Nanodiamond Solid-Phase Extraction and Triton X-114 Cloud Point Separation for Robust Fractionation and Shotgun Proteomics Analysis of the Human Serum Proteome.

Human serum is one of the most attractive specimens in biomarker research. However, its overcomplicated properties have hindered the analysis of low-abundance proteins by conventional mass spectrometry techniques. This work proposes an innovative strategy for utilizing nanodiamonds (NDs) in combination with Triton X-114 protein extraction to fractionate the crude serum to six pH-tuned fractions, simplifying the overall proteome and facilitating protein profiling with high efficiency. A total of 663 proteins are identified and evenly distributed among the fractions along with 39 FDA-approved biomarkers─a remarkable increase from the 230 proteins found in unfractionated crude serum. In the low-abundance protein section, 88 proteins with 7 FDA-approved biomarkers are detected─a marked increase from the 15 proteins (2 biomarkers) observed in the untreated sample. Notably, fractions at pH 11, derived from the aqueous phase of detergent separation, suggest potential applications in rapid and robust serum proteome analysis. Notably, by outlining the excellent properties of NDs for proteomic research, this work suggests a promising extraction protocol utilizing the great compatibility of NDs with streamlined serum proteomics and identifies potential avenues for future developments. Finally, we believe that this work not just improves shotgun proteomics but also opens up studies on the interaction between NDs and the human proteome. Data are available via ProteomeXchange with the identifier PXD029710.

Phosphorylation of the zinc finger transcriptional regulator ZAT6 by MPK6 regulates Arabidopsis seed germination under salt and osmotic stress.

C(2)H(2)-type zinc finger proteins (ZFPs) play diverse roles in plant response to abiotic stresses. ZAT6, an Arabidopsis C(2)H(2)-type ZFP, has been reported to regulate root development and nutrient stress responses. However, its roles in regulation of abiotic stress response are incompletely known. Here, we demonstrate that salt or osmotic stress triggers a strong increase in ZAT6 expression in leaves. Transgenic plants overexpressing ZAT6 showed improved seed germination under salt and osmotic stress. Intriguingly, ZAT6 interacts with a stress-responsive mitogen-activated protein kinase MPK6 in vitro and in planta. ZAT6 is phosphorylated by both recombinant and plant endogenous MPK6. Serine 8 and serine 223 in ZAT6 were identified as the sites phosphorylated by MPK6. In contrast to wild-type form of ZAT6, overexpression of phosphorylation mutant form did not display significantly enhanced salt and osmotic stress tolerance. Altogether, our results suggest that phosphorylation by MPK6 is required for the functional role of ZAT6 in seed germination under salt and osmotic stress.

Ethylene-responsive element-binding factor 5, ERF5, is involved in chitin-induced innate immunity response.

Our recent work demonstrated that chitin treatment modulated the expression of 118 transcription factor (TF) genes in Arabidopsis. To investigate the potential roles of these TF in chitin signaling and plant defense, we initiated an interaction study among these TF proteins, as well as two chitin-activated mitogen-activated protein kinases (MPK3 and MPK6), using a yeast two-hybrid system. This study revealed interactions among the following proteins: three ethylene-responsive element-binding factors (ERF), five WRKY transcription factors, one scarecrow-like (SCL), and the two MPK, in addition to many other interactions, reflecting a complex TF interaction network. Most of these interactions were subsequently validated by other methods, such as pull-down and in planta bimolecular fluorescence complementation assays. The key node ERF5 was shown to interact with multiple proteins in the network, such as ERF6, ERF8, and SCL13, as well as MPK3 and MPK6. Interestingly, ERF5 appeared to negatively regulate chitin signaling and plant defense against the fungal pathogen Alternaria brassicicola and positively regulate salicylic acid signaling and plant defense against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Therefore, ERF5 may play an important role in plant innate immunity, likely through coordinating chitin and other defense pathways in plants in response to different pathogens.

Phosphorylation by AtMPK6 is required for the biological function of AtMYB41 in Arabidopsis.

