Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation

Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phosphorylation. We demonstrate that metabolic labeling combined with PTM-specific enrichment does not measure effects of PTMs on protein stability. Rather, it reveals the relative order of PTM addition and removal along a protein's lifetime-a fundamentally different metric. This is due to interconversion of the measured proteoform species. Using this framework, we identify temporal phosphorylation sites on cell cycle-specific factors and protein complex assembly intermediates. Our results thus allow tying PTMs to the age of the modified proteins

Effect of Inoculation with Rhizobacteria and Arbuscular Mycorrhizal Fungi on Growth and Yield of Capsicum chinense Jacquin

We evaluated the effect of two rhizobacteria (Azotobacter chroococcum and Azospirillum brasilense) and a commercial product containing multiple strains of arbuscular mycorrhizal fungi (AMF) and an NPK fertiliser on the growth and yield of habanero chilli (Capsicum chinense Jacquin). All treatments were applied as single or combined inoculants, under nursery and field conditions, in a completely randomised design. The biofertilisers were applied to the roots by coating or dipping, with the inoculants in a solid or liquid support, respectively. At 30 days after inoculation, populations of 2.5×106 to 1.3×106 cfu g soil−1 of A. brasilense and 10.3×105 to 2.6×105 of A. chroococcum were detected in the rhizosphere of the crop. The prevalence of colonisation of plants inoculated with AMF ranged from 35 to 57%, with the greatest values recorded for the treatment involving single biofertilisation by root coating. In the nursery phase, single biofertilisation promoted a higher growth and nutrient content in the crop than combined biofertilisation. However, in the field phase the combined biofertilisation increased the nutrient content of the plant leaves, which was significantly greater than observed in the NPK treatment. The highest yields were recorded for the treatments involving a single inoculation of A. chroococcum and for those with the multi-strain of AMF, with average values of 2.5 and 2.3 kg plant−1 respectively, compared with 1.0 kg plant−1 obtained with the treatment in which NPK fertiliser was applied

Building a knowledge and innovation platform on diffuse and point soil contamination as base for (inter)national soil policies

This article highlights the importance of soil contamination, both from diffuse and point source pollution. It summarises a series of presentations at the Global Soil Week 2015 illustrating the current understanding of soil exposed to pollutants, including the main sources of contamination, the hazards and risks that pollutants in soil present for the environment and human health, as well as the possible ways to address the problem from both global and EU perspectives. It summarises the World Café discussions on four themes that participants identified as the key areas for further action: remediation of contaminated sites, alternatives to the use of chemicals and pollutants, harmonisation of monitoring and approaches and Knowledge and innovation platform.JRC.H.5-Land Resources Managemen

A framework approach for unravelling the impact of multiple factors influencing flooding

To have a better understanding of the influence of topographic, climatic, and, especially, anthropogenic factors on hydrological discharge and flooding, this study proposes a new framework approach using a set of methods to answer the questions why, where, when, and how flooding occurs. Including conditional inference tree (CIT), cross-correlation, and double-mass curves analysis, the approach is demonstrated in an application to the Wei River Basin, China. From the CIT analysis, dam construction period was identified as the most important factor (why), and the sub-catchment farthest upstream contributed the most to the flooding of the downstream floodplain (where). We then analysed the effect of the periods of dam construction on the time lag change (when) and the precipitation-discharge relationship (how) using cross-correlation analysis and double-mass curves analysis, respectively. The results suggested that the dam construction delayed the precipitation for 0.4days on average compared to before the dam construction period, and the discharge at the outlet of the basin was reduced by 44%. This framework approach is promising as it can quantitatively evaluate the importance of multiple factors on multiple years of flooding, while many studies evaluate single flooding events.</p

Imprints, Vol. 3

Imprints, Vol. 3 Laura Lundgren, Stephen F Austin State UniversitySandra L. Standley, Stephen F Austin State UniversityMelissa Miller, Stephen F Austin State UniversityCurtis Simmons, Stephen F Austin State UniversityVaughn Hamilton, Stephen F Austin State UniversitySteve Geissen, Stephen F Austin State UniversityEdward Shelton, Stephen F Austin State UniversityJames L. Choron, Stephen F Austin State UniversityAnderson Kelley, Stephen F Austin State UniversityAndrew J. Urbanus, Stephen F Austin State UniversityGordon Garrett Conner, Stephen F Austin State UniversityJames Chionsini Jr., Stephen F Austin State UniversityPaul M. Thomason, Stephen F Austin State UniversityCarol McBrayerJessica Anton, Stephen F Austin State University Download Download Full Text (5.7 MB) Description Imprints is the official publication for Sigma Tau Delta, the honorary English fraternity. The editors welcome creative works submitted by contributors and also publish winners of the annual T. E. Ferguson Writing Contest. Especially welcom are poems, fiction pieces and essays of no more than 5,000 words in length. At this time, we would like to express our gratitude to David Whitescarver, Sigma Tau Delta faculty advisor, for his unrelenting optimism and valuable help in the preparation of this journal

