The Effect of Phosphorylation on the Electron Capture Dissociation of Peptide Ions

The effect of site and frequency of phosphorylation on the electron capture dissociation of peptide ions has been investigated. The ECD of a suite of synthetic peptides (APLSFRGSLPKSYVK; one unmodified, three singly-phosphorylated, three-doubly phosphorylated, and one triplyphosphorylated); two tryptic phosphopeptides (YKVPQLEIVPNpSAEER, α-casein and FQpSEEQQQTEDELQDK, β-casein) and their unmodified counterparts, were determined over a range of ECD cathode potentials. The results show that, for doubly-charged precursor ions, the presence of phosphorylation has a deleterious effect on ECD sequence coverage. The fragmentation patterns observed suggest that for peptides with multiple basic residues, the phospho-groups exist in their deprotonated form and form salt-bridges with protonated amino acid side chains. The fragmentation observed for the acidic tryptic peptides suggested the presence of noncovalent interactions, which were perturbed on phosphorylation. Increasing the ECD electron energy significantly improves sequence coverage. Alternatively, improved sequence coverage can be achieved by performing ECD on triply-charged precursor ions. The findings are important for the understanding of gas-phase fragmentation of phosphopeptides

Numeracy skills and the numerate environment: affordances and demands

In the 2012 PIAAC Survey of Adult Skills of 23 industrialised countries, the UK (England & NI) scored below average on adult numeracy. Several recommendations focus on the need for (some) individuals in the population to undergo training. Yet, even in “high-performing countries” like the Netherlands, many adults (1.5M) score at or below PIAAC Level 1 (sometimes designated as “functionally innumerate”). The question arises as to how all of these people manage in important domains of their lives. In this article we aim to consider the context of the exercise of numeracy by adults, drawing on earlier research in mathematics education. We examine a recent conception of an adult’s ‘literate environment’ (EU HLG on Literacy, 2012), and extend this to reflect on the idea of an adult’s ‘numerate environment’. We consider the range of practices that particular adults may engage in, and the demands that these may make on the adult, the affordances the practices may offer; the latter include the opportunities, and the supports and / or barriers produced within these practices, and in cultures more generally, that may foster or impede an adult’s ongoing numerate development. We give examples of each of these aspects of adults’ numerate practices, and consider implications for the teaching, learning and development of numeracy

Ambient Intelligence through Image Retrieval

An ambient intelligent environment needs dynamic enrollment of strangers without too much human intervention. For this purpose, we propose an entity recognition process based on images captured with low-cost but widespread webcams and easy-to-deploy image processing techniques. We find that the use of levels of confidence in recognition due to different techniques and context-based image retrieval improves the process

Proteomic Analysis of a Noninvasive Human Model of Acute Inflammation and Its Resolution: The Twenty-one Day Gingivitis Model

The 21-day experimental gingivitis model, an established noninvasive model of inflammation in response to increasing bacterial accumulation in humans, is designed to enable the study of both the induction and resolution of inflammation. Here, we have analyzed gingival crevicular fluid, an oral fluid comprising a serum transudate and tissue exudates, by LC−MS/MS using Fourier transform ion cyclotron resonance mass spectrometry and iTRAQ isobaric mass tags, to establish meta-proteomic profiles of inflammation-induced changes in proteins in healthy young volunteers. Across the course of experimentally induced gingivitis, we identified 16 bacterial and 186 human proteins. Although abundances of the bacterial proteins identified did not vary temporally, Fusobacterium outer membrane proteins were detected. Fusobacterium species have previously been associated with periodontal health or disease. The human proteins identified spanned a wide range of compartments (both extracellular and intracellular) and functions, including serum proteins, proteins displaying antibacterial properties, and proteins with functions associated with cellular transcription, DNA binding, the cytoskeleton, cell adhesion, and cilia. PolySNAP3 clustering software was used in a multilayered analytical approach. Clusters of proteins that associated with changes to the clinical parameters included neuronal and synapse associated proteins

Electron capture dissociation mass spectrometry of phosphopeptides: Arginine and phosphoserine

AbstractWe have previously shown that the presence of phosphorylation can inhibit detection of electron capture dissociation (ECD) fragments of doubly charged peptide ions. The presence of non-covalent interactions, in the form of salt-bridges or ionic hydrogen bonds, prevents the separation of fragments following backbone cleavage. Here, we show the electron capture dissociation mass spectrometry of a suite of model peptides designed to investigate the relationship between phosphoserine and arginine position, namely AApSAnRAmKA (n=0–6, m=6–0), the presence of lysine residues (AApSAAKAARAKA) and AAApSARAAAAKAAAK, and the presence of proline A(A/P)ApSARAAA(A/P)KAAAK. The latter are analogous to the peptides studied previously. The results show that the presence of phosphoserine and basic amino acid residues alone does not inhibit ECD fragmentation, even when the number of basic amino acid residues is greater than the precursor charge state. Neither did the presence of proline in the peptide sequence suppress ECD backbone cleavage. Nevertheless, the presence and relative position of the phosphorylated residue do alter the observed backbone fragmentation abundance. In addition, the presence of phosphorylation appears to inhibit cleavage within the arginine side-chain regardless of the relative position of the arginine residue. The results suggest that ECD fragmentation behaviour is dependent on the three-dimensional structure of a peptide rather than its sequence

Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry.

