Identification of differentially regulated proteins in a patient with Leber's Congenital Amaurosis – a proteomic study

Background

Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed.

Results

We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ ^TM reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ ^TM reported intensities from Mascot output, into a valid PRIDE XML entry.

Conclusion

We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ ^TM data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from http://www.mcisb.org/software/PrideWizard.     

Health-Risk Behaviour in Deprived Neighbourhoods Compared with Non-Deprived Neighbourhoods: A Systematic Literature Review of Quantitative Observational Studies

Background

There has been increasing interest in neighbourhoods’ influence on individuals’ health-risk behaviours, such as smoking, alcohol consumption, physical activity and diet. The aim of this review was to systematically review recent studies on health-risk behaviour among adults who live in deprived neighbourhoods compared with those who live in non-deprived neighbourhoods and to summarise what kind of operationalisations of neighbourhood deprivation that were used in the studies.

Methods

PRISMA guidelines for systematic reviews were followed. Systematic searches were performed in PubMed, Embase, Web of Science and Sociological Abstracts using relevant search terms, Boolean operators, and truncation, and reference lists were scanned. Quantitative observational studies that examined health-risk behaviour in deprived neighbourhoods compared with non-deprived neighbourhoods were eligible for inclusion.

Results

The inclusion criteria were met by 22 studies. The available literature showed a positive association between smoking and physical inactivity and living in deprived neighbourhoods compared with non-deprived neighbourhoods. In regard to low fruit and vegetable consumption and alcohol consumption, the results were ambiguous, and no clear differences were found. Numerous different operationalisations of neighbourhood deprivation were used in the studies.

Conclusion

Substantial evidence indicates that future health interventions in deprived neighbourhoods should focus on smoking and physical inactivity. We suggest that alcohol interventions should be population based rather than based on the specific needs of deprived neighbourhoods. More research is needed on fruit and vegetable consumption. In future studies, the lack of a uniform operationalisation of neighbourhood deprivation must be addressed.     

Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridization between Betula pubescens and B. nana

Birches (Betula spp.) hybridize readily, confounding genetic signatures of refugial isolation and postglacial migration. We aimed to distinguish hybridization from range‐shift processes in the two widespread and cold‐adapted species B. nana and B. pubescens, previously shown to share a similarly east–west‐structured variation in plastid DNA (pDNA). We sampled the two species throughout their ranges and included reference samples of five other Betula species and putative hybrids. We analysed 901 individual plants using mainly nuclear high‐resolution markers (amplified fragment length polymorphisms; AFLPs); a subset of 64 plants was also sequenced for two pDNA regions. Whereas the pDNA variation as expected was largely shared between B. nana and B. pubescens, the two species were distinctly differentiated at AFLP loci. In B. nana, both the AFLP and pDNA results corroborated the former pDNA‐based hypothesis that it expanded from at least two major refugia in Eurasia, one south of and one east of the North European ice sheets. In contrast, B. pubescens showed a striking lack of geographic structuring of its AFLP variation. We identified a weak but significant increase in nuclear (AFLP) gene flow from B. nana into B. pubescens with increasing latitude, suggesting hybridization has been most frequent at the postglacial expansion front of B. pubescens and that hybrids mainly backcrossed to B. pubescens. Incongruence between pDNA and AFLP variation in B. pubescens can be explained by efficient expansion from a single large refugium combined with leading‐edge hybridization and plastid capture from B. nana during colonization of new territory already occupied by this more cold‐tolerant species.     

Effects of temperature and date of snowmelt on growth, reproduction, and flowering phenology in the arctic/alpine herb, Ranunculus glacialis

Changes in growing season temperature and duration may have profound effects on the population dynamics of arctic and alpine plant species in snow-bed and fell-field habitats. We examined how a typical herbaceous pioneer species, Ranunculus glacialis, responded to experimental climate change in open-top chambers for three seasons at an alpine site in southern Norway. Warming had no significant effect on any reproductive, growth or phenological variables, except for seed weight, which increased significantly during the first 2 ears. Despite large differences in average date of snowmelt among years, average reproductive output and ramet size differed little among years. Within-year variation in date of snowmelt had no impact on seed number or weight in either control or warmed plots. Leaf width and ramet leaf number decreased significantly with later snowmelt within a year. Experimental warming reduced the negative effect on ramet size of late snowmelt within a year to some extent. In general, R. glacialis reacts contrary to most other arctic/alpine species to experimental warming. Species with such low responsiveness to environmental conditions may be particularly vulnerable to climatic change, especially if their habitat is invaded by other species with higher phenotypic plasticity and a better competitive ability.     

