Transcriptome analysis reveals key genes involved in the resistance to Cryphonectria parasitica during early disease development in Chinese chestnut

BACKGROUND

Chestnut blight, one of the most serious branch diseases in Castanea caused by Cryphonectria parasitica, which has ravaged across American chestnut and most of European chestnut since the early twentieth century. Interestingly, the Chinese chestnut is strongly resistant to chestnut blight, shedding light on restoring the ecological status of Castanea plants severely affected by chestnut blight. To better explore the early defense of Chinese chestnut elicited in response to C. parasitica, the early stage of infection process of C. parasitica was observed and RNA sequencing-based transcriptomic profiling of responses of the chestnut blight-resistant wild resource 'HBY-1' at 0, 3 and 9 h after C. parasitica inoculation was performed.

RESULTS

First, we found that 9 h was a critical period for Chinese chestnut infected by C. parasitica, which was the basis of further study on transcriptional activation of Chinese chestnut in response to chestnut blight in the early stage. In the transcriptome analysis, a total of 283 differentially expressed genes were identified between T9 h and Mock9 h, and these DEGs were mainly divided into two clusters, one of which was metabolism-related pathways including biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, and photosynthesis; the other was related to plant-pathogen interaction and MAPK signal transduction. Meanwhile, the two clusters of pathways could be connected through junction among phosphatidylinositol signaling system, phytohormone signaling pathway and α-Linolenic acid metabolism pathway. It is worth noting that genes associated with JA biosynthesis and metabolic pathway were significantly up-regulated, revealing that the entire JA metabolic pathway was activated in Chinese chestnut at the early stage of chestnut blight infection.

CONCLUSION

We identified the important infection nodes of C. parasitica and observed the morphological changes of Chinese chestnut wounds at the early stage of infection. In response to chestnut blight, the plant hormone and MAPK signal transduction pathways, plant-pathogen interaction pathways and metabolism-related pathways were activated at the early stage. JA biosynthesis and metabolic pathway may be particularly involved in the Chinese chestnut resistance to chestnut blight. These results contributes to verifying the key genes involved in the resistance of Chinese chestnut to C. parasitica.

RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer

Tumors with mutations in chromatin regulators present attractive targets for DNA hypomethylating agent 5-aza-2'-deoxycytidine (DAC) therapy, which further disrupts cancer cells' epigenomic fidelity and reactivates transposable element (TE) expression to drive viral mimicry responses. SETD2 encodes a histone methyltransferase (H3K36me3) and is prevalently mutated in advanced kidney cancers. Here, we show that SETD2-mutant kidney cancer cells are especially sensitive in vitro and in vivo to DAC treatment. We find that the viral mimicry response are direct consequences of mis-splicing events, such as exon inclusions or extensions, triggered by DAC treatment in an SETD2-loss context. Comprehensive epigenomic analysis reveals H3K9me3 deposition, rather than DNA methylation dynamics, across intronic TEs might contribute to elevated mis-splicing rates. Through epigenomic and transcriptomic analyses, we show that SETD2-deficient kidney cancers are prone to mis-splicing, which can be therapeutically exacerbated with DAC treatment to increase viral mimicry activation and provide synergy with combinatorial immunotherapy approaches.

Scaling of Chinese urban CO2 emissions and multiple dimensions of city size

Cities are both the primary cause of global climate change and the key to the mitigation agenda. China's unprecedented urbanization has paralleled a growth in energy demand and urban areas have emerged as the crux of CO₂ emissions reduction in China. There is a crucial need for policymakers to understand how CO₂ emissions scale with city size and adopt economies of scale (cost savings) for mitigation, particularly through a multidimensional lens of city size. This study reveals a set of scaling relations between urban scope 1 CO₂ emissions and five dimensions of city size in 340 Chinese cities, including population (POP), built-up area (BA), building height (BH), specific built-up area (SBA), and built-up volume (BV). The findings show that CO₂ emissions in Chinese cities scale linearly with POP and BA but sublinearly with BA, SBA, and BV, and more diverse regimes exist across various geographic zones, population hierarchies, administrative hierarchies, and governance contexts. The prevalent sublinear scaling regime between CO₂ emissions and SBA and BV demonstrates the potential importance of optimizing the vertical built-up landscapes for establishing a zero‑carbon society. Furthermore, the top 10 % and bottom 10 % performance of individual cities in emissions identified by the Scale-Adjusted Metropolitan Indicator (SAMI) (the smaller the better) highlights the imprints of the socioeconomic context (e.g., Low Carbon City Initiative) on the scaling of CO₂ emissions in Chinese cities, which is critical for developing decarbonization strategies. Our multidimensional analysis can assist in the local-tailored low-carbon development of Chinese cities.

