Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method

The precision with which the dissociation constant, K_D, can be obtained from isothermal titration calorimetry depends on, among other factors, the concentrations of the interacting species. The so-called c value—the ratio of analyte concentration to K_D—should fall in the range of 1 to 1000 for reliable K_D determination. On the basis of simulated, noise-free data, Biswas and Tsodikov [5] recently suggested an optimal c value of 5 to 20. By contrast, we find an optimum at c > 40 on determining the K_D confidence intervals through simulations containing noise levels typical of state-of-the-art microcalorimeters.     

Selection of reference genes for gene expression studies in astrocytomas

This study was aimed to test a panel of six housekeeping genes (GAPDH, HPRT1, POLR2A, RPLP0, ACTB, and H3F) so as to identify and validate the most suitable reference genes for expression studies in astrocytomas. GAPDH was the most stable and HPRT1 was the least stable reference gene. The effect of reference gene selection on quantitative real-time polymerase chain reaction data interpretation was demonstrated, normalizing the expression data of a selected gene of interest. Thus, GAPDH may be recommended for data normalization in gene expression studies in astrocytomas. Nevertheless, a preliminary validation of reference gene stability is required prior to every study.     

Numerical solutions of the Lamm equation. III. Velocity centrifugation

We have generated solutions to the Lamm equation to examine the effects of concentration dependence on velocity experiments. Two forms of c dependence are considered: s/s₀ = 1 – kc and s/s₀ = (1 + kc)^?1. Features of these solutions are discussed. The magnitude of the errors resulting from the usual procedure of measuring the rate of movement of schlieren maxima or of the position at which the concentration is one half the plateau value have been examined. These errors are usually negligible after sufficient centrifugation time. The errors in using the half-plateau concentration are less than those using the movement of the peak. We have also examined a technique due to Fujita for determining D from boundary spreading when s/s₀ = (1+kc)^?1. This method is satisfactory when s/s₀ is actually of this form, or under certain limitations when s/s₀ = (1 + kc)^?1. Creeth has shown that under certain conditions the concentration gradient, curve remains virtually unchanged in shape after separating from the meniscus. When this occurs it is possible to estimate s/D from the data. The condition for such a steady state is that kc₀ be sufficiently large. Numerical confirmation of this method is presented in the final section.     

Comparison of PCR-RFLP with 21-plex PCR and rDNA Sequencing for Identification of Clinical Yeast Isolates

Non-albicans Candida species and other rare yeasts have emerged as major opportunistic pathogens in fungal infections. Identification of opportunistic yeasts in developing countries is mainly performed by phenotypic assay, which are time-consuming and prone to errors. The aim of the present study was to evaluate PCR-RFLP as a routinely used identification technique for the most clinically important Candida species in Iran and make a comparison with a novel multiplex PCR, called 21-plex PCR. One hundred and seventy-three yeast isolates from clinical sources were selected and identified with sequence analysis of the D1/D2 domains of rDNA (LSU rDNA) sequencing as the gold standard method. The results were compared with those obtained by PCR-RFLP using MspI restriction enzyme and the 21-plex PCR. PCR-RFLP correctly identified 93.4% of common pathogenic Candida species (C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and P. kudriavsevii (=?C. krusei)) and was able to identify 45.5% of isolates of the uncommon yeast species compared to the D1/D2 rDNA sequencing. Compared with PCR-RFLP, all common Candida species and 72.7% of uncommon yeast species were correctly identified by the 21-plex PCR. The application of the 21-plex PCR assay as a non-sequence-based molecular method for the identification of common and rare yeasts can reduce turnaround time and costs for the identification of clinically important yeasts and can be applied in resource-limited settings.

     

Stereoselective uptake and degradation of (±)‐o,p‐DDD pesticide stereomers in water‐sediment system

