Definitive screening design enables optimization of LC–ESI–MS/MS parameters in proteomics

In proteomics, more than 100,000 peptides are generated from the digestion of human cell lysates. Proteome samples have a broad dynamic range in protein abundance; therefore, it is critical to optimize various parameters of LC–ESI–MS/MS to comprehensively identify these peptides. However, there are many parameters for LC–ESI–MS/MS analysis. In this study, we applied definitive screening design to simultaneously optimize 14 parameters in the operation of monolithic capillary LC–ESI–MS/MS to increase the number of identified proteins and/or the average peak area of MS1. The simultaneous optimization enabled the determination of two-factor interactions between LC and MS. Finally, we found two parameter sets of monolithic capillary LC–ESI–MS/MS that increased the number of identified proteins by 8.1% or the average peak area of MS1 by 67%. The definitive screening design would be highly useful for high-throughput analysis of the best parameter set in LC–ESI–MS/MS systems.     

Effects of exposure to a time-varying 1.5 T magnetic field on the neurotransmitter-activated increase in intracellular Ca in relation to actin fiber and mitochondrial functions in bovine adrenal chromaffin cells

Background

It has been reported that exposure to electromagnetic fields influences intracellular signal transduction. We studied the effects of exposure to a time-varying 1.5 T magnetic field on membrane properties, membrane cation transport and intracellular Ca²⁺ mobilization in relation to signals. We also studied the mechanism of the effect of exposure to the magnetic field on intracellular Ca²⁺ release from Ca²⁺ stores in adrenal chromaffin cells.

Methods

We measured the physiological functions of ER, actin protein, and mitochondria with respect to a neurotransmitter-induced increase in Ca²⁺ in chromaffin cells exposed to the time-varying 1.5 T magnetic field for 2 h.

Results

Exposure to the magnetic field significantly reduced the increase in [Ca²⁺]i. The exposure depolarized the mitochondria membrane and lowered oxygen uptake, but did not reduce the intracellular ATP content. Magnetic field-exposure caused a morphological change in intracellular F-actin. F-actin in exposed cells seemed to be less dense than in control cells, but the decrease was smaller than that in cytochalasin D-treated cells. The increase in G-actin (i.e., the decrease in F-actin) due to exposure was recovered by jasplakinolide, but inhibition of Ca²⁺ release by the exposure was unaffected.

Conclusions and general significance

These results suggest that the magnetic field-exposure influenced both the ER and mitochondria, but the inhibition of Ca²⁺ release from ER was not due to mitochondria inhibition. The effect of eddy currents induced in the culture medium may indirectly influence intracellular actin and suppress the transient increase in [Ca²⁺]i.     

Role of dipeptidyl peptidase IV (DPP4) in the development of dyslipidemia: DPP4 contributes to the steroid metabolism pathway

AimsWe previously reported that dipeptidyl peptidase IV (DPP4)-deficient rats were susceptible to dyslipidemia induced by streptozotocin (STZ). Hence, it is suggested that DPP4 is important for lipid metabolism.Main methodsIn this study, to verify the role of DPP4 in the development of dyslipidemia, we carried out a microarray analysis of the livers of STZ-treated wild-type and DPP4-deficient rats and showed that the expression levels of genes involved in metabolic processes (steroid metabolic processes and cellular lipid metabolic processes) were significantly altered by STZ treatment.Key findingsIn the wild-type rats, the expression of hydroxysteroid (17-beta) dehydrogenase 2 (Hsd7b2), which catalyzes sex steroid synthesis from cholesterol, was significantly increased by about 15-fold after STZ treatment; however, it did not change in the DPP4-deficient rats. In the STZ untreated group of DPP4-deficient rats, the expression levels of cytochrome P450, subfamily 51 (Cyp51) and sterol-C4-methyl oxidase-like (Sc4mol), which catalyze intermediate steps in cholesterol synthesis, were significantly elevated compared to those of other groups. Similar results were demonstrated in HuH7-cells after DPP4 overexpression or the addition of human sera containing DPP4.SignificanceDPP4 is crucial for regulating the expression of factors related to steroid metabolism such as Cyp51, Sc4mol, and Hsd17b2, and DPP4 deficiency or inhibition may cause dyslipidemia.     

