Association between systemic inflammatory indicators with the survival of chronic kidney disease: a prospective study based on NHANES.

Background: systemic inflammation disorders were observed in chronic kidney disease (CKD). Whether the systemic inflammatory indicators could be optimal predictors for the survival of CKD remains less studied. Methods: In this study, participants were selected from the datasets of the National Health and Nutrition Examination Survey (NHANES) between 1999 to 2018 years. Four systemic inflammatory indicators were evaluated by the peripheral blood tests including systemic immune-inflammation index (SII, platelet*neutrophil/lymphocyte), neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-monocyte ratio (LMR). Kaplan-Meier curves, restricted cubic spline (RCS), and Cox regression analysis were used to evaluate the association between the inflammatory index with the all-cause mortality of CKD. Receiver operating characteristic (ROC) and concordance index (C-index) were used to determine the predictive accuracy of varied systemic inflammatory indicators. Sensitive analyses were conducted to validate the robustness of the main findings. Results: A total of 6,880 participants were included in this study. The mean age was 67.03 years old. Among the study population, the mean levels of systemic inflammatory indicators were 588.35 in SII, 2.45 in NLR, 133.85 in PLR, and 3.76 in LMR, respectively. The systemic inflammatory indicators of SII, NLR, and PLR were all significantly positively associated with the all-cause mortality of CKD patients, whereas the high value of LMR played a protectable role in CKD patients. NLR and LMR were the leading predictors in the survival of CKD patients [Hazard ratio (HR) =1.21, 95% confidence interval (CI): 1.07-1.36, p = 0.003 (3rd quartile), HR = 1.52, 95%CI: 1.35-1.72, p<0.001 (4th quartile) in NLR, and HR = 0.83, 95%CI: 0.75-0.92, p<0.001 (2nd quartile), HR = 0.73, 95%CI: 0.65-0.82, p<0.001 (3rd quartile), and = 0.74, 95%CI: 0.65-0.83, p<0.001 (4th quartile) in LMR], with a C-index of 0.612 and 0.624, respectively. The RCS curves showed non-linearity between systemic inflammatory indicators and all-cause mortality risk of the CKD population. Conclusion: Our study highlights that systemic inflammatory indicators are important for predicting the survival of the U.S. population with CKD. The systemic inflammatory indicators would add additional clinical value to the health care of the CKD population.

Economical Production of Phenazine-1-carboxylic Acid from Glycerol by Pseudomonas chlororaphis Using Cost-Effective Minimal Medium.

Phenazine compounds are widely used in agricultural control and the medicine industry due to their high inhibitory activity against pathogens and antitumor activity. The green and sustainable method of synthesizing phenazine compounds through microbial fermentation often requires a complex culture medium containing tryptone and yeast extract, and its cost is relatively high, which greatly limits the large-scale industrial production of phenazine compounds by fermentation. The aim of this study was to develop a cost-effective minimal medium for the efficient synthesis of phenazine compounds by Pseudomonas chlororaphis. Through testing the minimum medium commonly used by Pseudomonas, an ME medium for P. chlororaphis with a high production of phenazine compounds was obtained. Then, the components of the ME medium and the other medium were compared and replaced to verify the beneficial promoting effect of Fe2+ and NH4+ on phenazine compounds. A cost-effective general defined medium (GDM) using glycerol as the sole carbon source was obtained by optimizing the composition of the ME medium. Using the GDM, the production of phenazine compounds by P. chlororaphis reached 1073.5 mg/L, which was 1.3 times that achieved using a complex medium, while the cost of the GDM was only 10% that of a complex medium (e.g., the KB medium). Finally, by engineering the glycerol metabolic pathway, the titer of phenazine-1-carboxylic acid reached the highest level achieved using a minimum medium so far. This work demonstrates how we systematically analyzed and optimized the composition of the medium and integrated a metabolic engineering method to obtain the most cost-effective fermentation strategy.

Screening of Candidate Effectors from Magnaporthe oryzae by In Vitro Secretomic Analysis.

