Investigation of penetratin peptides. Part 1. The environment dependent conformational properties of penetratin and two of its derivatives.

The homeodomain, the DNA-binding domain of Antennapedia homeoprotein, is composed of three alpha-helices and one beta-turn between helices II and III. Its third helix from the N-terminal (helix III) can translocate through the cell membrane into the nucleus and can be used as an intracellular vehicle for the delivery of oligopeptides and oligonucleotides. To the best of our knowledge, this helix III, called penetratin, which consists of 16 amino acids, is internalized by cells in a specific, non-receptor-mediated manner. For a better understanding of the mechanism of the transfer, the structure of penetratin was examined in both extracellular matrix-mimetic and membrane-mimetic environments: 1H-NMR and CD spectroscopic measurements were performed in mixtures of TFE/water with different ratios. The molecular conformations of two analogue peptides [(6,14-Phe)-penetratin and a 12 amino acid penetratin derivative (peptide 3)] were also studied. An atomic level comprehensive analysis of penetratin and its two analogues was performed. In a membrane-mimetic solvent system (TFEd2/water = 9: 1), on the basis of 553 distance restraints, the 4-12 region of penetratin exhibits a bent, irregular helical structure on NMR examination. Interactions between hydrophobic amino acid residues in conjunction with H-bonds stabilize the secondary structure of the molecule. Thus, both derivatives adopt a helix-like conformation. However, while (6,14-Phe)-penetratin displays both alpha-helical and 310-helical features, the structure of peptide 3 is predominantly a 310-helix. Of the three peptides, surprisingly (6,14-Phe)-penetratin has the largest helical content. An increase in the polarity of the molecular environment gradually disintegrates these helix-like secondary structures. In a highly aqueous molecular system (TFEd2/water = 1 : 9), the fast exchange of multiple conformers leads to too few distance restraints being extracted, therefore the NMR structures can no longer be determined. The NMR data show that only short-range order can be traced in these peptides. Under these conditions, the molecules adopt nascent helix-like structures. On the other hand, CD spectra could be recorded at any TFE/water ratio and the conformational interconversion could therefore be monitored as a function of the polarity of the molecular environment. The CD data were analysed comprehensively by the quantitative deconvolution method (CCA+). All three penetratin peptides display helical conformational features in a low dielectric medium, with significant differences as a function of their amino acid composition. However, these conformational features are gradually lost during the shift from an apolar to a polar molecular environment.     

Biodiversity effects and transgressive overyielding

Aims The potential for mixtures of plant species to produce more biomass than every one of their constituent species in monoculture is still controversially discussed in the literature. Here we tested how this so-called transgressive overyielding is affected by variation between and within species in monoculture yields in biodiversity experiments.Methods We use basic statistical principles to calculate expected maximum monoculture yield in a species pool used for a biodiversity experiment. Using a real example we show how between- and within-species variance components in monoculture yields can be obtained. Combining the two components we estimate the importance of sampling bias in transgressive overyielding analysis.Important findings The net biodiversity effect (difference between mixture and average monoculture yield) needed to achieve transgressive overyielding increases with the number of species in a mixture and with the variation between constituent species in monoculture yields. If there is no significant variation between species, transgressive overyielding should not be calculated using the best monoculture, because in this case the difference between this species and the other species could exclusively reflect a sampling bias. The sampling bias decreases with increasing variation between species. Tests for transgressive overyielding require replicated species' monocultures. However, it can be doubted whether such an emphasis on monocultures in biodiversity experiments is justified if an analysis of transgressive overyielding is not the major goal.     

Odorant Receptor Inhibition Is Fundamental to Odor Encoding

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PCR-based assay for the rapid detection of fumonisin-producing Fusarium species in maize-based animal and poultry feeds in Karnataka,India

Abstract

One hundred and fourteen animal feedstuffs and eighty poultry feed mixtures commonly used for animal and poultry nutrition in Karnataka, India, were analysed for Fusarium contamination. The total counts of fusaria in animal feeds and poultry feed mixtures revealed a high incidence of F. verticillioides, being isolated from all positive samples. Most contaminated samples were maize pellets (71.4%), cotton seed (66.6%), maize powder (60%) and fine wheat bran (50%), respectively, while no Fusarium species was isolated from Bengal gram husk and wheat flakes. All the Fusarium species were identified by the PCR method using genus specific ITS and group specific FUM 1 primers. Of the 374 Fusarium isolates tested with ITS set of primers, all fusaria scored positive, whereas only 244 (65%) isolates tested positive with the FUM 1 set of primers. The specificity of the primers provides the basis for a simple, accurate and precise detection of Fusarium species that represents fumonisin producers, which are a considerable risk for animal, poultry and human health.     

D-L amino acid analysis using automated precolumn derivatization with 1-fluoro-2,4-dinitrophenyl-5-alanine amide

Summary An automated procedure for the precolumn derivatization of enantiomeric amino acid mixtures with 1-fluoro-2,4-dinitrophenyl-5-alanine amide and a liquid chromatographic method for the separation of the derivatives with UV detection are reported. The system described allows to perform routine analyses using microbore columns with a sensitivity at the picomol level. Improvements for the use of this reagent in the protocol of a subtractive Edman degradation procedure of peptides to determine the sequence position of amino acid residues with concomitant identification of their chirality are also described.     

