Effect of biotic and abiotic stresses on volatile emission of Achillea collina Becker ex Rchb

This study describes the application of headspace solid-phase microextraction (HS-SPME)–gas chromatography/mass spectrometry (GC/MS) to characterise the volatile fingerprint changes of Achillea collina, induced by aphids' infestation, mechanical damage and jasmonic acid (JA) treatment. The volatile organic compound profiles of A. collina, Prunus persica and Pisum sativum infested by Myzus persicae were also compared. Several changes were observed between control, infested, mechanically damaged and JA-treated plants, and new inducible volatile organic compounds (IVOCs) were emitted in response to biotic or abiotic stresses. Some of these were in common for all stresses and other compounds were in common only for two types of stress. Conversely some IVOCs were emitted only in response to the specific stimuli. The results suggested that there were species-specific and common IVOCs emitted by A. collina, P. persica and P. sativum in response to M. persicae infestation. In conclusion, HS-SPME–GC/MS seems to be a reliable analytical approach to study in vivo plant reaction to external stimuli.     

Identification of biotic and abiotic particles by using a combination of optical tweezers and in situ Raman spectroscopy.

A highly versatile setup, which introduces an optical gradient trap into a Raman spectrometer, is presented. The particular configuration, which consists of two lasers, makes trapping independent from the Raman excitation laser and allows a separate adjustment of the trapping and excitation wavelengths. Thus, the excitation wavelength can be chosen according to the needs of the application. We describe the successful application of an optical gradient trap on transparent as well as on reflective, metal-coated microparticles. Raman spectra were recorded from optically trapped polystyrene beads and from single biological cells (e.g., erythrocytes, yeast cells). Also, metal-coated microparticles were trapped and used as surface enhanced Raman spectroscopy (SERS) substrates for tests on yeast cells. Furthermore, the optical gradient trap was combined with a SERS fiber probe. Raman spectra were recorded from trapped red blood cells using the SERS fiber probe for excitation.     

Evaluation of the rate of abiotic and biotic degradation of oxo-degradable polyethylene

The recent introduction of oxo-degradable additive in the Argentinean market has motivated the study of the effect of abiotic (temperature and ultraviolet (UV) radiation) and biotic (aerobic in compost) degradation on the structure and mechanical behavior of films of polyethylene (PE) and oxo-degradable polyethylene (PE+AD).Physico-chemical tests show that the failure strain and the carbonyl index of degraded PE and PE+AD samples depend on the UV irradiation dose. Furthermore, the additive plays a crucial role in the degradation and subsequent decay of the molecular weight.It was observed that, for the same dose, the most deteriorated material was the one exposed to the lowest irradiance, emphasizing the importance of the time of exposure to UV radiation. The ratio between the irradiance and the critical dose, is a characteristic time associated to the sharp decay on the failure strain. The critical dose decreases significantly when increasing the temperature of the photo-degradation assay.PE is more susceptible to thermal degradation than PE+AD; the latter only degrades under thermal aging at the highest temperature.Initially biotic degradation in compost showed an increasing production of carbon dioxide for both previously UV-degraded and untreated PE+AD. It is also remarkable that UV-degraded samples of PE and PE+AD with differences in their abiotic degradation level, reached the same final biotic degradation level. It was observed that although the additive increased the abiotic photodegradation, the molecular weight reduction in compost was not enough to reach the maximum biotic degradation level established by international standards for biodegradable materials.     

Ionomic profiling of Nicotiana langsdorffii wild-type and mutant genotypes exposed to abiotic stresses

