Dataset Information

Digging deeper in Shanghai: towards a 'mechanism-rich' epidemiology.

ABSTRACT: BACKGROUND:There are very few close-up sociological or anthropological data informing epidemiological and psychiatric research design and/or contributing to our understanding of the relationship between mental health and specific forms of urban life. Furthermore, research on the relationships between urbanicity and mental disorder has paid little attention to the global diversity of urban experience, such as in cities in China, India and Brazil. METHODS:Two innovative methods can be employed to unveil the diversified urban experience of migrants in China, i.e. an ethnography-informed sociological deep surveying instrument and an ecological momentary assessment with a smartphone app. This article introduces the design and pilot survey of these new instruments towards a 'mechanism-rich' epidemiology. RESULTS:The ethnography-informed survey instrument enabled us to include some of the issues from the ethnography and successfully 'dig deeper' into respondents' social experience. The pilot of the smartphone app serves as 'proof of principle' that we can recruit respondents in Shanghai, and that we can receive and use the data. CONCLUSIONS:Both of these pilots have demonstrated good feasibility for studying mobility, urban life and mental health. Our next steps will be to extend the Shanghai sample, to use the app in Sao Paulo and Toronto and then hopefully in India and Africa.

SUBMITTER: Li J

PROVIDER: S-EPMC6822688 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Digging deeper in Shanghai: towards a 'mechanism-rich' epidemiology.

Li Jie J Manning Nick N Mechelli Andrea A

International health 20191001 S1

<h4>Background</h4>There are very few close-up sociological or anthropological data informing epidemiological and psychiatric research design and/or contributing to our understanding of the relationship between mental health and specific forms of urban life. Furthermore, research on the relationships between urbanicity and mental disorder has paid little attention to the global diversity of urban experience, such as in cities in China, India and Brazil.<h4>Methods</h4>Two innovative methods can ...[more]

PMID: 31670823

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Project description:Peptides presented by MHC molecules on the cell surface, or the immunopeptidome, play an important role in the adaptive arm of the immune response. Antigen processing for MHC class I molecules is a ubiquitous pathway present in all nucleated cells which generates and presents peptides of both self and non-self-origin. Peptides with post-translational modifications represent one category of peptides presented by MHC class I molecules. However, owing to the complexity of self-peptides presented by cells, the diversity of peptides with post-translational modifications is not well-studied. In this study, we carried out MHC Class I immunopeptidomics analysis of Loucy T-cell leukemia and A375 malignant melanoma cell line to characterize the diversity of post-translational modifications of MHC class I-bound peptides. Using high resolution mass spectrometry, we identified 25,761 MHC-bound peptides across both cell lines using Bolt and Sequest search engines. The enrichment method was highly specific as ~ 90% of the peptides were of typical length (8-12 amino acids long) and the motifs were expected based on previously reported motifs for MHC I alleles. Among the MHC-bound peptides, we identified phosphorylation as a major post-translational modification followed by deamidation. We observed site-specific localization of these post-translational modifications, at position P4 for phosphorylated peptides and position P3 for deamidated peptides. We identified a smaller number of peptides with acetylated and methylated lysine, possibly due to very low stoichiometric levels of these PTMs compared to phosphorylation and deamidation. Using PEAKS de novo sequencing algorithm, we identified spliced peptides that accounted for ~ 5-7% of MHC-bound peptides that were otherwise similar in their features as normal MHC-bound peptides. We validated the identity of several post-translationally modified peptides and spliced peptides through mass spectrometric analysis of synthetic peptides. Our study confirms post-translationally modified peptides to be present at low stoichiometric levels along with unusual spliced peptides through unbiased identification using high resolution mass spectrometry.Supplementary informationThe online version contains supplementary material available at 10.1007/s42485-021-00066-x.

Dataset Information

Digging deeper in Shanghai: towards a 'mechanism-rich' epidemiology.

Publications

Digging deeper in Shanghai: towards a 'mechanism-rich' epidemiology.

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