Mitogen-activated protein kinases (MPKs) are involved in a number of signaling pathways that control plant development and stress tolerance via the phosphorylation of target molecules. However, so far only a limited number of target molecules have been identified. Here, we provide evidence that MYB41 represents a new target of MPK6. MYB41 interacts with MPK6 not only in vitro but also in planta. MYB41 was phosphorylated by recombinant MPK6 as well as by plant MPK6. Ser(251) in MYB41 was identified as the site phosphorylated by MPK6. The phosphorylation of MYB41 by MPK6 enhanced its DNA binding to the promoter of a LTP gene. Interestingly, transgenic plants over-expressing MYB41(WT) showed enhanced salt tolerance, whereas transgenic plants over-expressing MYB41(S251A) showed decreased salt tolerance during seed germination and initial root growth. These results indicate that the phosphorylation of MYB41 by MPK6 is required for the biological function of MYB41 in salt tolerance.

Phosphorylation of the transcriptional regulator MYB44 by mitogen activated protein kinase regulates Arabidopsis seed germination.

The phytohormones abscisic acid (ABA) and gibberellic acid (GA) have antagonistic roles in the control of seed germination and seedling development. We report here that the transcriptional regulator MYB44 has a role in the control of seed germination in Arabidopsis thaliana. High levels of the MYB44 transcript are found in dry seeds but the transcript levels decrease during germination. The decrease in transcript level during germination is inhibited by the GA biosynthesis inhibitor paclobutrazol (PAC). MYB44 is phosphorylated by both recombinant and native forms of MPK3 and MPK6 at Ser(53) and Ser(145). Transgenic overexpression of MYB44 results in increased sensitivity of seed germination to ABA or PAC treatment. The PAC-insensitive germination phenotype of the myb44 mutant is complemented by overexpression of wild type MYB44 but not by overexpression of a mutant protein that lacks the MPK-target serines indicating that phosphorylation of MYB44 by MPKs is required for its biological function.

Identification of a C2H2-type zinc finger transcription factor (ZAT10) from Arabidopsis as a substrate of MAP kinase.

Mitogen-activated protein kinases (MAPKs or MPKs) are one of the most important and conserved signaling molecules in plants. MPKs can directly modulate gene expression by the phosphorylation of transcription factors. However, only a few target substrates of MPKs have been isolated. Here, we identified a C(2)H(2)-type zinc finger transcription factor from Arabidopsis, ZAT10, as a substrate of MPKs. Using in vitro and in vivo protein-protein interaction analyses, we demonstrated that ZAT10 directly interacted with MPK3 and MPK6. ZAT10 was phosphorylated by recombinant Arabidopsis MPK3 and MPK6 in a kinase assay. Furthermore, ZAT10 was also phosphorylated by native MPK3 and MPK6 prepared from Arabidopsis plants in an in-gel kinase assay. Mass spectrometry analysis of phosphopeptides was used to determine two MPK phosphorylation sites in ZAT10. These sites were verified by site-directed mutagenesis and in vitro kinase assays.

Arabidopsis MAP kinase phosphatase 1 is phosphorylated and activated by its substrate AtMPK6.

Arabidopsis MAP kinase phosphatase 1 (AtMKP1) is a member of the mitogen-activated protein kinase (MPK) phosphatase family, which negatively regulates AtMPKs. We have previously shown that AtMKP1 is regulated by calmodulin (CaM). Here, we examined the phosphorylation of AtMKP1 by its substrate AtMPK6. Intriguingly, AtMKP1 was phosphorylated by AtMPK6, one of AtMKP1 substrates. Four phosphorylation sites were identified by phosphoamino acid analysis, TiO(2) chromatography and mass spectrometric analysis. Site-directed mutation of these residues in AtMKP1 abolished the phosphorylation by AtMPK6. In addition, AtMKP1 interacted with AtMPK6 as demonstrated by the yeast two-hybrid system. Finally, the phosphatase activity of AtMKP1 increased approximately twofold following phosphorylation by AtMPK6. By in-gel kinase assays, we showed that AtMKP1 could be rapidly phosphorylated by AtMPK6 in plants. Our results suggest that the catalytic activity of AtMKP1 in plants can be regulated not only by Ca(2+)/CaM, but also by its physiological substrate, AtMPK6.

Plant-derived bioactive compounds produced by Streptomyces variabilis LCP18 associated with Litsea cubeba (Lour.) Pers as potential target to combat human pathogenic bacteria and human cancer cell lines.