Inhibition studies of the β-carbonic anhydrases from the bacterial pathogen Salmonella enterica serovar Typhimurium with sulfonamides and sulfamates

The two β-carbonic anhydrases (CAs, EC 4.2.1.1) from the bacterial pathogen Salmonella enterica serovar Typhimurium, stCA 1 and stCA 2, were investigated for their inhibition with a large panel of sulfonamides and sulfamates. Unlike inorganic anions, which are weak, millimolar inhibitors of the two enzymes [Vullo et al., Bioorg. Med. Chem. Lett.2011, 21, 3591], sulfonamides and sulfamates are effective micro-to nanomolar inhibitors of the two enzymes. Various types of inhibitors have been detected among the 38 investigated sulfonamides/sulfamates, with K(I)s in the range of 31 nM-5.87 μM. The best stCA 1 inhibitors were acetazolamide and benzolamide-based compounds, whereas the best stCA 2 inhibitors were sulfonylated benzenesulfonamides and amino-benzolamide derivatives (K(I)s in the range of 31-90 nM). 3-Fluoro-5-chloro-4-aminobenzolamide showed an inhibition constant of 51 nM against stCA 1 and of 38 nM against stCA 2, being the best inhibitor detected so far for these enzymes. As many strains of S. enterica show extensive resistance to classical antibiotics, inhibition of the β-CAs investigated here may be useful for developing novel antibacterials, targeting β-CAs which may be involved in pathogenicity and invasion of some bacteria.     

Reliability and validity of a Japanese version of the Oral Health Impact Profile for edentulous subjects

doi: 10.1111/j.1741‐2358.2011.00606.x Reliability and validity of a Japanese version of the Oral Health Impact Profile for edentulous subjects Objective: To evaluate the reliability and validity of the Japanese version of the Oral Health Impact Profile for edentulous (OHIP‐EDENT‐J) patients. Background: Oral Health Impact Profile for edentulous is an appropriate instrument for assessing the Quality of life (QOL) in edentulous patients. However, the reliability and validity of the Japanese version had not been evaluated. Methods: The study was conducted on 116 edentulous patients (Group A, requiring new dentures, n = 61; Group B, already having dentures, n = 55). Cronbach’s alpha (α) was used to measure internal consistency of the summary scores for OHIP‐EDENT‐J and various subscales in Groups A and B. The interclass correlation coefficient (ICC) and 95% confidence interval of the summary scores for OHIP‐EDENT‐J and subscales were calculated. The summary scores for OHIP‐EDENT‐J in Groups A and B were compared with evaluate content validity. The Spearman’s correlation coefficient between the summary scores for OHIP‐EDENT‐J and the satisfaction with dentures (100 mm VAS) was calculated for Groups A and B to evaluate concurrent validity. Results: The reliability of the summary scores for OHIP‐EDENT‐J was good (α = 0.93). The ICC of the summary scores for OHIP‐EDENT‐J was 0.85. Summary scores for OHIP‐EDENT‐J were significantly different (p = 0.027) between Group A and Group B, with Group A having the higher value. The Spearman’s correlation coefficient for the degree of satisfaction with dentures and the summary scores for OHIP‐EDENT‐J, calculated for Groups A and B (n = 107), was ?0.609. Conclusion: The OHIP‐EDENT‐J, a questionnaire on oral health–related QOL comprising 19 items, showed good reliability and validity for edentulous patients.     

