Environmental changes impact on vegetables physiology and nutrition - Gaps between vegetable and cereal crops.

Projected changes in climate patterns, increase of weather extreme, water scarcity, and land degradation are going to challenge agricultural production and food security. Currently, studies concerning effects of climate change on agriculture mainly focus on yield and quality of cereal crops. In contrast, there has been little attention on the effects of environmental changes on vegetables that are necessary and key nutrition component for human beings, but quite sensitive to these climatic changes. Therefore, we reviewed the main changes of environmental factors under the current scenario as well as the impacts of these factors on the physiological responses and nutritional alteration of vegetables and the key findings based on modelling. The gaps between cereal crops and vegetables were pinpointed and the actions to take in the future were proposed. The review will enhance our understanding concerning the effects of environmental changes on production, physiological responses, nutrition, and modelling of vegetable plants.

Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot.

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.

Disrupted gut microecology after high-dose 131I therapy and radioprotective effects of arachidonic acid supplementation.

BACKGROUND: Despite the potential radiotoxicity in differentiated thyroid cancer (DTC) patients with high-dose 131I therapy, the alterations and regulatory mechanisms dependent on intestinal microecology remain poorly understood. We aimed to identify the characteristics of the gut microbiota and metabolites in DTC patients suffering from high-dose 131I therapy and explore the radioprotective mechanisms underlying arachidonic acid (ARA) treatment. METHODS: A total of 102 patients with DTC were recruited, with fecal samples collected before and after 131I therapy for microbiome and untargeted and targeted metabolomic analyses. Mice were exposed to total body irradiation with ARA replenishment and antibiotic pretreatment and were subjected to metagenomic, metabolomic, and proteomic analyses. RESULTS: 131I therapy significantly changed the structure of gut microbiota and metabolite composition in patients with DTC. Lachnospiraceae were the most dominant bacteria after 131I treatment, and metabolites with decreased levels and pathways related to ARA and linoleic acid were observed. In an irradiation mouse model, ARA supplementation not only improved quality of life and recovered hematopoietic and gastrointestinal systems but also ameliorated oxidative stress and inflammation and preserved enteric microecology composition. Additionally, antibiotic intervention eliminated the radioprotective effects of ARA. Proteomic analysis and ursolic acid pretreatment showed that ARA therapy greatly influenced intestinal lipid metabolism in mice subjected to irradiation by upregulating the expression of hydroxy-3-methylglutaryl-coenzyme A synthase 1. CONCLUSION: These findings highlight that ARA, as a key metabolite, substantially contributes to radioprotection. Our study provides novel insights into the pivotal role that the microbiota-metabolite axis plays in radionuclide protection and offers effective biological targets for treating radiation-induced adverse effects.

Integrated microbiome and metabolome analysis reveals a distinct microbial and metabolic signature in Graves' disease and hypothyroidism.

Recent studies reveal that imbalanced microbiota is related to thyroid diseases. However, studies on the alterations in fecal metabolites in Graves' disease and clinical hypothyroidism patients are insufficient. Here, we identified 21 genera and 53 metabolites that were statistically significant among Graves' disease patients, hypothyroidism patients, and controls integrating microbiome and untargeted metabolome analysis. Disease groups revealed a decreased abundance in butyrate-producing microbiota and an increased abundance in potentially pathogenic microbiota. Lipids molecules were the major differential metabolites identified in all fecal samples. Network analysis recognized that microbiota may affect thyroid function by targeting specific metabolites. We further identified specific microbiota and metabolites that could distinguish Graves' disease patients, hypothyroidism patients, and controls. Our study reveals a distinct microbial and metabolic signature in hypothyroidism patients and Graves' disease patients and further validates the potential role of microbiota in thyroid diseases, providing new ideas for future research into the etiology and clinical intervention of thyroid diseases.

A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa.

Chaenomeles speciosa (2n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.

