Comparative transcriptome analysis reveals resistance-related genes and pathways in Musa acuminata banana 'Guijiao 9' in response to Fusarium wilt.

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases in bananas resulting in significant loss of Cavendish bananas production worldwide. Here we show the agronomic traits and the resistance of 'Guijiao 9' in the field trials from 2012 to 2017. And then we dissect and compare the transcriptome response from these two cultivars (cv. 'Guijiao 9' and cv. Williams) in an attempt to understand the molecular basis that contribute to the enhanced Foc tropical race 4 (Foc-TR4) resistance. 'Guijiao 9' is a Cavendish cultivar with strong resistance to Foc-TR4, which was reflected in a lower disease severity and incidence in glasshouse and field trails, when compared to the susceptible cultivar Williams. Gene expression profiles of 'Guijiao 9' and Williams were captured by performing RNA-Seq analysis on 16 biological samples collected over a six day period post inoculation with Foc-TR4. Transcriptional reprogramming in response to Foc-TR4 was detected in both genotypes but the response was more drastic in 'Guijiao 9' than in Williams. Specific genes involved in plant-pathogen interaction and defense signaling including MAPK, calcium, salicylic acid, jasmonic acid and ethylene pathways were analyzed and compared between 'Guijiao 9' and Williams. Genes associated with defense-related metabolites synthesis such as NB-LRR proteins, calmodulin-binding protein and phenylpropanoids biosynthesis genes were significantly up-regulated in 'Guijiao 9' resistant to Foc-TR4 infection. Taken together, this study highlights the important roles of plant hormone regulation and defense gene activation in mediating resistance in 'Guijiao 9'

Effect of cytokinins on shoot regeneration from cotyledon and leaf segment of stem mustard (Brassica juncea var. tsatsai)

Cotyledon and leaf segments of stem mustard (Brassica juncea var. tsatsai) were cultured on Murashige and Skoog medium supplemented with various concentrations of different cytokinins [6-benzyladenine (BA), N-(2-chloro-4-pyridyl)-n-phenylurea (CPPU), 6-furfurylaminopurine (KT) and thidiazuron (TDZ)] in combinations with different levels of ¿-naphthalene acetic acid (NAA). The shoot regeneration frequency of cotyledon and leaf segment was dependent on the kinds and concentrations of cytokinins used in the medium, while in most cases cotyledon gave high regeneration frequency than leaf segment. TDZ proved to be the best cytokinin to induce shoot from both cotyledon and leaf segments compared to BA, KT and CPPU. The highest frequency of shoot regeneration was 61.3¿67.9 % in cotyledon and 40.7¿52.4% in leaf segment respectively when 2.27 or 4.54 ¿M TDZ was combined with 5.37 ¿M NAA. Next to TDZ, CPPU was also very suitable to induce shoot formation both in cotyledon and leaf segment. When 1.61 ¿M CPPU was combined with 2.69 ¿M NAA, shoot regeneration frequency was 45.0% in cotyledon and 36.4% in leaf segment, respectively. It was also shown that KT and BA affected shoot regeneration from cotyledon and leaf segment, the shoot regeneration was greatly increased when NAA was added together with cytokinins. The efficient and reliable shoot regeneration system was developed in both cotyledon and leaf segments. This regeneration protocol may be applicable to the improvement of this crop by genetic engineering in the futur

Quantization and diagnosis of Shanghuo (Heatiness) in Chinese medicine using a diagnostic scoring scheme and salivary biochemical parameters

Background: This study aims to establish a diagnostic scoring scheme for Shanghuo (Heatiness) and to evaluate whether Shanghuo is associated with biochemical parameters of salivary lysozyme (LYZ), salivary secreted immunoglobulin (S-IgA), salivary amylase (AMS), and saliva flow rate (SFR). Methods: We collected 121 Shanghuo patients at the Affiliated Hospitals of Guangzhou University of Traditional Chinese Medicine in Guangdong Province, 60 cases as a Shanghuo recovered group, and 60 healthy cases as a healthy control group. The diagnostic scoring scheme was established by probability theory and maximum likelihood discriminatory analysis on the basis of epidemiology with the design of self-controlled clinical trial. Subsequently, we used the same methods to collect 120 Shanghuo patients, 60 Shanghuo recovered cases, and 60 healthy cases in both Hunan Province and Henan Province. The levels of LYZ, S-IgA, AMS, and SFR were tested when the patients suffered from Shanghuo or recovered, respectively. Results: The diagnostic score table for Shanghuo syndrome was established first. In the retrospective tests, the sensitivity, specificity, accuracy, and positive likelihood ratio of the diagnostic score table were 98.9%, 93.5%, 97.5%, and 14.34%, respectively. In the prospective tests, the corresponding values were 94.9%, 85.7%, 91.7%, and 6.64%, respectively. Shanghuo was classified into three degrees based on the diagnostic scores, common Shanghuo: 63–120; serious Shanghuo: 121–150; very serious Shanghuo: >150. A negative correlation was found between Shanghuo and S-IgA (R = -0.428; P = 0.000). The level of S-IgA was also affected by seasonal and regional factors. No significant correlations were found between Shanghuo and the levels of LYZ, AMS, and SFR. Conclusions: In this study, Shanghuo could be diagnosed by the combination of the diagnostic score table and S-lgA level