Levels of cadmium and mercury in the hair of Atlantic walruses (Odobenus rosmarus rosmarus) from Svalbard,Norway

Hair samples of 15 adult male Atlantic walruses (Odobenus rosmarus rosmarus) collected from anaesthetized individuals at Svalbard, Norway, were analysed for cadmium and total mercury. The mean level of cadmium was 0.860 ± 0.321 μg/g dry weight (median = 0.811, range = 0.349–1.51 μg/g dry weight) and the mean level of mercury was 0.235 ± 0.100 μg/g dry weight (median = 0.251, range = 0.121–0.424 μg/g dry weight). Levels of cadmium and mercury in hair of walruses from other areas are not known. Both cadmium and mercury levels in hair of walruses from Svalbard are relatively low compared to the levels found in the hair of other marine mammal species. It has been documented from a number of marine species, including marine mammals such as ringed seals and polar bears, that both cadmium and mercury levels at Svalbard are lower than in other areas. It is uncertain as to what degree levels in hair reflect levels in internal organs in walruses. In rare and highly endangered species or populations tissue samples can be difficult to collect. In walruses, it is possible to collect hair from anaesthetized individuals or at the haul-out sites during moult, to monitor heavy metal levels of the population. Accepted: 6 December 1998     

Alginate stability during high salt preservation of Ascophyllum nodosum

Formaldehyde is usually added to brown algae to avoid microbial growth during storage and to fix polyphenols in the algae before alginate extraction. Since formaldehyde is toxic, allergenic and possibly carcinogenic, dry salting of Ascophyllum nodosum was tested as an alternative. The seaweeds, harvested at locations with a salinity of about 30‰ from late autumn to early spring, were stored at 22±2 °C under compost-like conditions. Untreated samples of seaweed lost their quality as a raw material for alginate production within 14 days. Salted (20–22%) as well as formaldehyde treated seaweed was preserved for at least 46 days. Due to the reduced water activity and oxygen saturation in the dry salted seaweed, microbial growth and brown colouring reactions were suppressed. Economic factors must also be taken into account before large-scale applications are considered. This revised version was published online in June 2006 with corrections to the Cover Date.     

Direct determination of alginate content in brown algae by near infra-red (NIR) spectroscopy

The methods used to quantify total alginate in brown algal tissue are time-consuming and may also be misleading, so faster and simpler methods for measuring alginate content would be beneficial in a variety of applications. This study reports on the use of near infra-red (NIR) analysis to monitor the alginate content of Laminaria hyperborea stipe during biodegradation. NIR reflectance spectra were recorded for 78 different freeze-dried samples of its stipe. The samples were collected during several biological degradation experiments and the total alginate content varied from 2.2 to 40.8% Na-alginate (w/w), determined by established methods based on ion exchange. Data analysis was performed using multivariate calibration methods in order to relate the spectral data to the alginate content. PLS2 analysis revealed some dependence on material type, probably reflecting differences in polyphenol content. In the end, a PLS1 model with 9 components was selected. The calculated model was validated both with internal data and with an external test set. Internal full cross validation explained 96.6% of the variance in alginate content. The external validation showed that the PLS1 model was able to predict the alginate concentration with a root mean square prediction accuracy of 2.1%. This revised version was published online in June 2006 with corrections to the Cover Date.     

Factors Prior to Dry Period Associated with High and Low Levels of Cow Milk Somatic Cell Counts in Next Lactation

Data from a randomized controlled field study of selective dry cow therapy were used in which 686 cows had been allocated to 2 control groups (sampling only or placebo) or 2 therapy groups. Possible factors from previous lactation were assessed in determining their association with the probability of ‘failure’, designated as a cow milk somatic cell count (CMSCC) of greater than 399000 per ml in geometric mean of several measurements during subsequent lactation. Success cows were those with a CMSCC of less than 200000 per ml. For our analyses, this targeted 187 success cows and 186 failure cows. Therapy was given as a total dose of 400000 IU penicillin and 100 mg neomycin per infected quarter as dry cow preparation once, or as a lactation formula with a total dose of 1.2 million IU penicillin and 1200 mg dihydrostreptomycin per infected quarter during a 1-week period. Significant factors in the predictive model for success included therapy, low level of CMSCC (geometric mean of the 3 last tests) in previous lactation, low level of CMSCC (weighted by daily milk yield mean) in the herd, young cows, and not having had a case of treatment for chronic clinical mastitis. Additional information on the probability of failure in treated and untreated cows can be predicted by number of quarters infected with Staphylococcus aureus approximately 1.5 months before drying off. The models derived are considered for use as tools in selective treatment and culling decisions.