Molecular cloning and expression analysis of Myxovirus resistance gene in Yangzhou goose (Anser cygnoides domesticus)

1. Myxovirus resistance (Mx) is a protein produced by the interferon-induced natural immune response with broad spectrum antiviral function. However, the role and expression characteristics of the Mx gene in immune defence against viral infection in goose have not yet been reported.2. This study found a 2576 bp genomic sequence and a 2112 bp mRNA sequence for Mx, encoding 703 amino acids. Multiple sequence alignments of the amino acid sequences showed that the Yangzhou goose Mx (goMx) had 86.99% similarity to the mallard duck (Anas platyrhynchos).3. Tissue-specific expression profiling revealed that the expression of goMx was highest in the lung and spleen. Both poly (I:C) and GPV were found to elevate the expression of goMx. The upregulated expression of goMx was associated with interferon pathway-related genes IRF7, JAK1, STAT1, and STAT2. Furthermore, overexpression of goMx significantly activated the transcription of poly (I:C) induced TNF-α, IL-1β, IL-6, and IL-18.4. The findings of this study suggest that the goMx modulation of the antiviral response is mediated by the interferon pathway.

Artificial Intelligence-Assisted Evaluation of the Spatial Relationship between Brain Arteriovenous Malformations and the Corticospinal Tract to Predict Postsurgical Motor Defects

BACKGROUND AND PURPOSE

Preoperative evaluation of brain AVMs is crucial for the selection of surgical candidates. Our goal was to use artificial intelligence to predict postsurgical motor defects in patients with brain AVMs involving motor-related areas.

MATERIALS AND METHODS

Eighty-three patients who underwent microsurgical resection of brain AVMs involving motor-related areas were retrospectively reviewed. Four artificial intelligence-based indicators were calculated with artificial intelligence on TOF-MRA and DTI, including FN5mm/50mm (the proportion of fiber numbers within 5-50mm from the lesion border), FN10mm/50mm (the same but within 10-50mm), FP5mm/50mm (the proportion of fiber voxel points within 5-50mm from the lesion border), and FP10mm/50mm (the same but within 10-50mm). The association between the variables and long-term postsurgical motor defects was analyzed using univariate and multivariate analyses. Least absolute shrinkage and selection operator regression with the Pearson correlation coefficient was used to select the optimal features to develop the machine learning model to predict postsurgical motor defects. The area under the curve was calculated to evaluate the predictive performance.

RESULTS

In patients with and without postsurgical motor defects, the mean FN5mm/50mm, FN10mm/50mm, FP5mm/50mm, and FP10mm/50mm were 0.24 (SD, 0.24) and 0.03 (SD, 0.06), 0.37 (SD, 0.27) and 0.06 (SD, 0.08), 0.06 (SD, 0.10) and 0.01 (SD, 0.02), and 0.10 (SD, 0.12) and 0.02 (SD, 0.05), respectively. Univariate and multivariate logistic analyses identified FN10mm/50mm as an independent risk factor for long-term postsurgical motor defects (P = .002). FN10mm/50mm achieved a mean area under the curve of 0.86 (SD, 0.08). The mean area under the curve of the machine learning model consisting of FN10mm/50mm, diffuseness, and the Spetzler-Martin score was 0.88 (SD, 0.07).

CONCLUSIONS

The artificial intelligence-based indicator, FN10mm/50mm, can reflect the lesion-fiber spatial relationship and act as a dominant predictor for postsurgical motor defects in patients with brain AVMs involving motor-related areas.

Dehydrocostus Lactone Reduced Malignancy of HepG2 Human Hepatocellular Carcinoma Cells via Down-Regulation of the PI3K/AKT Signaling Pathway

We studied the effect of dehydrocostus lactone (DHL) on the biological characteristics of HepG2 human hepatocellular carcinoma cells. The inhibition of cell viability by different concentrations of DHL (10, 20, 40, 80, and 160 μmol/liter) was measured using MTT test. As the determined half-maximum inhibitory concentration (IC₅₀) was 20.33 μmol/liter, DHL in a concentration of 20 μmol/liter was used in further experiments. Cell proliferation, migration, invasion ability, and apoptosis were assessed by Ki-67 immunofluorescence, Transwell assay, and TUNEL analysis. The level of p-AKT protein was determined by Western blotting. DHL significantly inhibited the viability, proliferation, migration, and invasion of HepG2 cells in comparison with the control group, and induced cells apoptosis. DHL down-regulated the expression of p-AKT protein in the HepG2 cells in comparison with the control group. PI3K/AKT signaling pathway activator 740Y-P could block the above-mentioned effects of DHL. Thus, DHL inhibits the malignancy of HepG2 human hepatocellular carcinoma cells via down-regulation of PI3K/AKT signaling pathway.

