Multivariate analysis of volatile profiles in tea plant infested by tea green leafhopper Empoasca onukii Matsuda

Plant Growth Regulation - The tea green leafhopper (Empoasca onukii Matsuda) is a severe pest for the tea plant (Camellia sinensis (L.) O. Ktze), which significantly reduces the tea yields and...     

Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra

MOTIVATION: Independent component analysis (ICA) is a signal processing technique that can be utilized to recover independent signals from a set of their linear mixtures. We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling. The method is validated on simulated and experimental data for demonstrating its capability of correctly extracting protein profiles from MALDI-TOF mass spectra. RESULTS: The comparison on peak detection with an open-source and two commercial methods shows its superior reliability in reducing the false discovery rate of protein peak masses. Moreover, the integration of ICA and statistical tests for detecting the differences in peak intensities between experimental groups allows to identify protein peaks that could be indicators of a diseased state. This data-driven approach demonstrates to be a promising tool for biomarker-discovery studies based on MALDI-TOF MS technology. AVAILABILITY: The MATLAB implementation of the method described in the article and both simulated and experimental data are freely available at http://www.unich.it/proteomica/bioinf/.     

Quantal analysis of postsynaptic potentials at interneuronal synapses: Recovery of a signal from noise

Discrete distributions of amplitude of basic EPSP in vertebrate interneuronal synapses were obtained using the maximum likelihood method. Unequal intervals found between the values of calculated densities indicate the quantal nature of the signal. It was shown that quantal levels of nerve impulse transmission due to the structural arrangement of interneuronal connections may be distinguished using a binomial model, approximating as it does to empirical distributions. Systematic discrepancies between empirical and modeled distributions indicate the need to extend the model, however.A. A. Zhdanov State University, Leningrad; I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry; Academy of Sciences of the USSR, Leningrad. Translated from Neirofiziologiya, Vol. 20, No. 4, pp. 479–487, July–August, 1988.     

Reducing noise in computed correlation functions using techniques from signal processing

Time correlation functions invariably suffer from random noise, especially at longer time intervals for which fewer data pairs are available. This noise is particularly of concern when calculating correlations that cannot be averaged over per-molecule contributions, such as stress in molecular simulations. In this work, a set of methods based in signal processing has been developed to reduce the inherent noise that is present in time- and frequency-domain representations of correlation functions. The stress time autocorrelation function, which leads to stress relaxation modulus and complex modulus, is used as an example. The difference between initial and final values of a time correlation function over a finite time domain is found to create so-called ‘leakage’ of noise from disallowed into harmonic frequencies during fast Fourier transformation. Decreasing this leakage effect through reflection to negative time and through applying a window function reduces noise levels significantly. Removing frequency components of insignificant magnitudes also provides significant noise reduction. Applying moving averages in the frequency and time domains also contributes to noise reduction. Specific results obtained by applying these methods to a model asphalt system enable more clear physical interpretations of the underlying relaxations after dramatic noise level reductions were attained.     

Sugars as signal molecules in plant seed development.

Higher plants as sessile organisms react very flexible to environmental changes and stresses and use metabolites like glucose, sucrose and nitrate not only as nutrients but also as signals as part of their life strategies. The role of metabolites as signal molecules has attracted considerable interest during recent years. Data reviewed here for developing plant seeds suggest a trigger function of especially sugars also in development in that metabolic regulatory control can override developmental regulation, i.e., the developmental programme only continues normally if a certain metabolic state is sensed at a given time point in a given cell or tissue. Several experimental strategies have provided mainly correlative evidence that certain sugar levels and/or the resulting changes in osmotic values are necessary within defined tissues or cells to maintain a distinct stage of differentiation or to proceed with the developmental programme. In young legume seeds, but certainly also in other tissues, a high hexose (probably mainly glucose) level seems to maintain the capacity of cells to divide whereas - later in seed development - a certain sucrose level is necessary to induce storage-associated cell differentiation. A major determinant of embryo hexose levels in young legume seeds is an apoplastic invertase preferentially expressed in the inner cell layers of the seed coat. The enzyme cleaves the incoming photoassimilate sucrose into glucose and fructose. During development the tissue harbouring the invertase is degraded in a very specific spatial and temporal pattern as part of the developmental programme and is thus creating steep glucose gradients within the cotyledons. These gradients can be measured at nearly cellular resolution and were found to be correlated positively with cell division rate and negatively with cell differentiation and storage activities. A hexose and a sucrose transporter accumulating only in the epidermal cell layer of the cotyledons seem to be essential in creating and maintaining these gradients. To gain further insights into the role of metabolites, especially sugars, as triggers of developmental processes we foremost have to identify receptor molecules already characterised in yeast, and to describe and understand the signal transduction networks involved.     

