Integration of single-cell sequencing with machine learning and Mendelian randomization analysis identifies the NAP1L1 gene as a predictive biomarker for Alzheimer's disease

Background

The most effective approach to managing Alzheimer's disease (AD) lies in identifying reliable biomarkers for AD to forecast the disease in advance, followed by timely early intervention for patients.

Methods

Transcriptomic data on peripheral blood mononuclear cells (PBMCs) from patients with AD and the control group were collected, and preliminary data processing was completed using standardized analytical methods. PBMCs were initially segmented into distinct subpopulations, and the divisions were progressively refined until the most significantly altered cell populations were identified. A combination of high-dimensional weighted gene co-expression analysis (hdWGCNA), cellular communication, pseudotime analysis, and single-cell regulatory network inference and clustering (SCENIC) analysis was used to conduct single-cell transcriptomics analysis and identify key gene modules from them. Genes were screened using machine learning (ML) in the key gene modules, and internal and external dataset validations were performed using multiple ML methods to test predictive performance. Finally, bidirectional Mendelian randomization (MR) analysis, regional linkage analysis, and the Steiger test were employed to analyze the key gene.

Result

A significant decrease in non-classical monocytes was detected in PMBC of AD patients. Subsequent analyses revealed the inherent connection of non-classical monocytes to AD, and the NAP1L1 gene identified within its gene module appeared to exhibit some association with AD as well.

Conclusion

The NAP1L1 gene is a potential predictive biomarker for AD.

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Deciphering mitochondrial dysfunction: Pathophysiological mechanisms in vascular cognitive impairment

Vascular cognitive impairment (VCI) encompasses a range of cognitive deficits arising from vascular pathology. The pathophysiological mechanisms underlying VCI remain incompletely understood; however, chronic cerebral hypoperfusion (CCH) is widely acknowledged as a principal pathological contributor. Mitochondria, crucial for cellular energy production and intracellular signaling, can lead to numerous neurological impairments when dysfunctional. Recent evidence indicates that mitochondrial dysfunction-marked by oxidative stress, disturbed calcium homeostasis, compromised mitophagy, and anomalies in mitochondrial dynamics-plays a pivotal role in VCI pathogenesis. This review offers a detailed examination of the latest insights into mitochondrial dysfunction within the VCI context, focusing on both the origins and consequences of compromised mitochondrial health. It aims to lay a robust scientific groundwork for guiding the development and refinement of mitochondrial-targeted interventions for VCI.

[Propensity score matching analysis of the short-term efficacy of Kamikawa versus double- tract reconstruction in laparoscopic proximal gastric cancer surgery]

Objective: To compare the short-term efficacy of Kamikawa anastomosis and double-tract reconstruction (DTR) after proximal gastrectomy. Methods: This was a propensity score matched, retrospective, cohort study. Inclusion criteria comprised age 20-70 years, diagnosis of gastric cancer by pathological examination of preoperative endoscopic biopsies, tumor diameter ≤4 cm, and location in the upper 1/3 of the stomach (including the gastroesophageal junction), and TNM stage IA, IB, or IIA. The study cohort comprised 73 patients who had undergone laparoscopic proximal gastric cancer radical surgery in the Department of Gastroenterology, Tangdu Hospital, Air Force Medical University between June 2020 and February 2023, 19 of whom were in the Kamikawa group and 54 in the DTR group. After using R language to match the baseline characteristics of patients in a ratio of 1:2, there were 17 patients in the Kamikawa group and 34 in the DTR group. Surgery-related conditions, postoperative quality of life, and postoperative complications were compared between the two groups. Results: After propensity score matching, there were no statistically significant differences in baseline data between the two groups (P>0.05). Compared with the DTR group, the Kamikawa group had longer operative times (321.5±15.7 minutes vs. 296.8±26.1 minutes, t=32.056, P<0.001), longer anastomosis times (93.0±6.8 minutes vs. 45.3±7.7 minutes, t=56.303, P<0.001), and less bleeding (76 [54~103] mL vs.112 [82~148) mL, Z=71.536, P<0.001); these differences are statistically significant. There were no statistically significant differences between the two groups in tumor size, time to first postoperative passage of gas, postoperative hospital stay, number of lymph nodes removed, duration of lymph node dissection, or total hospitalization cost (all P>0.05). The median follow-up time was 6.1 ± 1.8 months. As to postoperative quality of life, the Kamikawa group had a lower rate of upper gastrointestinal contrast reflux than did the DTR group (0 vs. 29.4% [10/34], χ2=6.220, P=0.013); this difference is statistically significant. However, differences between the two groups in quality of life score on follow-up of 3 months and 6 months on the Gastroesophageal Reflux Disease (GERD) scale were not statistically significant (all P>0.05). The incidence of postoperative complications was 2/17 in the Kamikawa group, which is significantly lower than the 41.2% (14/34) in the DTR group (χ2=4.554, P=0.033). Conclusion: Kamikawa anastomosis and DTR are equally safe and effective procedures for reconstructing the digestive tract after proximal gastric surgery. Although Kamikawa anastomosis takes slightly longer and places higher demands on the surgical team, it is more effective at preventing postoperative reflux.

