A comprehensive guide for performing sample preparation and top-down protein analysis

© 2017 by the authors. Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O'Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single 'spots' in a polyacrylamide gel, allowing the quantitation of changes in a proteoform0s abundance to ascertain changes in an organism's phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the 'Top-Down'. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O'Farrell's paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism0s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer

Patterns of Exposure to Cumulative Risk Through Age 2 and Associations with Problem Behaviors at Age 4.5: Evidence from Growing Up in New Zealand.

Exposure to cumulative risk (CR) has important implications for child development, yet little is known about how frequency, persistence, and timing of CR exposure during early childhood predict behavioral problems already before school start. We examine prospective longitudinal associations between patterns of CR exposure from third trimester through 2 years and subsequent behavior problems at 4.5 years. In 6156 diverse children in the Growing Up in New Zealand longitudinal study, the presence of 12 risk factors, spanning maternal health, social status, and home and neighborhood environment, defined CR and were assessed at last trimester and 9 months and 2 years of age. At child age 4.5 years, mothers completed the Strengths and Difficulties Questionnaire, where a score ≥ 16 indicated an abnormal level of problem behaviors (ALPB). Children exposed to a CR ≥ 1 at least once in early development, compared to those with consistent CR = 0, showed a significantly higher likelihood of ALPB at 4.5 years. Consistent high exposure to CR ≥ 4 across all three assessments had the highest prevalence (44%) of ALPB at age 4.5. Children with high CR exposure on two of three, compared to on all three, time points in early development did not evidence a significantly reduced prevalence (32%-41%) of ALPB. The common co-occurrence of risk factors and their significant developmental impact when accumulated early in life underscore the need for systematic multisector intervention and policy implementation during pregnancy and shortly after birth to improve outcomes for vulnerable children

A Case of Urogenital Human Schistosomiasis from a Non-endemic Area

© 2015 Calvo-Cano et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Estimation of Dietary Iron Bioavailability from Food Iron Intake and Iron Status

Currently there are no satisfactory methods for estimating dietary iron absorption (bioavailability) at a population level, but this is essential for deriving dietary reference values using the factorial approach. The aim of this work was to develop a novel approach for estimating dietary iron absorption using a population sample from a sub-section of the UK National Diet and Nutrition Survey (NDNS). Data were analyzed in 873 subjects from the 2000–2001 adult cohort of the NDNS, for whom both dietary intake data and hematological measures (hemoglobin and serum ferritin (SF) concentrations) were available. There were 495 men aged 19–64 y (mean age 42.7±12.1 y) and 378 pre-menopausal women (mean age 35.7±8.2 y). Individual dietary iron requirements were estimated using the Institute of Medicine calculations. A full probability approach was then applied to estimate the prevalence of dietary intakes that were insufficient to meet the needs of the men and women separately, based on their estimated daily iron intake and a series of absorption values ranging from 1–40%. The prevalence of SF concentrations below selected cut-off values (indicating that absorption was not high enough to maintain iron stores) was derived from individual SF concentrations. An estimate of dietary iron absorption required to maintain specified SF values was then calculated by matching the observed prevalence of insufficiency with the prevalence predicted for the series of absorption estimates. Mean daily dietary iron intakes were 13.5 mg for men and 9.8 mg for women. Mean calculated dietary absorption was 8% in men (50th percentile for SF 85 µg/L) and 17% in women (50th percentile for SF 38 µg/L). At a ferritin level of 45 µg/L estimated absorption was similar in men (14%) and women (13%). This new method can be used to calculate dietary iron absorption at a population level using data describing total iron intake and SF concentration

A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease

Peer reviewedPublisher PD

Weak pairwise correlations imply strongly correlated network states in a neural population