To date, endophytic actinomycetes have been well-documented as great producers of novel antibiotics and important pharmaceutical leads. The present study aimed to evaluate potent bioactivities of metabolites synthesized by the strain LCP18 residing in the Vietnamese medicinal plant Litsea cubeba (Lour.) Pers towards human pathogenic bacteria and human cancer cell lines. Endophytic actinomycete strain LCP18 showed considerable inhibition against seven bacterial pathogens and three human tumor cell lines and was identified as species Streptomyces variabilis. Strain S. variabilis LCP18 was phenotypically resistant to fosfomycin, trimethoprim-sulfamethoxazole, dalacin, cefoxitin, rifampicin, and fusidic acid and harbored the two antibiotic biosynthetic genes such as PKS-II and NRPS. Further purification and structural elucidation of metabolites from the LCP18 extract revealed five plant-derived bioactive compounds including isopcrunetin, genistein, daidzein, syringic acid, and daucosterol. Among those, isoprunetin, genistein, and daidzein exhibited antibacterial activity against Salmonella typhimurium ATCC 14,028 and methicillin-resistant Staphylococcus epidermidis ATCC 35,984 with the MIC values ranging from 16 to 128 µg/ml. These plant-derived compounds also exhibited cytotoxic effects against human lung cancer cell line A549 with IC50 values of less than 46 µM. These findings indicated that endophytic S. variabilis LCP18 can be an alternative producer of plant-derived compounds which significantly show potential applications in combating bacterial infections and inhibition against lung cancer cell lines.

The Auxin Signaling Repressor IAA8 Promotes Seed Germination Through Down-Regulation of ABI3 Transcription in Arabidopsis.

Seed germination is a complex biological process controlled by various regulators, including phytohormones. Among these, abscisic acid and gibberellic acid inhibit and promote seed germination, respectively. Many studies have addressed the biological roles of auxin in plant growth and development, but very few have considered its role in seed germination. Here, we identified a novel function of the auxin signaling repressor Aux/IAA8 during seed germination. The IAA8 loss-of-function mutant iaa8-1 exhibited delayed seed germination. The phenotype of iaa8-1 was restored by ectopic expression of IAA8. Interestingly, IAA8 accumulated to high levels during seed germination, which was achieved not only by increased protein synthesis but also by the stabilization of IAA8 protein. We also showed that IAA8 down-regulates the transcription of ABSCISIC ACID INSENSITIVE3 (ABI3), a negative regulator of seed germination. Our study, thus strongly suggest that the auxin signaling repressor IAA8 acts as a positive regulator of seed germination in Arabidopsis thaliana.

High correlations between primary tumours and loco-regional metastatic lymph nodes in non-small-cell lung cancer with respect to glucose transporter type 1-mediated 2-deoxy-2-F18-fluoro-D-glucose uptake.

The purpose of the study was to investigate whether glucose transporter type 1 (Glut-1) mediated 2-deoxy-2-F18-fluoro-D-glucose (FDG) uptake of primary tumour is related to the likelihood of malignancy involvement in loco-regional lymph nodes (LNs) in 126 non-small-cell lung cancer (NSCLC) patients (M:F=103:23, age=65+/-9.7 years). Maximum standardised uptake values (maxSUV) and Glut-1 expression levels (determined by PET and immunostaining, respectively) of primary tumours and PET positive loco-regional LNs were compared. Significant correlations were found between malignant LNs and primary tumours with respect to maxSUV (r=0.6451, p<0.0001), %Glut-1 expression (r=0.8341, p<0.0001) and Glut-1 staining intensity (rho=0.827, p<0.0001). The area-under-curve value for LN differentiation using lymph node maxSUV was significantly higher in patients with a primary tumour maxSUV of >6 (AUC=0.775, p=0.0001). High correlations between the primary tumours and metastatic LNs in NSCLC with respect to the Glut-1 mediated FDG uptake may be useful for mediastinal LN discrimination by FDG-PET.

FDG uptake, glucose transporter type 1, and Ki-67 expressions in non-small-cell lung cancer: correlations and prognostic values.