ROS-mediated waterlogging memory, induced by priming, mitigates photosynthesis inhibition in tomato under waterlogging stress.

With global climate change, the frequency and intensity of waterlogging events are increasing due to frequent and heavy precipitation. Little is known however about the response of plants to repeated waterlogging stress events. The aim is to clarify physiological regulation mechanisms of tomato plants under repeated waterlogging stress, and whether Trichoderma harzianum can alleviate waterlogging injury. We identified two genotypes of tomato, 'MIX-002' and 'LA4440', as waterlogging tolerant and sensitive genotypes, respectively, based on plant biomass accumulation. The two tomato genotypes were subjected to a waterlogging priming treatment for 2 days (excess water for 1 cm above substrate surface) followed by a recovery stage for 2 days, and then a second waterlogging stress for 5 days (excess water for 1 cm above substrate surface) followed by a second recovery stage for 3 days. Leaf physiological, plant growth parameters, and the expression of five key genes were investigated. We found that the two genotypes responded differently to waterlogging priming and stress in terms of photosynthesis, reactive oxygen species (ROS), and osmotic regulatory mechanisms. Waterlogging stress significantly increased H2O2 content of 'MIX-002', while that of 'LA4440' had no significant change. Under waterlogging stress, photosynthesis of the two genotypes treated with waterlogging priming returned to the control level. However, Trichoderma harzianum treatment during the second recovery stage did not show positive mitigative effects. The plants of 'LA4440' with priming showed lower peroxidase (POD) activity and proline content but higher H2O2 content than that without priming under waterlogging stress. Under waterlogging stress with priming as compared to without priming, SODCC2 was downregulated in two tomatoes, and AGR2 and X92888 were upregulated in 'MIX-002' but downregulated in 'LA4440'. Overall, the two tomato genotypes exhibited distinct photosynthetic, ROS and osmotic regulatory mechanisms responding to the waterlogging stress. Waterlogging priming can induce stress memory by adjusting stomatal conductance, sustaining ROS homeostasis, regulating osmotic regulatory substances and key gene expressions mediated by H2O2, and thus alleviate the damage on tomato photosynthesis when waterlogging reoccurred.

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber.

Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.

CCL22 and CCL26 are potential biomarkers for predicting distant metastasis in thyroid carcinoma.

OBJECTIVES: Chemokines have been suggested to play significant roles in the progression of malignant cancers. This study aimed to identify the chemokines related to malignant progression in thyroid carcinoma. METHODS: The mRNA expression levels of 52 chemokines were compared between differentiated thyroid cancer (DTC) samples and normal thyroid tissues from The Cancer Genome Atlas database; survival analysis was then performed on the basis of differentially expressed chemokines. A retrospective study was conducted on the level of differentially expressed chemokines in 76 DTC patients. Functional pathway analysis was performed to explore chemokine-related regulatory mechanisms. RESULTS: We identified 20 chemokines with differentially expressed mRNA levels through publicly available data. High levels of CCL22 and CCL26 were found to be related with metastasis in clinical DTC samples. High levels of CCL22 were found to be significantly related to poor prognosis in DTC patients. Pathway analyses revealed that cytokines might affect cancer progression through cytokine-cytokine receptor and cytokine-interleukin interactions. CONCLUSIONS: CCL22 and CCL26 could serve as prognostic biomarkers in thyroid carcinoma.

Effect of low-dose radiation on thyroid function and the gut microbiota.