The environmental stereoselective uptake and degradation of (±)‐o,p‐DDD pesticide stereomers in water‐sediment system are described. The results were analyzed by artificial neural network model. The optimized experimental parameters were concentration of o,p‐DDD streamers (7.0 μg L^?1), experimental time (60 min), pH (6), dose (5.0 g L^?1), and temperature (25°C). The maximum uptake and degradation were 87% and 85% and 33.0% and 30.5% for (?)‐ and (+)‐stereomers of o,p‐DDD in 15‐day time. Both uptake and degraded phenomenon showed first‐order rate reaction. Thermodynamic variables indicated exothermic nature of uptake and degradation processes. The uptake and degradation were slightly higher for (?)‐stereomer than (+)‐stereomer of o,p‐DDD. It was assumed that both uptake and degradation processes are accountable for the removal of the streomers of o,p‐DDD from earth's ecosystem, but the uptake is responsible for major contribution. The magnitudes of relative errors obtained by artificial neural network model were in the range of ±0.2 to 3.5, indicating good applicability of the experimental data. The results are very useful to control the environmental contamination due to the chiral o,p‐DDD pesticide as its two enantiomers have different ecological toxicities.     

The effects of meteorological factors on airborne fungal spore concentration in two areas differing in urbanisation level

Although fungal spores are an ever-present component of the atmosphere throughout the year, their concentration oscillates widely. This work aims to establish correlations between fungal spore concentrations in Porto and Amares and meteorological data. The seasonal distribution of fungal spores was studied continuously (2005–2007) using volumetric spore traps. To determine the effect of meteorological factors (temperature, relative humidity and rainfall) on spore concentration, the Spearman rank correlation test was used. In both locations, the most abundant fungal spores were Cladosporium, Agaricus, Agrocybe, Alternaria and Aspergillus/Penicillium, the highest concentrations being found during summer and autumn. In the present study, with the exception of Coprinus and Pleospora, spore concentrations were higher in the rural area than in the urban location. Among the selected spore types, spring-autumn spores (Coprinus, Didymella, Leptosphaeria and Pleospora) exhibited negative correlations with temperature and positive correlations both with relative humidity and rainfall level. On the contrary, late spring-early summer (Smuts) and summer spores (Alternaria, Cladosporium, Epicoccum, Ganoderma, Stemphylium and Ustilago) exhibited positive correlations with temperature and negative correlations both with relative humidity and rainfall level. Rust, a frequent spore type during summer, had a positive correlation with temperature. Aspergillus/Penicillium, showed no correlation with the meteorological factors analysed. This knowledge can be useful for agriculture, allowing more efficient and reliable application of pesticides, and for human health, by improving the diagnosis and treatment of respiratory allergic disease.     

Selection of Stable Reference Genes for Quantitative Real-Time PCR on <i>Paeonia ostii</i> T. Hong et J. X. Zhang Leaves Exposed to Different Drought Stress Conditions

The definition of relatively stable expressed internal reference genes is essential in both traditional blotting quantification and as a modern data quantitative strategy. Appropriate internal reference genes can accurately standardize the expression abundance of target genes to avoid serious experimental errors. In this study, the expression profiles of ten candidate genes, ACT1, ACT2, GAPDH, eIF1, eIF2, α-TUB, β-TUB, TBP, RNA Pol II and RP II, were calculated for a suitable reference gene selection in Paeonia ostii T. Hong et J. X. Zhang leaves under various drought stress conditions. Data were processed by the four regularly used evaluation software. A comprehensive analysis revealed that RNA Pol II was the most stable gene and eIF2 was the least stable one. In addition, the geNorm program provided the optimal choice of two reference gene combination, RNA Pol II and β-TUB, for qRT-PCR normalization in P. ostii subjected to different drought stress levels. Our research provided convenience for gene expression analysis in P. ostii under drought stress and promoted research of effective methods to alleviate P. ostii drought stress in the future.     

Accurate kinetic parameter estimation during progress curve analysis of systems with endogenous substrate production

We have identified an error in the published integral form of the modified Michaelis–Menten equation that accounts for endogenous substrate production. The correct solution is presented and the error in both the substrate concentration, S, and the kinetic parameters V_m, K_m, and R resulting from the incorrect solution was characterized. The incorrect integral form resulted in substrate concentration errors as high as 50% resulting in 7–50% error in kinetic parameter estimates. To better reflect experimental scenarios, noise containing substrate depletion data were analyzed by both the incorrect and correct integral equations. While both equations resulted in identical fits to substrate depletion data, the final estimates of V_m, K_m, and R were different and K_m and R estimates from the incorrect integral equation deviated substantially from the actual values. Another observation was that at R = 0, the incorrect integral equation reduced to the correct form of the Michaelis–Menten equation. We believe this combination of excellent fits to experimental data, albeit with incorrect kinetic parameter estimates, and the reduction to the Michaelis–Menten equation at R = 0 is primarily responsible for the incorrectness to go unnoticed. However, the resulting error in kinetic parameter estimates will lead to incorrect biological interpretation and we urge the use of the correct integral form presented in this study. Biotechnol. Bioeng. 2011;108: 2499–2503. © 2011 Wiley Periodicals, Inc.     

