Positional proteomics reveals differences in N-terminal proteoform stability

To understand the impact of alternative translation initiation on a proteome, we performed a proteome-wide study on protein turnover using positional proteomics and ribosome profiling to distinguish between N-terminal proteoforms of individual genes. By combining pulsed SILAC with N-terminal COFRADIC, we monitored the stability of 1,941 human N-terminal proteoforms, including 147N-terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine. N-terminally truncated proteoforms were less abundant than canonical proteoforms and often displayed altered stabilities, likely attributed to individual protein characteristics, including intrinsic disorder, but independent of N-terminal amino acid identity or truncation length. We discovered that the removal of initiator methionine by methionine aminopeptidases reduced the stability of processed proteoforms, while susceptibility for N-terminal acetylation did not seem to influence protein turnover rates. Taken together, our findings reveal differences in protein stability between N-terminal proteoforms and point to a role for alternative translation initiation and co-translational initiator methionine removal, next to alternative splicing, in the overall regulation of proteome homeostasis

An integrated study resource for veterinary students at the University of Edinburgh: the library and the “Study Landscape”

In 2011 the Royal (Dick) School of Veterinary Studies moved its teaching and learning activities to one campus. The Lady Smith of Kelvin Veterinary Library now links to the Study Landscape, a student-centred space for self-directed learning. This allows students access to a range of physical and electronic resources including specimens and themed resources. This paper presents the practical experiences of the author in collaborating with academic and technical colleagues to populate the Study Landscape with appropriate resources. This collaboration has increased our understanding of the different learning resources used in veterinary medicine and can assist us in our provision of more ‘traditional’ library services to the Veterinary School

Shifting ranges and conservation challenges for lemurs in the face of climate change.

Geospatial modeling is one of the most powerful tools available to conservation biologists for estimating current species ranges of Earth's biodiversity. Now, with the advantage of predictive climate models, these methods can be deployed for understanding future impacts on threatened biota. Here, we employ predictive modeling under a conservative estimate of future climate change to examine impacts on the future abundance and geographic distributions of Malagasy lemurs. Using distribution data from the primary literature, we employed ensemble species distribution models and geospatial analyses to predict future changes in species distributions. Current species distribution models (SDMs) were created within the BIOMOD2 framework that capitalizes on ten widely used modeling techniques. Future and current SDMs were then subtracted from each other, and areas of contraction, expansion, and stability were calculated. Model overprediction is a common issue associated Malagasy taxa. Accordingly, we introduce novel methods for incorporating biological data on dispersal potential to better inform the selection of pseudo-absence points. This study predicts that 60% of the 57 species examined will experience a considerable range of reductions in the next seventy years entirely due to future climate change. Of these species, range sizes are predicted to decrease by an average of 59.6%. Nine lemur species (16%) are predicted to expand their ranges, and 13 species (22.8%) distribution sizes were predicted to be stable through time. Species ranges will experience severe shifts, typically contractions, and for the majority of lemur species, geographic distributions will be considerably altered. We identify three areas in dire need of protection, concluding that strategically managed forest corridors must be a key component of lemur and other biodiversity conservation strategies. This recommendation is all the more urgent given that the results presented here do not take into account patterns of ongoing habitat destruction relating to human activities

Fatty-acid uptake in prostate cancer cells using dynamic microfluidic raman technology

It is known that intake of dietary fatty acid (FA) is strongly correlated with prostate cancer progression but is highly dependent on the type of FAs. High levels of palmitic acid (PA) or arachidonic acid (AA) can stimulate the progression of cancer. In this study, a unique experimental set-up consisting of a Raman microscope, coupled with a commercial shear-flow microfluidic system is used to monitor fatty acid uptake by prostate cancer (PC-3) cells in real-time at the single cell level. Uptake of deuterated PA, deuterated AA, and the omega-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were monitored using this new system, while complementary flow cytometry experiments using Nile red staining, were also conducted for the validation of the cellular lipid uptake. Using this novel experimental system, we show that DHA and EPA have inhibitory effects on the uptake of PA and AA by PC-3 cells

Multi-Trophic Effects of Climate Change and Glacier Retreat in Mountain Rivers

Climate change is driving the thinning and retreat of many glaciers globally. Reductions of ice-melt inputs to mountain rivers are changing their physicochemical characteristics and, in turn, aquatic communities. Glacier-fed rivers can serve as model systems for investigations of climate-change effects on ecosystems because of their strong atmospheric–cryospheric links, high biodiversity of multiple taxonomic groups, and significant conservation interest concerning endemic species. From a synthesis of existing knowledge, we develop a new conceptual understanding of how reducing glacier cover affects organisms spanning multiple trophic groups. Although the response of macroinvertebrates to glacier retreat has been well described, we show that there remains a relative paucity of information for biofilm, microinvertebrate, and vertebrate taxa. Enhanced understanding of whole river food webs will improve the prediction of river-ecosystem responses to deglaciation while offering the potential to identify and protect a wider range of sensitive and threatened species

Walks4Work: Assessing the role of the natural environment in a workplace physical activity intervention