To provide a new insight into the response of plants to abiotic stresses, the ionomic profiles of Nicotiana langsdorffii specimens have been determined before and after exposure to toxic metals (chromium) or drought conditions. The plants were genetically transformed with the rat glucocorticoid receptor (GR) or the gene for Agrobacterium rhizogenes rolC, because these modifications are known to produce an imbalance in phytohormone equilibria and a significant change in the defence response of the plant. Elemental profiles were obtained by developing and applying analytical procedures based on inductively coupled plasma atomic emission and mass spectrometry (ICP–AES/MS). In particular, the removal of isobaric interferences affecting the determination of Cr and V by ICP–MS was accomplished by use of a dynamic reaction cell, after optimization of the relevant conditions. The combined use of ICP atomic emission and mass spectrometry enabled the determination of 29 major and trace elements (Ba, Bi, Ca, Cd, Co, Cr, Cu, Eu, Fe, Ga, K, Li, Mg, Mn, Mo, Na, P, Pb, Pt, Rb, S, Sb, Sn, Sr, Te, V, W, Y, and Zn) in different parts of the plants (roots, stems, and leaves), with high accuracy and precision. Multivariate data processing and study of element distribution patterns provided new information about the ionomic response of the target organism to chemical treatment or water stress. Genetic modification mainly affected the distribution of Bi, Cr, Mo, Na, and S, indicating that these elements were involved in biochemical processes controlled by the GR or rolC genes. Chemical stress strongly affected accumulation of several elements (Ba, Ca, Fe, Ga, K, Li, Mn, Mo, Na, P, Pb, Rb, S, Sn, Te, V, and Zn) in different ways; for Ca, Fe, K, Mn, Na, and P the effect was quite similar to that observed in other studies after treatment with other transition elements, for example Cu and Cd. The effect of water deficit was less evident, mainly consisting in a decrease of Ba, Cr, Na, and Sr in roots.

Hydrogen peroxide formation and decay in iron-rich geothermal waters: the relative roles of abiotic and biotic mechanisms

Hydrogen peroxide (H2O2) is widely distributed in surface waters where the primary photochemical formation pathway involves the interaction between dissolved organic carbon (DOC) and ultraviolet radiation (UVR). In laboratory studies using iron-rich water from Yellow-stone's Chocolate Pots spring, H2O2 formation depended on sample treatment (unfiltered, < 0.2 micron filtered, autoclaved) prior to irradiation, suggesting several formation pathways. Similar H2O2 formation in filtered and unfiltered water indicates that it is primarily soluble material that is responsible for H2O2 formation. H2O2 formation with soluble material probably includes only photochemical reactions with DOC and/or metals. Greater H2O2 formation in unfiltered and filtered water than in autoclaved water suggests that the agent(s) involved in H2O2 formation is (are) not stable at high temperatures and pressures and degrade to nonphotoreactive species. Such unstable agents may include DOC and/or dissolved complexes of iron or other metals. UVR absorbance occurs across the UV spectrum and, though slightly greater in the UVA range (320-400 nm), is similar to that of other surface waters. Increased UVR absorbance after autoclaving suggested degradation or alteration of some components, which in turn affected H2O2 formation. The spectral region used for irradiation affected net formation and yield. H2O2 formation in water irradiated with UVA radiation was 2.5-3 times that formed in water irradiated with UVB radiation (280-320 nm) in experiments using artificial light sources. Apparent quantum yields comparable to those reported by others could not be calculated because the instrumental designs are not the same. However, approximate quantum yields were calculated for these experiments but should be viewed with caution. Quantum yields were higher in these experiments (0.0040 mol H2O2 per mol photon at 310 nm and 0.0012 mol H2O2 per mol photon at 350 nm) than values reported by other researchers (< 0.0007 mol H2O2 per mol photon at 300 nm and < 0.0005 H2O2 per mol photon at 340 nm; [Scully, N. M., D. R. S. Lean, D. J. McQueen and W. J. Cooper (1996) Limnol. Oceanogr. 41, 540-548]). In natural solar source experiments, H2O2 formation was greater in experiments with UVA and photosynthetically active radiation (PAR; 400-700 nm) than with PAR alone or with UVB, UVA and PAR. However, H2O2 capacity (nM H2O2 W-1 h-1 m2) was greatest with UVB radiation and lowest with PAR radiation. Source regions could not be studied separately. Dark decay of H2O2 occurred via two mechanisms. The main mechanism responsible for H2O2 decay involved particulate matter (probably microorganisms), whereas a secondary mechanism involved soluble matter (i.e. DOC, metal ions and other dissolved species involved in Fenton reactions).     

