DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.     

Land surface phenology as an indicator of biodiversity patterns

With the rapid decline in biodiversity worldwide it is imperative to develop procedures for assessing changes in biodiversity across space. The synoptic view provided by imaging remote sensors constitutes a suitable approach for analyzing biodiversity from local to regional scales. A procedure based on the close relationship between floristic similarity and the similarity in land surface phenology was recently developed and successfully applied to assess diversity patterns using time series imagery acquired by the Moderate Resolution Imaging Spectro-radiometer (MODIS). However, as it depends on high temporal resolution remotely sensed data (e.g., MODIS), the procedure is constrained by the coarse spatial resolution characterizing these high temporal resolution data. Using an optimized technique for image fusion, we combined high temporal resolution data acquired by the MODIS sensor system with moderate spatial resolution data acquired by the Landsat TM/ETM+ sensor systems. Our results show that the MODIS/Landsat data fusion allows the characterization of land surface phenology at higher spatial resolutions, which better corresponded with information acquired within vegetation survey plots established in temperate montane forests located in Wolong Nature Reserve, Sichuan Province, China. As such, the procedure is useful for capturing changes in biodiversity induced by disturbances operating at large spatial scales and constitutes a suitable tool for monitoring and managing biodiversity.     

Insect pupil mechanisms

Summary The spectral characteristics of the pupil mechanism in blowfly photoreceptors and their dependence on light intensity have been investigated together with the intensity dependence of the receptor potential. The threshold for the pupil response as measured by reflectance is found at an intensity at which the peak of the receptor potential is about half maximal and the plateau potential starts to saturate. The reflectance saturates at about 3 log-units above threshold. The reflectance spectrum peaks near 620 nm, and its shape is independent of adaptation intensity. The absorbance change, measured by transmission, is extreme in the blue, at about 470 nm. The shape of the absorbance spectrum is slightly intensity dependent, presumably due to optical waveguide effects. The dynamic ranges of the light-induced reflectance and absorbance changes do not coincide. The reflectance change shows saturation at least 1 to 1.5 log units before the absorbance change saturates.     

Dispersion population models discrete in time and continuous in space

We analyze a discrete-time model of populations that grow and disperse in separate phases. The growth phase is a nonlinear process that allows for the effects of local crowding. The dispersion phase is a linear process that distributes the population throughout its spatial habitat. Our study quantifies the issues of survival and extinction, the existence and stability of nontrivial steady states, and the comparison of various dispersion strategies. Our results show that all of these issues are tied to the global nature of various model parameters. The extreme strategies of staying-in place and going-everywhere-uniformly are compared numerically to diffusion strategies in various contexts. We approach the mathematical analysis of our model from a functional analysis and an operator theory point of view. We use recent results from the theory of positive operators in Banach lattices.     

Modulation of connexon densities in gap junctions of horizontal cell perikarya and axon terminals in fish retina: effects of light/dark cycles,interruption of the optic nerve and application of dopamine

Summary In the fish retina, connexon densities of gap junctions in the outer horizontal cells are modulated in response to different light or dark adaptation times and wavelengths. We have examined whether the connexon density is a suitable parameter of gap junction coupling under in situ conditions. Short-term light adaptation evoked low connexon densities, regardless of whether white or red light was used. Short-term dark adaptation evoked high connexon densities; this was more pronounced in the axon terminal than in perikaryal gap junctions. Under a 12 h red light/12 h dark cycle, a significant difference in connexon densities between the light and the dark period could be established in the gap junctions of the perikarya and axon terminals. Under a white light/dark cycle, only the gap junctions of axon terminals showed a significant difference. Crushing of the optic nerve resulted in an increase in connexon densities; this was more pronounced in axon terminals than in perikarya. Dopamine injected into the right eye of white-light-adapted animals had no effect. However, dopamine prevented the effect of optic-nerve crushing on connexon density. The reaction of axon-terminal gap junctions to different conditions thus resembles that of perikaryal gap junctions, but is more intense. Axon terminals are therefore thought to play an important role in the adaptation process.     

