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.     

Fluorescence anisotropy from diphenylhexatriene in rat liver plasma membranes

Rat livers were fractionated to obtain intracellular membrane preparations and a highly purified preparation of bile canaliculi. The fraction containing bile canaliculi was homogenized and subfractionated to give fractions representing fragments of contiguous membrane and of canalicular microvilli. The relative purity and extent of contamination of each preparation was determined. When the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene was incorporated into aliquots of each fraction at the same probe: lipid ratio and the steady-state anisotropy of its fluorescence measured, it was found that the plasma membrane preparations were much more ordered than the intracellular membrane preparations. Of the plasma membrane preparations, that containing the canalicular microvilli was the most ordered, even allowing for any contribution of contaminants. Thus the microvillus membrane of the bile canaliculus appears to be the most ordered domain of the plasma membrane of the hepatocyte. The high order in this domain may be a factor in reducing the susceptibility to bile salt damage during bile secretion, since it is this region which is exposed to high concentrations of bile salts in vivo.     

A new approach to polarized fluorescence using phase and modulation fluorometry

In the preceding paper, an alternative method is described for obtaining information about the reorientational behavior of a fluorophore in a membrane system from frequency domain measurements. To demonstrate this new analysis procedure, we present data for the probe-molecule 1,6-diphenyl-1,3,5-hexatriene (DPH) in l--dimyristoyl- and l--dipalmitoylphosphatidylcholine (DMPC and DPPC) obtained with two different phase fluorometers: the SLM 4800A Subnanosecond Spectrofluorometer which has only three fixed frequencies available (6, 18 and 30 MHz) and the recently constructed continuously variable multifrequency phasefluorometer (Gratton and Limkeman 1983).It will be shown that reasonable information about the anisotropy behavior of a fluorophore can be obtained even if only three frequencies are used. The phase modulation technique was also used to check the new expression for the anisotropy, r(t), called the general model and introduced by Van der Meer et al. (1984). The parameters P ₂, P ₄ and D, obtained from the nonlinear least squares fit (Bevington 1969) for this general model, confirm the results from the pulse technique of Ameloot and coworkers (Ameloot et al. 1984; Pottel et al. 1986).     

Time-resolved fluorescence spectroscopy of lumazine protein from Photobacterium phosphoreum using synchrotron radiation

Time-resolved fluorescence on lumazine protein from Photobacterium phosphoreum was performed with synchrotron radiation as a source of continuously tunable excitation. The experiments yielded structural and dynamic details from which two aspects became apparent. From fluorescence anisotropy decay monitoring of lumazine fluorescence with different excitation wavelengths, the average correlation times were shown to change, which must indicate the presence of anisotropic motion of the protein. A similar study with 7-oxolumazine as the fluorescent ligand led to comparable results. The other remarkable observation dealt with the buildup of acceptor fluorescence, also observed with 7-oxolumazine although much less pronounced, which is caused by the finite energy transfer process between the single donor tryptophan and the energy accepting lumazine derivatives. Global analytical approaches in data analysis were used to yield realistic correlation times and reciprocal transfer rate constants. It was found that the tryptophan residue has a large motional freedom as also reported previously for this protein and for the related protein from P. leiognathi (Lee et al. 1985; Kulinski et al. 1987). The average distance between the tryptophan residue and the ligand donor-acceptor couple has been determined to be 2.7 nm for the same donor and two different acceptors.     

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.     

Anisotropy decay of fluorescence as an experimental approach to protein dynamics

This minireview makes an initial assessment of the progress made using anisotropy decay measurements for investigating the conformational changes and molecular dynamics in soluble systems. A critical analysis of available data is presented. The anisotropy decays of the tryptophan fluorescence of staphylococcal nuclease, adrenocorticotropin, melittin and of labeled transfer RNA were studied for investigating the functional conformational changes of these systems. The emissions of variously labeled immunoglobulins have been used to elucidate the conformations of these proteins before and after the binding of specific antibodies. Labeled myosin and its fragments have given information on the functional motions of the protein domains. The anisotropy decays of labeled and natural hemoglobin systems have been utilized for exploring the allosteric behavior of these molecules. The data suggest a wide applicability of this technique to the study of protein dynamics and conformational changes of macromolecules.     

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.     

Changes of fluorescence lifetime and rotational correlation time of bovine serum albumin labeled with 1-dimethylaminonaphthalene-5-sulfonyl chloride in guanidine and thermal denaturations

The nanosecond fluorescence depolarization method was applied to measure the fluorescence lifetime () and the rotational correlation time () of bovine serum albumin (BSA) labeled with 1-dimethylaminonaphthalene-5-sulfonyl chloride (dansyl-Cl). Changes of and of dansyl BSA in the guanidine denaturation and in the thermal denaturation were examined. In parallel, the secondary structural change of dansyl BSA was followed by circular dichroism measurements. The magnitude of was almost unchanged between 1 and 2 M guanidine, where the secondary structure of the protein was predominantly disrupted; whereas that of began to increase before the disruption of secondary structure in the guanidine denaturation. In the thermal denaturation, in contrast, changes of both and occurred in a temperature range where the secondary structure was predominantly disrupted. The volume of equivalent sphere (V _e ) and the axial ratio () for the BSA were 3.6–3.8×10^–19 cm³ and 3.6 at 2M guanidine as against 2.1×10^–19 cm³ and 2.2 in the absence of guanidine (25°C), respectively. The magnitudes ofV _e and were 4.9×10^–19 cm³ and 4.5 at 65°C, respectively. Although the secondary structural change of dansyl BSA was irreversible in the thermal denaturation,V _e and were reversible.