BACKGROUND: The thyroid-gut axis has a great influence on the maintenance of human health; however, we know very little about the effects of low-dose ionizing radiation (LDR) on thyroid hormone levels and gut microbiota composition. AIM: To investigate the potential effects of low-dose X-ray radiation to male C57BL/6J mice. METHODS: Peripheral blood was collected for enzyme-linked immunosorbent assay (ELISA), and stool samples were taken for 16S ribosomal RNA (rRNA) gene sequencing after irradiation. RESULTS: We found that LDR caused changes in thyroid stimulating hormone (TSH) levels in the irradiated mice, suggesting a dose-dependent response in thyroid function to ionizing radiation. No changes in the diversity and richness of the gut microbiota were observed in the LDR-exposed group in comparison to the controls. The abundance of Moraxellaceae and Enterobacteriaceae decreased in the LDR-exposed groups compared with the controls, and the Lachnospiraceae abundance increased in a dose-dependent manner in the radiated groups. And the abundances of uncultured_bacterium_g_Acinetobacter, uncultured_bacterium_ o_Mollicutes_RF39, uncultured_bacterium_g_Citrobacter, and uncultured_ bacterium_g_Lactococcus decreased in the radiated groups at the genus level, which showed a correlation with radiation exposure and diagnostic efficacy. Analysis of functional metabolic pathways revealed that biological metabolism was predicted to have an effect on functional activities, such as nucleotide metabolism, carbohydrate metabolism, and glycan biosynthesis and metabolism. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway annotation also suggested that changes in the gut microbiota were related to processing functions, including translation, replication and repair. CONCLUSION: LDR can change thyroid function and the gut microbiota, and changes in the abundances of bacteria are correlated with the radiation dose.

Dominant and Priming Role of Waterlogging in Tomato at e[CO2] by Multivariate Analysis.

The frequency of waterlogging episodes has increased due to unpredictable and intense rainfalls. However, less is known about waterlogging memory and its interaction with other climate change events, such as elevated CO2 concentration (e[CO2]). This study investigated the combined effects of e[CO2] and two rounds of waterlogging stress on the growth of cultivated tomato (Solanum lycopersicum) and wild tomato (S. pimpinellifolium). The aim is to elucidate the interaction between genotypes and environmental factors and thereby to improve crop resilience to climate change. We found that two rounds of treatments appeared to induce different acclimation strategies of the two tomato genotypes. S. pimpinellifolium responded more negatively to the first-time waterlogging than S. lycopersicum, as indicated by decreased photosynthesis and biomass loss. Nevertheless, the two genotypes respond similarly when waterlogging stress recurred, showing that they could maintain a higher leaf photosynthesis compared to single stress, especially for the wild genotype. This showed that waterlogging priming played a positive role in stress memory in both tomato genotypes. Multivariate analysis showed that waterlogging played a dominant role when combined with [CO2] for both the cultivated and wild tomato genotypes. This work will benefit agricultural production strategies by pinpointing the positive effects of e[CO2] and waterlogging memory.

Transcriptomic and Physiological Analyses Reveal Potential Genes Involved in Photoperiod-Regulated ß-Carotene Accumulation Mechanisms in the Endocarp of Cucumber (Cucumis sativus L.) Fruit.

The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit ß-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with ß-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced ß-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, ß-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces ß-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.

Evaluation and analysis of anxiety and depression symptoms for college students during COVID-19 pandemic.

