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.     

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.

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.     

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 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.     

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 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.     

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.     

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.     

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.     

LC-ESI-MS characterisation of phytoalexins induced in chickpea and pea tissues in response to a biotic elicitor of Hypnea musciformis (red algae)

A simple extraction procedure and HPLC method was developed to analyse the major and minor components of induced phytoalexins of elicited tissues (seeds) of chickpeas (Cicer arietinum L.) and peas (Pisum sativum L.) treated with a biotic elicitor (k-carrageenan) of Hypnea musciformis (red algae) from the Karachi coast. The level and timing of the induced phytoalexin production were estimated on the basis of various elicitor dilutions and as a function of time; the results are presented and discussed. A LC-ESI-MS/MS technique has been employed for the detection and characterisation of the induced phytochemical components (flavonoids and their glyco-conjugates). Nine flavonoids were identified from chickpeas: naringin, naringin malonate, liquiritigenin, naringenin, biochanin A, daidzein, formononetin, maackiain and medicarpin, while five flavonoids were identified from peas: afrormosin, anhydropisatin, pisatin, pseudobaptigenin and maackiain. These compounds play a vital role as phytoalexins because of their antimicrobial activity.     

The influence of biotic and abiotic factors on the rate of degradation of poly(lactic) acid (PLA) coupons buried in compost and soil

Poly(lactic) acid (PLA) is a compostable biopolymer and has been commercialised for the for the manufacture of short-shelf life products. As a result, increasing amounts of PLA are entering waste management systems and the environment; however, the degradation mechanism is unclear. While hydrolysis of the polymer occurs abiotically at elevated temperature in the presence of water, potential catalytic role for microbes in this process is yet to be established. In this study, we examined the degradation of PLA coupons from commercial packaging at a range of temperatures (25°, 37°, 45°, 50° and 55 °C) in soil and compost and compared with the degradation rates in sterile aqueous conditions by measuring loss of tensile strength and molecular weight (Mw). In addition, in order to assess the possible influence of abiotic soluble factors in compost and soil on degradation of PLA, degradation rates in microorganism-rich compost and soil were compared with sterile compost and soil extract at 50 °C. Temperature was determined to be the key parameter in PLA degradation and degradation rates in microorganism-rich compost and soil were faster than in sterile water at temperatures 45° and 50 °C determined by tensile strength and Mw loss. Furthermore, all tensile strength was lost faster after 30 and 36 days in microorganism-rich compost and soil, respectively, than in sterile compost and soil extract, 57 and 54 days, respectively at 50 °C. Significantly more Mw, 68% and 64%, was lost in compost and soil, respectively than in compost extract, Mw, 53%; and in soil extract, 57%. Therefore, degradation rates were faster in microorganism-rich compost and soil than in sterile compost and soil extract, which contained the abiotic soluble factors of compost and soil at 50 °C. These comparative studies support a direct role for microorganisms in PLA degradation at elevated temperatures in humid environments. No change in tensile strength or Mw was observed either 25° or 37 °C after 1 year suggesting that accumulation of PLA in the environment may cause future pollution issues.     

Identification of key residues for protein conformational transition using elastic network model

Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.     

Identification and quantification of protein carbonylation using light and heavy isotope labeled Girard's P reagent

Protein carbonyls are one of the most widely studied markers of oxidative stress. Determining increases in the concentration of protein carbonyls known to be associated with neurodegenerative diseases, heart disease, cancer and ageing. Identification of carbonylation sites in oxidized proteins has been a challenge. Even though recent advances in proteomics has facilitate the identification of carbonylation sites in oxidized proteins, confident identification remains a challenge due to the complicated nature of oxidative damage and the wide range of oxidative modifications. Here, we report the development of a multiplexing strategy that facilitates confident carbonylated peptide identification through a combination of heavy and light isotope coding and a multi-step filtering process. This procedure involves (1) labeling aliquots of oxidized proteins with heavy and light forms of Girard's reagent P (GPR) and combining them in a 1:1 ratio along with (2) LC/MS and MALDI-MS/MS analysis. The filtering process uses LC/MS and MALDI-MS/MS data to rule out false positives by rejecting peptide doublets that do not appear with the correct concentration ratio, retention time, tag number, or resolution. This strategy was used for the identification of heavily oxidized transferrin peptides and resulted in identification 13 distinct peptides. The competency of the method was validated in a complex mixture using oxidized transferrin in a yeast lysate as well as oxidized yeast. Twenty-five percent of the peptides identified in a pure oxidized sample of transferrin were successfully identified from the complex mixture. Analysis of yeast proteome stressed with hydrogen peroxide using this multiplexing strategy resulted in identification of 41 carbonylated peptides from 36 distinct proteins. Differential isotope coding of model peptides at different concentrations followed by mixing at different ratios was used to establish the linear dynamic range for quantification of carbonylated peptides using light and heavy forms of GPR.     

Investigations of residual stresses in carbon fibre/aluminium-composites using X-ray diffraction

Investigations of residual stresses have been carried out on unidirectionally carbon fibre reinforced aluminium using X-ray diffraction. It was found that the carbon exists in compression parallel to the fibre axis and in tension perpendicular to the fibre axis after the fabrication of the MMCs by a liquid infiltration process. Furthermore, it was observed that the intermetallic phase Al₃Ni was in tension (+ 100 MPa) parallel to the fibre axis and in considerable residual compression (– 400 MPa) perpendicular to the fibre axis.