Establishment of dual reverse transcriptase-polymerase chain reaction for detection system for Areca palm velarivirus 1.

Areca palm velarivirus 1 (APV1) is one of the main pathogen causing yellow leaf disease, and leading to considerable losses in the Areca palm industry. The detection methods for APV1 are primarily based on phenotype determination and molecular techniques, such as polymerase chain reaction (PCR). However, a single PCR has limitations in accuracy and sensitivity. Therefore, in the present study, we established a dual RT-PCR APV1-detection system with enhanced accuracy and sensitivity using two pairs of specific primers, YLDV2-F/YLDV2-R and YLDV4-F/YLDV4-R. Moreover, two cDNA fragments covering different regions of the viral genome were simultaneously amplified, with PCR amplicon of 311 and 499 bp, respectively. The dual RT-PCR detection system successfully amplified the two target regions of the APV1, demonstrating high specificity and sensitivity and compensating for the limitations of single-primer detection methods. We tested 60 Areca palm samples from different geographical regions, highlighting its advantages in that the dual RT-PCR system efficiently and accurately detected APV1 in samples across diverse areas. The dual RT-PCR APV1 detection system provides a rapid, accurate, and sensitive method for detecting the virus and offers valuable technical support for research in preventing and managing yellow leaf diseases caused by APV1 in Areca palms. Moreover, the findings of this study can serve as a reference for establishing similar plants viral detection systems in the future.

A mini review of Liparis species: an ornamental genus with considerable medicinal value.

The genus Liparis, a group of perennial ornamental herbs in the family Orchidaceae, is widely distributed in tropical and subtropical regions. Many species of the genus Liparis have been commonly used as traditional herbal medicines for the treatment of menorrhagia, haemoptysis, traumatic bleeding, snake bites, and pneumonia. This review describes the ornamental value of plants of the genus Liparis and summarises the chemical constituents and pharmacological activities reported during the last decade. The main chemical constituents of this genus are phenolic acids, alkaloids, flavonoids, etc. Most phenolic acids and alkaloids have a nervogenic acid skeleton, and most alkaloids also have a pyrrolizidine skeleton. Extracts from the genus Liparis plants showed significant haemostatic, antitumor, anti-inflammatory, hypolipidemic, antioxidant, and antibacterial activities. This paper proposed ideas and research directions for the future study of plants in the genus Liparis, providing valuable information for the development of new drugs and promoting their utilisation.

Efficacy and safety of prophylactic balloon occlusion in the management of placenta accreta spectrum disorder: a retrospective cohort study.

OBJECTIVE: Placenta accreta spectrum disorder (PAS) is a serious obstetric complication associated with significant maternal morbidity and mortality. Prophylactic balloon occlusion (PBO), as an intravascular interventional therapies, has emerged as a potential management strategy for controlling massive hemorrhage in patients with PAS. However, current evidence about the clinical application of PBO in PAS patients are still controversial. This study aimed to evaluate the effectiveness and safety of PBO in the management of PAS. METHODS: A retrospective cohort study including PAS patients underwent cesarean delivery was conducted in a tertiary hospital from January 2015 to March 2022. Included PAS patients were further divided into balloon and control groups by whether PBO was performed. Groups were compared for demographic characteristics, intraoperative and postoperative parameters, maternal and neonatal outcomes, PBO-related complication and follow up outcomes. Additionally, multivariate-logistic regression analysis was performed to determine the definitive associations between PBO and risk of massive hemorrhage and hysterectomy. RESULTS: A total of 285 PAS patients met the inclusion criteria were included, of which 57 PAS patients underwent PBO (PBO group) and 228 women performed cesarean section (CS) without PBO (control group). Irrespective of the differences of baseline characteristics between the two groups, PBO intervention did not reduce the blood loss, hysterectomy rate and postoperative hospital stay, but it prolonged the operation time and increased the cost of hospitalization (All P < 0.05) Additionally, there were no significant differences in postoperative complications, neonatal outcomes, and follow-up outcomes(All P > 0.05). In particular, patients undergoing PBO were more likely to develop the venous thrombosis postoperatively (P = 0.001). However, multivariate logistic regression analysis showed that PBO significantly decreased the risk of massive hemorrhage (OR 0.289, 95%CI:0.109-0.766, P = 0.013). The grade of PAS and MRI with S2 invasion were the significant risk factors affecting massive hemorrhage(OR:6.232 and OR:5.380, P<0.001). CONCLUSION: PBO has the potential to reduce massive hemorrhage in PAS patients undergoing CS. Obstetricians should, however, be aware of potential complications arising from the PBO. Additionally, MRI with S2 invasion and PAS grade will be useful to identify PAS patients who at high risk and may benefit from PBO. In brief, PBO seem to be a promising alternative for management of PAS, yet well-designed randomized controlled trials are needed to convincingly demonstrate its benefits and triage the necessity of PBO.