Plasmid profiles of Mycobacterium avium complex isolated from swine

Twenty strains of Mycobacterium avium complex (MAC) isolated from swine and five strains from humans were examined for drug susceptibility and plasmid content. Four strains of swine origin and two strains of human origin harbored plasmid DNAs differing in molecular weights. No relationship between plasmid contents and drug resistance was observed. Southern DNA-DNA hybridization showed that small plasmids from swine MAC strains were homologous to those from human origin at the nucleotide level.     

Antimicrobial agents from plants: antibacterial activity of plant volatile oils

The volatile oils of black pepper [Piper nigrum L. (Piperaceae)], clove [Syzygium aromaticum (L.) Merr. & Perry (Myrtaceae)], geranium [Pelargonium graveolens L'Herit (Geraniaceae)], nutmeg [Myristica fragrans Houtt. (Myristicaceae), oregano [Origanum vulgare ssp. hirtum (Link) Letsw. (Lamiaceae)] and thyme [Thymus vulgaris L. (Lamiaceae)] were assessed for antibacterial activity against 25 different genera of bacteria. These included animal and plant pathogens, food poisoning and spoilage bacteria. The volatile oils exhibited considerable inhibitory effects against all the organisms under test while their major components demonstrated various degrees of growth inhibition.     

Multivariate analysis of bacterial volatile compound profiles for discrimination between selected species and strains in vitro

Volatile compounds (VCs) are produced by all microorganisms as part of their normal metabolism. The aim of this study was to determine whether bacterial VC profiles could be used to discriminate between selected bacterial species and strains in vitro.Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) was used to quantify the concentration of 23 microbial VCs within the head-space of various bacterial monocultures, during both the logarithmic and stationary growth phases. In comparison with existing techniques, SIFT-MS enables quantitative, high throughput, real-time head-space analysis to be performed, without need for sample preparation. The results show that most VCs were produced by > 1 bacterial species or strain, and some were produced by all strains tested. Multivariate analysis using similarity matrices, cluster analysis and multidimensional scaling (MDS) was used to determine whether there was a characteristic VC profile at either the species or strain level. Significant discrimination of all bacterial species and strains was achieved by analysing the VC profiles, and the relative similarity of VC profiles could be differentiated in 2 or 3 dimensional space. This study has shown that there are significant differences in the volatile profiles obtained from various bacterial monocultures grown in vitro, and that the analysis techniques herein employed have the potential to differentiate samples at the strain level.     

Design of the Jacky dragon visual display: signal and noise characteristics in a complex moving environment

Visual systems are typically selective in their response to movement. This attribute facilitates the identification of functionally important motion events. Here we show that the complex push-up display produced by male Jacky dragons ( Amphibolurus muricatus) is likely to have been shaped by an interaction between typical signalling conditions and the sensory properties of receivers. We use novel techniques to define the structure of the signal and of a range of typical moving backgrounds in terms of direction, speed, acceleration and sweep area. Results allow us to estimate the relative conspicuousness of each motor pattern in the stereotyped sequence of which displays are composed. The introductory tail-flick sweeps a large region of the visual field, is sustained for much longer than other components, and has velocity characteristics that ensure it will not be filtered in the same way as wind-blown vegetation. These findings are consistent with the idea that the tail-flick has an alerting function. Quantitative analyses of movement-based signals can hence provide insights into sensory processes, which should facilitate identification of the selective forces responsible for structure. Results will complement the detailed models now available to account for the design of static visual signals.     

Comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data

We obtained 32K full-length cDNA sequence data from the rice full-length cDNA project and performed a homology search against NCBI GenBank data. We have also searched homologs of Arabidopsis and other plants' genes with the databases. Comparative analysis of calcium ion transport proteins revealed that the genes specific for muscle and nerve calcium signal transduction systems (VDCC, IP3 receptor, ryanodine receptor) are very different in animals and plants. In contrast, Ca elements with basic functions in cell responses (CNGC, iGlu receptor, Ca(2+)ATPase, Ca2+/Na(+)-K+ ion exchanger) are basically conserved between plants and animals. We also performed comparative analyses of calcium ion binding and/or controlling signal transduction proteins. Many genes specific for muscle and nerve tissue do not exist in plants. However, calcium ion signal transduction genes of basic functions of cell homeostasis and responses were well conserved; plants have developed a calcium ion interacting system that is more direct than in animals. Many species of plants have specifically modified calcium ion binding proteins (CPK, CRK), Ca2+/phospholipid-binding domains, and calcium storage proteins.     