Magnaporthe oryzae is the causal agent of rice blast, one of the most serious diseases of rice worldwide. Secreted proteins play essential roles during a M. oryzae-rice interaction. Although much progress has been made in recent decades, it is still necessary to systematically explore M. oryzae-secreted proteins and to analyze their functions. This study employs a shotgun-based proteomic analysis to investigate the in vitro secretome of M. oryzae by spraying fungus conidia onto the PVDF membrane to mimic the early stages of infection, during which 3315 non-redundant secreted proteins were identified. Among these proteins, 9.6% (319) and 24.7% (818) are classified as classically or non-classically secreted proteins, while the remaining 1988 proteins (60.0%) are secreted through currently unknown secretory pathway. Functional characteristics analysis show that 257 (7.8%) and 90 (2.7%) secreted proteins are annotated as CAZymes and candidate effectors, respectively. Eighteen candidate effectors are selected for further experimental validation. All 18 genes encoding candidate effectors are significantly up- or down-regulated during the early infection process. Sixteen of the eighteen candidate effectors cause the suppression of BAX-mediated cell death in Nicotiana benthamiana by using an Agrobacterium-mediated transient expression assay, suggesting their involvement in pathogenicity related to secretion effectors. Our results provide high-quality experimental secretome data of M. oryzae and will expand our knowledge on the molecular mechanisms of M. oryzae pathogenesis.

Evaluating the screening value of serum light chain ratio, ß2 microglobulin, lactic dehydrogenase and immunoglobulin in patients with multiple myeloma using ROC curves.

OBJECTIVE: Several laboratory and imaging assays are required to diagnose multiple myeloma (MM). Serum and urine immunofixation electrophoresis are two key assays to diagnose MM, while they have not been extensively utilized in Chinese hospitals. Serum light chain (sLC), ß2 microglobulin (ß2-MG), lactic dehydrogenase (LDH), and immunoglobulin (Ig) are routinely measured in the majority of Chinese hospitals. Imbalance of sLC ratio (involved light chain/uninvolved light chain) is frequently observed in MM patients. This study aimed to evaluate the screening value of sLC ratio, ß2-MG, LDH, and Ig in MM patients using receiver operating characteristic (ROC) curves. METHODS: Data of 303 suspected MM patients, who were admitted to the Taizhou Central Hospital between March 2015 and July 2021, were retrospectively analyzed. In total, 69 patients (MM arm) met the International Myeloma Working Group (IMWG) updated criteria for the diagnosis of MM, while 234 patients were non-MM (non-MM arm). All patients' sLC, ß2-MG, LDH, and Ig were measured using commercially available kits according to the manufacturer's instructions. The ROC curve analysis was employed to assess the screening value of sLC ratio, ß2-MG, LDH, creatinine (Cr) and Ig. The statistical analysis was carried out by SPSS 26.0 (IBM, Armonk, NY, USA) and MedCalc 19.0.4 (Ostend, Belgium) software. RESULTS: There was no significant difference between the MM and non-MM arms in terms of gender, age and Cr. The median sLC ratio in the MM arm was 11.5333, which was significantly higher than that of 1.9293 in the non-MM arm (P<0.001). The area under the curve (AUC) of sLC ratio was 0.875, which indicated a robust screening value. The optimal sensitivity and specificity were 81.16% and 94.87% respectively, when the sLC ratio was set as 3.2121. The serum levels of ß2-MG and Ig were higher in the MM arm than those in the non-MM arm (P<0.001). The AUC values of ß2-MG, LDH, and Ig were 0.843 (P<0.001), 0.547 (P = 0.2627), and 0.723 (P<0.001), respectively. The optimal cutoff values of ß2-MG, LDH, and Ig were 1.95 mg/L, 220 U/L, and 46.4 g/L respectively, in the context of screening value. The triple combination of sLC ratio (3.2121), ß2-MG (1.95 mg/L), and Ig (46.4 g/L) yielded a higher screening value compared with that of sLC ratio alone (AUC, 0.952; P<0.0001). The triple combination had a sensitivity of 94.20% and a specificity of 86.75%. The addition of LDH to the triple combination and formation of quadruple combination did not optimize the screening value, with AUC, sensitivity, and specificity of 0.952, 94.20%, and 85.47%, respectively. CONCLUSION: The triple combination strategy (sLC ratio, 3.2121; ß2-MG, 1.95 mg/L; Ig, 46.4 g/L) is accompanied by remarkable sensitivity and specificity for screening MM in Chinese hospitals.

A novel elicitor MoVcpo is necessary for the virulence of Magnaporthe oryzae and triggers rice defense responses.