Comparison of the ATP binding sites of protein kinases using conformationally diverse bisindolylmaleimides

The conformation of a bisindolylmaleimide may be controlled by the size of a macrocyclic ring in which it is constrained. A range of techniques were used to demonstrate that the tether controls both the ratio of the two limiting conformers (syn and anti) in solution and the extent of conjugation between the maleimide and indole rings. Screening the conformationally diverse bisindolylmaleimides against a panel of protein kinases allowed their ATP binding sites to be compared using a chemical approach which, like sequence alignment, does not require detailed structural information. This approach lead to the conclusion that several AGC group protein kinases (including PKCalpha, PKCbeta, MSK1, p70 S6K, PDK-1, and MAPKAP-K1alpha) may be best inhibited by bisindolylmaleimides which adopt a compressed approximately C2-symmetric anti conformation; in constrast, GSK3beta may be best inhibited by bisindolylmaleimides whose ground state is a distorted syn conformation. It is concluded that PDK-1, whose structure has been determined by X-ray crystallography, and its mutants, may serve as particularly useful surrogates for the study of PKC inhibitors.     

Identification of elements in plant drugs and their water infusion using X-ray fluorescence analysis

The present work gives preliminary results of analysis of drug mixtures (NEPHROSAL tea bag) and its water infusion. In a sample of dried drugs the elements K, Ca, Mn, Fe, Ni, Cu, Zn, Br, Rb, Sr, Pb were identified, whereas in their water infusion only Ca, Mn, Zn and Sr were found. The method applied was radionuclide X-ray fluorescence analysis using a radionuclide source¹⁰⁹Cd, a Si/Li semiconductor detector and a multichannel analyzer Canberra 8100.     

Kinetics of abiotic and biotic degradability of low-density polyethylene containing prodegradant additives and its effect on the growth of microbial communities

The kinetics of abiotic oxidation in the dark and the kinetics of biological mineralization in soil and in a compost environment of thermally oxidized LDPE were studied. It was demonstrated that different activation energies are obtained for the thermal oxidation, depending on the composition of the materials. Significantly higher levels of biodegradability have been obtained in a soil environment at 23 °C compared with the compost environment at 58 °C. After two years of mineralization, 91% conversion to carbon dioxide was obtained in the soil test, compared with 43% in the compost test. The differences between fungal, archaeal and bacterial community structures in soil and compost after 607 days of biodegradability assay were mapped out. It was found that the most dominant bacterial and fungal terminal restriction fragments (TRFs) in the compost containing the test material are significantly different from the TRFs in the other environments.     

Latent periodicity of serine-threonine and tyrosine protein kinases and other protein families

We identified latent periodicity in catalytic domains of approximately 85% of annotated serine-threonine and tyrosine protein kinases. Similar results were obtained for other 22 protein families and domains. We also designed the method of noise decomposition, which is aimed to distinguish between different periodicity types of the same period length. The method is to be used in conjunction with the method of cyclic profile alignment, and this combination is able to reveal structure-related or function-related patterns of latent periodicity. Possible origins of the periodic structure of protein kinase active sites are discussed. Summarizing, we presume that latent periodicity is the common property of many catalytic protein domains.     

Identification of plant sterols in hexaploid and tetraploid wheats using gas chromatography with mass spectrometry

Free sterols from hexaploid and tetraploid free-threshing wheats (Triticum aestivum L. and T. durum Desf.) and from their respective hulled wheats (T. spelta L. and T. dicoccon Schrank) were analysed by gas chromatography with mass spectrometry. The qualitative analysis of sterols showed a similar pattern either between hexaploid (T. aestivum, T. spelta) and tetraploid (T. durum, T. dicoccon) wheats or between free-threshing (T. aestivum, T. durum) and hulled (T. spelta, T. dicoccon) wheats. However, quantitative differences were found between tetraploid and hexaploid wheats, in that free sterol amounts in tetraploid wheats were 40% higher than in hexaploid ones. The mass spectra of the sterols were classified into four groups, taking into account the structural features of rings A and B. Typical mass spectral fragmentations of the four classes, and additional evidence related to the side chain of each molecule, were investigated together with their chromatographic behaviour, allowing identification of all the detected sterols.     

Identification and partial characterization of C-glycosylflavone markers in Asian plant dyes using liquid chromatography-tandem mass spectrometry

Flavonoids in the grasses (Poaceae family), Arthraxon hispidus (Thunb.) Makino and Miscanthus tinctorius (Steudel) Hackel have long histories of use for producing yellow dyes in Japan and China, but up to now there have been no analytical procedures for characterizing the dye components in textiles dyed with these materials. LC-MS analysis of plant material and of silk dyed with extracts of these plants shows the presence, primarily, of flavonoid C-glycosides, three of which have been tentatively identified as luteolin 8-C-rhamnoside, apigenin 8-C-rhamnoside and luteolin 8-C-(4-ketorhamnoside). Two of these compounds, luteolin 8-C-rhamnoside (M=432), apigenin 8-C-rhamnoside (M=416), along with the previously known tricin (M=330) and several other flavonoids that appear in varying amounts, serve as unique markers for identifying A. hispidus and M. tinctorius as the source of yellow dyes in textiles. Using this information, we have been able to identify grass-derived dyes in Japanese textiles dated to the Nara and Heian periods. However, due to the high variability in the amounts of various flavonoid components, our goal of distinguishing between the two plant sources remains elusive.     