Identification of immune infiltration and cuproptosis-related molecular clusters in tuberculosis

BackgroundTuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) infection. Cuproptosis is a novel cell death mechanism correlated with various diseases. This study sought to elucidate the role of cuproptosis-related genes (CRGs) in TB.MethodsBased on the GSE83456 dataset, we analyzed the expression profiles of CRGs and immune cell infiltration in TB. Based on CRGs, the molecular clusters and related immune cell infiltration were explored using 92 TB samples. The Weighted Gene Co-expression Network Analysis (WGCNA) algorithm was utilized to identify the co-expression modules and cluster-specific differentially expressed genes. Subsequently, the optimal machine learning model was determined by comparing the performance of the random forest (RF), support vector machine (SVM), generalized linear model (GLM), and eXtreme Gradient Boosting (XGB). The predictive performance of the machine learning model was assessed by generating calibration curves and decision curve analysis and validated in an external dataset.Results11 CRGs were identified as differentially expressed cuproptosis genes. Significant differences in immune cells were observed in TB patients. Two cuproptosis-related molecular clusters expressed genes were identified. Distinct clusters were identified based on the differential expression of CRGs and immune cells. Besides, significant differences in biological functions and pathway activities were observed between the two clusters. A nomogram was generated to facilitate clinical implementation. Next, calibration curves were generated, and decision curve analysis was conducted to validate the accuracy of our model in predicting TB subtypes. XGB machine learning model yielded the best performance in distinguishing TB patients with different clusters. The top five genes from the XGB model were selected as predictor genes. The XGB model exhibited satisfactory performance during validation in an external dataset. Further analysis revealed that these five model-related genes were significantly associated with latent and active TB.ConclusionOur study provided hitherto undocumented evidence of the relationship between cuproptosis and TB and established an optimal machine learning model to evaluate the TB subtypes and latent and active TB patients

Deletions in CWH43 cause idiopathic normal pressure hydrocephalus

Idiopathic normal pressure hydrocephalus (iNPH) is a neurological disorder that occurs in about 1% of individuals over age 60 and is characterized by enlarged cerebral ventricles, gait difficulty, incontinence, and cognitive decline. The cause and pathophysiology of iNPH are largely unknown. We performed whole exome sequencing of DNA obtained from 53 unrelated iNPH patients. Two recurrent heterozygous loss of function deletions in CWH43 were observed in 15% of iNPH patients and were significantly enriched 6.6-fold and 2.7-fold, respectively, when compared to the general population. Cwh43 modifies the lipid anchor of glycosylphosphatidylinositol-anchored proteins. Mice heterozygous for CWH43 deletion appeared grossly normal but displayed hydrocephalus, gait and balance abnormalities, decreased numbers of ependymal cilia, and decreased localization of glycosylphosphatidylinositol-anchored proteins to the apical surfaces of choroid plexus and ependymal cells. Our findings provide novel mechanistic insights into the origins of iNPH and demonstrate that it represents a distinct disease entity

Using aquatic animals as partners to increase yield and maintain soil nitrogen in the paddy ecosystems

Whether species coculture can overcome the shortcomings of crop monoculture requires additional study. Here, we show how aquatic animals (i.e. carp, crabs, and softshell turtles) benefit paddy ecosystems when cocultured with rice. Three separate field experiments and three separate mesocosm experiments were conducted. Each experiment included a rice monoculture (RM) treatment and a rice-aquatic animal (RA) coculture treatment; RA included feed addition for aquatic animals. In the field experiments, rice yield was higher with RA than with RM, and RA also produced aquatic animal yields that averaged 0.52–2.57 t ha-1. Compared to their corresponding RMs, the three RAs had significantly higher apparent nitrogen (N)-use efficiency and lower weed infestation, while soil N contents were stable over time. Dietary reconstruction analysis based on 13C and 15N showed that 16.0–50.2% of aquatic animal foods were from naturally occurring organisms in the rice fields. Stable-isotope-labeling (13C) in the field experiments indicated that the organic matter decomposition rate was greater with RA than with RM. Isotope 15N labeling in the mesocosm experiments indicated that rice used 13.0–35.1% of the aquatic animal feed-N. All these results suggest that rice-aquatic animal coculture increases food production, increases N-use efficiency, and maintains soil N content by reducing weeds and promoting decomposition and complementary N use. Our study supports the view that adding species to monocultures may enhance agroecosystem functions

Can edible mushrooms boost soil health in banana organic systems?