Determination of single-pore conductance from noise analysis. Influence of distribution in pore-amplitudes

For pores which can adopt only the open and closed states, the influence of the amplitude distribution of the single-pore conductance (γ, open state) on the covariance function is derived. It is shown that reliable mean values of γ (E(γ)) can be derived from noise analysis only if the variance in the amplitude distribution (σ_γ²) is known. In the past, σ_γ² was set always to zero, leading to an overestimation of E(γ). In the case of gramicidin-doped lipid bilayer membranes, this overestimation amounts to as much as 15% of the true value of E(γ).     

Determination of single-pore conductance from noise analysis. Influence of distribution in pore-amplitudes

For pores which can adopt only the open and closed states, the influence of the amplitude distribution of the single-pore conductance (gamma, open state) on the covariance function is derived. It is shown that reliable mean values of gamma (E(gamma)) can be derived from noise analysis only if the variance in the amplitude distribution (sigma gamma (2)) is known. In the past, sigma gamma (2) was set always to zero, leading to an overestimation of E(gamma). In the case of gramicidin-doped lipid bilayer membranes, this overestimation amounts to as much as 15% of the true value of E(gamma).     

Mitochondrial complex I function modulates volatile anesthetic sensitivity in C. elegans

Despite the widespread clinical use of volatile anesthetics, their mechanisms of action remain unknown [1-6]. An unbiased genetic screen in the nematode C. elegans for animals with altered volatile anesthetic sensitivity identified a mutant in a nuclear-encoded subunit of mitochondrial complex I [7,8]. This raised the question of whether mitochondrial dysfunction might be the primary mechanism by which volatile anesthetics act, rather than an untoward secondary effect [9,10]. We report here analysis of additional C. elegans mutations in orthologs of human genes that contribute to the formation of complex I, complex II, complex III, and coenzyme Q [11-14]. To further characterize the specific contribution of complex I, we generated four hypomorphic C. elegans mutants encoding different complex I subunits [15]. Our main finding is the identification of a clear correlation between complex I-dependent oxidative phosphorylation capacity and volatile anesthetic sensitivity. These extended data link a physiologic determinant of anesthetic action in a tractable animal model to similar clinical observations in children with mitochondrial myopathies [16]. This work is the first to specifically implicate complex I-dependent oxidative phosphorylation function as a primary mediator of volatile anesthetic effect.     

Tandem termination signal in plant mRNAs

It was proposed that if some mRNA characteristics resulted in a low efficiency of termination signal, an additional closely located stop codon (tandem stop codons) could be used to prevent the harmful readthrough. However, the role of tandem terminators in higher eukaryotes was not verified and remains hypothetical. In this work the sequence features of Arabidopsis thaliana and Oryza sativa mRNAs were analyzed. It was found that plant mRNAs with UGA terminator were characterized by a higher frequency of nonsense codons in the first triplet position of 3′-UTR that could result from a weak natural selection for “reserve” stop signal. Interestingly, the presence of tandem stop codons positively correlated with a specific amino acid composition in the C-terminal position of the encoded proteins. In particular, C-terminal glycine positively correlated with significantly higher frequencies of reserve terminators at the beginning positions of 3′-UTR in UGA-containing mRNAs. This finding coincides with some earlier observations concerning the role of glycine and its codons in inefficient termination of translation and recoding (e.g., 2A oligopeptide).     

Temperature stress causes different profiles of volatile compounds in two chemotypes of Salvia lavandulifolia Vahl.

In order to clarify volatile accumulation patterns along with their adaptability to temperature stress, replicas of two different accessions of Salvia lavandulifolia appointed as chemotypes (A and B) were subjected to increasing temperatures in environmental controlled cabins. Their respective volatile chemical profiles kept their integrity until reaching the growing temperature of 24 °C. Then, remarkable changes were observed. Stressed plants of both accessions showed an increase in the sesquiterpenic fraction and a decrease in the monoterpenic one, although changes in volatile percentages were highly related to the accession. Accession B overexpressed β-caryophyllene, caryophyllene oxide and manool when subjected to the higher temperature tested. On the other hand, accession A mainly showed a remarkable increase of β-bisabolene and viridiflorol. Furthermore, viridiflorol and manool have been confirmed as new chemotaxonomic markers for chemotypes A and B, respectively. The capacity to adjust the production of volatile compounds seems mostly attributed to the genetic background of the plant although more research is needed to understand the stress and its implications for the secondary metabolism. These results contribute remarkably to the chemical phenotyping of this species and may be useful for selection of genotypes.