Auxins of non-flowering plants. I. Occurrence of 3-indoleacetic acid and phenylacetic acid in vegetative and fertile fronds of the ostrich fern (Matteucia struthiopteris)

Gas chromatography-mass spectrometry evidence is presented for the presence of both phenylacetic acid (PAA) and 3-indoleacetic acid (IAA) in vegetative and fertile tissues of the sporophyte of the ostrich fern [ Matteucia struthiopteris (L.) Todaro]. 3-Indolepropionic acid, tryptamine and 3-indoleacetonitrile were not found in tissue extracts, although small amounts of 3-indolebutyric acid and tryptophol may have been present. PAA was present in amounts higher than those found in flowering plants, while LAA levels fall within the angiosperm range. The levels of both auxins were higher in the younger vegetative tissues than in mature vegetative or fertile pinnae. Recent evidence for the occurrence of angiosperm growth hormones in ferns is discussed.     

Smell the change: On the potential of gas‐chromatographic ion mobility spectrometry in ecosystem monitoring

Plant volatile organic compounds (pVOCs) are being recognized as an important factor in plant–environment interactions. Both the type and amount of the emissions appear to be heavily affected by climate change. A range of studies therefore has been directed toward understanding pVOC emissions, mostly under laboratory conditions (branch/leaf enclosure). However, there is a lack of rapid, sensitive, and selective analytical methods, and therefore, only little is known about VOC emissions under natural, outdoor conditions. An increased sensitivity and the identification of taxon‐specific patterns could turn VOC analysis into a powerful tool for the monitoring of atmospheric chemistry, ecosystems, and biodiversity, with far‐reaching relevance to the impact of climate change on pVOCs and vice versa. This study for the first time investigates the potential of ion mobility spectrometry coupled to gas‐chromatographic preseparation (GC‐IMS) to dramatically increase sensitivity and selectivity for continuous monitoring of pVOCs and to discriminate contributing plant taxa and their phenology. Leaf volatiles were analyzed for nine different common herbaceous plants from Germany. Each plant turned out to have a characteristic metabolite pattern. pVOC patterns in the field would thus reflect the composition of the vegetation, but also phenology (with herbaceous and deciduous plants contributing according to season). The technique investigated here simultaneously enables the identification and quantification of substances characteristic for environmental pollution such as industrial and traffic emissions or pesticides. GC‐IMS thus has an enormous potential to provide a broad range of data on ecosystem function. This approach with near‐continues measurements in the real plant communities could provide crucial insights on pVOC‐level emissions and their relation to climate and phenology and thus provide a sound basis for modeling climate change scenarios including pVOC emissions.     

Fabrication and characterization of noble crystalline silver nanoparticles from Pimenta dioica leave extract and analysis of chemical constituents for larvicidal applications

The current works report the bio-efficacy of Pimenta dioica leaf derived silver nanoparticles (Pd@AgNPs) and leaf extract obtained trough different solvents against the larvae of malaria, filarial and dengue vectors. Synthesis of silver nanoparticles (AgNPs) was done by adding 10 ml of P. dioica leaf extract into 90 ml of 1 mM silver nitrate solution, a slow colour change was observed depicting the formation of AgNPs. Further, Pd@AgNPs was confirmed through Ultraviolet–visible spectroscopy which exhibited characteristic absorption peak at 422 nm wavelength. X-ray diffraction and selected area electron diffraction analysis confirmed monodispersed and crystalline nature of Pd@AgNPs with 32 nm an average size. Scanning electron microscopy and transmission electron microscopy showed the most of Pd@AgNPs were spherical and triangular in shape and energy-dispersive X-ray spectroscopy revealed silver elemental nature of nanoparticles. Zeta potential of Pd@AgNPs is highly negative which confirmed its stable nature. Pd@AgNPs showed prominent absorption peaks at 1015, 1047, 1243, 1634, 2347, 2373, 2697 and 3840 cm^?1 which are corresponding to following compounds polysaccharides, carboxylic acids, water, alcohols, esters, ethers, amines, amides and phenol, respectively as reported by Fourier-transform infrared spectroscopy analysis. Gas chromatography–mass spectrometry and Liquid chromatography–mass spectrometry analysis revealed 39 and 70 compounds, respectively, which might be contributed for bio-reduction, capping, stabilization and larvicidal behavior of AgNPs. A comparable lethality (LC₅₀ and LC₉₀) was observed in case of Pd@AgNPs over leaf extract alone. The potential larvicidal activity of Pd@AgNPs was observed against the larvae of Aedes aegypti,(LC_50, 2.605; LC_90, 5.084 ppm) Anopheles stephensi (LC_50, 3.269; LC_90, 7.790 ppm) and Culex quinquefasciatus (LC_50, 5.373; LC_90, 14.738 ppm without affecting non-targeted organism, Mesocyclops thermocyclopoides after 72 hr of exposure. This study entails green chemistry behind synthesis of AgNPs which offers effective technique for mosquito control and other therapeutic applications.     

