell receptor (TCR) sequencing on 40 tumor regions from four LP patients. The landscape and ITH at the genomic and immunological levels in LP tumors were compared with multiple cancers that have previously been reported. The lymphocyte infiltration was further assessed by immunohistochemistry (IHC) in LP tumors. In total, we identified 6339 non-silent mutations from multi-samples, with a median tumor mutation burden (TMB) of 3.30 mutations per Mb, comparable to gastric adenocarcinoma from the Cancer Genome Atlas (TCGA) cohort (P = 0.53). An extremely high level of genomic ITH was observed, with only 12.42%, 5.37%, 5.35%, and 30.67% of mutations detectable across 10 regions within the same tumors of each patient, respectively. TCR sequencing revealed that TCR clonality was substantially lower in LP than in multi-cancers. IHC using antibodies against CD4, CD8, and PD-L1 demonstrated scant T-cell infiltration in the four LP tumors. Furthermore, profound TCR ITH was observed in all LP tumors, with no T-cell clones shared across tumor regions in any of the patients, while over 94% of T-cell clones were restricted to individual tumor regions. The Morisita overlap index (MOI) ranged from 0.21 to 0.66 among multi-regions within the same tumors, significantly lower than that of lung cancer (P = 0.002). Our results show that LP harbored extremely high genomic and TCR ITH and suppressed T-cell infiltration, suggesting a potential contribution to the frequent recurrence and poor therapeutic response of this adenocarcinoma

Carotenoid accumulation during tomato fruit ripening is modulated by the auxin-ethylene balance

Background : Tomato fruit ripening is controlled by ethylene and is characterized by a shift in color from green to red, a strong accumulation of lycopene, and a decrease in β-xanthophylls and chlorophylls. The role of other hormones, such as auxin, has been less studied. Auxin is retarding the fruit ripening. In tomato, there is no study of the carotenoid content and related transcript after treatment with auxin. Results : We followed the effects of application of various hormone-like substances to “Mature-Green” fruits. Application of an ethylene precursor (ACC) or of an auxin antagonist (PCIB) to tomato fruits accelerated the color shift, the accumulation of lycopene, α-, β-, and δ-carotenes and the disappearance of β-xanthophylls and chlorophyll b. By contrast, application of auxin (IAA) delayed the color shift, the lycopene accumulation and the decrease of chlorophyll a. Combined application of IAA + ACC led to an intermediate phenotype. The levels of transcripts coding for carotenoid biosynthesis enzymes, for the ripening regulator Rin, for chlorophyllase, and the levels of ethylene and abscisic acid (ABA) were monitored in the treated fruits. Correlation network analyses suggest that ABA, may also be a key regulator of several responses to auxin and ethylene treatments. Conclusions : The results suggest that IAA retards tomato ripening by affecting a set of (i) key regulators, such as Rin, ethylene and ABA, and (ii) key effectors, such as genes for lycopene and β-xanthophyll biosynthesis and for chlorophyll degradation

When politeness processing encounters failed syntactic/semantic processing

Previous studies have elucidated the neural mechanism of syntactic/semantic processing and pragmatic processing. However, the exact mechanisms by which these two aspects of processing interact during language comprehension remain unknown. In this event-related brain potential study, we examined the interaction between politeness processing and local syntactic/semantic processing of a phrase. We used a full factorial design that crossed politeness consistency with local syntactic/semantic coherence. Politeness violations elicited a P200 effect in the 190–320 ms range, centro-parietally distributed positivity in the 360–866 ms range, and pure local syntactic/semantic violation elicited a broad distributed positivity in the 362–868 ms range. Crucially, we found that event-related potential responses elicited by combined politeness and syntactic/semantic violations resemble those elicited by separate syntactic/semantic violations. These results indicated that local syntactic/semantic processing has a functional primacy over politeness processing. Furthermore, our results support the blocking hypothesis from a politeness processing perspective instead of the independent hypothesis

Reward expectation regulates brain responses to task-relevant and task-irrelevant emotional words: ERP evidence

We investigated the effect of reward expectation on the processing of emotional words in two experiments using event-related potentials (ERPs). A cue indicating the reward condition of each trial (incentive vs non-incentive) was followed by the presentation of a negative or neutral word, the target. Participants were asked to discrim inate the emotional content of the target word in Experiment 1 and to discriminate the color of the target word in Experiment 2, rendering the emotionality of the target word task-relevant in Experiment 1, but task-irrelevant in Experiment 2. The negative bias effect, in terms of the amplitude difference between ERPs for negative and neutral targets, was modulated by the task-set. In Experiment 1, P3(1) and early posterior negativity revealed a larger negative bias effect in the incentive condition than that in the non-incentive condition. However, in Experiment 2, P3(1) revealed a diminished negative bias effect in the incentive condition compared with that in the non-incentive condition. These results indicate that reward expectation improves top-down attentional concentration to task-relevant information, with enhanced sensitivity to the emotional content of target words when emotionality is task-relevant, but with reduced differential brain responses to emotional words when their content is task-irrelevant