Genome-Wide Identification of the CER Gene Family and Significant Features in Climate Adaptation of Castanea mollissima

The plant cuticle is the outermost layer of the aerial organs and an important barrier against biotic and abiotic stresses. The climate varies greatly between the north and south of China, with large differences in temperature and humidity, but Chinese chestnut is found in both regions. This study investigated the relationship between the wax layer of chestnut leaves and environmental adaptation. Firstly, semi-thin sections were used to verify that there is a significant difference in the thickness of the epicuticular wax layer between wild chestnut leaves in northwest and southeast China. Secondly, a whole-genome selective sweep was used to resequence wild chestnut samples from two typical regional populations, and significant genetic divergence was identified between the two populations in the CmCER1-1, CmCER1-5 and CmCER3 genes. Thirty-four CER genes were identified in the whole chestnut genome, and a series of predictive analyses were performed on the identified CmCER genes. The expression patterns of CmCER genes were classified into three trends-upregulation, upregulation followed by downregulation and continuous downregulation-when chestnut seedlings were treated with drought stress. Analysis of cultivars from two resource beds in Beijing and Liyang showed that the wax layer of the northern variety was thicker than that of the southern variety. For the Y-2 (Castanea mollissima genome sequencing material) cultivar, there were significant differences in the expression of CmCER1-1, CmCER1-5 and CmCER3 between the southern variety and the northern one-year-grafted variety. Therefore, this study suggests that the CER family genes play a role in environmental adaptations in chestnut, laying the foundation for further exploration of CmCER genes. It also demonstrates the importance of studying the adaptation of Chinese chestnut wax biosynthesis to the southern and northern environments.

[Analysis of the whole genome traceability and transmission path simulation experiment of the local cluster COVID-19 epidemic]

Objective: To trace and characterize the whole genome of SARS-CoV-2 of confirmed cases in the outbreak of COVID-19 on July 31, 2021 in Henan Province. Method: Genome-wide sequencing and comparative analysis were performed on positive nucleic acid samples of SARS-CoV-2 from 167 local cases related to the epidemic on July 31, 2021, to analyze the consistency and evolution of the whole genome sequence of virus. Results: Through high-throughput sequencing, a total of 106 cases of SARS-CoV-2 whole genome sequences were obtained. The results of genome analysis showed that the whole genome sequences of 106 cases belonged to the VOC/Delta variant strain (B.1.617.2 clade), and the whole genome sequences of 106 cases were shared with the genomes of 3 imported cases from Myanmar admitted to a hospital in Zhengzhou. On the basis of 45 nucleotide sites, 1-5 nucleotide variation sites were added, and the genome sequence was highly homologous. Conclusion: Combined with the comprehensive analysis of viral genomics, transmission path simulation experiments and epidemiology, it is determined that the local new epidemic in Henan Province is caused by imported cases in the nosocomial area, and the spillover has caused localized infection in the community. At the same time, it spills over to some provincial cities and results in localized clustered epidemics.

[Predictive models and prophylactic strategies for anastomotic leakage in colorectal surgery]

Anastomotic leakage (AL) has always been a persistent issue for colorectal surgeons. It is still difficult to reduce the incidence of AL despite the advances in technology and equipment. With the development of evidence-based medicine, increasing high-risk factors for AL have been identified. How to efficiently and systematically combine and quantify these isolated risk factors to provide a scientific early warning of AL in clinical practices and help surgeons in choosing the optimal prophylactic strategies, is of great significance for reducing the incidence of AL. There are generally two types of AL prediction models in colorectal surgery, including prognostic models (for preoperative and intraoperative AL prediction) and diagnostic models (for early warning and improving the early diagnosis rate of AL). Prophylactic strategies for AL include stabilizing the underlying diseases, improving anemia and hypoalbuminemia, choosing an appropriate operative time window, and emphasizing and improving anastomotic techniques (including choosing an appropriate size of stapler). However, a prophylactic ostomy is still the most common method for surgeons. However, how to reduce the morbidity of complications following prophylactic ostomy and how to avoid the conversion of the prophylactic stoma to permanent stoma need further study.

