Labeling of Bifidobacterium longum cells with 13C-substituted leucine for quantitative proteomic analyses

Stable isotope labeling of amino acids in cell culture was used for Bifidobacterium longum. A comprehensive proteomic strategy was developed and validated by designing an appropriate semidefined medium that allows stable replacement of natural leucine by [(13)C6]leucine. Using this strategy, proteins having variations of at least 50% in their expression rates can be quantified with great confidence.     

Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions

Since the discovery of several inherited diseases linked to the nuclear envelope the number of functions ascribed to this subcellular organelle has skyrocketed. However the molecular pathways underlying these functions are not clear in most cases, perhaps because of missing components. Several recent proteomic analyses of the nuclear envelope and nuclear pore complex proteomes have yielded not only enough missing components to potentially elucidate these pathways, but suggest an exponentially greater number of functions at the nuclear periphery than ever imagined. Many of these functions appear to derive from recapitulation of pathways utilized at the plasma membrane and from other membrane systems. Additionally, many proteins identified in the comparative nuclear envelope studies have sequence characteristics suggesting that they might also contribute to nuclear pore complex functions. In particular, the striking enrichment for proteins in the nuclear envelope fractions that carry phenylalanine-glycine (FG) repeats may be significant for the mechanism of nuclear transport. In retrospect, these findings are only surprising in context of the notion held for many years that the nuclear envelope was only a barrier protecting the genome. In fact, it is arguably the most complex membrane organelle in the cell.     

De novo peptide sequencing and quantitative profiling of complex protein mixtures using mass-coded abundance tagging

Proteomic studies require efficient, robust, and practical methods of characterizing proteins present in biological samples. Here we describe an integrated strategy for systematic proteome analysis based on differential guanidination of C-terminal lysine residues on tryptic peptides followed by capillary liquid chromatography-electrospray tandem mass spectrometry. The approach, termed mass-coded abundance tagging (MCAT), facilitates the automated, large-scale, and comprehensive de novo determination of peptide sequence and relative quantitation of proteins in biological samples in a single analysis. MCAT offers marked advantages as compared with previously described methods and is simple, economic, and effective when applied to complex proteomic mixtures. MCAT is used to identify proteins, including polymorphic variants, from complex mixtures and measure variation in protein levels from diverse cell types.     

Capture and analysis of quantitative proteomic data

Whilst the array of techniques available for quantitative proteomics continues to grow, the attendant bioinformatic software tools are similarly expanding in number. The data capture and analysis of such quantitative data is obviously crucial to the experiment and the methods used to process it will critically affect the quality of the data obtained. These tools must deal with a variety of issues, including identification of labelled and unlabelled peptide species, location of the corresponding MS scans in the experiment, construction of representative ion chromatograms, location of the true peptide ion chromatogram start and end, elimination of background signal in the mass spectrum and chromatogram and calculation of both peptide and protein ratios/abundances. A variety of tools and approaches are available, in part restricted by the nature of the experiment to be performed and available instrumentation. Currently, although there is no single consensus on precisely how to calculate protein and peptide abundances, many common themes have emerged which identify and reduce many of the key sources of error. These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge.     

The impact of Lake Victoria's lakefly abundance on Palearctic passerines

Wanink, J.H. & Goudswaard, K. 2000. The impact of Lake Victoria's lakefly abundance on Palearctic passerines. Ostrich 71 (1 & 2): 194–197.

In spite of an increase in lakeflies emerging from Lake Victoria, these periodically swarming insects remained an erratic food source for birds. However, even the relatively poor south-eastern shores were exploited by some Palearctic warblers on spring passage. Numbers and weights of Willow and Garden Warbler were correlated with lakefly abundance. The occurrence of lakefly swarms may trigger the birds' departure to the breeding areas, as the superabundance of food allows for rapid premigratory fattening.     

Optimal isolation of mitochondria for proteomic analyses

Considering the key role of mitochondria in cellular (dys)functions, we compared a standard isolation protocol, followed by lysis in urea/detergent buffer, with a commercially available isolation buffer that rapidly yields a mitochondrial protein fraction. The standard protocol yielded significantly better overall resolution and coverage of both the soluble and membrane mitochondrial proteomes; although the kit was faster, it resulted in recovery of only approximately 56% of the detectable proteome. The quality of “omic” analysis depends on sample handling; for large-scale protein studies, well-resolved proteomes are highly dependent on the purity of starting material and the rigor of the extraction protocol.     