Rice blast caused by Magnaporthe oryzae is one of the most important diseases of rice. Elicitors secreted by M. oryzae play important roles in the interaction with rice to facilitate fungal infection and disease development. In recent years, several elicitor proteins have been identified in M. oryzae, and their functions and importance are increasingly appreciated. In this study, we purified a novel elicitor-activity protein from M. oryzae, which was further identified as a vanadium chloroperoxidase (MoVcpo) by MAIDL TOF/TOF MS. The purified MoVcpo induced reactive oxygen species (ROS) accumulation in host cells, up-regulated the expression of multiple defense-related genes, thus significantly enhancing rice resistance against M. oryzae. These results suggested that MoVcpo functions as a pathogen-associated molecular pattern (PAMP) to trigger rice immunity. Furthermore, MoVcpo was highly expressed in the early stage of M. oryzae infection. Deletion of MoVcpo affected spore formation, conidia germination, cell wall integrity, and sensitivity to osmotic stress, but not fungal growth. Interestingly, compared with the wild-type, inoculation with MoVcpo deletion mutant on rice led to markedly induced ROS accumulation, increased expression of defense-related genes, but also lower disease severity, suggesting that MoVcpo acts as both an elicitor activating plant immune responses and a virulence factor facilitating fungal infection. These findings reveal a novel role for vanadium chloroperoxidase in fungal pathogenesis and deepen our understanding of M. oryzae-rice interactions.

FoCupin1, a Cupin_1 domain-containing protein, is necessary for the virulence of Fusarium oxysporum f. sp. cubense tropical race 4.

Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is an important soilborne fungal pathogen that causes the most devastating banana disease. Effectors secreted by microbes contribute to pathogen virulence on host plants in plant-microbe interactions. However, functions of Foc TR4 effectors remain largely unexplored. In this study, we characterized a novel cupin_1 domain-containing protein (FoCupin1) from Foc TR4. Sequence analysis indicated that the homologous proteins of FoCupin1 in phytopathogenic fungi were evolutionarily conserved. Furthermore, FoCupin1 could suppress BAX-mediated cell death and significantly downregulate the expression of defense-related genes in tobacco by using the Agrobacterium-mediated transient expression system. FoCupin1 was highly induced in the early stage of Foc TR4 infection. The deletion of FoCupin1 gene did not affect Foc TR4 growth and conidiation. However, FoCupin1 deletion significantly reduced Foc TR4 virulence on banana plants, which was further confirmed by biomass assay. The expression of the defense-related genes in banana was significantly induced after inoculation with FoCupin1 mutants. These results collectively indicate FoCupin1 is a putative effector protein that plays an essential role in Foc TR4 pathogenicity. These findings suggest a novel role for cupin_1 domain-containing proteins and deepen our understanding of effector-mediated Foc TR4 pathogenesis.

Deubiquitinase Ubp3 regulates ribophagy and deubiquitinates Smo1 for appressorium-mediated infection by Magnaporthe oryzae.

The Ubp family of deubiquitinating enzymes has been found to play important roles in plant-pathogenic fungi, but their regulatory mechanisms are still largely unknown. In this study, we revealed the regulatory mechanism of the deubiquitinating enzyme Ubp3 during the infection process of Magnaporthe oryzae. AUBP3 deletion mutant was severely defective in appressorium turgor accumulation, leading to the impairment of appressorial penetration. During appressorium formation, the mutant was also defective in glycogen and lipid metabolism. Interestingly, we found that nitrogen starvation and rapamycin treatment induced the ribophagy process in M. oryzae, which is closely dependent on Ubp3. In the ∆ubp3 mutant, the ribosome proteins and rRNAs were not well degraded on nitrogen starvation and rapamycin treatment. We also found that Ubp3 interacted with the GTPase-activating protein Smo1 and regulated its de-ubiquitination. Ubp3-dependent de-ubiquitination of Smo1 may be required for Smo1 to coordinate Ras signalling. Taken together, our results showed at least two roles of Ubp3 in M. oryzae: it regulates the ribophagy process and it regulates de-ubiquitination of GTPase-activating protein Smo1 for appressorium-mediated infection.

In Vitro Secretome Analysis Suggests Differential Pathogenic Mechanisms between Fusarium oxysporum f. sp. cubense Race 1 and Race 4.