Developing liquid chromatography ion mobility mass spectometry techniques

When a packet of ions in a buffer gas is exposed to a weak electric field, the ions will separate according to differences in their mobilities through the gas. This separation forms the basis of the analytical method known as ion mobility spectroscopy and is highly efficient, in that it can be carried out in a very short time frame (micro- to milliseconds). Recently, efforts have been made to couple the approach with liquid-phase separations and mass spectrometry in order to create a high-throughput and high-coverage approach for analyzing complex mixtures. This article reviews recent work to develop this approach for proteomics analyses. The instrumentation is described briefly. Several multidimensional data sets obtained upon analyzing complex mixtures are shown in order to illustrate the approach as well as provide a view of the limitations and required future work.     

Combination of size-exclusion chromatography and ion exchange adsorption for improving the proteomic analysis of plasma-derived extracellular vesicles

Extracellular vesicles (EVs) are lipid membrane vesicles released by live cells that carry a variety of biomolecules, including nucleic acids, lipids, and proteins. Recently, proteins in plasma-derived EVs have emerged as novel biomarkers with essential functions in the diagnosis and prognosis of human diseases. However, the current methods of isolating EVs from plasma often lead to coisolated impurities in biological fluids. Therefore, before performing any research protocol, the process of extracting EVs from plasma for proteomic analysis must be optimized. In this study, two EV isolation strategies, size exclusion chromatography (SEC) and SEC combined with ion exchange adsorption (SEC + IEA), were compared in terms of the purity and quantity of protein in EVs. Our results demonstrated that, compared to single-step SEC, SEC combined with IEA could produce plasma-derived EVs with a higher purity by decreasing the abundance of lipoprotein. Additionally, with MS analysis, we demonstrated that the combination approach maintained the stability and improved the purity of EVs in many plasma samples. Furthermore, by combining SEC with IEA, more cancer-associated proteins were detected in the plasma of various cancer samples.     

Evaluation of a low-cost calorimetric approach for rapid detection of tuberculosis and other mycobacteria in culture

Aims: The objective of this study was to evaluate the effectiveness of microcalorimetry in rapid detection of mycobacterium species using an inexpensive Isothermal microcalorimetry (IMC) instrument. In addition, we compared microcalorimetry with conventional monitoring techniques. Methods and Results: Isothermal microcalorimetry measures heat production rate and can provide rapid detection of living mycobacteria in clinical specimens. Using liquid medium showed that bacterial activity measured by IMC using a TAM Air^® agreed with the triphenyl tetrazolium chloride (TTC) assay. Using solid medium to enhance growth, fast‐growing mycobacteria detection was achieved between 26 and 53 h and slow‐growing mycobacteria detection was achieved between 54 and 298 h. In addition, the calorimetric data were analysed to estimate the growth rate and generation time of the mycobacteria monitored. Significance and Impact of the Study: Infections caused by mycobacteria are severe and difficult to treat. With 9·27 million new cases of tuberculosis in 2007, developing countries experience severe health and economic consequences owing to the lack of an affordable, fast detection method. Research‐grade IMC instruments are too expensive to use in developing countries. Our study demonstrates that less‐expensive instruments such as the TAM air ^® are adequate for mycobacteria detection and therefore establishes a clear proof of concept.     

Identification of benzophenanthridine alkaloids from Bocconia arborea by gas chromatography-mass spectrometry

A methanol extract of the bark of Bocconia arborea was fractionated on silica gel and the fractions analysed using gas chromatography coupled with mass spectrometry (GC-MS). Several benzophenanthridine alkaloids were identified including dihydrosanguinarine, oxysanguinarine, 11-acetonyldihydrochelerythrine, dihydrochelerythrine, chelerythrine, chelerythridimerine and angoline as the principal constituents. The results show that the direct GC-MS analysis of these alkaloids is possible with a clear distinction between the compounds. The technique is shown to be a valuable tool and an alternative technique to classical phytochemical procedures permitting the fast analysis of alkaloids mixtures.     

