Mapping differential interactomes by affinity purification coupled with data independent mass spectrometry acquisition

Characterizing changes in protein-protein interactions associated with sequence variants (e.g. disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies where cost and time are major considerations. To this end, we have coupled AP to data-independent mass spectrometric acquisition (SWATH), and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. Here, we use AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes, and propose a scalable pipeline for systems biology studies

Tumor-Shed PGE2 Impairs IL2Rγc-Signaling to Inhibit CD4+ T Cell Survival: Regulation by Theaflavins

BACKGROUND:Many tumors are associated with decreased cellular immunity and elevated levels of prostaglandin E2 (PGE2), a known inhibitor of CD4+ T cell activation and inducer of type-2 cytokine bias. However, the role of this immunomodulator in the survival of T helper cells remained unclear. Since CD4+ T cells play critical roles in cell-mediated immunity, detail knowledge of the effect tumor-derived PGE2 might have on CD4+ T cell survival and the underlying mechanism may, therefore, help to overcome the overall immune deviation in cancer. METHODOLOGY/PRINCIPAL FINDINGS:By culturing purified human peripheral CD4+ T cells or Jurkat cells with spent media of theaflavin- or celecoxib-pre-treated MCF-7 cells, we show that tumor-shed PGE2 severely impairs interleukin 2 receptor gammac (IL2Rgammac)-mediated survival signaling in CD4+ T cells. Indeed, tumor-shed PGE2 down-regulates IL2Rgammac expression, reduces phosphorylation as well as activation of Janus kinase 3 (Jak-3)/signal transducer and activator of transcription 5 (Stat-5) and decreases Bcl-2/Bax ratio thereby leading to activation of intrinsic apoptotic pathway. Constitutively active Stat-5A (Stat-5A1 6) over-expression efficiently elevates Bcl-2 levels in CD4+ T cells and protects them from tumor-induced death while dominant-negative Stat-5A over-expression fails to do so, indicating the importance of Stat-5A-signaling in CD4+ T cell survival. Further support towards the involvement of PGE2 comes from the results that (a) purified synthetic PGE2 induces CD4+ T cell apoptosis, and (b) when knocked out by small interfering RNA, cyclooxygenase-2 (Cox-2)-defective tumor cells fail to initiate death. Interestingly, the entire phenomena could be reverted back by theaflavins that restore cytokine-dependent IL2Rgammac/Jak-3/Stat-5A signaling in CD4+ T cells thereby protecting them from tumor-shed PGE2-induced apoptosis. CONCLUSIONS/SIGNIFICANCE:These data strongly suggest that tumor-shed PGE2 is an important factor leading to CD4+ T cell apoptosis during cancer and raise the possibility that theaflavins may have the potential as an effective immunorestorer in cancer-bearer

Unlocking the Transcriptomes of Two Carcinogenic Parasites, Clonorchis sinensis and Opisthorchis viverrini

The two parasitic trematodes, Clonorchis sinensis and Opisthorchis viverrini, have a major impact on the health of tens of millions of humans throughout Asia. The greatest impact is through the malignant cancer ( = cholangiocarcinoma) that these parasites induce in chronically infected people. Therefore, both C. sinensis and O. viverrini have been classified by the World Health Organization (WHO) as Group 1 carcinogens. Despite their impact, little is known about these parasites and their interplay with the host at the molecular level. Recent advances in genomics and bioinformatics provide unique opportunities to gain improved insights into the biology of parasites as well as their relationships with their hosts at the molecular level. The present study elucidates the transcriptomes of C. sinensis and O. viverrini using a platform based on next-generation (high throughput) sequencing and advanced in silico analyses. From 500,000 sequences, >50,000 sequences were assembled for each species and categorized as biologically relevant based on homology searches, gene ontology and/or pathway mapping. The results of the present study could assist in defining molecules that are essential for the development, reproduction and survival of liver flukes and/or that are linked to the development of cholangiocarcinoma. This study also lays a foundation for future genomic and proteomic research of C. sinensis and O. viverrini and the cancers that they are known to induce, as well as novel intervention strategies

Social media in undergraduate medical education: A systematic review.

INTRODUCTION: There are over 3.81 billion worldwide active social media (SoMe) users. SoMe are ubiquitous in medical education, with roles across undergraduate programmes, including professionalism, blended learning, well being and mentoring. Previous systematic reviews took place before recent explosions in SoMe popularity and revealed a paucity of high-quality empirical studies assessing its effectiveness in medical education. This review aimed to synthesise evidence regarding SoMe interventions in undergraduate medical education, to identify features associated with positive and negative outcomes. METHODS: Authors searched 31 key terms through seven databases, in addition to references, citation and hand searching, between 16 June and 16 July 2020. Studies describing SoMe interventions and research on exposure to existing SoMe were included. Title, abstract and full paper screening were undertaken independently by two reviewers. Included papers were assessed for methodological quality using the Medical Education Research Study Quality Instrument (MERSQI) and/or the Standards for Reporting Qualitative Research (SRQR) instrument. Extracted data were synthesised using narrative synthesis. RESULTS: 112 studies from 26 countries met inclusion criteria. Methodological quality of included studies had not significantly improved since 2013. Engagement and satisfaction with SoMe platforms in medical education are described. Students felt SoMe flattened hierarchies and improved communication with educators. SoMe use was associated with improvement in objective knowledge assessment scores and self-reported clinical and professional performance, however evidence for long term knowledge retention was limited. SoMe use was occasionally linked to adverse impacts upon mental and physical health. Professionalism was heavily investigated and considered important, though generally negative correlations between SoMe use and medical professionalism may exist. CONCLUSIONS: Social media is enjoyable for students who may improve short term knowledge retention and can aid communication between learners and educators. However, higher-quality study is required to identify longer-term impact upon knowledge and skills, provide clarification on professionalism standards and protect against harms

Ammonia: possible use for preserving fish

Eviscerated oil sardines (Sardinella longiceps) that have been treated with ammonia can be stored at a temperature of 25° to 30°C for more than 2 months without deterioration of their nutritive value. There is no measurable residue of ammonia in the final product

The effect of a supplementary protein food containing fish flour, groundnut flour and bengal gram flour and fortified with vitamins on the growth and nutritional status of children

A feeding experiment extending over a period of six months was carried out on 58 boys, aged 6 to 12 years, in a local boarding home in Mysore, to assess the effects of supplementing their diet daily, with 40 gm. of a protein food based on 2:1:1 blend of groundnut flour, Bengal gram flour and fish flour (from oil sardine) fortified with vitamins A and D, thiamine and riboflavin. The children were paired according to initial height and weight and the members of each pair allotted at random to the control and experimental groups. Values for weight, height, nutritional status, haemoglobin level and red blood cell count were recorded at the beginning and end of the experiment, for subjects in the control and experimental groups. All the children in the experimental group relished the protein supplement and none complained of digestive trouble. A highly significant increase in height, weight, red blood cell count and haemoglobin level of the subjects receiving the protein food supplement was observed as compared with the control group. Eighty per cent. of the subjects in the experimental group improved in their nutritional status as compared with only seventeen per cent. in the control group. None in the experimental group showed deterioration whereas seventeen per cent. of the subjects in the control group showed deterioration in their nutritional status