Banana Fusarium wilt, caused by the fungus pathogen Fusarium oxysporum f. sp. cubense (Foc), is a devastating disease that causes tremendous reductions in banana yield worldwide. Secreted proteins can act as pathogenicity factors and play important roles in the Foc-banana interactions. In this study, a shotgun-based proteomic approach was employed to characterize and compare the secretomes of Foc1 and Foc4 upon banana extract treatment, which detected 1183 Foc1 and 2450 Foc4 proteins. Comprehensive in silico analyses further identified 447 Foc1 and 433 Foc4 proteins in the classical and non-classical secretion pathways, while the remaining proteins might be secreted through currently unknown mechanisms. Further analyses showed that the secretomes of Foc1 and Foc4 are similar in their overall functional characteristics and share largely conserved repertoires of CAZymes and effectors. However, we also identified a number of potentially important pathogenicity factors that are differentially present in Foc1 and Foc4, which may contribute to their different pathogenicity against banana hosts. Furthermore, our quantitative PCR analysis revealed that genes encoding secreted pathogenicity factors differ significantly between Foc1 and Foc4 in their expression regulation in response to banana extract treatment. To our knowledge, this is the first experimental secretome analysis that focused on the pathogenicity mechanism in different Foc races. The results of this study provide useful resources for further exploration of the complicated pathogenicity mechanisms in Foc.

Marinobacter caseinilyticus sp. nov., Isolated from Saline Soil.

A Gram-stain-negative, motile, aerobic, rod-shaped bacterium with flagella, designated M3-13T, was isolated from a saline soil in Zhoushan, China. According to phylogenetic analysis based on 16S rRNA gene sequences, strain M3-13T was assigned to the genus Marinobacter with highest 16S rRNA gene sequence similarity of 97.7% to Marinobacter maroccanus LMG 30466T, followed by Marinobacter sediminum R65 T (97.5%) and M. salsuginis SD-14BT (97.2%). Digital DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain M3-13T and M. maroccanus LMG 30466T. Digital DDH estimation (19.8%) as well as ANI (72.98%) proved the dissimilarity of strain M3-13T. Optimal growth of the strain M3-13T was at 28-30 °C and at pH 8.0-8.5, in the presence of 3-6% (w/v) NaCl. The major fatty acids detected in strain M3-13T were C16:1 ω7c/C16:1 ω6c, C16:0, C18:1ω7c/C18:1 ω6c and C12:03-OH, and the predominant respiratory quinone was ubiquinone-9. The major polar lipids included diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophosphoglycolipid and one unidentified phosphoglycolipid. The DNA G+C content was 56.6%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain M3-13T belongs to the genus Marinobacter. Based on the polyphasic taxonomic characterization, strain M3-13T is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter caseinlyticus sp. nov. is proposed (type strain M3-13T = MCCC 1K04560T = KCTC 72043T).

Agromyces kandeliae sp. nov., isolated from rhizosphere soil of Kandelia candel in a mangrove.

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22T was isolated from the rhizosphere soil of mangrove plant, Kandelia candel collected in Zhangzhou, Fujian province, China. Strain Q22T was able to grow at 10-40 °C (optimum 30 °C), pH 5.5-9.0 (optimum 7.0-8.0) and with 0-5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain Q22T and the reference strains were 79.7-88.9% and 22.6-37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The major polar lipids of strain Q22T were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22T contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22T represents a novel species of the genus Agromyces, for which the name Agromyces kandeliae sp. nov. is proposed. The type strain is Q22T (=MCCC 1K03340T= KCTC 39961T).

Description of Erythrobacter mangrovi sp. nov., an aerobic bacterium from rhizosphere soil of mangrove plant (Kandelia candel).