Objectives The primary aim of this study was to examine the impact of physical activity (PA) in the natural environment (eg, "green exercise") on resting autonomic function in the Walks4Work intervention. A secondary aim was to assess the feasibility of Walks4Work in terms of adherence, change in PA levels, and cardiovascular health parameters. Methods In an 8-week randomized control trial, 94 office workers in an international company were allocated to one of three groups: control, nature (NW), or built (BW) lunchtime walking route. Both walking groups were required to undertake two lunchtime walks each week. The NW route centered around trees, maintained grass, and public footpaths. In contrast, the BW consisted of pavement routes through housing estates and industrial areas. Data were collected at baseline and following the intervention. To investigate the impact of the intervention, mixed-design analysis of variance (ANOVA) were performed. Results A total of 73 participants completed the intervention (drop-out rate of 22%). No difference was observed in resting autonomic function between the groups. Self-reported mental health improved for the NW group only. PA levels increased at the intervention mid-point for all groups combined but adherence to the intervention was low with rates of 42% and 43% within the BW and NW groups, respectively. Conclusion Accompanying a guideline of two active lunchtimes per week with low facilitator input appears inadequate for increasing the number of active lunchtimes and modifying cardiovascular health parameters in an office population. However, this population fell within normal ranges for cardiovascular measures and future research should consider investigating at-risk populations, particularly hypertensive individuals

Understanding the Links between Positive Wellbeing and Health

People with higher levels of positive wellbeing may enjoy better health and live longer, but it is not clear why. This thesis explores the notion that links between positive wellbeing and health-relevant biological correlates could provide some explanation for the relationship between positive wellbeing and health. Two complementary approaches were used. First, associations between the positive personality trait of resilience (the ability to withstand chronic stress or adversity) and various biological and psychological factors were explored using secondary data. Second, an intervention study was used to test causal mechanisms between changes in positive wellbeing and changes in biology. Resilience (from the Resilience Scale), psychosocial stressors and affect and wellbeing outcomes were assessed in around 200 healthy working women as part of the Daytracker study. Measures of cortisol and heart rate variability (HRV) were also collected across a work and leisure day. Results of regression analyses suggested that higher resilience was associated with greater HRV across the work period, but there was no association with cortisol. Resilience mediated the relationship between particular stressors and affect and wellbeing outcomes. A two week gratitude-based intervention in 119 healthy women was used to try to increase positive wellbeing. Psychological and biological factors (cortisol, blood pressure and heart rate) were assessed before and after the intervention. The gratitude condition was associated with increased optimism, reduced depressive symptoms and lower diastolic blood pressure. However, associations with measures of positive wellbeing were not robust. It was therefore not possible to demonstrate causal links between changes in positive wellbeing and changes in biology. Future studies could focus on strengthening positive wellbeing intervention tasks. Overall the results provided modest evidence for links between positive wellbeing and biological correlates of health. Resilience may provide cardiac health protective effects, since reduced HRV has previously been associated with increased cardiovascular disease incidence

Enteric glia mediate neuron death in colitis through purinergic pathways that require connexin-43 and nitric oxide

The concept of enteric glia as regulators of intestinal homeostasis is slowly gaining acceptance as a central concept in neurogastroenterology. Yet how glia contribute to intestinal disease is still poorly understood. Purines generated during inflammation drive enteric neuron death by activating neuronal P2X7 purine receptors (P2X7R), triggering ATP release via neuronal pannexin-1 channels that subsequently recruits intracellular calcium ([Ca(2+)]i) responses in the surrounding enteric glia. We tested the hypothesis that the activation of enteric glia contributes to neuron death during inflammation.We studied neuroinflammation in vivo using the 2,4-dinitrobenzenesulfonic acid model of colitis and in situ using whole-mount preparations of human and mouse intestine. Transgenic mice with a targeted deletion of glial connexin-43 (Cx43) [GFAP∷Cre (ERT2+/-)/Cx43(f/f) ] were used to specifically disrupt glial signaling pathways. Mice deficient in inducible nitric oxide (NO) synthase (iNOS (-/-)) were used to study NO production. Protein expression and oxidative stress were measured using immunohistochemistry and in situ Ca(2+) and NO imaging were used to monitor glial [Ca(2+)]i and [NO]i.Purinergic activation of enteric glia drove [Ca(2+)]i responses and enteric neuron death through a Cx43-dependent mechanism. Neurotoxic Cx43 activity, driven by NO production from glial iNOS, was required for neuron death. Glial Cx43 opening liberated ATP and Cx43-dependent ATP release was potentiated by NO.Our results show that the activation of glial cells in the context of neuroinflammation kills enteric neurons. Mediators of inflammation that include ATP and NO activate neurotoxic pathways that converge on glial Cx43 hemichannels. The glial response to inflammatory mediators might contribute to the development of motility disorders

DNA methylation governs the dynamic regulation of inflammation by apoptotic cells during efferocytosis

Efficient clearance of apoptotic cells (AC) is pivotal in preventing autoimmunity and is a potent immunosuppressive stimulus. However, activation of cells prior to apoptosis abolishes their immunoregulatory properties. Here we show using the antigen-induced model of arthritis that the degree of DNA methylation within AC confers their immunomodulatory plasticity. DNA isolated from resting and activated AC mimicked their respective immune effects. Demethylation of DNA abrogated the protective effect of AC whereas remethylation of AC DNA reversed the effects of activation and restored the ability to inhibit inflammation. Disease suppression or lack thereof was associated with TGFβ and IL-6 production respectively. Apoptotic CD4+ T cells from patients with rheumatoid arthritis and systemic lupus erythematosus were demethylated compared to healthy controls and favoured production of IL-6 when cultured with healthy macrophages, in contrast to the TGFβ produced in response to healthy AC. Our data implicate AC DNA methylation as the molecular switch that imprints their regulatory properties