Prevalence and influencing factors of depressive and anxiety symptoms among hospital-based healthcare workers during the surge period of the COVID-19 pandemic in the Chinese mainland: a multicenter cross-sectional study

BACKGROUND

From November 2022 to February 2023, the Chinese mainland experienced a surge in COVID-19 infection and hospitalization, and the hospital-based healthcare workers (HCWs) might suffer serious psychological crisis during this period. This study aims to assess the depressive and anxiety symptoms among HCWs during the surge of COVID-19 pandemic and to provide possible reference on protecting mental health of HCWs in future infectious disease outbreaks.

METHODS

A multicenter cross-sectional study was carried out among hospital-based HCWs in the Chinese mainland from 5 January to 9 February 2023. The PHQ-9 (nine-item Patient Health Questionnaire) and GAD-7 (seven-item Generalized Anxiety Disorder Questionnaire) were used to measure depressive and anxiety symptoms. Ordinal logistic regression analysis was performed to identify influencing factors.

RESULTS

A total of 6522 hospital-based HCWs in the Chinse mainland were included in this survey. The prevalence of depressive symptoms among the HCWs was 70.75%, and anxiety symptoms was 47.87%. The HCWs who perceived higher risk of COVID-19 infection and those who had higher work intensity were more likely to experience depressive and anxiety symptoms. Additionally, higher levels of mindfulness, resilience and perceived social support were negatively associated with depressive and anxiety symptoms.

CONCLUSION

This study revealed that a high proportion of HCWs in the Chinese mainland suffered from mental health disturbances during the surge of the COVID-19 pandemic. Resilience, mindfulness and perceived social support are important protective factors of HCWs' mental health. Tailored interventions, such as mindfulness practice, should be implemented to alleviate psychological symptoms of HCWs during the COVID-19 pandemic or other similar events in the future.

Effect of Segmental Abutting Esophagus-Sparing Technique to Reduce Severe Esophagitis in Limited-Stage Small-Cell Lung Cancer Patients Treated with Concurrent Hypofractionated Thoracic Radiation and Chemotherapy

PURPOSE/OBJECTIVE(S)

To evaluate the effect of segmental abutting esophagus-sparing (SAES) radiotherapy to reduce severe (G3+) acute esophagitis from 20% to 5% in patients with limited-stage small cell lung cancer (LS-SCLC) treated with concurrent chemoradiotherapy.

MATERIALS/METHODS

Patients with a clinical target volume (CTV) ≤1 cm close to the esophagus were enrolled in the experimental arm (45 Gy in 3 Gy daily fractions in 3 weeks) of an ongoing phase III randomized clinical trial (NCT02675088), which enrolled patients with histologically confirmed SCLC and clinically staged as LS or I-IIIB (AJCC 7th). This trial was designed to determine whether HYPO TRT (45 Gy in 3 Gy QD, experimental arm) has the same efficacy as CF TRT (60 Gy in 2 Gy QD, controlled arm) in patients with LS-SCLC. The whole esophagus was divided into the involved esophagus and abutting esophagus (AE) to receive different dose limitations according to the distance from the edge of the CTV. The primary endpoint was grade ≥ 3 acute esophagitis.