BACKGROUND: The mental health of students is affected by COVID-19. We aim to evaluate the anxiety and depression symptoms among college students during COVID-19 pandemic, analyze the influence factors that contribute to college students' anxiety and depression symptoms, and provide some suggestions for improving the mental health of college students. METHODS: With 179 college students participating, an online questionnaire consisting of a general questionnaire, Generalized Anxiety Disorder (GAD-7), and Patient Health Questionnaire (PHQ-9) was conducted in universities in Shanghai. The anxiety and depression symptoms among college students were evaluated using GAD-7 and PHQ-9 scales, and influence factors were analyzed using an unordered multi-class Logistic regression model. RESULTS: The reliability and validity of the GAD-7 and PHQ-9 scales were good (reliability ≥ 0.9, validity = 100%). The incidence of anxiety was 32.4%, of which were 23.5%, 8.4%, and 0.6% in mild, moderate, and severe, respectively; and the incidence of depression was 46.40%, of which in mild, moderate, moderate to severe, and severe were 28.5%, 10.1%, 7.3%, and 0.6%, respectively. Multivariate analysis revealed that male students with strong psychological quality, who were not easily affected by the COVID-19 pandemic, who received less negative or false information, and who had a strong grasp of psychology and related knowledge were less likely to suffer from mild or moderate anxiety symptoms [OR (95% CI) 0.18 (0.04, 0.81), 0.12 (0.05, 0.33), 0.23 (0.06, 0.89) and 0.07 (0.01, 0.74)]. Furthermore, college students who were not affected by the COVID-19 pandemic were less likely to suffer from mild, moderate, and moderate to severe depression symptoms [OR (95% CI) 0.23 (0.08, 0.65), 0.22 (0.05, 0.93), 0.10 (0.02, 0.54)]. CONCLUSION: The GAD-7 and PHQ-9 scales are suitable for evaluating anxiety and depression symptoms in college students. The COVID-19 pandemic was associated with a high incidence of anxiety and depression symptoms among college students, although gender and mental state fluctuations during the pandemic, negative and false information, and exposure to psychology and related courses were the main influencing factors.

Alterations of Gut Microbiome and Metabolite Profiles Associated With Anabatic Lipid Dysmetabolism in Thyroid Cancer.

Background: Currently, the high morbidity of individuals with thyroid cancer (TC) is an increasing health care burden worldwide. The aim of our study was to investigate the relationship among the gut microbiota community, metabolites, and the development of differentiated thyroid cancer. Methods: 16S rRNA gene sequencing and an integrated LC-MS-based metabolomics approach were performed to obtain the components and characteristics of fecal microbiota and metabolites from 50 patients with TC and 58 healthy controls (HCs). Results: The diversity and richness of the gut microbiota in the TC patients were markedly decreased. The composition of the gut microbiota was significantly altered, and the Bacteroides enterotype was the dominant enterotype in TC patients. Additionally, the diagnostic validity of the combined model (three genera and eight metabolites) and the metabolite model (six metabolites) were markedly higher than that of the microbial model (seven genera) for distinguishing TC patients from HCs. LEfSe analysis demonstrated that genera (g_Christensenellaceae_R-7_group, g_Eubacterium_coprostanoligenes_group) and metabolites [27-hydroxycholesterol (27HC), cholesterol] closely related to lipid metabolism were greatly reduced in the TC group. In addition, a clinical serum indicator (total cholesterol) and metabolites (27HC and cholesterol) had the strongest influence on the sample distribution. Furthermore, functional pathways related to steroid biosynthesis and lipid digestion were inhibited in the TC group. In the microbiota-metabolite network, 27HC was significantly related to metabolism-related microorganisms (g_Christensenellaceae_R-7_group). Conclusions: Our research explored the characteristics of the gut microecology of patients with TC. The findings of this study will help to discover risk factors that affect the occurrence and development of TC in the intestinal microecology.

Genome-Wide Identification of the B-Box Gene Family and Expression Analysis Suggests Their Potential Role in Photoperiod-Mediated ß-Carotene Accumulation in the Endocarp of Cucumber (Cucumis sativus L.) Fruit.

