Arabidopsis thaliana proteomics: from proteome to genome

Proteomics has become an important approach for investigating cellular processes and network functions. Significant improvements have been made during the last few years in technologies for high-throughput proteomics, both at the level of data analysis software and mass spectrometry hardware. As proteomics technologies advance and become more widely accessible, efforts of cataloguing and quantifying full proteomes are underway to complement other genomics approaches, such as RNA and metabolite profiling. Of particular interest is the application of proteome data to improve genome annotation and to include information on post-translational protein modifications with the annotation of the corresponding gene. This type of analysis requires a paradigm shift because amino acid sequences must be assigned to peptides without relying on existing protein databases. In this review, advances and current limitations of full proteome analysis are briefly highlighted using the model plant Arabidopsis thaliana as an example. Strategies to identify peptides are also discussed on the basis of MS/MS data in a protein database-independent approac

Social workers' workload survey: messages from the frontline: findings from the 2009 survey and interviews with senior managers

"The research findings which have been reported emerged from work commissioned to inform the Social Work Task Force but they also make a contribution to issues discussed in this section and to other social work debates. It is important to recognise that this was the most comprehensive diary exercise conducted with social workers in this country. The findings generated from the analysis of the diaries have provided the first systematic examination of how social workers use their time. Yet for the reasons examined in the report there are provisos regarding the representativeness of data which leads to the recommendation that the exercise should be repeated with an instrument which is redesigned to reflect lessons from this survey and with a larger negotiated sample, along the lines of the Teachers’ Workload Survey." - Page 138

Time, institutional support and quality of decision making in child protection:A cross-country analysis

This paper examines perceptions of time and institutional support for decision making and staff confidence in child welfare staffs ultimate decisions – examining differences and similarities between and within the service-oriented Nordic countries (Norway and Finland) and the risk-oriented Anglo-American countries (England and California). The study identifies a high degree of work pressure across all the countries, lines of predominantly vertical institutional support and relatively high confidence in decisions. Finland stands out with higher perceived work pressure and with a horizontal support line, whereas England stands out with workers having a lower degree of confidence in their own and others’ decisions

Semi-supervised LC/MS alignment for differential proteomics

Motivation: Mass spectrometry (MS) combined with high-performance liquid chromatography (LC) has received considerable attention for high-throughput analysis of proteomes. Isotopic labeling techniques such as ICAT [5,6] have been successfully applied to derive differential quantitative information for two protein samples, however at the price of significantly increased complexity of the experimental setup. To overcome these limitations, we consider a label-free setting where correspondences between elements of two samples have to be established prior to the comparative analysis. The alignment between samples is achieved by nonlinear robust ridge regression. The correspondence estimates are guided in a semi-supervised fashion by prior information which is derived from sequenced tandem mass spectra. Results: The semi-supervised method for finding correspondences was successfully applied to aligning highly complex protein samples, even if they exhibit large variations due to different biological conditions. A large-scale experiment clearly demonstrates that the proposed method bridges the gap between statistical data analysis and label-free quantitative differential proteomics. Availability: The software will be available on the website Contact: [email protected]