Electrochemical detection of mismatched DNA using a MutS probe

A direct and label-free electrochemical biosensor for the detection of the protein–mismatched DNA interaction was designed using immobilized N-terminal histidine tagged Escherichia coli. MutS on a Ni-NTA coated Au electrode. General electrochemical methods, cyclic voltammetry (CV), electrochemical quartz crystal microbalance (EQCM) and impedance spectroscopy, were used to ascertain the binding affinity of mismatched DNAs to the MutS probe. The direct results of CV and impedance clearly reveal that the interaction of MutS with the CC heteroduplex was much stronger than that with AT homoduplex, which was not differentiated in previous results (GT > CT > CC ≈ AT) of a gel mobility shift assay. The EQCM technique was also able to quantitatively analyze MutS affinity to heteroduplexes

Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides

BACKGROUND: Maize, a crop of global significance, is vulnerable to a variety of biotic stresses resulting in economic losses. Fusarium verticillioides (teleomorph Gibberella moniliformis) is one of the key fungal pathogens of maize, causing ear rots and stalk rots. To better understand the genetic mechanisms involved in maize defense as well as F. verticillioides virulence, a systematic investigation of the host-pathogen interaction is needed. The aim of this study was to computationally identify potential maize subnetwork modules associated with its defense response against F. verticillioides. RESULTS: We obtained time-course RNA-seq data from B73 maize inoculated with wild type F. verticillioides and a loss-of-virulence mutant, and subsequently established a computational pipeline for network-based comparative analysis. Specifically, we first analyzed the RNA-seq data by a cointegration-correlation-expression approach, where maize genes were jointly analyzed with known F. verticillioides virulence genes to find candidate maize genes likely associated with the defense mechanism. We predicted maize co-expression networks around the selected maize candidate genes based on partial correlation, and subsequently searched for subnetwork modules that were differentially activated when inoculated with two different fungal strains. Based on our analysis pipeline, we identified four potential maize defense subnetwork modules. Two were directly associated with maize defense response and were associated with significant GO terms such as GO:0009817 (defense response to fungus) and GO:0009620 (response to fungus). The other two predicted modules were indirectly involved in the defense response, where the most significant GO terms associated with these modules were GO:0046914 (transition metal ion binding) and GO:0046686 (response to cadmium ion). CONCLUSION: Through our RNA-seq data analysis, we have shown that a network-based approach can enhance our understanding of the complicated host-pathogen interactions between maize and F. verticillioides by interpreting the transcriptome data in a system-oriented manner. We expect that the proposed analytic pipeline can also be adapted for investigating potential functional modules associated with host defense response in diverse plant-pathogen interactions

Transjugular insertion of biliary stent in patients with malignant biliary obstruction complicated by ascites with/without coagulopathy: a prospective study of 12 patients

PURPOSEIn patients with malignant biliary obstruction complicated by massive ascites, when endoscopy fails, safe routes for biliary decompression are needed as an alternative to percutaneous approach. We aimed to evaluate the safety and effectiveness of transjugular insertion of biliary stent (TIBS) in patients with malignant biliary obstruction complicated by massive ascites with or without coagulopathy.METHODSFrom March 2012 to December 2017, a total of 12 consecutive patients with malignant biliary obstructions treated with TIBS were enrolled in this study. Five patients had jaundice and cholangitis, while seven had jaundice only. Clinical parameters including technical and clinical success rates and complications following TIBS were evaluated. Overall survival and stent occlusion-free survival were assessed using Kaplan-Meier analysis.RESULTSThe indications for transjugular approach were massive ascites with (n=2) or without (n=10) coagulopathy. TIBS was technically successful in 11 of 12 patients. Clinical success was defined as successful internal drainage and was achieved in eight patients. The mean serum bilirubin level was initially 13.9±6.3 mg/dL and decreased to 4.9±5.3 mg/dL within 1 month after stent placement (P = 0.037). Two patients had procedure-related complications (hemobilia). During the follow-up period (mean, 30 days; range, 1–146 days), all 12 patients died of disease progression. The median overall survival and stent occlusion-free survival times were 19 days (95% confidence interval [CI], 16–22 days) and 19 days (95% CI, 12–26 days), respectively. There was no stent dysfunction in the eight patients that had successful internal drainage.CONCLUSIONTIBS appears to be safe, technically feasible, and clinically effective for patients with malignant biliary obstruction complicated by massive ascites with or without coagulopathy