Carotenoids are indispensable to plants and essential for human nutrition and health. Carotenoid contents are strongly influenced by light through light-responsive genes such as B-Box (BBX) genes. BBX proteins, a class of zinc-finger transcription factors, mediate many light-signaling pathways, leading to the biosynthesis of important metabolites in plants. However, the identification of the BBX gene family and expression analysis in response to photoperiod-mediated carotenoid accumulation in cucumber remains unexplored. We performed a genome-wide study and determined the expression of cucumber BBX genes (hereafter referred to as CsaBBXs genes) in the endocarp of Xishuangbanna cucumber fruit (a special type of cucumber accumulating a high level of ß-carotene in the endocarp) using an RNA-seq analysis of plants previously subjected to two photoperiodic conditions. Here, 26 BBX family genes were identified in the cucumber genome and named serially CsaBBX1 through CsaBBX26. We characterized CsaBBX genes in terms of their phylogenetic relationships, exon-intron structures, cis-acting elements, and syntenic relationships with Arabidopsis thaliana (L.) Heynh. RNA-seq analysis revealed a varied expression of CsaBBX genes under photoperiod treatment. The analysis of CsaBBXs genes revealed a strong positive correlation between CsaBBX17 and carotenoid biosynthetic pathway genes (phytoene synthase, ζ-carotene desaturase, lycopene ε-cyclase, ß-carotene hydroxylase-1), thus suggesting its involvement in ß-carotene biosynthesis. Additionally, nine CsaBBX genes (CsaBBX 4,5,7,9,11, 13,15,17 and 22) showed a significant positive correlation with ß-carotene content. The selected CsaBBX genes were verified by qRT-PCR and confirmed the validity of RNA-seq data. The results of this study established the genome-wide analysis of the cucumber BBX family and provide a framework for understanding their biological role in carotenoid accumulation and photoperiodic responses. Further investigations of CsaBBX genes are vital since they are promising candidate genes for the functional analysis of carotenoid biosynthesis and can provide genetic tools for the molecular breeding of carotenoids in plants.

Salinity, waterlogging, and elevated [CO2] interact to induce complex responses in cultivated and wild tomato.

The effects of individual climatic factors on crops are well documented, whereas the interaction of such factors in combination has received less attention. The frequency of salinity and waterlogging stress is increasing with climate change, accompanied by elevated CO2 concentration (e[CO2]). This study explored how these three variables interacted and affected two tomato genotypes. Cultivated and wild tomato (Solanum lycopersicum and Solanum pimpinellifolium) were grown at ambient [CO2] and e[CO2], and subjected to salinity, waterlogging, and combined stress. Leaf photosynthesis, chlorophyll fluorescence, quenching analysis, pigment, and plant growth were analyzed. The response of tomatoes depended on both genotype and stress type. In cultivated tomato, photosynthesis was inhibited by salinity and combined stress, whereas in wild tomato, both salinity and waterlogging stress, alone and in combination, decreased photosynthesis. e[CO2] increased photosynthesis and biomass of cultivated tomato under salinity and combined stress compared with ambient [CO2]. Differences between tomato genotypes in response to individual and combined stress were observed in key photosynthetic and growth parameters. Hierarchical clustering and principal component analysis revealed genetic variations of tomatoes responding to the three climatic factors. Understanding the interacting effects of salinity and waterlogging with e[CO2] in tomato will facilitate improvement of crop resilience to climate change.

Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops.

The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.

Deep Learning for the Automatic Diagnosis and Analysis of Bone Metastasis on Bone Scintigrams.

OBJECTIVE: To develop an approach for automatically analyzing bone metastases (BMs) on bone scintigrams based on deep learning technology. METHODS: This research included a bone scan classification model, a regional segmentation model, an assessment model for tumor burden and a diagnostic report generation model. Two hundred eighty patients with BMs and 341 patients with non-BMs were involved. Eighty percent of cases were randomly extracted from two groups as training set. Remaining cases were as testing set. A deep residual convolutional neural network with different structures was used to determine whether metastatic bone lesions existed, regions of lesions were automatically segmented. Bone scan tumor burden index (BSTBI) was calculated; finally, diagnostic report could be automatically generated. The sensitivity, specificity and accuracy of classification model were compared with three physicians with different clinical experience. The Dice coefficient evaluated the effect of segmentation model and compared to the result of nnU-Net model. The correlation between BSTBI and blood alkaline phosphatase (ALP) level was analyzed to verify the efficiency of BSTBI. The performance of report generation model was evaluated by the accuracy of interpretation of report. RESULTS: In testing set, the sensitivity, specificity and accuracy of classification model were 92.59%, 85.51% and 88.62%, respectively. The accuracy showed no statistical difference with moderately and experienced physicians and obviously outperformed the inexperienced. The Dice coefficient of BMs area was 0.7387 in segmentation stage. Based on the whole model frame, our segmentation model outperformed the nnU-Net. BSTBI value changed as the BMs changed. There was a positive correlation between BSTBI and ALP level. The accuracy of report generation model was 78.05%. CONCLUSION: Deep learning based on automatic analysis frameworks for BMs can accurately identify BMs, preliminarily realize a fully automatic analysis process from raw data to report generation. BSTBI can be used as a quantitative evaluation indicator to assess the effect of therapy on BMs in different patients or in the same patient before and after treatment.

