A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment

The dynamics of a proteome can only be addressed with large-scale, high-throughput methods. To cope with the inherent complexity, techniques based on targeted quantification using proteotypic peptides are arising. This is an essential systems biology approach; however, for the exploratory discovery of unexpected markers, nontargeted detection of proteins, and protein modifications is indispensable. We present a rapid label-free shotgun proteomics approach that extracts relevant phenotype-specific peptide product ion spectra in an automated workflow without prior identification. These product ion spectra are subsequently sequenced with database search and de novo prediction algorithms. We analyzed six potato tuber cultivars grown on three plots of two geographically separated fields in Germany. For data mining about 1.5 million spectra from 107 analyses were aligned and statistically examined in approximately 1 day. Several cultivar-specific protein markers were detected. Based on de novo-sequencing a dominant protein polymorphism not detectable in the available EST-databases was assigned exclusively to a specific potato cultivar. The approach is applicable to organisms with unsequenced or incomplete genomes and to the automated extraction of relevant mass spectra that potentially cannot be identified by genome/EST-based search algorithms.     

Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.     

Spectral sensitivities of photoreceptors and their role in colour discrimination in the green-backed firecrown hummingbird (<Emphasis Type="Italic">Sephanoides sephaniodes</Emphasis>)

We studied the photopic spectral sensitivity in the green-backed firecrown, Sephanoides sephaniodes, a South American hummingbird, and its possible ecological relationship with preferred flowers and body colouration. Avian colour vision is in general tetrachromatic with at least four types of cones, which vary in sensitivity from the near ultraviolet (UV) to the red wavelength range. Hummingbirds represent an important family of birds, yet little is known about their eye sensitivity, especially about the role of photoreceptors and their oil droplet complements. The photopic electroretinogram shows a main sensitivity peak at 560 nm and a secondary peak in the UV, and may be explained by the presence of four single cones (lambda (max) at ~370, 440, 508 and 560 nm), and a double cone (lambda (max) at 560 nm) screened by oil droplets. The flowers preferred by the firecrown are those in which the red-green wavelength region predominates and have higher contrast than other flowers. The crown plumage of males is highly iridescent in the red wavelength range (peak at 650 nm) and UV; when plotted in a high-dimensional tetrachromatic space, it falls in a "red + UV" purple hue line, suggesting a potential significant communication signal for sexual differentiation.     

应用小波熵分析大鼠脑电信号的动态变化特性

应用小波熵（一种新的信号复杂度测量方法）分析大鼠在不同生理状态下脑电复杂度的动态时变特性。采用慢性埋植电极记录自由活动大鼠的皮层EEG,使用多分辨率小波变换将EEG信号分解为δ、θ、α和β四个分量,求得随时间变化的小波熵。结果表明：在清醒、慢波睡眠和快动眼睡眠三种生理状态下,EEG的小波熵之间存在显著差别,并且在不同时期其值与各个分解分量之间具有不同的关系,其中,慢波睡眠期小波熵还具有较明显的变化节律,反映了EEG微状态中慢波和纺锤波的互补性。由此可见,小波熵既能区别长时间段EEG复杂度之间的差别,又能反映EEG微状态的快速变化特性。     

Inherent and apparent optical measurements in the Hudson/Raritan Estuary

Duringan August, 1999 field campaign, measurements were made to establish hydrologicoptical properties of the Hudson/Raritan Estuary (New York-New Jersey): 1)concurrent above-and below-surface spectral irradiance; 2) sampling forlaboratory determination of inherent optical properties; and 3) concentrationsof optically-important water quality parameters. We used a bio optical modelbased on to predict thesubsurface irradiance reflectance from optically important water constituents.This model was then validated with the measured reflectance spectra from thefield spectroradiometers. Modeling of reflectance is a prerequisite forprocessing remote sensing data to desired thematic maps. These are key input tothe geographic information system (GIS) used to manage the water qualitycondition of the estuary.     

植物（口山）酮类化合物的波谱特征

结合大量文献和实验工作 ,对植物 (主要是獐牙菜属 )口山酮类化合物的波谱特征进行总结和归纳。     

Spectral Estimation by Variable Span Log Periodogram Smoothing: An Application to Annual Lynx Numbers

Spectral estimation is commonly based on smoothing the periodogram or its logarithm. In such a smoothing exercise, it is not entirely sensible to use the same bandwidth for all frequencies, since the smoothness of the underlying spectrum may vary. This note describes the use of a variable span smoother in estimating the log spectrum. An application to annual lynx data is presented.     

Spectral resolution of cardio-circulatory variations in men measured by autorhythmometry over 2 years

An analogue of the periodogram method for unequally spaced data is presented with a view to resolving the frequency structure of the observations. The algorithm is explicitly based on the sequential least squares procedure. In particular, the key concept is that the with-in-plot spectral analysis can be augmented by the between-plot information to make inferences about common characteristics. It is also shown how the between-plot random variations can be incorporated into the multiple harmonic regression model. A detailed spectral analysis investigates the periodic fluctuations in four cardio-circulatory variables, measured by autorhythmometric observation by eight men at rest and extending over a time span of 2 years. The spectral curves show the existence of circadian and circaseptan rhythmicities. The amplitude modulation of the dian rhythm by circaseptan variation is assimilated with the rhythmicity of work during the week. The blood-pressure variables situate their maximum annual peak in the winter period. These quasi-periodic fluctuations appear to be related to the amount of physical activity performed in time by the subjects.