Functional materials for microscale genomic and proteomic analyses

The design of functional materials for genomic and proteomic analyses in microscale systems has begun to mature, from materials designed for capillary-based electrophoresis systems to those tailored for microfluidic-based or 'chip-based' platforms. In particular, recent research has focused on evaluating different polymer chemistries for microchannel surface passivation and improved DNA separation matrix performance. Additionally, novel bioconjugate materials designed specifically for electrophoretic separations in microscale channels are facilitating new separation modalities.     

The impact of raptors on the abundance of upland passerines and waders

The issue of predator limitation of vertebrate prey populations is contentious, particularly when it involves species of economic or conservation value. In this paper, we examine the case of raptor predation on upland passerines and waders in Scotland. We analysed the abundance of five wader and passerine species on an upland sporting estate in southern Scotland during an eight-year period when hen harrier, peregrine and merlin numbers increased due to strict law enforcement. The abundance of meadow pipit and skylark declined significantly during this time. Golden plover also showed a declining trend, whereas curlew increased significantly and there was a near significant increase in lapwings. Contrasting the local population trends of these species with trends on nearby areas revealed higher rates of decline for meadow pipit and skylark at the site where raptors increased, but no differences in trends for any of the three wader species. There was a negative relationship between the number of breeding harriers and meadow pipit abundance the same year and between total annual raptor numbers and meadow pipit abundance. Predation rates of meadow pipit and skylark determined from observations at harrier nests suggested that predation in June was sufficient to remove up to 40% of the June meadow pipit population and up to 34% of the June skylark population. This 'quasi-natural' experiment suggests that harrier predation limited the abundance of their main prey, meadow pipit, and possibly the abundance of skylark. Thus, high densities of harriers may in theory reduce the abundance of the prey species which determine their breeding densities, potentially leading to lower harrier breeding densities in subsequent years. We found no evidence to suggest that raptor predation limited the populations of any of the three wader species. We infer that concerns over the impact of natural densities of hen harriers on vulnerable upland waders are unjustified.     

The impact of small chironomid grazers on epiphytic algal abundance and dispersion

• 1 A combination of field and laboratory experiments was used to assess the impact of chironomid grazers on taxonomic composition, abundance and dispersion of epiphytic algal assemblages.
• 2 In the laboratory, Psectrodadius sp. reduced the biovolume of algal species preferred as food and increased the degree of clumping of non-preferred species. Thienemanniella cf. fusca had both positive and negative effects (depending on the algal species) on the biovolumes of algal species preferred as food and increased the degree of clumping of non-preferred species.
• 3 In field exclosures, no effect of removal of chironomid larvae from the grazer assemblage could be detected in autumn or winter experiments. A third, longer removal experiment, conducted in summer, resulted in increased biovolumes of edible Cosmarium spp. and Aphanocapsa spp., preferred foods of chironomid larvae. Biovolumes of Lyngbya sp., Eulbochaete spp. and Oedogortium spp., filamentous taxa used extensively in larval case construction, also increased. Chironomid larvae had no effect on total algal biovolume or biovolume of large unicellular algae.
• 4 Chironomid larvae can influence epiphytic algal assemblages through selective grazing by reducing the biovolumes of preferred foods and through case-building activity by reducing the biovolumes of construction materials.

     

The dynamic range of human lightness perception

Natural viewing challenges the visual system with images that have a dynamic range of light intensity (luminance) that can approach 1,000,000:1 and that often exceeds 10,000:1 [1, 2]. The range of perceived surface reflectance (lightness), however, can be well approximated by the Munsell matte neutral scale (N 2.0/ to N 9.5/), consisting of surfaces whose reflectance varies by about 30:1. Thus, the visual system must map a large range of surface luminance onto a much smaller range of surface lightness. We measured this mapping in images with a dynamic range close to that of natural images. We studied simple images that lacked segmentation cues that would indicate multiple regions of illumination. We found a remarkable degree of compression: at a single image location, a stimulus luminance range of 5,905:1 can be mapped onto an extended lightness scale that has a reflectance range of 100:1. We characterized how the luminance-to-lightness mapping changes with stimulus context. Our data rule out theories that predict perceived lightness from luminance ratios or Weber contrast. A mechanistic model connects our data to theories of adaptation and provides insight about how the underlying visual response varies with context.     