Copper(II) complexes with tridentate pyrazole-based ligands: synthesis, characterization, DNA cleavage activity and cytotoxicity

Tridentate pyrazole-containing ligands of the Schiff base type, SalPz — HL¹, Cl₂SalPz — HL² and I₂SalPz — HL³, were used to prepare a series of new Cu(II) complexes (CuSalPz — 1, CuCl₂SalPz — 2 and CuI₂SalPz — 3). These new complexes have been studied by different analytical techniques (electrospray ionization mass spectrometry (ESI-MS), elemental analysis, FT-IR and EPR). The spectroscopic properties of 1-3 are consistent with the formation of Cu(II) complexes coordinated by monoanionic and tridentate (N,N,O)-chelators, behaving as monomeric species in aqueous solution, as shown by EPR studies. Crystals of 2 and 3, obtained by slow concentration of methanolic solutions of the compounds, were also analyzed by X-ray diffraction analysis. The X-ray structural study has shown that 2 crystallized as a dinuclear compound, [Cu₂(μ-Cl)₂(Cl₂SalPz)₂], while the solid state structure determined for 3 is best described by monomeric units of [CuCl(I₂SalPz)] displaying short Cu···Cl intermolecular contacts. The in vitro evaluation of 1-3 comprised the study of their DNA-cleaving ability using plasmid DNA and the assessment of their cytotoxic activity against several human cancer cell lines (PC-3 prostate, MCF-7 breast and A2780 and A2780cisR-ovary). The studies with plasmid DNA have shown that 2 and 3 induce extensive DNA cleavage in the presence of different additives. The cytotoxic activity of 2 and 3 is comparable to the one presented by cisplatin, with the exception of the A2780 cell line where cisplatin is more active. It has been found that the introduction of halogen substituents in the phenolate rings of the chelators enhanced the cytotoxicity of the respective Cu(II) complexes.     

Fungal growth inhibitory properties of new phytosphingolipid analogues

Aims: To study the growth inhibitory properties of a series of phytosphingosine (PHS) and phytoceramide (PHC) analogues. Methods and Results: A panel of two yeast (Candida albicans and Saccharomyces cerevisiae) and six moulds (Aspergillus repens, Aspergillus niger, Penicillium chrysogenum, Cladosporium cladosporioides, Arthroderma uncinatum and Penicillium funiculosum) has been used in this study. A series of new PHS and PHC analogues differing at the sphingoid backbone and the functional group at C1 position were synthesized. Conclusions: Among PHS analogues, 1‐azido derivative 1c, bearing the natural d ‐ribo stereochemistry, showed a promising growth inhibitory profile. Among PHC analogues, compound 12, with a bulky N‐pivaloyl group and a Z double bond at C3 position of the sphingoid chain, was the most active growth inhibitor. Minimal inhibitory concentration values were in the range of 23–48 μmol l^?1 for 1c and 44–87 μmol l^?1 for 12. Significance and Impact of the Study: Only scattered data on the antifungal activity of phytosphingolipids have been reported in the literature. This is the first time that a series of analogues of this kind are tested and compared to discern their structural requirements for antifungal activity.     

Integrated network analysis and machine learning approach for the identification of key genes of triple-negative breast cancer