RESULTS

From 1 May 2021 to 30 April 2022, 30 patients were enrolled and completed four cycles of planned chemotherapy and radiotherapy. Our patient population was predominantly male (66.7% men vs. 33.3% women), with a median age of 62 years. A majority of patients presented with Stage N2-3 (90.0%) and T2-4 (76.7%), in which 4 patients had ultracentral-located primary tumors. With the SAES technique, all dosimetric parameters were significantly reduced for the whole esophagus and AE. The maximal and mean dose of the esophagus (47.4±1.9 Gy and 13.5 ± 5.8 Gy, respectively) and AE (42.9±2.3 Gy and 8.6 ± 3.6 Gy, respectively) in the SAES plan were significantly lower than those (esophagus 48.0±1.9 Gy and 14.7± 6.1 Gy, AE 45.1±2.4 Gy and 9.8± 4.2 Gy, respectively) in the non-SAES plan. After the follow-up of more than 7 months (range, 7.0-18.1 months) for all patients, only one patient (3.3%, 95% CI 0.1%-17.2%) experienced grade 3 acute esophagitis and no grade 4-5 acute esophagitis happened (Table 3). For late toxicities, one patient suffered sustained grade 1 late esophagitis and all others had no symptoms of esophagitis. The rate of radiation pneumonitis was very low, with one grade 3 event and no grade 4-5 event. Twelve (40.0%) patients had G3+ hematologic toxic events, including 2 patients with febrile neutropenia. The 1-year OS, LRFS, DMFS and PFS was 96.4%, 88.7%, 78.4% and 64.3%, respectively. No patient developed local recurrence in the abutting esophagus-sparing region.

CONCLUSION

SAES radiotherapy has significant dosimetric advantages compared with standard radiotherapy, which are successfully translated into clinical benefits for patients with LS-SCLC treated with 45 Gy in 3 Gy daily fractions. This may facilitate dose escalation for TRT in LS-SCLC patients.

[Establishment of hysteroscopic scoring system of chronic endometritis and correlative analysis with pregnancy outcomes of in vitro fertilization-embryo transfer in infertile patients]

Objective: To establish a hysteroscopic chronic endometritis (hCE) scoring system for patients with chronic endometritis, and observe the correlation of hCE score with in vitro fertilization-embryo transfer (IVF-ET) pregnancy outcomes in infertile women. Methods: The study retrospectively investigated the correlation of morphologic features and hCE score with pregnancy outcomes during IVF-ET in infertile women with CE (n=429) at Yantai Yuhuangding Hospital between January 2017 and September 2018. The clinical pregnancy rate and live birth rate with different score levels (1-3,4-7 and 8-14) after IVF-ET treatment were analyzed. Multivariate regression analysis was performed to adjust for confounding factors. The correlation and regression between hCE score and pregnancy outcomes was analyzed by curve fitting. Results: The age of 429 patients [M(Q₁, Q₃)] was 31 (29, 35) years. There were 50.6% (217 cases), 35.4% (152 cases), and 14.0% (60 cases) of patients with hCE score of 1-3, 4-7, and 8-14, respectively. The pregnancy rates of the three groups were 60.8% (132 cases), 44.7% (68 cases) and 16.7% (10 cases), P<0.001; The live birth rates were 51.2% (111 cases), 36.8% (56 cases) and 13.3% (8 cases), respectively (P<0.001). Compared with patients with hCE of 1-3, pregnancy rates in those with hCE of 4-7 and 8-14 were lower, and the OR values were 0.521 (0.342-0.793) and 0.129 (0.062-0.268). The live birth rates in patients with hCE of 4-7 and 8-14 were lower than that in patients with hCE of 1-3, and the OR values were 0.570 (0.372-0.873) and 0.162 (0.073-0.360), all P<0.05. Quadratic curve fitting results showed that clinical pregnancy rate and live birth rate decreased with the increase of hCE score. Conclusions: With the increase of hCE score, the clinical pregnancy rate and live birth rate of patients gradually decrease. hCE 4 is an important cut-off threshold significantly affecting the pregnancy outcome.

Aneurysmal bone cyst of the temporal bone presenting with reversible vestibular impairment

BACKGROUND

Aneurysmal bone cysts are expansile benign lesions associated with compressive destruction and obscure pathogenesis. The most common sites of temporal bone involvement are the petrous apex, squamous portions and mastoid.