The foot posture index, ankle lunge test, Beighton scale and the lower limb assessment score in healthy children: a reliability study

<p>Abstract</p> <p>Background</p> <p>Outcome measures are important when evaluating treatments and physiological progress in paediatric populations. Reliable, relevant measures of foot posture are important for such assessments to be accurate over time. The aim of the study was to assess the intra- and inter-rater reliability of common outcome measures for paediatric foot conditions.</p> <p>Methods</p> <p>A repeated measures, same-subject design assessed the intra- and inter-rater reliability of measures of foot posture, joint hypermobility and ankle range: the Foot Posture Index (FPI-6), the ankle lunge test, the Beighton scale and the lower limb assessment scale (LLAS), used by two examiners in 30 healthy children (aged 7 to 15 years). The Oxford Ankle Foot Questionnaire (OxAFQ-C) was completed by participants and a parent, to assess the extent of foot and ankle problems.</p> <p>Results</p> <p>The OxAFQ-C demonstrated a mean (SD) score of 6 (6) in adults and 7(5) for children, showing good agreement between parents and children, and which indicates mid-range (transient) disability. Intra-rater reliability was good for the FPI-6 (ICC = 0.93 - 0.94), ankle lunge test (ICC = 0.85-0.95), Beighton scale (ICC = 0.96-0.98) and LLAS (ICC = 0.90-0.98). Inter-rater reliability was largely good for each of the: FPI-6 (ICC = 0.79), ankle lunge test (ICC = 0.83), Beighton scale (ICC = 0.73) and LLAS (ICC = 0.78).</p> <p>Conclusion</p> <p>The four measures investigated demonstrated adequate intra-rater and inter-rater reliability in this paediatric sample, which further justifies their use in clinical practice.</p

N-Glycans and Glycosylphosphatidylinositol-Anchor Act on Polarized Sorting of Mouse PrPC in Madin-Darby Canine Kidney Cells

The cellular prion protein (PrPC) plays a fundamental role in prion disease. PrPC is a glycosylphosphatidylinositol (GPI)-anchored protein with two variably occupied N-glycosylation sites. In general, GPI-anchor and N-glycosylation direct proteins to apical membranes in polarized cells whereas the majority of mouse PrPC is found in basolateral membranes in polarized Madin-Darby canine kidney (MDCK) cells. In this study we have mutated the first, the second, and both N-glycosylation sites of PrPC and also replaced the GPI-anchor of PrPC by the Thy-1 GPI-anchor in order to investigate the role of these signals in sorting of PrPC in MDCK cells. Cell surface biotinylation experiments and confocal microscopy showed that lack of one N-linked oligosaccharide leads to loss of polarized sorting of PrPC. Exchange of the PrPC GPI-anchor for the one of Thy-1 redirects PrPC to the apical membrane. In conclusion, both N-glycosylation and GPI-anchor act on polarized sorting of PrPC, with the GPI-anchor being dominant over N-glycans

Collection of human and environmental data on pesticide use in Europe and Argentina: Field study protocol for the SPRINT project

Current farm systems rely on the use of Plant Protection Products (PPP) to secure high productivity and control threats to the quality of the crops. However, PPP use may have considerable impacts on human health and the environment. A study protocol is presented aiming to determine the occurrence and levels of PPP residus in plants (crops), animals (livestock), humans and other non-target species (ecosystem representatives) for exposure modelling and impact assessment. To achieve this, we designed a cross-sectional study to compare conventional and organic farm systems across Europe. Environmental and biological samples were/are being/will be collected during the 2021 growing season, at 10 case study sites in Europe covering a range of climate zones and crops. An additional study site in Argentina will inform the impact of PPP use on growing soybean which is an important European protein-source in animal feed. We will study the impact of PPP mixtures using an integrated risk assessment methodology. The fate of PPP in environmental media (soil, water and air) and in the homes of farmers will be monitored. This will be complemented by biomonitoring to estimate PPP uptake by humans and farm animals (cow, goat, sheep and chicken), and by collection of samples from non-target species (earthworms, fish, aquatic and terrestrial macroinvertebrates, bats, and farm cats). We will use data on PPP residues in environmental and biological matrices to estimate exposures by modelling. These exposure estimates together with health and toxicity data will be used to predict the impact of PPP use on environment, plant, animal and human health. The outcome of this study will then be integrated with socio-economic information leading to an overall assessment used to identify transition pathways towards more sustainable plant protection and inform decision makers, practitioners and other stakeholders regarding farming practices and land use policy