Pixel-based analysis of multiple images for the identification of changes: a novel approach applied to unravel proteome patterns [corrected] of 2-D electrophoresis gel images

A novel approach for revealing patterns of proteome variation among series of 2-DE gel images is presented. The approach utilises image alignment to ensure that each pixel represents the same information across all gels. Gel images are normalised, and background corrected, followed by unfolding of the images to 1-D pixel vectors and analysing pixel vectors by multivariate data modelling. Information resulting from the data analysis is refolded back to the image domain for visualisation and interpretation. The method is rapid and suitable for automatic routines applied after the gel alignment. The approach is compared with spot volume analysis to illustrate how this approach can solve persistent problems like mismatch of protein spots, erroneous missing values and failure to detect variation in overlapping proteins. The method may also detect variation in the border area of saturated proteins. The approach is given the name pixel-based analysis of multiple images for the identification of changes (PMC). The method can be used for multiple images in general. Effects of pretreatment of the images are discussed.     

Vitamin E and selenium plasma concentrations in weanling pigs under field conditions in Norwegian pig herds

Background  

The status of α-tocopherol (vit E) and selenium (Se) has been shown to influence disease resistance in pigs, and may be important for the health of weanling pigs.     

Influence of nutrients on enhancing laccase production by Botryosphaeria rhodina MAMB-05.

The physiological requirements needed to enhance the production of laccases by the ascomycete Botryosphaeria rhodina MAMB-05 in submerged cultivation were examined under non-induced and induced (veratryl alcohol, VA) conditions. Under non-induced conditions (-VA), the initial pH, C:N ratio, and inorganic N source did not influence laccase production, in contrast to Tween 80, soybean oil, and copper, which significantly increased laccase production, and proline and urea, which suppressed laccase formation. In addition, Tween 60 could serve as the sole carbon source for the production of these enzymes. Under VA-induced conditions of fungal growth, factors such as inoculum type, time-point of addition of inducer, initial pH, C:N ratio, and type of N source, influenced the production of laccases; however, unlike the non-induced conditions, proline and urea did not act as suppressors. Each of these physiological conditions exerted different effects on biomass production. The nutritional conditions examined for B. rhodina MAMB-05 are discussed in relation to their influence on fungal growth and laccase production.     

Early trajectories of forest understory development on reclamation sites: influence of forest floor placement and a cover crop

We tested whether direct placement of forest floor material (FFM: litter, fibric, humus layers and surface mineral horizons) and sowing of a cover crop (Melilotus officinalis) could facilitate the establishment of native forest understory species at a reclaimed coal mine in Alberta, Canada. FFM was salvaged at two depths (15 and 40 cm) from a recently harvested native aspen forest and immediately placed at the same depths on the reclamation site. Total richness (approximately 61 species in 96 subplots) was similar in each of 3 years post‐placement; total richness for all 3 years combined was 87 including 34 typical boreal forest understory species plus 30 other natives. The deeper treatment reduced cover of all species, native and non‐native species in year 1. In year 3, the deeper treatment still had lower cover of non‐native species but had higher cover of forest understory species in years 2 and 3. The deeper treatment also resulted in lower species richness per plot, but only in year 1. In year 2 (when the biennial clover was at its tall stage), the cover crop treatment was associated with lower cover of non‐native species but did not affect the cover of native forest understory species. Direct placement of FFM can help facilitate establishment of a diverse native boreal forest understory in a reclaimed landscape. Although richness and cover may be initially higher with shallower salvage and placement, deeper salvage may ultimately be better for encouraging establishment of native forest understory species.     

Mucolipidosis Type IV Protein TRPML1‐Dependent Lysosome Formation

Lysosomes are dynamic organelles that undergo cycles of fusion and fission with themselves and with other organelles. Following fusion with late endosomes to form hybrid organelles, lysosomes are reformed as discrete organelles. This lysosome reformation or formation is a poorly understood process that has not been systematically analyzed and that lacks known regulators. In this study, we quantitatively define the multiple steps of lysosome formation and identify the first regulator of this process.      

Pitfalls in histone propionylation during bottom‐up mass spectrometry analysis

Despite their important role in regulating gene expression, posttranslational histone modifications remain technically challenging to analyze. For identification by bottom‐up MS, propionylation is required prior to and following trypsin digestion. Hereby, more hydrophobic peptides are generated enabling RP HPLC separation. When histone dynamics are studied in a quantitative manner, specificity, and efficiency of this chemical derivatization are crucial. Therefore we examined eight different protocols, including two different propionylation reagents. This revealed amidation (up to 70%) and methylation (up to 9%) of carboxyl groups as a side reaction. Moreover, incomplete (up to 85%) as well as a specific propionylation (up to 63%) can occur, depending on the protocol. These results highlight the possible pitfalls and implications for data analysis when doing bottom‐up MS on histones.