Gut microbiota changes and its potential relations with thyroid carcinoma.

Introduction: Emerging evidence suggests that the essence of life is the ecological balance of the neural, endocrine, metabolic, microbial, and immune systems. Gut microbiota have been implicated as an important factor affecting thyroid homeostasis. Objectives: This study aims to explore the relationship between gut microbiota and the development of thyroid carcinoma. Methods: Stool samples were collected from 90 thyroid carcinoma patients (TCs) and 90 healthy controls (HCs). Microbiota were analyzed using 16S ribosomal RNA gene sequencing. A cross-sectional study of an exploratory cohort of 60 TCs and 60 HCs was conducted. The gut microbiota signature of TCs was established by LEfSe, stepwise logistic regression, lasso regression, and random forest model analysis. An independent cohort of 30 TCs and 30 HCs was used to validate the findings. Functional prediction was achieved using Tax4Fun and PICRUSt2. TC patients were subsequently divided into subgroups to analyze the relationship between microbiota and metastatic lymphadenopathy. Results: In the exploratory cohorts, TCs had reduced richness and diversity of gut microbiota compared to HCs. No significant difference was found between TCs and HCs on the phylum level, though 70% of TCs had increased levels of Proteobacteria-types based on dominant microbiota typing. A prediction model of 10 genera generated with LEfSe analysis and lasso regression distinguished TCs from HCs with areas under the curves of 0.809 and 0.746 in the exploration and validation cohorts respectively. Functional prediction suggested that the microbial changes observed in TCs resulted in a decline in aminoacyl-tRNA biosynthesis, homologous recombination, mismatch repair, DNA replication, and nucleotide excision repair. A four-genus microbial signature was able to distinguish TC patients with metastatic lymphadenopathy from those without metastatic lymphadenopathy. Conclusion: Our study shows that thyroid carcinoma patients demonstrate significant changes in gut microbiota, which will help delineate the relationship between gut microbiota and TC pathogenesis.

Analysis of Genetic Alterations Related to DNA Methylation in Testicular Germ Cell Tumors Based on Data Mining.

Embryonal carcinoma (EC) and seminoma (SE) are both derived from germ cell neoplasia in situ but show big differences in growth patterns and clinical prognosis. Epigenetic regulation may play an important role in the development of EC and SE. This study investigated the DNA methylation-based genetic alterations between EC and SE by analyzing the datasets of mRNA expression and DNA methylation profiling. The datasets were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified between EC and SE by limma package in R environment. Gene function enrichment analysis of the DEGs was performed on the DAVID tool, the results of which suggested differences in capability of pluripotency and genomic stability between EC and SE. The minfi package and wANNOVAR tool were used to identify differentially methylated genes. A total of 37 genes were discovered with both mRNA expression and the accordant DNA methylation changes. The findings were verified by the sequencing data from The Cancer Genome Atlas database, and Kaplan-Meier survival analysis was performed. Finally, 5 genes (PRDM1, LMO2, FAM53B, HCN4, and FAM124B) were found that showed both low expression and high methylation in EC, and were significantly associated with relapse-free survival. The findings of methylation-based genetic features between EC and SE might be helpful in studying the role of DNA methylation in cancer development.