Systematic screening of protein modifications in four kinases using affinity enrichment and mass spectrometry analysis with unrestrictive sequence alignment

Protein kinases transfer phosphate groups from ATP to substrate proteins, they are known to be involved in diverse cellular processes. They are also important therapeutic targets in pharmaceutical design. Previous studies indicated that multiple post-translational modifications (PTMs) exist in kinases in addition to phosphorylation, and these PTMs play an important role in regulating kinases activities. Nevertheless, a comprehensive analysis for PTMs of kinases is insufficient due to technical limitations, which prevent us from better understanding their functional regulation. Here, we have developed a novel strategy that combines glutathione S-transferase tag affinity enrichment with nano-liquid chromatography coupled with tandem mass spectrometry analysis and non-restrictive protein sequence alignment for identification of diverse PTMs in four yeast kinases. The method allows us to enrich and analyze the entire protein isomers and to minimize the loss of all isomers of protein sample during protein purification. In our study, nineteen phosphorylation sites and several other types of PTMs sites were localized in 4 protein kinases. In addition, we found that some interesting mass shifts can not match those of the known PTMs. It suggested the existence of some undescribed PTMs in the proteins. Accordingly, this study showed that the novel strategy holds a great potential for identification of full-spectrum PTMs in proteins. Our data serves as a stepping stone for future functional studies.     

Identification and specificity profiling of protein prenyltransferase inhibitors using new fluorescent phosphoisoprenoids

Posttranslational modification of proteins with farnesyl and geranylgeranyl isoprenoids is a widespread phenomenon in eukaryotic organisms. Isoprenylation is conferred by three protein prenyltransferases: farnesyl transferase (FTase), geranylgeranyl transferase type-I (GGTase-I), and Rab geranylgeranyltransferase (RabGGTase). Inhibitors of these enzymes have emerged as promising therapeutic compounds for treatment of cancer, viral and parasite originated diseases, as well as osteoporosis. However, no generic nonradioactive protein prenyltransferase assay has been reported to date, complicating identification of enzyme-specific inhibitors. We have addressed this issue by developing two fluorescent analogues of farnesyl and geranylgeranyl pyrophosphates {3,7-dimethyl-8-(7-nitro-benzo[1,2,5]oxadiazol-4-ylamino)-octa-2,6-diene-1}pyrophosphate (NBD-GPP) and {3,7,11-trimethyl-12-(7-nitro-benzo[1,2,5]oxadiazo-4-ylamino)-dodeca-2,6,10-trien-1} pyrophosphate (NBD-FPP), respectively. We demonstrate that these compounds can serve as efficient lipid donors for prenyltransferases. Using these fluorescent lipids, we have developed two simple (SDS-PAGE and bead-based) in vitro prenylation assays applicable to all prenyltransferases. Using the SDS-PAGE assay, we found that, in contrast to previous reports, the tyrosine phosphatase PRL-3 may possibly be a dual substrate for both FTase and GGTase-I. The on-bead prenylation assay was used to identify prenyltransferase inhibitors that displayed nanomolar affinity for RabGGTase and FTase. Detailed analysis of the two inhibitors revealed a complex inhibition mechanism in which their association with the peptide binding site of the enzyme reduces the enzyme's affinity for lipid and peptide substrates without competing directly with their binding. Finally, we demonstrate that the developed fluorescent isoprenoids can directly and efficiently penetrate into mammalian cells and be incorporated in vivo into small GTPases.     

Comparative study of structure and properties of nucleoproteides synthesized using plant virus coat protein

The self-assembly of virus-like artificial particles from the coat protein of a helical virus (potato virus X) and nucleic acids (RNA and DNA) is studied. The structure and properties of the particles are investigated by transmission electron microscopy, atomic force microscopy, and enzymatic analysis.