Molecular cloning and expression analysis of ultraspiracle (USP) from the rice stem borer Chilo suppressalis

cDNA for ultraspiracle (USP) from the lepidopteran rice stem borer Chilo suppressalis was cloned using PCR techniques. The deduced amino acid sequence of C. suppressalis USP (CsUSP) was very similar to those of other lepidopteran USPs, especially to the Manduca sexta USP-2 isoform. Northern hybridization analysis detected a 6.5-kb message in the epidermis, fat body, and midgut of wandering larvae. CsUSP mRNA expression in the epidermis varied little during the last larval instar. Gel mobility shift assays showed that in vitro translated C. suppressalis ecdysone receptor (CsEcR) and CsUSP proteins bound to the Pal1 or Drosophila melanogaster hsp27 ecdysone response element as a heterodimer. In a ligand-receptor binding assay, [(3)H]ponasterone A ([(3)H]PoA) did not bind to individual CsEcR or CsUSP protein, but bound strongly to the CsEcR/CsUSP complex. [(3)H]PoA binding to CsEcR/CsUSP complex was competed by 20-hydroxyecdysone and a non-steroidal ecdysteroid agonist, RH-5992, but not by cholesterol, indicating that compounds with molting hormone activity against C. suppressalis can bind specifically to the CsEcR/CsUSP complex.     

Carbonic anhydrase inhibitors. Cloning, characterization and inhibition studies of the cytosolic isozyme III with anions

The cytosolic human carbonic anhydrase (hCA, EC 4.2.1.1) isozyme III (hCA III) has been cloned and purified by the GST-fusion protein method. Recombinant pure hCA III had the following kinetic parameters for the CO(2) hydration reaction at 20 degrees C and pH 7.5: k(cat) of 1.3 x 10(4) s(- 1) and k(cat)/K(M) of 2.5.10(5) M(- 1) s(- 1). The first detailed inhibition study of this enzyme with anions is reported. Inhibition data of the cytosolic isozymes hCA I - hCA III with a large number of anions (halides, pseudohalides, bicarbonate, carbonate, nitrate, nitrite, hydrosulfide, sulfate, sulfamic acid, sulfamide, etc.), were determined and these values are comparatively discussed for these three cytosolic isoforms. Fluoride, nitrate, nitrite, phenylboronic acid and phenylarsonic acid (as anions) were weak hCA III inhibitors (K(I)s of 21-78.5 mM), whereas bicarbonate, chloride, bromide, sulfate and several other simple anions showed K(I)s around 1 mM. The best hCA III inhibitors were carbonate, cyanide, thiocyanate, azide and hydrogensulfide, which showed K(I)s in the range of 10-90 microM. It is difficult to explain the inhibitory activity of carbonate (K(I) of 10 microM) against hCA III, also considering the fact that this ion has an affinity of 15-73 mM for hCA I and II and is in equilibrium with one of the substrates of this enzyme, i.e., bicarbonate, which is a much weaker inhibitor (K(I) of 0.74 mM against hCA III, of 12 mM against hCA I and of 85 mM against hCA II).     

Classical and three-dimensional QSAR for the inhibition of [3H]ponasterone A binding by diacylhydrazine-type ecdysone agonists to insect Sf-9 cells

The activity of 52 diacylhydrazine congeners was evaluated by measuring the inhibition of the incorporation of [3H]ponasterone A into intact Sf-9 cells. Eleven compounds were newly synthesized in this study. Results showed that the substitution of the 2-CH3 or 3-OCH3 moiety of methoxyfenozide with other groups or the removal of either group was unfavorable to the activity. The activity was quantitatively analyzed using both classical QSAR (Hansch-Fujita) and three-dimensional QSAR methods (comparative molecular field analysis, CoMFA). Sterically favorable fields were observed at the 3- and 4-positions of the benzene ring opposite from the t-butyl group (B-ring), and a sterically unfavorable field was evidenced at the 2-position. Another sterically unfavorable field developed surrounding the favorable field observed at the 4-position of the B-ring. Electrostatically negative fields were observed near the CO moiety, above the benzene ring, and at the 4-position of the B-ring. The optimum hydrophobicity of compounds in terms of their logP values was calculated to be approximately 4.1. Results of the three dimensional structure-activity relationship analyses were consistent with those obtained from the previously reported classical QSAR for 2-chlorobenzoyl analogs containing various para-substituents. The high activity of potent insecticides such as tebufenozide and chromafenozide were rationalized by CoMFA. Thus, this CoMFA result will be useful in the design of new compounds and in understanding the molecular mechanism of the ligand-receptor interactions.