Simultaneous electrochemical detection of both PSMA (+) and PSMA (-) prostate cancer cells using an RNA/peptide dual-aptamer probe

Using an RNA/peptide dual-aptamer probe, both PSMA (+) and PSMA (-) prostate cancer cells were simultaneously detected by electrochemical impedance spectroscopy. This approach can be applied as a general tool for early diagnosis of prostate cancer.CATALONA WJ, 1993, JAMA-J AM MED ASSOC, V270, P948Lupold SE, 2002, CANCER RES, V62, P4029Kue PF, 2002, INT J CANCER, V102, P572, DOI 10.1002/ijc.10734Drummond TG, 2003, NAT BIOTECHNOL, V21, P1192, DOI 10.1038/nbt873DARAIN F, 2004, BIOSENS BIOELECTRON, V20, P856Ban CG, 2004, NUCLEIC ACIDS RES, V32, DOI 10.1093/nar/gnh109Ghosh A, 2004, J CELL BIOCHEM, V91, P528, DOI 10.1002/jcb.10661LEVIN MA, 2005, J UROLOGY, V159, P475Rodriguez MC, 2005, CHEM COMMUN, P4267, DOI 10.1039/b506571bZitzmann S, 2005, CLIN CANCER RES, V11, P139Horninger W, 2001, CANCER-AM CANCER SOC, V91, P1667Lang SH, 2001, BRIT J CANCER, V85, P590Yamamoto T, 2001, UROLOGY, V58, P994Palecek E, 2002, CRIT REV ANAL CHEM, V32, P261Narain V, 2002, CANCER METAST REV, V21, P17Edwards S, 2005, BRIT J CANCER, V92, P376, DOI 10.1038/sj.bjc.6602261Postma R, 2005, EUR J CANCER, V41, P825, DOI 10.1016/j.ejca.2004.12.029Cahova-Kucharikova K, 2005, ANAL CHEM, V77, P2920Rahman MA, 2005, ANAL CHEM, V77, P4854, DOI 10.1021/ac050558vCho M, 2006, NUCLEIC ACIDS RES, V34, DOI 10.1093/nar/gkl364Farokhzad OC, 2006, P NATL ACAD SCI USA, V103, P6315, DOI 10.1073/pnas.0601755103Chu TC, 2006, CANCER RES, V66, P5989, DOI 10.1158/0008-5472.CAN-05-4583McNamara JO, 2006, NAT BIOTECHNOL, V24, P1005, DOI 10.1038/nbt1223Palecek E, 1998, BIOSENS BIOELECTRON, V13, P621Min K, 2008, BIOSENS BIOELECTRON, V23, P1819, DOI 10.1016/j.bios.2008.02.021CHO M, 2008, BMB REPORTS, V41, P119Kim D, 2007, J AM CHEM SOC, V129, P7661, DOI 10.1021/ja071471pMaalouf R, 2007, ANAL CHEM, V79, P4879, DOI 10.1021/ac070085nKRAHN MD, 1994, JAMA-J AM MED ASSOC, V272, P773

Association of appendicular skeletal muscle mass with carotid intima-media thickness according to body mass index in Korean adults

OBJECTIVES The combined effects of obesity and appendicular skeletal muscle (ASM) on atherosclerosis, especially in middleaged populations, remain poorly understood. This cross-sectional study investigated the effects of ASM on carotid intima-media thickness (IMT) according to body mass index (BMI) in middle-aged Korean adults. METHODS Herein, 595 men and 1,274 women aged 30-64 years completed questionnaires and underwent health examinations as part of the Cardiovascular and Metabolic Disease Etiology Research Center cohort. ASM was measured via bioelectrical impedance analysis and adjusted for weight (ASM/Wt). IMT was assessed using B-mode ultrasonography; highest quartile of IMT was defined as gender-specific top quartile of the IMT values. Higher BMIs was defined as a BMI over 25.0 kg/m2 . RESULTS Compared to the highest ASM/Wt quartile, the lowest ASM/Wt quartile was significantly associated with highest quartile of IMT in men with lower BMIs (adjusted odds ratio [aOR], 2.78; 95% confidence interval [CI], 1.09 to 7.13), but not in those with higher BMIs (aOR, 0.59; 95% CI, 0.24 to 1.91). In women, there was no significant association of low skeletal muscle mass with highest quartile of IMT, regardless of BMI. CONCLUSIONS Low appendicular skeletal muscle mass is associated with carotid arterial wall thickening in men with lower BMIs, but not in men with higher BMIs. Our findings suggest that the risk of atherosclerosis may be low in middle-aged Korean men with appropriate body weight and skeletal muscle mass maintenance