Identificaton of UV,green and red receptors,and their projection to lamina in the cabbage butterfly,Pieris rapae

Summary The photoreceptors in the compound eye of a cabbage butterfly, Pieris rapae, were examined by conventional and intracellular-labeling electron microscopy by the use of the cobalt(III)-lysine complex as an ionized marker. Five types of spectral sensitivity were recorded intracellularly in electrophysiological experiments. They peaked at about 340, 380, 480, 560 and 620 nm, respectively. One of the distal retinula cells (R2) was a UV receptor, whereas the R4 distal retinula cell was a green receptor. The basal retinula cell, R9, was found to be a red receptor; it was localized near the basement membrane, having a bilobed cell body with an individual nucleus in each lobe. A small number of rhabdomere microvilli were present in a narrow cytoplasmic bridge connecting the two lobes. The axons of six retinula cells (R3–R8) in each ommatidium terminated at the cartridge in the lamina (short visual fiber), whereas those of the other three retinula cells, R1, R2 and R9, extended to the medulla (long visual fiber). The information from the UV and red receptors is therefore probably delivered directly to the medulla neurons, independent of that from the other spectral receptor types.     

A model of proliferating cell populations with inherited cycle length

A mathematical model of cell population growth introduced by J. L. Lebowitz and S. I. Rubinow is analyzed. Individual cells are distinguished by age and cell cycle length. The cell cycle length is viewed as an inherited property determined at birth. The density of the population satisfies a first order linear partial differential equation with initial and boundary conditions. The boundary condition models the process of cell division of mother cells and the inheritance of cycle length by daughter cells. The mathematical analysis of the model employs the theory of operator semigroups and the spectral theory of linear operators. It is proved that the solutions exhibit the property of asynchronous exponential growth.     

Evolutionary analysis of the multigene pregnancy-specific β1-Glycoprotein family: Separation of historical and nonhistorical signals

The pregnancy-specific ₁-glycoproteins (PSG) form a large family of closely related proteins. Using newly developed methods of sequence analysis, in combination with protein modeling, we provide a framework for investigating the evolution and biological function of genes like the PSG. Evolutionary trees, based on C-terminal sequence, group PSG genes in a manner consistent with their genomic organization. Trees constructed using the N-terminal domain sequences are unreliable as an indicator of phylogeny because of non-neutral processes of sequence change. During duplication of the PSG genes, evolutionary pressures have resulted in a gradient of constrained change across each gene. The N-terminal domains show a nonrandom pattern of amino acid substitutions clustered in the immunoglobulin complementarity-determining region (CDR)-like regions, which appear to be important in the function of the protein.     

Spectral sensitivity of photoreceptors mediating phase-shifts of circadian rhythms in retinally degenerate CBA/J (rd/rd) and normal CBA/N (+/+) mice

Light-dark cycles are the most important time cue for the circadian system to entrain the endogenous circadian clock to the environmental 24 h cycle. Although photic entrainment of circadian rhythms is mediated by the eye in mammals, photoreceptors implicated in circadian photoreception remain unknown. In our previous study, retinally degenerate CBA/J (rd/rd) mice were found to have lower circadian photo-sensitivity for phase-shifting the locomotor activity rhythms than normal CBA/N(+/+) mice. In the present study, the spectral sensitivity for phase-shifting the rhythms was examined in order to characterize the photopigments involved in circadian photoreception of these mice. The spectral sensitivity of CBA/J-rd/rd mice clearly fitted to the Dartnall nomogram for a retinal₁-based pigment with a maximum at 480 nm, while the best fitted nomogram had a maximum at 500 nm in CBA/N- +/+ mice. These results suggest that circadian photopigments involved in CBA/J-rd/rd and CBA/N- +/+ mice may be different.     

竹红菌甲素在脂质体中的光谱性质和结合能力研究

竹红菌甲素在脂质体中的光谱性质和结合能力研究邹伟,安静仪,蒋丽金（中国科学院北京感光化学研究所,１００１０１）关键词竹红菌甲素;光谱特性;结合;脂质体竹红菌甲素（Ｒ人）是一种新型并配类光疗药物,临床上治疗一些皮肤病效果显著”’,研究表明ＨＡ对癌细胞有...