CASE REPORT

This paper reports a right temporal aneurysmal bone cyst in a 51-year-old man who presented clinically with facial palsy, and hearing loss and impaired vestibular function. Magnetic resonance imaging and computed tomography findings were consistent with a diagnosis of aneurysmal bone cyst. Inter-operative findings showed that the lesion had caused compressive damage to the internal auditory canal. Following surgical excision, the patient experienced vertigo, indicating recovery of vestibular function. Follow-up imaging revealed complete resection without clinical recurrence.

CONCLUSION

To our knowledge, this is the first report of aneurysmal bone cyst invasion of the inner auditory canal. Our clinical experience indicates that vestibular nerve damage recovery is relatively uncommon. This case report will hopefully inform future studies.

Foliar application of nanoceria attenuated cadmium stress in okra (Abelmoschus esculentus L.)

Foliar application of nanoparticles (NPs) as a means for ameliorating abiotic stress is increasingly employed in crop production. In this study, the potential of CeO₂-NPs as stress suppressants for cadmium (Cd)-stressed okra (Abelmoschus esculentus) plants was investigated, using two cycles of foliar application of CeO₂-NPs at 200, 400, and 600 mg/l. Compared to untreated stressed plants, Cd-stressed plants treated with CeO₂-NPs presented higher pigments (chlorophyll a and carotenoids). In contrast, foliar applications did not alter Cd root uptake and leaf bioaccumulation. Foliar CeO₂-NPs application modulated stress enzymes (APX, SOD, and GPx) in both roots and leaves of Cd-stressed plants, and led to decreases in Cd toxicity in plant's tissues. In addition, foliar application of CeO₂-NPs in Cd-stressed okra plants decreased fruit Cd contents, and improved fruit mineral elements and bioactive compounds. The infrared spectroscopic analysis of fruit tissues showed that foliar-applied CeO₂-NPs treatments did not induce chemical changes but induced conformational changes in fruit macromolecules. Additionally, CeO₂-NPs applications did not alter the eating quality indicator (Mg/K ratio) of okra fruits. Conclusively, the present study demonstrated that foliar application of CeO₂-NPs has the potential to ameliorate Cd toxicity in tissues and improve fruits of okra plants.

Morinda officinalis oligosaccharides mitigate depression-like behaviors in hypertension rats by regulating Mfn2-mediated mitophagy

OBJECTIVE

Patients with hypertension have a risk of depression. Morinda officinalis oligosaccharides (MOOs) have anti-depressant properties. In this study, we aimed to determine whether MOOs can improve the symptoms of depression in individuals with hypertension.

METHODS

Dahl salt-sensitive rats fed with a high-salt diet were stimulated by chronic unpredictable mild stress to mimic hypertension with depression. Primary astrocytes and neurons were isolated from these rats. Astrocytes underwent LPS stimulation to simulate the inflammatory astrocytes during depression. MOOs were administrated at 0.1 mg/g/day in vivo and 1.25, 2.5, and 5 mg/mL in vitro. Mitophagy was inhibited using 5 mM 3-methyladenine (3-MA). Astrocyte-mediated neurotoxicity was detected by co-culturing astrocytes and neurons.

RESULTS

MOOs decreased systolic pressure, diastolic pressure, and mean arterial pressure, thereby improving depression-like behavior, including behavioral despair, lack of enthusiasm, and loss of pleasure during hypertension with depression. Furthermore, MOOs inhibited inflammation, astrocytic dysfunction, and mitochondrial damage in the brain. Then, MOOs promoted autophagosome and lysosome enriched in mitochondria in LPS-stimulated astrocytes. MOOs suppressed mitochondrial damage and the release of tumor necrosis factor-α (TNF-α), interleukin (IL)-6, and IL-1β in astrocytes undergoing LPS stimulation. Importantly, MOOs rescued the impaired neurons co-cultured with astrocytes. The effects of MOOs on LPS-stimulated astrocytes were reversed by 3-MA. Finally, MOOs upregulated LPS-downregulated Mfn2 expression in astrocytes. Mfn2 inhibition partly reversed the effects of MOOs on hypertension with depression. Intriguingly, Mfn2 suppression activated PI3K/Akt/mTOR pathway during MOOs treatment.