Accurate and efficient method for quantification of urinary histamine by gas chromatography negative ion chemical ionization mass spectrometry

Because of the recognized inaccuracy and unreliability of currently available methods for the quantification of histamine in biological fluids, a method for quantification of urinary histamine by stable isotope dilution assay with negative ion chemical ionization mass spectrometry has been developed. Following the addition of [²H₄]histamine to 1 ml of urine, histamine is extracted into butanol, back-extracted into HCl, derivatized to the pentafluorobenzyl derivative (CH₂C₆F₅)₃-histamine, extracted into methylene chloride, and then quantified with negative ion chemical ionization mass spectrometry by selected ion monitoring of the ratio of ions $\text{m}\text{z}$$\text{430}\text{434}$. Twenty samples can be assayed in 2 days. Precision of the assay is ±2.7% and the accuracy is 97.6%. Lower limits of sensitivity are approximately 100–500 fg injected on-column. This assay provides a very sensitive, accurate, and efficient method for the quantification of histamine in human urine.     

Increased DNA Oxidation and Decreased Levels of Repair Products in Alzheimer's Disease Ventricular CSF

Abstract : One of the leading etiologic hypotheses regarding Alzheimer's disease (AD) is the involvement of free radical-mediated oxidative stress in neuronal degeneration. Although several recent studies show an increase in levels of brain DNA oxidation in both aging and AD, there have been no studies of levels of markers of DNA oxidation in ventricular CSF. This is a study of levels of 8-hydroxy-2'-deoxyguanosine (8-OHdG), the predominant marker of oxidative DNA damage, in intact DNA and as the "free" repair product that results from repair mechanisms. Free 8-OHdG was isolated from CSF from nine AD and five age-matched control subjects using solidphase extraction columns and measured using gas chromatography/mass spectrometry with selective ion monitoring. Intact DNA was isolated from the same samples and the levels of 8-OHdG determined in the intact structures. Quantification of results was carried out using stable isotope-labeled 8-OHdG. By using this sensitive methodology, statistically significant elevations ( p < 0.05) of 8-OHdG were observed in intact DNA in AD subjects compared with age-matched control subjects. In contrast, levels of free 8-OHdG, removed via repair mechanisms, were depleted significantly in AD samples ( p < 0.05). Our results demonstrate an increase in unrepaired oxygen radical-mediated damage in AD DNA as evidenced by the increased presence of 8-OHdG in intact DNA and decreased concentrations of the free repair product. These data suggest that the brain in AD may be subject to the double insult of increased oxidative stress, as well as deficiencies in repair mechanisms responsible for removal of oxidized bases.     

Detection of volatile compounds produced by microbial growth in urine by selected ion flow tube mass spectrometry (SIFT-MS)

Selected ion flow tube-mass spectrometry has been used to measure the volatile compounds occurring in the headspace of urine samples inoculated with common urinary tract infection (UTI)-causing microbes Escherichia coli, Proteus vulgaris, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Enterococcus faecalis, or Candida albicans. This technique has the potential to offer rapid and simple diagnosis of the causative agent of UTIs.     

Protein identification in cerebrospinal fluid using packed capillary liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry

The identification and characterization of proteins in complex biological samples such as body fluids, require powerful and reliable tools. Mass spectrometry is today one of the most important methods in such research. This paper reports on the results from the first experiment where a tryptic digest of cerebrospinal fluid was analyzed applying reversed phase liquid chromatography coupled on-line to a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer. In total, 70 204 peaks were detected, which originated from 16 296 isotopic clusters corresponding to 6551 unique peptide masses. From these masses, 39 proteins were identified in the sample. The amount of sample required for one experiment corresponds to 32 microL of cerebrospinal fluid.     

Molecular species analysis of lipids by metastable ion mass spectrometry

A convenient universal and fast mass spectrometrical method designed for the molecular species analysis of natural lipids is described. In contrast to the commonly employed procedures the method does not require chemical or enzymatic treatment and does not include chromatographic steps. The method relies on the recognition of ions characteristic of individual molecular species in the mass spectrum of a particular lipid fraction, that is accomplished on the basis of metastable ion spectra. The efficiency of this approach is demonstrated with a variety of natural lipids: triglycerides, glycerophospholipids, sphingomyelin and ornithinolipids. The advantages and limitations of the method as well as possible further developments are discussed.     

High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that separates gas-phase ions by their behavior in strong and weak electric fields. FAIMS is easily interfaced with electrospray ionization and has been implemented as an additional separation mode between liquid chromatography (LC) and mass spectrometry (MS) in proteomic studies. FAIMS separation is orthogonal to both LC and MS and is used as a means of on-line fractionation to improve the detection of peptides in complex samples. FAIMS improves dynamic range and concomitantly the detection limits of ions by filtering out chemical noise. FAIMS can also be used to remove interfering ion species and to select peptide charge states optimal for identification by tandem MS. Here, the authors review recent developments in LC-FAIMS-MS and its application to MS-based proteomics.     