Biological networks have so many possible states that exhaustive sampling is impossible. Successful analysis thus depends on simplifying hypotheses, but experiments on many systems hint that complicated, higher order interactions among large groups of elements play an important role. In the vertebrate retina, we show that weak correlations between pairs of neurons coexist with strongly collective behavior in the responses of ten or more neurons. Surprisingly, we find that this collective behavior is described quantitatively by models that capture the observed pairwise correlations but assume no higher order interactions. These maximum entropy models are equivalent to Ising models, and predict that larger networks are completely dominated by correlation effects. This suggests that the neural code has associative or error-correcting properties, and we provide preliminary evidence for such behavior. As a first test for the generality of these ideas, we show that similar results are obtained from networks of cultured cortical neurons.Comment: Full account of work presented at the conference on Computational and Systems Neuroscience (COSYNE), 17-20 March 2005, in Salt Lake City, Utah (http://cosyne.org

Abnormalities in autonomic function in obese boys at-risk for insulin resistance and obstructive sleep apnea.

Study objectivesCurrent evidence in adults suggests that, independent of obesity, obstructive sleep apnea (OSA) can lead to autonomic dysfunction and impaired glucose metabolism, but these relationships are less clear in children. The purpose of this study was to investigate the associations among OSA, glucose metabolism, and daytime autonomic function in obese pediatric subjects.MethodsTwenty-three obese boys participated in: overnight polysomnography; a frequently sampled intravenous glucose tolerance test; and recordings of spontaneous cardiorespiratory data in both the supine (baseline) and standing (sympathetic stimulus) postures.ResultsBaseline systolic blood pressure and reactivity of low-frequency heart rate variability to postural stress correlated with insulin resistance, increased fasting glucose, and reduced beta-cell function, but not OSA severity. Baroreflex sensitivity reactivity was reduced with sleep fragmentation, but only for subjects with low insulin sensitivity and/or low first-phase insulin response to glucose.ConclusionsThese findings suggest that vascular sympathetic activity impairment is more strongly affected by metabolic dysfunction than by OSA severity, while blunted vagal autonomic function associated with sleep fragmentation in OSA is enhanced when metabolic dysfunction is also present

Shifting Global Invasive Potential of European Plants with Climate Change

Global climate change and invasions by nonnative species rank among the top concerns for agents of biological loss in coming decades. Although each of these themes has seen considerable attention in the modeling and forecasting communities, their joint effects remain little explored and poorly understood. We developed ecological niche models for 1804 species from the European flora, which we projected globally to identify areas of potential distribution, both at present and across 4 scenarios of future (2055) climates. As expected from previous studies, projections based on the CGCM1 climate model were more extreme than those based on the HadCM3 model, and projections based on the a2 emissions scenario were more extreme than those based on the b2 emissions scenario. However, less expected were the highly nonlinear and contrasting projected changes in distributional areas among continents: increases in distributional potential in Europe often corresponded with decreases on other continents, and species seeing expanding potential on one continent often saw contracting potential on others. In conclusion, global climate change will have complex effects on invasive potential of plant species. The shifts and changes identified in this study suggest strongly that biological communities will see dramatic reorganizations in coming decades owing to shifting invasive potential by nonnative species

Exploring the “impact” in Impact sourcing ventures: a sociology of space perspective

Using qualitative methods this paper explores the lived experience of individuals employed in impact sourcing ventures. In doing so, the paper attempts to understand “impact” from the point of view of beneficiaries. The paper, drawing on Georg Simmel’s work on the sociology of space, explores how space influences the lived experience of beneficiaries in ImS ventures. The findings highlight the various strategies adopted by beneficiaries to navigate the dialectical tensions experienced as a result of living and working in the new (ImS workplace) and the old (community) space. The paper also draws attention to the multifaceted nature of impact

The Anatomy of International Students’ Acculturation in British Universities

The diversity of the student population in the UK Higher Education (HE) sector in recent times accentuates the notion of the world being a global village. The effect of this on the British economy is considerable in terms of scale and significance. Nevertheless, research attention that specifically explore how overseas students integrate into the UK culture in the extant literature remains inadequate. Accordingly, this interpretive research fills the lacuna by exploring the acculturation of overseas students in the UK using a London-based University as the contextual platform. It shows the challenges faced by overseas students in the country, which include culture shock, discrimination, and limited opportunity for interpersonal relationships, and pinpoints how they could be addressed. It offers HE Institutions strategic directions for creating value for their target students in the highly competitive education sector