A novel Gram-stain negative, aerobic, non-motile, rod-shaped bacterium, designated as strain EB310T, was isolated from rhizosphere soil of mangrove plant Kandelia candel in Fugong village, Zhangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EB310T belonged to the genus Erythrobacter, clustering with Erythrobacter pelagi JCM 17468T, Erythrobacter lutimaris KCTC 42109T and Erythrobacter marisflavi KCTC 62896T, and showed the highest 16S rRNA gene sequence similarity of 97.5% to Erythrobacter pelagi JCM 17468T. The genomic average nucleotide identity and in silico DNA-DNA hybridization values between strain EB310T and the reference strains were 71.0-75.5% and 19.8-20.0%, respectively. Growth ranges of the isolate occurred at 10-45 °C (optimum 28-30 °C), pH 5.5-9.5 (optimum pH 7.5) and 0-9.0% NaCl concentrations (optimum 2.0%, w/v). The strain did not produce bacteriochlorophyll a and flexirubin, but produced carotenoids. The strain contained Q-10 as the predominant ubiquinone and summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω6c/C18:1 ω7c) as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine. Differential phenotypic characteristics, together with chemotaxonomic, phylogenetic and genomic distinctiveness, indicated that strain EB310T is distinguishable from other members of the genus Erythrobacter. On the basis of the data exhibited, strain EB310T is considered to represent a novel species of the genus Erythrobacter, for which the name Erythrobacter mangrovi sp. nov., is proposed. The type strain is EB310T (= KCTC 72109T = MCCC 1K03690T). The genomic DNA G + C content is 62.9 mol%.

Discovery of Three 22-Membered Macrolides by Deciphering the Streamlined Genome of Mangrove-Derived Streptomyces sp. HM190.

Strain HM190, a moderate halophile, was isolated from rhizosphere soil of the mangrove Kandelia obovata in Fugong village, China. The 16S ribosomal RNA (rRNA) gene sequence and the results of phylogenetic analysis revealed that strain HM190 belonged to the genus Streptomyces and had the highest sequence similarity of 99.79% to Streptomyces heilongjiangensis NEAU-W2T. The complete genome of strain HM190 comprised 7,762,826 bp in a linear chromosome with 71.97% G + C content. According to antiSMASH analysis, a total of 30 biosynthetic gene clusters (BGCs) were predicted to be involved in secondary metabolism, 12 of which were responsible for the production of polyketide- and non-ribosomal peptide-derived secondary metabolites. Gene cluster 5 was responsible for macrolide biosynthesis in a strain-specific 126,331-bp genomic island belonging to the left-arm region. Combined genomics-metabolomics analysis led to the discovery of three 22-membered macrolides (compounds 1-3). Their structures were elucidated by using spectroscopic techniques including high-resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR). The absolute configurations of compounds 1-3 were determined by the X-ray single crystal diffraction and NMR data analysis. All three compounds displayed moderate cytotoxic activities toward tumor cell lines HepG2, A549, and HCT116.

Nitratireductor mangrovi sp. nov., a Nitrate-Reducing Bacterium Isolated from Mangrove Soil.

A Gram-stain-negative, non-motile and short-rod-shaped bacterium, designated as strain SY7T, was isolated from rhizosphere soil of the mangrove Kandelia obovata of Fugong village, in Zhangzhou, China. The isolate grew at 10-45 °C (optimum 30 °C), pH 6.0-10.0 (optimum pH 7.0) and 0-8% NaCl (optimum 3%, w/v). The 16S rRNA gene sequence and phylogenetic analysis revealed that strain SY7T located within the radiation of genus Nitratireductor and showed the highest sequence similarity of 97.23% to Nitratireductor pacificus MCCC 1A01024T. The DNA G+C content was 64.9%. In silico DNA-DNA hybridization and average nucleotide identity values between strain SY7T with reference strains of N. pacificus MCCC 1A01024T, N. basaltis KCTC 22119T and N. aquibiodomus DSM 15645T were 16.7%, 14.3%, 14.7% and 75.2%, 72.6%, 73.5%, respectively. The major isoprenoid quinone was Q-10. The dominant fatty acids were 11-methyl C18:1ω7c, iso-C17:0, C19:0ω8c cyclo and summed feature 8 (C18:1ω6c/C18:1ω7c), a profile that almost matched the other members of the genus Nitratireductor. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol. On the basis of the phenotypic, phylogenetic and chemotaxonomic analysis, strain SY7T represents a novel species of the genus Nitratireductor, for which the name Nitratireductor mangrovi sp. nov., is proposed. The type strain is SY7T (= KCTC 72110T = MCCC 1K03723T).

The Complete Genome of Emcibacter congregatus ZYLT, a Marine Bacterium Encoding a CRISPR-Cas 9 Immune System.