CONCLUSIONS

Astrocytes develop neuroinflammation in response to mitochondrial damage during hypertension with depression. MOOs upregulated Mfn2 expression to activate the PI3K/Akt/mTOR pathway-mediated mitophagy, thereby removing impaired mitochondria in astrocytes.

HIGHLIGHTS

1. MOOs have anti-hypertensive and anti-depressive properties. 2. MOOs inhibit inflammation and injury in astrocytes during hypertension with depression. 3. MOOs induce mitophagy activation in inflammatory astrocytes with mitochondrial damage. 4. MOOs upregulate Mfn2 expression in astrocytes. 5. Mfn2 activates mitophagy to resist mitochondrial damage in astrocytes.

Lost genome segments associate with trait diversity during rice domestication

BACKGROUND

DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication.

RESULTS

In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length.

CONCLUSIONS

We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Global whole-genome comparison and analysis to classify subpopulations and identify resistance genes in weedy rice relevant for improving crops

Common weedy rice plants are important genetic resources for modern breeding programs because they are the closest relatives to rice cultivars and their genomes contain elite genes. Determining the utility and copy numbers of WRKY and nucleotide-binding site (NBS) resistance-related genes may help to clarify their variation patterns and lead to crop improvements. In this study, the weedy rice line LM8 was examined at the whole-genome level. To identify the Oryza sativa japonica subpopulation that LM8 belongs to, the single nucleotide polymorphisms (SNPs) of 180 cultivated and 23 weedy rice varieties were used to construct a phylogenetic tree and a principal component analysis and STRUCTURE analysis were performed. The results indicated that LM8 with admixture components from japonica (GJ) and indica (XI) belonged to GJ-admixture (GJ-adm), with more than 60% of its genetic background derived from XI-2 (22.98%), GJ-tropical (22.86%), and GJ-subtropical (17.76%). Less than 9% of its genetic background was introgressed from weedy rice. Our results also suggested LM8 may have originated in a subtropical or tropical geographic region. Moreover, the comparisons with Nipponbare (NIP) and Shuhui498 (R498) revealed many specific structure variations (SVs) in the LM8 genome and fewer SVs between LM8 and NIP than between LM8 and R498. Next, 96 WRKY and 464 NBS genes were identified and mapped on LM8 chromosomes to eliminate redundancies. Three WRKY genes (ORUFILM02g002693, ORUFILM05g002725, and ORUFILM05g001757) in group III and one RNL [including the resistance to powdery mildew 8 (RPW8) domain, NBS, and leucine rich repeats (LRRs)] type NBS gene (ORUFILM12g000772) were detected in LM8. Among the NBS genes, the RPW8 domain was detected only in ORUFILM12g000772. This gene may improve plant resistance to pathogens as previously reported. Its classification and potential utility imply LM8 should be considered as a germplasm resource relevant for rice breeding programs.

Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains

The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F₂ generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F₂ populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.)

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Ethylene response factor MdERF4 and histone deacetylase MdHDA19 suppress apple fruit ripening through histone deacetylation of ripening-related genes

Histone deacetylase enzymes participate in the regulation of many aspects of plant development. However, the genome-level targets of histone deacetylation during apple (Malus domestica) fruit development have not been resolved in detail, and the mechanisms of regulation of such a process are unknown. We previously showed that the complex of ethylene response factor 4 (MdERF4) and the TOPLESS co-repressor (MdTPL4; MdERF4-MdTPL4) is constitutively active during apple fruit development (Hu et al., 2020), but whether this transcriptional repression complex is coupled to chromatin modification is unknown. Here, we show that a histone deacetylase (MdHDA19) is recruited to the MdERF4-MdTPL4 complex, thereby impacting fruit ethylene biosynthesis. Transient suppression of MdHDA19 expression promoted fruit ripening and ethylene production. To identify potential downstream target genes regulated by MdHDA19, we conducted chromatin immunoprecipitation (ChIP) sequencing of H3K9 and ChIP-quantitative polymerase chain reaction assays. We found that MdHDA19 affects ethylene production by facilitating H3K9 deacetylation and forms a complex with MdERF4-MdTPL4 to directly repress MdACS3a expression by decreasing the degree of acetylation. We demonstrate that an early-maturing-specific acetylation H3K9ac peak in MdACS3a and expression of MdACS3a were specifically up-regulated in fruit of an early-maturing, but not a late-maturing, cultivar. We provide evidence that a C-to-G mutation in the ethylene-responsive element binding factor-associated amphiphilic repression motif of MdERF4 reduces the repression of MdACS3a by the MdERF4-MdTPL4-MdHDA19 complex. Taken together, our results reveal that the MdERF4-MdTPL-MdHDA19 repressor complex participates in the epigenetic regulation of apple fruit ripening.