PURPOSE: FDG uptake mediated by glucose transporter type 1 (Glut-1) and tumor proliferative activity assessed by Ki-67 expression provide prognostic information in patients with non-small-cell lung cancer (NSCLC). Here, we compared the prognostic significances of FDG uptake, and of Glut-1 and Ki-67 expressions in patients with NSCLC. METHODS: NSCLC patients (n=53, F:M=16:37, age 61.9+/-12.1 years) who underwent curative resection after FDG-PET were enrolled. Thirty-one patients had stage I, 15 stage II, and 7 stage III disease. Patients were treated by surgery only (n=12), surgery plus adjuvant oral chemotherapy (n=32), or surgery plus adjuvant intravenous chemo- or radio-therapy (n=9). Maximum standardized FDG uptake values (maxSUV), and the Glut-1 and Ki-67 expressions of resected tumors were analyzed for correlations and relations with tumor recurrence. The median follow-up duration was 15 months. RESULTS: Thirteen (24.5%) of the 53 patients experienced recurrence during a median follow-up of 8 months and significant correlations were found between maxSUV, Glut-1, and Ki-67 expressions (r=0.48-0.79, p<0.001). Univariate analysis revealed that disease-free survival (DFS) was significantly correlated with maxSUV (<7 versus > or =7, p=0.001), % Ki-67 expression (<25% versus > or =25%, p=0.047), tumor size (<3 cm versus > or =3 cm, p=0.027), and tumor cell differentiation (well/moderate versus poor, p=0.011). However, multivariate Cox proportional analysis identified maxSUV as the only determinant of DFS (p=0.005). Patients with a maxSUV of > or =7 (n=14) had a significantly lower 1-year DFS rate (57.1%) than those with a maxSUV of <7 (n=39, 89.7%). CONCLUSION: FDG uptake is more valuable than Glut-1 or Ki-67 expression in terms of predicting prognosis in patients with resected NSCLC.

FDG-Avid Portal Vein Tumor Thrombosis from Hepatocellular Carcinoma in Contrast-Enhanced FDG PET/CT.

OBJECTIVES: In this study, we aimed to describe the characteristics of portal vein tumor thrombosis (PVTT), complicating hepatocellular carcinoma (HCC) in contrast-enhanced FDG PET/CT scan. METHODS: In this retrospective study, 9 HCC patients with FDG-avid PVTT were diagnosed by contrast-enhanced fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT), which is a combination of dynamic liver CT scan, multiphase imaging, and whole-body PET scan. PET and CT DICOM images of patients were imported into the PET/CT imaging system for the re-analysis of contrast enhancement and FDG uptake in thrombus, the diameter of the involved portal vein, and characteristics of liver tumors and metastasis. RESULTS: Two patients with previously untreated HCC and 7 cases with previously treated HCC had FDG-avid PVTT in contrast-enhanced FDG PET/CT scan. During the arterial phase of CT scan, portal vein thrombus showed contrast enhancement in 8 out of 9 patients (88.9%). PET scan showed an increased linear FDG uptake along the thrombosed portal vein in all patients. The mean greatest diameter of thrombosed portal veins was 1.8 ± 0.2 cm, which was significantly greater than that observed in normal portal veins (P<0.001). FDG uptake level in portal vein thrombus was significantly higher than that of blood pool in the reference normal portal vein (P=0.001). PVTT was caused by the direct extension of liver tumors. All patients had visible FDG-avid liver tumors in contrast-enhanced images. Five out of 9 patients (55.6%) had no extrahepatic metastasis, 3 cases (33.3%) had metastasis of regional lymph nodes, and 1 case (11.1%) presented with distant metastasis. The median estimated survival time of patients was 5 months. CONCLUSION: The intraluminal filling defect consistent with thrombous within the portal vein, expansion of the involved portal vein, contrast enhancement, and linear increased FDG uptake of the thrombus extended from liver tumor are findings of FDG-avid PVTT from HCC in contrast-enhanced FDG PET/CT.

Prognostic Value of Fluoro-D-glucose Uptake of Primary Tumor and Metastatic Lesions in Advanced Nonsmall Cell Lung Cancer.