Comparison of self-reported and accelerometer-assessed measurements of physical activity according to socio-demographic characteristics in Korean adults

OBJECTIVES Previous studies have shown relatively low correlations between self-reported and accelerometer-assessed physical activity (PA). However, this association differs by socio-demographic factors, and this relationship has not been fully investigated in the general population. Thus, we investigated the correlation between self-reported and accelerometer-assessed PA and whether it differed by demographic and socioeconomic factors among the Korean general population. METHODS This cross-sectional study included 623 participants (203 men and 420 women) aged 30 to 64 years, who completed a PA questionnaire and wore a wrist-worn accelerometer on the non-dominant wrist for 7 days. We examined the agreement for metabolic equivalent task minutes per week (MET-min/wk) between the 2 measures and calculated Spearman correlation coefficients according to demographic and socioeconomic factors. RESULTS The kappa coefficient between tertiles of self-reported and accelerometer-assessed total MET-min/wk was 0.16 in the total population, suggesting overall poor agreement. The correlation coefficient between the 2 measurements was 0.26 (p<0.001) in the total population, and the correlation tended to decrease with increasing age (p for trend <0.001) and depression scores (p for trend <0.001). CONCLUSIONS We found a low correlation between self-reported and accelerometer-assessed PA among healthy Korean adults, and the correlation decreased with age and depression score. When studying PA using accelerometers and/or questionnaires, age and depression need to be considered, as should differences between self-reported and accelerometer-assessed PA

Genome sequence of mungbean and insights into evolution within Vigna species

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis

Protein Kinase Cδ Stimulates Proteasome-Dependent Degradation of C/EBPα during Apoptosis Induction of Leukemic Cells

BACKGROUND:The precise regulation and maintenance of balance between cell proliferation, differentiation and death in metazoan are critical for tissue homeostasis. CCAAT/enhancer-binding protein alpha (C/EBPalpha) has been implicated as a key regulator of differentiation and proliferation in various cell types. Here we investigated the potential dynamic change and role of C/EBPalpha protein during apoptosis induction. METHODOLOGY/PRINCIPAL FINDINGS:Upon onset of apoptosis induced by various kinds of inducers such as NSC606985, etoposide and others, C/EBPalpha expression presented a profound down-regulation in leukemic cell lines and primary cells via induction of protein degradation and inhibition of transcription, as assessed respectively by cycloheximide inhibition test, real-time quantitative RT-PCR and luciferase reporter assay. Applying chemical inhibition, forced expression of dominant negative mutant and catalytic fragment (CF) of protein kinase Cdelta (PKCdelta), which was proteolytically activated during apoptosis induction tested, we showed that the active PKCdelta protein contributed to the increased degradation of C/EBPalpha protein. Three specific proteasome inhibitors antagonized C/EBPalpha degradation during apoptosis induction. More importantly, ectopic expression of PKCdelta-CF stimulated the ubiquitination of C/EBPalpha protein, while the chemical inhibition of PKCdelta action significantly inhibited the enhanced ubiquitination of C/EBPalpha protein under NSC606985 treatment. Additionally, silencing of C/EBPalpha expression by small interfering RNAs enhanced, while inducible expression of C/EBPalpha inhibited NSC606985/etoposide-induced apoptosis in leukemic cells. CONCLUSIONS/SIGNIFICANCE:These observations indicate that the activation of PKCdelta upon apoptosis results in the increased proteasome-dependent degradation of C/EBPalpha, which partially contributes to PKCdelta-mediated apoptosis