Supplemented phase diagrams for vitrification CPA cocktails: DP6, VS55 and M22

DP6, VS55 and M22 are the most commonly used cryoprotective agent (CPA) cocktails for vitrification experiments in tissues and organs. However, complete phase diagrams for the three CPAs are often unavailable or incomplete (only available for full strength CPAs) thereby hampering optimization of vitrification and rewarming procedures. In this paper, we used differential scanning calorimetry (DSC) to measure the transition temperatures including heterogeneous nucleation temperatures (T_het), glass transition temperatures (T_g), rewarming phase crystallization (devitrification and/or recrystallization) temperatures (T_d) and melting temperatures (T_m) while cooling or warming the CPA sample at 5 °C/min and plotted the obtained transition temperatures for different concentrations of CPAs into the phase diagrams. We also used cryomicroscopy cooling or warming the sample at the same rate to record the ice crystallization during the whole process, and we presented the cryomicroscopic images at the transition temperatures, which agreed with the DSC presented phenomena.

Network pharmacology and in vitro studies reveal the pharmacological effects and molecular mechanisms of Shenzhi Jiannao prescription against vascular dementia

Background

Shenzhi Jiannao (SZJN) prescription is a type of herbal formula adopted in the management of cognitive impairment and related disorders. However, its effects and related regulatory mechanisms on vascular dementia (VD) are elusive. Herein, network pharmacology prediction was employed to explore the pharmacological effects and molecular mechanisms of SZJN prescription on VD using network pharmacology prediction, and validated the results through in vitro experiments.

Methods

Through a search in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, chemical composition and targets for SZJN prescription were retrieved. The potential targets for VD were then obtained from the GeneCards and DisGeNET databases. The network was constructed that depicted the interactions between putative SZJN prescription and known therapeutic targets for VD using Cytoscape 3.7.1. Analysis of protein-protein interaction was achieved via STRING 11.0 software, followed by Gene Ontology (GO) functional enrichment and Kyoto Gene and Genome Encyclopedia (KEGG) pathway analyses. To validate the computer-predicted results, in vitro experiments based on an excitotoxic injury model were designed using glutamate-exposed PC12 cells, and treated with varying concentrations (low, 0.05; medium, 0.1 and high, 0.2 mg/mL) of SZJN prescription. Cell viability and cell death were detected using the IncuCyte imaging system. Moreover, the expression profiles of Caspase-3 were analyzed through qRT-PCR.

Results

Twenty-eight potentially active ingredients for SZJN prescription, including stigmasterol, beta-sitosterol, and kaempferol, plus 21 therapeutic targets for VD, including PTGS2, PTGS1, and PGR were revealed. The protein-protein interaction network was employed for the analysis of 20 target proteins, including CASP3, JUN, and AChE. The enrichment analysis demonstrated candidate targets of SZJN prescription were more frequently involved in neuroactive ligand-receptor interaction, calcium, apoptosis, and cholinergic synaptic signaling pathways. In vitro experiments revealed that SZJN prescription could significantly reverse glutamate-induced cell viability loss and cell death, and lower the levels of Caspase-3 mRNA in glutamate-induced PC12 cells.

Conclusions

Collectively, this study demonstrated that SZJN prescription exerted the effect of treating VD by regulating multi-targets and multi-channels with multi-components through the method of network pharmacology. Furthermore, in vitro results confirmed that SZJN prescription attenuated glutamate-induced neurotoxicity.

High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice

Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F₂ population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.