We used on-line electron capture dissociation (ECD) for the large scale identification and localization of sites of phosphorylation. Each FT-ICR ECD event was paired with a linear ion trap collision-induced dissociation (CID) event, allowing a direct comparison of the relative merits of ECD and CID for phosphopeptide identification and site localization. Linear ion trap CID was shown to be most efficient for phosphopeptide identification, whereas FT-ICR ECD was superior for localization of sites of phosphorylation. The combination of confident CID and ECD identification and confident CID and ECD localization is particularly valuable in cases where a phosphopeptide is identified just once within a phosphoproteomics experiment

Polygenic Risk Scoring is an Effective Approach to Predict Those Individuals Most Likely to Decline Cognitively Due to Alzheimer’s Disease

BACKGROUND: There is a clear need for simple and effective tests to identify individuals who are most likely to develop Alzheimer’s Disease (AD) both for the purposes of clinical trial recruitment but also for improved management of patients who may be experiencing early pre-clinical symptoms or who have clinical concerns. OBJECTIVES: To predict individuals at greatest risk of progression of cognitive impairment due to Alzheimer’s Disease in individuals from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) using a polygenic risk scoring algorithm. To compare the performance of a PRS algorithm in predicting cognitive decline against that of using the pTau/Aß1-42 ratio CSF biomarker profile. DESIGN: A longitudinal analysis of data from the Alzheimer’s Disease Neuroimaging Initiative study conducted across over 50 sites in the US and Canada. SETTING: Multi-center genetics study. PARTICPANTS: 515 subjects who upon entry to the study were diagnosed as cognitively normal or with mild cognitive impairment. MEASUREMENTS: Use of genotyping and/or whole genome sequencing data to calculate polygenic risk scores and assess ability to predict subsequent cognitive decline as measured by CDR-SB and ADAS-Cog13 over 4 years RESULTS: The overall performance for predicting those individuals who would decline by at least 15 ADAS-Cog13 points from a baseline mild cognitive impairment in 4 years was 72.8% (CI:67.9-77.7) AUC increasing to 79.1% (CI: 75.6-82.6) when also including cognitively normal participants. Assessing mild cognitive impaired subjects only and using a threshold of greater than 0.6, the high genetic risk participant group declined, on average, by 1.4 points (CDR-SB) more than the low risk group over 4 years. The performance of the PRS algorithm tested was similar to that of the pTau/Aß1-42 ratio CSF biomarker profile in predicting cognitive decline. CONCLUSION: Calculating polygenic risk scores offers a simple and effective way, using DNA extracted from a simple mouth swab, to select mild cognitively impaired patients who are most likely to decline cognitively over the next four years

Pathways to identity: using visualization to aid law enforcement in identification tasks

The nature of identity has changed dramatically in recent years and has grown in complexity. Identities are defined in multiple domains: biological and psychological elements strongly contribute, but biographical and cyber elements also are necessary to complete the picture. Law enforcement is beginning to adjust to these changes, recognizing identity’s importance in criminal justice. The SuperIdentity project seeks to aid law enforcement officials in their identification tasks through research of techniques for discovering identity traits, generation of statistical models of identity and analysis of identity traits through visualization. We present use cases compiled through user interviews in multiple fields, including law enforcement, and describe the modeling and visualization tools design to aid in those use cases

‘I think I'm more free with them'—Conflict, Negotiation and Change in Intergenerational Relations in African Families Living in Britain

While the family is increasingly being recognised as pivotal to migration, there remain too few studies examining how migration impacts on intergenerational relationships. Although traditional intergenerational gaps are intensified by migration, arguably there has been an over-emphasis on the divisions between ‘traditional’ parents and ‘modern’ children at the expense of examining the ways in which both generations adapt. As Foner and Dreby [2011. “Relations Between the Generations in Immigrant Families.” Annual Review of Sociology 37: 545–564] stress, the reality of post-migration intergenerational relations is inevitably more complex, requiring the examination of both conflict and cooperation. This article contributes to this growing literature by discussing British data from comparative projects on intergenerational relations in African families (in Britain, France and South Africa). It argues that particular understandings can be gained from examining the adaptation of parents and parenting strategies post-migration and how the reconfiguration of family relations can contribute to settlement. By focusing on how both parent and child generations engage in conflict and negotiation to redefine their relationships and expectations, it offers insight into how families navigate and integrate the values of two cultures. In doing so, it argues that the reconfiguration of gender roles as a result of migration offers families the space to renegotiate their relationships and make choices about what they transmit to the next generation

Cost-effectiveness of Dementia Care Mapping in care home settings – Evaluation of a randomised controlled trial

Background: Behaviours such as agitation impact on the quality of life of care home residents with dementia and increase health care use. Interventions to prevent these behaviours have little evidence supporting their effectiveness or cost-effectiveness. We conducted an economic evaluation alongside a trial assessing Dementia Care Mapping™ (DCM) versus usual care for reducing agitation and highlight methodological challenges of conducting evaluations in this population and setting. Methods: RCT data over 16 months from English care home residents with dementia (intervention n = 418; control n = 308) were analysed. We conducted a cost-utility analysis from the healthcare provider perspective. We gathered resource use and utility (EQ-5D-5L and DEMQoL-Proxy-U) from people living with dementia and proxy informants (staff and relatives). Data were analysed using seemingly unrelated regression, accounting for care home clustering and bootstrapping used to capture sampling uncertainty. Results: Costs were higher in the intervention arm than control arm (incremental = £1,479) due in part to high cost outliers. There were small QALY gains (incremental = 0.024) in favour of DCM. The base case ICER (£64,380 per QALY) suggests DCM is not cost-effective versus usual care. With the exception of analyses excluding high cost outliers, which suggested a potential for DCM to be cost-effective, sensitivity analyses corroborated the base case findings. Bootstrapped estimates suggested DCM had a low probability (p<0.20 where λ=£20,000) of being cost-effective versus control. Conclusion: DCM does not appear to be a cost-effective intervention versus usual care in this group and setting. The evaluation highlighted several methodological challenges relating to validity of utility assessments, loss to follow-up and compliance. Further research is needed on handling high cost individuals and capturing utility in this group