Manipulation of the rhizosphere can improve soil health; and foster sustainable management of pests and diseases. Biological inputs such as spent substrates from edible mushrooms (e.g., Pleurotus ostreatus) gardens offer sustainable alternatives on that direction. This work presents a meta-analysis of major trends in knowledge generation on edible mushroom use in agriculture, especially to benefit the crop rhizosphere. It further delves into a detailed synthesis of the effects of spent mushroom wastes (SMW) on the physical, chemical, and biological properties of the soil rhizosphere and agroecosystems. The review concludes by providing an outlook on how SMW can potentially support the management of key soil health challenges in organic banana production systems

Current state of Fusarium wilt of banana in the subtropics

The original publication is available at https://www.actahort.org/books/1272/1272_7.ht

Molecular diagnosis and vegetative compatibility group analysis of Fusarium Wilt of banana in Nepal

Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), is the most important constraint of the banana industry globally. In Nepal, epidemics resembling FWB have been increasingly observed on the Malbhog cultivar in the past several years. However, the disease has not been officially reported yet, and consequently, little is known about the pathogen present across the country. In this study, we characterized 13 fungal strains isolated from banana plants of the Malbhog cultivar (Silk, AAB) showing symptoms similar to FWB in banana plantations in Nepal. All of the strains were typed as belonging to the F. oxysporum and caused FWB symptoms when inoculated in the Malbhog and Cachaco (Bluggoe, ABB) cultivars. No symptoms were observed in the Williams cultivar (Cavendish, AAA). Vegetative compatibility group (VCG) analysis classified the strains as VCG 0124 or VCG 0125. PCR analyses conducted with primers specific for Foc race 1 (Foc R1) or Foc tropical race 4 (TR4) revealed that all the strains reacted positively for Foc R1 and none for TR4. Altogether, our results demonstrated that the pathogen populations causing FWB of the Malbhog cultivar in Nepal were Foc R1. This work reported, for the first time, the occurrence of FWB in Nepal. Further studies with larger Foc populations are needed to better understand disease epidemiology to design sustainable disease management strategies

Glucose and Palmitate Differentially Regulate PFKFB3/iPFK2 and Inflammatory Responses in Mouse Intestinal Epithelial Cells

The gene PFKFB3 encodes for inducible 6-phosphofructo-2-kinase, a glycolysis-regulatory enzyme that protects against diet-induced intestine inflammation. However, it is unclear how nutrient overload regulates PFKFB3 expression and inflammatory responses in intestinal epithelial cells (IECs). In the present study, primary IECs were isolated from small intestine of C57BL/6J mice fed a low-fat diet (LFD) or high-fat diet (HFD) for 12 weeks. Additionally, CMT-93 cells, a cell line for IECs, were cultured in low glucose (LG, 5.5 mmol/L) or high glucose (HG, 27.5 mmol/L) medium and treated with palmitate (50 mu mol/L) or bovine serum albumin (BSA) for 24 hr. These cells were analyzed for PFKFB3 and inflammatory markers. Compared with LFD, HFD feeding decreased IEC PFKFB3 expression and increased IEC proinflammatory responses. In CMT-93 cells, HG significantly increased PFKFB3 expression and proinflammatory responses compared with LG. Interestingly, palmitate decreased PFKFB3 expression and increased proinflammatory responses compared with BSA, regardless of glucose concentrations. Furthermore, HG significantly increased PFKFB3 promoter transcription activity compared with LG. Upon PFKFB3 overexpression, proinflammatory responses in CMT-93 cells were decreased. Taken together, these results indicate that in IECs glucose stimulates PFKFB3 expression and palmitate contributes to increased proinflammatory responses. Therefore, PFKFB3 regulates IEC inflammatory status in response to macronutrients.National Institutes of Health [HL108922, HL095556, R01DK095828, R01DK095862]; National Natural Science Foundation of China [81100562/H0711]; Hatch Program of National Institutes of Food and Agriculture (NIFA)SCI(E)[email protected]; [email protected]