Phosphoproteomic analysis using immobilized metal ion affinity chromatography on the basis of cellulose powder

Detailed characterization of phosphoproteins as well as other post-translationally modified proteins such as glycoproteins, is required to fully understand protein function and regulatory events in cells and organisms. Therefore, an experimental strategy for the isolation of phosphoproteins using a new immobilized metal ion affinity chromatograph (IMAC) material on the basis of cellulose has been developed and characterized. Different approaches have been used to test the material. Recovery rates were determined by 32P labelling of a myelin basic protein fragment and by reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry using a tryptic digest of the model protein bovine beta-casein. Selectivity was demonstrated by enrichment and separation of phosphopeptides from different samples, such as from a digest of horse myoglobin as well as from a digest of in vitro phosphorylated extracellular signal regulates kinase 2 (ERK2) mixed with synthetic phosphopeptides, phosphorylated on different amino acid residues. Furthermore, simplification and optimization of sample pretreatment was achieved by combining the separating (IMAC) and desalting (C18) step during preparative high performance liquid chromatography. The comparison between our material and a commercially available IMAC system (POROS 20 MC; Perspective BioSystems) emphasizes the competitiveness of the cellulose. Confirmed by the obtained data, the cellulose material performed as well as the commercially available sorbent, however with the advantage, that it can be produced rather easily and at very low cost.     

A possible role of alanine for ammonia transfer between astrocytes and glutamatergic neurons

The metabolism of [U-(13)C]lactate (1 mM) in the presence of unlabeled glucose (2.5 mM) was investigated in glutamatergic cerebellar granule cells, cerebellar astrocytes, and corresponding co-cultures. It was evident that lactate is primarily a neuronal substrate and that lactate produced glycolytically from glucose in astrocytes serves as a substrate in neurons. Alanine was highly enriched with (13)C in the neurons, whereas this was not the case in the astrocytes. Moreover, the cellular content and the amount of alanine released into the medium were higher in neurons than astrocytes. On incubation of the different cell types in medium containing alanine (1 mM), the astrocytes exhibited the highest level of accumulation. Altogether, these results indicate a preferential synthesis and release of alanine in glutamatergic neurons and uptake in cerebellar astrocytes. A new functional role of alanine may be suggested as a carrier of nitrogen from glutamatergic neurons to astrocytes, a transport that may operate to provide ammonia for glutamine synthesis in astrocytes and dispose of ammonia generated by the glutaminase reaction in glutamatergic neurons. Hence, a model of a glutamate-glutamine/lactate-alanine shuttle is presented. To elucidate if this hypothesis is compatible with the pattern of alanine metabolism observed in the astrocytes and neurons from cerebellum, the cells were incubated in a medium containing [(15)N]alanine (1 mM) and [5-(15)N]glutamine (0.5 mM), respectively. Additionally, neurons were incubated with [U-(13)C]glutamine to estimate the magnitude of glutamine conversion to glutamate. Alanine was labeled from [5-(15)N]glutamine to 3.3% and [U-(13)C]glutamate generated from [U-(13)C]glutamine was labeled to 16%. In spite of the modest labeling in alanine, it is clear that nitrogen from ammonia is transferred to alanine via transamination with glutamate formed by reductive amination of alpha-ketoglutarate. With regard to the astrocytic part of the shuttle, glutamine was labeled to 22% in one nitrogen atom whereas 3.2% was labeled in two when astrocytes were incubated in [(15)N]alanine. Moreover, in co-cultures, [U-(13)C]alanine labeled glutamate and glutamine equally, whereas [U-(13)C]lactate preferentially labeled glutamate. Altogether, these results support the role proposed above of alanine as a possible ammonia nitrogen carrier between glutamatergic neurons and surrounding astrocytes and they show that lactate is preferentially metabolized in neurons and alanine in astrocytes.     

选择反应监测技术在蛋白质组学研究中的应用

基于三重四极杆质谱仪的选择反应监测(SRM)技术是一种根据已有信息或理论信息靶向进行质谱信号采集的技术,具有高选择性、高重复性、高灵敏度、宽动态范围等特点,已被广泛应用于蛋白质组学研究,用于生物样本中蛋白质的绝对定量分析.本文对SRM技术的特点、发展过程、在蛋白质组学中的应用现状以及发展前景进行了概述.     