Saturation fluorescence labeling of proteins for proteomic analyses

We present here an optimized and cost-effective approach to saturation fluorescence labeling of protein thiols for proteomic analysis. We investigated a number of conditions and reagent concentrations, including the disulfide reducing agent tris(2-carboxyethyl)phosphine (TCEP), pH, incubation time, linearity of labeling, and saturating dye/protein thiol ratio with protein standards to gauge specific and nonspecific labeling. Efficacy of labeling under these conditions was quantified using specific fluorescence estimation, defined as the ratio of fluorescence pixel intensities and Coomassie-stained pixel intensities of bands after digital imaging. Factors leading to specific versus nonspecific labeling in the presence of thiourea are also discussed. We found that reproducible saturation of available Cys residues of the proteins used as labeling standards (human carbonic anhydrase I, enolase, and α-lactalbumin) is achieved at 50- to 100-fold excess of the uncharged maleimide-functionalized BODIPY dyes over Cys. We confirmed our previous findings, and those of others, that the maleimide dyes are not affected by the presence of 2 M thiourea. Moreover, we established that 2 mM TCEP used as reductant is optimal. We also established that labeling is optimal at pH 7.5 and complete after 30 min. Low nonspecific labeling was gauged by the inclusion of non-Cys-containing proteins (horse myoglobin and bovine carbonic anhydrase) to the labeling mixture. We also showed that the dye exhibits little to no effect on the two-dimensional mobilities of labeled proteins derived from cells.     

Self-similarity and the relationship between abundance and range size

Patterns in the relationships among the range, abundance, and distribution of species within a biome are of fundamental interest in ecology. A self-similarity condition, imposed at the community level and previously demonstrated to lead to the power-law form of the species-area relationship, is extended to the species level and shown to predict testable power-law relationships between range size and both species abundance and area of census cell across scales of spatial resolution. The predicted slopes of plots of log(range size) versus log(abundance) are shown to be in good agreement with data from British breeding bird and mammal censuses and with data on the distribution of fern species in old-growth forest. The predicted slopes of plots of log(range size) versus log (area of census cell) are consistent with the limited available data for British plant species. Self-similarity provides a testable theoretical framework for a unified understanding of patterns among the range, abundance, and distribution of species.     

The impact of fossils and taxon sampling on ancient molecular dating analyses

The number and complexity of molecular dating studies has increased over the past decade. Along with a broadening acceptance of their utility has come significant controversy over the methods and models that are appropriate, as well as the accuracy of the estimates yielded by molecular clock analyses. Radically different age estimates have been published for the same divergences from analyses of different datasets with different fossil constraints obtained with different methods, and the underlying explanation for these differences is often unclear. Here we utilize two previously published datasets to examine the effect of fossil calibrations and taxon sampling on the age estimates for two deep eukaryote divergences in an attempt to discern the relative impact of these factors. Penalized likelihood, non-parametric rate smoothing, and Bayesian methods were utilized to generate age estimates for the origin of the Metazoa from a 7-gene dataset and for the divergence of Eukaryotes from a 129-gene dataset. From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates. Concerns and recommendations for addressing these two factors when initiating a dating analysis are discussed.     

A review of quantitative methods for proteomic studies

An overview is provided of six strategies for relative or absolute quantitation of protein abundances that are widely used in proteomic studies. Strengths and limitations are discussed. Four of these involve stable isotope labeling and isotope ratio measurements by mass spectrometry. In another, mass spectra are used to deconvolute overlapping peptide HPLC peaks to provide relative quantitation based on peak areas. The sixth provides relative abundances of proteins based on 2-D gel arrays. It should be noted that these strategies measure peptide and protein abundances, and cannot directly assess changes in regulation or expression.     

Comparative proteomic and radiobiological analyses in human lung adenocarcinoma cells

In clinic, many non-small cell lung cancer (NSCLC) patients receive radiation therapy after chemotherapy failure. However, whether the multidrug resistance (MDR) can elevate the radioresistance (RDR) remains unclear. To evaluate the MDR's effect on the RDR, screen MDR- and RDR-related proteins in human lung adenocarcinoma (HLA) cells and tissues A549, and A549/DDP cells after irradiation were analyzed by colony-forming assay and flow cytometry. Two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) were utilized to identify differentially expressed proteins (DEPs) between them. The value of D0, Dq, and SF2 increased, the mean percentage in G2 phase and apoptosis rate significantly decreased in A549/DDP cells compared with A549 cells. 40 DEP points were found, and among them 27 were identified through proteomics. Four up-regulated proteins (HSPB1, Vimentin, Cofilin-1, and Annexin A4) in MDR cells compared with non-MDR cells, were confirmed by Western blot. Immuno-histochemistry showed that they were also over-expressed in MDR tissues compared with non-MDR counterparts of HLA. These results proved that the MDR in HLA cells and tissues increased the RDR. HSPB1, Vimentin, Cofilin-1, and Annexin A4 are potential biomarkers for predicting HLA response to MDR and RDR, and novel treatment targets of HLA.