Triple-negative breast cancer (TNBC) has attracted more attention compared with other breast cancer subtypes due to its aggressive nature, poor prognosis, and chemotherapy remains the mainstay of treatment with no other approved targeted therapy. Therefore, the study aimed to discover more promising therapeutic targets and investigating new insights of biological mechanism of TNBC. Six microarray data sets consisting of 463 non-TNBC and 405 TNBC samples were mined from Gene Expression Omnibus. The data sets were integrated by meta-analysis and identified 1075 differentially expressed genes. Protein-protein interaction network was constructed which consists of 486 nodes and 1932 edges, where 29 hub genes were obtained with high topological measures. Further, 16 features (hub genes), 12 upregulated (AURKB, CCNB2, CDC20, DDX18, EGFR, ENO1, MYC, NUP88, PLK1, PML, POLR2F, and SKP2) and four downregulated ( CCND1, GLI3, SKP1, and TGFB3) were selected through machine learning correlation based feature selection method on training data set. A naïve Bayes based classifier built using the expression profiles of 16 features (hub genes) accurately and reliably classify TNBC from non-TNBC samples in the validation test data set with a receiver operating curve of 0.93 to 0.98. Subsequently, Gene Ontology analysis revealed that the hub genes were enriched in mitotic cell cycle processes and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that they were enriched in cell cycle pathways. Thus, the identified key hub genes and pathways highlighted in the study would enhance the understanding of molecular mechanism of TNBC which may serve as potential therapeutic target.     

What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils?

We develop a theory for three states of equilibrium of amyloid peptides: the monomer, oligomer, and fibril. We assume that the oligomeric state is a disordered micellelike collection of a few peptide chains held together loosely by hydrophobic interactions into a spherical hydrophobic core. We assume that fibrillar amyloid chains are aligned and further stabilized by steric zipper interactions—hydrogen bonding, steric packing, and specific hydrophobic side-chain contacts. The model makes a broad set of predictions that are consistent with experimental results: 1), Similar to surfactant micellization, amyloid oligomerization should increase with peptide concentration in solution. 2), The onset of fibrillization limits the concentration of oligomers in the solution. 3), The extent of Aβ fibrillization increases with peptide concentration. 4), The predicted average fibril length versus monomer concentration agrees with data on α-synuclein. 5), Full fibril length distributions agree with data on α-synuclein. 6), Denaturants should melt out fibrils. And finally, 7), added salt should stabilize fibrils by reducing repulsions between amyloid peptide chains. It is of interest that small changes in solvent conditions can tip the equilibrium balance between oligomer and fibril and cause large changes in rates through effects on the transition-state barrier. This model may provide useful insights into the physical processes underlying amyloid diseases.     

Residues of Aliphatic and Polycyclic Aromatic Hydrocarbons in Some Fish Species of Lake Temsah,Ismailia, Egypt: An Analytical Search for Hydrocarbon Sources and Exposure Bioindicators

Residues of aliphatic and polycyclic aromatic hydrocarbons (PAHs) were monitored in some fish species collected from Temsah Lake, near Ismailia, Egypt. Fish were selected to represent different feeding habits and ecological niches in the lake's ecosystem. Fish samples were extracted using organic solvents, and residues of aliphatic and PAHs were separated using column chromatography and detected using gas liquid chromatography. Fish species were Clupea sirm, Mugil sehli, Mugil capito, Morone labrax, and Sciasna sp. Clupea sirm, a surface feeder fish had the highest concentration of aliphatic hydrocarbons, 320 ± 54 ng g^?1, while Morone labrax, a predatory fish that live in the water column, had the highest concentration of PAHs, 315.87 ± 46 ng g^?1. Even-number aliphatic hydrocarbons were more frequently detected in all fish species in comparison to odd-number aliphatic hydrocarbons, suggesting a petrogenic origin of these compounds. Meanwhile, the pattern of PAHs detected in the present study suggested that they originate from atmospheric deposition rather than land-based runoff. Morone labrax fish and Clupea sirm fish were the most suitable candidate bioindicators of exposure to aliphatic hydrocarbons and PAHs through fish consumption of the five fish species examined in this study.     

Comparison and Characterization of Microbial Communities in Sulfide-rich Wastewater with and without Propidium Monoazide Treatment

A 16S rRNA gene-based culture-independent approach was used to study the bacterial and archaeal communities in a sulfide-rich wastewater. Propidium Monoazide (PMA) treatment was applied to limit the analysis to the fraction of viable cells in environment. A total of 104 and 68 clones respective from bacterial clone library and archaeal library were picked and analyzed by restriction fragment length polymorphism (RFLP). 35 RFLP patterns from bacterial clone library and 10 RFLP patterns from archaeal clone library were unique and the respective clones were selected for sequencing. BLAST analysis and RFLP analysis showed that the bacterial clone library mainly consisted of Gammaproteobacteria (73%), Anaerolineae (6%), Bacilli (5%), Deltaproteobacteria (7%), Clostridia (4%), Bacteroidetes (1%), and Chlorobia (1%); Methanomicrobia (99%) and Thermococci (1%) were the only two lineages of the archaeal domains. This study gave a first insight into the overall microbial structure in a cloth printing and dyeing wastewater treatment plant with high concentration of sulfide and increased knowledge on the applicability of the PMA treatment in combination with PCR-based molecular techniques to analyze only viable cells in microbial ecology.     