固化金属离子亲和层析富集磷酸化多肽方法的选择及优化

在磷酸化蛋白质组学研究中,根据是否需要对待富集样品进行甲酯化处理,可将固化金属离子亲和层析（IMAC）方法分为两类,即需要甲酯化处理的IMAC方法（ME—IMAC）和不需要甲酯化处理的IMAC方法（Non—ME—IMAC）。要实现对磷酸化多肽的有效富集和鉴定,就必须对富集方法进行选择和优化。利用基质辅助激光解析离子化串联飞行时间质谱（MALDI—TOF—MS）对两种方法富集的磷酸化多肽进行了比较研究。结果表明,ME—IMAC方法容易发生样品丢失,质谱结果的分析也比较复杂,而Non—ME—IMAC方法则不仅操作简单而且富集效果理想。另外,优化了Non—ME—IMAC方法的实验条件,指出最佳的结合溶液是8％ACN／0．3％TFA,最佳的洗脱溶液是0．1mol／LEDTA（pH值8．0）,从而建立了一套完整而简单有效的磷酸化多肽富集方法。     

Identification and culturing of cyanobacteria isolated from freshwater bodies of Sri Lanka for biodiesel production

The present study was carried out to investigate cyanobacteria as a potential source for biodiesel production isolated from fresh water bodies of Sri Lanka. Semi mass culturing and mass culturing were carried out to obtain biomass for extracting total lipids. Fatty acid methyl ester (FAME) or biodiesel was produced from extracted lipid by trans-esterification reaction. FAME component was identified using gas chromatography (GC). Atotal of 74 uni-algal cultures were obtained from Biofuel and Bioenergy laboratory of the National Institute of Fundamental Studies (NIFS), Kandy, Sri Lanka. The total lipid content was recorded highest in Oscillatoria sp. (31.9 ± 2.01% of dry biomass) followed by Synechococcus sp. (30.6 ± 2.87%), Croococcidiopsis sp. (22.7 ± 1.36%), Leptolyngbya sp. (21.15 ± 1.99%), Limnothrixsp. (20.73 ± 3.26%), Calothrix sp. (18.15 ± 4.11%) and Nostoc sp. (15.43 ± 3.89%), Cephalothrixsp. (13.95 ± 4.27%), Cephalothrix Komarekiana (13.8 ± 3.56%) and Westiellopsisprolifica (12.80 ± 1.97%). FAME analysis showed cyanobacteria contain Methyl palmitoleate, Linolelaidic acid methyl ester, Cis-8,11,14-eicosatrienoic acid methyl ester, Cis-10-heptadecanoic acid methyl ester, Methyl myristate, Methyl pentadecanoate, Methyl octanoate, Methyl decanoate, Methyl laurate, Methyl tridecanoate, Methyl palmitoleate, Methyl pentadeconoate, Methyl heptadeconoate, Linolaidic acid methyl ester, Methyl erucate, Methyl myristate, Myristoloeic acid, Methyl palmitate, Cis-9-oleic acid methyl ester, Methyl arachidate and Cis-8,11,14-ecosatrieconoic acid methyl ester. The present study revealed that cyanobacteria isolated from Sri Lanka are potential source for biodiesel industry because of their high fatty acid content. Further studies are required to optimize the mass culture conditions to increase thelipid content from cyanobacterial biomass along with the research in the value addition to the remaining biomass.     

A systematical analysis of tryptic peptide identification with reverse phase liquid chromatography and electrospray ion trap mass spectrometry

In this study we systematically analyzed the elution condition of tryptic peptides and the characteristics of identified peptides in reverse phase liquid chromatography and electrospray tandem mass spectrometry (RPLC-MS/MS) analysis. Following protein digestion with trypsin, the peptide mixture was analyzed by on-line RPLC-MS/MS. Bovine serum albumin (BSA) was used to optimize acetonitrile (ACN) elution gradient for tryptic peptides, and Cytochrome C was used to retest the gradient and the sensitivity of LC-MS/MS. The characteristics of identified peptides were also analyzed. In our experiments, the suitable ACN gradient is 5% to 30% for tryptic peptide elution and the sensitivity of LC-MS/MS is 50 fmol.Analysis of the tryptic peptides demonstrated that longer (more than 10 amino acids) and multi-charge state ( 2, 3) peptides are likely to be identified, and the hydropathicity of the peptides might not be related to whether it is more likely to be identified or not. The number of identified peptides for a protein might be used to estimate its loading amount under the same sample background. Moreover, in this study the identified peptides present three types of redundancy, namely identification, charge, and sequence redundancy, which may repress low abundance protein identification.