Integrated transcriptomics and metabolomics analyses of the effects of bagging treatment on carotenoid biosynthesis and regulation of Areca catechu L.

Introduction: Fresh Aareca nut fruit for fresh fruit chewing commonly found in green or dark green hues. Despite its economic significance, there is currently insufficient research on the study of color and luster of areca. And the areca nut fruits after bagging showed obvious color change from green to tender yellow. In the study, we tried to explain this interesting variation in exocarp color. Methods: Fruits were bagged (with a double-layered black interior and yellow exterior) 45 days after pollination and subsequently harvested 120 days after pollination. In this study, we examined the the chlorophyll and carotenoid content of pericarp exocarp, integrated transcriptomics and metabolomics to study the effects of bagging on the carotenoid pathway at the molecular level. Results: It was found that the chlorophyll and carotenoid content of bagged areca nut (YP) exocarp was significantly reduced. A total of 21 differentially expressed metabolites (DEMs) and 1784 differentially expressed genes (DEGs) were screened by transcriptomics and metabolomics. Three key genes in the carotenoid biosynthesis pathway as candidate genes for qPCR validation by co-analysis, which suggested their role in the regulation of pathways related to crtB, crtZ and CYP707A. Discussion: We described that light intensity may appear as a main factor influencing the noted shift from green to yellow and the ensuing reduction in carotenoid content after bagging.

HIPK3 maintains sensitivity to platinum drugs and prevents disease progression in gastric cancer.

In the realm of cancer therapeutics and resistance, kinases play a crucial role, particularly in gastric cancer (GC). Our study focused on platinum-based chemotherapy resistance in GC, revealing a significant reduction in homeodomain-interacting protein kinase 3 (HIPK3) expression in platinum-resistant tumors through meticulous analysis of transcriptome datasets. In vitro and in vivo experiments demonstrated that HIPK3 knockdown enhanced tumor proliferation and metastasis, while upregulation had the opposite effect. We identified the myocyte enhancer factor 2C (MEF2C) as a transcriptional regulator of HIPK3 and uncovered HIPK3's role in downregulating the morphogenesis regulator microtubule-associated protein (MAP7) through ubiquitination. Phosphoproteome profiling revealed HIPK3's inhibitory effects on mTOR and Wnt pathways crucial in cell proliferation and movement. A combined treatment strategy involving oxaliplatin, rapamycin, and IWR1-1-endo effectively overcame platinum resistance induced by reduced HIPK3 expression. Monitoring HIPK3 levels could serve as a GC malignancy and platinum resistance indicator, with our proposed treatment strategy offering novel avenues for reversing resistance in gastric cancer.

Epstein-Barr virus-based prognostic model in nodular sclerosis classic Hodgkin lymphoma.

The role of Epstein-Barr virus (EBV) in lymphoma cells of nodular sclerosis classic Hodgkin lymphoma (NScHL) is controversial. Our aim was to explore this and establish a clinically feasible model for risk stratification. We interrogated data from 542 consecutive subjects with NScHL receiving ABVD therapy and demonstrated EBV-infection in their lymphoma cells with EBV-encoded small RNAs (EBERs) in situ hybridization. Subjects were divided into training and validation datasets. As data from the training dataset suggested EBERs-positivity was the only independent prognostic factor for both progression-free survival (PFS) and overall survival (OS), we developed corresponding prognostic models based on it. Our models showed excellent performance in both training and validation cohort. These data indicate the close association of EBV infection and the outcomes of persons with NScHL receiving ABVD. Additionally, our newly developed models should help physicians estimate prognosis and select individualized therapy.

Protective effects of Liupao tea against high-fat diet/cold exposure-induced irritable bowel syndrome in rats.