23种中草药体外抗菌活性筛选

为研究23种中草药的80%乙醇提取物对4种临床常见致病菌的体外抗菌活性,该研究用琼脂扩散法测定抑菌圈直径,微量肉汤培养基倍比稀释法测定最低抑菌浓度(minimum inhibitory concentration,MIC)和最低杀菌浓度(minimum bactericidal/fungicidal concentration,MBC/MFC)。结果表明:滇龙胆草、金丝梅、溪黄草等16种提取物对金黄色葡萄球菌的MIC/MBC值在0.19～3.12 mg·mL^-1之间,有很强的抑菌活性。头花蓼、淡竹叶、半枝莲等14种提取物对铜绿假单胞菌的MIC/MBC值在1.56～6.25 mg·mL(-1)之间,有较强的抑菌活性。除槐角外,其余提取物对大肠埃希菌的MIC/MBC值均在3.12～12.5 mg·mL^-1之间,有较强的抑菌活性。黄藤、藿香提取物对白色念珠菌的MIC/MFC值在0.78～6.25 mg·mL^-1之间,有较强的抑菌活性;滇龙胆草、金丝梅、水杨梅、苦参、胡椒、赶黄草、荜菝、淡竹叶提取物对白色念珠菌的MIC/MFC值...     

Prostaglandin F(2alpha) regulates cytokine responses of mast cells through the receptors for prostaglandin E

There is an increasing body of evidence that prostanoids modulate mast cell functions and contribute to the development of allergic inflammation. The present study aimed to identify an undetermined function of prostaglandin (PG) F_2α in mast cell activation and the signaling mechanism involved in it. Simultaneous quantification of prostanoids by liquid chromatography/tandem mass spectrometry revealed the constitutive release of PGF_2α, thromboxane B₂, and 6-keto-PGF_1α from bone marrow-derived mast cells (BMMCs). Upon activation of BMMCs by lipopolysaccharide, the cytokine production in BMMCs was enhanced when the culture was supplemented with PGF_2α. However, F prostanoid receptor—a selective receptor for PGF_2α—was not detected in BMMCs. Further investigations performed using prostanoid receptor antagonists revealed an alternative mechanism wherein the receptors for PGE species—E prostanoid receptors—mediated the PGF_2α signal in BMMCs. The present study provides an insight into a novel function of PGF_2α, i.e., an autocrine accelerator for mast cell activation.     

Ion channels in the immune system as targets for immunosuppression

The discovery of a diverse and unique subset of ion channels in T lymphocytes has led to a rapidly growing body of knowledge about their functional roles in the immune system. Potent and specific blockers have provided molecules tools to probe channel structure—function relations and to elucidate the involvement of K⁺, Ca²⁺, and Cl⁻ channels in T-cell activation and cell volume regulation. Recent advances in analyzing Kv1.3 channel structure—function relationships have defined binding sites for channel blockers, which have now been shown to be effective in suppressing T-cell function in vivo. Ion channels may provide excellent pharmaceutical targets for modulating immune system function.     

In vitro biopesticide effect of alkaloids and flavonoids of some plants against Fusarium oxysporum

Alkaloids and flavonoids of three plants, namely Withania somnifera, Euphorbia hirta and Terminalia chebula, were tested for their antifungal potential against plant pathogenic fungi Fusarium oxysporum. The spore counting technique was followed for the antibiotic properties of the extracts tested at three different concentrations (2.5, 5 and 10?mg/ml). Results revealed that the bound flavonoid of root of W. somnifera and free flavonoids of stem bark and fruits of T. chebula totally inhibited spore germination of the fungi (100%). The range of minimum inhibitory concentration and minimum fungicidal concentration of extracts recorded was 0.039–0.625 and 0.039–1.25?mg/ml, respectively. Bound flavonoids of selected plants were more effective than free flavonoids and alkaloids. The study suggests that both alkaloids and flavonoids extracts of selected plants have a potential antifungal properties for the control of diseases of various crops.