Emcibacter congregatus ZYLT was isolated from a sediment sample cultured in situ in a coast located in the East China Sea. The genome of E. congregatus ZYLT was sequenced and assembled into one single circular chromosome with the size of 4,189,011 bp and G+C content of 52.6%. Genomic annotation showed that E. congregatus ZYLT had an intact Type II-C CRISPR-Cas system consists of three cas genes (cas 9, cas 1, and cas 2), 34 direct repeat sequences with the length of 36 bp, and 33 spacers. The predicted Cas 9 protein was smaller than most of existing genome editing tools. This structure might have potential in developing new gene editing system and uncovering the regulatory mechanisms of CRISPR-Cas system. Besides, the comparison between E. congregatus ZYLT and its relative species living in neritic environments unraveled some common traits of the defective strategies of these bacteria to face inshore challenges including the motility, multidrug resistance, and universal efflux pumps.

Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid.

BACKGROUND: Salicylic acid (SA) is a significant signaling molecule that induces rice resistance against pathogen invasion. Protein phosphorylation carries out an important regulatory function in plant defense responses, while the global phosphoproteome changes in rice response to SA-mediated defense response has not been reported. In this study, a comparative phosphoproteomic profiling was conducted by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) analysis, with two near-isogenic rice cultivars after SA treatment. RESULTS: Thirty-seven phosphoprotein spots were differentially expressed after SA treatment, twenty-nine of which were identified by MALDI-TOF/TOF MS, belonging to nine functional categories. Phosphoproteins involved in photosynthesis, antioxidative enzymes, molecular chaperones were similarly expressed in the two cultivars, suggesting SA might alleviate decreases in plant photosynthesis, regulate the antioxidant defense activities, thus improving basal resistance response in both cultivars. Meanwhile, phosphoproteins related to defense, carbohydrate metabolism, protein synthesis and degradation were differentially expressed, suggesting phosphorylation regulation mediated by SA may coordinate complex cellular activities in the two cultivars. Furthermore, the phosphorylation sites of four identified phosphoproteins were verified by NanoLC-MS/MS, and phosphorylated regulation of three enzymes (cinnamoyl-CoA reductase, phosphoglycerate mutase and ascorbate peroxidase) was validated by activity determination. CONCLUSIONS: Our study suggested that phosphorylation regulation mediated by SA may contribute to the different resistance response of the two cultivars. To our knowledge, this is the first report to measure rice phosphoproteomic changes in response to SA, which provides new insights into molecular mechanisms of SA-induced rice defense.

Data set from the phosphoproteomic analysis of Magnaporthe oryzae-responsive proteins in susceptible and resistant rice cultivars.

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is the most destructive disease of rice and causes tremendous losses of rice yield worldwide. To explore the molecular mechanisms involved in the rice-M. oryzae interaction, we conducted a time-course phosphoproteomic analysis of leaf samples from resistant and susceptible rice cultivars infected with M. oryzae. This data article contains additional results and analysis of M. oryzae-regulated phosphoproteins in rice leaves [1]. We report the analysis of M. oryzae-regulated phosphoproteins at all time points, including Venn diagram analysis, close-up views, relative intensities, and functional category, and the MS spectra of representative phosphoprotein and representative phosphorylated peptides.

Comparative phosphoproteome analysis of Magnaporthe oryzae-responsive proteins in susceptible and resistant rice cultivars.