Liupao tea as a type of dark tea can relieve irritable bowel syndrome by regulating gut microbiota, but the mechanism has not been fully explained. An ultra-high performance liquid chromatography along with quadrupole time of flight tandem mass spectrometry was used to analyze the phytochemicals in Liupao tea. Then, we explored the effects of Liupao tea against IBS. From the results of chemical analysis, we identified catechins, polyphenols, amino acids, caffeine, polysaccharides and other components in Liupao tea. The open-field test, gastrointestinal function-related indexes, histochemical assays, measurements of cytokine and aquaporin 3 (AQP3), and determination of serum metabolites were utilized to monitor the physiological consequences of Liupao tea administration in rats with irritable bowel syndrome. The results showed that Liupao tea had a significant protective effect on irritable bowel syndrome. Liupao tea increased locomotive velocity while reducing interleukin-6, interleukin-1ß, and tumor necrosis factor-α levels, as well as gastrointestinal injury. Moreover, Liupao tea increased the AQP3 levels of renal tissues but reduced the AQP3 levels of gastrointestinal tissues. Liupao tea reduced the Firmicutes/Bacteroides ratio and significantly reconstructed the microbial pattern. Liupao tea relieved irritable bowel syndrome by repairing gastrointestinal dysfunction, regulating the secretion of pro-inflammatory cytokines, modulating water metabolism, and restoring microbial homeostasis.

Factors influencing loyalty to online health consultation platform: a cross-strait cultural perspective.

BACKGROUND: The geographical, cultural, and linguistic proximity between Taiwan and Mainland China has facilitated rapid growth of cross-strait interactions. Both countries have developed online health consultation platforms on the Internet for the public to access healthcare related information. This study examines factors that influence loyalty to a specific online health consultation platform (OHCP) from a cross-strait perspective. METHODS: Based on the Expectation Confirmation Theory and the combined Trust, Perceived Health Risks and Culture, we examine factors that influence loyalty to OHCPs among cross-strait users by investigating the roles of trust, perceived health risks, and culture. Data was collected through a questionnaire survey. RESULTS: The research models used provide a high-power explanation of loyalty to OHCPs. Results generally align with those of previous studies, with the exception of the relationships between Perceived Health Risks and Perceived Usefulness, Perceived Usefulness and Loyalty, Confirmation and Satisfaction, and Trust and Loyalty. In other words, culture may have moderated these relationships. CONCLUSIONS: Findings can help promote OHCPs among cross-strait users to make things easier for patients, and further reduce the load on the emergency department, especially in view of the still ongoing issues related to global outbreak of Coronavirus disease by facilitating early detection of potential cases.

An ultrasensitive solid-state ECL biosensor based on synergistic effect between Zn-NGQDs and porphyrin-based MOF as "on-off-on" platform.

To develop an ultra-sensitive solid-state electrochemiluminescence (ECL) biosensor for detection of miRNA 24, three different forms of porphyrin metal-organic framework (MOF) nanomaterials with good biocompatibility were synthesized through small molecule ligand modulation. We investigated various properties of synthesized MOFs in the presence of different small molecule ligands. The as-obtained 2D MOF nanodisk exhibited high ECL intensity and outstanding stability in the presence of a co-reactant at low concentrations. We also synthesized zinc-based quantum dots (Zn-NGQDs) with excellent photovoltaic properties by doping zinc dithiothreitol (DTT-Zn) into quantum dots. Accordingly, an enzyme-free solid-state ECL biosensor for miRNA 24 based on the "on-off-on" signal conversion strategy was created. Dependent on the synergy between the luminophor 2D MOF and Zn-NGQDs, the biosensor achieves a wide linear range from 1.00 × 10-16 to 1.00 × 10-10 mol·L-1 and an exceedingly low detection limit of 0.03 fM. Furthermore, the ECL biosensor exhibits outstanding selectivity, repeatability, and stability. The method has great potential for investigating sensitive detection models for various biomolecules and the design of highly efficient MOF luminescent materials.

Clinicopathological, etiological and molecular characteristics of intrahepatic cholangiocarcinoma subtypes classified by mucin production and immunohistochemical features.

BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) can be divided into two morphological subtypes: large duct type and small duct type ICC. This study aims to verify the feasibility of the classification criteria and clinicopathological characteristics of ICC. RESEARCH DESIGN AND METHODS: ICC patients were divided into the large and small type ICC by morphological and immunohistochemical patterns. Subsequently, clinicopathological data of the two groups was compared and the multivariate COX regression was used to verify the clinical significance of ICC subtypes. In addition, IDH1/2 mutation, KRAS mutation and FGFR2 translocation was also evaluated. RESULTS: Totally, 32, 61 and 13 tumors were defined as large, small and the indeterminate-duct type ICC respectively. Clinicopathologically, the large and small duct type ICC showed distinct morphological features. Compared with the small duct type ICC, the large duct type ICC had higher levels of serum tumor markers, vascular invasion, lymph node metastasis, and postoperative recurrence. Furthermore, positive FGFR2 rearrangement occurred only in small duct type ICC and IDH1/2 was mutated mainly in small duct type ICC. CONCLUSIONS: The subclassification system was applicable and the ICC subtypes had distinct clinicopathological characteristics, prognostic outcome, and IDH1/2 mutation pattern.

miR-29a-3p promotes the regulatory role of eicosapentaenoic acid in the NLRP3 inflammasome and autophagy in microglial cells.

Eicosapentaenoic acid (EPA) has been reported to play an anti-inflammatory and antioxidative stress role in a series of human diseases, including major depressive disorder. However, its exact mechanism is still largely unknown. Mouse BV-2 cells were treated with lipopolysaccharide (LPS) to induce an in vitro inflammatory cell model of depression. Cytotoxic effects were assessed with MTT and lactate dehydrigebase release assays. Cytokine mediators were elevated by western blot and enzyme-linked immunosorbent assays. Autophagy-relators were determined by immunofluorescence and western blot analyses. Interaction relationships among molecules were evaluated utilizing chromatin immunoprecipitation and dual luciferase assays. Methylated miR-29a-3p was detected via methylation-specific polymerase chain reaction. EPA treatment at 60 µM had no cytotoxic effects on BV2 cells and significantly inhibited the LPS-induced inflammatory response and NLRP3 inflammasome but activated autophagy, while all these effects were reversed by the autophagy inhibitor 3-MA. Importantly, miR-29a-3p exhibited a role similar to that of EPA in LPS-treated BV2 cells. Mechanistically, EPA treatment elevated miR-29a-3p by repressing its promoter methylation. MAPK8 was a direct target of miR-29a-3p. Inhibition of miR-29a-3p greatly diminished the regulatory roles mediated by EPA in LPS-treated BV2 cells, while these roles were further impeded after MAPK8 silencing. To conclude, our data demonstrated that EPA treatment alleviated LPS-induced NLRP3 inflammasomes by activating autophagy via regulation of miR-29a-3p/MAPK8 signaling, which further elucidates the potential antidepressant mechanism of EPA.

Leukemic cells resist lysosomal inhibition through the mitochondria-dependent reduction of intracellular pH and oxidants.

Acidic lysosomes are indispensable for cancer development and linked to chemotherapy resistance. Chloroquine (CQ) and functional analogues have been considered as a potential solution to overcome the cancer progression and chemoresistance by inhibiting the lysosome-mediated autophagy and multidrug exocytosis. However, their anti-cancer efficacy in most clinical trials demonstrated modest improvement. In this study, we investigated the detailed mechanisms underlying the acquired resistance of K562 leukemic cells to CQ treatment. In response to 5-80 µM CQ, the lumen pH of endosomal-lysosomal system immediately increased and gradually reached dynamic equilibrium within 24 h. Leukemic cells produced more acidic organelles to tolerate 5-10 µM CQ. CQ (20-80 µM) concentration-dependently triggered cytosolic pH (pHi) rise, G0/G1 arrest, mitochondrial depolarization/fragmentation, and necrotic/apoptotic cell death. Oxidant induction by CQ was responsible for the mitochondria-dependent cytotoxicity and partial pHi elevation. Cells that survived the CQ cytotoxicity were accompanied with increased mitochondria. Under the 80 µM CQ challenge, co-treatment with the inhibitor of F0 part of mitochondrial H+-ATP synthase, oligomycin (40 nM), prevented the elevation of oxidants as well as pHi, and attenuated stresses on mitochondria, cell survival, and cell proliferation. Besides, oligomycin-treated cells obviously displayed the lysosomal peripheralization and plasma membrane blebbing, suggesting that these cells were in process of lysosomal exocytosis and microvesicle release. Enhanced motion of these secretory processes allowed the cells to exclude CQ and repair necrotic injury. Together, the oxidant production and the proton dynamic interconnection among lysosomes, mitochondria, and cytosol are crucial for leukemic susceptibility to lysosomotropic chemotherapeutics.