Competition as a source of errors in RAPD analysis

We have used artificial 11 DNA mixtures of all pairwise combinations of four doubled haploid Brassica napus lines to test the ability of RAPDs to function as reliable dominant genetic markers. In situations where a specific RAPD band is present in one homozygous line but absent in the other, the band is expected in the artificial heterozygote, i.e. in the 11 DNA mixture. In 84 of all 613 heterozygous situations analysed, the expected band failed to amplify in the RAPD reaction. Thus, RAPD markers will lead to an erroneous genetic interpretation in 14% of all cases. In contrast, the formation of non-parental heteroduplex bands was found at a frequency of only 0.2%. Analysis of 1 1 mixtures using (1) a different set of optimized reaction conditions and (2) a material with low genomic complexity (Bacillus cereus) gave identical results. Serial dilutions of one genome into another, in steps of 10%, showed that all of the polymorphic bands decreased in intensity as a linear function of their respective proportion in the mixture. In dilutions with water no differences in band intensity were detected. Thus, competition occurs in the amplification of all RAPD fragments and is a major source of genotyping errors in RAPD analysis.     

Degradation of the herbicide diclofop-methyl in soil and influence of pesticide mixtures on its persistence

The degradation of the herbicide [¹⁴C]-diclofopmethyl was investigated in moist parabrown podzol soil at 22°C. Radiochemical procedures were used to monitor the herbicide breakdown. The mineralization of the uniformly labelled aromatic ring was pursued by trapping the¹⁴CO₂ generated for 96 days. Diclofop-methyl was rapidly degraded in the soil with a half-life of about 8 days. The major breakdown product was the corresponding acid-diclofop, formed by a very rapid hydrolysis of the esterbond. With time the acid appeared to undergo strong binding or complexing to the soil. An intermediate 4-(2,4-dichlorophenoxy) phenol was recovered from the treated soil. Concentration of the phenoxyphenol increased upto 6 days followed by quick decline. Insecticide combination of parathion + Demeton-Smethylsulphoxide partially inhibited diclofop degradation in the soil     

Permeability of bilayers composed of mixtures of saturated phospholipids

Liposomes composed of an equimolar binary mixture of phospholipids were formed from a series of saturated phosphatidylcholines (PC) and phosphatidylethanolamines (PE). Mixtures were chosen such that the two phospholipids differed either in terms of head group alone, chain length alone, or both head group and chain length. Cation effluxes, both with and without ionophores (nigericin and valinomycin) were measured over a range of temperatures that encompassed the regions of phase separation for these different lipid mixtures. There was a good correlation between the temperatures at which permeability maxima and phase separation occur. For phospholipid mixtures with the same acyl chain but different head groups (PC vs. PE), the PC component ‘controls’ permeability. For mixtures of PCs differing in chain length, the short chain lipid dominates the permeability pattern particularly if the chain lengths are sufficiently different. Lipids differing in both head group and chain length give rise to more complex permeability patterns. The results of the present study are interpreted in terms of a model in which one of the lipid components of the mixture may specifically congregate at defects between co-existing phases and thus ‘regulate’ permeability.     

Simple luminescence method for estimation of benzo[a]pyrene in a complex mixture of polycyclic aromatic hydrocarbons without a pre‐separation procedure

Benzo[a]pyrene causes cancer at cellular level and is widely present in the environment. Conventional spectroscopic methods for analysis of this compound need a pre‐separation procedure due to severe spectral overlap from other polycyclic aromatic hydrocarbons. We report a simple method that avoids spectral overlap of benzo[a]pyrene from other impurities or polycyclic aromatic hydrocarbons (PAHs), thus it can easily identify benzo[a]pyrene in a complex PAH mixture. The method could easily identify benzo[a]pyrene in an 18‐component PAH mixture. Calibration plots in methanol solution and in micellar media show a good linearity (R > 0.9997) in the benzo[a]pyrene concentration range generally found in the environment. The method gives a detection limit of 1.52 × 10^?9 mol/L in CTAB micellar medium and 2.55 × 10^?9 mol/L in methanol solution. The proposed method is selective, sensitive and fast. The fluorescence response of benzo[a]pyrene is found to be a potential candidate to sense the critical micellar concentration (CMC) of CTAB micelles. Copyright © 2003 John Wiley & Sons, Ltd.     

Determining the optimal size of small molecule mixtures for high throughput NMR screening

High-throughput screening (HTS) using NMR spectroscopy has become a common component of the drug discovery effort and is widely used throughout the pharmaceutical industry. NMR provides additional information about the nature of small molecule-protein interactions compared to traditional HTS methods. In order to achieve comparable efficiency, small molecules are often screened as mixtures in NMR-based assays. Nevertheless, an analysis of the efficiency of mixtures and a corresponding determination of the optimum mixture size (OMS) that minimizes the amount of material and instrumentation time required for an NMR screen has been lacking. A model for calculating OMS based on the application of the hypergeometric distribution function to determine the probability of a hit for various mixture sizes and hit rates is presented. An alternative method for the deconvolution of large screening mixtures is also discussed. These methods have been applied in a high-throughput NMR screening assay using a small, directed library.