To assess the prognostic value of maximum standardized uptake value (maxSUV) of the primary tumor (maxSUVpt), maxSUV of whole-body tumors (maxSUVwb) and sum of maximum standardized uptake value (sumaxSUV) measured by the sum of maxSUVs of the primary tumor, metastatic lymph nodes, and metastatic lesions per each organ on fluoro-D-glucose-positron emission tomography/computed tomography in advanced non-small cell lung cancer (NSCLC). Eighty-three patients (49 male, 34 female) with advanced NSCLC were enrolled. Seventeen patients had Stage IIIA, 21 Stage IIIB, and 45 Stage IV. maxSUVpt, maxSUVwb, sumaxSUV, age, gender, tumor-cell type, T stage, N stage, overall stage, primary tumor size, and specific treatment were analyzed for correlation with overall survival. Median follow-up duration was 13 months. Fifty patients were dead during a median follow-up time of 11 months and 33 patients were alive with a median time of 15 months. Univariate analysis revealed that overall survival was significantly correlated with sumaxSUV (≥35 vs. <35, P = 0.004), T stage (T4 vs. T1-T3, P = 0.025), overall stage (IV vs. III, P = 0.002), gender (male vs. female, P = 0.029) and specific treatment (no vs. yes, P = 0.011). maxSUVpt and maxSUVwb were not correlated with overall survival with P value of 0.139 and 0.168, respectively. Multivariate analysis identified sumaxSUV, T stage, gender, and specific treatment as independent prognostic indicators. Patients with a sumaxSUV of ≥35 were 1.921 times more likely to die than those with a sumaxSUV of < 35 (P = 0.047). Median survival time was 14 months for patients with sumaxSUV ≥ 35 compared with 20 months for those with sumaxSUV < 35. In patients with metastatic NSCLC, sumaxSUV with cut-off of 35 was much more significant for survival prognosis (P = 0.021). sumaxSUV is a new prognostic measure, independent of tumor stage, gender, and specific treatment in advanced NSCLC. sumaxSUV may be better than maxSUVpt and maxSUVwb in prediction of survival. A large prospective cohort study is necessary to validate these results.

Tumor Burden Assessed by the Maximum Standardized Uptake Value and Greatest Diameter on FDG-PET Predicts Prognosis in Untreated Diffuse Large B-cell Lymphoma.

PURPOSE: It is uncertain whether the tumor burden as assessed using FDG-PET has prognostic significance in newly diagnosed diffuse large B-cell lymphoma (DLBCL). The authors undertook this study to determine whether a parameter that reflects both FDG uptake magnitude and the greatest tumor diameter is a prognostic indicator in DLBCL. MATERIALS AND METHODS: Forty-two DLBCL patients (age, 57.4 ± 15.5 years; male/female = 25/17; stage I/II/III/IV=5/17/10/10) who underwent FDG-PET before chemotherapy were enrolled. A lesion with the highest maximum standardized uptake value (MaxSUV) on the PET image was selected, and size-incorporated MaxSUV (SIMaxSUV) of mass was calculated as MaxSUV × greatest diameter (mm) on the transaxial PET image. Median follow-up duration was 20.0 months. RESULTS: Twelve (28.6% = 12/42) patients experienced disease progression, and 10 (23.8% = 10/42) died during follow-up. Among six variables [Ann Arbor stage, %Ki-67 expression, International Prognostic Index (IPI), MaxSUV, greatest diameter, and SIMaxSUV] investigated, only SIMaxSUV was found to be a single determinant of progression-free and overall survivals by multivariate analyses (p < 0.05). CONCLUSION: These results suggest that SIMaxSUV, a new FDG-PET parameter that incorporates FDG uptake magnitude and the greatest tumor diameter, may be a useful indicator of prognosis in untreated DLBCL.

Cadmium activates Arabidopsis MPK3 and MPK6 via accumulation of reactive oxygen species.

Cadmium (Cd) is a non-essential toxic heavy metal that influences normal growth and development of plants. However, the molecular mechanisms by which plants recognize and respond to Cd remain poorly understood. We show that, in Arabidopsis, Cd activates the mitogen-activated protein kinases, MPK3 and MPK6, in a dose-dependent manner. Following treatment with Cd, these two MAPKs exhibited much higher activity in the roots than in the leaves, and pre-treatment with the reactive oxygen species (ROS) scavenger, glutathione, effectively inhibited their activation. These results suggest that the Cd sensing signaling pathway uses a build-up of ROS to trigger activation of Arabidopsis MPK3 and MPK6.