Understanding the microfluidic generation of double emulsion droplets with alginate shell.

The monodisperse double emulsions obtained by microfluidic method can serve as ideal templates for preparing core-shell alginate microcapsules, which have attracted much attention in biological applications, such as drug delivery systems and cell encapsulation, tissue engineering. However, the formation behavior and dynamic analysis of double emulsion with an alginate shell is still unclear due to the complex rheological behavior of alginate solutions. Herein, we employ a dual-coaxial microfluidic device to generate the high-quality double emulsion droplets with alginate shell, focusing on the effects of the fluid properties of alginate solution in the middle phase (viscosity, µm) and the fluid flow rate on the droplet formation mechanism. As the viscosity of the middle fluid (µm) increased, the size of compound droplets (D2) increased and the size of inner droplets (D1) decreased, and the break-up regimes occurred a dripping-to-jetting transition when µm = 160 mPa s. The number of encapsulated inner droplets can be predicted and precisely controlled by regulating the generation frequency of inner (f1) and outer droplets (f2). The breakup dynamics of the alginate thread are also analyzed by using the volume-of-fluid/continuum-surface-force (VOF/CSF) method. The results show that the pressure and velocity in the neck of pinch-off is lower in the jetting than that in the dripping regime. This study will provide useful guidance for the rational design and controllable preparation of core-shell alginate microcapsules.

Reliability and validity of the repetitive behavior scale-revised for young Chinese children with autism spectrum disorder in Jiangxi Province.

Restricted and repetitive behaviors (RRBs) are one of the two main diagnostic features of autism spectrum disorder (ASD). To date, a growing body of research on RRB in children with ASD has recently attracted academic attention. The Repetitive Behavior Scale-Revised (RBS-R) was primarily intended for use in evaluating RRBs observed in ASD. This study recruited 381 Chinese children with ASD aged 2-4 years to measure the reliability and validity of the RBS-R. Confirmatory factor analysis (CFA) was applied to the structuring models of the four proposed structural models, indicating that a 6-factor model demonstrated good internal consistency and the best fit based on common overall fit indices. These findings suggest the utility of the Chinese version of RBS-R.

Early Growth Response 1 Strengthens Pol-III-Directed Transcription and Transformed Cell Proliferation by Controlling PTEN/AKT Signalling Activity.

RNA polymerase III (Pol III) products play essential roles in ribosome assembly, protein synthesis, and cell survival. Deregulation of Pol-III-directed transcription is closely associated with tumorigenesis. However, the regulatory pathways or factors controlling Pol-III-directed transcription remain to be investigated. In this study, we identified a novel role of EGR1 in Pol-III-directed transcription. We found that Filamin A (FLNA) silencing stimulated EGR1 expression at both RNA and protein levels. EGR1 expression positively correlated with Pol III product levels and cell proliferation activity. Mechanistically, EGR1 downregulation dampened the occupancies of Pol III transcription machinery factors at the loci of Pol III target genes. Alteration of EGR1 expression did not affect the expression of p53, c-MYC, and Pol III general transcription factors. Instead, EGR1 activated RhoA expression and inhibited PTEN expression in several transformed cell lines. We found that PTEN silencing, rather than RhoA overexpression, could reverse the inhibition of Pol-III-dependent transcription and cell proliferation caused by EGR1 downregulation. EGR1 could positively regulate AKT phosphorylation levels and is required for the inhibition of Pol-III-directed transcription mediated by FLNA. The findings from this study indicate that EGR1 can promote Pol-III-directed transcription and cell proliferation by controlling the PTEN/AKT signalling pathway.

Proteomic profiling identifies novel diagnostic biomarkers and molecular subtypes for mucinous tubular and spindle cell carcinoma of the kidney.