To explore the molecular mechanisms involved in the rice-Magnaporthe oryzae interaction, we conducted a time-course phosphoproteomic analysis of leaf samples from resistant and susceptible rice cultivars infected with M. oryzae, with emphasis on the initial biotrophic phase of the interaction. Phosphoproteomic profiling analysis led to the identification of 56 M. oryzae-regulated phosphoprotein spots. MALDI-TOF/TOF analysis unveiled 53 phosphoproteins belonging to 12 functional categories. Phosphorylation within 7 identified phosphoproteins was verified by mapping the phosphorylation sites by nanoLC-MS/MS. Although the phosphoproteins involved in photosynthesis, antioxidation, and protein folding showed similar changes in both compatible and incompatible interactions, differential regulation between the two interactions was documented for the phosphorylation status of defense-related proteins, signaling-related proteins, microtubule-associated proteins, energy-related enzymes, and amino acid synthesis-related proteins. Rice resistance is likely related to several rapidly and strongly triggered signal transduction cascades (e.g., Rac GTPases- and H2O2-mediated rice defense signaling) resulting in a multiple-level activation of defense responses. The six differentially expressed mRNA encoding proteins were measured by quantitative real-time PCR (qRT-PCR). This study provides useful clues for the further exploration of the sophisticated regulatory mechanisms of M. oryzae-rice interactions. BIOLOGICAL SIGNIFICANCE: Although large-scale identification of phosphorylated proteins has been carried out in rice, there is little report on the rice phosphoproteome in response to pathogens in general and in response to M. oryzae in particular. In this study, a time-course comparative phosphoproteomics was performed to analyze the changes of phosphoprotein profiles in rice leaves during early compatible and incompatible interactions with M. oryzae by using a combination of PEG prefractionation, Al(OH)3-MOAC, 2-DE, Pro-Q DPS and mass spectrometry. Fifty-six M. oryzae-regulated phosphoproteins were identified successfully and phosphorylation within 7 identified phosphoproteins was verified by mapping the phosphorylation sites by nanoLC-MS/MS. Our study provides novel insights into the functions of proteins involved in rice resistance and the molecular mechanism of rice resistance against M. oryzae. Furthermore, we propose the working model for the signaling pathways of rice defense in response to M. oryzae.

Quantitative analysis of APC promoter methylation in hepatocellular carcinoma and its prognostic implications.

The present study aimed to quantitatively determine the aberrant methylation signal of the adenomatous polyposis coli (APC) gene in hepatocellular carcinoma (HCC), and to evaluate whether hypermethylation of the APC promoter could be a prognostic biomarker for HCC. Taqman probe-based quantitative methylation-specific polymerase chain reaction was performed to identify the APC promoter methylation levels in 57 HCC and corresponding non-tumorous liver tissues. In the present study, the methylation level of the APC promoter was upregulated by 4.51-fold in the HCC tissues compared with the non-cancerous tissues (P=0.0003). With regard to the clinicopathological data, the methylation level of the APC promoter in the HCC samples was higher in the patients with larger tumors when the cut-off was set at 4 cm (P=0.0008), and in the older patients when the cut-off was set at 60 years old (P=0.0438). However, the methylation status in the HCC samples appeared not to affect the overall patient survival rate (P=0.1684). The findings of the present study showed that APC promoter hypermethylation accumulates during the development of HCC, but that it may not be a promising prognostic biomarker for HCC.

Comparative proteomic analysis of methyl jasmonate-induced defense responses in different rice cultivars.

Jasmonate is an important endogenous chemical signal that plays a role in modulation of plant defense responses. To understand its mechanisms in regulation of rice resistance against the fungal pathogen Magnaporthe oryzae, comparative phenotype and proteomic analyses were undertaken using two near-isogenic cultivars with different levels of disease resistance. Methyl-jasmonate (MeJA) treatment significantly enhanced the resistance against M. oryzae in both cultivars but the treated resistant cultivar maintained a higher level of resistance than the same treated susceptible cultivars. Proteomic analysis revealed 26 and 16 MeJA-modulated proteins in resistant and susceptible cultivars, respectively, and both cultivars shared a common set of 13 proteins. Cumulatively, a total of 29 unique MeJA-influenced proteins were identified with many of them known to be associated with plant defense response and ROS accumulation. Consistent with the findings of proteomic analysis, MeJA treatment increased ROS accumulation in both cultivars with the resistant cultivar showing higher levels of ROS production and cell membrane damage than the susceptible cultivar. Taken together, our data add a new insight into the mechanisms of overall MeJA-induced rice defense response and provide a molecular basis of using MeJA to enhance fungal disease resistance in resistant and susceptible rice cultivars.

Review: Recent application of chiral liquid chromatography-tandem mass spectrometric methods for enantiomeric pharmaceutical and biomedical determinations.

The technology of analyzing the pharmacological and toxicological properties of chiral drugs has become more commonly utilized since the knowledge of the biological actions of enantiomers has been gradually acquired during the last few decades. This work reviews the applications of chiral liquid chromatography coupled to tandem mass spectrometry (LC-MS) for the analysis of chiral pharmaceuticals since 2005. The enantioselective determinations in pharmaceutical and biomedical fields with LC-MS are classified based on three mobile phase modes, including normal phase, reversed phase and polar organic solvent, in terms of their compatibility with various ionization sources and specific applications.