Prevalence of USP and hlyA Genes and Association with Drug Resistance in Uropathogenic Escherichia coli Isolated from Patients in a Tertiary Hospital from Southeast China

E. coli was cultured from the urine of patients from the tertiary hospital located in Southeast China from 2017 to 2019. The species were identified, drug sensitivity test was performed, and the presence of the virulence genes USP and hlyA was determined. A total of 483 strains of E. coli were isolated, including 132 from patients with urinary tract infection (UTI). The resistance to ciprofloxacin was more common in non-UTI patients, while resistance to gentamycin was significantly higher in the UTI group. In the UTI group, the proportions of isolated bacteria with the virulence USP (40.15%) and hlyA (8.33%) genes were significantly higher than in the non-UTI group (19.60 and 2.56%, respectively). The rate of resistance of E. coli toward levofloxacin in the USP⁺ group was significantly (p<0.05) higher than in the USP- group. Thus, we revealed the differences in the rate of drug resistance and prevalence of USP and hlyA between the UTI and non-UTI groups. Furthermore, the presence of the USP gene was found to be associated with greater resistance to levofloxacin.

Isolated hand weakness due to brain lesion

When hand weakness is linked to a brain lesion, there is risk of misdiagnosis. A case of hand weakness related to stroke is presented. The electromyography report indicated a segmental lesion of the median nerve at the wrist. Thus, the patient was initially diagnosed with carpal tunnel syndrome, and was referred to the orthopedic department for release surgery. Because the symptom was immediate and did not include hand numbness, the orthopedic surgeon ruled out the previous diagnosis and ordered a head CT scan, which revealed stroke. Aspirin and other medications were given. Percutaneous carotid balloon angioplasty with stent implantation and percutaneous vertebral artery balloon angioplasty were performed. The weakness of the left hand was greatly improved. So far, only a few cases suggest that hand weakness may be linked to stroke. Therefore, physicians should pay attention to physical examination.

Comparison of pathogenicity of porcine deltacoronavirus CZ2020 from cell culture and intestinal contents in 27-day-old piglets

Porcine deltacoronavirus (PDCoV) is an emenging swine enteropathogenic coronavirus that can cause high mortality rate. It affects pigs of all ages, but most several in neonatal piglets. Little is known regarding the pathogenicity of PDCoV against 27-day-old piglets. In this study, 27-day-old piglets were experimentally infected with PDCoV CZ2020 from cell culture, the challenged piglets do not have obvious symptoms from 1 to 7 days post-challenge (DPC), while viral shedding was detected in rectal swab at 1 DPC. Tissues of small intestines displayed slight macroscopic and microscopic lesions with no viral antigen detection. On the other hand, 27-day-old piglets were infected with PDCoV from intestinal contents, the piglets developed mild to severe diarrhea, shedding increasing from 2 to 7 DPC, and developed macroscopic and microscopic lesions in small intestines with clear viral antigen confirmed by immunohistochemistry staining. Indicating the small intestine was still the major target organ in PDCoV-challenged pigs at the age of 27-day-old. Diarrhea caused by PDCoV from intestinal contents in 27-day-old piglets is less reported. Thus, our results might provide new insights into the pathogenesis of PDCoV.

Preparation and characterization of ZnO/graphene/graphene oxide/multi-walled carbon nanotube composite aerogels

ZnO/Graphene (G)/Graphene Oxide (GO)/Multi-walled Carbon Nanotube (MCNT) composite aerogels with a three-dimensional porous structure were prepared by the sol-gel method under average temperature and alkaline conditions, combined with freeze-drying process and heat treatment process. The photocatalytic degradation of Rhodamine B (RhB) was mainly studied. The scanning electron microscope (SEM) test results showed that the morphology uniformity of the ZnO/G/GO/MCNT composite aerogel was significantly enhanced, which effectively solving the agglomeration problem of MCNT and ZnO. The photocatalytic degradation test results of RhB show that due to the synergistic effect of physical adsorption and photocatalytic degradation, the total degradation efficiency of RhB by ZnO/G/GO/MCNT could reach 86.8%, which is 3.3 times higher than that of ZnO. In addition, the synergistic effect of ZnO and G effectively hinders the recombination of photo-generated electron-hole pairs and enhances photocatalytic activity. The ZnO/G/GO/MCNT composite aerogel can be applied in the visible light catalytic degradation of water pollution.