Mucinous tubular and spindle cell carcinoma (MTSCC) is a relatively rare renal epithelial neoplasm resembling type 1 papillary renal cell carcinoma (PRCC) morphologically and immunohistochemically. The accurate diagnosis of MTSCC remains a challenge. Here, by using proteomic profiling, we characterized MTSCC and PRCC to identify diagnostic biomarkers. We found that the MTSCC tumor proteome was significantly enriched in B-cell-mediated immunity when compared with the proteome of adjacent normal tissues of MTSCC or tumors of PRCC. Importantly, we identified MZB1, VCAN, and SOSTDC1 as diagnostic biomarkers to distinguish MTSCC from the solid variant of type 1 PRCC, with an AUC of 0.985 when combined. MZB1 was inversely correlated with tumor clinical stage and may play an anti-tumor role by activating the complement system. Finally, unsupervised clustering revealed two molecular subtypes of MTSCC, displaying different morphology, expression signatures of oxidative phosphorylation, and aggravation. In summary, our analyses identified a three-protein diagnostic panel and molecular subtypes for MTSCC. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Two Facile Aniline-Based Hypercrosslinked Polymer Adsorbents for Highly Efficient Iodine Capture and Removal.

Effective capture and safe disposal of radioactive iodine (129I or 131I) during nuclear power generation processes have always been a worldwide environmental concern. Low-cost and high-efficiency iodine removal materials are urgently needed. In this study, we synthesized two aniline-based hypercrosslinked polymers (AHCPs), AHCP-1 and AHCP-2, for iodine capture in both aqueous and gaseous phases. They are obtained by aniline polymerization through Friedel-Crafts alkylation and Scholl coupling reaction, respectively, with high chemical and thermal stability. Notably, AHCP-1 exhibits record-high static iodine adsorption (250 wt%) in aqueous solution. In the iodine vapor adsorption, AHCP-2 presents an excellent total iodine capture (596 wt%), surpassing the most reported amorphous polymer adsorbents. The rich primary amine groups of AHCPs promote the rapid physical capture of iodine from iodine water and iodine vapor. Intrinsic features such as low-cost preparation, good recyclability, as well as excellent performance in iodine capture indicate that the AHCPs can be used as potential candidates for the removal of iodine from radioactive wastewater and gas mixtures.

Protein powder derived nitrogen-doped carbon supported atomically dispersed iron sites for selective oxidation of ethylbenzene.

Atomically dispersed Fe species embedded in the nitrogen-containing carbon supports (Fe1/NC) are successfully synthesized using a ball milling approach, with commercial protein powder as the nitrogen source. The catalyst exhibits outstanding performance in the oxidation of aromatic compounds containing saturated C-H bonds into corresponding ketones under ambient conditions, which is superior to those of a nanoparticle catalyst (Fen/NC) and a metal-free catalyst (NC).

Applications of Multi-Omics Technologies for Crop Improvement.

Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.

The genomic architecture of EBV and infected gastric tissue from precursor lesions to carcinoma.

BACKGROUND: Epstein-Barr virus (EBV)-associated gastric carcinomas (EBVaGCs) present unique molecular signatures, but the tumorigenesis of EBVaGCs and the role EBV plays during this process remain poorly understood. METHODS: We applied whole-exome sequencing, EBV genome sequencing, and whole-genome bisulfite sequencing to multiple samples (n = 123) derived from the same patients (n = 25), which covered saliva samples and different histological stages from morphologically normal epithelial tissues to dysplasia and EBVaGCs. We compared the genomic landscape between EBVaGCs and their precursor lesions and traced the clonal evolution for each patient. We also analyzed genome sequences of EBV from samples of different histological types. Finally, the key molecular events promoting the tumor evolution were demonstrated by MTT, IC50, and colony formation assay in vitro experiments and in vivo xenograft experiments. RESULTS: Our analysis revealed increasing mutational burden and EBV load from normal tissues and low-grade dysplasia (LD) to high-grade dysplasia (HD) and EBVaGCs, and oncogenic amplifications occurred late in EBVaGCs. Interestingly, within each patient, EBVaGCs and HDs were monoclonal and harbored single-strain-originated EBV, but saliva or normal tissues/LDs had different EBV strains from that in EBVaGCs. Compared with precursor lesions, tumor cells showed incremental methylation in promotor regions, whereas EBV presented consistent hypermethylation. Dominant alterations targeting the PI3K-Akt and Wnt pathways were found in EBV-infected cells. The combinational inhibition of these two pathways in EBV-positive tumor cells confirmed their synergistic function. CONCLUSIONS: We portrayed the (epi) genomic evolution process of EBVaGCs, revealed the extensive genomic diversity of EBV between tumors and normal tissue sites, and demonstrated the synergistic activation of the PI3K and Wnt pathways in EBVaGCs, offering a new potential treatment strategy for this disease.